@article{wangRoleUpf2pPhosphorylation2006, title = {Role for {{Upf2p}} Phosphorylation in {{Saccharomyces}} Cerevisiae Nonsense-Mediated {{mRNA}} Decay}, author = {Wang, W. and Cajigas, I.J. and Peltz, S.W. and Wilkinson, M.F. and Gonzalez, C.I.}, year = 2006, month = may, journal = {Molecular and Cellular Biology}, volume = {26}, number = {9}, eprint = {16611983}, eprinttype = {pubmed}, pages = {3390–3400}, issn = {0270-7306}, doi = {10.1128/MCB.26.9.3390-3400.2006}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16611983}, abstract = {Premature termination (nonsense) codons trigger rapid mRNA decay by the nonsense-mediated mRNA decay (NMD) pathway. Two conserved proteins essential for NMD, UPF1 and UPF2, are phosphorylated in higher eukaryotes. The phosphorylation and dephosphorylation of UPF1 appear to be crucial for NMD, as blockade of either event in Caenorhabditis elegans and mammals largely prevents NMD. The universality of this phosphorylation/dephosphorylation cycle pathway has been questioned, however, because the well-studied Saccharomyces cerevisiae NMD pathway has not been shown to be regulated by phosphorylation. Here, we used in vitro and in vivo biochemical techniques to show that both S. cerevisiae Upf1p and Upf2p are phosphoproteins. We provide evidence that the phosphorylation of the N-terminal region of Upf2p is crucial for its interaction with Hrp1p, an RNA-binding protein that we previously showed is essential for NMD. We identify specific amino acids in Upf2p’s N-terminal domain, including phosphorylated serines, which dictate both its interaction with Hrp1p and its ability to elicit NMD. Our results indicate that phosphorylation of UPF1 and UPF2 is a conserved event in eukaryotes and for the first time provide evidence that Upf2p phosphorylation is crucial for NMD.}, pmid = {16611983}, keywords = {Adaptor Proteins Signal Transducing,Amino Acid Sequence,Codon,Codon Nonsense,In Vitro,Molecular Sequence Data,mRNA Cleavage and Polyadenylation Factors,nosource,Phosphoproteins,Phosphorylation,Proteins,RNA Helicases,RNA Messenger,RNA Stability,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Trans-Activators} } % == BibTeX quality report for wangRoleUpf2pPhosphorylation2006: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{glasserFunctionalConsiderationsGranulocyte1979, title = {Functional Considerations of Granulocyte Concentrates Used for Clinical Transfusions}, author = {Glasser, L}, year = {1979 Jan-Feb}, journal = {Transfusion}, volume = {19}, number = {1}, eprint = {373176}, eprinttype = {pubmed}, pages = {1–6}, issn = {0041-1132}, url = {http://www.ncbi.nlm.nih.gov/pubmed/373176}, pmid = {373176}, keywords = {Blood Preservation,Blood Specimen Collection,Blood Transfusion,Granulocytes,Humans,Leukemia,Neutrophils,nosource,Phagocytosis} }

@article{leliveltYeastUpfProteins1999, title = {Yeast {{Upf}} Proteins Required for {{RNA}} Surveillance Affect Global Expression of the Yeast Transcriptome}, author = {Lelivelt, M J and Culbertson, M R}, year = 1999, month = oct, journal = {Molecular and Cellular Biology}, volume = {19}, number = {10}, pages = {6710–6719}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, doi = {10.1128/MCB.19.10.6710}, url = {http://mcb.asm.org/cgi/content/abstract/19/10/6710}, abstract = {mRNAs are monitored for errors in gene expression by RNA surveillance, in which mRNAs that cannot be fully translated are degraded by the nonsense-mediated mRNA decay pathway (NMD). RNA surveillance ensures that potentially deleterious truncated proteins are seldom made. NMD pathways that promote surveillance have been found in a wide range of eukaryotes. In Saccharomyces cerevisiae, the proteins encoded by the UPF1, UPF2, and UPF3 genes catalyze steps in NMD and are required for RNA surveillance. In this report, we show that the Upf proteins are also required to control the total accumulation of a large number of mRNAs in addition to their role in RNA surveillance. High-density oligonucleotide arrays were used to monitor global changes in the yeast transcriptome caused by loss of UPF gene function. Null mutations in the UPF genes caused altered accumulation of hundreds of mRNAs. The majority were increased in abundance, but some were decreased. The same mRNAs were affected regardless of which of the three UPF gene was inactivated. The proteins encoded by UPF-dependent mRNAs were broadly distributed by function but were underrepresented in two MIPS (Munich Information Center for Protein Sequences) categories: protein synthesis and protein destination. In a UPF(+) strain, the average level of expression of UPF-dependent mRNAs was threefold lower than the average level of expression of all mRNAs in the transcriptome, suggesting that highly abundant mRNAs were underrepresented. We suggest a model for how the abundance of hundreds of mRNAs might be controlled by the Upf proteins.}, keywords = {0,Adaptor Proteins Signal Transducing,DECAY,expression,Fungal Proteins,gene,Gene Expression,Gene Expression Profiling,Gene Expression Regulation Fungal,GENE-EXPRESSION,Genes,Genetic,genetics,mRNA,mRNA decay,Munich Information Center for Protein Sequences,Mutation,MUTATIONS,NMD,nosource,Oligonucleotide Array Sequence Analysis,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Rna,RNA Helicases,RNA Messenger,RNA Processing Post-Transcriptional,RNA Stability,RNA-Binding Proteins,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,Trans-Activators,Transcription Genetic,UPF,Upf1,UPF3,yeast} } % == BibTeX quality report for leliveltYeastUpfProteins1999: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{patzoldWhyPpr1pWeak2001, title = {Why {{Ppr1p}} Is a Weak Activator of Transcription.}, author = {P{"a}tzold, A J and Lehming, N}, year = 2001, month = apr, journal = {FEBS Letters}, volume = {494}, number = {1-2}, eprint = {11297736}, eprinttype = {pubmed}, pages = {64–68}, issn = {0014-5793}, doi = {10.1016/S0014-5793(01)02312-2}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11297736}, abstract = {Upon uracil depletion, the transcriptional activator Ppr1p stimulates expression of the Saccharomyces cerevisiae URA3 gene only four-fold. We performed a split-ubiquitin screen with Tup1p as bait, and we found that the global repressor Tup1p interacts with the transcriptional activator Ppr1p both in vivo and in vitro. The interaction is biologically significant, since the deletion of the TUP1 gene as well as the removal of the Tup1p-binding domain from Ppr1p results in an increased expression of the URA3 gene. Our results suggest that Tup1p blocks Ppr1p directly, and that Ppr1p is a weak activator of transcription because of its interaction with Tup1p. Thus we were able to demonstrate that the global repressor Tup1p can modulate transcription by interacting with an activator.}, pmid = {11297736}, keywords = {DNA-Binding Proteins,DNA-Binding Proteins: genetics,DNA-Binding Proteins: metabolism,Fungal,Fungal Proteins,Fungal Proteins: genetics,Gene Expression Regulation,Gene Expression Regulation Fungal,Gene Expression RegulationFungal,Genetic,genetics,In Vitro,metabolism,nosource,Nuclear Proteins,Proteins,Recombinant Fusion Proteins,Recombinant Fusion Proteins: genetics,Recombinant Fusion Proteins: metabolism,Repressor Proteins,Repressor Proteins: genetics,Research SupportNon-U.S.Gov’t,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Trans-Activators,Trans-Activators: genetics,Trans-Activators: metabolism,Transcription,Transcription Factors,Transcription Factors: genetics,Transcription Factors: metabolism,Transcription Genetic,TranscriptionGenetic} } % == BibTeX quality report for patzoldWhyPpr1pWeak2001: % ? unused Journal abbr (“FEBS Lett.”)

@article{maquatWhenCellsStop1995, title = {When Cells Stop Making Sense: Effects of Nonsense Codons on {{RNA}} Metabolism in Vertebrate Cells.}, author = {Maquat, L E}, year = 1995, month = jul, journal = {RNA (New York, N.Y.)}, volume = {1}, number = {5}, pages = {453–465}, publisher = {Cold Spring Harbor Laboratory Press}, issn = {1355-8382}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1482424/}, abstract = {It appears that no organism is immune to the effects of nonsense codons on mRNA abundance. The study of how nonsense codons alter RNA metabolism is still at an early stage, and our current understanding derives more from incidental vignettes than from experimental undertakings that address molecular mechanisms. Challenges for the future include identifying the gene products and RNA sequences that function in nonsense mediated RNA loss, resolving the cause and consequences of there apparently being more than one cellular site and mechanism for nonsense-mediated RNA loss, and understanding how these sites and mechanisms are related to both constitutive and specialized pathways of pre-mRNA processing and mRNA decay.}, keywords = {Animals,Base Sequence,Cell Compartmentation,Codon,Codon Nonsense,Feedback,Half-Life,metabolism,Models Genetic,Molecular Sequence Data,NMD,No DOI found,nosource,Review,Rna,RNA Messenger,RNA Precursors,RNA Processing Post-Transcriptional,Vertebrates} } % == BibTeX quality report for maquatWhenCellsStop1995: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{myerViralSmallNuclear1992, title = {Viral Small Nuclear Ribonucleoproteins Bind a Protein Implicated in Messenger {{RNA}} Destabilization}, author = {Myer, V E and Lee, S I and Steitz, J A}, year = 1992, month = feb, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {89}, number = {4}, pages = {1296–1300}, publisher = {National Acad Sciences}, issn = {0027-8424}, url = {http://www.pnas.org/content/89/4/1296.short}, abstract = {Herpesvirus saimiri (HVS) is one of several primate viruses that carry genes for small RNAs. The five H. saimiri-encoded U RNAs (HSURs) are the most abundant viral transcripts expressed in transformed marmoset T lymphocytes. They assemble with host proteins common to spliceosomal small nuclear ribonucleoproteins (snRNPs). HSURs 1, 2, and 5 exhibit sequences at their 5’ ends identical to the AUUUA motif, which targets a number of protooncogene, cytokine, and lymphokine mRNAs for rapid degradation. We show that a 32-kDa protein previously demonstrated to bind to the 3’ untranslated region of several unstable messages can be UV crosslinked specifically to HSUR 1, 2, and 5 transcripts in vitro, as well as to endogenous HSUR snRNPs. Our results suggest an unusual role for these viral snRNPs: HSURs may function to attenuate the rapid degradation of certain cellular mRNAs, thereby facilitating viral transformation of host T lymphocytes.}, keywords = {Base Sequence,Binding Sites,Cloning Molecular,Cloning- Molecular,Herpesvirus 2 Saimiriine,Herpesvirus 2- Saimiriine,Molecular Sequence Data,nosource,Nuclear Proteins,Protein Binding,Ribonucleoproteins,Ribonucleoproteins Small Nuclear,Ribonucleoproteins- Small Nuclear,RNA Messenger,RNA Viral,RNA- Messenger,RNA- Viral,Ultraviolet Rays} } % == BibTeX quality report for myerViralSmallNuclear1992: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{zhaoViralInfectionsCell2005, title = {Viral Infections and Cell Cycle {{G2}}/{{M}} Regulation}, author = {Zhao, Richard Y and Elder, Robert T}, year = 2005, month = mar, journal = {Cell Research}, volume = {15}, number = {3}, eprint = {15780175}, eprinttype = {pubmed}, pages = {143–149}, issn = {1001-0602}, doi = {10.1038/sj.cr.7290279}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15780175}, abstract = {Progression of cells from G2 phase of the cell cycle to mitosis is a tightly regulated cellular process that requires activation of the Cdc2 kinase, which determines onset of mitosis in all eukaryotic cells. In both human and fission yeast (Schizosaccharomyces pombe) cells, the activity of Cdc2 is regulated in part by the phosphorylation status of tyrosine 15 (Tyr15) on Cdc2, which is phosphorylated by Wee1 kinase during late G2 and is rapidly dephosphorylated by the Cdc25 tyrosine phosphatase to trigger entry into mitosis. These Cdc2 regulators are the downstream targets of two well-characterized G2/M checkpoint pathways which prevent cells from entering mitosis when cellular DNA is damaged or when DNA replication is inhibited. Increasing evidence suggests that Cdc2 is also commonly targeted by viral proteins, which modulate host cell cycle machinery to benefit viral survival or replication. In this review, we describe the effect of viral protein R (Vpr) encoded by human immunodeficiency virus type 1 (HIV-1) on cell cycle G2/M regulation. Based on our current knowledge about this viral effect, we hypothesize that Vpr induces cell cycle G2 arrest through a mechanism that is to some extent different from the classic G2/M checkpoints. One the unique features distinguishing Vpr-induced G2 arrest from the classic checkpoints is the role of phosphatase 2A (PP2A) in Vpr-induced G2 arrest. Interestingly, PP2A is targeted by a number of other viral proteins including SV40 small T antigen, polyomavirus T antigen, HTLV Tax and adenovirus E4orf4. Thus an in-depth understanding of the molecular mechanisms underlying Vpr-induced G2 arrest will provide additional insights into the basic biology of cell cycle G2/M regulation and into the biological significance of this effect during host-pathogen interactions.}, pmid = {15780175}, keywords = {CDC2 Protein Kinase,DNA Damage,DNA Replication,DNA Viral,DNA- Viral,G2 Phase,Genes vpr,Genes- vpr,HIV Infections,HIV-1,Humans,Mitosis,nosource,Phosphorylation,Schizosaccharomyces,Virus Replication} } % == BibTeX quality report for zhaoViralInfectionsCell2005: % ? unused Journal abbr (“Cell Res”)

@article{xuVersatileRoleHnRNP2001, title = {Versatile Role for {{hnRNP D}} Isoforms in the Differential Regulation of Cytoplasmic {{mRNA}} Turnover}, author = {Xu, N and Chen, C Y and Shyu, A B}, year = 2001, month = oct, journal = {Molecular and Cellular Biology}, volume = {21}, number = {20}, pages = {6960–6971}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, doi = {10.1128/MCB.21.20.6960-6971.2001}, url = {http://mcb.asm.org/cgi/content/abstract/21/20/6960}, abstract = {An important emerging theme is that heterogeneous nuclear ribonucleoproteins (hnRNPs) not only function in the nucleus but also control the fates of mRNAs in the cytoplasm. Here, we show that hnRNP D plays a versatile role in cytoplasmic mRNA turnover by functioning as a negative regulator in an isoform-specific and cell-type-dependent manner. We found that hnRNP D discriminates among the three classes of AU-rich elements (AREs), most effectively blocking rapid decay directed by class II AREs found in mRNAs encoding cytokines. Our experiments identified the overlapping AUUUA motifs, one critical characteristic of class II AREs, to be the key feature recognized in vivo by hnRNP D for its negative effect on ARE-mediated mRNA decay. The four hnRNP D isoforms, while differing in their ability to block decay of ARE-containing mRNAs, all potently inhibited mRNA decay directed by another mRNA cis element that shares no sequence similarity with AREs, the purine-rich c-fos protein-coding region determinant of instability. Further experiments indicated that different mechanisms underlie the inhibitory effect of hnRNP D on the two distinct mRNA decay pathways. Our study identifies a potential mechanism by which cytoplasmic mRNA turnover can be differentially and selectively regulated by hnRNP D isoforms in mammalian cells. Our results support the notion that hnRNP D serves as a key factor broadly involved in general mRNA decay.}, keywords = {3T3 Cells,Amino Acid Motifs,Animals,Blotting Western,Blotting- Western,Cytokines,Cytoplasm,Heterogeneous-Nuclear Ribonucleoproteins,Mice,Microscopy Fluorescence,Microscopy- Fluorescence,nosource,Plasmids,Protein Binding,Protein Isoforms,Protein Structure Tertiary,Protein Structure- Tertiary,Proto-Oncogene Proteins c-fos,Ribonucleoproteins,RNA,RNA Messenger,RNA- Messenger,Time Factors} } % == BibTeX quality report for xuVersatileRoleHnRNP2001: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{heUpf1pNmd2pUpf3p2001, title = {Upf1p, {{Nmd2p}}, and {{Upf3p}} Regulate the Decapping and Exonucleolytic Degradation of Both Nonsense-Containing {{mRNAs}} and Wild-Type {{mRNAs}}}, author = {He, F and Jacobson, A}, year = 2001, month = mar, journal = {Molecular and Cellular Biology}, volume = {21}, number = {5}, pages = {1515–1530}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, doi = {10.1128/MCB.21.5.1515-1530.2001}, url = {http://mcb.asm.org/cgi/content/abstract/21/5/1515}, abstract = {In Saccharomyces cerevisiae, rapid degradation of nonsense-containing mRNAs requires the decapping enzyme Dcp1p, the 5’-to-3’ exoribonuclease Xrn1p, and the three nonsense-mediated mRNA decay (NMD) factors, Upf1p, Nmd2p, and Upf3p. To identify specific functions for the NMD factors, we analyzed the mRNA decay phenotypes of yeast strains containing deletions of DCP1 or XRN1 and UPF1, NMD2, or UPF3. Our results indicate that Upf1p, Nmd2p, and Upf3p regulate decapping and exonucleolytic degradation of nonsense-containing mRNAs. In addition, we show that these factors also regulate the same processes in the degradation of wild-type mRNAs. The participation of the NMD factors in general mRNA degradation suggests that they may regulate an aspect of translation termination common to all transcripts.}, keywords = {Adaptor Proteins Signal Transducing,Alleles,Blotting Northern,Exoribonucleases,Fungal Proteins,Gene Deletion,Gene Expression Regulation Fungal,Mutation,nosource,Phenotype,Protein Biosynthesis,RNA,RNA Caps,RNA Helicases,RNA Messenger,RNA-Binding Proteins,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Trans-Activators} } % == BibTeX quality report for heUpf1pNmd2pUpf3p2001: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{heUpf1pNmd2pUpf3p1997, title = {Upf1p, {{Nmd2p}}, and {{Upf3p}} Are Interacting Components of the Yeast Nonsense-Mediated {{mRNA}} Decay Pathway.}, author = {He, F and Brown, A H and Jacobson, A}, year = 1997, month = mar, journal = {Molecular and Cellular Biology}, volume = {17}, number = {3}, pages = {1580–1594}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, doi = {10.1128/MCB.17.3.1580}, url = {http://mcb.asm.org/cgi/content/abstract/17/3/1580}, abstract = {Rapid turnover of nonsense-containing mRNAs in Saccharomyces cerevisiae is dependent on Upf1p, Nmd2p, and Upf3p, the products of the UPF1, NMD2/UPF2, and UPF3 genes, respectively. We showed previously that Upf1p and Nmd2p interact and that this interaction is required for nonsense-mediated mRNA decay (F. He and A. Jacobson, Genes Dev. 9:437-454, 1995; F. He, A. H. Brown, and A. Jacobson, RNA 2:153-170, 1996). In this study we have used the yeast two-hybrid system to define other protein-protein interactions among the essential components of this decay pathway. Nmd2p-Upf3p and Upf1p-Upf3p interactions were identified, and the respective domains involved in these interactions were delineated by deletion analysis. The domains of Upf1p and Upf3p putatively involved in their mutual interaction were found to correspond to the domains on the two proteins which interact with Nmd2p, suggesting that Nmd2p bridges Upf1p and Upf3p. This conclusion was reinforced by experiments showing that: (i) deletion of NMD2 completely abolishes interactions between Upf1p and Upf3p and (ii) overexpression of full-length Nmd2p or Nmd2p fragments that retain Upf1p- and Upf3p-interacting domains promotes 10- to 200-fold enhancement of Upf1p-Nmd2p-Upf3p complex formation. These results; the observation that cells harboring either single or multiple deletions of UPF1, NMD2, and UPF3 inhibit nonsense-mediated mRNA decay to the same extent; and an analysis of the possible targets of a dominant-negative NMD2 allele indicate that Upf1p, Nmd2p, Upf3p, and at least one other factor are functionally dependent, interacting components of the yeast nonsense-mediated mRNA decay pathway.}, keywords = {2 hybrid,2-hybrid,Adaptor Proteins Signal Transducing,COMPONENT,DECAY,Fungal Proteins,mRNA,mRNA decay,NMD,nosource,Recombinant Fusion Proteins,RNA Fungal,RNA Helicases,RNA Messenger,RNA-Binding Proteins,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Sequence Deletion,Trans-Activators,Upf1,UPF3,yeast,Zinc Fingers} } % == BibTeX quality report for heUpf1pNmd2pUpf3p1997: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{maderazoUpf1pControlNonsense2000, title = {Upf1p Control of Nonsense {{mRNA}} Translation Is Regulated by {{Nmd2p}} and {{Upf3p}}}, author = {Maderazo, A B and He, F and Mangus, D A and Jacobson, A}, year = 2000, month = jul, journal = {Molecular and Cellular Biology}, volume = {20}, number = {13}, pages = {4591–4603}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, doi = {10.1128/MCB.20.13.4591-4603.2000}, url = {http://mcb.asm.org/cgi/content/abstract/20/13/4591}, abstract = {Upf1p, Nmd2p, and Upf3p regulate the degradation of yeast mRNAs that contain premature translation termination codons. These proteins also appear to regulate the fidelity of termination, allowing translational suppression in their absence. Here, we have devised a novel quantitative assay for translational suppression, based on a nonsense allele of the CAN1 gene (can1-100), and used it to determine the regulatory roles of the UPF/NMD gene products. Deletion of UPF1, NMD2, or UPF3 stabilized the can1-100 transcript and promoted can1-100 nonsense suppression. Changes in mRNA levels were not the basis of suppression, however, since deletion of DCP1 or XRN1 or high-copy-number can1-100 expression in wild-type cells caused an increase in mRNA abundance similar to that obtained in upf/nmd cells but did not result in comparable suppression. can1-100 suppression was highest in cells harboring a deletion of UPF1, and overexpression of UPF1 in cells with individual or multiple upf/nmd mutations lowered the level of nonsense suppression without affecting the abundance of the can1-100 mRNA. Our findings indicate that Nmd2p and Upf3p regulate Upf1p activity and that Upf1p plays a critical role in promoting termination fidelity that is independent of its role in regulating mRNA decay. Consistent with these relationships, Upf1p, Nmd2p, and Upf3p were shown to be present at 1, 600, 160, and 80 molecules per cell, levels that underscored the importance of Upf1p but minimized the likelihood that these proteins were associated with all ribosomes or that they functioned as a stoichiometric complex.}, keywords = {Adaptor Proteins Signal Transducing,Amino Acid Transport Systems,CAENORHABDITIS-ELEGANS,Codon,Codon Nonsense,COMPLEX,COMPLEXES,DECAPPING ENZYME,DECAY,DECAY PATHWAY,degradation,expression,Fidelity,Fungal Proteins,gene,Gene Expression Regulation Fungal,Membrane Transport Proteins,MESSENGER-RNA TURNOVER,mRNA,mRNA decay,Mutation,MUTATIONS,nonsense suppression,nosource,protein,Protein Biosynthesis,Proteins,ribosome,Ribosomes,RNA Caps,RNA Helicases,RNA Messenger,RNA-Binding Proteins,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,suppression,Suppression Genetic,SURVEILLANCE COMPLEX,termination,TERMINATION CODON,Trans-Activators,Transcription Genetic,translation,TRANSLATION TERMINATION,Upf1,UPF3,XRN1,yeast,Yeasts} } % == BibTeX quality report for maderazoUpf1pControlNonsense2000: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{hannonUnlockingPotentialHuman2004, title = {Unlocking the Potential of the Human Genome with {{RNA}} Interference}, author = {Hannon, Gregory J and Rossi, John J}, year = 2004, month = sep, journal = {Nature}, volume = {431}, number = {7006}, pages = {371–378}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature02870}, url = {http://www.nature.com/nature/journal/v431/n7006/full/nature02870.html?lang=en}, abstract = {The discovery of RNA interference (RNAi) may well be one of the transforming events in biology in the past decade. RNAi can result in gene silencing or even in the expulsion of sequences from the genome. Harnessed as an experimental tool, RNAi has revolutionized approaches to decoding gene function. It also has the potential to be exploited therapeutically, and clinical trials to test this possibility are already being planned.}, keywords = {Animals,Drug Evaluation Preclinical,Gene Therapy,Genome Human,Genomics,Humans,nosource,RNA Interference,RNA Small Interfering} }

@article{studerUnfoldingMRNASecondary2006, title = {Unfolding of {{mRNA}} Secondary Structure by the Bacterial Translation Initiation Complex}, author = {Studer, Sean M and Joseph, Simpson}, year = 2006, month = apr, journal = {Molecular Cell}, volume = {22}, number = {1}, pages = {105–115}, publisher = {Elsevier}, issn = {1097-2765}, doi = {10.1016/j.molcel.2006.02.014}, url = {http://linkinghub.elsevier.com/retrieve/pii/S109727650600116X}, abstract = {Translation initiation is a key step for regulating the level of numerous proteins within the cell. In bacteria, the 30S initiation complex directly binds to the translation initiation region (TIR) of the mRNA. How the ribosomal 30S subunit assembles on highly structured TIR is not known. Using fluorescence-based experiments, we assayed 12 different mRNAs that form secondary structures with various stabilities and contain Shine-Dalgarno (SD) sequences of different strengths. A strong correlation was observed between the stability of the mRNA structure and the association and dissociation rate constants. Interestingly, in the presence of initiation factors and initiator tRNA, the association kinetics of structured mRNAs showed two distinct phases. The second phase was found to be important for unfolding structured mRNAs to form a stable 30S initiation complex. We show that unfolding of structured mRNAs requires a SD sequence, the start codon, fMet-tRNA(fMet), and the GTP bound form of initiation factor 2 bound to the 30S subunit.}, keywords = {Codon Initiator,Eukaryotic Initiation Factor-2,Kinetics,nosource,Nucleic Acid Conformation,Peptide Chain Initiation Translational,Protein Biosynthesis,RNA Bacterial,RNA Messenger,RNA Ribosomal,RNA Transfer Met} } % == BibTeX quality report for studerUnfoldingMRNASecondary2006: % ? unused Journal abbr (“Mol. Cell”)

@article{matlinUnderstandingAlternativeSplicing2005, title = {Understanding Alternative Splicing: Towards a Cellular Code}, author = {Matlin, Arianne J and Clark, Francis and Smith, Christopher W J}, year = 2005, month = may, journal = {Nature Reviews. Molecular Cell Biology}, volume = {6}, number = {5}, pages = {386–398}, publisher = {Nature Publishing Group}, issn = {1471-0072}, doi = {10.1038/nrm1645}, url = {http://www.nature.com/nrm/journal/v6/n5/abs/nrm1645.html}, abstract = {In violation of the ‘one gene, one polypeptide’ rule, alternative splicing allows individual genes to produce multiple protein isoforms - thereby playing a central part in generating complex proteomes. Alternative splicing also has a largely hidden function in quantitative gene control, by targeting RNAs for nonsense-mediated decay. Traditional gene-by-gene investigations of alternative splicing mechanisms are now being complemented by global approaches. These promise to reveal details of the nature and operation of cellular codes that are constituted by combinations of regulatory elements in pre-mRNA substrates and by cellular complements of splicing regulators, which together determine regulated splicing pathways.}, keywords = {Alternative Splicing,Animals,nosource,Spliceosomes} } % == BibTeX quality report for matlinUnderstandingAlternativeSplicing2005: % ? Possibly abbreviated journal title Nature Reviews. Molecular Cell Biology % ? unused Journal abbr (“Nat. Rev. Mol. Cell Biol”)

@article{hamiltonTwoClassesShort2002, title = {Two Classes of Short Interfering {{RNA}} in {{RNA}} Silencing}, author = {Hamilton, Andrew and Voinnet, Olivier and Chappell, Louise and Baulcombe, David}, year = 2002, month = sep, journal = {The EMBO Journal}, volume = {21}, number = {17}, pages = {4671–4679}, publisher = {Nature Publishing Group}, issn = {0261-4189}, doi = {10.1093/emboj/cdf464}, url = {http://www.nature.com/emboj/journal/v21/n17/abs/7594680a.html}, abstract = {RNA silencing is a eukaryotic genome defence system that involves processing of double-stranded RNA (dsRNA) into 21-26 nt, short interfering RNA (siRNA). The siRNA mediates suppression of genes corresponding to the dsRNA through targeted RNA degradation. In some plant systems there are additional silencing processes, involving systemic spread of silencing and RNA-directed methylation/transcriptional suppression of homologous genomic DNA. We show here that siRNAs produced in plants from a green fluorescent protein (GFP) transgene are in short (21-22 nt) and long (24-26 nt) size classes, whereas those from endogenous retroelements are only in the long class. Viral suppressors of RNA silencing and mutations in Arabidopsis indicate that these classes of siRNA have different roles. The long siRNA is dispensable for sequence-specific mRNA degradation, but correlates with systemic silencing and methylation of homologous DNA. Conversely, the short siRNA class correlates with mRNA degradation but not with systemic signalling or methylation. These findings reveal an unexpected level of complexity in the RNA silencing pathway in plants that may also apply in animals.}, keywords = {Adaptation Physiological,Adaptation- Physiological,Arabidopsis,Caulimovirus,Gene Silencing,Genes Reporter,Genes Viral,Genes- Reporter,Genes- Viral,Green Fluorescent Proteins,Luminescent Proteins,nosource,Plant Leaves,Plants Genetically Modified,Plants- Genetically Modified,Promoter Regions Genetic,Promoter Regions- Genetic,Recombinant Fusion Proteins,Retroelements,Rhizobium radiobacter,RNA Double-Stranded,RNA Plant,RNA Small Interfering,RNA Untranslated,RNA Viral,RNA- Double-Stranded,RNA- Plant,RNA- Small Interfering,RNA- Untranslated,RNA- Viral,Tobacco,Transgenes} } % == BibTeX quality report for hamiltonTwoClassesShort2002: % ? unused Journal abbr (“EMBO J”)

@article{blanchardTRNASelectionKinetic2004, title = {{{tRNA}} Selection and Kinetic Proofreading in Translation}, author = {Blanchard, Scott C and Gonzalez, Ruben L and Kim, Harold D and Chu, Steven and Puglisi, Joseph D}, year = 2004, month = oct, journal = {Nature Structural & Molecular Biology}, volume = {11}, number = {10}, pages = {1008–1014}, publisher = {Nature Publishing Group}, issn = {1545-9993}, doi = {10.1038/nsmb831}, url = {http://www.nature.com/nsmb/journal/v11/n10/abs/nsmb831.html}, abstract = {Using single-molecule methods we observed the stepwise movement of aminoacyl-tRNA (aa-tRNA) into the ribosome during selection and kinetic proofreading using single-molecule fluorescence resonance energy transfer (smFRET). Intermediate states in the pathway of tRNA delivery were observed using antibiotics and nonhydrolyzable GTP analogs. We identified three unambiguous FRET states corresponding to initial codon recognition, GTPase-activated and fully accommodated states. The antibiotic tetracycline blocks progression of aa-tRNA from the initial codon recognition state, whereas cleavage of the sarcin-ricin loop impedes progression from the GTPase-activated state. Our data support a model in which ribosomal recognition of correct codon-anticodon pairs drives rotational movement of the incoming complex of EF-Tu-GTP-aa-tRNA toward peptidyl-tRNA during selection on the ribosome. We propose a mechanistic model of initial selection and proofreading.}, keywords = {Codon,Energy Transfer,Fluorescence,GTP Phosphohydrolases,nosource,Protein Biosynthesis,RNA Transfer,RNA- Transfer} } % == BibTeX quality report for blanchardTRNASelectionKinetic2004: % ? unused Journal abbr (“Nat. Struct. Mol. Biol”)

@article{jacobsIdentificationFunctionalEndogenous2006, title = {Identification of Functional, Endogenous Programmed -1 Ribosomal Frameshift Signals in the Genome of {{Saccharomyces}} Cerevisiae}, author = {Jacobs, J. L. and Belew, A. T. and Rakauskaite, R. and Dinman, J. D.}, year = 2006, month = dec, journal = {Nucleic Acids Research}, volume = {35}, number = {1}, pages = {165–174}, issn = {0305-1048}, doi = {10.1093/nar/gkl1033}, url = {http://nar.oxfordjournals.org/content/35/1/165.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1802563&tool=pmcentrez&rendertype=abstract http://www.nar.oxfordjournals.org/cgi/doi/10.1093/nar/gkl1033}, abstract = {In viruses, programmed -1 ribosomal frameshifting (-1 PRF) signals direct the translation of alternative proteins from a single mRNA. Given that many basic regulatory mechanisms were first discovered in viral systems, the current study endeavored to: (i) identify -1 PRF signals in genomic databases, (ii) apply the protocol to the yeast genome and (iii) test selected candidates at the bench. Computational analyses revealed the presence of 10 340 consensus -1 PRF signals in the yeast genome. Of the 6353 yeast ORFs, 1275 contain at least one strong and statistically significant -1 PRF signal. Eight out of nine selected sequences promoted efficient levels of PRF in vivo. These findings provide a robust platform for high throughput computational and laboratory studies and demonstrate that functional -1 PRF signals are widespread in the genome of Saccharomyces cerevisiae. The data generated by this study have been deposited into a publicly available database called the PRFdb. The presence of stable mRNA pseudoknot structures in these -1 PRF signals, and the observation that the predicted outcomes of nearly all of these genomic frameshift signals would direct ribosomes to premature termination codons, suggest two possible mRNA destabilization pathways through which -1 PRF signals could post-transcriptionally regulate mRNA abundance.}, pmid = {17158156}, keywords = {0,ACID,Base Sequence,BIOLOGY,CEREVISIAE,chemistry,Codon,CODONS,Computational Biology,Data Interpretation,Data InterpretationStatistical,DATABASE,Databases,DatabasesNucleic Acid,frameshift,Frameshifting,FrameshiftingRibosomal,Fungal,Fungal: chemistry,Gene Expression Regulation,Gene Expression RegulationFungal,Genetic,genetics,Genome,GenomeFungal,genomic,Genomics,IDENTIFICATION,IDENTIFY,IN-VIVO,Internet,La,MECHANISM,MECHANISMS,Messenger,Messenger: chemistry,microbiology,Molecular Sequence Data,MOLECULAR-GENETICS,mRNA,nosource,Nucleic Acid,Nucleic Acid Conformation,PATHWAY,PREMATURE TERMINATION CODON,protein,Proteins,pseudoknot,pseudoknot structure,Regulatory Sequences,Regulatory SequencesRibonucleic Acid,Ribonucleic Acid,RIBONUCLEIC-ACID,Ribosomal,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,ribosome,Ribosomes,Rna,RNA,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,SIGNAL,Statistical,structure,Support,SYSTEM,SYSTEMS,termination,TERMINATION CODON,TERMINATION-CODON,translation,Viruses,yeast} }

@article{belewPRFdbDatabaseComputationally2008, title = {{{PRFdb}}: {{A}} Database of Computationally Predicted Eukaryotic Programmed -1 Ribosomal Frameshift Signals}, author = {Belew, Ashton T and Hepler, Nicholas L and Jacobs, Jonathan L and Dinman, Jonathan D}, year = 2008, journal = {BMC Genomics}, volume = {9}, number = {1}, pages = {339–47}, issn = {1471-2164}, doi = {10.1186/1471-2164-9-339}, url = {http://www.biomedcentral.com/1471-2164/9/339}, abstract = {BACKGROUND: The Programmed Ribosomal Frameshift Database (PRFdb) provides an interface to help researchers identify potential programmed -1 ribosomal frameshift (-1 PRF) signals in eukaryotic genes or sequences of interest. RESULTS: To identify putative -1 PRF signals, sequences are first imported from whole genomes or datasets, e.g. the yeast genome project and mammalian gene collection. They are then filtered through multiple algorithms to identify potential -1 PRF signals as defined by a heptameric slippery site followed by an mRNA pseudoknot. The significance of each candidate -1 PRF signal is evaluated by comparing the predicted thermodynamic stability (DeltaG degrees ) of the native mRNA sequence against a distribution of DeltaG degrees values of a pool of randomized sequences derived from the original. The data have been compiled in a user-friendly, easily searchable relational database. CONCLUSION: The PRFdB enables members of the research community to determine whether genes that they are investigating contain potential -1 PRF signals, and can be used as a metasource of information for cross referencing with other databases. It is available on the web at http://dinmanlab.umd.edu/prfdb}, keywords = {Algorithms,BIOLOGY,Computational Biology,DATABASE,Database Management Systems,Databases,EUKARYOTIC GENES,frameshift,FrameshiftingRibosomal,gene,Genes,Genetic,genetics,Genome,IDENTIFY,INFORMATION,interface,Internet,La,MOLECULAR-GENETICS,mRNA,nosource,pseudoknot,RIBOSOMAL FRAMESHIFT,sequence,SEQUENCES,SIGNAL,SITE,slippery site,stability,Support,thermodynamic stability,User-Computer Interface,yeast} }

@article{belewEndogenousRibosomalFrameshift2010, title = {Endogenous Ribosomal Frameshift Signals Operate as {{mRNA}} Destabilizing Elements through at Least Two Molecular Pathways in Yeast}, author = {Belew, A. T. and Advani, V. M. and Dinman, J. D.}, year = 2010, month = nov, journal = {Nucleic Acids Research}, volume = {39}, number = {7}, pages = {2799–2808}, publisher = {Oxford Univ Press}, issn = {0305-1048}, doi = {10.1093/nar/gkq1220}, url = {http://nar.oxfordjournals.org/content/39/7/2799.short http://www.nar.oxfordjournals.org/cgi/doi/10.1093/nar/gkq1220}, keywords = {nosource} }

@article{buchanTRNAPropertiesHelp2006, title = {{{tRNA}} Properties Help Shape Codon Pair Preferences in Open Reading Frames}, author = {Buchan, J Ross and Aucott, Lorna S and Stansfield, Ian}, year = 2006, journal = {Nucleic Acids Research}, volume = {34}, number = {3}, pages = {1015–1027}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gkj488}, url = {http://nar.oxfordjournals.org/content/34/3/1015.short}, abstract = {Translation elongation is an accurate and rapid process, dependent upon efficient juxtaposition of tRNAs in the ribosomal A- and P-sites. Here, we sought evidence of A- and P-site tRNA interaction by examining bias in codon pair choice within open reading frames from a range of genomes. Three distinct and marked effects were revealed once codon and dipeptide biases had been subtracted. First, in the majority of genomes, codon pair preference is primarily determined by a tetranucleotide combination of the third nucleotide of the P-site codon, and all 3 nt of the A-site codon. Second, pairs of rare codons are generally under-used in eukaryotes, but over-used in prokaryotes. Third, the analysis revealed a highly significant effect of tRNA-mediated selection on codon pairing in unicellular eukaryotes, Bacillus subtilis, and the gamma proteobacteria. This was evident because in these organisms, synonymous codons decoded in the A-site by the same tRNA exhibit significantly similar P-site pairing preferences. Codon pair preference is thus influenced by the identity of A-site tRNAs, in combination with the P-site codon third nucleotide. Multivariate analysis identified conserved nucleotide positions within A-site tRNA sequences that modulate codon pair preferences. Structural features that regulate tRNA geometry within the ribosome may govern genomic codon pair patterns, driving enhanced translational fidelity and/or rate.}, keywords = {Bacillus subtilis,Bacteria,Base Pairing,Cluster Analysis,Codon,Gammaproteobacteria,Genomics,nosource,Open Reading Frames,RNA Transfer,Yeasts} } % == BibTeX quality report for buchanTRNAPropertiesHelp2006: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{oconnorTRNAImbalancePromotes1998, title = {{{tRNA}} Imbalance Promotes -1 Frameshifting via near-Cognate Decoding.}, author = {O’Connor, M}, year = 1998, month = jun, journal = {Journal of Molecular Biology}, volume = {279}, number = {4}, eprint = {9642056}, eprinttype = {pubmed}, pages = {727–736}, issn = {0022-2836}, doi = {10.1006/jmbi.1998.1832}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9642056}, abstract = {tRNAGly1 is the Escherichia coli glycine tRNA specific for GGG codons. A genetic selection for multicopy suppressors of a frameshift mutation has shown that increased levels of wild-type tRNAGly1 causes -1 frameshifting. Analysis of the suppression spectrum of this multicopy suppressor and peptide sequencing of the suppressed protein product showed that it promoted GG doublet decoding at the near-cognate GGA codons. It is proposed that increasing the concentration of the GGG-specific tRNAGly1 relative to the cognate GGA-decoding tRNAGly2 allows the near-cognate tRNA to read GGA codons. Near-cognate decoding of GGA codons by tRNAGly1 can occur by a two-out-of-three reading mechanism, in which only the first two bases of the GGA codon are paired with the anticodon, thus permitting doublet translocations. In mycoplasmas, a single tRNA typically decodes all four triplets of a codon family and introduction of a feature of the Mypoplasma mycoides tRNAGly responsible for non-discriminate decoding, a C at position 32, into the anticodon E. coli tRNAGly1, enhanced the efficiency of doublet decoding.}, pmid = {9642056}, keywords = {Bacterial,Bacterial: genetics,Escherichia coli,Escherichia coli: genetics,Frameshift Mutation,Gene Expression Regulation,Gene Expression Regulation Bacterial,Gly,Gly: genetics,nosource,Protein Biosynthesis,RNA,RNA Bacterial,RNA Transfer Gly,Transfer} } % == BibTeX quality report for oconnorTRNAImbalancePromotes1998: % ? unused Journal abbr (“J. Mol. Biol”)

@article{blanchardTRNADynamicsRibosome2004, title = {{{tRNA}} Dynamics on the Ribosome during Translation}, author = {Blanchard, Scott C and Kim, Harold D and Gonzalez, Ruben L and Puglisi, Joseph D and Chu, Steven}, year = 2004, month = aug, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {35}, eprint = {15317937}, eprinttype = {pubmed}, pages = {12893–12898}, issn = {0027-8424}, doi = {10.1073/pnas.0403884101}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15317937}, abstract = {Using single-molecule fluorescence spectroscopy, time-resolved conformational changes between fluorescently labeled tRNA have been characterized within surface-immobilized ribosomes proceeding through a complete cycle of translation elongation. Fluorescence resonance energy transfer was used to observe aminoacyl-tRNA (aa-tRNA) stably accommodating into the aminoacyl site (A site) of the ribosome via a multistep, elongation factor-Tu dependent process. Subsequently, tRNA molecules, bound at the peptidyl site and A site, fluctuate between two configurations assigned as classical and hybrid states. The lifetime of classical and hybrid states, measured for complexes carrying aa-tRNA and peptidyl-tRNA at the A site, shows that peptide bond formation decreases the lifetime of the classical-state tRNA configuration by approximately 6-fold. These data suggest that the growing peptide chain plays a role in modulating fluctuations between hybrid and classical states. Single-molecule fluorescence resonance energy transfer was also used to observe aa-tRNA accommodation coupled with elongation factor G-mediated translocation. Dynamic rearrangements in tRNA configuration are also observed subsequent to the translocation reaction. This work underscores the importance of dynamics in ribosome function and demonstrates single-particle enzymology in a system of more than two components.}, pmid = {15317937}, keywords = {A SITE,A-SITE,BOND FORMATION,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,DYNAMICS,elongation,ELONGATION-FACTOR-TU,Energy Transfer,enzymology,FACTOR TU,Fluorescence,Fluorescence Resonance Energy Transfer,La,Microscopy Fluorescence,nosource,peptide bond formation,Protein Biosynthesis,ribosome,Ribosomes,RNA Transfer,SITE,SPECTROSCOPY,SYSTEM,Time Factors,translation,translocation,tRNA} } % == BibTeX quality report for blanchardTRNADynamicsRibosome2004: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{hoggUpf1Senses3UTR2010, title = {Upf1 {{Senses}} 3{\(\prime\)}{{UTR Length}} to {{Potentiate mRNA Decay}}}, author = {Hogg, J. Robert and Goff, Stephen P.}, year = 2010, month = oct, journal = {Cell}, volume = {143}, number = {3}, pages = {379–389}, publisher = {Elsevier}, issn = {00928674}, doi = {10.1016/j.cell.2010.10.005}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867410011414}, keywords = {nosource} } % == BibTeX quality report for hoggUpf1Senses3UTR2010: % ? Title looks like it was stored in title-case in Zotero

@article{hosodaTranslationTerminationFactor2003, title = {Translation Termination Factor {{eRF3}} Mediates {{mRNA}} Decay through the Regulation of Deadenylation}, author = {Hosoda, Nao and Kobayashi, Tetsuo and Uchida, Naoyuki and Funakoshi, Yuji and Kikuchi, Yoshiko and Hoshino, Shinichi and Katada, Toshiaki}, year = 2003, month = oct, journal = {The Journal of Biological Chemistry}, volume = {278}, number = {40}, pages = {38287–38291}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.C300300200}, url = {http://www.jbc.org/content/278/40/38287.short}, abstract = {Messenger RNA decay, which is a regulated process intimately linked to translation, begins with the deadenylation of the poly(A) tail at the 3’ end. However, the precise mechanism triggering the first step of mRNA decay and its relationship to translation have not been elucidated. Here, we show that the translation termination factor eRF3 mediates mRNA deadenylation and decay in the yeast Saccharomyces cerevisiae. The N-domain of eRF3, which is not necessarily required for translation termination, interacts with the poly(A)-binding protein PABP. When this interaction is blocked by means of deletion or overexpression of the N-domain of eRF3, half-lives of all mRNAs are prolonged. The eRF3 mutant lacking the N-domain is deficient in the poly(A) shortening. Furthermore, the eRF3-mediated mRNA decay requires translation to proceed, especially ribosomal transition through the termination codon. These results indicate that the N-domain of eRF3 mediates mRNA decay by regulating deadenylation in a manner coupled to translation.}, keywords = {Codon,Fungal Proteins,Models Biological,Models Genetic,Models- Biological,Models- Genetic,nosource,Peptide Termination Factors,Poly A,Poly(A)-Binding Proteins,Precipitin Tests,Prions,Protein Binding,Protein Biosynthesis,Protein Structure Tertiary,Protein Structure- Tertiary,RNA,RNA Messenger,RNA- Messenger,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Time Factors} } % == BibTeX quality report for hosodaTranslationTerminationFactor2003: % ? unused Journal abbr (“J. Biol. Chem”)

@article{burckTranslationalSuppressorsAntisuppressors1999, title = {Translational Suppressors and Antisuppressors Alter the Efficiency of the {{Ty1}} Programmed Translational Frameshift.}, author = {Burck, C L and Chernoff, Y O and Liu, R and Farabaugh, P J and Liebman, S W}, year = 1999, month = nov, journal = {RNA (New York, N.Y.)}, volume = {5}, number = {11}, pages = {1451–1457}, issn = {1355-8382}, url = {http://rnajournal.cshlp.org/content/5/11/1451.short}, abstract = {Certain viruses, transposons, and cellular genes have evolved specific sequences that induce high levels of specific translational errors. Such “programmed misreading” can result in levels of frameshifting or nonsense codon readthrough that are up to 1,000-fold higher than normal. Here we determine how a number of mutations in yeast affect the programmed misreading used by the yeast Ty retrotransposons. These mutations have previously been shown to affect the general accuracy of translational termination. We find that among four nonsense suppressor ribosomal mutations tested, one (a ribosomal protein mutation) enhanced the efficiency of the Tyl frameshifting, another (an rRNA mutation) reduced frameshifting, and two others (another ribosomal protein mutation and another rRNA mutation) had no effect. Three antisuppressor rRNA mutations all reduced Tyl frameshifting; however the antisuppressor mutation in the ribosomal protein did not show any effect. Among nonribosomal mutations, the allosuppressor protein phosphatase mutation enhanced Tyl frameshifting, whereas the partially inactive prion form of the release factor eRF3 caused a slight decrease, if any effect. A mutant form of the other release factor, eRF1, also had no effect on frameshifting. Our data suggest that Ty frameshifting is under the control of the cellular translational machinery. Surprisingly we find that translational suppressors can affect Ty frameshifting in either direction, whereas antisuppressors have either no effect or cause a decrease.}, pmid = {10580473}, keywords = {Base Sequence,beta-Galactosidase,Codon,Escherichia coli,Frameshifting Ribosomal,Mutagenesis Insertional,nosource,programmed misreading,Protein Biosynthesis,rdna,Retroelements,retrotransposon,Saccharomyces cerevisiae,Suppression Genetic,translational accuracy,yeast} } % == BibTeX quality report for burckTranslationalSuppressorsAntisuppressors1999: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{gaoTranslationalRecodingSignals2003, title = {Translational Recoding Signals between Gag and Pol in Diverse {{LTR}} Retrotransposons}, author = {Gao, Xiang and Havecker, Ericka R and Baranov, Pavel V and Atkins, John F and Voytas, Daniel F}, year = 2003, month = dec, journal = {RNA (New York, N.Y.)}, volume = {9}, number = {12}, pages = {1422–1430}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, doi = {10.1261/rna.5105503}, url = {http://www.rnajournal.org/cgi/doi/10.1261/rna.5105503 http://rnajournal.cshlp.org/content/9/12/1422.short}, abstract = {Because of their compact genomes, retroelements (including retrotransposons and retroviruses) employ a variety of translational recoding mechanisms to express Gag and Pol. To assess the diversity of recoding strategies, we surveyed gag/pol gene organization among retroelements from diverse host species, including elements exhaustively recovered from the genome sequences of Caenorhabditis elegans, Drosophila melanogaster, Schizosaccharomyces pombe, Candida albicans, and Arabidopsis thaliana. In contrast to the retroviruses, which typically encode pol in the -1 frame relative to gag, nearly half of the retroelements surveyed encode a single gag-pol open reading frame. This was particularly true for the Ty1/copia group retroelements. Most animal Ty3/gypsy retroelements, on the other hand, encode gag and pol in separate reading frames, and likely express Pol through +1 or -1 frameshifting. Conserved sequences conforming to slippery sites that specify viral ribosomal frameshifting were identified among retroelements with pol in the -1 frame. None of the plant retroelements encoded pol in the -1 frame relative to gag; however, two closely related plant Ty3/gypsy elements encode pol in the +1 frame. Interestingly, a group of plant Ty1/copia retroelements encode pol either in a +1 frame relative to gag or in two nonoverlapping reading frames. These retroelements have a conserved stem-loop at the end of gag, and likely express pol either by a novel means of internal ribosomal entry or by a bypass mechanism.}, keywords = {animal,Base Sequence,BIOLOGY,Caenorhabditis,Caenorhabditis elegans,CAENORHABDITIS-ELEGANS,Candida albicans,Codon Terminator,Conserved Sequence,development,DIVERSITY,DNA,Drosophila,Drosophila melanogaster,DROSOPHILA-MELANOGASTER,ELEGANS,ELEMENTS,FRAME,frameshifting,Frameshifting,Gag,Gag-pol,gene,Genes gag,Genes pol,Genetic,genetics,Genome,human,INTERNAL RIBOSOMAL ENTRY,La,MECHANISM,MECHANISMS,Molecular Sequence Data,nosource,OPEN READING FRAME,Open Reading Frames,ORGANIZATION,Phylogeny,pol,Protein Biosynthesis,READING FRAME,Reading Frames,recoding,Repetitive Sequences Nucleic Acid,Retroelements,retrotransposon,RETROVIRUSES,ribosomal frameshifting,Schizosaccharomyces,sequence,Sequence Homology Nucleic Acid,SEQUENCES,SIGNAL,SITE,SITES,slippery site,STEM-LOOP,translational regulation} } % == BibTeX quality report for gaoTranslationalRecodingSignals2003: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{farabaughTranslationalFrameshiftingImplications2000, title = {Translational Frameshifting: Implications for the Mechanism of Translational Frame Maintenance}, author = {Farabaugh, P J}, year = 2000, journal = {Progress in Nucleic Acid Research and Molecular Biology}, volume = {64}, eprint = {10697409}, eprinttype = {pubmed}, pages = {131–170}, issn = {0079-6603}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10697409}, abstract = {The ribosome rapidly translates the information in the nucleic sequence of mRNA into the amino acid sequence of proteins. As with any biological process, translation is not completely accurate; it must compromise the antagonistic demands of increased speed and greater accuracy. Yet, reading-frame errors are especially infrequent, occurring at least 10 times less frequently than other errors. How do ribosomes maintain the reading frame so faithfully? Geneticists have addressed this question by identifying suppressors that increase error frequency. Most familiar are the frameshift suppressor tRNAs, though other suppressors include mutant forms of rRNA, ribosomal proteins, or translation factors. Certain mRNA sequences can also program frameshifting by normal ribosomes. The models of suppression and programmed frameshifting describe apparently quite different mechanisms. Contemporary work has questioned the long-accepted model for frameshift suppression by mutant tRNAs, and a unified explanation has been proposed for both phenomena. The Quadruplet Translocation Model proposes that suppressor tRNAs cause frameshifting by recognizing an expanded mRNA codon. The new data are inconsistent with this model for some tRNAs, implying the model may be invalid for all. A new model for frameshift suppression involves slippage caused by a weak, near-cognate codon.anticodon interaction. This strongly resembles the mechanism of +1 programmed frameshifting. This may mean that infrequent frameshift errors by normal ribosomes may result from two successive errors: misreading by a near-cognate tRNA, which causes a subsequent shift in reading frame. Ribosomes may avoid phenotypically serious frame errors by restricting apparently innocuous errors of sense.}, pmid = {10697409}, keywords = {Anticodon,Frameshifting Ribosomal,Models Genetic,nosource,RNA Transfer,Suppression Genetic} } % == BibTeX quality report for farabaughTranslationalFrameshiftingImplications2000: % ? unused Journal abbr (“Prog. Nucleic Acid Res. Mol. Biol”)

@article{dreherTranslationalControlPositive2006, title = {Translational Control in Positive Strand {{RNA}} Plant Viruses}, author = {Dreher, Theo W and Miller, W Allen}, year = 2006, month = jan, journal = {Virology}, volume = {344}, number = {1}, pages = {185–197}, publisher = {Elsevier}, issn = {0042-6822}, doi = {10.1016/j.virol.2005.09.031}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0042682205005799}, abstract = {The great variety of genome organizations means that most plant positive strand viral RNAs differ from the standard 5’-cap/3’-poly(A) structure of eukaryotic mRNAs. The cap and poly(A) tail recruit initiation factors that support the formation of a closed loop mRNA conformation, the state in which translation initiation is most efficient. We review the diverse array of cis-acting sequences present in viral mRNAs that compensate for the absence of a cap, poly(A) tail, or both. We also discuss the cis-acting sequences that control translation strategies that both amplify the coding potential of a genome and regulate the accumulations of viral gene products. Such strategies include leaky scanning initiation of translation of overlapping open reading frames, stop codon readthrough, and ribosomal frameshifting. Finally, future directions for research on the translation of plant positive strand viruses are discussed.}, keywords = {0,3,3’ Untranslated Regions,Cap,Codon,Codon Terminator,Codon- Terminator,CodonTerminator,CONFORMATION,FRAME,Frameshifting,Frameshifting Ribosomal,Frameshifting- Ribosomal,FrameshiftingRibosomal,gene,GENE-PRODUCT,genetics,Genome,GENOME ORGANIZATION,Genome Viral,Genome- Viral,GenomeViral,initiation,INITIATION-FACTOR,La,LOOP,metabolism,microbiology,mRNA,nosource,OPEN READING FRAME,Open Reading Frames,ORGANIZATION,Plant Viruses,poly(A),POLY(A) TAIL,PRODUCT,PRODUCTS,protein,Protein Biosynthesis,Proteins,READING FRAME,Reading Frames,readthrough,REGION,Review,ribosomal frameshifting,Rna,Rna Caps,RNA Caps,RNA Viruses,scanning,sequence,SEQUENCES,STOP CODON,structure,Support,translation,TRANSLATION INITIATION,Untranslated Regions,Viral Proteins,VIRAL-RNA,Viruses} }

@article{mendezTranslationalControlCPEB2001, title = {Translational Control by {{CPEB}}: A Means to the End}, author = {Mendez, R and Richter, J D}, year = 2001, month = jul, journal = {Nature Reviews. Molecular Cell Biology}, volume = {2}, number = {7}, pages = {521–529}, publisher = {Nature Publishing Group}, issn = {1471-0072}, doi = {10.1038/35080081}, url = {http://www.nature.com/nrm/journal/v2/n7/abs/nrm0701_521a.html http://goldfarb.bioweb.hunter.cuny.edu/files/Public/BIOL470.58-BIOL790.61/Topic 3 Synaptic Plasticity/Mendez.Richter.NatRev.2001.pdf http://goldfarb.bioweb.hunter.cuny.edu/files/Public/BIOL470.58-BIOL790.61/Topic 3 Synaptic Plasticity/Mendez.Richter.NatRev.2001.pdf}, abstract = {The regulated translation of messenger RNA is essential for cell-cycle progression, establishment of the body plan during early development, and modulation of key activities in the central nervous system. Cytoplasmic polyadenylation, which is one mechanism of controlling translation, is driven by CPEB–a highly conserved, sequence-specific RNA-binding protein that binds to the cytoplasmic polyadenylation element, and modulates translational repression and mRNA localization. What are the features and functions of this multifaceted protein?}, keywords = {Animals,Cell Cycle,Cytoplasm,Gene Expression Regulation,Humans,Models Biological,Models- Biological,Molecular Structure,mRNA Cleavage and Polyadenylation Factors,Neuronal Plasticity,nosource,Oocytes,Phylogeny,Protein Biosynthesis,RNA Messenger,RNA- Messenger,RNA-Binding Proteins,Transcription Factors,Xenopus laevis,Xenopus Proteins} } % == BibTeX quality report for mendezTranslationalControlCPEB2001: % ? Possibly abbreviated journal title Nature Reviews. Molecular Cell Biology % ? unused Journal abbr (“Nat. Rev. Mol. Cell Biol”)

@article{stahlTranslationalAccuracyExponential2004, title = {Translational Accuracy during Exponential, Postdiauxic, and Stationary Growth Phases in {{Saccharomyces}} Cerevisiae}, author = {Stahl, Guillaume and Salem, Samia N Ben and Chen, Lifeng and Zhao, Bing and Farabaugh, Philip J}, year = 2004, month = apr, journal = {Eukaryotic Cell}, volume = {3}, number = {2}, pages = {331–338}, publisher = {Am Soc Microbiol}, issn = {1535-9778}, doi = {10.1128/EC.3.2.331-338.2004}, url = {http://ec.asm.org/cgi/content/abstract/3/2/331}, abstract = {When the yeast Saccharomyces cerevisiae shifts from rapid growth on glucose to slow growth on ethanol, it undergoes profound changes in cellular metabolism, including the destruction of most of the translational machinery. We have examined the effect of this metabolic change, termed the diauxic shift, on the frequency of translational errors. Recoding sites are mRNA sequences that increase the frequency of translational errors, providing a convenient reporter of translational accuracy. We found that the diauxic shift causes no overall change in translational accuracy but does cause a strong reduction in the frequency of one type of programmed error: Ty +1 frameshifting. Genetic data suggest that this effect may be due to changes in the relative amounts of tRNA participating in translation elongation. We discuss possible implications for expression strategies that use recoding.}, keywords = {+1 frameshifting,accuracy,CEREVISIAE,Codon,elongation,ERRORS,Ethanol,expression,Frameshifting,Frameshifting Ribosomal,Genetic,Glucose,GROWTH,La,metabolism,mRNA,nosource,Protein Biosynthesis,recoding,Retroelements,RNA Transfer Amino Acyl,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,SITE,SITES,translation,tRNA,Ty,yeast} }

@article{culbertsonTranscriptSelectionRecruitment2005, title = {Transcript Selection and the Recruitment of {{mRNA}} Decay Factors for {{NMD}} in {{Saccharomyces}} Cerevisiae}, author = {Culbertson, Michael R and {Neeno-Eckwall}, Eric}, year = 2005, month = sep, journal = {RNA (New York, N.Y.)}, volume = {11}, number = {9}, pages = {1333–1339}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, doi = {10.1261/rna.2113605}, url = {http://rnajournal.cshlp.org/content/11/9/1333.short}, abstract = {In Saccharomyces cerevisiae, nonsense-mediated mRNA decay (NMD) requires Upf1p, Upf2p, and Upf3p to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target Cbc-bound or eIF-4E-bound transcripts. Extremely low concentrations of the Upf proteins relative to the total pool of transcripts make it difficult to understand how nonsense transcripts are selectively recruited. To stimulate debate, we propose two alternative mechanisms for selecting nonsense transcripts for NMD and for assembling components of the surveillance complex, one for the first (pioneer) round of translation, called “nuclear marking,” and the other for subsequent rounds, called “reverse assembly.” The model is designed to accommodate (1) the low abundance of NMD factors, (2) the role of nucleocytoplasmic shuttling proteins in NMD, (3) the independent and nonobligate order of assembly of two different subcomplexes of NMD factors, and (4) the ability of NMD to simultaneously reduce or eliminate the synthesis of truncated proteins produced by nonsense transcripts while down-regulating but not completely eliminating functional proteins produced from error-free NMD-sensitive transcripts}, keywords = {Animals,Codon Nonsense,nosource,RNA Messenger,RNA Processing Post-Transcriptional,RNA-Binding Proteins,Saccharomyces cerevisiae,Transcription Genetic} } % == BibTeX quality report for culbertsonTranscriptSelectionRecruitment2005: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{nudlerTranscriptionElongationStructural1999, title = {Transcription Elongation: Structural Basis and Mechanisms 1}, author = {Nudler, E}, year = 1999, month = apr, journal = {Journal of Molecular Biology}, volume = {288}, number = {1}, pages = {1–12}, publisher = {Elsevier}, issn = {0022-2836}, doi = {10.1006/jmbi.1999.2641}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(99)92641-4}, abstract = {A ternary complex composed of RNA polymerase (RNAP), DNA template, and RNA transcript is the central intermediate in the transcription cycle responsible for the elongation of the RNA chain. Although the basic biochemistry of RNAP functioning is well understood, little is known about the underlying structural determinants. The absence of high- resolution structural data has hampered our understanding of RNAP mechanism. However, recent work suggests a structure-function model of the ternary elongation complex, if not at a defined structural level, then at least as a conceptual view, such that key components of RNAP are defined operationally on the basis of compelling biochemical, protein chemical, and genetic data. The model has important implications for mechanisms of transcription elongation and also for initiation and termination.}, keywords = {Bacterial Proteins,Binding Sites,DNA,DNA-Directed RNA Polymerases,Escherichia coli,Macromolecular Substances,Models Genetic,nosource,Protein Binding,RNA Messenger,Structure-Activity Relationship,Transcription Genetic} } % == BibTeX quality report for nudlerTranscriptionElongationStructural1999: % ? unused Journal abbr (“J. Mol. Biol”)

@article{buhlerTranscriptionalSilencingNonsense2005, title = {Transcriptional Silencing of Nonsense Codon-Containing Immunoglobulin Minigenes}, author = {B{"u}hler, Marc and Mohn, Fabio and Stalder, Lukas and M{"u}hlemann, Oliver}, year = 2005, month = apr, journal = {Molecular Cell}, volume = {18}, number = {3}, eprint = {15866173}, eprinttype = {pubmed}, pages = {307–317}, publisher = {Elsevier}, issn = {1097-2765}, doi = {10.1016/j.molcel.2005.03.030}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15866173 http://linkinghub.elsevier.com/retrieve/pii/S1097276505012232}, abstract = {Cells possess mechanisms to prevent synthesis of potentially deleterious truncated proteins caused by premature translation-termination codons (PTCs). Here, we show that PTCs can induce silencing of transcription of its cognate gene. We demonstrate for immunoglobulin (Ig)-mu minigenes expressed in HeLa cells that this transcriptional silencing is PTC specific and reversible by treatment of the cells with histone deacetylase inhibitors. Furthermore, PTC-containing Ig-mu minigenes are significantly more associated with K9-methylated histone H3 and less associated with acetylated H3 than the PTC-free Ig-mu minigene. This nonsense-mediated transcriptional gene silencing (NMTGS) is also observed with an Ig-gamma minigene, but not with several classic NMD reporter genes, suggesting that NMTGS might be specific for Ig genes. NMTGS represents a nonsense surveillance mechanism by which truncation of a gene’s open reading frame (ORF) induces transcriptional silencing through chromatin remodeling. Remarkably, NMTGS is inhibited by overexpression of the putative siRNase 3’hExo, suggesting that siRNA-like molecules are involved in NMTGS.}, keywords = {Base Sequence,Codon Nonsense,Exonucleases,Gene Silencing,Genes Immunoglobulin,Genes Reporter,Hela Cells,Histone Deacetylase Inhibitors,Histone Deacetylases,Histones,Humans,Immunoglobulins,Lysine,Methylation,nosource,RNA Interference,Sequence Alignment,Transcription Genetic} } % == BibTeX quality report for buhlerTranscriptionalSilencingNonsense2005: % ? unused Journal abbr (“Mol. Cell”)

@article{nasmythTranscriptionalRegulationYeast1987, title = {Transcriptional Regulation in the Yeast Life Cycle}, author = {Nasmyth, K and Shore, D}, year = 1987, month = sep, journal = {Science (New York, N.Y.)}, volume = {237}, number = {4819}, pages = {1162–1170}, publisher = {American Association for the Advancement of Science}, issn = {0036-8075}, url = {http://www.sciencemag.org/content/237/4819/1162.short}, abstract = {The transition from haploid to diploid in homothallic yeast involves a defined sequence of events which are regulated at the level of transcription. Transcription factors encoded by SWI genes activate the HO endonuclease gene at a precise stage in the cell cycle of mother cells. The HO endonuclease initiates a transposition event which activates genes of the opposite mating type by causing them to move away from a silencer element. The activated mating type genes then regulate genes involved in cell signaling such as the mating type-specific pheromones and their receptors. Since HO is only activated in one of the sister cells after division (the mother), adjacent cells of opposite mating type are generated which respond to each others’ secreted pheromones by inducing genes involved in conjugation. This leads to the formation of a diploid in which many of the genes involved in mating and mating-type switching become repressed due to the heterozygosity of the mating-type locus. This article summarizes what is known about these transcriptional controls and discusses possible parallels in higher eukaryotes.}, keywords = {Crosses Genetic,Gene Expression Regulation,Genes Fungal,Genes Mating Type Fungal,nosource,Saccharomyces cerevisiae,Transcription Genetic} } % == BibTeX quality report for nasmythTranscriptionalRegulationYeast1987: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”)

@article{bekaertComputationalModel12003, title = {Towards a Computational Model for -1 Eukaryotic Frameshifting Sites}, author = {Bekaert, Micha{"e}l and Bidou, Laure and Denise, Alain and {Duchateau-Nguyen}, Guillemette and Forest, Jean-Paul and Froidevaux, Christine and Hatin, Isabelle and Rousset, Jean-Pierre and Termier, Michel}, year = 2003, month = feb, journal = {Bioinformatics (Oxford, England)}, volume = {19}, number = {3}, eprint = {12584117}, eprinttype = {pubmed}, pages = {327–335}, publisher = {Oxford Univ Press}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btf868}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12584117 http://bioinformatics.oxfordjournals.org/content/19/3/327.short}, abstract = {MOTIVATION: Unconventional decoding events are now well acknowledged, but not yet well formalized. In this study, we present a bioinformatics analysis of eukaryotic -1 frameshifting, in order to model this event. RESULTS: A consensus model has already been established for -1 frameshifting sites. Our purpose here is to provide new constraints which make the model more precise. We show how a machine learning approach can be used to refine the current model. We identify new properties that may be involved in frameshifting. Each of the properties found was experimentally validated. Initially, we identify features of the overall model that are to be simultaneously satisfied. We then focus on the following two components: the spacer and the slippery sequence. As a main result, we point out that the identity of the primary structure of the so-called spacer is of great importance. AVAILABILITY: Sequences of the oligonucleotides in the functional tests are available at http://www.igmors.u-psud.fr/rousset/bioinformatics/.}, keywords = {0,Algorithms,analysis,Animals,Artificial Intelligence,Base Sequence,Birds,COMPONENT,Computer Simulation,decoding,DNA Ribosomal Spacer,Eukaryotic Cells,Frameshifting,Frameshifting Ribosomal,Gene Expression Regulation,Gene Expression Regulation Viral,GENE-EXPRESSION,genomic,Haplorhini,Humans,Models Genetic,Molecular Sequence Data,MUTATIONAL ANALYSIS,nosource,RIBOSOMAL FRAMESHIFT,RNA PSEUDOKNOT,ROUS-SARCOMA VIRUS,sequence,Sequence Analysis RNA,SIGNAL,structure,translation,Viruses} } % == BibTeX quality report for bekaertComputationalModel12003: % ? unused Journal abbr (“Bioinformatics”)

@article{plantTorsionalRestraintNew2005, title = {Torsional Restraint: A New Twist on Frameshifting Pseudoknots.}, author = {Plant, Ewan P and Dinman, Jonathan D}, year = 2005, month = jan, journal = {Nucleic Acids Research}, volume = {33}, number = {6}, pages = {1825–1833}, issn = {1362-4962}, doi = {10.1093/nar/gki329}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1072802&tool=pmcentrez&rendertype=abstract}, abstract = {mRNA pseudoknots have a stimulatory function in programmed -1 ribosomal frameshifting (-1 PRF). Though we previously presented a model for how mRNA pseudoknots might activate the mechanism for -1 PRF, it did not address the question of the role that they may play in positioning the mRNA relative to the ribosome in this process [E. P. Plant, K. L. M. Jacobs, J. W. Harger, A. Meskauskas, J. L. Jacobs, J. L. Baxter, A. N. Petrov and J. D. Dinman (2003) RNA, 9, 168-174]. A separate ‘torsional restraint’ model suggests that mRNA pseudoknots act to increase the fraction of ribosomes directed to pause with the upstream heptameric slippery site positioned at the ribosome’s A- and P-decoding sites [J. D. Dinman (1995) Yeast, 11, 1115-1127]. Here, experiments using a series of ‘pseudo-pseudoknots’ having different degrees of rotational freedom were used to test this model. The results of this study support the mechanistic hypothesis that -1 ribosomal frameshifting is enhanced by torsional resistance of the mRNA pseudoknot.}, pmid = {15800212}, keywords = {0,Base Sequence,BIOLOGY,chemistry,D,Frameshifting,Frameshifting Ribosomal,FrameshiftingRibosomal,Genetic,genetics,La,M,MECHANISM,Messenger,Messenger: chemistry,Messenger: metabolism,metabolism,microbiology,MODEL,Models,Models Genetic,ModelsGenetic,Molecular Sequence Data,MOLECULAR-GENETICS,mRNA,nosource,Nucleic Acid Conformation,Protein Biosynthesis,pseudoknot,pseudoknots,Research SupportU.S.Gov’tP.H.S.,RESISTANCE,Ribosomal,ribosomal frameshifting,ribosome,Ribosomes,Ribosomes: metabolism,Rna,RNA,RNA Messenger,RNAMessenger,Rotation,SERIES,SITE,SITES,slippery site,Support,UPSTREAM,yeast} } % == BibTeX quality report for plantTorsionalRestraintNew2005: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{arfvidssonTimeminimizedDeterminationRibosome2003a, title = {Time-Minimized Determination of Ribosome and {{tRNA}} Levels in Bacterial Cells Using Flow Field-Flow Fractionation}, author = {Arfvidsson, Cecilia and Wahlund, Karl Gustav}, year = 2003, month = feb, journal = {Analytical Biochemistry}, volume = {313}, number = {1}, eprint = {12576061}, eprinttype = {pubmed}, pages = {76–85}, issn = {0003-2697}, doi = {10.1016/S0003-2697(02)00541-9}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12576061}, abstract = {The evaluation of the translation capacity of cells that produce recombinant proteins can be made by monitoring their ribosomal composition. In a previous use of asymmetrical flow field-flow fractionation (AsFlFFF) for this purpose the overall analysis time was more than 1 h and 40 min, based on a standard protocol for cell harvest, washing, cell disruption, and the final 8-min AsFlFFF determination of ribosome and subunits. In the present work the overall analysis time was reduced to 16 min. The washing step was deleted and a time-consuming freeze-thaw cycle. Cell disruption was obtained by a time-minimized lysozyme and detergent treatment for 1.5 min, respectively. The ribosomal material was finally fractionated and quantified in only 6 min, without previous centrifugation, using AsFlFFF. The great time reduction will enable the future use of AsFlFFF at-line to a growing cell cultivation, continuously monitoring the change in ribosomal composition or in other applications requiring high sample throughput. To demonstrate the high efficiency of the method the ribosome and tRNA composition in an Escherichia coli cultivation was monitored every half an hour, giving 18 measurements across the complete growth curve, a frequency of data enough to make decisions about induction or termination of the cultivation.}, pmid = {12576061}, keywords = {analysis,Bacteria,Bacterial,Cell Fractionation,CELLS,chemistry,DISRUPTION,efficiency,Escherichia coli,ESCHERICHIA-COLI,GROWTH,La,metabolism,Methods,nosource,protein,Proteins,Recombinant Proteins,Research SupportNon-U.S.Gov’t,ribosome,Ribosomes,Rna,RNA Transfer,RNATransfer,SUBUNIT,SUBUNITS,termination,translation,tRNA} } % == BibTeX quality report for arfvidssonTimeminimizedDeterminationRibosome2003a: % ? unused Journal abbr (“Anal. Biochem”)

@article{greiveThinkingQuantitativelyTranscriptional2005, title = {Thinking Quantitatively about Transcriptional Regulation}, author = {Greive, Sandra J and {}{von Hippel}, Peter H}, year = 2005, month = mar, journal = {Nature Reviews. Molecular Cell Biology}, volume = {6}, number = {3}, pages = {221–232}, publisher = {Nature Publishing Group}, issn = {1471-0072}, doi = {10.1038/nrm1588}, url = {http://www.nature.com/nrm/journal/v6/n3/abs/nrm1588.html}, abstract = {By thinking about the chemical and physical mechanisms that are involved in the stepwise elongation of RNA transcripts, we can begin to understand the way that these mechanisms are controlled within the cell to reflect the different requirements for transcription that are posed by various metabolic, developmental and disease states. Here, we focus on the mechanistic details of the single-nucleotide addition (or excision) cycle in the transcription process, as this is the level at which many regulatory mechanisms function and can be explained in quantitative terms.}, keywords = {DNA Helicases,DNA-Directed RNA Polymerases,Escherichia coli,Gene Expression Regulation Bacterial,nosource,Operon,Transcription Genetic} } % == BibTeX quality report for greiveThinkingQuantitativelyTranscriptional2005: % ? Possibly abbreviated journal title Nature Reviews. Molecular Cell Biology % ? unused Journal abbr (“Nat. Rev. Mol. Cell Biol”)

@article{vilelaYeastTranscriptionFactor1998, title = {The Yeast Transcription Factor Genes {{YAP1}} and {{YAP2}} Are Subject to Differential Control at the Levels of Both Translation and {{mRNA}} Stability}, author = {Vilela, C and Linz, B and {Rodrigues-Pousada}, C and McCarthy, J E}, year = 1998, month = mar, journal = {Nucleic Acids Research}, volume = {26}, number = {5}, pages = {1150–1159}, publisher = {Oxford Univ Press}, issn = {0305-1048}, url = {http://nar.oxfordjournals.org/content/26/5/1150.short}, abstract = {Two forms of post-transcriptional control direct differential expression of the Saccharomyces cerevisiae genes encoding the AP1-like transcription factors Yap1p and Yap2p. The mRNAs of these genes contain respectively one (YAP1 uORF) and two (YAP2 uORF1 and uORF2) upstream open reading frames. uORF-mediated modulation of post-termination events on the 5’-untranslated region (5’-UTR) directs differential control not only of translation but also of mRNA decay. Translational control is defined by two types of uORF function. The YAP1 -type uORF allows scanning 40S subunits to proceed via leaky scanning and re-initiation to the major ORF, whereas the YAP2 -type acts to block ribosomal scanning by promoting efficient termination. At the same time, the YAP2 uORFs define a new type of mRNA destabilizing element. Both post-termination ribosome scanning behaviour and mRNA decay are influenced by the coding sequence and mRNA context of the respective uORFs, including downstream elements. Our data indicate that release of post-termination ribosomes promotes largely upf -independent accelerated decay. It follows that translational termination on the 5’-UTR of a mature, non-aberrant yeast mRNA can trigger destabilization via a different pathway to that used to rid the cell of mRNAs containing premature stop codons. This route of control of non-aberrant mRNA decay influences the stress response in yeast. It is also potentially relevant to expression of the sizable number of eukaryotic mRNAs that are now recognized to contain uORFs.}, keywords = {Base Sequence,DNA Fungal,DNA-Binding Proteins,Drug Stability,Fungal Proteins,Gene Expression Regulation Fungal,Genes Fungal,Molecular Sequence Data,nosource,Open Reading Frames,Protein Biosynthesis,RNA Fungal,RNA Messenger,RNA Processing Post-Transcriptional,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Transcription Factors} } % == BibTeX quality report for vilelaYeastTranscriptionFactor1998: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{bouleYeastPif1pHelicase2005, title = {The Yeast {{Pif1p}} Helicase Removes Telomerase from Telomeric {{DNA}}}, author = {Boul{'e}, Jean-Baptiste and Vega, Leticia R and Zakian, Virginia A}, year = 2005, month = nov, journal = {Nature}, volume = {438}, number = {7064}, pages = {57–61}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature04091}, url = {http://www.nature.com/nature/journal/v438/n7064/abs/nature04091.html}, abstract = {Telomeres are the physical ends of eukaryotic chromosomes. Genetic studies have established that the baker’s yeast Pif1p DNA helicase is a negative regulator of telomerase, the specialized reverse transcriptase that maintains telomeric DNA, but the biochemical basis for this inhibition was unknown. Here we show that in vitro, Pif1p reduces the processivity of telomerase and releases telomerase from telomeric oligonucleotides. The released telomerase is enzymatically active because it is able to lengthen a challenger oligonucleotide. In vivo, overexpression of Pif1p reduces telomerase association with telomeres, whereas depleting cells of Pif1p increases the levels of telomere-bound Est1p, a telomerase subunit that is present on the telomere when telomerase is active. We propose that Pif1p helicase activity limits telomerase action both in vivo and in vitro by displacing active telomerase from DNA ends.}, keywords = {Chromosomes Fungal,DNA Helicases,DNA Primers,DNA-Binding Proteins,nosource,Protein Binding,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Substrate Specificity,Telomerase,Telomere} }

@article{gonzalezYeastHnRNPlikeProtein2000, title = {The Yeast {{hnRNP-like}} Protein {{Hrp1}}/{{Nab4}} Marks a Transcript for Nonsense-Mediated {{mRNA}} Decay.}, author = {Gonz{'a}lez, C I and {Ruiz-Echevarr{'i}a}, M J and Vasudevan, S and Henry, M F and Peltz, S W}, year = 2000, month = mar, journal = {Molecular Cell}, volume = {5}, number = {3}, eprint = {10882134}, eprinttype = {pubmed}, pages = {489–499}, publisher = {Elsevier}, issn = {1097-2765}, doi = {10.1016/S1097-2765(00)80443-8}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10882134 http://linkinghub.elsevier.com/retrieve/pii/s1097-2765(00)80443-8 http://www.sciencedirect.com/science/article/pii/s1097-2765(00)80443-8}, abstract = {The nonsense-mediated mRNA decay (NMD) pathway monitors premature translation termination and degrades aberrant mRNAs. In yeast, it has been proposed that a surveillance complex searches 3’ of a nonsense codon for a downstream sequence element (DSE) associated with RNA-binding proteins. An interaction between the complex and the DSE-binding protein(s) triggers NMD. Here we describe the identification and characterization of the Hrp1/Nab4 protein as a DSE-binding factor that activates NMD. Mutations in HRP1 stabilize nonsense-containing transcripts without affecting the decay of wild-type mRNAs. Hrp1p binds specifically to a DSE-containing RNA and interacts with Upf1p, a component of the surveillance complex. A mutation in HRP1 that stabilizes nonsense-containing mRNAs abolishes its affinity for the DSE and fails to interact with Upf1p. We present a model describing how Hrp1p marks a transcript for rapid decay.}, pmid = {10882134}, keywords = {20337982,Biological Transport,Cell Nucleus,Cell Nucleus: metabolism,Codon,Codon Nonsense,CodonNonsense,COMPLEX,COMPLEXES,COMPONENT,Cytoplasm,Cytoplasm: metabolism,DECAY,Fungal,Fungal Proteins,Fungal Proteins: metabolism,Fungal: metabolism,Genetic,genetics,Heterogeneous-Nuclear Ribonucleoproteins,IDENTIFICATION,Messenger,Messenger: metabolism,metabolism,microbiology,Models,Models Genetic,ModelsGenetic,mRNA,mRNA Cleavage and Polyadenylation Factors,mRNA decay,Mutation,MUTATIONS,NMD,Nonsense,nosource,Nuclear Proteins,Nuclear Proteins: metabolism,Phosphoglycerate Kinase,Phosphoglycerate Kinase: genetics,protein,Protein Binding,Protein Biosynthesis,Proteins,Ribonucleoproteins,Ribonucleoproteins: genetics,Ribonucleoproteins: metabolism,Rna,RNA,RNA Fungal,RNA Helicases,RNA Helicases: metabolism,RNA Messenger,RNA Stability,RNA-Binding Proteins,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism,RNAFungal,RNAMessenger,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae: genetics,search,sequence,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,termination,translation,TranslationGenetic,Untranslated Regions,yeast} } % == BibTeX quality report for gonzalezYeastHnRNPlikeProtein2000: % ? unused Journal abbr (“Mol. Cell”)

@article{kebaaraUpfdependentDecayWildtype2003, title = {The {{Upf-dependent}} Decay of Wild-Type {{PPR1 mRNA}} Depends on Its 5’-{{UTR}} and First 92 {{ORF}} Nucleotides}, author = {Kebaara, B and Nazarenus, T and Taylor, R and Forch, A and Atkin, A L}, year = 2003, month = jun, journal = {Nucleic Acids Research}, volume = {31}, number = {12}, pages = {3157–3165}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gkg430}, url = {http://www.nar.oupjournals.org/cgi/doi/10.1093/nar/gkg430 http://nar.oxfordjournals.org/content/31/12/3157.short}, abstract = {mRNAs containing premature translation termination codons (nonsense mRNAs) are targeted for deadenylation-independent degradation in a mechanism that depends on Upf1p, Upf2p and Upf3p. This decay pathway is often called nonsense- mediated mRNA decay (NMD). Nonsense mRNAs are decapped by Dcp1p and then degraded 5’ to 3’ by Xrn1p. In the yeast Saccharomyces cerevisiae, a significant number of wild-type mRNAs accumulate in upf mutants. Wild-type PPR1 mRNA is one of these mRNAs. Here we show that PPR1 mRNA degradation depends on the Upf proteins, Dcp1p, Xrn1p and Hrp1p. We have mapped an Upf1p-dependent destabilizing element to a region located within the 5’-UTR and the first 92 bases of the PPR1 ORF. This element targets PPR1 mRNA for Upf-dependent decay by a novel mechanism.}, keywords = {0,3,5’ Untranslated Regions,5’-UTR,ACID,Adaptor Proteins Signal Transducing,BASE,Base Sequence,BASES,CEREVISIAE,chemistry,CLEAVAGE,Codon,CODONS,DECAY,DECAY PATHWAY,degradation,DNA-BINDING,DNA-Binding Proteins,Endoribonucleases,Exoribonucleases,genetics,Helicase,La,MECHANISM,metabolism,mRNA,mRNA Cleavage and Polyadenylation Factors,mRNA decay,MUTANTS,NMD,NONSENSE,nosource,Nucleotides,Open Reading Frames,PATHWAY,physiology,Polyadenylation,protein,Proteins,REGION,Regulatory Sequences Ribonucleic Acid,Regulatory SequencesRibonucleic Acid,RIBONUCLEIC-ACID,Rna,RNA Cap-Binding Proteins,RNA Fungal,RNA HELICASE,RNA Helicases,RNA Messenger,RNA Stability,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAFungal,RNAMessenger,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,Sequence Deletion,SEQUENCES,supportu.s.gov’tnon-p.h.s.,TARGET,termination,TERMINATION CODON,TERMINATION-CODON,Trans-Activators,transcription,TRANSCRIPTION FACTOR,Transcription Factors,translation,TRANSLATION TERMINATION,Untranslated Regions,UPF,Upf1,UPF1 PROTEIN,UPF3,WILD-TYPE,yeast} } % == BibTeX quality report for kebaaraUpfdependentDecayWildtype2003: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{czaplinskiSurveillanceComplexInteracts1998, title = {The Surveillance Complex Interacts with the Translation Release Factors to Enhance Termination and Degrade Aberrant {{mRNAs}}.}, author = {Czaplinski, K and {Ruiz-Echevarria}, M J and Paushkin, S V and Han, X and Weng, Y and Perlick, H A and Dietz, H C and {Ter-Avanesyan}, M D and Peltz, S W}, year = 1998, month = jun, journal = {Genes & Development}, volume = {12}, number = {11}, pages = {1665–1677}, publisher = {Cold Spring Harbor Lab}, issn = {0890-9369}, doi = {10.1101/gad.12.11.1665}, url = {http://www.genesdev.org/cgi/doi/10.1101/gad.12.11.1665 http://genesdev.cshlp.org/content/12/11/1665.short}, abstract = {The nonsense-mediated mRNA decay pathway is an example of an evolutionarily conserved surveillance pathway that rids the cell of transcripts that contain nonsense mutations. The product of the UPF1 gene is a necessary component of the putative surveillance complex that recognizes and degrades aberrant mRNAs. Recent results indicate that the Upf1p also enhances translation termination at a nonsense codon. The results presented here demonstrate that the yeast and human forms of the Upf1p interact with both eukaryotic translation termination factors eRF1 and eRF3. Consistent with Upf1p interacting with the eRFs, the Upf1p is found in the prion-like aggregates that contain eRF1 and eRF3 observed in yeast [PSI+] strains. These results suggest that interaction of the Upf1p with the peptidyl release factors may be a key event in the assembly of the putative surveillance complex that enhances translation termination, monitors whether termination has occurred prematurely, and promotes degradation of aberrant transcripts.}, keywords = {ATPase,COMPLEX,COMPLEXES,Fungal Proteins,GTPase,Humans,mrna,mRNA,mrna decay,NMD,nonsense mutation,nonsense-mediated decay,nosource,Peptide Termination Factors,Protein Biosynthesis,release factors,ribosome,RNA Helicases,RNA Messenger,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,sup35,sup45,surveillence complex,termination,Trans-Activators,Transcription Genetic,translation,translation termination,Upf1} } % == BibTeX quality report for czaplinskiSurveillanceComplexInteracts1998: % ? unused Journal abbr (“Genes & Dev.”)

@article{kadlecStructuralBasisInteraction2004, title = {The Structural Basis for the Interaction between Nonsense-Mediated {{mRNA}} Decay Factors {{UPF2}} and {{UPF3}}}, author = {Kadlec, Jan and Izaurralde, Elisa and Cusack, Stephen}, year = 2004, month = apr, journal = {Nature Structural & Molecular Biology}, volume = {11}, number = {4}, pages = {330–337}, publisher = {Nature Publishing Group}, issn = {1545-9993}, doi = {10.1038/nsmb741}, url = {http://www.nature.com/nsmb/journal/v11/n4/abs/nsmb741.html}, abstract = {Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons. Three ‘up-frameshift’ proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast to human. We present a crystal structure at a resolution of 1.95 A of the complex between the interacting domains of human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain). The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b RNP domain, which is generally used by these domains to bind nucleic acids. We show that the UPF3b RNP does not bind RNA, whereas the UPF2 construct and the complex do. Our results advance understanding of the molecular mechanisms underlying the NMD quality control process.}, keywords = {Amino Acid Sequence,Animals,Binding Sites,Conserved Sequence,Humans,Models Molecular,Models- Molecular,Molecular Sequence Data,nosource,Protein Structure Secondary,Protein Structure- Secondary,RNA Messenger,RNA- Messenger,RNA-Binding Proteins,Sequence Alignment,Sequence Homology Amino Acid,Sequence Homology- Amino Acid,Transcription Factors} } % == BibTeX quality report for kadlecStructuralBasisInteraction2004: % ? unused Journal abbr (“Nat. Struct. Mol. Biol”)

@article{gerhardStatusQualityExpansion2004, title = {The Status, Quality, and Expansion of the {{NIH}} Full-Length {{cDNA}} Project: The {{Mammalian Gene Collection}} ({{MGC}}).}, author = {Gerhard, Daniela S and Wagner, Lukas and Feingold, Elise A and Shenmen, Carolyn M and Grouse, Lynette H and Schuler, Greg and Klein, Steven L and Old, Susan and Rasooly, Rebekah and Good, Peter and Guyer, Mark and Peck, Allison M and Derge, Jeffery G and Lipman, David and Collins, Francis S and Jang, Wonhee and Sherry, Steven and Feolo, Mike and Misquitta, Leonie and Lee, Eduardo and Rotmistrovsky, Kirill and Greenhut, Susan F and Schaefer, Carl F and Buetow, Kenneth and Bonner, Tom I and Haussler, David and Kent, Jim and Kiekhaus, Mark and Furey, Terry and Brent, Michael and Prange, Christa and Schreiber, Kirsten and Shapiro, Nicole and Bhat, Narayan K and Hopkins, Ralph F and Hsie, Florence and Driscoll, Tom and Soares, M Bento and Casavant, Tom L and Scheetz, Todd E and {Brown-stein}, Michael J and Usdin, Ted B and Toshiyuki, Shiraki and Carninci, Piero and Piao, Yulan and Dudekula, Dawood B and Ko, Minoru S H and Kawakami, Koichi and Suzuki, Yutaka and Sugano, Sumio and Gruber, C E and Smith, M R and Simmons, Blake and Moore, Troy and Waterman, Richard and Johnson, Stephen L and Ruan, Yijun and Wei, Chia Lin and Mathavan, S and Gunaratne, Preethi H and Wu, Jiaqian and Garcia, Angela M and Hulyk, Stephen W and Fuh, Edwin and Yuan, Ye and Sneed, Anna and Kowis, Carla and Hodgson, Anne and Muzny, Donna M and McPherson, John and Gibbs, Richard A and Fahey, Jessica and Helton, Erin and Ketteman, Mark and Madan, Anuradha and Rodrigues, Stephanie and Sanchez, Amy and Whiting, Michelle and Madari, Anup and Young, Alice C and Wetherby, Keith D and Granite, Steven J and Kwong, Peggy N and Brinkley, Charles P and Pearson, Russell L and Bouffard, Gerard G and Blakesly, Robert W and Green, Eric D and Dickson, Mark C and Rodriguez, Alex C and Grimwood, Jane and Schmutz, Jeremy and Myers, Richard M and Butterfield, Yaron S N and Griffith, Malachi and Griffith, Obi L and Krzywinski, Martin I and Liao, Nancy and Morin, Ryan and Morrin, Ryan and Palmquist, Diana and Petrescu, Anca S and Skalska, Ursula and Smailus, Duane E and Stott, Jeff M and Schnerch, Angelique and Schein, Jacqueline E and Jones, Steven J M and Holt, Robert A and Baross, Agnes and Marra, Marco A and Clifton, Sandra and Makowski, Kathryn A and Bosak, Stephanie and Malek, Joel}, year = 2004, month = oct, journal = {Genome Research}, volume = {14}, number = {10B}, eprint = {15489334}, eprinttype = {pubmed}, pages = {2121–2127}, issn = {1088-9051}, doi = {10.1101/gr.2596504}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15489334}, abstract = {The National Institutes of Health’s Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5’-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.}, pmid = {15489334}, keywords = {Animals,Cloning Molecular,Computational Biology,DNA Complementary,DNA Primers,Gene Library,Humans,Mice,National Institutes of Health (U.S.),nosource,Open Reading Frames,Rats,United States,Xenopus laevis,Zebrafish} } % == BibTeX quality report for gerhardStatusQualityExpansion2004: % ? unused Journal abbr (“Genome Res”)

@article{sherlockStanfordMicroarrayDatabase2001, title = {The {{Stanford Microarray Database}}}, author = {Sherlock, G and {Hernandez-Boussard}, T and Kasarskis, A and Binkley, G and Matese, J C and Dwight, S S and Kaloper, M and Weng, S and Jin, H and Ball, C A and Eisen, M B and Spellman, P T and Brown, P O and Botstein, D and Cherry, J M}, year = 2001, month = jan, journal = {Nucleic Acids Research}, volume = {29}, number = {1}, pages = {152–155}, publisher = {Oxford Univ Press}, issn = {1362-4962}, url = {http://nar.oxfordjournals.org/content/29/1/152.short}, abstract = {The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two immediate goals for SMD are to serve as a storage site for microarray data from ongoing research at Stanford University, and to facilitate the public dissemination of that data once published, or released by the researcher. Of paramount importance is the connection of microarray data with the biological data that pertains to the DNA deposited on the microarray (genes, clones etc.). SMD makes use of many public resources to connect expression information to the relevant biology, including SGD [Ball,C.A., Dolinski,K., Dwight,S.S., Harris,M.A., Issel-Tarver,L., Kasarskis,A., Scafe,C.R., Sherlock,G., Binkley,G., Jin,H. et al. (2000) Nucleic Acids Res., 28, 77-80], YPD and WormPD [Costanzo,M.C., Hogan,J.D., Cusick,M.E., Davis,B.P., Fancher,A.M., Hodges,P.E., Kondu,P., Lengieza,C., Lew-Smith,J.E., Lingner,C. et al. (2000) Nucleic Acids Res., 28, 73-76], Unigene [Wheeler,D.L., Chappey,C., Lash,A.E., Leipe,D.D., Madden,T.L., Schuler,G.D., Tatusova,T.A. and Rapp,B.A. (2000) Nucleic Acids Res., 28, 10-14], dbEST [Boguski,M.S., Lowe,T.M. and Tolstoshev,C.M. (1993) Nature Genet., 4, 332-333] and SWISS-PROT [Bairoch,A. and Apweiler,R. (2000) Nucleic Acids Res., 28, 45-48] and can be accessed at http://genome-www.stanford.edu/microarray.}, keywords = {Animals,Databases Factual,Databases- Factual,Gene Expression Profiling,Gene Expression Regulation Developmental,Gene Expression Regulation Neoplastic,Gene Expression Regulation- Developmental,Gene Expression Regulation- Neoplastic,Humans,Information Services,Internet,nosource,Oligonucleotide Array Sequence Analysis} } % == BibTeX quality report for sherlockStanfordMicroarrayDatabase2001: % ? Title looks like it was stored in title-case in Zotero % ? unused Journal abbr (“Nucleic Acids Res”)

@article{brodersenSocialLifeRibosomal2005, title = {The Social Life of Ribosomal Proteins}, author = {Brodersen, Ditlev E and Nissen, Poul}, year = 2005, month = may, journal = {The FEBS Journal}, volume = {272}, number = {9}, pages = {2098–2108}, publisher = {Wiley Online Library}, issn = {1742-464X}, doi = {10.1111/j.1742-4658.2005.04651.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2005.04651.x/full}, abstract = {Ribosomal proteins hold a unique position in biology because their function is so closely tied to the large rRNAs of the ribosomes in all kingdoms of life. Following the determination of the complete crystal structures of both the large and small ribosomal subunits from bacteria, the functional role of the proteins has often been overlooked when focusing on rRNAs as the catalysts of translation. In this review we highlight some of the many known and important functions of ribosomal proteins, both during translation on the ribosome and in a wider context.}, keywords = {0,Bacteria,Bacterial,Bacterial Proteins,Binding Sites,BIOLOGY,chemistry,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,genetics,Humans,La,metabolism,Models Molecular,ModelsMolecular,Molecular Biology,nosource,peptidyl transferase,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,POSITION,protein,Protein Biosynthesis,Protein Conformation,Proteins,Review,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNA Messenger,RNA Transfer,RNAMessenger,RNATransfer,rRNA,Structural,structure,SUBUNIT,SUBUNITS,Transferases,translation} } % == BibTeX quality report for brodersenSocialLifeRibosomal2005: % ? unused Journal abbr (“FEBS J.”)

@article{ben-porathSignalsPathwaysActivating2005, title = {The Signals and Pathways Activating Cellular Senescence}, author = {{Ben-Porath}, Ittai and Weinberg, Robert A}, year = 2005, month = may, journal = {The International Journal of Biochemistry & Cell Biology}, volume = {37}, number = {5}, pages = {961–976}, publisher = {Elsevier}, issn = {1357-2725}, doi = {10.1016/j.biocel.2004.10.013}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1357272504003875}, abstract = {Cellular senescence is a program activated by normal cells in response to various types of stress. These include telomere uncapping, DNA damage, oxidative stress, oncogene activity and others. Senescence can occur following a period of cellular proliferation or in a rapid manner in response to acute stress. Once cells have entered senescence, they cease to divide and undergo a series of dramatic morphologic and metabolic changes. Cellular senescence is thought to play an important role in tumor suppression and to contribute to organismal aging, but a detailed description of its physiologic occurrence in vivo is lacking. Recent studies have provided important insights regarding the manner by which different stresses and stimuli activate the signaling pathways leading to senescence. These studies reveal that a population of growing cells may suffer from a combination of different physiologic stresses acting simultaneously. The signaling pathways activated by these stresses are funneled to the p53 and Rb proteins, whose combined levels of activity determine whether cells enter senescence. Here we review recent advances in our understanding of the stimuli that trigger senescence, the molecular pathways activated by these stimuli, and the manner by which these signals determine the entry of a population of cells into senescence.}, keywords = {Cell Aging,Cyclin-Dependent Kinase Inhibitor p16,DNA Damage,Gene Expression Regulation,Humans,nosource,Oncogenes,Oxidative Stress,Retinoblastoma Protein,Signal Transduction,Telomere,Tumor Suppressor Protein p53} } % == BibTeX quality report for ben-porathSignalsPathwaysActivating2005: % ? unused Journal abbr (“Int. J. Biochem. Cell Biol”)

@article{wangRoleUpfProteins2001, title = {The Role of {{Upf}} Proteins in Modulating the Translation Read-through of Nonsense-Containing Transcripts}, author = {Wang, W and Czaplinski, K and Rao, Y and Peltz, S W}, year = 2001, month = feb, journal = {The EMBO Journal}, volume = {20}, number = {4}, pages = {880–890}, publisher = {Nature Publishing Group}, issn = {0261-4189}, doi = {10.1093/emboj/20.4.880}, url = {http://www.nature.com/emboj/journal/v20/n4/abs/7593593a.html}, abstract = {The yeast UPF1, UPF2 and UPF3 genes encode trans-acting factors of the nonsense-mediated mRNA decay pathway. In addition, the upf1Delta strain demonstrates a nonsense suppression phenotype and Upf1p has been shown to interact with the release factors eRF1 and eRF3. In this report, we show that both upf2Delta and upf3Delta strains demonstrate a nonsense suppression phenotype independent of their effect on mRNA turnover. We also demonstrate that Upf2p and Upf3p interact with eRF3, and that their ability to bind eRF3 correlates with their ability to complement the nonsense suppression phenotype. In vitro experiments demonstrate that Upf2p, Upf3p and eRF1 compete with each other for interacting with eRF3. Con versely, Upf1p binds to a different region of eRF3 and can form a complex with these factors. These results suggest a sequential surveillance complex assembly pathway, which occurs during the premature translation termination process. We propose that the observed nonsense suppression phenotype in the upfDelta strains can be attributed to a defect in the surveillance complex assembly.}, keywords = {0,Alleles,assembly,cancer,Codon,Codon Nonsense,CodonNonsense,COMPLEX,COMPLEXES,DECAY,Epistasis Genetic,EpistasisGenetic,Fungal Proteins,gene,Genes,Genetic,genetics,In Vitro,IN-VITRO,La,microbiology,mRNA,mRNA decay,nonsense suppression,nosource,Phenotype,physiology,protein,Protein Biosynthesis,Proteins,readthrough,RELEASE FACTORS,Rna,RNA Messenger,RNAMessenger,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,suppression,termination,translation,TRANSLATION TERMINATION,TranslationGenetic,turnover,UPF,Upf1,UPF3,yeast} } % == BibTeX quality report for wangRoleUpfProteins2001: % ? unused Journal abbr (“EMBO J.”)

@article{espelRoleAUrichElements2005, title = {The Role of the {{AU-rich}} Elements of {{mRNAs}} in Controlling Translation}, author = {Espel, Enric}, year = 2005, month = feb, journal = {Seminars in Cell & Developmental Biology}, volume = {16}, number = {1}, eprint = {15659340}, eprinttype = {pubmed}, pages = {59–67}, issn = {1084-9521}, doi = {10.1016/j.semcdb.2004.11.008}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15659340}, abstract = {Adenosine- and uridine-rich elements (AREs) located in 3’-untranslated regions are the best-known determinants of RNA instability. These elements have also been shown to control translation in certain mRNAs, including mRNAs for prominent pro-inflammatory and tumor growth-related proteins, and physiological anti-inflammatory processes that target ARE-controlled translation of mRNAs coding for pro-inflammatory proteins have been described. A major research effort is now being made to understand the mechanisms by which the translation of these mRNAs is controlled and the signalling pathways involved. This review focuses on the role of ARE-containing gene translation in inflammation, and the disease models that have improved our understanding of ARE-mediated translational control.}, pmid = {15659340}, keywords = {3’ Untranslated Regions,Adenosine,nosource,Protein Biosynthesis,RNA Messenger,Signal Transduction,T-Lymphocytes,Uridine} } % == BibTeX quality report for espelRoleAUrichElements2005: % ? unused Journal abbr (“Semin. Cell Dev. Biol”)

@article{napthineRoleRNAPseudoknot1999a, title = {The Role of {{RNA}} Pseudoknot Stem 1 Length in the Promotion of Efficient - 1 Ribosomal Frameshifting}, author = {Napthine, S and Liphardt, J and Bloys, A and Routledge, S and Brierley, I}, year = 1999, month = may, journal = {Journal of Molecular Biology}, volume = {288}, number = {3}, eprint = {10329144}, eprinttype = {pubmed}, pages = {305–320}, issn = {0022-2836}, doi = {10.1006/jmbi.1999.2688}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10329144}, abstract = {The ribosomal frameshifting signal present in the genomic RNA of the coronavirus infectious bronchitis virus (IBV) contains a classic hairpin-type RNA pseudoknot that is believed to possess coaxially stacked stems of 11 bp (stem 1) and 6 bp (stem 2). We investigated the influence of stem 1 length on the frameshift process by measuring the frameshift efficiency in vitro of a series of IBV-based pseudoknots whose stem 1 length was varied from 4 to 13 bp in single base-pair increments. Efficient frameshifting depended upon the presence of a minimum of 11 bp; pseudoknots with a shorter stem 1 were either non- functional or had reduced frameshift efficiency, despite the fact that a number of them had a stem 1 with a predicted stability equal to or greater than that of the wild-type IBV pseudoknot. An upper limit for stem 1 length was not determined, but pseudoknots containing a 12 or 13 bp stem 1 were fully functional. Structure probing analysis was carried out on RNAs containing either a ten or 11 bp stem 1; these experiments confirmed that both RNAs formed pseudoknots and appeared to be indistinguishable in conformation. Thus the difference in frameshifting efficiency seen with the two structures was not simply due to an inability of the 10 bp stem 1 construct to fold into a pseudoknot. In an attempt to identify other parameters which could account for the poor functionality of the shorter stem 1-containing pseudoknots, we investigated, in the context of the 10 bp stem 1 construct, the influence on frameshifting of altering the slippery sequence-pseudoknot spacing distance, loop 2 length, and the number of G residues at the bottom of the 5’-arm of stem 1. For each parameter, it was possible to find a condition where a modest stimulation of frameshifting was observable (about twofold, from seven to a maximal 17 %), but we were unable to find a situation where frameshifting approached the levels seen with 11 bp stem 1 constructs (48-57 %). Furthermore, in the next smaller construct (9 bp stem 1), changing the bottom four base-pairs to G.C (the optimal base composition) only stimulated frameshifting from 3 to 6 %, an efficiency about tenfold lower than seen with the 11 bp construct. Thus stem 1 length is a major factor in determining the functionality of this class of pseudoknot and this has implications for models of the frameshift process. Copyright 1999 Academic Press}, pmid = {10329144}, keywords = {99262844,analysis,Base Composition,Base Sequence,chemistry,efficiency,frameshift,Frameshifting,Frameshifting Ribosomal,FrameshiftingRibosomal,genetics,genomic,In Vitro,IN-VITRO,Infectious bronchitis virus,metabolism,models,Mutagenesis Site-Directed,MutagenesisSite-Directed,nosource,Nucleic Acid Conformation,pathology,pseudoknot,ribosomal frameshifting,RIBOSOMAL FRAMESHIFTING SIGNAL,Rna,RNA,RNA Probes,RNA PSEUDOKNOT,SIGNAL,stability,structure,supportnon-u.s.gov’t,virology,virus} } % == BibTeX quality report for napthineRoleRNAPseudoknot1999a: % ? unused Journal abbr (“J. Mol. Biol”)

@article{leThermodynamicStabilityStatistical1989, title = {Thermodynamic Stability and Statistical Significance of Potential Stem-Loop Structures Situated at the Frameshift Sites of Retroviruses}, author = {Le, S Y and Chen, J H and Maizel, J V}, year = 1989, month = aug, journal = {Nucleic Acids Research}, volume = {17}, number = {15}, pages = {6143–6152}, publisher = {Oxford Univ Press}, issn = {0305-1048}, doi = {10.1093/nar/17.15.6143}, url = {http://nar.oxfordjournals.org/content/17/15/6143.short}, abstract = {RNA stem-loop structures situated just 3’ to the frameshift sites of the retroviral gag-pol or gag-pro and pro-pol regions may make important contributions to frame-shifting in retroviruses. In this study, the thermodynamic stability and statistical significance of such secondary structural features relative to others in the sequence have been assessed using a newly developed method that combines calculations of the lowest free energy of formation of RNA secondary structures and the Monte Carlo simulations. Our results show that stem-loop structures situated just 3’ to the frameshift sites are both highly stable and statistically significant relative to others in the gag-pol or gag-pro and pro-pol junction domains (both 300 nucleotides upstream and downstream from the possible frameshift sites are included) of Rous sarcoma virus (RSV), human immunodeficiency virus (HIV-1), bovine leukemia virus (BLV), human T-cell leukemia virus type II (HTLV-II), and mouse mammary tumor virus (MMTV). No other more stable, or significant folding regions are predicted in these domains.}, keywords = {0,3,Avian Sarcoma Viruses,Base Sequence,BIOLOGY,cancer,DOMAIN,DOMAINS,DOWNSTREAM,Drug Stability,frameshift,Frameshifting,Gag,Gag-pol,gene,Gene Products gag,Gene Productsgag,GENE-PRODUCT,genetics,Hiv-1,HIV-1,human,Human T-lymphotropic virus 2,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,La,LEUKEMIA,Leukemia Virus Bovine,Leukemia VirusBovine,Mammary Tumor Virus Mouse,Mammary Tumor VirusMouse,MMTV,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleotides,PRODUCT,PRODUCTS,protein,Protein Biosynthesis,Proteins,REGION,Research SupportU.S.Gov’tP.H.S.,Retroviridae,Retroviridae Proteins,RETROVIRUSES,Rna,RNA SECONDARY STRUCTURE,RNA Viral,RnaViral,Sarcoma VirusesAvian,SECONDARY STRUCTURE,sequence,SITE,SITES,stability,STEM-LOOP,Structural,STRUCTURAL FEATURES,structure,thermodynamic stability,Thermodynamics,UPSTREAM,virus} } % == BibTeX quality report for leThermodynamicStabilityStatistical1989: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{rakwalskaRibosomeboundChaperonesRAC2004, title = {The Ribosome-Bound Chaperones {{RAC}} and {{Ssb1}}/2p Are Required for Accurate Translation in {{Saccharomyces}} Cerevisiae}, author = {Rakwalska, Magdalena and Rospert, Sabine}, year = 2004, month = oct, journal = {Molecular and Cellular Biology}, volume = {24}, number = {20}, pages = {9186–9197}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, doi = {10.1128/MCB.24.20.9186-9197.2004}, url = {http://mcb.asm.org/cgi/content/full/24/20/9186?view=full&pmid=15456889}, abstract = {The chaperone homologs RAC (ribosome-associated complex) and Ssb1/2p are anchored to ribosomes; Ssb1/2p directly interacts with nascent polypeptides. The absence of RAC or Ssb1/2p results in a similar set of phenotypes, including hypersensitivity against the aminoglycoside paromomycin, which binds to the small ribosomal subunit and compromises the fidelity of translation. In order to understand this phenomenon we measured the frequency of translation termination and misincorporation in vivo and in vitro with a novel reporter system. Translational fidelity was impaired in the absence of functional RAC or Ssb1/2p, and the effect was further enhanced by paromomycin. The mutant strains suffered primarily from a defect in translation termination, while misincorporation was compromised to a lesser extent. Consistently, a low level of soluble translation termination factor Sup35p enhanced growth defects in the mutant strains. Based on the combined data we conclude that RAC and Ssb1/2p are crucial in maintaining translational fidelity beyond their postulated role as chaperones for nascent polypeptides.}, keywords = {Adenosine Triphosphatases,Amino Acid Sequence,Anti-Bacterial Agents,assays,Base Sequence,CEREVISIAE,COMPLEX,COMPLEXES,DNA-Binding Proteins,Drug gradient,Drug Resistance,Fidelity,Gene Expression Regulation Fungal,Genes Reporter,GROWTH,homolog,HSP70 Heat-Shock Proteins,In Vitro,IN-VITRO,IN-VIVO,La,Macromolecular Substances,misincorporation,Molecular Chaperones,Molecular Sequence Data,nosource,Paromomycin,Peptide Termination Factors,Phenotype,Point Mutation,POLYPEPTIDE,POLYPEPTIDES,Protein Binding,Protein Biosynthesis,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SUBUNIT,SYSTEM,termination,translation,TRANSLATION TERMINATION,translational fidelity} } % == BibTeX quality report for rakwalskaRibosomeboundChaperonesRAC2004: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{polacekRibosomalPeptidylTransferase2005, title = {The Ribosomal Peptidyl Transferase Center: Structure, Function, Evolution, Inhibition}, author = {Polacek, Norbert and Mankin, Alexander S}, year = {2005 Sep-Oct}, journal = {Critical Reviews in Biochemistry and Molecular Biology}, volume = {40}, number = {5}, pages = {285–311}, publisher = {Informa UK Ltd UK}, issn = {1040-9238}, doi = {10.1080/10409230500326334}, url = {http://informahealthcare.com/doi/abs/10.1080/10409230500326334}, abstract = {The ribosomal peptidyl transferase center (PTC) resides in the large ribosomal subunit and catalyzes the two principal chemical reactions of protein synthesis: peptide bond formation and peptide release. The catalytic mechanisms employed and their inhibition by antibiotics have been in the focus of molecular and structural biologists for decades. With the elucidation of atomic structures of the large ribosomal subunit at the dawn of the new millennium, these questions gained a new level of molecular significance. The crystallographic structures compellingly confirmed that peptidyl transferase is an RNA enzyme. This places the ribosome on the list of naturally occurring ribozymes that outlived the transition from the pre-biotic RNA World to contemporary biology. Biochemical, genetic and structural evidence highlight the role of the ribosome as an entropic catalyst that accelerates peptide bond formation primarily by substrate positioning. At the same time, peptide release should more strongly depend on chemical catalysis likely involving an rRNA group of the PTC. The PTC is characterized by the most pronounced accumulation of universally conserved rRNA nucleotides in the entire ribosome. Thus, it came as a surprise that recent findings revealed an unexpected high level of variation in the mode of antibiotic binding to the PTC of ribosomes from different organisms.}, keywords = {Anti-Bacterial Agents,antibiotic,antibiotics,BINDING,BIOLOGY,BOND FORMATION,Catalysis,enzyme,Evolution,Evolution Molecular,Genetic,genomic,Genomics,INHIBITION,La,MECHANISM,MECHANISMS,Models Molecular,nosource,Nucleotides,peptide bond formation,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,protein,protein synthesis,PROTEIN-SYNTHESIS,RELEASE,RIBOSOMAL PEPTIDYL TRANSFERASE,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNA Catalytic,RNA world,rRNA,Structural,structure,SUBUNIT,TRANSFERASE CENTER,WORLD} } % == BibTeX quality report for polacekRibosomalPeptidylTransferase2005: % ? unused Journal abbr (“Crit. Rev. Biochem. Mol. Biol”)

@article{beringerRibosomalPeptidylTransferase2007, title = {The Ribosomal Peptidyl Transferase.}, author = {Beringer, Malte and Rodnina, Marina V}, year = 2007, month = may, journal = {Molecular Cell}, volume = {26}, number = {3}, eprint = {17499039}, eprinttype = {pubmed}, pages = {311–321}, publisher = {Elsevier}, issn = {1097-2765}, doi = {10.1016/j.molcel.2007.03.015}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17499039 http://linkinghub.elsevier.com/retrieve/pii/S1097276507001852 http://www.sciencedirect.com/science/article/pii/S1097276507001852}, abstract = {Peptide bond formation on the ribosome takes place in an active site composed of RNA. Recent progress of structural, biochemical, and computational approaches has provided a fairly detailed picture of the catalytic mechanism of the reaction. The ribosome accelerates peptide bond formation by lowering the activation entropy of the reaction due to positioning the two substrates, ordering water in the active site, and providing an electrostatic network that stabilizes the reaction intermediates. Proton transfer during the reaction appears to be promoted by a concerted proton shuttle mechanism that involves ribose hydroxyl groups on the tRNA substrate.}, pmid = {17499039}, keywords = {0,activation,ACTIVE-SITE,Bacteria,Bacteria: metabolism,Base Sequence,Binding Sites,Biochemistry,BOND FORMATION,Catalysis,chemistry,Crystallization,Germany,INTERMEDIATE,La,MECHANISM,metabolism,Models,Models Molecular,ModelsMolecular,Molecular,nosource,peptide bond formation,peptidyl transferase,Peptidyl Transferases,Peptidyl Transferases: chemistry,Peptidyl Transferases: metabolism,PEPTIDYL-TRANSFERASE,protein,Protein Biosynthesis,Protein Conformation,Proteins,PROTON,Review,Ribose,Ribosomal,RIBOSOMAL PEPTIDYL TRANSFERASE,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: metabolism,RIBOSOMAL-PROTEIN,ribosome,Rna,RNA,RNA Ribosomal,RNA Transfer,RNARibosomal,RNATransfer,SITE,Structural,Support,Transfer,Transfer: chemistry,Transfer: metabolism,Transferases,tRNA,Water} } % == BibTeX quality report for beringerRibosomalPeptidylTransferase2007: % ? unused Journal abbr (“Mol. Cell”)

@article{vrekenRatelimitingStepYeast1992, title = {The Rate-Limiting Step in Yeast {{PGK1 mRNA}} Degradation Is an Endonucleolytic Cleavage in the 3’-Terminal Part of the Coding Region.}, author = {Vreken, P and Rau{'e}, H A}, year = 1992, month = jul, journal = {Molecular and Cellular Biology}, volume = {12}, number = {7}, pages = {2986–2996}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, url = {http://mcb.asm.org/cgi/content/abstract/12/7/2986 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=364512&tool=pmcentrez&rendertype=abstract http://mcb.asm.org/content/12/7/2986.short}, abstract = {Insertion of an 18-nucleotide-long poly(G) tract into the 3’-terminal untranslated region of yeast phosphoglycerate kinase (PGK1) mRNA increases its chemical half-life by about a factor of 2 (P. Vreken, R. Van der Veen, V. C. H. F. de Regt, A. L. de Maat, R. J. Planta, and H. A. Rau'e, Biochimie 73:729-737, 1991). In this report, we show that this insertion also causes the accumulation of a degradation intermediate extending from the poly(G) sequence down to the transcription termination site. Reverse transcription and S1 nuclease mapping experiments demonstrated that this intermediate is the product of shorter-lived primary fragments resulting from endonucleolytic cleavage immediately downstream from the U residue of either of two 5’-GGUG-3’ sequences present between positions 1100 and 1200 close to the 3’ terminus (position 1251) of the coding sequence. Similar endonucleolytic cleavages appear to initiate degradation of wild-type PGK1 mRNA. Insertion of a poly(G) tract just upstream from the AUG start codon resulted in the accumulation of a 5’-terminal degradation intermediate extending from the insertion to the 1100-1200 region. RNase H degradation in the presence of oligo(dT) demonstrated that the wild-type and mutant PGK1 mRNAs are deadenylated prior to endonucleolytic cleavage and that the half-life of the poly(A) tail is three- to sixfold lower than that of the remainder of the mRNA. Thus, the endonucleolytic cleavage constitutes the rate-limiting step in degradation of both wild-type and mutant PGK1 transcripts, and the resulting fragments are degraded by a 5’—-3’ exonuclease, which appears to be severely retarded by a poly(G) sequence.}, pmid = {1320194}, keywords = {Base Sequence,Chromosome Mapping,Endonucleases,Endonucleases: metabolism,Genetic,Half-Life,Messenger,Messenger: metabolism,Molecular Sequence Data,nosource,Nucleic Acid,Nucleic Acid Conformation,Phosphoglycerate Kinase,Phosphoglycerate Kinase: metabolism,Poly A,Poly A: metabolism,Poly U,Poly U: metabolism,Protein Biosynthesis,Regulatory Sequences,Regulatory Sequences Nucleic Acid,Regulatory Sequences- Nucleic Acid,RNA,RNA Messenger,RNA- Messenger,Transcription,Transcription Genetic,Transcription- Genetic,Transformation,Transformation Genetic,Transformation- Genetic} } % == BibTeX quality report for vrekenRatelimitingStepYeast1992: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{leedsProductYeastUPF11991, title = {The Product of the Yeast {{UPF1}} Gene Is Required for Rapid Turnover of {{mRNAs}} Containing a Premature Translational Termination Codon.}, author = {Leeds, P and Peltz, S W and Jacobson, A and Culbertson, M R}, year = 1991, month = dec, journal = {Genes & Development}, volume = {5}, number = {12A}, pages = {2303–2314}, publisher = {Cold Spring Harbor Lab}, issn = {0890-9369}, url = {http://genesdev.cshlp.org/content/5/12a/2303.short}, abstract = {mRNA decay rates often increase when translation is terminated prematurely due to a frameshift or nonsense mutation. We have identified a yeast gene, UPF1, that codes for a trans-acting factor whose function is necessary for enhanced turnover of mRNAs containing a premature stop codon. In the absence of UPF1 function, frameshift or nonsense mutations in the HIS4 or LEU2 genes that normally cause rapid mRNA decay fail to have this effect. Instead, the mRNAs decay at rates similar to the corresponding wild-type mRNAs. The stabilization of frameshift or nonsense mRNAs observed in upf1- strains does not appear to result from enhanced readthrough of the termination signal. Loss of UPF1 function has no effect on the accumulation or stability of HIS4+ or LEU2+ mRNA, suggesting that the UPF1 product functions only in response to a premature termination signal. When we examined the accumulation and stability of other wild-type mRNAs in the presence or absence of UPF1, including MAT alpha 1, STE3, ACT1, PGK1, PAB1, and URA3 mRNAs, only the URA3 transcript was affected. On the basis of these and other results, the UPF1 product appears to participate in a previously uncharacterized pathway leading to the degradation of a limited class of yeast transcripts.}, keywords = {Base Sequence,Cloning Molecular,Codon,DNA,Fungal Proteins,Histidine,Molecular Sequence Data,Mutation,nosource,Peptide Chain Termination Translational,Plasmids,Protein Biosynthesis,Ribosomes,RNA Fungal,RNA Messenger,Saccharomyces cerevisiae,Terminator Regions Genetic} } % == BibTeX quality report for leedsProductYeastUPF11991: % ? unused Journal abbr (“Genes Dev”)

@article{chiuPioneerTranslationInitiation2004, title = {The Pioneer Translation Initiation Complex Is Functionally Distinct from but Structurally Overlaps with the Steady-State Translation Initiation Complex}, author = {Chiu, Shang-Yi and Lejeune, Fabrice and Ranganathan, Aparna C and Maquat, Lynne E}, year = 2004, month = apr, journal = {Genes & Development}, volume = {18}, number = {7}, pages = {745–754}, publisher = {Cold Spring Harbor Lab}, issn = {0890-9369}, doi = {10.1101/gad.1170204}, url = {http://genesdev.cshlp.org/content/18/7/745.short}, abstract = {The bulk of cellular proteins derive from the translation of eukaryotic translation initiation factor (eIF)4E-bound mRNA. However, recent studies of nonsense-mediated mRNA decay (NMD) indicate that cap-binding protein (CBP)80-bound mRNA, which is a precursor to eIF4E-bound mRNA, can also be translated during a pioneer round of translation. Here, we report that the pioneer round, which can be assessed by measuring NMD, is not inhibited by 4E-BP1, which is known to inhibit steady-state translation by competing with eIF4G for binding to eIF4E. Therefore, at least in this way, the pioneer round of translation is distinct from steady-state translation. eIF4GI, poly(A)-binding protein (PABP)1, eIF3, eIF4AI, and eIF2alpha coimmunopurify with both CBP80 and eIF4E, which suggests that each factor functions in both modes of translation. Consistent with roles for PABP1 and eIF2alpha in the pioneer round of translation, PABP-interacting protein 2, which is known to destabilize PABP1 binding to poly(A) and inhibit steady-state translation, as well as inactive eIF2alpha, which is also known to inhibit steady-state translation, also inhibit NMD. Polysome profiles indicate that CBP80-bound mRNAs are translated less efficiently than their eIF4E-bound counterparts.}, keywords = {0,Adaptor Proteins Signal Transducing,Animals,BINDING,Blotting Western,BlottingWestern,Caenorhabditis,Caenorhabditis elegans,Caenorhabditis elegans Proteins,CAENORHABDITIS-ELEGANS,Cap,Cap binding,Carrier Proteins,Cercopithecus aethiops,Codon,Codon Nonsense,CodonNonsense,COMPLEX,COMPLEXES,Cos Cells,COS Cells,DECAY,eIF3,ELEGANS,Eukaryotic Initiation Factor-2,Eukaryotic Initiation Factor-3,Eukaryotic Initiation Factor-4E,Eukaryotic Initiation Factor-4G,EUKARYOTIC TRANSLATION,FACTOR 4G,genetics,human,Humans,initiation,INITIATION-FACTOR,La,luciferase,Luciferases,metabolism,mRNA,mRNA decay,NMD,NONSENSE,nonsense-mediated mRNA decay,nosource,Nuclear Cap-Binding Protein Complex,Peptide Chain Initiation,Peptide Chain Initiation Translational,phosphoprotein,Phosphoproteins,poly(A),POLY(A)-BINDING PROTEIN,Poly(A)-Binding Protein I,Precipitin Tests,PRECURSOR,protein,Protein Biosynthesis,PROTEIN COMPLEX,Proteins,Reverse Transcriptase Polymerase Chain Reaction,Rna,Rna Caps,RNA Caps,RNA Messenger,RNAMessenger,supportu.s.gov’tp.h.s.,translation,TRANSLATION INITIATION,TranslationGenetic} } % == BibTeX quality report for chiuPioneerTranslationInitiation2004: % ? unused Journal abbr (“Genes Dev.”)

@article{ottoPathwayHCVIRESmediated2004, title = {The Pathway of {{HCV IRES-mediated}} Translation Initiation}, author = {Otto, Geoff A and Puglisi, Joseph D}, year = 2004, month = oct, journal = {Cell}, volume = {119}, number = {3}, pages = {369–380}, publisher = {Elsevier}, issn = {0092-8674}, doi = {10.1016/j.cell.2004.09.038}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867404008918}, abstract = {The HCV internal ribosome entry site (IRES) directly regulates the assembly of translation initiation complexes on viral mRNA by a sequential pathway that is distinct from canonical eukaryotic initiation. The HCV IRES can form a binary complex with an eIF-free 40S ribosomal subunit. Next, a 48S-like complex assembles at the AUG initiation codon upon association of eIF3 and ternary complex. 80S complex formation is rate limiting and follows the GTP-dependent association of the 60S subunit. Efficient assembly of the 48S-like and 80S complexes on the IRES mRNA is dependent upon maintenance of the highly conserved HCV IRES structure. This revised model of HCV IRES translation initiation provides a context to understand the function of different HCV IRES domains during translation initiation.}, keywords = {Base Sequence,Hela Cells,Hepacivirus,Hepatitis C,Humans,Molecular Sequence Data,nosource,Protein Biosynthesis,Ribosomal Proteins,Ribosomes,RNA Viral,Sucrose} }

@article{yusupovaPathMessengerRNA2001, title = {The Path of Messenger {{RNA}} through the Ribosome}, author = {Yusupova, G Z and Yusupov, M M and Cate, J H and Noller, H F}, year = 2001, month = jul, journal = {Cell}, volume = {106}, number = {2}, pages = {233–241}, publisher = {Elsevier}, issn = {0092-8674}, doi = {10.1016/S0092-8674(01)00435-4}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867401004354}, abstract = {Using X-ray crystallography, we have directly observed the path of mRNA in the 70S ribosome in Fourier difference maps at 7 A resolution. About 30 nucleotides of the mRNA are wrapped in a groove that encircles the neck of the 30S subunit. The Shine-Dalgarno helix is bound in a large cleft between the head and the back of the platform. At the interface, only about eight nucleotides (-1 to +7), centered on the junction between the A and P codons, are exposed, and bond almost exclusively to 16S rRNA. The mRNA enters the ribosome around position +13 to +15, the location of downstream pseudoknots that stimulate -1 translational frame shifting.}, keywords = {Bacteriophage T4,Base Pairing,Base Sequence,Binding Sites,chemistry,Codon,Crystallography,Crystallography X-Ray,CrystallographyX-Ray,DNA-Binding Proteins,Escherichia coli,Fourier Analysis,Frameshifting Ribosomal,FrameshiftingRibosomal,genetics,MESSENGER-RNA,metabolism,Models Molecular,ModelsMolecular,Molecular Sequence Data,mRNA,nosource,Nucleic Acid Conformation,Nucleotides,Protein Binding,Protein Conformation,Protein Subunits,pseudoknot,pseudoknots,ribosome,Ribosomes,Rna,RNA Messenger,RNA Ribosomal 16S,RNAMessenger,RNARibosomal16S,rRNA,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Thermus thermophilus,Viral Proteins} }

@article{draperThemesRNAproteinRecognition1999, title = {Themes in {{RNA-protein}} Recognition}, author = {Draper, D E}, year = 1999, month = oct, journal = {Journal of Molecular Biology}, volume = {293}, number = {2}, pages = {255–270}, publisher = {Elsevier}, issn = {0022-2836}, doi = {10.1006/jmbi.1999.2991}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283699929911}, abstract = {Atomic resolution structures are now available for more than 20 complexes of proteins with specific RNAs. This review examines two main themes that appear in this set of structures. A “groove binder” class of proteins places a protein structure (alpha-helix, 310-helix, beta-ribbon, or irregular loop) in the groove of an RNA helix, recognizing both the specific sequence of bases and the shape or dimensions of the groove, which are sometimes distorted from the normal A-form. A second class of proteins uses beta-sheet surfaces to create pockets that examine single-stranded RNA bases. Some of these proteins recognize completely unstructured RNA, and in others RNA secondary structure indirectly promotes binding by constraining bases in an appropriate orientation. Thermodynamic studies have shown that binding specificity is generally a function of several factors, including base-specific hydrogen bonds, non-polar contacts, and mutual accommodation of the protein and RNA-binding surfaces. The recognition strategies and structural frameworks used by RNA binding proteins are not exotically different from those employed by DNA-binding proteins, suggesting that the two kinds of nucleic acid-binding proteins have not evolved independently.}, keywords = {Animals,Binding Sites,DNA-Binding Proteins,Humans,nosource,Nucleic Acid Conformation,Protein Structure Secondary,Protein Structure- Secondary,RNA,RNA-Binding Proteins,Static Electricity} } % == BibTeX quality report for draperThemesRNAproteinRecognition1999: % ? unused Journal abbr (“J. Mol. Biol”)

@article{zenkinMechanismDNAReplication2006, title = {The Mechanism of {{DNA}} Replication Primer Synthesis by {{RNA}} Polymerase}, author = {Zenkin, Nikolay and Naryshkina, Tatyana and Kuznedelov, Konstantin and Severinov, Konstantin}, year = 2006, month = feb, journal = {Nature}, volume = {439}, number = {7076}, pages = {617–620}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature04337}, url = {http://www.nature.com/nature/journal/vaop/ncurrent/full/nature04337.html}, abstract = {RNA primers for DNA replication are usually synthesized by specialized enzymes, the primases. However, some replication systems have evolved to use cellular DNA-dependent RNA polymerase for primer synthesis. The main requirement for the replication primer, an exposed RNA 3’ end annealed to the DNA template, is not compatible with known conformations of the transcription elongation complex, raising a question of how the priming is achieved. Here we show that a previously unrecognized kind of transcription complex is formed during RNA polymerase-catalysed synthesis of the M13 bacteriophage replication primer. The complex contains an overextended RNA-DNA hybrid bound in the RNA-polymerase trough that is normally occupied by downstream double-stranded DNA, thus leaving the 3’ end of the RNA available for interaction with DNA polymerase. Transcription complexes with similar topology may prime the replication of other bacterial mobile elements and may regulate transcription elongation under conditions that favour the formation of an extended RNA-DNA hybrid.}, keywords = {Bacteriophage M13,DNA Replication,DNA Viral,DNA-Directed DNA Polymerase,DNA-Directed RNA Polymerases,nosource,Nucleic Acid Heteroduplexes,Nucleic Acid Hybridization,RNA,RNA Viral} }

@article{strausbergMammalianGeneCollection1999, title = {The Mammalian Gene Collection}, author = {Strausberg, R L and Feingold, E A and Klausner, R D and Collins, F S}, year = 1999, month = oct, journal = {Science (New York, N.Y.)}, volume = {286}, number = {5439}, pages = {455–457}, publisher = {American Association for the Advancement of Science}, issn = {0036-8075}, doi = {10.1126/science.286.5439.455}, url = {http://www.sciencemag.org/content/286/5439/455.short}, abstract = {The Mammalian Gene Collection (MGC) project is a new effort by the NIH to generate full-length complementary DNA (cDNA) resources. This project will provide publicly accessible resources to the full research community. The MGC project entails the production of libraries, sequencing, and database and repository development, as well as the support of library construction, sequencing, and analytic technologies dedicated to the goal of obtaining a full set of human and other mammalian full-length (open reading frame) sequences and clones of expressed genes.}, keywords = {0,Animals,Base Sequence,cancer,Computational Biology,DATABASE,Databases Factual,DatabasesFactual,development,Dna,DNA Complementary,DNAComplementary,Expressed Sequence Tags,FRAME,gene,Gene Library,Genes,genetics,Genome,Genome Human,GenomeHuman,human,human genome,Humans,La,library,Mammals,Mice,National Institutes of Health (U.S.),nosource,OPEN READING FRAME,Private Sector,Public Sector,READING FRAME,sequence,Sequence Analysis DNA,Sequence AnalysisDNA,SEQUENCES,Support,United States} } % == BibTeX quality report for strausbergMammalianGeneCollection1999: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”)

@article{rivasLanguageRNAFormal2000, title = {The Language of {{RNA}}: A Formal Grammar That Includes Pseudoknots}, author = {Rivas, E and Eddy, S R}, year = 2000, month = apr, journal = {Bioinformatics (Oxford, England)}, volume = {16}, number = {4}, pages = {334–340}, publisher = {Oxford Univ Press}, issn = {1367-4803}, doi = {10.1093/bioinformatics/16.4.334}, url = {http://bioinformatics.oxfordjournals.org/content/16/4/334.short}, abstract = {MOTIVATION: In a previous paper, we presented a polynomial time dynamic programming algorithm for predicting optimal RNA secondary structure including pseudoknots. However, a formal grammatical representation for RNA secondary structure with pseudoknots was still lacking. RESULTS: Here we show a one-to-one correspondence between that algorithm and a formal transformational grammar. This grammar class encompasses the context-free grammars and goes beyond to generate pseudoknotted structures. The pseudoknot grammar avoids the use of general context-sensitive rules by introducing a small number of auxiliary symbols used to reorder the strings generated by an otherwise context-free grammar. This formal representation of the residue correlations in RNA structure is important because it means we can build full probabilistic models of RNA secondary structure, including pseudoknots, and use them to optimally parse sequences in polynomial time.}, keywords = {Algorithms,chemistry,dynamic programming,Genetic,genetics,La,MODEL,models,nosource,Nucleic Acid Conformation,pseudoknot,pseudoknots,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,Rna,RNA,RNA SECONDARY STRUCTURE,RULES,SECONDARY STRUCTURE,sequence,SEQUENCES,structure} } % == BibTeX quality report for rivasLanguageRNAFormal2000: % ? unused Journal abbr (“Bioinformatics.”)

@article{cobucci-ponzanoGeneArchaealAlphaLfucosidase2006, title = {The Gene of an Archaeal Alpha-{{L-fucosidase}} Is Expressed by Translational Frameshifting}, author = {{Cobucci-Ponzano}, Beatrice and Conte, Fiorella and Benelli, Dario and Londei, Paola and Flagiello, Angela and Monti, Maria and Pucci, Piero and Rossi, Mos{`e} and Moracci, Marco}, year = 2006, journal = {Nucleic Acids Research}, volume = {34}, number = {15}, eprint = {16920738}, eprinttype = {pubmed}, pages = {4258–4268}, issn = {1362-4962}, doi = {10.1093/nar/gkl574}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16920738}, abstract = {The standard rules of genetic translational decoding are altered in specific genes by different events that are globally termed recoding. In Archaea recoding has been unequivocally determined so far only for termination codon readthrough events. We study here the mechanism of expression of a gene encoding for a alpha-l-fucosidase from the archaeon Sulfolobus solfataricus (fucA1), which is split in two open reading frames separated by a -1 frameshifting. The expression in Escherichia coli of the wild-type split gene led to the production by frameshifting of full-length polypeptides with an efficiency of 5%. Mutations in the regulatory site where the shift takes place demonstrate that the expression in vivo occurs in a programmed way. Further, we identify a full-length product of fucA1 in S.solfataricus extracts, which translate this gene in vitro by following programmed -1 frameshifting. This is the first experimental demonstration that this kind of recoding is present in Archaea.}, pmid = {16920738}, keywords = {alpha-L-Fucosidase,Archaea,Codon,decoding,efficiency,Escherichia coli,ESCHERICHIA-COLI,expression,EXTRACTS,FRAME,Frameshift Mutation,Frameshifting,Frameshifting Ribosomal,FrameshiftingRibosomal,gene,Gene Expression Regulation Archaeal,Gene Expression RegulationArchaeal,Genes,Genetic,genetics,IDENTIFY,In Vitro,IN-VITRO,IN-VIVO,La,MECHANISM,Mutation,MUTATIONS,nosource,OPEN READING FRAME,Open Reading Frames,physiology,POLYPEPTIDE,POLYPEPTIDES,PRODUCT,protein,READING FRAME,Reading Frames,readthrough,recoding,REGULATORY SITE,Research SupportNon-U.S.Gov’t,RULES,SITE,Sulfolobus,Sulfolobus solfataricus,termination,TERMINATION CODON,TERMINATION-CODON,TRANSLATIONAL FRAMESHIFTING,WILD-TYPE} } % == BibTeX quality report for cobucci-ponzanoGeneArchaealAlphaLfucosidase2006: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{barilFrameshiftStimulatorySignal2003, title = {The Frameshift Stimulatory Signal of Human Immunodeficiency Virus Type 1 Group {{O}} Is a Pseudoknot}, author = {Baril, Martin and Dulude, Dominic and Steinberg, Sergey V and {Brakier-Gingras}, L{'e}a}, year = 2003, month = aug, journal = {Journal of Molecular Biology}, volume = {331}, number = {3}, pages = {571–583}, publisher = {Elsevier}, issn = {0022-2836}, doi = {10.1016/S0022-2836(03)00784-8}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283603007848}, abstract = {Human immunodeficiency virus type 1 (HIV-1) requires a programmed -1 ribosomal frameshift to produce Gag-Pol, the precursor of its enzymatic activities. This frameshift occurs at a slippery sequence on the viral messenger RNA and is stimulated by a specific structure, downstream of the shift site. While in group M, the most abundant HIV-1 group, the frameshift stimulatory signal is an extended bulged stem-loop, we show here, using a combination of mutagenesis and probing studies, that it is a pseudoknot in group O. The mutagenesis and probing studies coupled to an in silico analysis show that group O pseudoknot is a hairpin-type pseudoknot with two coaxially stacked stems of eight base-pairs (stem 1 and stem 2), connected by single-stranded loops of 2nt (loop 1) and 20nt (loop 2). Mutations impairing formation of stem 1 or stem 2 of the pseudoknot reduce frameshift efficiency, whereas compensatory changes that allow re-formation of these stems restore the frameshift efficiency to near wild-type level. The difference between the frameshift stimulatory signal of group O and group M supports the hypothesis that these groups originate from a different monkey to human transmission.}, keywords = {analysis,Base Sequence,BASE-PAIR,Cell Line,Computer Simulation,DOWNSTREAM,efficiency,frameshift,Frameshifting Ribosomal,Gag-pol,Hiv-1,HIV-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,Humans,IMMUNODEFICIENCY-VIRUS,IN-SILICO,La,LOOP,M,MESSENGER-RNA,Models Molecular,Molecular Sequence Data,Mutagenesis,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,PRECURSOR,pseudoknot,Regulatory Sequences Ribonucleic Acid,REQUIRES,RIBOSOMAL FRAMESHIFT,Rna,RNA Viral,sequence,Sequence Analysis DNA,SIGNAL,SITE,STEM-LOOP,structure,Support,TYPE-1,virus,WILD-TYPE} } % == BibTeX quality report for barilFrameshiftStimulatorySignal2003: % ? unused Journal abbr (“J. Mol. Biol”)

@article{dinmanFrameshiftSignalHIV12002, title = {The Frameshift Signal of {{HIV-1}} Involves a Potential Intramolecular Triplex {{RNA}} Structure.⬚ ⬚}, author = {Dinman, Jonathan D and Richter, Sara and Plant, Ewan P and Taylor, Ronald C and Hammell, Amy B and Rana, Tariq M}, year = 2002, month = apr, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {8}, eprint = {11959986}, eprinttype = {pubmed}, pages = {5331–5336}, publisher = {National Acad Sciences}, issn = {0027-8424}, doi = {10.1073/pnas.082102199}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11959986}, abstract = {Programmed ribosomal frameshifting presents an attractive target for anti-retroviral chemotherapies, and the ⬚cis⬚-acting mRNA elements that promote programmed -1 ribosomal frameshifting present a natural target for rational drug design. It has been commonly accepted that the HIV-1 frameshifting signal is special because its downstream enhancer element consists of a simple mRNA stem-loop rather than a more complex secondary structure such as a pseudoknot. Here, we present three lines of evidence, bioinformatic, structural, and genetic, showing that the biologically relevant HIV-1 frameshift signal contains a complex RNA structure that likely contains an extended RNA triple helix region. We suggest that the potential intramolecular triplex structure is essential for viral propagation and viability, and that small molecules targeted to this RNA structure may possess anti-retroviral activities.}, keywords = {Anti-HIV Agents,Base Sequence,COMPLEX,COMPLEXES,Databases as Topic,DNA,ELEMENTS,frameshift,Frameshift Mutation,Frameshifting,Genetic,Hela Cells,Hiv-1,HIV-1,Humans,Molecular Sequence Data,mRNA,nosource,Nucleic Acid Conformation,Plasmids,pseudoknot,Ribonucleases,ribosomal frameshifting,Rna,RNA,RNA Messenger,SIGNAL,Structural,structure,Structure-Activity Relationship,yeast,Yeasts} } % == BibTeX quality report for dinmanFrameshiftSignalHIV12002: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{geerlingsFinalStepFormation2000a, title = {The Final Step in the Formation of {{25S rRNA}} in {{Saccharomyces}} Cerevisiae Is Performed by 5’–{\(>\)}3’ Exonucleases}, author = {Geerlings, T H and Vos, J C and Rau{'e}, H A}, year = 2000, month = dec, journal = {RNA (New York, N.Y.)}, volume = {6}, number = {12}, eprint = {11142370}, eprinttype = {pubmed}, pages = {1698–1703}, issn = {1355-8382}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11142370}, abstract = {The final stage in the formation of the two large subunit rRNA species in Saccharomyces cerevisiae is the removal of internal transcribed spacer 2 (ITS2) from the 27SB precursors. This removal is initiated by endonucleolytic cleavage approximately midway in ITS2. The resulting 7S pre-rRNA, which is easily detectable, is then converted into 5.8S rRNA by the concerted action of a number of 3’–{\(>\)}5’ exonucleases, many of which are part of the exosome. So far the complementary precursor to 25S rRNA resulting from the initial cleavage in ITS2 has not been detected and the manner of its conversion into the mature species is unknown. Using various yeast strains that carry different combinations of wild-type and mutant alleles of the major 5’–{\(>\)}3’ exonucleases Rat1p and Xrn1p, we now demonstrate the existence of a short-lived 25.5S pre-rRNA whose 5’ end is located closely downstream of the previously mapped 3’ end of 7S pre-rRNA. The 25.5S pre-rRNA is converted into mature 25S rRNA by rapid exonucleolytic trimming, predominantly carried out by Rat1p. In the absence of Rat1p, however, the removal of the ITS2 sequences from 25.5S pre-rRNA can also be performed by Xrn1p, albeit somewhat less efficiently.}, pmid = {11142370}, keywords = {Base Sequence,DNA Fungal,DNA Intergenic,Exoribonucleases,Fungal Proteins,Molecular Sequence Data,nosource,RNA Fungal,RNA Polymerase I,RNA Precursors,RNA Processing Post-Transcriptional,RNA Ribosomal,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Transcription Genetic} } % == BibTeX quality report for geerlingsFinalStepFormation2000a: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{mitchellExosomeConservedEukaryotic1997a, title = {The Exosome: A Conserved Eukaryotic {{RNA}} Processing Complex Containing Multiple 3’–{\(>\)}5’ Exoribonucleases}, author = {Mitchell, P and Petfalski, E and Shevchenko, A and Mann, M and Tollervey, D}, year = 1997, month = nov, journal = {Cell}, volume = {91}, number = {4}, eprint = {9390555}, eprinttype = {pubmed}, pages = {457–466}, issn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9390555}, abstract = {We identified a complex in S. cerevisiae, the “exosome,” consisting of the five essential proteins Rrp4p, Rrp41p, Rrp42p, Rrp43p, and Rrp44p (Dis3p). Remarkably, four of these proteins are homologous to characterized bacterial 3’–{\(>\)}5’ exoribonucleases; Rrp44p is homologous to RNase II, while Rrp41p, Rrp42p, and Rrp43p are related to RNase PH. Recombinant Rrp4p, Rrp44p, and Rrp41p are 3’–{\(>\)}5’ exoribonucleases in vitro that have distributive, processive, and phosphorolytic activities, respectively. All components of the exosome are required for 3’ processing of the 5.8S rRNA. Human Rrp4p is found in a comparably sized complex, and expression of the hRRP4 gene in yeast complements the rrp4-1 mutation. We conclude that the exosome constitutes a highly conserved eukaryotic RNA processing complex.}, pmid = {9390555}, keywords = {Amino Acid Sequence,Exoribonucleases,Fungal Proteins,Genetic Complementation Test,Hela Cells,Humans,Molecular Sequence Data,Molecular Weight,Multienzyme Complexes,Mutation,nosource,Recombinant Fusion Proteins,RNA Processing Post-Transcriptional,RNA Ribosomal 5.8S,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins} }

@article{lejeuneExonJunctionComplex2002, title = {The Exon Junction Complex Is Detected on {{CBP80-bound}} but Not {{eIF4E-bound mRNA}} in Mammalian Cells: Dynamics of {{mRNP}} Remodeling}, author = {Lejeune, Fabrice and Ishigaki, Yasuhito and Li, Xiaojie and Maquat, Lynne E}, year = 2002, month = jul, journal = {The EMBO Journal}, volume = {21}, number = {13}, pages = {3536–3545}, publisher = {Nature Publishing Group}, issn = {0261-4189}, doi = {10.1093/emboj/cdf345}, url = {http://www.nature.com/emboj/journal/v21/n13/abs/7594563a.html}, abstract = {Newly spliced mRNAs in mammalian cells are characterized by a complex of proteins at exon-exon junctions. This complex recruits Upf3 and Upf2, which function in nonsense-mediated mRNA decay (NMD). Both Upf proteins are detected on mRNA bound by the major nuclear cap-binding proteins CBP80/CBP20 but not mRNA bound by the major cytoplasmic cap-binding protein eIF4E. These and other data indicate that NMD targets CBP80-bound mRNA during a ‘pioneer’ round of translation, but whether nuclear eIF4E also binds nascent but dead-end transcripts is unclear. Here we provide evidence that nuclear CBP80 but not nuclear eIF4E is readily detected in association with intron-containing RNA and the C-terminal domain of RNA polymerase II. Consistent with this evidence, we demonstrate that RNPS1, Y14, SRm160, REF/Aly, TAP, Upf3X and Upf2 are detected in the nuclear fraction on CBP80-bound but not eIF4E-bound mRNA. Each of these proteins is also detected on CBP80-bound mRNA in the cytoplasmic fraction, indicating a presence on mRNA after export. The dynamics of mRNP composition before and after mRNA export are discussed.}, keywords = {Animals,Antigens Nuclear,Antigens Polyomavirus Transforming,Biological Transport,Cercopithecus aethiops,COS Cells,Cytoplasm,DNA-Binding Proteins,Eukaryotic Initiation Factor-4E,Exons,Globins,Introns,Macromolecular Substances,nosource,Nuclear Matrix-Associated Proteins,Nuclear Proteins,Peptide Initiation Factors,Protein Interaction Mapping,Protein Structure Tertiary,Ribonucleoproteins,RNA Cap-Binding Proteins,RNA Caps,RNA Messenger,RNA Polymerase II,RNA Precursors,RNA Processing Post-Transcriptional,RNA-Binding Proteins,Simian virus 40,Transcription Factors,Transfection} } % == BibTeX quality report for lejeuneExonJunctionComplex2002: % ? unused Journal abbr (“EMBO J”)

@article{shatkinEndsAffairCapping2000, title = {The Ends of the Affair: Capping and Polyadenylation}, author = {Shatkin, A J and Manley, J L}, year = 2000, month = oct, journal = {Nature Structural & Molecular Biology}, volume = {7}, number = {10}, pages = {838–842}, publisher = {Nature Publishing Group}, issn = {1072-8368}, doi = {10.1038/79583}, url = {http://www.nature.com/nsmb/journal/v7/n10/abs/nsb1000_838.html}, abstract = {Nearly all mRNAs are post-transcriptionally modified at their 5’ and 3’ ends, by capping and polyadenylation, respectively. These essential modifications are of course chemically quite distinct, as are the enzymatic complexes responsible for their synthesis. But recent studies have uncovered some similarities as well. For example, both involve entirely protein machinery, which is now the exception rather than the rule in RNA processing and modification reactions, and the two reactions share one important factor, namely RNA polymerase II. In this brief review, we describe progress in understanding the enzymes and factors that participate in these two processes, highlighting the evolutionary conservation, from yeast to humans, that has become apparent.}, keywords = {20473219,animal,Animals,COMPLEX,COMPLEXES,DNA Polymerase II,enzyme,enzymology,genetics,human,metabolism,modification,mRNA,nosource,Poly A,polymerase,protein,Review,Rna,Rna Caps,RNA Caps,RNA Messenger,RNA Polymerase II,RNA Processing Post-Transcriptional,RNA Processing- Post-Transcriptional,RNA ProcessingPost-Transcriptional,RNA- Messenger,RNAMessenger,Saccharomyces cerevisiae,supportu.s.gov’tp.h.s.,Transcription Genetic,Transcription- Genetic,TranscriptionGenetic,yeast} } % == BibTeX quality report for shatkinEndsAffairCapping2000: % ? unused Journal abbr (“Nat. Struct. Biol”)

@article{ichoDoublestrandedRNAGenome1989, title = {The Double-Stranded {{RNA}} Genome of Yeast Virus {{L-A}} Encodes Its Own Putative {{RNA}} Polymerase by Fusing Two Open Reading Frames.}, author = {Icho, T and Wickner, R B}, year = 1989, month = apr, journal = {The Journal of Biological Chemistry}, volume = {264}, number = {12}, eprint = {2651431}, eprinttype = {pubmed}, pages = {6716–6723}, issn = {0021-9258}, doi = {10.1016/S0021-9258(18)83488-3}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2651431}, abstract = {The L-A double-stranded RNA virus of Saccharomyces cerevisiae encodes its major coat protein (80 kDa) and a minor single-stranded RNA binding protein (180 kDa) that has immunological cross-reactivity with the major coat protein. The sequence of L-A cDNA clones revealed two open reading frames (ORF), ORF1 and ORF2. These two reading frames overlap by 130 base pairs and ORF2 is in the -1 reading frame with respect to ORF1. Although the major coat protein of the viral particles is encoded by ORF1, the 180-kDa protein is derived from the entire double-stranded RNA genome by fusing ORF1 and ORF2, probably by a -1 translational frameshift. Within the overlapping region is a sequence similar to that producing a -1 frameshift by “simultaneous slippage” in retroviruses. The coding sequence of ORF2 shows a pattern characteristic of viral RNA-dependent RNA polymerases of icosahedral (+)-strand RNA viruses. Thus, the 180-kDa protein is analogous to gag-pol fusion proteins.}, pmid = {2651431}, keywords = {Amino Acid Sequence,Base Sequence,Capsid,DNA-Directed RNA Polymerases,DOUBLE-STRANDED-RNA,Frameshifting,Genes,Genes Viral,Genome,Hydrogen Bonding,L-A,La,Molecular Sequence Data,Molecular Weight,nosource,Open Reading Frames,polymerase,Restriction Mapping,Rna,RNA Double-Stranded,RNA Viral,Saccharomyces cerevisiae,sequence,virus,yeast} } % == BibTeX quality report for ichoDoublestrandedRNAGenome1989: % ? unused Journal abbr (“J. Biol. Chem”)

@article{collerDEADBoxHelicase2001, title = {The {{DEAD}} Box Helicase, {{Dhh1p}}, Functions in {{mRNA}} Decapping and Interacts with Both the Decapping and Deadenylase Complexes.}, author = {Coller, J M and Tucker, M and Sheth, U and {Valencia-Sanchez}, M A and Parker, R}, year = 2001, month = dec, journal = {RNA (New York, N.Y.)}, volume = {7}, number = {12}, pages = {1717–1727}, issn = {1355-8382}, url = {http://rnajournal.cshlp.org/content/7/12/1717.short}, abstract = {A major pathway of mRNA turnover in eukaryotic cells initiates with deadenylation, leading to mRNA decapping and subsequent 5’ to 3’ exonuclease digestion. We show that a highly conserved member of the DEAD box family of helicases, Dhh1p, stimulates mRNA decapping in yeast. In dhh1delta mutants, mRNAs accumulate as deadenylated, capped species. Dhh1p’s effects on decapping only occur on normal messages as nonsense-mediated decay still occurs in dhh1delta mutants. The role of Dhh1p in decapping appears to be direct, as Dhh1p physically interacts with several proteins involved in mRNA decapping including the decapping enzyme Dcp1p, as well as Lsm1p and Pat1p/Mrt1p, which function to enhance the decapping rate. Additional observations suggest Dhh1p functions to coordinate distinct steps in mRNA function and decay. Dhh1p also associates with Pop2p, a subunit of the mRNA deadenylase. In addition, genetic phenotypes suggest that Dhh1p also has a second biological function. Interestingly, Dhh1p homologs in others species function in maternal mRNA storage. This provides a novel link between the mechanisms of decapping and maternal mRNA translational repression.}, pmid = {11780629}, keywords = {Amino Acid Sequence,Conserved Sequence,DEAD-box RNA Helicases,deadenylase,decapping,Endoribonucleases,Fungal Proteins,helicase,Models Genetic,mrna turnover,nosource,Protein Biosynthesis,Proto-Oncogene Proteins,Ribonucleases,RNA Cap-Binding Proteins,RNA Caps,RNA Helicases,RNA Messenger Stored,RNA Nucleotidyltransferases,RNA Stability,RNA-Binding Proteins,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins} } % == BibTeX quality report for collerDEADBoxHelicase2001: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{sergievConservedAsiteFinger2005, title = {The Conserved {{A-site}} Finger of the 23 {{S rRNA}}: {{Just}} One of the Intersubunit Bridges or a Part of the Allosteric Communication Pathway?}, author = {Sergiev, Petr V and Kiparisov, Sergey V and Burakovsky, Dmitry E and Lesnyak, Dmitry V and Leonov, Andrei A and Bogdanov, Alexey A and Dontsova, Olga A}, year = 2005, month = oct, journal = {Journal of Molecular Biology}, volume = {353}, number = {1}, pages = {116–123}, publisher = {Elsevier}, issn = {0022-2836}, doi = {10.1016/j.jmb.2005.08.006}, url = {http://linkinghub.elsevier.com/retrieve/pii/S002228360500906X}, abstract = {During the translocation of tRNAs and mRNA relative to the ribosome, the B1a, B1b and B1c bridges undergo the most extensive conformational changes among the bridges between the large and the small ribosomal subunits. The B1a bridge, also called the “A-site finger” (ASF), is formed by the 23S rRNA helix 38, which is located right above the ribosomal A-site. Here, we deleted part of the ASF so that the B1a intersubunit bridge could not be formed (DeltaB1a). The mutation led to a less efficient subunit association. A number of functional activities of the DeltaB1a ribosomes, such as tRNA binding to the P and A-sites, translocation and EF-G-related GTPase reaction were preserved. A moderate decrease in EF-G-related GTPase stimulation by the P-site occupation by deacylated tRNA was observed. This suggests that the B1a bridge is not involved in the most basic steps of the elongation cycle, but rather in the fine-tuning of the ribosomal activity. Chemical probing of ribosomes carrying the ASF truncation revealed structural differences in the 5S rRNA and in the 23S rRNA helices located between the peptidyltransferase center and the binding site of the elongation factors. Interestingly, reactivity changes were found in the P-loop, an important functional region of the 23S rRNA. It is likely that the A-site finger, in addition to its role in subunit association, forms part of the system of allosteric signal exchanges between the small subunit decoding center and the functional centers on the large subunit.}, keywords = {0,5S rRNA,A SITE,A-SITE,A-SITES,Allosteric Regulation,ASSOCIATION,Base Sequence,BINDING,BINDING-SITE,BIOLOGY,Catalysis,chemistry,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,Conserved Sequence,decoding,elongation,ELONGATION CYCLE,elongation factors,ELONGATION-FACTORS,FORM,genetics,GTP,GTP Phosphohydrolase,GTP Phosphohydrolases,GTPase,La,metabolism,Models Molecular,Models- Molecular,Models-Molecular,ModelsMolecular,Molecular Sequence Data,mRNA,Mutation,nosource,Nucleic Acid Conformation,P and A sites,P loop,P SITE,P-SITE,PATHWAY,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,REGION,Research Support-Non-U.S.Gov’t,Research SupportNon-U.S.Gov’t,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNA Ribosomal 23S,RNA Transfer,RNA- Ribosomal- 23S,RNA- Transfer,RNA-Ribosomal-23S,RNA-Transfer,RNARibosomal23S,RNATransfer,rRNA,SIGNAL,SITE,Structural,SUBUNIT,subunit association,SUBUNITS,SYSTEM,translocation,tRNA,tRNA binding} } % == BibTeX quality report for sergievConservedAsiteFinger2005: % ? unused Journal abbr (“J. Mol. Biol”)

@article{karolClosestLivingRelatives2001, title = {The Closest Living Relatives of Land Plants}, author = {Karol, K G and McCourt, R M and Cimino, M T and Delwiche, C F}, year = 2001, month = dec, journal = {Science (New York, N.Y.)}, volume = {294}, number = {5550}, pages = {2351–2353}, publisher = {American Association for the Advancement of Science}, issn = {0036-8075}, doi = {10.1126/science.1065156}, url = {http://www.sciencemag.org/content/294/5550/2351.short}, abstract = {The embryophytes (land plants) have long been thought to be related to the green algal group Charophyta, though the nature of this relationship and the origin of the land plants have remained unresolved. A four-gene phylogenetic analysis was conducted to investigate these relationships. This analysis supports the hypothesis that the land plants are placed phylogenetically within the Charophyta, identifies the Charales (stoneworts) as the closest living relatives of plants, and shows the Coleochaetales as sister to this Charales/land plant assemblage. The results also support the unicellular flagellate Mesostigma as the earliest branch of the charophyte lineage. These findings provide insight into the nature of the ancestor of plants, and have broad implications for understanding the transition from aquatic green algae to terrestrial plants.}, keywords = {Algae Green,ATP Synthetase Complexes,Bayes Theorem,DNA Plant,Evolution,Genes Plant,Genes rRNA,Likelihood Functions,Mitochondrial Proteins,nosource,Phylogeny,Plant Physiological Phenomena,Plant Proteins,Plants,Polymerase Chain Reaction,Ribulose-Bisphosphate Carboxylase,Sequence Analysis DNA} } % == BibTeX quality report for karolClosestLivingRelatives2001: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”)

@article{fedorCatalyticDiversityRNAs2005, title = {The Catalytic Diversity of {{RNAs}}.}, author = {Fedor, Martha J and Williamson, James R}, year = 2005, month = may, journal = {Nature Reviews. Molecular Cell Biology}, volume = {6}, number = {5}, eprint = {15956979}, eprinttype = {pubmed}, pages = {399–412}, publisher = {Nature Publishing Group}, issn = {1471-0072}, doi = {10.1038/nrm1647}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15956979 http://www.nature.com/nrm/journal/v6/n5/abs/nrm1647.html}, abstract = {The natural RNA enzymes catalyse phosphate-group transfer and peptide-bond formation. Initially, metal ions were proposed to supply the chemical versatility that nucleotides lack. In the ensuing decades, structural and mechanistic studies have substantially altered this initial viewpoint. Whereas self-splicing ribozymes clearly rely on essential metal-ion cofactors, self-cleaving ribozymes seem to use nucleotide bases for their catalytic chemistry. Despite the overall differences in chemical features, both RNA and protein enzymes use similar catalytic strategies.}, pmid = {15956979}, keywords = {Animals,Base Sequence,Catalysis,Catalytic,Catalytic: chemistry,Catalytic: metabolism,Introns,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Protein Biosynthesis,Ribosomes,Ribosomes: metabolism,RNA,RNA Catalytic,RNA Splicing} } % == BibTeX quality report for fedorCatalyticDiversityRNAs2005: % ? Possibly abbreviated journal title Nature Reviews. Molecular Cell Biology % ? unused Journal abbr (“Nat. Rev. Mol. Cell Biol”)

@article{iborraCaseNuclearTranslation2004, title = {The Case for Nuclear Translation}, author = {Iborra, Francisco J and Jackson, Dean A and Cook, Peter R}, year = 2004, month = nov, journal = {Journal of Cell Science}, volume = {117}, number = {Pt 24}, pages = {5713–5720}, publisher = {Company of Biologists}, issn = {0021-9533}, doi = {10.1242/jcs.01538}, url = {http://jcs.biologists.org/content/117/24/5713.short}, abstract = {Although it is frequently assumed that translation does not occur in eukaryotic nuclei, recent evidence suggests that some translation can take place and that it is closely coupled to transcription. The first evidence concerns the destruction of nuclear mRNAs containing premature termination codons by nonsense-mediated decay (NMD). Only ribosomes can detect termination codons, and as some NMD occurs within the nuclear fraction, active nuclear ribosomes could perform the required detection. The second evidence is the demonstration that tagged amino acids are incorporated into nascent polypeptides in a nuclear process coupled to transcription. The third evidence is that components involved in translation, NMD and transcription colocalize, coimmunoprecipitate and co-purify. All these results are simply explained if nuclear ribosomes scan nascent transcripts for premature termination codons at the site of transcription. Alternatively, the scanning needed for NMD might take place at the nuclear membrane, and contaminating cytoplasmic ribosomes might give the appearance of some nuclear translation. We argue, however, that the balance of evidence favours bona fide nuclear translation.}, keywords = {Animals,Cell Nucleus,Codon Nonsense,Codon Terminator,Codon- Nonsense,Codon- Terminator,Cytoplasm,Humans,Immunoprecipitation,Models Biological,Models Theoretical,Models- Biological,Models- Theoretical,nosource,Peptides,Protein Biosynthesis,Ribosomes,RNA Messenger,RNA Transfer,RNA- Messenger,RNA- Transfer,Transcription Genetic,Transcription- Genetic} } % == BibTeX quality report for iborraCaseNuclearTranslation2004: % ? unused Journal abbr (“J. Cell. Sci”)

@article{wiluszCaptotailGuideMRNA2001, title = {The Cap-to-Tail Guide to {{mRNA}} Turnover}, author = {Wilusz, C J and Wormington, M and Peltz, S W}, year = 2001, month = apr, journal = {Nature Reviews. Molecular Cell Biology}, volume = {2}, number = {4}, pages = {237–246}, publisher = {Nature Publishing Group}, issn = {1471-0072}, doi = {10.1038/35067025}, url = {http://www.nature.com/nrm/journal/v2/n4/abs/nrm0401_237a.html}, abstract = {The levels of cellular messenger RNA transcripts can be regulated by controlling the rate at which the mRNA decays. Because decay rates affect the expression of specific genes, they provide a cell with flexibility in effecting rapid change. Moreover, many clinically relevant mRNAs–including several encoding cytokines, growth factors and proto-oncogenes–are regulated by differential RNA stability. But what are the sequence elements and factors that control the half-lives of mRNAs?}, keywords = {Animals,Base Sequence,Half-Life,Humans,Kinetics,nosource,Poly A,Protein Biosynthesis,RNA Caps,RNA Processing Post-Transcriptional,RNA Processing- Post-Transcriptional,RNA Stability} } % == BibTeX quality report for wiluszCaptotailGuideMRNA2001: % ? Possibly abbreviated journal title Nature Reviews. Molecular Cell Biology % ? unused Journal abbr (“Nat. Rev. Mol. Cell Biol”)

@article{wahleBiochemistry3endCleavage1992, title = {The Biochemistry of 3’-End Cleavage and Polyadenylation of Messenger {{RNA}} Precursors}, author = {Wahle, E and Keller, W}, year = 1992, journal = {Annual Review of Biochemistry}, volume = {1960}, number = {8}, pages = {419–440}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, issn = {0066-4154}, doi = {10.1146/annurev.bi.61.070192.002223}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.bi.61.070192.002223 http://www.annualreviews.org/doi/pdf/10.1146/annurev.bi.61.070192.002223}, keywords = {Animals,Base Sequence,Binding Sites,biozentrum,depart m e n,Humans,klingelbergstrasse 70,nosource,Plants,Poly A,RNA Messenger,RNA Precursors,RNA Processing Post-Transcriptional,Saccharomyces cerevisiae,t of cell biology,university of basel} } % == BibTeX quality report for wahleBiochemistry3endCleavage1992: % ? unused Journal abbr (“Annu. Rev. Biochem”)

@article{plant9angstromSolutionHow2003, title = {The 9-Angstrom Solution: {{How mRNA}} Pseudoknots Promote Efficient Programmed -1 Ribosomal Frameshifting}, author = {Plant, Ewan P and Jacobs, Kristi L Muldoon and Harger, Jason W and Meskauskas, Arturas and Jacobs, Jonathan L and Baxter, Jennifer L and Petrov, Alexey N and Dinman, Jonathan D}, year = 2003, month = feb, journal = {RNA (New York, N.Y.)}, volume = {9}, number = {2}, pages = {168–174}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, doi = {10.1261/rna.2132503}, url = {isi:000181281600004 http://rnajournal.cshlp.org/content/9/2/168.short}, abstract = {There is something special about mRNA pseudoknots that allows them to elicit efficient levels of programmed -1 ribosomal frameshifting. Here, we present a synthesis of recent crystallographic, molecular, biochemical, and genetic studies to explain this property. Movement of 9 A by the anticodon loop of the aminoacyl-tRNA at the accommodation step normally pulls the downstream mRNA a similar distance along with it. We suggest that the downstream mRNA pseudoknot provides resistance to this movement by becoming wedged into the entrance of the ribosomal mRNA tunnel. These two opposing forces result in the creation of a local region of tension in the mRNA between the A-site codon and the mRNA pseudoknot. This can be relieved by one of two mechanisms; unwinding the pseudoknot, allowing the downstream region to move forward, or by slippage of the proximal region of the mRNA backwards by one base. The observed result of the latter mechanism is a net shift of reading frame by one base in the 5’ direction, that is, a -1 ribosomal frameshift.}, keywords = {0,A-SITE,after a generation spent,ANGSTROM RESOLUTION,Anticodon,Bacteria,Codon,crys-,CRYSTAL-STRUCTURE,enjoying a renaissance,frameshift,Frameshifting,Frameshifting Ribosomal,function,GENE-EXPRESSION,Genetic,genetic code,Genetic Code,have given us,IMMUNODEFICIENCY-VIRUS,in the shadows,MECHANISM,MECHANISMS,MESSENGER-RNA,Movement,mRNA,nosource,PEPTIDYL-TRANSFERASE,PROTEIN-SYNTHESIS,pseudoknot,recent breakthroughs in x-ray,recoding,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,ribosome,Ribosomes,RNA Messenger,SACCHAROMYCES-CEREVISIAE,SLIPPAGE,structure,structure/function,tallography and cryoelectron microscopy,the ribosome is,Thermodynamics,translation,TY1 RETROTRANSPOSITION,VIRAL-RNA PSEUDOKNOT,virus} } % == BibTeX quality report for plant9angstromSolutionHow2003: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{anderson35Degradation1998, title = {The 3’ to 5’ Degradation of Yeast {{mRNAs}} Is a General Mechanism for {{mRNA}} Turnover That Requires the {{SKI2 DEVH}} Box Protein and 3’ to 5’ Exonucleases of the Exosome Complex.}, author = {Anderson, J S and Parker, R P}, year = 1998, month = mar, journal = {The EMBO Journal}, volume = {17}, number = {5}, pages = {1497–1506}, publisher = {Nature Publishing Group}, issn = {0261-4189}, doi = {10.1093/emboj/17.5.1497}, url = {http://www.nature.com/emboj/journal/v17/n5/abs/7590864a.html}, abstract = {One major pathway of mRNA decay in yeast occurs by deadenylation-dependent decapping, which exposes the transcript to 5’ to 3’ exonucleolytic degradation. We show that a second general pathway of mRNA decay in yeast occurs by 3’ to 5’ degradation of the transcript. We also show that the SKI2, SKI3, SKI6/RRP41, SKI8 and RRP4 gene products are required for 3’ to 5’ decay of mRNA. The Ski6p/Rrp41p protein has homology to the Escherichia coli 3’ to 5’ exoribonuclease RNase PH, and both the Ski6p/Rrp41p and Rrp4p proteins are components of a multiprotein complex, termed the exosome, that contains at least three polypeptides with 3’ to 5’ exoribonuclease activities. These observations suggest that the exosome may be the nucleolytic activity that degrades the body of the mRNA in a 3’ to 5’ direction, and the exosome’s activity on mRNAs may be modulated by Ski2p, Ski3p and Ski8p. Blocking both 3’ to 5’ and 5’ to 3’ decay leads to inviability, and conditional double mutants show extremely long mRNA half-lives. These observations argue that efficient mRNA turnover is required for viability and that we have identified the two major pathways of mRNA decay in yeast.}, keywords = {degradation,Endoribonucleases,Exoribonucleases,exosome,Fungal Proteins,Genes Fungal,Genes Lethal,mRNA,mRNA decay,Mutation,nosource,Phenotype,Phosphoglycerate Kinase,Poly G,protein,Proteins,RNA Cap-Binding Proteins,RNA Fungal,RNA Messenger,RNA Ribosomal 5.8S,RNA-Binding Proteins,Saccharomyces cerevisiae Proteins,SKI,translation,turnover,yeast,Yeasts} } % == BibTeX quality report for anderson35Degradation1998: % ? unused Journal abbr (“EMBO J.”)

@article{blackburnTelomeresTelomeraseTheir2005, title = {Telomeres and Telomerase: Their Mechanisms of Action and the Effects of Altering Their Functions}, author = {Blackburn, Elizabeth H}, year = 2005, month = feb, journal = {FEBS Letters}, volume = {579}, number = {4}, pages = {859–862}, publisher = {Elsevier}, issn = {0014-5793}, doi = {10.1016/j.febslet.2004.11.036}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579304014267}, abstract = {The molecular features of telomeres and telomerase are conserved among most eukaryotes. How telomerase and telomeres function and how they interact to promote the chromosome-stabilizing properties of telomeres are discussed here.}, keywords = {Apoptosis,Chromosome Aberrations,DNA-Binding Proteins,Humans,Neoplasms,nosource,Telomerase,Telomere} } % == BibTeX quality report for blackburnTelomeresTelomeraseTheir2005: % ? unused Journal abbr (“FEBS Lett”)

@article{enomotoTelomereCapComponents2004, title = {Telomere Cap Components Influence the Rate of Senescence in Telomerase-Deficient Yeast Cells}, author = {Enomoto, Shinichiro and Glowczewski, Lynn and {Lew-Smith}, Jodi and Berman, Judith G}, year = 2004, month = jan, journal = {Molecular and Cellular Biology}, volume = {24}, number = {2}, pages = {837–845}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, doi = {10.1128/​MCB.24.2.837-845.2004}, url = {PM:14701754 http://mcb.asm.org/cgi/content/abstract/24/2/837}, abstract = {Cells lacking telomerase undergo senescence, a progressive reduction in cell division that involves a cell cycle delay and culminates in “crisis,” a period when most cells become inviable. In telomerase-deficient Saccharomyces cerevisiae cells lacking components of the nonsense-mediated mRNA decay (NMD) pathway (Upf1,Upf2, or Upf3 proteins), senescence is delayed, with crisis occurring approximately 10 to 25 population doublings later than in Upf+ cells. Delayed senescence is seen in upfDelta cells lacking the telomerase holoenzyme components Est2p and TLC1 RNA, as well as in cells lacking the telomerase regulators Est1p and Est3p. The delay of senescence in upfDelta cells is not due to an increased rate of survivor formation. Rather, it is caused by alterations in the telomere cap, composed of Cdc13p, Stn1p, and Ten1p. In upfDelta mutants, STN1 and TEN1 levels are increased. Increasing the levels of Stn1p and Ten1p in Upf+ cells is sufficient to delay senescence. In addition, cdc13-2 mutants exhibit delayed senescence rates similar to those of upfDelta cells. Thus, changes in the telomere cap structure are sufficient to affect the rate of senescence in the absence of telomerase. Furthermore, the NMD pathway affects the rate of senescence in telomerase-deficient cells by altering the stoichiometry of telomere cap components.}, keywords = {0,Adaptor Proteins Signal Transducing,Base Sequence,BIOLOGY,Cap,CAP STRUCTURE,cell cycle,Cell Cycle,Cell Cycle Proteins,Cell Division,CELLS,CEREVISIAE,chemistry,Codon,Codon Nonsense,Codon-Nonsense,CodonNonsense,COMPONENT,COMPONENTS,cytology,DECAY,development,Dna,DNA Fungal,DNA-BINDING,DNA-Binding Proteins,DNA-Fungal,DNAFungal,enzymology,Fungal Proteins,Genes Fungal,Genes-Fungal,GenesFungal,Genetic,genetics,Helicase,La,metabolism,Models Biological,Models-Biological,ModelsBiological,mRNA,mRNA decay,MUTANTS,Mutation,NMD,NONSENSE,nonsense-mediated mRNA decay,nosource,PATHWAY,protein,Proteins,Rad52 DNA Repair and Recombination Protein,REVERSE-TRANSCRIPTASE,Rna,RNA Fungal,RNA HELICASE,RNA Helicases,RNA Messenger,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNA-Fungal,RNA-Messenger,RNAFungal,RNAMessenger,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,structure,support-u.s.gov’t-p.h.s.,supportu.s.gov’tp.h.s.,Telomerase,Telomere,Telomere-Binding Proteins,Trans-Activators,ultrastructure,Upf1,UPF1 PROTEIN,UPF3,yeast,YEAST-CELLS} } % == BibTeX quality report for enomotoTelomereCapComponents2004: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{dongTelomeraseRegulationFunction2005, title = {Telomerase: Regulation, Function and Transformation}, author = {Dong, Carolyn K and Masutomi, Kenkichi and Hahn, William C}, year = 2005, month = may, journal = {Critical Reviews in ooncology/Hematology}, volume = {54}, number = {2}, pages = {85–93}, publisher = {Elsevier}, issn = {1040-8428}, doi = {10.1016/j.critrevonc.2004.12.005}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1040842804002240}, abstract = {Work from several laboratories over the past decade indicates that the acquisition of constitutive telomerase expression is a critical step during the malignant transformation of human cells. Normal human cells transiently express low levels of telomerase, the ribonucleoprotein responsible for extending and maintaining telomeres, and exhibit telomere shortening after extended passage, whereas most cancers exhibit constitutive telomerase expression and maintain telomeres at stable lengths. These observations establish a direct connection between immortalization and stabilization of telomere structure. However, recent work suggests that telomerase also contributes to cancer development beyond its role in maintaining stable telomere lengths. In this review, we summarize recent observations that support the concept that telomerase plays multiple roles in facilitating human cell transformation.}, keywords = {Cell Aging,Cell Transformation Neoplastic,Humans,Neoplasms,nosource,Telomerase} } % == BibTeX quality report for dongTelomeraseRegulationFunction2005: % ? unused Journal abbr (“Crit. Rev. Oncol. Hematol”)

@article{nakamuraTelomeraseCatalyticSubunit1997, title = {Telomerase Catalytic Subunit Homologs from Fission Yeast and Human}, author = {Nakamura, T M and Morin, G B and Chapman, K B and Weinrich, S L and Andrews, W H and Lingner, J and Harley, C B and Cech, T R}, year = 1997, month = aug, journal = {Science (New York, N.Y.)}, volume = {277}, number = {5328}, pages = {955–959}, issn = {0036-8075}, url = {http://www.sciencemag.org/content/277/5328/955.short}, abstract = {Catalytic protein subunits of telomerase from the ciliate Euplotes aediculatus and the yeast Saccharomyces cerevisiae contain reverse transcriptase motifs. Here the homologous genes from the fission yeast Schizosaccharomyces pombe and human are identified. Disruption of the S. pombe gene resulted in telomere shortening and senescence, and expression of mRNA from the human gene correlated with telomerase activity in cell lines. Sequence comparisons placed the telomerase proteins in the reverse transcriptase family but revealed hallmarks that distinguish them from retroviral and retrotransposon relatives. Thus, the proposed telomerase catalytic subunits are phylogenetically conserved and represent a deep branch in the evolution of reverse transcriptases.}, pmid = {9252327}, keywords = {Amino Acid Sequence,Binding Sites,Catalysis,Cell Line,DNA-Binding Proteins,Evolution Molecular,Genes Fungal,Humans,Introns,Molecular Sequence Data,nosource,Phylogeny,Proteins,Retroelements,RNA,RNA Messenger,RNA-Directed DNA Polymerase,Schizosaccharomyces,Schizosaccharomyces pombe Proteins,Sequence Alignment,Telomerase,Telomere} } % == BibTeX quality report for nakamuraTelomeraseCatalyticSubunit1997: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”)

@article{shethTargetingAberrantMRNAs2006, title = {Targeting of Aberrant {{mRNAs}} to Cytoplasmic Processing Bodies}, author = {Sheth, Ujwal and Parker, Roy}, year = 2006, month = jun, journal = {Cell}, volume = {125}, number = {6}, pages = {1095–1109}, publisher = {Elsevier}, issn = {0092-8674}, doi = {10.1016/j.cell.2006.04.037}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867406006192}, abstract = {In eukaryotes, a specialized pathway of mRNA degradation termed nonsense-mediated decay (NMD) functions in mRNA quality control by recognizing and degrading mRNAs with aberrant termination codons. We demonstrate that NMD in yeast targets premature termination codon (PTC)-containing mRNA to P-bodies. Upf1p is sufficient for targeting mRNAs to P-bodies, whereas Upf2p and Upf3p act, at least in part, downstream of P-body targeting to trigger decapping. The ATPase activity of Upf1p is required for NMD after the targeting of mRNAs to P-bodies. Moreover, Upf1p can target normal mRNAs to P-bodies but not promote their degradation. These observations lead us to propose a new model for NMD wherein two successive steps are used to distinguish normal and aberrant mRNAs.}, keywords = {Adaptor Proteins Signal Transducing,Adaptor Proteins- Signal Transducing,Codon Nonsense,Codon- Nonsense,Cytoplasmic Structures,Models Biological,Models- Biological,nosource,RNA Fungal,RNA Helicases,RNA Messenger,RNA Stability,RNA Transport,RNA- Fungal,RNA- Messenger,RNA-Binding Proteins,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Trans-Activators} }

@article{jacobsSystematicAnalysisBicistronic2004, title = {Systematic Analysis of Bicistronic Reporter Assay Data}, author = {Jacobs, Jonathan L and Dinman, Jonathan D}, year = 2004, month = nov, journal = {Nucleic Acids Research}, volume = {32}, number = {20}, pages = {e160-e170}, issn = {1362-4962}, doi = {10.1093/nar/gnh157}, url = {http://nar.oxfordjournals.org/content/32/20/e160.short}, abstract = {Bicistronic reporter assay systems have become a mainstay of molecular biology. While the assays themselves encompass a broad range of diverse and unrelated experimental protocols, the numerical data garnered from these experiments often have similar statistical properties. In general, a primary dataset measures the paired expression of two internally controlled reporter genes. The expression ratio of these two genes is then normalized to an external control reporter. The end result is a ‘ratio of ratios’ that is inherently sensitive to propagation of the error contributed by each of the respective numerical components. The statistical analysis of this data therefore requires careful handling in order to control for the propagation of error and its potentially misleading effects. A careful survey of the literature found no consistent method for the statistical analysis of data generated from these important and informative assay systems. In this report, we present a detailed statistical framework for the systematic analysis of data obtained from bicistronic reporter assay systems. Specifically, a dual luciferase reporter assay was employed to measure the efficiency of four programmed -1 frameshift signals. These frameshift signals originate from the L-A virus, the SARS-associated Coronavirus and computationally identified frameshift signals from two Saccharomyces cerevisiae genes. Furthermore, these statistical methods were applied to prove that the effects of anisomycin on programmed -1 frameshifting are statistically significant. A set of Microsoft Excel spreadsheets, which can be used as templates for data generated by dual reporter assay systems, and an online tutorial are available at our website (http://dinmanlab.umd.edu/statistics). These spreadsheets could be easily adapted to any bicistronic reporter assay system.}, pmid = {15561995}, keywords = {analysis,anisomycin,assays,bicistronic,BIOLOGY,CEREVISIAE,COMPONENT,COMPONENTS,Coronavirus,Data Interpretation,Data Interpretation Statistical,efficiency,expression,frameshift,Frameshifting,Frameshifting Ribosomal,gene,Gene Expression,Genes,Genes Reporter,Genetic,Genetic Techniques,genetics,Internet,L-A,L-A-VIRUS,La,luciferase,Luciferases,Luciferases: genetics,Methods,microbiology,MOLECULAR-GENETICS,nosource,Probability,PROPAGATION,Reporter,REQUIRES,Ribosomal,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,SACCHAROMYCES-CEREVISIAE,Sample Size,SIGNAL,Statistical,SYSTEM,SYSTEMS,TEMPLATE,Templates,virus} } % == BibTeX quality report for jacobsSystematicAnalysisBicistronic2004: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{johnsonSyntheticLethalitySep11995, title = {Synthetic Lethality of Sep1 (Xrn1) Ski2 and Sep1 (Xrn1) Ski3 Mutants of {{Saccharomyces}} Cerevisiae Is Independent of Killer Virus and Suggests a General Role for These Genes in Translation Control}, author = {Johnson, A W and Kolodner, R D}, year = 1995, month = may, journal = {Molecular and Cellular Biology}, volume = {15}, number = {5}, eprint = {7739552}, eprinttype = {pubmed}, pages = {2719–2727}, issn = {0270-7306}, doi = {10.1128/MCB.15.5.2719}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7739552}, abstract = {Strand exchange protein 1 (Sep1) (also referred to as exoribonuclease I [Xrn1]) from Saccharomyces cerevisiae has been implicated in DNA recombination, RNA turnover, karyogamy, and G4 DNA pairing among other disparate cellular processes. Using a genetic approach to study the role of SEP1/XRN1 in mitotic yeast cells, we identified mutations in the genes superkiller 2 (SKI2) and superkiller 3 (SKI3) as synthetically lethal with an sep1 null mutation. The SKI genes are thought to comprise an intracellular antiviral system controlling the expression of killer toxin from double-stranded RNA virus found in many yeast strains. However, the lethality of sep1 ski2 and sep1 ski3 mutants was independent of the L-A and M viruses, suggesting that the SKI genes act in a general cellular process in addition to virus control. We propose that Sep1/Xrn1 and Ski2 both act to block translation on transcripts targeted for degradation. Using a temperature-sensitive allele of SEP1/XRN1, we show that double mutants display a synthetic cell cycle arrest in late G1 at Start.}, pmid = {7739552}, keywords = {antiviral,Base Sequence,cancer,cell cycle,degradation,Deoxyribonucleases,Dna,DNA Fungal,DNA Primers,DOUBLE-STRANDED-RNA,Exoribonucleases,expression,Fungal Proteins,G1 Phase,gene,Genes,Genes Fungal,Genes Lethal,Genetic,killer,killer toxin,L-A,La,Molecular Sequence Data,Mutation,MUTATIONS,nosource,Phenotype,protein,Protein Biosynthesis,Rna,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SKI,SYSTEM,toxin,translation,turnover,virus,XRN1,yeast} } % == BibTeX quality report for johnsonSyntheticLethalitySep11995: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{weingerSubstrateassistedCatalysisPeptide2004, title = {Substrate-Assisted Catalysis of Peptide Bond Formation by the Ribosome}, author = {Weinger, Joshua S and Parnell, K Mark and Dorner, Silke and Green, Rachel and Strobel, Scott A}, year = 2004, month = nov, journal = {Nature Structural & Molecular Biology}, volume = {11}, number = {11}, pages = {1101–1106}, publisher = {Nature Publishing Group}, issn = {1545-9993}, doi = {10.1038/nsmb841}, url = {http://www.nature.com/nsmb/journal/v11/n11/abs/nsmb841.html}, abstract = {The ribosome accelerates the rate of peptide bond formation by at least 10(7)-fold, but the catalytic mechanism remains controversial. Here we report evidence that a functional group on one of the tRNA substrates plays an essential catalytic role in the reaction. Substitution of the P-site tRNA A76 2’ OH with 2’ H or 2’ F results in at least a 10(6)-fold reduction in the rate of peptide bond formation, but does not affect binding of the modified substrates. Such substrate-assisted catalysis is relatively uncommon among modern protein enzymes, but it is a property predicted to be essential for the evolution of enzymatic function. These results suggest that substrate assistance has been retained as a catalytic strategy during the evolution of the prebiotic peptidyl transferase center into the modern ribosome.}, keywords = {Base Sequence,BINDING,BOND FORMATION,Catalysis,Catalytic Domain,enzyme,Enzymes,Escherichia coli,Evolution,Evolution Molecular,Kinetics,La,Lysine,MECHANISM,Methionine,Models Biological,Models Chemical,Molecular Sequence Data,nosource,P SITE,P-SITE,peptide bond formation,Peptides,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,protein,Protein Transport,ribosome,Ribosomes,RNA Messenger,RNA Transfer,Substrate Specificity,Time Factors,TRANSFERASE CENTER,tRNA} } % == BibTeX quality report for weingerSubstrateassistedCatalysisPeptide2004: % ? unused Journal abbr (“Nat. Struct. Mol. Biol”)

@article{gaoStudyStructuralDynamics2003, title = {Study of the {{Structural Dynamics}} of the {{E}}. Coli {{70S Ribosome Using Real-Space Refinement}}}, author = {Gao, Haixiao and Sengupta, Jayati and Valle, Mikel and Korostelev, Andrei and Eswar, Narayanan and Stagg, Scott M and Van Roey, Patrick and Agrawal, Rajendra K and Harvey, Stephen C and Sali, Andrej and Chapman, Michael S and Frank, Joachim}, year = 2003, month = jun, journal = {Cell}, volume = {113}, number = {6}, eprint = {12809609}, eprinttype = {pubmed}, pages = {789–801}, publisher = {Elsevier}, issn = {0092-8674}, doi = {10.1016/S0092-8674(03)00427-6}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12809609}, abstract = {Cryo-EM density maps showing the 70S ribosome of E. coli in two different functional states related by a ratchet-like motion were analyzed using real-space refinement. Comparison of the two resulting atomic models shows that the ribosome changes from a compact structure to a looser one, coupled with the rearrangement of many of the proteins. Furthermore, in contrast to the unchanged inter-subunit bridges formed wholly by RNA, the bridges involving proteins undergo large conformational changes following the ratchet-like motion, suggesting an important role of ribosomal proteins in facilitating the dynamics of translation.}, keywords = {5S rRNA,Bacterial Proteins,Escherichia coli,Macromolecular Substances,models,Models Molecular,Molecular Conformation,Molecular Weight,Movement,nosource,protein,Protein Biosynthesis,Protein Structure Quaternary,Protein Structure Tertiary,Proteins,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNA,Structural,structure,translation} }

@article{shenStructuresRequiredPolyA2007, title = {Structures Required for Poly({{A}}) Tail-Independent Translation Overlap with, but Are Distinct from, Cap-Independent Translation and {{RNA}} Replication Signals at the 3’ End of {{Tobacco}} Necrosis Virus {{RNA}}.}, author = {Shen, Ruizhong and Miller, W Allen}, year = 2007, month = feb, journal = {Virology}, volume = {358}, number = {2}, pages = {448–458}, issn = {0042-6822}, doi = {10.1016/j.virol.2006.08.054}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1995077&tool=pmcentrez&rendertype=abstract}, abstract = {Tobacco necrosis necrovirus (TNV) RNA lacks both a 5’ cap and a poly(A) tail but is translated efficiently, owing in part to a Barley yellow dwarf virus (BYDV)-like cap-independent translation element (BTE) in its 3’ untranslated region (UTR). Here, we identify sequence downstream of the BTE that is necessary for poly(A) tail-independent translation in vivo by using RNA encoding a luciferase reporter gene flanked by viral UTRs. Deletions and point mutations caused loss of translation that was restored by adding a poly(A) tail, and not by adding a 5’ cap. The two 3’-proximal stem-loops in the viral genome contribute to poly(A) tail-independent translation, as well as RNA replication. For all necroviruses, we predict a conserved 3’ UTR secondary structure that includes the BTE at one end of a long helical axis and the stem-loops required for poly(A) tail-independent translation and RNA replication at the other end. This work shows that a viral genome can harbor distinct cap- and poly(A) tail-mimic sequences in the 3’ UTR.}, pmid = {17023016}, keywords = {3,3’ Untranslated Regions,3’ Untranslated Regions: chemistry,3’ Untranslated Regions: physiology,Avena sativa,barley yellow dwarf virus-like,Base Sequence,Genome,Genome Viral,Molecular Sequence Data,necrovirus,nosource,Nucleic Acid Conformation,Protein Biosynthesis,Protoplasts,RNA,RNA Viral,stem-loop structure,tombusviridae,Tombusviridae,Tombusviridae: genetics,translation element,translational control,untranslated region,Viral,Viral: biosynthesis} }

@article{schuwirthStructuresBacterialRibosome2005, title = {Structures of the Bacterial Ribosome at 3.5 {{A}} Resolution}, author = {Schuwirth, Barbara S and Borovinskaya, Maria A and Hau, Cathy W and Zhang, Wen and {Vila-Sanjurjo}, Ant{'o}n and Holton, James M and Cate, Jamie H Doudna}, year = 2005, month = nov, journal = {Science (New York, N.Y.)}, volume = {310}, number = {5749}, pages = {827–834}, publisher = {American Association for the Advancement of Science}, issn = {1095-9203}, doi = {10.1126/science.1117230}, url = {http://www.sciencemag.org/content/310/5749/827.short http://www.ncbi.nlm.nih.gov/pubmed/16272117}, abstract = {We describe two structures of the intact bacterial ribosome from Escherichia coli determined to a resolution of 3.5 angstroms by x-ray crystallography. These structures provide a detailed view of the interface between the small and large ribosomal subunits and the conformation of the peptidyl transferase center in the context of the intact ribosome. Differences between the two ribosomes reveal a high degree of flexibility between the head and the rest of the small subunit. Swiveling of the head of the small subunit observed in the present structures, coupled to the ratchet-like motion of the two subunits observed previously, suggests a mechanism for the final movements of messenger RNA (mRNA) and transfer RNAs (tRNAs) during translocation.}, pmid = {16272117}, keywords = {Bacterial,Bacterial: chemistry,Bacterial: metabolism,Binding Sites,chemistry,CONFORMATION,Crystallization,Crystallography,Crystallography X-Ray,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: biosynthesis,Escherichia coli Proteins: chemistry,Escherichia coli: chemistry,Escherichia coli: ultrastructure,ESCHERICHIA-COLI,Hydrogen Bonding,interface,La,Magnesium,Magnesium: metabolism,MECHANISM,Messenger,MESSENGER-RNA,Messenger: chemistry,Messenger: metabolism,Models,Models Molecular,Molecular,Movement,mRNA,nosource,Nucleic Acid Conformation,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,Peptidyl Transferases,Peptidyl Transferases: chemistry,PEPTIDYL-TRANSFERASE,Protein Biosynthesis,Protein Conformation,RESOLUTION,Ribosomal,Ribosomal Proteins,Ribosomal Proteins: chemistry,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,Ribosomal: chemistry,ribosome,Ribosomes,Ribosomes: chemistry,Ribosomes: ultrastructure,Rna,RNA Bacterial,RNA Messenger,RNA Ribosomal,RNA Transfer,structure,SUBUNIT,SUBUNITS,Transfer,TRANSFER-RNA,Transfer: chemistry,Transfer: metabolism,TRANSFERASE CENTER,translocation,tRNA,X-Ray} } % == BibTeX quality report for schuwirthStructuresBacterialRibosome2005: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”)

@article{tuStructuresMLSBKAntibiotics2005, title = {Structures of {{MLSBK}} Antibiotics Bound to Mutated Large Ribosomal Subunits Provide a Structural Explanation for Resistance}, author = {Tu, Daqi and Blaha, Gregor and Moore, Peter B and Steitz, Thomas A}, year = 2005, month = apr, journal = {Cell}, volume = {121}, number = {2}, pages = {257–270}, publisher = {Elsevier}, issn = {0092-8674}, doi = {10.1016/j.cell.2005.02.005}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0092-8674(05)00116-9}, abstract = {Crystal structures of H. marismortui large ribosomal subunits containing the mutation G2099A (A2058 in E. coli) with erythromycin, azithromycin, clindamycin, virginiamycin S, and telithromycin bound explain why eubacterial ribosomes containing the mutation A2058G are resistant to them. Azithromycin binds almost identically to both G2099A and wild-type subunits, but the erythromycin affinity increases by more than 10(4)-fold, implying that desolvation of the N2 of G2099 accounts for the low wild-type affinity for macrolides. All macrolides bind similarly to the H. marismortui subunit, but their binding differs significantly from what has been reported in the D. radioidurans subunit. The synergy in the binding of streptogramins A and B appears to result from a reorientation of the base of A2103 (A2062, E. coli) that stacks between them. The structure of large subunit containing a three residue deletion mutant of L22 shows a change in the L22 structure and exit tunnel shape that illuminates its macrolide resistance phenotype.}, keywords = {Anti-Bacterial Agents,antibiotic,antibiotics,Azithromycin,BASE,BINDING,Binding Sites,Clindamycin,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,Crystallography,D,Drug Resistance Bacterial,E,Erythromycin,Escherichia coli,Haloarcula marismortui,Ketolides,La,Macrolides,Mutation,nosource,Phenotype,Protein Binding,RESISTANCE,RESISTANT,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,RNA Ribosomal 23S,S,Structural,structure,SUBUNIT,SUBUNITS,Virginiamycin,WILD-TYPE} }

@article{hansenStructuresFiveAntibiotics2003, title = {Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit}, author = {Hansen, Jeffrey L and Moore, Peter B and Steitz, Thomas A}, year = 2003, month = jul, journal = {Journal of Molecular Biology}, volume = {330}, number = {5}, pages = {1061–1075}, publisher = {Elsevier}, issn = {0022-2836}, doi = {10.1016/S0022-2836(03)00668-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283603006685}, abstract = {Structures of anisomycin, chloramphenicol, sparsomycin, blasticidin S, and virginiamycin M bound to the large ribosomal subunit of Haloarcula marismortui have been determined at 3.0A resolution. Most of these antibiotics bind to sites that overlap those of either peptidyl-tRNA or aminoacyl-tRNA, consistent with their functioning as competitive inhibitors of peptide bond formation. Two hydrophobic crevices, one at the peptidyl transferase center and the other at the entrance to the peptide exit tunnel play roles in binding these antibiotics. Midway between these crevices, nucleotide A2103 of H.marismortui (2062 Escherichia coli) varies in its conformation and thereby contacts antibiotics bound at either crevice. The aromatic ring of anisomycin binds to the active-site hydrophobic crevice, as does the aromatic ring of puromycin, while the aromatic ring of chloramphenicol binds to the exit tunnel hydrophobic crevice. Sparsomycin contacts primarily a P-site bound substrate, but also extends into the active-site hydrophobic crevice. Virginiamycin M occupies portions of both the A and P-site, and induces a conformational change in the ribosome. Blasticidin S base-pairs with the P-loop and thereby mimics C74 and C75 of a P-site bound tRNA.}, keywords = {0,anisomycin,Anisomycin,Anti-Bacterial Agents,antibiotic,antibiotics,BASE-PAIR,BINDING,Binding Competitive,Binding Sites,BindingCompetitive,BOND FORMATION,chemistry,Chloramphenicol,CONFORMATION,CONFORMATIONAL CHANGE,CONFORMATIONAL-CHANGE,Crystallography X-Ray,CrystallographyX-Ray,Electrons,Escherichia coli,ESCHERICHIA-COLI,Haloarcula,Haloarcula marismortui,INHIBITOR,Ions,La,M,metabolism,Models Molecular,ModelsMolecular,nosource,Nucleosides,P loop,P SITE,P-SITE,peptide bond formation,Peptides,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Protein Conformation,Puromycin,RESOLUTION,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNA Transfer,RNATransfer,S,SITE,SITES,sparsomycin,Sparsomycin,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,TRANSFERASE CENTER,tRNA,Virginiamycin} } % == BibTeX quality report for hansenStructuresFiveAntibiotics2003: % ? unused Journal abbr (“J. Mol. Biol”)

@article{grailleStructureYeastDom342008, title = {Structure of Yeast {{Dom34}}: A Protein Related to Translation Termination Factor {{Erf1}} and Involved in {{No-Go}} Decay}, author = {Graille, Marc and Chaillet, Maxime and {}{van Tilbeurgh}, Herman}, year = 2008, month = mar, journal = {The Journal of Biological Chemistry}, volume = {283}, number = {11}, eprint = {18180287}, eprinttype = {pubmed}, pages = {7145–7154}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.M708224200}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18180287 http://www.jbc.org/content/283/11/7145.short}, abstract = {The yeast protein Dom34 has been described to play a critical role in a newly identified mRNA decay pathway called No-Go decay. This pathway clears cells from mRNAs inducing translational stalls through endonucleolytic cleavage. Dom34 is related to the translation termination factor eRF1 and physically interacts with Hbs1, which is itself related to eRF3. We have solved the 2.5-A resolution crystal structure of Saccharomyces cerevisiae Dom34. This protein is organized in three domains with the central and C-terminal domains structurally homologous to those from eRF1. The N-terminal domain of Dom34 is different from eRF1. It adopts a Sm-fold that is often involved in the recognition of mRNA stem loops or in the recruitment of mRNA degradation machinery. The comparison of eRF1 and Dom34 domains proposed to interact directly with eRF3 and Hbs1, respectively, highlights striking structural similarities with eRF1 motifs identified to be crucial for the binding to eRF3. In addition, as observed for eRF1 that enhances eRF3 binding to GTP, the interaction of Dom34 with Hbs1 results in an increase in the affinity constant of Hbs1 for GTP but not GDP. Taken together, these results emphasize that eukaryotic cells have evolved two structurally related complexes able to interact with ribosomes either paused at a stop codon or stalled in translation by the presence of a stable stem loop and to trigger ribosome release by catalyzing chemical bond hydrolysis.}, isbn = {2005512028}, pmid = {18180287}, keywords = {Amino Acid,Amino Acid Sequence,Binding Sites,Cell Cycle Proteins,Cell Cycle Proteins: chemistry,Cell Cycle Proteins: physiology,Crystallography,Crystallography X-Ray,Endoribonucleases,GTP-Binding Proteins,GTP-Binding Proteins: metabolism,Guanosine Diphosphate,Guanosine Diphosphate: chemistry,Guanosine Triphosphate,Guanosine Triphosphate: chemistry,HSP70 Heat-Shock Proteins,HSP70 Heat-Shock Proteins: metabolism,Messenger,Messenger: metabolism,Molecular Conformation,Molecular Sequence Data,nosource,Peptide Elongation Factors,Peptide Elongation Factors: metabolism,Peptide Termination Factors,Peptide Termination Factors: chemistry,Protein Structure,Protein Structure Tertiary,Ribosomes,Ribosomes: metabolism,RNA,RNA Messenger,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: chemistry,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae Proteins: physiology,Saccharomyces cerevisiae: metabolism,Sequence Homology,Sequence Homology Amino Acid,Tertiary,X-Ray,X-Ray: methods} } % == BibTeX quality report for grailleStructureYeastDom342008: % ? unused Journal abbr (“J. Biol. Chem”)

@article{agalarovStructureS15S6S18rRNAComplex2000, title = {Structure of the {{S15}},{{S6}},{{S18-rRNA}} Complex: Assembly of the {{30S}} Ribosome Central Domain}, author = {Agalarov, S C and Sridhar Prasad, G and Funke, P M and Stout, C D and Williamson, J R}, year = 2000, month = apr, journal = {Science (New York, N.Y.)}, volume = {288}, number = {5463}, eprint = {10753109}, eprinttype = {pubmed}, pages = {107–113}, issn = {0036-8075}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10753109}, abstract = {The crystal structure of a 70-kilodalton ribonucleoprotein complex from the central domain of the Thermus thermophilus 30S ribosomal subunit was solved at 2.6 angstrom resolution. The complex consists of a 104-nucleotide RNA fragment composed of two three-helix junctions that lie at the end of a central helix, and the ribosomal proteins S15, S6, and S18. S15 binds the ribosomal RNA early in the assembly of the 30S ribosomal subunit, stabilizing a conformational reorganization of the two three-helix junctions that creates the RNA fold necessary for subsequent binding of S6 and S18. The structure of the complex demonstrates the central role of S15-induced reorganization of central domain RNA for the subsequent steps of ribosome assembly.}, pmid = {10753109}, keywords = {Amino Acid Sequence,Bacterial Proteins,Base Pairing,Base Sequence,Binding Sites,Crystallography X-Ray,Models Molecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Protein Binding,Protein Conformation,Protein Structure Secondary,Protein Structure Tertiary,Ribonucleoproteins,Ribosomal Protein S6,Ribosomal Proteins,Ribosomes,RNA Bacterial,RNA Ribosomal,Thermus thermophilus} } % == BibTeX quality report for agalarovStructureS15S6S18rRNAComplex2000: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”)

@article{spahnStructure80SRibosome2001a, title = {Structure of the {{80S}} Ribosome from {{Saccharomyces}} Cerevisiae–{{tRNA-}} Ribosome and Subunit-Subunit Interactions}, author = {Spahn, C M and Beckmann, R and Eswar, N and Penczek, P A and Sali, A and Blobel, G and Frank, J}, year = 2001, month = nov, journal = {Cell}, volume = {107}, number = {3}, eprint = {11701127}, eprinttype = {pubmed}, pages = {373–386}, issn = {0092-8674}, doi = {10.1016/S0092-8674(01)00539-6}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11701127}, abstract = {A cryo-EM reconstruction of the translating yeast 80S ribosome was analyzed. Computationally separated rRNA and protein densities were used for docking of appropriately modified rRNA models and homology models of yeast ribosomal proteins. The core of the ribosome shows a remarkable degree of conservation. However, some significant differences in functionally important regions and dramatic changes in the periphery due to expansion segments and additional ribosomal proteins are evident. As in the bacterial ribosome, bridges between the subunits are mainly formed by RNA contacts. Four new bridges are present at the periphery. The position of the P site tRNA coincides precisely with its prokaryotic counterpart, with mainly rRNA contributing to its molecular environment. This analysis presents an exhaustive inventory of an eukaryotic ribosome at the molecular level.}, pmid = {11701127}, keywords = {0,analysis,Bacterial,Base Sequence,Binding Sites,chemistry,Cryoelectron Microscopy,genetics,La,metabolism,Methods,models,Models Molecular,ModelsMolecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,P-SITE,protein,Proteins,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNA,RNA Fungal,RNA Ribosomal,RNA Ribosomal 18S,RNA Ribosomal 5.8S,RNA Transfer,RNAFungal,RNARibosomal,RNARibosomal18S,RNARibosomal5.8S,RNATransfer,rRNA,Saccharomyces,Saccharomyces cerevisiae,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,tRNA,ultrastructure,yeast} }

@article{brierleyStructureFunctionStimulatory2001, title = {Structure and Function of the Stimulatory {{RNAs}} Involved in Programmed Eukaryotic-1 Ribosomal Frameshifting}, author = {Brierley, I and Pennell, S}, year = 2001, journal = {Cold Spring Harbor Symposia on Quantitative Biology}, volume = {66:233-48.}, eprint = {12762025}, eprinttype = {pubmed}, pages = {233–248}, issn = {0091-7451}, doi = {10.1101/sqb.2001.66.233}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12762025}, pmid = {12762025}, keywords = {Avian Sarcoma Viruses,Base Sequence,Binding Sites,chemistry,Frameshift Mutation,Frameshifting,Gene Products gag,Gene Productsgag,genetics,Models Molecular,ModelsMolecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Oncogenic Viruses,pathology,Review,ribosomal frameshifting,Rna,RNA Ribosomal,RNARibosomal,Sarcoma VirusesAvian,Signal Transduction,structure,supportnon-u.s.gov’t,virology} } % == BibTeX quality report for brierleyStructureFunctionStimulatory2001: % ? unused Journal abbr (“Cold Spring Harb. Symp. Quant. Biol”)

@article{bottgerStructuralBasisSelectivity2001, title = {Structural Basis for Selectivity and Toxicity of Ribosomal Antibiotics}, author = {B{"o}ttger, E C and Springer, B and Prammananan, T and Kidan, Y and Sander, P}, year = 2001, month = apr, journal = {EMBO Reports}, volume = {2}, number = {4}, pages = {318–323}, publisher = {Nature Publishing Group}, issn = {1469-221X}, doi = {10.1093/embo-reports/kve062}, url = {http://www.nature.com/embor/journal/v2/n4/abs/embor447.html}, abstract = {Ribosomal antibiotics must discriminate between bacterial and eukaryotic ribosomes to various extents. Despite major differences in bacterial and eukaryotic ribosome structure, a single nucleotide or amino acid determines the selectivity of drugs affecting protein synthesis. Analysis of resistance mutations in bacteria allows the prediction of whether cytoplasmic or mitochondrial ribosomes in eukaryotic cells will be sensitive to the drug. This has important implications for drug specificity and toxicity. Together with recent data on the structure of ribosomal subunits these data provide the basis for development of new ribosomal antibiotics by rationale drug design.}, keywords = {Alleles,Anti-Bacterial Agents,Cytoplasm,Databases Factual,Drug Design,Lincomycin,Macrolides,Mitochondria,Mutation,Mycobacterium smegmatis,nosource,Plasmids,Ribosomes,RNA Ribosomal 16S,Structure-Activity Relationship,Time Factors,Virginiamycin} } % == BibTeX quality report for bottgerStructuralBasisSelectivity2001: % ? unused Journal abbr (“EMBO Rep”)

@article{leeStructuralFunctionalInsights2007, title = {Structural and Functional Insights into {{Dom34}}, a Key Component of No-Go {{mRNA}} Decay.}, author = {Lee, Hyung Ho and Kim, Youn-Sung and Kim, Kyoung Hoon and Heo, Inha and Kim, Sang Kyu and Kim, Olesya and Kim, Hye Kyung and Yoon, Ji Young and Kim, Hyoun Sook and Kim, Do Jin and Lee, Sang Jae and Yoon, Hye Jin and Kim, Soon Jong and Lee, Byung Gil and Song, Hyun Kyu and Kim, V Narry and Park, Chung-Mo and Suh, Se Won}, year = 2007, month = sep, journal = {Molecular Cell}, volume = {27}, number = {6}, eprint = {17889667}, eprinttype = {pubmed}, pages = {938–950}, issn = {1097-2765}, doi = {10.1016/j.molcel.2007.07.019}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17889667}, abstract = {The yeast protein Dom34 is a key component of no-go decay, by which mRNAs with translational stalls are endonucleolytically cleaved and subsequently degraded. However, the identity of the endoribonuclease is unknown. Homologs of Dom34, called Pelota, are broadly conserved in eukaryotes and archaea. To gain insights into the structure and function of Dom34/Pelota, we have determined the structure of Pelota from Thermoplasma acidophilum (Ta Pelota) and investigated the ribonuclease activity of Dom34/Pelota. The structure of Ta Pelota is tripartite, and its domain 1 has the RNA-binding Sm fold. We have discovered that Ta Pelota has a ribonuclease activity and that its domain 1 is sufficient for the catalytic activity. We also demonstrate that domain 1 of Dom34 has an endoribonuclease activity against defined RNA substrates containing a stem loop, which supports a direct catalytic role of yeast Dom34 in no-go mRNA decay.}, pmid = {17889667}, keywords = {Amino Acid Motifs,Amino Acid Sequence,Archaeal Proteins,Archaeal Proteins: chemistry,Archaeal Proteins: metabolism,Binding Sites,Cell Cycle Proteins,Cell Cycle Proteins: chemistry,Cell Cycle Proteins: metabolism,Endoribonucleases,Humans,Messenger,Messenger: chemistry,Messenger: metabolism,Models,Models Molecular,Molecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Peptide Termination Factors,Peptide Termination Factors: chemistry,Protein,Protein Structure,Protein Structure Quaternary,Protein Structure Secondary,Quaternary,Ribonucleases,Ribonucleases: metabolism,RNA,RNA Messenger,RNA Stability,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: chemistry,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: enzymology,Secondary,Solutions,Structural Homology,Structural Homology Protein,Substrate Specificity,Thermoplasma,Thermoplasma: enzymology} } % == BibTeX quality report for leeStructuralFunctionalInsights2007: % ? unused Journal abbr (“Mol. Cell”)

@article{gromadskiStreptomycinInterferesConformational2004, title = {Streptomycin Interferes with Conformational Coupling between Codon Recognition and {{GTPase}} Activation on the Ribosome}, author = {Gromadski, Kirill B and Rodnina, Marina V}, year = 2004, month = apr, journal = {Nature Structural & Molecular Biology}, volume = {11}, number = {4}, pages = {316–322}, publisher = {Nature Publishing Group}, issn = {1545-9993}, doi = {10.1038/nsmb742}, url = {http://www.nature.com/nsmb/journal/v11/n4/abs/nsmb742.html}, abstract = {Aminoacyl-tRNAs (aa-tRNAs) are selected by the ribosome through a kinetically controlled induced fit mechanism. Cognate codon recognition induces a conformational change in the decoding center and a domain closure of the 30S subunit. We studied how these global structural rearrangements are related to tRNA discrimination by using streptomycin to restrict the conformational flexibility of the 30S subunit. The antibiotic stabilized aa-tRNA on the ribosome both with a cognate and with a near-cognate codon in the A site. Streptomycin altered the rates of GTP hydrolysis by elongation factor Tu (EF-Tu) on cognate and near-cognate codons, resulting in almost identical rates of GTP hydrolysis and virtually complete loss of selectivity. These results indicate that movements within the 30S subunit at the streptomycin-binding site are essential for the coupling between base pair recognition and GTP hydrolysis, thus modulating the fidelity of aa-tRNA selection.}, keywords = {0,A SITE,A-SITE,activation,antibiotic,BASE,BASE-PAIR,Binding Sites,chemistry,Codon,CODON RECOGNITION,CODONS,CONFORMATIONAL CHANGE,CONFORMATIONAL-CHANGE,decoding,DOMAIN,drug effects,EFTu,elongation,ELONGATION-FACTOR-TU,Escherichia coli,FACTOR TU,Fidelity,genetics,GTP,GTP Phosphohydrolase,GTP Phosphohydrolases,GTPase,Hydrolysis,Kinetics,La,MECHANISM,metabolism,Movement,nosource,pharmacology,RECOGNITION,ribosome,Ribosomes,Rna,RNA Transfer Met,RNATransferMet,SELECTION,SITE,Streptomycin,Structural,SUBUNIT,supportnon-u.s.gov’t,tRNA} } % == BibTeX quality report for gromadskiStreptomycinInterferesConformational2004: % ? unused Journal abbr (“Nat. Struct. Mol. Biol”)

@article{schroederStrategiesRNAFolding2004, title = {Strategies for {{RNA}} Folding and Assembly}, author = {Schroeder, Ren{'e}e and Barta, Andrea and Semrad, Katharina}, year = 2004, month = nov, journal = {Nature Reviews. Molecular Cell Biology}, volume = {5}, number = {11}, eprint = {15520810}, eprinttype = {pubmed}, pages = {908–919}, issn = {1471-0072}, doi = {10.1038/nrm1497}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15520810}, abstract = {RNA is structurally very flexible, which provides the basis for its functional diversity. An RNA molecule can often adopt different conformations, which enables the regulation of its function through folding. Proteins help RNAs reach their functionally active conformation by increasing their structural stability or by chaperoning the folding process. Large, dynamic RNA-protein complexes, such as the ribosome or the spliceosome, require numerous proteins that coordinate conformational switches of the RNA components during assembly and during their respective activities.}, pmid = {15520810}, keywords = {Adenosine Triphosphate,Amino Acid Sequence,Base Sequence,Catalysis,Molecular Chaperones,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Protein Conformation,Protein Structure Tertiary,Protein Structure- Tertiary,Proteins,RNA,RNA Catalytic,RNA- Catalytic,Spliceosomes} } % == BibTeX quality report for schroederStrategiesRNAFolding2004: % ? Possibly abbreviated journal title Nature Reviews. Molecular Cell Biology % ? unused Journal abbr (“Nat. Rev. Mol. Cell Biol”)

@article{pillsburySteepestDescentCalculation2005, title = {Steepest Descent Calculation of {{RNA}} Pseudoknots}, author = {Pillsbury, M and Orland, Henri and Zee, A}, year = 2005, month = jul, journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, volume = {72}, number = {1 Pt 1}, eprint = {16090005}, eprinttype = {pubmed}, pages = {011911}, issn = {1539-3755}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16090005}, abstract = {We enumerate possible topologies of pseudoknots in single-stranded RNA molecules. We use a steepest-descent approximation in the large N matrix field theory, and a Feynman diagram formalism to describe the resulting pseudoknot structure.}, pmid = {16090005}, keywords = {Biophysics,Models Statistical,Models Theoretical,Normal Distribution,nosource,Nucleic Acid Conformation,RNA,Statistics as Topic,Thermodynamics} } % == BibTeX quality report for pillsburySteepestDescentCalculation2005: % ? Possibly abbreviated journal title Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics % ? unused Journal abbr (“Phys Rev E Stat Nonlin Soft Matter Phys”)

@article{meyerStatisticalEvidenceConserved2005, title = {Statistical Evidence for Conserved, Local Secondary Structure in the Coding Regions of Eukaryotic {{mRNAs}} and Pre-{{mRNAs}}}, author = {Meyer, Irmtraud M and Mikl{'o}s, Istv{'a}n}, year = 2005, journal = {Nucleic Acids Research}, volume = {33}, number = {19}, pages = {6338–6348}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gki923}, url = {http://nar.oxfordjournals.org/content/33/19/6338.short}, abstract = {Owing to the degeneracy of the genetic code, protein-coding regions of mRNA sequences can harbour more than only amino acid information. We search the mRNA sequences of 11 human protein-coding genes for evolutionarily conserved secondary structure elements using RNA-Decoder, a comparative secondary structure prediction program that is capable of explicitly taking the known protein-coding context of the mRNA sequences into account. We detect well-defined, conserved RNA secondary structure elements in the coding regions of the mRNA sequences and show that base-paired codons strongly correlate with sparse codons. We also investigate the role of repetitive elements in the formation of secondary structure and explain the use of alternate start codons in the caveolin-1 gene by a conserved secondary structure element overlapping the nominal start codon. We discuss the functional roles of our novel findings in regulating the gene expression on mRNA level. We also investigate the role of secondary structure on the correct splicing of the human CFTR gene. We study the wild-type version of the pre-mRNA as well as 29 variants with synonymous mutations in exon 12. By comparing our predicted secondary structures to the experimentally determined splicing efficiencies, we find with weak statistical significance that pre-mRNAs with high-splicing efficiencies have different predicted secondary structures than pre-mRNAs with low-splicing efficiencies.}, keywords = {Animals,Cats,Cattle,Codon,Codon Initiator,Computational Biology,Cystic Fibrosis Transmembrane Conductance Regulator,Data Interpretation Statistical,Dogs,Evolution Molecular,Exons,Gene Expression Regulation,Humans,Mice,nosource,Nucleic Acid Conformation,Rabbits,Rats,Repetitive Sequences Nucleic Acid,RNA Messenger,RNA Precursors,RNA Splicing,Software} } % == BibTeX quality report for meyerStatisticalEvidenceConserved2005: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{preissStartingProteinSynthesis2003, title = {Starting the Protein Synthesis Machine: Eukaryotic Translation Initiation}, author = {Preiss, Thomas and W Hentze, Matthias}, year = 2003, month = dec, journal = {BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology}, volume = {25}, number = {12}, pages = {1201–1211}, publisher = {Wiley Online Library}, issn = {0265-9247}, doi = {10.1002/bies.10362}, url = {http://onlinelibrary.wiley.com/doi/10.1002/bies.10362/abstract}, abstract = {The final assembly of the protein synthesis machinery occurs during translation initiation. This delicate process involves both ends of eukaryotic messenger RNAs as well as multiple sequential protein-RNA and protein-protein interactions. As is expected from its critical position in the gene expression pathway between the transcriptome and the proteome, translation initiation is a selective and highly regulated process. This synopsis summarises the current status of the field and identifies intriguing open questions.}, keywords = {5’ Untranslated Regions,Animals,Codon Initiator,Codon- Initiator,Eukaryotic Initiation Factors,Fungal Proteins,Humans,Models Biological,Models Genetic,Models- Biological,Models- Genetic,nosource,Peptide Chain Initiation Translational,Peptide Chain Initiation- Translational,Protein Binding,Protein Biosynthesis,Ribosomes,RNA Messenger,RNA- Messenger} } % == BibTeX quality report for preissStartingProteinSynthesis2003: % ? unused Journal abbr (“Bioessays”)

@article{heStabilizationRibosomeAssociation1993, title = {Stabilization and Ribosome Association of Unspliced Pre-{{mRNAs}} in a Yeast Upf1- Mutant}, author = {He, F and Peltz, S W and Donahue, J L and Rosbash, M and Jacobson, A}, year = 1993, month = aug, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {90}, number = {15}, pages = {7034–7038}, publisher = {National Acad Sciences}, issn = {0027-8424}, url = {http://www.pnas.org/content/90/15/7034.short}, abstract = {Nonsense-mediated mRNA decay, the accelerated turnover of mRNAs transcribed from genes containing early nonsense mutations, is dependent on the product of the UPF1 gene in yeast. Mutations that inactivate UPF1 lead to the selective stabilization of mRNAs containing early nonsense mutations but have no effect on the half-lives of almost all other mRNAs. Since the transcripts of nonsense alleles are not typical cellular constituents, we sought to identify those RNAs that comprise normal substrates of the nonsense-mediated mRNA decay pathway. Many yeast pre-mRNAs contain early in-frame nonsense codons and we consider it possible that a role of this pathway is to accelerate the degradation of pre-mRNAs present in the cytoplasm. Consistent with this hypothesis, we find that, in a strain lacking UPF1 function, the CYH2, RP51B, and MER2 pre-mRNAs are stabilized 2- to 5-fold and are associated with ribosomes. We conclude that a major source of early nonsense codon-containing cytoplasmic transcripts in yeast is pre-mRNAs and that the UPF1 protein may be part of a cellular system that ensures that potentially deleterious nonsense fragments of polypeptides do not accumulate.}, keywords = {Gene Expression Regulation Fungal,Genes Fungal,Introns,nosource,Nucleic Acid Precursors,Protein Biosynthesis,Ribosomes,RNA Fungal,RNA Messenger,RNA Splicing,Saccharomyces cerevisiae} } % == BibTeX quality report for heStabilizationRibosomeAssociation1993: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{padgettSplicingMessengerRNA1986, title = {Splicing of Messenger {{RNA}} Precursors.}, author = {Padgett, R A and Grabowski, P J and Konarska, M M and Seiler, S and Sharp, P A}, year = 1986, month = jan, journal = {Annual Review of Biochemistry}, volume = {55}, number = {1}, eprint = {2943217}, eprinttype = {pubmed}, pages = {1119–1150}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, issn = {0066-4154}, doi = {10.1146/annurev.bi.55.070186.005351}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2943217 http://www.annualreviews.org/doi/pdf/10.1146/annurev.bi.55.070186.005351}, pmid = {2943217}, keywords = {Animals,Base Sequence,Biological Evolution,Evolution,Gene Expression Regulation,Humans,Messenger,Messenger: genetics,Messenger: metabolism,Mutation,nosource,Nucleic Acid Precursors,Nucleic Acid Precursors: genetics,Nucleic Acid Precursors: metabolism,Ribonucleoproteins,Ribonucleoproteins Small Nuclear,Ribonucleoproteins- Small Nuclear,Ribonucleoproteins: metabolism,RNA,RNA Messenger,RNA Splicing,RNA- Messenger,Small Nuclear} } % == BibTeX quality report for padgettSplicingMessengerRNA1986: % ? unused Journal abbr (“Annu. Rev. Biochem”)

@article{suaySpecificRoles52005, title = {Specific Roles of 5’ {{RNA}} Secondary Structures in Stabilizing Transcripts in Chloroplasts}, author = {Suay, Loreto and Salvador, Maria L and Abesha, Emnet and Klein, Uwe}, year = 2005, journal = {Nucleic Acids Research}, volume = {33}, number = {15}, pages = {4754–4761}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gki760}, url = {http://nar.oxfordjournals.org/content/33/15/4754.short}, abstract = {RNA secondary structures, e.g. stem-loops that are often found at the 5’ and 3’ ends of mRNAs, are in many cases known to be crucial for transcript stability but their role in prolonging the lifetime of transcripts remains elusive. In this study we show for an essential RNA-stabilizing stem-loop at the 5’ end of rbcL gene transcripts in Chlamydomonas that it neither prevents ribonucleases from binding to the RNA nor impedes their movement along the RNA strand. The stem-loop has a formative function in that it mediates folding of a short sequence around its base into a specific RNA conformation, consisting of a helical and single-stranded region, i.e. the real structure required for longevity of rbcL transcripts in chloroplasts. Disturbing this structure renders transcripts completely unstable, even if the sequence of this element is not altered. The requirement of a specific 5’ sequence and structure for RNA longevity suggests an interaction of this element with a trans-acting factor that protects transcripts from rapid degradation in chloroplasts.}, keywords = {5’ Untranslated Regions,Animals,Base Sequence,Chlamydomonas,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Ribulose-Bisphosphate Carboxylase,RNA Chloroplast,RNA Messenger,RNA Stability} } % == BibTeX quality report for suaySpecificRoles52005: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{pisarevSpecificFunctionalInteractions2006, title = {Specific Functional Interactions of Nucleotides at Key -3 and +4 Positions Flanking the Initiation Codon with Components of the Mammalian {{48S}} Translation Initiation Complex.}, author = {Pisarev, Andrey V and Kolupaeva, Victoria G and Pisareva, Vera P and Merrick, William C and Hellen, Christopher U T and Pestova, Tatyana V}, year = 2006, month = mar, journal = {Genes & Development}, volume = {20}, number = {5}, eprint = {16510876}, eprinttype = {pubmed}, pages = {624–636}, issn = {0890-9369}, doi = {10.1101/gad.1397906}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16510876 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1410799&tool=pmcentrez&rendertype=abstract}, abstract = {Eukaryotic initiation factor (eIF) 1 maintains the fidelity of initiation codon selection and enables mammalian 43S preinitiation complexes to discriminate against AUG codons with a context that deviates from the optimum sequence GCC(A/G)CCAUGG, in which the purines at (-)3 and (+)4 positions are most important. We hypothesize that eIF1 acts by antagonizing conformational changes that occur in ribosomal complexes upon codon-anticodon base-pairing during 48S initiation complex formation, and that the role of (-)3 and (+)4 context nucleotides is to stabilize these changes by interacting with components of this complex. Here we report that U and G at (+)4 both UV-cross-linked to ribosomal protein (rp) S15 in 48S complexes. However, whereas U cross-linked strongly to C(1696) and less well to AA(1818-1819) in helix 44 of 18S rRNA, G cross-linked exclusively to AA(1818-1819). U at (-)3 cross-linked to rpS5 and eIF2alpha, whereas G cross-linked only to eIF2alpha. Results of UV cross-linking experiments and of assays of 48S complex formation done using alpha-subunit-deficient eIF2 indicate that eIF2alpha’s interaction with the (-)3 purine is responsible for recognition of the (-)3 context position by 43S complexes and suggest that the (+)4 purine/AA(1818-1819) interaction might be responsible for recognizing the (+)4 position.}, pmid = {16510876}, keywords = {Animals,Cattle,Codon,Codon Initiator,Eukaryotic Initiation Factor-1,Eukaryotic Initiation Factor-1: chemistry,Eukaryotic Initiation Factor-1: genetics,Eukaryotic Initiation Factor-1: metabolism,Eukaryotic Initiation Factors,Eukaryotic Initiation Factors: chemistry,Eukaryotic Initiation Factors: genetics,Eukaryotic Initiation Factors: metabolism,Guanosine,Guanosine: analogs & derivatives,Guanosine: chemistry,Guanosine: metabolism,Initiator,Initiator: metabolism,Messenger,Messenger: metabolism,Models,Models Molecular,Molecular,Molecular Structure,nosource,Peptide Chain Initiation,Peptide Chain Initiation Translational,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,RNA,RNA Messenger,Thionucleosides,Thionucleosides: chemistry,Thionucleosides: metabolism,Thiouridine,Thiouridine: chemistry,Thiouridine: metabolism,Translational} } % == BibTeX quality report for pisarevSpecificFunctionalInteractions2006: % ? unused Journal abbr (“Genes Dev”)

@article{muldoon-jacobsSpecificEffectsRibosomethethered2006, title = {Specific Effects of Ribosome-Thethered Molecular Chaperones on Programmed -1 Ribosomal Frameshifting.}, author = {{Muldoon-Jacobs}, Kristi L and Dinman, Jonathan D}, year = 2006, month = apr, journal = {Eukaryotic Cell}, volume = {5}, number = {4}, pages = {762–770}, publisher = {Am Soc Microbiol}, issn = {1535-9778}, doi = {10.1128/EC.5.4.762-770.2006}, url = {http://ec.asm.org/cgi/content/abstract/5/4/762}, abstract = {The ribosome-associated molecular chaperone complexes RAC (Ssz1p/Zuo1p) and Ssb1p/Ssb2p expose a link between protein folding and translation. Disruption of the conserved nascent peptide-associated complex results in cell growth and translation fidelity defects. To better understand the consequences of deletion of either RAC or Ssb1p/2p, experiments relating to cell growth and programmed ribosomal frameshifting (PRF) were assayed. Genetic analyses revealed that deletion of Ssb1p/Ssb2p or of Ssz1p/Zuo1p resulted in specific inhibition of -1 PRF and defects in Killer virus maintenance, while no effects were observed on +1 PRF. These factors may provide a new set of targets to exploit against viruses that use -1 PRF. Quantitative measurements of growth profiles of isogenic wild-type and mutant cells showed that translational inhibitors exacerbate underlying growth defects in these mutants. Previous studies have identified -1 PRF signals in yeast chromosomal genes and have demonstrated an inverse relationship between -1 PRF efficiency and mRNA stability. Analysis of published DNA microarray experiments reveals conditions under which Ssb1, Ssb2, Ssz1, and Zuo1 transcript levels are regulated independently of those of genes encoding ribosomal proteins. Thus, the findings presented here suggest that these trans-acting factors could be used by cells to posttranscriptionally regulate gene expression through -1 PRF.}, keywords = {analysis,CELLS,chaperone,CHROMOSOMAL GENES,COMPLEX,COMPLEXES,DISRUPTION,Dna,DNA-Binding Proteins,efficiency,expression,Fidelity,Frameshift Mutation,Frameshifting,Frameshifting Ribosomal,gene,Gene Expression,GENE-EXPRESSION,Genes,Genetic,GROWTH,HSP70 Heat-Shock Proteins,INHIBITION,INHIBITOR,inhibitors,killer,killer virus,Models Molecular,Molecular Chaperones,mRNA,mRNA stability,MUTANTS,nosource,protein,Protein Folding,Protein Processing Post-Translational,Proteins,QUANTITATIVE MEASUREMENT,Repressor Proteins,ribosomal frameshifting,Ribosomal Proteins,RIBOSOMAL-PROTEIN,Ribosomes,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SIGNAL,stability,TARGET,TRANS-ACTING FACTORS,TRANSCRIPT,translation,virus,Viruses,WILD-TYPE,yeast} }

@article{stapleSolutionStructureHIV12003, title = {Solution Structure of the {{HIV-1}} Frameshift Inducing Stem-Loop {{RNA}}}, author = {Staple, David W and Butcher, Samuel E}, year = 2003, month = aug, journal = {Nucleic Acids Research}, volume = {31}, number = {15}, eprint = {12888491}, eprinttype = {pubmed}, pages = {4326–4331}, issn = {1362-4962}, doi = {10.1093/nar/gkg654}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12888491}, abstract = {The translation of reverse transcriptase and other essential viral proteins from the HIV-1 Pol mRNA requires a programmed -1 ribosomal frameshift. This frameshift is induced by two highly conserved elements within the HIV-1 mRNA: a slippery sequence comprised of a UUUUUUA heptamer, and a downstream stem-loop structure. We have determined the structure of the HIV-1 frameshift inducing RNA stem-loop, using multidimensional heteronuclear nuclear magnetic resonance (NMR) methods. The 22 nucleotide RNA solution structure [root mean squared deviation (r.m.s.d.) = 1.2 A] was determined from 475 nuclear Overhauser effect (NOE)-derived distance restrains, 20 residual dipolar couplings and direct detection of hydrogen bonds via scalar couplings. We find that the frameshift inducing stem-loop is an A-form helix capped by a structured ACAA tetraloop. The ACAA tetraloop is stabilized by an equilateral 5’ and 3’ stacking pattern, a sheared A-A pair and a cross-strand hydrogen bond. Unexpectedly, the ACAA tetraloop structure is nearly identical to a known tetraloop fold, previously identified in the RNase III recognition site from Saccharomyces cerevisiae.}, pmid = {12888491}, keywords = {3,Adenine,Base Sequence,CEREVISIAE,DOWNSTREAM,ELEMENTS,frameshift,Frameshifting Ribosomal,Hiv-1,HIV-1,Hydrogen Bonding,La,Methods,Models Molecular,mRNA,NMR,nosource,nuclear magnetic resonance,Nuclear Magnetic Resonance Biomolecular,NUCLEAR-MAGNETIC-RESONANCE,Nucleic Acid Conformation,pol,protein,Proteins,RECOGNITION,REQUIRES,REVERSE-TRANSCRIPTASE,RIBOSOMAL FRAMESHIFT,Rna,RNA Viral,RNAse,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SITE,STEM-LOOP,structure,translation,Viral Proteins} } % == BibTeX quality report for stapleSolutionStructureHIV12003: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{stapleSolutionStructureThermodynamic2005, title = {Solution Structure and Thermodynamic Investigation of the {{HIV-1}} Frameshift Inducing Element}, author = {Staple, David W and Butcher, Samuel E}, year = 2005, month = jun, journal = {Journal of Molecular Biology}, volume = {349}, number = {5}, pages = {1011–1023}, publisher = {Elsevier}, issn = {0022-2836}, doi = {10.1016/j.jmb.2005.03.038}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283605003189}, abstract = {Expression of the HIV reverse transcriptase and other essential viral enzymes requires a -1 translational frameshift. The frameshift event is induced by two highly conserved RNA elements within the HIV-1 mRNA: a UUUUUUA heptamer known as the slippery sequence, and a downstream RNA structure. Here, we report structural and thermodynamic evidence that the HIV-1 frameshift site RNA forms a stem-loop and lower helix separated by a three-purine bulge. We have determined the structure of the 45 nucleotide frameshift site RNA using multidimensional heteronuclear nuclear magnetic resonance (NMR) methods. The upper helix is highly thermostable (T(m){\(>\)}90 degrees C), forming 11 Watson-Crick base-pairs capped by a stable ACAA tetraloop. The eight base-pair lower helix was found to be only moderately stable (T(m)=47 degrees C). A three-purine bulge separates the highly stable upper helix from the lower helix. Base stacking in the bulge forms a wedge, introducing a 60 degrees bend between the helices. Interestingly, this bend is similar to those seen in a number of frameshift inducing pseudoknots for which structures have been solved. The lower helix must denature to allow the ribosome access to the slippery site, but likely functions as a positioning element that enhances frameshift efficiency.}, keywords = {0,BASE,BASE-PAIR,chemistry,DOWNSTREAM,efficiency,ELEMENTS,enzyme,Enzymes,expression,FORM,frameshift,Frameshifting Ribosomal,FrameshiftingRibosomal,Gene Expression Regulation Viral,Gene Expression RegulationViral,genetics,HIV,Hiv-1,HIV-1,Humans,La,Metals,Methods,Models Molecular,ModelsMolecular,mRNA,NMR,nosource,nuclear magnetic resonance,Nuclear Magnetic Resonance Biomolecular,Nuclear Magnetic ResonanceBiomolecular,NUCLEAR-MAGNETIC-RESONANCE,Nucleic Acid Conformation,pseudoknot,pseudoknots,REQUIRES,Research SupportN.I.H.Extramural,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,REVERSE-TRANSCRIPTASE,ribosome,Ribosomes,Rna,RNA Stability,RNA Viral,RnaViral,sequence,SITE,slippery site,Solutions,STEM-LOOP,Structural,structure,Thermodynamics} } % == BibTeX quality report for stapleSolutionStructureThermodynamic2005: % ? unused Journal abbr (“J. Mol. Biol”)

@article{vandykeSiteFunctionalInteraction2003, title = {Site of Functional Interaction of Release Factor 1 with the Ribosome}, author = {Van Dyke, Natalya and Murgola, Emanuel J}, year = 2003, month = jun, journal = {Journal of Molecular Biology}, volume = {330}, number = {1}, pages = {9–13}, publisher = {Elsevier}, issn = {0022-2836}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283603005370}, abstract = {Ribosomal protein L11 consists of a C-terminal and an N-terminal domain. To determine the importance of each domain for interaction with release factor 1, which works specifically at the UAG termination codon, we constructed Escherichia coli strains lacking either the entire L11 protein or just the N-terminal portion. Strains lacking L11 exhibited UAG suppression, defective growth, and high-temperature lethality, phenotypes that were reversed by expression of L11 protein from a plasmid. Strains lacking only the N-terminal portion of L11 grew well at physiological temperatures and survived at high temperature, but they were defective in UAG-dependent termination. Our results show for the first time that it is precisely the N-terminal part of ribosomal protein L11 that is required for the functional interaction of release factor 1 with the ribosome in the cell.}, keywords = {Binding Sites,Cell Division,Electrophoresis Gel Two-Dimensional,Escherichia coli,Escherichia coli Proteins,Mutation,nosource,Peptide Termination Factors,Ribosomal Proteins,Ribosomes,Suppression Genetic,Temperature} } % == BibTeX quality report for vandykeSiteFunctionalInteraction2003: % ? unused Journal abbr (“J. Mol. Biol”)

@article{chomczynskiSinglestepMethodRNA1987, title = {Single-Step Method of {{RNA}} Isolation by Acid Guanidinium Thiocyanate-Phenol-Chloroform Extraction}, author = {Chomczynski, P and Sacchi, N}, year = 1987, month = apr, journal = {Analytical Biochemistry}, volume = {162}, number = {1}, pages = {156–159}, publisher = {Elsevier}, issn = {0003-2697}, doi = {10.1006/abio.1987.9999}, url = {http://linkinghub.elsevier.com/retrieve/pii/0003269787900212}, abstract = {A new method of total RNA isolation by a single extraction with an acid guanidinium thiocyanate-phenol-chloroform mixture is described. The method provides a pure preparation of undegraded RNA in high yield and can be completed within 4 h. It is particularly useful for processing large numbers of samples and for isolation of RNA from minute quantities of cells or tissue samples.}, keywords = {Animals,Cell Line,Chloroform,Guanidine,Guanidines,Humans,Hydrogen-Ion Concentration,Mammary Glands Animal,nosource,Phenol,Phenols,Rats,RNA,Solutions} } % == BibTeX quality report for chomczynskiSinglestepMethodRNA1987: % ? unused Journal abbr (“Anal. Biochem”)

@article{sanbonmatsuSimulatingMovementTRNA2005, title = {Simulating Movement of {{tRNA}} into the Ribosome during Decoding}, author = {Sanbonmatsu, Kevin Y and Joseph, Simpson and Tung, Chang-Shung}, year = 2005, month = oct, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {44}, eprint = {16249344}, eprinttype = {pubmed}, pages = {15854–15859}, publisher = {National Acad Sciences}, issn = {0027-8424}, doi = {10.1073/pnas.0503456102}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16249344}, abstract = {Decoding is the key step during protein synthesis that enables information transfer from RNA to protein, a process critical for the survival of all organisms. We have used large-scale (2.64 x 10(6) atoms) all-atom simulations of the entire ribosome to understand a critical step of decoding. Although the decoding problem has been studied for more than four decades, the rate-limiting step of cognate tRNA selection has only recently been identified. This step, known as accommodation, involves the movement inside the ribosome of the aminoacyl-tRNA from the partially bound “A/T” state to the fully bound “A/A” state. Here, we show that a corridor of 20 universally conserved ribosomal RNA bases interacts with the tRNA during the accommodation movement. Surprisingly, the tRNA is impeded by the A-loop (23S helix 92), instead of enjoying a smooth transition to the A/A state. In particular, universally conserved 23S ribosomal RNA bases U2492, C2556, and C2573 act as a 3D gate, causing the acceptor stem to pause before allowing entrance into the peptidyl transferase center. Our simulations demonstrate that the flexibility of the acceptor stem of the tRNA, in addition to flexibility of the anticodon arm, is essential for tRNA selection. This study serves as a template for simulating conformational changes in large ({\(>\)}10(6) atoms) biological and artificial molecular machines.}, keywords = {Anticodon,BASE,BASES,Biological Transport,BIOLOGY,Computer Simulation,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,Conserved Sequence,decoding,INFORMATION,Kinetics,La,Models Molecular,Movement,nosource,Nucleic Acid Conformation,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNA Transfer,RNA Transfer Amino Acyl,SELECTION,TEMPLATE,TRANSFERASE CENTER,tRNA} } % == BibTeX quality report for sanbonmatsuSimulatingMovementTRNA2005: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{shahSimianVirus402004, title = {Simian Virus 40 and Human Disease}, author = {Shah, Keerti V}, year = 2004, month = dec, journal = {The Journal of Infectious Diseases}, volume = {190}, number = {12}, pages = {2061–2064}, publisher = {Oxford University Press}, issn = {0022-1899}, doi = {10.1086/425999}, url = {http://jid.oxfordjournals.org/content/190/12/2061.short}, keywords = {Animals,Drug Contamination,Humans,Neoplasms,nosource,Poliovirus Vaccine Inactivated,Poliovirus Vaccine- Inactivated,Polyomavirus Infections,Risk Factors,Simian virus 40,Tumor Virus Infections,Zoonoses} } % == BibTeX quality report for shahSimianVirus402004: % ? unused Journal abbr (“J. Infect. Dis”)

@article{jacksSignalsRibosomalFrameshifting1988, title = {Signals for Ribosomal Frameshifting in the {{Rous Sarcoma Virus}} Gag-Pol Region.}, author = {Jacks, T and Madhani, H D and Masiarz, F R and Varmus, H E}, year = 1988, month = nov, journal = {Cell}, volume = {55}, number = {3}, pages = {447–458}, publisher = {Elsevier}, issn = {0092-8674}, doi = {10.1016/0092-8674(88)90031-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867488900311 http://www.sciencedirect.com/science/article/pii/0092867488900311}, abstract = {The gag-pol protein of Rous sarcoma virus (RSV), the precursor to the enzymes responsible for reverse transcription and integration, is expressed from two genes that lie in different translational reading frames by ribosomal frameshifting. Here, we localize the site of frameshifting and show that the frameshifting reaction is mediated by slippage of two adjacent tRNAs by a single nucleotide in the 5’ direction. The gag terminator, which immediately follows the frameshift site, is not required for frameshifting. Other suspected retroviral frameshift sites mediate frameshifting when placed at the end of RSV gag. Mutations in RSV pol also affect synthesis of the gag-pol protein in vitro. The effects of these mutations best correlate with the potential to form an RNA stem-loop structure adjacent to the frameshift site. A short sequence of RSV RNA, 147 nucleotides in length, containing the frameshift site and stem-loop structure, is sufficient to direct frameshifting in a novel genetic context.}, keywords = {Amino Acid Sequence,Avian Sarcoma Viruses,Base Sequence,Chromosome Deletion,enzyme,Enzymes,FORM,FRAME,frameshift,Frameshifting,Gag,Gag-pol,gene,Gene Products gag,Gene Products- gag,Genes,Genes Viral,Genes- Viral,Genetic,In Vitro,IN-VITRO,Molecular Sequence Data,Mutation,MUTATIONS,nosource,Nucleotides,pol,PRECURSOR,protein,Protein Biosynthesis,Protein Conformation,READING FRAME,Reading Frames,Retroviridae Proteins,ribosomal frameshifting,Ribosomes,Rna,RNA Transfer Leu,RNA Viral,RNA- Transfer- Leu,RNA- Viral,sequence,SIGNAL,SITE,SITES,SLIPPAGE,slippery site,STEM-LOOP,structure,transcription,tRNA,virus} }

@article{czaplinskiShouldWeKill1999, title = {Should We Kill the Messenger? {{The}} Role of the Surveillance Complex in Translation Termination and {{mRNA}} Turnover}, author = {Czaplinski, K and {Ruiz-Echevarria}, M J and Gonz{'a}lez, C I and Peltz, S W}, year = 1999, month = aug, journal = {BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology}, volume = {21}, number = {8}, eprint = {10440865}, eprinttype = {pubmed}, pages = {685–696}, publisher = {Wiley Online Library}, issn = {0265-9247}, doi = {10.1002/(SICI)1521-1878(199908)21:8<685::AID-BIES8>3.0.CO;2-4}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10440865 http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1521-1878(199908)21:8<685::AID-BIES8>3.0.CO;2-4/abstract}, abstract = {Eukaryotes have evolved conserved mechanisms to rid cells of faulty gene products that can interfere with cell function. mRNA surveillance is an example of a pathway that monitors the translation termination process and promotes degradation of transcripts harboring premature translation termination codons. Studies on the mechanism of mRNA surveillance in yeast and humans suggest a common mechanism where a “surveillance complex” monitors the translation process and determines whether translation termination has occurred at the correct position within the mRNA. A model will be presented that suggests that the surveillance complex assesses translation termination by monitoring the transition of an RNP as it is converted from a nuclear to a cytoplasmic form during the initial rounds of translation. Copyright 1999 John Wiley & Sons, Inc}, keywords = {99369634,animal,Animals,cancer,Codon,Codon Terminator,Codon- Terminator,CodonTerminator,COMPLEX,COMPLEXES,degradation,gene,Gene Expression Regulation,Genetic,genetics,human,MECHANISM,MECHANISMS,metabolism,microbiology,Models Biological,Models- Biological,ModelsBiological,mRNA,Mutation,NMD,nosource,Peptide Chain Termination,Peptide Chain Termination Translational,Peptide Chain Termination- Translational,Review,RNA Fungal,RNA Messenger,RNA- Fungal,RNA- Messenger,RNAFungal,RNAMessenger,Saccharomyces cerevisiae,termination,translation,turnover,yeast} } % == BibTeX quality report for czaplinskiShouldWeKill1999: % ? unused Journal abbr (“Bioessays”)

@article{gurvichSequencesThatDirect2003, title = {Sequences That Direct Significant Levels of Frameshifting Are Frequent in Coding Regions of {{Escherichia}} Coli}, author = {Gurvich, Olga L and Baranov, Pavel V and Zhou, Jiadong and Hammer, Andrew W and Gesteland, Raymond F and Atkins, John F}, year = 2003, month = nov, journal = {The EMBO Journal}, volume = {22}, number = {21}, pages = {5941–5950}, publisher = {Nature Publishing Group}, issn = {0261-4189}, doi = {10.1093/emboj/cdg561}, url = {http://onlinelibrary.wiley.com/doi/10.1093/emboj/cdg561/full http://www.nature.com/emboj/journal/v22/n21/abs/7595471a.html http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=275418&tool=pmcentrez&rendertype=abstract}, abstract = {It is generally believed that significant ribosomal frameshifting during translation does not occur without a functional purpose. The distribution of two frameshift-prone sequences, A_AAA_AAG and CCC_TGA, in coding regions of Escherichia coli has been analyzed. Although a moderate level of selection against the first sequence is evident, 68 genes contain A_AAA_AAG and 19 contain CCC_TGA. The majority of those tested in their genomic context showed {\(>\)}1% frameshifting. Comparative sequence analysis was employed to assess a potential biological role for frameshifting in decoding these genes. Two new candidates, in pheL and ydaY, for utilized frameshifting have been identified in addition to those previously known in dnaX and nine insertion sequence elements. For the majority of the shift-prone sequences no functional role can be attributed to them, and the frameshifting is likely erroneous. However, none of frameshift sequences is in the 306 most highly expressed genes. The unexpected conclusion is that moderate frameshifting during expression of at least some other genes is not sufficiently harmful for cells to trigger strong negative evolutionary pressure.}, pmid = {14592990}, keywords = {0,analysis,Bacterial,Bacterial: genetics,Base Sequence,CELLS,CODING REGION,Codon,Codon: genetics,decoding,DNA,DNA Bacterial,dnaX,ELEMENTS,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: biosynthesis,Escherichia coli Proteins: genetics,Escherichia coli: genetics,Escherichia coli: metabolism,ESCHERICHIA-COLI,expression,frameshift,frameshifting,Frameshifting,Frameshifting Ribosomal,gene,Genes,Genes Bacterial,Genetic,genetics,genomic,genomics,human,La,nosource,proline,Recombinant Fusion Proteins,Recombinant Fusion Proteins: biosynthesis,Recombinant Fusion Proteins: genetics,REGION,Ribosomal,ribosomal frameshifting,Ribosomes,Ribosomes: metabolism,SELECTION,sequence,Sequence Analysis,SEQUENCE-ANALYSIS,SEQUENCES,translation,translational} } % == BibTeX quality report for gurvichSequencesThatDirect2003: % ? unused Journal abbr (“EMBO J.”)

@article{mendellSeparableRolesRent12002, title = {Separable Roles for Rent1/{{hUpf1}} in Altered Splicing and Decay of Nonsense Transcripts}, author = {Mendell, Joshua T and {}{ap Rhys}, Colette M J and Dietz, Harry C}, year = 2002, month = oct, journal = {Science (New York, N.Y.)}, volume = {298}, number = {5592}, pages = {419–422}, publisher = {American Association for the Advancement of Science}, issn = {1095-9203}, doi = {10.1126/science.1074428}, url = {http://www.sciencemag.org/content/298/5592/419.short http://www.ncbi.nlm.nih.gov/pubmed/12228722}, abstract = {The mechanism by which disruption of reading frame can influence pre-messenger RNA (pre-mRNA) processing is poorly understood. We assessed the role of factors essential for nonsense-mediated mRNA decay (NMD) in nonsense-mediated altered splicing (NAS) with the use of RNA interference (RNAi) in mammalian cells. Inhibition of rent1/hUpf1 expression abrogated both NMD and NAS of nonsense T cell receptor beta transcripts. In contrast, inhibition of rent2/hUpf2 expression did not disrupt NAS despite achieving comparable stabilization of nonsense transcripts. We also demonstrate that NAS and NMD are genetically separable functions of rent1/hUpf1. Additionally, rent1/hUpf1 enters the nucleus where it may directly influence early events in mRNA biogenesis. This provides compelling evidence that NAS relies on a component of the nonsense surveillance machinery but is not an indirect consequence of NMD.}, pmid = {12228722}, keywords = {0,ACID,ACIDS,Active Transport,Active Transport Cell Nucleus,Active Transport- Cell Nucleus,Active Transport-Cell Nucleus,Active TransportCell Nucleus,Alternative Splicing,Amino Acid Substitution,BIOGENESIS,Blotting,Blotting Northern,Blotting- Northern,Blotting-Northern,BlottingNorthern,Cell Nucleus,Cell Nucleus: metabolism,CELLS,Codon,Codon Nonsense,Codon- Nonsense,Codon-Nonsense,CodonNonsense,COMPONENT,Cytoplasm,Cytoplasm: metabolism,DECAY,DISRUPTION,Equilibrative-Nucleoside Transporter 2,Equilibrative-Nucleoside Transporter 2: genetics,Equilibrative-Nucleoside Transporter 2: metabolism,expression,Fatty Acids,Fatty Acids Unsaturated,Fatty Acids- Unsaturated,Fatty Acids-Unsaturated,Fatty AcidsUnsaturated,FRAME,FUSION PROTEIN,Gene Silencing,Genes,Genes T-Cell Receptor beta,Genes- T-Cell Receptor beta,Genes-T-Cell Receptor beta,GenesT-Cell Receptor beta,Genetic,genetics,Hela Cells,Helicase,human,Humans,INHIBITION,La,MAMMALIAN-CELLS,MECHANISM,Messenger,Messenger: genetics,Messenger: metabolism,metabolism,mRNA,mRNA decay,Mutation,NMD,Nonsense,NONSENSE,nonsense-mediated mRNA decay,Northern,nosource,pharmacology,PRE-MESSENGER-RNA,protein,Proteins,rat,READING FRAME,Recombinant Fusion Proteins,Recombinant Fusion Proteins: metabolism,Rna,RNA HELICASE,RNA Helicases,RNA Helicases: genetics,RNA Helicases: metabolism,RNA Interference,RNA Messenger,RNA Small Interfering,RNA- Messenger,RNA- Small Interfering,RNA-Messenger,RNA-Small Interfering,RNAMessenger,RNASmall Interfering,Small Interfering,Small Interfering: metabolism,splicing,Support,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SURVEILLANCE,T,T-Cell Receptor beta,Trans-Activators,Trans-Activators: genetics,Trans-Activators: metabolism,TRANSCRIPT,transcription,TRANSCRIPTION FACTOR,Transcription Factors,Transcription Factors: genetics,Transcription Factors: metabolism,Unsaturated,Unsaturated: pharmacology,Upf1,UPF1 PROTEIN} } % == BibTeX quality report for mendellSeparableRolesRent12002: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”)

@article{wilkinsonSelective2hydroxylAcylation2006, title = {Selective 2’-Hydroxyl Acylation Analyzed by Primer Extension ({{SHAPE}}): Quantitative {{RNA}} Structure Analysis at Single Nucleotide Resolution}, author = {Wilkinson, Kevin A and Merino, Edward J and Weeks, Kevin M}, year = 2006, journal = {Nature Protocols}, volume = {1}, number = {3}, pages = {1610–1616}, issn = {1750-2799}, doi = {10.1038/nprot.2006.249}, url = {pm:17406453 http://www.nature.com/nprot/journal/v1/n3/abs/nprot.2006.249.html}, abstract = {Selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) interrogates local backbone flexibility in RNA at single-nucleotide resolution under diverse solution environments. Flexible RNA nucleotides preferentially sample local conformations that enhance the nucleophilic reactivity of 2’-hydroxyl groups toward electrophiles, such as N-methylisatoic anhydride (NMIA). Modified sites are detected as stops in an optimized primer extension reaction, followed by electrophoretic fragment separation. SHAPE chemistry scores local nucleotide flexibility at all four ribonucleotides in a single experiment and discriminates between base-paired versus unconstrained or flexible residues with a dynamic range of 20-fold or greater. Quantitative SHAPE reactivity information can be used to establish the secondary structure of an RNA, to improve the accuracy of structure prediction algorithms, to monitor structural differences between related RNAs or a single RNA in different states, and to detect ligand binding sites. SHAPE chemistry rarely needs significant optimization and requires two days to complete for an RNA of 100-200 nucleotides.}, pmid = {17406453}, keywords = {0,accuracy,Acylation,Algorithms,analysis,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,chemistry,CONFORMATION,Dna,DNA Primers,Electrophoresis,genetics,INFORMATION,La,Molecular Structure,nosource,Nucleic Acid Conformation,NUCLEOTIDE RESOLUTION,Nucleotides,PREDICTION,primer extension,REQUIRES,RESIDUES,RESOLUTION,Ribonucleotides,Rna,RNA,SECONDARY STRUCTURE,Sequence Analysis RNA,Sequence Analysis-RNA,Sequence AnalysisRNA,SITE,SITES,Structural,structure,Structure-Activity Relationship,Support} } % == BibTeX quality report for wilkinsonSelective2hydroxylAcylation2006: % ? unused Journal abbr (“Nat.Protoc.”)

@article{percudaniSelectionWobblePosition1999, title = {Selection at the Wobble Position of Codons Read by the Same {{tRNA}} in {{Saccharomyces}} Cerevisiae.}, author = {Percudani, R and Ottonello, S}, year = 1999, month = dec, journal = {Molecular Biology and Evolution}, volume = {16}, number = {12}, pages = {1752–1762}, publisher = {SMBE}, issn = {0737-4038}, url = {http://mbe.oxfordjournals.org/content/16/12/1752.short}, abstract = {The transfer RNA gene complement of Saccharomyces cerevisiae was utilized for a whole-genome analysis of the deviation from a neutral usage of pyrimidine-ending cognate codons, that is, codons read by a single tRNA species having either inosine or guanosine as the first anticodon base. Mutational pressure at the wobble position was estimated from the base composition of the noncoding portion of the yeast genome. The selective pressure for translational efficiency was inferred from the degree of codon adaptation to tRNA gene redundancy and from mRNA abundance data derived from yeast transcriptome analysis. Amino acid conservation in orthologous comparisons with wholly sequenced microbial genomes was used to estimate translational accuracy requirements. A close correspondence was observed between the usage of wobble position pyrimidines and the frequency predicted by mutational bias. However, in the case of four cognate pairs (Gly: ggu/ggc; Asn: aau/aac; Phe: uuu/uuc; Tyr: uau/ uac) all read by guanosine-starting anticodons, we found evidence for a strong selective pressure driven by translational efficiency. Only for the glycine pair, wobble pyrimidine choice also appears to fulfill a translational accuracy requirement. Wobble pyrimidine selection is strictly related to the number of hydrogen bonds formed by alternative cognate codons: whenever a different number of hydrogen bonds can be formed at the wobble position, there is selection against six- or nine-hydrogen-bonded codon-anticodon pairs. Our results indicate that an intrinsic codon preference, critically dependent on the stability of codon-anticodon interaction and mainly reflecting selection for the optimization of translational efficiency, is built into the translational apparatus.}, keywords = {Codon,Genome Fungal,nosource,Open Reading Frames,Protein Biosynthesis,Pyrimidines,RNA Transfer,Saccharomyces cerevisiae,Sequence Alignment} } % == BibTeX quality report for percudaniSelectionWobblePosition1999: % ? unused Journal abbr (“Mol. Biol. Evol”)

@article{alkemarSecondaryStructureTwo2004, title = {Secondary Structure of Two Regions in Expansion Segments {{ES3}} and {{ES6}} with the Potential of Forming a Tertiary Interaction in Eukaryotic {{40S}} Ribosomal Subunits}, author = {Alkemar, Gunnar and Nyg{}rd, Odd}, year = 2004, month = mar, journal = {RNA (New York, N.Y.)}, volume = {10}, number = {3}, eprint = {14970386}, eprinttype = {pubmed}, pages = {403–411}, issn = {1355-8382}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14970386}, abstract = {The 18S rRNA of the small eukaryotic ribosomal subunit contains several expansion segments. Electron microscopy data indicate that two of the largest expansion segments are juxtaposed in intact 40S subunits, and data from phylogenetic sequence comparisons indicate that these two expansion segments contain complementary sequences that could form a direct tertiary interaction on the ribosome. We have investigated the secondary structure of the two expansion segments in the region around the putative tertiary interaction. Ribosomes from yeast, wheat, and mouse-three organisms representing separate eukaryotic kingdoms-were isolated, and the structure of ES3 and part of the ES6 region were analyzed using the single-strand-specific chemical reagents CMCT and DMS and the double-strand-specific ribonuclease V1. The modification patterns were analyzed by primer extension and gel electrophoresis on an ABI 377 automated DNA sequencer. The investigated sequences were relatively exposed to chemical and enzymatic modification. This is in line with their indicated location on the surface at the solvent side of the subunit. The complementary ES3 and ES6 sequences were clearly inaccessible to single-strand modification, but available for cleavage by double-strand-specific RNase V1. The results are compatible with a direct helical interaction between bases in ES3 and ES6. Almost identical results were obtained with ribosomes from the three organisms investigated.}, pmid = {14970386}, keywords = {Animals,Base Sequence,Mice,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Ribosomes,RNA Ribosomal 18S,Saccharomyces cerevisiae,Sequence Analysis RNA,Triticum} } % == BibTeX quality report for alkemarSecondaryStructureTwo2004: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{marczinkeSecondaryStructureMutational1998, title = {Secondary Structure and Mutational Analysis of the Ribosomal Frameshift Signal of Rous Sarcoma Virus1}, author = {Marczinke, B and Fisher, R and Vidakovic, M and Bloys, A J and Brierley, I}, year = 1998, month = nov, journal = {Journal of Molecular Biology}, volume = {284}, number = {2}, pages = {205–225}, publisher = {Elsevier}, issn = {0022-2836}, doi = {10.1006/jmbi.1998.2186}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(98)92186-6}, abstract = {Expression of the Gag-Pol polyprotein of Rous sarcoma virus (RSV) requires a -1 ribosomal frameshifting event at the overlap region of the gag and pol open reading frames. The signal for frameshifting is composed of two essential mRNA elements; a slippery sequence (AAAUUUA) where the ribosome changes reading frame, and a stimulatory RNA structure located immediately downstream. This RNA is predicted to be a complex stem-loop but may also form an RNA pseudoknot. We have investigated the structure of the RSV frameshift signal by a combination of enzymatic and chemical structure probing and site- directed mutagenesis. The stimulatory RNA is indeed a complex stem-loop with a long stable stem and two additional stem-loops contained as substructures within the main loop region. The substructures are not however required for frameshifting. Evidence for an additional interaction between a stretch of nucleotides in the main loop and a region downstream to generate an RNA pseudoknot was obtained from an analysis of the frameshifting properties of RSV mutants translated in the rabbit reticulocyte lysate in vitro translation system. Mutations that disrupted the predicted pseudoknot-forming sequences reduced frameshifting but when the mutations were combined and should re-form the pseudoknot, frameshifting was restored to a level approaching that of the wild-type construct. It was also observed that the predicted pseudoknot-forming regions had reduced sensitivity to cleavage by the single-stranded probe imidazole. Overall, however, the structure probing data indicate that the pseudoknot interaction is weak and may form transiently. In comparison to other characterised RNA structures present at viral frameshift signals, the RSV stimulator falls into a novel group. It cannot be considered to be a simple hairpin-loop yet it is distinct from other well characterised frameshift-inducing RNA pseudoknots in that the overall contribution of the RSV pseudoknot to frameshifting is less dramatic. Copyright 1998 Academic Press}, keywords = {99033042,analysis,Avian Sarcoma Viruses,Base Sequence,chemistry,CLEAVAGE,COMPLEX,COMPLEXES,Computer Simulation,ELEMENTS,expression,frameshift,Frameshifting,Frameshifting Ribosomal,FrameshiftingRibosomal,Fusion Proteins gag-pol,Fusion Proteinsgag-pol,Gag,Gag-pol,genetics,In Vitro,in vitro translation,IN-VITRO,lysate,Models Molecular,ModelsMolecular,Molecular Sequence Data,mRNA,Mutagenesis,Mutagenesis Site-Directed,MutagenesisSite-Directed,Mutation,MUTATIONAL ANALYSIS,MUTATIONS,nosource,Nucleic Acid Conformation,Nucleotides,Open Reading Frames,pathology,pol,pseudoknot,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,ribosome,Rna,RNA PSEUDOKNOT,RNA Viral,RnaViral,Sarcoma VirusesAvian,sequence,SIGNAL,structure,supportnon-u.s.gov’t,SYSTEM,translation,virus} } % == BibTeX quality report for marczinkeSecondaryStructureMutational1998: % ? unused Journal abbr (“J. Mol. Biol”)

@article{bairdSearchingIRES2006, title = {Searching for {{IRES}}}, author = {Baird, Stephen D and Turcotte, Marcel and Korneluk, Robert G and Holcik, Martin}, year = 2006, month = oct, journal = {RNA (New York, N.Y.)}, volume = {12}, number = {10}, pages = {1755–1785}, issn = {1355-8382}, doi = {10.1261/rna.157806}, url = {http://rnajournal.cshlp.org/content/12/10/1755.short}, abstract = {The cell has many ways to regulate the production of proteins. One mechanism is through the changes to the machinery of translation initiation. These alterations favor the translation of one subset of mRNAs over another. It was first shown that internal ribosome entry sites (IRESes) within viral RNA genomes allowed the production of viral proteins more efficiently than most of the host proteins. The RNA secondary structure of viral IRESes has sometimes been conserved between viral species even though the primary sequences differ. These structures are important for IRES function, but no similar structure conservation has yet to be shown in cellular IRES. With the advances in mathematical modeling and computational approaches to complex biological problems, is there a way to predict an IRES in a data set of unknown sequences? This review examines what is known about cellular IRES structures, as well as the data sets and tools available to examine this question. We find that the lengths, number of upstream AUGs, and %GC content of 5’-UTRs of the human transcriptome have a similar distribution to those of published IRES-containing UTRs. Although the UTRs containing IRESes are on the average longer, almost half of all 5’-UTRs are long enough to contain an IRES. Examination of the available RNA structure prediction software and RNA motif searching programs indicates that while these programs are useful tools to fine tune the empirically determined RNA secondary structure, the accuracy of de novo secondary structure prediction of large RNA molecules and subsequent identification of new IRES elements by computational approaches, is still not possible.}, pmid = {16957278}, keywords = {5’ Untranslated Regions,Algorithms,Animals,Base Sequence,Databases Nucleic Acid,Genetic Complementation Test,Humans,ires,Models Molecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,prediction software,Protein Biosynthesis,Ribosomes,rna,RNA Viral,RNA-Binding Proteins,secondary structure,Software,Thermodynamics} } % == BibTeX quality report for bairdSearchingIRES2006: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? Title looks like it was stored in title-case in Zotero % ? unused Journal abbr (“RNA”)

@article{wilkinsonRNASurveillanceNuclear2002, title = {{{RNA}} Surveillance by Nuclear Scanning?}, author = {Wilkinson, Miles F and Shyu, Ann-Bin}, year = 2002, month = jun, journal = {Nature Cell Biology}, volume = {4}, number = {6}, pages = {E144–E147}, publisher = {Nature Publishing Group}, issn = {1465-7392}, doi = {10.1038/ncb0602-e144}, url = {http://www.nature.com/ncb/journal/v4/n6/abs/ncb0602-e144.html}, abstract = {There are many quality-control mechanisms that ensure high fidelity of gene expression. One of these is the nonsense-mediated decay (NMD) pathway, which destroys aberrant mRNAs that contain premature termination codons generated as a result of biosynthetic errors or random and programmed gene mutations. Two complexes that initially bind to RNA in the nucleus have been suggested to be involved in NMD in the cytoplasm. Here we propose an alternative model that involves nuclear scanning, on the basis of recent evidence for nuclear translation.}, keywords = {Animals,Codon Nonsense,Codon- Nonsense,Gene Expression Regulation,Mammals,nosource,Nuclear Proteins,RNA Precursors} } % == BibTeX quality report for wilkinsonRNASurveillanceNuclear2002: % ? unused Journal abbr (“Nat. Cell Biol”)

@article{nollerRNAStructureReading2005, title = {{{RNA}} Structure: Reading the Ribosome.}, author = {Noller, Harry F}, year = 2005, month = sep, journal = {Science (New York, N.Y.)}, volume = {309}, number = {5740}, pages = {1508–1514}, publisher = {American Association for the Advancement of Science}, issn = {1095-9203}, doi = {10.1126/science.1111771}, url = {http://www.sciencemag.org/content/309/5740/1508.short}, abstract = {The crystal structures of the ribosome and its subunits have increased the amount of information about RNA structure by about two orders of magnitude. This is leading to an understanding of the principles of RNA folding and of the molecular interactions that underlie the functional capabilities of the ribosome and other RNA systems. Nearly all of the possible types of RNA tertiary interactions have been found in ribosomal RNA. One of these, an abundant tertiary structural motif called the A-minor interaction, has been shown to participate in both aminoacyl-transfer RNA selection and in peptidyl transferase; it may also play an important role in the structural dynamics of the ribosome.}, pmid = {16141058}, keywords = {0,AMINOACYL-TRANSFER RNA,AMINOACYL-TRANSFER-RNA,BIOLOGY,chemistry,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,crystallography,Crystallography X-Ray,CrystallographyX-Ray,DYNAMICS,INFORMATION,La,models,Models Molecular,ModelsMolecular,molecular,Molecular Biology,nosource,nucleic acid conformation,Nucleic Acid Conformation,peptidyl transferase,PEPTIDYL-TRANSFERASE,Research SupportN.I.H.Extramural,Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,Review,ribosomal,ribosomal chemistry,ribosomal RNA,RIBOSOMAL-RNA,ribosome,ribosomes,Ribosomes,ribosomes chemistry,rna,Rna,RNA,rna chemistry,RNA folding,RNA Ribosomal,RNA Transfer,RNARibosomal,RNATransfer,SELECTION,Structural,structure,SUBUNIT,SUBUNITS,SYSTEM,SYSTEMS,transfer,transfer chemistry,x ray} } % == BibTeX quality report for nollerRNAStructureReading2005: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”)

@article{merinoRNAStructureAnalysis2005, title = {{{RNA}} Structure Analysis at Single Nucleotide Resolution by Selective 2’-Hydroxyl Acylation and Primer Extension ({{SHAPE}})}, author = {Merino, Edward J and Wilkinson, Kevin A and Coughlan, Jennifer L and Weeks, Kevin M}, year = 2005, month = mar, journal = {Journal of the American Chemical Society}, volume = {127}, number = {12}, eprint = {15783204}, eprinttype = {pubmed}, pages = {4223–4231}, publisher = {ACS Publications}, issn = {0002-7863}, doi = {10.1021/ja043822v}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15783204}, abstract = {The reactivity of an RNA ribose hydroxyl is shown to be exquisitely sensitive to local nucleotide flexibility because a conformationally constrained adjacent 3’-phosphodiester inhibits formation of the deprotonated, nucleophilic oxyanion form of the 2’-hydroxyl group. Reaction with an appropriate electrophile, N-methylisatoic anhydride, to form a 2’-O-adduct thus can be used to monitor local structure at every nucleotide in an RNA. We develop a quantitative approach involving Selective 2’-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) to map the structure of and to distinguish fine differences in structure for tRNAAsp transcripts at single nucleotide resolution. Modest extensions of the SHAPE approach will allow RNA structure to be monitored comprehensively and at single nucleotide resolution for RNAs of arbitrary sequence and structural complexity and under diverse solution environments.}, keywords = {0,ACID,ACIDS,Acylation,analysis,Anhydrides,Anthranilic Acids,chemistry,FORM,genetics,La,metabolism,nosource,Nucleic Acid Conformation,NUCLEOTIDE RESOLUTION,primer extension,RESOLUTION,Ribose,Rna,RNA,RNA Transfer Asp,RNATransferAsp,sequence,Structural,structure,Structure-Activity Relationship,Support,TRANSCRIPT} } % == BibTeX quality report for merinoRNAStructureAnalysis2005: % ? unused Journal abbr (“J. Am. Chem. Soc”)

@article{galleiRNARecombinationVivo2004, title = {{{RNA}} Recombination in Vivo in the Absence of Viral Replication}, author = {Gallei, Andreas and Pankraz, Alexander and Thiel, Heinz-J{"u}rgen and Becher, Paul}, year = 2004, month = jun, journal = {Journal of Virology}, volume = {78}, number = {12}, pages = {6271–6281}, publisher = {Am Soc Microbiol}, issn = {0022-538X}, doi = {10.1128/JVI.78.12.6271-6281.2004}, url = {http://jvi.asm.org/cgi/content/abstract/78/12/6271}, abstract = {To study fundamental aspects of RNA recombination, an in vivo RNA recombination system was established. This system allowed the efficient generation of recombinant cytopathogenic pestiviruses after transfection of synthetic, nonreplicatable, subgenomic transcripts in cells infected with a replicating noncytopathogenic virus. Studies addressing the interplay between RNA recombination and replication revealed that cotransfection of noninfected cells with various pairs of nonreplicatable RNA derivatives also led to the emergence of recombinant viral genomes. Remarkably, homologous and nonhomologous recombination occurred between two overlapping transcripts, each lacking different essential parts of the viral RNA-dependent RNA polymerase (RdRp) gene. Apart from the generally accepted viral replicative copy choice recombination, our results prove the existence of a viral RdRp-independent mechanism of RNA recombination that occurs in vivo. It appears likely that such a mechanism not only contributes to the evolution of RNA viruses but also leads to the generation of recombinant cellular RNAs.}, keywords = {Amino Acid Sequence,Animals,Base Sequence,Cattle,Cell Line,Diarrhea Viruses Bovine Viral,Diarrhea Viruses- Bovine Viral,Genome Viral,Genome- Viral,Molecular Sequence Data,nosource,Recombination Genetic,Recombination- Genetic,RNA Replicase,RNA Viral,RNA- Viral,Transfection,Virus Replication} } % == BibTeX quality report for galleiRNARecombinationVivo2004: % ? unused Journal abbr (“J. Virol”)

@article{mackeRNAMotifRNASecondary2001, title = {{{RNAMotif}}, an {{RNA}} Secondary Structure Definition and Search Algorithm}, author = {Macke, T J and Ecker, D J and Gutell, R R and Gautheret, D and Case, D A and Sampath, R}, year = 2001, month = nov, journal = {Nucleic Acids Research}, volume = {29}, number = {22}, eprint = {11713323}, eprinttype = {pubmed}, pages = {4724–4735}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/29.22.4724}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11713323 http://nar.oxfordjournals.org/content/29/22/4724.short}, abstract = {RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures are assembled from a collection of RNA structural motifs. These basic building blocks are used repeatedly, and in various combinations, to form different RNA types and define their unique structural and functional properties. Identification of recurring RNA structural motifs will therefore enhance our understanding of RNA structure and help associate elements of RNA structure with functional and regulatory elements. Our goal was to develop a computer program that can describe an RNA structural element of any complexity and then search any nucleotide sequence database, including the complete prokaryotic and eukaryotic genomes, for these structural elements. Here we describe in detail a new computational motif search algorithm, RNAMotif, and demonstrate its utility with some motif search examples. RNAMotif differs from other motif search tools in two important aspects: first, the structure definition language is more flexible and can specify any type of base-base interaction; second, RNAMotif provides a user controlled scoring section that can be used to add capabilities that patterns alone cannot provide.}, keywords = {3’ Untranslated Regions,5’ Untranslated Regions,Algorithms,Base Sequence,computer,CRYSTAL-STRUCTURE,DATABASE,ELEMENTS,Escherichia coli,Genome,GENOMIC DNA-SEQUENCES,Humans,IDENTIFICATION,INTERNAL LOOP/BULGE,IRON-RESPONSIVE ELEMENT,La,LOOP-E,MESSENGER-RNA,Molecular Sequence Data,MUSCULAR-DYSTROPHY,nosource,Nucleic Acid Conformation,RIBOSOMAL-SUBUNIT,Rna,RNA,RNA Bacterial,RNA Ribosomal 16S,RNA Ribosomal 23S,RNA- Bacterial,RNA- Ribosomal- 16S,RNA- Ribosomal- 23S,search,sequence,Sequence Alignment,SRP RNA,Structural,structure} } % == BibTeX quality report for mackeRNAMotifRNASecondary2001: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{leRNAMoleculesStructure2002, title = {{{RNA}} Molecules with Structure Dependent Functions Are Uniquely Folded}, author = {Le, Shu-Yun and Zhang, Kaizhong and Maizel, Jacob V}, year = 2002, month = aug, journal = {Nucleic Acids Research}, volume = {30}, number = {16}, eprint = {12177299}, eprinttype = {pubmed}, pages = {3574–3582}, issn = {1362-4962}, doi = {10.1093/nar/gkf473}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12177299}, abstract = {Cis-acting elements in post-transcriptional regulation of gene expression are often correlated with distinct local RNA secondary structure. These structures are expected to be significantly more ordered than those anticipated at random because of evolutionary constraints and intrinsic structural properties. In this study, we introduce a computing method to calculate two quantitative measures, NRd and Stscr, for estimating the uniqueness of an RNA secondary structure. NRd is a normalized score based on evaluating how different a natural RNA structure is from those predicted for its randomly shuffled variants. The lower the score NRd the more well ordered is the natural RNA structure. The statistical significance of NRd compared with that computed from structural comparisons among large numbers of randomly permuted sequences is represented by a standardized score, STSCR: We tested the method on the trans-activation response element and Rev response element of HIV-1 mRNA, internal ribosome entry sequence of hepatitis C virus, Tetrahymena thermophila rRNA intron, 100 tRNAs and 14 RNase P RNAs. Our data indicate that functional RNA structures have high Stscr, while other structures have low Stscr. We conclude that RNA functional molecules and/or cis-acting elements with structure dependent functions possess well ordered conformations and they are uniquely folded as measured by this technique.}, pmid = {12177299}, keywords = {0,Animals,Base Sequence,BIOLOGY,cancer,chemistry,Computational Biology,CONFORMATION,ELEMENTS,Endoribonucleases,expression,gene,Gene Expression,GENE-EXPRESSION,genetics,Hepacivirus,HEPATITIS-C,HIV Long Terminal Repeat,Hiv-1,HIV-1,INTERNAL RIBOSOME ENTRY,INTRON,Introns,La,Molecular Sequence Data,mRNA,nosource,Nucleic Acid Conformation,post-transcriptional regulation,POSTTRANSCRIPTIONAL REGULATION,regulation,Regulatory Sequences Nucleic Acid,Regulatory Sequences- Nucleic Acid,Regulatory SequencesNucleic Acid,Ribonuclease P,ribosome,Rna,RNA,RNA Catalytic,RNA Ribosomal,RNA SECONDARY STRUCTURE,RNA Transfer,RNA Viral,RNA- Catalytic,RNA- Ribosomal,RNA- Transfer,RNA- Viral,RNACatalytic,RNARibosomal,RNAse,RNATransfer,RnaViral,rRNA,SECONDARY STRUCTURE,sequence,SEQUENCES,Structural,structure,Tetrahymena,Tetrahymena thermophila,tRNA,virus} } % == BibTeX quality report for leRNAMoleculesStructure2002: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{gonsalvezRNALocalizationYeast2005, title = {{{RNA}} Localization in Yeast: Moving towards a Mechanism}, author = {Gonsalvez, Graydon B and Urbinati, Carl R and Long, Roy M}, year = 2005, month = jan, journal = {Biology of the Cell / Under the Auspices of the European Cell Biology Organization}, volume = {97}, number = {1}, pages = {75–86}, issn = {0248-4900}, doi = {10.1042/BC20040066}, url = {http://www.biolcell.org/boc/097/0075/boc0970075.htm}, abstract = {RNA localization is a widely utilized strategy employed by cells to spatially restrict protein function. In Saccharomyces cerevisiae asymmetric sorting of mRNA to the bud has been reported for at least 24 mRNAs. The mechanism by which the mRNAs are trafficked to the bud, illustrated by ASH1 mRNA, involves recognition of cis-acting localization elements present in the mRNA by the RNA-binding protein, She2p. The She2p/mRNA complex subsequently associates with the myosin motor protein, Myo4p, through an adapter, She3p. This ribonucleoprotein complex is transported to the distal tip of the bud along polarized actin cables. While the mechanism by which ASH1 mRNA is anchored at the bud tip is unknown, current data point to a role for translation in this process, and the rate of translation of Ash1p during the transport phase is regulated by the cis-acting localization elements. Subcellular sorting of mRNA in yeast is not limited to the bud; certain mRNAs corresponding to nuclear-encoded mitochondrial proteins are specifically sorted to the proximity of mitochondria. Analogous to ASH1 mRNA localization, mitochondrial sorting requires cis-acting elements present in the mRNA, though trans-acting factors involved with this process remain to be identified. This review aims to discuss mechanistic details of mRNA localization in S. cerevisiae.}, pmid = {15601259}, keywords = {Cell Polarity,Cytoskeleton,DNA-Binding Proteins,Mitochondria,nosource,Protein Biosynthesis,Repressor Proteins,RNA Messenger,RNA- Messenger,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins} } % == BibTeX quality report for gonsalvezRNALocalizationYeast2005: % ? unused Journal abbr (“Biol. Cell”)

@article{hannonRNAInterference2002, title = {{{RNA}} Interference}, author = {Hannon, Gregory J}, year = 2002, month = jul, journal = {Nature}, volume = {418}, number = {6894}, eprint = {12110901}, eprinttype = {pubmed}, pages = {244–251}, issn = {0028-0836}, doi = {10.1038/418244a}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12110901 http://www.nature.com/nature/journal/v418/n6894/full/418244a.html?lang=en}, abstract = {A conserved biological response to double-stranded RNA, known variously as RNA interference (RNAi) or post-transcriptional gene silencing, mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes. RNAi has been cultivated as a means to manipulate gene expression experimentally and to probe gene function on a whole-genome scale.}, pmid = {12110901}, keywords = {Animals,Gene Silencing,Genetic Techniques,Genome,Models Genetic,Models- Genetic,nosource,RNA Double-Stranded,RNA Processing Post-Transcriptional,RNA Processing- Post-Transcriptional,RNA- Double-Stranded} }

@article{chenRNAFoldingEnergy2000, title = {{{RNA}} Folding Energy Landscapes}, author = {Chen, S J and Dill, K A}, year = 2000, month = jan, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {2}, eprint = {10639133}, eprinttype = {pubmed}, pages = {646–651}, publisher = {National Acad Sciences}, issn = {0027-8424}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10639133}, abstract = {Using a statistical mechanical treatment, we study RNA folding energy landscapes. We first validate the theory by showing that, for the RNA molecules we tested having only secondary structures, this treatment (i) predicts about the same native structures as the Zuker method, and (ii) qualitatively predicts the melting curve peaks and shoulders seen in experiments. We then predict thermodynamic folding intermediates. For one hairpin sequence, unfolding is a simple unzipping process. But for another sequence, unfolding is more complex. It involves multiple stable intermediates and a rezipping into a completely non-native conformation before unfolding. The principle that emerges, for which there is growing experimental support, is that although protein folding tends to involve highly cooperative two-state thermodynamic transitions, without detectable intermediates, the folding of RNA secondary structures may involve rugged landscapes, often with more complex intermediate states.}, keywords = {Base Sequence,Escherichia coli,Models Chemical,Molecular Sequence Data,Morpholines,Mutation,nosource,Nucleic Acid Conformation,Nucleic Acid Denaturation,Operon,Potassium Chloride,RNA,RNA Messenger,RNA Ribosomal 23S,RNA Ribosomal 5S,Temperature,Thermodynamics} } % == BibTeX quality report for chenRNAFoldingEnergy2000: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{chenRNAFoldingConformational2008, title = {{{RNA}} Folding: Conformational Statistics, Folding Kinetics, and Ion Electrostatics}, author = {Chen, Shi-Jie}, year = 2008, journal = {Annual Review of Biophysics}, volume = {37}, pages = {197–214}, publisher = {NIH Public Access}, issn = {1936-122X}, doi = {10.1146/annurev.biophys.37.032807.125957}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2473866/}, abstract = {RNA folding is a remarkably complex problem that involves ion-mediated electrostatic interaction, conformational entropy, base pairing and stacking, and noncanonical interactions. During the past decade, results from a variety of experimental and theoretical studies pointed to (a) the potential ion correlation effect in Mg2+-RNA interactions, (b) the rugged energy landscapes and multistate RNA folding kinetics even for small RNA systems such as hairpins and pseudoknots, (c) the intraloop interactions and sequence-dependent loop free energy, and (d) the strong nonadditivity of chain entropy in RNA pseudoknot and other tertiary folds. Several related issues, which have not been thoroughly resolved, require combined approaches with thermodynamic and kinetic experiments, statistical mechanical modeling, and all-atom computer simulations.}, keywords = {Binding Sites,Computer Simulation,Ions,Kinetics,Models Chemical,Models Molecular,Models- Chemical,Models- Molecular,nosource,Nucleic Acid Conformation,RNA,Static Electricity} } % == BibTeX quality report for chenRNAFoldingConformational2008: % ? unused Journal abbr (“Annu Rev Biophys”)

@article{fillmanRNADecappingOutside2005, title = {{{RNA}} Decapping inside and Outside of Processing Bodies}, author = {Fillman, Christy and {Lykke-Andersen}, Jens}, year = 2005, month = jun, journal = {Current Opinion in Cell Biology}, volume = {17}, number = {3}, pages = {326–331}, publisher = {Elsevier}, issn = {0955-0674}, doi = {10.1016/j.ceb.2005.04.002}, url = {http://linkinghub.elsevier.com/retrieve/pii/S095506740500044X}, abstract = {Decapping is a central step in eukaryotic mRNA turnover. Recent studies have identified several factors involved in catalysis and regulation of decapping. These include the following: an mRNA decapping complex containing the proteins Dcp1 and Dcp2; a nucleolar decapping enzyme, X29, involved in the degradation of U8 snoRNA and perhaps of other capped nuclear RNAs; and a decapping ‘scavenger’ enzyme, DcpS, that hydrolyzes the cap structure resulting from complete 3’-to-5’ degradation of mRNAs by the exosome. Several proteins that stimulate mRNA decapping by the Dcp1:Dcp2 complex co-localize with Dcp1 and Dcp2, together with Xrn1, a 5’-to-3’ exonuclease, to structures in the cytoplasm called processing bodies. Recent evidence suggests that the processing bodies may constitute specialized cellular compartments of mRNA turnover, which suggests that mRNA and protein localization may be integral to mRNA decay.}, keywords = {Animals,Cytoplasmic Structures,Endoribonucleases,Humans,Models Biological,Models- Biological,nosource,RNA Caps,RNA Stability,RNA-Binding Proteins} } % == BibTeX quality report for fillmanRNADecappingOutside2005: % ? unused Journal abbr (“Curr. Opin. Cell Biol”)

@article{sunoharaRibosomeStallingTranslation2004, title = {Ribosome Stalling during Translation Elongation Induces Cleavage of {{mRNA}} Being Translated in {{Escherichia}} Coli}, author = {Sunohara, Takafumi and Jojima, Kaoru and Tagami, Hideaki and Inada, Toshifumi and Aiba, Hiroji}, year = 2004, month = apr, journal = {The Journal of Biological Chemistry}, volume = {279}, number = {15}, pages = {15368–15375}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.M312805200}, url = {http://www.jbc.org/content/279/15/15368.short}, abstract = {Recently, it has been found that ribosome pausing at stop codons caused by certain nascent peptides induces cleavage of mRNA in Escherichia coli cells (1, 2). The question we addressed in the present study is whether mRNA cleavage occurs when translation elongation is prevented. We focused on a specific peptide sequence (AS17), derived from SecM, that is known to cause elongation arrest. When the crp-crr fusion gene encoding CRP-AS17-IIA(Glc) was expressed, cAMP receptor protein (CRP) proteins truncated around the arrest sequence were efficiently produced, and they were tagged by the transfer-messenger RNA (tmRNA) system. Northern blot analysis revealed that both truncated upstream crp and downstream crr mRNAs were generated along with reduced amounts of the full-length crp-crr mRNA. The truncated crp mRNA dramatically decreased in the presence of tmRNA due to rapid degradation. The 3’ ends of truncated crp mRNA correspond well to the C termini of the truncated CRP proteins. We conclude that ribosome stalling by the arrest sequence induces mRNA cleavage near the arrest point, resulting in nonstop mRNAs that are recognized by tmRNA. We propose that the mRNA cleavage induced by ribosome stalling acts in concert with the tmRNA system as a way to ensure quality control of protein synthesis and possibly to regulate the expression of certain genes.}, keywords = {Adenosine Triphosphatases,Amino Acid Sequence,Bacterial Proteins,Base Sequence,Blotting Northern,Blotting Western,Cell Division,Codon,Codon Terminator,Cyclic AMP,Escherichia coli,Mass Spectrometry,Membrane Transport Proteins,Models Biological,Models Genetic,Molecular Sequence Data,nosource,Peptides,Plasmids,Protein Biosynthesis,Protein Structure Tertiary,Recombinant Fusion Proteins,Ribosomes,RNA,RNA Messenger} } % == BibTeX quality report for sunoharaRibosomeStallingTranslation2004: % ? unused Journal abbr (“J. Biol. Chem”)

@article{greenRibosomesTranslation1997, title = {Ribosomes and Translation.}, author = {Green, R and Noller, H F}, year = 1997, journal = {Annual Review of Biochemistry}, volume = {66:679-716.}, eprint = {9242921}, eprinttype = {pubmed}, pages = {679–716}, issn = {0066-4154}, doi = {10.1146/annurev.biochem.66.1.679}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9242921}, abstract = {The ribosome is a large multifunctional complex composed of both RNA and proteins. Biophysical methods are yielding low-resolution structures of the overall architecture of ribosomes, and high-resolution structures of individual proteins and segments of rRNA. Accumulating evidence suggests that the ribosomal RNAs play central roles in the critical ribosomal functions of tRNA selection and binding, translocation, and peptidyl transferase. Biochemical and genetic approaches have identified specific functional interactions involving conserved nucleotides in 16S and 23S rRNA. The results obtained by these quite different approaches have begun to converge and promise to yield an unprecedented view of the mechanism of translation in the coming years.}, pmid = {9242921}, keywords = {animal,Animals,BINDING,chemistry,COMPLEX,COMPLEXES,Fidelity,Genetic,human,Humans,MECHANISM,Methods,nosource,Nucleotides,peptidyl transferase,physiology,protein,Protein Biosynthesis,Proteins,Review,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,rRNA,structure,Structure-Activity Relationship,translation,Translation-Genetic,TranslationGenetic,translocation,tRNA} } % == BibTeX quality report for greenRibosomesTranslation1997: % ? unused Journal abbr (“Annu. Rev. Biochem”)

@article{nielsenRIBOSOMEINACTIVATINGPROTEINSPlant2001, title = {{{RIBOSOME-INACTIVATING PROTEINS}}: {{A Plant Perspective}}}, author = {Nielsen, Kirsten and Boston, Rebecca S}, year = 2001, month = jun, journal = {Annual Review of Plant Physiology and Plant Molecular Biology}, volume = {52}, number = {1}, pages = {785–816}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, issn = {1040-2519}, doi = {10.1146/annurev.arplant.52.1.785}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.arplant.52.1.785}, abstract = {Ribosome-inactivating proteins (RIPs) are toxic N-glycosidases that depurinate the universally conserved alpha-sarcin loop of large rRNAs. This depurination inactivates the ribosome, thereby blocking its further participation in protein synthesis. RIPs are widely distributed among different plant genera and within a variety of different tissues. Recent work has shown that enzymatic activity of at least some RIPs is not limited to site-specific action on the large rRNAs of ribosomes but extends to depurination and even nucleic acid scission of other targets. Characterization of the physiological effects of RIPs on mammalian cells has implicated apoptotic pathways. For plants, RIPs have been linked to defense by antiviral, antifungal, and insecticidal properties demonstrated in vitro and in transgenic plants. How these effects are brought about, however, remains unresolved. At the least, these results, together with others summarized here, point to a complex biological role. With genetic, genomic, molecular, and structural tools now available for integrating different experimental approaches, we should further our understanding of these multifunctional proteins and their physiological functions in plants.}, keywords = {nosource} } % == BibTeX quality report for nielsenRIBOSOMEINACTIVATINGPROTEINSPlant2001: % ? Title looks like it was stored in title-case in Zotero % ? unused Journal abbr (“Annu. Rev. Plant Physiol. Plant Mol. Biol”)

@article{lindsleyRibosomeBypassingElicited2003, title = {Ribosome Bypassing Elicited by {{tRNA}} Depletion}, author = {Lindsley, Dale and Gallant, Jonathan and Guarneros, Gabriel}, year = 2003, month = jun, journal = {Molecular Microbiology}, volume = {48}, number = {5}, pages = {1267–1274}, publisher = {Wiley Online Library}, issn = {0950-382X}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2003.03514.x/full}, abstract = {Ribosome bypassing refers to the ability of the ribosome::peptidyl-tRNA complex to slide down the message without translation to a site several or dozens of nucleotides downstream and resume protein chain elongation there. The product is an isoform of a protein with a ‘coding’ gap corresponding to the region of the message which was bypassed. Previous work showed that ribosome bypassing was strongly stimulated at ‘hungry’ codons calling for a tRNA whose aminoacylation was limited. We have now used the ‘minigene’ phenomenon to ascertain whether depletion of the pool of specific isoacceptors has a similar effect. High level expression of plasmid-borne minigenes results in the sequestration as peptidyl-tRNA of tRNA cognate to the last triplet of the minigene, thereby limiting protein synthesis for lack of the tRNA in question. We find that induction of a minigene ending in AUA stimulates bypassing at an AUA codon, but not in a control sequence with AGA at the test position; induction of a minigene ending in AGA stimulates bypassing at the latter but not the former. Induction of the AUA minigene also stimulates both leftward and rightward frameshifting at ‘shifty’ sequences containing an AUA codon. The normal, background frequency of bypassing at an AUA codon is markedly reduced by increasing the cellular level of the tRNA which reads the codon. Thus, the frequency of bypassing can be increased or decreased by lowering or raising the concentration of a relevant tRNA isoacceptor. These observations suggest that the occurrence of ribosome bypassing reflects the length of the pause at a given codon.}, keywords = {Amino Acid Sequence,Base Sequence,Codon,Escherichia coli,Frameshifting Ribosomal,Genes,Molecular Sequence Data,nosource,Plasmids,Ribosomes,RNA Transfer} } % == BibTeX quality report for lindsleyRibosomeBypassingElicited2003: % ? unused Journal abbr (“Mol. Microbiol”)

@article{cukrasRibosomalProteinsS122003, title = {Ribosomal Proteins {{S12}} and {{S13}} Function as Control Elements for Translocation of the {{mRNA}}:{{tRNA}} Complex.}, author = {Cukras, Anthony R and Southworth, Daniel R and Brunelle, Julie L and Culver, Gloria M and Green, Rachel}, year = 2003, month = aug, journal = {Molecular Cell}, volume = {12}, number = {2}, pages = {321–328}, publisher = {Elsevier}, issn = {1097-2765}, doi = {10.1016/S1097-2765(03)00275-2}, url = {⬚http://download.molecule.org/pdfs/1097-2765/PIIS1097276503002752.pdf⬚⬚⬚ ⬚⬚}, abstract = {Translocation of the mRNA:tRNA complex through the ⬚ribosome⬚ is promoted by elongation factor G (EF-G) during the translation cycle. Previous studies established that modification of ribosomal proteins with thiol-specific reagents promotes this event in the absence of EF-G. Here we identify two small subunit interface proteins S12 and S13 that are essential for maintenance of a pretranslocation state. Omission of these proteins using in vitro reconstitution procedures yields ribosomal particles that translate in the absence of enzymatic factors. Conversely, replacement of cysteine residues in these two proteins yields ribosomal particles that are refractive to stimulation with thiol-modifying reagents. These data support a model where S12 and S13 function as control elements for the more ancient rRNA- and tRNA-driven movements of translocation.}, keywords = {Biological Transport,COMPLEX,COMPLEXES,Cysteine,EF-G,ELEMENTS,elongation,ELONGATION-FACTOR-G,Escherichia coli,Escherichia coli Proteins,IDENTIFY,In Vitro,IN-VITRO,interface,MODEL,Models Molecular,modification,Movement,Mutagenesis Site-Directed,nosource,PARTICLES,Peptide Elongation Factor G,Phenylalanine,protein,Protein Binding,Protein Structure Secondary,Proteins,Recombinant Proteins,RECONSTITUTION,RESIDUES,Ribosomal Proteins,ribosome,RNA Messenger,RNA Transfer,rRNA,SUBUNIT,Support,Time Factors,translation,translocation} } % == BibTeX quality report for cukrasRibosomalProteinsS122003: % ? unused Journal abbr (“Mol. Cell”)

@article{wilsonRibosomalProteinsSpotlight2005, title = {Ribosomal Proteins in the Spotlight}, author = {Wilson, Daniel N and Nierhaus, Knud H}, year = {2005 Sep-Oct}, journal = {Critical Reviews in Biochemistry and Molecular Biology}, volume = {40}, number = {5}, pages = {243–267}, publisher = {Informa UK Ltd UK}, issn = {1040-9238}, doi = {10.1080/10409230500256523}, url = {http://informahealthcare.com/doi/abs/10.1080/10409230500256523}, abstract = {The assignment of specific ribosomal functions to individual ribosomal proteins is difficult due to the enormous cooperativity of the ribosome; however, important roles for distinct ribosomal proteins are becoming evident. Although rRNA has a major role in certain aspects of ribosomal function, such as decoding and peptidyl-transferase activity, ribosomal proteins are nevertheless essential for the assembly and optimal functioning of the ribosome. This is particularly true in the context of interactions at the entrance pore for mRNA, for the translation-factor binding site and at the tunnel exit, where both chaperones and complexes associated with protein transport through membranes bind.}, keywords = {0,analysis,Animals,assembly,ASSIGNMENT,BINDING,BINDING-SITE,biosynthesis,chaperone,chemistry,COMPLEX,COMPLEXES,decoding,Evolution Molecular,EvolutionMolecular,Germany,Humans,La,metabolism,Models Molecular,ModelsMolecular,Molecular Chaperones,mRNA,nosource,peptidyl transferase,PEPTIDYL-TRANSFERASE,Peptidyltransferase,physiology,protein,Protein Transport,Proteins,Review,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Rna,RNA Ribosomal,RNARibosomal,rRNA,SITE,TRANSPORT} } % == BibTeX quality report for wilsonRibosomalProteinsSpotlight2005: % ? unused Journal abbr (“Crit. Rev. Biochem. Mol. Biol”)

@article{serganovRibosomalProteinS152003, title = {Ribosomal Protein {{S15}} Represses Its Own Translation via Adaptation of an {{rRNA-like}} Fold within Its {{mRNA}}}, author = {Serganov, Alexander and Polonskaia, Ann and Ehresmann, Bernard and Ehresmann, Chantal and Patel, Dinshaw J}, year = 2003, month = apr, journal = {The EMBO Journal}, volume = {22}, number = {8}, pages = {1898–1908}, publisher = {Nature Publishing Group}, issn = {0261-4189}, doi = {10.1093/emboj/cdg170}, url = {http://www.nature.com/emboj/journal/v22/n8/abs/7595079a.html}, abstract = {The 16S rRNA-binding ribosomal protein S15 is a key component in the assembly of the small ribosomal subunit in bacteria. We have shown that S15 from the extreme thermophile Thermus thermophilus represses the translation of its own mRNA in vitro, by interacting with the leader segment of its mRNA. The S15 mRNA-binding site was characterized by footprinting experiments, deletion analysis and site-directed mutagenesis. S15 binding triggers a conformational rearrangement of its mRNA into a fold that mimics the conserved three-way junction of the S15 rRNA-binding site. This conformational change masks the ribosome entry site, as demonstrated by direct competition between the ribosomal subunit and S15 for mRNA binding. A comparison of the T.thermophilus and Escherichia coli regulation systems reveals that the two regulatory mRNA targets do not share any similarity and that the mechanisms of translational inhibition are different. Our results highlight an astonishing plasticity of mRNA in its ability to adapt to evolutionary constraints, that contrasts with the extreme conservation of the rRNA-binding site.}, keywords = {Bacterial Proteins,Binding Sites,nosource,Nucleic Acid Conformation,Protein Binding,Protein Biosynthesis,Protein Footprinting,Repressor Proteins,Ribosomal Proteins,Ribosomes,RNA Messenger,Thermus thermophilus} } % == BibTeX quality report for serganovRibosomalProteinS152003: % ? unused Journal abbr (“EMBO J”)

@article{meskauskasRibosomalProteinL52001, title = {Ribosomal Protein {{L5}} Helps Anchor Peptidyl-{{tRNA}} to the {{P-site}} in {{Saccharomyces}} Cerevisiae}, author = {Meskauskas, A and Dinman, J D}, year = 2001, month = aug, journal = {RNA (New York, N.Y.)}, volume = {7}, number = {8}, pages = {1084–1096}, publisher = {Cambridge Univ Press}, issn = {1355-8382}, doi = {10.1017/S1355838201001480}, url = {http://journals.cambridge.org/abstract_S1355838201001480}, abstract = {Our previous demonstration that mutants of 5S rRNA called mof9 can specifically alter efficiencies of programmed ribosomal frameshifting (PRF) suggested a role for this ubiquitous molecule in the maintenance of translational reading frame, though the repetitive nature of the 5S rDNA gene ({\(>\)}100 copies/cell) inhibited more detailed analyses. However, given the known interactions between 5S rRNA and ribosomal protein L5 (previously called L1 or YL3) encoded by an essential, single-copy gene, we monitored the effects of a series of well-defined rpl5 mutants on PRF and virus propagation. Consistent with the mof9 results, we find that the rpl5 mutants promoted increased frameshifting efficiencies in both the -1 and +1 directions, and conferred defects in the ability of cells to propagate two endogenous viruses. Biochemical analyses demonstrated that mutant ribosomes had decreased affinities for peptidyl-tRNA. Pharmacological studies showed that sparsomycin, a peptidyltransferase inhibitor that specifically increases the binding of peptidyl-tRNA with ribosomes, was antagonistic to the frameshifting defects of the most severe mutant, and the extent of sparsomycin resistance correlated with the severity of the frameshifting defects in all of the mutants. These results provide biochemical and physiological evidence that one function of L5 is to anchor peptidyl-tRNA to the P-site. A model is presented describing how decreased affinity of ribosomes for peptidyl-tRNA can affect both -1 and +1 frameshifting, and for the effects of sparsomycin.}, keywords = {+1 frameshifting,0,5S rRNA,Alleles,anisomycin,Anisomycin,antagonists & inhibitors,antibiotic,antibiotics,Antibiotics Antineoplastic,Antibiotics- Antineoplastic,AntibioticsAntineoplastic,BINDING,chemistry,Dose-Response Relationship Drug,Dose-Response Relationship- Drug,Dose-Response RelationshipDrug,efficiency,Frameshift Mutation,Frameshifting,gene,Genetic,genetics,L1,L5,La,metabolism,microbiology,Mutation,nosource,P-SITE,Peptidyl Transferases,Peptidyltransferase,pharmacology,Phenotype,Plasmids,protein,Protein Biosynthesis,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,Proteins,rDNA,Retroelements,ribosomal frameshifting,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNA Transfer,RNA- Transfer,RNATransfer,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sparsomycin,Sparsomycin,supportu.s.gov’tp.h.s.,Time Factors,TranslationGenetic,virus} } % == BibTeX quality report for meskauskasRibosomalProteinL52001: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA.”)

@article{somogyiRibosomalPausingTranslation1993, title = {Ribosomal Pausing during Translation of an {{RNA}} Pseudoknot.}, author = {Somogyi, P and Jenner, A J and Brierley, I and Inglis, S C}, year = 1993, month = nov, journal = {Molecular and Cellular Biology}, volume = {13}, number = {11}, pages = {6931–6940}, issn = {0270-7306}, url = {http://mcb.asm.org/cgi/content/abstract/13/11/6931}, abstract = {The genomic RNA of the coronavirus infectious bronchitis virus contains an efficient ribosomal frameshift signal which comprises a heptanucleotide slippery sequence followed by an RNA pseudoknot structure. The presence of the pseudoknot is essential for high-efficiency frameshifting, and it has been suggested that its function may be to slow or stall the ribosome in the vicinity of the slippery sequence. To test this possibility, we have studied translational elongation in vitro on mRNAs engineered to contain a well-defined pseudoknot-forming sequence. Insertion of the pseudoknot at a specific location within the influenza virus PB1 mRNA resulted in the production of a new translational intermediate corresponding to the size expected for ribosomal arrest at the pseudoknot. The appearance of this protein was transient, indicating that it was a true paused intermediate rather than a dead-end product, and mutational analysis confirmed that its appearance was dependent on the presence of a pseudoknot structure within the mRNA. These observations raise the possibility that a pause is required for the frameshift process. The extent of pausing at the pseudoknot was compared with that observed at a sequence designed to form a simple stem-loop structure with the same base pairs as the pseudoknot. This structure proved to be a less effective barrier to the elongating ribosome than the pseudoknot and in addition was unable to direct efficient ribosomal frameshifting, as would be expected if pausing plays an important role in frameshifting. However, the stem-loop was still able to induce significant pausing, and so this effect alone may be insufficient to account for the contribution of the pseudoknot to frameshifting.}, pmid = {8413285}, keywords = {Animals,Base Composition,Base Sequence,DNA Primers,Frameshift Mutation,Frameshifting,Infectious bronchitis virus,Kinetics,Molecular Sequence Data,Multiple DOI,Mutagenesis Site-Directed,nonfile,nosource,Nucleic Acid Conformation,Open Reading Frames,Orthomyxoviridae,pausing,Plasmids,Protein Biosynthesis,pseudoknot,Rabbits,Restriction Mapping,Reticulocytes,Ribosomes,Rna,RNA Messenger,RNA PSEUDOKNOT,RNA Viral,Transcription Genetic,translation,virus} } % == BibTeX quality report for somogyiRibosomalPausingTranslation1993: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{kontosRibosomalPausingFrameshifter2001a, title = {Ribosomal Pausing at a Frameshifter {{RNA}} Pseudoknot Is Sensitive to Reading Phase but Shows Little Correlation with Frameshift Efficiency}, author = {Kontos, H and Napthine, S and Brierley, I}, year = 2001, month = dec, journal = {Molecular and Cellular Biology}, volume = {21}, number = {24}, eprint = {11713298}, eprinttype = {pubmed}, pages = {8657–8670}, issn = {0270-7306}, doi = {10.1128/MCB.21.24.8657-8670.2001}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11713298}, abstract = {Here we investigated ribosomal pausing at sites of programmed -1 ribosomal frameshifting, using translational elongation and ribosome heelprint assays. The site of pausing at the frameshift signal of infectious bronchitis virus (IBV) was determined and was consistent with an RNA pseudoknot-induced pause that placed the ribosomal P- and A-sites over the slippery sequence. Similarly, pausing at the simian retrovirus 1 gag/pol signal, which contains a different kind of frameshifter pseudoknot, also placed the ribosome over the slippery sequence, supporting a role for pausing in frameshifting. However, a simple correlation between pausing and frameshifting was lacking. Firstly, a stem-loop structure closely related to the IBV pseudoknot, although unable to stimulate efficient frameshifting, paused ribosomes to a similar extent and at the same place on the mRNA as a parental pseudoknot. Secondly, an identical pausing pattern was induced by two pseudoknots differing only by a single loop 2 nucleotide yet with different functionalities in frameshifting. The final observation arose from an assessment of the impact of reading phase on pausing. Given that ribosomes advance in triplet fashion, we tested whether the reading frame in which ribosomes encounter an RNA structure (the reading phase) would influence pausing. We found that the reading phase did influence pausing but unexpectedly, the mRNA with the pseudoknot in the phase which gave the least pausing was found to promote frameshifting more efficiently than the other variants. Overall, these experiments support the view that pausing alone is insufficient to mediate frameshifting and additional events are required. The phase dependence of pausing may be indicative of an activity in the ribosome that requires an optimal contact with mRNA secondary structures for efficient unwinding.}, pmid = {11713298}, keywords = {0,animal,Animals,assays,Base Sequence,chemistry,efficiency,elongation,frameshift,Frameshift Mutation,Frameshifting,Infectious bronchitis virus,La,metabolism,Molecular Sequence Data,mRNA,Mutagenesis Site-Directed,MutagenesisSite-Directed,nosource,Nucleic Acid Conformation,pathology,pausing,physiology,Plasmids,Protein Biosynthesis,pseudoknot,Rabbits,Reticulocytes,retrovirus,ribosomal frameshifting,ribosome,Ribosomes,Rna,RNA,RNA Messenger,RNA PSEUDOKNOT,RNAMessenger,sequence,SIGNAL,structure,Support,supportnon-u.s.gov’t,Time Factors,TranslationGenetic,virology,virus} } % == BibTeX quality report for kontosRibosomalPausingFrameshifter2001a: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{brierleyRibosomalFrameshiftingViral1995a, title = {Ribosomal Frameshifting Viral {{RNAs}}}, author = {Brierley, I}, year = 1995, month = aug, journal = {The Journal of General Virology}, volume = {76 ( Pt 8)}, eprint = {7636469}, eprinttype = {pubmed}, pages = {1885–1892}, issn = {0022-1317}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7636469}, pmid = {7636469}, keywords = {Animals,Base Sequence,Humans,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Protein Biosynthesis,Reading Frames,Ribosomes,RNA Viral,RNA Viruses} } % == BibTeX quality report for brierleyRibosomalFrameshiftingViral1995a: % ? unused Journal abbr (“J. Gen. Virol”)

@article{dinmanRibosomalFrameshiftingEfficiency1992, title = {Ribosomal Frameshifting Efficiency and Gag/Gag-Pol Ratio Are Critical for Yeast {{M1}} Double-Stranded {{RNA}} Virus Propagation.}, author = {Dinman, J D and Wickner, R B}, year = 1992, month = jun, journal = {Journal of Virology}, volume = {66}, number = {6}, pages = {3669–3676}, publisher = {Am Soc Microbiol}, issn = {0022-538X}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=241150&tool=pmcentrez&rendertype=abstract http://www.ncbi.nlm.nih.gov/pubmed/1583726 http://jvi.asm.org/cgi/content/abstract/66/6/3669}, abstract = {About 1.9% of ribosomes translating the gag open reading frame of the yeast L-A double-stranded RNA virus positive strand undergo a -1 frameshift and continue translating in the pol open reading frame to make a 170-kDa gag-pol fusion protein. The importance of frameshifting efficiency for viral propagation was tested in a system where the M1 (killer toxin-encoding) satellite RNA is supported by a full-length L-A cDNA clone. Either increasing or decreasing the frameshift efficiency more than twofold by alterations in the slippery site disrupted viral propagation. A threefold increase caused by a chromosomal mutation, hsh1 (high shifter), had the same effect. Substituting a +1 ribosomal frameshift site from Ty1 with the correct efficiency also allowed support of M1 propagation. The normal -1 frameshift efficiency is similar to the observed molar ratio in viral particles of the 170-kDa gag-pol protein to the 70-kDa gag gene product, the major coat protein. The results are interpreted in terms of a packaging model for L-A.}, pmid = {1583726}, keywords = {Amino Acyl,Amino Acyl: metabolism,Base Sequence,Double-Stranded,Double-Stranded: metabolism,Frameshift Mutation,Frameshift Mutation: drug effects,Fungal Proteins,Fungal Proteins: pharmacology,Fusion Proteins,Fusion Proteins gag-pol,Fusion Proteins- gag-pol,gag,gag-pol,gag-pol: metabolism,gag: metabolism,Gene Products,Gene Products gag,Gene Products- gag,Genetic,Host-Parasite Interactions,Killer Factors,Killer Factors Yeast,Killer Factors- Yeast,Models,Models Genetic,Models- Genetic,Molecular Sequence Data,Mutation,nosource,Nucleic Acid Conformation,Proteins,Proteins: pharmacology,Ribosomes,Ribosomes: metabolism,RNA,RNA Double-Stranded,RNA Transfer Amino Acyl,RNA Viral,RNA Viruses,RNA Viruses: drug effects,RNA Viruses: growth & development,RNA- Double-Stranded,RNA- Transfer- Amino Acyl,RNA- Viral,Saccharomyces cerevisiae,Saccharomyces cerevisiae: metabolism,Transfer,Viral,Viral: metabolism,Virus Replication,Yeast} } % == BibTeX quality report for dinmanRibosomalFrameshiftingEfficiency1992: % ? unused Journal abbr (“J. Virol”)

@article{mejlhedeRibosomal1Frameshifting1999, title = {Ribosomal -1 Frameshifting during Decoding of {{Bacillus}} Subtilis Cdd Occurs at the Sequence {{CGA AAG}}}, author = {Mejlhede, N and Atkins, J F and Neuhard, J}, year = 1999, month = may, journal = {Journal of Bacteriology}, volume = {181}, number = {9}, eprint = {10217788}, eprinttype = {pubmed}, pages = {2930–2937}, issn = {0021-9193}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10217788}, abstract = {During translation of the Bacillus subtilis cdd gene, encoding cytidine deaminase (CDA), a ribosomal -1 frameshift occurs near the stop codon, resulting in a CDA subunit extended by 13 amino acids. The frequency of the frameshift is approximately 16%, and it occurs both when the cdd gene is expressed from a multicopy plasmid in Escherichia coli and when it is expressed from the chromosomal copy in B. subtilis. As a result, heterotetrameric forms of the enzyme are formed in vivo along with the dominant homotetrameric species. The different forms have approximately the same specific activity. The cdd gene was cloned in pUC19 such that the lacZ’ gene of the vector followed the cdd gene in the -1 reading frame immediately after the cdd stop codon. By using site-directed mutagenesis of the cdd-lacZ’ fusion, it was shown that frameshifting occurred at the sequence CGA AAG, 9 bp upstream of the in-frame cdd stop codon, and that it was stimulated by a Shine-Dalgarno-like sequence located 14 bp upstream of the shift site. The possible function of this frameshift in gene expression is discussed.}, pmid = {10217788}, keywords = {Amino Acid Sequence,Bacillus subtilis,Base Sequence,Codon Terminator,Codon- Terminator,Cytidine Deaminase,DNA Mutational Analysis,Frameshifting Ribosomal,Frameshifting- Ribosomal,Isoenzymes,Molecular Sequence Data,Mutagenesis Site-Directed,Mutagenesis- Site-Directed,nosource,RNA Messenger,RNA- Messenger} } % == BibTeX quality report for mejlhedeRibosomal1Frameshifting1999: % ? unused Journal abbr (“J. Bacteriol”)

@article{feinbergRibose2hydroxylGroups2006, title = {Ribose 2’-Hydroxyl Groups in the 5’ Strand of the Acceptor Arm of {{P-site tRNA}} Are Not Essential for {{EF-G}} Catalyzed Translocation}, author = {Feinberg, Jason S and Joseph, Simpson}, year = 2006, month = apr, journal = {RNA (New York, N.Y.)}, volume = {12}, number = {4}, pages = {580–588}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, doi = {10.1261/rna.2290706}, url = {http://rnajournal.cshlp.org/content/12/4/580.short}, abstract = {The coupled movement of tRNA-mRNA complex through the ribosome is a fundamental step during the protein elongation process. We demonstrate that the ribosome will translocate a P-site-bound tRNA(Met) with a break in the phosphodiester backbone between positions 17 and 18 in the D-loop. Crystallographic data showed that the acceptor arms of P- and E-site tRNA interact extensively with the ribosomal large subunit. Therefore, we used this fragmented P-site-bound tRNA(Met) to investigate the contributions of single 2’-hydroxyl groups in the 5’ strand of the acceptor arm for translocation into the ribosomal E-site. EF-G-dependent translocation of the tRNAs was monitored using a toeprinting assay and a fluorescence-based rapid kinetic method. Surprisingly, our results show that none of the 2’-hydroxyl groups in the 5’ strand of the acceptor arm of P-site-bound tRNA(Met) between positions 1-17 play a critical role during translocation. This suggests that either these 2’-hydroxyl groups are not important for translocation or they are redundant and the three-dimensional shape of the P-site tRNA is more important for translocation.}, keywords = {Biological Transport,Catalysis,ef-g,Electrophoresis Polyacrylamide Gel,Fluorescence,Kinetics,mechanism,mrna,nosource,Peptide Elongation Factor G,Ribose,ribosome,RNA Transfer Met,translocation,trna} } % == BibTeX quality report for feinbergRibose2hydroxylGroups2006: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{williamsResumingTranslationTmRNA1999, title = {Resuming Translation on {{tmRNA}}: A Unique Mode of Determining a Reading Frame}, author = {Williams, K P and Martindale, K A and Bartel, D P}, year = 1999, month = oct, journal = {The EMBO Journal}, volume = {18}, number = {19}, eprint = {10508174}, eprinttype = {pubmed}, pages = {5423–5433}, publisher = {Nature Publishing Group}, issn = {0261-4189}, doi = {10.1093/emboj/18.19.5423}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10508174 http://www.nature.com/emboj/journal/v18/n19/abs/7591949a.html}, abstract = {The bacterial ribosome switches from an mRNA lacking an in-frame stop codon and resumes translation on a specialized RNA known as tmRNA, SsrA or 10Sa RNA. We find that the ribosome can reach and use the extreme 3’ terminal codon of the defective mRNA prior to switching. The first triplet to be translated in tmRNA (the resume codon) is determined at two levels: distant elements in tmRNA restrict resume codon choice to a narrow window and local upstream elements provide precision. Insights from a randomization-selection experiment secure the alignment of tmRNA sequences from diverse species. The triplet UA(A/G) (normally recognized as a stop codon by release factor-1) is strongly conserved two nucleotides upstream of the resume codon. The central adenosine of this triplet is essential for tmRNA activity. The reading frame of tmRNA is determined differently from all other known reading frames in that the first translated codon is not specified by a particular tRNA anticodon.}, keywords = {Amino Acid Sequence,Base Sequence,Codon,Escherichia coli,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Open Reading Frames,Phylogeny,Protein Biosynthesis,RNA Bacterial,RNA- Bacterial} } % == BibTeX quality report for williamsResumingTranslationTmRNA1999: % ? unused Journal abbr (“EMBO J”)

@article{goldbachResistanceMechanismsPlant2003, title = {Resistance Mechanisms to Plant Viruses: An Overview}, author = {Goldbach, Rob and Bucher, Etienne and Prins, Marcel}, year = 2003, month = apr, journal = {Virus Research}, volume = {92}, number = {2}, pages = {207–212}, publisher = {Elsevier}, issn = {0168-1702}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0168170202003532}, abstract = {To obtain virus-resistant host plants, a range of operational strategies can be followed nowadays. While for decades plant breeders have been able to introduce natural resistance genes in susceptible genotypes without knowing precisely what these resistance traits were, currently a growing number of (mostly) dominant resistance genes have been cloned and analyzed. This has led not only to a better understanding of the plant’s natural defence systems, but also opened the way to use these genes beyond species borders. Besides using natural resistance traits, also several novel, “engineered” forms of virus resistance have been developed over the past 15 years. The first successes were obtained embarking from the principle of pathogen-derived resistance (PDR) by transforming host plants with viral genes or sequences with the purpose to block a specific step during virus multiplication in the plant. As an unforeseen spin-off of these investments, the phenomenon of post-translational gene silencing (PTGS) was discovered, which to date is by far the most successful way to engineer resistance. It is generally believed that PTGS reflects a natural defence system of the plant, and part of the hypothesized components required for PTGS have been identified. As counteracting strategy, and confirming PTGS to be a natural phenomenon, a considerable number of viruses have acquired gene functions by which they can suppress PTGS. In addition to PDR and PTGS, further strategies for engineered virus resistance have been explored, including the use of pokeweed antiviral protein (PAP), 2’,5’-oligoadenylate synthetase and “plantibodies”. This paper will give a brief overview of the major strategies that have become operational during the past 10 years.}, keywords = {Gene Silencing,nosource,Plant Diseases,Plant Proteins,Plant Viruses,Plants,Plants Genetically Modified,RNA Interference,Transcription Genetic,Viral Proteins} } % == BibTeX quality report for goldbachResistanceMechanismsPlant2003: % ? unused Journal abbr (“Virus Res”)

@article{namyReprogrammedGeneticDecoding2004, title = {Reprogrammed Genetic Decoding in Cellular Gene Expression}, author = {Namy, Olivier and Rousset, Jean-Pierre and Napthine, Sawsan and Brierley, Ian}, year = 2004, month = jan, journal = {Molecular Cell}, volume = {13}, number = {2}, pages = {157–168}, publisher = {Elsevier}, issn = {1097-2765}, doi = {10.1016/S1097-2765(04)00031-0}, url = {http://www.sciencedirect.com/science/article/pii/S1097276504000310 http://linkinghub.elsevier.com/retrieve/pii/S1097276504000310}, abstract = {Reprogrammed genetic decoding signals in mRNAs productively overwrite the normal decoding rules of translation. These “recoding” signals are associated with sites of programmed ribosomal frameshifting, hopping, termination codon suppression, and the incorporation of the unusual amino acids selenocysteine and pyrrolysine. This review summarizes current knowledge of the structure and function of recoding signals in cellular genes, the biological importance of recoding in gene regulation, and ways to identify new recoded genes.}, keywords = {ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,Animals,Base Sequence,Codon,decoding,Escherichia coli,expression,Frameshifting,gene,Gene Expression,gene regulation,GENE-EXPRESSION,Genes,Genetic,hopping,Humans,IDENTIFY,La,Lysine,Molecular Sequence Data,mRNA,nosource,pathology,Protein Biosynthesis,recoding,regulation,Review,ribosomal frameshifting,RNA Messenger,RULES,Saccharomyces cerevisiae,Selenocysteine,SIGNAL,SITE,SITES,structure,suppression,termination,TERMINATION CODON,TERMINATION-CODON,translation,virology} } % == BibTeX quality report for namyReprogrammedGeneticDecoding2004: % ? unused Journal abbr (“Mol. Cell”)

@article{eckerleReplicationRNASegments2002, title = {Replication of the {{RNA}} Segments of a Bipartite Viral Genome Is Coordinated by a Transactivating Subgenomic {{RNA}}}, author = {Eckerle, Lance D and Ball, L Andrew}, year = 2002, month = apr, journal = {Virology}, volume = {296}, number = {1}, pages = {165–176}, publisher = {Elsevier}, issn = {0042-6822}, doi = {10.1006/viro.2002.1377}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0042682202913772}, abstract = {The insect nodavirus Flock house virus (FHV) has a small genome divided between two segments of positive-sense RNA, RNA1 and RNA2. RNA1 encodes the RNA-dependent RNA polymerase (RdRp) catalytic subunit and templates the synthesis of a subgenomic RNA (RNA3) that encodes two small nonstructural proteins. Replication of RNA2, which encodes a precursor to the viral capsid proteins, suppresses RNA3 synthesis. Here we report that RNA1 mutants deficient in RNA3 synthesis failed to support RNA2 replication. This effect was not caused by alterations in the RdRp catalytic subunit nor by a lack of the proteins encoded by RNA3. Furthermore, RNA3 supplied in trans from an exogenous source restored RNA2 replication. These data indicate that RNA3 transactivates the replication of RNA2, a novel property for a viral RNA. We propose that the RNA3 dependence of RNA2 replication serves to coordinate replication of the FHV genome segments.}, keywords = {Animals,Capsid,Cell Line,Cricetinae,Genome Viral,Mutation,Nodaviridae,nosource,Protein Precursors,Replicon,RNA Replicase,RNA Viral,Transcriptional Activation,Viral Nonstructural Proteins} }

@article{ballReplicationGenomicRNA1994, title = {Replication of the Genomic {{RNA}} of a Positive-Strand {{RNA}} Animal Virus from Negative-Sense Transcripts}, author = {Ball, L A}, year = 1994, month = dec, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {26}, pages = {12443–12447}, publisher = {National Acad Sciences}, issn = {0027-8424}, url = {http://www.pnas.org/content/91/26/12443.short}, abstract = {Studies of RNA replication among the positive-strand RNA animal viruses have been hindered by the apparent inability of their RNA-dependent RNA polymerases to initiate replication on the corresponding negative-sense RNAs. However, here I report that in the case of the nodavirus flock house virus (FHV), which has a bipartite positive-sense RNA genome, the viral RNA replicase can replicate a negative-sense transcript of the genome segment that encodes the viral capsid proteins. For this work, the FHV replication cycle was experimentally reconstructed in baby hamster kidney cells that were transfected with specialized transcription plasmids designed to direct the synthesis of RNAs which corresponded closely to the two genome segments of FHV. The RNA replicase encoded by the larger genome segment could utilize either the positive or the negative strand of the smaller segment as a template, and it catalyzed RNA replication to produce similar RNA products in the two situations. Surprisingly, studies of the nucleotide sequences that were required for replication showed that the 3’ end of the negative-strand RNA contained only a minimal cis-acting signal. The success of these experiments will facilitate further studies of the cis- and trans-acting factors involved in the recognition and replication of negative-sense RNA in this system.}, keywords = {Base Sequence,Capsid,Cell Line,Cloning Molecular,Molecular Sequence Data,nosource,Plasmids,RNA Catalytic,RNA Replicase,RNA Viral,RNA Viruses,Templates Genetic,Virus Replication} } % == BibTeX quality report for ballReplicationGenomicRNA1994: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{bhattacharyyaReliefMicroRNAmediatedTranslational2006, title = {Relief of {{microRNA-mediated}} Translational Repression in Human Cells Subjected to Stress}, author = {Bhattacharyya, Suvendra N and Habermacher, Regula and Martine, Ursula and Closs, Ellen I and Filipowicz, Witold}, year = 2006, month = jun, journal = {Cell}, volume = {125}, number = {6}, pages = {1111–1124}, publisher = {Elsevier}, issn = {0092-8674}, doi = {10.1016/j.cell.2006.04.031}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867406005800}, abstract = {In metazoans, most microRNAs imperfectly base-pair with the 3’ untranslated region (3’UTR) of target mRNAs and prevent protein accumulation by either repressing translation or inducing mRNA degradation. Examples of specific mRNAs undergoing microRNA-mediated repression are numerous, but whether the repression is a reversible process remains largely unknown. Here we show that cationic amino acid transporter 1 (CAT-1) mRNA and reporters bearing its 3’UTR can be relieved from the microRNA miR-122-induced inhibition in human hepatocarcinoma cells subjected to different stress conditions. The derepression of CAT-1 mRNA is accompanied by its release from cytoplasmic processing bodies and its recruitment to polysomes. The derepression requires binding of HuR, an AU-rich-element binding protein, to the 3’UTR of CAT-1 mRNA. We propose that proteins interacting with the 3’UTR will generally act as modifiers altering the potential of miRNAs to repress gene expression.}, keywords = {3’ Untranslated Regions,Amino Acids,Antigens Surface,Antigens- Surface,Arsenites,Cationic Amino Acid Transporter 1,Cell Line Tumor,Cell Line- Tumor,Culture Media,Cytoplasmic Structures,Humans,MicroRNAs,nosource,Oxidative Stress,Protein Binding,Protein Biosynthesis,RNA Stability,RNA Transport,RNA-Binding Proteins,Sodium Compounds,Thapsigargin,Up-Regulation} }

@article{atkinRelationshipYeastPolyribosomes1997, title = {Relationship between Yeast Polyribosomes and {{Upf}} Proteins Required for Nonsense {{mRNA}} Decay}, author = {Atkin, A L and Schenkman, L R and Eastham, M and Dahlseid, J N and Lelivelt, M J and Culbertson, M R}, year = 1997, month = aug, journal = {The Journal of Biological Chemistry}, volume = {272}, number = {35}, pages = {22163–22172}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.272.35.22163}, url = {http://www.jbc.org/content/272/35/22163.short}, abstract = {In yeast, the accelerated rate of decay of nonsense mutant mRNAs, called nonsense-mediated mRNA decay, requires three proteins, Upf1p, Upf2p, and Upf3p. Single, double, and triple disruptions of the UPF genes had nearly identical effects on nonsense mRNA accumulation, suggesting that the encoded proteins function in a common pathway. We examined the distribution of epitope-tagged versions of Upf proteins by sucrose density gradient fractionation of soluble lysates and found that all three proteins co-distributed with 80 S ribosomal particles and polyribosomes. Treatment of lysates with RNase A caused a coincident collapse of polyribosomes and each Upf protein into fractions containing 80 S ribosomal particles, as expected for proteins that are associated with polyribosomes. Mutations in the cysteine-rich (zinc finger) and RNA helicase domains of Upf1p caused loss of function, but the mutant proteins remained polyribosome-associated. Density gradient profiles for Upf1p were unchanged in the absence of Upf3p, and although similar, were modestly shifted to fractions lighter than those containing polyribosomes in the absence of Upf2p. Upf2p shifted toward heavier polyribosome fractions in the absence of Upf1p and into fractions containing 80 S particles and lighter fractions in the absence of Upf3p. Our results suggest that the association of Upf2p with polyribosomes typically found in a wild-type strain depends on the presence and opposing effects of Upf1p and Upf3p.}, keywords = {0,Adaptor Proteins Signal Transducing,ASSOCIATION,CEREVISIAE,Codon,Codon Nonsense,CodonNonsense,Cysteine,DECAY,DISRUPTION,DISRUPTIONS,DOMAIN,DOMAINS,Fungal Proteins,gene,Genes,genetics,Helicase,La,lysate,metabolism,mRNA,mRNA decay,Mutagenesis Site-Directed,MutagenesisSite-Directed,Mutation,MUTATIONS,NONSENSE,nonsense-mediated mRNA decay,nosource,PARTICLES,PATHWAY,Polyribosomes,protein,Proteins,REQUIRES,Rna,RNA HELICASE,RNA Helicases,RNA Messenger,RNA-Binding Proteins,RNAMessenger,RNAse,S,S-CEREVISIAE,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Solubility,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Trans-Activators,UPF,Upf1,UPF1 PROTEIN,UPF3,WILD-TYPE,yeast} } % == BibTeX quality report for atkinRelationshipYeastPolyribosomes1997: % ? unused Journal abbr (“J. Biol. Chem”)

@article{rajkowitschReinitiationRecyclingAre2004, title = {Reinitiation and Recycling Are Distinct Processes Occurring Downstream of Translation Termination in Yeast}, author = {Rajkowitsch, Lukas and Vilela, Cristina and Berthelot, Karine and Ramirez, Carmen Velasco and McCarthy, John E G}, year = 2004, month = jan, journal = {Journal of Molecular Biology}, volume = {335}, number = {1}, eprint = {14659741}, eprinttype = {pubmed}, pages = {71–85}, issn = {0022-2836}, doi = {10.1016/j.jmb.2003.10.049}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14659741}, abstract = {The circularisation model of the polysome suggests that ribosome recycling is facilitated by 5’-3’ interactions mediated by the cap-binding complex eIF4F and the poly(A)-binding protein, Pab1. Alternatively, downstream of a short upstream open reading frame (uORF) in the 5’ untranslated region of a gene, posttermination ribosomes can maintain the competence to (re)initiate translation. Our data show that recycling and reinitiation must be distinct processes in Saccharomyces cerevisiae. The role of the 3’UTR in recycling was assessed by restricting ribosome movement along the mRNA using a poly(G) stretch or the mammalian iron regulatory protein bound to the iron responsive element. We find that although 3’UTR structure can influence translation, the main pathway of ribosome recycling does not depend on scanning-like movement through the 3’UTR. Changes in termination kinetics or disruption of the Pab1-eIF4F interaction do not affect recycling, yet the maintenance of normal in vivo mRNP structure is important to this process. Using bicistronic ACT1-LUC constructs, elongating yeast ribosomes were found to maintain the competence to (re)initiate over only short distances. Thus, as the first ORF to be translated is progressively truncated, reinitiation downstream of an uORF of 105nt is found to be just detectable, and increases markedly in efficiency as uORF length is reduced to 15nt. Experiments using a strain mutated in the Cca1 nucleotidyltransferase suggest that the uORF length-dependence of changes in reinitiation competence is affected by peptide elongation kinetics, but that ORF length per se may also be relevant.}, pmid = {14659741}, keywords = {0,Base Sequence,bicistronic,Cap binding,CAP-BINDING COMPLEX,CEREVISIAE,Codon,Codon Terminator,Codon-Terminator,CodonTerminator,COMPLEX,COMPLEXES,DISRUPTION,DOWNSTREAM,efficiency,elongation,Eukaryotic Initiation Factor-4F,FRAME,gene,Gene Components,genetics,IN-VIVO,initiation,Kinetics,La,metabolism,MODEL,Movement,mRNA,nosource,OPEN READING FRAME,PATHWAY,Peptide Chain Initiation,Peptide Chain Initiation Translational,Peptide Chain Termination,Peptide Chain Termination Translational,physiology,POLY(A)-BINDING PROTEIN,Poly(A)-Binding Protein I,protein,Protein Binding,Protein Biosynthesis,READING FRAME,REGION,ribosome,Ribosomes,Rna,RNA Messenger,RNA-Messenger,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,structure,support-non-u.s.gov’t,supportnon-u.s.gov’t,termination,translation,TRANSLATION TERMINATION,Translation-Genetic,TranslationGenetic,uORF,UPSTREAM,yeast,Yeasts} } % == BibTeX quality report for rajkowitschReinitiationRecyclingAre2004: % ? unused Journal abbr (“J. Mol. Biol”)

@article{cowlingRegulationMRNACap2010, title = {Regulation of {{mRNA}} Cap Methylation.}, author = {Cowling, Victoria H}, year = 2010, month = jan, journal = {The Biochemical Journal}, volume = {425}, number = {2}, pages = {295–302}, publisher = {Portland Press Ltd}, issn = {1470-8728}, doi = {10.1042/BJ20091352}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825737/ http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2825737&tool=pmcentrez&rendertype=abstract}, abstract = {The 7-methylguanosine cap added to the 5’ end of mRNA is essential for efficient gene expression and cell viability. Methylation of the guanosine cap is necessary for the translation of most cellular mRNAs in all eukaryotic organisms in which it has been investigated. In some experimental systems, cap methylation has also been demonstrated to promote transcription, splicing, polyadenylation and nuclear export of mRNA. The present review discusses how the 7-methylguanosine cap is synthesized by cellular enzymes, the impact that the 7-methylguanosine cap has on biological processes, and how the mRNA cap methylation reaction is regulated.}, pmid = {20025612}, keywords = {Gene Expression Regulation,Guanosine,Methylation,nosource,RNA Caps,Transcription Genetic,Transcription- Genetic,undefined} } % == BibTeX quality report for cowlingRegulationMRNACap2010: % ? unused Journal abbr (“Biochem. J”)

@article{lemmRegulationCmycMRNA2002, title = {Regulation of C-Myc {{mRNA}} Decay by Translational Pausing in a Coding Region Instability Determinant}, author = {Lemm, Ira and Ross, Jeff}, year = 2002, month = jun, journal = {Molecular and Cellular Biology}, volume = {22}, number = {12}, pages = {3959–3969}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, url = {http://mcb.asm.org/cgi/content/abstract/22/12/3959}, abstract = {A 249-nucleotide coding region instability determinant (CRD) destabilizes c-myc mRNA. Previous experiments identified a CRD-binding protein (CRD-BP) that appears to protect the CRD from endonuclease cleavage. However, it was unclear why a CRD-BP is required to protect a well-translated mRNA whose coding region is covered with ribosomes. We hypothesized that translational pausing in the CRD generates a ribosome-deficient region downstream of the pause site, and this region is exposed to endonuclease attack unless it is shielded by the CRD-BP. Transfection and cell-free translation experiments reported here support this hypothesis. Ribosome pausing occurs within the c-myc CRD in tRNA-depleted reticulocyte translation reactions. The pause sites map to a rare arginine (CGA) codon and to an adjacent threonine (ACA) codon. Changing these codons to more common codons increases translational efficiency in vitro and increases mRNA abundance in transfected cells. These data suggest that c-myc mRNA is rapidly degraded unless it is (i) translated without pausing or (ii) protected by the CRD-BP when pausing occurs. Additional mapping experiments suggest that the CRD is bipartite, with several upstream translation pause sites and a downstream endonuclease cleavage site.}, keywords = {Animals,Arginine,Codon,nosource,Protein Biosynthesis,Proto-Oncogene Proteins c-myc,Rabbits,Rats,Reticulocytes,Ribosomes,RNA Messenger,RNA Stability,RNA Transfer,RNA- Messenger,RNA- Transfer,RNA-Binding Proteins} } % == BibTeX quality report for lemmRegulationCmycMRNA2002: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{muhlradRecognitionYeastMRNAs1999, title = {Recognition of Yeast {{mRNAs}} as “Nonsense Containing” Leads to Both Inhibition of {{mRNA}} Translation and {{mRNA}} Degradation: Implications for the Control of {{mRNA}} Decapping}, author = {Muhlrad, D and Parker, R}, year = 1999, month = nov, journal = {Molecular Biology of the Cell}, volume = {10}, number = {11}, pages = {3971–3978}, publisher = {Am Soc Cell Biol}, issn = {1059-1524}, doi = {10.1091/mbc.10.11.3971}, url = {http://www.molbiolcell.org/content/10/11/3971.short}, abstract = {A critical step in the degradation of many eukaryotic mRNAs is a decapping reaction that exposes the transcript to 5’ to 3’ exonucleolytic degradation. The dual role of the cap structure as a target of mRNA degradation and as the site of assembly of translation initiation factors has led to the hypothesis that the rate of decapping would be specified by the status of the cap binding complex. This model makes the prediction that signals that promote mRNA decapping should also alter translation. To test this hypothesis, we examined the decapping triggered by premature termination codons to determine whether there is a down-regulation of translation when mRNAs were recognized as “nonsense containing.” We constructed an mRNA containing a premature stop codon in which we could measure the levels of both the mRNA and the polypeptide encoded upstream of the premature stop codon. Using this system, we analyzed the effects of premature stop codons on the levels of protein being produced per mRNA. In addition, by using alterations either in cis or in trans that inactivate different steps in the recognition and degradation of nonsense-containing mRNAs, we demonstrated that the recognition of a nonsense codon led to a decrease in the translational efficiency of the mRNA. These observations argue that the signal from a premature termination codon impinges on the translation machinery and suggest that decapping is a consequence of the change in translational status of the mRNA.}, keywords = {assembly,BINDING,Blotting Northern,Blotting-Northern,BlottingNorthern,Cap,Cap binding,Codon,Codon Nonsense,Codon Terminator,Codon-Nonsense,Codon-Terminator,CodonNonsense,CodonTerminator,COMPLEX,COMPLEXES,Copper,degradation,efficiency,Fungal Proteins,genetics,INHIBITION,initiation,metabolism,metallothionein,Metallothionein,mRNA,nosource,Phenotype,protein,Protein Biosynthesis,Rna Caps,RNA Caps,RNA Messenger,RNA-Messenger,RNAMessenger,SIGNAL,STOP CODON,structure,support-non-u.s.gov’t,supportnon-u.s.gov’t,SYSTEM,termination,translation,TRANSLATION INITIATION,Translation-Genetic,TranslationGenetic,yeast,Yeasts} } % == BibTeX quality report for muhlradRecognitionYeastMRNAs1999: % ? unused Journal abbr (“Mol. Biol. Cell”)

@article{baranovRecodingTranslationalBifurcations2002, title = {Recoding: Translational Bifurcations in Gene Expression}, author = {Baranov, Pavel V and Gesteland, Raymond F and Atkins, John F}, year = 2002, month = mar, journal = {Gene}, volume = {286}, number = {2}, pages = {187–201}, issn = {0378-1119}, doi = {10.1016/S0378-1119(02)00423-7}, url = {PM:11943474 http://www.sciencedirect.com/science/article/pii/S0378111902004237 http://www.ncbi.nlm.nih.gov/pubmed/11943474}, abstract = {During the expression of a certain genes standard decoding is over-ridden in a site or mRNA specific manner. This recoding occurs in response to special signals in mRNA and probably occurs in all organisms. This review deals with the function and distribution of recoding with a focus on the ribosomal frameshifting used for gene expression in bacteria. (C) 2002 Elsevier Science B.V. All rights reserved}, isbn = {1180158539}, pmid = {11943474}, keywords = {0,16S,16S: genetics,A SITE,A-SITE,Animals,Bacteria,Bacteria: classification,Bacteria: genetics,Bacterial,Base Sequence,classification,codon redefinition,decoding,ESCHERICHIA-COLI,expression,Frameshifting,Frameshifting Ribosomal,Frameshifting-Ribosomal,FrameshiftingRibosomal,GAMMA-SUBUNIT,gene,Gene Expression,Gene Expression Regulation,Gene Expression Regulation Bacterial,Gene Expression Regulation-Bacterial,Gene Expression RegulationBacterial,GENE-EXPRESSION,Genes,Genetic,Genetic Code,Genetic Code: genetics,genetics,human,Humans,La,MESSENGER-RNA,Molecular Sequence Data,mRNA,MYCOPLASMA-HYORHINIS,nosource,ORNITHINE DECARBOXYLASE ANTIZYME,Phylogeny,programmed frameshifting,Protein Biosynthesis,Protein Biosynthesis: genetics,readthrough,recoding,RELEASE FACTOR-II,Review,Ribosomal,ribosomal frameshifting,RIBOSOMAL FRAMESHIFTING SIGNAL,Ribosomal: genetics,Rna,RNA Ribosomal 16S,RNA-Ribosomal-16S,RNARibosomal16S,SELENOCYSTEINE INSERTION,SIGNAL,SITE,STOP CODON,Support,THIOREDOXIN REDUCTASE,translation,translational bypass} }

@article{harjuRapidIsolationYeast2004, title = {Rapid Isolation of Yeast Genomic {{DNA}}: {{Bust}} n’ {{Grab}}}, author = {Harju, Susanna and Fedosyuk, Halyna and Peterson, Kenneth R}, year = 2004, month = apr, journal = {BMC Biotechnology}, volume = {4}, number = {1}, eprint = {15102338}, eprinttype = {pubmed}, pages = {8}, publisher = {BioMed Central Ltd}, issn = {1472-6750}, doi = {10.1186/1472-6750-4-8}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15102338}, abstract = {BACKGROUND: Mutagenesis of yeast artificial chromosomes (YACs) often requires analysis of large numbers of yeast clones to obtain correctly targeted mutants. Conventional ways to isolate yeast genomic DNA utilize either glass beads or enzymatic digestion to disrupt yeast cell wall. Using small glass beads is messy, whereas enzymatic digestion of the cells is expensive when many samples need to be analyzed. We sought to develop an easier and faster protocol than the existing methods for obtaining yeast genomic DNA from liquid cultures or colonies on plates. RESULTS: Repeated freeze-thawing of cells in a lysis buffer was used to disrupt the cells and release genomic DNA. Cell lysis was followed by extraction with chloroform and ethanol precipitation of DNA. Two hundred ng–3 microg of genomic DNA could be isolated from a 1.5 ml overnight liquid culture or from a large colony. Samples were either resuspended directly in a restriction enzyme/RNase cocktail mixture for Southern blot hybridization or used for several PCR reactions. We demonstrated the utility of this method by showing an analysis of yeast clones containing a mutagenized human beta-globin locus YAC. CONCLUSION: An efficient, inexpensive method for obtaining yeast genomic DNA from liquid cultures or directly from colonies was developed. This protocol circumvents the use of enzymes or glass beads, and therefore is cheaper and easier to perform when processing large numbers of samples.}, keywords = {Blotting Southern,Blotting- Southern,Chromosomes Artificial Yeast,Chromosomes- Artificial- Yeast,DNA Fungal,DNA- Fungal,Genome Fungal,Genome- Fungal,Globins,Mycology,nosource,Polymerase Chain Reaction,Saccharomyces cerevisiae} } % == BibTeX quality report for harjuRapidIsolationYeast2004: % ? unused Journal abbr (“BMC Biotechnol”)

@article{yiQuantitationTelomeraseComponents2001, title = {Quantitation of Telomerase Components and {{hTERT mRNA}} Splicing Patterns in Immortal Human Cells}, author = {Yi, X and Shay, J W and Wright, W E}, year = 2001, month = dec, journal = {Nucleic Acids Research}, volume = {29}, number = {23}, pages = {4818–4825}, publisher = {Oxford Univ Press}, issn = {1362-4962}, url = {http://nar.oxfordjournals.org/content/29/23/4818.short}, abstract = {Telomerase is a reverse transcriptase that adds telomeric repeats to chromosomal ends. In most normal human somatic cells, telomerase is repressed and telomeres progressively shorten, leading to limited proliferative life-span. Telomerase reactivation is associated with cellular immortalization and is a frequent event during tumorigenesis. The telomerase ribonucleoprotein complex consists of two essential components, a catalytic protein subunit [human telomerase reverse transcriptase (hTERT)] and a template RNA (hTR). hTR is constitutively expressed, while hTERT is almost universally absent in telomerase-negative cells. Although repression of telomerase is transcriptional in telomerase-negative cells, post-transcriptional and assembly processes are likely to play important roles in regulating telomerase activity in those that are telomerase-positive. The telomerase transcript can also be alternatively spliced into a variety of non-functional forms. To establish the quantitative relationships between telomerase activity and its various components, we determined the numbers of molecules of hTR and hTERT mRNA, and the levels of alternatively spliced hTERT mRNA variants in normal, in vitro immortalized and cancer cell lines. We report here that there is surprisingly little variation in the proportion of alternatively spliced forms of hTERT in different cell lines. The only variation observed occurred when a change in splicing to non-functional forms appeared in response to conditions that repress telomerase activity in IDH4 cells. We also found that most telomerase-positive cell lines only contain a few molecules of potentially functional hTERT mRNA, and there is a correlation between telomerase activity and the levels of both hTR and hTERT +alpha+beta mRNA.}, keywords = {Alternative Splicing,Cell Line,DNA-Binding Proteins,Humans,nosource,RNA Messenger,RNA Untranslated,Telomerase,Tumor Cells Cultured} } % == BibTeX quality report for yiQuantitationTelomeraseComponents2001: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{maquatQualityControlMRNA2001, title = {Quality Control of {{mRNA}} Function.}, author = {Maquat, L E and Carmichael, G G}, year = 2001, month = jan, journal = {Cell}, volume = {104}, number = {2}, eprint = {11207359}, eprinttype = {pubmed}, pages = {173–176}, issn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11207359 http://yadda.icm.edu.pl/yadda/element/bwmeta1.element.elsevier-6c662c7a-1c70-3fbe-a6ad-db75d6a02295/c/00000247.pdf}, pmid = {11207359}, keywords = {Biological Transport,Cell Nucleus,Cytoplasm,nosource,Protein Biosynthesis,Quality Control,RNA Double-Stranded,RNA Messenger,RNA Precursors,RNA Processing Post-Transcriptional,Transcription Genetic} }

@article{mitchellPurificationYeastExosome2001, title = {Purification of Yeast Exosome.}, author = {Mitchell, P}, year = 2001, journal = {Methods in Enzymology}, volume = {342}, eprint = {11586908}, eprinttype = {pubmed}, pages = {356–364}, issn = {0076-6879}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11586908}, pmid = {11586908}, keywords = {Chromatography Affinity,Multienzyme Complexes,nosource,Saccharomyces cerevisiae} } % == BibTeX quality report for mitchellPurificationYeastExosome2001: % ? unused Journal abbr (“Meth. Enzymol”)

@article{baranovPsiteTRNACrucial2004, title = {P-Site {{tRNA}} Is a Crucial Initiator of Ribosomal Frameshifting}, author = {Baranov, Pavel V and Gesteland, Raymond F and Atkins, John F}, year = 2004, month = feb, journal = {RNA (New York, N.Y.)}, volume = {10}, number = {2}, pages = {221–230}, issn = {1355-8382}, doi = {10.1261/rna.5122604}, url = {http://rnajournal.cshlp.org/content/10/2/221.short}, abstract = {The expression of some genes requires a high proportion of ribosomes to shift at a specific site into one of the two alternative frames. This utilized frameshifting provides a unique tool for studying reading frame control. Peptidyl-tRNA slippage has been invoked to explain many cases of programmed frameshifting. The present work extends this to other cases. When the A-site is unoccupied, the P-site tRNA can be repositioned forward with respect to mRNA (although repositioning in the minus direction is also possible). A kinetic model is presented for the influence of both, the cognate tRNAs competing for overlapping codons in A-site, and the stabilities of P-site tRNA:mRNA complexes in the initial and new frames. When the A-site is occupied, the P-site tRNA can be repositioned backward. Whether frameshifting will happen depends on the ability of the A-site tRNA to subsequently be repositioned to maintain physical proximity of the tRNAs. This model offers an alternative explanation to previously published mechanisms of programmed frameshifting, such as out-of-frame tRNA binding, and a different perspective on simultaneous tandem tRNA slippage.}, pmid = {14730021}, keywords = {A SITE,A-SITE,Animals,Anticodon,BINDING,Codon,CODONS,COMPLEX,COMPLEXES,expression,FRAME,frameshifting,Frameshifting,Frameshifting Ribosomal,gene,Genes,Genetic,genetics,human,Humans,kinetic model,La,MECHANISM,MECHANISMS,MODEL,mRNA,nosource,P SITE,P-SITE,programmed frameshifting,READING FRAME,Reading Frames,recoding,REQUIRES,ribosomal frameshifting,ribosome,Ribosomes,RNA Transfer,SITE,SLIPPAGE,stability,translation,tRNA,tRNA binding} } % == BibTeX quality report for baranovPsiteTRNACrucial2004: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA.”)

@article{staplePseudoknotsRNAStructures2005, title = {Pseudoknots: {{RNA}} Structures with Diverse Functions}, author = {Staple, David W and Butcher, Samuel E}, year = 2005, month = jun, journal = {PLoS Biology}, volume = {3}, number = {6}, pages = {e213}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0030213}, url = {http://dx.plos.org/10.1371/journal.pbio.0030213}, pmid = {15941360}, keywords = {Base Composition,Molecular Sequence Data,nosource,Nucleic Acid Conformation,RNA,RNA Viral,RNA- Viral,SARS Virus,Sequence Analysis RNA,Sequence Analysis- RNA} } % == BibTeX quality report for staplePseudoknotsRNAStructures2005: % ? unused Journal abbr (“PLoS Biol”)

@article{barrettePseudoknotsPrionProtein2001, title = {Pseudoknots in Prion Protein {{mRNAs}} Confirmed by Comparative Sequence Analysis and Pattern Searching}, author = {Barrette, I and Poisson, G and Gendron, P and Major, F}, year = 2001, month = feb, journal = {Nucleic Acids Research}, volume = {29}, number = {3}, pages = {753–758}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/29.3.753}, url = {http://nar.oxfordjournals.org/content/29/3/753.short}, abstract = {The human prion gene contains five copies of a 24 nt repeat that is highly conserved among species. An analysis of folding free energies of the human prion mRNA, in particular in the repeat region, suggested biased codon selection and the presence of RNA patterns. In particular, pseudoknots, similar to the one predicted by Wills in the human prion mRNA, were identified in the repeat region of all available prion mRNAs available in GenBank, but not those of birds and the red slider turtle. An alignment of these mRNAs, which share low sequence homology, shows several co-variations that maintain the pseudoknot pattern. The presence of pseudoknots in yeast Sup35p and Rnq1 suggests acquisition in the prokaryotic era. Computer generated three-dimensional structures of the human prion pseudoknot highlight protein and RNA interaction domains, which suggest a possible effect in prion protein translation. The role of pseudoknots in prion diseases is discussed as individuals with extra copies of the 24 nt repeat develop the familial form of Creutzfeldt-Jakob disease.}, keywords = {3,alignment,analysis,Base Sequence,Codon,computer,CREUTZFELDT-JAKOB-DISEASE,disease,DOMAIN,DOMAINS,DYNAMICS,gene,human,Humans,initiation,INSERTIONAL MUTATION,MESSENGER-RNA,mRNA,nosource,Nucleic Acid Conformation,PATTERNS,PREDICTION,prion,Prions,PRNP GENE,protein,PrPC Proteins,pseudoknot,pseudoknots,RECOGNITION,REGION,Rna,RNA Messenger,SECONDARY STRUCTURE,SELECTION,sequence,Sequence Alignment,Sequence Analysis,STEM-LOOP,structure,Thermodynamics,translation,yeast} } % == BibTeX quality report for barrettePseudoknotsPrionProtein2001: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{gavinProteomeSurveyReveals2006, title = {Proteome Survey Reveals Modularity of the Yeast Cell Machinery}, author = {Gavin, Anne-Claude and Aloy, Patrick and Grandi, Paola and Krause, Roland and Boesche, Markus and Marzioch, Martina and Rau, Christina and Jensen, Lars Juhl and Bastuck, Sonja and D{"u}mpelfeld, Birgit and Edelmann, Angela and Heurtier, Marie-Anne and Hoffman, Verena and Hoefert, Christian and Klein, Karin and Hudak, Manuela and Michon, Anne-Marie and Schelder, Malgorzata and Schirle, Markus and Remor, Marita and Rudi, Tatjana and Hooper, Sean and Bauer, Andreas and Bouwmeester, Tewis and Casari, Georg and Drewes, Gerard and Neubauer, Gitte and Rick, Jens M and Kuster, Bernhard and Bork, Peer and Russell, Robert B and {Superti-Furga}, Giulio}, year = 2006, month = mar, journal = {Nature}, volume = {440}, number = {7084}, pages = {631–636}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature04532}, url = {http://www.nature.com/nature/journal/v440/n7084/abs/nature04532.html}, abstract = {Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. Here we report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry. Through systematic tagging of open reading frames (ORFs), the majority of complexes were purified several times, suggesting screen saturation. The richness of the data set enabled a de novo characterization of the composition and organization of the cellular machinery. The ensemble of cellular proteins partitions into 491 complexes, of which 257 are novel, that differentially combine with additional attachment proteins or protein modules to enable a diversification of potential functions. Support for this modular organization of the proteome comes from integration with available data on expression, localization, function, evolutionary conservation, protein structure and binary interactions. This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling.}, keywords = {Genome Fungal,Genome- Fungal,Multiprotein Complexes,nosource,Open Reading Frames,Phenotype,Proteome,Proteomics,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins} }

@article{kresslerProteinTransactingFactors1999, title = {Protein Trans-Acting Factors Involved in Ribosome Biogenesis in {{Saccharomyces}} Cerevisiae}, author = {Kressler, D and Linder, P and {}{de La Cruz}, J}, year = 1999, month = dec, journal = {Molecular and Cellular Biology}, volume = {19}, number = {12}, eprint = {10567516}, eprinttype = {pubmed}, pages = {7897–7912}, issn = {0270-7306}, doi = {10.1128/MCB.19.12.7897}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10567516}, pmid = {10567516}, keywords = {0,Adenosine,Adenosine Triphosphate,animal,Animals,Endoribonucleases,Exoribonucleases,Fungal Proteins,Helicase,human,Humans,La,metabolism,nosource,physiology,protein,Proteins,Review,ribosome,ribosome biogenesis,Ribosomes,Rna,RNA Helicases,RNA Precursors,RNA Processing Post-Transcriptional,RNA ProcessingPost-Transcriptional,RNA Ribosomal,RNARibosomal,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportnon-u.s.gov’t} } % == BibTeX quality report for kresslerProteinTransactingFactors1999: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{horsfieldProkaryoticRibosomesRecode1995, title = {Prokaryotic Ribosomes Recode the {{HIV-1}} Gag-Pol-1 Frameshift Sequence by an {{E}}/{{P}} Site Post-Translocation Simultaneous Slippage Mechanism}, author = {Horsfield, J A and Wilson, D N and Mannering, S A and Adamski, F M and Tate, W P}, year = 1995, month = may, journal = {Nucleic Acids Research}, volume = {23}, number = {9}, eprint = {7784201}, eprinttype = {pubmed}, pages = {1487–1494}, issn = {0305-1048}, doi = {10.1093/nar/23.9.1487}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7784201}, abstract = {The mechanism favoured for -1 frameshifting at typical retroviral sites is a pre-translocation simultaneous slippage model. An alternative post-translocation mechanism would also generate the same protein sequence across the frameshift site and therefore in this study the strategic placement of a stop codon has been used to distinguish between the two mechanisms. A 26 base pair frameshift sequence from the HIV-1 gag-pol overlap has been modified to include a stop codon immediately 3’ to the heptanucleotide frameshift signal, where it often occurs naturally in retroviral recoding sites. Stop codons at the 3’-end of the heptanucleotide sequence decreased the frame-shifting efficiency on prokaryote ribosomes and the recording event was further depressed when the levels of the release factors in vivo were increased. In the presence of elevated levels of a defective release factor 2, frameshifting efficiency in vivo was increased in the constructs containing the stop codons recognized specifically by that release factor. These results are consistent with the last six nucleotides of the heptanucleotide slippery sequence occupying the ribosomal E and P sites, rather than the P and A sites, with the next codon occupying the A site and therefore with a post-translocation rather than a pre-translocation -1 slippage model.}, pmid = {7784201}, keywords = {3,3’-END,A SITE,A-SITE,A-SITES,Bacteria,BASE,Base Sequence,BASE-PAIR,Codon,CODONS,E,efficiency,ERRORS,Escherichia coli,ESCHERICHIA-COLI,frameshift,Frameshift Mutation,Frameshifting,Gag-pol,gene,GENE-EXPRESSION,Hiv-1,HIV-1,IMMUNODEFICIENCY-VIRUS,IN-VIVO,MECHANISM,MECHANISMS,MODEL,Molecular Sequence Data,MUTANTS,nosource,Nucleotides,P and A sites,P SITE,P-SITE,P-SITES,protein,Protein Biosynthesis,PROTEIN-SYNTHESIS,recoding,RELEASE FACTOR-II,RELEASE FACTORS,ribosome,Ribosomes,RNA Messenger,sequence,SIGNAL,SITE,SITES,SLIPPAGE,STOP CODON,termination,TRANSFER-RNA} } % == BibTeX quality report for horsfieldProkaryoticRibosomesRecode1995: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{sungProkaryoticEukaryoticTranslational2003, title = {Prokaryotic and Eukaryotic Translational Machineries Respond Differently to the Frameshifting {{RNA}} Signal from Plant or Animal Virus}, author = {Sung, Deukyong and Kang, Hunseung}, year = 2003, month = apr, journal = {Virus Research}, volume = {92}, number = {2}, pages = {165–170}, publisher = {Elsevier}, issn = {0168-1702}, doi = {10.1016/S0168-1702(03)00042-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/s016817020300042x}, abstract = {Many mutational and structural analyses of the RNA signals propose a hypothesis that programmed frameshifting occurs by a specific interaction between ribosome and frameshifting signals comprised of a shifty site and a downstream RNA structure, in which the exact nature of the interaction has not yet been proven. To address this question, we analyzed the frameshifting sequence elements from animal or plant virus in yeast and Escherichia coli. Frameshifting efficiencies varied in yeast, but not in E coli, depending on the specific conformation of mouse mammary tumor virus (MMTV) RNA pseudoknot. Similar changes in frameshifting efficiencies were observed in yeast, but not in E coli, for the mutations in frameshifting sequence elements from cereal yellow dwarf virus serotype RPV (CYDV-RPV). The differential response of MMTV or CYDV-RPV frameshifting signal to prokaryotic and eukaryotic translational machineries implies that ribosome pausing alone is insufficient to mediate frameshifting, and additional events including specific interaction between ribosome and RNA structural element are required for efficient frameshifting. These results supports the hypothesis that frameshifting occurs by a specific interaction between ribosome and frameshifting signal. (C) 2003 Elsevier Science B.V. All rights reserved}, keywords = {0,animal,Animals,Base Sequence,Cereals,CONFORMATION,CYDV,DOWNSTREAM,E,efficiency,ELEMENTS,Escherichia coli,ESCHERICHIA-COLI,Frameshifting,Frameshifting Ribosomal,GENE-EXPRESSION,Mammary Tumor Virus Mouse,MAMMARY-TUMOR VIRUS,MESSENGER-RNA,Mice,MMTV,Molecular Sequence Data,Mutation,MUTATIONS,nosource,pausing,Plant Viruses,programmed frameshifting,Protein Biosynthesis,pseudoknot,RETROVIRAL RNA,ribosome,ribosome-RNA interaction,Rna,RNA PSEUDOKNOT,RNA Viral,Saccharomyces cerevisiae,sequence,SIGNAL,SITE,Structural,structure,Support,SYSTEMS,virus,yeast,YELLOW DWARF VIRUS} } % == BibTeX quality report for sungProkaryoticEukaryoticTranslational2003: % ? unused Journal abbr (“Virus Res”)

@article{farabaughProgrammedTranslationalFrameshifting1996, title = {Programmed Translational Frameshifting.}, author = {Farabaugh, P J}, year = 1996, month = mar, journal = {Microbiology and Molecular Biology Reviews}, volume = {60}, number = {1}, pages = {103–134}, publisher = {Am Soc Microbiol}, issn = {0146-0749}, doi = {10.1128/mr.60.1.103-134.1996}, url = {http://mmbr.asm.org/cgi/reprint/60/1/103.pdf}, keywords = {Amino Acid Sequence,Animals,Base Sequence,Frameshifting,Frameshifting Ribosomal,Molecular Sequence Data,nosource,Review,review article,ribosomal frameshifting,RNA Transfer} } % == BibTeX quality report for farabaughProgrammedTranslationalFrameshifting1996: % ? unused Journal abbr (“Microbiol. Rev”)

@article{licznarProgrammedTranslational12003, title = {Programmed Translational -1 Frameshifting on Hexanucleotide Motifs and the Wobble Properties of {{tRNAs}}}, author = {Licznar, Patricia and Mejlhede, Nina and Pr{`e}re, Marie-Fran{}oise and Wills, Norma and Gesteland, Raymond F and Atkins, John F and Fayet, Olivier}, year = 2003, month = sep, journal = {The EMBO Journal}, volume = {22}, number = {18}, eprint = {12970189}, eprinttype = {pubmed}, pages = {4770–4778}, issn = {0261-4189}, doi = {10.1093/emboj/cdg465}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12970189}, abstract = {Programmed -1 ribosomal frameshifting, involving tRNA re-pairing from an AAG codon to an AAA codon, has been reported to occur at the sequences CGA AAG and CAA AAG. In this study, using the recoding region of insertion sequence IS3, we have investigated the influence on frameshifting in Escherichia coli of the first codon of this type of motif by changing it to all other NNA codons. Two classes of NNA codons were distinguished, depending on whether they favor or limit frameshifting. Their degree of shiftiness is correlated with wobble propensity, and base 34 modification, of their decoding tRNAs. A more flexible anticodon loop very likely makes the tRNAs with extended wobble more prone to liberate the third codon base, A, for re-pairing of tRNA(Lys) in the -1 frame}, pmid = {12970189}, keywords = {0,Anticodon,ANTICODON LOOP,BASE,Base Sequence,Codon,CODONS,decoding,disease,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,FRAME,Frameshift Mutation,Frameshifting,Genetic,genetics,human,immunology,Kinetics,La,LOOP,modification,Molecular Sequence Data,MOTIFS,nosource,Nucleic Acid Conformation,Plasmids,Protein Biosynthesis,recoding,REGION,ribosomal frameshifting,RNA Bacterial,RNA Transfer,RNA- Bacterial,RNA- Transfer,S,sequence,SEQUENCES,tRNA} } % == BibTeX quality report for licznarProgrammedTranslational12003: % ? unused Journal abbr (“EMBO J.”)

@article{brierleyProgrammedRibosomalFrameshifting2005, title = {Programmed Ribosomal Frameshifting in {{HIV-1}} and the {{SARS-CoV}}}, author = {Brierley, Ian and Dos Ramos, Francisco J}, year = 2005, month = nov, journal = {Virus Research}, volume = {119}, number = {1}, pages = {29–42}, publisher = {Elsevier}, issn = {0168-1702}, doi = {10.1016/j.virusres.2005.10.008}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0168170205003217 PM:16310880}, abstract = {Ribosomal frameshifting is a mechanism of gene expression used by several RNA viruses to express replicase enzymes. This article focuses on frameshifting in two human pathogens, the retrovirus human immunodeficiency virus type 1 (HIV-1) and the coronavirus responsible for severe acute respiratory syndrome (SARS). The nature of the frameshift signals of HIV-1 and the SARS-CoV will be described and the impact of this knowledge on models of frameshifting will be considered. The role of frameshifting in the replication cycle of the two pathogens and potential antiviral therapies targeting frameshifting will also be discussed.}, keywords = {antiviral,Base Sequence,Coronavirus,enzyme,Enzymes,expression,frameshift,Frameshifting,Frameshifting Ribosomal,Frameshifting- Ribosomal,gene,Gene Expression,Gene Expression Regulation Viral,Gene Expression Regulation- Viral,GENE-EXPRESSION,Hiv-1,HIV-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,Humans,IMMUNODEFICIENCY-VIRUS,La,MECHANISM,MODEL,models,Molecular Sequence Data,No DOI found,nosource,Nucleic Acid Conformation,pathology,Protein Biosynthesis,Regulatory Sequences Ribonucleic Acid,Regulatory Sequences- Ribonucleic Acid,REPLICASE,REPLICATION,retrovirus,ribosomal frameshifting,Rna,RNA Viral,RNA Viruses,RNA- Viral,SARS,SARS Virus,Severe Acute Respiratory Syndrome,SIGNAL,Syndrome,therapy,TYPE-1,virology,virus,Viruses} } % == BibTeX quality report for brierleyProgrammedRibosomalFrameshifting2005: % ? unused Journal abbr (“Virus Res.”)

@article{baranovProgrammedRibosomalFrameshifting2005, title = {Programmed Ribosomal Frameshifting in Decoding the {{SARS-CoV}} Genome}, author = {Baranov, Pavel V and Henderson, Clark M and Anderson, Christine B and Gesteland, Raymond F and Atkins, John F and Howard, Michael T}, year = 2005, month = feb, journal = {Virology}, volume = {332}, number = {2}, pages = {498–510}, publisher = {Elsevier}, issn = {0042-6822}, doi = {10.1016/j.virol.2004.11.038}, url = {http://linkinghub.elsevier.com/retrieve/pii/S004268220400813X}, abstract = {Programmed ribosomal frameshifting is an essential mechanism used for the expression of orf1b in coronaviruses. Comparative analysis of the frameshift region reveals a universal shift site U_UUA_AAC, followed by a predicted downstream RNA structure in the form of either a pseudoknot or kissing stem loops. Frameshifting in SARS-CoV has been characterized in cultured mammalian cells using a dual luciferase reporter system and mass spectrometry. Mutagenic analysis of the SARS-CoV shift site and mass spectrometry of an affinity tagged frameshift product confirmed tandem tRNA slippage on the sequence U_UUA_AAC. Analysis of the downstream pseudoknot stimulator of frameshifting in SARS-CoV shows that a proposed RNA secondary structure in loop II and two unpaired nucleotides at the stem I-stem II junction in SARS-CoV are important for frameshift stimulation. These results demonstrate key sequences required for efficient frameshifting, and the utility of mass spectrometry to study ribosomal frameshifting.}, keywords = {analysis,Base Sequence,Cell Line,CELLS,Coronavirus,decoding,DOWNSTREAM,E,expression,FORM,frameshift,Frameshifting,Frameshifting Ribosomal,Genes Reporter,Genetic,genetics,Genome,Genome Viral,human,Humans,La,LOOP,luciferase,Luciferases,MAMMALIAN-CELLS,MECHANISM,Models Molecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleotides,PRODUCT,pseudoknot,REGION,ribosomal frameshifting,Rna,RNA SECONDARY STRUCTURE,RNA Viral,SARS Virus,SECONDARY STRUCTURE,sequence,Sequence Alignment,SEQUENCES,SITE,SLIPPAGE,Spectrometry Mass Electrospray Ionization,STEM-LOOP,structure,SYSTEM,tRNA} }

@article{ivanovProgrammedFrameshiftingSynthesis1998, title = {Programmed Frameshifting in the Synthesis of Mammalian Antizyme Is +1 in Mammals, Predominantly +1 in Fission Yeast, but -2 in Budding Yeast.}, author = {Ivanov, I P and Gesteland, R F and Matsufuji, S and Atkins, J F}, year = 1998, month = oct, journal = {RNA (New York, N.Y.)}, volume = {4}, number = {10}, eprint = {9769097}, eprinttype = {pubmed}, pages = {1230–1238}, issn = {1355-8382}, doi = {10.1017/S1355838298980864}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9769097}, abstract = {The coding sequence for mammalian ornithine decarboxylase antizyme is in two different partially overlapping reading frames with no independent ribosome entry to the second ORF. Immediately before the stop codon of the first ORF, a proportion of ribosomes undergo a quadruplet translocation event to shift to the +1 reading frame of the second and main ORF. The proportion that frameshifts is dependent on the polyamine level and, because the product antizyme is a negative regulator of intracellular polyamine levels, the frameshifting acts to complete an autoregulatory circuit by sensing polyamine levels. An mRNA element just 5’ of the shift site and a 3’ pseudoknot are important for efficient frameshifting. Previous work has shown that a cassette with the mammalian shift site and associated signals directs efficient shifting in the budding yeast Saccharomyces cerevisiae at the same codon to the correct frame, but that the shift is -2 instead of +1. The product contains an extra amino acid corresponding to the shift site. The present work shows efficient frameshifting also occurs in the fission yeast, Schizosaccharomyces pombe. This frameshifting is 80% +1 and 20% -2. The response of S. pombe translation apparatus to the mammalian antizyme recoding signals is more similar to that of the mammalian system than to that of S. cerevisiae. S. pombe provides a good model system for genetic studies on the mechanism of at least this type of programmed mammalian frameshifting.}, pmid = {9769097}, keywords = {Amino Acid Sequence,Animals,antizyme,Base Sequence,Cell-Free System,Codon,Enzyme Inhibitors,frameshift,Frameshifting,Frameshifting Ribosomal,Genetic,genetics,human,Mammals,MECHANISM,Molecular Sequence Data,mRNA,nosource,Nucleic Acid Conformation,Ornithine Decarboxylase,ORNITHINE DECARBOXYLASE ANTIZYME,polyamine,programmed frameshifting,Proteins,pseudoknot,Rats,recoding,Regulatory Sequences Nucleic Acid,ribosome,Ribosomes,RNA Messenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Schizosaccharomyces,sequence,Sequence Analysis,SIGNAL,STOP CODON,SYSTEM,translation,translocation,yeast} } % == BibTeX quality report for ivanovProgrammedFrameshiftingSynthesis1998: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA.”)

@article{dosramosProgrammedX22121Ribosomal2004, title = {Programmed# X22121 Ribosomal Frameshifting in the {{SARS}} Coronavirus}, author = {Dos Ramos, F and Carrasco, M and Doyle, T and Brierley, I}, year = 2004, month = dec, journal = {Biochemical Society Transactions}, volume = {32}, number = {Pt 6}, eprint = {15506971}, eprinttype = {pubmed}, pages = {1081–1083}, publisher = {London: The Society, 1973-}, issn = {0300-5127}, doi = {10.1042/BST0321081}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15506971 http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Programmed+-1+ribosomal+frameshifting+in+the+SARS+coronavirus#0}, abstract = {Programmed -1 ribosomal frameshifting is an alternate mechanism of translation used by coronavirus to synthesize replication proteins encoded by two overlapping open reading frames. For some coronaviruses, the mRNA cis-acting stimulatory structures involved in this process have been characterized, but their precise contribution to ribosomal frameshifting is not completely understood. Recently, a novel coronavirus was identified as the causative agent of the severe acute respiratory syndrome. This review describes the mRNA motifs involved in programmed -1 ribosomal frameshifting in this virus.}, keywords = {Amino Acid Sequence,Base Sequence,Coronavirus,FRAME,Frameshift Mutation,Frameshifting,Genome Viral,Genome- Viral,La,MECHANISM,Molecular Sequence Data,MOTIFS,mRNA,No DOI found,nosource,Nucleic Acid Conformation,OPEN READING FRAME,Open Reading Frames,protein,Proteins,READING FRAME,Reading Frames,REPLICATION,Review,ribosomal frameshifting,Ribosomes,SARS,SARS Virus,Severe Acute Respiratory Syndrome,Signal Transduction,structure,translation,virus} } % == BibTeX quality report for dosramosProgrammedX22121Ribosomal2004: % ? unused Journal abbr (“Biochem. Soc. Trans”)

@article{brierleyProbingMechanismRibosomal1993, title = {Probing the Mechanism of Ribosomal Frameshifting on Viral {{RNAs}}}, author = {Brierley, I}, year = 1993, month = nov, journal = {Biochemical Society Transactions}, volume = {21}, number = {4}, pages = {822–826}, issn = {0300-5127}, url = {http://www.biochemsoctrans.org/bst/021/bst0210822.htm}, pmid = {8132074}, keywords = {Base Sequence,Frameshift Mutation,Molecular Sequence Data,nosource,Open Reading Frames,Ribosomes,RNA Transfer,RNA Viral} } % == BibTeX quality report for brierleyProbingMechanismRibosomal1993: % ? unused Journal abbr (“Biochem. Soc. Trans”)

@article{greenPremRNASplicing1986, title = {Pre-{{mRNA}} Splicing}, author = {Green, M R}, year = 1986, journal = {Annual Review of Genetics}, volume = {20}, number = {1}, pages = {671–708}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, issn = {0066-4197}, doi = {10.1146/annurev.ge.20.120186.003323}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.ge.20.120186.003323}, keywords = {Animals,Base Sequence,Humans,Introns,nosource,Nucleic Acid Conformation,Nucleic Acid Precursors,Poly A,Ribonucleoproteins,Ribonucleoproteins Small Nuclear,Ribonucleoproteins- Small Nuclear,RNA Caps,RNA Messenger,RNA Precursors,RNA Splicing,RNA- Messenger,Saccharomyces cerevisiae} } % == BibTeX quality report for greenPremRNASplicing1986: % ? unused Journal abbr (“Annu. Rev. Genet”)

@article{zukerPredictionRNASecondary1994, title = {Prediction of {{RNA}} Secondary Structure by Energy Minimization}, author = {Zuker, M}, year = 1994, journal = {Methods in Molecular Biology (Clifton, N.J.)}, volume = {25}, eprint = {7516239}, eprinttype = {pubmed}, pages = {267–294}, issn = {1064-3745}, doi = {10.1385/0-89603-276-0:267}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7516239}, pmid = {7516239}, keywords = {Base Composition,Base Sequence,Consensus Sequence,DNA,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Repetitive Sequences Nucleic Acid,RNA,Software,Thermodynamics} } % == BibTeX quality report for zukerPredictionRNASecondary1994: % ? Possibly abbreviated journal title Methods in Molecular Biology (Clifton, N.J.) % ? unused Journal abbr (“Methods Mol. Biol”)

@article{witwerPredictionConsensusRNA2004, title = {Prediction of Consensus {{RNA}} Secondary Structures Including Pseudoknots}, author = {Witwer, Christina and Hofacker, Ivo L and Stadler, Peter F}, year = {2004 Apr-Jun}, journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics / IEEE, ACM}, volume = {1}, number = {2}, pages = {66–77}, publisher = {IEEE}, issn = {1545-5963}, doi = {10.1109/TCBB.2004.22}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1350749}, abstract = {Most functional RNA molecules have characteristic structures that are highly conserved in evolution. Many of them contain pseudoknots. Here, we present a method for computing the consensus structures including pseudoknots based on alignments of a few sequences. The algorithm combines thermodynamic and covariation information to assign scores to all possible base pairs, the base pairs are chosen with the help of the maximum weighted matching algorithm. We applied our algorithm to a number of different types of RNA known to contain pseudoknots. All pseudoknots were predicted correctly and more than 85 percent of the base pairs were identified.}, keywords = {Algorithms,Base Pairing,Base Sequence,Computational Biology,Models Molecular,Models- Molecular,nosource,Nucleic Acid Conformation,RNA,RNA Bacterial,RNA- Bacterial,Sequence Alignment,Thermodynamics} } % == BibTeX quality report for witwerPredictionConsensusRNA2004: % ? unused Journal abbr (“IEEE/ACM Trans Comput Biol Bioinform”)

@article{freyhultPredictingRNAStructure2005, title = {Predicting {{RNA}} Structure Using Mutual Information}, author = {Freyhult, Eva and Moulton, Vincent and Gardner, Paul}, year = 2005, journal = {Applied Bioinformatics}, volume = {4}, number = {1}, eprint = {16000013}, eprinttype = {pubmed}, pages = {53–59}, issn = {1175-5636}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16000013}, abstract = {BACKGROUND: With the ever-increasing number of sequenced RNAs and the establishment of new RNA databases, such as the Comparative RNA Web Site and Rfam, there is a growing need for accurately and automatically predicting RNA structures from multiple alignments. Since RNA secondary structure is often conserved in evolution, the well known, but underused, mutual information measure for identifying covarying sites in an alignment can be useful for identifying structural elements. This article presents MIfold, a MATLAB toolbox that employs mutual information, or a related covariation measure, to display and predict conserved RNA secondary structure (including pseudoknots) from an alignment. RESULTS: We show that MIfold can be used to predict simple pseudoknots, and that the performance can be adjusted to make it either more sensitive or more selective. We also demonstrate that the overall performance of MIfold improves with the number of aligned sequences for certain types of RNA sequences. In addition, we show that, for these sequences, MIfold is more sensitive but less selective than the related RNAalifold structure prediction program and is comparable with the COVE structure prediction package. CONCLUSION: MIfold provides a useful supplementary tool to programs such as RNA Structure Logo, RNAalifold and COVE, and should be useful for automatically generating structural predictions for databases such as Rfam.}, pmid = {16000013}, keywords = {Algorithms,Base Sequence,Computer Graphics,Computer Simulation,Models Molecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,RNA,Sequence Alignment,Sequence Analysis RNA,Software,User-Computer Interface} } % == BibTeX quality report for freyhultPredictingRNAStructure2005: % ? unused Journal abbr (“Appl. Bioinformatics”)

@article{ieongPredictingRNASecondary2003, title = {Predicting {{RNA}} Secondary Structures with Arbitrary Pseudoknots by Maximizing the Number of Stacking Pairs}, author = {Ieong, Samuel and Kao, Ming-Yang and Lam, Tak-Wah and Sung, Wing-Kin and Yiu, Siu-Ming}, year = 2003, month = jan, journal = {Journal of Computational Biology: A Journal of Computational Molecular Cell Biology}, volume = {10}, number = {6}, pages = {981–995}, issn = {1066-5277}, doi = {10.1089/106652703322756186}, url = {http://online.liebertpub.com/doi/abs/10.1089/106652703322756186 http://www.ncbi.nlm.nih.gov/pubmed/14980021}, abstract = {The paper investigates the computational problem of predicting RNA secondary structures. The general belief is that allowing pseudoknots makes the problem hard. Existing polynomial-time algorithms are heuristic algorithms with no performance guarantee and can handle only limited types of pseudoknots. In this paper, we initiate the study of predicting RNA secondary structures with a maximum number of stacking pairs while allowing arbitrary pseudoknots. We obtain two approximation algorithms with worst-case approximation ratios of 1/2 and 1/3 for planar and general secondary structures, respectively. For an RNA sequence of n bases, the approximation algorithm for planar secondary structures runs in O(n(3)) time while that for the general case runs in linear time. Furthermore, we prove that allowing pseudoknots makes it NP-hard to maximize the number of stacking pairs in a planar secondary structure. This result is in contrast with the recent NP-hard results on psuedoknots which are based on optimizing some general and complicated energy functions.}, pmid = {14980021}, keywords = {Algorithms,approximation algorithms,Base Pairing,Base Sequence,Computational Biology,Computational Biology: methods,computational complexity,Molecular Sequence Data,nosource,Nucleic Acid Conformation,pseudoknots,RNA,rna secondary structures,RNA: chemistry,RNA: genetics,stacking pairs} } % == BibTeX quality report for ieongPredictingRNASecondary2003: % ? unused Journal abbr (“J. Comput. Biol”)

@article{wangPrecisionFunctionalSpecificity2002, title = {Precision and Functional Specificity in {{mRNA}} Decay}, author = {Wang, Yulei and Liu, Chih Long and Storey, John D and Tibshirani, Robert J and Herschlag, Daniel and Brown, Patrick O}, year = 2002, month = apr, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {9}, eprint = {11972065}, eprinttype = {pubmed}, pages = {5860–5865}, issn = {0027-8424}, doi = {10.1073/pnas.092538799}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11972065}, abstract = {Posttranscriptional processing of mRNA is an integral component of the gene expression program. By using DNA microarrays, we precisely measured the decay of each yeast mRNA, after thermal inactivation of a temperature-sensitive RNA polymerase II. The half-lives varied widely, ranging from approximately 3 min to more than 90 min. We found no simple correlation between mRNA half-lives and ORF size, codon bias, ribosome density, or abundance. However, the decay rates of mRNAs encoding groups of proteins that act together in stoichiometric complexes were generally closely matched, and other evidence pointed to a more general relationship between physiological function and mRNA turnover rates. The results provide strong evidence that precise control of the decay of each mRNA is a fundamental feature of the gene expression program in yeast.}, pmid = {11972065}, keywords = {0,3,Codon,COMPLEX,COMPLEXES,COMPONENT,DECAY,Dna,DNA MICROARRAYS,expression,gene,Gene Expression,GENE-EXPRESSION,Glycolysis,La,metabolism,Models Genetic,Models- Genetic,ModelsGenetic,mRNA,mRNA decay,mRNA turnover,nosource,Oligonucleotide Array Sequence Analysis,physiology,Poly A,polymerase,protein,Proteins,ribosome,Rna,RNA Messenger,RNA Polymerase II,RNA Processing Post-Transcriptional,RNA Processing- Post-Transcriptional,RNA ProcessingPost-Transcriptional,RNA- Messenger,RNA-POLYMERASE,RNA-POLYMERASE-II,RNAMessenger,Saccharomyces cerevisiae,SPECIFICITY,supportu.s.gov’tp.h.s.,Temperature,Time Factors,Transcription Genetic,Transcription- Genetic,TranscriptionGenetic,turnover,yeast} } % == BibTeX quality report for wangPrecisionFunctionalSpecificity2002: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{lomakinPositionEukaryoticInitiation2003, title = {Position of Eukaryotic Initiation Factor {{eIF1}} on the {{40S}} Ribosomal Subunit Determined by Directed Hydroxyl Radical Probing}, author = {Lomakin, Ivan B and Kolupaeva, Victoria G and Marintchev, Assen and Wagner, Gerhard and Pestova, Tatyana V}, year = 2003, month = nov, journal = {Genes & Development}, volume = {17}, number = {22}, pages = {2786–2797}, publisher = {Cold Spring Harbor Lab}, issn = {0890-9369}, doi = {10.1101/gad.1141803}, url = {http://genesdev.cshlp.org/content/17/22/2786.short}, abstract = {Eukaryotic initiation factor (eIF) eIF1 maintains the fidelity of initiation codon selection by enabling 43S complexes to reject codon-anticodon mismatches, to recognize the initiation codon context, and to discriminate against establishing a codon-anticodon interaction with AUGs located {\(<\)}8 nt from the 5’-end of mRNA. To understand how eIF1 plays its discriminatory role, we determined its position on the 40S ribosomal subunit using directed hydroxyl radical cleavage. The cleavage of 18S rRNA in helices 23b, 24a, and 44 by hydroxyl radicals generated from Fe(II) tethered to seven positions on the surface of eIF1 places eIF1 on the interface surface of the platform of the 40S subunit in the proximity of the ribosomal P-site. The position of eIF1 on the 40S subunit suggests that although eIF1 is unable to inspect the region of initiation codon directly, its position close to the P-site is very favorable for an indirect mechanism of eIF1’s action by influencing the conformation of the platform of the 40S subunit and the positions of mRNA and initiator tRNA in initiation complexes. Unexpectedly, the position of eIF1 on the 40S subunit was strikingly similar to the position on the 30S ribosomal subunit of the sequence and structurally unrelated C-terminal domain of prokaryotic initiation factor IF3, which also participates in initiation codon selection in prokaryotes.}, keywords = {0,Animals,AUG,Binding Sites,chemistry,CLEAVAGE,Codon,Codon Initiator,CODON-ANTICODON INTERACTION,CodonInitiator,COMPLEX,COMPLEXES,CONFORMATION,DOMAIN,eIF1,Eukaryotic Initiation Factor-1,Eukaryotic Initiation Factor-3,FE(II),Fidelity,FUSION PROTEIN,genetics,human,Humans,Hydroxyl Radical,immunology,initiation,INITIATION-FACTOR,interface,La,MECHANISM,metabolism,microbiology,Models Molecular,ModelsMolecular,mRNA,nosource,Nucleic Acid Conformation,P SITE,P-SITE,Peptide Chain Initiation,Peptide Chain Initiation Translational,POSITION,POSITIONS,PROKARYOTES,protein,Protein Binding,Protein Footprinting,Protein Structure Tertiary,Protein StructureTertiary,Protein Subunits,Proteins,Recombinant Fusion Proteins,REGION,RIBOSOMAL-SUBUNIT,Ribosomes,Rna,RNA Messenger,RNA Ribosomal,RNAMessenger,RNARibosomal,rRNA,SELECTION,sequence,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,tRNA} } % == BibTeX quality report for lomakinPositionEukaryoticInitiation2003: % ? unused Journal abbr (“Genes Dev.”)

@article{hudakPokeweedAntiviralProtein1999, title = {Pokeweed Antiviral Protein Accesses Ribosomes by Binding to {{L3}}}, author = {Hudak, K A and Dinman, J D and Tumer, N E}, year = 1999, month = feb, journal = {The Journal of Biological Chemistry}, volume = {274}, number = {6}, pages = {3859–3864}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.274.6.3859}, url = {http://www.jbc.org/content/274/6/3859.short}, abstract = {Pokeweed antiviral protein (PAP), a 29-kDa ribosome-inactivating protein, catalytically removes an adenine residue from the conserved alpha-sarcin loop of the large rRNA, thereby preventing the binding of eEF-2.GTP complex during protein elongation. Because the alpha-sarcin loop has been placed near the peptidyltransferase center in Escherichia coli ribosomes, we investigated the effects of alterations at the peptidyltransferase center on the activity of PAP. We demonstrate here that a chromosomal mutant of yeast, harboring the mak8-1 allele of peptidyltransferase-linked ribosomal protein L3 (RPL3), is resistant to the cytostatic effects of PAP. Unlike wild-type yeast, ribosomes from mak8-1 cells are not depurinated when PAP expression is induced in vivo, indicating that wild-type L3 is required for ribosome depurination. Co-immunoprecipitation studies show that PAP binds directly to L3 or Mak8-1p in vitro but does not physically interact with ribosome-associated Mak8-1p. L3 is required for PAP to bind to ribosomes and depurinate the 25 S rRNA, suggesting that it is located in close proximity to the alpha-sarcin loop. These results demonstrate for the first time that a ribosomal protein provides a receptor site for an ribosome-inactivating protein and allows depurination of the target adenine.}, keywords = {99121133,antiviral,Antiviral Agents,BINDING,COMPLEX,COMPLEXES,drug effects,elongation,Escherichia coli,ESCHERICHIA-COLI,expression,In Vitro,IN-VITRO,IN-VIVO,L3,metabolism,N-Glycosyl Hydrolases,nosource,PAP,pathology,Peptidyltransferase,pharmacology,Plant Proteins,Pokeweed antiviral protein,Precipitin Tests,protein,Protein Binding,Purines,Ribosomal Proteins,ribosome,Ribosome Inactivating Proteins Type 1,Ribosomes,rRNA,yeast} } % == BibTeX quality report for hudakPokeweedAntiviralProtein1999: % ? unused Journal abbr (“J. Biol. Chem”)

@article{pricePoisedPolymerasesYour2008, title = {Poised Polymerases: On Your Mark…Get Set…Go!}, author = {Price, David H}, year = 2008, month = apr, journal = {Molecular Cell}, volume = {30}, number = {1}, pages = {2006–2009}, issn = {1097-4164}, doi = {10.1016/j.molcel.2008.03.001}, url = {http://www.sciencedirect.com/science/article/pii/S1097276508001561}, abstract = {Recent global analyses have determined that many Drosophila and human genes have engaged polymerase molecules trapped immediately downstream of promoters. These results strongly implicate RNA polymerase II elongation control as a major regulator of differentiation and development.}, pmid = {18406322}, keywords = {Animals,Gene Expression Regulation,Humans,nosource,Positive Transcriptional Elongation Factor B,Promoter Regions Genetic,Protein Biosynthesis,RNA Polymerase II,Transcription Genetic} } % == BibTeX quality report for pricePoisedPolymerasesYour2008: % ? unused Journal abbr (“Mol. Cell”)

@article{vimaladithanPeptidyltRNAsPromoteTranslational1995, title = {Peptidyl-{{tRNAs}} Promote Translational Frameshifting}, author = {Vimaladithan, A and Pande, S and Zhao, H and Farabaugh, P J}, year = 1995, journal = {Nucleic Acids Symposium Series}, number = {33}, eprint = {8643366}, eprinttype = {pubmed}, pages = {190–193}, issn = {0261-3166}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8643366}, abstract = {Programmed translational frameshifting is a ubiquitous, though rare, mechanism of gene expression in prokaryotes and eukaryotes. Research on many such sites has led to a general understanding that frameshifting depends on slippage of one or two ribosome-bound tRNAs on the mRNA. We recently found an example of an efficient frameshift in the Ty3 retrotransposon of the yeast Saccharomyces cerevisiae which occurs without tRNA slippage. Frameshifting appears to occur by misplacement of aminoacyl-tRNA in the ribosomal A site. Most of the eight tRNAs which induce measurable amounts of +1 frameshifting are predicted to slip only very poorly. In fact, frameshifting by tRNA slippage appears an unusual event in yeast, and where it occurs depends on peptidyl-tRNAs which employ two-out-of-three decoding. In addition, frameshifting either by slippage or by aminoacyl-tRNA misplacement depends on adequate availability of the first +1 frame tRNA. We present two models to explain how the tRNA which reads the shifted frame codon could promote +1 translational frameshifting.}, pmid = {8643366}, keywords = {Base Sequence,Codon,Frameshifting Ribosomal,Fungal Proteins,Models Biological,nosource,Peptide Elongation Factor 1,Peptide Elongation Factors,Retroelements,RNA Transfer Amino Acyl,Saccharomyces cerevisiae} } % == BibTeX quality report for vimaladithanPeptidyltRNAsPromoteTranslational1995: % ? unused Journal abbr (“Nucleic Acids Symp. Ser”)

@article{gilesPackagingReverseTranscription2004, title = {Packaging and Reverse Transcription of {{snRNAs}} by Retroviruses May Generate Pseudogenes}, author = {Giles, Keith E and Caputi, Massimo and Beemon, Karen L}, year = 2004, month = feb, journal = {RNA (New York, N.Y.)}, volume = {10}, number = {2}, eprint = {14730028}, eprinttype = {pubmed}, pages = {299–307}, issn = {1355-8382}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14730028}, abstract = {Retroviruses specifically package two copies of their RNA genome in each viral particle, along with some small cellular RNAs, including tRNAs and 7S L RNA. We show here that Rous sarcoma virus (RSV) also packages U6 snRNA at approximately one copy per virion. In addition, trace amounts of U1 and U2 snRNAs were detected in purified virus by Northern blotting. U6 snRNA comigrated with the RSV 70S genomic RNA dimer on sucrose gradients. We observed reverse transcription of U6 snRNA in an endogenous reaction in which RSV particles were the source of both reverse transcriptase and RNA substrates. This finding led us to examine mammalian genomic sequences for the presence of snRNA pseudogenes. A survey of the human, mouse, and rat genomes revealed a high number of spliceosomal snRNA pseudogenes. U6 pseudogenes were the most abundant, with approximately 200 copies in each genome. In the human genome, 67% of U6 snRNA pseudogenes, and a significant number of the other snRNA pseudogenes, were associated with LINE, SINE, or retroviral LTR repeat sequences. We propose that the packaging of snRNAs in retroviral particles leads to their reverse transcription in an infected cell and the integration of snRNA/viral recombinants into the host genome.}, pmid = {14730028}, keywords = {Animals,Avian Sarcoma Viruses,Humans,Long Interspersed Nucleotide Elements,Mice,nosource,Pseudogenes,Rats,RNA Small Nuclear,RNA- Small Nuclear,Sequence Analysis DNA,Sequence Analysis- DNA,Short Interspersed Nucleotide Elements,Terminal Repeat Sequences,Transcription Genetic,Transcription- Genetic} } % == BibTeX quality report for gilesPackagingReverseTranscription2004: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{stillmanOriginRecognitionChromosome2005, title = {Origin Recognition and the Chromosome Cycle}, author = {Stillman, Bruce}, year = 2005, month = feb, journal = {FEBS Letters}, volume = {579}, number = {4}, eprint = {15680967}, eprinttype = {pubmed}, pages = {877–884}, issn = {0014-5793}, doi = {10.1016/j.febslet.2004.12.011}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15680967}, abstract = {Prior to the initiation of DNA replication, chromosomes must establish a biochemical mark that permits the recruitment in S phase of the DNA replication machinery that copies DNA. The process of chromosome replication in eukaryotes also must be coordinated with segregation of the duplicated chromosomes to daughter cells during mitosis. Protein complexes that utilize ATP coordinate events at origins of DNA replication and later they participate in the initiation of DNA replication. In eukaryotes, some of these proteins also play a part in later processes that ensure accurate inheritance of chromosomes in mitosis, including spindle attachment of chromosomes, accurate duplication of centrosomes and cytokinesis. A perspective of how ATP-dependent proteins accomplish this task in eukaryotes is discussed.}, pmid = {15680967}, keywords = {Archaea,Cell Cycle,Chromosome Segregation,Chromosomes,DNA Replication,Eukaryotic Cells,nosource,Replication Origin,Simian virus 40} } % == BibTeX quality report for stillmanOriginRecognitionChromosome2005: % ? unused Journal abbr (“FEBS Lett”)

@article{hamoshOnlineMendelianInheritance2005, title = {Online {{Mendelian Inheritance}} in {{Man}} ({{OMIM}}), a Knowledgebase of Human Genes and Genetic Disorders.}, author = {Hamosh, Ada and Scott, Alan F and Amberger, Joanna S and Bocchini, Carol A and McKusick, Victor A}, year = 2005, month = jan, journal = {Nucleic Acids Research}, volume = {33}, number = {Database issue}, pages = {D514-517}, issn = {1362-4962}, doi = {10.1093/nar/gki033}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=539987&tool=pmcentrez&rendertype=abstract http://nar.oxfordjournals.org/content/33/suppl_1/D514.short}, abstract = {Online Mendelian Inheritance in Man (OMIM) is a comprehensive, authoritative and timely knowledgebase of human genes and genetic disorders compiled to support human genetics research and education and the practice of clinical genetics. Started by Dr Victor A. McKusick as the definitive reference Mendelian Inheritance in Man, OMIM (http://www.ncbi.nlm.nih.gov/omim/) is now distributed electronically by the National Center for Biotechnology Information, where it is integrated with the Entrez suite of databases. Derived from the biomedical literature, OMIM is written and edited at Johns Hopkins University with input from scientists and physicians around the world. Each OMIM entry has a full-text summary of a genetically determined phenotype and/or gene and has numerous links to other genetic databases such as DNA and protein sequence, PubMed references, general and locus-specific mutation databases, HUGO nomenclature, MapViewer, GeneTests, patient support groups and many others. OMIM is an easy and straightforward portal to the burgeoning information in human genetics.}, pmid = {15608251}, keywords = {Chromosome Mapping,Databases,Databases Genetic,Genes,Genetic,Genetic Diseases,Genetic Diseases Inborn,Humans,Inborn,Inborn: genetics,nosource,Phenotype,User-Computer Interface} } % == BibTeX quality report for hamoshOnlineMendelianInheritance2005: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{dahlbergNuclearTranslationWhat2003, title = {Nuclear Translation: What Is the Evidence?}, author = {Dahlberg, James E and Lund, Elsebet and Goodwin, Elizabeth B}, year = 2003, month = jan, journal = {Rna-A Publication of the Rna Society}, volume = {9}, number = {1}, eprint = {12554869}, eprinttype = {pubmed}, pages = {1–8}, issn = {1355-8382}, doi = {10.1261/rna.2121703}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12554869}, abstract = {Recently, several reports have been published in support of the idea that protein synthesis occurs in both the nucleus and the cytoplasm. This proposal has generated a great deal of excitement because, if true, it would mean that our thinking about the compartmentalization of cell functions would have to be re-evaluated. The significance and broad implications of this phenomenon require that the experimental evidence used to support it be carefully evaluated. Here, we critique the published evidence in support of, or in opposition to, the question of whether translation occurs in the nucleus. Arguments in support of nuclear translation focus on three issues: (1) the presence of translation factors and ribosomal components in the nucleus, and their recruitment to sites of transcription; (2) amino acid incorporation in isolated nuclei and in nuclei under conditions that should not permit protein import; and (3) the fact that nuclear translation would account for observations that are otherwise difficult to explain. Arguments against nuclear translation emphasize the absence (or low abundance) from nuclei of many translation factors; the likely inactivity of nascent ribosomes; and the loss of translation activity as nuclei are purified from contaminating cytoplasm. In our opinion, all of the experiments on nuclear translation published to date lack critical controls and, therefore, are not compelling; also, traditional mechanisms can explain the observations for which nuclear translation has been invoked. Thus, while we cannot rule out nuclear translation, in the absence of better supporting data we are reluctant to believe it occurs.}, pmid = {12554869}, keywords = {3,ACID,AMINO-ACID,CAP-BINDING COMPLEX,Cell Nucleus,COMPONENT,COMPONENTS,Cytoplasm,E,EXON JUNCTION COMPLEX,Gene Expression,INITIATION-FACTOR,LUMENAL CA2+ STORES,MAMMALIAN-CELLS,MECHANISM,MECHANISMS,MESSENGER-RNA SURVEILLANCE,nonsense-mediated decay,nosource,PREMATURE TERMINATION CODON,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,RECRUITMENT,Review,ribosome,RIBOSOME SYNTHESIS,Ribosomes,SACCHAROMYCES-CEREVISIAE,SITE,SITES,Support,transcription,translation} } % == BibTeX quality report for dahlbergNuclearTranslationWhat2003: % ? unused Journal abbr (“RNA”)

@article{mendellNovelUpf2pOrthologues2000, title = {Novel {{Upf2p}} Orthologues Suggest a Functional Link between Translation Initiation and Nonsense Surveillance Complexes}, author = {Mendell, J T and Medghalchi, S M and Lake, R G and Noensie, E N and Dietz, H C}, year = 2000, month = dec, journal = {Molecular and Cellular Biology}, volume = {20}, number = {23}, pages = {8944–8957}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, doi = {10.1128/MCB.20.23.8944-8957.2000}, url = {http://mcb.asm.org/cgi/content/abstract/20/23/8944}, abstract = {Transcripts harboring premature signals for translation termination are recognized and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay (NMD). In addition to protecting cells by preventing the translation of potentially deleterious truncated peptides, studies have suggested that NMD plays a broader role in the regulation of the steady-state levels of physiologic transcripts. In Saccharomyces cerevisiae, three trans-acting factors (Upf1p to Upf3p) are required for NMD. Orthologues of Upf1p have been identified in numerous species, showing that the NMD machinery, at least in part, is conserved through evolution. In this study, we demonstrate additional functional conservation of the NMD pathway through the identification of Upf2p homologues in Schizosaccharomyces pombe and humans (rent2). Disruption of S. pombe UPF2 established that this gene is required for NMD in fission yeast. rent2 was demonstrated to interact directly with rent1, a known trans-effector of NMD in mammalian cells. Additionally, fragments of rent2 were shown to possess nuclear targeting activity, although the native protein localizes to the cytoplasmic compartment. Finally, novel functional domains of Upf2p and rent2 with homology to eukaryotic initiation factor 4G (eIF4G) and other translational regulatory proteins were identified. Directed mutations within these so-called eIF4G homology (4GH) domains were sufficient to abolish the function of S. pombe Upf2p. Furthermore, using the two-hybrid system, we obtained evidence for direct interaction between rent2 and human eIF4AI and Sui1, both components of the translation initiation complex. Based on these findings, a novel model in which Upf2p and rent2 effects decreased translation and accelerated decay of nonsense transcripts through competitive interactions with eIF4G-binding partners is proposed.}, keywords = {Adaptor Proteins Signal Transducing,Amino Acid Sequence,animal,Animals,Cell Compartmentation,Codon Nonsense,CodonNonsense,COMPLEX,COMPLEXES,COMPONENT,Cytoplasm,DECAY,Eukaryotic Cells,Eukaryotic Initiation Factor-4G,Evolution,Fungal Proteins,gene,Genetic,human,Humans,IDENTIFICATION,initiation,metabolism,Mice,Models Genetic,ModelsGenetic,Molecular Sequence Data,mRNA,mRNA decay,Mutation,MUTATIONS,NMD,nosource,Peptide Chain Initiation,Peptide Chain Initiation Translational,Peptide Initiation Factors,Peptides,protein,Protein Binding,Proteins,regulation,RNA Messenger,RNA Stability,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Schizosaccharomyces,Sequence Homology Amino Acid,Sequence HomologyAmino Acid,SIGNAL,Species Specificity,sui1,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,termination,Tissue Distribution,Trans-Activators,translation,TRANSLATION INITIATION,TRANSLATION TERMINATION,yeast} } % == BibTeX quality report for mendellNovelUpf2pOrthologues2000: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{kalhorNovelMethyltransferaseModified2003, title = {Novel Methyltransferase for Modified Uridine Residues at the Wobble Position of {{tRNA}}}, author = {Kalhor, Hamid R and Clarke, Steven}, year = 2003, month = dec, journal = {Molecular and Cellular Biology}, volume = {23}, number = {24}, pages = {9283–9292}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, url = {http://mcb.asm.org/cgi/content/full/23/24/9283?view=full&pmid=14645538}, abstract = {We have identified a novel tRNA methyltransferase in Saccharomyces cerevisiae that we designate Trm9. This enzyme, the product of the YML014w gene, catalyzes the esterification of modified uridine nucleotides, resulting in the formation of 5-methylcarbonylmethyluridine in tRNA(Arg3) and 5-methylcarbonylmethyl-2-thiouridine in tRNA(Glu). In intact yeast cells, disruption of the TRM9 gene results in the complete loss of these modified wobble bases and increased sensitivity at 37 degrees C to paromomycin, a translational inhibitor. These results suggest a role for this potentially reversible methyl esterification reaction when cells are under stress.}, keywords = {Amino Acid Sequence,Base Sequence,DNA Fungal,DNA- Fungal,Gene Deletion,Genes Fungal,Genes- Fungal,Methylation,Molecular Sequence Data,Mutation,nosource,Protein Biosynthesis,RNA Fungal,RNA Transfer,RNA Transfer Arg,RNA Transfer Glu,RNA- Fungal,RNA- Transfer,RNA- Transfer- Arg,RNA- Transfer- Glu,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Sequence Homology Amino Acid,Sequence Homology- Amino Acid,Substrate Specificity,Temperature,tRNA Methyltransferases,Uridine} } % == BibTeX quality report for kalhorNovelMethyltransferaseModified2003: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{olsthoornNovelApplicationSRNA2004, title = {Novel Application of {{sRNA}}: Stimulation of Ribosomal Frameshifting}, author = {Olsthoorn, R C L and Laurs, M and Sohet, F and Hilbers, C W and Heus, H A and Pleij, C W A}, year = 2004, month = nov, journal = {RNA (New York, N.Y.)}, volume = {10}, number = {11}, eprint = {15496520}, eprinttype = {pubmed}, pages = {1702–1703}, issn = {1355-8382}, doi = {10.1261/rna.7139704}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15496520}, abstract = {Small RNAs play an important role in regulation of gene expression in eukaryotic and eubacterial cells by modulating gene expression both at the level of transcription and translation. Here, we show that short complementary RNAs can also affect gene expression by stimulating ribosomal frameshifting in vitro. This finding has important implications for understanding the process of ribosomal frameshifting and for the potential application of small RNAs in the treatment of diseases that are due to frameshift mutations.}, pmid = {15496520}, keywords = {Base Pairing,CELLS,chemistry,Codon,Codon Terminator,COMPLEMENTARY RNA,disease,Enhancer Elements Genetic,expression,frameshift,Frameshift Mutation,Frameshifting,Frameshifting Ribosomal,gene,Gene Expression,Gene Expression Regulation,GENE-EXPRESSION,In Vitro,IN-VITRO,La,Mutation,MUTATIONS,nosource,Oligonucleotides,Open Reading Frames,Protein Biosynthesis,Recombinant Fusion Proteins,regulation,ribosomal frameshifting,Ribosomes,Rna,RNA Interference,RNA Messenger,RNA Small Interfering,Thermodynamics,transcription,Transcription Genetic,translation} } % == BibTeX quality report for olsthoornNovelApplicationSRNA2004: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{vasudevanNonstopDecayaNew2002, title = {Non-Stop Decay–a New {{mRNA}} Surveillance Pathway}, author = {Vasudevan, Shobha and Peltz, Stuart W and Wilusz, Carol J}, year = 2002, month = sep, journal = {BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology}, volume = {24}, number = {9}, eprint = {12210514}, eprinttype = {pubmed}, pages = {785–788}, issn = {0265-9247}, doi = {10.1002/bies.10153}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12210514}, abstract = {Gene expression is an inherently complex process and errors often occur during the transcription and processing of mRNAs. Several surveillance mechanisms have evolved to check the fidelity at each step of mRNA manufacture. Two recent reports describe the identification of a novel pathway in eukaryotes that recognizes and degrades mRNAs that lack a stop codon. The non-stop decay mechanism releases ribosomes stalled at the 3’ end of a mRNA and stimulates the exosome to rapidly degrade the transcript.}, pmid = {12210514}, keywords = {3’ Untranslated Regions,Adaptor Proteins Signal Transducing,Adaptor Proteins- Signal Transducing,Binding Sites,Cell Nucleus,Codon Terminator,Codon- Terminator,Cytoplasm,Fungal Proteins,GTP-Binding Proteins,Models Biological,Models- Biological,nosource,Protein Binding,Ribosomes,RNA Messenger,RNA- Messenger,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins} } % == BibTeX quality report for vasudevanNonstopDecayaNew2002: % ? unused Journal abbr (“Bioessays”)

@article{mendellNonsenseSurveillanceRegulates2004, title = {Nonsense Surveillance Regulates Expression of Diverse Classes of Mammalian Transcripts and Mutes Genomic Noise}, author = {Mendell, Joshua T and Sharifi, Neda A and Meyers, Jennifer L and {Martinez-Murillo}, Francisco and Dietz, Harry C}, year = 2004, month = oct, journal = {Nature Genetics}, volume = {36}, number = {10}, pages = {1073–1078}, publisher = {Nature Publishing Group}, issn = {1061-4036}, doi = {10.1038/ng1429}, url = {http://www.nature.com/ng/journal/v36/n10/abs/ng1429.html}, abstract = {Premature termination codons induce rapid transcript degradation in eukaryotic cells through nonsense-mediated mRNA decay (NMD). This pathway can modulate phenotypes arising from nonsense or frameshift mutations, but little is known about the physiologic role of NMD in higher eukaryotes. To address this issue, we examined expression profiles in mammalian cells depleted of Rent1 (also called hUpf1), a factor essential for NMD. Upregulated transcripts included those with upstream open reading frames in the 5’ untranslated region, alternative splicing that introduces nonsense codons or frameshifts, introns in the 3’ untranslated region or selenocysteine codons. Transcripts derived from ancient transposons and endogenous retroviruses were also upregulated. These RNAs are unified by the presence of a spliced intron at least 50 nucleotides downstream of a termination codon, a context sufficient to initiate NMD. Consistent with direct regulation by NMD, representative upregulated transcripts decayed more slowly in cells deficient in NMD. In addition, inhibition of NMD induced by amino acid starvation upregulated transcripts that promote amino acid homeostasis. These results document that nonsense surveillance is a crucial post-transcriptional regulatory event that influences the expression of broad classes of physiologic transcripts, has been functionally incorporated into essential homeostatic mechanisms and suppresses expression of evolutionary remnants.}, keywords = {0,3,ACID,ACIDS,Alternative Splicing,Amino Acids,AMINO-ACID,AMINO-ACIDS,CELLS,Codon,Codon Nonsense,CodonNonsense,CODONS,DECAY,degradation,DOWNSTREAM,Endogenous Retroviruses,Eukaryotic Cells,expression,FRAME,frameshift,Frameshift Mutation,Gene Expression Regulation,Genetic,genetics,genomic,Hela Cells,human,Humans,INHIBITION,INTRON,Introns,La,MAMMALIAN-CELLS,MECHANISM,MECHANISMS,metabolism,Molecular Sequence Data,mRNA,mRNA decay,Mutation,MUTATIONS,NMD,NONSENSE,nonsense-mediated mRNA decay,nosource,Nucleotides,OPEN READING FRAME,Open Reading Frames,PATHWAY,Phenotype,PREMATURE TERMINATION CODON,protein,READING FRAME,Reading Frames,REGION,regulation,RETROVIRUSES,Rna,RNA Messenger,RNA Processing Post-Transcriptional,RNA ProcessingPost-Transcriptional,RNA Stability,RNAMessenger,Selenocysteine,splicing,SURVEILLANCE,termination,TERMINATION CODON,TERMINATION-CODON,Trans-Activators,TRANSCRIPT,UPSTREAM} } % == BibTeX quality report for mendellNonsenseSurveillanceRegulates2004: % ? unused Journal abbr (“Nat. Genet”)

@article{inacioNonsenseMutationsClose2004, title = {Nonsense Mutations in Close Proximity to the Initiation Codon Fail to Trigger Full Nonsense-Mediated {{mRNA}} Decay}, author = {In{'a}cio, Angela and Silva, Ana Lu{'i}sa and Pinto, Joana and Ji, Xinjun and Morgado, Ana and Almeida, F{'a}tima and Faustino, Paula and Lavinha, Jo{~a}o and Liebhaber, Stephen A and Rom{~a}o, Lu{'i}sa}, year = 2004, month = jul, journal = {The Journal of Biological Chemistry}, volume = {279}, number = {31}, pages = {32170–32180}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.M405024200}, url = {http://www.jbc.org/content/279/31/32170.short}, abstract = {Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism that degrades mRNAs containing premature translation termination codons. In mammalian cells, a termination codon is ordinarily recognized as “premature” if it is located greater than 50-54 nucleotides 5’ to the final exon-exon junction. We have described a set of naturally occurring human beta-globin gene mutations that apparently contradict this rule. The corresponding beta-thalassemia genes contain nonsense mutations within exon 1, and yet their encoded mRNAs accumulate to levels approaching wild-type beta-globin (beta(WT)) mRNA. In the present report we demonstrate that the stabilities of these mRNAs with nonsense mutations in exon 1 are intermediate between beta(WT) mRNA and beta-globin mRNA carrying a prototype NMD-sensitive mutation in exon 2 (codon 39 nonsense; beta 39). Functional analyses of these mRNAs with 5’-proximal nonsense mutations demonstrate that their relative resistance to NMD does not reflect abnormal RNA splicing or translation re-initiation and is independent of promoter identity and erythroid specificity. Instead, the proximity of the nonsense codon to the translation initiation AUG constitutes a major determinant of NMD. Positioning a termination mutation at the 5’ terminus of the coding region blunts mRNA destabilization, and this effect is dominant to the “50-54 nt boundary rule.” These observations impact on current models of NMD.}, keywords = {Animals,Cell Line,Codon,Codon Initiator,Codon Nonsense,Codon Terminator,DNA,Exons,Genes Dominant,Globins,Hela Cells,Humans,Introns,Mice,Mutation,nosource,Oligonucleotides,Open Reading Frames,Plasmids,Polyribosomes,Promoter Regions Genetic,Protein Biosynthesis,Protein Structure Tertiary,Reverse Transcriptase Polymerase Chain Reaction,Ribonucleases,RNA Messenger,RNA Splicing,Sucrose,Time Factors,Transfection} } % == BibTeX quality report for inacioNonsenseMutationsClose2004: % ? unused Journal abbr (“J. Biol. Chem”)

@article{contiNonsensemediatedMRNADecay2005, title = {Nonsense-Mediated {{mRNA}} Decay: Molecular Insights and Mechanistic Variations across Species}, shorttitle = {Nonsense-Mediated {{mRNA}} Decay}, author = {Conti, Elena and Izaurralde, Elisa}, year = 2005, month = jun, journal = {Current Opinion in Cell Biology}, volume = {17}, number = {3}, pages = {316–325}, issn = {0955-0674}, doi = {10.1016/j.ceb.2005.04.005}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0955067405000475}, abstract = {Nonsense-mediated mRNA decay (NMD) is an mRNA surveillance pathway that ensures the rapid degradation of mRNAs containing premature translation termination codons (PTCs), thereby preventing the synthesis of truncated and potentially harmful proteins. In addition, this pathway regulates the expression of approximately 10% of the transcriptome and is essential in mice. Although NMD is conserved in eukaryotes, recent studies in several organisms have revealed that different mechanisms have evolved to discriminate natural from premature stop codons and to degrade the targeted mRNAs. With the elucidation of the first crystal structures of components of the NMD machinery, the way is paved towards a molecular understanding of the protein interaction network underlying this process.}, pmid = {15901503}, keywords = {0,Animals,BIOLOGY,Codon,Codon Nonsense,Codon-Nonsense,CodonNonsense,CODONS,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,DECAY,degradation,Exoribonucleases,expression,genetics,Humans,La,MECHANISM,MECHANISMS,metabolism,Mice,Models Biological,Models Molecular,Models-Biological,Models-Molecular,ModelsBiological,ModelsMolecular,Molecular Biology,mRNA,mRNA decay,Multiprotein Complexes,NMD,NONSENSE,nonsense-mediated mRNA decay,nosource,Nuclear Proteins,PATHWAY,Phosphorylation,protein,Proteins,Research Support-Non-U.S.Gov’t,Research SupportNon-U.S.Gov’t,Review,Rna,RNA Messenger,RNA Stability,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNA-Messenger,RNAMessenger,Species Specificity,STOP CODON,structure,SURVEILLANCE,termination,TERMINATION CODON,TERMINATION-CODON,translation,TRANSLATION TERMINATION} } % == BibTeX quality report for contiNonsensemediatedMRNADecay2005: % ? unused Library catalog (“CrossRef”)

@article{maquatNonsensemediatedMRNADecay2001, title = {Nonsense-Mediated {{mRNA}} Decay: Insights into Mechanism from the Cellular Abundance of Human {{Upf1}}, {{Upf2}}, {{Upf3}}, and {{Upf3X}} Proteins}, author = {Maquat, L E and Serin, G}, year = 2001, month = jan, journal = {Cold Spring Harbor Symposia on Quantitative Biology}, volume = {66:313-20.}, number = {1}, pages = {313–320}, publisher = {Cold Spring Harbor Laboratory Press}, issn = {0091-7451}, doi = {10.1101/sqb.2001.66.313}, url = {http://symposium.cshlp.org/cgi/doi/10.1101/sqb.2001.66.313 http://symposium.cshlp.org/content/66/313.short http://www.cshl-symposium.org/doi/abs/10.1101/sqb.2001.66.313}, isbn = {0879696192}, keywords = {animal,Animals,Codon Nonsense,CodonNonsense,DECAY,genetics,Hela Cells,human,Humans,Kinetics,Mammals,MECHANISM,metabolism,Models Genetic,ModelsGenetic,mRNA,mRNA decay,nosource,protein,Proteins,RNA Messenger,RNA-Binding Proteins,RNAMessenger,supportu.s.gov’tp.h.s.,Trans-Activators,Transcription Factors,Upf1,UPF3} } % == BibTeX quality report for maquatNonsensemediatedMRNADecay2001: % ? unused Journal abbr (“Cold Spring Harb. Symp. Quant. Biol”)

@article{gonzalezNonsensemediatedMRNADecay2001, title = {Nonsense-Mediated {{mRNA}} Decay in {{Saccharomyces}} Cerevisiae.}, author = {Gonz{'a}lez, C I and Bhattacharya, A and Wang, W and Peltz, S W}, year = 2001, month = aug, journal = {Gene}, volume = {274}, number = {1-2}, pages = {15–25}, publisher = {Elsevier}, issn = {0378-1119}, doi = {10.1016/S0378-1119(01)00552-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0378111901005522 http://www.ncbi.nlm.nih.gov/pubmed/11674994 http://www.ncbi.nlm.nih.gov/pubmed/21918884}, abstract = {Cell survival depends on the precise and correct production of polypeptides. Eukaryotic cells have evolved conserved proofreading mechanisms to get rid of incomplete and potentially deleterious proteins. The nonsense-mediated mRNA decay (NMD) pathway is an example of a surveillance mechanism that monitors premature translation termination and promotes degradation of aberrant transcripts that code for nonfunctional or even harmful proteins. In this review we will describe our current knowledge of the NMD pathway, analyzing primarily the results obtained from the yeast Saccharomyces cerevisiae, but establishing functional comparisons with those obtained in higher eukaryotes. Based on these observations, we present two related working models to explain how this surveillance pathway recognizes and selectively degrades aberrant mRNAs.}, pmid = {11674994}, keywords = {0,Biological,Cell Survival,Codon,Codon Nonsense,CodonNonsense,DECAY,degradation,Eukaryotic Cells,Fungal,Gene Expression Regulation,Gene Expression Regulation Fungal,Gene Expression RegulationFungal,Genetic,genetics,La,MECHANISM,MECHANISMS,Messenger,Messenger: genetics,Messenger: metabolism,metabolism,microbiology,models,Models,Models Biological,ModelsBiological,mRNA,mRNA decay,NMD,Nonsense,Nonsense: genetics,nosource,proofreading,protein,Proteins,Review,Rna,RNA,RNA Messenger,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,SACCHAROMYCES-CEREVISIAE,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,termination,translation,yeast} }

@article{maquatNonsensemediatedMRNADecay2005, title = {Nonsense-Mediated {{mRNA}} Decay in Mammals}, author = {Maquat, Lynne E}, year = 2005, month = may, journal = {Journal of Cell Science}, volume = {118}, number = {Pt 9}, pages = {1773–1776}, publisher = {Company of Biologists}, issn = {0021-9533}, doi = {10.1242/jcs.01701}, url = {http://jcs.biologists.org/content/118/9/1773.full}, keywords = {Animals,Codon Nonsense,Cytoplasm,Exons,Humans,Mice,Models Biological,Mutation,nosource,RNA Messenger,Subcellular Fractions} } % == BibTeX quality report for maquatNonsensemediatedMRNADecay2005: % ? unused Journal abbr (“J. Cell. Sci”)

@article{lejeuneNonsensemediatedMRNADecay2003, title = {Nonsense-Mediated {{mRNA}} Decay in Mammalian Cells Involves Decapping, Deadenylating, and Exonucleolytic Activities}, author = {Lejeune, Fabrice and Li, Xiaojie and Maquat, Lynne E}, year = 2003, month = sep, journal = {Molecular Cell}, volume = {12}, number = {3}, pages = {675–687}, publisher = {Elsevier}, issn = {1097-2765}, doi = {10.1016/S1097-2765(03)00349-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276503003496}, abstract = {Nonsense-mediated mRNA decay (NMD) is a mechanism by which cells recognize and degrade mRNAs that prematurely terminate translation. To date, the polarity and enzymology of NMD in mammalian cells is unknown. We show here that downregulating the Dcp2 decapping protein or the PM/Scl100 component of the exosome (1) significantly increases the abundance of steady-state nonsense-containing but not nonsense-free mRNAs, and (2) significantly slows the decay rate of transiently induced nonsense-containing but not nonsense-free mRNA. Downregulating poly(A) ribonuclease (PARN) also increases the abundance of nonsense-containing mRNAs. Furthermore, NMD factors Upf1, Upf2, and Upf3X coimmunopurify with the decapping enzyme Dcp2, the putative 5’–{\(>\)}3’ exonuclease Rat1, the proven 5’–{\(>\)}3’ exonuclease Xrn1, exosomal components PM/Scl100, Rrp4, and Rrp41, and PARN. From these and other data, we conclude that NMD in mammalian cells degrades mRNAs from both 5’ and 3’ ends by recruiting decapping and 5’–{\(>\)}3’ exonuclease activities as well as deadenylating and 3’–{\(>\)}5’ exonuclease activities.}, keywords = {0,3,Animals,CELLS,Codon,Codon Nonsense,CodonNonsense,COMPONENT,COMPONENTS,DECAPPING ENZYME,DECAY,Down-Regulation,Endoribonucleases,enzyme,enzymology,Exonucleases,Exoribonucleases,exosome,genetics,Hela Cells,human,Humans,La,MAMMALIAN-CELLS,Mammals,MECHANISM,metabolism,mRNA,mRNA decay,NMD,NONSENSE,nonsense-mediated mRNA decay,nosource,Nuclear Proteins,poly(A),protein,Proteins,Rna,RNA Messenger,RNAMessenger,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,transcription,TRANSCRIPTION FACTOR,Transcription Factors,Transcription Genetic,TranscriptionGenetic,translation,Upf1,XRN1} } % == BibTeX quality report for lejeuneNonsensemediatedMRNADecay2003: % ? unused Journal abbr (“Mol. Cell”)

@article{frischmeyerNonsensemediatedMRNADecay1999, title = {Nonsense-Mediated {{mRNA}} Decay in Health and Disease}, author = {Frischmeyer, P A and Dietz, H C}, year = 1999, journal = {Human Molecular Genetics}, volume = {8}, number = {10}, eprint = {10469842}, eprinttype = {pubmed}, pages = {1893–1900}, issn = {0964-6906}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10469842}, abstract = {All eukaryotes possess the ability to detect and degrade transcripts harboring premature signals for the termination of translation. Despite the ubiquitous nature of nonsense-mediated mRNA decay (NMD) and its demonstrated role in the modulation of phenotypes resulting from selected nonsense alleles, very little is known regarding its basic mechanism or the selective pressure for complete evolutionary conservation of this function. This review will present the current models of NMD that have been generated during the study of model organisms and mammalian cells. The physiological burden of nonsense transcripts and the emerging view that NMD plays a broad and critical role in the regulation of gene expression will also be discussed. Such issues are relevant to the proposal that pharmacological manipulation of NMD will find therapeutic application.}, pmid = {10469842}, keywords = {Adaptor Proteins Signal Transducing,Adaptor Proteins- Signal Transducing,Animals,Codon Nonsense,Codon- Nonsense,Fungal Proteins,Gene Expression Regulation,Genetic Diseases Inborn,Genetic Diseases- Inborn,Humans,Models Genetic,Models- Genetic,nosource,RNA Messenger,RNA Stability,RNA- Messenger,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Trans-Activators} } % == BibTeX quality report for frischmeyerNonsensemediatedMRNADecay1999: % ? unused Journal abbr (“Hum. Mol. Genet”)

@article{gatfieldNonsensemediatedMessengerRNA2004, title = {Nonsense-Mediated Messenger {{RNA}} Decay Is Initiated by Endonucleolytic Cleavage in {{Drosophila}}}, author = {Gatfield, David and Izaurralde, Elisa}, year = 2004, month = jun, journal = {Nature}, volume = {429}, number = {6991}, pages = {575–578}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature02559}, url = {http://www.nature.com/nature/journal/v429/n6991/abs/nature02559.html}, abstract = {In eukaryotic cells, messenger RNAs harbouring premature termination codons (PTCs) are rapidly degraded by a conserved post-transcriptional mechanism referred to as nonsense-mediated mRNA decay (NMD), which prevents the synthesis of truncated proteins that could be deleterious for the cell. Studies in yeast and mammals indicate that degradation by means of this pathway can occur from both the 5’ end of the message (involving decapping and 5’-to-3’ exonucleolytic digestion by XRN1) or the 3’ end (through accelerated deadenylation and exosome-mediated 3’-to-5’ decay). Here we show that, contrary to expectation, degradation of PTC-containing messages in Drosophila is initiated by endonucleolytic cleavage(s) in the vicinity of the nonsense codon. The resulting 5’ fragment is rapidly degraded by exonucleolytic digestion by the exosome, whereas the 3’ fragment is degraded by XRN1. This decay route is shown for several PTC-containing reporters, as well as an endogenous mRNA that is naturally regulated by NMD. We conclude that, despite conservation in the NMD machinery, PTC-containing transcripts are degraded in Drosophila by a mechanism that differs considerably from those described in yeast and mammals.}, keywords = {Animals,Cell Line,Codon Nonsense,Drosophila melanogaster,Drosophila Proteins,Endoribonucleases,Exoribonucleases,Models Genetic,nosource,RNA Messenger,RNA Stability} }

@article{huuskoNonsensemediatedDecayMicroarray2004, title = {Nonsense-Mediated Decay Microarray Analysis Identifies Mutations of {{EPHB2}} in Human Prostate Cancer}, author = {Huusko, Pia and {Ponciano-Jackson}, Damaris and Wolf, Maija and Kiefer, Jeff A and Azorsa, David O and Tuzmen, Sukru and Weaver, Don and Robbins, Christiane and Moses, Tracy and Allinen, Minna and Hautaniemi, Sampsa and Chen, Yidong and Elkahloun, Abdel and Basik, Mark and Bova, G Steven and Bubendorf, Lukas and Lugli, Alessandro and Sauter, Guido and Schleutker, Johanna and Ozcelik, Hilmi and Elowe, Sabine and Pawson, Tony and Trent, Jeffrey M and Carpten, John D and Kallioniemi, Olli-P and Mousses, Spyro}, year = 2004, month = sep, journal = {Nature Genetics}, volume = {36}, number = {9}, pages = {979–983}, publisher = {Nature Publishing Group}, issn = {1061-4036}, doi = {10.1038/ng1408}, url = {http://www.nature.com/ng/journal/vaop/ncurrent/full/ng1408.html}, abstract = {The identification of tumor-suppressor genes in solid tumors by classical cancer genetics methods is difficult and slow. We combined nonsense-mediated RNA decay microarrays and array-based comparative genomic hybridization for the genome-wide identification of genes with biallelic inactivation involving nonsense mutations and loss of the wild-type allele. This approach enabled us to identify previously unknown mutations in the receptor tyrosine kinase gene EPHB2. The DU 145 prostate cancer cell line, originating from a brain metastasis, carries a truncating mutation of EPHB2 and a deletion of the remaining allele. Additional frameshift, splice site, missense and nonsense mutations are present in clinical prostate cancer samples. Transfection of DU 145 cells, which lack functional EphB2, with wild-type EPHB2 suppresses clonogenic growth. Taken together with studies indicating that EphB2 may have an essential role in cell migration and maintenance of normal tissue architecture, our findings suggest that mutational inactivation of EPHB2 may be important in the progression and metastasis of prostate cancer.}, keywords = {Cell Line Tumor,Cell Line- Tumor,Codon Nonsense,Codon- Nonsense,Emetine,Genes Tumor Suppressor,Genes- Tumor Suppressor,Humans,Male,Molecular Sequence Data,Mutation,nosource,Oligonucleotide Array Sequence Analysis,Prostatic Neoplasms,Receptor EphB2,Receptor- EphB2,RNA Stability,Transfection} } % == BibTeX quality report for huuskoNonsensemediatedDecayMicroarray2004: % ? unused Journal abbr (“Nat. Genet”)

@article{kuperwasserNonsensemediatedDecayDoes2004, title = {Nonsense-Mediated Decay Does Not Occur within the Yeast Nucleus}, author = {Kuperwasser, Nicolas and Brogna, Saverio and Dower, Ken and Rosbash, Michael}, year = 2004, month = dec, journal = {RNA (New York, N.Y.)}, volume = {10}, number = {12}, eprint = {15547136}, eprinttype = {pubmed}, pages = {1907–1915}, issn = {1355-8382}, doi = {10.1261/rna.7132504}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15547136}, abstract = {Nonsense-mediated decay (NMD) is a eukaryotic regulatory process that degrades mRNAs with premature termination codons (PTCs). Although NMD is a translation-dependent process, there is evidence from mammalian systems that PTC recognition and mRNA degradation takes place in association with nuclei. Consistent with this notion, degradation of mammalian PTC-containing mRNAs occurs when they are bound by the cap binding complex (CBC) during a “pioneer” round of translation. Moreover, there are reports indicating that a PTC can trigger other nuclear events such as alternative splicing, abnormal 3’ end processing, and accumulation of pre-mRNA at transcription sites. To examine whether a PTC can elicit similar nuclear events in yeast, we used RNA export-defective mutants to sequester mRNAs within nuclei. The results indicate that nuclear PTC-containing yeast RNAs are NMD insensitive. We also observed by fluorescent in situ hybridization that there was no PTC effect on mRNA accumulated at the site of transcription. Finally, we show that yeast NMD occurs minimally if at all on CBC-bound transcripts, arguing against a CBC-mediated pioneer round of translation in yeast. The data taken together indicate that there are no direct consequences of a PTC within the yeast nucleus.}, pmid = {15547136}, keywords = {0,3,Alternative Splicing,ASSOCIATION,BINDING,BIOLOGY,Cap,Cap binding,Cell Nucleus,CEREVISIAE,Codon,Codon Nonsense,Codon- Nonsense,CodonNonsense,CODONS,COMPLEX,COMPLEXES,DECAY,degradation,Genes Reporter,Genes- Reporter,GenesReporter,genetics,GREEN FLUORESCENT PROTEIN,Green Fluorescent Proteins,Heat-Shock Response,in situ hybridization,In Situ Hybridization Fluorescence,In Situ Hybridization- Fluorescence,In Situ HybridizationFluorescence,La,metabolism,mRNA,MUTANTS,NMD,NONSENSE,nonsense-mediated decay,nosource,PREMATURE TERMINATION CODON,protein,Proteins,RECOGNITION,Research SupportU.S.Gov’tP.H.S.,Rna,RNA Cap-Binding Proteins,RNA Fungal,RNA Messenger,RNA- Fungal,RNA- Messenger,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SITE,SITES,splicing,SYSTEM,SYSTEMS,termination,TERMINATION CODON,TERMINATION-CODON,TRANSCRIPT,transcription,transcription site,TRANSCRIPTION SITES,translation,yeast} } % == BibTeX quality report for kuperwasserNonsensemediatedDecayDoes2004: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{maderazoNonsensecontainingMRNAsThat2003, title = {Nonsense-Containing {{mRNAs}} That Accumulate in the Absence of a Functional Nonsense-Mediated {{mRNA}} Decay Pathway Are Destabilized Rapidly upon Its Restitution}, author = {Maderazo, Alan B and Belk, Jonathan P and He, Feng and Jacobson, Allan}, year = 2003, month = feb, journal = {Molecular and Cellular Biology}, volume = {23}, number = {3}, pages = {842–851}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, doi = {10.1128/MCB.23.3.842-851.2003}, url = {http://mcb.asm.org/cgi/content/abstract/23/3/842}, abstract = {Nonsense-mediated mRNA decay (NMD) is a conserved proofreading mechanism that protects eukaryotic cells from the potentially deleterious effects of truncated proteins. Studies of Saccharomyces cerevisiae imply that NMD is a predominantly cytoplasmic decay pathway, while studies of mammalian systems suggest that decay of most substrate mRNAs may occur while they are still associated with the nucleus, possibly during a round of translation that occurs during their export to the cytoplasm. Complete entry of the latter mRNAs into the cytoplasm appears to render them immune to further NMD; i.e., they escape further susceptibility to this decay pathway. To determine if yeast cytoplasmic nonsense-containing mRNAs that evade decay are subsequently immune to NMD, we examined the consequences of placing each of the three UPF/NMD genes under the control of a galactose-inducible promoter. The decay kinetics of ADE2 and PGK1 nonsense-containing mRNAs were then analyzed when expression of UPF1, NMD2, or UPF3 was either repressed or subsequently induced. Results from these experiments demonstrated that activation of NMD caused rapid and immediate degradation of both substrate transcripts, with half-lives of both stable mRNA populations shortened to approximately 7 min. These findings make it unlikely that yeast nonsense-containing mRNAs can escape degradation by NMD and indicate that such mRNAs are available to this decay pathway at each round of translation.}, keywords = {3’-END FORMATION,Adaptor Proteins Signal Transducing,Animals,Carboxy-Lyases,Cell Nucleus,Codon Nonsense,Cytoplasm,DECAPPING ENZYME,DEPENDENT GLUTATHIONE-PEROXIDASE-1,EXON-EXON JUNCTIONS,Galactose,Gene Expression,Genes Fungal,Humans,MESSENGER-RNA DECAY,nosource,RNA Fungal,RNA Helicases,RNA Messenger,RNA Stability,RNA-Binding Proteins,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SHUTTLE VECTORS,SURVEILLANCE COMPLEX,Trans-Activators,TRANSLATION TERMINATION,TRIOSEPHOSPHATE ISOMERASE} } % == BibTeX quality report for maderazoNonsensecontainingMRNAsThat2003: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{workmanNoEvidenceThat1999, title = {No Evidence That {{mRNAs}} Have Lower Folding Free Energies than Random Sequences with the Same Dinucleotide Distribution}, author = {Workman, C and Krogh, A}, year = 1999, month = dec, journal = {Nucleic Acids Research}, volume = {27}, number = {24}, pages = {4816–4822}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/27.24.4816}, url = {http://nar.oxfordjournals.org/content/27/24/4816.short}, abstract = {This work investigates whether mRNA has a lower estimated folding free energy than random sequences. The free energy estimates are calculated by the mfold program for prediction of RNA secondary structures. For a set of 46 mRNAs it is shown that the predicted free energy is not significantly different from random sequences with the same dinucleotide distribution. For random sequences with the same mononucleotide distribution it has previously been shown that the native mRNA sequences have a lower predicted free energy, which indicates a more stable structure than random sequences. However, dinucleotide content is important when assessing the significance of predicted free energy as the physical stability of RNA secondary structure is known to depend on dinucleotide base stacking energies. Even known RNA secondary structures, like tRNAs, can be shown to have predicted free energies indistinguishable from randomized sequences. This suggests that the predicted free energy is not always a good determinant for RNA folding.}, keywords = {0,analysis,Animals,BASE,Base Composition,Base Sequence,chemistry,Databases Factual,Databases-Factual,DatabasesFactual,Dinucleoside Phosphates,Humans,La,MFOLD,Mice,Models Molecular,Models-Molecular,ModelsMolecular,mRNA,nosource,Nucleic Acid Conformation,Phosphates,PREDICTION,Research Support-Non-U.S.Gov’t,Research SupportNon-U.S.Gov’t,Rna,RNA folding,RNA Messenger,RNA SECONDARY STRUCTURE,RNA-Messenger,RNAMessenger,SECONDARY STRUCTURE,sequence,Sequence Analysis,SEQUENCE-ANALYSIS,SEQUENCES,stability,structure,Thermodynamics,tRNA} } % == BibTeX quality report for workmanNoEvidenceThat1999: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{wolfNMDMicroarrayAnalysis2005, title = {{{NMD}} Microarray Analysis for Rapid Genome-Wide Screen of Mutated Genes in Cancer}, author = {Wolf, Maija and Edgren, Henrik and Muggerud, Aslaug and Kilpinen, Sami and Huusko, Pia and S{}rlie, Therese and Mousses, Spyro and Kallioniemi, Olli}, year = 2005, journal = {Cellular Oncology: The Official Journal of the International Society for Cellular Oncology}, volume = {27}, number = {3}, pages = {169–173}, publisher = {IOS Press}, issn = {1570-5870}, url = {http://iospress.metapress.com/index/5NW6JR6ENFVEMHA3.pdf}, abstract = {Gene mutations play a critical role in cancer development and progression, and their identification offers possibilities for accurate diagnostics and therapeutic targeting. Finding genes undergoing mutations is challenging and slow, even in the post-genomic era. A new approach was recently developed by Noensie and Dietz to prioritize and focus the search, making use of nonsense-mediated mRNA decay (NMD) inhibition and microarray analysis (NMD microarrays) in the identification of transcripts containing nonsense mutations. We combined NMD microarrays with array-based CGH (comparative genomic hybridization) in order to identify inactivation of tumor suppressor genes in cancer. Such a “mutatomics” screening of prostate cancer cell lines led to the identification of inactivating mutations in the EPHB2 gene. Up to 8% of metastatic uncultured prostate cancers also showed mutations of this gene whose loss of function may confer loss of tissue architecture. NMD microarray analysis could turn out to be a powerful research method to identify novel mutated genes in cancer cell lines, providing targets that could then be further investigated for their clinical relevance and therapeutic potential.}, keywords = {Animals,Cell Line Tumor,Cell Line- Tumor,Codon Nonsense,Codon- Nonsense,Emetine,Genetic Testing,Humans,Male,Mutation,Neoplasms,nosource,Oligonucleotide Array Sequence Analysis,Prostatic Neoplasms,Protein Synthesis Inhibitors,Receptor EphB2,Receptor- EphB2,RNA Neoplasm,RNA Stability,RNA- Neoplasm} } % == BibTeX quality report for wolfNMDMicroarrayAnalysis2005: % ? unused Journal abbr (“Cell. Oncol”)

@article{singhNewInsightsFormation2003, title = {New Insights into the Formation of Active Nonsense-Mediated Decay Complexes}, author = {Singh, Guramrit and {Lykke-Andersen}, Jens}, year = 2003, month = sep, journal = {Trends in Biochemical Sciences}, volume = {28}, number = {9}, pages = {464–466}, publisher = {Elsevier}, issn = {0968-0004}, doi = {10.1016/S0968-0004(03)00176-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000403001762}, abstract = {In the nonsense-mediated mRNA decay (NMD) pathway, an exon-junction protein complex (EJC) and hUpf proteins mediate rapid downregulation of aberrant mRNAs that terminate translation upstream of the last splice junction. Two EJC subunits, Y14 and RNPS1, have been proposed to act as a link between splicing and NMD by recruiting hUpf3 and the other hUpf proteins. New studies now present evidence that Y14 is directly involved in NMD, and that Y14 is required for hUpf3 activity. These findings suggest unforeseen intricacies in the formation of active NMD complexes.}, keywords = {0,Animals,BIOLOGY,Codon,Codon Nonsense,CodonNonsense,COMPLEX,COMPLEXES,DECAY,Eukaryotic Cells,Exons,genetics,human,Humans,La,Macromolecular Substances,Macromolecular Systems,metabolism,mRNA,mRNA decay,NMD,NONSENSE,nonsense-mediated decay,nonsense-mediated mRNA decay,nosource,PATHWAY,physiology,protein,Protein Biosynthesis,PROTEIN COMPLEX,Protein Subunits,Proteins,Review,Rna,RNA Messenger,RNA Splicing,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAMessenger,splicing,SUBUNIT,SUBUNITS,SYSTEM,SYSTEMS,translation,TranslationGenetic,UPSTREAM} } % == BibTeX quality report for singhNewInsightsFormation2003: % ? unused Journal abbr (“Trends Biochem. Sci”)

@article{hilbersNewDevelopmentsStructure1998, title = {New Developments in Structure Determination of Pseudoknots}, author = {Hilbers, C W and Michiels, P J and Heus, H A}, year = 1998, journal = {Biopolymers}, volume = {48}, number = {2-3}, eprint = {10333742}, eprinttype = {pubmed}, pages = {137–153}, issn = {0006-3525}, doi = {10.1002/(SICI)1097-0282(1998)48:2<137::AID-BIP4>3.0.CO;2-H}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10333742}, abstract = {Recently, several high-resolution structures of-RNA pseudoknots have become available. Here we review the progress in this area. The majority of the structures obtained belong to the classical or H-type pseudoknot family. The most complicated pseudoknot structure elucidated so far is the Hepatitis Delta Virus ribozyme, which forms a nested double pseudoknot. In particular, the structure-function relationships of the H-type pseudoknots involved in translational frameshifting have received much attention. All molecules considered show interesting new structural motifs.}, pmid = {10333742}, keywords = {Base Sequence,Hepatitis Delta Virus,Molecular Sequence Data,nosource,Nucleic Acid Conformation,RNA,RNA Catalytic,Structure-Activity Relationship} }

@article{pringleMutationsRibosomalProtein2004, title = {Mutations in Ribosomal Protein {{L3}} and {{23S}} Ribosomal {{RNA}} at the Peptidyl Transferase Centre Are Associated with Reduced Susceptibility to Tiamulin in {{Brachyspira}} Spp. Isolates}, author = {Pringle, M{"a}rit and Poehlsgaard, Jacob and Vester, Birte and Long, Katherine S}, year = 2004, month = dec, journal = {Molecular Microbiology}, volume = {54}, number = {5}, pages = {1295–1306}, publisher = {Wiley Online Library}, issn = {0950-382X}, doi = {10.1111/j.1365-2958.2004.04373.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2004.04373.x/full}, abstract = {The pleuromutilin antibiotic tiamulin binds to the ribosomal peptidyl transferase centre. Three groups of Brachyspira spp. isolates with reduced tiamulin susceptibility were analysed to define resistance mechanisms to the drug. Mutations were identified in genes encoding ribosomal protein L3 and 23S rRNA at positions proximal to the peptidyl transferase centre. In two groups of laboratory-selected mutants, mutations were found at nucleotide positions 2032, 2055, 2447, 2499, 2504 and 2572 of 23S rRNA (Escherichia coli numbering) and at amino acid positions 148 and 149 of ribosomal protein L3 (Brachyspira pilosicoli numbering). In a third group of clinical B. hyodysenteriae isolates, only a single mutation at amino acid 148 of ribosomal protein L3 was detected. Chemical footprinting experiments show a reduced binding of tiamulin to ribosomal subunits from mutants with decreased susceptibility to the drug. This reduction in drug binding is likely the resistance mechanism for these strains. Hence, the identified mutations located near the tiamulin binding site are predicted to be responsible for the resistance phenotype. The positions of the mutated residues relative to the bound drug advocate a model where the mutations affect tiamulin binding indirectly through perturbation of nucleotide U2504.}, keywords = {ACID,Amino Acid Substitution,AMINO-ACID,Anti-Bacterial Agents,antibiotic,antibiotics,Bacterial Proteins,Base Sequence,BINDING,BINDING-SITE,Diterpenes,DNA Mutational Analysis,Drug Resistance Bacterial,Escherichia coli,ESCHERICHIA-COLI,gene,Genes,L3,La,MECHANISM,MECHANISMS,MODEL,Models Molecular,Molecular Sequence Data,MUTANTS,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,peptidyl transferase,PEPTIDYL-TRANSFERASE,Phenotype,POSITION,POSITIONS,protein,Protein Synthesis Inhibitors,RESIDUES,RESISTANCE,RIBOSOMAL PEPTIDYL TRANSFERASE,Ribosomal Proteins,ribosomal RNA,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,Rna,RNA Bacterial,RNA Ribosomal 23S,rRNA,SITE,Spirochaetales,SUBUNIT,SUBUNITS} } % == BibTeX quality report for pringleMutationsRibosomalProtein2004: % ? unused Journal abbr (“Mol. Microbiol”)

@article{brierleyMutationalAnalysisSlipperysequence1992a, title = {Mutational Analysis of the “Slippery-Sequence” Component of a Coronavirus Ribosomal Frameshifting Signal}, author = {Brierley, I and Jenner, A J and Inglis, S C}, year = 1992, month = sep, journal = {Journal of Molecular Biology}, volume = {227}, number = {2}, eprint = {1404364}, eprinttype = {pubmed}, pages = {463–479}, issn = {0022-2836}, doi = {10.1016/0022-2836(92)90901-U}, url = {http://www.ncbi.nlm.nih.gov/pubmed/1404364}, abstract = {The ribosomal frameshift signal in the genomic RNA of the coronavirus IBV is composed of two elements, a heptanucleotide “slippery-sequence” and a downstream RNA pseudoknot. We have investigated the kinds of slippery sequence that can function at the IBV frameshift site by analysing the frameshifting properties of a series of slippery-sequence mutants. We firstly confirmed that the site of frameshifting in IBV was at the heptanucleotide stretch UUUAAAC, and then used our knowledge of the pseudoknot structure and a suitable reporter gene to prepare an expression construct that allowed both the magnitude and direction of ribosomal frameshifting to be determined for candidate slippery sequences. Our results show that in almost all of the sequences tested, frameshifting is strictly into the -1 reading frame. Monotonous runs of nucleotides, however, gave detectable levels of a -2/+1 frameshift product, and U stretches in particular gave significant levels (2% to 21%). Preliminary evidence suggests that the RNA pseudoknot may play a role in influencing frameshift direction. The spectrum of slip-sequences tested in this analysis included all those known or suspected to be utilized in vivo. Our results indicate that triplets of A, C, G and U are functional when decoded in the ribosomal P-site following slippage (XXXYYYN) although C triplets were the least effective. In the A-site (XXYYYYN), triplets of C and G were non-functional. The identity of the nucleotide at position 7 of the slippery sequence (XXXYYYN) was found to be a critical determinant of frameshift efficiency and we show that a hierarchy of frameshifting exists for A-site codons. These observations lead us to suggest that ribosomal frameshifting at a particular site is determined, at least in part, by the strength of the interaction of normal cellular tRNAs with the A-site codon and does not necessarily involve specialized “shifty” tRNAs.}, pmid = {1404364}, keywords = {A-SITE,analysis,Base Sequence,Cloning Molecular,Codon,COMPONENT,Coronaviridae,DNA Viral,efficiency,expression,frameshift,Frameshifting,gene,Gene Expression Regulation Viral,genomic,IN-VIVO,Molecular Sequence Data,Mutagenesis Site-Directed,MUTATIONAL ANALYSIS,nosource,Nucleotides,Open Reading Frames,P-SITE,Plasmids,pseudoknot,Regulatory Sequences Nucleic Acid,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,RIBOSOMAL FRAMESHIFTING SIGNAL,Ribosomes,Rna,RNA PSEUDOKNOT,RNA Transfer,RNA Viral,sequence,SIGNAL,structure,tRNA} } % == BibTeX quality report for brierleyMutationalAnalysisSlipperysequence1992a: % ? unused Journal abbr (“J. Mol. Biol”)

@article{sungMutationalAnalysisRNA1998, title = {Mutational Analysis of the {{RNA}} Pseudoknot Involved in Efficient Ribosomal Frameshifting in Simian Retrovirus-1}, author = {Sung, D and Kang, H}, year = 1998, month = mar, journal = {Nucleic Acids Research}, volume = {26}, number = {6}, pages = {1369–1372}, publisher = {Oxford Univ Press}, issn = {0305-1048}, doi = {10.1093/nar/26.6.1369}, url = {http://nar.oxfordjournals.org/content/26/6/1369.short}, abstract = {Mutational effects on frameshifting efficiency of the RNA pseudoknot involved in ribosomal frameshifting in simian retrovirus-1 (SRV-1) have been investigated. The primary sequence and the proposed secondary structure of the SRV-1 pseudoknot are similar to those of other efficient frameshifting pseudoknots in mouse mammary tumor virus (MMTV) and feline immunodeficiency virus (FIV), where an unpaired adenine nucleotide intercalates between stem 1 and stem 2. In SRV-1 pseudoknot, the adenine nucleotide in between stem 1 and stem 2 has a potential to form an AU base pair with the last uridine nucleotide in the loop 2, resulting in a continuous A-form helix with coaxially stacked stem 1 and stem 2. To test whether this AU base pairing and coaxial stacking of stem 1 and stem 2 is absolutely required for efficient frameshifting in SRV-1, a series of mutants changing this potential A.U base pair to either G.C base pair or A.A, A.G, A.C, G.A, G.G mismatch is generated, and their frameshifting efficiencies are investigated in vitro using rabbit reticulocyte lysate translation assay. The frameshifting abilities of these mutant pseudoknots are similar to that of the wild-type pseudoknot, suggesting that the A*U base pair in between stem 1 and stem 2 is not necessary to promote efficient frameshifting in SRV-1. These results reveal that coaxial stacking of stem 1 and stem 2 with a Watson-Crick A.U base pair in between two stems is not a required structural feature of the pseudoknot for promoting efficient frameshifting in SRV-1. Our mutational data suggest that SRV-1 pseudoknot adopts similar structural features common to other efficient frameshifting pseudoknots as observed in MMTV and FIV.}, keywords = {Adenine,analysis,Animals,BASE,Base Composition,Base Pairing,Base Sequence,BASE-PAIR,Cats,efficiency,Frameshifting,Frameshifting Ribosomal,GENE-EXPRESSION,IDENTIFICATION,Immunodeficiency Virus Feline,IMMUNODEFICIENCY-VIRUS,In Vitro,IN-VITRO,LOOP,lysate,Mammary Tumor Virus Mouse,Mice,MMTV,Mutagenesis Site-Directed,MUTANTS,Mutation,MUTATIONAL ANALYSIS,nosource,Nucleic Acid Conformation,pseudoknot,pseudoknots,Rabbits,Reticulocytes,Retroviruses Simian,ribosomal frameshifting,Rna,RNA PSEUDOKNOT,RNA Viral,SECONDARY STRUCTURE,sequence,SERIES,SIGNAL,SIMIAN RETROVIRUS-1,Species Specificity,Structural,structure,translation,TRANSLATIONAL SUPPRESSION,Uridine,virus} } % == BibTeX quality report for sungMutationalAnalysisRNA1998: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{brierleyMutationalAnalysisRNA1991a, title = {Mutational Analysis of the {{RNA}} Pseudoknot Component of a Coronavirus Ribosomal Frameshifting Signal.}, author = {Brierley, I and Rolley, N J and Jenner, A J and Inglis, S C}, year = 1991, month = aug, journal = {Journal of Molecular Biology}, volume = {220}, number = {4}, eprint = {1880803}, eprinttype = {pubmed}, pages = {889–902}, issn = {0022-2836}, doi = {10.1016/0022-2836(91)90361-9}, url = {http://www.ncbi.nlm.nih.gov/pubmed/1880803}, abstract = {The genomic RNA of the coronavirus IBV contains an efficient ribosomal frameshift signal at the junction of the overlapping 1a and 1b open reading frames. The signal is comprised of two elements, a heptanucleotide “slip-site” and a downstream tertiary RNA structure in the form of an RNA pseudoknot. We have investigated the structure of the pseudoknot and its contribution to the frameshift process by analysing the frameshifting properties of a series of pseudoknot mutants. Our results show that the pseudoknot structure closely resembles that which can be predicted from current building rules, although base-pair formation at the region where the two pseudoknot stems are thought to stack co-axially is not a pre-requisite for efficient frameshifting. The stems, however, must be in close proximity to generate a functional structure. In general, the removal of a single base-pair contact in either stem is sufficient to reduce or abolish frameshifting. No primary sequence determinants in the stems or loops appear to be involved in the frameshift process; as long as the overall structure is maintained, frameshifting is highly efficient. Thus, small insertions into the pseudoknot loops and a deletion in loop 2 that reduced its length to the predicted functional minimum did not influence frameshifting. However, a large insertion (467 nucleotides) into loop 2 abolished frameshifting. A simple stem-loop structure with a base-paired stem of the same length and nucleotide composition as the stacked stems of the pseudoknot could not functionally replace the pseudoknot, suggesting that some particular conformational feature of the pseudoknot determines its ability to promote frameshifting.}, pmid = {1880803}, keywords = {analysis,Base Sequence,Cloning Molecular,COMPONENT,Coronaviridae,DNA Mutational Analysis,Frameshifting,Gene Expression Regulation Viral,Genes Overlapping,Hydrogen Bonding,Molecular Sequence Data,MUTATIONAL ANALYSIS,nosource,Nucleic Acid Conformation,Protein Biosynthesis,pseudoknot,ribosomal frameshifting,RIBOSOMAL FRAMESHIFTING SIGNAL,Rna,RNA Messenger,RNA PSEUDOKNOT,RNA Viral,SIGNAL,Structure-Activity Relationship,virus} } % == BibTeX quality report for brierleyMutationalAnalysisRNA1991a: % ? unused Journal abbr (“J. Mol. Biol”)

@article{gregoryMutationalAnalysis16S2005a, title = {Mutational Analysis of {{16S}} and {{23S rRNA}} Genes of {{Thermus}} Thermophilus}, author = {Gregory, Steven T and Carr, Jennifer F and {Rodriguez-Correa}, Daniel and Dahlberg, Albert E}, year = 2005, month = jul, journal = {Journal of Bacteriology}, volume = {187}, number = {14}, eprint = {15995195}, eprinttype = {pubmed}, pages = {4804–4812}, issn = {0021-9193}, doi = {10.1128/JB.187.14.4804-4812.2005}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15995195}, abstract = {Structural studies of the ribosome have benefited greatly from the use of organisms adapted to extreme environments. However, little is known about the mechanisms by which ribosomes or other ribonucleoprotein complexes have adapted to functioning under extreme conditions, and it is unclear to what degree mutant phenotypes of extremophiles will resemble those of their counterparts adapted to more moderate environments. It is conceivable that phenotypes of mutations affecting thermophilic ribosomes, for instance, will be influenced by structural adaptations specific to a thermophilic existence. This consideration is particularly important when using crystal structures of thermophilic ribosomes to interpret genetic results from nonextremophilic species. To address this issue, we have conducted a survey of spontaneously arising antibiotic-resistant mutants of the extremely thermophilic bacterium Thermus thermophilus, a species which has featured prominently in ribosome structural studies. We have accumulated over 20 single-base substitutions in T. thermophilus 16S and 23S rRNA, in the decoding site and in the peptidyltransferase active site of the ribosome. These mutations produce phenotypes that are largely identical to those of corresponding mutants of mesophilic organisms encompassing a broad phylogenetic range, suggesting that T. thermophilus may be an ideal model system for the study of ribosome structure and function.}, pmid = {15995195}, keywords = {0,16S,analysis,Anti-Bacterial Agents,Bacteria,Bacterial,Base Sequence,BIOLOGY,COMPLEX,COMPLEXES,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,decoding,Dna,DNA Primers,drug effects,gene,Genes,Genetic,genetics,La,MECHANISM,MECHANISMS,MODEL,Models Molecular,ModelsMolecular,Molecular Biology,Molecular Sequence Data,Mutagenesis,MUTANTS,Mutation,MUTATIONAL ANALYSIS,MUTATIONS,nosource,Nucleic Acid Conformation,Peptidyltransferase,pharmacology,Phenotype,Research SupportN.I.H.Extramural,Research SupportU.S.Gov’tP.H.S.,RIBONUCLEOPROTEIN,ribosome,Ribosomes,Rna,RNA Bacterial,RNA Ribosomal 16S,RNA Ribosomal 23S,RNABacterial,RNARibosomal16S,RNARibosomal23S,rRNA,rRNA genes,SITE,Structural,structure,SYSTEM,T,THERMOPHILIC BACTERIUM,Thermus,Thermus thermophilus,THERMUS-THERMOPHILUS} } % == BibTeX quality report for gregoryMutationalAnalysis16S2005a: % ? unused Journal abbr (“J. Bacteriol”)

@article{falaheeMutantsTranslationalComponents1988, title = {Mutants of Translational Components That Alter Reading Frame by Two Steps Forward or One Step Back.}, author = {Falahee, M B and Weiss, R B and O’Connor, M and Doonan, S and Gesteland, R F and Atkins, J F}, year = 1988, month = dec, journal = {The Journal of Biological Chemistry}, volume = {263}, number = {34}, eprint = {2848024}, eprinttype = {pubmed}, pages = {18099–18103}, publisher = {ASBMB}, issn = {0021-9258}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2848024 http://www.jbc.org/content/263/34/18099.short}, abstract = {External suppressors, sufS, of a -1 frameshift mutant cause ribosomes to shift into the -1 frame when reading the sequence CAG GGA GUG. The resulting product is not Gln-Gly-Val but Gln-Gly-Ser with Ser being encoded by the underlined AGU. The alleles investigated are approximately 2% efficient in causing frameshifting. Two other suppressors, hopR and hopE of the same -1 frameshift mutant, cause some ribosomes reading the sequence GUG UG to decode a single amino acid, Val, from the five nucleotides. The possibility is considered that peptidyl-tRNA(Val) dissociates from the mRNA, but re-pairs in a triplet manner after the mRNA slips forward by two bases.}, pmid = {2848024}, keywords = {Amino Acid Sequence,Bacterial,Bacterial Proteins,Bacterial Proteins: genetics,Base Sequence,Codon,Escherichia coli,Escherichia coli: genetics,Genes,Genes Bacterial,Genetic,Genetic Vectors,Messenger,Molecular Sequence Data,Mutation,nosource,Plasmids,Protein Biosynthesis,Ribosomes,Ribosomes: metabolism,RNA,RNA Messenger,Suppression,Suppression Genetic} } % == BibTeX quality report for falaheeMutantsTranslationalComponents1988: % ? unused Journal abbr (“J. Biol. Chem”)

@article{oconnorMultipleDefectsTranslation2004, title = {Multiple Defects in Translation Associated with Altered Ribosomal Protein {{L4}}}, author = {O’Connor, Michael and Gregory, Steven T and Dahlberg, Albert E}, year = 2004, journal = {Nucleic Acids Research}, volume = {32}, number = {19}, pages = {5750–5756}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gkh913}, url = {http://nar.oxfordjournals.org/content/32/19/5750.short}, abstract = {The ribosomal proteins L4 and L22 form part of the peptide exit tunnel in the large ribosomal subunit. In Escherichia coli, alterations in either of these proteins can confer resistance to the macrolide antibiotic, erythromycin. The structures of the 30S as well as the 50S subunits from each antibiotic resistant mutant differ from wild type in distinct ways and L4 mutant ribosomes have decreased peptide bond-forming activity. Our analyses of the decoding properties of both mutants show that ribosomes carrying the altered L4 protein support increased levels of frameshifting, missense decoding and readthrough of stop codons during the elongation phase of protein synthesis and stimulate utilization of non-AUG codons and mutant initiator tRNAs at initiation. L4 mutant ribosomes are also altered in their interactions with a range of 30S-targeted antibiotics. In contrast, the L22 mutant is relatively unaffected in both decoding activities and antibiotic interactions. These results suggest that mutations in the large subunit protein L4 not only alter the structure of the 50S subunit, but upon subunit association, also affect the structure and function of the 30S subunit.}, keywords = {0,antibiotic,antibiotics,ASSOCIATION,chemistry,Codon,Codon Terminator,CODONS,CodonTerminator,decoding,drug effects,elongation,Erythromycin,Escherichia coli,ESCHERICHIA-COLI,FORM,Frameshifting,Frameshifting Ribosomal,FrameshiftingRibosomal,genetics,INHIBITOR,inhibitors,initiation,La,metabolism,MUTANTS,Mutation,Mutation Missense,MutationMissense,MUTATIONS,nosource,pharmacology,physiology,protein,Protein Biosynthesis,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,Proteins,readthrough,Research SupportU.S.Gov’tP.H.S.,RESISTANCE,RESISTANT,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNA Messenger,RNA Transfer Met,RNAMessenger,RNATransferMet,STOP CODON,structure,SUBUNIT,subunit association,SUBUNITS,Support,SYNTHESIS INHIBITORS,translation,tRNA,WILD-TYPE} } % == BibTeX quality report for oconnorMultipleDefectsTranslation2004: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{wagnerMRNASurveillancePerfect2002, title = {{{mRNA}} Surveillance: The Perfect Persist}, author = {Wagner, Eileen and {Lykke-Andersen}, Jens}, year = 2002, month = aug, journal = {Journal of Cell Science}, volume = {115}, number = {Pt 15}, pages = {3033–3038}, publisher = {Company of Biologists}, issn = {0021-9533}, url = {http://jcs.biologists.org/content/115/15/3033.short}, abstract = {In eukaryotes, an elaborate set of mechanisms has evolved to ensure that the multistep process of gene expression is accurately executed and adapted to cellular needs. The mRNA surveillance pathway works in this context by assessing the quality of mRNAs to ensure that they are suitable for translation. mRNA surveillance facilitates the detection and destruction of mRNAs that contain premature termination codons by a process called nonsense-mediated decay. Moreover, recent studies have shown that a distinct mRNA surveillance process, called nonstop decay, is responsible for depleting mRNAs that lack in-frame termination codons. mRNA surveillance thereby prevents the synthesis of truncated and otherwise aberrant proteins, which can have dominant-negative and other deleterious effects.}, keywords = {Animals,Codon Nonsense,Codon- Nonsense,Eukaryotic Cells,Gene Expression Regulation,Humans,nosource,Protein Biosynthesis,Proteins,RNA Helicases,RNA Messenger,RNA- Messenger,Trans-Activators} } % == BibTeX quality report for wagnerMRNASurveillancePerfect2002: % ? unused Journal abbr (“J. Cell. Sci”)

@article{hillerenMRNASurveillanceEukaryotes1999, title = {{{mRNA}} Surveillance in Eukaryotes: Kinetic Proofreading of Proper Translation Termination as Assessed by {{mRNP}} Domain Organization?}, author = {Hilleren, P and Parker, R}, year = 1999, month = jun, journal = {RNA (New York, N.Y.)}, volume = {5}, number = {6}, pages = {711–719}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, doi = {10.1017/S1355838299990519}, url = {http://rnajournal.cshlp.org/content/5/6/711.short}, abstract = {In the last few years it has become clear that a conserved mRNA degradation system, referred to as mRNA surveillance, exists in eukaryotic cells to degrade aberrant mRNAs. This process plays an important role in checking that mRNAs have been properly synthesized and functions, at least in part, to increase the fidelity of gene expression by degrading aberrant mRNAs that, if translated, would produce truncated proteins. A critical issue is how normal and aberrant mRNAs are distinguished and how that distinction leads to differences in mRNA stability. Recent results suggest a model with three main points. First, mRNPs have a domain organization that is, in part, a reflection of the completion of nuclear pre-mRNA processing events. Second, the critical aspect of distinguishing a normal from an aberrant mRNA is the environment of the translation termination codon as determined by the organization of the mRNP domains. Third, the cell distinguishes proper from improper termination through an internal clock that is the rate of ATP hydrolysis by Upf1p. If termination is completed before ATP hydrolysis, the mRNA is protected from mRNA degradation. Conversely, if termination is slow, then ATP hydrolysis and a structural rearrangement occurs before termination is completed, which affects the fate of the terminating ribosome in a manner that fails to stabilize the mRNA. This proposed system of distinguishing normal from aberrant transcripts is similar to, but distinct from other systems of kinetic proofreading that affect the accuracy of other biogenic processes such as translation accuracy and spliceosome assembly.}, keywords = {3’ Untranslated Regions,39 utr,99303364,accuracy,animal,Animals,assembly,ATP,chemistry,Codon,degradation,Endoribonucleases,Eukaryotic Cells,expression,Fidelity,gene,Gene Expression,GENE-EXPRESSION,human,Humans,Hydrolysis,mecha-,metabolism,mRNA,mrna turnover,mrnas are distinguished from,nism by which aberrant,nmd,NMD,nosource,physiology,proofreading,protein,Protein Biosynthesis,Proteins,Review,Ribonucleoproteins,ribosome,Ribosomes,RNA Helicases,RNA Messenger,RNAMessenger,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,stability,Structural,surveillance refers to a,SYSTEM,termination,Terminator Regions (Genetics),Terminator Regions Genetic,the process of mrna,Trans-Activators,translation,TranslationGenetic,upf1,what is mrna surveillance} } % == BibTeX quality report for hillerenMRNASurveillanceEukaryotes1999: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{seffensMRNAsHaveGreater1999, title = {{{mRNAs}} Have Greater Negative Folding Free Energies than Shuffled or Codon Choice Randomized Sequences}, author = {Seffens, W and Digby, D}, year = 1999, month = apr, journal = {Nucleic Acids Research}, volume = {27}, number = {7}, pages = {1578–1584}, publisher = {Oxford Univ Press}, issn = {0305-1048}, doi = {10.1093/nar/27.7.1578}, url = {http://nar.oxfordjournals.org/content/27/7/1578.short}, abstract = {An examination of 51 mRNA sequences in GenBank has revealed that calculated mRNA folding is more stable than expected by chance. Free energy minimization calculations of native mRNA sequences are more negative than randomized mRNA sequences with the same base composition and length. Randomization of the coding region of genes yields folding free energies of less negative magnitude than the original native mRNA sequence. Randomization of codon choice, while still preserving original base composition, also results in less stable mRNAs. This suggests that a bias in the selection of codons favors the potential formation of mRNA structures which contribute to folding stability.}, keywords = {0,BASE,Base Composition,chemistry,CODING REGION,Codon,CODONS,gene,Genes,La,mRNA,nosource,Nucleic Acid Conformation,REGION,Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,Rna,RNA Messenger,RNAMessenger,SELECTION,sequence,SEQUENCES,stability,structure,SYSTEM,SYSTEMS} } % == BibTeX quality report for seffensMRNAsHaveGreater1999: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{kawaguchiMRNASequenceFeatures2005, title = {{{mRNA}} Sequence Features That Contribute to Translational Regulation in {{Arabidopsis}}}, author = {Kawaguchi, Riki and {Bailey-Serres}, Julia}, year = 2005, journal = {Nucleic Acids Research}, volume = {33}, number = {3}, pages = {955–965}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gki240}, url = {http://nar.oxfordjournals.org/content/33/3/955.short}, abstract = {DNA microarrays were used to evaluate the regulation of the proportion of individual mRNA species in polysomal complexes in leaves of Arabidopsis thaliana under control growth conditions and following a mild dehydration stress (DS). The analysis determined that the percentage of an individual gene transcript in polysomes (ribosome loading) ranged from over 95 to {\(<\)}5%. DS caused a decrease in ribosome loading from 82 to 72%, with maintained polysome association for over 60% of the mRNAs with an increased abundance. To identify sequence features responsible for translational regulation, ribosome loading values and features of full-length mRNA sequences were compared. mRNAs with extreme length or high GU content in the 5’-untranslated regions (5’-UTRs) were generally poorly translated. Under DS, mRNAs with both a high GC content in the 5’-UTR and long open reading frame showed a significant impairment in ribosome loading. Evaluation of initiation A+1UG codon context revealed distinctions in the frequency of adenine in nucleotides -10 to -1 (especially at -4 and -3) in mRNAs with different ribosome loading values. Notably, the mRNA features that contribute to translational regulation could not fully explain the variation in ribosome loading, indicating that additional factors contribute to translational regulation in Arabidopsis.}, keywords = {3’ Untranslated Regions,5’ Untranslated Regions,Arabidopsis,Codon,Codon Initiator,Gene Expression Profiling,Gene Expression Regulation Plant,nosource,Oligonucleotide Array Sequence Analysis,Open Reading Frames,Polyribosomes,Protein Biosynthesis,Regulatory Sequences Ribonucleic Acid,Ribosomes,RNA Messenger,RNA Plant} } % == BibTeX quality report for kawaguchiMRNASequenceFeatures2005: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{dahlseidMRNAsEncodingTelomerase2003, title = {{{mRNAs}} Encoding Telomerase Components and Regulators Are Controlled by {{UPF}} Genes in {{Saccharomyces}} Cerevisiae}, author = {Dahlseid, Jeffrey N and {Lew-Smith}, Jodi and Lelivelt, Michael J and Enomoto, Shinichiro and Ford, Amanda and Desruisseaux, Michelle and McClellan, Mark and Lue, Neal and Culbertson, Michael R and Berman, Judith}, year = 2003, month = feb, journal = {Eukaryotic Cell}, volume = {2}, number = {1}, pages = {134–142}, publisher = {Am Soc Microbiol}, issn = {1535-9778}, doi = {10.1128/​EC.2.1.134-142.2003}, url = {http://ec.asm.org/cgi/content/abstract/2/1/134 http://ec.asm.org/content/2/1/134.short}, abstract = {Telomeres, the chromosome ends, are maintained by a balance of activities that erode and replace the terminal DNA sequences. Furthermore, telomere-proximal genes are often silenced in an epigenetic manner. In Saccharomyces cerevisiae, average telomere length and telomeric silencing are reduced by loss of function of UPF genes required in the nonsense-mediated mRNA decay (NMD) pathway. Because NMD controls the mRNA levels of several hundred wild-type genes, we tested the hypothesis that NMD affects the expression of genes important for telomere functions. In upf mutants, high-density oligonucleotide microarrays and Northern blots revealed that the levels of mRNAs were increased for genes encoding the telomerase catalytic subunit (Est2p), in vivo regulators of telomerase (Est1p, Est3p, Stn1p, and Ten1p), and proteins that affect telomeric chromatin structure (Sas2p and Orc5p). We investigated whether overexpressing these genes could mimic the telomere length and telomeric silencing phenotypes seen previously in upf mutant strains. Increased dosage of STN1, especially in combination with increased dosage of TEN1, resulted in reduced telomere length that was indistinguishable from that in upf mutants. Increased levels of STN1 together with EST2 resulted in reduced telomeric silencing like that of upf mutants. The half-life of STN1 mRNA was not altered in upf mutant strains, suggesting that an NMD-controlled transcription factor regulates the levels of STN1 mRNA. Together, these results suggest that NMD maintains the balance of gene products that control telomere length and telomeric silencing primarily by maintaining appropriate levels of STN1, TEN1, and EST2 mRNA.}, keywords = {0,cell cycle,Cell Cycle Proteins,CEREVISIAE,chemistry,Chromatin,Codon,Codon Nonsense,Codon-Nonsense,CodonNonsense,COMPONENT,COMPONENTS,DECAY,Dna,DNA sequence,DNA-Binding Proteins,enzymology,expression,gene,Gene Dosage,Gene Expression Regulation Enzymologic,Gene Expression Regulation Fungal,Gene Expression Regulation-Enzymologic,Gene Expression Regulation-Fungal,Gene Expression RegulationEnzymologic,Gene Expression RegulationFungal,Gene Silencing,GENE-PRODUCT,Genes,Genes Regulator,Genes-Regulator,GenesRegulator,genetics,Half-Life,Helicase,IN-VIVO,La,mRNA,mRNA decay,MUTANTS,Mutation,NMD,NONSENSE,nonsense-mediated mRNA decay,nosource,PATHWAY,Phenotype,physiology,PRODUCT,PRODUCTS,protein,Proteins,REVERSE-TRANSCRIPTASE,Rna,RNA HELICASE,RNA Helicases,RNA Messenger,RNA-Messenger,RNAMessenger,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,structure,SUBUNIT,support-non-u.s.gov’t,support-u.s.gov’t-non-p.h.s.,support-u.s.gov’t-p.h.s.,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Telomerase,Telomere,Telomere-Binding Proteins,transcription,TRANSCRIPTION FACTOR,UPF,Upf1,UPF1 PROTEIN,WILD-TYPE} }

@article{peltzMRNADestabilizationTriggered1993, title = {{{mRNA}} Destabilization Triggered by Premature Translational Termination Depends on at Least Three Cis-Acting Sequence Elements and One Trans-Acting Factor.}, author = {Peltz, S W and Brown, A H and Jacobson, A}, year = 1993, month = sep, journal = {Genes & Development}, volume = {7}, number = {9}, pages = {1737–1754}, issn = {0890-9369}, doi = {10.1101/gad.7.9.1737}, url = {http://www.genesdev.org/cgi/doi/10.1101/gad.7.9.1737 http://genesdev.cshlp.org/content/7/9/1737.short}, abstract = {Nonsense mutations in a gene can accelerate the decay rate of the mRNA transcribed from that gene, a phenomenon we describe as nonsense-mediated mRNA decay. Using amber (UAG) mutants of the yeast PGK1 gene as a model system, we find that nonsense-mediated mRNA decay is position dependent, that is, nonsense mutations within the initial two-thirds of the PGK1-coding region accelerate the decay rate of the PGK1 transcript {\(<\)} or = 12-fold, whereas nonsense mutations within the carboxy-terminal third of the coding region have no effect on mRNA decay. Moreover, we find that this position effect reflects (1) a requirement for sequences 3’ to the nonsense mutation that may be necessary for translational reinitiation or pausing, and (2) the presence of an additional sequence that, when translated, inactivates the nonsense-mediated mRNA decay pathway. This stabilizing element is positioned within the coding region such that it constitutes the boundary between nonsense mutations that do or do not affect mRNA decay. Rapid decay of PGK1 nonsense-containing transcripts is also dependent on the status of the UPF1 gene. Regardless of the position of an amber codon in the PGK1 gene, deletion of the UPF1 gene restores wild-type decay rates to nonsense-containing PGK1 transcripts.}, pmid = {8370523}, keywords = {1993,22,Base Sequence,by changes in the,changes in the expression,Codon,DNA Fungal,ELEMENTS,Fungal Proteins,Molecular Sequence Data,mRNA,mrna decay,Mutation,nonsense mutations,nonsense-mediated decay,nosource,of,Phosphoglycerate Kinase,Protein Biosynthesis,protein-coding region,received april 21,revised version accepted june,RNA Helicases,RNA Messenger,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,sequence,specific genes are manifested,steady-,termination,Terminator Regions Genetic,to a first approximation,Trans-Activators,Transcription Factors,translational termination,UPF,upf1 gene} } % == BibTeX quality report for peltzMRNADestabilizationTriggered1993: % ? unused Journal abbr (“Genes & Dev.”)

@article{dornerMononucleotideDerivativesRibosomal2003, title = {Mononucleotide Derivatives as Ribosomal {{P-site}} Substrates Reveal an Important Contribution of the 2’-{{OH}} to Activity}, author = {Dorner, Silke and Panuschka, Claudia and Schmid, Walther and Barta, Andrea}, year = 2003, month = nov, journal = {Nucleic Acids Research}, volume = {31}, number = {22}, eprint = {14602912}, eprinttype = {pubmed}, pages = {6536–6542}, issn = {1362-4962}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14602912}, abstract = {The chemical synthesis of various acylaminoacylated mononucleotides is described and their activities as donor substrates for the ribosomal peptide synthesis were investigated using PhetRNA(Phe) as an acceptor. This minimal reaction was characterized in detail and was shown to be stimulated by CMP, cytidine and cytosine. By using several cytidine and cytosine analogs evidence is provided that this enhancement is rather caused by base pairing to rRNA, followed by a structural change, than by a base mediated general acid/base catalysis. Only derivatives of AMP proved active as P-site substrates. Further, a significant contribution of the 2’-OH to activity was indicated by the finding that AcLeu-dAMP was inactive as donor substrate, although it is a good inhibitor of peptide bond formation and thus, is presumably bound to the P-site. However, Di(AcLeu)-2’-OCH(3)-Ade and DiAcLeu-AMP were moderately active in this assay suggesting that the reactivity of the 3’-acylaminoacid ester is stimulated by the presence of the 2’-oxygen group. A model is discussed how further interactions of the 2’-OH in the transition state might influence peptidyl transferase activity.}, pmid = {14602912}, keywords = {Binding Sites,Cytidine,Cytidine Monophosphate,Cytosine,Dose-Response Relationship Drug,nosource,Nucleotides,Peptide Biosynthesis,Peptidyl Transferases,Ribosomes,RNA Ribosomal,RNA Transfer Phe} } % == BibTeX quality report for dornerMononucleotideDerivativesRibosomal2003: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{swankMolecularWeightAnalysis1971, title = {Molecular Weight Analysis of Oligopeptides by Electrophoresis in Polyacrylamide Gel with Sodium Dodecyl Sulfate}, author = {Swank, R T and Munkres, K D}, year = 1971, month = feb, journal = {Analytical Biochemistry}, volume = {39}, number = {2}, pages = {462–477}, publisher = {Elsevier}, issn = {0003-2697}, url = {http://linkinghub.elsevier.com/retrieve/pii/0003269771904362}, keywords = {Acrylates,Bacitracin,Buffers,Cyanides,Cytochromes,Detergents,Electrophoresis,Gels,Glucagon,Insulin,Methods,Molecular Weight,Myoglobin,nosource,Ovalbumin,Peptides,Polymers,Polymyxins,Staining and Labeling,Sulfuric Acids,Trypsin Inhibitors,Urea} } % == BibTeX quality report for swankMolecularWeightAnalysis1971: % ? unused Journal abbr (“Anal. Biochem”)

@article{iborraMolecularCrosstalkTranscription2004, title = {Molecular Cross-Talk between the Transcription, Translation, and Nonsense-Mediated Decay Machineries}, author = {Iborra, Francisco J and Escargueil, Alexandre E and Kwek, Kon Y and Akoulitchev, Alexandre and Cook, Peter R}, year = 2004, month = feb, journal = {Journal of Cell Science}, volume = {117}, number = {Pt 6}, pages = {899–906}, publisher = {Company of Biologists}, issn = {0021-9533}, doi = {10.1242/jcs.00933}, url = {http://jcs.biologists.org/content/117/6/899.short}, abstract = {It is widely believed that translation occurs only in the cytoplasm of eukaryotes, but recent results suggest some takes place in nuclei, coupled to transcription. Support for this heterodoxy comes from studies of the nonsense-mediated decay (NMD) pathway; this pathway probably uses ribosomes to proofread messenger RNAs. We find components of the machineries involved in transcription, translation and NMD colocalise, interact and copurify, and that interactions between them are probably mediated by the C-terminal domain of the catalytic subunit of RNA polymerase II. These results are simply explained if the NMD machinery uses nuclear ribosomes to translate - and so proofread - newly made transcripts; then, faulty transcripts and any truncated peptides produced by nuclear translation would be degraded.}, keywords = {Animals,Antibiotics Antineoplastic,Antigens CD2,Catalytic Domain,Cell Nucleus,Codon Nonsense,COS Cells,Cricetinae,Cytoplasm,Fatty Acids Unsaturated,Genetic Vectors,Hela Cells,Humans,Karyopherins,Models Biological,nosource,Protein Biosynthesis,Receptors Cytoplasmic and Nuclear,Recombinant Proteins,RNA Messenger,RNA Polymerase II,RNA Stability,Transcription Factors,Transcription Genetic} } % == BibTeX quality report for iborraMolecularCrosstalkTranscription2004: % ? unused Journal abbr (“J. Cell. Sci”)

@article{pasqualiModularRNAArchitecture2005, title = {Modular {{RNA}} Architecture Revealed by Computational Analysis of Existing Pseudoknots and Ribosomal {{RNAs}}}, author = {Pasquali, Samuela and Gan, Hin Hark and Schlick, Tamar}, year = 2005, journal = {Nucleic Acids Research}, volume = {33}, number = {4}, pages = {1384–1398}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gki267}, url = {http://nar.oxfordjournals.org/content/33/4/1384.short}, abstract = {Modular architecture is a hallmark of RNA structures, implying structural, and possibly functional, similarity among existing RNAs. To systematically delineate the existence of smaller topologies within larger structures, we develop and apply an efficient RNA secondary structure comparison algorithm using a newly developed two-dimensional RNA graphical representation. Our survey of similarity among 14 pseudoknots and subtopologies within ribosomal RNAs (rRNAs) uncovers eight pairs of structurally related pseudoknots with non-random sequence matches and reveals modular units in rRNAs. Significantly, three structurally related pseudoknot pairs have functional similarities not previously known: one pair involves the 3’ end of brome mosaic virus genomic RNA (PKB134) and the alternative hammerhead ribozyme pseudoknot (PKB173), both of which are replicase templates for viral RNA replication; the second pair involves structural elements for translation initiation and ribosome recruitment found in the viral internal ribosome entry site (PKB223) and the V4 domain of 18S rRNA (PKB205); the third pair involves 18S rRNA (PKB205) and viral tRNA-like pseudoknot (PKB134), which probably recruits ribosomes via structural mimicry and base complementarity. Additionally, we quantify the modularity of 16S and 23S rRNAs by showing that RNA motifs can be constructed from at least 210 building blocks. Interestingly, we find that the 5S rRNA and two tree modules within 16S and 23S rRNAs have similar topologies and tertiary shapes. These modules can be applied to design novel RNA motifs via build-up-like procedures for constructing sequences and folds.}, keywords = {Algorithms,Base Sequence,Computational Biology,Computer Graphics,Models Molecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,RNA,RNA Catalytic,RNA Ribosomal,RNA Ribosomal 16S,RNA Ribosomal 23S,RNA Viral} } % == BibTeX quality report for pasqualiModularRNAArchitecture2005: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{suMinorGrooveRNA1999, title = {Minor Groove {{RNA}} Triplex in the Crystal Structure of a Ribosomal Frameshifting Viral Pseudoknot}, author = {Su, L and Chen, L and Egli, M and Berger, J M and Rich, A}, year = 1999, month = mar, journal = {Nature Structural Biology}, volume = {6}, number = {3}, pages = {285–292}, issn = {1072-8368}, doi = {10.1038/6722}, url = {http://www.nature.com/nsmb/journal/v6/n3/abs/nsb0399_285.html}, abstract = {Many viruses regulate translation of polycistronic mRNA using a -1 ribosomal frameshift induced by an RNA pseudoknot. A pseudoknot has two stems that form a quasi-continuous helix and two connecting loops. A 1.6 A crystal structure of the beet western yellow virus (BWYV) pseudoknot reveals rotation and a bend at the junction of the two stems. A loop base is inserted in the major groove of one stem with quadruple-base interactions. The second loop forms a new minor-groove triplex motif with the other stem, involving 2’-OH and triple-base interactions, as well as sodium ion coordination. Overall, the number of hydrogen bonds stabilizing the tertiary interactions exceeds the number involved in Watson-Crick base pairs. This structure will aid mechanistic analyses of ribosomal frameshifting.}, pmid = {10074948}, keywords = {99173243,chemistry,CRYSTAL-STRUCTURE,Crystallography X-Ray,Crystallography-X-Ray,CrystallographyX-Ray,frameshift,Frameshifting,Frameshifting Ribosomal,Frameshifting-Ribosomal,FrameshiftingRibosomal,Ions,Luteovirus,mRNA,No DOI found,nosource,Nucleic Acid Conformation,pseudoknot,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,Rna,RNA Messenger,RNA PSEUDOKNOT,RNA Viral,RNA-Messenger,Rna-Viral,RNAMessenger,RnaViral,Sodium,structure,support-non-u.s.gov’t,support-u.s.gov’t-non-p.h.s.,support-u.s.gov’t-p.h.s.,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,translation,virus,Water} } % == BibTeX quality report for suMinorGrooveRNA1999: % ? unused Journal abbr (“Nat. Struct. Biol”)

@article{kimMildTemperatureShock1983, title = {Mild Temperature Shock Alters the Transcription of a Discrete Class of {{Saccharomyces}} Cerevisiae Genes.}, author = {Kim, C H and Warner, J R}, year = 1983, month = mar, journal = {Molecular and Cellular Biology}, volume = {3}, number = {3}, pages = {457–465}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=368555&tool=pmcentrez&rendertype=abstract http://mcb.asm.org/cgi/content/abstract/3/3/457}, abstract = {In Saccharomyces cerevisiae the synthesis of ribosomal proteins declines temporarily after a culture has been subjected to a mild temperature shock, i.e., a shift from 23 to 36 degrees C, each of which support growth. Using cloned genes for several S. cerevisiae ribosomal proteins, we found that the changes in the synthesis of ribosomal proteins parallel the changes in the concentration of mRNA of each. The disappearance and reappearance of the mRNA is due to a brief but severe inhibition of the transcription of each of the ribosomal protein genes, although the total transcription of mRNA in the cells is relatively unaffected by the temperature shock. The precisely coordinated response of these genes, which are scattered throughout the genome, suggests that either they or the enzyme which transcribes them has unique properties. In certain S. cerevisiae mutants, the synthesis of ribosomal proteins never recovers from a temperature shift. Yet both the decline and the resumption of transcription of these genes during the 30 min after the temperature shift are indistinguishable from those in wild-type cells. The failure of the mutant cells to grow at the restrictive temperature appears to be due to their inability to process the RNA transcribed from genes which have introns (Rosbash et al., Cell 24:679-686, 1981), a large proportion of which appear to be ribosomal protein genes.}, pmid = {6341818}, keywords = {Genetic,Messenger,Messenger: analysis,nosource,Ribosomal Proteins,Ribosomal Proteins: biosynthesis,Ribosomal Proteins: genetics,RNA,RNA Messenger,RNA- Messenger,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Temperature,Transcription,Transcription Genetic,Transcription- Genetic} } % == BibTeX quality report for kimMildTemperatureShock1983: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{bartelMicroRNAsGenomicsBiogenesis2004, title = {{{MicroRNAs}}: Genomics, Biogenesis, Mechanism, and Function}, author = {Bartel, David P}, year = 2004, month = jan, journal = {Cell}, volume = {116}, number = {2}, pages = {281–297}, publisher = {Elsevier}, issn = {0092-8674}, doi = {10.1016/S0092-8674(04)00045-5}, url = {http://www.sciencedirect.com/science/article/pii/S0092867404000455}, abstract = {MicroRNAs (miRNAs) are endogenous approximately 22 nt RNAs that can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes.}, keywords = {Animals,Base Sequence,Caenorhabditis elegans,Drosophila,Genome,Humans,MicroRNAs,Models Biological,Molecular Sequence Data,nosource,Phenotype,Plant Proteins,Protein Biosynthesis,RNA Small Interfering,Species Specificity,Transcription Genetic} }

@article{lynchMessengerRNASurveillance2003, title = {Messenger {{RNA}} Surveillance and the Evolutionary Proliferation of Introns}, author = {Lynch, Michael and Kewalramani, Avinash}, year = 2003, month = apr, journal = {Molecular Biology and Evolution}, volume = {20}, number = {4}, eprint = {12654936}, eprinttype = {pubmed}, pages = {563–571}, publisher = {SMBE}, issn = {0737-4038}, doi = {10.1093/molbev/msg068}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12654936 http://mbe.oxfordjournals.org/content/20/4/563.short}, abstract = {The mechanisms responsible for the proliferation and subsequent stabilization of introns within the eukaryotic lineage have remained elusive. In the early stages of eukaryotic evolution, most introns may have been mildly deleterious at the time of insertion, but enough of them eventually acquired integral roles in transcript processing that few eukaryotic species can any longer survive without them. We suggest that the proliferation of spliceosomal introns was facilitated by the evolution of nonsense-mediated decay, an ancient and (in many cases) intron-dependent mechanism for eliminating aberrant mRNA molecules resulting from errors in transcription and splicing and from mutations at the DNA level. The spatial distribution of introns, as revealed by whole-genome analysis, is consistent with expectations for a model in which maximum protective coverage of a gene stochastically evolves over time.}, pmid = {12654936}, keywords = {Alternative Splicing,Alternative Splicing: genetics,Eukaryotic Cells,Evolution,Evolution Molecular,Exons,Exons: genetics,Gene Expression Regulation,Gene Expression Regulation: genetics,Genetic,genome complexity,genome evolution,introns,Introns,Introns: genetics,Messenger,Messenger: genetics,Models,Models Genetic,Molecular,mrna processing,mrna surveillance,nonsense-mediated decay,nosource,null,RNA,RNA Messenger,Spliceosomes,Spliceosomes: genetics} } % == BibTeX quality report for lynchMessengerRNASurveillance2003: % ? unused Journal abbr (“Mol. Biol. Evol”)

@article{grunberg-managoMessengerRNAStability1999, title = {Messenger {{RNA}} Stability and Its Role in Control of Gene Expression in Bacteria and Phages}, author = {{Grunberg-Manago}, M}, year = 1999, journal = {Annual Review of Genetics}, volume = {33}, pages = {193–227}, issn = {0066-4197}, doi = {10.1146/annurev.genet.33.1.193}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.genet.33.1.193}, abstract = {The stability of mRNA in prokaryotes depends on multiple factors and it has not yet been possible to describe the process of mRNA degradation in terms of a unique pathway. However, important advances have been made in the past 10 years with the characterization of the cis-acting RNA elements and the trans-acting cellular proteins that control mRNA decay. The trans-acting proteins are mainly four nucleases, two endo- (RNase E and RNase III) and two exonucleases (PNPase and RNase II), and poly(A) polymerase. RNase E and PNPase are found in a multienzyme complex called the degradosome. In addition to the host nucleases, phage T4 encodes a specific endonuclease called RegB. The cis-acting elements that protect mRNA from degradation are stable stem-loops at the 5’ end of the transcript and terminators or REP sequences at their 3’ end. The rate-limiting step in mRNA decay is usually an initial endonucleolytic cleavage that often occurs at the 5’ extremity. This initial step is followed by directional 3’ to 5’ degradation by the two exonucleases. Several examples, reviewed here, indicate that mRNA degradation is an important step at which gene expression can be controlled. This regulation can be either global, as in the case of growth rate-dependent control, or specific, in response to changes in the environmental conditions.}, pmid = {10690408}, keywords = {a,and,autoregulation,Bacteria,Bacteriophages,been possible to describe,degradation in terms,depends on multiple factors,Gene Expression Regulation Bacterial,Gene Expression Regulation Viral,it has not yet,mrna,nosource,of mrna in prokaryotes,pnpase,poly,polymerase,Ribonucleases,RNA Messenger,rnase e,rnase ii,rnase iii,s abstract the stability,stability,the process of mrna,Transcription Genetic} } % == BibTeX quality report for grunberg-managoMessengerRNAStability1999: % ? unused Journal abbr (“Annu. Rev. Genet”)

@article{dreyfussMessengerRNAbindingProteinsMessages2002, title = {Messenger-{{RNA-binding}} Proteins and the Messages They Carry}, author = {Dreyfuss, Gideon and Kim, V Narry and Kataoka, Naoyuki}, year = 2002, month = mar, journal = {Nature Reviews. Molecular Cell Biology}, volume = {3}, number = {3}, pages = {195–205}, publisher = {Nature Publishing Group}, issn = {1471-0072}, doi = {10.1038/nrm760}, url = {http://www.nature.com/nrm/journal/v3/n3/abs/nrm760.html}, abstract = {From sites of transcription in the nucleus to the outreaches of the cytoplasm, messenger RNAs are associated with RNA-binding proteins. These proteins influence pre-mRNA processing as well as the transport, localization, translation and stability of mRNAs. Recent discoveries have shown that one group of these proteins marks exon exon junctions and has a role in mRNA export. These proteins communicate crucial information to the translation machinery for the surveillance of nonsense mutations and for mRNA localization and translation.}, keywords = {Animals,Cytoplasm,Exons,Heterogeneous-Nuclear Ribonucleoproteins,Humans,Models Biological,nosource,Ribonucleoproteins,RNA Messenger,RNA Splicing,RNA-Binding Proteins} } % == BibTeX quality report for dreyfussMessengerRNAbindingProteinsMessages2002: % ? Possibly abbreviated journal title Nature Reviews. Molecular Cell Biology % ? unused Journal abbr (“Nat. Rev. Mol. Cell Biol”)

@article{lejeuneMechanisticLinksNonsensemediated2005, title = {Mechanistic Links between Nonsense-Mediated {{mRNA}} Decay and Pre-{{mRNA}} Splicing in Mammalian Cells}, author = {Lejeune, Fabrice and Maquat, Lynne E}, year = 2005, month = jun, journal = {Current Opinion in Cell Biology}, volume = {17}, number = {3}, pages = {309–315}, publisher = {Elsevier}, issn = {0955-0674}, doi = {10.1016/j.ceb.2005.03.002}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0955-0674(05)00042-6}, abstract = {Nonsense-mediated mRNA decay (NMD) generally involves nonsense codon recognition by translating ribosomes at a position approximately 25 nts upstream of a splicing-generated exon junction complex of proteins. As such, NMD provides a means to degrade abnormal mRNAs that encode potentially deleterious truncated proteins. Additionally, an estimated one-third of naturally occurring, alternatively spliced mRNAs is also targeted for NMD. Given the extraordinary frequency of alternative splicing together with data indicating that naturally occurring transcripts other than alternatively spliced mRNAs are likewise targeted for NMD, it is believed that mammalian cells routinely utilize NMD to achieve proper levels of gene expression.}, keywords = {Animals,Codon Nonsense,Exons,Gene Expression Regulation,Humans,Models Biological,nosource,RNA Messenger,RNA Splicing,RNA Stability} } % == BibTeX quality report for lejeuneMechanisticLinksNonsensemediated2005: % ? unused Journal abbr (“Curr. Opin. Cell Biol”)

@article{hillerenMechanismsMRNASurveillance1999, title = {Mechanisms of {{mRNA}} Surveillance in Eukaryotes}, author = {Hilleren, P and Parker, R}, year = 1999, journal = {Annual Review of Genetics}, volume = {33}, number = {1}, eprint = {10690409}, eprinttype = {pubmed}, pages = {229–260}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, issn = {0066-4197}, doi = {10.1146/annurev.genet.33.1.229}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10690409 http://www.annualreviews.org/doi/abs/10.1146/annurev.genet.33.1.229}, abstract = {A conserved mRNA degradation system, referred to as mRNA surveillance, exists in eukaryotic cells to degrade aberrant mRNAs. A defining aspect of aberrant transcripts is that the spatial relationship between the termination codon and specific downstream sequence information has been altered. A key, yet unknown, feature of the mRNA surveillance system is how this spatial relationship is assessed in individual transcripts. Two views have emerged to describe how discrimination between proper and improper termination might occur. In the first view, a surveillance complex assembles onto the mRNA after translation termination, and scans the mRNA in a 3’ to 5’ direction for a limited distance. If specific downstream sequence information is encountered during this scanning, then the surveillance complex targets the transcript for rapid decay. An alternate view suggests that the downstream sequence information influences how translation termination occurs. This view encompasses several ideas including: (a) The architecture of the mRNP can alter the rate of key steps in translation termination; (b) the discrimination between a proper and improper termination occurs via an internal, Upf1-dependent, timing mechanism; and (c) proper termination results in the restructuring of the mRNP to a form that promotes mRNA stability. This proposed model for mRNA surveillance is similar to other systems of kinetic proofreading that monitor the accuracy of other biogenic processes such as translation and spliceosome assembly.}, keywords = {a defining aspect of,Animals,Eukaryotic Cells,exists in eukaryotic cells,kinetic proofreading,lance,mrna biogenesis,mrna degradation system,mrnp remodeling,nonsense decay,nosource,Peptide Chain Termination Translational,Protein Biosynthesis,referred to as mrna,RNA Messenger,s abstract a conserved,surveil-,termination,to degrade aberrant mrnas,Transcription Genetic,translation} } % == BibTeX quality report for hillerenMechanismsMRNASurveillance1999: % ? unused Journal abbr (“Annu. Rev. Genet”)

@article{blackMechanismsAlternativePremessenger2003, title = {Mechanisms of Alternative Pre-Messenger {{RNA}} Splicing}, author = {Black, Douglas L}, year = 2003, month = jan, journal = {Annual Review of Biochemistry}, volume = {72}, number = {1}, pages = {291–336}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, issn = {0066-4154}, doi = {10.1146/annurev.biochem.72.121801.161720}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.biochem.72.121801.161720 http://www.ncbi.nlm.nih.gov/pubmed/12626338}, abstract = {Alternative pre-mRNA splicing is a central mode of genetic regulation in higher eukaryotes. Variability in splicing patterns is a major source of protein diversity from the genome. In this review, I describe what is currently known of the molecular mechanisms that control changes in splice site choice. I start with the best-characterized systems from the Drosophila sex determination pathway, and then describe the regulators of other systems about whose mechanisms there is some data. How these regulators are combined into complex systems of tissue-specific splicing is discussed. In conclusion, very recent studies are presented that point to new directions for understanding alternative splicing and its mechanisms.}, pmid = {12626338}, keywords = {alternative splicing,Alternative Splicing,Animals,binding proteins,Drosophila,Drosophila: genetics,Drosophila: growth & development,Drosophila: metabolism,Exons,Exons: genetics,f abstract alternative pre-mrna,Introns,Introns: genetics,is a major source,Messenger,Messenger: genetics,Messenger: metabolism,mode of genetic regula-,nosource,of protein,Organ Specificity,protein diversity,regulatory mechanisms,rna,RNA,RNA Messenger,RNA Precursors,RNA Precursors: genetics,RNA Precursors: metabolism,RNA-Binding Proteins,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism,Sex Determination (Genetics),Sex Determination Processes,spliceosome,Spliceosomes,Spliceosomes: metabolism,splicing is a central,tion in higher eukaryotes,Transcription Factors,Transcription Factors: metabolism,variability in splicing patterns} } % == BibTeX quality report for blackMechanismsAlternativePremessenger2003: % ? unused Journal abbr (“Annu. Rev. Biochem”)

@article{caponigroMechanismsControlMRNA1996, title = {Mechanisms and Control of {{mRNA}} Turnover in {{Saccharomyces}} Cerevisiae}, author = {Caponigro, G and Parker, R}, year = 1996, month = mar, journal = {Microbiology and Molecular Biology Reviews}, volume = {60}, number = {1}, pages = {233–249}, publisher = {Am Soc Microbiol}, issn = {0146-0749}, url = {http://mmbr.asm.org/cgi/reprint/60/1/233.pdf}, keywords = {Base Sequence,MECHANISM,MECHANISMS,Molecular Sequence Data,mRNA,NMD,nosource,Review,review article,RNA Fungal,RNA Messenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,turnover} } % == BibTeX quality report for caponigroMechanismsControlMRNA1996: % ? unused Journal abbr (“Microbiol. Rev”)

@article{trobroMechanismPeptideBond2005, title = {Mechanism of Peptide Bond Synthesis on the Ribosome}, author = {Trobro, Stefan and Aqvist, Johan}, year = 2005, month = aug, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {35}, pages = {12395–12400}, publisher = {National Acad Sciences}, issn = {0027-8424}, doi = {10.1073/pnas.0504043102}, url = {http://www.pnas.org/content/102/35/12395.short}, abstract = {With the emergence of atomic-resolution crystal structures of bacterial ribosomal subunits, major advances in eliciting structure-function relationships of the translation process are underway. Nevertheless, the detailed mechanism of peptide bond synthesis that occurs on the large ribosomal subunit remains unknown. Separate x-ray structures of aminoacyl-tRNA and peptidyl-tRNA analogues bound to the ribosomal A- and P-sites, however, allow for structural modeling of the active complex in catalysis. Here, we combine available structural data to construct such a model of the peptidyl transfer reaction center with bound substrates. Molecular dynamics and free energy perturbation simulations then are used in combination with an empirical valence bond description of the reaction energy surface to examine possible catalytic mechanisms. Already, simulations of the reactant and tetrahedral intermediate states reveal a stable, preorganized H-bond network poised for catalysis. The most favorable mechanism is found not to involve any general acid-base catalysis by ribosomal groups but an intra-reactant proton shuttling via the P-site adenine O2’ oxygen, which follows the attack of the A-site alpha-amino group on the P-site ester. The calculated rate enhancement for this mechanism is approximately 10(5), and the catalytic effect is found to be entirely of entropic origin, in accordance with recent experimental data, and is associated with the reduction of solvent reorganization energy rather than with substrate alignment or proximity. This mechanism also explains the inability of 2’-deoxyadenine P-site substrates to promote peptidyl transfer. The observed H-bond network suggests an important structural role of several universally conserved rRNA residues.}, isbn = {0504043102}, pmid = {16116099}, keywords = {Binding Sites,Biophysical Phenomena,Biophysics,Crystallography X-Ray,Macromolecular Substances,Models Chemical,Models Molecular,nosource,Peptide Biosynthesis,Peptides,Ribosomes,RNA Transfer Amino Acyl,Thermodynamics} } % == BibTeX quality report for trobroMechanismPeptideBond2005: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{mattapallilMassiveInfectionLoss2005, title = {Massive Infection and Loss of Memory {{CD4}}+ {{T}} Cells in Multiple Tissues during Acute {{SIV}} Infection}, author = {Mattapallil, Joseph J and Douek, Daniel C and Hill, Brenna and Nishimura, Yoshiaki and Martin, Malcolm and Roederer, Mario}, year = 2005, month = apr, journal = {Nature}, volume = {434}, number = {7037}, pages = {1093–1097}, issn = {1476-4687}, doi = {10.1038/nature03501}, url = {http://molpath.ucsd.edu/PDF/Richman_CelBiol.pdf}, abstract = {It has recently been established that both acute human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) infections are accompanied by a dramatic and selective loss of memory CD4+ T cells predominantly from the mucosal surfaces. The mechanism underlying this depletion of memory CD4+ T cells (that is, T-helper cells specific to previously encountered pathogens) has not been defined. Using highly sensitive, quantitative polymerase chain reaction together with precise sorting of different subsets of CD4+ T cells in various tissues, we show that this loss is explained by a massive infection of memory CD4+ T cells by the virus. Specifically, 30-60% of CD4+ memory T cells throughout the body are infected by SIV at the peak of infection, and most of these infected cells disappear within four days. Furthermore, our data demonstrate that the depletion of memory CD4+ T cells occurs to a similar extent in all tissues. As a consequence, over one-half of all memory CD4+ T cells in SIV-infected macaques are destroyed directly by viral infection during the acute phase-an insult that certainly heralds subsequent immunodeficiency. Our findings point to the importance of reducing the cell-associated viral load during acute infection through therapeutic or vaccination strategies.}, pmid = {15793563}, keywords = {Acute Disease,Animals,CD4-Positive T-Lymphocytes,CD8-Positive T-Lymphocytes,Cell Death,Humans,Immunologic Memory,Macaca mulatta,nosource,Receptors CCR5,RNA Messenger,Simian Acquired Immunodeficiency Syndrome,Simian immunodeficiency virus,Viral Load} }

@article{koMappingEssentialStructures2006, title = {Mapping the Essential Structures of Human Ribosomal Protein {{L7}} for Nuclear Entry, Ribosome Assembly and Function}, author = {Ko, J-R and Wu, Jing-Ying and Kirby, R and Li, I-Fang and Lin, Alan}, year = 2006, month = jul, journal = {FEBS Letters}, volume = {580}, number = {16}, pages = {3804–3810}, publisher = {Elsevier}, issn = {0014-5793}, doi = {10.1016/j.febslet.2006.05.073}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579306006910}, abstract = {Human large subunit protein L7 carries multiple nuclear localization signals (NLS) in its structure: there are three monobasic partite NLSs at the NH2-region of the first 54 amino acid residues and a bipartite in the middle section at position of 156-167. The C-region of the last 50 amino acid residues displays membrane binding nature, and might involve in forming a nuclear microbody for pre-nucleolar ribosome assembly. The middle section covers 144 amino acid residues which are essential for the structure and function of ribosome. This is evident from findings that truncated L7 without the NH2-region or the C-region, or missing both regions, is capable of reaching nucleolus and incorporating in ribosome, however, only ribosomes bearing truncated L7 without the NH2-region is capable of engaging in polysome formation. Combining with the phylogenic findings from homologous sequence alignment, the NH2-region of L7, besides being as a eukaryotic expansion segment, can be excluded from building a functional eukaryotic ribosome.}, keywords = {Amino Acid Sequence,Animals,Cell Nucleus,Hela Cells,Humans,Microbodies,Molecular Sequence Data,Mutation,nosource,Protein Transport,Recombinant Proteins,Ribosomal Proteins,Ribosomes,Sequence Alignment} } % == BibTeX quality report for koMappingEssentialStructures2006: % ? unused Journal abbr (“FEBS Lett”)

@article{belgraderMammalianNonsenseCodons1994, title = {Mammalian Nonsense Codons Can Be Cis Effectors of Nuclear {{mRNA}} Half-Life.}, author = {Belgrader, P and Cheng, J and Zhou, X and Stephenson, L S and Maquat, L E}, year = 1994, month = dec, journal = {Molecular and Cellular Biology}, volume = {14}, number = {12}, pages = {8219–8228}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, url = {http://mcb.asm.org/cgi/content/abstract/14/12/8219}, abstract = {Frameshift and nonsense mutations within the gene for human triosephosphate isomerase (TPI) that generate a nonsense codon within the first three-fourths of the protein coding region have been found to reduce the abundance of the product mRNA that copurifies with nuclei. The cellular process and location of the nonsense codon-mediated reduction have proven difficult to elucidate for technical reasons. We show here, using electron microscopy to judge the purity of isolated nuclei, that the previously established reduction to 25% of the normal mRNA level is evident for nuclei that are free of detectable cytoplasmic contamination. Therefore, the reduction is likely to be characteristic of bona fide nuclear RNA. Fully spliced nuclear mRNA is identified by Northern (RNA) blot hybridization and a reverse transcription-PCR assay as the species that undergoes decay in experiments that used the human c-fos promoter to elicit a burst and subsequent shutoff of TPI gene transcription upon the addition of serum to serum-deprived cells. Finally, the finding that deletion of a 5’ splice site of the TPI gene results predominantly but not exclusively in the removal by splicing (i.e., skipping) of the upstream exon as a part of the flanking introns has been used to demonstrate that decay is specific to those mRNA products that maintain the nonsense codon. This result, together with our previous results that implicate translation by ribosomes and charged tRNAs in the decay mechanism, indicate that nonsense codon recognition takes place after splicing and triggers decay solely in cis. The possibility that decay takes place during the process of mRNA export from the nucleus to the cytoplasm is discussed.}, keywords = {Animals,Base Sequence,Cell Nucleus,Codon Nonsense,DNA Primers,Gene Expression Regulation Enzymologic,Genes fos,Mice,Molecular Sequence Data,nosource,Recombinant Fusion Proteins,RNA Messenger,RNA Splicing,Triose-Phosphate Isomerase} } % == BibTeX quality report for belgraderMammalianNonsenseCodons1994: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{clarkMammalianGenePEG102007, title = {Mammalian Gene {{PEG10}} Expresses Two Reading Frames by High Efficiency -1 Frameshifting in Embryonic-Associated Tissues.}, author = {Clark, Michael B and J{"a}nicke, Martina and Gottesb{"u}hren, Undine and Kleffmann, Torsten and Legge, Michael and Poole, Elizabeth S and Tate, Warren P}, year = 2007, month = dec, journal = {The Journal of Biological Chemistry}, volume = {282}, number = {52}, pages = {37359–37369}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.M705676200}, url = {http://www.jbc.org/content/282/52/37359.short http://www.ncbi.nlm.nih.gov/pubmed/17942406}, abstract = {Paternally expressed gene 10 (PEG10) is a mammalian gene that is essential for embryonic development in mice. The gene contains two overlapping open reading frames (ORF1 and ORF2) and is derived from a retroelement that acquired a cellular function. It is not known if both reading frames are required for PEG10 function. Synthesis of ORF2 would be possible only if programmed -1 frameshifting occurred during ORF1 translation. In this study the frameshifting activity of PEG10 was analyzed in vivo, and a potential role for ORF2 was investigated. Phylogenetic analysis demonstrated that PEG10 is highly conserved in therian mammals, with all species retaining the elements necessary for frameshifting as well as functional motifs in each ORF. The frameshift site of PEG10 was highly active in cultured cells and produced the ORF1-2 protein. In mice, endogenous ORF1 and an ORF1-2 frameshift protein were detected in the developing placenta and amniotic membrane from 9.5 days post-coitus through to term with a very high frameshift efficiency ({\(>\)}60%). Mutagenesis of the active site motif of a putative protease within ORF2 showed that this enzyme is active and participates in post-translational processing of PEG10 ORF1-2. Both PEG10 proteins were also detected in first trimester human placenta. By contrast, neither protein expression nor frameshifting was detected in adult mouse tissues. These studies imply that the ORF1-2 protein, synthesized utilizing the most efficient -1 frameshift mechanism yet documented in vivo, will have an essential function that is intrinsic to the importance of PEG10 in mammals.}, pmid = {17942406}, keywords = {ACTIVE-SITE,Adult,Amino Acid,Amino Acid Sequence,analysis,Animals,Base Sequence,Biochemistry,CELLS,Cercopithecus aethiops,development,Developmental,efficiency,ELEMENTS,Embryo,Embryo Mammalian,enzyme,expression,FRAME,frameshift,Frameshift Mutation,Frameshifting,gene,Gene Expression Regulation,Gene Expression Regulation Developmental,human,Humans,IN-VIVO,Inbred C57BL,La,Mammalian,Mammalian: metabolism,Mammals,MECHANISM,Mice,Mice Inbred C57BL,Molecular Sequence Data,MOTIFS,Mutagenesis,nosource,Nuclear Proteins,Nuclear Proteins: genetics,Nuclear Proteins: physiology,Nucleic Acid,OPEN READING FRAME,Open Reading Frames,Placenta,Placenta: metabolism,protein,Proteins,READING FRAME,Reading Frames,Sequence Homology,Sequence Homology Amino Acid,Sequence Homology Nucleic Acid,SITE,Support,Transcription Factors,Transcription Factors: genetics,Transcription Factors: physiology,translation} } % == BibTeX quality report for clarkMammalianGenePEG102007: % ? unused Journal abbr (“J. Biol. Chem”)

@article{atkinsLowActivityGalactosidase1972, title = {Low Activity of -Galactosidase in Frameshift Mutants of {{Escherichia}} Coli}, author = {Atkins, J F and Elseviers, D and Gorini, L}, year = 1972, month = may, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {69}, number = {5}, eprint = {4556457}, eprinttype = {pubmed}, pages = {1192–1195}, issn = {0027-8424}, url = {http://www.ncbi.nlm.nih.gov/pubmed/4556457}, abstract = {16 lac frameshift mutants induced by an acridine derivative, ICR-191D, in E. coli are leaky for beta-galactosidase activity. Activities of all mutants differ from each other and from the wild type in their stability to thermal denaturation. The leakiness is under ribosomal control, since it is strongly reduced by strA restrictive mutations and is restored by ram mutations that reverse restriction. Addition of streptomycin during growth has an effect similar to the presence of the ram mutation. These ribosomal alterations do not modify the thermal stability of the enzyme.It is suggested that the leakiness is due to an infrequent 2- or 4-base reading close to the frameshift mutation site. The possibility that not only the ribosome, but also the reading context in the messenger, plays a role in securing code fidelity is discussed.}, pmid = {4556457}, keywords = {Acridines,Escherichia coli,Galactosidases,Genetic Code,Genotype,Hot Temperature,Lactose,Mutation,nosource,Operon,Ribosomes,Streptomycin,Suppression Genetic} } % == BibTeX quality report for atkinsLowActivityGalactosidase1972: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{culbertsonLookingMRNADecay2003, title = {Looking at {{mRNA}} Decay Pathways through the Window of Molecular Evolution}, author = {Culbertson, Michael R and Leeds, Peter F}, year = 2003, month = apr, journal = {Current Opinion in Genetics & Development}, volume = {13}, number = {2}, pages = {207–214}, issn = {0959-437X}, doi = {10.1016/S0959-437X(03)00014-5}, url = {http://www.sciencedirect.com/science/article/pii/S0959437X03000145 http://linkinghub.elsevier.com/retrieve/pii/S0959437X03000145}, abstract = {In eukaryotes, mRNAs are monitored for errors in gene expression by RNA surveillance where untranslatable mRNAs are selectively degraded by the nonsense-mediated mRNA decay (NMD) pathway. Depending on the organism, three to seven genes are required for NMD. Besides RNA surveillance, the genes required for NMD serve a second purpose by controlling the overall abundance of a substantial fraction of the transcriptome.}, pmid = {12672499}, keywords = {0,Animals,DECAY,DECAY PATHWAY,decay pathways,ERRORS,Evolution,Evolution Molecular,EvolutionMolecular,expression,gene,Gene Expression,GENE-EXPRESSION,Genes,genetics,Helicase,human,Humans,La,M,metabolism,mRNA,mRNA decay,NMD,nonsense-mediated mRNA decay,nosource,PATHWAY,Phylogeny,protein,Review,Rna,RNA HELICASE,RNA Helicases,RNA Messenger,RNAMessenger,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Sequence Alignment,Sequence Analysis Protein,Sequence AnalysisProtein,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SURVEILLANCE,Trans-Activators,Upf1,UPF1 PROTEIN} } % == BibTeX quality report for culbertsonLookingMRNADecay2003: % ? unused Journal abbr (“Curr. Opin. Genet. Dev”)

@article{khodurskyLifeTranscriptionrevisitingFate2003, title = {Life after Transcription–Revisiting the Fate of Messenger {{RNA}}}, author = {Khodursky, Arkady B and Bernstein, Jonathan A}, year = 2003, month = mar, journal = {Trends in Genetics: TIG}, volume = {19}, number = {3}, pages = {113–115}, publisher = {Elsevier}, issn = {0168-9525}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0168952502000471}, abstract = {Recently, several groups have used high-density DNA microarrays to study mRNA turnover. These new data suggest that decay contributes significantly to determining mRNA levels, and they should prompt us to refocus our attention on the regulatory potential of mRNA decay.}, keywords = {Models Genetic,nosource,Oligonucleotide Array Sequence Analysis,RNA Messenger,RNA Processing Post-Transcriptional,Transcription Genetic} } % == BibTeX quality report for khodurskyLifeTranscriptionrevisitingFate2003: % ? unused Journal abbr (“Trends Genet”)

@article{keelingLeakyTerminationPremature2004, title = {Leaky Termination at Premature Stop Codons Antagonizes Nonsense-Mediated {{mRNA}} Decay in {{S}}. Cerevisiae}, author = {Keeling, Kim M and Lanier, Jessica and Du, Ming and {Salas-Marco}, Joe and Gao, Lin and {Kaenjak-Angeletti}, Anisa and Bedwell, David M}, year = 2004, month = apr, journal = {RNA (New York, N.Y.)}, volume = {10}, number = {4}, eprint = {15037778}, eprinttype = {pubmed}, pages = {691–703}, issn = {1355-8382}, doi = {10.1261/rna.5147804}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15037778}, abstract = {The Nonsense-Mediated mRNA Decay (NMD) pathway mediates the rapid degradation of mRNAs that contain premature stop mutations in eukaryotic organisms. It was recently shown that mutations in three yeast genes that encode proteins involved in the NMD process, UPF1, UPF2, and UPF3, also reduce the efficiency of translation termination. In the current study, we compared the efficiency of translation termination in a upf1Delta strain and a [PSI(+)] strain using a collection of translation termination reporter constructs. The [PSI(+)] state is caused by a prion form of the polypeptide chain release factor eRF3 that limits its availability to participate in translation termination. In contrast, the mechanism by which Upf1p influences translation termination is poorly understood. The efficiency of translation termination is primarily determined by a tetranucleotide termination signal consisting of the stop codon and the first nucleotide immediately 3’ of the stop codon. We found that the upf1Delta mutation, like the [PSI(+)] state, decreases the efficiency of translation termination over a broad range of tetranucleotide termination signals in a unique, context-dependent manner. These results suggest that Upf1p may associate with the termination complex prior to polypeptide chain release. We also found that the increase in readthrough observed in a [PSI(+)]/upf1Delta strain was larger than the readthrough observed in strains carrying either defect alone, indicating that the upf1Delta mutation and the [PSI(+)] state influence the termination process in distinct ways. Finally, our analysis revealed that the mRNA destabilization associated with NMD could be separated into two distinct forms that correlated with the extent the premature stop codon was suppressed. The minor component of NMD was a 25% decrease in mRNA levels observed when readthrough was {\(>\)}/=0.5%, while the major component was represented by a larger decrease in mRNA abundance that was observed only when readthrough was}, pmid = {15037778}, keywords = {0,3,analysis,CEREVISIAE,Codon,Codon Nonsense,Codon-Nonsense,CodonNonsense,CODONS,COMPLEX,COMPLEXES,COMPONENT,DECAY,degradation,efficiency,FORM,gene,Genes,Genes Reporter,Genes-Reporter,GenesReporter,genetics,Helicase,La,MECHANISM,metabolism,microbiology,mRNA,mRNA decay,Mutation,MUTATIONS,NMD,NONSENSE,nonsense-mediated mRNA decay,nosource,PATHWAY,Peptide Chain Termination,Peptide Chain Termination Translational,Peptide Termination Factors,physiology,POLYPEPTIDE,POLYPEPTIDE-CHAIN,prion,Prions,protein,Proteins,readthrough,RELEASE,release factor,Rna,RNA HELICASE,RNA Helicases,RNA Messenger,RNA-Messenger,RNAMessenger,S,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SIGNAL,STOP CODON,support-non-u.s.gov’t,support-u.s.gov’t-p.h.s.,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SURVEILLANCE,termination,Trans-Activators,translation,TRANSLATION TERMINATION,Upf1,UPF1 PROTEIN,UPF3,yeast} } % == BibTeX quality report for keelingLeakyTerminationPremature2004: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{lopinskiKineticsRibosomalPausing2000, title = {Kinetics of Ribosomal Pausing during Programmed -1 Translational Frameshifting}, author = {Lopinski, J D and Dinman, J D and Bruenn, J A}, year = 2000, month = feb, journal = {Molecular and Cellular Biology}, volume = {20}, number = {4}, pages = {1095–1103}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, doi = {10.1128/​MCB.20.4.1095-1103.2000}, url = {http://mcb.asm.org/cgi/content/abstract/20/4/1095 http://mcb.highwire.org/cgi/content/abstract/20/4/1095}, abstract = {In the Saccharomyces cerevisiae double-stranded RNA virus, programmed -1 ribosomal frameshifting is responsible for translation of the second open reading frame of the essential viral RNA. A typical slippery site and downstream pseudoknot are necessary for this frameshifting event, and previous work has demonstrated that ribosomes pause over the slippery site. The translational intermediate associated with a ribosome paused at this position is detected, and, using in vitro translation and quantitative heelprinting, the rates of synthesis, the ribosomal pause time, the proportion of ribosomes paused at the slippery site, and the fraction of paused ribosomes that frameshift are estimated. About 10% of ribosomes pause at the slippery site in vitro, and some 60% of these continue in the -1 frame. Ribosomes that continue in the -1 frame pause about 10 times longer than it takes to complete a peptide bond in vitro. Altering the rate of translational initiation alters the rate of frameshifting in vivo. Our in vitro and in vivo experiments can best be interpreted to mean that there are three methods by which ribosomes pass the frameshift site, only one of which results in frameshifting.}, keywords = {Base Sequence,Binding Sites,DOUBLE-STRANDED-RNA,frameshift,Frameshifting,Frameshifting Ribosomal,In Vitro,in vitro translation,IN-VITRO,IN-VIVO,initiation,killer,Kinetics,L-A,Methods,Models Genetic,nosource,Nucleic Acid Conformation,pausing,pseudoknot,ribosomal frameshifting,ribosome,Ribosomes,Rna,RNA Viral,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,slippery site,Totiviridae,translation,virus} } % == BibTeX quality report for lopinskiKineticsRibosomalPausing2000: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{gromadskiKineticDeterminantsHighfidelity2004, title = {Kinetic Determinants of High-Fidelity {{tRNA}} Discrimination on the Ribosome}, author = {Gromadski, Kirill B and Rodnina, Marina V}, year = 2004, month = jan, journal = {Molecular Cell}, volume = {13}, number = {2}, pages = {191–200}, publisher = {Elsevier}, issn = {1097-2765}, doi = {10.1016/S1097-2765(04)00005-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/s109727650400005x}, abstract = {The ribosome selects aminoacyl-tRNA (aa-tRNA) matching to the mRNA codon from the bulk of non-matching aa-tRNAs in two consecutive selection steps, initial selection and proofreading. Here we report the kinetic analysis of selection taking place under conditions where the overall selectivity was close to values observed in vivo and initial selection and proofreading contributed about equally. Comparison of the rate constants shows that the 350-fold difference in stabilities of cognate and near-cognate codon-anticodon complexes is not used for tRNA selection due to high rate of GTP hydrolysis in the cognate complex. tRNA selection at the initial selection step is entirely kinetically controlled and is due to much faster (650-fold) GTP hydrolysis of cognate compared to near-cognate substrate.}, keywords = {0,analysis,Binding Sites,chemistry,Codon,COMPLEX,COMPLEXES,elongation,ELONGATION-FACTOR-TU,Escherichia coli,FACTOR TU,GTP,GTP Phosphohydrolase,GTP Phosphohydrolases,Guanosine,Guanosine Triphosphate,Hydrolysis,IN-VIVO,Kinetics,La,metabolism,Models Biological,Models Genetic,ModelsBiological,ModelsGenetic,mRNA,nosource,Peptide Elongation Factor Tu,proofreading,Protein Binding,ribosome,Ribosomes,Rna,RNA Messenger,RNA Transfer,RNA Transfer Amino Acyl,RNAMessenger,RNATransfer,RNATransferAmino Acyl,SELECTION,stability,supportnon-u.s.gov’t,Thermodynamics,Time Factors,tRNA} } % == BibTeX quality report for gromadskiKineticDeterminantsHighfidelity2004: % ? unused Journal abbr (“Mol. Cell”)

@article{byersKillingMessengerNew2002a, title = {Killing the Messenger: New Insights into Nonsense-Mediated {{mRNA}} Decay}, author = {Byers, Peter H}, year = 2002, month = jan, journal = {The Journal of Clinical Investigation}, volume = {109}, number = {1}, eprint = {11781342}, eprinttype = {pubmed}, pages = {3–6}, issn = {0021-9738}, doi = {10.1172/JCI14841}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11781342}, pmid = {11781342}, keywords = {Animals,Caenorhabditis elegans,Cell Nucleus,Codon Nonsense,Codon Terminator,Cytoplasm,Humans,Models Biological,Mutation,nosource,Protein Biosynthesis,RNA Fungal,RNA Helminth,RNA Messenger,Saccharomyces cerevisiae} } % == BibTeX quality report for byersKillingMessengerNew2002a: % ? unused Journal abbr (“J. Clin. Invest”)

@article{cochellaIsolationAntibioticResistance2004, title = {Isolation of Antibiotic Resistance Mutations in the {{rRNA}} by Using an in Vitro Selection System}, author = {Cochella, Luisa and Green, Rachel}, year = 2004, month = mar, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {11}, pages = {3786–3791}, publisher = {National Acad Sciences}, issn = {0027-8424}, doi = {10.1073/pnas.0307596101}, url = {http://www.pnas.org/content/101/11/3786.short}, abstract = {Genetic, biochemical, and structural data support an essential role for the ribosomal RNA in all steps of the translation process. Although in vivo genetic selection techniques have been used to identify mutations in the rRNAs that result in various miscoding phenotypes and resistance to known ribosome-targeted antibiotics, these are limited because the resulting mutant ribosomes must be only marginally disabled if they are able to support growth of the cell. Furthermore, in vivo, it is not possible to control the environment in precise ways that might allow for the isolation of certain types of rRNA variants. To overcome these limitations, we have developed an in vitro selection system for the isolation of functionally competent ribosomal particles from populations containing variant rRNAs. Here, we describe this system and present an example of its application to the selection of antibiotic resistance mutations. From a pool of 4,096 23S rRNA variants, a double mutant (A2058U/A2062G) was isolated after iteration of the selection process. This mutant was highly resistant to clindamycin in in vitro translation reactions and yet was not viable in Escherichia coli. These data establish that this system has the potential to identify mutations in the rRNA not readily accessed by comparable in vivo systems, thus allowing for more exhaustive ribosomal genetic screens.}, keywords = {0,antibiotic,antibiotics,BIOLOGY,Clindamycin,Drug Resistance Bacterial,Drug ResistanceBacterial,Escherichia coli,ESCHERICHIA-COLI,Genetic,genetics,GROWTH,IDENTIFY,In Vitro,in vitro translation,IN-VITRO,IN-VIVO,La,metabolism,Mutation,MUTATIONS,nosource,PARTICLES,Phenotype,RESISTANCE,RESISTANCE MUTATIONS,RESISTANT,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNA Ribosomal,RNARibosomal,rRNA,SELECTION,Streptavidin,Structural,Support,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,SYSTEMS,techniques,translation} } % == BibTeX quality report for cochellaIsolationAntibioticResistance2004: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{tanguayIsolationCharacterization102kilodalton1996a, title = {Isolation and Characterization of the 102-Kilodalton {{RNA-binding}} Protein That Binds to the 5’ and 3’ Translational Enhancers of Tobacco Mosaic Virus {{RNA}}}, author = {Tanguay, R L and Gallie, D R}, year = 1996, month = jun, journal = {The Journal of Biological Chemistry}, volume = {271}, number = {24}, eprint = {8663059}, eprinttype = {pubmed}, pages = {14316–14322}, issn = {0021-9258}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8663059}, abstract = {Tobacco mosaic virus (TMV) is a positive-sense, single-stranded RNA virus the genome of which acts as a mRNA in the cytoplasm. On infection, TMV mRNA is efficiently and selectively translated by the host translation machinery despite the lack of a poly(A) tail, which is normally required for efficient translation. Both the 68-base 5’ leader (Omega) and the 205-base 3’ untranslated region of TMV promote efficient translation. A 25-base poly(CAA) region within Omega and the upstream pseudoknot domain, a 72-base region composed of three RNA pseudoknots, are responsible for the translational regulation. We have identified, purified, and characterized a 102-kDa RNA-binding protein (p102) from wheat that binds specifically to the poly(CAA) region within Omega and the upstream pseudoknot domain within the TMV 3’ untranslated region. Polyclonal antibodies raised against wheat p102 were used to demonstrate that p102 is widely conserved in plant species. Moreover, specific RNA binding activity was detected in all plant species tested. Addition of anti-p102 antibodies to an in vitro translation lysate derived from wheat germ repressed translation, which was subsequently reversed by supplementing the lysate with p102. These findings suggest that this protein may play an important role in determining translational efficiency in plants.}, pmid = {8663059}, keywords = {Antibodies,Base Sequence,Binding Sites,Electrophoresis Polyacrylamide Gel,Heparin,Molecular Sequence Data,Molecular Weight,nosource,Nucleic Acid Conformation,Protein Biosynthesis,RNA Messenger,RNA Viral,RNA-Binding Proteins,Substrate Specificity,Tobacco Mosaic Virus,Triticum} } % == BibTeX quality report for tanguayIsolationCharacterization102kilodalton1996a: % ? unused Journal abbr (“J. Biol. Chem”)

@article{atkinsIntricaciesRibosomalFrameshifting1999, title = {Intricacies of Ribosomal Frameshifting}, author = {Atkins, J F and Gesteland, R F}, year = 1999, month = mar, journal = {Nature Structural Biology}, volume = {6}, number = {3}, pages = {206–207}, publisher = {NATURE AMERICA INC}, issn = {1072-8368}, doi = {10.1038/6642}, url = {http://lsb2.uah.edu/chenlq/publications/nsb0399_206.pdf}, keywords = {Frameshifting Ribosomal,Frameshifting- Ribosomal,Magnetic Resonance Spectroscopy,nosource,Nucleic Acid Conformation,RNA Messenger,RNA- Messenger} } % == BibTeX quality report for atkinsIntricaciesRibosomalFrameshifting1999: % ? unused Journal abbr (“Nat. Struct. Biol”)

@article{jacobsonInterrelationshipsPathwaysMRNA1996, title = {Interrelationships of the Pathways of {{mRNA}} Decay and Translation in Eukaryotic Cells.}, author = {Jacobson, A and Peltz, S W}, year = 1996, journal = {Annual Review of Biochemistry}, volume = {65}, pages = {693–739}, issn = {0066-4154}, doi = {10.1146/annurev.bi.65.070196.003401}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.bi.65.070196.003401}, abstract = {While the potential importance of mRNA stability to the regulation of gene expression has been recognized, the structures and mechanisms involved in the determination of individual mRNA decay rates have just begun to be elucidated, particularly in mammalian systems and yeast. It is now well established that mRNA decay is not a default process, in which an array of nonspecific nucleases degrades indiscriminately based on target size or ribosome protection of the substrate. Rather, like transcription, RNA processing, and translation, mRNA decay is a precise process dependent on a variety of specific cis-acting sequences and trans-acting factors. Entry into the pathways of mRNA decay is triggered by at least three types of initiating event: poly(A) shortening, arrest of translation at a premature nonsense codon, and endonucleolytic cleavage. Steps subsequent to poly(A) shortening or premature translational termination converge in a pathway that progresses from removal of the 5’ cap to exonucleolytic digestion of the body of the mRNA. mRNA fragments generated by endonucleolytic cleavage are most likely removed by exonucleolytic decay as well, but these events have not been characterized in detail. Nucleases and other factors (including mRNA sequence elements and autoregulatory proteins) required for the promotion or inhibition of these pathways have been identified by both biochemical and genetic methods and systematic attempts to understand their respective roles have begun. mRNA sequences whose presence or absence has marked effects on mRNA decay rates include the ubiquitous cap and poly(A) tail, sequences that comprise endonuclease cleavage sites, and sequences that promote poly(A) shortening. The latter are found in the 3’-UTR (untranslated region) and in coding regions. Evidence that poly(A) stimulates translation initiation, that some destabilization sequences must be translated in order to function, and that premature translation termination promotes rapid mRNA decay indicates a close linkage between the elements regulating mRNA decay and components of the protein synthesis apparatus. This linkage, and other data, leads us to propose a model for a functional mRNP. In this model, interactions between factors associated with opposite ends of an mRNA stimulate translation initiation and minimize the rate of entry into the pathways of mRNA decay. Events that initiate mRNA decay are postulated to be those that can disrupt this functional complex and create substrates for exonucleolytic digestion.}, pmid = {8811193}, keywords = {Animals,DECAY,Endonucleases,Eukaryotic Cells,Hydrolysis,mRNA,mRNA decay,nosource,Poly A,Protein Biosynthesis,Review,RNA Messenger,translation} } % == BibTeX quality report for jacobsonInterrelationshipsPathwaysMRNA1996: % ? unused Journal abbr (“Annu. Rev. Biochem”)

@article{imanishiIntegrativeAnnotation210372004, title = {Integrative Annotation of 21,037 Human Genes Validated by Full-Length {{cDNA}} Clones}, author = {Imanishi, Tadashi and Itoh, Takeshi and Suzuki, Yutaka and O’Donovan, Claire and Fukuchi, Satoshi and Koyanagi, Kanako O and Barrero, Roberto A and Tamura, Takuro and {Yamaguchi-Kabata}, Yumi and Tanino, Motohiko and Yura, Kei and Miyazaki, Satoru and Ikeo, Kazuho and Homma, Keiichi and Kasprzyk, Arek and Nishikawa, Tetsuo and Hirakawa, Mika and {Thierry-Mieg}, Jean and {Thierry-Mieg}, Danielle and Ashurst, Jennifer and Jia, Libin and Nakao, Mitsuteru and Thomas, Michael A and Mulder, Nicola and Karavidopoulou, Youla and Jin, Lihua and Kim, Sangsoo and Yasuda, Tomohiro and Lenhard, Boris and Eveno, Eric and Suzuki, Yoshiyuki and Yamasaki, Chisato and Takeda, Jun-ichi and Gough, Craig and Hilton, Phillip and Fujii, Yasuyuki and Sakai, Hiroaki and Tanaka, Susumu and Amid, Clara and Bellgard, Matthew and Bonaldo, Maria de Fatima and Bono, Hidemasa and Bromberg, Susan K and Brookes, Anthony J and Bruford, Elspeth and Carninci, Piero and Chelala, Claude and Couillault, Christine and {}{de Souza}, Sandro J and Debily, Marie-Anne and Devignes, Marie-Dominique and Dubchak, Inna and Endo, Toshinori and Estreicher, Anne and Eyras, Eduardo and {Fukami-Kobayashi}, Kaoru and Gopinath, Gopal R and Graudens, Esther and Hahn, Yoonsoo and Han, Michael and Han, Ze-Guang and Hanada, Kousuke and Hanaoka, Hideki and Harada, Erimi and Hashimoto, Katsuyuki and Hinz, Ursula and Hirai, Momoki and Hishiki, Teruyoshi and Hopkinson, Ian and Imbeaud, Sandrine and Inoko, Hidetoshi and Kanapin, Alexander and Kaneko, Yayoi and Kasukawa, Takeya and Kelso, Janet and Kersey, Paul and Kikuno, Reiko and Kimura, Kouichi and Korn, Bernhard and Kuryshev, Vladimir and Makalowska, Izabela and Makino, Takashi and Mano, Shuhei and {Mariage-Samson}, Regine and Mashima, Jun and Matsuda, Hideo and Mewes, Hans-Werner and Minoshima, Shinsei and Nagai, Keiichi and Nagasaki, Hideki and Nagata, Naoki and Nigam, Rajni and Ogasawara, Osamu and Ohara, Osamu and Ohtsubo, Masafumi and Okada, Norihiro and Okido, Toshihisa and Oota, Satoshi and Ota, Motonori and Ota, Toshio and Otsuki, Tetsuji and {Piatier-Tonneau}, Dominique and Poustka, Annemarie and Ren, Shuang-Xi and Saitou, Naruya and Sakai, Katsunaga and Sakamoto, Shigetaka and Sakate, Ryuichi and Schupp, Ingo and Servant, Florence and Sherry, Stephen and Shiba, Rie and Shimizu, Nobuyoshi and Shimoyama, Mary and Simpson, Andrew J and Soares, Bento and Steward, Charles and Suwa, Makiko and Suzuki, Mami and Takahashi, Aiko and Tamiya, Gen and Tanaka, Hiroshi and Taylor, Todd and Terwilliger, Joseph D and Unneberg, Per and Veeramachaneni, Vamsi and Watanabe, Shinya and Wilming, Laurens and Yasuda, Norikazu and Yoo, Hyang-Sook and Stodolsky, Marvin and Makalowski, Wojciech and Go, Mitiko and Nakai, Kenta and Takagi, Toshihisa and Kanehisa, Minoru and Sakaki, Yoshiyuki and Quackenbush, John and Okazaki, Yasushi and Hayashizaki, Yoshihide and Hide, Winston and Chakraborty, Ranajit and Nishikawa, Ken and Sugawara, Hideaki and Tateno, Yoshio and Chen, Zhu and Oishi, Michio and Tonellato, Peter and Apweiler, Rolf and Okubo, Kousaku and Wagner, Lukas and Wiemann, Stefan and Strausberg, Robert L and Isogai, Takao and Auffray, Charles and Nomura, Nobuo and Gojobori, Takashi and Sugano, Sumio}, year = 2004, month = jun, journal = {PLoS Biology}, volume = {2}, number = {6}, pages = {e162}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0020162}, url = {http://dx.plos.org/10.1371/journal.pbio.0020162}, abstract = {The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.}, pmid = {15103394}, keywords = {Alternative Splicing,Computational Biology,Databases Genetic,DNA Complementary,Genes,Genome Human,Humans,Internet,Microsatellite Repeats,nosource,Open Reading Frames,Polymorphism Genetic,Polymorphism Single Nucleotide,Protein Structure Tertiary} } % == BibTeX quality report for imanishiIntegrativeAnnotation210372004: % ? unused Journal abbr (“PLoS Biol”)

@article{schellIntegrationSplicingTransport2002, title = {Integration of Splicing, Transport and Translation to Achieve {{mRNA}} Quality Control by the Nonsense-Mediated Decay Pathway}, author = {Schell, Thomas and Kulozik, Andreas E and Hentze, Matthias W}, year = 2002, journal = {Genome Biology}, volume = {3}, number = {3}, pages = {REVIEWS1006}, issn = {1465-6914}, url = {http://www.biomedcentral.com/content/pdf/gb-2002-3-3-reviews1006.pdf}, abstract = {When pre-mRNAs are spliced, a multi-component complex is deposited onto them, close to the sites of intron removal. New findings suggest that these exon-exon junction complexes and the complexes that bind mRNA caps are key effectors of the fate of spliced mRNAs and may regulate whether mRNAs containing premature stop codons are degraded.}, pmid = {11897029}, keywords = {Animals,Codon Nonsense,Exons,Humans,Models Genetic,nosource,Protein Biosynthesis,Quality Control,RNA Cap-Binding Proteins,RNA Messenger,RNA Splicing,RNA-Binding Proteins} } % == BibTeX quality report for schellIntegrationSplicingTransport2002: % ? unused Journal abbr (“Genome Biol”)

@article{ballIntegratingFunctionalGenomic2000, title = {Integrating Functional Genomic Information into the {{Saccharomyces}} Genome Database}, author = {Ball, C A and Dolinski, K and Dwight, S S and Harris, M A and {Issel-Tarver}, L and Kasarskis, A and Scafe, C R and Sherlock, G and Binkley, G and Jin, H and Kaloper, M and Orr, S D and Schroeder, M and Weng, S and Zhu, Y and Botstein, D and Cherry, J M}, year = 2000, month = jan, journal = {Nucleic Acids Research}, volume = {28}, number = {1}, pages = {77–80}, publisher = {Oxford Univ Press}, issn = {0305-1048}, doi = {10.1093/nar/28.1.77}, url = {http://nar.oxfordjournals.org/content/28/1/77.short}, abstract = {The Saccharomyces Genome Database (SGD) stores and organizes information about the nearly 6200 genes in the yeast genome. The information is organized around the ‘locus page’ and directs users to the detailed information they seek. SGD is endeavoring to integrate the existing information about yeast genes with the large volume of data generated by functional analyses that are beginning to appear in the literature and on web sites. New features will include searches of systematic analyses and Gene Summary Paragraphs that succinctly review the literature for each gene. In addition to current information, such as gene product and phenotype descriptions, the new locus page will also describe a gene product’s cellular process, function and localization using a controlled vocabulary developed in collaboration with two other model organism databases. We describe these developments in SGD through the newly reorganized locus page. The SGD is accessible via the WWW at http://genome-www.stanford.edu/Saccharomyces/}, keywords = {DATABASE,Database Management Systems,Databases,Databases Factual,DatabasesFactual,development,gene,GENE-PRODUCT,Genes,Genetic,genetics,Genome,Genome Fungal,GenomeFungal,genomic,INFORMATION,Internet,La,LOCALIZATION,MODEL,nosource,Phenotype,PRODUCT,Review,Saccharomyces,Saccharomyces Genome Database,search,SGD,SITE,SITES,Support,yeast} } % == BibTeX quality report for ballIntegratingFunctionalGenomic2000: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{ruanILMWebServer2004, title = {{{ILM}}: A Web Server for Predicting {{RNA}} Secondary Structures with Pseudoknots}, author = {Ruan, Jianhua and Stormo, Gary D and Zhang, Weixiong}, year = 2004, month = jul, journal = {Nucleic Acids Research}, volume = {32}, number = {Web Server issue}, pages = {W146-W149}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gkh444}, url = {http://nar.oxfordjournals.org/content/32/suppl_2/W146.short}, abstract = {The ILM web server provides a web interface to two algorithms, iterated loop matching and maximum weighted matching, for efficiently predicting RNA secondary structures with pseudoknots. The algorithms can utilize either thermodynamic or comparative information or both, and thus can work on both aligned and individual sequences. Predicted secondary structures are presented in several formats compatible with a variety of existing visualization tools. The service can be accessed at http://cic.cs.wustl.edu/RNA/.}, keywords = {Algorithms,chemistry,computer,interface,Internet,La,LOOP,No DOI found,nosource,Nucleic Acid Conformation,pseudoknot,pseudoknots,Rna,RNA,RNA SECONDARY STRUCTURE,SECONDARY STRUCTURE,sequence,Sequence Analysis RNA,Sequence AnalysisRNA,SEQUENCES,Software,structure,User-Computer Interface} } % == BibTeX quality report for ruanILMWebServer2004: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{gutellIdentifyingConstraintsHigherorder1992, title = {Identifying Constraints on the Higher-Order Structure of {{RNA}}: Continued Development and Application of Comparative Sequence Analysis Methods.}, author = {Gutell, R R and Power, A and Hertz, G Z and Putz, E J and Stormo, G D}, year = 1992, month = nov, journal = {Nucleic Acids Research}, volume = {20}, number = {21}, pages = {5785–5795}, publisher = {Oxford Univ Press}, issn = {0305-1048}, doi = {10.1093/nar/20.21.5785}, url = {http://nar.oxfordjournals.org/content/20/21/5785.short}, abstract = {Comparative sequence analysis addresses the problem of RNA folding and RNA structural diversity, and is responsible for determining the folding of many RNA molecules, including 5S, 16S, and 23S rRNAs, tRNA, RNAse P RNA, and Group I and II introns. Initially this method was utilized to fold these sequences into their secondary structures. More recently, this method has revealed numerous tertiary correlations, elucidating novel RNA structural motifs, several of which have been experimentally tested and verified, substantiating the general application of this approach. As successful as the comparative methods have been in elucidating higher-order structure, it is clear that additional structure constraints remain to be found. Deciphering such constraints requires more sensitive and rigorous protocols, in addition to RNA sequence datasets that contain additional phylogenetic diversity and an overall increase in the number of sequences. Various RNA databases, including the tRNA and rRNA sequence datasets, continue to grow in number as well as diversity. Described herein is the development of more rigorous comparative analysis protocols. Our initial development and applications on different RNA datasets have been very encouraging. Such analyses on tRNA, 16S and 23S rRNA are substantiating previously proposed associations and are now beginning to reveal additional constraints on these molecules. A subset of these involve several positions that correlate simultaneously with one another, implying units larger than a basepair can be under a phylogenetic constraint.}, keywords = {Base Sequence,Databases Factual,Molecular Sequence Data,nosource,Nucleic Acid Conformation,RNA Ribosomal,RNA Transfer,Sequence Alignment,Sequence Analysis RNA} } % == BibTeX quality report for gutellIdentifyingConstraintsHigherorder1992: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{hammellIdentificationPutativeProgrammed1999, title = {Identification of Putative Programmed -1 Ribosomal Frameshift Signals in Large {{DNA}} Databases.}, author = {Hammell, A B and Taylor, R C and Peltz, S W and Dinman, J D}, year = 1999, month = may, journal = {Genome Research}, volume = {9}, number = {5}, eprint = {10330121}, eprinttype = {pubmed}, pages = {417–427}, issn = {1088-9051}, doi = {10.1101/gr.9.5.417}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10330121}, abstract = {The ⬚cis⬚-acting elements that promote efficient ribosomal frameshifting in the -1 (5’) direction have been well characterized in several viral systems. Results from many studies have convincingly demonstrated that the basic molecular mechanisms governing programmed -1 ribosomal frameshifting are almost identical from yeast to humans. We are interested in testing the hypothesis that programmed -1 ribosomal frameshifting can be utilized to control cellular gene expression. Toward this end, a computer program was designed to search large DNA databases for consensus -1 ribosomal frameshift signals. The results demonstrated that consensus programmed -1 ribosomal frameshift signals can be identified in a substantial number of chromosomally encoded mRNAs, and that they occur with frequencies from 2- to 6-fold greater than random in all of the databases searched. A preliminary survey of the databases resulting from the computer searches found that consensus frameshift signals are present in at least 21 homologous genes from different species, 2 of which are nearly identical, suggesting evolutionary conservation of function. We show that four previously described missense alleles of genes which are linked to human diseases would disrupt putative programmed -1 ribosomal frameshift signals, suggesting that the frameshift signal may be involved in the normal expression of these genes. We also demonstrate that signals found in the yeast ⬚RAS1⬚ and the human ⬚CCR5⬚ genes were able to promote significant levels of programmed -1 ribosomal frameshifting. The significance of these frameshifting signals in controlling gene expression is not known however.}, pmid = {10330121}, keywords = {Alleles,Amino Acid Sequence,Animals,Base Sequence,Chickens,computer,DATABASE,Databases Factual,disease,Dna,DNA,ELEMENTS,expression,frameshift,Frameshifting,Frameshifting Ribosomal,gene,Gene Expression,GENE-EXPRESSION,Genes,genomic,human,Humans,IDENTIFICATION,MECHANISM,MECHANISMS,Mice,Molecular Sequence Data,mRNA,NMD,nosource,Rats,Regulatory Sequences Nucleic Acid,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,search,SIGNAL,Swine,SYSTEM,yeast} } % == BibTeX quality report for hammellIdentificationPutativeProgrammed1999: % ? unused Journal abbr (“Genome Res.”)

@article{meskauskasIdentificationFunctionallyImportant2005, title = {Identification of Functionally Important Amino Acids of Ribosomal Protein {{L3}} by Saturation Mutagenesis.}, author = {Meskauskas, Arturas and Petrov, Alexey N and Dinman, Jonathan D}, year = 2005, month = dec, journal = {Molecular and Cellular Biology}, volume = {25}, number = {24}, pages = {10863–10874}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, doi = {10.1128/MCB.25.24.10863-10874.2005}, url = {http://mcb.asm.org/cgi/content/abstract/25/24/10863}, abstract = {There is accumulating evidence that many ribosomal proteins are involved in shaping rRNA into their functionally correct conformations through RNA-protein interactions. Moreover, although rRNA seems to play the central role in all aspects of ribosome function, ribosomal proteins may be involved in facilitating communication between different functional regions in ribosome, as well as between the ribosome and cellular factors. In an effort to more fully understand how ribosomal proteins may influence ribosome function, we undertook large-scale mutational analysis of ribosomal protein L3, a core protein of the large subunit that has been implicated in numerous ribosome-associated functions in the past. A total of 98 different rpl3 alleles were genetically characterized with regard to their effects on killer virus maintenance, programmed -1 ribosomal frameshifting, resistance/hypersensitivity to the translational inhibitor anisomycin and, in specific cases, the ability to enhance translation of a reporter mRNA lacking the 5’ (7)mGppp cap structure and 3’ poly(A) tail. Biochemical studies reveal a correlation between an increased affinity for aminoacyl-tRNA and the extent of anisomycin resistance and a decreased peptidyltransferase activity and increased frameshifting efficiency. Immunoblot analyses reveal that the superkiller phenotype is not due to a defect in the ability of ribosomes to recruit the Ski-complex, suggesting that the defect lies in a reduced ability of mutant ribosomes to distinguish between cap(+)/poly(A)(+) and cap(-)/poly(A)(-) mRNAs. The results of these analyses are discussed with regard to how protein-rRNA interactions may affect ribosome function.}, keywords = {3,ACID,ACIDS,Alleles,Amino Acid Sequence,Amino Acid Substitution,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,anisomycin,Anisomycin,Cap,CAP STRUCTURE,CONFORMATION,Drug Resistance Fungal,Drug Resistance- Fungal,efficiency,Frameshifting,Frameshifting Ribosomal,Frameshifting- Ribosomal,IDENTIFICATION,INHIBITOR,killer,killer virus,L3,mRNA,Mutagenesis,Mutation,MUTATIONAL ANALYSIS,nosource,Peptidyltransferase,Phenotype,protein,Protein Conformation,Proteins,REGION,RESISTANCE,ribosomal frameshifting,Ribosomal Proteins,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNA Caps,RNA Messenger,RNA Ribosomal,RNA Transfer Amino Acyl,RNA- Messenger,RNA- Ribosomal,RNA- Transfer- Amino Acyl,rRNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,structure,SUBUNIT,translation,virus,Viruses} } % == BibTeX quality report for meskauskasIdentificationFunctionallyImportant2005: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{herrickIdentificationComparisonStable1990, title = {Identification and Comparison of Stable and Unstable {{mRNAs}} in {{Saccharomyces}} Cerevisiae.}, author = {Herrick, D and Parker, R and Jacobson, A}, year = 1990, month = may, journal = {Molecular and Cellular Biology}, volume = {10}, number = {5}, pages = {2269–2284}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, doi = {10.1128/MCB.10.5.2269.Updated}, url = {http://mcb.asm.org/cgi/content/abstract/10/5/2269 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=360574&tool=pmcentrez&rendertype=abstract}, abstract = {We developed a procedure to measure mRNA decay rates in the yeast Saccharomyces cerevisiae and applied it to the determination of half-lives for 20 mRNAs encoded by well-characterized genes. The procedure utilizes Northern (RNA) or dot blotting to quantitate the levels of individual mRNAs after thermal inactivation of RNA polymerase II in an rpb1-1 temperature-sensitive mutant. We compared the results of this procedure with results obtained by two other procedures (approach to steady-state labeling and inhibition of transcription with Thiolutin) and also evaluated whether heat shock alter mRNA decay rates. We found that there are no significant differences in the mRNA decay rates measured in heat-shocked and non-heat-shocked cells and that, for most mRNAs, different procedures yield comparable relative decay rates. Of the 20 mRNAs studied, 11, including those encoded by HIS3, STE2, STE3, and MAT alpha 1, were unstable (t1/2 less than 7 min) and 4, including those encoded by ACT1 and PGK1, were stable (t1/2 greater than 25 min). We have begun to assess the basis and significance of such differences in the decay rates of these two classes of mRNA. Our results indicate that (i) stable and unstable mRNAs do not differ significantly in their poly(A) metabolism; (ii) deadenylation does not destabilize stable mRNAs; (iii) there is no correlation between mRNA decay rate and mRNA size; (iv) the degradation of both stable and unstable mRNAs depends on concomitant translational elongation; and (v) the percentage of rare codons present in most unstable mRNAs is significantly higher than in stable mRNAs.}, pmid = {2183028}, keywords = {Blotting,Blotting Northern,Codon,Cycloheximide,Cycloheximide: pharmacology,Fungal,Fungal: drug effects,Fungal: genetics,Gene Expression Regulation,Gene Expression Regulation Fungal,Genes,Genes Fungal,Hot Temperature,Messenger,Messenger: genetics,Messenger: metabolism,Molecular Weight,Northern,nosource,Poly A,Poly A: genetics,Protein Biosynthesis,Pyrrolidinones,Pyrrolidinones: pharmacology,RNA,RNA Fungal,RNA Messenger,RNA Polymerase II,RNA Polymerase II: metabolism,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism} } % == BibTeX quality report for herrickIdentificationComparisonStable1990: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{zhangIdentificationCharacterizationSequence1995, title = {Identification and Characterization of a Sequence Motif Involved in Nonsense-Mediated {{mRNA}} Decay.}, author = {Zhang, S and {Ruiz-Echevarria}, M J and Quan, Y and Peltz, S W}, year = 1995, month = apr, journal = {Molecular and Cellular Biology}, volume = {15}, number = {4}, eprint = {7891717}, eprinttype = {pubmed}, pages = {2231–2244}, issn = {0270-7306}, doi = {10.1128/MCB.15.4.2231}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7891717}, abstract = {In both prokaryotes and eukaryotes, nonsense mutations in a gene can enhance the decay rate or reduce the abundance of the mRNA transcribed from that gene, and we call this process nonsense-mediated mRNA decay. We have been investigating the cis-acting sequences involved in this decay pathway. Previous experiments have demonstrated that, in addition to a nonsense codon, specific sequences 3’ of a nonsense mutation, which have been defined as downstream elements, are required for mRNA destabilization. The results presented here identify a sequence motif (TGYYGATGYYYYY, where Y stands for either T or C) that can predict regions in genes that, when positioned 3’ of a nonsense codon, promote rapid decay of its mRNA. Sequences harboring two copies of the motif from five regions in the PGK1, ADE3, and HIS4 genes were able to function as downstream elements. In addition, four copies of this motif can function as an independent downstream element. The sequences flanking the motif played a more significant role in modulating its activity when fewer copies of the sequence motif were present. Our results indicate the sequences 5’ of the motif can modulate its activity by maintaining a certain distance between the sequence motif and the termination codon. We also suggest that the sequences 3’ of the motif modulate the activity of the downstream element by forming RNA secondary structures. Consistent with this view, a stem-loop structure positioned 3’ of the sequence motif can enhance the activity of the downstream element. This sequence motif is one of the few elements that have been identified that can predict regions in genes that can be involved in mRNA turnover. The role of these sequences in mRNA decay is discussed.}, pmid = {7891717}, keywords = {Alcohol Oxidoreductases,Aminohydrolases,Base Sequence,Codon,DECAY,DNA Mutational Analysis,downstream element,Formate-Tetrahydrofolate Ligase,Fungal Proteins,Genes Fungal,Half-Life,IDENTIFICATION,Models Genetic,Molecular Sequence Data,mRNA,mRNA decay,Mutagenesis Insertional,nosource,Phosphoglycerate Kinase,Protein Biosynthesis,Pyrophosphatases,RNA Fungal,RNA Messenger,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,sequence,Sequence Deletion,Sequence Homology Nucleic Acid,Transcription Factors,UPF} } % == BibTeX quality report for zhangIdentificationCharacterizationSequence1995: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{shigemotoIdentificationCharacterisationDevelopmentally2001a, title = {Identification and Characterisation of a Developmentally Regulated Mammalian Gene That Utilises -1 Programmed Ribosomal Frameshifting}, author = {Shigemoto, K and Brennan, J and Walls, E and Watson, C J and Stott, D and Rigby, P W and Reith, A D}, year = 2001, month = oct, journal = {Nucleic Acids Research}, volume = {29}, number = {19}, eprint = {11574691}, eprinttype = {pubmed}, pages = {4079–4088}, issn = {1362-4962}, doi = {10.1093/nar/29.19.4079}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11574691}, abstract = {Translational recoding of mRNA through a -1 ribosomal slippage mechanism has been observed in RNA viruses and retrotransposons of both eukaryotes and prokaryotes. Whilst this provides a potentially powerful mechanism of gene regulation, the utilization of -1 translational frameshifting in regulating mammalian gene expression has remained obscure. Here we report a mammalian gene, Edr, which provides the first example of -1 translational recoding in a eukaryotic cellular gene. In addition to bearing functional frameshift elements that mediate expression of distinct polypeptides, Edr bears both CCHC zinc-finger and putative aspartyl protease catalytic site retroviral-like motifs, indicative of a relic retroviral-like origin for Edr. These features, coupled with conservation of Edr as a single copy gene in mouse and man and striking spatio-temporal regulation of expression during embryogenesis, suggest that Edr plays a functionally important role in mammalian development.}, pmid = {11574691}, keywords = {Amino Acid Motifs,Amino Acid Sequence,Animals,Aspartic Acid Endopeptidases,Base Sequence,Carrier Proteins,Chromosome Mapping,Conserved Sequence,development,ELEMENTS,expression,frameshift,Frameshifting,Frameshifting Ribosomal,gene,Gene Expression,Gene Expression Regulation Developmental,GENE-EXPRESSION,Genome Viral,Humans,IDENTIFICATION,MECHANISM,Mice,Molecular Sequence Data,mRNA,Muscle Skeletal,nosource,Nucleic Acid Conformation,Peptides,recoding,regulation,retrotransposon,Retroviridae,ribosomal frameshifting,Rna,RNA Messenger,RNA Viruses,Sequence Homology Amino Acid,SLIPPAGE,Tissue Distribution,Zinc Fingers} } % == BibTeX quality report for shigemotoIdentificationCharacterisationDevelopmentally2001a: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{wittmannHUPF2SilencingIdentifies2006, title = {{{hUPF2}} Silencing Identifies Physiologic Substrates of Mammalian Nonsense-Mediated {{mRNA}} Decay}, author = {Wittmann, J{"u}rgen and Hol, Elly M and J{"a}ck, Hans-Martin}, year = 2006, month = feb, journal = {Molecular and Cellular Biology}, volume = {26}, number = {4}, pages = {1272–1287}, issn = {0270-7306}, doi = {10.1128/MCB.26.4.1272-1287.2006}, url = {http://mcb.asm.org/cgi/content/abstract/26/4/1272}, abstract = {Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic surveillance pathway that selectively degrades aberrant mRNAs with premature termination codons (PTCs). Although a small number of cases exist in mammals, where NMD controls levels of physiologic PTC transcripts, it is still unclear whether the engagement of NMD in posttranscriptional control of gene expression is a more prevalent phenomenon. To identify physiologic NMD substrates and to study how NMD silencing affects the overall dynamics of a cell, we stably down-regulated hUPF2, the human homolog of the yeast NMD factor UPF2, by RNA interference. As expected, hUPF2-silenced HeLa cells were impaired in their ability to recognize ectopically expressed aberrant PTC transcripts. Surprisingly, hUPF2 silencing did not affect cell growth and viability but clearly diminished phosphorylation of hUPF1, suggesting a role of hUPF2 in modulating NMD activity through phosphorylation of hUPF1. Genome-wide DNA microarray expression profiling identified 37 novel up-regulated and 57 down-regulated transcripts in hUPF2-silenced cells. About 60% of the up-regulated mRNAs carry typical NMD motifs. Hence, NMD is important not only for maintaining the transcriptome integrity by removing nonfunctional and aberrant PTC-bearing transcripts but also for posttranscriptional control of selected physiologic transcripts with NMD features.}, pmid = {16449641}, keywords = {0,Base Sequence,Cell Proliferation,Cell Survival,CELLS,Codon,Codon Nonsense,CodonNonsense,CODONS,DECAY,Dna,DNA Complementary,DNAComplementary,DYNAMICS,expression,gene,Gene Expression,Gene Expression Profiling,Gene Silencing,GENE-EXPRESSION,genetics,Germany,GROWTH,Hela Cells,HELA-CELLS,homolog,human,HUMAN HOMOLOG,Humans,IDENTIFY,immunology,La,Mammals,metabolism,MOTIFS,mRNA,mRNA decay,NMD,nonfile,NONSENSE,nonsense-mediated mRNA decay,nosource,PATHWAY,Phosphorylation,PREMATURE TERMINATION CODON,protein,Research SupportNon-U.S.Gov’t,Rna,RNA Interference,RNA Messenger,RNA Small Interfering,RNA Stability,RNAMessenger,RNASmall Interfering,SURVEILLANCE,termination,TERMINATION CODON,TERMINATION-CODON,Trans-Activators,TRANSCRIPT,transcription,TRANSCRIPTION FACTOR,Transcription Factors,Transfection,yeast} } % == BibTeX quality report for wittmannHUPF2SilencingIdentifies2006: % ? unused Journal abbr (“Mol. Cell. Biol.”)

@article{farabaughHowTranslationalAccuracy1999, title = {How Translational Accuracy Influences Reading Frame Maintenance.}, author = {Farabaugh, P J and Bj{"o}rk, G R}, year = 1999, month = mar, journal = {The EMBO Journal}, volume = {18}, number = {6}, pages = {1427–1434}, publisher = {Nature Publishing Group}, issn = {0261-4189}, doi = {10.1093/emboj/18.6.1427}, url = {http://onlinelibrary.wiley.com/doi/10.1093/emboj/18.6.1427/full http://www.nature.com/emboj/journal/v18/n6/abs/7591574a.html}, abstract = {Most missense errors have little effect on protein function, since they only exchange one amino acid for another. However, processivity errors, frameshifting or premature termination result in a synthesis of an incomplete peptide. There may be a connection between missense and processivity errors, since processivity errors now appear to result from a second error occurring after recruitment of an errant aminoacyl-tRNA, either spontaneous dissociation causing premature termination or translational frameshifting. This is clearest in programmed translational frameshifting where the mRNA programs errant reading by a near-cognate tRNA; this error promotes a second frameshifting error (a dual-error model of frameshifting). The same mechanism can explain frameshifting by suppressor tRNAs, even those with expanded anticodon loops. The previous model that suppressor tRNAs induce quadruplet translocation now appears incorrect for most, and perhaps for all of them. We suggest that the ‘spontaneous’ tRNA-induced frameshifting and ‘programmed’ mRNA-induced frameshifting use the same mechanism, although the frequency of frameshifting is very different. This new model of frameshifting suggests that the tRNA is not acting as the yardstick to measure out the length of the translocation step. Rather, the translocation of 3 nucleotides may be an inherent feature of the ribosome.}, keywords = {99177158,accuracy,Anticodon,appeared to use an,Base Pairing,Base Sequence,dual-error model,expanded 4-nucleotide anticodon to,frameshift,Frameshift Mutation,frameshift suppressor trnas that,Frameshifting,MECHANISM,missense errors,Models Genetic,mRNA,Mutation Missense,nosource,Nucleic Acid Conformation,Nucleotides,protein,Protein Biosynthesis,read a 4-nucleotide,Reading Frames,ribosome,Ribosomes,RNA Transfer,termination,translation,translocation,tRNA,yardstick model} } % == BibTeX quality report for farabaughHowTranslationalAccuracy1999: % ? unused Journal abbr (“EMBO J.”)

@article{eddyHowRNAFolding2004, title = {How Do {{RNA}} Folding Algorithms Work?}, author = {Eddy, Sean R}, year = 2004, month = nov, journal = {Nature Biotechnology}, volume = {22}, number = {11}, pages = {1457–1458}, publisher = {New York, NY: Nature Pub. Co., 1996-}, issn = {1087-0156}, doi = {10.1038/nbt1104-1457}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:How+do+RNA+folding+algorithms+work?#0}, abstract = {Programs such as MFOLD and ViennaRNA are widely used to predict RNA secondary structures. How do these algorithms work? Why can’t they predict RNA pseudoknots? How accurate are they, and will they get better?}, keywords = {Algorithms,Base Sequence,Computer Simulation,Models Chemical,Models Molecular,Models- Chemical,Models- Molecular,Molecular Sequence Data,nosource,RNA,Sequence Analysis RNA,Sequence Analysis- RNA} } % == BibTeX quality report for eddyHowRNAFolding2004: % ? unused Journal abbr (“Nat. Biotechnol”)

@article{renHotKnotsHeuristicPrediction2005, title = {{{HotKnots}}: Heuristic Prediction of {{RNA}} Secondary Structures Including Pseudoknots}, author = {Ren, Jihong and Rastegari, Baharak and Condon, Anne and Hoos, Holger H}, year = 2005, month = oct, journal = {RNA (New York, N.Y.)}, volume = {11}, number = {10}, pages = {1494–1504}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, doi = {10.1261/rna.7284905}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1370833&tool=pmcentrez&rendertype=abstract http://www.ncbi.nlm.nih.gov/pubmed/16199760 http://rnajournal.cshlp.org/content/11/10/1494.short}, abstract = {We present HotKnots, a new heuristic algorithm for the prediction of RNA secondary structures including pseudoknots. Based on the simple idea of iteratively forming stable stems, our algorithm explores many alternative secondary structures, using a free energy minimization algorithm for pseudoknot free secondary structures to identify promising candidate stems. In an empirical evaluation of the algorithm with 43 sequences taken from the Pseudobase database and from the literature on pseudoknotted structures, we found that overall, in terms of the sensitivity and specificity of predictions, HotKnots outperforms the well-known Pseudoknots algorithm of Rivas and Eddy and the NUPACK algorithm of Dirks and Pierce, both based on dynamic programming approaches for limited classes of pseudoknotted structures. It also outperforms the heuristic Iterated Loop Matching algorithm of Ruan and colleagues, and in many cases gives better results than the genetic algorithm from the STAR package of van Batenburg and colleagues and the recent pknotsRG-mfe algorithm of Reeder and Giegerich. The HotKnots algorithm has been implemented in C/C++ and is available from http://www.cs.ubc.ca/labs/beta/Software/HotKnots.}, pmid = {16199760}, keywords = {Algorithms,Base Pairing,Base Sequence,chemistry,Comparative Study,Computational Biology,computer,DATABASE,dynamic programming,Genetic,GENETIC ALGORITHM,heuristic algorithms,IDENTIFY,La,LOOP,Molecular Sequence Data,nosource,Nucleic Acid,Nucleic Acid Conformation,PREDICTION,Predictive Value of Tests,pseudoknot,pseudoknots,Rna,RNA,RNA SECONDARY STRUCTURE,rna secondary structure prediction,RNA: chemistry,SECONDARY STRUCTURE,Sensitivity and Specificity,sequence,Sequence Analysis,Sequence Analysis RNA,Sequence AnalysisRNA,Sequence Homology,Sequence Homology Nucleic Acid,Sequence HomologyNucleic Acid,SEQUENCES,Software,SPECIFICITY,structure} } % == BibTeX quality report for renHotKnotsHeuristicPrediction2005: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA.”)

@article{wilkinsonHighthroughputSHAPEAnalysis2008, title = {High-Throughput {{SHAPE}} Analysis Reveals Structures in {{HIV-1}} Genomic {{RNA}} Strongly Conserved across Distinct Biological States}, author = {Wilkinson, Kevin A and Gorelick, Robert J and Vasa, Suzy M and Guex, Nicolas and Rein, Alan and Mathews, David H and Giddings, Morgan C and Weeks, Kevin M}, year = 2008, month = apr, journal = {PLoS Biology}, volume = {6}, number = {4}, pages = {e96}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0060096}, url = {http://dx.plos.org/10.1371/journal.pbio.0060096}, abstract = {Replication and pathogenesis of the human immunodeficiency virus (HIV) is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We invent high-throughput SHAPE (selective 2’-hydroxyl acylation analyzed by primer extension) technology, which uses many of the same tools as DNA sequencing, to quantify RNA backbone flexibility at single-nucleotide resolution and from which robust structural information can be immediately derived. We analyze the structure of HIV-1 genomic RNA in four biologically instructive states, including the authentic viral genome inside native particles. Remarkably, given the large number of plausible local structures, the first 10% of the HIV-1 genome exists in a single, predominant conformation in all four states. We also discover that noncoding regions functioning in a regulatory role have significantly lower (p-value {\(<\)} 0.0001) SHAPE reactivities, and hence more structure, than do viral coding regions that function as the template for protein synthesis. By directly monitoring protein binding inside virions, we identify the RNA recognition motif for the viral nucleocapsid protein. Seven structurally homologous binding sites occur in a well-defined domain in the genome, consistent with a role in directing specific packaging of genomic RNA into nascent virions. In addition, we identify two distinct motifs that are targets for the duplex destabilizing activity of this same protein. The nucleocapsid protein destabilizes local HIV-1 RNA structure in ways likely to facilitate initial movement both of the retroviral reverse transcriptase from its tRNA primer and of the ribosome in coding regions. Each of the three nucleocapsid interaction motifs falls in a specific genome domain, indicating that local protein interactions can be organized by the long-range architecture of an RNA. High-throughput SHAPE reveals a comprehensive view of HIV-1 RNA genome structure, and further application of this technology will make possible newly informative analysis of any RNA in a cellular transcriptome.}, pmid = {18447581}, keywords = {0,Acylation,Amino Acid Sequence,analysis,Base Sequence,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,chemistry,CODING REGION,CONFORMATION,Dna,DNA Primers,DOMAIN,genetics,Genome,Genome Viral,Genome-Viral,GenomeViral,genomic,GENOMIC RNA,HIV,Hiv-1,HIV-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,Humans,IDENTIFY,IMMUNODEFICIENCY-VIRUS,INFORMATION,La,metabolism,Models Biological,Models-Biological,ModelsBiological,Molecular Sequence Data,MOTIFS,Movement,nosource,Nucleic Acid Conformation,NUCLEOCAPSID PROTEIN,Nucleocapsid Proteins,packaging,PARTICLES,primer extension,protein,Protein Binding,protein synthesis,PROTEIN-SYNTHESIS,Proteins,RECOGNITION,REGION,REPLICATION,RESOLUTION,REVERSE-TRANSCRIPTASE,ribosome,Rna,RNA Messenger,RNA recognition,RNA Transfer Lys,RNA Viral,RNA-Messenger,RNA-Transfer-Lys,Rna-Viral,RNAMessenger,RNATransferLys,RnaViral,SITE,SITES,Structural,structure,Structure-Activity Relationship,Support,TARGET,TEMPLATE,Transcription Genetic,Transcription-Genetic,TranscriptionGenetic,tRNA,United States,Virion,VIRIONS,virus} } % == BibTeX quality report for wilkinsonHighthroughputSHAPEAnalysis2008: % ? unused Journal abbr (“PLoS Biol”)

@article{dickHeterologousComplementationReveals1998, title = {Heterologous Complementation Reveals That Mutant Alleles of {{QSR1}} Render {{60S}} Ribosomal Subunits Unstable and Translationally Inactive}, author = {Dick, F A and Trumpower, B L}, year = 1998, month = may, journal = {Nucleic Acids Research}, volume = {26}, number = {10}, pages = {2442–2448}, publisher = {Oxford Univ Press}, issn = {0305-1048}, doi = {10.1093/nar/26.10.2442}, url = {http://nar.oxfordjournals.org/content/26/10/2442.short}, abstract = {QSR1 is a highly conserved gene which encodes a 60S ribosomal subunit protein that is required for joining of large and small ribosomal subunits. In this report we demonstrate heterologous complementation of a yeast QSR1 deletion strain with both the human and corn homologs and show that the human and corn proteins are assembled into hybrid yeast/human and yeast/corn ribosomes. While the homologous genes complement lethality of the QSR1 deletion, they also result in a diminished growth rate. Analyses of the translation rates of ribosomes containing the human and corn proteins reveal a partial loss of function. Velocity gradient analyses of the hybrid ribosomes after exposure to high concentrations of salt indicate that the decreased activity is due to lability of the hybrid 60S subunits.}, keywords = {0,60S subunit,Alleles,Amino Acid Sequence,Biochemistry,CEREVISIAE,Corn,ENCODES,Fungal Proteins,gene,Genes,Genetic Complementation Test,genetics,GROWTH,homolog,human,Humans,La,Molecular Sequence Data,Mutation,nosource,Peptide Chain Elongation Translational,Peptide Chain ElongationTranslational,pharmacology,Polyribosomes,Potassium,Potassium Chloride,protein,Protein Biosynthesis,Proteins,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Sequence Homology Nucleic Acid,Sequence HomologyNucleic Acid,Species Specificity,SUBUNIT,SUBUNITS,Support,translation,yeast,Zea mays} } % == BibTeX quality report for dickHeterologousComplementationReveals1998: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{zavialovGuaninenucleotideExchangeRibosomebound2005, title = {Guanine-Nucleotide Exchange on Ribosome-Bound Elongation Factor {{G}} Initiates the Translocation of {{tRNAs}}}, author = {Zavialov, Andrey V and Hauryliuk, Vasili V and Ehrenberg, M{}ns}, year = 2005, journal = {Journal of Biology}, volume = {4}, number = {2}, eprint = {15985150}, eprinttype = {pubmed}, pages = {9}, publisher = {BioMed Central Ltd}, issn = {1475-4924}, doi = {10.1186/jbiol24}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15985150}, abstract = {BACKGROUND: During the translation of mRNA into polypeptide, elongation factor G (EF-G) catalyzes the translocation of peptidyl-tRNA from the A site to the P site of the ribosome. According to the ‘classical’ model, EF-G in the GTP-bound form promotes translocation, while hydrolysis of the bound GTP promotes dissociation of the factor from the post-translocation ribosome. According to a more recent model, EF-G operates like a ‘motor protein’ and drives translocation of the peptidyl-tRNA after GTP hydrolysis. In both the classical and motor protein models, GDP-to-GTP exchange is assumed to occur spontaneously on ‘free’ EF-G even in the absence of a guanine-nucleotide exchange factor (GEF). RESULTS: We have made a number of findings that challenge both models. First, free EF-G in the cell is likely to be in the GDP-bound form. Second, the ribosome acts as the GEF for EF-G. Third, after guanine-nucleotide exchange, EF-G in the GTP-bound form moves the tRNA2-mRNA complex to an intermediate translocation state in which the mRNA is partially translocated. Fourth, subsequent accommodation of the tRNA2-mRNA complex in the post-translocation state requires GTP hydrolysis. CONCLUSION: These results, in conjunction with previously published cryo-electron microscopy reconstructions of the ribosome in various functional states, suggest a novel mechanism for translocation of tRNAs on the ribosome by EF-G. Our observations suggest that the ribosome is a universal guanosine-nucleotide exchange factor for EF-G as previously shown for the class-II peptide-release factor 3.}, keywords = {3,A SITE,A-SITE,BIOLOGY,COMPLEX,COMPLEXES,Cryoelectron Microscopy,EF-G,elongation,ELONGATION-FACTOR-G,Escherichia coli,FORM,GTP,Guanine Nucleotides,GUANINE-NUCLEOTIDE,GUANINE-NUCLEOTIDE EXCHANGE,GUANINE-NUCLEOTIDE-EXCHANGE,Hydrolysis,INTERMEDIATE,La,MECHANISM,MODEL,models,Models Biological,MOF,Molecular Biology,mRNA,nosource,P SITE,P-SITE,Peptide Elongation Factor G,POLYPEPTIDE,protein,Protein Biosynthesis,REQUIRES,ribosome,Ribosomes,RNA Transfer Amino Acyl,SITE,translation,translocation,tRNA} } % == BibTeX quality report for zavialovGuaninenucleotideExchangeRibosomebound2005: % ? unused Journal abbr (“J. Biol”)

@article{kroganGlobalLandscapeProtein2006, title = {Global Landscape of Protein Complexes in the Yeast {{Saccharomyces}} Cerevisiae}, author = {Krogan, Nevan J and Cagney, Gerard and Yu, Haiyuan and Zhong, Gouqing and Guo, Xinghua and Ignatchenko, Alexandr and Li, Joyce and Pu, Shuye and Datta, Nira and Tikuisis, Aaron P and Punna, Thanuja and {Peregr{'i}n-Alvarez}, Jos{'e} M and Shales, Michael and Zhang, Xin and Davey, Michael and Robinson, Mark D and Paccanaro, Alberto and Bray, James E and Sheung, Anthony and Beattie, Bryan and Richards, Dawn P and Canadien, Veronica and Lalev, Atanas and Mena, Frank and Wong, Peter and Starostine, Andrei and Canete, Myra M and Vlasblom, James and Wu, Samuel and Orsi, Chris and Collins, Sean R and Chandran, Shamanta and Haw, Robin and Rilstone, Jennifer J and Gandi, Kiran and Thompson, Natalie J and Musso, Gabe and St Onge, Peter and Ghanny, Shaun and Lam, Mandy H Y and Butland, Gareth and {Altaf-Ul}, Amin M and Kanaya, Shigehiko and Shilatifard, Ali and O’Shea, Erin and Weissman, Jonathan S and Ingles, C James and Hughes, Timothy R and Parkinson, John and Gerstein, Mark and Wodak, Shoshana J and Emili, Andrew and Greenblatt, Jack F}, year = 2006, month = mar, journal = {Nature}, volume = {440}, number = {7084}, pages = {637–643}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature04670}, url = {http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature04670.html}, abstract = {Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ionization-time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein-protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.}, keywords = {Conserved Sequence,Evolution,Mass Spectrometry,Multiprotein Complexes,nosource,Protein Binding,Proteome,Proteomics,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins} }

@article{vegaGettingEndTelomerase2003, title = {Getting to the End: Telomerase Access in Yeast and Humans}, author = {Vega, Leticia R and Mateyak, Maria K and Zakian, Virginia A}, year = 2003, month = dec, journal = {Nature Reviews. Molecular Cell Biology}, volume = {4}, number = {12}, pages = {948–959}, publisher = {Nature Publishing Group}, issn = {1471-0072}, doi = {10.1038/nrm1256}, url = {http://www.nature.com/nrm/journal/v4/n12/abs/nrm1256.html}, keywords = {Base Sequence,Cell Nucleolus,DNA Damage,DNA Fungal,DNA Replication,Fungal Proteins,Humans,nosource,Telomerase,Telomere,Telomere-Binding Proteins} } % == BibTeX quality report for vegaGettingEndTelomerase2003: % ? Possibly abbreviated journal title Nature Reviews. Molecular Cell Biology % ? unused Journal abbr (“Nat. Rev. Mol. Cell Biol”)

@article{heGenomewideAnalysisMRNAs2003, title = {Genome-Wide Analysis of {{mRNAs}} Regulated by the Nonsense-Mediated and 5’ to 3’ {{mRNA}} Decay Pathways in Yeast.}, author = {He, Feng and Li, Xiangrui and Spatrick, Phyllis and Casillo, Ryan and Dong, Shuyun and Jacobson, Allan}, year = 2003, month = dec, journal = {Molecular Cell}, volume = {12⬚ ⬚}, number = {6}, eprint = {14690598}, eprinttype = {pubmed}, pages = {1439–1452}, publisher = {Elsevier}, issn = {1097-2765}, doi = {10.1016/S1097-2765(03)00446-5}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14690598 http://www.sciencedirect.com/science/article/pii/S1097276503004465}, abstract = {Transcripts regulated by the yeast nonsense-mediated and 5’ to 3’ mRNA decay pathways were identified by expression profiling of wild-type, upf1Delta, nmd2Delta, upf3Delta, dcp1Delta, and xrn1Delta cells. This analysis revealed that inactivation of Upf1p, Nmd2p, or Upf3p has identical effects on global RNA accumulation; inactivation of Dcp1p or Xrn1p exhibits both common and unique effects on global RNA accumulation but causes upregulation of only a small fraction of transcripts; and the majority of transcripts upregulated in upf/nmd strains are also upregulated to similar extents in dcp1Delta and xrn1Delta strains. Our results define the core transcripts regulated by NMD, identify several novel structural classes of NMD substrates, demonstrate that nonsense-containing mRNAs are primarily degraded by the 5’ to 3’ decay pathway even in the absence of functional NMD, and indicate that 3’ to 5’ decay, not 5’ to 3’ decay, may be the major mRNA decay activity in yeast cells.}, keywords = {3,analysis,Cluster Analysis,Codon Nonsense,Codon- Nonsense,DECAY,DECAY PATHWAY,decay pathways,Endoribonucleases,Exoribonucleases,Gene Expression Profiling,Gene Expression Regulation Fungal,Gene Expression Regulation- Fungal,Genome Fungal,Genome- Fungal,micorarray,mRNA,mRNA decay,nosource,Oligonucleotide Array Sequence Analysis,Open Reading Frames,PATHWAY,Reproducibility of Results,RNA Cap-Binding Proteins,RNA Fungal,RNA Messenger,RNA- Fungal,RNA- Messenger,RNA-Binding Proteins,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,yeast} } % == BibTeX quality report for heGenomewideAnalysisMRNAs2003: % ? unused Journal abbr (“Mol. Cell”)

@article{velichutinaGeneticInteractionYeast2001, title = {Genetic Interaction between Yeast {{Saccharomyces}} Cerevisiae Release Factors and the Decoding Region of 18 {{S rRNA1}}}, author = {Velichutina, I V and Hong, J Y and Mesecar, A D and Chernoff, Y O and Liebman, S W}, year = 2001, month = jan, journal = {Journal of Molecular Biology}, volume = {305}, number = {4}, pages = {715–727}, publisher = {Elsevier}, issn = {0022-2836}, doi = {10.1006/jmbi.2000.4329}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283600943298}, abstract = {Functional and structural similarities between tRNA and eukaryotic class 1 release factors (eRF1) described previously, provide evidence for the molecular mimicry concept. This concept is supported here by the demonstration of a genetic interaction between eRF1 and the decoding region of the ribosomal RNA, the site of tRNA-mRNA interaction. We show that the conditional lethality caused by a mutation in domain 1 of yeast eRF1 (P86A), that mimics the tRNA anticodon stem-loop, is rescued by compensatory mutations A1491G (rdn15) and U1495C (hyg1) in helix 44 of the decoding region and by U912C (rdn4) and G886A (rdn8) mutations in helix 27 of the 18 S rRNA. The rdn15 mutation creates a C1409-G1491 base-pair in yeast rRNA that is analogous to that in prokaryotic rRNA known to be important for high-affinity paromomycin binding to the ribosome. Indeed, rdn15 makes yeast cells extremely sensitive to paromomycin, indicating that the natural high resistance of the yeast ribosome to paromomycin is, in large part, due to the absence of the 1409-1491 base-pair. The rdn15 and hyg1 mutations also partially compensate for inactivation of the eukaryotic release factor 3 (eRF3) resulting from the formation of the [PSI+] prion, a self-reproducible termination-deficient conformation of eRF3. However, rdn15, but not hyg1, rescues the conditional cell lethality caused by a GTPase domain mutation (R419G) in eRF3. Other antisuppressor rRNA mutations, rdn2(G517A), rdn1T(C1054T) and rdn12A(C526A), strongly inhibit [PSI+]-mediated stop codon read-through but do not cure cells of the [PSI+] prion. Interestingly, cells bearing hyg1 seem to enable [PSI+] strains to accumulate larger Sup35p aggregates upon Sup35p overproduction, suggesting a lower toxicity of overproduced Sup35p when the termination defect, caused by [PSI+], is partly relieved.}, keywords = {0,3,Anti-Bacterial Agents,AntibioticsAminoglycoside,Anticodon,Base Pairing,Base Sequence,BASE-PAIR,BINDING,BIOLOGY,biosynthesis,CELLS,CEREVISIAE,CHAIN TERMINATION,chemistry,Codon,Codon Terminator,CodonTerminator,CONFORMATION,cytology,decoding,DECODING REGION,DOMAIN,drug effects,Drug Resistance Microbial,Drug ResistanceMicrobial,Frameshift Mutation,Fungal Proteins,Genes Fungal,Genes Lethal,GenesFungal,GenesLethal,Genetic,genetics,GTPase,La,metabolism,Molecular Biology,Molecular Mimicry,Mutation,MUTATIONS,nosource,Paromomycin,Peptide Chain Termination,Peptide Termination Factors,pharmacology,prion,protein,Protein Biosynthesis,Proteins,READ-THROUGH,readthrough,REGION,RELEASE,release factor,RELEASE FACTORS,RESISTANCE,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNA Ribosomal 18S,RNARibosomal18S,rRNA,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SITE,STEM-LOOP,STOP CODON,Structural,Support,supportu.s.gov’tp.h.s.,Suppression Genetic,SuppressionGenetic,termination,termination defect,toxicity,TranslationGenetic,tRNA,yeast,YEAST-CELLS} } % == BibTeX quality report for velichutinaGeneticInteractionYeast2001: % ? unused Journal abbr (“J. Mol. Biol”)

@article{martinGeneticExplorationInteractive1990, title = {Genetic Exploration of Interactive Domains in {{RNA}} Polymerase {{II}} Subunits.}, author = {Martin, C and Okamura, S and Young, R}, year = 1990, month = may, journal = {Molecular and Cellular Biology}, volume = {10}, number = {5}, pages = {1908–1914}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, url = {http://mcb.asm.org/cgi/content/abstract/10/5/1908}, abstract = {The two large subunits of RNA polymerase II, RPB1 and RPB2, contain regions of extensive homology to the two large subunits of Escherichia coli RNA polymerase. These homologous regions may represent separate protein domains with unique functions. We investigated whether suppressor genetics could provide evidence for interactions between specific segments of RPB1 and RPB2 in Saccharomyces cerevisiae. A plasmid shuffle method was used to screen thoroughly for mutations in RPB2 that suppress a temperature-sensitive mutation, rpb1-1, which is located in region H of RPB1. All six RPB2 mutations that suppress rpb1-1 were clustered in region I of RPB2. The location of these mutations and the observation that they were allele specific for suppression of rpb1-1 suggests an interaction between region H of RPB1 and region I of RPB2. A similar experiment was done to isolate and map mutations in RPB1 that suppress a temperature-sensitive mutation, rpb2-2, which occurs in region I of RPB2. These suppressor mutations were not clustered in a particular region. Thus, fine structure suppressor genetics can provide evidence for interactions between specific segments of two proteins, but the results of this type of analysis can depend on the conditional mutation to be suppressed.}, keywords = {Alleles,Chromosome Mapping,Cloning Molecular,DNA Mutational Analysis,Genes Fungal,Genetic Complementation Test,Macromolecular Substances,nosource,RNA Polymerase II,Saccharomyces cerevisiae,Suppression Genetic} } % == BibTeX quality report for martinGeneticExplorationInteractive1990: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{kebaaraGeneticBackgroundAffects2003, title = {Genetic Background Affects Relative Nonsense {{mRNA}} Accumulation in Wild-Type and Upf Mutant Yeast Strains}, author = {Kebaara, Bessie and Nazarenus, Tara and Taylor, Rachel and Atkin, Audrey L}, year = 2003, month = jun, journal = {Current Genetics}, volume = {43}, number = {3}, pages = {171–177}, publisher = {Springer}, issn = {0172-8083}, doi = {10.1007/s00294-003-0386-3}, url = {http://www.springerlink.com/index/KABCCRHR8JR94DN8.pdf}, abstract = {The Saccharomyces cerevisiae nonsense-mediated mRNA decay (NMD) pathway targets mRNAs with premature stop codons and some wild-type mRNAs for accelerated decay. Upf1p, Upf2p and Upf3p are required for NMD. NMD-targeted mRNAs are degraded rapidly in wild-type cells and stabilized in upf1, upf2 or upf3 mutants. We report here that the relative CYH2 pre-mRNA/mRNA accumulation is enhanced in cells derived from a W303 background, compared with a variety of commonly used strains. The enhanced CYH2 pre-mRNA accumulation phenotype results from a larger difference in mRNA half-lives in the W303 strains than two previously used strains. This phenotype can be selected in crosses and is also seen in upf2 and upf3 mutants. These results suggest there are genes that influence the efficiency of NMD and that yeast strains derived from the W303 background may be useful for measurement of abundance and half-lives of low abundance, short-lived NMD substrates.}, keywords = {Adaptor Proteins Signal Transducing,Blotting Northern,Codon Nonsense,Crosses Genetic,nosource,RNA Helicases,RNA Stability,RNA-Binding Proteins,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Trans-Activators,Transformation Genetic} } % == BibTeX quality report for kebaaraGeneticBackgroundAffects2003: % ? unused Journal abbr (“Curr. Genet”)

@article{taylorGeneSetCoregulated2005a, title = {Gene Set Coregulated by the {{Saccharomyces}} Cerevisiae Nonsense-Mediated {{mRNA}} Decay Pathway}, author = {Taylor, Rachel and Kebaara, Bessie Wanja and Nazarenus, Tara and Jones, Ashley and Yamanaka, Rena and Uhrenholdt, Rachel and Wendler, Jason P and Atkin, Audrey L}, year = 2005, month = dec, journal = {Eukaryotic Cell}, volume = {4}, number = {12}, eprint = {16339724}, eprinttype = {pubmed}, pages = {2066–2077}, issn = {1535-9778}, doi = {10.1128/EC.4.12.2066-2077.2005}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16339724}, abstract = {The nonsense-mediated mRNA decay (NMD) pathway has historically been thought of as an RNA surveillance system that degrades mRNAs with premature translation termination codons, but the NMD pathway of Saccharomyces cerevisiae has a second role regulating the decay of some wild-type mRNAs. In S. cerevisiae, a significant number of wild-type mRNAs are affected when NMD is inactivated. These mRNAs are either wild-type NMD substrates or mRNAs whose abundance increases as an indirect consequence of NMD. A current challenge is to sort the mRNAs that accumulate when NMD is inactivated into direct and indirect targets. We have developed a bioinformatics-based approach to address this challenge. Our approach involves using existing genomic and function databases to identify transcription factors whose mRNAs are elevated in NMD-deficient cells and the genes that they regulate. Using this strategy, we have investigated a coregulated set of genes. We have shown that NMD regulates accumulation of ADR1 and GAL4 mRNAs, which encode transcription activators, and that Adr1 is probably a transcription activator of ATS1. This regulation is physiologically significant because overexpression of ADR1 causes a respiratory defect that mimics the defect seen in strains with an inactive NMD pathway. This strategy is significant because it allows us to classify the genes regulated by NMD into functionally related sets, an important step toward understanding the role NMD plays in the normal functioning of yeast cells.}, pmid = {16339724}, keywords = {0,Binding Sites,CELLS,CEREVISIAE,Codon,Codon Nonsense,CodonNonsense,CODONS,Computational Biology,DATABASE,Databases,DECAY,DECAY PATHWAY,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,gene,Gene Expression Regulation Fungal,Gene Expression RegulationFungal,Genes,Genes Fungal,GenesFungal,genetics,Genome Fungal,GenomeFungal,genomic,growth & development,Half-Life,IDENTIFY,Kinetics,La,metabolism,mRNA,mRNA decay,NMD,NONSENSE,nonsense-mediated mRNA decay,nosource,Open Reading Frames,OVEREXPRESSION,PATHWAY,physiology,Promoter Regions (Genetics),Promoter Regions Genetic,protein,Protein Binding,Proteins,regulation,Research SupportU.S.Gov’tNon-P.H.S.,Rna,RNA Messenger,RNAMessenger,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SURVEILLANCE,SYSTEM,TARGET,termination,TERMINATION CODON,TERMINATION-CODON,Trans-Activators,transcription,TRANSCRIPTION FACTOR,Transcription Factors,translation,TRANSLATION TERMINATION,Up-Regulation,WILD-TYPE,yeast,YEAST-CELLS} }

@article{hudakGenerationPokeweedAntiviral2004, title = {Generation of Pokeweed Antiviral Protein Mutations in {{Saccharomyces}} Cerevisiae: Evidence That Ribosome Depurination Is Not Sufficient for Cytotoxicity}, author = {Hudak, Katalin A and Parikh, Bijal A and Di, Rong and Baricevic, Marianne and Santana, Maria and Seskar, Mirjana and Tumer, Nilgun E}, year = 2004, journal = {Nucleic Acids Research}, volume = {32}, number = {14}, pages = {4244–4256}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gkh757}, url = {http://nar.oxfordjournals.org/content/32/14/4244.short}, abstract = {Pokeweed antiviral protein (PAP) is a ribosome-inactivating protein that depurinates the highly conserved alpha-sarcin/ricin loop in the large rRNA. Here, using site-directed mutagenesis and systematic deletion analysis from the 5’ and the 3’ ends of the PAP cDNA, we identified the amino acids important for ribosome depurination and cytotoxicity of PAP. Truncating the first 16 amino acids of PAP eliminated its cytotoxicity and the ability to depurinate ribosomes. Ribosome depurination gradually decreased upon the sequential deletion of C-terminal amino acids and was abolished when a stop codon was introduced at Glu-244. Cytotoxicity of the C-terminal deletion mutants was lost before their ability to depurinate ribosomes. Mutations in Tyr-123 at the active site affected cytotoxicity without altering the ribosome depurination ability. Total translation was not inhibited in yeast expressing the non-toxic Tyr-123 mutants, although ribosomes were depurinated. These mutants depurinated ribosomes only during their translation and could not depurinate ribosomes in trans in a translation-independent manner. A mutation in Leu-71 in the central domain affected cytotoxicity without altering the ability to depurinate ribosomes in trans and inhibit translation. These results demonstrate that the ability to depurinate ribosomes in trans in a catalytic manner is required for the inhibition of translation, but is not sufficient for cytotoxicity.}, keywords = {0,3,ACID,ACIDS,Adenine,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,antiviral,BIOLOGY,CEREVISIAE,chemistry,Codon,DOMAIN,drug effects,genetics,INHIBITION,La,LOOP,metabolism,Mutagenesis,Mutagenesis Site-Directed,MutagenesisSite-Directed,MUTANTS,Mutation,MUTATIONS,N-Glycosyl Hydrolases,nosource,PAP,pathology,PHYTOLACCA-AMERICANA,Plant Proteins,Pokeweed antiviral protein,protein,Protein Biosynthesis,Protein Structure Tertiary,Protein StructureTertiary,Proteins,ribosome,ribosome depurination,Ribosome Inactivating Proteins Type 1,ribosome-inactivating protein,Ribosomes,Rna,RNA Ribosomal,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Sequence Deletion,SITE,STOP CODON,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,toxicity,Transformation Genetic,TransformationGenetic,translation,TranslationGenetic,yeast} } % == BibTeX quality report for hudakGenerationPokeweedAntiviral2004: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{collerGeneralTranslationalRepression2005, title = {General Translational Repression by Activators of {{mRNA}} Decapping}, author = {Coller, Jeff and Parker, Roy}, year = 2005, month = sep, journal = {Cell}, volume = {122}, number = {6}, eprint = {16179257}, eprinttype = {pubmed}, pages = {875–886}, issn = {0092-8674}, doi = {10.1016/j.cell.2005.07.012}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16179257}, abstract = {Translation and mRNA degradation are affected by a key transition where eukaryotic mRNAs exit translation and assemble an mRNP state that accumulates into processing bodies (P bodies), cytoplasmic sites of mRNA degradation containing non-translating mRNAs, and mRNA degradation machinery. We identify the decapping activators Dhh1p and Pat1p as functioning as translational repressors and facilitators of P body formation. Strains lacking both Dhh1p and Pat1p show strong defects in mRNA decapping and P body formation and are blocked in translational repression. Contrastingly, overexpression of Dhh1p or Pat1p causes translational repression, P body formation, and arrests cell growth. Dhh1p, and its human homolog, RCK/p54, repress translation in vitro, and Dhh1p function is bypassed in vivo by inhibition of translational initiation. These results identify a broadly acting mechanism of translational repression that targets mRNAs for decapping and functions in translational control. We propose this mechanism is competitively balanced with translation, and shifting this balance is an important basis of translational control.}, pmid = {16179257}, keywords = {Cytoplasmic Granules,DEAD-box RNA Helicases,DNA-Binding Proteins,Gene Silencing,Humans,nosource,Proto-Oncogene Proteins,RNA Helicases,RNA Messenger,RNA Nucleotidyltransferases,RNA Stability,RNA- Messenger,RNA-Binding Proteins,Saccharomyces cerevisiae Proteins,Time Factors} }

@article{preissFactorsMechanismsTranslation1999, title = {From Factors to Mechanisms: Translation and Translational Control in Eukaryotes}, author = {Preiss, T and Hentze, M W}, year = 1999, month = oct, journal = {Current Opinion in Genetics & Development}, volume = {9}, number = {5}, pages = {515–521}, publisher = {Elsevier}, issn = {0959-437X}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0959437X99000052}, abstract = {Biochemical and genetic studies are revealing a network of interactions between eukaryotic translation initiation factors, further refining or redefining perceptions of their function. The notion of translated mRNA as a ‘closed-loop’ has gained support from the identification of physical and functional interactions between the two mRNA ends and their associated factors. Translational control mechanisms are beginning to unravel in sufficient detail to pinpoint the affected step in the initiation pathway.}, keywords = {Eukaryotic Cells,nosource,Protein Biosynthesis,Ribosomes,RNA Messenger,RNA- Messenger} } % == BibTeX quality report for preissFactorsMechanismsTranslation1999: % ? unused Journal abbr (“Curr. Opin. Genet. Dev”)

@article{condronFrameshiftingGene101991, title = {Frameshifting in Gene 10 of Bacteriophage {{T7}}.}, author = {Condron, B G and Atkins, J F and Gesteland, R F}, year = 1991, month = nov, journal = {Journal of Bacteriology}, volume = {173}, number = {21}, pages = {6998–7003}, publisher = {Am Soc Microbiol}, issn = {0021-9193}, doi = {10.1128/jb.173.21.6998-7003.1991}, url = {http://jb.asm.org/cgi/content/abstract/173/21/6998}, abstract = {Gene 10 of bacteriophage T7, which encodes the most abundant capsid protein, has two products: a major product, 10A (36 kDa), and a minor product, 10B (41 kDa). 10B is produced by frameshifting into the -1 frame near the end of the 10A coding frame and is incorporated into the capsid. The frameshift occurs at a frequency of about 10% and is conserved in bacteriophage T3. This study shows that sequences important to frameshifting include the originally proposed frameshift site, consisting of overlapping phenylalanine codons and the 3’ noncoding region that includes the transcriptional terminator over 200 bases downstream of the frameshift site. The frameshift occurs at the overlapping phenylalanine codons as determined from peptide sequencing data. Complementation studies show that there is only a very weak phenotype associated with phage infections in which there is no 10A frameshifting. Capsids from such infections are devoid of 10B and are as stable as wild-type capsids.}, keywords = {Amino Acid Sequence,Base Sequence,Capsid,Capsid Proteins,Codon,DNA Viral,DnaViral,frameshift,Frameshifting,gene,Gene Expression Regulation Viral,Gene Expression RegulationViral,Genetic,genetics,human,Molecular Sequence Data,nosource,Phenotype,protein,RNA Viral,RnaViral,sequence,supportnon-u.s.gov’t,T-Phages} } % == BibTeX quality report for condronFrameshiftingGene101991: % ? unused Journal abbr (“J. Bacteriol”)

@article{paillartFirstSnapshotsHIV12004, title = {First Snapshots of the {{HIV-1 RNA}} Structure in Infected Cells and in Virions}, author = {Paillart, Jean-Christophe and Dettenhofer, Markus and Yu, Xiao-Fang and Ehresmann, Chantal and Ehresmann, Bernard and Marquet, Roland}, year = 2004, month = nov, journal = {The Journal of Biological Chemistry}, volume = {279}, number = {46}, pages = {48397–48403}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.M408294200}, url = {http://www.jbc.org/content/279/46/48397.short}, abstract = {With the increasing interest of RNAs in regulating a range of cell biological processes, very little is known about the structure of RNAs in tissue culture cells. We focused on the 5’-untranslated region of the human immunodeficiency virus type 1 RNA genome, a highly conserved RNA region, which contains structural domains that regulate key steps in the viral replication cycle. Up until now, structural information only came from in vitro studies. Here, we developed chemical modification assays to test nucleotide accessibility directly in infected cells and viral particles, thus circumventing possible biases and artifacts linked to in vitro assays. The secondary structure of the 5’-untranslated region in infected cells points to the existence of the various stem-loop motifs associated to distinct functions, proposed from in vitro probing, mutagenesis, and phylogeny. However, compared with in vitro data, subtle differences were observed in the dimerization initiation site hairpin, and none of the proposed long range interactions were observed between the functional domains. Moreover, no global RNA rearrangement was observed; structural differences between infected cells and viral particles were limited to the primer binding site, which became protected against chemical modification upon tRNA(3) (Lys) annealing in virions and to the main packaging signal. In addition, our data suggested that the genomic RNA could already dimerize in the cytoplasm of infected cells. Taken together, our results provided the first analysis of the dynamic of RNA structure of the human immunodeficiency virus type 1 RNA genome during virus assembly ex vivo.}, keywords = {5’ Untranslated Regions,Base Sequence,Cell Line,Dimerization,Genome Viral,HIV-1,Humans,Molecular Sequence Data,nosource,Nucleic Acid Conformation,RNA Viral,Virion,Virus Replication} } % == BibTeX quality report for paillartFirstSnapshotsHIV12004: % ? unused Journal abbr (“J. Biol. Chem”)

@article{jacksExpressionRousSarcoma1985, title = {Expression of the {{Rous Sarcoma Virus}} Pol Gene by Ribosomal Frameshifting.}, author = {Jacks, T and Varmus, H E}, year = 1985, month = dec, journal = {Science (New York, N.Y.)}, volume = {230}, number = {4731}, eprint = {2416054}, eprinttype = {pubmed}, pages = {1237–1242}, issn = {0036-8075}, doi = {10.1126/science.2416054}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2416054 http://www.sciencemag.org/content/230/4731/1237.short}, abstract = {The pol gene of Rous sarcoma virus is positioned downstream of the gag gene in a different, briefly overlapping reading frame; nevertheless, the primary translation product of pol is a gag-pol fusion protein. Two mechanisms, ribosomal frameshifting and RNA splicing, have been considered to explain this phenomenon. The frameshifting model is supported by synthesis of both gag protein and gag-pol fusion protein in a cell-free mammalian translation system programmed by a single RNA species that was synthesized from cloned viral DNA with a bacteriophage RNA polymerase. Under these conditions, the ratio of the gag protein to the fusion protein (about 20 to 1) is similar to that previously observed in infected cells, the frameshifting is specific for the gag-pol junction, and it is unaffected by large deletions in gag. In addition, synthesis of the fusion protein is ten times less efficient in an Escherichia coli cell-free translation system and cannot be explained by transcriptional errors or in vitro modification of the RNA. Ribosomal frameshifting may affect production of other proteins in higher eukaryotes, including proteins encoded by several retroviruses and transposable elements.}, pmid = {2416054}, keywords = {Animals,Avian Sarcoma Viruses,Avian Sarcoma Viruses: genetics,Base Sequence,Cell-Free System,expression,Frameshifting,gag,gene,Gene Expression Regulation,Gene Products,Gene Products gag,Messenger,Messenger: genetics,Molecular Weight,nosource,pol,Protein Biosynthesis,Rabbits,Retroviridae Proteins,Retroviridae Proteins: genetics,ribosomal frameshifting,Ribosomes,Ribosomes: metabolism,RNA,RNA Messenger,RNA Viral,RNA-Directed DNA Polymerase,RNA-Directed DNA Polymerase: genetics,Viral,Viral: genetics,virus} } % == BibTeX quality report for jacksExpressionRousSarcoma1985: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”)

@article{ganExploringRepertoireRNA2003, title = {Exploring the Repertoire of {{RNA}} Secondary Motifs Using Graph Theory; Implications for {{RNA}} Design}, author = {Gan, Hin Hark and Pasquali, Samuela and Schlick, Tamar}, year = 2003, month = jun, journal = {Nucleic Acids Research}, volume = {31}, number = {11}, pages = {2926–2943}, publisher = {Oxford Univ Press}, issn = {1362-4962}, url = {http://nar.oxfordjournals.org/content/31/11/2926.short}, abstract = {Understanding the structural repertoire of RNA is crucial for RNA genomics research. Yet current methods for finding novel RNAs are limited to small or known RNA families. To expand known RNA structural motifs, we develop a two-dimensional graphical representation approach for describing and estimating the size of RNA’s secondary structural repertoire, including naturally occurring and other possible RNA motifs. We employ tree graphs to describe RNA tree motifs and more general (dual) graphs to describe both RNA tree and pseudoknot motifs. Our estimates of RNA’s structural space are vastly smaller than the nucleotide sequence space, suggesting a new avenue for finding novel RNAs. Specifically our survey shows that known RNA trees and pseudoknots represent only a small subset of all possible motifs, implying that some of the ‘missing’ motifs may represent novel RNAs. To help pinpoint RNA-like motifs, we show that the motifs of existing functional RNAs are clustered in a narrow range of topological characteristics. We also illustrate the applications of our approach to the design of novel RNAs and automated comparison of RNA structures; we report several occurrences of RNA motifs within larger RNAs. Thus, our graph theory approach to RNA structures has implications for RNA genomics, structure analysis and design.}, keywords = {Algorithms,Base Sequence,Computational Biology,Databases Nucleic Acid,Databases- Nucleic Acid,Genomics,Models Molecular,Models Theoretical,Models- Molecular,Models- Theoretical,Molecular Sequence Data,nosource,Nucleic Acid Conformation,RNA} } % == BibTeX quality report for ganExploringRepertoireRNA2003: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{zhangEvidenceThatTranslation1997, title = {Evidence That Translation Reinitiation Abrogates Nonsense-Mediated {{mRNA}} Decay in Mammalian Cells}, author = {Zhang, J and Maquat, L E}, year = 1997, month = feb, journal = {The EMBO Journal}, volume = {16}, number = {4}, pages = {826–833}, publisher = {Nature Publishing Group}, issn = {0261-4189}, doi = {10.1093/emboj/16.4.826}, url = {http://www.nature.com/emboj/journal/v16/n4/abs/7590076a.html}, abstract = {Nonsense codons upstream of and including position 192 of the human gene for triosephosphate isomerase (TPI) have been found to reduce the abundance of TPI mRNA to approximately 25% of normal. The reduction is due to the decay of newly synthesized TPI mRNA that co-purifies with nuclei. TPI mRNA that co-purifies with cytoplasm is immune to nonsense-mediated decay. Until now, a nonsense codon at position 23 has been the 5’-most nonsense codon that has been analyzed. Here, we provide evidence that a nonsense codon at position 1, 2 or 10 reduces the abundance of nucleus-associated TPI mRNA to an average of only 84% of normal because translation reinitiates at the methionine codon at position 14. First, converting codon 14 to one for valine increased the effectiveness with which an upstream nonsense codon reduces mRNA abundance. Second, when TPI gene sequences, including codon 14, were fused upstream of and in-frame to the translational reading frame of an Escherichia coli chloramphenicol acetyl transferase (CAT) gene that lacked an initiation codon, a nonsense codon at TPI position 1 or 2 allowed for the production of TPI-CAT that was an estimated 14 amino acids smaller than TPI-CAT produced by a nonsense-free gene, whereas a nonsense codon at TPI position 23 precluded the production of TPI-CAT. These and related findings lend credence to the concept that the nonsense-mediated reduction in the half-life of nucleus-associated TPI mRNA involves cytoplasmic ribosomes.}, keywords = {Animals,Codon Nonsense,Codon- Nonsense,DNA Recombinant,DNA- Recombinant,Exons,Humans,L Cells (Cell Line),Metallothionein,Methionine,Mice,nosource,Peptide Chain Initiation Translational,Peptide Chain Initiation- Translational,Promoter Regions Genetic,Promoter Regions- Genetic,RNA Messenger,RNA- Messenger,Transfection,Triose-Phosphate Isomerase} } % == BibTeX quality report for zhangEvidenceThatTranslation1997: % ? unused Journal abbr (“EMBO J”)

@article{gallantEvidenceThatBypassing2003, title = {Evidence That the Bypassing Ribosome Travels through the Coding Gap}, author = {Gallant, Jonathan and Bonthuis, Paul and Lindsley, Dale}, year = 2003, month = nov, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {23}, eprint = {14576279}, eprinttype = {pubmed}, pages = {13430–13435}, issn = {0027-8424}, doi = {10.1073/pnas.2233745100}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14576279}, abstract = {In translational bypassing, a peptidyl-tRNA::ribosome complex skips over a number of nucleotides in a messenger sequence and resumes protein chain elongation after a “landing site” downstream of the bypassed region. The present experiments demonstrate that the complex “scans” processively through the bypassed region. This conclusion rests on three observations. (i) When two potential “landing sites” are present, the protein sequence of the product shows that virtually all ribosomes land at the first and virtually none at the second. (ii) In such a sequence with two landing sites, the presence of a terminator triplet in phase in the coding region immediately after the first landing site drastically reduces the efficiency of bypassing. (iii) Internally complementary sequences that can form a stable stemloop in the bypassed region significantly reduce the efficiency of bypassing. We analyze bypassing from a given “takeoff” site to “landing sites” at different distances downstream so as to derive estimates of the frequency of ribosome takeoff and of the stability of the bypassing complex.}, pmid = {14576279}, keywords = {0,Amino Acid Sequence,Base Sequence,beta-Galactosidase,Binding Sites,chemistry,CODING REGION,COMPLEX,COMPLEXES,DOWNSTREAM,efficiency,elongation,FORM,Genome,La,metabolism,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleotides,Oligonucleotides,PLASMID,Plasmids,PRODUCT,protein,Protein Biosynthesis,REGION,ribosome,Ribosomes,Rna,RNA Messenger,RNA Transfer,RNA-Messenger,RNA-Transfer,RNAMessenger,RNATransfer,sequence,SEQUENCES,SITE,SITES,stability,support-u.s.gov’t-p.h.s.,supportu.s.gov’tp.h.s.,Translation-Genetic,TranslationGenetic} } % == BibTeX quality report for gallantEvidenceThatBypassing2003: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{lewisEvidenceWidespreadCoupling2003, title = {Evidence for the Widespread Coupling of Alternative Splicing and Nonsense-Mediated {{mRNA}} Decay in Humans}, author = {Lewis, Benjamin P and Green, Richard E and Brenner, Steven E}, year = 2003, month = jan, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {1}, pages = {189–192}, publisher = {National Acad Sciences}, issn = {0027-8424}, doi = {10.1073/pnas.0136770100}, url = {http://www.pnas.org/content/100/1/189.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=140922&tool=pmcentrez&rendertype=abstract}, abstract = {To better understand the role of alternative splicing, we conducted a large-scale analysis of reliable alternative isoforms of known human genes. Each isoform was classified according to its splice pattern and supporting evidence. We found that one-third of the alternative transcripts examined contain premature termination codons, and most persist even after rigorous filtering by multiple methods. These transcripts are apparent targets of nonsense-mediated mRNA decay (NMD), a surveillance mechanism that selectively degrades nonsense mRNAs. Several of these transcripts are from genes for which alternative splicing is known to regulate protein expression by generating alternate isoforms that are differentially subjected to NMD. We propose that regulated unproductive splicing and translation (RUST), through the coupling of alternative splicing and NMD, may be a pervasive, underappreciated means of regulating protein expression.}, pmid = {12502788}, keywords = {Alternative Splicing,Alternative Splicing: genetics,analysis,Chromosome Mapping,Codon,Codon Nonsense,Codon Terminator,CODONS,DECAY,DIVERSITY,E,ELEGANS,EST,EXON-EXON JUNCTIONS,Expressed Sequence Tags,expression,gene,Gene Library,Genes,Genome,Genome Human,human,Human,HUMAN GENES,human genome,Humans,LARGE-SCALE ANALYSIS,MECHANISM,MECHANISMS,Messenger,MESSENGER-RNA SURVEILLANCE,Messenger: genetics,Methods,Microbial,mRNA,mRNA decay,NMD,Nonsense,NONSENSE,nonsense-mediated mRNA decay,Nonsense: genetics,nosource,POSITION,PREMATURE TERMINATION CODON,protein,RefSeq,regulated unproductive splicing and translation,regulation,RNA,RNA Messenger,S,sequence,splicing,SURVEILLANCE,TARGET,termination,TERMINATION CODON,TERMINATION-CODON,Terminator,Terminator: genetics,TRANSCRIPT,translation} } % == BibTeX quality report for lewisEvidenceWidespreadCoupling2003: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{derebailEvidenceDifferentialEffects2003, title = {Evidence for the Differential Effects of Nucleocapsid Protein on Strand Transfer in Various Regions of the {{HIV}} Genome}, author = {Derebail, Suchitra S and Heath, Megan J and DeStefano, Jeffrey J}, year = 2003, month = may, journal = {The Journal of Biological Chemistry}, volume = {278}, number = {18}, pages = {15702–15712}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.M211701200}, url = {http://www.jbc.org/content/278/18/15702.short}, abstract = {An in vitro strand transfer assay that mimicked recombinational events occurring during reverse transcription in HIV-1 was used to assess the role of nucleocapsid protein (NC) in strand transfer. Strand transfer in highly structured nucleic acid species from the U3 3’ long terminal repeats, gag-pol frameshift region, and Rev response element were strongly enhanced by NC. In contrast, weakly structured templates from the env and pol-vif regions transferred well without NC and showed lower enhancement. The lack of strong polymerase pause sites in the latter regions demonstrated that non-pause driven mechanisms could also promote transfer. Assays conducted using NC zinc finger mutants supported a differential role for the two fingers in strand transfer with finger 1 (N-terminal) being more important on highly structured RNAs. Overall this report suggests a role for structural intricacies of RNA templates in determining the extent of influence of NC on recombination and illustrates that strand transfer may occur by several different mechanisms depending on the structural nature of the RNA.}, keywords = {Base Sequence,Genome Viral,HIV,Molecular Sequence Data,nosource,Nucleocapsid Proteins,Recombination Genetic,RNA Viral,Zinc Fingers} } % == BibTeX quality report for derebailEvidenceDifferentialEffects2003: % ? unused Journal abbr (“J. Biol. Chem”)

@article{ishigakiEvidencePioneerMRNA2001, title = {Evidence for a {{Pioneer Round}} of {{mRNA Translation}}:: {{mRNAs Subject}} to {{Nonsense-Mediated Decay}} in {{Mammalian Cells Are Bound}} by {{CBP80}} and {{CBP20}}}, author = {Ishigaki, Y and Li, X and Serin, G and Maquat, L E}, year = 2001, month = sep, journal = {Cell}, volume = {106}, number = {5}, pages = {607–617}, issn = {0092-8674}, doi = {10.1016/S0092-8674(01)00475-5}, url = {http://www.sciencedirect.com/science/article/pii/S0092867401004755}, abstract = {Nonsense-mediated decay (NMD) eliminates mRNAs that prematurely terminate translation. We used antibody to the nuclear cap binding protein CBP80 or its cytoplasmic counterpart eIF4E to immunopurify RNP containing nonsense-free or nonsense-containing transcripts. Data indicate that NMD takes place in association with CBP80. We defined other components of NMD-susceptible mRNP as CBP20, PABP2, eIF4G, and the NMD factors Upf2 and Upf3. Consistent with the dependence of NMD on translation, the NMD of CBP80-bound mRNA is blocked by cycloheximide or suppressor tRNA. These findings provide evidence that translation can take place in association with CBP80. They also indicate that CBP80-bound mRNA undergoes a “pioneer” round of translation, before CBP80-CBP20 are replaced by eIF4E, and Upf2 and Upf3 proteins dissociate from upstream of exon-exon junctions.}, pmid = {11551508}, keywords = {3T3 Cells,Alpha-Globulins,animal,Animals,Antibodies,antibody,BINDING,BINDING-PROTEIN,Cap,Cap binding,Cell Nucleus,Codon Nonsense,Codon-Nonsense,CodonNonsense,COMPONENT,Cos Cells,COS Cells,Cross-Linking Reagents,Cycloheximide,DECAY,Eukaryotic Initiation Factor-4G,genetics,Globins,Glutathione Peroxidase,human,Humans,Immunoblotting,Macromolecular Substances,Macromolecular Systems,metabolism,Mice,Models Biological,Models-Biological,ModelsBiological,mRNA,NMD,nonsense-mediated decay,nosource,Peptide Initiation Factors,pharmacology,Poly(A)-Binding Proteins,protein,Protein Biosynthesis,Protein Synthesis Inhibitors,Proteins,Reverse Transcriptase Polymerase Chain Reaction,RNA Cap-Binding Proteins,Rna Caps,RNA Caps,RNA Messenger,RNA-Binding Proteins,RNA-Messenger,RNAMessenger,support-u.s.gov’t-p.h.s.,supportu.s.gov’tp.h.s.,Transfection,translation,Translation-Genetic,TranslationGenetic,tRNA,UPF3} } % == BibTeX quality report for ishigakiEvidencePioneerMRNA2001: % ? Title looks like it was stored in title-case in Zotero

@article{inge-vechtomovEukaryoticReleaseFactors2003a, title = {Eukaryotic Release Factors ({{eRFs}}) History}, author = {{Inge-Vechtomov}, Sergei and Zhouravleva, Galina and Philippe, Michel}, year = {2003 May-Jun}, journal = {Biology of the Cell / Under the Auspices of the European Cell Biology Organization}, volume = {95}, number = {3-4}, pages = {195–209}, publisher = {Ivry sur Seine, France: Publie par la Societe francaise de microscopie electronique avec le concours du Centre national de la recherche scientifique et de l’Institut national de sante et de la recherche medicale,[1981-}, issn = {0248-4900}, url = {http://www.biolcell.cn/boc/095/0195/boc0950195.pdf}, abstract = {In the present review, we describe the history of the identification of the eukaryotic translation termination factors eRF1 and eRF3. As in the case of several proteins involved in general and essential processes in all cells (e.g., DNA replication, gene expression regulation.) the strategies and methodologies used to identify these release factors were first established in prokaryotes. The genetic investigations in Saccharomyces cerevisiae have made a major contribution in the field. A large amount of data have been produced, from which it was concluded that the SUP45 and SUP35 genes were controlling translation termination but were also involved in other functions important for the cell organization and the cell cycle accomplishment. This does not seem to be restricted to yeast but is also probably the case in eukaryotes in general. The biochemical studies of the proteins encoded by the higher eukaryote homologs of SUP45 and SUP35 were efficient and permitted the identification of eRF1 as being the key protein in the termination process, eRF3 having a stimulating role. Around 25 years were needed after the identification of sup45 and sup35 mutants for the characterization of their gene products as eRF1 and eRF3, respectively. It also has to be pointed out that if the results came first from bacteria, the identification of RF3 and eRF3 was made practically at the same time. Moreover, eRF1 was the first crystal structure obtained for a class-1 release factor, the bacterial RF2 structure came later. The goal is now to understand at the molecular level the roles of both eRF1 and eRF3 in addition to their translation termination functions.}, keywords = {Animals,Eukaryotic Cells,History 20th Century,History 21st Century,Humans,Molecular Biology,Molecular Structure,nosource,Peptide Termination Factors,Prions,Protein Biosynthesis,Saccharomyces cerevisiae Proteins,Yeasts} } % == BibTeX quality report for inge-vechtomovEukaryoticReleaseFactors2003a: % ? unused Journal abbr (“Biol. Cell”)

@article{collerEukaryoticMRNADecapping2004, title = {Eukaryotic {{mRNA}} Decapping.}, author = {Coller, Jeff and Parker, Roy}, year = 2004, month = jan, journal = {Annual Review of Biochemistry}, volume = {73}, eprint = {15189161}, eprinttype = {pubmed}, pages = {861–890}, issn = {0066-4154}, doi = {10.1146/annurev.biochem.73.011303.074032}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15189161}, abstract = {Eukaryotic mRNAs are primarily degraded by removal of the 3’ poly(A) tail, followed either by cleavage of the 5’ cap structure (decapping) and 5’-{\(>\)}3’ exonucleolytic digestion, or by 3’ to 5’ degradation. mRNA decapping represents a critical step in turnover because this permits the degradation of the mRNA and is a site of numerous control inputs. Recent analyses suggest decapping of an mRNA consists of four central and related events. These include removal, or inactivation, of the poly(A) tail as an inhibitor of decapping, exit from active translation, assembly of a decapping complex on the mRNA, and sequestration of the mRNA into discrete cytoplasmic foci where decapping can occur. Each of these steps is a demonstrated, or potential, site for the regulation of mRNA decay. We discuss the decapping process in the light of these central properties, which also suggest fundamental aspects of cytoplasmic mRNA physiology that connect decapping, translation, and storage of mRNA.}, pmid = {15189161}, keywords = {Biological,Codon,Codon Nonsense,Endoribonucleases,Endoribonucleases: metabolism,Eukaryotic Cells,Macromolecular Substances,Models,Models Biological,Nonsense,nosource,Organelles,Organelles: metabolism,Poly(A)-Binding Proteins,Poly(A)-Binding Proteins: metabolism,Ribonucleoproteins,Ribonucleoproteins: chemistry,Ribonucleoproteins: metabolism,Ribosomes,Ribosomes: metabolism,RNA Caps,RNA Caps: chemistry,RNA Caps: genetics,RNA Caps: metabolism,RNA Stability} } % == BibTeX quality report for collerEukaryoticMRNADecapping2004: % ? unused Journal abbr (“Annu. Rev. Biochem”)

@article{nonetEucaryoticRNAPolymerase1987, title = {Eucaryotic {{RNA}} Polymerase Conditional Mutant That Rapidly Ceases {{mRNA}} Synthesis.}, author = {Nonet, M and Scafe, C and Sexton, J and Young, R}, year = 1987, month = may, journal = {Molecular and Cellular Biology}, volume = {7}, number = {5}, pages = {1602–1611}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, url = {http://mcb.asm.org/cgi/content/abstract/7/5/1602}, abstract = {We have isolated a yeast conditional mutant which rapidly ceases synthesis of mRNA when subjected to the nonpermissive temperature. This mutant (rpb1-1) was constructed by replacing the wild-type chromosomal copy of the gene encoding the largest subunit of RNA polymerase II with one mutagenized in vitro. The rapid cessation of mRNA synthesis in vivo and the lack of RNA polymerase II activity in crude extracts indicate that the mutant possesses a functionally defective, rather than an assembly-defective, RNA polymerase II. The shutdown in mRNA synthesis in the rpb1-1 mutant has pleiotropic effects on the synthesis of other RNAs and on the heat shock response. This mutant provides direct evidence that the RPB1 protein has a functional role in mRNA synthesis.}, keywords = {0,biosynthesis,Chromosome Mapping,Fungal Proteins,gene,Genes Lethal,GenesLethal,genetics,Heat,Hot Temperature,In Vitro,IN-VITRO,IN-VIVO,La,mRNA,Multiple DOI,Mutation,nonfile,nosource,polymerase,protein,Proteins,Rna,RNA Fungal,RNA Messenger,RNA Polymerase II,RNAFungal,RNAMessenger,Saccharomyces cerevisiae,SUBUNIT,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Temperature,Transcription Genetic,TranscriptionGenetic,yeast} } % == BibTeX quality report for nonetEucaryoticRNAPolymerase1987: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{beringerEssentialMechanismsCatalysis2005, title = {Essential Mechanisms in the Catalysis of Peptide Bond Formation on the Ribosome}, author = {Beringer, Malte and Bruell, Christian and Xiong, Liqun and Pfister, Peter and Bieling, Peter and Katunin, Vladimir I and Mankin, Alexander S and B{"o}ttger, Erik C and Rodnina, Marina V}, year = 2005, month = oct, journal = {The Journal of Biological Chemistry}, volume = {280}, number = {43}, pages = {36065–36072}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.M507961200}, url = {http://www.jbc.org/content/280/43/36065.short}, abstract = {Peptide bond formation is the main catalytic function of the ribosome. The mechanism of catalysis is presumed to be highly conserved in all organisms. We tested the conservation by comparing mechanistic features of the peptidyl transfer reaction on ribosomes from Escherichia coli and the Gram-positive bacterium Mycobacterium smegmatis. In both cases, the major contribution to catalysis was the lowering of the activation entropy. The rate of peptide bond formation was pH independent with the natural substrate, amino-acyl-tRNA, but was slowed down 200-fold with decreasing pH when puromycin was used as a substrate analog. Mutation of the conserved base A2451 of 23 S rRNA to U did not abolish the pH dependence of the reaction with puromycin in M. smegmatis, suggesting that A2451 did not confer the pH dependence. However, the A2451U mutation alters the structure of the peptidyl transferase center and changes the pattern of pH-dependent rearrangements, as probed by chemical modification of 23 S rRNA. A2451 seems to function as a pivot point in ordering the structure of the peptidyl transferase center rather than taking part in chemical catalysis.}, keywords = {Alleles,Binding Sites,Catalysis,Conserved Sequence,Entropy,Escherichia coli,Hydrogen-Ion Concentration,Kinetics,Mutagenesis,Mutation,Mycobacterium smegmatis,nosource,Peptides,Plasmids,Point Mutation,Protein Conformation,Puromycin,Ribosomes,RNA,RNA Ribosomal 23S,RNA Transfer,Substrate Specificity,Thermodynamics,Time Factors} } % == BibTeX quality report for beringerEssentialMechanismsCatalysis2005: % ? unused Journal abbr (“J. Biol. Chem”)

@article{parkerErrorsAlternativesReading1989, title = {Errors and Alternatives in Reading the Universal Genetic Code.}, author = {Parker, J}, year = 1989, month = sep, journal = {Microbiology and Molecular Biology Reviews}, volume = {53}, number = {3}, pages = {273–298}, issn = {0146-0749}, doi = {10.1128/mr.53.3.273-298.1989}, url = {http://mmbr.asm.org/cgi/reprint/53/3/273.pdf}, pmid = {2677635}, keywords = {Acylation,Base Sequence,Codon,DNA Bacterial,DNA Fungal,DNA Replication,Genetic Code,Mutation,nosource,Protein Biosynthesis,Review} } % == BibTeX quality report for parkerErrorsAlternativesReading1989: % ? unused Journal abbr (“Microbiol. Rev”)

@article{domaEndonucleolyticCleavageEukaryotic2006, title = {Endonucleolytic Cleavage of Eukaryotic {{mRNAs}} with Stalls in Translation Elongation}, author = {Doma, Meenakshi K and Parker, Roy}, year = 2006, month = mar, journal = {Nature}, volume = {440}, number = {7083}, eprint = {16554824}, eprinttype = {pubmed}, pages = {561–564}, issn = {1476-4687}, doi = {10.1038/nature04530}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16554824}, abstract = {A fundamental aspect of the biogenesis and function of eukaryotic messenger RNA is the quality control systems that recognize and degrade non-functional mRNAs. Eukaryotic mRNAs where translation termination occurs too soon (nonsense-mediated decay) or fails to occur (non-stop decay) are rapidly degraded. We show that yeast mRNAs with stalls in translation elongation are recognized and targeted for endonucleolytic cleavage, referred to as ‘no-go decay’. The cleavage triggered by no-go decay is dependent on translation and involves Dom34p and Hbs1p. Dom34p and Hbs1p are similar to the translation termination factors eRF1 and eRF3 (refs 3, 4), indicating that these proteins might function in recognizing the stalled ribosome and triggering endonucleolytic cleavage. No-go decay provides a mechanism for clearing the cell of stalled translation elongation complexes, which could occur as a result of damaged mRNAs or ribosomes, or as a mechanism of post-transcriptional control.}, pmid = {16554824}, keywords = {0,3,BIOGENESIS,BIOLOGY,cell cycle,Cell Cycle Proteins,CEREVISIAE,CLEAVAGE,COMPLEX,COMPLEXES,DECAY,elongation,elongation factors,ELONGATION-FACTORS,Endoribonucleases,Genes Reporter,Genes-Reporter,GenesReporter,genetics,GTP-Binding Proteins,heat shock proteins,HEAT-SHOCK,HEAT-SHOCK PROTEIN,HEAT-SHOCK PROTEINS,HSP70 Heat-Shock Proteins,La,MECHANISM,MESSENGER-RNA,metabolism,mRNA,nonsense-mediated decay,nosource,Peptide Chain Elongation Translational,Peptide Chain Elongation-Translational,Peptide Chain ElongationTranslational,Peptide Elongation Factors,physiology,protein,Proteins,Quality Control,QUALITY-CONTROL,Research Support-N.I.H.-Extramural,Research Support-Non-U.S.Gov’t,Research SupportN.I.H.Extramural,Research SupportNon-U.S.Gov’t,ribosome,Ribosomes,Rna,RNA Fungal,RNA Messenger,RNA Stability,RNA-Fungal,RNA-Messenger,RNAFungal,RNAMessenger,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SYSTEM,SYSTEMS,termination,translation,TRANSLATION TERMINATION,yeast} }

@article{lejeuneEIF4GRequiredPioneer2004, title = {{{eIF4G}} Is Required for the Pioneer Round of Translation in Mammalian Cells}, author = {Lejeune, Fabrice and Ranganathan, Aparna C and Maquat, Lynne E}, year = 2004, month = oct, journal = {Nature Structural & Molecular Biology}, volume = {11}, number = {10}, pages = {992–1000}, publisher = {Nature Publishing Group}, issn = {1545-9993}, doi = {10.1038/nsmb824}, url = {PM:15361857 http://www.ncbi.nlm.nih.gov/pubmed/15361857 http://www.nature.com/nsmb/journal/v11/n10/abs/nsmb824.html}, abstract = {Nonsense-mediated mRNA decay (NMD) in mammalian cells targets cap-binding protein 80 (CBP80)-bound mRNA during or after a pioneer round of translation. It is unknown whether eukaryotic translation initiation factor 4G (eIF4G) functions in the pioneer round. We show that baculovirus-produced CBP80 and CBP20 independently interact with eIF4GI. The interactions between eIF4G and the heterodimer CBP80/20 suggest that eIF4G has a function in the pioneer initiation complex rather than merely a presence during remodeling to the steady-state complex. First, NMD is inhibited upon eIF4G cleavage by HIV-2 or poliovirus 2A protease. Second, eIF4GI coimmunopurifies with pre-mRNA, indicating that it associates with transcripts before the pioneer round. Third, eIF4G immunopurifies with Upf NMD factors and eIF4AIII, which are constituents of the pioneer translation initiation complex. We propose a model in which eIF4G serves to connect CBP80/20 with other initiation factors during the pioneer round of translation.}, keywords = {Animals,Base Sequence,Cap binding,CELLS,CLEAVAGE,COMPLEX,COMPLEXES,COS Cells,DECAY,DNA Primers,EUKARYOTIC TRANSLATION,FACTOR 4G,Hiv-2,initiation,INITIATION-FACTOR,La,MAMMALIAN-CELLS,MODEL,mRNA,mRNA decay,NMD,nonsense-mediated mRNA decay,nosource,protein,Protein Binding,Protein Biosynthesis,RNA Messenger,TARGET,TRANSCRIPT,translation,TRANSLATION INITIATION,UPF} } % == BibTeX quality report for lejeuneEIF4GRequiredPioneer2004: % ? unused Journal abbr (“Nat. Struct. Mol. Biol”)

@article{clareEfficientTranslationalFrameshifting1988, title = {Efficient Translational Frameshifting Occurs within a Conserved Sequence of the Overlap between the Two Genes of a Yeast {{Ty1}} Transposon}, author = {Clare, J J and Belcourt, M and Farabaugh, P J}, year = 1988, month = sep, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {85}, number = {18}, pages = {6816–6820}, publisher = {National Acad Sciences}, issn = {0027-8424}, doi = {10.1073/pnas.85.18.6816}, url = {http://www.pnas.org/content/85/18/6816.short}, abstract = {The Ty (transposon yeast) family of retroviral-like transposons include two genes, TYA and TYB, analogous to the gag and pol genes of metazoan retroviruses. TYB lies downstream of TYA, the two genes overlapping by 38 base pairs. The primary translation product of TYB is a TYA/TYB fusion protein whose expression has been inferred to occur by translational frameshifting within the overlap region. We show that the event leading to expression of TYB is very efficient, resulting in 20% read-through into TYB from TYA. We demonstrate that the Ty mRNA is colinear with the DNA sequence of the element, eliminating any pretranslational model for TYB expression. Frameshifting requires no particular sequence of the upstream TYA gene, nor any global RNA structure. Surprisingly, it can be promoted by a 14-base-pair oligonucleotide of the overlap region. The ability of this oligonucleotide to function is inhibited when it is positioned immediately downstream of an initiator AUG. We conclude that the TYB gene is expressed by an efficient ribosomal frameshifting event requiring a small oligonucleotide sequence derived from the TYA/TYB overlap region.}, keywords = {88320527,Amino Acid Sequence,Base Sequence,beta-Galactosidase,Cloning Molecular,Cloning- Molecular,Cloning-Molecular,CloningMolecular,Conserved Sequence,Dna,DNA Transposable Elements,Endonucleases,expression,Frameshifting,Gag,gene,Genes,genetics,metabolism,microbiology,Molecular Sequence Data,mRNA,nosource,protein,Protein Biosynthesis,readthrough,ribosomal frameshifting,Rna,Saccharomyces cerevisiae,sequence,Single-Strand Specific DNA and RNA Endonucleases,structure,support-non-u.s.gov’t,support-u.s.gov’t-p.h.s.,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,translation,Translation-Genetic,TranslationGenetic,Ty,Ty1,yeast} } % == BibTeX quality report for clareEfficientTranslationalFrameshifting1988: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{howardEfficientStimulationSitespecific2004, title = {Efficient Stimulation of Site-Specific Ribosome Frameshifting by Antisense Oligonucleotides}, author = {Howard, Michael T and Gesteland, Raymond F and Atkins, John F}, year = 2004, month = oct, journal = {RNA (New York, N.Y.)}, volume = {10}, number = {10}, pages = {1653–1661}, issn = {1355-8382}, doi = {10.1261/rna.7810204}, url = {http://rnajournal.cshlp.org/content/10/10/1653.short}, abstract = {Evidence is presented that morpholino, 2’-O-methyl, phosphorothioate, and RNA antisense oligonucleotides can direct site-specific -1 translational frameshifting when annealed to mRNA downstream from sequences where the P- and A-site tRNAs are both capable of repairing with -1 frame codons. The efficiency of ribosomes shifting into the new frame can be as high as 40%, determined by the sequence of the frameshift site, as well as the location, sequence composition, and modification of the antisense oligonucleotide. These results demonstrate that a perfect duplex formed by complementary oligonucleotides is sufficient to induce high level -1 frameshifting. The implications for the mechanism of action of natural programmed translational frameshift stimulators are discussed.}, pmid = {15383681}, keywords = {-o-methyl,0,2,A SITE,A-SITE,Animals,antisense,Base Sequence,chemistry,Codon,CODONS,DOWNSTREAM,drug effects,E,efficiency,FRAME,frameshift,frameshifting,Frameshifting,Frameshifting Ribosomal,FrameshiftingRibosomal,Genetic,genetics,human,In Vitro,La,LOCATION,luciferase,Luciferases,MECHANISM,metabolism,modification,morpholino,mRNA,nosource,Oligonucleotides,Oligoribonucleotides,Oligoribonucleotides Antisense,OligoribonucleotidesAntisense,pharmacology,phosphorothioate,protein,Proteins,Rabbits,recoding,Recombinant Proteins,Reticulocytes,ribosome,Ribosomes,Rna,sequence,SEQUENCES,SITE,site specific,supportu.s.gov’tp.h.s.,TRANSLATIONAL FRAMESHIFTING,tRNA} } % == BibTeX quality report for howardEfficientStimulationSitespecific2004: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{buhlerEfficientDownregulationImmunoglobulin2004, title = {Efficient Downregulation of Immunoglobulin Mu {{mRNA}} with Premature Translation-Termination Codons Requires the 5’-Half of the {{VDJ}} Exon}, author = {B{"u}hler, Marc and Paillusson, Alexandra and M{"u}hlemann, Oliver}, year = 2004, month = jan, journal = {Nucleic Acids Research}, volume = {32}, number = {11}, pages = {3304–3315}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gkh651}, url = {http://nar.oxfordjournals.org/content/32/11/3304.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=443527&tool=pmcentrez&rendertype=abstract http://ukpmc.ac.uk/articles/PMC443527}, abstract = {Premature translation-termination codons (PTCs) elicit rapid degradation of the mRNA by a process called nonsense-mediated mRNA decay (NMD). NMD appears to be significantly more efficient for mRNAs of genes belonging to the immunoglobulin superfamily, which frequently acquire PTCs during VDJ rearrangment, than for mRNAs of other genes. To identify determinants for efficient NMD, we developed a minigene system derived from a mouse immunoglobulin micro gene (Ig-micro) and measured the effect of PTCs at different positions on the mRNA level. This revealed that PTCs located downstream of the V-D junction in the VDJ exon of Ig-micro minigenes and of endogenous Ig-micro genes elicit very strong mRNA downregulation, whereas NMD efficiency decreases gradually further upstream in the V segment where a PTC was inserted. Interestingly, two PTCs are in positions where they usually do not trigger NMD ({\(<\)}50 nt from the 3’-most 5’ splice site) still resulted in reduced mRNA levels. Using a set of hybrid constructs comprised of Ig-micro and an inefficient substrate for NMD, we identified a 177 nt long element in the V segment that is necessary for efficient downregulation of PTC-containing hybrid transcripts. Moreover, deletion of this NMD-promoting element from the Ig-micro minigene results in loss of strong NMD.}, pmid = {15210863}, keywords = {Animals,B-Lymphocyte,Codon,Codon Terminator,Codon- Terminator,Down-Regulation,Exons,Gene Rearrangement,Gene Rearrangement B-Lymphocyte Heavy Chain,Gene Rearrangement- B-Lymphocyte- Heavy Chain,Heavy Chain,Hela Cells,Humans,Hybridomas,Immunoglobulin Fragments,Immunoglobulin Fragments: genetics,Immunoglobulin mu-Chains,Immunoglobulin mu-Chains: genetics,Immunoglobulin mu-Chains: metabolism,Immunoglobulin Variable Region,Immunoglobulin Variable Region: genetics,Messenger,Messenger: chemistry,Messenger: metabolism,Mice,nosource,Protein Biosynthesis,Regulatory Sequences,Regulatory Sequences Ribonucleic Acid,Regulatory Sequences- Ribonucleic Acid,Ribonucleic Acid,RNA,RNA Messenger,RNA Stability,RNA- Messenger,Sequence Deletion,Terminator} } % == BibTeX quality report for buhlerEfficientDownregulationImmunoglobulin2004: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{amraniEarlyNonsenseMRNA2006, title = {Early Nonsense: {{mRNA}} Decay Solves a Translational Problem}, author = {Amrani, Nadia and Sachs, M. S. S. and Jacobson, Allan}, year = 2006, month = jun, journal = {Nature Reviews Molecular Cell Biology}, volume = {7}, number = {6}, pages = {415–425}, publisher = {Nature Publishing Group}, issn = {1471-0072}, doi = {10.1038/nrm1942}, url = {http://www.nature.com/nrm/journal/v7/n6/abs/nrm1942.html}, abstract = {Gene expression is highly accurate and rarely generates defective proteins. Several mechanisms ensure this fidelity, including specialized surveillance pathways that rid the cell of mRNAs that are incompletely processed or that lack complete open reading frames. One such mechanism, nonsense-mediated mRNA decay, is triggered when ribosomes encounter a premature translation-termination–or nonsense–codon. New evidence indicates that the specialized factors that are recruited for this process not only promote rapid mRNA degradation, but are also required to resolve a poorly dissociable termination complex.}, keywords = {3’ Untranslated Regions,Animals,Codon Nonsense,Codon Terminator,Codon- Nonsense,Codon- Terminator,nosource,Protein Biosynthesis,Ribosomes,RNA Messenger,RNA Stability,RNA- Messenger,Transcription Genetic,Transcription- Genetic} }

@article{darzacqDynamicsTranscriptionMRNA2005, title = {Dynamics of Transcription and {{mRNA}} Export}, author = {Darzacq, Xavier and Singer, Robert H and {Shav-Tal}, Yaron}, year = 2005, month = jun, journal = {Current Opinion in Cell Biology}, volume = {17}, number = {3}, pages = {332–339}, publisher = {Elsevier}, issn = {0955-0674}, doi = {10.1016/j.ceb.2005.04.004}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0955067405000463}, abstract = {Understanding the different molecular mechanisms responsible for gene expression has been a central interest of molecular biologists for several decades. Transcription, the initial step of gene expression, consists of converting the genetic code into a dynamic messenger RNA that will specify a required cellular function following translocation to the cytoplasm and translation. We now possess an in-depth understanding of the mechanism and regulations of transcription. By contrast, an understanding of the dynamics of an individual gene’s expression in real time is just beginning to emerge following recent technological developments.}, keywords = {Active Transport Cell Nucleus,Animals,Cell Nucleus,DNA-Directed RNA Polymerases,Gene Expression Regulation,Humans,Kinetics,Models Genetic,nosource,RNA Messenger,RNA Transport,Transcription Factor TFIIH,Transcription Factors,Transcription Factors TFII,Transcription Genetic} } % == BibTeX quality report for darzacqDynamicsTranscriptionMRNA2005: % ? unused Journal abbr (“Curr. Opin. Cell Biol”)

@article{hermannDrugsTargetingRibosome2005, title = {Drugs Targeting the Ribosome}, author = {Hermann, Thomas}, year = 2005, month = jun, journal = {Current Opinion in Structural Biology}, volume = {15}, number = {3}, pages = {355–366}, publisher = {Elsevier}, issn = {0959-440X}, doi = {10.1016/j.sbi.2005.05.001}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0959440X05000850}, abstract = {Several classes of clinically important antibiotics target the bacterial ribosome, where they interfere with microbial protein synthesis. Structural studies of the interaction of antibiotics with the ribosome have revealed that these small molecules recognize predominantly the rRNA components. Over the past two years, three-dimensional structures of ribosome-antibiotic complexes have been determined, providing a detailed picture of the binding sites and mechanism of action of antibacterials, including ‘blockbuster’ drugs such as the macrolides. Structure-based approaches have come to fruition that comprise the design and crystal structure analysis of novel semi-synthetic antibiotics that target the ribosome decoding site.}, keywords = {Anti-Bacterial Agents,Binding Sites,Drug Delivery Systems,Drug Design,Models Chemical,Models Molecular,nosource,Protein Binding,Ribosomes,RNA Bacterial,RNA Ribosomal} } % == BibTeX quality report for hermannDrugsTargetingRibosome2005: % ? unused Journal abbr (“Curr. Opin. Struct. Biol”)

@article{millsDrosophilaARSsContain1986, title = {Drosophila {{ARSs}} Contain the Yeast {{ARS}} Consensus Sequence and a Replication Enhancer}, author = {Mills, J S and Kingsman, A J and Kingsman, S M}, year = 1986, month = aug, journal = {Nucleic Acids Research}, volume = {14}, number = {16}, pages = {6633–6648}, publisher = {Oxford Univ Press}, issn = {0305-1048}, url = {http://nar.oxfordjournals.org/content/14/16/6633.short}, abstract = {A number of restriction fragments that function as autonomously replicating sequences (ARSs) in yeast have been isolated from Drosophila melanogaster DNA. The behaviour in yeast of plasmids containing Drosophila ARS elements was studied and compared to that exhibited by the archetypal yeast ARS-1 plasmid. ARS functions were localised by subcloning and BAL-31 deletion analysis. These studies demonstrated the structural and functional complexity of Drosophila ARSs. Each Drosophila ARS element has at least two domains, one essential for replication (the replication sequence, RS) and a second (the replication enhancer, RE) which is essential for maximum function of the RS. The RS of three Drosophila ARSs was shown to contain a sequence identical to an 11 bp yeast ARS consensus sequence (5’ A/T TTTATPuTTT A/T 3’). These observations lend support to the hypothesis that heterologous ARS elements may be of biological significance.}, keywords = {Animals,Base Sequence,DNA Fungal,DNA Replication,Drosophila melanogaster,Enhancer Elements Genetic,Escherichia coli,Genes,Genes Fungal,Genes Regulator,Genetic Vectors,nosource,Plasmids,Saccharomyces cerevisiae} } % == BibTeX quality report for millsDrosophilaARSsContain1986: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{sachsDownstreamControlUpstream2006, title = {Downstream Control of Upstream Open Reading Frames}, author = {Sachs, Matthew S and Geballe, Adam P}, year = 2006, month = apr, journal = {Genes & Development}, volume = {20}, number = {8}, pages = {915–921}, publisher = {Cold Spring Harbor Lab}, issn = {0890-9369}, doi = {10.1101/gad.1427006}, url = {http://genesdev.cshlp.org/content/20/8/915.short}, keywords = {3’ Untranslated Regions,Animals,Humans,nosource,Nucleic Acid Conformation,Open Reading Frames,RNA Messenger} } % == BibTeX quality report for sachsDownstreamControlUpstream2006: % ? unused Journal abbr (“Genes Dev”)

@article{quiggleDonorSiteRibosomal1981, title = {Donor Site of Ribosomal Peptidyltransferase: Investigation of Substrate Specificity Using 2’(3’)-{{O-}}({{N-acylaminoacyl}}) Dinucleoside Phosphates as Models of the 3’-Terminus of {{N-acylaminoacyl}} Transfer Ribonucleic Acid}, author = {Quiggle, K and Kumar, G and Ott, T W and Ryu, E K and Chl{'a}dek, S}, year = 1981, month = jun, journal = {Biochemistry}, volume = {20}, number = {12}, pages = {3480–3485}, publisher = {ACS Publications}, issn = {0006-2960}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00515a027}, keywords = {Acyltransferases,Escherichia coli,Kinetics,nosource,Oligonucleotides,Peptidyl Transferases,Ribosomes,RNA Transfer,Structure-Activity Relationship,Substrate Specificity} }

@article{aravaDissectingEukaryoticTranslation2005, title = {Dissecting Eukaryotic Translation and Its Control by Ribosome Density Mapping}, author = {Arava, Yoav and Boas, F Edward and Brown, Patrick O and Herschlag, Daniel}, year = 2005, journal = {Nucleic Acids Research}, volume = {33}, number = {8}, pages = {2421–2432}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gki331}, url = {http://nar.oxfordjournals.org/content/33/8/2421.short}, abstract = {Translation of an mRNA is generally divided into three stages: initiation, elongation and termination. The relative rates of these steps determine both the number and position of ribosomes along the mRNA, but traditional velocity sedimentation assays for the translational status of mRNA determine only the number of bound ribosomes. We developed a procedure, termed Ribosome Density Mapping (RDM), that uses site-specific cleavage of polysomal mRNA followed by separation on a sucrose gradient and northern analysis, to determine the number of ribosomes associated with specified portions of a particular mRNA. This procedure allows us to test models for translation and its control, and to examine properties of individual steps of translation in vivo. We tested specific predictions from the current model for translational control of GCN4 expression in yeast and found that ribosomes were differentially associated with the uORFs elements and coding region under different growth conditions, consistent with this model. We also mapped ribosome density along the ORF of several mRNAs, to probe basic kinetic properties of translational steps in yeast. We found no detectable decline in ribosome density between the 5’ and 3’ ends of the ORFs, suggesting that the average processivity of elongation is very high. Conversely, there was no queue of ribosomes at the termination site, suggesting that termination is not very slow relative to elongation and initiation. Finally, the RDM results suggest that less frequent initiation of translation on mRNAs with longer ORFs is responsible for the inverse correlation between ORF length and ribosomal density that we observed in a global analysis of translation. These results provide new insights into eukaryotic translation in vivo.}, keywords = {0,3,analysis,assays,biosynthesis,CEREVISIAE,chemistry,CLEAVAGE,CODING REGION,DNA-BINDING,DNA-Binding Proteins,ELEMENTS,elongation,EUKARYOTIC TRANSLATION,expression,GCN,GCN4,Gene Expression Regulation Fungal,Gene Expression Regulation-Fungal,Gene Expression RegulationFungal,Genetic Techniques,genetics,GROWTH,IN-VIVO,initiation,kinase,La,mapping,metabolism,MODEL,models,Models Genetic,Models-Genetic,ModelsGenetic,mRNA,nosource,Open Reading Frames,Peptide Chain Elongation Translational,Peptide Chain Elongation-Translational,Peptide Chain ElongationTranslational,Peptide Chain Initiation Translational,Peptide Chain Initiation-Translational,Peptide Chain InitiationTranslational,Peptide Chain Termination Translational,Peptide Chain Termination-Translational,Peptide Chain TerminationTranslational,POSITION,PREDICTION,protein,Protein Biosynthesis,Protein Kinases,PROTEIN-KINASE,Proteins,REGION,Research Support-Non-U.S.Gov’t,Research SupportNon-U.S.Gov’t,ribosome,Ribosomes,Rna,RNA Messenger,RNA-Messenger,RNAMessenger,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SITE,site specific,termination,translation,uORF,yeast} } % == BibTeX quality report for aravaDissectingEukaryoticTranslation2005: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{salas-marcoDiscriminationDefectsElongation2005, title = {Discrimination between Defects in Elongation Fidelity and Termination Efficiency Provides Mechanistic Insights into Translational Readthrough}, author = {{Salas-Marco}, Joe and Bedwell, David M}, year = 2005, month = may, journal = {Journal of Molecular Biology}, volume = {348}, number = {4}, pages = {801–815}, publisher = {Elsevier}, issn = {0022-2836}, doi = {10.1016/j.jmb.2005.03.025}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283605002949}, abstract = {The suppression of stop codons (termed translational readthrough) can be caused by a decreased accuracy of translation elongation or a reduced efficiency of translation termination. In previous studies, the inability to determine the extent to which each of these distinct processes contributes to a readthrough phenotype has limited our ability to evaluate how defects in the translational machinery influence the overall termination process. Here, we describe the combined use of misincorporation and readthrough reporter systems to determine which of these mechanisms contributes to translational readthrough in Saccharomyces cerevisiae. The misincorporation reporter system was generated by introducing a series of near-cognate mutations into functionally important residues in the firefly luciferase gene. These constructs allowed us to monitor the incidence of elongation errors by monitoring the level of firefly luciferase activity from a mutant allele inactivated by a single missense mutation. In this system, an increase in luciferase activity should reflect an increased level of misincorporation of the wild-type amino acid that provides an estimate of the overall fidelity of translation elongation. Surprisingly, we found that growth in the presence of paromomycin stimulated luciferase activity for only a small subset of the mutant proteins examined. This suggests that the ability of this aminoglycoside to induce elongation errors is limited to a subset of near-cognate mismatches. We also found that a similar bias in near-cognate misreading could be induced by the expression of a mutant form of ribosomal protein (r-protein) S9B or by depletion of r-protein L12. We used this misincorporation reporter in conjunction with a readthrough reporter system to show that alterations at different regions of the ribosome influence elongation fidelity and termination efficiency to different extents.}, keywords = {0,accuracy,ACID,AMINO-ACID,Aspartic Acid,Base Sequence,CEREVISIAE,Codon,Codon Terminator,CODONS,CodonTerminator,deficiency,drug effects,efficiency,elongation,enzymology,ERRORS,expression,Fidelity,FIREFLY LUCIFERASE,FORM,gene,Gene Expression Regulation Fungal,Gene Expression RegulationFungal,Genes Reporter,GenesReporter,genetics,GROWTH,Helicase,La,luciferase,Luciferases,Luciferases Firefly,LuciferasesFirefly,MECHANISM,MECHANISMS,metabolism,microbiology,misincorporation,Mutagenesis,Mutation,MUTATIONS,nosource,Paromomycin,Peptide Chain Elongation Translational,Peptide Chain ElongationTranslational,Peptide Chain Termination Translational,Peptide Chain TerminationTranslational,pharmacology,Phenotype,protein,Proteins,readthrough,REGION,Research SupportN.I.H.Extramural,Research SupportU.S.Gov’tP.H.S.,RESIDUES,Ribosomal Proteins,ribosome,Rna,RNA HELICASE,RNA Helicases,RNA Transfer,RNATransfer,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SERIES,STOP CODON,suppression,SYSTEM,SYSTEMS,termination,TERMINATION EFFICIENCY,translation,TRANSLATION TERMINATION,TRANSLATIONAL READTHROUGH,Upf1,UPF1 PROTEIN,WILD-TYPE} } % == BibTeX quality report for salas-marcoDiscriminationDefectsElongation2005: % ? unused Journal abbr (“J. Mol. Biol”)

@article{kangDirectStructuralEvidence1998, title = {Direct Structural Evidence for Formation of a Stem-Loop Structure Involved in Ribosomal Frameshifting in Human Immunodeficiency Virus Type 1.}, author = {Kang, H}, year = 1998, month = apr, journal = {Biochimica Et Biophysica Acta}, volume = {1397}, number = {1}, eprint = {9545540}, eprinttype = {pubmed}, pages = {73–78}, issn = {0006-3002}, doi = {10.1016/S0167-4781(98)00004-9}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9545540}, abstract = {Programmed ribosomal frameshifting in viral messenger RNA occurs in response to neighboring sequence elements consisting of: a frameshift site, a spacer, and a downstream enhancer sequence. In human immunodeficiency virus type 1 (HIV-1) mRNA, this sequence element has a potential to form either a stem-loop or a pseudoknot structure. Based on many mutational studies, the stem-loop structure has been proposed for the downstream enhancer region of the HIV-1 mRNA. This stimulatory stem-loop structure is separated from the shift site by a spacer of seven nucleotides. In contrast, a recent report has proposed an alternative model in which the bases in the spacer sequence form a pseudoknot structure as the downstream enhancer sequence [Du et al., Biochemistry 35 (1996) 4187-4198.]. Using UV melting and enzymatic mapping analyses, we have investigated the conformation of the sequence region involved in ribosomal frameshifting in HIV-1. Our S1, V1, and T1 endonuclease mappings, together with UV melting analysis, clearly indicate that this sequence element of the HIV-1 mRNA frameshift site forms a stem-loop structure, not a pseudoknot structure. This finding further supports the stem-loop structure proposed by many mutational studies for the downstream enhancer sequence of the HIV-1 mRNA.}, pmid = {9545540}, keywords = {analysis,aspergillus nuclease s1,chemistry,ELEMENTS,Endoribonucleases,enhancer elements (genetics),Enhancer Elements Genetic,frameshift,Frameshifting,Frameshifting Ribosomal,FrameshiftingRibosomal,genetics,HIV,Hiv-1,HIV-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,mapping,MESSENGER-RNA,metabolism,models,mRNA,Mutation,nosource,Nucleic Acid Conformation,Nucleotides,pseudoknot,ribonuclease t1,Ribonuclease T1,ribosomal frameshifting,Rna,RNA Viral,RnaViral,sequence,Single-Strand Specific DNA and RNA Endonucleases,Structural,structure,Support,ultraviolet rays,Ultraviolet Rays,virus} } % == BibTeX quality report for kangDirectStructuralEvidence1998: % ? unused Journal abbr (“Biochim. Biophys. Acta”)

@article{abbondanzieriDirectObservationBasepair2005, title = {Direct Observation of Base-Pair Stepping by {{RNA}} Polymerase}, author = {Abbondanzieri, Elio A and Greenleaf, William J and Shaevitz, Joshua W and Landick, Robert and Block, Steven M}, year = 2005, month = nov, journal = {Nature}, volume = {438}, number = {7067}, eprint = {16284617}, eprinttype = {pubmed}, pages = {460–465}, issn = {1476-4687}, doi = {10.1038/nature04268}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16284617}, abstract = {During transcription, RNA polymerase (RNAP) moves processively along a DNA template, creating a complementary RNA. Here we present the development of an ultra-stable optical trapping system with ngstr"om-level resolution, which we used to monitor transcriptional elongation by single molecules of Escherichia coli RNAP. Records showed discrete steps averaging 3.7 +/- 0.6 A, a distance equivalent to the mean rise per base found in B-DNA. By combining our results with quantitative gel analysis, we conclude that RNAP advances along DNA by a single base pair per nucleotide addition to the nascent RNA. We also determined the force-velocity relationship for transcription at both saturating and sub-saturating nucleotide concentrations; fits to these data returned a characteristic distance parameter equivalent to one base pair. Global fits were inconsistent with a model for movement incorporating a power stroke tightly coupled to pyrophosphate release, but consistent with a brownian ratchet model incorporating a secondary NTP binding site.}, pmid = {16284617}, keywords = {Base Pairing,DNA,DNA-Directed RNA Polymerases,Escherichia coli,Kinetics,Models Biological,Movement,nosource,Nucleotides,Optics and Photonics,Sensitivity and Specificity,Templates Genetic,Transcription Genetic} }

@article{paillartDimerizationRetroviralGenomic1996, title = {Dimerization of Retroviral Genomic {{RNAs}}: Structural and Functional Implications}, author = {Paillart, J C and Marquet, R and Skripkin, E and Ehresmann, C and Ehresmann, B}, year = 1996, journal = {Biochimie}, volume = {78}, number = {7}, pages = {639–653}, publisher = {Elsevier}, issn = {0300-9084}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0300908496800101}, abstract = {Retroviruses are a family of widespread small animal viruses at the origin of a diversity of diseases. They share common structural and functional properties such as reverse transcription of their RNA genome and integration of the proviral DNA into the host genome, and have the particularity of packaging a diploid genome. The genome of all retroviruses is composed of two homologous RNA molecules that are non-covalently linked near their 5’ end in a region called the dimer linkage structure (DLS). There is now considerable evidence that a specific site (or sites) in the 5’ leader region of all retroviruses, located either upstream or/and downstream of the major splice donor site, is involved in the dimer linkage. For MoMuLV and especially HIV-1, it was shown that dimerization is initiated at a stem-loop structure named the dimerization initiation site (DIS). The DIS of HIV-1 and related regions in other retroviruses corresponds to a highly conserved structure with a self-complementary loop sequence, that is involved in a typical loop-loop ‘kissing’ complex which can be further stabilized by long distance interactions or by conformational rearrangements. RNA interactions involved in the viral RNA dimer were postulated to regulate several key steps in retroviral cycle, such as: i) translation and encapsidation: the arrest of gag translation imposed by the highly structured DLS-encapsidation signal would leave the RNA genome available for the encapsidation machinery; and ii) recombination during reverse transcription: the presence of two RNA molecules in particles would be necessary for variability and viability of virus progeny and the ordered structure imposed by the DLS would be required for efficient reverse transcription.}, keywords = {Animals,Base Sequence,HIV-1,Humans,Microscopy Electron,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Rats,Retroviridae,RNA Viral,Sequence Analysis DNA} }

@article{heathDifferingRolesCterminal2003, title = {Differing Roles of the {{N-}} and {{C-terminal}} Zinc Fingers in Human Immunodeficiency Virus Nucleocapsid Protein-Enhanced Nucleic Acid Annealing}, author = {Heath, Megan J and Derebail, Suchitra S and Gorelick, Robert J and DeStefano, Jeffrey J}, year = 2003, month = aug, journal = {The Journal of Biological Chemistry}, volume = {278}, number = {33}, pages = {30755–30763}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.M303819200}, url = {http://www.jbc.org/content/278/33/30755.short}, abstract = {The replication process of human immunodeficiency virus requires a number of nucleic acid annealing steps facilitated by the hybridization and helix-destabilizing activities of human immunodeficiency virus nucleocapsid (NC) protein. NC contains two CCHC zinc finger motifs numbered 1 and 2 from the N terminus. The amino acids surrounding the CCHC residues differ between the two zinc fingers. Assays were preformed to investigate the activities of the fingers by determining the effect of mutant and wild-type proteins on annealing of 42-nucleotide RNA and DNA complements. The mutants 1.1 NC and 2.2 NC had duplications of the N- and C-terminal zinc fingers in positions 1 and 2. The mutant 2.1 NC had the native zinc fingers with their positions switched. Annealing assays were completed with unstructured and highly structured oligonucleotide complements. 2.2 NC had a near wild-type level of annealing of unstructured nucleic acids, whereas it was completely unable to stimulate annealing of highly structured nucleic acids. In contrast, 1.1 NC was able to stimulate annealing of both unstructured and structured substrates, but to a lesser degree than the wild-type protein. Results suggest that finger 1 has a greater role in unfolding of strong secondary structures, whereas finger 2 serves an accessory role that leads to a further increase in the rate of annealing.}, keywords = {DNA Complementary,Fluorescence Resonance Energy Transfer,HIV-1,Mutation,nosource,Nucleic Acid Conformation,Nucleocapsid Proteins,Oligonucleotides,Protein Structure Tertiary,RNA,Zinc Fingers} } % == BibTeX quality report for heathDifferingRolesCterminal2003: % ? unused Journal abbr (“J. Biol. Chem”)

@article{kislauskisDeterminantsMRNALocalization1992, title = {Determinants of {{mRNA}} Localization}, author = {Kislauskis, E H and Singer, R H}, year = 1992, month = dec, journal = {Current Opinion in Cell Biology}, volume = {4}, number = {6}, pages = {975–978}, publisher = {Elsevier}, issn = {0955-0674}, url = {http://linkinghub.elsevier.com/retrieve/pii/095506749290128Y}, abstract = {RNA localization provides a mechanism for protein targeting within developing or differentiating cells. Specific cis-acting sequences on mRNA mediate this process. Such ‘localizer’ or ‘zipcode’ nucleic acid sequences have been restricted to the 3’ untranslated region of several mRNAs. The presence of genetic information denoting a spatial component of translation adds a new dimension to gene expression.}, keywords = {Animals,nosource,RNA Messenger} } % == BibTeX quality report for kislauskisDeterminantsMRNALocalization1992: % ? unused Journal abbr (“Curr. Opin. Cell Biol”)

@article{mcgarryDestabilizationSiteCodonanticodon2005, title = {Destabilization of the {{P}} Site Codon-Anticodon Helix Results from Movement of {{tRNA}} into the {{P}}/{{E}} Hybrid State within the Ribosome}, author = {McGarry, Kevin G and Walker, Sarah E and Wang, Huanyu and Fredrick, Kurt}, year = 2005, month = nov, journal = {Molecular Cell}, volume = {20}, number = {4}, pages = {613–622}, publisher = {Elsevier}, issn = {1097-2765}, doi = {10.1016/j.molcel.2005.10.007}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276505016771}, abstract = {Retention of the reading frame in ribosomal complexes after single-round translocation depends on the acylation state of the tRNA. When tRNA lacking a peptidyl group is translocated to the P site, the mRNA slips to allow re-pairing of the tRNA with a nearby out-of-frame codon. Here, we show that this ribosomal activity results from movement of tRNA into the P/E hybrid state. Slippage of mRNA is suppressed by 3’ truncation of the translocated tRNA, increased MgCl2 concentration, and mutation C2394A of the 50S E site, and each of these conditions inhibits P/E-state formation. Mutation G2252U of the 50S P site stimulates mRNA slippage, suggesting that decreased affinity of tRNA for the P/P state also destabilizes mRNA in the complex. The effects of G2252U are suppressed by C2394A, further implicating the P/E state in mRNA destabilization. This work uncovers a functional attribute of the P/E state crucial for understanding translation.}, keywords = {0,3,Acylation,Anticodon,Binding Sites,biosynthesis,Codon,COMPLEX,COMPLEXES,E,E site,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,FRAME,genetics,La,Magnesium,Magnesium Chloride,metabolism,microbiology,Movement,mRNA,Mutation,nosource,Nucleic Acid Conformation,P SITE,P-SITE,Peptide Chain Elongation Translational,Peptide Chain ElongationTranslational,Peptides,physiology,protein,Protein Biosynthesis,Protein Transport,Proteins,READING FRAME,Research SupportN.I.H.Extramural,Research SupportNon-U.S.Gov’t,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Rna,RNA Messenger,RNA Ribosomal,RNA Stability,RNA Transfer,RNA Transfer Amino Acyl,RNAMessenger,RNARibosomal,RNATransfer,RNATransferAmino Acyl,SITE,SLIPPAGE,Support,Transfer RNA Aminoacylation,translation,translocation,tRNA} } % == BibTeX quality report for mcgarryDestabilizationSiteCodonanticodon2005: % ? unused Journal abbr (“Mol. Cell”)

@article{mehtaDerepressionHer2UORF2006, title = {Derepression of the {{Her-2 uORF}} Is Mediated by a Novel Post-Transcriptional Control Mechanism in Cancer Cells.}, author = {Mehta, Anuradha and Trotta, Christopher R and Peltz, Stuart W}, year = 2006, month = apr, journal = {Genes & Development}, volume = {20}, number = {8}, pages = {939–953}, publisher = {Cold Spring Harbor Lab}, issn = {0890-9369}, doi = {10.1101/gad.1388706}, url = {http://genesdev.cshlp.org/content/20/8/939.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1472302&tool=pmcentrez&rendertype=abstract}, abstract = {Transcripts harboring 5’ upstream open reading frames (uORFs) are often found in genes controlling cell growth including receptors, oncogenes, or growth factors. uORFs can modulate translation or RNA stability and mediate inefficient translation of these potent proteins under normal conditions. In dysregulated cancer cells, where the gene product, for example Her-2 receptor, is overexpressed, post-transcriptional processes must exist that serve to override the inhibitory effects of the uORFs. The 5’ untranslated region (UTR) of Her-2 mRNA contains a short uORF that represses translation of the downstream coding region. We demonstrate that in Her-2 overexpressing breast cancer cells, the 3’ UTR of the Her-2 mRNA can override translational inhibition mediated by the Her-2 uORF. Within this 3’ UTR, a translational derepression element (TDE) that binds to a 38-kDa protein was identified. These results define a novel biological mechanism in which translational control of genes harboring a 5’ uORF can be modulated by elements in their 3’ UTRs.}, pmid = {16598037}, keywords = {2005,2006,21,5 and 3,5 and 3 utrs,a critical role for,Base Sequence,biochemical pathways responsible,Cell Line,Cell Line Tumor,DNA Primers,erbB-2,erbB-2: genetics,Fluorescence,her-2,her-2 receptor in the,Humans,Immunoprecipitation,many studies have established,Messenger,Messenger: genetics,Microscopy,Microscopy Fluorescence,Mutagenesis,nosource,Open Reading Frames,Post-Transcriptional,Protein Biosynthesis,received october 27,Receptor,Receptor erbB-2,revised version accepted february,RNA,RNA Messenger,RNA Processing,RNA Processing Post-Transcriptional,the,Tumor,uorf,utrs} } % == BibTeX quality report for mehtaDerepressionHer2UORF2006: % ? unused Journal abbr (“Genes Dev”)

@article{hamacherDependencyMapProteins2006, title = {Dependency Map of Proteins in the Small Ribosomal Subunit}, author = {Hamacher, Kay and Trylska, Joanna and McCammon, J Andrew}, year = 2006, month = feb, journal = {PLoS Computational Biology}, volume = {2}, number = {2}, pages = {80–87}, publisher = {Public Library of Science San Francisco, USA}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.0020010}, url = {http://dx.plos.org/10.1371/journal.pcbi.0020010}, abstract = {The assembly of the ribosome has recently become an interesting target for antibiotics in several bacteria. In this work, we extended an analytical procedure to determine native state fluctuations and contact breaking to investigate the protein stability dependence in the 30S small ribosomal subunit of Thermus thermophilus. We determined the causal influence of the presence and absence of proteins in the 30S complex on the binding free energies of other proteins. The predicted dependencies are in overall agreement with the experimentally determined assembly map for another organism, Escherichia coli. We found that the causal influences result from two distinct mechanisms: one is pure internal energy change, the other originates from the entropy change. We discuss the implications on how to target the ribosomal assembly most effectively by suggesting six proteins as targets for mutations or other hindering of their binding. Our results show that by blocking one out of this set of proteins, the association of other proteins is eventually reduced, thus reducing the translation efficiency even more. We could additionally determine the binding dependency of THX–a peptide not present in the ribosome of E. coli–and suggest its assembly path.}, keywords = {Computational Biology,Entropy,Escherichia coli,Models Biological,Models Statistical,Models- Biological,Models- Statistical,Monte Carlo Method,nosource,Peptides,Ribosomal Proteins,Ribosomes,Software,Thermodynamics,Thermus thermophilus} } % == BibTeX quality report for hamacherDependencyMapProteins2006: % ? unused Journal abbr (“PLoS Comput. Biol”)

@article{miyaoDeletionRNAPolymerase2001, title = {Deletion of the {{RNA}} Polymerase Subunit {{RPB4}} Acts as a Global, Not Stress-Specific, Shut-off Switch for {{RNA}} Polymerase {{II}} Transcription at High Temperatures}, author = {Miyao, T and Barnett, J D and Woychik, N A}, year = 2001, month = dec, journal = {The Journal of Biological Chemistry}, volume = {276}, number = {49}, eprint = {11577101}, eprinttype = {pubmed}, pages = {46408–46413}, issn = {0021-9258}, doi = {10.1074/jbc.M107012200}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11577101}, abstract = {We used whole genome expression analysis to investigate the changes in the mRNA profile in cells lacking the Saccharomyces cerevisiae RNA polymerase II subunit RPB4 (Delta RPB4). Our results indicated that an essentially complete shutdown of transcription occurs upon temperature shift of this conditionally lethal mutant; 98% of mRNA transcript levels decrease at least 2-fold, 96% at least 4-fold. This data was supported by in vivo experiments that revealed a rapid and greater than 5-fold decline in steady state poly(A) RNA levels after the temperature shift. Expression of several individual genes, measured by Northern analysis, was also consistent with the whole genome expression profile. Finally we demonstrated that the loss of RNA polymerase II activity causes secondary effects on RNA polymerase I, but not RNA polymerase III, transcription. The transcription phenotype of the Delta RPB4 mutant closely mirrors that of the temperature-sensitive rpb1-1 mutant frequently implemented as a tool to inactivate the RNA polymerase II in vivo. Therefore, the Delta RPB4 mutant can be used to easily design strains that enable the study of distinct post-transcriptional cellular processes in the absence of RNA polymerase II transcription.}, pmid = {11577101}, keywords = {0,analysis,Base Sequence,Dna,DNA Primers,expression,gene,Genes,Genetic,genetics,Genome,IN-VIVO,La,microbiology,mRNA,nosource,Phenotype,physiology,poly(A),polymerase,Rna,RNA Messenger,RNA Polymerase I,RNA Polymerase II,RNA Polymerase III,RNA-Messenger,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Sequence Deletion,SUBUNIT,support-u.s.gov’t-p.h.s.,supportu.s.gov’tp.h.s.,Temperature,transcription,Transcription Genetic,Transcription-Genetic,TranscriptionGenetic} } % == BibTeX quality report for miyaoDeletionRNAPolymerase2001: % ? unused Journal abbr (“J. Biol. Chem”)

@article{meskauskasDelayedRRNAProcessing2003, title = {Delayed {{rRNA}} Processing Results in Significant Ribosome Biogenesis and Functional Defects}, author = {Meskauskas, Arturas and Baxter, Jennifer L and Carr, Edward A and Yasenchak, Jason and Gallagher, Jennifer E G and Baserga, Susan J and Dinman, Jonathan D}, year = 2003, month = mar, journal = {Molecular and Cellular Biology}, volume = {23}, number = {5}, pages = {1602–1613}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, doi = {10.1128/MCB.23.5.1602-1613.2003}, url = {http://mcb.asm.org/cgi/content/abstract/23/5/1602}, abstract = {mof6-1 was originally isolated as a recessive mutation in Saccharomyces cerevisiae which promoted increased efficiencies of programmed -1 ribosomal frameshifting and rendered cells unable to maintain the killer virus. Here, we demonstrate that mof6-1 is a unique allele of the histone deacetylase RPD3, that the deacetylase function of Rpd3p is required for controlling wild-type levels of frameshifting and virus maintenance, and that the closest human homolog can fully complement these defects. Loss of the Rpd3p-associated histone deacetylase function, either by mutants of rpd3 or loss of the associated gene product Sin3p or Sap30p, results in a delay in rRNA processing rather than in an rRNA transcriptional defect. This results in production of ribosomes having lower affinities for aminoacyl-tRNA and diminished peptidyltransferase activities. We hypothesize that decreased rates of peptidyl transfer allow ribosomes with both A and P sites occupied by tRNAs to pause for longer periods of time at -1 frameshift signals, promoting increased programmed -1 ribosomal frameshifting efficiencies and subsequent loss of the killer virus. The frameshifting defect is accentuated when the demand for ribosomes is highest, suggesting that rRNA posttranscriptional modification is the bottleneck in ribosome biogenesis.}, keywords = {Alleles,Amino Acid Motifs,Anti-Bacterial Agents,Cloning Molecular,Cloning- Molecular,drugs,Electrophoresis Gel Two-Dimensional,Electrophoresis- Gel- Two-Dimensional,Frameshift Mutation,Frameshifting,Gene Deletion,Genes Recessive,Genes- Recessive,Heterochromatin,Histone Deacetylase,Histone Deacetylases,killer,Methionine,Models Genetic,Models- Genetic,Mutation,nosource,Peptidyl Transferases,Peptidyltransferase,Phenotype,Plasmids,Protein Synthesis Inhibitors,Puromycin,ribosome,ribosome biogenesis,Ribosomes,RNA Processing Post-Transcriptional,RNA Processing- Post-Transcriptional,RNA Ribosomal,RNA Transfer,RNA- Ribosomal,RNA- Transfer,RPD3,rRNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Temperature,Time Factors,Transcription Factors,Transcription Genetic,Transcription- Genetic,virus} } % == BibTeX quality report for meskauskasDelayedRRNAProcessing2003: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{agrisDecodingGenomeModified2004, title = {Decoding the Genome: A Modified View}, author = {Agris, Paul F. PF}, year = 2004, month = jan, journal = {Nucleic acids research}, volume = {32}, number = {1}, pages = {223–238}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gkh185}, url = {http://nar.oxfordjournals.org/content/32/1/223.short http://www.ncbi.nlm.nih.gov/pubmed/14715921 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=384350&tool=pmcentrez&rendertype=abstract}, abstract = {Transfer RNA’s role in decoding the genome is critical to the accuracy and efficiency of protein synthesis. Though modified nucleosides were identified in RNA 50 years ago, only recently has their importance to tRNA’s ability to decode cognate and wobble codons become apparent. RNA modifications are ubiquitous. To date, some 100 different posttranslational modifications have been identified. Modifications of tRNA are the most extensively investigated; however, many other RNAs have modified nucleosides. The modifications that occur at the first, or wobble position, of tRNA’s anticodon and those 3’-adjacent to the anticodon are of particular interest. The tRNAs most affected by individual and combinations of modifications respond to codons in mixed codon boxes where distinction of the third codon base is important for discriminating between the correct cognate or wobble codons and the incorrect near-cognate codons (e.g. AAA/G for lysine versus AAU/C asparagine). In contrast, other modifications expand wobble codon recognition, such as U*U base pairing, for tRNAs that respond to multiple codons of a 4-fold degenerate codon box (e.g. GUU/A/C/G for valine). Whether restricting codon recognition, expanding wobble, enabling translocation, or maintaining the messenger RNA, reading frame modifications appear to reduce anticodon loop dynamics to that accepted by the ribosome. Therefore, we suggest that anticodon stem and loop domain nucleoside modifications allow a limited number of tRNAs to accurately and efficiently decode the 61 amino acid codons by selectively restricting some anticodon-codon interactions and expanding others.}, pmid = {14715921}, keywords = {0,accuracy,ACID,AMINO-ACID,Animals,Anticodon,ANTICODON LOOP,Anticodon: chemistry,Anticodon: genetics,Anticodon: metabolism,Asparagine,BASE,Base Pairing,Base Sequence,chemistry,Codon,CODON RECOGNITION,Codon: chemistry,Codon: genetics,Codon: metabolism,CODONS,decoding,DOMAIN,DYNAMICS,efficiency,FRAME,Genetic Code,genetics,Genome,Humans,La,LOOP,Lysine,MESSENGER-RNA,metabolism,modification,nosource,Nucleosides,POSITION,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,READING FRAME,RECOGNITION,Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,Review,ribosome,Rna,RNA,RNA Transfer,RNATransfer,Structural,Thermodynamics,Transfer,TRANSFER-RNA,Transfer: chemistry,Transfer: genetics,Transfer: metabolism,translocation,tRNA} } % == BibTeX quality report for agrisDecodingGenomeModified2004: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{orbanDecayMRNAsTargeted2005, title = {Decay of {{mRNAs}} Targeted by {{RISC}} Requires {{XRN1}}, the {{Ski}} Complex, and the Exosome}, author = {Orban, Tamas I and Izaurralde, Elisa}, year = 2005, month = apr, journal = {RNA (New York, N.Y.)}, volume = {11}, number = {4}, pages = {459–469}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, doi = {10.1261/rna.7231505}, url = {http://rnajournal.cshlp.org/content/11/4/459.short}, abstract = {RNA interference (RNAi) is a conserved RNA silencing pathway that leads to sequence-specific mRNA decay in response to the presence of double-stranded RNA (dsRNA). Long dsRNA molecules are first processed by Dicer into 21-22-nucleotide small interfering RNAs (siRNAs). The siRNAs are incorporated into a multimeric RNA-induced silencing complex (RISC) that cleaves mRNAs at a site determined by complementarity with the siRNAs. Following this initial endonucleolytic cleavage, the mRNA is degraded by a mechanism that is not completely understood. We investigated the decay pathway of mRNAs targeted by RISC in Drosophila cells. We show that 5’ mRNA fragments generated by RISC cleavage are rapidly degraded from their 3’ ends by the exosome, whereas the 3’ fragments are degraded from their 5’ ends by XRN1. Exosome-mediated decay of the 5’ fragments requires the Drosophila homologs of yeast Ski2p, Ski3p, and Ski8p, suggesting that their role as regulators of exosome activity is conserved. Our findings indicate that mRNAs targeted by siRNAs are degraded from the ends generated by RISC cleavage, without undergoing decapping or deadenylation.}, keywords = {Acyltransferases,Animals,Cell Line,Drosophila melanogaster,Drosophila Proteins,Exoribonucleases,nosource,Nuclear Proteins,RNA Interference,RNA Messenger,RNA Stability,RNA- Messenger,RNA-Induced Silencing Complex,Saccharomyces cerevisiae Proteins} } % == BibTeX quality report for orbanDecayMRNAsTargeted2005: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{shethDecappingDecayMessenger2003, title = {Decapping and Decay of Messenger {{RNA}} Occur in Cytoplasmic Processing Bodies}, author = {Sheth, Ujwal and Parker, Roy}, year = 2003, month = may, journal = {Science (New York, N.Y.)}, volume = {300}, number = {5620}, pages = {805–808}, publisher = {American Association for the Advancement of Science}, issn = {1095-9203}, doi = {10.1126/science.1082320}, url = {http://www.sciencemag.org/content/300/5620/805.short}, abstract = {A major pathway of eukaryotic messenger RNA (mRNA) turnover begins with deadenylation, followed by decapping and 5’ to 3’ exonucleolytic decay. We provide evidence that mRNA decapping and 5’ to 3’ degradation occur in discrete cytoplasmic foci in yeast, which we call processing bodies (P bodies). First, proteins that activate or catalyze decapping are concentrated in P bodies. Second, inhibiting mRNA turnover before decapping leads to loss of P bodies; however, inhibiting turnover at, or after, decapping, increases the abundance and size of P bodies. Finally, mRNA degradation intermediates are localized to P bodies. These results define the flux of mRNAs between polysomes and P bodies as a critical aspect of cytoplasmic mRNA metabolism and a possible site for regulation of mRNA degradation.}, keywords = {Capsid Proteins,Cytoplasm,Cytoplasmic Granules,Cytoplasmic Structures,DEAD-box RNA Helicases,DNA-Binding Proteins,Endoribonucleases,Green Fluorescent Proteins,Luminescent Proteins,Models Biological,nosource,Polyribosomes,Protein Biosynthesis,Recombinant Fusion Proteins,Ribonucleases,RNA Cap-Binding Proteins,RNA Caps,RNA Fungal,RNA Helicases,RNA Messenger,RNA-Binding Proteins,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins} } % == BibTeX quality report for shethDecappingDecayMessenger2003: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”)

@article{sherryDbSNPNCBIDatabase2001, title = {{{dbSNP}}: The {{NCBI}} Database of Genetic Variation}, author = {Sherry, S T and Ward, M H and Kholodov, M and Baker, J and Phan, L and Smigielski, E M and Sirotkin, K}, year = 2001, month = jan, journal = {Nucleic Acids Research}, volume = {29}, number = {1}, pages = {308–311}, publisher = {Oxford Univ Press}, issn = {1362-4962}, url = {http://nar.oxfordjournals.org/content/29/1/308.short}, abstract = {In response to a need for a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, the National Center for Biotechnology Information (NCBI) has established the dbSNP database [S.T.Sherry, M.Ward and K. Sirotkin (1999) Genome Res., 9, 677-679]. Submissions to dbSNP will be integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data. The complete contents of dbSNP are available to the public at website: http://www.ncbi.nlm.nih.gov/SNP. The complete contents of dbSNP can also be downloaded in multiple formats via anonymous FTP at ftp://ncbi.nlm.nih.gov/snp/.}, keywords = {Animals,Biotechnology,Databases Factual,Databases- Factual,Genetic Variation,Humans,Information Services,Internet,National Institutes of Health (U.S.),National Library of Medicine (U.S.),nosource,Polymorphism Single Nucleotide,Polymorphism- Single Nucleotide,United States} } % == BibTeX quality report for sherryDbSNPNCBIDatabase2001: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{wohlgemuthOptimizationSpeedAccuracy2010, title = {Optimization of Speed and Accuracy of Decoding in Translation}, author = {Wohlgemuth, Ingo and Pohl, Corinna and Rodnina, Marina V}, year = 2010, month = sep, journal = {The EMBO Journal}, volume = {29}, number = {21}, pages = {3701–3709}, publisher = {Nature Publishing Group}, issn = {0261-4189}, doi = {10.1038/emboj.2010.229}, url = {http://www.nature.com/emboj/journal/v29/n21/abs/emboj2010229a.html}, keywords = {nosource} } % == BibTeX quality report for wohlgemuthOptimizationSpeedAccuracy2010: % ? unused Journal abbr (“EMBO J”)

@article{wiluszCurbingNonsenseActivation2001, title = {Curbing the Nonsense: The Activation and Regulation of {{mRNA}} Surveillance}, author = {Wilusz, C J and Wang, W and Peltz, S W}, year = 2001, month = nov, journal = {Genes & Development}, volume = {15}, number = {21}, eprint = {11691829}, eprinttype = {pubmed}, pages = {2781–2785}, issn = {0890-9369}, doi = {10.1101/gad.943701}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11691829}, pmid = {11691829}, keywords = {0,activation,animal,Animals,Cell Line,chemistry,Codon,Codon Nonsense,Codon- Nonsense,CodonNonsense,enzyme,Enzyme Inhibitors,Gene Expression Regulation,Genetic,genetics,human,Humans,kinase,La,metabolism,Metalloendopeptidases,microbiology,Models Biological,Models- Biological,ModelsBiological,mRNA,nosource,pharmacology,Phosphorylation,physiology,protein,Protein Kinases,regulation,Review,Rna,RNA Messenger,RNA- Messenger,RNAMessenger,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for wiluszCurbingNonsenseActivation2001: % ? unused Journal abbr (“Genes Dev.”)

@article{pallanCrystalStructureLuteoviral2005, title = {Crystal Structure of a Luteoviral {{RNA}} Pseudoknot and Model for a Minimal Ribosomal Frameshifting Motif}, author = {Pallan, Pradeep S and Marshall, William S and Harp, Joel and Jewett, Frederic C and Wawrzak, Zdzislaw and Brown, Bernard A and Rich, Alexander and Egli, Martin}, year = 2005, month = aug, journal = {Biochemistry}, volume = {44}, number = {34}, pages = {11315–11322}, publisher = {ACS Publications}, issn = {0006-2960}, doi = {10.1021/bi051061i}, url = {http://pubs.acs.org/doi/abs/10.1021/bi051061i}, abstract = {To understand the role of structural elements of RNA pseudoknots in controlling the extent of -1-type ribosomal frameshifting, we determined the crystal structure of a high-efficiency frameshifting mutant of the pseudoknot from potato leaf roll virus (PLRV). Correlations of the structure with available in vitro frameshifting data for PLRV pseudoknot mutants implicate sequence and length of a stem-loop linker as modulators of frameshifting efficiency. Although the sequences and overall structures of the RNA pseudoknots from PLRV and beet western yellow virus (BWYV) are similar, nucleotide deletions in the linker and adjacent minor groove loop abolish frameshifting only with the latter. Conversely, mutant PLRV pseudoknots with up to four nucleotides deleted in this region exhibit nearly wild-type frameshifting efficiencies. The crystal structure helps rationalize the different tolerances for deletions in the PLRV and BWYV RNAs, and we have used it to build a three-dimensional model of the PRLV pseudoknot with a four-nucleotide deletion. The resulting structure defines a minimal RNA pseudoknot motif composed of 22 nucleotides capable of stimulating -1-type ribosomal frameshifts.}, keywords = {0,Base Sequence,chemistry,crystal structure,CRYSTAL-STRUCTURE,Crystallography X-Ray,Crystallography-X-Ray,CrystallographyX-Ray,efficiency,ELEMENTS,frameshift,Frameshifting,Frameshifting Ribosomal,Frameshifting-Ribosomal,FrameshiftingRibosomal,genetics,In Vitro,IN-VITRO,La,LOOP,Luteovirus,MODEL,Models Molecular,Models-Molecular,ModelsMolecular,MUTANTS,nosource,Nucleic Acid Conformation,Nucleotides,Potatoes,pseudoknot,pseudoknots,REGION,Research Support-N.I.H.-Extramural,Research Support-Non-U.S.Gov’t,Research Support-U.S.Gov’t-Non-P.H.S.,Research Support-U.S.Gov’t-P.H.S.,Research SupportN.I.H.Extramural,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,Rna,RNA PSEUDOKNOT,RNA Viral,Rna-Viral,RnaViral,sequence,SEQUENCES,Solanum tuberosum,STEM-LOOP,Structural,structure,Thermodynamics,virology,virus,WILD-TYPE} }

@article{spahnCryoEMVisualizationViral2004, title = {Cryo-{{EM Visualization}} of a {{Viral Internal Ribosome Entry Site Bound}} to {{Human Ribosomes}}:: {{The IRES Functions}} as an {{RNA-Based Translation Factor}}}, author = {Spahn, Christian M T and Jan, Eric and Mulder, Anke and Grassucci, Robert A and Sarnow, Peter and Frank, Joachim}, year = 2004, month = aug, journal = {Cell}, volume = {118}, number = {4}, pages = {465–475}, publisher = {Elsevier}, issn = {0092-8674}, doi = {10.1016/j.cell.2004.08.001}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867404007469}, abstract = {Internal initiation of protein synthesis in eukaryotes is accomplished by recruitment of ribosomes to structured internal ribosome entry sites (IRESs), which are located in certain viral and cellular messenger RNAs. An IRES element in cricket paralysis virus (CrPV) can directly assemble 80S ribosomes in the absence of canonical initiation factors and initiator tRNA. Here we present cryo-EM structures of the CrPV IRES bound to the human ribosomal 40S subunit and to the 80S ribosome. The CrPV IRES adopts a defined, elongate structure within the ribosomal intersubunit space and forms specific contacts with components of the ribosomal A, P, and E sites. Conformational changes in the ribosome as well as within the IRES itself show that CrPV IRES actively manipulates the ribosome. CrPV-like IRES elements seem to act as RNA-based translation factors.}, keywords = {0,chemistry,COMPONENT,COMPONENTS,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,Conserved Sequence,Cricket paralysis virus,Cryoelectron Microscopy,E,E site,ELEMENTS,Escherichia coli,FORM,Hela Cells,human,Humans,initiation,INITIATION-FACTOR,INTERNAL RIBOSOME ENTRY,La,MESSENGER-RNA,MESSENGER-RNAS,metabolism,Methods,Models Molecular,ModelsMolecular,nosource,protein,Protein Binding,Protein Biosynthesis,Protein Conformation,protein synthesis,PROTEIN-SYNTHESIS,RECRUITMENT,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,ribosome,RIBOSOME ENTRY SITE,RIBOSOME ENTRY SITES,Ribosomes,Rna,RNA Messenger,RNA Transfer,RNA Viral,RNAMessenger,RNATransfer,RnaViral,SITE,SITES,structure,SUBUNIT,translation,tRNA,virus,VISUALIZATION} } % == BibTeX quality report for spahnCryoEMVisualizationViral2004: % ? Title looks like it was stored in title-case in Zotero

@article{hoangCreatingRibosomesAllRNA2004, title = {Creating Ribosomes with an All-{{RNA 30S}} Subunit {{P}} Site}, author = {Hoang, Lee and Fredrick, Kurt and Noller, Harry F}, year = 2004, month = aug, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {34}, pages = {12439–12443}, publisher = {National Acad Sciences}, issn = {0027-8424}, doi = {10.1073/pnas.0405227101}, url = {http://www.pnas.org/content/101/34/12439.short}, abstract = {Ribosome crystal structures have revealed that two small subunit proteins, S9 and S13, have C-terminal tails, which, together with several features of 16S rRNA, contact the anticodon stem-loop of P-site tRNA. To test the functional importance of these protein tails, we created genomic deletions of the C-terminal regions of S9 and S13. All of the tail deletions, including double mutants containing deletions in both S9 and S13, were viable, showing that Escherichia coli cells can synthesize all of their proteins by using ribosomes that contain 30S P sites composed only of RNA. However, these mutants have slower growth rates, indicating that the tails may play a supporting functional role in translation. In vitro analysis shows that 30S subunits purified from the S13 deletion mutants have a generally decreased affinity for tRNA, whereas deletion of the S9 tail selectively affects the binding of tRNAs whose anticodon stem sequences are most divergent from that of initiator tRNA.}, keywords = {0,16S,Amino Acid Sequence,analysis,Anticodon,Base Sequence,BINDING,BIOLOGY,CELLS,chemistry,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,genetics,genomic,GROWTH,In Vitro,IN-VITRO,La,metabolism,Models Molecular,ModelsMolecular,Molecular Sequence Data,MUTANTS,Mutation,nosource,Nucleic Acid Conformation,P SITE,P-SITE,P-SITES,protein,Protein Structure Tertiary,Protein StructureTertiary,Protein Subunits,Proteins,REGION,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNA Transfer,RNATransfer,rRNA,sequence,SEQUENCES,SITE,SITES,STEM-LOOP,structure,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,translation,tRNA} } % == BibTeX quality report for hoangCreatingRibosomesAllRNA2004: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{gygiCorrelationProteinMRNA1999, title = {Correlation between Protein and {{mRNA}} Abundance in Yeast}, author = {Gygi, S P and Rochon, Y and Franza, B R and Aebersold, R}, year = 1999, month = mar, journal = {Molecular and Cellular Biology}, volume = {19}, number = {3}, eprint = {10022859}, eprinttype = {pubmed}, pages = {1720–1730}, issn = {0270-7306}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10022859}, abstract = {We have determined the relationship between mRNA and protein expression levels for selected genes expressed in the yeast Saccharomyces cerevisiae growing at mid-log phase. The proteins contained in total yeast cell lysate were separated by high-resolution two-dimensional (2D) gel electrophoresis. Over 150 protein spots were excised and identified by capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein spots were quantified by metabolic labeling and scintillation counting. Corresponding mRNA levels were calculated from serial analysis of gene expression (SAGE) frequency tables (V. E. Velculescu, L. Zhang, W. Zhou, J. Vogelstein, M. A. Basrai, D. E. Bassett, Jr., P. Hieter, B. Vogelstein, and K. W. Kinzler, Cell 88:243-251, 1997). We found that the correlation between mRNA and protein levels was insufficient to predict protein expression levels from quantitative mRNA data. Indeed, for some genes, while the mRNA levels were of the same value the protein levels varied by more than 20-fold. Conversely, invariant steady-state levels of certain proteins were observed with respective mRNA transcript levels that varied by as much as 30-fold. Another interesting observation is that codon bias is not a predictor of either protein or mRNA levels. Our results clearly delineate the technical boundaries of current approaches for quantitative analysis of protein expression and reveal that simple deduction from mRNA transcript analysis is insufficient.}, pmid = {10022859}, keywords = {Codon,Fungal Proteins,Gene Expression Regulation Fungal,Gene Expression Regulation- Fungal,nosource,RNA Fungal,RNA Messenger,RNA- Fungal,RNA- Messenger,Saccharomyces cerevisiae} } % == BibTeX quality report for gygiCorrelationProteinMRNA1999: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{kiefCoordinateControlSyntheses1981, title = {Coordinate Control of Syntheses of Ribosomal Ribonucleic Acid and Ribosomal Proteins during Nutritional Shift-up in {{Saccharomyces}} Cerevisiae.}, author = {Kief, D R and Warner, J R}, year = 1981, month = nov, journal = {Molecular and Cellular Biology}, volume = {1}, number = {11}, pages = {1007–1015}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, url = {http://mcb.asm.org/cgi/content/abstract/1/11/1007}, abstract = {We investigated the regulation of ribosome synthesis in Saccharomyces cerevisiae growing at different rates and in response to a growth stimulus. The ribosome content and the rates of synthesis of ribosomal ribonucleic acid and of ribosomal proteins were compared in cultures growing in minimal medium with either glucose or ethanol as a carbon source. The results demonstrated that ribosome content is proportional to growth rate. Moreover, these steady-state concentrations are regulated at the level of synthesis of ribosomal precursor ribonucleic acid and of ribosomal proteins. When cultures growing on ethanol were enriched with glucose, the rate of ribosomal ribonucleic acid synthesis, measured by pulsing cells with [methyl-3H]methionine, increased by 40% within 5 min, doubled within 15 min, and reached a steady state characteristic of the new growth medium by 30 min. Labeling with [3H]leucine reveal a coordinate increase in the rate of synthesis of 30 or more ribosomal proteins as compared with that of total cellular proteins. Their synthesis was stimulated approximately 2.5-fold within 15 min and nearly 4-fold within 60 min. The data suggest that S. cerevisiae responds to a growth stimulus by preferential stimulation of the synthesis of ribosomal ribonucleic acid and ribosomal proteins.}, keywords = {82271822,biosynthesis,Carbon,carbon source,Cell Division,Comparative Study,Culture Media,Ethanol,Fungal Proteins,Glucose,media,metabolism,Multiple DOI,nonfile,nosource,Nucleic Acid Precursors,protein,Protein Biosynthesis,Proteins,regulation,Ribosomal Proteins,ribosome,RNA Ribosomal,RNARibosomal,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Transcription Genetic,TranscriptionGenetic,TranslationGenetic} } % == BibTeX quality report for kiefCoordinateControlSyntheses1981: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{cesareniControlColE1DNA1982, title = {Control of {{ColE1 DNA}} Replication: The Rop Gene Product Negatively Affects Transcription from the Replication Primer Promoter}, author = {Cesareni, G and Muesing, M A and Polisky, B}, year = 1982, month = oct, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {79}, number = {20}, pages = {6313–6317}, publisher = {National Acad Sciences}, issn = {0027-8424}, url = {http://www.pnas.org/content/79/20/6313.short}, abstract = {A 600-base-pair region essential for ColE1 and pMBl plasmid replication contains two promoters responsible for the synthesis of two RNA molecules central to copy number control. One promoter directs synthesis of the primer RNA precursor. The second promoter directs the synthesis of a small RNA molecule, RNAl, which acts in trans to inhibit processing of the RNA primer precursor. We have fused each promoter to the beta-galactosidase structural gene contained in a lambda phage. Expression of the RNAl promoter in lysogens is not influenced by the presence of wild-type pMBl or ColEl plasmids residing in the cell. Transcription from the RNA primer promoter, however, is repressed by the product of a trans-acting plasmid gene product, which we have designated rop (for repressor of primer). The rop gene maps downstream from the replication origin in a region that encodes a polypeptide of 63 amino acids whose sequence is completely conserved in pMBl and ColE1. We propose that this polypeptide is the rop gene product and that it regulates plasmid DNA replication by modulating the initiation of transcription of the primer RNA precursor.}, keywords = {Amino Acid Sequence,Bacterial Proteins,Bacteriocin Plasmids,Base Sequence,Chromosome Mapping,DNA Replication,Gene Expression Regulation,Genes Bacterial,nosource,Operon,Plasmids,RNA Bacterial,Transcription Genetic} } % == BibTeX quality report for cesareniControlColE1DNA1982: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{xuConservedTranslationalFrameshift2004, title = {Conserved Translational Frameshift in {{dsDNA}} Bacteriophage Tail Assembly Genes}, author = {Xu, Jun and Hendrix, Roger W and Duda, Robert L}, year = 2004, month = oct, journal = {Molecular Cell}, volume = {16}, number = {1}, pages = {11–21}, publisher = {Elsevier}, issn = {1097-2765}, doi = {10.1016/j.molcel.2004.09.006}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276504005398}, abstract = {A programmed translational frameshift similar to frameshifts in retroviral gag-pol genes and bacterial insertion elements was found to be strongly conserved in tail assembly genes of dsDNA phages and to be independent of sequence similarities. In bacteriophage lambda, this frameshift controls production of two proteins with overlapping sequences, gpG and gpGT, that are required for tail assembly. We developed bioinformatic approaches to identify analogous -1 frameshifting sites and experimentally confirmed our predictions for five additional phages. Clear evidence was also found for an unusual but analogous -2 frameshift in phage Mu. Frameshifting sites could be identified for most phages with contractile or noncontractile tails whose length is controlled by a tape measure protein. Phages from a broad spectrum of hosts spanning Eubacteria and Archaea appear to conserve this frameshift as a fundamental component of their tail assembly mechanisms, supporting the idea that their tail genes share a common, distant ancestry.}, keywords = {Amino Acid Sequence,Bacteriophage mu,Bacteriophages,Base Sequence,Conserved Sequence,DNA Viruses,Evolution Molecular,Evolution- Molecular,Frameshift Mutation,Molecular Sequence Data,nosource,Viral Proteins} } % == BibTeX quality report for xuConservedTranslationalFrameshift2004: % ? unused Journal abbr (“Mol. Cell”)

@article{ivanovConservationPolyamineRegulation2000, title = {Conservation of Polyamine Regulation by Translational Frameshifting from Yeast to Mammals}, author = {Ivanov, I P and Matsufuji, S and Murakami, Y and Gesteland, R F and Atkins, J F}, year = 2000, month = apr, journal = {The EMBO Journal}, volume = {19}, number = {8}, pages = {1907–1917}, publisher = {Nature Publishing Group}, issn = {0261-4189}, doi = {10.1093/emboj/19.8.1907}, url = {http://www.nature.com/emboj/journal/v19/n8/abs/7593016a.html}, abstract = {Regulation of ornithine decarboxylase in vertebrates involves a negative feedback mechanism requiring the protein antizyme. Here we show that a similar mechanism exists in the fission yeast Schizosaccharomyces pombe. The expression of mammalian antizyme genes requires a specific +1 translational frameshift. The efficiency of the frameshift event reflects cellular polyamine levels creating the autoregulatory feedback loop. As shown here, the yeast antizyme gene and several newly identified antizyme genes from different nematodes also require a ribosomal frameshift event for their expression. Twelve nucleotides around the frameshift site are identical between S.pombe and the mammalian counterparts. The core element for this frameshifting is likely to have been present in the last common ancestor of yeast, nematodes and mammals.}, keywords = {0,Amino Acid Sequence,Animals,antizyme,Caenorhabditis elegans,Conserved Sequence,efficiency,Evolution Molecular,expression,Feedback,frameshift,Frameshift Mutation,Frameshifting,gene,Gene Deletion,Genes,Genetic,genetics,human,Humans,Mammals,MECHANISM,Molecular Sequence Data,Mutagenesis,nosource,Nucleotides,Ornithine Decarboxylase,polyamine,Polyamines,protein,Protein Biosynthesis,Proteins,Putrescine,regulation,RIBOSOMAL FRAMESHIFT,Schizosaccharomyces,Sequence Homology Amino Acid,Spermidine,Spermine,Transcription Genetic,yeast} } % == BibTeX quality report for ivanovConservationPolyamineRegulation2000: % ? unused Journal abbr (“EMBO J.”)

@article{gaschConservationEvolutionCisregulatory2004, title = {Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi}, author = {Gasch, Audrey P and Moses, Alan M and Chiang, Derek Y and Fraser, Hunter B and Berardini, Mark and Eisen, Michael B}, year = 2004, month = dec, journal = {PLoS Biology}, volume = {2}, number = {12}, pages = {e398}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0020398}, url = {http://dx.plos.org/10.1371/journal.pbio.0020398}, abstract = {Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by examining the cis-regulatory elements that govern the expression of coregulated genes. We first identified groups of coregulated Saccharomyces cerevisiae genes enriched for genes with known upstream or downstream cis-regulatory sequences. Reasoning that many of these gene groups are coregulated in related species as well, we performed similar analyses on orthologs of coregulated S. cerevisiae genes in 13 other ascomycete species. We find that many species-specific gene groups are enriched for the same flanking regulatory sequences as those found in the orthologous gene groups fromS. cerevisiae, indicating that those regulatory systems have been conserved in multiple ascomycete species. In addition to these clear cases of regulatory conservation, we find examples of cis-element evolution that suggest multiple modes of regulatory diversification, including alterations in transcription factor-binding specificity, incorporation of new gene targets into an existing regulatory system, and cooption of regulatory systems to control a different set of genes. We investigated one example in greater detail by measuring the in vitro activity of the S. cerevisiae transcription factor Rpn4p and its orthologs from Candida albicans and Neurospora crassa. Our results suggest that the DNA binding specificity of these proteins has coevolved with the sequences found upstream of the Rpn4p target genes and suggest that Rpn4p has a different function in N. crassa.}, pmid = {15534694}, keywords = {Amino Acid Motifs,Amino Acid Sequence,Ascomycota,Binding Competitive,Candida albicans,Cloning Molecular,Conserved Sequence,DNA,DNA-Binding Proteins,Evolution Molecular,Gene Expression Regulation Fungal,Genes Regulator,Genome Fungal,Models Statistical,Molecular Sequence Data,Multigene Family,Neurospora crassa,nosource,Open Reading Frames,Phylogeny,Plasmids,Proteasome Endopeptidase Complex,Protein Binding,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Sequence Homology Amino Acid,Species Specificity,Transcription Factors} } % == BibTeX quality report for gaschConservationEvolutionCisregulatory2004: % ? unused Journal abbr (“PLoS Biol”)

@article{kangConformationNonframeshiftingRNA1996, title = {Conformation of a Non-Frameshifting {{RNA}} Pseudoknot from Mouse Mammary Tumor Virus}, author = {Kang, H and Hines, J V and Tinoco, I}, year = 1996, month = may, journal = {Journal of Molecular Biology}, volume = {259}, number = {1}, eprint = {8648641}, eprinttype = {pubmed}, pages = {135–147}, issn = {0022-2836}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8648641}, abstract = {The solution conformation of an RNA pseudoknot, which is a mutant of the pseudoknot required for ribosomal frameshifting in mouse mammary tumor virus, has been determined by NMR. The 32-nucleotide RNA pseudoknot does not promote efficient frameshifting, although its sequence is very similar to the efficient frameshifting pseudoknot whose structure was recently determined by our group. 13C-labeling of the RNA and 13C-edited NMR techniques were used to facilitate spectral assignment. The three-dimensional structure of the RNA pseudoknot was determined by restrained molecular dynamics based on NMR-derived interproton distances and torsion angle constraints. The conformation is very different from that previously determined for the efficient-frameshifting pseudoknot. Two unpaired nucleotides are stacked between stem 1 and stem 2, in contrast to the one unpaired nucleotide at the same junction region as found previously. The two stems of the pseudoknot are not coaxial, they are twisted and bent relative to each other. Loop 2 does not cross the shallow minor groove of stem 1, in contrast to the pseudoknots with one or no intervening nucleotides between the stems. The fact that a specific conformation is required for efficient frameshifting implies a specific interaction of the pseudoknot with the ribosome.}, pmid = {8648641}, keywords = {Base Sequence,Magnetic Resonance Spectroscopy,Mammary Tumor Virus Mouse,Mammary Tumor Virus- Mouse,Models Molecular,Models- Molecular,Molecular Sequence Data,Mutation,nosource,Nucleic Acid Conformation,Protein Biosynthesis,Protons,RNA Viral,RNA- Viral,Sequence Homology Nucleic Acid,Sequence Homology- Nucleic Acid,Thermodynamics} } % == BibTeX quality report for kangConformationNonframeshiftingRNA1996: % ? unused Journal abbr (“J. Mol. Biol”)

@article{caoComputationalModelingExperimental2003, title = {Computational Modeling and Experimental Analysis of Nonsense-Mediated Decay in Yeast}, author = {Cao, Dan and Parker, Roy}, year = 2003, month = may, journal = {Cell}, volume = {113}, number = {4}, pages = {533–545}, publisher = {Elsevier}, issn = {0092-8674}, doi = {10.1016/S0092-8674(03)00353-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867403003532}, abstract = {A conserved mRNA surveillance system, referred to as nonsense-mediated decay (NMD), exists in eukaryotic cells to degrade mRNAs containing nonsense codons. This process is important in checking that mRNAs; have been properly synthesized and functions, at least in part, to increase the fidelity of gene expression by degrading aberrant mRNAs; that, if translated, would produce truncated proteins. Using computational modeling and experimental analysis, we define the alterations in mRNA turnover triggered by NMD in yeast. We demonstrate that the nonsense-containing transcripts are efficiently recognized, targeted for deadenylation-independent decapping, and show NMD triggered accelerated deadenylation regardless of the position of the nonsense codon. We also show that 5’ nonsense codons trigger faster rates of decapping than 3’ nonsense codons, thereby providing a mechanistic basis for the polar effect of NMD. Finally, we construct a computational model that accurately describes the process of NMD and serves as an explanatory and predictive tool}, keywords = {Adenine,analysis,Base Sequence,Codon,Codon Nonsense,DEADENYLATION,DECAY,ELEMENTS,Eukaryotic Cells,expression,Fidelity,gene,Gene Expression,Gene Expression Regulation Fungal,GENE-EXPRESSION,Genes Regulator,MECHANISMS,MESSENGER-RNA SURVEILLANCE,Models Biological,mRNA,MUTATIONS,NMD,nonsense-mediated decay,nosource,protein,Proteins,RNA Messenger,SACCHAROMYCES-CEREVISIAE,stability,SYSTEM,TRANSLATION INITIATION,turnover,yeast,Yeasts} }

@article{majorComputationalMethodsRNA2001, title = {Computational Methods for {{RNA}} Structure Determination}, author = {Major, F and Griffey, R}, year = 2001, month = jun, journal = {Current Opinion in Structural Biology}, volume = {11}, number = {3}, pages = {282–286}, publisher = {Elsevier}, issn = {0959-440X}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0959-440x(00)00203-7}, abstract = {During the past year, major improvements have been made in methods used to solve RNA structures from crystals, find RNA patterns in sequence data and determine RNA secondary structure. Computational methods for assisting an interactive computer graphics human modeler, searching the conformational space of RNA tertiary structure, studying the dynamics of complexes involving RNA and simulating RNA catalytic activities have also been advanced.}, keywords = {Base Sequence,Crystallography X-Ray,Crystallography- X-Ray,Magnetic Resonance Spectroscopy,Models Molecular,Models- Molecular,nosource,Nucleic Acid Conformation,RNA} } % == BibTeX quality report for majorComputationalMethodsRNA2001: % ? unused Journal abbr (“Curr. Opin. Struct. Biol”)

@article{shahComputationalIdentificationPutative2002, title = {Computational Identification of Putative Programmed Translational Frameshift Sites}, author = {Shah, Atul A and Giddings, Michael C and Parvaz, Jasmin B and Gesteland, Raymond F and Atkins, John F and Ivanov, Ivaylo P}, year = 2002, month = aug, journal = {Bioinformatics (Oxford, England)}, volume = {18}, number = {8}, pages = {1046–1053}, publisher = {Oxford Univ Press}, issn = {1367-4803}, doi = {10.1093/bioinformatics/18.8.1046}, url = {http://bioinformatics.oxfordjournals.org/content/18/8/1046.short}, abstract = {Motivation: In an effort to identify potential programmed frameshift sites by statistical analysis, we explore the hypothesis that selective pressure would have rendered such sites underabundant and underrepresented in protein-coding sequences. We developed a computer program to compare the frequencies of k-length subsequences of nucleotides with the frequencies predicted by a zero order Markov chain determined by the codon bias of the same set of sequences. The program was used to calculate and evaluate the distribution of 7-base oligonucleotides in the 6000+ putative protein-coding sequences of S. cerevisiae preliminary to the laboratory testing of the most highly underrepresented oligos for frameshifting efficiency. Results: Among the most significant results is the finding that the heptanucleotides CUU-AGG-C and CUU-AGU-U, sites of the programmed +1 translational frameshifts required for the production in yeast of actin filament- binding protein ABP140 and telomerase subunit EST3, respectively, rank among the least represented of phase I heptanucleotides in the coding sequences of S. cerevisiae. Laboratory experiments demonstrated that other underrepresented heptanucleotides identified by the program, for example GGU-CAG-A, are also prone to significant translational frameshifting, suggesting the possibility that genes containing other underrepresented heptamers may also encode transframe products. Availability: The program is available for download from http://www.gesteland.genetics.utah.edu/freqAnalysis Contact: ivaylo.ivanov@m.cc.utah.edu Supplementary Information: Complete results from the analysis of S. cerevisiae are available on http://www.gesteland.genetics.utah.edu/freqAnalysis}, keywords = {Algorithms,analysis,Base Composition,Base Sequence,BINDING,BINDING PROTEIN,BINDING-PROTEIN,Codon,computer,Databases Genetic,Databases- Genetic,DNA,efficiency,frameshift,Frameshift Mutation,Frameshifting,gene,Gene Expression Regulation,Genes,Genetic,genetics,genomic,human,IDENTIFICATION,La,Models Genetic,Models Statistical,Models- Genetic,Models- Statistical,Molecular Sequence Data,nosource,Nucleotides,Oligonucleotides,protein,Protein Biosynthesis,Reproducibility of Results,Saccharomyces,Sensitivity and Specificity,sequence,Sequence Analysis DNA,Sequence Analysis- DNA,SEQUENCES,Software,SUBUNIT,Telomerase,yeast} } % == BibTeX quality report for shahComputationalIdentificationPutative2002: % ? unused Journal abbr (“Bioinformatics.”)

@article{plantComparativeStudyEffects2006, title = {Comparative Study of the Effects of Heptameric Slippry Site Composition on -1 Frameshifting among Different Translational Assay Systems.}, author = {Plant, Ewan P and Dinman, Jonathan D}, year = 2006, month = apr, journal = {RNA (New York, N.Y.)}, volume = {12}, number = {4}, pages = {666–673}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, doi = {10.1261/rna.2225206}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1421095&tool=pmcentrez&rendertype=abstract http://rnajournal.cshlp.org/content/12/4/666.short}, abstract = {Studies of programmed -1 ribosomal frameshifting (-1 PRF) have been approached over the past two decades by many different laboratories using a diverse array of virus-derived frameshift signals in translational assay systems derived from a variety of sources. Though it is generally acknowledged that both absolute and relative -1 PRF efficiency can vary in an assay system-dependent manner, no methodical study of this phenomenon has been undertaken. To address this issue, a series of slippery site mutants of the SARS-associated coronavirus frameshift signal were systematically assayed in four different eukaryotic translational systems. HIV-1 promoted frameshifting was also compared between Escherichia coli and a human T-cell line expression systems. The results of these analyses highlight different aspects of each system, suggesting in general that (1) differences can be due to the assay systems themselves; (2) phylogenetic differences in ribosome structure can affect frameshifting efficiency; and (3) care must be taken to employ the closest phylogenetic match between a specific -1 PRF signal and the choice of translational assay system.}, pmid = {16497657}, keywords = {3,Base Sequence,Cell Line,Codon,Comparative Study,Coronavirus,efficiency,Escherichia coli,Escherichia coli: genetics,ESCHERICHIA-COLI,expression,frameshift,frameshifting,Frameshifting,Frameshifting Ribosomal,Hiv-1,HIV-1,human,Humans,LINE,Mutagenesis,Mutagenesis Site-Directed,MUTANTS,nosource,Oligonucleotides,Plasmids,Ribosomal,ribosomal frameshifting,ribosome,SERIES,SIGNAL,SITE,Site-Directed,slippery site,structure,SYSTEM,SYSTEMS,T-Lymphocytes,T-Lymphocytes: metabolism,virus} } % == BibTeX quality report for plantComparativeStudyEffects2006: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{wellsCircularizationMRNAEukaryotic1998, title = {Circularization of {{mRNA}} by Eukaryotic Translation Initiation Factors}, author = {Wells, S E and Hillner, P E and Vale, R D and Sachs, A B}, year = 1998, month = jul, journal = {Molecular Cell}, volume = {2}, number = {1}, pages = {135–140}, publisher = {Elsevier}, issn = {1097-2765}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276500801227}, abstract = {Communication between the 5’ cap structure and 3’ poly(A) tail of eukaryotic mRNA results in the synergistic enhancement of translation. The cap and poly(A) tail binding proteins, eIF4E and Pab1p, mediate this effect in the yeast S. cerevisiae through their interactions with different parts of the translation factor eIF4G. Here, we demonstrate the reconstitution of an eIF4E/eIF4G/Pab1p complex with recombinant proteins, and show by atomic force microscopy that the complex can circularize capped, polyadenylated RNA. Our results suggest that formation of circular mRNA by translation factors could contribute to the control of mRNA expression in the eukaryotic cell.}, keywords = {Eukaryotic Initiation Factor-4E,Eukaryotic Initiation Factor-4G,Fungal Proteins,Glutathione Transferase,Macromolecular Substances,Microscopy Atomic Force,Microscopy- Atomic Force,nosource,Nucleic Acid Conformation,Peptide Fragments,Peptide Initiation Factors,Poly(A)-Binding Proteins,Protein Biosynthesis,Recombinant Fusion Proteins,RNA,RNA Fungal,RNA Messenger,RNA- Fungal,RNA- Messenger,RNA-Binding Proteins,Saccharomyces cerevisiae} } % == BibTeX quality report for wellsCircularizationMRNAEukaryotic1998: % ? unused Journal abbr (“Mol. Cell”)

@article{manktelowCharacterizationFrameshiftSignal2005, title = {Characterization of the Frameshift Signal of {{Edr}}, a Mammalian Example of Programmed -1 Ribosomal Frameshifting.}, author = {Manktelow, Emily and Shigemoto, Kazuhiro and Brierley, Ian}, year = 2005, month = jan, journal = {Nucleic Acids Research}, volume = {33}, number = {5}, pages = {1553–1563}, issn = {1362-4962}, doi = {10.1093/nar/gki299}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1065257&tool=pmcentrez&rendertype=abstract http://nar.oxfordjournals.org/content/33/5/1553.short}, abstract = {The ribosomal frameshifting signal of the mouse embryonal carcinoma differentiation regulated (Edr) gene represents the sole documented example of programmed -1 frameshifting in mammalian cellular genes [Shigemoto,K., Brennan,J., Walls,E,. Watson,C.J., Stott,D., Rigby,P.W. and Reith,A.D. (2001), Nucleic Acids Res., 29, 4079-4088]. Here, we have employed site-directed mutagenesis and RNA structure probing to characterize the Edr signal. We began by confirming the functionality and magnitude of the signal and the role of a GGGAAAC motif as the slippery sequence. Subsequently, we derived a model of the Edr stimulatory RNA and assessed its similarity to those stimulatory RNAs found at viral frameshift sites. We found that the structure is an RNA pseudoknot possessing features typical of retroviral frameshifter pseudoknots. From these experiments, we conclude that the Edr signal and by inference, the human orthologue PEG10, do not represent a novel ‘cellular class’ of programmed -1 ribosomal frameshift signal, but rather are similar to viral examples, albeit with some interesting features. The similarity to viral frameshift signals may complicate the design of antiviral therapies that target the frameshift process.}, pmid = {15767280}, keywords = {0,ACID,ACIDS,Animals,antiviral,Base Sequence,biosynthesis,Carrier Proteins,Carrier Proteins: biosynthesis,Carrier Proteins: genetics,chemistry,frameshift,Frameshifting,Frameshifting Ribosomal,FrameshiftingRibosomal,gene,Genes,genetics,human,La,Messenger,Messenger: chemistry,Mice,MODEL,Molecular Sequence Data,Mutagenesis,Mutagenesis Site-Directed,MutagenesisSite-Directed,nosource,Nucleic Acid Conformation,Nucleic Acids,pathology,protein,Proteins,Proteins: genetics,pseudoknot,pseudoknots,Research SupportNon-U.S.Gov’t,Ribosomal,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,RIBOSOMAL FRAMESHIFTING SIGNAL,Rna,RNA,RNA Messenger,RNA PSEUDOKNOT,RNAMessenger,sequence,SIGNAL,SITE,Site-Directed,SITES,structure,TARGET,therapy,virology} } % == BibTeX quality report for manktelowCharacterizationFrameshiftSignal2005: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{bhattacharyaCharacterizationBiochemicalProperties2000, title = {Characterization of the Biochemical Properties of the Human {{Upf1}} Gene Product That Is Involved in Nonsense-Mediated {{mRNA}} Decay.}, author = {Bhattacharya, A and Czaplinski, K and Trifillis, P and He, F and Jacobson, A and Peltz, S W}, year = 2000, month = sep, journal = {RNA (New York, N.Y.)}, volume = {6}, number = {9}, pages = {1226–1235}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, url = {http://rnajournal.cshlp.org/content/6/9/1226.short}, abstract = {The Upf1 protein in yeast has been implicated in the modulation of efficient translation termination as well as in the accelerated turnover of mRNAs containing premature stop codons, a phenomenon called nonsense-mediated mRNA decay (NMD). A human homolog of the yeast UPF1, termed HUpf1/RENT1, has also been identified. The HUpf1 has also been shown to play a role in NMD in mammalian cells. Comparison of the yeast and human UPF1 proteins demonstrated that the amino terminal cysteine/histidine-rich region and the region comprising the domains that define this protein as a superfamily group I helicase have been conserved. The yeast Upf1p demonstrates RNA-dependent ATPase and 5’ –{\(>\)} 3’ helicase activities. In this paper, we report the expression, purification, and characterization of the activities of the human Upf1 protein. We demonstrate that human Upf1 protein displays a nucleic-acid-dependent ATPase activity and a 5’–{\(>\)} 3’ helicase activity. Furthermore, human Upf1 is an RNA-binding protein whose RNA-binding activity is modulated by ATP. Taken together, these results indicate that the activities of the Upf1 protein are conserved across species, reflecting the conservation of function of this protein throughout evolution.}, keywords = {Adenosine Triphosphatases,DNA Helicases,Electrophoresis Polyacrylamide Gel,Humans,Mutation,nosource,Recombinant Proteins,RNA,RNA Helicases,RNA-Binding Proteins,Trans-Activators} } % == BibTeX quality report for bhattacharyaCharacterizationBiochemicalProperties2000: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{haganCharacterizationCisactingSequences1995, title = {Characterization of Cis-Acting Sequences and Decay Intermediates Involved in Nonsense-Mediated {{mRNA}} Turnover.}, author = {Hagan, K W and {Ruiz-Echevarria}, M J and Quan, Y and Peltz, S W}, year = 1995, month = feb, journal = {Molecular and Cellular Biology}, volume = {15}, number = {2}, eprint = {7823948}, eprinttype = {pubmed}, pages = {809–823}, issn = {0270-7306}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7823948}, abstract = {Several lines of evidence indicate that the processes of mRNA turnover and translation are intimately linked and that understanding this relationship is critical to elucidating the mechanism of mRNA decay. One clear example of this relationship is the observation that nonsense mutations can accelerate the decay of mRNAs in a process that we term nonsense-mediated mRNA decay. The experiments described here demonstrate that in the yeast Saccharomyces cerevisiae premature translational termination within the initial two-thirds of the PGK1 coding region accelerates decay of that transcript regardless of which of the stop codons is used. Nonsense mutations within the last quarter of the coding region have no effect on PGK1 mRNA decay. The sequences required for nonsense-mediated mRNA decay include a termination codon and specific sequences 3’ to the nonsense mutation. Translation of two-thirds of the PGK1 coding region inactivates the nonsense-mediated mRNA decay pathway. This observation explains why carboxyl-terminal nonsense mutations are resistant to accelerated decay. Characterization of the decay of nonsense-containing HIS4 transcripts yielded results mirroring those described above, suggesting that the sequence requirements described for the PGK1 transcript are likely to be a general characteristic of this decay pathway. In addition, an analysis of the decay intermediates of nonsense-containing mRNAs indicates that nonsense-mediated mRNA decay flows through a pathway similar to that described for a class of wild-type transcripts. The initial cleavage event occurs near the 5’ terminus of the nonsense-containing transcript and is followed by 5’–{\(>\)}3’ exonucleolytic digestion. A model for nonsense-mediated mRNA decay based on these results is discussed.}, pmid = {7823948}, keywords = {Alleles,Base Sequence,Exodeoxyribonuclease V,Exodeoxyribonucleases,Genes Fungal,Histones,Models Genetic,Molecular Sequence Data,Mutagenesis Site-Directed,nosource,Oligodeoxyribonucleotides,Phosphoglycerate Kinase,Plasmids,Protein Biosynthesis,Recombinant Proteins,RNA Messenger,Saccharomyces cerevisiae,Substrate Specificity,Transcription Genetic} } % == BibTeX quality report for haganCharacterizationCisactingSequences1995: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{yslaChapter3Assays2008, title = {Chapter 3. {{Assays}} of Adenylate Uridylate-Rich Element-Mediated {{mRNA}} Decay in Cells}, author = {Ysla, Riza M and Wilson, Gerald M and Brewer, Gary}, year = 2008, journal = {Methods in Enzymology}, volume = {449}, pages = {47–71}, publisher = {Elsevier}, issn = {1557-7988}, doi = {10.1016/S0076-6879(08)02403-8}, url = {http://www.sciencedirect.com/science/article/pii/S0076687908024038 ?http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B7CV2-4VK64G8-8-1&_cdi=18066&_user=961305&_orig=search&_coverDate=12/31/2008&_sk=995509999&view=c&wchp=dGLzVlz-zSkzV&md5=ba58f71d0a}, abstract = {The abundance of a cytoplasmic mRNA in eukaryotes often determines the level of the encoded protein product. The rates at which an mRNA is synthesized, exported, and degraded collectively contribute to its abundance in all cell types. Numerous mRNAs, particularly those encoding structural proteins, are very stable, with half-lives in the order of many hours. In contrast, mRNAs encoding regulatory proteins, including oncoproteins, cytokines, and signaling proteins, are relatively unstable with half-lives of an hour or less. As a result, modest changes in their decay rates affect their levels over a relatively short time period. This is particularly important to ensure rapid responses to extracellular signaling events. Messenger RNAs often harbor sequence elements that dictate their degradation rates. Adenylate uridylate (A+U)-rich elements (AREs), first identified in 1986, are perhaps the best characterized sequences that promote rapid mRNA degradation. These elements, localized within 3’-untranslated regions, sometimes contain AUUUA pentamers within an overall U-rich sequence, but this does not always define a bona fide ARE. Thus, experimental validation is essential before bestowing upon a suspected A+U-rich sequence the title of “ARE.” This chapter describes a reporter gene system that permits quantitative assessment of the effects of candidate A+U-rich sequences on mRNA half-life. This system employs tetracycline-controlled transcriptional silencing of the reporter gene, isolation of total-cell RNA at selected time points, quantitative reverse transcriptase polymerase chain reaction analysis of reporter mRNA levels, and nonlinear regression analysis of mRNA level as a function of time to quantitatively define parameters describing mRNA decay kinetics. Finally, this chapter describes more specialized assays to characterize ARE-mediated mRNA decay pathways, including deadenylation, and discusses decapping.⬚ ⬚}, keywords = {3’ UNTRANSLATED REGION,3’ Untranslated Regions,3’-UNTRANSLATED REGION,Adenine,analysis,assays,CELLS,Cytokines,DEADENYLATION,DECAY,DECAY PATHWAY,decay pathways,DECAY-,DECAY;,degradation,ELEMENTS,gene,Half-Life,Hela Cells,Humans,Kinetics,MESSENGER-RNA,MESSENGER-RNAS,mRNA,mRNA decay,nosource,PATHWAY,polymerase,Polymerase Chain Reaction,PRODUCT,protein,Proteins,REGION,Reverse Transcriptase Polymerase Chain Reaction,REVERSE-TRANSCRIPTASE,Rna,RNA decay-,RNA decay;,RNA Stability,RNA-Tetracycline repressible,RNA;Tetracycline repressible,sequence,SEQUENCES,Signal Transduction,Structural,SYSTEM,Uracil} } % == BibTeX quality report for yslaChapter3Assays2008: % ? unused Journal abbr (“Meth. Enzymol”)

@article{hosodaCBP80PromotesInteraction2005, title = {{{CBP80}} Promotes Interaction of {{Upf1}} with {{Upf2}} during Nonsense-Mediated {{mRNA}} Decay in Mammalian Cells}, author = {Hosoda, Nao and Kim, Yoon Ki and Lejeune, Fabrice and Maquat, Lynne E}, year = 2005, month = oct, journal = {Nature Structural & Molecular Biology}, volume = {12}, number = {10}, pages = {893–901}, publisher = {Nature Publishing Group}, issn = {1545-9993}, doi = {10.1038/nsmb995}, url = {http://www.nature.com/nsmb/journal/v12/n10/abs/nsmb995.html}, abstract = {In mammalian cells, nonsense-mediated messenger RNA decay (NMD) targets newly synthesized nonsense-containing mRNA bound by the cap-binding-protein heterodimer CBP80-CBP20 and at least one exon-junction complex (EJC). An EJC includes the NMD factors Upf3 or Upf3X and Upf2, and Upf2 recruits Upf1. Once this pioneer translation initiation complex is remodeled so that CBP80-CBP20 is replaced by eukaryotic initiation factor 4E, the mRNA is no longer detectably targeted for NMD. Here, we provide evidence that CBP80 augments the efficiency of NMD but not of Staufen1 (Stau1)-mediated mRNA decay (SMD). SMD depends on the recruitment of Upf1 by the RNA-binding protein Stau1 but does not depend on the other Upf proteins. We find that CBP80 interacts with Upf1 and promotes the interaction of Upf1 with Upf2 but not with Stau1.}, keywords = {Adaptor Proteins Signal Transducing,Carrier Proteins,Codon Nonsense,Cytoskeletal Proteins,Down-Regulation,Hela Cells,Humans,nosource,Nuclear Cap-Binding Protein Complex,Phosphoproteins,RNA Messenger,RNA Stability,RNA-Binding Proteins,Trans-Activators,Transcription Factors} } % == BibTeX quality report for hosodaCBP80PromotesInteraction2005: % ? unused Journal abbr (“Nat. Struct. Mol. Biol”)

@article{gaoCapbindingProtein1mediated2005, title = {Cap-Binding Protein 1-Mediated and Eukaryotic Translation Initiation Factor {{4E-mediated}} Pioneer Rounds of Translation in Yeast}, author = {Gao, Qinshan and Das, Biswadip and Sherman, Fred and Maquat, Lynne E}, year = 2005, month = mar, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {12}, pages = {4258–4263}, publisher = {National Acad Sciences}, issn = {0027-8424}, doi = {10.1073/pnas.0500684102}, url = {http://www.pnas.org/content/102/12/4258.short}, abstract = {Nonsense-mediated mRNA decay (NMD) in mammalian cells is restricted to newly synthesized mRNA that is bound at the 5’ cap by the major nuclear cap-binding complex and at splicing-generated exon-exon junctions by exon junction complexes. This messenger ribonucleoprotein has been called the pioneer translation initiation complex and, accordingly, NMD occurs as a consequence of nonsense codon recognition during a pioneer round of translation. Here, we characterize the nature of messenger ribonucleoprotein that is targeted for NMD in Saccharomyces cerevisiae. Data indicate that NMD targets both cap-binding complex (Cbc)1p- and eukaryotic translation initiation factor (eIF)4E-bound mRNAs, unlike in mammalian cells, where NMD does not detectably target eIF4E-bound mRNA. First, intron-containing pre-mRNAs in yeast are detectably bound by either Cbc1p, or, unlike in mammalian cells, eIF4E, indicating that mRNAs can be derived from either Cbc1p- or eIF4E-bound pre-mRNAs. Second, the ratio of nonsense-containing Cbc1p-bound mRNA to nonsense-free Cbc1p-bound mRNA, which was {\(<\)} 0.4 for those mRNAs tested here, is essentially identical to the ratio of the corresponding nonsense-containing eIF4E-bound mRNA to nonsense-free eIF4E-bound mRNA, and both ratios increase in cells treated with the translational inhibitor cycloheximide (CHX). These data, together with data presented here and elsewhere showing that Cbc1p-bound transcripts are precursors to eIF4E-bound transcripts, demonstrate that Cbc1p-bound mRNA is targeted for NMD. In support of the idea that eIF4E-bound mRNA is also targeted for NMD, eIF4E-bound mRNA is targeted for NMD in strains that lack Cbc1p. These results suggest that both Cbc1p- and eIF4E-mediated pioneer rounds of translation occur in yeast.}, keywords = {Base Sequence,Cap,Cap binding,CAP-BINDING COMPLEX,CELLS,CEREVISIAE,Codon,CODON RECOGNITION,COMPLEX,COMPLEXES,Cycloheximide,DECAY,DNA Fungal,Eukaryotic Initiation Factor-4E,EUKARYOTIC TRANSLATION,EXON,EXON JUNCTION COMPLEX,EXON-EXON JUNCTIONS,Ferrochelatase,Genes Fungal,INHIBITOR,initiation,INITIATION-FACTOR,La,MAMMALIAN-CELLS,Models Biological,mRNA,mRNA decay,NMD,NONSENSE,nonsense-mediated mRNA decay,nosource,PRECURSOR,protein,Protein Biosynthesis,RECOGNITION,RIBONUCLEOPROTEIN,RNA Cap-Binding Proteins,RNA Fungal,RNA Messenger,RNA Precursors,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Support,TARGET,TRANSCRIPT,translation,TRANSLATION INITIATION,yeast} } % == BibTeX quality report for gaoCapbindingProtein1mediated2005: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{huBioinformaticIdentificationCandidate2005, title = {Bioinformatic Identification of Candidate Cis -Regulatory Elements Involved in Human {{mRNA}} Polyadenylation}, author = {Hu, Jun and Lutz, Carol S and Wilusz, Jeffrey and Tian, Bin}, year = 2005, month = oct, journal = {RNA (New York, N.Y.)}, volume = {11}, number = {10}, eprint = {16131587}, eprinttype = {pubmed}, pages = {1485–1493}, issn = {1355-8382}, doi = {10.1261/rna.2107305}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16131587}, abstract = {Polyadenylation is an essential step for the maturation of almost all cellular mRNAs in eukaryotes. In human cells, most poly(A) sites are flanked by the upstream AAUAAA hexamer or a close variant, and downstream U/GU-rich elements. In yeast and plants, additional cis elements have been found to be located upstream of the poly(A) site, including UGUA, UAUA, and U-rich elements. In this study, we have developed a computer program named PROBE (Polyadenylation-Related Oligonucleotide Bidimensional Enrichment) to identify cis elements that may play regulatory roles in mRNA polyadenylation. By comparing human genomic sequences surrounding frequently used poly(A) sites with those surrounding less frequently used ones, we found that cis elements occurring in yeast and plants also exist in human poly(A) regions, including the upstream U-rich elements, and UAUA and UGUA elements. In addition, several novel elements were found to be associated with human poly(A) sites, including several G-rich elements. Thus, we suggest that many cis elements are evolutionarily conserved among eukaryotes, and human poly(A) sites have an additional set of cis elements that may be involved in the regulation of mRNA polyadenylation.}, pmid = {16131587}, keywords = {cis elements,Computational Biology,Genome Human,Humans,nosource,Poly A,polyadenylation,Polyadenylation,regulation,Regulatory Sequences Nucleic Acid,RNA Messenger} } % == BibTeX quality report for huBioinformaticIdentificationCandidate2005: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{panopoulosBiochemicalEvidenceTranslational2004, title = {Biochemical Evidence of Translational Infidelity and Decreased Peptidyltransferase Activity by a Sarcin/Ricin Domain Mutation of Yeast {{25S rRNA}}}, author = {Panopoulos, Panagiotis and Dresios, John and Synetos, Dennis}, year = 2004, journal = {Nucleic Acids Research}, volume = {32}, number = {18}, pages = {5398–5408}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gkh860}, url = {http://nar.oxfordjournals.org/content/32/18/5398.short}, abstract = {A C–{\(>\)}U mutation (rdn5) in the conserved sarcin/ricin domain of yeast 25S rRNA has been shown to cause translational suppression and paromomycin resistance. It also separates the killing from the misreading effect of this antibiotic. We confirm these findings and provide in vitro evidence that rdn5 causes a 3-fold increase in translational errors and resistance to paromomycin. The role of this 25S rRNA domain in ribosome’s decoding function was further demonstrated when 60S subunits from rdn5 cells were combined with 40S subunits from cells carrying an error-prone mutation in the eukaryotic accuracy center ribosomal protein S23, an homologue of Escherichia coli S12. These hybrids exhibited an error frequency similar to that of rdn5 alone, despite the error-prone mutation in S23. This was accompanied by extreme resistance to paromomycin, unlike the effects of the individual mutations. Furthermore, rdn5 lowers peptidyltransferase activity measured as a second-order rate constant (kcat/K(s)) corresponding to the rate of peptide bond formation. This mutation was also found to affect translocation. Elongation factor 2 (EF2)-dependent translocation of Ac-Phe-tRNA from the A- to P-site was achieved at an EF2 concentration 3.5 times lower than in wild type. In conclusion, the sarcin/ricin domain of 25S rRNA influences decoding, peptide bond formation and translocation.}, keywords = {0,60S subunit,accuracy,ACCURACY CENTER,ALPHA-SARCIN,Anti-Bacterial Agents,antibiotic,BOND FORMATION,Cell Division,CELLS,chemistry,decoding,DOMAIN,drug effects,Drug Resistance Fungal,Drug ResistanceFungal,elongation,Endoribonucleases,enzymology,ERRORS,Escherichia coli,ESCHERICHIA-COLI,Fungal Proteins,genetics,In Vitro,IN-VITRO,INHIBITOR,inhibitors,La,metabolism,Mutation,MUTATIONS,nosource,P SITE,P-SITE,Paromomycin,PAROMOMYCIN-RESISTANCE,peptide bond formation,Peptides,peptidyl transferase,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,Peptidyltransferase,pharmacology,Polyribosomes,protein,Protein Biosynthesis,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,Proteins,Research SupportNon-U.S.Gov’t,RESISTANCE,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Ricin,Rna,RNA Ribosomal,RNA Transfer,RNARibosomal,RNATransfer,rRNA,Saccharomyces cerevisiae,sarcin/ricin domain,SUBUNIT,SUBUNITS,suppression,SYNTHESIS INHIBITORS,Transferases,TRANSLATIONAL SUPPRESSION,translocation,WILD-TYPE,yeast} } % == BibTeX quality report for panopoulosBiochemicalEvidenceTranslational2004: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{curranBaseSubstitutionsTRNA1986, title = {Base Substitutions in the {{tRNA}} Anticodon Arm Do Not Degrade the Accuracy of Reading Frame Maintenance}, author = {Curran, J F and Yarus, M}, year = 1986, month = sep, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {83}, number = {17}, eprint = {2428035}, eprinttype = {pubmed}, pages = {6538–6542}, issn = {0027-8424}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2428035}, abstract = {We have examined the activities of a set of 34 site-directed mutants of tRNA Su7 for their ability to shift reading frame during translation of amber codons in vivo. The set includes variants at every position in the distal three base pairs of the anticodon stem and saturates the anticodon loop, with the exception of the anticodon itself. Most anticodon-stem mutations were made pairwise to preserve the secondary structure of that region. Variants of the Hirsh (A24) coding alteration were also tested. The mutations have varied and often dramatic effects on the ability of Su7 to act in translation, which indicates that they cause distortions of the codon-anticodon complex. However, none of the tested mutations affects the intrinsic accuracy of translocation, which we show to be very high. These results suggest that translocation must be independent of the conformational detail of the codon-anticodon complex and stand in contrast to frameshifts that occur when tRNAs misread codons. We suggest that when the tRNA is properly paired to the codon, translocation proceeds normally. Thus, we conclude that selection of a cognate tRNA ensures highly accurate reading frame maintenance. As a corollary, inefficient amber suppressors are not inefficient because they frameshift. Instead, they are likely to fail because a release factor translates the amber codon.}, pmid = {2428035}, keywords = {Anticodon,Escherichia coli,Mutation,nosource,Nucleic Acid Conformation,Protein Biosynthesis,RNA Bacterial,RNA Transfer,RNA- Bacterial,RNA- Transfer,Structure-Activity Relationship,Suppression Genetic,Suppression- Genetic} } % == BibTeX quality report for curranBaseSubstitutionsTRNA1986: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{malloryViralSuppressorRNA2002, title = {A Viral Suppressor of {{RNA}} Silencing Differentially Regulates the Accumulation of Short Interfering {{RNAs}} and Micro-{{RNAs}} in Tobacco}, author = {Mallory, Allison C and Reinhart, Brenda J and Bartel, David and Vance, Vicki B and Bowman, Lewis H}, year = 2002, month = nov, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {23}, eprint = {12403829}, eprinttype = {pubmed}, pages = {15228–15233}, issn = {0027-8424}, doi = {10.1073/pnas.232434999}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12403829}, abstract = {Two major classes of small noncoding RNAs have emerged as important regulators of gene expression in eukaryotes, the short interfering RNAs (siRNAs) associated with RNA silencing and endogenous micro-RNAs (miRNAs) implicated in regulation of gene expression. Helper component-proteinase (HC-Pro) is a viral protein that blocks RNA silencing in plants. Here we examine the effect of HC-Pro on the accumulation of siRNAs and endogenous miRNAs. siRNAs were analyzed in transgenic tobacco plants silenced in response to three different classes of transgenes: sense-transgenes, inverted-repeat transgenes, and amplicon-transgenes. HC-Pro suppressed silencing in each line, blocking accumulation of the associated siRNAs and allowing accumulation of transcripts from the previously silenced loci. HC-Pro-suppression of silencing in the inverted-repeat- and amplicon-transgenic lines was accompanied by the apparent accumulation of long double-stranded RNAs and proportional amounts of small RNAs that are larger than the siRNAs that accumulate during silencing. Analysis of these results suggests that HC-Pro interferes with silencing either by inhibiting siRNA processing from double-stranded RNA precursors or by destabilizing siRNAs. In contrast to siRNAs, the accumulation of endogenous miRNAs was greatly enhanced in all of the HC-Pro-expressing lines. Thus, our results demonstrate that accumulation of siRNAs and miRNAs in plants can be differentially regulated by a viral protein. The fact that HC-Pro affects the miRNA pathway raises the possibility that this pathway is targeted by plant viruses as a means to control gene expression in the host.}, pmid = {12403829}, keywords = {Glucuronidase,nosource,Plants Genetically Modified,RNA Double-Stranded,RNA Interference,RNA Plant,RNA Small Interfering,Tobacco} } % == BibTeX quality report for malloryViralSuppressorRNA2002: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{chenAUrichElementsCharacterization1995, title = {{{AU-rich}} Elements: Characterization and Importance in {{mRNA}} Degradation}, author = {Chen, C Y and Shyu, A B}, year = 1995, month = nov, journal = {Trends in Biochemical Sciences}, volume = {20}, number = {11}, pages = {465–470}, publisher = {Elsevier}, issn = {0968-0004}, doi = {10.1016/S0968-0004(00)89102-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000400891021 http://www.sciencedirect.com/science/article/pii/S0968000400891021}, abstract = {Adenylate/uridylate-rich elements (AREs) are found in the 3’ untranslated region (UTR) of many messenger RNAs (mRNAs) that code for proto-oncogenes, nuclear transcription factors and cytokines. They represent the most common determinant of RNA stability in mammalian cells. Moreover, ARE-directed mRNA degradation is influenced by many exogenous factors, including phorbol esters, calcium ionophores, cytokines and transcription inhibitors. These observations suggest that AREs play a critical role in the regulation of gene expression during cell growth and differentiation, and in the immune response.}, keywords = {Adenine,Animals,Base Composition,Conserved Sequence,Gene Expression Regulation,nosource,Protein Biosynthesis,RNA Messenger,RNA-Binding Proteins,Signal Transduction,Transcription Genetic,Uracil} } % == BibTeX quality report for chenAUrichElementsCharacterization1995: % ? unused Journal abbr (“Trends Biochem. Sci”)

@article{ramakrishnanAtomicStructuresLast2001, title = {Atomic Structures at Last: The Ribosome in 2000}, author = {Ramakrishnan, V and Moore, P B}, year = 2001, month = apr, journal = {Current Opinion in Structural Biology}, volume = {11}, number = {2}, pages = {144–154}, publisher = {Elsevier}, issn = {0959-440X}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0959-440x(00)00184-6}, abstract = {Last year, atomic structures of the 50S ribosomal subunit from Haloarcula marismortui and of the 30S ribosomal subunit from Thermus thermophilus were published. A year before that, a 7.8 A resolution electron density map of the 70S ribosome from T. thermophilus appeared. This information is revolutionizing our understanding of protein synthesis.}, keywords = {Binding Sites,Crystallography,Microscopy Atomic Force,Microscopy Electron,nosource,Peptide Elongation Factor G,Ribosomes,RNA Transfer} } % == BibTeX quality report for ramakrishnanAtomicStructuresLast2001: % ? unused Journal abbr (“Curr. Opin. Struct. Biol”)

@article{cardosoTobaccoNecrosisVirus2004, title = {A {{Tobacco}} Necrosis Virus {{D}} Isolate from {{Olea}} Europaea {{L}}.: Viral Characterization and Coat Protein Sequence Analysis}, author = {Cardoso, J M S and F{'e}lix, M R and Oliveira, S and Clara, M I E}, year = 2004, month = jun, journal = {Archives of Virology}, volume = {149}, number = {6}, eprint = {15168200}, eprinttype = {pubmed}, pages = {1129–1138}, issn = {0304-8608}, doi = {10.1007/s00705-003-0258-7}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15168200}, abstract = {A virus isolated from Olea europaea L. grown in Portugal, was identified as a member of the species Tobacco necrosis virus D (TNV-D, genus Necrovirus, family Tombusviridae), based on the molecular and serological properties of the purified virus particles. The genomic region encoding the coat protein (CP) of this isolate (named GP isolate) was amplified by RT-PCR and the cDNA was cloned and sequenced. The CP gene encodes a predicted protein of 269 amino acids showing high identity (86.2%) to TNV-D coat protein sequence. Phylogenetic analysis based on necroviruses CP sequences, confirmed GP as a TNV-D isolate. The alignment with homologous TNV-D CP sequences revealed four conserved amino acids involved in Ca(2+) binding as well as the plant virus icosahedral capsid protein “S’ signature. Based on the determined nucleotide sequence, specific primers were designed and successfully used in RT-PCR for virus diagnosis in naturally infected olive trees.}, pmid = {15168200}, keywords = {Amino Acid Sequence,Capsid Proteins,Cloning Molecular,Cloning- Molecular,Genes Viral,Genes- Viral,Molecular Sequence Data,nosource,Olea,Phylogeny,Plant Diseases,Portugal,Reverse Transcriptase Polymerase Chain Reaction,Sequence Alignment,Sequence Homology Amino Acid,Sequence Homology- Amino Acid,Tobacco Mosaic Virus} } % == BibTeX quality report for cardosoTobaccoNecrosisVirus2004: % ? unused Journal abbr (”Arch. Virol”)

@article{hennellyTimeresolvedInvestigationRibosomal2005, title = {A Time-Resolved Investigation of Ribosomal Subunit Association}, author = {Hennelly, Scott P and Antoun, Ayman and Ehrenberg, M{}ns and Gualerzi, Claudio O and Knight, William and Lodmell, J Stephen and Hill, Walter E}, year = 2005, month = mar, journal = {Journal of Molecular Biology}, volume = {346}, number = {5}, eprint = {15713478}, eprinttype = {pubmed}, pages = {1243–1258}, issn = {0022-2836}, doi = {10.1016/j.jmb.2004.12.054}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15713478}, abstract = {The notion that the ribosome is dynamic has been supported by various biochemical techniques, as well as by differences observed in high-resolution structures of ribosomal complexes frozen in various functional states. Yet, the mechanisms and extent of rRNA dynamics are still largely unknown. We have used a novel, fast chemical-modification technique to provide time-resolved details of 16 S rRNA structural changes that occur as bridges are formed between the ribosomal subunits as they associate. Association of different 16 S rRNA regions was found to be a sequential, multi-step process involving conformational rearrangements within the 30 S subunit. Our results suggest that key regions of 16 S rRNA, necessary for decoding and tRNA A-site binding, are structurally altered in a time-dependent manner by association with the 50 S ribosomal subunits.}, pmid = {15713478}, keywords = {0,16S,30 S,30-S,A SITE,A-SITE,ASSOCIATION,Bacterial,Base Pairing,BINDING,Binding Sites,CHEMICAL MODIFICATION,chemistry,COMPLEX,COMPLEXES,Crystallography X-Ray,CrystallographyX-Ray,decoding,DYNAMICS,Escherichia coli,La,MECHANISM,MECHANISMS,metabolism,Models Molecular,ModelsMolecular,nosource,Nucleic Acid Conformation,Protein Conformation,REGION,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNA Bacterial,RNA Ribosomal 16S,RNA Transfer,RNABacterial,RNARibosomal16S,RNATransfer,rRNA,S,Structural,structure,SUBUNIT,subunit association,SUBUNITS,Support,techniques,Time Factors,tRNA} } % == BibTeX quality report for hennellyTimeresolvedInvestigationRibosomal2005: % ? unused Journal abbr (“J. Mol. Biol”)

@article{plantThreestemmedMRNAPseudoknot2005, title = {A Three-Stemmed {{mRNA}} Pseudoknot in the {{SARS}} Coronavirus Frameshift Signal}, author = {Plant, Ewan P and {P{'e}rez-Alvarado}, Gabriela C and Jacobs, Jonathan L and Mukhopadhyay, Bani and Hennig, Mirko and Dinman, Jonathan D}, year = 2005, month = jun, journal = {PLoS Biology}, volume = {3}, number = {6}, eprint = {15884978}, eprinttype = {pubmed}, pages = {e172}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0030172}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15884978}, abstract = {A wide range of RNA viruses use programmed -1 ribosomal frameshifting for the production of viral fusion proteins. Inspection of the overlap regions between ORF1a and ORF1b of the SARS-CoV genome revealed that, similar to all coronaviruses, a programmed -1 ribosomal frameshift could be used by the virus to produce a fusion protein. Computational analyses of the frameshift signal predicted the presence of an mRNA pseudoknot containing three double-stranded RNA stem structures rather than two. Phylogenetic analyses showed the conservation of potential three-stemmed pseudoknots in the frameshift signals of all other coronaviruses in the GenBank database. Though the presence of the three-stemmed structure is supported by nuclease mapping and two-dimensional nuclear magnetic resonance studies, our findings suggest that interactions between the stem structures may result in local distortions in the A-form RNA. These distortions are particularly evident in the vicinity of predicted A-bulges in stems 2 and 3. In vitro and in vivo frameshifting assays showed that the SARS-CoV frameshift signal is functionally similar to other viral frameshift signals: it promotes efficient frameshifting in all of the standard assay systems, and it is sensitive to a drug and a genetic mutation that are known to affect frameshifting efficiency of a yeast virus. Mutagenesis studies reveal that both the specific sequences and structures of stems 2 and 3 are important for efficient frameshifting. We have identified a new RNA structural motif that is capable of promoting efficient programmed ribosomal frameshifting. The high degree of conservation of three-stemmed mRNA pseudoknot structures among the coronaviruses suggests that this presents a novel target for antiviral therapeutics.}, pmid = {15884978}, keywords = {3,Animals,antiviral,assays,BIOLOGY,Cercopithecus aethiops,Coronavirus,DATABASE,DOUBLE-STRANDED-RNA,efficiency,frameshift,Frameshift Mutation,Frameshifting,FUSION PROTEIN,Genetic,genetics,Genome,In Vitro,IN-VITRO,IN-VIVO,La,mapping,Messenger,Messenger: chemistry,Messenger: genetics,Molecular Sequence Data,MOLECULAR-GENETICS,mRNA,Mutagenesis,Mutation,No DOI found,nosource,nuclear magnetic resonance,NUCLEAR-MAGNETIC-RESONANCE,Nucleic Acid Conformation,Open Reading Frames,protein,Proteins,pseudoknot,pseudoknot structure,pseudoknots,REGION,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,Rna,RNA,RNA Messenger,RNA Viral,RNA Viruses,SARS,SARS Virus,SARS Virus: genetics,sequence,SEQUENCES,SIGNAL,Structural,structure,SYSTEM,SYSTEMS,TARGET,United States,Vero Cells,Viral,Viral: chemistry,Viral: genetics,virus,Viruses,yeast} } % == BibTeX quality report for plantThreestemmedMRNAPseudoknot2005: % ? unused Journal abbr (“PLoS Biol”)

@article{shuaiTemperatureSensitiveMutant1991, title = {A Temperature Sensitive Mutant of {{Saccharomyces}} Cerevisiae Defective in Pre-{{rRNA}} Processing}, author = {Shuai, K and Warner, J R}, year = 1991, month = sep, journal = {Nucleic Acids Research}, volume = {19}, number = {18}, eprint = {1923772}, eprinttype = {pubmed}, pages = {5059–5064}, issn = {0305-1048}, url = {http://www.ncbi.nlm.nih.gov/pubmed/1923772}, abstract = {A recessive temperature sensitive mutant has been isolated that is defective in ribosomal RNA processing. By Northern analysis, this mutant was found to accumulate three novel rRNA species: 23S’, 18S’ and 7S’, each of which contains sequences from the spacer region between 25S and 18S rRNA. 35S pre-rRNA accumulates, while the level of the 20S and 27S rRNA processing intermediates is depressed. Pulse-chase analysis demonstrates that the processing of 35S pre-rRNA is slowed. The defect in the mutant appears to be at the first processing step, which generates 20S and 27S rRNA. 7S’ RNA is a form of 5.8S RNA whose 5’ end is extended by 149 nucleotides to a position just 5 nucleotides downstream of the normal cleavage site that produces 20S and 27S rRNA. 7S’ RNA can assemble into 60S ribosomal subunits, but such subunits are relatively ineffective in joining polyribosomes. A single lesion is responsible for the pre-rRNA processing defect and the temperature sensitivity. The affected gene is designated RRP2.}, pmid = {1923772}, keywords = {Blotting Northern,Blotting- Northern,Mutation,nosource,Oligonucleotide Probes,Ribosomes,RNA Precursors,RNA Ribosomal,RNA Ribosomal 18S,RNA Ribosomal 23S,RNA- Ribosomal,RNA- Ribosomal- 18S,RNA- Ribosomal- 23S,Saccharomyces cerevisiae,Temperature} } % == BibTeX quality report for shuaiTemperatureSensitiveMutant1991: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{korzhevaStructuralModelTranscription2000, title = {A Structural Model of Transcription Elongation}, author = {Korzheva, N and Mustaev, A and Kozlov, M and Malhotra, A and Nikiforov, V and Goldfarb, A and Darst, S A}, year = 2000, month = jul, journal = {Science (New York, N.Y.)}, volume = {289}, number = {5479}, eprint = {10915625}, eprinttype = {pubmed}, pages = {619–625}, issn = {0036-8075}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10915625}, abstract = {The path of the nucleic acids through a transcription elongation complex was tracked by mapping cross-links between bacterial RNA polymerase (RNAP) and transcript RNA or template DNA onto the x-ray crystal structure. In the resulting model, the downstream duplex DNA is nestled in a trough formed by the beta’ subunit and enclosed on top by the beta subunit. In the RNAP channel, the RNA/DNA hybrid extends from the enzyme active site, along a region of the beta subunit harboring rifampicin resistance mutations, to the beta’ subunit “rudder.” The single-stranded RNA is then extruded through another channel formed by the beta-subunit flap domain. The model provides insight into the functional properties of the transcription complex.}, pmid = {10915625}, keywords = {Binding Sites,Cross-Linking Reagents,Crystallography X-Ray,DNA,DNA Primers,DNA-Directed RNA Polymerases,Models Molecular,Mutation,nosource,Nucleic Acid Conformation,Nucleic Acid Hybridization,Oligodeoxyribonucleotides,Oligoribonucleotides,Protein Conformation,Protein Structure Tertiary,RNA Messenger,Templates Genetic,Thermus,Transcription Genetic} } % == BibTeX quality report for korzhevaStructuralModelTranscription2000: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”)

@article{noensieStrategyDiseaseGene2001, title = {A Strategy for Disease Gene Identification through Nonsense-Mediated {{mRNA}} Decay Inhibition}, author = {Noensie, E N and Dietz, H C}, year = 2001, month = may, journal = {Nature Biotechnology}, volume = {19}, number = {5}, eprint = {11329012}, eprinttype = {pubmed}, pages = {434–439}, issn = {1087-0156}, doi = {10.1038/88099}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11329012}, abstract = {Premature termination codons (PTCs) have been shown to initiate degradation of mutant transcripts through the nonsense-mediated messenger RNA (mRNA) decay (NMD) pathway. We report a strategy, termed gene identification by NMD inhibition (GINI), to identify genes harboring nonsense codons that underlie human diseases. In this strategy, the NMD pathway is pharmacologically inhibited in cultured patient cells, resulting in stabilization of nonsense transcripts. To distinguish stabilized nonsense transcripts from background transcripts upregulated by drug treatment, drug-induced expression changes are measured in control and disease cell lines with complementary DNA (cDNA) microarrays. Transcripts are ranked by a nonsense enrichment index (NEI), which relates expression changes for a given transcript in NMD-inhibited control and patient cell lines. The most promising candidates can be selected using information such as map location or biological function; however, an important advantage of the GINI strategy is that a priori information is not essential for disease gene identification. GINI was tested on colon cancer and Sandhoff disease cell lines, which contained previously characterized nonsense mutations in the MutL homolog 1 (MLH1) and hexosaminidase B (HEXB) genes, respectively. A list of genes was produced in which the MLH1 and HEXB genes were among the top 1% of candidates, thus validating the strategy.}, pmid = {11329012}, keywords = {Adaptor Proteins,Adaptor Proteins Signal Transducing,Bacterial Proteins,Bacterial Proteins: drug effects,Bacterial Proteins: genetics,beta-Hexosaminidase beta Chain,beta-N-Acetylhexosaminidases,Carrier Proteins,Cell Line,Codon,Codon Nonsense,Codon Terminator,Colonic Neoplasms,Colonic Neoplasms: drug therapy,Colonic Neoplasms: genetics,Cultured,DNA-Binding Proteins,Hexosaminidase B,Humans,Male,Messenger,Messenger: isolation & purification,Neoplasm Proteins,Neoplasm Proteins: drug effects,Neoplasm Proteins: genetics,Nonsense,nosource,Nuclear Proteins,Oligonucleotide Array Sequence Analysis,Peptide Chain Termination,Peptide Chain Termination Translational,RNA,RNA Messenger,Sandhoff Disease,Sandhoff Disease: drug therapy,Sandhoff Disease: genetics,Signal Transducing,Terminator,Terminator: genetics,Translational,Translational: genetics,Tumor Cells,Tumor Cells Cultured,Tumor Suppressor Protein p53,Tumor Suppressor Protein p53: drug effects,Tumor Suppressor Protein p53: genetics} } % == BibTeX quality report for noensieStrategyDiseaseGene2001: % ? unused Journal abbr (“Nat. Biotechnol”)

@article{jagannathanAssemblyCentralDomain2003a, title = {Assembly of the Central Domain of the {{30S}} Ribosomal Subunit: Roles for the Primary Binding Ribosomal Proteins {{S15}} and {{S8}}}, author = {Jagannathan, Indu and Culver, Gloria M}, year = 2003, month = jul, journal = {Journal of Molecular Biology}, volume = {330}, number = {2}, eprint = {12823975}, eprinttype = {pubmed}, pages = {373–383}, issn = {0022-2836}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12823975}, abstract = {Assembly of the 30S ribosomal subunit occurs in a highly ordered and sequential manner. The ordered addition of ribosomal proteins to the growing ribonucleoprotein particle is initiated by the association of primary binding proteins. These proteins bind specifically and independently to 16S ribosomal RNA (rRNA). Two primary binding proteins, S8 and S15, interact exclusively with the central domain of 16S rRNA. Binding of S15 to the central domain results in a conformational change in the RNA and is followed by the ordered assembly of the S6/S18 dimer, S11 and finally S21 to form the platform of the 30S subunit. In contrast, S8 is not part of this major platform assembly branch. Of the remaining central domain binding proteins, only S21 association is slightly dependent on S8. Thus, although S8 is a primary binding protein that extensively contacts the central domain, its role in assembly of this domain remains unclear. Here, we used directed hydroxyl radical probing from four unique positions on S15 to assess organization of the central domain of 16S rRNA as a consequence of S8 association. Hydroxyl radical probing of Fe(II)-S15/16S rRNA and Fe(II)-S15/S8/16S rRNA ribonucleoprotein particles reveal changes in the 16S rRNA environment of S15 upon addition of S8. These changes occur predominantly in helices 24 and 26 near previously identified S8 binding sites. These S8-dependent conformational changes are consistent with 16S rRNA folding in complete 30S subunits. Thus, while S8 binding is not absolutely required for assembly of the platform, it appears to affect significantly the 16S rRNA environment of S15 by influencing central domain organization.}, pmid = {12823975}, keywords = {Binding Sites,Cysteine,Escherichia coli,Escherichia coli Proteins,Hydroxyl Radical,Iron,Macromolecular Substances,Models Molecular,nosource,Nucleic Acid Conformation,Protein Binding,Protein Engineering,Recombinant Proteins,Ribosomal Proteins,Ribosomes,RNA Bacterial,RNA Ribosomal 16S,Thermus thermophilus} } % == BibTeX quality report for jagannathanAssemblyCentralDomain2003a: % ? unused Journal abbr (“J. Mol. Biol”)

@article{takaiSingleUridineModification1999, title = {A Single Uridine Modification at the Wobble Position of an Artificial {{tRNA}} Enhances Wobbling in an {{Escherichia}} Coli Cell-Free Translation System}, author = {Takai, K and Okumura, S and Hosono, K and Yokoyama, S and Takaku, H}, year = 1999, month = mar, journal = {FEBS Letters}, volume = {447}, number = {1}, eprint = {10218569}, eprinttype = {pubmed}, pages = {1–4}, issn = {0014-5793}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10218569}, abstract = {5-Methoxyuridine was introduced into the first position of the anticodon of the unmodified form of tRNA(1Ser) from Escherichia coli. The codon reading efficiencies of this tRNA (tRNA(5-methoxyuridine UGA)) relative to those of the unmodified counterpart (tRNA(UGA)) were measured in a cell-free translation system. tRNA(5-methoxyuridine UGA) was more efficient than tRNA(UGA) in the reading of the UCU and UCG codons and was less efficient in the reading of the UCA codon. Thus, the single modification of U to 5-methoxyuridine can enhance the wobble readings.}, pmid = {10218569}, keywords = {Amino Acid Sequence,Anticodon,Base Sequence,Cell-Free System,Codon,Escherichia coli,Models Genetic,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Protein Biosynthesis,RNA Transfer Ser,Uridine} } % == BibTeX quality report for takaiSingleUridineModification1999: % ? unused Journal abbr (“FEBS Lett”)

@article{sugimotoSimpleEfficientMethod1989, title = {A Simple and Efficient Method for the Oligonucleotide-Directed Mutagenesis Using Plasmid {{DNA}} Template and Phosphorothioate-Modified Nucleotide}, author = {Sugimoto, M and Esaki, N and Tanaka, H and Soda, K}, year = 1989, month = jun, journal = {Analytical Biochemistry}, volume = {179}, number = {2}, eprint = {2549807}, eprinttype = {pubmed}, pages = {309–311}, issn = {0003-2697}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2549807}, abstract = {We have developed a simple and efficient method for oligonucleotide-directed mutagenesis with double-stranded (plasmid) DNA as a template. The template was simply and rapidly prepared by cell lysis and the following DNA denaturation with alkali. The chain elongation was performed with phosphorothioate-modified nucleotide at 37 degrees C. After the selective digestion of original DNA with NciI and exonuclease III, the desired mutated gene was obtained at a high frequency (about 70%).}, pmid = {2549807}, keywords = {Amino Acid Sequence,Base Sequence,Deoxycytosine Nucleotides,Deoxyribonucleases Type II Site-Specific,DNA,DNA Restriction Enzymes,Exodeoxyribonucleases,Molecular Sequence Data,Mutation,nosource,Nucleic Acid Hybridization,Oligonucleotides,Plasmids,Thionucleotides} } % == BibTeX quality report for sugimotoSimpleEfficientMethod1989: % ? unused Journal abbr (“Anal. Biochem”)

@article{gariSetVectorsTetracyclineregulatable1997, title = {A Set of Vectors with a Tetracycline-Regulatable Promoter System for Modulated Gene Expression in {{Saccharomyces}} Cerevisiae}, author = {Gar{'i}, E and Piedrafita, L and Aldea, M and Herrero, E}, year = 1997, month = jul, journal = {Yeast (Chichester, England)}, volume = {13}, number = {9}, eprint = {9234672}, eprinttype = {pubmed}, pages = {837–848}, publisher = {Wiley Online Library}, issn = {0749-503X}, doi = {10.1002/(SICI)1097-0061(199707)13:9<837::AID-YEA145>3.0.CO;2-T}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9234672 http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0061(199707)13:9<837::AID-YEA145>3.0.CO;2-T/pdf}, abstract = {A set of Saccharomyces cerevisiae expression vectors has been developed in which transcription is driven by a hybrid tetO-CYC1 promoter through the action of a tetR-VP16 (tTA) activator. Expression from the promoter is regulated by tetracycline or derivatives. Various modalities of promoter and activator are used in order to achieve different levels of maximal expression. In the presence of antibiotic in the growth medium at concentrations that do not affect cell growth, expression from the tetO promoter is negligible, and upon antibiotic removal induction ratios of up to 1000-fold are observed with a lacZ reporter system. With the strongest system, overexpression levels comparable with those observed with GAL1-driven promoters are reached. For each particular promoter/tTA combination, expression can be modulated by changing the tetracycline concentration in the growth medium. These vectors may be useful for the study of the function of essential genes in yeast, as well as for phenotypic analysis of genes in overexpression conditions, without restrictions imposed by growth medium composition.}, keywords = {0,analysis,antibiotic,Base Sequence,CEREVISIAE,derivatives,Dna,DNA Fungal,DNA Primers,DNAFungal,drug effects,expression,gene,Gene Expression,Gene Expression Regulation Fungal,Gene Expression RegulationFungal,GENE-EXPRESSION,Genes,Genes Fungal,GenesFungal,Genetic,Genetic Vectors,genetics,GROWTH,La,media,Molecular Sequence Data,nosource,Operator Regions (Genetics),Operator Regions Genetic,OVEREXPRESSION,pharmacology,PLASMID,Plasmids,PROMOTER,Promoter Regions (Genetics),Promoter Regions Genetic,PROMOTERS,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SYSTEM,Tetracycline,Tetracycline Resistance,Trans-Activators,transcription,vector,vectors,yeast} } % == BibTeX quality report for gariSetVectorsTetracyclineregulatable1997: % ? unused Journal abbr (“Yeast”)

@article{nagyRuleTerminationcodonPosition1998, title = {A Rule for Termination-Codon Position within Intron-Containing Genes: When Nonsense Affects {{RNA}} Abundance}, author = {Nagy, E and Maquat, L E}, year = 1998, month = jun, journal = {Trends in Biochemical Sciences}, volume = {23}, number = {6}, eprint = {9644970}, eprinttype = {pubmed}, pages = {198–199}, issn = {0968-0004}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9644970}, pmid = {9644970}, keywords = {Animals,Codon Nonsense,Codon Terminator,Humans,Introns,nosource,RNA Messenger} } % == BibTeX quality report for nagyRuleTerminationcodonPosition1998: % ? unused Journal abbr (“Trends Biochem. Sci”)

@article{birnboimRapidAlkalineExtraction1983a, title = {A Rapid Alkaline Extraction Method for the Isolation of Plasmid {{DNA}}}, author = {Birnboim, H C}, year = 1983, journal = {Methods in Enzymology}, volume = {100}, eprint = {6353143}, eprinttype = {pubmed}, pages = {243–255}, issn = {0076-6879}, url = {http://www.ncbi.nlm.nih.gov/pubmed/6353143}, pmid = {6353143}, keywords = {Cloning Molecular,DNA Bacterial,Electrophoresis Agar Gel,Escherichia coli,Indicators and Reagents,nosource,Nucleic Acid Hybridization,Plasmids} } % == BibTeX quality report for birnboimRapidAlkalineExtraction1983a: % ? unused Journal abbr (“Meth. Enzymol”)

@article{plantProgrammed1Ribosomal2004, title = {A Programmed -1 Ribosomal Frameshift Signal Can Function as a Cis-Acting {{mRNA}} Destabilizing Element}, author = {Plant, Ewan P and Wang, Pinger and Jacobs, Jonathan L and Dinman, Jonathan D}, year = 2004, journal = {Nucleic Acids Research}, volume = {32}, number = {2}, eprint = {14762205}, eprinttype = {pubmed}, pages = {784–790}, issn = {1362-4962}, doi = {10.1093/nar/gkh256}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14762205}, abstract = {Nonsense-mediated mRNA decay (NMD) directs rapid degradation of premature termination codon (PTC)-containing mRNAs, e.g. those containing frameshift mutations. Many viral mRNAs encode polycistronic messages where programmed -1 ribosomal frameshift (-1 PRF) signals direct ribosomes to synthesize polyproteins. A previous study, which identified consensus -1 PRF signals in the yeast genome, found that, in contrast to viruses, the majority of predicted -1 PRF events would direct translating ribosomes to PTCs. Here we tested the hypothesis that a -1 PRF signal can function as a cis-acting mRNA destabilizing element by inserting an L-A viral -1 PRF signal into a PGK1 reporter construct in the ‘genomic’ orientation. The results show that even low levels of -1 PRF are sufficient to target the reporter mRNA for degradation via the NMD pathway, with half-lives similar to messages containing in-frame PTCs. The demonstration of an inverse correlation between frameshift efficiency and mRNA half-lives suggests that modulation of -1 PRF frequencies can be used to post-transcriptionally regulate gene expression. Analysis of the mRNA decay profiles of the frameshift-signal- containing reporter mRNAs also supports the notion that NMD remains active on mRNAs beyond the ‘pioneer round’ of translation in yeast.}, pmid = {14762205}, keywords = {analysis,BIOLOGY,Codon,Codon Nonsense,DECAY,degradation,efficiency,expression,frameshift,Frameshift Mutation,Frameshifting,Frameshifting Ribosomal,Fungal,Fungal: genetics,Fungal: metabolism,gene,Gene Expression,GENE-EXPRESSION,Genes,Genes Fungal,Genes Reporter,Genetic,genetics,Genome,genomic,Half-Life,L-A,La,MESSAGE,Messenger,Messenger: genetics,Messenger: metabolism,microbiology,Models,Models Genetic,MOLECULAR-GENETICS,mRNA,mRNA decay,Mutation,MUTATIONS,NMD,Nonsense,nonsense-mediated mRNA decay,Nonsense: genetics,nosource,PATHWAY,POLYPROTEIN,Polyproteins,Polyproteins: genetics,PREMATURE TERMINATION CODON,Regulatory Sequences,Regulatory Sequences Ribonucleic Acid,Reporter,Reporter: genetics,Ribonucleic Acid,Ribonucleic Acid: genetics,Ribosomal,RIBOSOMAL FRAMESHIFT,Ribosomal: genetics,ribosome,Ribosomes,Ribosomes: metabolism,RNA,RNA Fungal,RNA Messenger,RNA Stability,RNA Transport,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae: genetics,SIGNAL,Support,TARGET,termination,TERMINATION CODON,TERMINATION-CODON,translation,yeast} } % == BibTeX quality report for plantProgrammed1Ribosomal2004: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{hentzePerfectMessageRNA1999, title = {A Perfect Message: {{RNA}} Surveillance and Nonsense-Mediated Decay}, author = {Hentze, M W and Kulozik, A E}, year = 1999, month = feb, journal = {Cell}, volume = {96}, number = {3}, eprint = {10025395}, eprinttype = {pubmed}, pages = {307–310}, issn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10025395}, pmid = {10025395}, keywords = {99148262,animal,Animals,Cell Nucleus,Codon Nonsense,Codon- Nonsense,CodonNonsense,DECAY,expression,gene,Gene Expression,GENE-EXPRESSION,genetics,human,Humans,metabolism,NMD,nonsense-mediated decay,nosource,physiology,Review,Rna,RNA,RNA Messenger,RNA- Messenger,RNAMessenger,Saccharomyces cerevisiae} }

@article{chanPathwayTransmissionAllosteric2006, title = {A Pathway for the Transmission of Allosteric Signals in the Ribosome through a Network of {{RNA}} Tertiary Interactions}, author = {Chan, Yuen-Ling and Dresios, John and Wool, Ira G}, year = 2006, month = feb, journal = {Journal of Molecular Biology}, volume = {355}, number = {5}, eprint = {16359709}, eprinttype = {pubmed}, pages = {1014–1025}, issn = {0022-2836}, doi = {10.1016/j.jmb.2005.11.037}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16359709}, abstract = {There are a large number of tertiary contacts between nucleotides in 23S rRNA, but which are of functional importance is not known. Disruption of one between A2662 in the sarcin/ricin loop (SRL) and A2531 in the peptidyl-transferase center (PTC) has adverse effects on cell growth and on the ability of ribosomes to catalyze some but not other partial reactions of elongation. A lethal A2662C mutation is suppressed by a concomitant lethal A2531 mutation. Ribosomes with non-lethal A2531 mutations, treated with base-specific reagents, have alterations of nucleotides in the PTC (home of A2531) and, more significantly, in nucleotides in the SRL and in the GTPase center. The results suggest that the function of ribosomal centers is coordinated by a set of sequential conformational changes in rRNA that are a response to signals transmitted through a network of tertiary interactions.}, pmid = {16359709}, keywords = {0,Allosteric Regulation,BIOLOGY,chemistry,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,DISRUPTION,elongation,genetics,GROWTH,GTPase,La,LOOP,metabolism,Models Molecular,ModelsMolecular,Molecular Biology,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Nucleotides,PATHWAY,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,physiology,protein,Protein Subunits,Research SupportN.I.H.Extramural,ribosome,Ribosomes,Rna,RNA Ribosomal,RNARibosomal,rRNA,SIGNAL,Signal Transduction,SUBUNIT,SUBUNITS,transmission} } % == BibTeX quality report for chanPathwayTransmissionAllosteric2006: % ? unused Journal abbr (“J. Mol. Biol”)

@article{dirksPartitionFunctionAlgorithm2003, title = {A Partition Function Algorithm for Nucleic Acid Secondary Structure Including Pseudoknots}, author = {Dirks, Robert M and Pierce, Niles A}, year = 2003, month = oct, journal = {Journal of Computational Chemistry}, volume = {24}, number = {13}, eprint = {12926009}, eprinttype = {pubmed}, pages = {1664–1677}, issn = {0192-8651}, doi = {10.1002/jcc.10296}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12926009}, abstract = {Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most physically relevant pseudoknots. We describe an O(N(5)) dynamic programming algorithm, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of secondary structures. Hence, it is possible to determine the probability of sampling the lowest energy structure, or any other structure of particular interest. This capability motivates the use of the partition function for the design of DNA or RNA molecules for bioengineering applications.}, pmid = {12926009}, keywords = {Algorithms,Computational Biology,DNA,Models Molecular,Models- Molecular,nosource,Nucleic Acid Conformation,RNA,Thermodynamics} } % == BibTeX quality report for dirksPartitionFunctionAlgorithm2003: % ? unused Journal abbr (“J Comput Chem”)

@article{ivanovSURVEYSUMMARYAntizyme2000, title = {{{SURVEY AND SUMMARY}}: Antizyme Expression: A Subversion of Triplet Decoding, Which Is Remarkably Conserved by Evolution, Is a Sensor for an Autoregulatory Circuit.}, author = {Ivanov, I P and Gesteland, R F and Atkins, J F}, year = 2000, month = sep, journal = {Nucleic Acids Research}, volume = {28}, number = {17}, pages = {3185–3196}, publisher = {Oxford University Press}, issn = {1362-4962}, doi = {10.1093/nar/28.17.3185}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC110703/}, abstract = {The efficiency of programmed ribosomal frameshifting in decoding antizyme mRNA is the sensor for an autoregulatory circuit that controls cellular polyamine levels in organisms ranging from the yeast Schizosaccharomyces pombe to Drosophila to mammals. Comparison of the frameshift sites and flanking stimulatory signals in many organisms now permits a reconstruction of the likely evolutionary path of the remarkably conserved mRNA sequences involved in the frameshifting.}, keywords = {0,Animals,antizyme,Base Sequence,chemistry,Codon,Conserved Sequence,decoding,Drosophila,efficiency,Evolution,Evolution Molecular,Evolution- Molecular,EvolutionMolecular,expression,Feedback,frameshift,Frameshifting,Frameshifting Ribosomal,Frameshifting- Ribosomal,FrameshiftingRibosomal,Genetic,genetics,human,Humans,La,Mammals,metabolism,Molecular Sequence Data,mRNA,nosource,Nucleic Acid Conformation,Phylogeny,polyamine,Polyamines,Regulatory Sequences Nucleic Acid,Regulatory Sequences- Nucleic Acid,Regulatory SequencesNucleic Acid,Review,ribosomal frameshifting,Rna,RNA Catalytic,RNA Messenger,RNA- Catalytic,RNA- Messenger,RNACatalytic,RNAMessenger,Schizosaccharomyces,sequence,Sequence Alignment,SEQUENCES,SIGNAL,SITE,SITES,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,yeast} } % == BibTeX quality report for ivanovSURVEYSUMMARYAntizyme2000: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{hargerVivoDualluciferaseAssay2003, title = {An ⬚in Vivo⬚ Dual-Luciferase Assay System for Studying Translational Recoding in the Yeast ⬚{{Saccharomyces}} Cerevisiae ⬚}, author = {Harger, Jason W and Dinman, Jonathan D}, year = 2003, month = aug, journal = {RNA (New York, N.Y.)}, volume = {9}, number = {8}, pages = {1019–1024}, issn = {1355-8382}, doi = {10.1261/rna.5930803}, url = {http://www.rnajournal.org/cgi/doi/10.1261/rna.5930803 http://rnajournal.cshlp.org/content/9/8/1019.short}, abstract = {A new in vivo assay system has been developed to study programmed⬚ frameshifting in the yeast ⬚Saccharomyces cerevisiae⬚. Frameshift signals are inserted between the ⬚Renilla⬚ and firefly luciferase reporter genes contained in a yeast expression vector and the two activities are directly measured from cell lysates in one tube. Similar to other bicistronic reporter systems, this one allows the efficient estimation of recoding efficiency by comparison of the normalized activity ratios from each luciferase protein. The assay system has been applied to HIV-1 and L-A directed programmed -1 frameshifting and Ty⬚1⬚ and Ty⬚3⬚ directed +1 frameshifting. The assay system is amenable to high-throughput screening. ⬚}, pmid = {12869712}, keywords = {+1 frameshifting,Animals,Base Sequence,Beetles,bicistronic,CEREVISIAE,efficiency,expression,frameshift,frameshifting,Frameshifting,Frameshifting Ribosomal,gene,Genes,Genes Reporter,Hiv-1,IN-VIVO,L-A,La,luciferase,Luciferases,lysate,Molecular Sequence Data,nosource,programmed frameshifting,protein,Protein Biosynthesis,recoding,ribosome,RNA Messenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SIGNAL,SYSTEM,translation,Ty1,vector,virus,yeast} } % == BibTeX quality report for hargerVivoDualluciferaseAssay2003: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{hargerIntegratedModelProgrammed2002, title = {An “Integrated Model” of Programmed Ribosomal Frameshifting}, author = {Harger, Jason W and Meskauskas, Arturas and Dinman, Jonathan D}, year = 2002, month = sep, journal = {Trends in Biochemical Sciences}, volume = {27}, number = {9}, pages = {448–454}, publisher = {Elsevier}, issn = {0968-0004}, doi = {10.1016/S0968-0004(02)02149-7}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000402021497 http://www.sciencedirect.com/science/article/pii/S0968000402021497}, abstract = {Many viral mRNAs, including those of HIV-1, can make translating ribosomes change reading frame. Altering the efficiencies of programmed ribosomal frameshift (PRF) inhibits viral propagation. As a new target for potential antiviral agents, it is therefore important to understand how PRF is controlled. Incorporation of the current models describing PRF into the context of the translation elongation cycle leads us to propose an ‘integrated model’ of PRF both as a guide towards further characterization of PRF at the molecular and biochemical levels, and for the identification of new targets for antiviral therapeutics.}, keywords = {antiviral,Antiviral Agents,EF-1,EF-2,efficiency,elongation,frameshift,Frameshifting,Frameshifting Ribosomal,Frameshifting- Ribosomal,Gag/Gag-pol ratio,Hiv-1,IDENTIFICATION,killer,L-A,M1,models,mRNA,nosource,Peptide Chain Elongation Translational,Peptide Chain Elongation- Translational,peptidyl-transfer,Reading Frames,Review,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,ribosome,Ribosomes,translation,tRNA,Ty,viral propagation,virus} } % == BibTeX quality report for hargerIntegratedModelProgrammed2002: % ? unused Journal abbr (“Trends Biochem. Sci”)

@article{bekaertExtendedSignalInvolved2005, title = {An Extended Signal Involved in Eukaryotic -1 Frameshifting Operates through Modification of the {{E}} Site {{tRNA}}}, author = {Bekaert, Micha{"e}l and Rousset, Jean-Pierre}, year = 2005, month = jan, journal = {Molecular Cell}, volume = {17}, number = {1}, eprint = {15629717}, eprinttype = {pubmed}, pages = {61–68}, issn = {1097-2765}, doi = {10.1016/j.molcel.2004.12.009}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15629717}, abstract = {By using a sensitive search program based on hidden Markov models (HMM), we identified 74 viruses carrying frameshift sites among 1500 fully sequenced virus genomes. These viruses are clustered in specific families or genera. Sequence analysis of the frameshift sites identified here, along with previously characterized sites, identified a strong bias toward the two nucleotides 5’ of the shifty heptamer signal. Functional analysis in the yeast Saccharomyces cerevisiae demonstrated that high frameshifting efficiency is correlated with the presence of a Psi39 modification in the tRNA present in the E site of the ribosome at the time of frameshifting. These results demonstrate that an extended signal is involved in eukaryotic frameshifting and suggest additional interactions between tRNAs and the ribosome during decoding.}, pmid = {15629717}, keywords = {0,analysis,Base Sequence,CEREVISIAE,decoding,E,E site,efficiency,FAMILY,frameshift,Frameshifting,Frameshifting Ribosomal,FrameshiftingRibosomal,functional analysis,genetics,Genome,Genome Viral,GenomeViral,Intramolecular Transferases,La,metabolism,MODEL,models,modification,nosource,Nucleotides,Plant Viruses,protein,Proteins,Research SupportNon-U.S.Gov’t,ribosome,Ribosomes,Rna,RNA Transfer,RNA Viral,RNATransfer,RnaViral,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,search,sequence,Sequence Analysis,SEQUENCE-ANALYSIS,SIGNAL,SITE,SITES,tRNA,virus,Viruses,yeast} } % == BibTeX quality report for bekaertExtendedSignalInvolved2005: % ? unused Journal abbr (“Mol. Cell”)

@article{qianNewModelPhenotypic1998, title = {A New Model for Phenotypic Suppression of Frameshift Mutations by Mutant {{tRNAs}}}, author = {Qian, Q and Li, J N and Zhao, H and Hagervall, T G and Farabaugh, P J and Bj{"o}rk, G R}, year = 1998, month = mar, journal = {Molecular Cell}, volume = {1}, number = {4}, eprint = {9660932}, eprinttype = {pubmed}, pages = {471–482}, issn = {1097-2765}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9660932}, abstract = {According to the prevailing model, frameshift-suppressing tRNAs with an extra nucleotide in the anticodon loop suppress +1 frameshift mutations by recognizing a four-base codon and promoting quadruplet translocation. We present three sets of experiments that suggest a general alternative to this model. First, base modification should actually block such a four-base interaction by two classical frameshift suppressors. Second, for one Salmonella suppressor tRNA, it is not mutant tRNA but a structurally normal near cognate that causes the +1 shift in-frame. Finally, frameshifting occurs in competition with normal decoding of the next in-frame codon, consistent with an event that occurs in the ribosomal P site after the translocation step. These results suggest an alternative model involving peptidyl-tRNA slippage at the classical CCC-N and GGG-N frameshift suppression sites.}, pmid = {9660932}, keywords = {Anticodon,DNA Primers,Frameshift Mutation,Gene Expression Regulation Bacterial,Gene Expression Regulation Fungal,Gene Expression Regulation- Bacterial,Gene Expression Regulation- Fungal,Guanosine,nosource,Nucleic Acid Conformation,Phenotype,Protein Biosynthesis,RNA Messenger,RNA Transfer,RNA- Messenger,RNA- Transfer,Saccharomyces cerevisiae,Salmonella typhimurium} } % == BibTeX quality report for qianNewModelPhenotypic1998: % ? unused Journal abbr (“Mol. Cell”)

@article{pfafflNewMathematicalModel2001, title = {A New Mathematical Model for Relative Quantification in Real-Time {{RT-PCR}}}, author = {Pfaffl, M W}, year = 2001, month = may, journal = {Nucleic Acids Research}, volume = {29}, number = {9}, eprint = {11328886}, eprinttype = {pubmed}, pages = {e45}, issn = {1362-4962}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11328886}, abstract = {Use of the real-time polymerase chain reaction (PCR) to amplify cDNA products reverse transcribed from mRNA is on the way to becoming a routine tool in molecular biology to study low abundance gene expression. Real-time PCR is easy to perform, provides the necessary accuracy and produces reliable as well as rapid quantification results. But accurate quantification of nucleic acids requires a reproducible methodology and an adequate mathematical model for data analysis. This study enters into the particular topics of the relative quantification in real-time RT-PCR of a target gene transcript in comparison to a reference gene transcript. Therefore, a new mathematical model is presented. The relative expression ratio is calculated only from the real-time PCR efficiencies and the crossing point deviation of an unknown sample versus a control. This model needs no calibration curve. Control levels were included in the model to standardise each reaction run with respect to RNA integrity, sample loading and inter-PCR variations. High accuracy and reproducibility ({\(<\)}2.5% variation) were reached in LightCycler PCR using the established mathematical model.}, pmid = {11328886}, keywords = {Animals,DNA Primers,Gene Expression Regulation,Models Theoretical,nosource,Reference Standards,Reproducibility of Results,Reverse Transcriptase Polymerase Chain Reaction,RNA Messenger,Sensitivity and Specificity,Time Factors,Transcription Genetic} } % == BibTeX quality report for pfafflNewMathematicalModel2001: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{pedersenEvolutionaryModelProteincoding2004, title = {An Evolutionary Model for Protein-Coding Regions with Conserved {{RNA}} Structure}, author = {Pedersen, Jakob Skou and Forsberg, Roald and Meyer, Irmtraud Margret and Hein, Jotun}, year = 2004, month = oct, journal = {Molecular Biology and Evolution}, volume = {21}, number = {10}, pages = {1913–1922}, publisher = {SMBE}, issn = {0737-4038}, doi = {10.1093/molbev/msh199}, url = {http://mbe.oxfordjournals.org/content/21/10/1913.short}, abstract = {Here we present a model of nucleotide substitution in protein-coding regions that also encode the formation of conserved RNA structures. In such regions, apparent evolutionary context dependencies exist, both between nucleotides occupying the same codon and between nucleotides forming a base pair in the RNA structure. The overlap of these fundamental dependencies is sufficient to cause “contagious” context dependencies which cascade across many nucleotide sites. Such large-scale dependencies challenge the use of traditional phylogenetic models in evolutionary inference because they explicitly assume evolutionary independence between short nucleotide tuples. In our model we address this by replacing context dependencies within codons by annotation-specific heterogeneity in the substitution process. Through a general procedure, we fragment the alignment into sets of short nucleotide tuples based on both the protein coding and the structural annotation. These individual tuples are assumed to evolve independently, and the different tuple sets are assigned different annotation-specific substitution models shared between their members. This allows us to build a composite model of the substitution process from components of traditional phylogenetic models. We applied this to a data set of full-genome sequences from the hepatitis C virus where five RNA structures are mapped within the coding region. This allowed us to partition the effects of selection on different structural elements and to test various hypotheses concerning the relation of these effects. Of particular interest, we found evidence of a functional role of loop and bulge regions, as these were shown to evolve according to a different and more constrained selective regime than the nonpairing regions outside the RNA structures. Other potential applications of the model include comparative RNA structure prediction in coding regions and RNA virus phylogenetics.}, keywords = {Base Sequence,Conserved Sequence,Evolution Molecular,Models Genetic,nosource,Nucleic Acid Conformation,Phylogeny,Proteins,RNA,Sequence Alignment,Sequence Analysis RNA} } % == BibTeX quality report for pedersenEvolutionaryModelProteincoding2004: % ? unused Journal abbr (“Mol. Biol. Evol”)

@article{valencia-sanchezEnemyFlyReconnaissance2004, title = {An Enemy within: Fly Reconnaissance Deploys an Endonuclease to Destroy Nonsense-Containing {{mRNA}}}, author = {{Valencia-S{'a}nchez}, Marco A and Maquat, Lynne E}, year = 2004, month = nov, journal = {Trends in Cell Biology}, volume = {14}, number = {11}, pages = {594–597}, publisher = {Elsevier}, issn = {0962-8924}, doi = {10.1016/j.tcb.2004.09.010}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0962892404002612 http://www.ncbi.nlm.nih.gov/pubmed/15519847}, abstract = {Quality-control mechanisms function in cells to ensure proper gene expression. Nonsense-mediated mRNA decay (NMD) is one such mechanism and it degrades abnormal mRNAs that contain a premature-termination codon. Although NMD is conserved in all eukaryotes that have been examined, it can manifest mechanistic differences in different organisms. A recent study using Drosophila melanogaster describes a new mechanistic twist to NMD.}, keywords = {Animals,Codon Initiator,Codon Nonsense,Drosophila melanogaster,Endonucleases,nosource,RNA Messenger,RNA Stability} } % == BibTeX quality report for valencia-sanchezEnemyFlyReconnaissance2004: % ? unused Journal abbr (“Trends Cell Biol”)

@article{savelsberghElongationFactorGinduced2003, title = {An Elongation Factor {{G-induced}} Ribosome Rearrangement Precedes {{tRNA-mRNA}} Translocation}, author = {Savelsbergh, Andreas and Katunin, Vladimir I and Mohr, Dagmar and Peske, Frank and Rodnina, Marina V and Wintermeyer, Wolfgang}, year = 2003, month = jun, journal = {Molecular Cell}, volume = {11}, number = {6}, pages = {1517–1523}, publisher = {Elsevier}, issn = {1097-2765}, doi = {10.1016/S1097-2765(03)00230-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/s1097276503002302}, abstract = {The elongation cycle of protein synthesis is completed by translocation, a rearrangement during which two tRNAs bound to the mRNA move on the ribosome. The reaction is promoted by elongation factor G (EF-G) and accelerated by GTP hydrolysis. Here we report a pre-steady-state kinetic analysis of translocation. The kinetic model suggests that GTP hydrolysis drives a conformational rearrangement of the ribosome that precedes and limits the rates of tRNA-mRNA translocation and Pi release from EF-G.GDP.Pi. The latter two steps are intrinsically rapid and take place at random. These results indicate that the energy of GTP hydrolysis is utilized to promote the ribosome rearrangement and to bias spontaneous fluctuations within the ribosome-EF-G complex toward unidirectional movement of mRNA and tRNA.}, keywords = {0,70S RIBOSOME,AMINOACYL-TRANSFER-RNA,analysis,Animals,COMPLEX,COMPLEXES,CONFORMATIONAL-CHANGE,EF-G,elongation,Energy Metabolism,FACTOR TU,GTP,GTPASE ACTIVITY,Guanosine Diphosphate,Guanosine Triphosphate,Humans,Hydrolysis,Kinetics,MECHANISM,Models Biological,Movement,mRNA,nosource,Peptide Elongation Factor G,Phosphates,protein,protein synthesis,PROTEIN-SYNTHESIS,RECOGNITION,ribosome,Ribosomes,RNA Messenger,RNA Transfer,Time Factors,translation,translocation,Translocation Genetic,tRNA} } % == BibTeX quality report for savelsberghElongationFactorGinduced2003: % ? unused Journal abbr (“Mol. Cell”)

@article{suAtypicalRNAPseudoknot2005, title = {An Atypical {{RNA}} Pseudoknot Stimulator and an Upstream Attenuation Signal for -1 Ribosomal Frameshifting of {{SARS}} Coronavirus}, author = {Su, Mei-Chi and Chang, Chung-Te and Chu, Chiu-Hui and Tsai, Ching-Hsiu and Chang, Kung-Yao}, year = 2005, journal = {Nucleic Acids Research}, volume = {33}, number = {13}, pages = {4265–4275}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gki731}, url = {http://nar.oxfordjournals.org/content/33/13/4265.short}, abstract = {The -1 ribosomal frameshifting requires the existence of an in cis RNA slippery sequence and is promoted by a downstream stimulator RNA. An atypical RNA pseudoknot with an extra stem formed by complementary sequences within loop 2 of an H-type pseudoknot is characterized in the severe acute respiratory syndrome coronavirus (SARS CoV) genome. This pseudoknot can serve as an efficient stimulator for -1 frameshifting in vitro. Mutational analysis of the extra stem suggests frameshift efficiency can be modulated via manipulation of the secondary structure within the loop 2 of an infectious bronchitis virus-type pseudoknot. More importantly, an upstream RNA sequence separated by a linker 5’ to the slippery site is also identified to be capable of modulating the -1 frameshift efficiency. RNA sequence containing this attenuation element can downregulate -1 frameshifting promoted by an atypical pseudoknot of SARS CoV and two other pseudoknot stimulators. Furthermore, frameshift efficiency can be reduced to half in the presence of the attenuation signal in vivo. Therefore, this in cis RNA attenuator represents a novel negative determinant of general importance for the regulation of -1 frameshift efficiency, and is thus a potential antiviral target.}, keywords = {0,ACID,analysis,antiviral,Base Sequence,chemistry,Coronavirus,Down-Regulation,DOWNSTREAM,efficiency,frameshift,Frameshifting,Frameshifting Ribosomal,Frameshifting-Ribosomal,FrameshiftingRibosomal,Gene Expression Regulation Viral,Gene Expression Regulation-Viral,Gene Expression RegulationViral,genetics,Genome,In Vitro,IN-VITRO,IN-VIVO,La,LOOP,Molecular Sequence Data,MUTATIONAL ANALYSIS,nosource,Nucleic Acid Conformation,pseudoknot,regulation,Regulatory Sequences Ribonucleic Acid,Regulatory Sequences-Ribonucleic Acid,Regulatory SequencesRibonucleic Acid,REQUIRES,Research Support-Non-U.S.Gov’t,Research SupportNon-U.S.Gov’t,RIBONUCLEIC-ACID,ribosomal frameshifting,Rna,RNA PSEUDOKNOT,RNA Viral,Rna-Viral,RnaViral,SARS,Sars Virus,SARS Virus,SECONDARY STRUCTURE,sequence,SEQUENCES,Severe Acute Respiratory Syndrome,SIGNAL,SITE,slippery site,structure,TARGET,UPSTREAM} } % == BibTeX quality report for suAtypicalRNAPseudoknot2005: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{schwartzAnalysesFrameshiftingUUUpyrimidine1997, title = {Analyses of Frameshifting at {{UUU-pyrimidine}} Sites.}, author = {Schwartz, R and Curran, J F}, year = 1997, month = may, journal = {Nucleic Acids Research}, volume = {25}, number = {10}, pages = {2005–2011}, issn = {0305-1048}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=146683&tool=pmcentrez&rendertype=abstract}, abstract = {Others have recently shown that the UUU phenylalanine codon is highly frameshift-prone in the 3’(rightward) direction at pyrimidine 3’contexts. Here, several approaches are used to analyze frameshifting at such sites. The four permutations of the UUU/C (phenylalanine) and CGG/U (arginine) codon pairs were examined because they vary greatly in their expected frameshifting tendencies. Furthermore, these synonymous sites allow direct tests of the idea that codon usage can control frameshifting. Frameshifting was measured for these dicodons embedded within each of two broader contexts: the Escherichia coli prfB (RF2 gene) programmed frameshift site and a ‘normal’ message site. The principal difference between these contexts is that the programmed frameshift contains a purine-rich sequence upstream of the slippery site that can base pair with the 3’end of 16 S rRNA (the anti-Shine-Dalgarno) to enhance frameshifting. In both contexts frameshift frequencies are highest if the slippery tRNAPhe is capable of stable base pairing in the shifted reading frame. This requirement is less stringent in the RF2 context, as if the Shine-Dalgarno interaction can help stabilize a quasi-stable rephased tRNA:message complex. It was previously shown that frameshifting in RF2 occurs more frequently if the codon 3’to the slippery site is read by a rare tRNA. Consistent with that earlier work, in the RF2 context frameshifting occurs substantially more frequently if the arginine codon is CGG, which is read by a rare tRNA. In contrast, in the ‘normal’ context frameshifting is only slightly greater at CGG than at CGU. It is suggested that the Shine-Dalgarno-like interaction elevates frameshifting specifically during the pause prior to translation of the second codon, which makes frameshifting exquisitely sensitive to the rate of translation of that codon. In both contexts frameshifting increases in a mutant strain that fails to modify tRNA base A37, which is 3’of the anticodon. Thus, those base modifications may limit frameshifting at UUU codons. Finally, statistical analyses show that UUU Ynn dicodons are extremely rare in E.coli genes that have highly biased codon usage.}, pmid = {9115369}, keywords = {Arg,Arg: genetics,Arginine,Arginine: genetics,Base Composition,Base Sequence,Codon,DNA Primers,Escherichia coli,Escherichia coli: genetics,Frameshifting,Frameshifting Ribosomal,Genetic Techniques,nosource,Phe,Phe: genetics,Phenylalanine,Phenylalanine: genetics,Plasmids,Polymerase Chain Reaction,Polymerase Chain Reaction: methods,Protein Biosynthesis,Restriction Mapping,Ribosomal,RNA,RNA Transfer Arg,RNA Transfer Phe,Salmonella,Salmonella: genetics,Transfer,Uracil} } % == BibTeX quality report for schwartzAnalysesFrameshiftingUUUpyrimidine1997: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{dirksAlgorithmComputingNucleic2004, title = {An Algorithm for Computing Nucleic Acid Base-Pairing Probabilities Including Pseudoknots}, author = {Dirks, Robert M and Pierce, Niles A}, year = 2004, month = jul, journal = {Journal of Computational Chemistry}, volume = {25}, number = {10}, pages = {1295–1304}, publisher = {Wiley Online Library}, issn = {0192-8651}, doi = {10.1002/jcc.20057}, url = {pm:15139042 http://onlinelibrary.wiley.com/doi/10.1002/jcc.20057/full}, abstract = {Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base-pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed by backtracking through the partition function algorithm, applying a particular transformation at each step. This transformation is applicable to any partition function algorithm that follows the same basic dynamic programming paradigm. Base-pairing probabilities are useful for analyzing the equilibrium ensemble properties of natural and engineered nucleic acids, as demonstrated for a human telomerase RNA and a synthetic DNA nanostructure.}, keywords = {0,ACID,ACIDS,Algorithms,Base Pairing,Base Sequence,chemistry,Computational Biology,Dna,DNA,dynamic programming,human,Humans,La,Models Molecular,Models-Molecular,ModelsMolecular,nosource,Nucleic Acid Conformation,Nucleic Acids,pseudoknot,pseudoknots,Rna,RNA,SECONDARY STRUCTURE,sequence,structure,support-non-u.s.gov’t,support-u.s.gov’t-non-p.h.s.,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,Telomerase,Thermodynamics,TRANSFORMATION} } % == BibTeX quality report for dirksAlgorithmComputingNucleic2004: % ? unused Journal abbr (“J.Comput.Chem.”)

@article{cochellaActiveRoleTRNA2005, title = {An Active Role for {{tRNA}} in Decoding beyond Codon: Anticodon Pairing}, author = {Cochella, Luisa and Green, Rachel}, year = 2005, month = may, journal = {Science (New York, N.Y.)}, volume = {308}, number = {5725}, pages = {1178–1180}, publisher = {American Association for the Advancement of Science}, issn = {1095-9203}, doi = {10.1126/science.1111408}, url = {http://www.sciencemag.org/content/308/5725/1178.short}, abstract = {During transfer RNA (tRNA) selection, a cognate codon:anticodon interaction triggers a series of events that ultimately results in the acceptance of that tRNA into the ribosome for peptide-bond formation. High-fidelity discrimination between the cognate tRNA and near- and noncognate ones depends both on their differential dissociation rates from the ribosome and on specific acceleration of forward rate constants by cognate species. Here we show that a mutant tRNA(Trp) carrying a single substitution in its D-arm achieves elevated levels of miscoding by accelerating these forward rate constants independent of codon:anticodon pairing in the decoding center. These data provide evidence for a direct role for tRNA in signaling its own acceptance during decoding and support its fundamental role during the evolution of protein synthesis.}, keywords = {Anticodon,Base Pairing,BIOLOGY,Codon,Codon Terminator,codon:anticodon,CONSTANTS,decoding,Dipeptides,Evolution,Genetic,genetics,GTP Phosphohydrolases,Guanosine Triphosphate,Hydrolysis,Kinetics,La,Mutation,nosource,Nucleic Acid Conformation,peptide bond formation,Peptide Elongation Factor Tu,PEPTIDE-BOND FORMATION,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,ribosome,Ribosomes,Rna,RNA Messenger,RNA Transfer Trp,SELECTION,SERIES,Support,TRANSFER-RNA,tRNA} } % == BibTeX quality report for cochellaActiveRoleTRNA2005: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”)

@article{storzAbundanceRNARegulators2005, title = {An Abundance of {{RNA}} Regulators}, author = {Storz, Gisela and Altuvia, Shoshy and Wassarman, Karen M}, year = 2005, journal = {Annual Review of Biochemistry}, volume = {74}, eprint = {15952886}, eprinttype = {pubmed}, pages = {199–217}, issn = {0066-4154}, doi = {10.1146/annurev.biochem.74.082803.133136}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15952886}, abstract = {The importance of small, noncoding RNAs that act as regulators of transcription, of RNA modification or stability, and of mRNA translation is becoming increasingly apparent. Here we discuss current knowledge of regulatory RNA function and review how the RNAs have been identified in a variety of organisms. Many of the regulatory RNAs act through base-pairing interactions with target RNAs. The base-pairing RNAs can be grouped into two general classes: those that are encoded on the opposite strand of their target RNAs such that they contain perfect complementarity with their targets, and those that are encoded at separate locations on the chromosome and have imperfect base-pairing potential with their targets. Other regulatory RNAs act by modifying protein activity, in some cases by mimicking the structures of other RNA or DNA molecules.}, pmid = {15952886}, keywords = {abstract the importance of,and of mrna translation,Animals,Antisense,antisense rna,Antisense: chemistry,Antisense: genetics,Antisense: metabolism,as regulators of,Base Pairing,Base Sequence,Gene Expression,Genetic,Humans,is becoming,Mice,microrna,Molecular Sequence Data,noncoding rna,noncoding rnas that act,nosource,Nucleic Acid Conformation,of rna modification or,Protein Biosynthesis,RNA,RNA Antisense,RNA Small Interfering,RNA Small Nucleolar,RNA Stability,RNA Untranslated,small,Small Interfering,Small Interfering: chemistry,Small Interfering: genetics,Small Interfering: metabolism,Small Nucleolar,Small Nucleolar: chemistry,Small Nucleolar: genetics,Small Nucleolar: metabolism,small rna,stability,transcription,Transcription,Transcription Genetic,Untranslated,Untranslated: chemistry,Untranslated: genetics,Untranslated: metabolism} } % == BibTeX quality report for storzAbundanceRNARegulators2005: % ? unused Journal abbr (“Annu. Rev. Biochem”)

@article{konnoMinimumStructureAminoglycosides2004, title = {A Minimum Structure of Aminoglycosides That Causes an Initiation Shift of Trans-Translation}, author = {Konno, Takayuki and Takahashi, Toshiharu and Kurita, Daisuke and Muto, Akira and Himeno, Hyouta}, year = 2004, journal = {Nucleic Acids Research}, volume = {32}, number = {14}, eprint = {15295039}, eprinttype = {pubmed}, pages = {4119–4126}, issn = {1362-4962}, doi = {10.1093/nar/gkh750}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15295039}, abstract = {Trans-translation is an unusual translation in which transfer-messenger RNA plays a dual function–as a tRNA and an mRNA–to relieve the stalled translation on the ribosome. It has been shown that paromomycin, a typical member of a 4,5-disubstituted class of aminoglycosides, causes a shift of the translation-resuming point on the tmRNA by -1 during trans-translation. To address the molecular basis of this novel effect, we examined the effects of various aminoglycosides that can bind around the A site of the small subunit of the ribosome on trans-translation in vitro. Tobramycin and gentamicin, belonging to the 4,6-disubstituted class of aminoglycosides having rings I and II similar to those in the 4,5-disubstituted class, possess similar effects. Neamine, which has only rings I and II, a common structure shared by 4,5- and 4,6-disubstituted classes of aminoglycosides, was sufficient to cause an initiation shift of trans-translation. In contrast, streptomycin or hygromycin B, lacking ring I, did not cause an initiation shift. The effect of each aminoglycoside on trans-translation coincides with that on conformational change in the A site of the small subunit of the ribosome revealed by recent structural studies: paromomycin, tobramycin and geneticin which is categorized into the gentamicin subclass, but not streptomycin and hygromycin B, flip out two conserved adenine bases at 1492 and 1493 from the A site helix. The pattern of initiation shifts by paromomycin fluctuates with variation of mutations introduced into a region upstream of the initiation point.}, pmid = {15295039}, keywords = {Aminoglycosides,Frameshifting Ribosomal,Framycetin,Hygromycin B,Mutation,nosource,Paromomycin,Protein Biosynthesis,RNA Bacterial,Streptomycin} } % == BibTeX quality report for konnoMinimumStructureAminoglycosides2004: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{namyMechanicalExplanationRNA2006, title = {A Mechanical Explanation of {{RNA}} Pseudoknot Function in Programmed Ribosomal Frameshifting}, author = {Namy, Olivier and Moran, Stephen J and Stuart, David I and Gilbert, Robert J C and Brierley, Ian}, year = 2006, month = may, journal = {Nature}, volume = {441}, number = {7090}, eprint = {16688178}, eprinttype = {pubmed}, pages = {244–247}, issn = {1476-4687}, doi = {10.1038/nature04735}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16688178}, abstract = {The triplet-based genetic code requires that translating ribosomes maintain the reading frame of a messenger RNA faithfully to ensure correct protein synthesis. However, in programmed -1 ribosomal frameshifting, a specific subversion of frame maintenance takes place, wherein the ribosome is forced to shift one nucleotide backwards into an overlapping reading frame and to translate an entirely new sequence of amino acids. This process is indispensable in the replication of numerous viral pathogens, including HIV and the coronavirus associated with severe acute respiratory syndrome, and is also exploited in the expression of several cellular genes. Frameshifting is promoted by an mRNA signal composed of two essential elements: a heptanucleotide ‘slippery’ sequence and an adjacent mRNA secondary structure, most often an mRNA pseudoknot. How these components operate together to manipulate the ribosome is unknown. Here we describe the observation of a ribosome-mRNA pseudoknot complex that is stalled in the process of -1 frameshifting. Cryoelectron microscopic imaging of purified mammalian 80S ribosomes from rabbit reticulocytes paused at a coronavirus pseudoknot reveals an intermediate of the frameshifting process. From this it can be seen how the pseudoknot interacts with the ribosome to block the mRNA entrance channel, compromising the translocation process and leading to a spring-like deformation of the P-site transfer RNA. In addition, we identify movements of the likely eukaryotic ribosomal helicase and confirm a direct interaction between the translocase eEF2 and the P-site tRNA. Together, the structural changes provide a mechanical explanation of how the pseudoknot manipulates the ribosome into a different reading frame.}, pmid = {16688178}, keywords = {ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,Animals,Biological,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,Coronavirus,Coronavirus: genetics,ELEMENTS,expression,FRAME,FRAME MAINTENANCE,Frameshift Mutation,Frameshift Mutation: genetics,Frameshifting,Frameshifting Ribosomal,gene,Genes,Genetic,Genetic Code,GENETIC-CODE,Helicase,HIV,IDENTIFY,INTERMEDIATE,La,Messenger,MESSENGER-RNA,Messenger: chemistry,Messenger: genetics,Messenger: metabolism,Models,Models Biological,Models Molecular,Molecular,Movement,mRNA,nosource,Nucleic Acid Conformation,P SITE,P-SITE,pathology,protein,protein synthesis,PROTEIN-SYNTHESIS,pseudoknot,Rabbits,READING FRAME,REPLICATION,REQUIRES,Reticulocytes,Ribosomal,ribosomal frameshifting,Ribosomal: physiology,ribosome,Ribosomes,Ribosomes: chemistry,Ribosomes: genetics,Ribosomes: metabolism,Rna,RNA,RNA Messenger,RNA PSEUDOKNOT,RNA Transfer,SECONDARY STRUCTURE,sequence,Severe Acute Respiratory Syndrome,SIGNAL,Structural,structure,Syndrome,Transfer,TRANSFER-RNA,Transfer: chemistry,Transfer: genetics,Transfer: metabolism,translocation,tRNA,virology} }

@article{kimAlternativeSplicingCurrent2008, title = {Alternative Splicing: Current Perspectives}, author = {Kim, Eddo and Goren, Amir and Ast, Gil}, year = 2008, month = jan, journal = {BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology}, volume = {30}, number = {1}, pages = {38–47}, issn = {0265-9247}, doi = {10.1002/bies.20692}, url = {http://onlinelibrary.wiley.com/doi/10.1002/bies.20692/full http://www.ncbi.nlm.nih.gov/pubmed/18081010}, abstract = {Alternative splicing is a well-characterized mechanism by which multiple transcripts are generated from a single mRNA precursor. By allowing production of several protein isoforms from one pre-mRNA, alternative splicing contributes to proteomic diversity. But what do we know about the origin of this mechanism? Do the same evolutionary forces apply to alternatively and constitutively splice exons? Do similar forces act on all types of alternative splicing? Are the products generated by alternative splicing functional? Why is “improper” recognition of exons and introns allowed by the splicing machinery? In this review, we summarize the current knowledge regarding these issues from an evolutionary perspective.}, pmid = {18081010}, keywords = {Alternative Splicing,Alternative Splicing: physiology,Animals,Biological,Cell Physiological Phenomena,Evolution,Evolution Molecular,Exons,Genetic,Humans,Introns,Models,Models Biological,Molecular,nosource,Open Reading Frames,Open Reading Frames: genetics,Selection,Selection Genetic} } % == BibTeX quality report for kimAlternativeSplicingCurrent2008: % ? unused Journal abbr (“Bioessays”)

@article{cuccureseAlternativeSplicingNonsensemediated2005, title = {Alternative Splicing and Nonsense-Mediated {{mRNA}} Decay Regulate Mammalian Ribosomal Gene Expression}, author = {Cuccurese, Monica and Russo, Giulia and Russo, Annapina and Pietropaolo, Concetta}, year = 2005, journal = {Nucleic Acids Research}, volume = {33}, number = {18}, pages = {5965–5977}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gki905}, url = {http://nar.oxfordjournals.org/content/33/18/5965.short}, abstract = {Messenger RNAs containing premature stop codons are generally targeted for degradation through nonsense-mediated mRNA decay (NMD). This mechanism degrades aberrant transcripts derived from mutant genes containing nonsense or frameshift mutations. Wild-type genes also give rise to transcripts targeted by NMD. For example, some wild-type genes give rise to alternatively spliced transcripts that are targeted for decay by NMD. In Caenorhabditis elegans, the ribosomal protein (rp) L12 gene generates a nonsense codon-bearing alternatively spliced transcript that is induced in an autoregulatory manner by the rpL12 protein. By pharmacologically blocking the NMD pathway, we identified alternatively spliced mRNA transcripts derived from the human rpL3 and rpL12 genes that are natural targets of NMD. The deduced protein sequence of these alternatively spliced transcripts suggests that they are unlikely to encode functional ribosomal proteins. Overexpression of rpL3 increased the level of the alternatively spliced rpL3 mRNA and decreased the normally expressed rpL3. This indicates that rpL3 regulates its own production by a negative feedback loop and suggests the possibility that NMD participates in this regulatory loop by degrading the non-functional alternatively spliced transcript.}, keywords = {Alternative Splicing,Animals,Base Sequence,Cattle,Cell Line Tumor,Codon Nonsense,Humans,Introns,Mice,Molecular Sequence Data,nosource,Rats,Ribosomal Proteins,RNA Messenger,RNA Stability,Transcription Genetic} } % == BibTeX quality report for cuccureseAlternativeSplicingNonsensemediated2005: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{kleeneAlternativePatternsTranscription2003, title = {Alternative Patterns of Transcription and Translation of the Ribosomal Protein {{L32 mRNA}} in Somatic and Spermatogenic Cells in Mice}, author = {Kleene, Kenneth C and Cataldo, Leah and Mastrangelo, Mary-Ann and Tagne, Jean-Bosco}, year = 2003, month = nov, journal = {Experimental Cell Research}, volume = {291}, number = {1}, pages = {101–110}, publisher = {Elsevier}, issn = {0014-4827}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014482703003392}, abstract = {The patterns of transcription and translation of the ribosomal protein L32 (Rpl32) mRNA differ greatly in adult testis and somatic tissues. Northern blots reveal that the levels of Rpl32 mRNA are four- to five-fold higher in prepubertal and adult testes, and purified pachytene spermatocytes and round spermatids than in a variety of nongrowing adult somatic tissues. 5’ RACE demonstrates that transcription in 8-day prepubertal testis, which lacks meiotic and haploid cells, strongly prefers the same start site in the 5’ terminal oligopyrimidine tract (5’ TOP) that is used is somatic cells. The 5’ TOP is a cis element that inhibits translation of many mRNAs in nongrowing somatic cells. Although the sizes of deadenylated Rpl32 mRNAs are indistinguishable in somatic and spermatogenic cells, transcription initiates at 11 sites over a 31-nt segment in adult testis and approximately 62% of Rpl32 mRNAs lack a 5’ TOP. In agreement with previous studies, low levels of cycloheximide increase the proportions and sizes of polysomes in absorbance profiles, and increase the proportions and sizes of polysomes translating four 5’ TOP mRNA species including the Rpl32 mRNA in 8-day seminiferous tubules. In contrast, cycloheximide has little or no effect on the absorbance profiles and distribution of Rpl32 mRNA and 5’ TOP mRNAs in adult seminiferous tubules. The failure of cycloheximide to increase the size of polysomes in adult seminiferous tubules implies a block in the pathway by which ribosomes are recruited onto translationally active mRNAs.}, keywords = {Aging,Animals,Codon Terminator,Cycloheximide,Gene Expression Regulation Developmental,Male,Mice,nosource,Polyribosomes,Protein Biosynthesis,Protein Synthesis Inhibitors,Ribosomal Proteins,RNA 5’ Terminal Oligopyrimidine Sequence,RNA Messenger,Spermatids,Spermatocytes,Spermatogenesis,Testis,Transcription Genetic} } % == BibTeX quality report for kleeneAlternativePatternsTranscription2003: % ? unused Journal abbr (“Exp. Cell Res”)

@article{mckeownAlternativeMRNASplicing1992, title = {Alternative {{mRNA}} Splicing}, author = {McKeown, M}, year = 1992, journal = {Annual Review of Cell Biology}, volume = {8}, eprint = {1335742}, eprinttype = {pubmed}, pages = {133–155}, issn = {0743-4634}, doi = {10.1146/annurev.cb.08.110192.001025}, url = {http://www.ncbi.nlm.nih.gov/pubmed/1335742}, pmid = {1335742}, keywords = {Amino Acid Sequence,Animals,Antigens CD45,Antigens Polyomavirus Transforming,Antigens- CD45,Antigens- Polyomavirus Transforming,Base Sequence,Calcitonin,Calcitonin Gene-Related Peptide,Consensus Sequence,DNA Transposable Elements,Drosophila melanogaster,Drosophila Proteins,Exons,Female,Genes ras,Genes Suppressor,Genes- ras,Genes- Suppressor,Humans,Male,Molecular Sequence Data,nosource,Ribonucleoproteins,RNA Messenger,RNA Precursors,RNA Splicing,RNA- Messenger,Sequence Alignment,Sequence Homology Amino Acid,Sequence Homology- Amino Acid,Sex Differentiation} } % == BibTeX quality report for mckeownAlternativeMRNASplicing1992: % ? unused Journal abbr (“Annu. Rev. Cell Biol”)

@article{cornishLoop2Cytidinestem2005, title = {A Loop 2 Cytidine-Stem 1 Minor Groove Interaction as a Positive Determinant for Pseudoknot-Stimulated -1 Ribosomal Frameshifting}, author = {Cornish, Peter V and Hennig, Mirko and Giedroc, David P}, year = 2005, month = sep, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {36}, eprint = {16123125}, eprinttype = {pubmed}, pages = {12694–12699}, issn = {0027-8424}, doi = {10.1073/pnas.0506166102}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16123125}, abstract = {The molecular determinants of stimulation of -1 programmed ribosomal frameshifting (-1 PRF) by RNA pseudoknots are poorly understood. Sugarcane yellow leaf virus (ScYLV) encodes a 28-nt mRNA pseudoknot that promotes -1 PRF between the P1 (protease) and P2 (polymerase) genes in plant luteoviruses. The solution structure of the ScYLV pseudoknot reveals a well ordered loop 2 (L2) that exhibits continuous stacking of A20 through C27 in the minor groove of the upper stem 1 (S1), with C25 flipped out of the triple-stranded stack. Five consecutive triple base pairs flank the helical junction where the 3’ nucleotide of L2, C27, adopts a cytidine 27 N3-cytidine 14 2’-OH hydrogen bonding interaction with the C14-G7 base pair. This interaction is isosteric with the adenosine N1-2’-OH interaction in the related mRNA from beet western yellows virus (BWYV); however, the ScYLV and BWYV mRNA structures differ in their detailed L2-S1 hydrogen bonding and L2 stacking interactions. Functional analyses of ScYLV/BWYV chimeric pseudoknots reveal that the ScYLV RNA stimulates a higher level of -1 PRF (15 +/- 2%) relative to the BWYV pseudoknot (6 +/- 1%), a difference traced largely to the identity of the 3’ nucleotide of L2 (C27 vs. A25 in BWYV). Strikingly, C27A ScYLV RNA is a poor frameshift stimulator (2.0%) and is destabilized by approximately 1.5 kcal x mol(-1) (pH 7.0, 37 degrees C) with respect to the wild-type pseudoknot. These studies establish that the precise network of weak interactions nearest the helical junction in structurally similar pseudoknots make an important contribution to setting the frameshift efficiency in mRNAs.}, pmid = {16123125}, keywords = {3,Adenosine,BASE,Base Sequence,BASE-PAIR,Cytidine,efficiency,ENCODES,frameshift,Frameshifting,Frameshifting Ribosomal,gene,Genes,Hydrogen,Hydrogen Bonding,L2,La,LOOP,Magnetic Resonance Spectroscopy,Molecular Sequence Data,mRNA,Mutation,nosource,Nucleic Acid Conformation,Plant Viruses,polymerase,pseudoknot,pseudoknots,ribosomal frameshifting,Rna,RNA Messenger,RNA PSEUDOKNOT,RNA Viral,structure,Thermodynamics,virus,WILD-TYPE} } % == BibTeX quality report for cornishLoop2Cytidinestem2005: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{domeierLinkRNAInterference2000, title = {A Link between {{RNA}} Interference and Nonsense-Mediated Decay in {{Caenorhabditis}} Elegans}, author = {Domeier, M E and Morse, D P and Knight, S W and Portereiko, M and Bass, B L and Mango, S E}, year = 2000, month = sep, journal = {Science (New York, N.Y.)}, volume = {289}, number = {5486}, eprint = {10988072}, eprinttype = {pubmed}, pages = {1928–1931}, issn = {0036-8075}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10988072}, abstract = {Double-stranded RNA (dsRNA) inhibits expression of homologous genes by a process involving messenger RNA degradation. To gain insight into the mechanism of degradation, we examined how RNA interference is affected by mutations in the smg genes, which are required for nonsense-mediated decay. For three of six smg genes tested, mutations resulted in animals that were initially silenced by dsRNA but then recovered; wild-type animals remained silenced. The levels of target messenger RNAs were restored during recovery, and RNA editing and degradation of the dsRNA were identical to those of the wild type. We suggest that persistence of RNA interference relies on a subset of smg genes.}, pmid = {10988072}, keywords = {Adenosine Deaminase,Alleles,Animals,Caenorhabditis elegans,Caenorhabditis elegans Proteins,Gene Silencing,Helminth Proteins,Mutation,Myosin Heavy Chains,Nonmuscle Myosin Type IIB,nosource,Phosphoproteins,Reverse Transcriptase Polymerase Chain Reaction,RNA Double-Stranded,RNA Helminth,RNA Stability,RNA- Double-Stranded,RNA- Helminth} } % == BibTeX quality report for domeierLinkRNAInterference2000: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”)

@article{marie-egyptienneHumanTetrahymenaPseudoknotChimeric2005, title = {A Human-{{Tetrahymena}} Pseudoknot Chimeric Telomerase {{RNA}} Reconstitutes a Nonprocessive Enzyme in Vitro That Is Defective in Telomere Elongation}, author = {{Marie-Egyptienne}, Delphine T and Cerone, Maria Antonietta and {Londo{~n}o-Vallejo}, J Arturo and Autexier, Chantal}, year = 2005, journal = {Nucleic Acids Research}, volume = {33}, number = {17}, eprint = {16192571}, eprinttype = {pubmed}, pages = {5446–5457}, issn = {1362-4962}, doi = {10.1093/nar/gki848}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16192571}, abstract = {The phylogenetically-derived secondary structures of telomerase RNAs (TR) from ciliates, yeasts and vertebrates are surprisingly conserved and contain a pseudoknot domain at a similar location downstream of the template. As the pseudoknot domains of Tetrahymena TR (tTR) and human TR (hTR) mediate certain similar functions, we hypothesized that they might be functionally interchangeable. We constructed a chimeric TR (htTR) by exchanging the hTR pseudoknot sequences for the tTR pseudoknot region. The chimeric RNA reconstituted human telomerase activity when coexpressed with hTERT in vitro, but exhibited defects in repeat addition processivity and levels of DNA synthesis compared to hTR. Activity was dependent on tTR sequences within the chimeric RNA. htTR interacted with hTERT in vitro and dimerized predominantly via a region of its hTR backbone, the J7b/8a loop. Introduction of htTR in telomerase-negative cells stably expressing hTERT did not reconstitute an active enzyme able to elongate telomeres. Thus, our results indicate that the chimeric RNA reconstituted a weakly active nonprocessive human telomerase enzyme in vitro that was defective in telomere elongation in vivo. This suggests that there may be species-specific requirements for pseudoknot functions.}, pmid = {16192571}, keywords = {Animals,Cell Line,Dimerization,DNA-Binding Proteins,Humans,Mutation,nosource,Nucleic Acid Conformation,Polymerase Chain Reaction,RNA,Telomerase,Telomere,Tetrahymena} } % == BibTeX quality report for marie-egyptienneHumanTetrahymenaPseudoknotChimeric2005: % ? unused Journal abbr (“Nucleic Acids Res”)

@article{huangHeuristicApproachDetecting2005, title = {A Heuristic Approach for Detecting {{RNA H-type}} Pseudoknots}, author = {Huang, Chun-Hsiang and Lu, Chin Lung and Chiu, Hsien-Tai}, year = 2005, month = sep, journal = {Bioinformatics (Oxford, England)}, volume = {21}, number = {17}, eprint = {15994188}, eprinttype = {pubmed}, pages = {3501–3508}, issn = {1367-4803}, doi = {10.1093/bioinformatics/bti568}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15994188}, abstract = {MOTIVATION: RNA H-type pseudoknots are ubiquitous pseudoknots that are found in almost all classes of RNA and thought to play very important roles in a variety of biological processes. Detection of these RNA H-type pseudoknots can improve our understanding of RNA structures and their associated functions. However, the currently existing programs for detecting such RNA H-type pseudoknots are still time consuming and sometimes even ineffective. Therefore, efficient and effective tools for detecting the RNA H-type pseudoknots are needed. RESULTS: In this paper, we have adopted a heuristic approach to develop a novel tool, called HPknotter, for efficiently and accurately detecting H-type pseudoknots in an RNA sequence. In addition, we have demonstrated the applicability and effectiveness of HPknotter by testing on some sequences with known H-type pseudoknots. Our approach can be easily extended and applied to other classes of more general pseudoknots. AVAILABILITY: The web server of our HPknotter is available for online analysis at http://bioalgorithm.life.nctu.edu.tw/HPKNOTTER/ CONTACT: cllu@mail.nctu.edu.tw, chiu@cc.nctu.edu.tw}, pmid = {15994188}, keywords = {Algorithms,Base Sequence,Computer Simulation,Models Chemical,Models Molecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Sequence Analysis RNA} } % == BibTeX quality report for huangHeuristicApproachDetecting2005: % ? unused Journal abbr (“Bioinformatics”)

@article{aresHandfulIntroncontainingGenes1999, title = {A Handful of Intron-Containing Genes Produces the Lion’s Share of Yeast {{mRNA}}}, author = {Ares, M and Grate, L and Pauling, M H}, year = 1999, month = sep, journal = {RNA (New York, N.Y.)}, volume = {5}, number = {9}, eprint = {10496214}, eprinttype = {pubmed}, pages = {1138–1139}, issn = {1355-8382}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10496214}, pmid = {10496214}, keywords = {Databases Factual,expression levels,Gene Expression Regulation Fungal,Genome Fungal,genomics,introns,Introns,Mutagenesis,nificance of introns in,nosource,Protein Biosynthesis,Ribosomes,RNA Messenger,RNA Small Nuclear,Saccharomyces cerevisiae,separate pieces of informa-,sig-,the budding yeast saccharomyces,the functional and evolutionary,tion that bear on,two studies have provided} } % == BibTeX quality report for aresHandfulIntroncontainingGenes1999: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{fialcowitzHairpinlikeStructureAUrich2005, title = {A Hairpin-like Structure within an {{AU-rich mRNA-destabilizing}} Element Regulates Trans-Factor Binding Selectivity and {{mRNA}} Decay Kinetics}, author = {Fialcowitz, Elizabeth J and Brewer, Brandy Y and Keenan, Bridget P and Wilson, Gerald M}, year = 2005, month = jun, journal = {The Journal of Biological Chemistry}, volume = {280}, number = {23}, eprint = {15809297}, eprinttype = {pubmed}, pages = {22406–22417}, issn = {0021-9258}, doi = {10.1074/jbc.M500618200}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15809297}, abstract = {In mammals, rapid mRNA turnover directed by AU-rich elements (AREs) is mediated by selective association of cellular ARE-binding proteins. These trans-acting factors display overlapping RNA substrate specificities and may act to either stabilize or destabilize targeted transcripts; however, the mechanistic features of AREs that promote preferential binding of one trans-factor over another are not well understood. Here, we describe a hairpin-like structure adopted by the ARE from tumor necrosis factor alpha (TNFalpha) mRNA that modulates its affinity for selected ARE-binding proteins. In particular, association of the mRNA-destabilizing factor p37(AUF1) was strongly inhibited by adoption of the higher order ARE structure, whereas binding of the inducible heat shock protein Hsp70 was less severely compromised. By contrast, association of the mRNA-stabilizing protein HuR was only minimally affected by changes in ARE folding. Consistent with the inverse relationship between p37(AUF1) binding affinity and the stability of ARE folding, mutations that stabilized the ARE hairpin also inhibited its ability to direct rapid mRNA turnover in transfected cells. Finally, phylogenetic analyses and structural modeling indicate that TNFalpha mRNA sequences flanking the ARE are highly conserved and may stabilize the hairpin fold in vivo. Taken together, these data suggest that local higher order structures involving AREs may function as potent regulators of mRNA turnover in mammalian cells by modulating trans-factor binding selectivity.}, pmid = {15809297}, keywords = {0,ASSOCIATION,AU-RICH ELEMENTS,Base Sequence,BINDING,Biochemistry,BIOLOGY,Cations,CELLS,chemistry,Complementary,Complementary: metabolism,Computational Biology,D,DECAY,Dna,DNA,DNA Complementary,DNA- Complementary,DNAComplementary,Dose-Response Relationship,Dose-Response Relationship Drug,Dose-Response Relationship- Drug,Dose-Response RelationshipDrug,Drug,ELEMENTS,Fluorescence,Fluorescence Resonance Energy Transfer,genetics,Glutathione,Glutathione Transferase,Glutathione Transferase: metabolism,Heat,heat shock proteins,HEAT-SHOCK,HEAT-SHOCK PROTEIN,HEAT-SHOCK PROTEINS,Heterogeneous-Nuclear Ribonucleoprotein D,Heterogeneous-Nuclear Ribonucleoprotein D: chemist,Heterogeneous-Nuclear Ribonucleoprotein D: genetic,Heterogeneous-Nuclear Ribonucleoprotein D: metabol,HSP70 Heat-Shock Proteins,HSP70 Heat-Shock Proteins: chemistry,Humans,IN-VIVO,Kinetics,La,Magnesium,Magnesium: chemistry,MAMMALIAN-CELLS,Mammals,Messenger,Messenger: metabolism,metabolism,Molecular Biology,Molecular Sequence Data,mRNA,mRNA decay,mRNA turnover,Mutagenesis,Mutagenesis Site-Directed,Mutagenesis- Site-Directed,MutagenesisSite-Directed,Mutation,MUTATIONS,nosource,Nucleic Acid,Nucleic Acid Conformation,Phylogeny,protein,Protein Binding,Protein Folding,Proteins,Recombinant Proteins,Recombinant Proteins: chemistry,RIBONUCLEOPROTEIN,Rna,RNA,RNA Messenger,RNA- Messenger,RNA: chemistry,RNAMessenger,sequence,Sequence Homology,Sequence Homology Nucleic Acid,Sequence Homology- Nucleic Acid,Sequence HomologyNucleic Acid,SEQUENCES,Site-Directed,SPECIFICITY,SPECTROSCOPY,stability,Structural,structure,Substrate Specificity,SUBSTRATE-SPECIFICITY,Support,Temperature,Time Factors,TRANS-ACTING FACTORS,TRANSCRIPT,Transfection,Tumor Necrosis Factor-alpha,Tumor Necrosis Factor-alpha: chemistry,turnover} } % == BibTeX quality report for fialcowitzHairpinlikeStructureAUrich2005: % ? unused Journal abbr (“J. Biol. Chem”)

@article{askreeGenomewideScreenSaccharomyces2004, title = {A Genome-Wide Screen for {{Saccharomyces}} Cerevisiae Deletion Mutants That Affect Telomere Length}, author = {Askree, Syed H and Yehuda, Tal and Smolikov, Sarit and Gurevich, Raya and Hawk, Joshua and Coker, Carrie and Krauskopf, Anat and Kupiec, Martin and McEachern, Michael J}, year = 2004, month = jun, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {23}, eprint = {15161972}, eprinttype = {pubmed}, pages = {8658–8663}, issn = {0027-8424}, doi = {10.1073/pnas.0401263101}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15161972}, abstract = {Telomeres are nucleoprotein structures present at the ends of eukaryotic chromosomes that play a central role in guarding the integrity of the genome by protecting chromosome ends from degradation and fusion. Length regulation is central to telomere function. To broaden our knowledge about the mechanisms that control telomere length, we have carried out a systematic examination of approximately 4,800 haploid deletion mutants of Saccharomyces cerevisiae for telomere-length alterations. By using this screen, we have identified {\(>\)}150 candidate genes not previously known to affect telomere length. In two-thirds of the identified mutants, short telomeres were observed; whereas in one-third, telomeres were lengthened. The genes identified are very diverse in their functions, but certain categories, including DNA and RNA metabolism, chromatin modification, and vacuolar traffic, are overrepresented. Our results greatly enlarge the number of known genes that affect telomere metabolism and will provide insights into how telomere function is linked to many other cellular processes.}, pmid = {15161972}, keywords = {0,Base Sequence,CEREVISIAE,Chromatin,Chromosomes,degradation,Dna,DNA Fungal,DNAFungal,gene,Gene Deletion,Genes,Genetic,genetics,Genome,Genome Fungal,GenomeFungal,La,MECHANISM,MECHANISMS,metabolism,modification,MUTANTS,Mutation,nosource,Phenotype,regulation,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Telomere} } % == BibTeX quality report for askreeGenomewideScreenSaccharomyces2004: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{willsFunctional1Ribosomal2006, title = {A Functional -1 Ribosomal Frameshift Signal in the Human Paraneoplastic {{Ma3}} Gene}, author = {Wills, Norma M and Moore, Barry and Hammer, Andrew and Gesteland, Raymond F and Atkins, John F}, year = 2006, month = mar, journal = {The Journal of Biological Chemistry}, volume = {281}, number = {11}, eprint = {16407312}, eprinttype = {pubmed}, pages = {7082–7088}, issn = {0021-9258}, doi = {10.1074/jbc.M511629200}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16407312}, abstract = {A bioinformatics approach to finding new cases of -1 frameshifting in the expression of human genes revealed a classical retrovirus-like heptanucleotide shift site followed by a potential structural stimulator in the paraneoplastic antigen Ma3 and Ma5 genes. Analysis of the sequence 3’ of the shift site demonstrated that an RNA pseudoknot in Ma3 is important for promoting efficient -1 frame-shifting. Ma3 is a member of a family of six genes in humans whose protein products contain homology to retroviral Gag proteins. The -1 frameshift site and pseudoknot structure are conserved in other mammals, but there are some sequence differences. Although the functions of the Ma genes are unknown, the serious neurological effects of ectopic expression in tumor cells indicate their importance in the brain.}, pmid = {16407312}, keywords = {3,analysis,ANTIGEN,Antigens,Antigens Neoplasm,Base Sequence,Binding Sites,Cell Line,Cell Line Tumor,CELLS,Cloning,Cloning Molecular,Computational Biology,expression,FAMILY,frameshift,Frameshift Mutation,Frameshifting,gag,Gag,gag: genetics,gene,Gene Products,Gene Products gag,Genes,Genetic,genetics,Glutathione Transferase,Glutathione Transferase: metabolism,human,HUMAN GENES,Humans,La,Luciferases,Luciferases: metabolism,Mammals,Messenger,Messenger: metabolism,Molecular,Molecular Sequence Data,Mutation,Neoplasm,Neoplasm: genetics,Neoplasm: metabolism,nosource,Nucleic Acid Conformation,Open Reading Frames,Phylogeny,protein,Protein,Proteins,pseudoknot,pseudoknot structure,Retroviridae,Retroviridae: genetics,Retroviridae: metabolism,RIBOSOMAL FRAMESHIFT,Rna,RNA,RNA Messenger,RNA PSEUDOKNOT,sequence,Sequence Analysis,Sequence Analysis Protein,SIGNAL,SITE,Structural,structure,Tumor} } % == BibTeX quality report for willsFunctional1Ribosomal2006: % ? unused Journal abbr (“J. Biol. Chem”)

@article{amraniFauxUTRPromotes2004, title = {A Faux 3’-{{UTR}} Promotes Aberrant Termination and Triggers Nonsense-Mediated {{mRNA}} Decay}, author = {Amrani, N. and Ganesan, R. and Kervestin, S. and Mangus, D.A. and Ghosh, S. and Jacobson, A.}, year = 2004, month = nov, journal = {Nature}, volume = {432}, number = {7013}, pages = {112–118}, doi = {10.1038/nature03060}, url = {PM:15525991}, abstract = {Nonsense-mediated messenger RNA decay (NMD) is triggered by premature translation termination, but the features distinguishing premature from normal termination are unknown. One model for NMD suggests that decay-inducing factors bound to mRNAs during early processing events are routinely removed by elongating ribosomes but remain associated with mRNAs when termination is premature, triggering rapid turnover. Recent experiments challenge this notion and suggest a model that posits that mRNA decay is activated by the intrinsically aberrant nature of premature termination. Here we use a primer extension inhibition (toeprinting) assay to delineate ribosome positioning and find that premature translation termination in yeast extracts is indeed aberrant. Ribosomes encountering premature UAA or UGA codons in the CAN1 mRNA fail to release and, instead, migrate to upstream AUGs. This anomaly depends on prior nonsense codon recognition and is eliminated in extracts derived from cells lacking the principal NMD factor, Upf1p, or by flanking the nonsense codon with a normal 3’-untranslated region (UTR). Tethered poly(A)-binding protein (Pab1p), used as a mimic of a normal 3’-UTR, recruits the termination factor Sup35p (eRF3) and stabilizes nonsense-containing mRNAs. These findings indicate that efficient termination and mRNA stability are dependent on a properly configured 3’-UTR}, keywords = {0,3,3’ UNTRANSLATED REGION,3’ Untranslated Regions,3’ Untranslated Regions: genetics,3’ Untranslated Regions: metabolism,3’ UTR,3’-UNTRANSLATED REGION,3’-UTR,AUG,Base Sequence,Binding Sites,Cell Extracts,CELLS,Codon,Codon Nonsense,CODON RECOGNITION,CodonNonsense,CODONS,Cycloheximide,Cycloheximide: pharmacology,DECAY,EXTRACTS,Fungal,Fungal: genetics,Fungal: metabolism,Genetic,genetics,INHIBITION,La,MESSENGER-RNA,metabolism,microbiology,MODEL,MOLECULAR-GENETICS,mRNA,mRNA decay,mRNA stability,NMD,Nonsense,NONSENSE,nonsense-mediated mRNA decay,Nonsense: genetics,nosource,Peptide Chain Termination,Peptide Chain Termination Translational,Peptide Chain TerminationTranslational,pharmacology,POLY(A)-BINDING PROTEIN,primer extension,protein,RECOGNITION,REGION,RELEASE,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,ribosome,Ribosomes,Rna,RNA,RNA Fungal,RNA Stability,RNAFungal,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,stability,termination,toeprinting,translation,TRANSLATION TERMINATION,Translational,Translational: genetics,turnover,UAA,Untranslated Regions,UPSTREAM,yeast} }

@article{shirleyFactorRequiredNonsensemediated1998, title = {A Factor Required for Nonsense-Mediated {{mRNA}} Decay in Yeast Is Exported from the Nucleus to the Cytoplasm by a Nuclear Export Signal Sequence}, author = {Shirley, R L and Lelivelt, M J and Schenkman, L R and Dahlseid, J N and Culbertson, M R}, year = 1998, month = nov, journal = {Journal of Cell Science}, volume = {111 ( Pt 21)}, eprint = {9763508}, eprinttype = {pubmed}, pages = {3129–3143}, issn = {0021-9533}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9763508}, abstract = {In Saccharomyces cerevisiae, Upf3p is required for nonsense-mediated mRNA decay (NMD). Although localized primarily in the cytoplasm, Upf3p contains three sequence elements that resemble nuclear localization signals (NLSs) and two sequence elements that resemble nuclear export signals (NESs). We found that a cytoplasmic reporter protein localized to the nucleus when fused to any one of the three NLS-like sequences of Upf3p. A nuclear reporter protein localized to the cytoplasm when fused to one of the NES-like sequences (NES-A). We present evidence that NES-A functions to signal the export of Upf3p from the nucleus. Combined alanine substitutions in the NES-A element caused a re-distribution of Upf3p to a subnuclear location identified as the nucleolus and conferred an Nmd- phenotype. Single mutations in NES-A failed to affect the distribution of Upf3p and were Nmd+. When an NES element from HIV-1 Rev was inserted near the C terminus of a mutant Upf3p containing multiple mutations in NES-A, the cytoplasmic distribution typical of wild-type Upf3p was restored but the cells remained phenotypically Nmd-. These results suggest that NES-A is a functional nuclear export signal. Combined mutations in NES-A may cause multiple defects in protein function leading to an Nmd- phenotype even when export is restored.}, pmid = {9763508}, keywords = {Amino Acid Substitution,Biological Transport,Cell Nucleus,Cytoplasm,Fungal Proteins,Gene Dosage,Genes Reporter,Genes rev,HIV-1,nosource,Point Mutation,Protein Sorting Signals,Recombinant Fusion Proteins,Regulatory Sequences Nucleic Acid,RNA Fungal,RNA Messenger,RNA Processing Post-Transcriptional,RNA-Binding Proteins,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins} } % == BibTeX quality report for shirleyFactorRequiredNonsensemediated1998: % ? unused Journal abbr (“J. Cell. Sci”)

@article{rivasDynamicProgrammingAlgorithm1999, title = {A Dynamic Programming Algorithm for {{RNA}} Structure Prediction Including Pseudoknots}, author = {Rivas, E and Eddy, S R}, year = 1999, month = feb, journal = {Journal of Molecular Biology}, volume = {285}, number = {5}, eprint = {9925784}, eprinttype = {pubmed}, pages = {2053–2068}, issn = {0022-2836}, doi = {10.1006/jmbi.1998.2436}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9925784}, abstract = {We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of O(N6) in time and O(N4) in storage. The description of the algorithm is complex, which led us to adopt a useful graphical representation (Feynman diagrams) borrowed from quantum field theory. We present an implementation of the algorithm that generates the optimal minimum energy structure for a single RNA sequence, using standard RNA folding thermodynamic parameters augmented by a few parameters describing the thermodynamic stability of pseudoknots. We demonstrate the properties of the algorithm by using it to predict structures for several small pseudoknotted and non-pseudoknotted RNAs. Although the time and memory demands of the algorithm are steep, we believe this is the first algorithm to be able to fold optimal (minimum energy) pseudoknotted RNAs with the accepted RNA thermodynamic model.}, pmid = {9925784}, keywords = {Algorithms,alignment,BINDING,COMPLEX,COMPLEXES,COMPUTER-SIMULATION,dynamic programming,GENETIC ALGORITHM,HIV Reverse Transcriptase,Models Genetic,MOSAIC-VIRUS RNA,nosource,Nucleic Acid Conformation,Nucleotides,pknots,pseudoknot,pseudoknots,Rna,RNA,RNA Transfer,RNA Viral,SECONDARY STRUCTURE,secondary structure prediction,sequence,SEQUENCES,stability,structure,thermodynamic stability,Thermodynamics} } % == BibTeX quality report for rivasDynamicProgrammingAlgorithm1999: % ? unused Journal abbr (“J. Mol. Biol”)

@article{grentzmannDualluciferaseReporterSystem1998, title = {A Dual-Luciferase Reporter System for Studying Recoding Signals}, author = {Grentzmann, G and Ingram, J A and Kelly, P J and Gesteland, R F and Atkins, J F}, year = 1998, month = apr, journal = {RNA (New York, N.Y.)}, volume = {4}, number = {4}, eprint = {9630253}, eprinttype = {pubmed}, pages = {479–486}, issn = {1355-8382}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9630253}, abstract = {A new reporter system has been developed for measuring translation coupling efficiency of recoding mechanisms such as frameshifting or readthrough. A recoding test sequence is cloned in between the renilla and firefly luciferase reporter genes and the two luciferase activities are subsequently measured in the same tube. The normalized ratio of the two activities is proportional to the efficiency with which the ribosome “reads” the recoding signal making the transition from one open reading frame to the next. The internal control from measuring both activities provides a convenient and reliable assay of efficiency. This is the first enzymatic dual reporter assay suitable for in vitro translation. Translation signals can be tested in vivo and in vitro from a single construct, which allows an intimate comparison between the two systems. The assay is applicable for high throughput screening procedures. The dual-luciferase reporter system has been applied to in vivo and in vitro recoding of HIV-1 gag-pol, MMTV gag-pro, MuLV gag-pol, and human antizyme.}, pmid = {9630253}, keywords = {Amino Acid Sequence,Animals,antizyme,assays,Base Sequence,Beetles,Cnidaria,frameshift,Frameshifting,Fusion Proteins gag-pol,Genes Reporter,Genetic Code,Genetic Vectors,HIV,HIV-1,Humans,In Vitro,IN-VITRO,IN-VIVO,luciferase,Luciferases,Mammary Tumor Virus Mouse,MMTV,Molecular Sequence Data,No DOI found,nosource,Ornithine Decarboxylase,Protein Biosynthesis,pseudoknot,Reading Frames,recoding,ribosomal frameshifting,SIGNAL,Simian virus 40,SYSTEM} } % == BibTeX quality report for grentzmannDualluciferaseReporterSystem1998: % ? Possibly abbreviated journal title RNA (New York, N.Y.) % ? unused Journal abbr (“RNA”)

@article{shyamsundarDNAMicroarraySurvey2005, title = {A {{DNA}} Microarray Survey of Gene Expression in Normal Human Tissues}, author = {Shyamsundar, Radha and Kim, Young H and Higgins, John P and Montgomery, Kelli and Jorden, Michelle and Sethuraman, Anand and {}{van de Rijn}, Matt and Botstein, David and Brown, Patrick O and Pollack, Jonathan R}, year = 2005, journal = {Genome Biology}, volume = {6}, number = {3}, eprint = {15774023}, eprinttype = {pubmed}, pages = {R22}, issn = {1465-6914}, doi = {10.1186/gb-2005-6-3-r22}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15774023}, abstract = {BACKGROUND: Numerous studies have used DNA microarrays to survey gene expression in cancer and other disease states. Comparatively little is known about the genes expressed across the gamut of normal human tissues. Systematic studies of global gene-expression patterns, by linking variation in the expression of specific genes to phenotypic variation in the cells or tissues in which they are expressed, provide clues to the molecular organization of diverse cells and to the potential roles of the genes. RESULTS: Here we describe a systematic survey of gene expression in 115 human tissue samples representing 35 different tissue types, using cDNA microarrays representing approximately 26,000 different human genes. Unsupervised hierarchical cluster analysis of the gene-expression patterns in these tissues identified clusters of genes with related biological functions and grouped the tissue specimens in a pattern that reflected their anatomic locations, cellular compositions or physiologic functions. In unsupervised and supervised analyses, tissue-specific patterns of gene expression were readily discernable. By comparative hybridization to normal genomic DNA, we were also able to estimate transcript abundances for expressed genes. CONCLUSIONS: Our dataset provides a baseline for comparison to diseased tissues, and will aid in the identification of tissue-specific functions. In addition, our analysis identifies potential molecular markers for detection of injury to specific organs and tissues, and provides a foundation for selection of potential targets for selective anticancer therapy.}, pmid = {15774023}, keywords = {Cluster Analysis,Gene Expression Profiling,Genomics,Humans,nosource,Oligonucleotide Array Sequence Analysis,RNA Messenger,Tissue Distribution} } % == BibTeX quality report for shyamsundarDNAMicroarraySurvey2005: % ? unused Journal abbr (“Genome Biol”)

@article{solingerActivesiteMutationsXrn1p1999, title = {Active-Site Mutations in the {{Xrn1p}} Exoribonuclease of {{Saccharomyces}} Cerevisiae Reveal a Specific Role in Meiosis}, author = {Solinger, J A and Pascolini, D and Heyer, W D}, year = 1999, month = sep, journal = {Molecular and Cellular Biology}, volume = {19}, number = {9}, eprint = {10454540}, eprinttype = {pubmed}, pages = {5930–5942}, issn = {0270-7306}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10454540}, abstract = {Xrn1p of Saccharomyces cerevisiae is a major cytoplasmic RNA turnover exonuclease which is evolutionarily conserved from yeasts to mammals. Deletion of the XRN1 gene causes pleiotropic phenotypes, which have been interpreted as indirect consequences of the RNA turnover defect. By sequence comparisons, we have identified three loosely defined, common 5’-3’ exonuclease motifs. The significance of motif II has been confirmed by mutant analysis with Xrn1p. The amino acid changes D206A and D208A abolish singly or in combination the exonuclease activity in vivo. These mutations show separation of function. They cause identical phenotypes to that of xrn1Delta in vegetative cells but do not exhibit the severe meiotic arrest and the spore lethality phenotype typical for the deletion. In addition, xrn1-D208A does not cause the severe reduction in meiotic popout recombination in a double mutant with dmc1 as does xrn1Delta. Biochemical analysis of the DNA binding, exonuclease, and homologous pairing activity of purified mutant enzyme demonstrated the specific loss of exonuclease activity. However, the mutant enzyme is competent to promote in vitro assembly of tubulin into microtubules. These results define a separable and specific function of Xrn1p in meiosis which appears unrelated to its RNA turnover function in vegetative cells.}, pmid = {10454540}, keywords = {Amino Acid Sequence,Animals,Base Sequence,Catalytic Domain,Conserved Sequence,DNA Fungal,DNA Primers,DNA- Fungal,Exoribonucleases,Meiosis,Microtubules,Molecular Sequence Data,Mutation,nosource,Phenotype,RNA Fungal,RNA Messenger,RNA- Fungal,RNA- Messenger,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Sequence Homology Amino Acid,Sequence Homology- Amino Acid,Substrate Specificity} } % == BibTeX quality report for solingerActivesiteMutationsXrn1p1999: % ? unused Journal abbr (“Mol. Cell. Biol”)

@article{freyhultComparisonRNAFolding2005, title = {A Comparison of {{RNA}} Folding Measures}, author = {Freyhult, Eva and Gardner, Paul P and Moulton, Vincent}, year = 2005, journal = {BMC Bioinformatics}, volume = {6}, eprint = {16202126}, eprinttype = {pubmed}, pages = {241}, issn = {1471-2105}, doi = {10.1186/1471-2105-6-241}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16202126}, abstract = {BACKGROUND: In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs) fold in a more well-defined manner than random sequences. In this paper, we investigate several existing measures for how well an RNA sequence folds, and compare the behaviour of these measures over a large range of Rfam ncRNA families. Such measures can be useful in, for example, identifying novel ncRNAs, and indicating the presence of alternate RNA foldings. RESULTS: Our analysis shows that ncRNAs, but not mRNAs, in general have lower minimal free energy (MFE) than random sequences with the same dinucleotide frequency. Moreover, even when the MFE is significant, many ncRNAs appear to not have a unique fold, but rather several alternative folds, at least when folded in silico. Furthermore, we find that the six investigated measures are correlated to varying degrees. CONCLUSION: Due to the correlations between the different measures we find that it is sufficient to use only two of them in RNA folding studies, one to test if the sequence in question has lower energy than a random sequence with the same dinucleotide frequency (the Z-score) and the other to see if the sequence has a unique fold (the average base-pair distance, D).}, pmid = {16202126}, keywords = {0,analysis,BASE-PAIR,chemistry,Comparative Study,D,FAMILY,IN-SILICO,La,Models Molecular,Models- Molecular,ModelsMolecular,mRNA,Multiple DOI,nonfile,nosource,Protein Folding,Research SupportNon-U.S.Gov’t,Rna,RNA folding,RNA Untranslated,RNA- Untranslated,RNAUntranslated,sequence,Sequence Alignment,SEQUENCES} }

@article{yarianAccurateTranslationGenetic2002, title = {Accurate Translation of the Genetic Code Depends on {{tRNA}} Modified Nucleosides}, author = {Yarian, Connie and Townsend, Hannah and Czestkowski, Wojciech and Sochacka, Elzbieta and Malkiewicz, Andrzej J and Guenther, Richard and Miskiewicz, Agnieszka and Agris, Paul F}, year = 2002, month = may, journal = {The Journal of Biological Chemistry}, volume = {277}, number = {19}, eprint = {11861649}, eprinttype = {pubmed}, pages = {16391–16395}, issn = {0021-9258}, doi = {10.1074/jbc.M200253200}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11861649}, abstract = {Transfer RNA molecules translate the genetic code by recognizing cognate mRNA codons during protein synthesis. The anticodon wobble at position 34 and the nucleotide immediately 3’ to the anticodon triplet at position 37 display a large diversity of modified nucleosides in the tRNAs of all organisms. We show that tRNA species translating 2-fold degenerate codons require a modified U(34) to enable recognition of their cognate codons ending in A or G but restrict reading of noncognate or near-cognate codons ending in U and C that specify a different amino acid. In particular, the nucleoside modifications 2-thiouridine at position 34 (s(2)U(34)), 5-methylaminomethyluridine at position 34 (mnm(5)U(34)), and 6-threonylcarbamoyladenosine at position 37 (t(6)A(37)) were essential for Watson-Crick (AAA) and wobble (AAG) cognate codon recognition by tRNA(UUU)(Lys) at the ribosomal aminoacyl and peptidyl sites but did not enable the recognition of the asparagine codons (AAU and AAC). We conclude that modified nucleosides evolved to modulate an anticodon domain structure necessary for many tRNA species to accurately translate the genetic code.}, pmid = {11861649}, keywords = {Adenosine,Asparagine,Base Pairing,Base Sequence,Codon,Genetic Code,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleosides,Protein Biosynthesis,Protein Structure Tertiary,Protein Structure- Tertiary,Ribosomes,RNA,RNA Messenger,RNA Ribosomal 16S,RNA Transfer,RNA- Messenger,RNA- Ribosomal- 16S,RNA- Transfer,Thiouridine,Uridine} } % == BibTeX quality report for yarianAccurateTranslationGenetic2002: % ? unused Journal abbr (“J. Biol. Chem”)

@article{amraniAberrantTerminationTriggers2006, title = {Aberrant Termination Triggers Nonsense-Mediated {{mRNA}} Decay}, author = {Amrani, N. and Dong, S. and He, F. and Ganesan, R. and Ghosh, S. and Kervestin, S. and Li, C. and Mangus, D. A. A. and Spatrick, P. and Jacobson, A.}, year = 2006, month = feb, journal = {Biochemical Society Transactions}, volume = {34}, number = {1}, pages = {39}, publisher = {London: The Society, 1973-}, issn = {0300-5127}, doi = {10.1042/BST20060039}, url = {http://www.biochemsoctrans.cn/bst/034/0039/0340039.pdf}, abstract = {NMD (nonsense-mediated mRNA decay) is a cellular quality-control mechanism in which an otherwise stable mRNA is destabilized by the presence of a premature termination codon. We have defined the set of endogenous NMD substrates, demonstrated that they are available for NMD at every round of translation, and showed that premature termination and normal termination are not equivalent biochemical events. Premature termination is aberrant, and its NMD-stimulating defects can be reversed by the presence of tethered poly(A)-binding protein (Pab1p) or tethered eRF3 (eukaryotic release factor 3) (Sup35p). Thus NMD appears to be triggered by a ribosome’s failure to terminate adjacent to a properly configured 3’-UTR (untranslated region), an event that may promote binding of the UPF/NMD factors to stimulate mRNA decapping.}, keywords = {3’ Untranslated Regions,Codon Nonsense,Codon- Nonsense,nosource,Peptide Termination Factors,Poly(A)-Binding Protein I,Prions,Protein Biosynthesis,RNA Messenger,RNA- Messenger,Saccharomyces cerevisiae Proteins} }

@article{weil3UTRSequence2006, title = {A 3{\(\prime\)} {{UTR}} Sequence Stabilizes Termination Codons in the Unspliced {{RNA}} of {{Rous}} Sarcoma Virus}, author = {Weil, J. E. E. and Beemon, K. L. L.}, year = 2006, month = jan, journal = {Rna}, volume = {12}, number = {1}, pages = {102}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, doi = {10.1261/rna.2129806}, url = {http://rnajournal.cshlp.org/content/12/1/102.short}, abstract = {Eukaryotic cells target mRNAs to the nonsense-mediated mRNA decay (NMD) pathway when translation terminates within the coding region. In mammalian cells, this is presumably due to a downstream signal deposited during pre-mRNA splicing. In contrast, unspliced retroviral RNA undergoes NMD in chicken cells when premature termination codons (PTCs) are present in the gag gene. Surprisingly, deletion of a 401-nt 3’ UTR sequence immediately downstream of the normal gag termination codon caused this termination event to be recognized as premature. We termed this 3’ UTR region the Rous sarcoma virus (RSV) stability element (RSE). The RSE also stabilized the viral RNA when placed immediately downstream of a PTC in the gag gene. Deletion analysis of the RSE indicated a smaller functional element. We conclude that this 3’ UTR sequence stabilizes termination codons in the RSV RNA, and termination codons not associated with such an RSE sequence undergo NMD.}, keywords = {0,3,3’ Untranslated Regions,analysis,Animals,Avian Sarcoma Viruses,BIOLOGY,CELLS,Cells Cultured,Cells- Cultured,CellsCultured,Chick Embryo,CODING REGION,Codon,Codon Nonsense,Codon Terminator,Codon- Nonsense,Codon- Terminator,CodonNonsense,CODONS,CodonTerminator,DECAY,DOWNSTREAM,Eukaryotic Cells,Gag,gene,Genes Viral,Genes- Viral,GenesViral,genetics,IMMEDIATELY DOWNSTREAM,La,MAMMALIAN-CELLS,metabolism,mRNA,mRNA decay,NMD,NONSENSE,nonsense-mediated mRNA decay,nosource,PATHWAY,PREMATURE TERMINATION CODON,Protein Biosynthesis,REGION,Research SupportN.I.H.Extramural,Research SupportNon-U.S.Gov’t,RETROVIRAL RNA,Rna,RNA,RNA Stability,Sarcoma VirusesAvian,sequence,SIGNAL,splicing,stability,TARGET,termination,TERMINATION CODON,TERMINATION-CODON,Transfection,translation,Untranslated Regions,VIRAL-RNA,virus} }

@article{dinman1RibosomalFrameshift1991, title = {A -1 Ribosomal Frameshift in a Double-Stranded {{RNA}} Virus of Yeast Forms a Gag-Pol Fusion Protein}, author = {Dinman, J D and Icho, T and Wickner, R B}, year = 1991, month = jan, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {88}, number = {1}, pages = {174–178}, publisher = {National Acad Sciences}, issn = {0027-8424}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=50772&tool=pmcentrez&rendertype=abstract http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:A+-1+ribosomal+frameshift+in+a+double-stranded+RNA+virus+of+yeast+forms+a+gag-pol+fusion+protein#0 http://www.pnas.org/content/88/1/174.short}, abstract = {The L-A double-stranded RNA (dsRNA) virus of Saccharomyces cerevisiae has two open reading frames (ORFs). ORF1 encodes the 80-kDa major coat protein (gag). ORF2, which is expressed only as a 180-kDa fusion protein with ORF1, encodes a single-stranded RNA-binding domain and has the consensus sequence for RNA-dependent RNA polymerases of (+)-strand and double-stranded RNA viruses (pol). We show that the 180-kDa protein is formed by -1 ribosomal frame-shifting by a mechanism indistinguishable from that of retro-viruses. Analysis of the “slippery site” suggests that a low probability of unpairing of the aminoacyl-tRNA from the 0-frame codon at the ribosomal A site reduces the efficiency of frameshifting more than the reluctance of a given tRNA to have its wobble base mispaired. Frameshifting of L-A requires a pseudoknot structure just downstream of the shift site. The efficiency of the L-A frameshift site is 1.8%, similar to the observed molar ratio in viral particles of the 180-kDa fusion protein to the major coat protein.}, pmid = {1986362}, keywords = {Amino Acid Sequence,Base Sequence,Double-Stranded,Double-Stranded: genetics,frameshift,Frameshift Mutation,Frameshifting,Fusion Proteins,Fusion Proteins gag-pol,gag-pol,Gag-pol,gag-pol: genetics,Genetic,Genetic Vectors,L-A,La,Molecular Sequence Data,Mutagenesis,Mutagenesis Site-Directed,nosource,Oligonucleotide Probes,Open Reading Frames,Plasmids,protein,Protein Biosynthesis,pseudoknot,RIBOSOMAL FRAMESHIFT,Ribosomes,Ribosomes: metabolism,Rna,RNA,RNA Double-Stranded,RNA Viruses,RNA Viruses: genetics,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Site-Directed,slippery site,Transcription,Transcription Genetic,virus} } % == BibTeX quality report for dinman1RibosomalFrameshift1991: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{barry1RibosomalFrameshift2002, title = {A -1 Ribosomal Frameshift Element That Requires Base Pairing across Four Kilobases Suggests a Mechanism of Regulating Ribosome and Replicase Traffic on a Viral {{RNA}}}, author = {Barry, Jennifer K and Miller, W Allen}, year = 2002, month = aug, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {17}, pages = {11133–11138}, issn = {0027-8424}, doi = {10.1073/pnas.162223099}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:A+-1+ribosomal+frameshift+element+that+requires+base+pairing+across+four+kilobases+suggests+a+mechanism+of+regulating+ribosome+and+replicase+traffic+on+a+viral+RNA#0}, abstract = {Programmed -1 ribosomal frameshifting is necessary for translation of the polymerase genes of many viruses. In addition to the consensus elements in the mRNA around the frameshift site, we found previously that frameshifting on Barley yellow dwarf virus RNA requires viral sequence located four kilobases downstream. By using dual luciferase reporter constructs, we now show that a predicted loop in the far downstream frameshift element must base pair to a bulge in a bulged stem loop adjacent to the frameshift site. Introduction of either two or six base mismatches in either the bulge or the far downstream loop abolished frameshifting, whereas mutations in both sites that restored base pairing reestablished frameshifting. Likewise, disruption of this base pairing abolished viral RNA replication in plant cells, and restoration of base pairing completely reestablished virus replication. We propose a model in which Barley yellow dwarf virus uses this and another long-distance base-pairing event required for cap-independent translation to allow the replicase copying from the 3’ end to shut off translation of upstream ORFs and free the RNA of ribosomes to allow unimpeded replication. This would be a means of solving the “problem,” common to positive strand RNA viruses, of competition between ribosomes and replicase for the same RNA template.}, pmid = {12149516}, keywords = {0,3’ Untranslated Regions,Animals,Base Pair Mismatch,Base Pairing,Base Sequence,Cloning Molecular,frameshift,Frameshifting,Frameshifting Ribosomal,gene,Genes,La,luciferase,Luciferases,Luteovirus,Molecular Sequence Data,mRNA,Mutagenesis,Mutation,nosource,Nucleic Acid Conformation,Open Reading Frames,pathology,polymerase,Protein Biosynthesis,Recombinant Proteins,ribosomal frameshifting,ribosome,Ribosomes,Rna,RNA Replicase,RNA Viral,RNA Viruses,Scyphozoa,sequence,translation,virus,Virus Replication} } % == BibTeX quality report for barry1RibosomalFrameshift2002: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”)

@article{UNAIDSWHOGlobal2001, title = {{{UNAIDS}}/{{WHO}} Global {{AIDS}} Statistics}, year = 2001, month = jun, journal = {AIDS Care}, volume = {13}, number = {3}, pages = {408}, keywords = {Acquired Immunodeficiency Syndrome,epidemiology,human,nosource,Statistics,World Health,World Health Organization} } % == BibTeX quality report for UNAIDSWHOGlobal2001: % Missing required field ‘author’

@book{UNAIDSUnitedNations2007a, title = {{{UNAIDS}}: {{United Nations}} 2006 {{Report}} on the Global {{AIDS}} Epidemic}, year = 2007, volume = {10}, publisher = {UNAIDS}, address = {Geneva, Switzerland}, url = {⬚http://data.unaids.org/pub/GlobalReport/2006/2006_GR-ExecutiveSummary_en.pdf ⬚}, isbn = {92 9 173511 6}, keywords = {AIDS,nosource} } % == BibTeX quality report for UNAIDSUnitedNations2007a: % Missing required field ‘author/editor’

@article{abbottTranslationFactorsSickness2004, title = {Translation Factors: In Sickness and in Health}, author = {Abbott, C. M. and Proud, C. G.}, year = 2004, month = jan, journal = {Trends in biochemical sciences}, volume = {29}, number = {1}, pages = {25–31}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000403002998 http://www.sciencedirect.com/science/article/pii/S0968000403002998}, abstract = {It has been known for many years that aberrant levels of the factors involved in translation of mRNA can contribute to disease, most notably cancer. However, despite the wealth of information gathered about initiation and elongation factors from biochemical studies in mammalian cells, and from mutation analysis in lower organisms, little was known until recently about the effects that mutations in these factors could have on cellular function in higher organisms. In the past few years, this balance has started to be redressed, and we are at a fascinating stage in the molecular pathology of translation factors. It has been discovered recently that mutations in subunits of eukaryotic initiation factor 2B (eIF2B) underlie the neurodegenerative disease termed ‘vanishing white matter’}, keywords = {0,Amino Acid Sequence,analysis,Animals,cancer,CELLS,disease,elongation,elongation factors,ELONGATION-FACTORS,Eukaryotic Initiation Factors,Genetic,Genetic DiseasesInborn,genetics,human,initiation,INITIATION-FACTOR,La,MAMMALIAN-CELLS,Molecular Sequence Data,mRNA,Mutation,MUTATIONS,nosource,pathology,Review,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,translation,TranslationGenetic} }

@article{abdelmajidReleaseMetaphaseBlock1993, title = {Release from the Metaphase {{I}} Block in Invertebrate Oocytes: Possible Involvement of {{Ca2}}+/Calmodulin Kinase {{III}}.}, author = {Abdelmajid, H. and {Leclerc-David}, C. and Moreau, M. and Gurrier, P. and Ryazanov, A.G.}, year = 1993, journal = {Int.J.Dev.Biol.}, volume = {37}, pages = {279–290}, keywords = {Ca2+,cyclins,degradation,EF-2,EF-2 kinase,No DOI found,nosource,protein,protein synthesis} } % == BibTeX quality report for abdelmajidReleaseMetaphaseBlock1993: % ? Possibly abbreviated journal title Int.J.Dev.Biol.

@article{abouEfficientlyExpressed8S1995, title = {An Efficiently Expressed 5.{{8S rRNA}} ‘tag’ for in Vivo Studies of Yeast {{rRNA}} Biosynthesis and Function}, author = {Abou, Elela S. and Good, L. and Nazar, R. N.}, year = 1995, month = jun, journal = {Biochimica et biophysica acta}, volume = {1262}, number = {2-3}, pages = {164–167}, abstract = {Inefficient expression or detrimental markers have limited mutational analyses of eukaryotic 5.8S rRNA and the associated rDNA transcribed spacers. We have found a neutral, 4-base insertion mutation that effectively tags the 5.8S rRNA for improved studies of rRNA expression, processing and function. Cells expressing the tagged rDNA plasmid contain 50-60% mutant 5.8S rRNA, but show a normal growth rate and polysomal profile and a constant distribution of tagged 5.8S rRNA. The high level of expression also demonstrates that plasmid-associated rDNA is preferentially transcribed over chromosomal copies}, keywords = {5S rRNA,95322459,analysis,Base Sequence,biosynthesis,DNARibosomal,expression,Genetic,genetics,metabolism,Molecular Sequence Data,Mutation,nosource,RNARibosomal,rRNA,Saccharomyces cerevisiae,Sequence Tagged Sites,supportnon-u.s.gov’t,yeast} }

@article{abouRole8SRRNA1997, title = {Role of the 5.{{8S rRNA}} in Ribosome Translocation}, author = {Abou, Elela S. and Nazar, R.N.}, year = 1997, month = may, journal = {Nucleic Acids Res.}, volume = {25}, number = {9}, pages = {1788–1794}, abstract = {Studies on the inhibition of protein synthesis by specific anti 5.8S rRNA oligonucleotides have suggested that this RNA plays an important role in eukaryotic ribosome function. Mutations in the 5. 8S rRNA can inhibit cell growth and compromise protein synthesis in vitro . Polyribosomes from cells expressing these mutant 5.8S rRNAs are elevated in size and ribosome-associated tRNA. Cell free extracts from these cells also are more sensitive to antibiotics which act on the 60S ribosomal subunit by inhibiting elongation. The extracts are especially sensitive to cycloheximide and diphtheria toxin which act specifically to inhibit translocation. Studies of ribosomal proteins show no reproducible changes in the core proteins, but reveal reduced levels of elongation factors 1 and 2 only in ribosomes which contain large amounts of mutant 5.8S rRNA. Polyribosomes from cells which are severely inhibited, but contain little mutant 5.8S rRNA, do not show the same reductions in the elongation factors, an observation which underlines the specific nature of the change. Taken together the results demonstrate a defined and critical function for the 5.8S rRNA, suggesting that this RNA plays a role in ribosome translocation}, keywords = {97263805,antibiotics,Biological Transport,chemistry,Cycloheximide,Diphtheria Toxin,elongation,Genetic,genetics,metabolism,Mutagenesis,Mutation,No DOI found,nosource,Oligonucleotides,Peptide Elongation Factors,protein,protein synthesis,Proteins,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNARibosomal5.8S,rRNA,supportnon-u.s.gov’t,toxin,translocation,tRNA} } % == BibTeX quality report for abouRole8SRRNA1997: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{abovichTwoGenesRibosomal1984, title = {Two Genes for Ribosomal Protein 51 of {{Saccharomyces}} Cerevisiae Complement and Contribute to the Ribosomes}, author = {Abovich, N. and Rosbash, M.}, year = 1984, journal = {Mol.Cell Biol.}, volume = {4}, number = {9}, pages = {1871–1879}, abstract = {We cloned and sequenced the second gene coding for yeast ribosomal protein 51 (RP51B). When the DNA sequence of this gene was compared with the DNA sequence of RP51A (J.L. Teem and M. Rosbash, Proc. Natl. Acad. Sci. U.S.A. 80:4403–4407, 1983), the following conclusions emerged: both genes code for a protein of 135 amino acids; both open reading frames are interrupted by a single intron which occurs directly after the initiating methionine; the open reading frames are 96% homologous and code for the same protein with the exception of the carboxy-terminal amino acid; DNA sequence homology outside of the coding region is extremely limited. The cloned genes, in combination with the one-step gene disruption techniques of Rothstein (R. J. Rothstein, Methods Enzymol. 101:202-211, 1983), were used to generate haploid strains containing mutations in the RP51A or RP51B genes or in both. Strains missing a normal RP51A gene grew poorly (180-min generation time versus 130 min for the wild type), whereas strains carrying a mutant RP51B were relatively normal. Strains carrying mutations in the two genes grew extremely poorly (6 to 9 h), which led us to conclude that RP51A and RP51B were both expressed. The results of Northern blot and primer extension experiments indicate that strains with a wild-type copy of the RP51B gene and a mutant (or deleted) RP51A gene grow slowly because of an insufficient amount of RP51 mRNA. The growth defect was completely rescued with additional copies of RP51B. The data suggest that RP51A contributes more RP51 mRNA (and more RP51 protein) than does RP51B and that intergenic dosage compensation, sufficient to rescue the growth defect of strains missing a wild-type RP51A gene, does not take place}, keywords = {85036340,Amino Acids,Base Sequence,CloningMolecular,Comparative Study,Dna,DNA Restriction Enzymes,Escherichia coli,Genes,GenesFungal,GenesStructural,genetics,Genotype,metabolism,Methods,mRNA,Multiple DOI,Mutation,nonfile,nosource,Open Reading Frames,Plasmids,primer extension,protein,Ribosomal Proteins,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,sequence,Species Specificity,supportu.s.gov’tp.h.s.,techniques,yeast} } % == BibTeX quality report for abovichTwoGenesRibosomal1984: % ? Possibly abbreviated journal title Mol.Cell Biol.

@article{abovichEffectRP51Gene1985, title = {Effect of {{RP51}} Gene Dosage Alterations on Ribosome Synthesis in {{Saccharomyces}} Cerevisiae}, author = {Abovich, N. and Gritz, L. and Tung, L. and Rosbash, M.}, year = 1985, month = dec, journal = {Mol.Cell Biol.}, volume = {5}, number = {12}, pages = {3429–3435}, abstract = {The Saccharomyces cerevisiae ribosomal protein rp51 is encoded by two interchangeable genes, RP51A and RP51B. We altered the RP51 gene dose by creating deletions of the RP51A or RP51B genes or both. Deletions of both genes led to spore inviability, indicating that rp51 is an essential ribosomal protein. From single deletion studies in haploid cells, we concluded that there was no intergenic dosage compensation at the level of mRNA abundance or mRNA utilization (translational efficiency), although phenotypic analysis had previously indicated a small compensation effect on growth rate. Similarly, deletions in diploid strains indicated that no strong mechanisms exist for intragenic dosage compensation; in all cases, a decreased dose of RP51 genes was characterized by a slow growth phenotype. A decreased dose of RP51 genes also led to insufficient amounts of 40S ribosomal subunits, as evidenced by a dramatic accumulation of excess 60S ribosomal subunits. We conclude that inhibition of 40S synthesis had little or no effect on the synthesis of the 60S subunit components. Addition of extra copies of rp51 genes led to extra rp51 protein synthesis. The additional rp51 protein was rapidly degraded. We propose that rp51 and perhaps many ribosomal proteins are normally oversynthesized, but the unassembled excess is degraded, and that the apparent compensation seen in haploids, i.e., the fact that the growth rate of mutant strains is less depressed than the actual reduction in mRNA, is a consequence of this excess which is spared from proteolysis under this circumstance}, keywords = {60S subunit,86310821,analysis,biosynthesis,Diploidy,efficiency,Gene Amplification,Genes,GenesFungal,genetics,Haploidy,metabolism,mRNA,Multiple DOI,Mutation,nonfile,nosource,Phenotype,protein,Protein ProcessingPost-Translational,protein synthesis,Proteins,Ribosomal Proteins,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for abovichEffectRP51Gene1985: % ? Possibly abbreviated journal title Mol.Cell Biol.

@article{abrahamEffectProteinSynthesis1983, title = {Effect of Protein Synthesis Inhibitors on the Fidelity of Translation in Eukaryotic Systems}, author = {Abraham, A. K. and Pihl, A.}, year = 1983, month = nov, journal = {Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression}, volume = {741}, number = {2}, pages = {197–203}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0167478183900593}, abstract = {Factors influencing the accuracy of poly(U)-directed poly(Phe) synthesis in a wheat germ and in a reticulocyte system were studied. Addition of preformed phenylalanyl-tRNA, as well as increasing the ratio of poly(U) to ribosomes, significantly enhanced the poly(Phe) synthesis and concurrently reduced the misincorporation of leucine. The protein synthesis inhibitors cycloheximide, abrin and ricin had little or no effect on the misreading when the system was supplemented with 100 microM phenylalanyl-tRNA, but they reduced the relatively high error rate observed when the poly(U) system was not supplemented with the cognate substrate. Raising the incubation temperature enhanced the accuracy to the same extent whether or not ricin was present i.e., at widely different rates of elongation. The results show that the translational accuracy is not linked to the elongation rate as such. Translational inhibitors affect the fidelity by influencing the kinetics of the system. In systems containing limiting concentrations of cognate substrate, translational inhibitors will cause an increase in the limiting aminoacyl-tRNA species and thereby increase fidelity}, keywords = {Abrin,accuracy,animal,Cell-Free System,Cycloheximide,drug effects,elongation,Fidelity,genetics,Kinetics,Leucine,nosource,Peptide Chain Elongation,pharmacology,Plant Proteins,Poly U,protein,protein synthesis,Protein Synthesis Inhibitors,Rabbits,Reticulocytes,ribosome,Ribosomes,Ricin,supportnon-u.s.gov’t,Temperature,translation,TranslationGenetic,Wheat} }

@article{ackerReconstitutionYeastTranslation2007, title = {Reconstitution of Yeast Translation Initiation}, author = {Acker, M. G. and Kolitz, S. E. and Mitchell, S. F. and Nanda, J. S. and Lorsch, J. R.}, year = 2007, journal = {Methods in enzymology}, volume = {430}, pages = {111–145}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0076687907300062}, abstract = {To facilitate the mechanistic dissection of eukaryotic translation initiation we have reconstituted the steps of this process using purified Saccharomyces cerevisiae components. This system provides a bridge between biochemical studies in vitro and powerful yeast genetic techniques, and complements existing reconstituted mammalian translation systems (Benne and Hershey, 1978; Pestova and Hellen, 2000; Pestova et al., 1998; Trachsel et al., 1977). The following describes methods for synthesizing and purifying the components of the yeast initiation system and assays useful for its characterization}, keywords = {0,assays,Biophysics,CEREVISIAE,chemistry,COMPONENT,COMPONENTS,Escherichia coli,Eukaryotic Initiation Factor-1,Eukaryotic Initiation Factor-2,EUKARYOTIC TRANSLATION,Genetic,Genetic Techniques,genetics,In Vitro,IN-VITRO,initiation,isolation & purification,La,metabolism,Methionine,Methionine-tRNA Ligase,Methods,nosource,protein,Protein Biosynthesis,Protein Isoforms,Proteins,RECONSTITUTION,Ribosome SubunitsLargeEukaryotic,Ribosome SubunitsSmallEukaryotic,Rna,RNAFungal,RNARibosomal,RNATransferMet,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Support,SYSTEM,SYSTEMS,techniques,translation,TRANSLATION INITIATION,yeast} }

@book{actonAnalysisStraightLineData1966, title = {Analysis of {{Straight-Line Data}}.}, author = {Acton, F.S.}, year = 1966, publisher = {Dover Press}, address = {New York}, keywords = {analysis,nosource} } % == BibTeX quality report for actonAnalysisStraightLineData1966: % ? Title looks like it was stored in title-case in Zotero

@article{adamsFunctionsRelationshipsTyVLP1987, title = {The Functions and Relationships of {{Ty-VLP}} Proteins in Yeast Reflect Those of Mammalian Retroviral Proteins}, author = {Adams, S. E. and Mellor, J. and Gull, K. and Sim, R. B. and Tuite, M. F. and Kingsman, S. M. and Kingsman, A. J.}, year = 1987, month = apr, journal = {Cell}, volume = {49}, number = {1}, pages = {111–119}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867487907616}, abstract = {We have identified the major structural core proteins of Ty virus-like particles (Ty-VLPs) and shown that they are generated by proteolytic cleavage of the primary translation product of TYA, p1. This precursor protein is therefore functionally similar to the gag precursor of retroviruses. Cleavage is mediated by a Ty-encoded protease located at the 5’ region of TYB and is accompanied by a change in particle morphology. p1 contains sufficient information for the assembly of a pre-Ty-VLP complex, which does not require the presence of either Ty protease or reverse transcriptase. The results indicate that the requirements and pathway of Ty-VLP formation reflect the initial stages of mammalian retroviral assembly and further support the idea of a common origin for Ty elements and retroviruses}, keywords = {87159539,Amino Acid Sequence,Base Sequence,Chromosome Deletion,Comparative Study,DNA Transposable Elements,Escherichia coli,Fungal Proteins,Gag,GenesFungal,GenesStructural,Genetic Vectors,genetics,Mutation,nosource,protein,Proteins,Retroviridae,Retroviridae Proteins,Saccharomyces cerevisiae,Species Specificity,Structural,Structure-Activity Relationship,Support,supportnon-u.s.gov’t,translation,Ty,yeast} }

@article{adamsEukaryoticInitiationComplex1975, title = {Eukaryotic Initiation Complex Formation. {{Evidence}} for Two Distinct Pathways.}, author = {Adams, S. L. and Safer, B. and Anderson, W. F. and Merrick, W. C.}, year = 1975, month = dec, journal = {Journal of Biological Chemistry}, volume = {250}, number = {23}, pages = {9083}, publisher = {ASBMB}, url = {http://www.jbc.org/content/250/23/9083.short}, abstract = {Two distinct pathways have been elucidated which lead to the formation of an AUG-dependent initiation complex. One pathway involves the use of initiation factor M1 (IF-M1) to promote AUG-dependent binding of the initiator tRNA to the 40 S subunit, followed by joining of the 60 S subunit in the presence of IF-M2A, IF-M2B, and GTP. The second pathway involves the IF-MP-directed binding of initiator tRNA to the 40 S subunit via a ternary complex of IF-MP-GTP-Met-tRNAf. This reaction does not require AUG codon. However, subsequent formation of an 80 S initiation complex (as determined by methionyl-puromycin synthesis) required AUG as well as IF-M2A, IF-M2B, and GTP. Since both pathways require the same complementary initiation factors (at the same level), it would appear that the only difference is the manner in which the initiator tRNA is bound to the 40 S subunit, either by IF-M1 or IF-MP. Examination of the requirements for endogenous mRNA-directed methionyl-puromycin synthesis indicates a greater difference between IF-MP and IF-M1 in that only IF-MP was capable of forming an 80 S initiation complex which was sensitive to puromycin}, keywords = {0,animal,AUG,BINDING,Binding Sites,Codon,COMPLEX,COMPLEX-FORMATION,COMPLEXES,GTP,Guanosine,Guanosine Triphosphate,initiation,INITIATION-FACTOR,La,M1,metabolism,nosource,PATHWAY,Peptide Chain Initiation,Peptide Initiation Factors,Protein Binding,Puromycin,Rabbits,Reticulocytes,Ribosomes,S,SUBUNIT,tRNA} }

@article{agarwalCelltyperestrictedBindingTranscription2000, title = {Cell-Type-Restricted Binding of the Transcription Factor {{NFAT}} to a Distal {{IL-4}} Enhancer in Vivo}, author = {Agarwal, S. and Avni, O. and Rao, A.}, year = 2000, month = jun, journal = {Immunity}, volume = {12}, number = {6}, pages = {643–652}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1074761300802150}, abstract = {By DNase I hypersensitivity analysis, we have identified an inducible, cyclosporin A-sensitive enhancer located 3’ of the interleukin-4 (IL-4) gene. The enhancer binds the Th2-specific transcription factor GATA3 in vivo but is not perceptibly influenced by the absence of a second Th2-specific factor, cMaf. The antigen-inducible transcription factor NFAT1 binds the IL-4 enhancer and the IL-4 promoter only in stimulated Th2 cells; conversely, NFAT1 binds to the interferon (IFN)-gamma promoter only in stimulated Th1 cells. Our results support a model whereby transcription factors such as NFAT1, which are nonselectively induced in antigen-stimulated T cells, gain access to cytokine regulatory regions only in the appropriate subset of differentiated T cells in vivo. This restricted access enables antigen-dependent and subset-specific transcription of cytokine genes}, keywords = {3’ Untranslated Regions,3’ UTR,analysis,animal,Base Sequence,Binding Sites,Clone Cells,Cyclosporine,Cytokines,Deoxyribonuclease I,DNA-Binding Proteins,drug effects,enhancer elements (genetics),Gene Expression Regulation,Genes,genetics,immunology,Interleukin-4,metabolism,Mice,MiceInbred C57BL,Molecular Sequence Data,nosource,pharmacology,physiology,Proto-Oncogene Proteins,Regulatory SequencesNucleic Acid,Support,Th2 Cells,Trans-Activators,transcription,Transcription Factors} }

@article{agmonRibosomalCrystallographyFlexible2004, title = {Ribosomal Crystallography: A Flexible Nucleotide Anchoring {{tRNA}} Translocation, Facilitates Peptide-Bond Formation, Chirality Discrimination and Antibiotics Synergism}, author = {Agmon, I. and Amit, M. and Auerbach, T. and Bashan, A. and Baram, D. and Bartels, H. and Berisio, R. and Greenberg, I. and Harms, J. and Hansen, H. A. S. and others}, year = 2004, month = jun, journal = {FEBS Letters}, volume = {567}, number = {1}, pages = {20–26}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S001457930400362X}, abstract = {The linkage between internal ribosomal symmetry and transfer RNA (tRNA) positioning confirmed positional catalysis of amino-acid polymerization. Peptide bonds are formed concurrently with tRNA-3’ end rotatory motion, in conjunction with the overall messenger RNA (mRNA)/tRNA translocation. Accurate substrate alignment, mandatory for the processivity of protein biosynthesis, is governed by remote interactions. Inherent flexibility of a conserved nucleotide, anchoring the rotatory motion, facilitates chirality discrimination and antibiotics synergism. Potential tRNA interactions explain the universality of the tRNA CCA-end and P-site preference of initial tRNA. The interactions of protein L2 tail with the symmetry-related region periphery explain its conservation and its contributions to nascent chain elongation}, keywords = {0,ACID,ACIDS,alignment,Amino Acids,AMINO-ACID,AMINO-ACIDS,Anti-Bacterial Agents,antibiotic,antibiotics,Azithromycin,BIOLOGY,biosynthesis,Catalysis,chemistry,conserved nucleotide,Crystallography,CrystallographyX-Ray,elongation,L2,La,MESSENGER-RNA,metabolism,Methods,ModelsMolecular,nosource,P SITE,P-SITE,peptide bond formation,PEPTIDE-BOND FORMATION,Peptides,pharmacology,protein,Protein Isoforms,Protein StructureTertiary,Protein Transport,PROTEIN-BIOSYNTHESIS,REGION,Review,Ribosomes,Rna,RNAMessenger,RNATransfer,Structural,Substrate Specificity,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,TRANSFER-RNA,translocation,tRNA,ultrastructure,Virginiamycin} }

@article{agoXrayStructurePokeweed1994, title = {X-Ray Structure of a Pokeweed Antiviral Protein, Coded by a New Genomic Clone, at 0.23 Nm Resolution. {{A}} Model Structure Provides a Suitable Electrostatic Field for Substrate Binding}, author = {Ago, H. and Kataoka, J. and Tsuge, H. and Habuka, N. and Inagaki, E. and Noma, M. and Miyano, M.}, year = 1994, month = oct, journal = {Eur.J.Biochem.}, volume = {225}, number = {1}, pages = {369–374}, abstract = {We have determined the crystal structure of alpha-pokeweed antiviral protein, a member of ribosome-inactivating proteins, at 0.23 nm resolution, by the molecular-replacement method. The crystals belong to the space group P2(1)2(1)2 with unit-cell dimensions a = 4.71, b = 11.63 and c = 4.96 nm, and contain one protein molecule/asymmetric unit based on a crystal volume/unit protein molecular mass of 2.1 x 10(-3) nm3/Da. The crystallographic residual value was reduced to 17.2% (0.6- 0.23 nm resolution) with root-mean-square deviations in bond lengths of 1.9 pm and bond angles of 2.2 degrees. The C alpha-C alpha distance map shows that alpha-pokeweed antiviral protein is composed of three modules, the N-terminal (Ala1-Leu76), the central (Tyr77-Lys185) and the C-terminal (Tyr186-Thr266) modules. The substrate-binding site is formed as a cleft between the central and C-terminal modules and all the active residues exist on the central module. The electrostatic potential around the substrate-binding site shows that the central and C-terminal module sides of this cleft have a negatively and a positively charged region, respectively. This charge distribution in the protein seems to provide a suitable interaction with the substrate rRNA}, keywords = {95010127,Amino Acid Sequence,antiviral,Antiviral Agents,Binding Sites,biosynthesis,chemistry,CloningMolecular,Comparative Study,CrystallographyX-Ray,genomic,metabolism,Methods,ModelsMolecular,Molecular Sequence Data,nosource,Plant Proteins,Pokeweed antiviral protein,protein,Protein StructureSecondary,Proteins,Recombinant Proteins,rRNA,Sequence HomologyAmino Acid,structure} } % == BibTeX quality report for agoXrayStructurePokeweed1994: % ? Possibly abbreviated journal title Eur.J.Biochem.

@article{agrawalDirectVisualizationEsite1996a, title = {Direct Visualization of {{A-}}, {{P-}}, and {{E-site}} Transfer {{RNAs}} in the ⬚{{Escherichia}} Coli⬚ Ribosome.}, author = {Agrawal, R.K. and Penczek, P. and Grassucci, R.A. and Li, Y. and Leith, A. and Nierhaus, K.H. and Frank, J.}, year = 1996, journal = {Science}, volume = {271}, pages = {1000–1002}, doi = {10.1126/science.271.5251.1000}, keywords = {Escherichia coli,nosource,ribosome,Rna,structure} }

@article{agrawalEFGdependentGTPHydrolysis1999, title = {{{EF-G-dependent GTP}} Hydrolysis Induces Translocation Accompanied by Large Conformational Changes in the {{70S}} Ribosome}, author = {Agrawal, R.K. and Heagle, A.B. and Penczek, P. and Grassucci, R.A. and Frank, J.}, year = 1999, month = jul, journal = {Nature Structural & Molecular Biology}, volume = {6}, number = {7}, pages = {643–647}, publisher = {Nature Publishing Group}, doi = {10.1038/10695}, url = {http://www.nature.com/nsmb/journal/v6/n7/abs/nsb0799_643.html}, abstract = {Cryo-electron microscopy has been used to visualize elongation factor G (EF-G) on the 70S ribosome in GDP and GTP states. GTP hydrolysis is required for binding of all the domains of EF-G to the pretranslocational complex and for the completion of translocation, in addition, large conformational changes have been identified in the ribosome, The head of the 30S subunit shifts toward the L1 protein side, and the L7/L12 stalk becomes bifurcated upon EF-G binding. Upon GTP hydrolysis, the bifurcation is reversed and an are-like connection is formed between the base of the stalk and EF-G}, keywords = {70S RIBOSOME,BASE,BINDING,COMPLEX,COMPLEXES,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,Cryoelectron Microscopy,CRYSTAL-STRUCTURE,DOMAIN,DOMAINS,EF-G,elongation,ELONGATION-FACTOR-G,ESCHERICHIA-COLI RIBOSOME,GTP,Hydrolysis,L1,MECHANISM,nosource,protein,PROTEIN L7/L12,RESOLUTION,ribosome,SITE,SUBUNIT,TRANSFER-RNA,translocation,TU,VISUALIZATION} }

@article{agrawalVisualizationTRNAMovements2000, title = {Visualization of {{tRNA}} Movements on the {{Escherichia}} Coli {{70S}} Ribosome during the Elongation Cycle}, author = {Agrawal, R.K. and Spahn, C.M. and Penczek, P. and Grassucci, R.A. and Nierhaus, K.H. and Frank, J.}, year = 2000, journal = {J. Biol. Chem.}, volume = {150}, number = {3}, pages = {447–460}, publisher = {Rockefeller Univ Press}, doi = {10.1083/jcb.150.3.447}, abstract = {Three-dimensional cryomaps have been reconstructed for tRNA-ribosome complexes in pre- and posttranslocational states at 17-A resolution. The positions of tRNAs in the A and P sites in the pretranslocational complexes and in the P and E sites in the posttranslocational complexes have been determined. Of these, the P-site tRNA position is the same as seen earlier in the initiation-like fMet-tRNA(f)(Met)-ribosome complex, where it was visualized with high accuracy. Now, the positions of the A- and E-site tRNAs are determined with similar accuracy. The positions of the CCA end of the tRNAs at the A site are different before and after peptide bond formation. The relative positions of anticodons of P- and E-site tRNAs in the posttranslocational state are such that a codon-anticodon interaction at the E site appears feasible}, keywords = {20391969,accuracy,Anticodon,Comparative Study,Cryoelectron Microscopy,CrystallographyX-Ray,elongation,Escherichia coli,genetics,Image ProcessingComputer-Assisted,ModelsMolecular,Movement,nosource,Peptide Chain Elongation,ribosome,Ribosomes,RNATransfer,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,tRNA,ultrastructure} } % == BibTeX quality report for agrawalVisualizationTRNAMovements2000: % ? Possibly abbreviated journal title J. Biol. Chem. % ? unused Journal abbr (“J.Cell Biol.”)

@article{agrawalLocalizationL11Protein2001a, title = {Localization of {{L11}} Protein on the Ribosome and Elucidation of Its Involvement in {{EF-G-dependent}} Translocation}, author = {Agrawal, R.K. and Linde, J. and Sengupta, J. and Nierhaus, K.H. and Frank, J.}, year = 2001, journal = {J.Mol Biol}, volume = {311}, number = {4}, pages = {777–787}, doi = {10.1006/jmbi.2001.4907}, url = {PM:11518530}, abstract = {L11 protein is located at the base of the L7/L12 stalk of the 50 S subunit of the Escherichia coli ribosome. Because of the flexible nature of the region, recent X-ray crystallographic studies of the 50 S subunit failed to locate the N-terminal domain of the protein. We have determined the position of the complete L11 protein by comparing a three-dimensional cryo-EM reconstruction of the 70 S ribosome, isolated from a mutant lacking ribosomal protein L11, with the three-dimensional map of the wild-type ribosome. Fitting of the X-ray coordinates of L11-23 S RNA complex and EF-G into the cryo-EM maps combined with molecular modeling, reveals that, following EF-G-dependent GTP hydrolysis, domain V of EF-G intrudes into the cleft between the 23 S ribosomal RNA and the N-terminal domain of L11 (where the antibiotic thiostrepton binds), causing the N-terminal domain to move and thereby inducing the formation of the arc-like connection with the G’ domain of EF-G. The results provide a new insight into the mechanism of EF-G-dependent translocation}, keywords = {0,antibiotic,BASE,chemistry,COMPLEX,COMPLEXES,Cryoelectron Microscopy,CrystallographyX-Ray,DOMAIN,DOMAIN-V,E,EF-G,elongation,ELONGATION-FACTOR-G,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,Gene Deletion,genetics,GTP,Guanosine,Guanosine Triphosphate,Hydrolysis,La,LOCALIZATION,MECHANISM,metabolism,ModelsMolecular,nosource,Peptide Elongation Factor G,POSITION,protein,Protein Binding,Protein StructureQuaternary,Protein StructureTertiary,Protein Subunits,Proteins,REGION,Ribosomal Proteins,ribosomal RNA,RIBOSOMAL-PROTEIN,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,S,SUBUNIT,SUBUNITS,Support,Thiostrepton,translocation,ultrastructure,WILD-TYPE} } % == BibTeX quality report for agrawalLocalizationL11Protein2001a: % ? Possibly abbreviated journal title J.Mol Biol

@article{agrisWobblePositionModified1991, title = {Wobble Position Modified Nucleosides Evolved to Select Transfer {{RNA}} Codon Recognition: A Modified-Wobble Hypothesis}, author = {Agris, P.F.}, year = 1991, month = nov, journal = {Biochimie}, volume = {73}, number = {11}, pages = {1345–1349}, publisher = {Elsevier}, doi = {10.1016/0300-9084(91)90163-U}, url = {http://linkinghub.elsevier.com/retrieve/pii/030090849190163U}, abstract = {While recognized that some wobble exists in the base pairing of the first base of the tRNA anticodon with the third of the codon, specific base modifications have evolved to select particular codons. This modified-wobble theory would be exemplified by a single codon recognition imposed on the anticodon by modification of the tRNA wobble position nucleoside}, keywords = {0,Anticodon,BASE,Base Pairing,Biochemistry,Codon,CODON RECOGNITION,CODONS,Genetic Code,genetics,La,ModelsGenetic,modification,nosource,Nucleosides,POSITION,RECOGNITION,Rna,RNATransfer,Support,TRANSFER-RNA,tRNA} }

@article{agrisUnconventionalStructureTRNA1997a, title = {Unconventional Structure of {{tRNA}}({{Lys}}){{SUU}} Anticodon Explains {{tRNA}}’s Role in Bacterial and Mammalian Ribosomal Frameshifting and Primer Selection by {{HIV-1}}}, author = {Agris, P.F. and Guenther, R. and Ingram, P.C. and Basti, M.M. and Stuart, J.W. and Sochacka, E. and Malkiewicz, A.}, year = 1997, month = apr, journal = {RNA}, volume = {3}, number = {4}, pages = {420–428}, keywords = {Anticodon,Bacterial,Dna,Escherichia coli,frameshift,Frameshifting,No DOI found,nosource,Oligonucleotides,polymerase,protein,Proteins,ribosomal frameshifting,Structural,structure,translation,tRNA} }

@article{agrisTRNAsWobbleDecoding2007, title = {{{tRNA}}‘s Wobble Decoding of the Genome: 40 Years of Modification}, author = {Agris, P.F. and Vendeix, F.A. and Graham, W.D.}, year = 2007, month = feb, journal = {Journal of molecular biology}, volume = {366}, number = {1}, pages = {1–13}, publisher = {Elsevier}, doi = {10.1016/j.jmb.2006.11.046}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(06)01586-5}, abstract = {The genetic code is degenerate, in that 20 amino acids are encoded by 61 triplet codes. In 1966, Francis Crick hypothesized that the cell’s limited number of tRNAs decoded the genome by recognizing more than one codon. The ambiguity of that recognition resided in the third base-pair, giving rise to the Wobble Hypothesis. Post-transcriptional modifications at tRNA’s wobble position 34, especially modifications of uridine 34, enable wobble to occur. The Modified Wobble Hypothesis proposed in 1991 that specific modifications of a tRNA wobble nucleoside shape the anticodon architecture in such a manner that interactions were restricted to the complementary base plus a single wobble pairing for amino acids with twofold degenerate codons. However, chemically different modifications at position 34 would expand the ability of a tRNA to read three or even four of the fourfold degenerate codons. One foundation of Crick’s Wobble Hypothesis was that a near-constant geometry of canonical base-pairing be maintained in forming all three base-pairs between the tRNA anticodon and mRNA codon on the ribosome. In accepting an aminoacyl-tRNA, the ribosome requires maintenance of a specific geometry for the anticodon-codon base-pairing. However, it is the post-transcriptional modifications at tRNA wobble position 34 and purine 37, 3’-adjacent to the anticodon, that pre-structure the anticodon domain to ensure the correct codon binding. The modifications create both the architecture and the stability needed for decoding through restraints on anticodon stereochemistry and conformational space, and through selective hydrogen bonding. A physicochemical understanding of modified nucleoside contributions to the tRNA anticodon domain architecture and its decoding of the genome has advanced RNA world evolutionary theory, the principles of RNA chemistry, and the application of this knowledge to the introduction of new amino acids to proteins}, keywords = {ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,Anticodon,BASE,Base Pairing,BASE-PAIR,BINDING,Biochemistry,chemistry,Codon,CODONS,decoding,DOMAIN,Genetic,Genetic Code,GENETIC-CODE,Genome,Hydrogen,Hydrogen Bonding,La,modification,mRNA,nosource,POSITION,posttranscriptional modification,protein,Proteins,RECOGNITION,REQUIRES,ribosome,Rna,RNA world,stability,Structural,Support,tRNA,Uridine,WORLD} } % == BibTeX quality report for agrisTRNAsWobbleDecoding2007: % ? unused Journal abbr (“J.Mol.Biol”)

@article{ahmedMolecularTargetViral1999, title = {A {{Molecular Target}} for {{Viral Killer Toxin}}:: {{TOK1 Potassium Channels}}}, author = {Ahmed, A. and Sesti, F. and Ilan, N. and Shih, T. M. and Sturley, S. L. and Goldstein, S. A. N.}, year = 1999, month = oct, journal = {Cell}, volume = {99}, number = {3}, pages = {283–291}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867400816591}, abstract = {Killer strains of S. cerevisiae harbor double-stranded RNA viruses and secrete protein toxins that kill virus-free cells. The K1 killer toxin acts on sensitive yeast cells to perturb potassium homeostasis and cause cell death. Here, the toxin is shown to activate the plasma membrane potassium channel of S. cerevisiae, TOK1. Genetic deletion of TOK1 confers toxin resistance; overexpression increases susceptibility. Cells expressing TOK1 exhibit toxin-induced potassium flux; those without the gene do not. K1 toxin acts in the absence of other viral or yeast products: toxin synthesized from a cDNA increases open probability of single TOK1 channels (via reversible destabilization of closed states) whether channels are studied in yeast cells or X. laevis oocytes}, keywords = {20021615,Genetic,killer toxin,L-A,nosource,Oocytes,Potassium,protein,Rna,RNA Viruses,toxin,yeast} } % == BibTeX quality report for ahmedMolecularTargetViral1999: % ? Title looks like it was stored in title-case in Zotero

@article{aignerEuplotesTelomeraseContains2000, title = {Euplotes Telomerase Contains an {{La}} Motif Protein Produced by Apparent Translational Frameshifting}, author = {Aigner, S. and Lingner, J. and Goodrich, K. J. and Grosshans, C. A. and Shevchenko, A. and Mann, M. and Cech, T. R.}, year = 2000, month = nov, journal = {The EMBO Journal}, volume = {19}, number = {22}, pages = {6230–6239}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/emboj/journal/v19/n22/abs/7593435a.html}, abstract = {Telomerase is the ribonucleoprotein enzyme responsible for the replication of chromosome ends in most eukaryotes. In the ciliate Euplotes aediculatus, the protein p43 biochemically co-purifies with active telomerase and appears to be stoichiometric with both the RNA and the catalytic protein subunit of this telomerase complex. Here we describe cloning of the gene for p43 and present evidence that it is an authentic component of the telomerase holoenzyme. Comparison of the nucleotide sequence of the cloned gene with peptide sequences of the protein suggests that production of full-length p43 relies on a programmed ribosomal frameshift, an extremely rare translational mechanism. Anti-p43 antibodies immunodeplete telomerase RNA and telomerase activity from E.aediculatus nuclear extracts, indicating that the vast majority of mature telomerase complexes in the cell are associated with p43. The sequence of p43 reveals similarity to the La autoantigen, an RNA-binding protein involved in maturation of RNA polymerase III transcripts, and recombinant p43 binds telomerase RNA in vitro. By analogy to other La proteins, p43 may function in chaperoning the assembly and/or facilitating nuclear retention of telomerase}, keywords = {+1 frameshifting,Antibodies,antibody,cancer,chemistry,cloning,frameshift,Frameshifting,homolog,In Vitro,La,nosource,polymerase,protein,Proteins,Rna,RNA Polymerase III,sequence} }

@article{alkaradaghiStructureElongationFactor1996, title = {The Structure of Elongation Factor {{G}} in Complex with {{GDP}}: Conformational Flexibility and Nucleotide Exchange}, author = {{}{al Karadaghi}, S. and Aevarsson, A. and Garber, M. and Zheltonosova, J. and Liljas, A.}, year = 1996, month = may, journal = {Structure.}, volume = {4}, number = {5}, pages = {555–565}, publisher = {Elsevier}, doi = {10.1016/S0969-2126(96)00061-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0969212696000615}, abstract = {BACKGROUND: Elongation factor G (EF-G) catalyzes the translocation step of translation. During translocation EF-G passes through four main conformational states: the GDP complex, the nucleotide-free state, the GTP complex, and the GTPase conformation. The first two of these conformations have been previously investigated by crystallographic methods. RESULTS: The structure of EF-G-GDP has been refined at 2.4 A resolution. Comparison with the nucleotide-free structure reveals that, upon GDP release, the phosphate-binding loop (P-loop) adopts a closed conformation. This affects the position of helix CG, the switch II loop and domains II, IV and V. Asp83 has a conformation similar to the conformation of the corresponding residue in the EF-Tu/EF-Ts complex. The magnesium ion is absent in EF-G-GDP. CONCLUSIONS: The results illustrate that conformational changes in the P-loop can be transmitted to other parts of the structure. A comparison of the structures of EF-G and EF-Tu suggests that EF-G, like EF-Tu, undergoes a transition with domain rearrangements. The conformation of EF-G-GDP around the nucleotide-binding site may be related to the mechanism of nucleotide exchange}, keywords = {Binding Sites,chemistry,Comparative Study,Crystallography,EFTu,elongation,GTP,GTP Phosphohydrolase-Linked Elongation Factors,GTPase,Guanosine Diphosphate,Magnesium,metabolism,Methods,ModelsMolecular,nosource,Peptide Elongation Factor G,Peptide Elongation Factors,physiology,Protein Conformation,Protein StructureTertiary,structure,supportnon-u.s.gov’t,translation,TranslationGenetic,translocation} } % == BibTeX quality report for alkaradaghiStructureElongationFactor1996: % ? Possibly abbreviated journal title Structure.

@article{alamStructuralStudiesRNA1999, title = {Structural Studies of the {{RNA}} Pseudoknot Required for Readthrough of the Gag-Termination Codon of Murine Leukemia Virus1}, author = {Alam, S. L. and Wills, N. M. and Ingram, J. A. and Atkins, J. F.}, year = 1999, month = may, journal = {Journal of Molecular Biology}, volume = {288}, number = {5}, pages = {837–852}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283699927134 http://www.sciencedirect.com/science/article/pii/S0022283699927134}, abstract = {Retroviruses, such as murine leukemia virus (MuLV), whose gag and pol genes are in the same reading frame but separated by a UAG stop codon, require that 5-10 % of ribosomes decode the UAG as an amino acid and continue translation to synthesize the Gag-Pol fusion polyprotein. A specific pseudoknot located eight nucleotides 3’ of the UAG is required for this redefinition of the UAG stop codon. The structural probing and mutagenic analyses presented here provide evidence that loop I of the pseudoknot is one nucleotide, stem II has seven base-pairs, and the nucleotides 3’ of stem II are important for function. Stem II is more resistant to single-strand-specific probes than stem I. Sequences upstream of the UAG codon allow formation of two competing structures, a stem-loop and the pseudoknot. Copyright 1998 Academic Press}, keywords = {99264408,Aldehydes,Antiviral Agents,chemistry,Codon,Dose-Response RelationshipDrug,Gag,Gag-pol,Gene Productsgag,Genes,genetics,Leukemia VirusesMurine,ModelsGenetic,MuLV,Mutagenesis,nosource,Nucleic Acid Conformation,pharmacology,physiology,pseudoknot,readthrough,ribosome,Ribosomes,Rna,sequence,Structural,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,translation,TranslationGenetic,virus} }

@article{alaniMethodGeneDisruption1987, title = {A Method for Gene Disruption That Allows Repeated Use of {{URA3}} Selection in the Construction of Multiply Disrupted Yeast Strains.}, author = {Alani, E. and Cao, L. and Kleckner, N.}, year = 1987, journal = {Genetics}, volume = {116}, pages = {541–545}, keywords = {hisG::URA3,Methods,Multiple DOI,nonfile,nosource,yeast} }

@article{alexeevaInteractionMRNAEscherichia1996, title = {Interaction of {{mRNA}} with the {{Escherichia}} Coli Ribosome: Accessibility of Phosphorothioate-Containing {{mRNA}} Bound to Ribosomes for Iodine Cleavage}, author = {Alexeeva, E.V. and Shpanchenko, O.V. and Dontsova, O.A. and Bogdanov, A.A. and Nierhaus, K.H.}, year = 1996, month = jun, journal = {Nucleic acids research}, volume = {24}, number = {12}, pages = {2228–2235}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/24.12.2228}, url = {http://nar.oxfordjournals.org/content/24/12/2228.short}, abstract = {The contacts of phosphate groups in mRNAs with ribosomes were studied. Two mRNAs were used: one mRNA contained in the middle two defined codons to construct the pre- and the post-translocational states, the other was a sequence around the initiation site of the natural cro- mRNA. Phosphorothioate nucleotides were randomly incorporated at a few A, G, U or C positions during in vitro transcription. Iodine can cleave the thioated positions if they are not shielded by ribosomal components. Only a few minor differences in iodine cleavage of ribosome bound and non-bound mRNA were observed: the nucleotide two positions upstream of the decoding codons (i.e. those codons involved in codon- anticodon interactions) showed a reduced accessibility for iodine and the nucleotide immediately following the decoding codons an enhanced accessibility in both elongating states. In initiating ribosomes where the mRNA contained a strong Shine-Dalgarno sequence, at least five phosphates were additionally slightly protected covering the Shine- Dalgarno sequence and nucleotides downstream including the initiator AUG in the P site (Al, G3, G-2, G-5 and A-7). The low contact levels of the phosphates in the mRNA with the elongating ribosome strikingly contrast with the pronounced contact patterns previously described for tRNAs. The data obtained in this study, as well as results of previous studies, suggest that mRNA regions downstream and upstream of decoding codons form only weak contacts with ribosomal components and that the mRNA thus is mainly fixed by codon-anticodon interaction on the elongating ribosome}, keywords = {0,Anticodon,Base Sequence,Binding Sites,Codon,Escherichia coli,genetics,In Vitro,initiation,Iodine,La,metabolism,Molecular Sequence Data,mRNA,nosource,Nucleotides,Peptide Chain Elongation,Phosphates,protein,Proteins,Repressor Proteins,ribosome,Ribosomes,Rna,RNAMessenger,sequence,supportnon-u.s.gov’t,Thionucleotides,transcription,tRNA} } % == BibTeX quality report for alexeevaInteractionMRNAEscherichia1996: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{algireDevelopmentCharacterizationReconstituted2002, title = {Development and Characterization of a Reconstituted Yeast Translation Initiation System}, author = {Algire, M. A. and Maag, D. and Savio, P. and Acker, M. G. and Tarun, S. Z. and Sachs, A. B. and Asano, K. and Nielsen, K. H. and Olsen, D. S. and Phan, L. and Hinnebusch, A. G. and Lorsch, J. R.}, year = 2002, month = mar, journal = {RNA}, volume = {8}, number = {3}, pages = {382–397}, url = {PM:12008673}, abstract = {To provide a bridge between in vivo and in vitro studies of eukaryotic translation initiation, we have developed a reconstituted translation initiation system using components from the yeast Saccharomyces cerevisiae. We have purified a minimal set of initiation factors (elFs) that, together with yeast 80S ribosomes, GTP, and initiator methionyl-tRNA, are sufficient to assemble active initiation complexes on a minimal mRNA template. The kinetics of various steps in the pathway of initiation complex assembly and the formation of the first peptide bond in vitro have been explored. The formation of active initiation complexes in this system is dependent on ribosomes, mRNA, Met-tRNAi, GTP hydrolysis, elF1, elF1A, elF2, elF5, and elF5B. Our data indicate that elF1 and elF1A both facilitate the binding of the elF2 x GTP x Met-tRNAi complex to the 40S ribosomal subunit to form the 43S complex. elF5 stimulates a step after 43S complex formation, consistent with its proposed role in activating GTP hydrolysis by elF2 upon initiation codon recognition. The presence of elF5B is required for the joining of the 40S and 60S subunits to form the 80S initiation complex. The step at which each of these factors acts in this reconstituted system is in agreement with previous data from in vivo studies and work using reconstituted mammalian systems, indicating that the system recapitulates fundamental events in translation initiation in eukaryotic cells. This system should allow us to couple powerful yeast genetic and molecular biological experiments with in vitro kinetic and biophysical experiments, yielding a better understanding of the molecular mechanics of this central, complex process}, keywords = {0,60S subunit,assembly,BINDING,CELLS,CEREVISIAE,chemistry,Codon,CODON RECOGNITION,COMPLEX,COMPLEX-FORMATION,COMPLEXES,COMPONENT,COMPONENTS,development,Eukaryotic Cells,EUKARYOTIC TRANSLATION,FORM,Genetic,genetics,GTP,GTP-Binding Proteins,Guanosine,Guanosine Triphosphate,human,Hydrolysis,In Vitro,IN-VITRO,IN-VIVO,initiation,INITIATION-FACTOR,isolation & purification,Kinetics,La,metabolism,mRNA,nosource,PATHWAY,Peptide Chain Initiation,Peptide Initiation Factors,physiology,protein,Proteins,RECOGNITION,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNAMessenger,RNATransferMet,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,SYSTEM,SYSTEMS,TEMPLATE,translation,TRANSLATION INITIATION,yeast} }

@article{aliDeletionConservedCentral2006, title = {Deletion of a Conserved, Central Ribosomal Intersubunit {{RNA}} Bridge}, author = {Ali, I.K. and Lancaster, L. and Feinberg, J. and Joseph, S. and Noller, H.F.}, year = 2006, journal = {Mol Cell}, volume = {23}, number = {6}, pages = {865–874}, doi = {10.1016/j.molcel.2006.08.011}, url = {PM:16973438}, abstract = {Elucidation of the structure of the ribosome has stimulated numerous proposals for the roles of specific rRNA elements, including the universally conserved helix 69 (H69) of 23S rRNA, which forms intersubunit bridge B2a and contacts the D stems of A- and P-site tRNAs. H69 has been proposed to be involved not only in subunit association and tRNA binding but also in initiation, translocation, translational accuracy, the peptidyl transferase reaction, and ribosome recycling. Consistent with such proposals, deletion of H69 confers a dominant lethal phenotype. Remarkably, in vitro assays show that affinity-purified Deltah69 ribosomes have normal translational accuracy, synthesize a full-length protein from a natural mRNA template, and support EF-G-dependent translocation at wild-type rates. However, Deltah69 50S subunits are unable to associate with 30S subunits in the absence of tRNA, are defective in RF1-catalyzed peptide release, and can be recycled in the absence of RRF}, keywords = {0,accuracy,assays,ASSOCIATION,Base Sequence,BINDING,BIOLOGY,chemistry,Conserved Sequence,D,E,ELEMENTS,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,FORM,genetics,In Vitro,IN-VITRO,initiation,La,metabolism,Molecular Biology,mRNA,nosource,Nucleic Acid Conformation,P SITE,P-SITE,Peptide Termination Factors,peptidyl transferase,PEPTIDYL-TRANSFERASE,Phenotype,physiology,protein,Protein Biosynthesis,Proteins,RELEASE,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Rna,RNAMessenger,RNARibosomal23S,RNATransfer,rRNA,Sequence Deletion,structure,SUBUNIT,subunit association,SUBUNITS,Support,TEMPLATE,termination,translocation,tRNA,tRNA binding,WILD-TYPE} }

@article{almazanConstructionSevereAcute2006, title = {Construction of a Severe Acute Respiratory Syndrome Coronavirus Infectious {{cDNA}} Clone and a Replicon to Study Coronavirus {{RNA}} Synthesis}, author = {Almazan, F. and DeDiego, M.L. and Galan, C. and Escors, D. and Alvarez, E. and Ortego, J. and Sola, I. and Zuniga, S. and Alonso, S. and Moreno, J.L. and Nogales, A. and Capiscol, C. and Enjuanes, L.}, year = 2006, month = nov, journal = {J.Virol.}, volume = {80}, number = {21}, pages = {10900–10906}, doi = {10.1128/JVI.00385-06}, url = {PM:16928748}, abstract = {The engineering of a full-length infectious cDNA clone and a functional replicon of the severe acute respiratory syndrome coronavirus (SARS-CoV) Urbani strain as bacterial artificial chromosomes (BACs) is described in this study. In this system, the viral RNA was expressed in the cell nucleus under the control of the cytomegalovirus promoter and further amplified in the cytoplasm by the viral replicase. Both the infectious clone and the replicon were fully stable in Escherichia coli. Using the SARS-CoV replicon, we have shown that the recently described RNA-processing enzymes exoribonuclease, endoribonuclease, and 2’-O-ribose methyltransferase were essential for efficient coronavirus RNA synthesis. The SARS reverse genetic system developed as a BAC constitutes a useful tool for the study of fundamental viral processes and also for developing genetically defined vaccines}, keywords = {0,3,Animals,Bacterial,Base Sequence,BIOLOGY,biosynthesis,Cell Line,Cell Nucleus,Cercopithecus aethiops,Chromosomes,ChromosomesArtificialBacterial,CloningMolecular,Coronavirus,Cricetinae,Cytoplasm,Dna,DNAComplementary,DnaViral,enzyme,Enzymes,Escherichia coli,ESCHERICHIA-COLI,Genetic,genetics,Humans,La,metabolism,METHYLTRANSFERASE,Molecular Sequence Data,nosource,PROMOTER,REPLICASE,Replicon,Rna,RnaViral,SARS,Sars Virus,Severe Acute Respiratory Syndrome,Support,Syndrome,SYSTEM,Vero Cells,VIRAL-RNA} } % == BibTeX quality report for almazanConstructionSevereAcute2006: % ? Possibly abbreviated journal title J.Virol.

@article{altamuraNAM7NuclearGene1992, title = {{{NAM7}} Nuclear Gene Encodes a Novel Member of a Family of Helicases with a {{Z1-6n-ligand}} Motif and Is Involved in Mitochondrial Functions in {{Saccharomyces}} Cerevisiae}, author = {Altamura, N. and Groudinsky, O. and Dujardin, G. and Slonimski, P. P.}, year = 1992, journal = {J. Mol. Biol}, volume = {224}, pages = {575–587}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:?NAM7?+nuclear+gene+encodes+a+novel+member+of+a+family+of+helicases+with+a+Z1-6n-ligand+motif+and+is+involved+in+mitochondrial+functions+in+?Saccharomyces+cerevisiae?.#0}, keywords = {Helicase,NMD,nonsense-mediated decay,nosource,Saccharomyces,Saccharomyces cerevisiae,Upf1,yeast} } % == BibTeX quality report for altamuraNAM7NuclearGene1992: % ? Possibly abbreviated journal title J. Mol. Biol

@article{altchulBasicLocalAlignment1990, title = {Basic Local Alignment Search Tool}, author = {Altchul, S. F. and Gish, W. and Miller, E. and Myers, E. W. and Lipman, D. J. and Altschul, S. F. and Miller, W.}, year = 1990, journal = {Journal of molecular biology}, volume = {215}, number = {3}, pages = {403–410}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283605803602}, keywords = {alignment,BLAST,computer,nosource,search} }

@article{amarantosIdentificationSpermineBinding2002, title = {The Identification of Spermine Binding Sites in {{16S rRNA}} Allows Interpretation of the Spermine Effect on Ribosomal {{30S}} Subunit Functions}, author = {Amarantos, I. and Zarkadis, I. K. and Kalpaxis, D. L.}, year = 2002, month = jul, journal = {Nucleic acids research}, volume = {30}, number = {13}, pages = {2832}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/30/13/2832.short}, abstract = {A photoreactive analogue of spermine, N-1-azidobenzamidino (ABA)-spermine, was covalently attached after irradiation to Escherichia coli 30S ribosomal subunits or naked 16S rRNA. By means of RNase H digestion and primer extension, the cross-linking sites of ABA-spermine in naked 16S rRNA were characterised and compared with those identified in 30S subunits. The 5’ domain, the internal and terminal loops of helix H24, as well as the upper part of helix H44 in naked 16S rRNA, were found to be preferable binding sites for polyamines. Association of 16S rRNA with ribosomal proteins facilitated its interaction with photoprobe, except for 530 stem-loop nt, whose modification by ABA-spermine was abolished. Association of 30S with 50S subunits, poly(U) and AcPhe-tRNA (complex C) further altered the susceptibility of ABA-spermine cross-linking to 16S rRNA. Complex C, modified in its 30S subunit by ABA-spermine, reacted with puromycin similarly to non-photolabelled complex. On the contrary, poly(U)-programmed 70S ribosomes reconstituted from photolabelled 30S subunits and untreated 50S subunits bound AcPhe-tRNA more efficiently than untreated ribosomes, but were less able to recognise and reject near cognate aminoacyl-tRNA. The above can be interpreted in terms of conformational changes in 16S rRNA, induced by the incorporation of ABA-spermine}, keywords = {0,70S RIBOSOME,BINDING,Binding Sites,BINDING-SITE,COMPLEX,COMPLEXES,CONFORMATIONAL-CHANGE,CROSS-LINKING,CRYSTAL-STRUCTURES,DECODING REGION,Escherichia coli,ESCHERICHIA-COLI,ESCHERICHIA-COLI RIBOSOMES,IDENTIFICATION,LOOP,MESSENGER-RNA,modification,nosource,P-SITE,PEPTIDE-BOND FORMATION,PHOTOAFFINITY POLYAMINES,polyamine,Polyamines,primer extension,protein,Proteins,Puromycin,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,RNAse,rRNA,SITE,SITES,SUBUNIT,TRANSFER-RNA} }

@article{amortIntactRiboseMoiety2007, title = {An Intact Ribose Moiety at {{A2602}} of {{23S rRNA}} Is Key to Trigger Peptidyl-{{tRNA}} Hydrolysis during Translation Termination}, author = {Amort, M. and Wotzel, B. and {Bakowska-Zywicka}, K. and Erlacher, M. D. D. and Micura, R. and Polacek, N.}, year = 2007, month = jul, journal = {Nucleic Acids Research}, volume = {35}, number = {15}, pages = {5130}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/35/15/5130.short}, abstract = {Peptide bond formation and peptidyl-tRNA hydrolysis are the two elementary chemical reactions of protein synthesis catalyzed by the ribosomal peptidyl transferase ribozyme. Due to the combined effort of structural and biochemical studies, details of the peptidyl transfer reaction have become increasingly clearer. However, significantly less is known about the molecular events that lead to peptidyl-tRNA hydrolysis at the termination phase of translation. Here we have applied a recently introduced experimental system, which allows the ribosomal peptidyl transferase center (PTC) to be chemically engineered by the introduction of non-natural nucleoside analogs. By this approach single functional group modifications are incorporated, thus allowing their functional contributions in the PTC to be unravelled with improved precision. We show that an intact ribose sugar at the 23S rRNA residue A2602 is crucial for efficient peptidyl-tRNA hydrolysis, while having no apparent functional relevance for transpeptidation. Despite the fact that all investigated active site residues are universally conserved, the removal of the complete nucleobase or the ribose 2’-hydroxyl at A2602, U2585, U2506, A2451 or C2063 has no or only marginal inhibitory effects on the overall rate of peptidyl-tRNA hydrolysis. These findings underscore the exceptional functional importance of the ribose moiety at A2602 for triggering peptide release}, keywords = {3,ACTIVE-SITE,BOND FORMATION,chemistry,genomic,Genomics,Hydrolysis,La,modification,nosource,peptide bond formation,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,peptidyl-transfer,PEPTIDYL-TRANSFERASE,protein,protein synthesis,PROTEIN-SYNTHESIS,RELEASE,RESIDUES,Ribose,RIBOSOMAL PEPTIDYL TRANSFERASE,ribozyme,rRNA,SITE,Structural,SYSTEM,termination,TRANSFERASE CENTER,translation,TRANSLATION TERMINATION} }

@article{anandTranslationElongationFactor2001, title = {Translation Elongation Factor 1 Functions in the Yeast {{Saccharomyces}} Cerevisiae}, author = {Anand, M. and Valente, L. and {Carr-Schmid}, A. and Munshi, R. and Olarewaju, O. and Ortiz, P.A. and Kinzy, T.G.}, year = 2001, journal = {Cold Spring Harb.Symp.Quant.Biol.}, volume = {66:439-48.}, pages = {439–448}, doi = {10.1101/sqb.2001.66.439}, keywords = {Amino Acid Sequence,Base Sequence,CEREVISIAE,chemistry,CrystallographyX-Ray,DNA Primers,elongation,Genetic,genetics,Kinetics,M,microbiology,ModelsGenetic,Molecular Sequence Data,MOLECULAR-GENETICS,nosource,Nuclear Proteins,Peptide Chain Elongation,Peptide Elongation Factor 1,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Sequence Alignment,Sequence HomologyAmino Acid,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Transcription Factors,translation,TranslationGenetic,yeast} } % == BibTeX quality report for anandTranslationElongationFactor2001: % ? Possibly abbreviated journal title Cold Spring Harb.Symp.Quant.Biol.

@article{anandFunctionalInteractionsYeast2002, title = {Functional Interactions between Yeast Translation Elongation Factors {{eEF1A}} and {{eEF3}}}, author = {Anand, M. and Chakraburtty, K. and Marton, M. J. and Hinnebusch, A. G. and Kinzy, T. G.}, year = 2002, month = dec, journal = {J.Biol.Chem.}, volume = {.}, abstract = {The translation elongation machinery in fungi differs from other eukaryotes in its dependence upon the eukaryotic Elongation Factor 3 (eEF3). eEF3 is essential in vivo and required for each cycle of the translation elongation process in vitro. Models predict eEF3 impacts on the delivery of cognate aminoacyl-tRNA, a function performed by eEF1A, by removing deacylated tRNA from the ribosomal Exit site. In order to dissect eEF3 function and its link to the A-site activities of eEF1A, we have identified a temperature sensitive allele of the YEF3 gene. The F650S substitution, located between the two ATP binding cassettes, reduces both ribosome-dependent and intrinsic ATPase activities. in vivo this mutation increases sensitivity to aminoglycosidic drugs, causes a 50% reduction of total protein synthesis at permissive temperatures, slows run off of polyribosomes, and reduces binding to eEF1A. Reciprocally, excess eEF3 confers synthetic slow growth, increased drug sensitivity and reduced translation in an allele specific fashion with an E122K mutation in the GTP-binding domain of eEF1A. In addition, this mutant form of eEF1A shows reduced binding of eEF3. Thus, optimal in vivo interactions between eEF3 and eEF1A are critical for protein synthesis}, keywords = {A-SITE,ATP,ATPase,drugs,elongation,Fungi,Genetic,genetics,immunology,In Vitro,IN-VITRO,IN-VIVO,microbiology,models,Mutation,No DOI found,nosource,Polyribosomes,protein,protein synthesis,PROTEIN-SYNTHESIS,Temperature,translation,tRNA,yeast} } % == BibTeX quality report for anandFunctionalInteractionsYeast2002: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{andersenStructureEEF3Mechanism2006, title = {Structure of {{eEF3}} and the Mechanism of Transfer {{RNA}} Release from the {{E-site}}}, author = {Andersen, C. B. F. and Becker, T. and Blau, M. and Anand, M. and Halic, M. and Balar, B. and Mielke, T. and Boesen, T. and Pedersen, J. S. and Spahn, C. M. T. and others}, year = 2006, month = oct, journal = {Nature}, volume = {443}, number = {7112}, pages = {663–668}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature05126.html}, abstract = {Elongation factor eEF3 is an ATPase that, in addition to the two canonical factors eEF1A and eEF2, serves an essential function in the translation cycle of fungi. eEF3 is required for the binding of the aminoacyl-tRNA-eEF1A-GTP ternary complex to the ribosomal A-site and has been suggested to facilitate the clearance of deacyl-tRNA from the E-site. Here we present the crystal structure of Saccharomyces cerevisiae eEF3, showing that it consists of an amino-terminal HEAT repeat domain, followed by a four-helix bundle and two ABC-type ATPase domains, with a chromodomain inserted in ABC2. Moreover, we present the cryo-electron microscopy structure of the ATP-bound form of eEF3 in complex with the post-translocational-state 80S ribosome from yeast. eEF3 uses an entirely new factor binding site near the ribosomal E-site, with the chromodomain likely to stabilize the ribosomal L1 stalk in an open conformation, thus allowing tRNA release}, keywords = {A SITE,A-SITE,ATPase,BINDING,BINDING-SITE,BIOLOGY,CEREVISIAE,COMPLEX,COMPLEXES,CONFORMATION,Cryoelectron Microscopy,crystal structure,CRYSTAL-STRUCTURE,DOMAIN,DOMAINS,E site,elongation,FORM,Fungi,Heat,L1,La,MECHANISM,Molecular Biology,nosource,RELEASE,ribosome,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SITE,Structural,structure,TRANSFER-RNA,translation,tRNA,yeast} }

@article{andersenStructuralBasisNucleotide2000a, title = {Structural Basis for Nucleotide Exchange and Competition with {{tRNA}} in the Yeast Elongation Factor Complex {{eEF1A}}:{{eEF1Balpha}}}, author = {Andersen, G.R. and Pedersen, L. and Valente, L. and Chatterjee, I. and Kinzy, T.G. and Kjeldgaard, M. and Nyborg, J.}, year = 2000, month = nov, journal = {Mol.Cell}, volume = {6}, number = {5}, pages = {1261–1266}, doi = {10.1016/S1097-2765(00)00122-2}, url = {PM:0011106763}, abstract = {The crystal structure of a complex between the protein biosynthesis elongation factor eEF1A (formerly EF-1alpha) and the catalytic C terminus of its exchange factor, eEF1Balpha (formerly EF-1beta), was determined to 1.67 A resolution. One end of the nucleotide exchange factor is buried between the switch 1 and 2 regions of eEF1A and destroys the binding site for the Mg(2+) ion associated with the nucleotide. The second end of eEF1Balpha interacts with domain 2 of eEF1A in the region hypothesized to be involved in the binding of the CCA-aminoacyl end of the tRNA. The competition between eEF1Balpha and aminoacylated tRNA may be a central element in channeling the reactants in eukaryotic protein synthesis. The recognition of eEF1A by eEF1Balpha is very different from that observed in the prokaryotic EF-Tu:EF-Ts complex. Recognition of the switch 2 region in nucleotide exchange is, however, common to the elongation factor complexes and those of Ras:Sos and Arf1:Sec7}, keywords = {0,biosynthesis,elongation,La,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Structural,structure,tRNA,yeast} } % == BibTeX quality report for andersenStructuralBasisNucleotide2000a: % ? Possibly abbreviated journal title Mol.Cell

@article{andersenCrystalStructuresNucleotide2001, title = {Crystal Structures of Nucleotide Exchange Intermediates in the {{eEF1A- eEF1Balpha}} Complex}, author = {Andersen, G. R. and Valente, L. and Pedersen, L. and Kinzy, T. G. and Nyborg, J.}, year = 2001, month = jun, journal = {Nature Structural Biology}, volume = {8}, number = {6}, pages = {531–534}, url = {PM:11373622}, abstract = {In the elongation cycle of protein biosynthesis, the nucleotide exchange factor eEF1Balpha catalyzes the exchange of GDP bound to the G- protein, eEF1A, for GTP. To obtain more information about the recently solved eEF1A-eEF1Balpha structure, we determined the structures of the eEF1A-eEF1Balpha-GDP-Mg2+, eEF1A-eEF1Balpha-GDP and eEF1A-eEF1Balpha- GDPNP complexes at 3.0, 2.4 and 2.05 A resolution, respectively. Minor changes, specifically around the nucleotide binding site, in eEF1A and eEF1Balpha are consistent with in vivo data. The base, sugar and alpha- phosphate bind as in other known nucleotide G-protein complexes, whereas the beta- and gamma-phosphates are disordered. A mutation of Lys 205 in eEF1Balpha that inserts into the Mg2+ binding site of eEF1A is lethal. This together with the structures emphasizes the essential role of Mg2+ in nucleotide exchange in the eEF1A-eEF1Balpha complex}, keywords = {0,Amino Acid Substitution,analogs & derivatives,Binding Sites,biosynthesis,Carbohydrates,chemistry,CrystallographyX-Ray,drug effects,elongation,genetics,GTP,Guanosine Diphosphate,IN-VIVO,La,Lysine,Magnesium,metabolism,ModelsMolecular,Mutation,nosource,Orotic Acid,Peptide Elongation Factor 1,pharmacology,protein,Protein Conformation,Structural,structure,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Yeasts} }

@article{andersenElongationFactorsProtein2003, title = {Elongation Factors in Protein Biosynthesis}, author = {Andersen, G. R. and Nissen, P. and Nyborg, J.}, year = 2003, journal = {Trends in biochemical sciences}, volume = {28}, number = {8}, pages = {434–441}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000403001622}, abstract = {Translation elongation factors are the workhorses of protein synthesis on the ribosome. They assist in elongating the nascent polypeptide chain by one amino acid at a time. The general biochemical outline of the translation elongation cycle is well preserved in all biological kingdoms. Recently, there has been structural insight into the effects of antibiotics on elongation. These structures provide a scaffold for understanding the biological function of elongation factors before high-resolution structures of such factors in complex with ribosomes are obtained. Very recent structures of the yeast translocation factor and its complex with the antifungal drug sordarin reveal an unexpected conformational flexibility that might be crucial to the mechanism of translocation}, keywords = {0,ACID,AMINO-ACID,antibiotic,antibiotics,AntibioticsAntifungal,Antifungal Agents,BIOLOGY,biosynthesis,chemistry,COMPLEX,COMPLEXES,elongation,ELONGATION CYCLE,elongation factors,ELONGATION-FACTORS,Escherichia coli,INHIBITOR,La,MECHANISM,metabolism,ModelsMolecular,nosource,Peptide Elongation Factors,pharmacology,physiology,POLYPEPTIDE,POLYPEPTIDE-CHAIN,protein,Protein Conformation,Protein StructureTertiary,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-BIOSYNTHESIS,PROTEIN-SYNTHESIS,Review,ribosome,Ribosomes,sordarin,Structural,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYNTHESIS INHIBITORS,Thermus thermophilus,translation,translocation,yeast} }

@article{andersonPUB1MajorNuclear1993, title = {{{PUB1}} Is a Major Nuclear and Cytoplasmic Polyadenylated {{RNA-binding}} Protein in {{Saccharomyces}} Cerevisiae.}, author = {Anderson, J.T. and Paddy, M.R. and Swanson, M.S.}, year = 1993, month = oct, journal = {Molecular and cellular biology}, volume = {13}, number = {10}, pages = {6102–6113}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/13/10/6102}, abstract = {Proteins that directly associate with nuclear polyadenylated RNAs, or heterogeneous nuclear RNA-binding proteins (hnRNPs), and those that associate with cytoplasmic mRNAs, or mRNA-binding proteins (mRNPs), play important roles in regulating gene expression at the posttranscriptional level. Previous work with a variety of eukaryotic cells has demonstrated that hnRNPs are localized predominantly within the nucleus whereas mRNPs are cytoplasmic. While studying proteins associated with polyadenylated RNAs in Saccharomyces cerevisiae, we discovered an abundant polyuridylate-binding protein, PUB1, which appears to be both an hnRNP and an mRNP. PUB1 and PAB1, the polyadenylate tail-binding protein, are the two major proteins cross-linked by UV light to polyadenylated RNAs in vivo. The deduced primary structure of PUB1 indicates that it is a member of the ribonucleoprotein consensus sequence family of RNA-binding proteins and is structurally related to the human hnRNP M proteins. Even though the PUB1 protein is a major cellular polyadenylated RNA-binding protein, it is nonessential for cell growth. Indirect cellular immunofluorescence combined with digital image processing allowed a detailed comparison of the intracellular distributions of PUB1 and PAB1. While PAB1 is predominantly, and relatively uniformly, distributed within the cytoplasm, PUB1 is localized in a nonuniform pattern throughout both the nucleus and the cytoplasm. The cytoplasmic distribution of PUB1 is considerably more discontinuous than that of PAB1. Furthermore, sucrose gradient sedimentation analysis demonstrates that PAB1 cofractionates with polyribosomes whereas PUB1 does not. These results suggest that PUB1 is both an hnRNP and an mRNP and that it may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm}, keywords = {0,analysis,animal,Base Sequence,Cell Nucleus,CELLS,CEREVISIAE,Consensus Sequence,Cytoplasm,Dna,DNAFungal,Eukaryotic Cells,expression,FAMILY,Fluorescent Antibody Technique,Fungal Proteins,gene,Gene Expression,GENE-EXPRESSION,genetics,GROWTH,growth & development,Hela Cells,human,immunology,IN-VIVO,isolation & purification,La,M,metabolism,microbiology,Molecular Sequence Data,mRNA,Multiple DOI,nonfile,nosource,Poly A,POLY(A)-BINDING PROTEIN,Poly(A)-Binding Proteins,Polymerase Chain Reaction,Polyribosomes,protein,Proteins,RIBONUCLEOPROTEIN,Rna,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAFungal,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Xenopus} } % == BibTeX quality report for andersonPUB1MajorNuclear1993: % ? unused Journal abbr (“Mol Cell Biol.”)

@article{andersonPosttranscriptionalControlCytokine2008a, title = {Post-Transcriptional Control of Cytokine Production}, author = {Anderson, P.}, year = 2008, month = apr, journal = {Nature Immunology}, volume = {9}, number = {4}, pages = {353–359}, publisher = {New York: Nature America, c2000-}, doi = {10.1038/ni1584}, url = {http://anderson.bwh.harvard.edu/03-Lab Publications/03-pdf publication links/23_NatImmunol08.pdf}, abstract = {The cytokine-encoding messenger RNA (mRNA) molecules transcribed in the nucleus acquire a protein coat that facilitates nuclear export, influences cytoplasmic localization, and determines stability and translational competence. The composition of this coat is determined by sequence elements that recruit proteins that influence the rate of translation and/or mRNA decay. Some of these regulatory proteins direct their associated mRNA molecules to discrete cytoplasmic foci (stress granules and processing bodies) that are essential in ‘programming’ mRNA ‘metabolism’. Studies have begun to identify how these various mechanisms are integrated and regulated to determine the amount of cytokine production in cells involved in immune responses. Understanding of these mechanisms has identified targets for the development of new classes of immunomodulatory drugs}, keywords = {0,Animals,antagonists & inhibitors,biosynthesis,BODIES,CELLS,Cytokines,DECAY,development,drugs,ELEMENTS,genetics,Humans,IDENTIFY,immunology,La,LOCALIZATION,MECHANISM,MECHANISMS,MESSENGER-RNA,metabolism,mRNA,mRNA decay,nosource,physiology,protein,Proteins,Review,Rna,RNA ProcessingPost-Transcriptional,RNAMessenger,sequence,stability,Stress,Support,TARGET,translation} } % == BibTeX quality report for andersonPosttranscriptionalControlCytokine2008a: % ? unused Journal abbr (“Nat.Immunol.”)

@article{anderssonRamRibosomesAre1983a, title = {Ram Ribosomes Are Defective Proofeaders.}, author = {Andersson, D.I. and Kurland, C.G.}, year = 1983, journal = {Mol.Gen.Genet.}, volume = {191}, pages = {378–381}, doi = {10.1007/BF00425749}, keywords = {E.coli,nosource,proofreading,ram,ribosome,Ribosomes,translation} } % == BibTeX quality report for anderssonRamRibosomesAre1983a: % ? Possibly abbreviated journal title Mol.Gen.Genet.

@article{anderssonAlphaBetaHSQCalphaBeta1998, title = {An [Alpha]/[Beta]-{{HSQC-}}[Alpha]/[Beta] {{Experiment}} for {{Spin-State Selective Editing}} of {{IS Cross Peaks}}}, author = {Andersson, P. and Annila, A. and Otting, G.}, year = 1998, journal = {Journal of Magnetic Resonance}, volume = {133}, number = {2}, pages = {364–367}, publisher = {Elsevier}, doi = {10.1006/jmre.1998.1492}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1090780798914926}, abstract = {A generalized version of the TROSY experiment allows the spin-state selective editing of the four multiplet components of 15N-1H cross peaks of amide groups in proteins into four different subspectra, with no penalty in sensitivity. An improvement by 2 in sensitivity results, if only two of the four multiplet components are selected. Use of the experiment for the measurement of 1JHN coupling constants is discussed. A water flip-back version of the experiment is demonstrated with a 45 kDa fragment of 15N/2H labeled Staphylococcus aureus gyrase B. Copyright 1998 Academic Press}, keywords = {COMPONENT,COMPONENTS,COUPLING-CONSTANTS,La,nosource,protein,Proteins,STAPHYLOCOCCUS-AUREUS,Water} } % == BibTeX quality report for anderssonAlphaBetaHSQCalphaBeta1998: % ? unused Journal abbr (“J.Magn Reson.”)

@article{angus-hillRsc3Rsc30Zinc2001, title = {A {{Rsc3}}/{{Rsc30}} Zinc Cluster Dimer Reveals Novel Roles for the Chromatin Remodeler {{RSC}} in Gene Expression and Cell Cycle Control}, author = {{Angus-Hill}, M.L. and Schlichter, A. and Roberts, D. and {Erdjument-Bromage}, H. and Tempst, P. and Cairns, B.R.}, year = 2001, month = apr, journal = {Mol.Cell}, volume = {7}, number = {4}, pages = {741–751}, doi = {10.1016/S1097-2765(01)00219-2}, url = {PM:11336698}, abstract = {Chromatin remodeling complexes perform central roles in transcriptional regulation. Here, we identify Rsc3 and Rsc30 as novel components of the essential yeast remodeler RSC complex. Rsc3 and Rsc30 function requires their zinc cluster domain, a known site-specific DNA binding motif. RSC3 is essential, and rsc3 Ts- mutants display a G2/M cell cycle arrest involving the spindle assembly checkpoint pathway, whereas rsc30Delta mutants are viable and osmosensitive. Rsc3 and Rsc30 interact functionally and also physically as a stable Rsc3/Rsc30 heteromeric complex. However, DNA microarray analysis with rsc3 or rsc30 mutants reveals different effects on the expression levels of ribosomal protein genes and cell wall genes. We propose that Rsc3 and Rsc30 interact physically but have different roles in targeting or regulating RSC}, keywords = {0,analysis,assembly,Base Sequence,BINDING,BINDING MOTIF,cell cycle,Cell Wall,CEREVISIAE,chemistry,Chromatin,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,DIMER,Dimerization,Dna,DNA-BINDING,DNA-Binding Proteins,DOMAIN,expression,G2 Phase,gene,Gene Expression,Gene Expression RegulationFungal,GENE-EXPRESSION,Genes,Genescdc,GenesLethal,genetics,IDENTIFY,La,Leucine Zippers,metabolism,Mitosis,Mitotic Spindle Apparatus,Molecular Sequence Data,MutagenesisSite-Directed,MUTANTS,nosource,Nuclear Proteins,PATHWAY,physiology,protein,Protein StructureSecondary,Protein StructureTertiary,Proteins,regulation,REQUIRES,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,Ribosomal Proteins,RIBOSOMAL-PROTEIN,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,site specific,Temperature,transcription,TRANSCRIPTION FACTOR,Transcription Factors,yeast,Yeasts,Zinc} } % == BibTeX quality report for angus-hillRsc3Rsc30Zinc2001: % ? Possibly abbreviated journal title Mol.Cell

@article{antaoThermodynamicStudyUnusually1991a, title = {A Thermodynamic Study of Unusually Stable {{RNA}} and {{DNA}} Hairpins}, author = {Antao, V.P. and Lai, S.Y. and Tinoco, I.}, year = 1991, month = nov, journal = {Nucleic Acids Res.}, volume = {19}, number = {21}, pages = {5901–5905}, doi = {10.1093/nar/19.21.5901}, url = {PM:1719483}, abstract = {About 70% of the RNA tetra-loop sequences identified in ribosomal RNAs from different organisms fall into either (UNCG) or (GNRA) families (where N = A, C, G, or U; and R = A or G). RNA hairpins with these loop sequences form unusually stable tetra-loop structures. We have studied the RNA hairpin GGAC(UUCG)GUCC and several sequence variants to determine the effect of changing the loop sequence and the loop-closing base pair on the thermodynamic stability of (UNCG) tetra-loops. The hairpin GGAG(CUUG)CUCC with the conserved loop G(CUUG)C was also unusually stable. We have determined melting temperatures (Tm), and obtained thermodynamic parameters for DNA hairpins with sequences analogous to stable RNA hairpins with (UNCG), C(GNRA)G, C(GAUA)G, and G(CUUG)C loops. DNA hairpins with (TTCG), (dUdUCG), and related sequences in the loop, unlike their RNA counterparts, did not form unusually stable hairpins. However, DNA hairpins with the consensus loop sequence C(GNRA)G were very stable compared to hairpins with C(TTTT)G or C(AAAA)G loops. The C(GATA)G and G(CTTG)C loops were also extra stable. The relative stabilities of the unusually stable DNA hairpins are similar to those observed for their RNA analogs}, keywords = {0,BASE,Base Sequence,BASE-PAIR,chemistry,Comparative Study,Consensus Sequence,CONSERVED LOOP,Dna,FAMILY,FORM,genetics,HAIRPINS,La,LOOP,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Oligonucleotides,ribosomal RNA,RIBOSOMAL-RNA,Rna,sequence,SEQUENCES,stability,stable RNA,structure,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Temperature,thermodynamic stability} } % == BibTeX quality report for antaoThermodynamicStudyUnusually1991a: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{antaoThermodynamicParametersLoop1992, title = {Thermodynamic Parameters for Loop Formation in {{RNA}} and {{DNA}} Hairpin Tetraloops}, author = {Antao, V.P. and Tinoco, I.}, year = 1992, month = feb, journal = {Nucleic acids research}, volume = {20}, number = {4}, pages = {819–824}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/20.4.819}, url = {http://nar.oxfordjournals.org/content/20/4/819.short}, abstract = {We determined the melting temperatures (Tm) and thermodynamic parameters of 15 RNA and 19 DNA hairpins at 1 M NaCl, 0.01 M sodium phosphate, 0.1 mM EDTA, at pH 7. All these hairpins have loops of four bases, the most common loop size in 16S and 23S ribosomal RNAs. The RNA hairpins varied in loop sequence, loop-closing base pair (A.U, C.G, or G.C), base sequence of the stem, and stem size (four or five base pairs). The DNA hairpins varied in loop sequence, loop-closing base pair (C.G, or G.C), and base sequence of the four base-pair stem. Thermodynamic properties of a hairpin may be represented by nearest-neighbor interactions of the stem plus contributions from the loop. Thus, we obtained thermodynamic parameters for the formation of RNA and DNA tetraloops. For the tetraloops we studied, a free energy of loop formation (at 37 degrees C) of about +3 kcal/mol is most common for either RNA or DNA. There are extra stable loops with delta G degrees 37 near +1 kcal/mol, but the sequences are not necessarily the same for RNA and DNA. The closing base pair is also important; changing from C.G to G.C lowered the stability of several tetraloops in both RNA and DNA. These values will be useful in predicting RNA and DNA secondary structures}, keywords = {0,16S,BASE,Base Sequence,BASE-PAIR,BASES,chemistry,Dna,HAIRPINS,La,LOOP,M,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Oligodeoxyribonucleotides,Oligoribonucleotides,ribosomal RNA,RIBOSOMAL-RNA,Rna,SECONDARY STRUCTURE,sequence,SEQUENCES,Sodium,stability,structure,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Temperature,Thermodynamics} } % == BibTeX quality report for antaoThermodynamicParametersLoop1992: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{anthonyAffinityLabelingEukaryotic1990, title = {Affinity Labeling of Eukaryotic Initiation Factor 2 and Elongation Factor 1 [Alpha][Beta][Gamma] with {{GTP}} Analogs}, author = {Anthony, D.D. and Kinzy, T.G. and Merrick, W.C.}, year = 1990, month = aug, journal = {Archives of biochemistry and biophysics}, volume = {281}, number = {1}, pages = {157–162}, publisher = {Elsevier}, doi = {10.1016/0003-9861(90)90426-Y}, url = {http://linkinghub.elsevier.com/retrieve/pii/000398619090426Y}, keywords = {Amino Acid Sequence,elongation,GTP,initiation,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,sequence,Support} }

@article{applequistCloningCharacterizationHUPF11997, title = {Cloning and Characterization of {{HUPF1}}, a Human Homolog of the ⬚{{Saccharomyces}} Cerevisiae⬚ Nonsense {{mRNA-reducing UPF1}} Protein.}, author = {Applequist, S.E. and Sleg, M. and Roman, C. and Jack, H.}, year = 1997, month = feb, journal = {Nucleic acids research}, volume = {25}, number = {4}, pages = {814–821}, publisher = {Oxford Univ Press}, issn = {0305-1048}, doi = {10.1093/nar/25.4.814}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=146496&tool=pmcentrez&rendertype=abstract http://nar.oxfordjournals.org/content/25/4/814.short}, abstract = {Levels of most nonsense mRNAs are normally reduced in prokaryotes and eukaryotes when compared with that of corresponding functional mRNAs. Genes encoding polypeptides that selectively reduce levels of nonsense mRNA have so far only been identified in simple eukaryotes. We have now cloned a human cDNA whose deduced amino acid sequence shows the highest degree of homology to that of UPF1, a bona fide Saccharomyces cerevisiae group I RNA helicase required for accelerated degradation of nonsense mRNA. Based on the total sequence of the shorter yeast UPF1 protein, the overall identity between the human protein and UPF1 is 51%. Besides NTPase and other RNA helicase consensus motifs, UPF1 and its human homolog also share similar putative zinc finger motifs that are absent in other group I RNA helicases. Northern blot analysis with the human cDNA probe revealed two transcripts in several human cell lines. Further, antibodies raised against a synthetic peptide of the human polypeptide detected a single 130 kDa polypeptide on Western blots from human and mouse cells. Finally, immunofluorescence and Western blot analyses revealed that the human and mouse polypeptides, like yeast UPF1, are expressed in the cytoplasm, but not in the nucleus. We have thus identified the first mammalian homolog of yeast UPF1, a protein that regulates levels of nonsense mRNA, and we tentatively name this protein human HUPF1 (for human homolog of UPF1).}, pmid = {9064659}, keywords = {Amino Acid,Amino Acid Sequence,Animals,B-Lymphocytes,Base Sequence,Chromosomes,cloning,Cloning,Codon,Complementary,Complementary: analysis,Cultured,Cytoplasm,Cytoplasm: metabolism,DNA,Fungal Proteins,Fungal Proteins: biosynthesis,Fungal Proteins: chemistry,Fungal Proteins: genetics,Gene Library,homolog,human,Human,Humans,Hybridomas,Messenger,Messenger: metabolism,Mice,Molecular,Molecular Sequence Data,Nonsense,nonsense-mediated decay,nosource,Pair 19,protein,RNA,RNA Helicases,RNA Nucleotidyltransferases,RNA Nucleotidyltransferases: biosynthesis,RNA Nucleotidyltransferases: chemistry,RNA Nucleotidyltransferases: genetics,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae: genetics,Sequence Homology,Trans-Activators,Tumor Cells,Upf1} } % == BibTeX quality report for applequistCloningCharacterizationHUPF11997: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{aravaGenomewideAnalysisMRNA2003a, title = {Genome-Wide Analysis of {{mRNA}} Translation Profiles in {{Saccharomyces}} Cerevisiae}, author = {Arava, Y. and Wang, Y.L. and Storey, J.D. and Liu, C.L. and Brown, P.O. and Herschlag, D.}, year = 2003, month = apr, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {7}, pages = {3889–3894}, doi = {10.1073/pnas.0635171100}, url = {ISI:000182058400066}, abstract = {We have analyzed the translational status of each mRNA in rapidly growing Saccharomyces cerevisiae. mRNAs were separated by velocity sedimentation on a sucrose gradient, and 14 fractions across the gradient were analyzed by quantitative microarray analysis, providing a profile of ribosome association with mRNAs for thousands of genes. For most genes, the majority of mRNA molecules were associated with ribosomes and presumably engaged in translation. This systematic approach enabled us to recognize genes with unusual behavior. For 43 genes, most mRNA molecules were not associated with ribosomes, suggesting that they may be translationally controlled. For 53 genes, including GCN4, CPA1, and ICY2, three genes for which translational control is known to play a key role in regulation, most mRNA molecules were associated with a single ribosome. The number of ribosomes associated with mRNAs increased with increasing length of the putative protein-coding sequence, consistent with longer transit times for ribosomes translating longer coding sequences. The density at which ribosomes were distributed on each mRNA (i.e., the number of ribosomes per unit ORF length) was well below the maximum packing density for nearly all mRNAs, consistent with initiation as the rate-limiting step in translation. Global analysis revealed an unexpected correlation: Ribosome density decreases with increasing ORF length: Models to account for this surprising observation are discussed}, keywords = {analysis,ASSOCIATION,CEREVISIAE,coding sequence,D,DNA MICROARRAYS,ESCHERICHIA-COLI,GCN4,gene,GENE-EXPRESSION,Genes,IDENTIFICATION,initiation,MESSENGER-RNA TRANSLATION,MODEL,models,mRNA,nosource,POLYPEPTIDE,PROTEIN-SYNTHESIS,regulation,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,translation,yeast} }

@article{arbustiniMitochondrialDNAMutations1998, title = {Mitochondrial {{DNA}} Mutations and Mitochondrial Abnormalities in Dilated Cardiomyopathy}, author = {Arbustini, E. and Diegoli, M. and Fasani, R. and Grasso, M. and Morbini, P. and Banchieri, N. and Bellini, O. and Dal Bello, B. and Pilotto, A. and Magrini, G. and Campana, C. and Fortina, P. and Gavazzi, A. and Narula, J. and Vigano, M.}, year = 1998, month = nov, journal = {American Journal of Pathology}, volume = {153}, number = {5}, pages = {1501–1510}, publisher = {ASIP}, doi = {10.1016/S0002-9440(10)65738-0}, url = {http://amjpathol.highwire.org/cgi/content/abstract/153/5/1501}, abstract = {Mitochondrial (mt)DNA defects, both deletions and tRNA point mutations, have been associated with cardiomyopathies. The aim of the study was to determine the prevalence of pathological mtDNA mutations and to assess associated defects of mitochondrial enzyme activity in dilated cardiomyopathy (DCM) patients with ultrastructural abnormalities of cardiac mitochondria. In a large cohort of 601 DCM patients we performed conventional light and electron microscopy on endomyocardial biopsy samples. Cases with giant organelles, angulated, tubular, and concentric cristae, and crystalloid or osmiophilic inclusion bodies were selected for mtDNA analysis. Mutation screening techniques, automated DNA sequencing, restriction enzyme digestion, and densitometric assays were performed to identify mtDNA mutations, assess heteroplasmy, and quantify the amount of mutant in myocardial and blood DNA. Of 601 patients (16 to 63 years; mean, 43.5 +/- 12.7 years), 85 had ultrastructural evidence of giant organelles, with abnormal cristae and inclusion bodies; 19 of 85 (22.35%) had heteroplasmic mtDNA mutations (9 tRNA, 5 rRNA, and 4 missense, one in two patients) that were not found in 111 normal controls and in 32 DCM patients without the above ultrastructural mitochondrial abnormalities. In all cases, the amount of mutant was higher in heart than in blood. In hearts of patients that later underwent transplantation, cytochrome c oxidase (Cox) activity was significantly lower in cases with mutations than in those without or controls (P = 0.0008). NADH dehydrogenase activity was only slightly reduced in cases with mutations (P = 0.0388), whereas succinic dehydrogenase activity did not significantly differ between DCM patients with mtDNA mutations and those without or controls. The present study represents the first attempt to detect a morphological, easily identifiable marker to guide mtDNA mutation screening. Pathological mtDNA mutations are associated with ultrastructurally abnormal mitochondria, and reduced Cox activity in a small subgroup of non-otherwise-defined, idiopathic DCMs, in which mtDNA defects may constitute the basis for, or contribute to, the development of congestive heart failure}, keywords = {0,16S,Adolescent,Adult,analysis,assays,Biopsy,blood,BODIES,CardiomyopathyDilated,Cytochrome c,DEHYDROGENASE,development,Dna,DNAMitochondrial,E,ELECTRON-MICROSCOPY,enzyme,Female,genetics,heart,Humans,IDENTIFY,La,Male,MARKER,metabolism,Middle Aged,mitochondria,MitochondriaHeart,Mutation,MutationMissense,MUTATIONS,NADH Dehydrogenase,nosource,Organelles,pathology,Point Mutation,Polymerase Chain Reaction,PolymorphismGenetic,Research SupportNon-U.S.Gov’t,Rna,RNARibosomal,RNARibosomal16S,RNATransfer,rRNA,Succinate Dehydrogenase,techniques,tRNA} } % == BibTeX quality report for arbustiniMitochondrialDNAMutations1998: % ? unused Journal abbr (“Am.J.Pathol.”)

@article{arnoldActionNterminalAcetyltransferases1999, title = {The Action of {{N-terminal}} Acetyltransferases on Yeast Ribosomal Proteins}, author = {Arnold, R.J. and Polevoda, B. and Reilly, J.P. and Sherman, F.}, year = 1999, month = dec, journal = {Journal of Biological Chemistry}, volume = {274}, number = {52}, pages = {37035–37040}, publisher = {ASBMB}, doi = {10.1074/jbc.274.52.37035}, url = {http://www.jbc.org/content/274/52/37035.short}, abstract = {Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to determine the state of N-terminal acetylation of 68 ribosomal proteins from a normal strain of Saccharomyces cerevisiae and from the ard1-Delta, nat3-Delta, and mak3-Delta mutants (), each lacking a catalytic subunit of three different N-terminal acetyltransferases. A total 30 of the of 68 ribosomal proteins were N-terminal-acetylated, and 24 of these (80%) were NatA substrates, unacetylated in solely the ard1-Delta mutant and having mainly Ac-Ser- termini and a few with Ac-Ala- or Ac-Thr- termini. Only 4 (13%) were NatB substrates, unacetylated in solely the nat3-Delta mutant, and having Ac-Met-Asp- or Ac-Met-Glu- termini. No NatC substrates were uncovered, e.g. unacetylated in solely mak3-Delta mutants, consistent with finding that none of the ribosomal proteins had Ac-Met-Ile-, Ac-Met-Leu-, or Ac-Met-Phe- termini. Interestingly, two new types of the unusual NatD substrates were uncovered, having either Ac-Ser-Asp-Phe- or Ac-Ser-Asp-Ala- termini that were unacetylated in the ard1-Delta mutant, and only partially acetylated in the mak3-Delta mutant and, for one case, also only partially in the nat3-Delta mutant. We suggest that the acetylation of NatD substrates requires not only Ard1p and Nat1p, but also auxiliary factors that are acetylated by the Mak3p and Nat3p N-terminal acetyltransferases}, keywords = {0,Acetylation,Acetyltransferases,Arylamine N-Acetyltransferase,CEREVISIAE,chemistry,Fungal Proteins,La,matrix assisted laser,metabolism,Methylation,MUTANTS,N-ACETYLTRANSFERASE,NatA,nosource,Phosphorylation,protein,Proteins,REQUIRES,Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,Ribosomal Proteins,RIBOSOMAL-PROTEIN,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUBUNIT,yeast} } % == BibTeX quality report for arnoldActionNterminalAcetyltransferases1999: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{aronInhibitionHerpesSimplex1980, title = {Inhibition of Herpes Simplex Virus Multiplication by the Pokeweed Antiviral Protein.}, author = {Aron, G.M. and Irvin, J.D.}, year = 1980, month = jun, journal = {Antimicrobial Agents and Chemotherapy}, volume = {17}, number = {6}, pages = {1032–1033}, publisher = {Am Soc Microbiol}, doi = {10.1128/AAC.17.6.1032}, url = {http://aac.asm.org/cgi/content/abstract/17/6/1032}, abstract = {The pokeweed antiviral protein inhibited the multiplication of herpes simplex virus type 1 in cell culture. The extent of antiviral activity was proportional to the length of time that the antiviral protein was present postinfection. The results demonstrate that the continued presence of the pokeweed antiviral protein is necessary for the maximum inhibition of virus yields}, keywords = {antiviral,nosource,PAP,Pokeweed antiviral protein,protein,virus} }

@article{asaiEscherichiaColiStrain1999, title = {An {{Escherichia}} Coli Strain with All Chromosomal {{rRNA}} Operons Inactivated: Complete Exchange of {{rRNA}} Genes between Bacteria}, author = {Asai, T. and Zaporojets, D. and Squires, C. and Squires, C.L.}, year = 1999, month = mar, journal = {Proceedings of the National Academy of Sciences}, volume = {96}, number = {5}, pages = {1971–1976}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.96.5.1971}, url = {http://www.pnas.org/content/96/5/1971.short}, abstract = {Current global phylogenies are built predominantly on rRNA sequences. However, an experimental system for studying the evolution of rRNA is not readily available, mainly because the rRNA genes are highly repeated in most experimental organisms. We have constructed an Escherichia coli strain in which all seven chromosomal rRNA operons are inactivated by deletions spanning the 16S and 23S coding regions. A single E. coli rRNA operon carried by a multicopy plasmid supplies 16S and 23S rRNA to the cell. By using this strain we have succeeded in creating microorganisms that contain only a foreign rRNA operon derived from either Salmonella typhimurium or Proteus vulgaris, microorganisms that have diverged from E. coli about 120-350 million years ago. We also were able to replace the E. coli rRNA operon with an E. coli/yeast hybrid one in which the GTPase center of E. coli 23S rRNA had been substituted by the corresponding domain from Saccharomyces cerevisiae. These results suggest that, contrary to common belief, coevolution of rRNA with many other components in the translational machinery may not completely preclude the horizontal transfer of rRNA genes}, keywords = {0,16S,Bacteria,Bacterial,Base Sequence,BIOLOGY,CEREVISIAE,ChromosomesBacterial,CODING REGION,Comparative Study,COMPONENT,COMPONENTS,DOMAIN,E,Escherichia coli,ESCHERICHIA-COLI,Evolution,gene,Genes,GenesBacterial,genetics,growth & development,GTPase,La,microbiology,Molecular Biology,nosource,Operon,Phylogeny,PLASMID,Polymerase Chain Reaction,REGION,Restriction Mapping,Rna,RNABacterial,RNARibosomal,RNARibosomal16S,RNARibosomal23S,rRNA,rRNA genes,rRNA Operon,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Salmonella typhimurium,sequence,Sequence Deletion,SEQUENCES,Support,SYSTEM} } % == BibTeX quality report for asaiEscherichiaColiStrain1999: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{asakuraIsolationCharacterizationNovel1998a, title = {Isolation and Characterization of a Novel Actin Filament-Binding Protein from {{Saccharomyces}} Cerevisiae.}, author = {Asakura, T. and Sasaki, T. and Nagano, F. and Satoh, A. and Obaishi, H. and Nishioka, H. and Imamura, H. and Hotta, K. and Tanaka, K. and Nakanishi, H. and Takai, Y.}, year = 1998, month = jan, journal = {Oncogene}, volume = {16}, number = {1}, eprint = {9467951}, eprinttype = {pubmed}, pages = {121–130}, doi = {10.1038/sj.onc.1201487}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9467951}, abstract = {We purified a novel actin filament (F-actin)-binding protein from the soluble fraction of Saccharomyces cerevisiae by successive column chromatographies by use of the 125I-labeled F-actin blot overlay method. The purified protein showed a minimum Mr of about 140 kDa on SDS-polyacrylamide gel electrophoresis and we named it ABP140. A search with the partial amino acid sequences of ABP140 against the Saccharomyces Genome Database revealed that the open reading frame of the ABP140 gene (ABP140) corresponded to YOR239W fused with YOR240W by the +1 translational frame shift. The encoded protein consisted of 628 amino acids with a calculated Mr of 71,484. The recombinant protein interacted with F-actin and showed the activity to crosslink F-actin into a bundle. Indirect immunofluorescence study demonstrated that ABP140 was colocalized with both cortical actin patches and cytoplasmic actin cables in intact cells. However, elimination of ABP140 by gene disruption did not show a deleterious effect on cell growth or affect the organization of F-actin. These results indicate that ABP140 is not required for cell growth but may be involved in the reorganization of F-actin in the budding yeast}, keywords = {+1 frameshifting,98127445,Actins,Amino Acid Sequence,Amino Acids,Base Sequence,Chromatography,Cytosol,Electrophoresis,genetics,genomic,isolation &,metabolism,Microfilament Proteins,Molecular Sequence Data,nosource,Open Reading Frames,Peptide Mapping,protein,purification,Recombinant Proteins,Saccharomyces,Saccharomyces cerevisiae,search,sequence,supportnon-u.s.gov’t,yeast} }

@article{asanoConservationDiversityEukaryotic1997, title = {Conservation and Diversity of Eukaryotic Translation Initiation Factor {{eIF3}}}, author = {Asano, K. and Kinzy, T.G. and Merrick, W.C. and Hershey, J.W.}, year = 1997, month = jan, journal = {Journal of Biological Chemistry}, volume = {272}, number = {2}, pages = {1101–1109}, publisher = {ASBMB}, doi = {10.1074/jbc.272.2.1101}, url = {http://www.jbc.org/content/272/2/1101.short}, keywords = {Amino Acid Sequence,analysis,Antibodies,antibody,cloning,eIF3,homolog,human,initiation,mRNA,nosource,protein,Proteins,ribosome,Ribosomes,sequence,translation,yeast} }

@article{asanoMultifactorComplexEIFI2001, title = {A Multifactor Complex of {{eIFI}}, {{cIF2}}, {{eIF3}}, {{eIF5}}, and {{tRNA}}(i)({{Met}}) Promotes Initiation Complex Assembly and Couples {{GTP}} Hydrolysis to {{AUG}} Recognition}, author = {Asano, K. and Phan, L. and Valasek, L. and Schoenfeld, L.W. and Shalev, A. and Clayton, J. and Nielsen, K. and Donahue, T.F. and Hinnebusch, A.G.}, year = 2001, journal = {Cold Spring Harbor Symposia on Quantitative Biology}, volume = {66}, pages = {403–415}, doi = {10.1101/sqb.2001.66.403}, url = {ISI:000180643700041}, keywords = {0,3 EIF3,Animals,assembly,AUG,Base Sequence,Binding Sites,Child,COMPLEX,COMPLEXES,Conserved Sequence,development,eIF1,eIF3,EIF5,Eukaryotic Initiation Factor-1,Eukaryotic Initiation Factor-2,Eukaryotic Initiation Factor-3,Eukaryotic Initiation Factor-5,EUKARYOTIC TRANSLATION INITIATION-FACTOR-3,Evolution,gene,gene regulation,genetics,GTP,GUANINE-NUCLEOTIDE EXCHANGE,Guanosine,Guanosine Triphosphate,human,Hydrolysis,initiation,La,MESSENGER-RNA,metabolism,nosource,Peptide Chain InitiationTranslational,Protein Biosynthesis,PROTEIN COMPLEX,PRT1 PROTEIN,RECOGNITION,regulation,Review,RIBOSOME BINDING,Rna,RNATransferMet,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,START CODON,SUBUNIT} }

@article{asanoAnalysisReconstitutionTranslation2002, title = {Analysis and Reconstitution of Translation Initiation in Vitro}, author = {Asano, K. and Phan, L. and Krishnamoorthy, T. and Pavitt, G.D. and Gomez, E. and Hannig, E.M. and Nika, J. and Donahue, T.F. and Huang, H.K. and Hinnebusch, A.G.}, year = 2002, journal = {Guide to Yeast Genetics and Molecular and Cell Biology, Pt C}, volume = {351}, pages = {221–247}, publisher = {Elsevier}, doi = {10.1016/S0076-6879(02)51850-4}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0076687902518504}, keywords = {0,ACID INSERTION MODULE,analysis,BINDING,EIF5,FACTOR-II,gene,GUANINE-NUCLEOTIDE-EXCHANGE,In Vitro,IN-VITRO,initiation,La,MESSENGER-RNA,nosource,PROTEIN COMPLEX,PRT1,Review,TRANSFER-RNA FORMYLTRANSFERASE,translation,TRANSLATION INITIATION,YEAST SACCHAROMYCES-CEREVISIAE} }

@article{atkinMajorityYeastUPF11995, title = {The Majority of Yeast {{UPF1}} Co-Localizes with Polyribosomes in the Cytoplasm.}, author = {Atkin, A.L. and Altamura, N. and Leeds, P. and Culbertson, M.R.}, year = 1995, journal = {Molecular biology of the cell}, volume = {6}, number = {5}, pages = {611–625}, publisher = {American Society for Cell Biology}, doi = {10.1091/mbc.6.5.611}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC301219/}, keywords = {nosource,Polyribosomes,translation,UPF,Upf1,yeast} } % == BibTeX quality report for atkinMajorityYeastUPF11995: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{atkinsGeneticDissectionBasis1991, title = {Towards a Genetic Dissection of the Basis of Triplet Decoding, and Its Natural Subversion: Programmed Reading Frame Shifts and Hops.}, author = {Atkins, J.F. and Weills, R.B. and Thompson, S. and Gesteland, R.F.E.}, year = 1991, journal = { review of genetics}, volume = {25}, number = {1}, pages = {201–228}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, doi = {10.1146/annurev.ge.25.120191.001221}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.ge.25.120191.001221}, keywords = {decoding,frameshifting,Frameshifting,Genetic,hopping,nosource,Review,review article,suppressors,translation} } % == BibTeX quality report for atkinsGeneticDissectionBasis1991: % ? unused Journal abbr (“Annu.Rev.Genet.”)

@article{atkinsonSecondaryStructuresStarvationinduced1997, title = {Secondary Structures and Starvation-Induced Frameshifting}, author = {Atkinson, J. and Dodge, M. and Gallant, J.}, year = 1997, month = nov, journal = {Molecular Microbiology}, volume = {26}, number = {4}, pages = {747–753}, publisher = {Wiley Online Library}, doi = {10.1046/j.1365-2958.1997.6101959.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.1997.6101959.x/abstract}, keywords = {Bacterial,Codon,frameshift,Frameshifting,Genetic,genetics,nosource,Nucleotides,regulation,sequence,structure,tRNA} }

@article{atwaterRegulatedMRNAStability1990, title = {Regulated {{mRNA}} Stability.}, author = {Atwater, J.A. and Wisdom, R. and Verma, I.M.}, year = 1990, journal = {Annual review of genetics}, volume = {24}, number = {1}, pages = {519–541}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, doi = {10.1146/annurev.ge.24.120190.002511}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.ge.24.120190.002511}, keywords = {cancer,mRNA,nosource,stability} } % == BibTeX quality report for atwaterRegulatedMRNAStability1990: % ? unused Journal abbr (“Ann.Rev.Genet.”)

@article{auerbachRibosomalAntibioticsStructural2004, title = {Ribosomal Antibiotics: Structural Basis for Resistance, Synergism and Selectivity}, author = {Auerbach, T. and Bashan, A. and Yonath, A.}, year = 2004, month = nov, journal = {Trends Biotechnol.}, volume = {22}, number = {11}, pages = {570–576}, publisher = {Elsevier}, doi = {10.1016/j.tibtech.2004.09.006}, url = {PM:15491801}, abstract = {Various antibiotics bind to ribosomes at functionally relevant locations such as the peptidyl-transferase center (PTC) and the exit tunnel for nascent proteins. High-resolution structures of antibiotics bound to ribosomal particles from a eubacterium that is similar to pathogens and an archaeon that shares properties with eukaryotes are deciphering subtle differences in these highly conserved locations that lead to drug selectivity and thereby facilitate clinical usage. These structures also show that members of antibiotic families with structural differences might bind to specific ribosomal pockets in different modes dominated by their chemical properties. Similarly, the chemical properties of drugs might govern variations in the nature of seemingly identical mechanisms of drug resistance. The observed variability in binding modes justifies expectations for structural design of improved antibiotic properties}, keywords = {0,Anti-Bacterial Agents,antibiotic,antibiotics,BINDING,Binding Sites,BIOLOGY,chemistry,Drug Delivery Systems,drug effects,Drug Resistance,Drug ResistanceBacterial,Drug Synergism,drugs,Eubacterium,FAMILY,immunology,La,LOCATION,MECHANISM,MECHANISMS,Methods,ModelsChemical,ModelsImmunological,ModelsMolecular,nosource,PARTICLES,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,pharmacology,protein,Protein Binding,Proteins,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,RESISTANCE,Review,Ribosomal Proteins,ribosome,Ribosomes,Sensitivity and Specificity,Structural,STRUCTURAL BASIS,structure,Structure-Activity Relationship} } % == BibTeX quality report for auerbachRibosomalAntibioticsStructural2004: % ? Possibly abbreviated journal title Trends Biotechnol.

@article{auronFunctionalOrganizationLarge1981, title = {Functional Organization of the Large Ribosomal Subunit of {{Bacillus}} Stearothermophilus.}, author = {Auron, P.E. and Fahnestock, S.R.}, year = 1981, month = oct, journal = {Journal of Biological Chemistry}, volume = {256}, number = {19}, pages = {10105–10110}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(19)68749-1}, url = {http://www.jbc.org/content/256/19/10105.short}, abstract = {Bacillus stearothermophilus 50 S ribosomal subunits active in polyphenylalanine (polyPhe) synthesis were reconstituted from a mixture of purified proteins and RNA. Proteins were omitted one at a time, and the resulting particles were examined by sucrose gradient sedimentation and assayed for polyPhe synthesis, peptidyltransferase activity, and in some cases binding of elongation factor EF-G and GTP, and association with a (20 S . Phe-tRNA . poly(U)) complex. Based on their effect on polyPhe synthesis and peptidyltransferase activity, the proteins were grouped into four functional categories. The set of proteins most strongly required for peptidyltransferase activity, which must include the protein or proteins most directly involved in the active center, consists of proteins (probable Escherichia coli homologs in parentheses) B-L3 (E-L2), B-L4 (E-L4), B-L5 (E-L5), B-L6 (E-L3 or E- L6), B-L18 (E-L14), B-L20b (E-L16), and B-L25 (E-L20). Several proteins affected both polyPhe synthesis and peptidyltransferase activity more weakly. Only four proteins were required for polyPhe synthesis but not for peptidyltransferase activity, B-L2 (E-L1), B-L8 (E-L10), B-L13 (E- L7/L12), and B-L11(E-L11). The results indicate that the peptidyltransferase center is tightly integrated into the cooperative body of the 50 S subunit and that the (B-L8 . B-L13) complex is relatively independent of this cooperative domain}, keywords = {0,analysis,Bacillus stearothermophilus,BINDING,Cell Fractionation,elongation,Escherichia coli,GTP,homolog,Kinetics,La,metabolism,nosource,Peptidyltransferase,protein,Proteins,Ribosomal Proteins,Ribosomes,Rna,supportu.s.gov’tp.h.s.,TranslationGenetic,ultrastructure} } % == BibTeX quality report for auronFunctionalOrganizationLarge1981: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{avarssonStructurebasedSequenceAlignment1995, title = {Structure-Based Sequence Alignment of Elongation Factors {{Tu}} and {{G}} with Related {{GTPases}} Involved in Translation}, author = {Avarsson, A.}, year = 1995, month = dec, journal = {Journal of Molecular Evolution}, volume = {41}, number = {6}, pages = {1096–1104}, publisher = {Springer}, url = {http://www.springerlink.com/index/m6k17262mv84g330.pdf}, keywords = {alignment,EFTu,elongation,Escherichia coli,GTPase,human,initiation,No DOI found,nosource,protein,Proteins,ribosome,sequence,Structural,structure,translation} }

@article{babalRegulationOrnithineDecarboxylase2001, title = {Regulation of Ornithine Decarboxylase Activity and Polyamine Transport by Agmatine in Rat Pulmonary Artery Endothelial Cells}, author = {Babal, P. and Ruchko, M. and Campbell, C.C. and Gilmour, S.P. and Mitchell, J.L. and Olson, J.W. and Gillespie, M.N.}, year = 2001, month = feb, journal = {Journal of Pharmacology and Experimental Therapeutics}, volume = {296}, number = {2}, pages = {372–377}, publisher = {ASPET}, url = {ISI:000166462700019 http://jpet.aspetjournals.org/content/296/2/372.short}, abstract = {Agmatine, a product of arginine decarboxylation in mammalian cells, is believed to govern cell polyamines by inducing antizyme, which in turn suppresses ornithine decarboxylase (ODC) activity and polyamine uptake. However, since agmatine is structurally similar to the polyamines, it is possible that it exerts antizyme-independent actions on polyamine regulatory pathways. The present study determined whether agmatine inhibited ODC activity and polyamine transport in rat pulmonary artery endothelial cells (PAECs) by an antizyme-dependent mechanism. Agmatine caused time-dependent reductions in ODC activity, which occurred before increases in antizyme. Interventions that suppressed proteosome function caused large increases in ODC activity but failed to attenuate inhibitory effects of agmatine. When agmatine was present in the culture medium, C-14-polyamine uptake was competitively inhibited as evidenced by substantial elevations in Km values. If PAECs were incubated with agmatine for periods sufficient to increase antizyme, there were modest decreases in Vmax for putrescine and spermidine but not for spermine. These effects of agmatine on polyamine transport were insensitive to protein synthesis inhibition. Collectively, our findings show that agmatine decreases ODC activity and polyamine transport in PAECs, but a causal role for antizyme in these actions of agmatine is difficult to establish. Nevertheless, these observations are consistent with a model in which PAECs express both antizyme-1 and -2, but only the latter contributes to agmatine-mediated suppression of ODC activity}, keywords = {antizyme,Arginine,CELLS,CLONIDINE-DISPLACING SUBSTANCE,Culture Media,FEEDBACK REPRESSION,HYPERTENSION,IMIDAZOLINE RECEPTORS,INHIBITION,M,MAMMALIAN-CELLS,MECHANISM,media,MODEL,NEUROTRANSMITTER,NITRIC-OXIDE SYNTHASE,No DOI found,nosource,Ornithine Decarboxylase,polyamine,Polyamines,PROLIFERATION,protein,protein synthesis,protein synthesis inhibition,PROTEIN-SYNTHESIS,rat,regulation,S,SMOOTH-MUSCLE CELLS,Spermidine,suppression,TRANSPORT} }

@article{badisSnoRNAThatGuides2003a, title = {A {{snoRNA}} That Guides the Two Most Conserved Pseudouridine Modifications within {{rRNA}} Confers a Growth Advantage in Yeast}, author = {Badis, G. and {Fromont-Racine}, M. and Jacquier, A.}, year = 2003, month = jul, journal = {Rna-A Publication of the Rna Society}, volume = {9}, number = {7}, pages = {771–779}, doi = {10.1261/rna.5240503}, url = {ISI:000183699600001}, abstract = {Ribosomal RNAs contain a number of modified nucleotides. The most abundant nucleotide modifications found within rRNAs fall into two types: 2’-O-ribose methylations and pseudouridylations. In eukaryotes, small nucleolar guide RNAs, the snoRNAs that are the RNA components of the snoRNPs, specify the position of these modifications. The 2’-O-ribose methylations and pseudouridylations are guided by the box C/D and box H/ACA snoRNAs, respectively. The role of these modifications in rRNA remains poorly understood as no clear phenotype has yet been assigned to the absence of specific 2’-O-ribose methylations or pseudouridylations. Only very recently, a slight translation defect and perturbation of polysome profiles was reported in yeast for the absence of the Psi at position 2919 within the LSU rRNA. Here we report the identification and characterization in yeast of a novel intronic H/ACA snoRNA that we called snR191 and that guides pseudouridylation at positions 2258 and 2260 in the LSU rRNA. Most interestingly, these two modified bases are the most conserved pseudouridines from bacteria to human in rRNA. The corresponding human snoRNA is hU19. We show here that, in yeast, the presence of this snoRNA, and hence, most likely, of the conserved pseudouridines it specifies, is not essential for viability but provides a growth advantage to the cell}, keywords = {0,Bacteria,BINDING,COMPONENT,COMPONENTS,ELEMENTS,ESCHERICHIA-COLI,FIBRILLARIN,FORM PSEUDOURIDINES,H-ACA snoRNA,human,IDENTIFICATION,Methylation,modification,MUTATIONS,nosource,NUCLEOTIDE RESOLUTION,Nucleotides,Phenotype,Pseudouridine,pseudouridylation,psi,RESIDUES,RIBOSOMAL-RNA,ribosome,Rna,rRNA,Saccharomyces cerevisiae,SMALL NUCLEOLAR RNAS,stable RNA,translation,yeast} }

@misc{baherIntegratedDatabaseSupport1992, title = {Integrated Database to Support Research On⬚ {{Escherichia}} Coli⬚.}, author = {Baher, A. and Dunham, G. and Ginaburg, A. and Hagstrom, R. and Joerg, D. and Krazik, T. and Matsuda, H. and Michaels, G. and Overbeek, R. and Smith, C. and Taylor, R. and Yoshida, K. and Zawada, D.}, year = 1992, publisher = {{Math and Computer Science Division, Argonne National Laboratory}}, keywords = {Escherichia coli,nosource,Support} }

@article{baimMutationAllowingMRNA1985, title = {A Mutation Allowing an {{mRNA}} Secondary Structure Diminishes Translation of {{Saccharomyces}} Cerevisiae Iso-1-Cytochrome c}, author = {Baim, S.B. and Pietras, D.F. and Eustice, D.C. and Sherman, F.}, year = 1985, journal = {Molecular & Cellular Biology}, volume = {5}, number = {8}, pages = {1839–1846}, abstract = {The CYC1-239-O mutation in the yeast Saccharomyces cerevisiae produces a -His-Leu- replacement of the normal -Ala-Gly- sequence at amino acid positions 5 and 6, which lie within a dispensable region of iso-1-cytochrome c; this mutation can accommodate the formation of a hairpin structure at the corresponding site in the mRNA. The amount of the altered protein was diminished to 20% of the wild-type level, whereas the amount of the mRNA remained normal. However, in contrast to the normal CYC1+ mRNA that is associated mainly with four to seven ribosomes, the bulk of the CYC1-239-O mRNA is associated with one to four ribosomes. These results suggest that the stable secondary structure within the translated region of the CYC1 mRNA diminishes translation by inhibiting elongation}, keywords = {elongation,mRNA,Multiple DOI,Mutation,nonfile,nosource,polysomes,protein,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,sequence,structure,translation,yeast} }

@article{bakerSuppressionHumanColorectal1990, title = {Suppression of Human Colorectal Carcinoma Cell Growth by Wild-Type P53}, author = {Baker, S.J. and Markowitz, S. and Fearon, E.R. and Willson, J.K. and Vogelstein, B.}, year = 1990, journal = {Science}, volume = {249}, number = {4971}, pages = {912–915}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.2144057}, url = {http://www.sciencemag.org/content/249/4971/912.short}, abstract = {Mutations of the p53 gene occur commonly in colorectal carcinomas and the wild-type p53 allele is often concomitantly deleted. These findings suggest that the wild-type gene may act as a suppressor of colorectal carcinoma cell growth. To test this hypothesis, wild-type or mutant human p53 genes were transfected into human colorectal carcinoma cell lines. Cells transfected with the wild-type gene formed colonies five- to tenfold less efficiently than those transfected with a mutant p53 gene. In those colonies that did form after wild-type gene transfection, the p53 sequences were found to be deleted or rearranged, or both, and no exogenous p53 messenger RNA expression was observed. In contrast, transfection with the wild-type gene had no apparent effect on the growth of epithelial cells derived from a benign colorectal tumor that had only wild-type p53 alleles. Immunocytochemical techniques demonstrated that carcinoma cells expressing the wild-type gene did not progress through the cell cycle, as evidenced by their failure to incorporate thymidine into DNA. These studies show that the wild-type gene can specifically suppress the growth of human colorectal carcinoma cells in vitro and that an in vivo-derived mutation resulting in a single conservative amino acid substitution in the p53 gene product abrogates this suppressive ability}, keywords = {90364409,Amino Acid Substitution,cell cycle,Cell Division,Cell Line,cell lines,Colonic Neoplasms,cytology,Dna,DNA Replication,expression,gene,Genes,genetics,human,In Vitro,IN-VITRO,MESSENGER-RNA,Mutation,nosource,Nuclear Proteins,Oncogene Proteins,p53,Phosphoproteins,physiology,Plasmids,Rectal Neoplasms,Rna,RNAMessenger,sequence,supportu.s.gov’tp.h.s.,suppression,techniques,Transfection,Tumor CellsCultured} }

@article{bakinFourNewlyLocated1993, title = {Four Newly Located Pseudouridylate Residues in {{Escherichia}} Coli {{23S}} Ribosomal {{RNA}} Are All at the Peptidyltransferase Center: Analysis by the Application of a New Sequencing Technique}, author = {Bakin, A. and Ofengand, J.}, year = 1993, journal = {Biochemistry}, volume = {32}, number = {37}, pages = {9754–9762}, publisher = {ACS Publications}, doi = {10.1021/bi00088a030}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00088a030}, abstract = {A new technique has been developed for the facile location of pseudouridylate (psi) residues in any RNA molecule. The method uses two known modification procedures which in combination uniquely identify U residues which have been converted into psi. The first procedure involves reaction of all U-like and G-like residues with N-cyclohexyl- N’-beta-(4-methylmorpholinium)ethylcarbodiimide p-tosylate (CMC), followed by alkaline removal of all CMC groups except those linked to the N3 of psi. This stops reverse transcription, resulting in a gel band which identifies the U residue. The second procedure is uridine- specific hydrazinolysis which cleaves the RNA chain at all U residues and produces a gel band upon reverse transcription. psi residues, being resistant to hydrazinolysis, are not cleaved and do not stop reverse transcription. This leads to the absence of a band at psi residues. The combined method can also distinguish psi from 5-methyluridine, 4- thiouridine, uridine-5-oxyacetic acid, and 2-thio-5- methylaminomethyluridine as shown by treating rRNA and tRNA species known to contain these modified bases at defined sites. By this procedure, four new sites for psi in Escherichia coli 23S RNA were discovered, and one was disproven. The four new sites are at positions 2457, 2504, 2580, and 2605. The erroneous site is at position 2555. These four new psi residues, which are all in or within 2-3 residues of the peptidyltransferase ring, are thus in a position to play a functional and/or structural role at the peptidyltransferase center.(ABSTRACT TRUNCATED AT 250 WORDS)}, keywords = {0,analysis,Base Sequence,chemistry,enzymology,Escherichia coli,Hydrazines,Hydrogen Bonding,La,modification,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Peptidyltransferase,Pseudouridine,psi,Ribosomes,Rna,RNARibosomal23S,rRNA,Structural,Thiouridine,transcription,tRNA,Uridine} }

@article{bakinMapping13Pseudouridine1995, title = {Mapping of the 13 Pseudouridine Residues in {{Saccharomyces}} Cerevisiae Small Subunit Ribosomal {{RNA}} to Nucleotide Resolution}, author = {Bakin, A. and Ofengand, J.}, year = 1995, journal = {Nucleic acids research}, volume = {23}, number = {16}, pages = {3290–3294}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/23.16.3290}, url = {http://nar.oxfordjournals.org/content/23/16/3290.short}, abstract = {The number and location of all of the pseudouridine (phi) residues in Saccharomyces cerevisiae small subunit (SSU) ribosomal RNA have been determined by a reverse transcriptase sequencing method [Bakin, A. and Ofengand, J., 1993, Biochemistry, 32, 9754-9762]. Thirteen residues were found in addition to the previously described m1acp3 phi 1189. The residues were scattered throughout the molecule with three being in expansion segments. No phi was found in the three highly conserved single-stranded sequence elements common to all SSU RNAs. Specifically, phi 563, the analog of phi 516 (Escherichia coli) and phi 517 (Bacillus subtilis) were not found. Eight of the phi were located identically to those in mammalian SSU RNA and three were near to mammalian phi residues in the secondary structure. There was no discernible correlation between the sites for phi and the known locations of the methylated nucleosides as exists in large subunit (LSU) RNAs. Comparison of the structural context in which phi was found in SSU RNA with that in LSU RNA showed a differential bias suggestive of possible different roles for phi in the two rRNAs. This work also identified the locations of three putative new modified bases in SSU rRNA, and revealed 15 sequence differences between the yeast strain used here and the reported sequence}, keywords = {0,Bacillus subtilis,BASE,Base Sequence,BASES,Biochemistry,BIOLOGY,CEREVISIAE,chemistry,Chromosome Mapping,Dna,ELEMENTS,Escherichia coli,ESCHERICHIA-COLI,genetics,Humans,La,LOCATION,mapping,Methods,Molecular Biology,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleosides,NUCLEOTIDE RESOLUTION,polymerase,Pseudouridine,RESIDUES,RESOLUTION,REVERSE-TRANSCRIPTASE,ribosomal RNA,RIBOSOMAL-RNA,Rna,RNA-Directed DNA Polymerase,RNAFungal,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SECONDARY STRUCTURE,sequence,Sequence AnalysisRNA,SITE,SITES,Structural,structure,SUBUNIT,yeast} } % == BibTeX quality report for bakinMapping13Pseudouridine1995: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{balasundaramSpermidineDeficiencyIncreases1994a, title = {Spermidine Deficiency Increases +1 Ribosomal Frameshifting Efficiency and Inhibits {{Ty}}⬚1⬚ Retrotransposition in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Balasundaram, D. and Dinman, J.D. and Wickner, R.B. and Tabor, C.W. and Tabor, H.}, year = 1994, journal = {Proc.Natl.Acad.Sci.USA}, volume = {91}, pages = {172–176}, doi = {10.1073/pnas.91.1.172}, keywords = {efficiency,Frameshifting,Gag/Gag-pol ratio,nosource,Polyamines,ribosomal frameshifting,Saccharomyces,Saccharomyces cerevisiae,Ty1,viral particle assembly} } % == BibTeX quality report for balasundaramSpermidineDeficiencyIncreases1994a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{balasundaramTwoEssentialGenes1994a, title = {Two Essential Genes in the Biosynthesis of Polyamines That Modulate +1 Ribosomal Frameshifting In⬚ {{Saccharomyces}} Cerevisiae⬚.}, author = {Balasundaram, D. and Dinman, J.D. and Tabor, C.W. and Tabor, H.}, year = 1994, journal = {J.Bacteriol.}, volume = {176}, pages = {7126–7128}, doi = {10.1128/jb.176.22.7126-7128.1994}, keywords = {biosynthesis,Frameshifting,Gag/Gag-pol ratio,gene,Genes,nosource,Polyamines,ribosomal frameshifting,Saccharomyces,Saccharomyces cerevisiae} } % == BibTeX quality report for balasundaramTwoEssentialGenes1994a: % ? Possibly abbreviated journal title J.Bacteriol.

@article{baldariNovelLeaderPeptide1987, title = {A Novel Leader Peptide Which Allows Efficient Secretion of a Fragment of Human Interleukin {{1B}} in {{Saccharomyces}} Cerevisiae.}, author = {Baldari, C.J. and Murray, H. and Ghiara, H. and Cesareni, G. and Galeotti, C.L.}, year = 1987, journal = {EMBO J.}, volume = {6}, pages = {229–234}, doi = {10.1002/j.1460-2075.1987.tb04743.x}, keywords = {GAL inducible,human,leu2-d,nosource,pEMBLyex4,Saccharomyces,Saccharomyces cerevisiae} } % == BibTeX quality report for baldariNovelLeaderPeptide1987: % ? Possibly abbreviated journal title EMBO J.

@article{balzariniConcomitantCombinationTherapy1996, title = {Concomitant Combination Therapy for {{HIV}} Infection Preferable over Sequential Therapy with {{3TC}} and Non-Nucleoside Reverse Transcriptase Inhibitors}, author = {Balzarini, J. and Pelemans, H. and Karlsson, A. and De ClercQ, E. and Kleim, J.P.}, year = 1996, month = nov, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {93}, number = {23}, pages = {13152–13157}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.93.23.13152}, url = {http://www.pnas.org/content/93/23/13152.short}, keywords = {HIV,Mutation,nosource,virus} }

@article{banPlacementProteinRNA1999, title = {Placement of Protein and {{RNA}} Structures into a 5 {{A-resolution}} Map of the {{50S}} Ribosomal Subunit.}, author = {Ban, N. and Nissen, P. and Hansen, J. and Capel, M. and Moore, P.B. and Steitz, T.A.}, year = 1999, journal = {Nature}, volume = {400}, number = {6747}, pages = {841–847}, publisher = {Nature Publishing Group}, doi = {10.1038/23641}, url = {http://www.nature.com/nature/journal/v400/n6747/abs/400841a0.html}, abstract = {We have calculated at 5.0 A resolution an electron-density map of the large 50S ribosomal subunit from the bacterium Haloarcula marismortui by using phases derived from four heavy-atom derivatives, intercrystal density averaging and density-modification procedures. More than 300 base pairs of A-form RNA duplex have been fitted into this map, as have regions of non-A-form duplex, single-stranded segments and tetraloops. The long rods of RNA crisscrossing the subunit arise from the stacking of short, separate double helices, not all of which are A-form, and in many places proteins crosslink two or more of these rods. The polypeptide exit channel was marked by tungsten cluster compounds bound in one heavy-atom-derivatized crystal. We have determined the structure of the translation-factor-binding centre by fitting the crystal structures of the ribosomal proteins L6, L11 and L14, the sarcin-ricin loop RNA, and the RNA sequence that binds L11 into the electron density. We can position either elongation factor G or elongation factor Tu complexed with an aminoacylated transfer RNA and GTP onto the factor-binding centre in a manner that is consistent with results from biochemical and electron microscopy studies}, keywords = {99404611,Archaeal Proteins,Bacteria,chemistry,CrystallographyX-Ray,elongation,GTP,Haloarcula marismortui,nosource,Nucleic Acid Conformation,protein,Protein Conformation,Proteins,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNAArchaeal,RNARibosomal,sequence,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,ultrastructure} }

@article{banCompleteAtomicStructure2000, title = {The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 {{A}} Resolution.}, author = {Ban, N. and Nissen, P. and Hansen, J. and Moore, P.B. and Steitz, T.A.}, year = 2000, month = aug, journal = {Science}, volume = {289}, number = {5481}, pages = {905–920}, publisher = {American Association for the Advancement of Science}, issn = {00368075}, doi = {10.1126/science.289.5481.905}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.289.5481.905 http://www.sciencemag.org/content/289/5481/905.short}, abstract = {The large ribosomal subunit catalyzes peptide bond formation and binds initiation, termination, and elongation factors. We have determined the crystal structure of the large ribosomal subunit from Haloarcula marismortui at 2.4 angstrom resolution, and it includes 2833 of the subunit’s 3045 nucleotides and 27 of its 31 proteins. The domains of its RNAs all have irregular shapes and fit together in the ribosome like the pieces of a three-dimensional jigsaw puzzle to form a large, monolithic structure. Proteins are abundant everywhere on its surface except in the active site where peptide bond formation occurs and where it contacts the small subunit. Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit’s interior}, keywords = {Archaeal Proteins,Base Sequence,Binding Sites,chemistry,Conserved Sequence,Crystallography-X-Ray,CrystallographyX-Ray,elongation,Haloarcula marismortui,initiation,metabolism,Models-Molecular,ModelsMolecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleotides,protein,Protein Conformation,Protein Folding,Proteins,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNA-Archaeal,RNA-Ribosomal-23S,RNA-Ribosomal-5S,RNAArchaeal,RNARibosomal23S,RNARibosomal5S,structure,ultrastructure} }

@article{banerjeeIncreasedGenomeInstability2004, title = {Increased Genome Instability and Telomere Length in the Elg1-Deficient {{Saccharomyces}} Cerevisiae Mutant Are Regulated by {{S-phase}} Checkpoints}, author = {Banerjee, S. and Myung, K.}, year = 2004, month = dec, journal = {Eukaryotic Cell}, volume = {3}, number = {6}, pages = {1557–1566}, publisher = {Am Soc Microbiol}, doi = {10.1128/EC.3.6.1557-1566.2004}, url = {http://ec.asm.org/cgi/content/abstract/3/6/1557}, abstract = {Gross chromosomal rearrangements (GCRs) are frequently observed in cancer cells. Abnormalities in different DNA metabolism including DNA replication, cell cycle checkpoints, chromatin remodeling, telomere maintenance, and DNA recombination and repair cause GCRs in Saccharomyces cerevisiae. Recently, we used genome-wide screening to identify several genes the deletion of which increases GCRs in S. cerevisiae. Elg1, which was discovered during this screening, functions in DNA replication by participating in an alternative replication factor complex. Here we further characterize the GCR suppression mechanisms observed in the elg1Delta mutant strain in conjunction with the telomere maintenance role of Elg1. The elg1Delta mutation enhanced spontaneous DNA damage and resulted in GCR formation. However, DNA damage due to inactivation of Elg1 activates the intra-S checkpoints, which suppress further GCR formation. The intra-S checkpoints activated by the elg1Delta mutation also suppress GCR formation in strains defective in the DNA replication checkpoint. Lastly, the elg1Delta mutation increases telomere size independently of other previously known telomere maintenance proteins such as the telomerase inhibitor Pif1 or the telomere size regulator Rif1. The increase in telomere length caused by the elg1Delta mutation was suppressed by a defect in the DNA replication checkpoint, which suggests that DNA replication surveillance by Dpb11-Mec1/Tel1-Dun1 also has an important role in telomere length regulation}, keywords = {0,Base Sequence,BIOLOGY,cancer,Carrier Proteins,cell cycle,CELLS,CEREVISIAE,Chromatin,COMPLEX,COMPLEXES,Dna,DNA Damage,DNA Helicases,DNA Repair,DNA Replication,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,gene,Gene Deletion,Genes,Genetic,genetics,Genome,GenomeFungal,Genomic Instability,Helicase,human,human genome,IDENTIFY,INHIBITOR,La,MECHANISM,MECHANISMS,metabolism,Methyl Methanesulfonate,Molecular Biology,Molecular Sequence Data,Mutagens,Mutation,nosource,pharmacology,physiology,protein,Proteins,RECOMBINATION,RecombinationGenetic,regulation,REPLICATION,REPRESSOR,Repressor Proteins,S,S Phase,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Sequence HomologyNucleic Acid,suppression,SURVEILLANCE,Telomerase,Telomere,Telomere-Binding Proteins,Time Factors,ultrastructure} } % == BibTeX quality report for banerjeeIncreasedGenomeInstability2004: % ? unused Journal abbr (“Eukaryot.Cell”)

@article{barakEnhancedRibosomeFrameshifting1996, title = {Enhanced Ribosome Frameshifting in Stationary Phase Cells}, author = {Barak, Z. and Gallant, J. and Lindsley, D. and Kwieciszewki, B. and Heidel, D.}, year = 1996, month = oct, journal = {Journal of Molecular Biology}, volume = {263}, number = {2}, pages = {140–148}, publisher = {Elsevier}, doi = {10.1006/jmbi.1996.0565}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283696905653}, abstract = {We have examined the effect of growth phase in Escherichia coli on the a translation of a plasmid-borne lacZ gene in which active enzyme synthesis requires a leftward frameshift. During the log phase of growth, the differential rate of enzyme synthesis is very low. It increases by about two orders of magnitude during the small amount of protein synthesis which occurs at the end of log phase and the early part of stationary pi-case. The increase is sufficient to increase the enzyme’s specific activity in crude extracts to 30 times more than it would be if the log-phase differential rate continued unchanged. No such large increase is observed with a zero-frame lacZ(+) control gene on the same plasmid under the control of the same promoter; a significant but much smaller increase is observed with a zero-frame control containing an in-frame terminator tripler in the region of the required frameshift. Protein sequence analysis of the enzyme made from the frameshift reporter in stationary cells shows that the increased enzyme synthesis is due to frameshifting, and not due to termination and reinitiation. The frameshift occurs at or right after the sequence U UUC AAG, an intrinsically shifty site. (C) 1996 Academic Press Limited}, keywords = {analysis,CELLS,enzyme,Escherichia coli,ESCHERICHIA-COLI,expression,EXTRACTS,frameshift,Frameshifting,gene,GROWTH,HUNGRY CODON,nosource,PLASMID,PROMOTER,protein,protein synthesis,PROTEIN-SYNTHESIS,REGION,REQUIRES,ribosome,sequence,Sequence Analysis,SITE,stationary phase,suppression,termination,translation} }

@article{baranovNewTechniqueCharacterization1997a, title = {A New Technique for the Characterization of Long-Range Tertiary Contacts in Large {{RNA}} Molecules: Insertion of a Photolabel at a Selected Position in {{16S rRNA}} within the {{Escherichia}} Coli Ribosome}, author = {Baranov, P.V. and Dokudovskaya, S.S. and Oretskaya, T.S. and Dontsova, O.A. and Bogdanov, A.A. and Brimacombe, R.}, year = 1997, month = jun, journal = {Nucleic Acids Res.}, volume = {25}, number = {12}, pages = {2266–2273}, doi = {10.1093/nar/25.12.2266}, url = {PM:9171076}, abstract = {A new approach for inserting a photo-label at a selected position within the long ribosomal RNA molecules has been developed. The Escherichia coli 16S rRNA was cleaved at a single internucleotide bond, 1141-1142, with RNase H in the presence of a complementary chimeric oligonucleotide. 4-Thiouridine 5’, 3’-diphosphate was ligated to the 3’- end of the 5’fragment at the cleavage site with T4 RNA ligase. The 16S rRNA fragments containing this added photo-reactive nucleotide were assembled together with total 30S ribosomal proteins into small ribosomal subunits. The ability of such 30S particles containing fragmented rRNA to form 70S ribosomes has been demonstrated previously. Crosslinks were induced within the 30S subunits by mild UV irradiation. The sites of crosslinking within the 16S rRNA were then analyzed using RNase H digestion and reverse transcription. Two crosslinks from the thio-nucleotide attached to nt C1141 of 16S rRNA were observed, namely to nt U1295 and G1272. These results are in agreement with the established proximity of helix 39 and 41 in the 3D structure of the 30S ribosomal subunit, as shown by other intra RNA crosslinking data. These data furthermore allow us to refine the structural arrangement of helices 41 and 39 relative to one another}, keywords = {0,analogs & derivatives,ATP,Bacteriophage T4,Base Sequence,chemical synthesis,chemistry,Chimera,Cross-Linking Reagents,Dna,enzymology,Escherichia coli,Indicators and Reagents,La,metabolism,ModelsMolecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Oligoribonucleotides,polymerase,protein,Proteins,Ribonuclease HCalf Thymus,Ribosomal Proteins,ribosome,Ribosomes,Rna,Rna Ligase (Atp),RNA-Directed DNA Polymerase,RNARibosomal16S,RNAse,rRNA,Structural,structure,Substrate Specificity,supportnon-u.s.gov’t,transcription,ultraviolet rays,Uridine,Uridine Diphosphate} } % == BibTeX quality report for baranovNewTechniqueCharacterization1997a: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{baranovNewFeatures23S1998, title = {New Features of {{23S}} Ribosomal {{RNA}} Folding: The Long Helix 41-42 Makes a” {{U-turn}}” inside the Ribosome.}, author = {Baranov, P.V. and Gurvich, O.L. and Bogdanov, A.A. and Brimacombe, R. and Dontsova, O.A.}, year = 1998, month = jun, journal = {RNA}, volume = {4}, number = {6}, pages = {658–668}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838298980104}, url = {http://rnajournal.cshlp.org/content/4/6/658.short}, abstract = {23S rRNA from Escherichia coli was cleaved at single internucleotide bonds using ribonuclease H in the presence of appropriate chimeric oligonucleotides; the individual cleavage sites were between residues 384 and 385, 867 and 868, 1045 and 1046, and 2510 and 2511, with an additional fortuitous cleavage at positions 1117 and 1118. In each case, the 3’ terminus of the 5’ fragment was ligated to radioactively labeled 4-thiouridine 5’-,3’-biphosphate (“psUp”), and the cleaved 23S rRNA carrying this label was reconstituted into 50S subunits. The 50S subunits were able to associate normally with 30S subunits to form 70S ribosomes. Intra-RNA crosslinks from the 4-thiouridine residues were induced by irradiation at 350 nm, and the crosslink sites within the 23S rRNA were analyzed. The rRNA molecules carrying psUp at positions 867 and 1117 showed crosslinks to nearby positions on the opposite strand of the same double helix where the cleavage was located, and no crosslinking was detected from position 2510. In contrast, the rRNA carrying psUp at position 384 showed crosslinking to nt 420 (and sometimes also to 416 and 425) in the neighboring helix in 23S rRNA, and the rRNA with psUp at position 1045 gave a crosslink to residue 993. The latter crosslink demonstrates that the long helix 41-42 of the 23S rRNA (which carries the region associated with GTPase activity) must double back on itself, forming a “U-turn” in the ribosome. This result is discussed in terms of the topography of the GTPase region in the 50S subunit, and its relation to the locations of the 5S rRNA and the peptidyl transferase center}, keywords = {0,5S rRNA,analogs & derivatives,Base Sequence,chemistry,Cross-Linking Reagents,Escherichia coli,GTPase,La,metabolism,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Oligonucleotides,peptidyl transferase,Peptidyltransferase,Ribonuclease HCalf Thymus,ribosome,Ribosomes,Rna,RNARibosomal23S,RNARibosomal5S,rRNA,supportnon-u.s.gov’t,Thiouridine,Uridine,Uridine Diphosphate} }

@article{baranovDatabaseRibosomalCross1998, title = {The {{Database}} of {{Ribosomal Cross}} Links ({{DRC}})}, author = {Baranov, P.V. and Sergiev, P.V. and Dontsova, O.A. and Bogdanov, A.A. and Brimacombe, R.}, year = 1998, month = jan, journal = {Nucleic Acids Research}, volume = {26}, number = {1}, pages = {187–189}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/26.1.187}, url = {http://nar.oxfordjournals.org/content/26/1/187.short}, abstract = {The Database of Ribosomal Cross-links (DRC) provides a complete collection of all the published data produced by cross-linking studies on the Escherichia coli ribosome, as well as on its components and functional ligands. The DRC currently includes data on 986 cross-links from {\(>\)}100 research papers, yielded by {\(>\)}40 different reagents. For each cross-link, information is given concerning its location in the ribosome, the chemical or photochemical reagent applied, a brief description of the method(s) used to locate the cross-link, and the literature reference. The DRC is freely available via the World Wide Web at: http://Ribosome.Genebee.MSU.SU/DRC/ or at http://WWW:MPIMG- Berlin-Dahlem.MPG.DE/[symbol: see text]baranov/DRC/}, keywords = {0,chemistry,Computer Communication Networks,Cross-Linking Reagents,DatabasesFactual,Escherichia coli,Forecasting,Information Storage and Retrieval,La,nosource,ribosome,Ribosomes} } % == BibTeX quality report for baranovDatabaseRibosomalCross1998: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{baranovRECODEDatabaseFrameshifting2001, title = {{{RECODE}}: A Database of Frameshifting, Bypassing and Codon Redefinition Utilized for Gene Expression}, author = {Baranov, P.V. and Gurvich, O.L. and Fayet, O. and Prere, M.F. and Miller, W.A. and Gesteland, R.F. and Atkins, J.F. and Giddings, M.C.}, year = 2001, month = jan, journal = {Nucleic Acids Research}, volume = {29}, number = {1}, pages = {264–267}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/29.1.264}, url = {http://nar.oxfordjournals.org/content/29/1/264.short}, abstract = {The RECODE database is a compilation of ‘programmed’ translational recoding events taken from the scientific literature and personal communications. The database deals with programmed ribosomal frameshifting, codon redefinition and translational bypass occurring in a variety of organisms. The entries for each event include the sequences of the corresponding genes, their encoded proteins for both the normal and alternate decoding, the types of the recoding events involved, trans-factors and cis-elements that influence recoding. The database is freely available at http://recode.genetics.utah.edu/}, keywords = {Codon,codon redefinition,DATABASE,decoding,efficiency,expression,Frameshifting,gene,Gene Expression,GENE-EXPRESSION,Genes,human,nosource,protein,Proteins,recoding,ribosomal frameshifting,sequence,SEQUENCES,translational bypass} }

@article{baranovRecode20032003, title = {Recode 2003}, author = {Baranov, P.V. and Gurvich, O.L. and Hammer, A.W. and Gesteland, R.F. and Atkins, J.F.}, year = 2003, month = jan, journal = {Nucleic Acids Research}, volume = {31}, number = {1}, pages = {87–89}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkg024}, url = {http://nar.oxfordjournals.org/content/31/1/87.short}, abstract = {The RECODE database is a compilation of translational recoding events (programmed ribosomal frameshifting, codon redefinition and translational bypass). The database provides information about the genes utilizing these events for their expression, recoding sites, stimulatory sequences and other relevant information. The Database is freely available at http://recode.genetics.utah.edu/}, keywords = {Codon,codon redefinition,DATABASE,expression,Frameshifting,gene,Genes,human,nosource,recoding,ribosomal frameshifting,sequence,translational bypass} } % == BibTeX quality report for baranovRecode20032003: % ? Title looks like it was stored in title-case in Zotero

@article{barikSitedirectedMutagenesisVitro1996, title = {Site-Directed Mutagenesis in Vitro by Megaprimer {{PCR}}}, author = {Barik, S.}, year = 1996, journal = {METHODS IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-}, volume = {57}, pages = {203–215}, publisher = {Springer}, url = {http://www.springerlink.com/index/T72388T844442260.pdf}, keywords = {0,Amino Acid Sequence,Base Sequence,Biochemistry,BIOLOGY,chemistry,Dna,DNA Primers,DNARecombinant,genetics,In Vitro,IN-VITRO,isolation & purification,La,Methods,Molecular Biology,Molecular Sequence Data,Mutagenesis,MutagenesisSite-Directed,No DOI found,nosource,PCR,Polymerase Chain Reaction,Review,Support,TemplatesGenetic} } % == BibTeX quality report for barikSitedirectedMutagenesisVitro1996: % ? unused Journal abbr (“Methods Mol.Biol.”)

@article{barre-sinoussiIsolationTlymphotropicRetrovirus1983, title = {Isolation of a {{T-lymphotropic}} Retrovirus from a Patient at Risk for Acquired Immune Deficiency Syndrome ({{AIDS}})}, author = {{Barre-Sinoussi}, F. and Chermann, J.C. and Rey, F. and Nugeyre, M.T. and Chamaret, S. and Gruest, J. and Dauguet, C. and {Axler-Blin}, C. and {Vezinet-Brun}, F. and Rouzioux, C. and Rozenbaum, W. and Montagnier, L.}, year = 1983, month = may, journal = {Science}, volume = {220}, number = {4599}, pages = {868–871}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.6189183}, url = {http://www.sciencemag.org/content/220/4599/868.short PM:6189183}, abstract = {A retrovirus belonging to the family of recently discovered human T-cell leukemia viruses (HTLV), but clearly distinct from each previous isolate, has been isolated from a Caucasian patient with signs and symptoms that often precede the acquired immune deficiency syndrome (AIDS). This virus is a typical type-C RNA tumor virus, buds from the cell membrane, prefers magnesium for reverse transcriptase activity, and has an internal antigen (p25) similar to HTLV p24. Antibodies from serum of this patient react with proteins from viruses of the HTLV-I subgroup, but type-specific antisera to HTLV-I do not precipitate proteins of the new isolate. The virus from this patient has been transmitted into cord blood lymphocytes, and the virus produced by these cells is similar to the original isolate. From these studies it is concluded that this virus as well as the previous HTLV isolates belong to a general family of T-lymphotropic retroviruses that are horizontally transmitted in humans and may be involved in several pathological syndromes, including AIDS}, keywords = {0,Acquired Immunodeficiency Syndrome,Adult,AIDS,Animals,Antibodies,AntibodiesViral,antibody,ANTIGEN,blood,Cell Membrane,CELLS,CellsCultured,deficiency,DISCOVERY,Dna,FAMILY,HIV,Hiv-1,human,Humans,immunology,isolation & purification,La,LEUKEMIA,Magnesium,Male,metabolism,microbiology,MicroscopyElectron,nosource,polymerase,protein,Proteins,Retroviridae,retrovirus,RETROVIRUSES,REVERSE-TRANSCRIPTASE,Rna,RNA-Directed DNA Polymerase,Syndrome,T-Lymphocytes,Tumor Virus Infections,virus,Viruses} }

@article{barrettImmunologicalIdentityProteins1984a, title = {Immunological Identity of Proteins That Bind Stored {{5S RNA}} in {{Xenopus}} Oocytes}, author = {Barrett, P. and Johnson, R.M. and Sommerville, J.}, year = 1984, journal = {Exp.Cell Res.}, volume = {153}, number = {2}, pages = {299–307}, doi = {10.1016/0014-4827(84)90602-5}, abstract = {In small oocytes of Xenopus laevis, the three most abundant proteins are isolated as basic polypeptides with molecular weights of 48 kD (P48), 43 kD (P43) and 40 kD (P40, also known as transcription factor IIIA). All three proteins share common properties in being able to bind specifically ribosomal 5S RNA molecules and influence, in different ways, their rates of production and utilization. It has been shown by biochemical analysis and immunological characterization that the three proteins are structurally distinct and are most probably the products of different genes. Immunostaining and radio-immunoassays indicate that both P48 and P43 have diverged considerably in structure between the amphibian genera Xenopus and Triturus. Antibodies raised against the transcription factor for Xenopus laevis 5S RNA genes (P40/TFIIIA) do not cross-react with the transcription factor isolated from oocytes of the closely related species Xenopus borealis. A protein equivalent of TFIIIA is not found in 5S RNA-containing RNP storage particles of Triturus oocytes. The functions of the three Xenopus oocyte proteins in transporting 5S RNA between different cellular compartments are considered in the light of these variations}, keywords = {5S rRNA,84236521,analysis,animal,Antibodies,antibody,Cross Reactions,Female,gene,Genes,immunology,metabolism,Molecular Weight,nosource,Oocytes,protein,Protein Binding,Proteins,Radioimmunoassay,Rna,RNARibosomal,rRNA,Staining,structure,supportnon-u.s.gov’t,transcription,Triturus,Xenopus,Xenopus laevis} } % == BibTeX quality report for barrettImmunologicalIdentityProteins1984a: % ? Possibly abbreviated journal title Exp.Cell Res.

@article{bartelMicroRNAsRootPlant2003, title = {{{MicroRNAs}}: At the Root of Plant Development?}, author = {Bartel, B. and Bartel, D.P.}, year = 2003, month = jun, journal = {Plant Physiology}, volume = {132}, number = {2}, pages = {709–717}, publisher = {Am Soc Plant Biol}, doi = {10.1104/pp.103.023630}, url = {http://www.plantphysiol.org/content/132/2/709.short}, keywords = {0,development,genetics,growth & development,La,metabolism,MicroRNAs,nosource,Plant Proteins,Plant Roots,protein,Proteins,Rna,RNAMessenger,RnaPlant,RNASmall Interfering,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,TranscriptionGenetic} } % == BibTeX quality report for bartelMicroRNAsRootPlant2003: % ? unused Journal abbr (“Plant Physiol”)

@incollection{bartelTwohybridSystemYeast1993, title = {The Two-Hybrid System of Yeast.}, booktitle = {Cellular {{Interactions}} in {{Development}}.}, author = {Bartel, P.L. and Chien, C.-T. and Sternglanz, R. and Fields, S.}, year = 1993, pages = {153–179}, publisher = {Oxford University Press}, address = {Oxford, England}, collaborator = {Hartley, D.A.}, keywords = {2-hybrid system,Methods,nosource,yeast} }

@article{bashanStructuralBasisRibosomal2003, title = {Structural Basis of the Ribosomal Machinery for Peptide Bond Formation, Translocation, and Nascent Chain Progression}, author = {Bashan, A. and Agmon, I. and Zarivach, R. and Schluenzen, F. and Harms, J. and Berisio, R. and Bartels, H. and Franceschi, F. and Auerbach, T. and Hansen, H.A. and Kossoy, E. and Kessler, M. and Yonath, A.}, year = 2003, month = jan, journal = {Molecular cell}, volume = {11}, number = {1}, pages = {91–102}, publisher = {Elsevier}, doi = {10.1016/S1097-2765(03)00009-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276503000091}, abstract = {Crystal structures of tRNA mimics complexed with the large ribosomal subunit of Deinococcus radiodurans indicate that remote interactions determine the precise orientation of tRNA in the peptidyl-transferase center (PTC). The PTC tolerates various orientations of puromycin derivatives and its flexibility allows the conformational rearrangements required for peptide-bond formation. Sparsomycin binds to A2602 and alters the PTC conformation. H69, the intersubunit-bridge connecting the PTC and decoding site, may also participate in tRNA placement and translocation. A spiral rotation of the 3’ end of the A-site tRNA around a 2-fold axis of symmetry identified within the PTC suggests a unified ribosomal machinery for peptide-bond formation, A-to-P-site translocation, and entrance of nascent proteins into the exit tunnel. Similar 2-fold related regions, detected in all known structures of large ribosomal subunits, indicate the universality of this mechanism}, keywords = {0,3,A SITE,A-SITE,Bacterial,Bacterial Proteins,BIOLOGY,BOND FORMATION,Catalytic Domain,chemistry,CONFORMATION,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,CrystallographyX-Ray,decoding,Deinococcus,derivatives,genetics,INHIBITOR,La,MECHANISM,metabolism,ModelsMolecular,Molecular Structure,nosource,Nucleic Acid Conformation,peptide bond formation,PEPTIDE-BOND FORMATION,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,protein,Protein Conformation,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,Proteins,Puromycin,REGION,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,Rna,RNATransferAmino Acyl,SITE,sparsomycin,Structural,STRUCTURAL BASIS,structure,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYNTHESIS INHIBITORS,TranslationGenetic,translocation,tRNA} } % == BibTeX quality report for bashanStructuralBasisRibosomal2003: % ? unused Journal abbr (“Mol Cell”)

@article{bassMaizeRibosomeinactivatingProtein1992, title = {A Maize Ribosome-Inactivating Protein Is Controlled by the Transcriptional Activator {{Opaque-2}}}, author = {Bass, H.W. and Webster, C. and OBrian, G.R. and Roberts, J.K. and Boston, R.S.}, year = 1992, journal = {Plant Cell}, volume = {4}, number = {2}, pages = {225–234}, keywords = {Multiple DOI,nonfile,nosource,protein} }

@article{bateyPreparationIsotopicallyEnriched1995a, title = {Preparation of Isotopically Enriched {{RNAs}} for Heteronuclear {{NMR}}.}, author = {Batey, R.T. and Battiste, J.L. and Williamson, J.R.}, year = 1995, journal = {Methods in enzymology}, volume = {261}, eprint = {8569501}, eprinttype = {pubmed}, pages = {300–322}, doi = {10.1016/S0076-6879(95)61015-4}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8569501}, keywords = {0,Bacterial,Base Sequence,BIOLOGY,chemistry,ChromatographyHigh Pressure Liquid,Culture Media,Deoxyribonucleotides,Escherichia coli,genetics,Gram-Negative Aerobic Bacteria,growth & development,Hydrolysis,isolation & purification,Isotope Labeling,La,Magnetic Resonance Spectroscopy,media,metabolism,Molecular Sequence Data,NMR,nosource,Ribonucleotides,Rna,RNABacterial,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,TranscriptionGenetic} } % == BibTeX quality report for bateyPreparationIsotopicallyEnriched1995a: % ? unused Journal abbr (“Methods Enzymol.”)

@article{baxCorrelationProtonN151983a, title = {Correlation of {{Proton}} and {{N-15 Chemical-Shifts}} by {{Multiple Quantum Nmr}}}, author = {Bax, A. and Griffey, R.H. and Hawkins, B.L.}, year = 1983, journal = {Journal of Magnetic Resonance}, volume = {55}, number = {2}, pages = {301–315}, url = {ISI:A1983RR92300012}, keywords = {NMR,No DOI found,nosource} } % == BibTeX quality report for baxCorrelationProtonN151983a: % ? Title looks like it was stored in title-case in Zotero

@article{baxDipolarCouplingsMacromolecular2001, title = {Dipolar Couplings in Macromolecular Structure Determination}, author = {Bax, A. and Kontaxis, G. and Tjandra, N.}, year = 2001, journal = {Methods Enzymol.}, volume = {339}, pages = {127–174}, doi = {10.1016/S0076-6879(01)39313-8}, url = {PM:11462810}, keywords = {0,ACID,ACIDS,chemistry,disease,Hydrogen,Kidney,La,Macromolecular Systems,Magnetic Resonance Spectroscopy,Methods,Micelles,ModelsChemical,ModelsMolecular,Molecular Structure,Nitrogen,Nitrogen Isotopes,nosource,Nucleic Acids,protein,Proteins,Purple Membrane,Review,statistics & numerical data,structure,SYSTEM,SYSTEMS,Ubiquitins} } % == BibTeX quality report for baxDipolarCouplingsMacromolecular2001: % ? Possibly abbreviated journal title Methods Enzymol.

@article{baxter-roshekOptimizationRibosomeStructure2007a, title = {Optimization of Ribosome Structure and Function by {{rRNA}} Base Modification.}, author = {{Baxter-Roshek}, J.L. and Petrov, A.N. and Dinman, J.D.}, year = 2007, journal = {PLoS ONE}, volume = {2}, number = {1}, pages = {e174}, doi = {10.1371/journal.pone.0000174}, url = {http://dx.plos.org/10.1371/journal.pone.0000174}, abstract = {⬚2Background. ⬚ Translating mRNA sequences into functional proteins is a fundamental process necessary for the viability of organisms throughout all kingdoms of life. The ribosome carries out this process with a delicate balance between speed and accuracy. This work investigates how ribosome structure and function are affected by rRNA base modification. The prevailing view is that rRNA base modifications serve to fine-tune ribosome structure and function. ⬚Methodology/Principal Findings:⬚ To test this hypothesis, yeast strains deficient in rRNA modifications in the ribosomal peptidyltransferase center were monitored for changes in and translational fidelity. These studies revealed allele-specific sensitivity to translational inhibitors, changes in reading frame maintenance, nonsense suppression and aa-tRNA selection. Ribosomes isolated from two mutants with the most pronounced phenotypic changes had increased affinities for aa-tRNA, and surprisingly, increased rates of peptidyltransfer as monitored by the puromycin assay. rRNA chemical analyses of one of these mutants identified structural changes in five specific bases associated with the ribosomal A-site. ⬚Conclusions/Significance:⬚ Together, the data suggest that modification of these bases fine tune the structure of the A-site region of the large subunit so as to assure correct positioning of critical rRNA bases involved in aa-tRNA accommodation into the PTC, of the eEF-1A⬚aa-tRNA⬚GTP ternary complex with the GTPase associated center, and of the aa-tRNA in the A-site. These findings represent a direct demonstration in support of the prevailing hypothesis that rRNA modifications serve to optimize rRNA structure for production of accurate and efficient ribosomes.}, keywords = {A SITE,A-SITE,accuracy,BASE,BASES,COMPLEX,COMPLEXES,Fidelity,FRAME,FRAME MAINTENANCE,GTPase,INHIBITOR,inhibitors,modification,mRNA,MUTANTS,NONSENSE,nonsense suppression,nosource,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,protein,Proteins,Puromycin,READING FRAME,REGION,ribosome,Ribosomes,rRNA,SELECTION,sequence,SEQUENCES,Structural,structure,SUBUNIT,Support,suppression,translational fidelity,yeast} }

@article{beckenbachSingleNucleotideFrameshifts2005a, title = {Single Nucleotide +1 Frameshifts in an Apparently Functional Mitochondrial Cytochrome b Gene in Ants of the Genus {{Polyrhachis}}}, author = {Beckenbach, A.T. and Robson, S.K. and Crozier, R.H.}, year = 2005, month = feb, journal = {J.Mol.Evol.}, volume = {60}, number = {2}, pages = {141–152}, doi = {10.1007/s00239-004-0178-5}, url = {PM:15785844}, abstract = {Twelve of 30 species examined in the ant genus Polyrhachis carry single nucleotide insertions at one or two positions within the mitochondrial cytochrome b (cytb) gene. Two of the sites are present in more than one species. Nucleotide substitutions in taxa carrying insertions show the strong codon position bias expected of functional protein coding genes, with substitutions concentrated in the third positions of the original reading frame. This pattern of evolution of the sequences strongly suggests that they are functional cytb sequences. This result is not the first report of +1 frameshift insertions in animal mitochondrial genes. A similar site was discovered in vertebrates, where single nucleotide frameshift insertions in many birds and a turtle were reported by Mindell et al. (Mol Biol Evol 15:1568, 1998). They hypothesized that the genes are correctly decoded by a programmed frameshift during translation. The discovery of four additional sites gives us the opportunity to look for common features that may explain how programmed frameshifts can arise. The common feature appears to be the presence of two consecutive rare codons at the insertion site. We hypothesize that the second of these codons is not efficiently translated, causing a pause in the translation process. During the stall the weak wobble pairing of the tRNA bound in the peptidyl site of the ribosome, together with an exact Watson-Crick codon-anticodon pairing in the +1 position, allows translation to continue in the +1 reading frame. The result of these events is an adequate level of translation of a full-length and fully functional protein. A model is presented for decoding of these mitochondrial genes, consistent with known features of programmed translational frameshifting in the yeast TY1 and TY3 retrotransposons}, keywords = {0,Amino Acid Sequence,animal,Animals,Ants,Base Sequence,chemistry,Codon,CODONS,Comparative Study,Cytochrome b,Cytochromes b,decoding,DISCOVERY,Dna,DNAMitochondrial,Evolution,EvolutionMolecular,FRAME,frameshift,Frameshift Mutation,Frameshifting,gene,Genes,GenesInsect,genetics,La,MODEL,ModelsGenetic,Molecular Sequence Data,nosource,Nucleic Acid Conformation,POSITION,POSITIONS,protein,READING FRAME,Research SupportNon-U.S.Gov’t,retrotransposon,ribosome,Rna,RNATransfer,sequence,SEQUENCES,SITE,SITES,Species Specificity,translation,TRANSLATIONAL FRAMESHIFTING,tRNA,Ty1,TY3,Vertebrates,yeast} } % == BibTeX quality report for beckenbachSingleNucleotideFrameshifts2005a: % ? Possibly abbreviated journal title J.Mol.Evol.

@article{beckettGeneticControlBiochemical1941, title = {Genetic Control of Biochemical Reactions in ⬚{{Neurospora}}⬚.}, author = {Beckett, G.J. and Tatum, E.L.}, year = 1941, journal = {Proc.Natl.Adac.Sci.USA}, volume = {27}, pages = {499–506}, doi = {10.1073/pnas.27.11.499}, keywords = {gene,Genetic,nosource,protein} } % == BibTeX quality report for beckettGeneticControlBiochemical1941: % ? Possibly abbreviated journal title Proc.Natl.Adac.Sci.USA

@article{beckmannArchitectureProteinconductingChannel2001, title = {Architecture of the Protein-Conducting Channel Associated with the Translating {{80S}} Ribosome}, author = {Beckmann, R. and Spahn, C.M. and Eswar, N. and Helmers, J. and Penczek, P.A. and Sali, A. and Frank, J. and Blobel, G.}, year = 2001, month = nov, journal = {Cell}, volume = {107}, number = {3}, pages = {361–372}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(01)00541-4}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867401005414}, abstract = {In vitro assembled yeast ribosome-nascent chain complexes (RNCs) containing a signal sequence in the nascent chain were immunopurified and reconstituted with the purified protein-conducting channel (PCC) of yeast endoplasmic reticulum, the Sec61 complex. A cryo-EM reconstruction of the RNC-Sec61 complex at 15.4 A resolution shows a tRNA in the P site. Distinct rRNA elements and proteins of the large ribosomal subunit form four connections with the PCC across a gap of about 10-20 A. Binding of the PCC influences the position of the highly dynamic rRNA expansion segment 27. The RNC-bound Sec61 complex has a compact appearance and was estimated to be a trimer. We propose a binary model of cotranslational translocation entailing only two basic functional states of the translating ribosome-channel complex}, keywords = {0,Base Sequence,BINDING,chemistry,genetics,In Vitro,IN-VITRO,La,Membrane Proteins,metabolism,Molecular Sequence Data,nosource,Nucleic Acid Conformation,protein,Proteins,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNAFungal,RNATransfer,rRNA,Saccharomyces cerevisiae,sequence,SIGNAL,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,TranslationGenetic,translocation,tRNA,ultrastructure,yeast} }

@article{beelmanDifferentialEffectsTranslational1994, title = {Differential Effects of Translational Inhibition in Cis and in Trans on the Decay of the Unstable Yeast {{MFA2 mRNA}}.}, author = {Beelman, C.A. and Parker, R.}, year = 1994, month = apr, journal = {Journal of Biological Chemistry}, volume = {269}, number = {13}, pages = {9687–9692}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(17)36937-5}, url = {http://www.jbc.org/content/269/13/9687.short}, abstract = {Several observations in eukaryotic cells suggest that the processes of translation and mRNA turnover are interrelated. To understand this relationship, we examined the effects of translational inhibition on the decay of the unstable yeast MFA2 mRNA, which is degraded in a 5’ to 3’ direction following deadenylation (1). Although inhibition of translation in cis stabilizes several unstable mammalian transcripts, inhibiting translation of the MFA2 mRNA in cis, by the insertion of a large stem-loop structure in the 5’-untranslated region (UTR), did not affect the half-life, deadenylation rate, or appearance of specific decay intermediates. Therefore, efficient translational elongation on the MFA2 mRNA is not a requirement for the normal rate, or mechanism, of degradation of this transcript. In contrast, inhibition of translation in trans, by the addition of cycloheximide, stabilized the deadenylated form of MFA2 mRNA. Furthermore, the MFA2 transcripts that were not translated due to a stem-loop in the 5’-UTR were also stabilized in the presence of cycloheximide, suggesting that cycloheximide is likely to affect mRNA stability indirectly. These results suggest possible relationships between the mechanisms of mRNA decay and the translational process}, keywords = {94193652,Base Sequence,biosynthesis,Cycloheximide,degradation,drug effects,elongation,Eukaryotic Cells,Gene Expression RegulationFungal,GenesFungal,genetics,isolation & purification,Kinetics,metabolism,Molecular Sequence Data,mRNA,mRNA decay,MutagenesisInsertional,MutagenesisSite-Directed,nosource,Oligodeoxyribonucleotides,pharmacology,Plasmids,RNAFungal,RNAMessenger,Saccharomyces cerevisiae,stability,structure,supportu.s.gov’tp.h.s.,TranscriptionGenetic,translation,TranslationGenetic,turnover,yeast} } % == BibTeX quality report for beelmanDifferentialEffectsTranslational1994: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{beierMisreadingTerminationCodons2001, title = {Misreading of Termination Codons in Eukaryotes by Natural Nonsense Suppressor {{tRNAs}}}, author = {Beier, H. and Grimm, M.}, year = 2001, month = dec, journal = {Nucleic acids research}, volume = {29}, number = {23}, pages = {4767–4782}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/29.23.4767}, url = {http://nar.oxfordjournals.org/content/29/23/4767.short}, abstract = {Translational stop codon readthrough provides a regulatory mechanism of gene expression that is extensively utilised by positive-sense ssRNA viruses. The misreading of termination codons is achieved by a variety of naturally occurring suppressor tRNAs whose structure and function is the subject of this survey. All of the nonsense suppressors characterised to date (with the exception of selenocysteine tRNA) are normal cellular tRNAs that are primarily needed for reading their cognate sense codons. As a consequence, recognition of stop codons by natural suppressor tRNAs necessitates unconventional base pairings in anticodon-codon interactions. A number of intrinsic features of the suppressor tRNA contributes to the ability to read non-cognate codons. Apart from anticodon-codon affinity, the extent of base modifications within or 3’ of the anticodon may up- or down-regulate the efficiency of suppression. In order to out-compete the polypeptide chain release factor an absolute prerequisite for the action of natural suppressor tRNAs is a suitable nucleotide context, preferentially at the 3’ side of the suppressed stop codon. Three major types of viral readthrough sites, based on similar sequences neighbouring the leaky stop codon, can be defined. It is discussed that not only RNA viruses, but also the eukaryotic host organism might gain some profit from cellular suppressor tRNAs}, keywords = {0,3,Animals,Anticodon,BASE,Base Pairing,Base Sequence,chemistry,Codon,CODONS,CodonTerminator,efficiency,expression,gene,Gene Expression,Gene Expression RegulationViral,GENE-EXPRESSION,genetics,La,MECHANISM,modification,Molecular Sequence Data,NONSENSE,nosource,Peptide Chain TerminationTranslational,physiology,POLYPEPTIDE,POLYPEPTIDE-CHAIN,readthrough,RECOGNITION,RELEASE,release factor,Research SupportNon-U.S.Gov’t,Review,Rna,RNA Viruses,RNAChloroplast,RNATransfer,RnaViral,Selenocysteine,sequence,SEQUENCES,SITE,SITES,STOP CODON,structure,suppression,termination,TERMINATION CODON,TERMINATION-CODON,tRNA,Viruses} } % == BibTeX quality report for beierMisreadingTerminationCodons2001: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{belcourtRibosomalFrameshiftingYeast1990, title = {Ribosomal Frameshifting in the Yeast Retrotransposon {{Ty}}: {{tRNAs}} Induce Slippage on a 7 Nucleotide Minimal Site.}, author = {Belcourt, M.F. and Farabaugh, P.J.}, year = 1990, journal = {Cell}, volume = {62}, number = {2}, pages = {339–352}, publisher = {Elsevier}, doi = {10.1016/0092-8674(90)90371-K}, url = {http://linkinghub.elsevier.com/retrieve/pii/009286749090371K}, keywords = {Frameshifting,nosource,ribosomal frameshifting,tRNA,Ty,Ty1,yeast} }

@article{belovaNovelSiteAntibiotic2001a, title = {A Novel Site of Antibiotic Action in the Ribosome: Interaction of Evernimicin with the Large Ribosomal Subunit}, author = {Belova, L. and Tenson, T. and Xiong, L. and McNicholas, P.M. and Mankin, A.S.}, year = 2001, month = mar, journal = {Proc.Natl.Acad.Sci.U.S.A}, volume = {98}, number = {7}, pages = {3726–3731}, doi = {10.1073/pnas.071527498}, url = {PM:11259679}, abstract = {Evernimicin (Evn), an oligosaccharide antibiotic, interacts with the large ribosomal subunit and inhibits bacterial protein synthesis. RNA probing demonstrated that the drug protects a specific set of nucleotides in the loops of hairpins 89 and 91 of 23S rRNA in bacterial and archaeal ribosomes. Spontaneous Evn-resistant mutants of Halobacterium halobium contained mutations in hairpins 89 and 91 of 23S rRNA. In the ribosome tertiary structure, rRNA residues involved in interaction with the drug form a tight cluster that delineates the drug-binding site. Resistance mutations in the bacterial ribosomal protein L16, which is shown to be homologous to archaeal protein L10e, cluster to the same region as the rRNA mutations. The Evn-binding site overlaps with the binding site of initiation factor 2. Evn inhibits activity of initiation factor 2 in vitro, suggesting that the drug interferes with formation of the 70S initiation complex. The site of Evn binding and its mode of action are distinct from other ribosome-targeted antibiotics. This antibiotic target site can potentially be used for the development of new antibacterial drugs}, keywords = {0,antibiotic,antibiotics,AntibioticsAminoglycoside,Bacterial,BINDING,Binding Sites,BINDING-SITE,chemistry,COMPLEX,COMPLEXES,development,drug effects,Drug ResistanceMicrobial,drugs,FORM,genetics,HAIRPINS,Halobacterium,Halobacterium halobium,In Vitro,IN-VITRO,initiation,INITIATION-FACTOR,isolation & purification,La,LOOP,ModelsMolecular,MutagenesisSite-Directed,MUTANTS,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Nucleotides,pharmacology,protein,protein synthesis,PROTEIN-SYNTHESIS,REGION,RESIDUES,RESISTANCE,RESISTANCE MUTATIONS,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNAArchaeal,RNABacterial,RNARibosomal23S,rRNA,SITE,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,TARGET} } % == BibTeX quality report for belovaNovelSiteAntibiotic2001a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.U.S.A

@article{benaliConstructionVariabilityMap1999, title = {Construction of a Variability Map for Eukaryotic Large Subunit Ribosomal {{RNA}}}, author = {Ben Ali, A. and Wuyts, J. and De Wachter, R. and Meyer, A. and {Van de}, Peer Y.}, year = 1999, month = jul, journal = {Nucleic acids research}, volume = {27}, number = {14}, pages = {2825–2831}, publisher = {Oxford Univ Press}, url = {PM:10390522 http://nar.oxfordjournals.org/content/27/14/2825.short}, abstract = {In this paper, we present a variability map of the eukaryotic large subunit ribosomal RNA, showing the distribution of variable and conserved sites in this molecule. The variability of each site in this map is indicated by means of a colored dot. Construction of the variability map was based on the substitution rate calibration (SRC) method, in which the substitution rate of each nucleotide site is computed by looking at the frequency with which sequence pairs differ at that site as a function of their evolutionary distance. Variability maps constructed by this method provide a much more accurate and objective description of site-to-site variability than visual inspection of sequence alignments}, keywords = {0,alignment,animal,Base Sequence,chemistry,Conserved Sequence,Eukaryotic Cells,Gene Frequency,genetics,Internet,La,Molecular Weight,No DOI found,nosource,Nucleic Acid Conformation,Plants,ribosomal RNA,RIBOSOMAL-RNA,Rna,RNARibosomal,Saccharomyces cerevisiae,sequence,Sequence Alignment,SITE,SITES,SUBUNIT,supportnon-u.s.gov’t,Variation (Genetics)} } % == BibTeX quality report for benaliConstructionVariabilityMap1999: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{benardSki6pHomologRNAprocessing1998, title = {Ski6p Is a Homolog of {{RNA-processing}} Enzymes That Affects Translation of Non-Poly({{A}}) {{mRNAs}} and {{60S}} Ribosomal Subunit Biogenesis.}, author = {Benard, L. and Carroll, K. and Valle, R.P.C. and Wickner, R.B.}, year = 1998, journal = {Molecular and cellular biology}, volume = {18}, number = {5}, pages = {2688–2696}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.18.5.2688}, url = {http://mcb.asm.org/cgi/content/abstract/18/5/2688}, abstract = {We mapped and cloned SKI6 of Saccharomyces cerevisiae, a gene that represses the copy number of the L-A double-stranded RNA virus, and found that it encodes an essential 246-residue protein with homology to a tRNA-processing enzyme, RNase PH. The ski6-2 mutant expressed electroporated non-poly(A) luciferase mRNAs 8- to 10-fold better than did the isogenic wild type. No effect of ski6-2 on expression of uncapped or normal mRNAs was found. Kinetics of luciferase synthesis and direct measurement of radiolabeled electroporated mRNA indicate that the primary effect of Ski6p was on efficiency of translation rather than on mRNA stability. Both ski6 and ski2 mutants show hypersensitivity to hygromycin, suggesting functional alteration of the translation apparatus. The ski6-2 mutant has normal amounts of 40S and 60S ribosomal subunits but accumulates a 38S particle containing 5’-truncated 25S rRNA but no 5.8S rRNA, apparently an incomplete or degraded 60S subunit. This suggests an abnormality in 60S subunit assembly. The ski6-2 mutation suppresses the poor expression of the poly(A)- viral mRNA in a strain deficient in the 60S ribosomal protein L4. Thus, a ski6 mutation bypasses the requirement of the poly(A) tail for translation, allowing better translation of non-poly(A) mRNA, including the L-A virus mRNA which lacks poly(A). We speculate that the derepressed translation of non-poly(A) mRNAs is due to abnormal (but full-size) 60S subunits.}, keywords = {60S subunit,assembly,CEREVISIAE,DOUBLE-STRANDED-RNA,efficiency,ENCODES,enzyme,expression,gene,homolog,Kinetics,L-A,L-A-VIRUS,La,luciferase,mRNA,mRNA stability,MUTANTS,Mutation,nosource,poly(A),POLY(A) TAIL,protein,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,Rna,RNAse,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SKI,SKI2,stability,SUBUNIT,SUBUNITS,translation,virus,WILD-TYPE} } % == BibTeX quality report for benardSki6pHomologRNAprocessing1998: % ? unused Journal abbr (“Mol.Cell.Biol.”)

@article{benardSki7AntiviralProtein1999, title = {The Ski7 Antiviral Protein Is an {{EF1-alpha}} Homolog That Blocks Expression of Non-{{Poly}} ({{A}}) {{mRNA}} in {{Saccharomyces}} Cerevisiae}, author = {Benard, L. and Carroll, K. and Valle, R.C.P. and Masison, d.C. and Wickner, R.B.}, year = 1999, month = apr, journal = {Journal of Virology}, volume = {73}, number = {4}, pages = {2893–2900}, publisher = {Am Soc Microbiol}, doi = {10.1128/JVI.73.4.2893-2900.1999}, url = {http://jvi.asm.org/cgi/content/abstract/73/4/2893}, abstract = {We mapped and cloned SKI7, a gene that negatively controls the copy number of L-A and M double-stranded RNA viruses in Saccharomyces cerevisiae. We found that it encodes a nonessential 747-residue protein with similarities to two translation factors, Hbs1p and EF1-alpha. The ski7 mutant was hypersensitive to hygromycin B, a result also suggesting a role in translation. The SKI7 product repressed the expression of nonpolyadenylated [non-poly(A)] mRNAs, whether capped or uncapped, thus explaining why Ski7p inhibits the propagation of the yeast viruses, whose mRNAs lack poly(A). The dependence of the Ski7p effect on 3’ RNA structures motivated a study of the expression of capped non-poly(A) luciferase mRNAs containing 3’ untranslated regions (3’UTRs) differing in length. In a wild-type strain, increasing the length of the 3’UTR increased luciferase expression due to both increased rates and duration of translation. Overexpression of Ski7p efficiently cured the satellite virus M2 due to a twofold-increased repression of non-poly(A) mRNA expression. Our experiments showed that Ski7p is part of the Ski2p-Ski3p-Ski8p antiviral system because a single ski7 mutation derepresses the expression of non-poly(A) mRNA as much as a quadruple ski2 ski3 ski7 ski8 mutation, and the effect of the overexpression of Ski7p is not obtained unless other SKI genes are functional. ski1/xrn1Delta ski2Delta and ski1/xrn1Delta ski7Delta mutants were viable but temperature sensitive for growth}, keywords = {99173984,Amino Acid Sequence,antiviral,CloningMolecular,disease,expression,Fungal Proteins,gene,Gene Expression RegulationFungal,Gene Expression RegulationViral,Genes,Genetic,genetics,homolog,L-A,La,luciferase,Molecular Sequence Data,mRNA,Mutation,nosource,poly(A),protein,Rna,RNA Viruses,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,Sequence Alignment,SKI,structure,Temperature,Transcription Factors,translation,virology,virus,yeast} } % == BibTeX quality report for benardSki7AntiviralProtein1999: % ? unused Journal abbr (“J.Virol.”)

@article{benkoCompetitionSterolBiosynthetic2000, title = {Competition between a Sterol Biosynthetic Enzyme and {{tRNA}} Modification in Addition to Changes in the Protein Synthesis Machinery Causes Altered Nonsense Suppression}, author = {Benko, A.L. and Vaduva, G. and Martin, N.C. and Hopper, A.K.}, year = 2000, month = jan, journal = {Proceedings of the National Academy of Sciences}, volume = {97}, number = {1}, pages = {61–66}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.97.1.61}, url = {http://www.pnas.org/content/97/1/61.short}, abstract = {The Saccharomyces cerevisiae Mod5 protein catalyzes isopentenylation of A to i(6)A on tRNAs in the nucleus, cytosol, and mitochondria. The substrate for Mod5p, dimethylallyl pyrophosphate, is also a substrate for Erg20p that catalyzes an essential step in sterol biosynthesis. Changing the distribution of Mod5p so that less Mod5p is present in the cytosol decreases i(6)A on cytosolic tRNAs and alters tRNA-mediated nonsense suppression. We devised a colony color/growth assay to assess tRNA-mediated nonsense suppression and used it to search for genes, which, when overexpressed, affect nonsense suppression. We identified SAL6, TEF4, and YDL219w, all of which likely affect nonsense suppression via alteration of the protein synthesis machinery. We also identified ARC1, whose product interacts with aminoacyl synthetases. Interestingly, we identified ERG20. Midwestern analysis showed that yeast cells overproducing Erg20p have reduced levels of i(6)A on tRNAs. Thus, Erg20p appears to affect nonsense suppression by competing with Mod5p for substrate. Identification of ERG20 reveals that yeast have a limited pool of dimethylallyl pyrophosphate. It also demonstrates that disrupting the balance between enzymes that use dimethylallyl pyrophosphate as substrate affects translation}, keywords = {0,Alkyl and Aryl Transferases,analysis,biosynthesis,Canavanine,Cell Division,CELLS,CEREVISIAE,Codon,CodonNonsense,Cytosol,drug effects,enzyme,Enzymes,Fungal Proteins,gene,Gene Dosage,Gene Expression RegulationFungal,Genes,genetics,Hemiterpenes,IDENTIFICATION,Isopentenyladenosine,La,metabolism,mitochondria,modification,Mutation,NONSENSE,nonsense suppression,nosource,Organophosphorus Compounds,pharmacology,PLASMID,Plasmids,PRODUCT,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Research SupportU.S.Gov’tNon-P.H.S.,Rna,RNATransfer,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,search,Sterols,suppression,SuppressionGenetic,Transferases,translation,tRNA,yeast,YEAST-CELLS} } % == BibTeX quality report for benkoCompetitionSterolBiosynthetic2000: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{berchtoldCrystalStructureActive1993, title = {Crystal Structure of Active Elongation Factor {{Tu}} Reveals Major Domain Rearrangements.}, author = {Berchtold, H. and Reshetnikova, L. and Reiser, C.O. and Schirmer, N.K. and Sprinzl, M. and Hilgenfeld, R.}, year = 1993, month = sep, journal = {Nature}, volume = {365}, number = {6442}, pages = {126–132}, publisher = {Nature Publishing Group}, doi = {10.1038/365126a0}, url = {http://www.nature.com/nature/journal/v365/n6442/abs/365126a0.html}, keywords = {BINDING,EFTu,elongation,GTP,GTPase,nosource,ribosome,Rna,SIGNAL,structure} }

@article{bergstromRegulatoryAutonomyMolecular1995, title = {Regulatory Autonomy and Molecular Characterization of the {{Drosophila}} out at First Gene}, author = {Bergstrom, D.E. and Merli, C.A. and Cygan, J.A. and Shelby, R. and Blackman, R.K.}, year = 1995, month = mar, journal = {Genetics}, volume = {139}, number = {3}, pages = {1331–1346}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/139.3.1331}, url = {http://www.genetics.org/content/139/3/1331.short}, keywords = {cloning,Codon,development,Drosophila,expression,gene,Genes,Mutation,nosource,Open Reading Frames,protein,Proteins,readthrough,Rna,STOP CODON,suppression,transcription,translation} }

@article{berkStructuralBasisMRNA2006, title = {Structural Basis for {{mRNA}} and {{tRNA}} Positioning on the Ribosome}, author = {Berk, V. and Zhang, W. and Pai, R.D. and Cate, J.H.}, year = 2006, month = oct, journal = {Proceedings of the National Academy of Sciences}, volume = {103}, number = {43}, pages = {15830–15834}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.0607541103}, url = {http://www.pnas.org/content/103/43/15830.short}, abstract = {Protein synthesis requires the accurate positioning of mRNA and tRNA in the peptidyl-tRNA site of the ribosome. Here we describe x-ray crystal structures of the intact bacterial ribosome from Escherichia coli in a complex with mRNA and the anticodon stem-loop of P-site tRNA. At 3.5-A resolution, these structures reveal rearrangements in the intact ribosome that clamp P-site tRNA and mRNA on the small ribosomal subunit. Binding of the anticodon stem-loop of P-site tRNA to the ribosome is sufficient to lock the head of the small ribosomal subunit in a single conformation, thereby preventing movement of mRNA and tRNA before mRNA decoding}, keywords = {0,Anticodon,Bacterial,Base Sequence,BINDING,BIOLOGY,chemistry,COMPLEX,COMPLEXES,CONFORMATION,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,CrystallographyX-Ray,decoding,Escherichia coli,ESCHERICHIA-COLI,genetics,La,metabolism,ModelsMolecular,Movement,mRNA,nosource,Nucleic Acid Conformation,P SITE,P-SITE,protein,Protein Binding,protein synthesis,PROTEIN-SYNTHESIS,Proteins,REQUIRES,RESOLUTION,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNAMessenger,RNATransfer,SITE,STEM-LOOP,Structural,STRUCTURAL BASIS,structure,SUBUNIT,Support,tRNA} } % == BibTeX quality report for berkStructuralBasisMRNA2006: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{berkInsightsProteinBiosynthesis2007, title = {Insights into Protein Biosynthesis from Structures of Bacterial Ribosomes}, author = {Berk, V. and Cate, J.H.}, year = 2007, month = jun, journal = {Current opinion in structural biology}, volume = {17}, number = {3}, pages = {302–309}, publisher = {Elsevier}, doi = {10.1016/j.sbi.2007.05.009}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0959-440x(07)00074-7}, abstract = {Understanding the structural basis of protein biosynthesis on the ribosome remains a challenging problem for cryo-electron microscopy and X-ray crystallography. Recent high-resolution structures of the Escherichia coli 70S ribosome without ligands, and of the Thermus thermophilus and E. coli 70S ribosomes with bound mRNA and tRNAs, reveal many new features of ribosome dynamics and ribosome-ligand interactions. In addition, the first high-resolution structures of the L7/L12 stalk of the ribosome, responsible for translation factor binding and GTPase activation, reveal the structural basis of the high degree of flexibility in this region of the ribosome. These structures provide groundbreaking insights into the mechanism of protein synthesis at the level of ribosome architecture, ligand binding and ribosome dynamics}, keywords = {70S RIBOSOME,activation,Bacterial,BINDING,BIOLOGY,biosynthesis,Cryoelectron Microscopy,Crystallography,DYNAMICS,E,Escherichia coli,ESCHERICHIA-COLI,GTPase,La,Ligands,MECHANISM,mRNA,nosource,protein,Protein Biosynthesis,protein synthesis,PROTEIN-BIOSYNTHESIS,PROTEIN-SYNTHESIS,REGION,ribosome,Ribosomes,Structural,STRUCTURAL BASIS,structure,Thermus,Thermus thermophilus,THERMUS-THERMOPHILUS,translation,tRNA} } % == BibTeX quality report for berkInsightsProteinBiosynthesis2007: % ? unused Journal abbr (“Curr.Opin.Struct.Biol”)

@article{bermanoTissuespecificRegulationSelenoenzyme1995, title = {Tissue-Specific Regulation of Selenoenzyme Gene Expression during Selenium Deficiency in Rats.}, author = {Bermano, G. and Nicol, F. and Dyer, J.A. and Sunde, R.A. and Beckett, G.J. and Arthur, J.R. and Hesketh, J.E.}, year = 1995, month = oct, journal = {Biochemical Journal}, volume = {311 ( Pt 2)}, number = {Pt 2}, pages = {425–430}, publisher = {Portland Press Ltd}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1136017/}, abstract = {Regulation of synthesis of the selenoenzymes cytosolic glutathione peroxidase (GSH-Px), phospholipid hydroperoxide glutathione peroxidase (PHGSH-Px) and type-1 iodothyronine 5’-deiodinase (5’IDI) was investigated in liver, thyroid and heart of rats fed on diets containing 0.405, 0.104 (Se-adequate), 0.052, 0.024 or 0.003 mg of Se/kg. Severe Se deficiency (0.003 mg of Se/kg) caused almost total loss of GSH-Px activity and mRNA in liver and heart. 5’IDI activity decreased by 95% in liver and its mRNA by 50%; in the thyroid, activity increased by 15% and mRNA by 95%. PHGSH-Px activity was reduced by 75% in the liver and 60% in the heart but mRNA levels were unchanged; in the thyroid, PHGSH-Px activity was unaffected by Se depletion but its mRNA increased by 52%. Thus there is differential regulation of the three mRNAs and subsequent protein synthesis within and between organs, suggesting both that mechanisms exist to channel Se for synthesis of a particular enzyme and that there is tissue-specific regulation of selenoenzyme mRNAs. During Se depletion, the levels of selenoenzyme mRNA did not necessarily parallel the changes in enzyme activity, suggesting a distinct mechanism for regulating mRNA levels. Nuclear run- off assays with isolated liver nuclei showed severe Se deficiency to have no effect on transcription of the three genes, suggesting that there is post-transcriptional control of the three selenoenzymes, probably involving regulation of mRNA stability}, keywords = {0,animal,assays,BlottingNorthern,Comparative Study,deficiency,Diet,Dna,DNA Probes,enzymology,expression,gene,Gene Expression,Gene Expression RegulationEnzymologic,GENE-EXPRESSION,Genes,genetics,Glutathione Peroxidase,heart,Hormones,Iodide Peroxidase,La,Liver,Male,metabolism,mRNA,Myocardium,No DOI found,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,rat,Rats,regulation,Rna,RNAMessenger,Selenium,stability,supportnon-u.s.gov’t,Thyroid Gland,Thyroid Hormones,transcription} } % == BibTeX quality report for bermanoTissuespecificRegulationSelenoenzyme1995: % ? unused Journal abbr (“Biochem.J.”)

@article{bermanoRole3Untranslated1996, title = {Role of the 3’ Untranslated Region in the Regulation of Cytosolic Glutathione Peroxidase and Phospholipid-Hydroperoxide Glutathione Peroxidase Gene Expression by Selenium Supply}, author = {Bermano, G. and Arthur, J.R. and Hesketh, J.E.}, year = 1996, month = dec, journal = {Biochemical Journal}, volume = {320 ( Pt 3)}, number = {Pt 3}, pages = {891–895}, publisher = {Portland Press Ltd}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1218012/}, abstract = {Selenium is an essential nutrient and synthesis of selenoproteins is affected by limited selenium supply. During selenium deficiency there is a differential regulation of selenoprotein synthesis and gene expression; for example, there is a decrease in abundance of mRNA for cytosolic glutathione peroxidase (cGSH-Px) and a preservation of mRNA for phospholipid-hydroperoxide glutathione peroxidase (PHGSH-Px). This difference is not due to an alteration in the rate of transcription but might reflect differences in translation. The aim of the present work was to assess the role of cGSH-Px and PHGSH-Px 3’ untranslated regions (UTRs) in the regulation of selenoprotein mRNA stability and translation by using H4-II-E-C3 cells transfected with different constructs containing a type I iodothyronine deiodinase-coding region linked to different selenoprotein mRNA 3’ UTRs. Translational efficiency results showed that the efficiency of the 3’ UTRs in permitting selenocysteine incorporation is similar in selenium-replete conditions but, when selenium is limiting, the 3’ UTR of cGSH-Px is less efficient than the 3’ UTR of PHGSH-Px. The results suggest that the 3’ UTR of these selenoprotein mRNA species influences their extent of translation when selenium levels are low. The different sensitivity of the 3’ UTRs to selenium deficiency can explain the differential effect that selenium deficiency has on cGSH-Px and PHGSH-Px activity and mRNA levels, stability and translation. This might be partly responsible for channelling selenium for synthesis of PHGSH-Px rather than cGSH-Px}, keywords = {0,animal,BlottingNorthern,CarcinomaHepatocellular,Chimeric Proteins,Cytosol,deficiency,drug effects,efficiency,enzymology,expression,gene,Gene Expression,Gene Expression RegulationNeoplastic,GENE-EXPRESSION,genetics,Glutathione Peroxidase,Iodide Peroxidase,La,Lipid Peroxides,metabolism,mRNA,No DOI found,nosource,pharmacology,Phospholipids,Plasmids,protein,Proteins,Rats,regulation,Rna,RNAMessenger,Selenium,stability,supportnon-u.s.gov’t,transcription,Transfection,translation,TranslationGenetic,Tumor CellsCultured,Untranslated Regions} } % == BibTeX quality report for bermanoRole3Untranslated1996: % ? unused Journal abbr (“Biochem.J.”)

@article{bernabeuPeptidylTransferaseBacterial1979, title = {Peptidyl Transferase of Bacterial Ribosome: Resistance to Proteinase {{K}}}, author = {Bernabeu, C. and Conde, P. and Vazquez, D. and Ballesta, J.P.}, year = 1979, month = feb, journal = {European Journal of Biochemistry}, volume = {93}, number = {3}, pages = {527–533}, publisher = {Wiley Online Library}, doi = {10.1111/j.1432-1033.1979.tb12851.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1979.tb12851.x/abstract}, abstract = {70-S ribosomes and 50-S ribosomal subunits from Escherichia coli D10 were treated with proteinase K for increasing periods of time. Peptidyl transferase activity and sparsomycin-induced binding of (U)C-A-C-C-A- [3H]Leu-Ac were tested in the treated particles, the binding of the substrate being more sensitive to the protease than peptide bond formation. Comparison of the amounts of proteins present in the treated particles with the residual activity indicates that only proteins L3 and L14 are released at a similar rate to that at which peptidyl transferase activity is lost. Proteins related to this ribosomal activity by other techniques are lost at a faster rate than the activity itself. In addition, the results indicate that sparsomycin stimulates the binding of the substrate by a different mechanism from that which inhibits peptide bond formation}, keywords = {0,Acyltransferases,analogs & derivatives,Bacterial,BINDING,Endopeptidases,enzymology,Escherichia coli,ESCHERICHIA-COLI,L3,La,Leucine,metabolism,nosource,Oligoribonucleotides,peptidyl transferase,Peptidyltransferase,pharmacology,protein,Proteins,Ribosomal Proteins,ribosome,Ribosomes,sparsomycin,techniques} } % == BibTeX quality report for bernabeuPeptidylTransferaseBacterial1979: % ? unused Journal abbr (“Eur.J.Biochem.”)

@article{bernacchiAminoglycosideBindingHIV12007, title = {Aminoglycoside Binding to the {{HIV-1 RNA}} Dimerization Initiation Site: Thermodynamics and Effect on the Kissing-Loop to Duplex Conversion}, author = {Bernacchi, S. and Freisz, S. and Maechling, C. and Spiess, B. and Marquet, R. and Dumas, P. and Ennifar, E.}, year = 2007, journal = {Nucleic Acids Research}, volume = {35}, number = {21}, pages = {7128–7139}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkm856}, url = {http://nar.oxfordjournals.org/content/35/21/7128.short}, abstract = {Owing to a striking, and most likely fortuitous, structural and sequence similarity with the bacterial 16 S ribosomal A site, the RNA kissing-loop complex formed by the HIV-1 genomic RNA dimerization initiation site (DIS) specifically binds 4,5-disubstituted 2-deoxystreptamine (2-DOS) aminoglycoside antibiotics. We used chemical probing, molecular modeling, isothermal titration calorimetry (ITC) and UV melting to investigate aminoglycoside binding to the DIS loop-loop complex. We showed that apramycin, an aminoglycoside containing a bicyclic moiety, also binds the DIS, but in a different way than 4,5-disubstituted 2-DOS aminoglycosides. The determination of thermodynamic parameters for various aminoglycosides revealed the role of the different rings in the drug-RNA interaction. Surprisingly, we found that the affinity of lividomycin and neomycin for the DIS (K(d) approximately 30 nM) is significantly higher than that obtained in the same experimental conditions for their natural target, the bacterial A site (K(d) approximately 1.6 microM). In good agreement with their respective affinity, aminoglycoside increase the melting temperature of the loop-loop interaction and also block the conversion from kissing-loop complex to extended duplex. Taken together, our data might be useful for selecting new molecules with improved specificity and affinity toward the HIV-1 DIS RNA}, keywords = {0,5’ Untranslated Regions,A SITE,A-SITE,AMINOGLYCOSIDE ANTIBIOTICS,Aminoglycosides,analogs & derivatives,Anti-Bacterial Agents,antibiotic,antibiotics,antiviral,Antiviral Agents,Bacterial,BINDING,Binding Sites,Calorimetry,chemistry,Cinnamates,COMPLEX,COMPLEXES,Dimerization,genetics,genomic,GENOMIC RNA,Hiv-1,Hygromycin B,initiation,INITIATION SITE,La,ModelsMolecular,Nebramycin,Neomycin,nosource,Nucleic Acid Conformation,Paromomycin,REGION,Rna,RnaViral,S,sequence,SITE,SPECIFICITY,Structural,Support,TARGET,Temperature,Thermodynamics,Untranslated Regions} } % == BibTeX quality report for bernacchiAminoglycosideBindingHIV12007: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{bertramEndlessPossibilitiesTranslation2001, title = {Endless Possibilities: Translation Termination and Stop Codon Recognition}, author = {Bertram, G. and Innes, S. and Minella, O. and Richardson, J.P. and Stansfield, I.}, year = 2001, month = feb, journal = {Microbiology-Uk}, volume = {147}, number = {Pt 2}, pages = {255–269}, publisher = {Soc General Microbiol}, doi = {10.1099/00221287-147-2-255}, url = {http://mic.sgmjournals.org/cgi/content/abstract/147/2/255}, keywords = {0,3,animal,antagonists & inhibitors,BIOLOGY,biosynthesis,Codon,CODON RECOGNITION,CodonNonsense,CodonTerminator,ESCHERICHIA-COLI RIBOSOMES,genetics,La,MESSENGER-RNA,metabolism,Mice,MURINE LEUKEMIA-VIRUS,No DOI found,NONSENSE,nonsense suppression,nosource,Peptide Termination Factors,PEPTIDYL-TRANSFER-RNA,PRION-LIKE FACTOR,protein,protein synthesis,Proteins,RECOGNITION,release factor,RELEASE FACTOR RF3,Review,RIBOSOME RECYCLING FACTOR,STOP CODON,STOP CODON RECOGNITION,supportnon-u.s.gov’t,termination,TOBACCO MOSAIC-VIRUS,translation,TRANSLATION TERMINATION,TranslationGenetic,YEAST SACCHAROMYCES-CEREVISIAE,YELLOW DWARF VIRUS} } % == BibTeX quality report for bertramEndlessPossibilitiesTranslation2001: % ? unused Journal abbr (“Microbiology”)

@article{bertrandInfluenceStackingPotential2002, title = {Influence of the Stacking Potential of the Base 3’ of Tandem Shift Codons on -1 Ribosomal Frameshifting Used for Gene Expression}, author = {Bertrand, C. and Prere, M.F. and Gesteland, R.F. and Atkins, J.F. and Fayet, O.}, year = 2002, month = jan, journal = {RNA.}, volume = {8}, number = {1}, pages = {16–28}, publisher = {Cambridge Univ Press}, doi = {10.1017/S1355838202012086}, url = {http://journals.cambridge.org/abstract_S1355838202012086}, abstract = {Translating ribosomes can shift reading frame at specific sites with high efficiency for gene expression purposes. The most common type of shift to the -1 frame involves a tandem realignment of two anticodons from pairing with mRNA sequence of the form X XXY YYZ to XXX YYY Z where the spaces indicate the reading frame. The predominant -1 shift site of this type in eubacteria is A AAA AAG. The present work shows that in Escherichia coli the identity of the 6 nt 3’ of this sequence can be responsible for a 14-fold variation in frameshift frequency. The first 3’ nucleotide has the primary effect, with, in order of decreasing efficiency, U {\(>\)} C {\(>\)} A {\(>\)} G. This effect is independent of other stimulators of frameshifting. It is detected with other X XXA AAG sequences, but not with several other heptameric -1 shift sites. Pairing of E. coli tRNALYS with AAG is especially weak at the third codon position. We propose that strong stacking of purines 3’ of AAG stabilizes pairing of tRNALys, diminishing the chance of codon:anticodon dissociation that is a prerequisite for the realignment involved in frameshifting}, keywords = {0,Anticodon,Base Sequence,chemistry,Codon,codon:anticodon,CodonTerminator,efficiency,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,expression,frameshift,Frameshifting,FrameshiftingRibosomal,gene,Gene Expression,Gene Expression RegulationBacterial,GENE-EXPRESSION,GenesBacterial,GenesReporter,genetics,La,metabolism,Molecular Sequence Data,mRNA,Mutagenesis,nosource,Nucleic Acid Conformation,Nucleotides,protein,Proteins,Purines,ribosomal frameshifting,ribosome,Ribosomes,Rna,RNA 3’ End Processing,RNA Stability,RNAMessenger,RNATransfer,sequence,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for bertrandInfluenceStackingPotential2002: % ? Possibly abbreviated journal title RNA.

@article{bessarabCompleteCDNASequence2000, title = {The Complete {{cDNA}} Sequence of a Type {{II Trichomonas}} Vaginalis Virus}, author = {Bessarab, I.N. and Liu, H.W. and Ip, C.F. and Tai, J.H.}, year = 2000, month = feb, journal = {Virology}, volume = {267}, number = {2}, pages = {350–359}, publisher = {Elsevier}, doi = {10.1006/viro.1999.0129}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0042682299901290}, abstract = {Trichomonas vaginalis viruses (TVV), which may regulate P270 gene expression in the protozoan pathogen T: vaginalis, are a group of divergent double-stranded (ds) RNA viruses. In the present study, the complete 4674-bp cDNA sequence of a 4.6-kb ds RNA from a newly identified TVV2-1 isolate was determined. The sequence of the plus-strand mRNA contains four open reading frames, which encode overlapping cap and pol genes in the reading frame 2 and reading frame 1, respectively, and two putative serine-threonine-rich basic proteins VP3 and VP4 in the third reading frame. An 85-kDa capsid protein and a 180-kDa CAP-POL fusion protein were identified in crude viruses by Western blotting experiments using antisera raised against gene-specific oligopeptides. In conjunction with the presence of a potential ribosomal slippery heptanucleotide G GGC CCC within the overlap of the cap and pol genes, these observations suggest that the pol gene of TVV2-1 is translated via a -1 ribosomal frameshifting event during translation of the cap gene. Our results also provide insight into the conservation among divergent dsRNA species from TW and suggest that the genome of TVV2-1 may encode two extra genes in addition to the cap and pol genes. (C) 2000 Academic Press}, keywords = {Cap,Capsid,DOUBLE-STRANDED-RNA,expression,FIREFLY LUCIFERASE,FRAME,Frameshifting,gene,Gene Expression,GENE-EXPRESSION,Genes,Genome,GIARDIA-LAMBLIA,IDENTIFICATION,MESSENGER-RNA,mRNA,nosource,OPEN READING FRAME,Open Reading Frames,ORGANIZATION,pol,protein,Proteins,READING FRAME,Reading Frames,ribosomal frameshifting,Rna,RNA Viruses,SACCHAROMYCES-CEREVISIAE,sequence,T,T-VAGINALIS,translation,virus,yeast} }

@article{bettinardiMissenseMutationsFas1997, title = {Missense Mutations in the {{Fas}} Gene Resulting in Autoimmune Lymphoproliferative Syndrome: A Molecular and Immunological Analysis}, author = {Bettinardi, A. and Brugnoni, D. and {Quiros-Roldan}, E. and Malagoli, A. and La Grutta, S. and Correra, A. and Notarangelo, L.D.}, year = 1997, month = feb, journal = {Blood}, volume = {89}, number = {3}, pages = {902–909}, publisher = {American Society of Hematology}, doi = {10.1182/blood.V89.3.902}, url = {http://bloodjournal.hematologylibrary.org/content/89/3/902.short}, keywords = {activation,analysis,development,disease,expression,Frameshifting,gene,Genes,human,Mice,Mutation,nosource,regulation} }

@article{betzelCrystalStructureDomain1994, title = {Crystal Structure of Domain {{A}} of {{Thermus}} Flavus {{5S rRNA}} and the Contribution of Water Molecules to Its Structure}, author = {Betzel, C. and Lorenz, S. and Furste, J.P. and Bald, R. and Zhang, M. and Schneider, T.R. and Wilson, K.S. and Erdmann, V.A.}, year = 1994, journal = {FEBS letters}, volume = {351}, number = {2}, pages = {159–164}, publisher = {Elsevier}, doi = {10.1016/0014-5793(94)00834-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/0014579394008345}, abstract = {This is the first high resolution crystal structure of an RNA molecule made by solid phase chemical synthesis and representing a natural RNA. The structure of the domain A of Thermus flavus ribosomal 5S RNA is refined to R = 18% at 2.4 A including 159 solvent molecules. Most of the 2’-hydroxyl groups as well as the phosphate oxygens are involved either in specific hydrogen bonds in intermolecular contacts or to solvent molecules. The two U-G and G-U base-pairs are stabilized by H-bonds supplied via three water molecules to compensate for the lack of base-pair hydrogen bonds. The structure shows for the first time in detail the importance of highly ordered internal water in stabilizing an RNA structure}, keywords = {0,5S RNA,5S rRNA,Base Sequence,BASE-PAIR,chemical synthesis,chemistry,crystal structure,CRYSTAL-STRUCTURE,CrystallographyX-Ray,DOMAIN,Hydrogen,Hydrogen Bonding,La,ModelsMolecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Research SupportNon-U.S.Gov’t,RESOLUTION,Rna,RNARibosomal5S,rRNA,structure,Thermus,Water} } % == BibTeX quality report for betzelCrystalStructureDomain1994: % ? unused Journal abbr (“FEBS Lett.”)

@article{beusYeastNOP2Encodes1994a, title = {Yeast ⬚{{NOP2}}⬚ Encodes an Essential Nucleolar Protein with Homology to a Human Proliferation Marker.}, author = {Beus, e. and Brokenbrough, J.S. and Hong, B. and Aris, J.P.}, year = 1994, journal = {J.Cell Biol.}, volume = {127}, pages = {1799–1813}, doi = {10.1083/jcb.127.6.1799}, keywords = {human,nosource,protein,ribosome,yeast} } % == BibTeX quality report for beusYeastNOP2Encodes1994a: % ? Possibly abbreviated journal title J.Cell Biol.

@article{bhatEssentialRoleRibosomal2004, title = {Essential Role of Ribosomal Protein {{L11}} in Mediating Growth Inhibition-Induced P53 Activation}, author = {Bhat, K.P. and Itahana, K. and Jin, A. and Zhang, Y.}, year = 2004, month = jun, journal = {The EMBO journal}, volume = {23}, number = {12}, pages = {2402–2412}, publisher = {Nature Publishing Group}, doi = {10.1038/sj.emboj.7600247}, url = {http://www.nature.com/emboj/journal/v23/n12/abs/7600247a.html}, abstract = {The ribosomal protein L11 binds to and suppresses the E3 ligase function of HDM2, thus activating p53. Despite being abundant as a component of the 60S large ribosomal subunit, L11 does not induce p53 under normal growth conditions. In search of mechanisms controlling L11-HDM2 interaction, we found that the induction of p53 under growth inhibitory conditions, such as low dose of actinomycin D or serum depletion, can be significantly attenuated by knocking down L11, indicating the importance of L11 in mediating these growth inhibitory signals to p53. We show that L11 is not regulated by transcription or protein stability and its level remains relatively constant during serum starvation. However, serum starvation induces translocation of L11 from the nucleolus to the nucleoplasm, where it participates in a complex with HDM2. We propose that the nucleolus acts as a barrier to prevent L11 interacting with HDM2 during normal growth. Growth inhibition, presumably through suppression of rRNA production in the nucleolus, facilitates translocation of L11 to the nucleoplasm, thus activating p53 through inhibiting HDM2}, keywords = {0,activation,Amino Acid Sequence,cancer,cell cycle,Cell Division,Cell LineTumor,COMPLEX,COMPLEXES,COMPONENT,Culture Media,Culture MediaSerum-Free,D,GROWTH,human,INHIBITION,La,MECHANISM,MECHANISMS,media,metabolism,Molecular Sequence Data,nosource,nucleolus,p53,physiology,protein,Protein p53,Protein Transport,Proteins,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,rRNA,search,SIGNAL,stability,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,suppression,transcription,translocation} } % == BibTeX quality report for bhatEssentialRoleRibosomal2004: % ? unused Journal abbr (“EMBO J.”)

@article{bianchiHowTelomeraseReaches2008, title = {How Telomerase Reaches Its End: Mechanism of Telomerase Regulation by the Telomeric Complex}, author = {Bianchi, A. and Shore, D.}, year = 2008, month = jul, journal = {Molecular cell}, volume = {31}, number = {2}, pages = {153–165}, publisher = {Elsevier}, doi = {10.1016/j.molcel.2008.06.013}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276508004310}, abstract = {The telomerase enzyme, which synthesizes telomeric DNA repeats, is regulated in cis at individual chromosome ends by the telomeric protein/DNA complex in a manner dependent on telomere repeat-array length. A dynamic interplay between telomerase-inhibiting factors bound at duplex DNA repeats and telomerase-promoting ones bound at single-stranded terminal DNA overhangs appears to modulate telomerase activity and to be directly related to the transient deprotection of telomeres. We discuss recent advances on the mechanism of telomerase regulation at chromosome ends in both yeast and mammalian systems}, keywords = {0,Animals,antagonists & inhibitors,BIOLOGY,cell cycle,COMPLEX,COMPLEXES,cytology,Dna,DNA Replication,enzyme,Genetic,genetics,Humans,La,MECHANISM,metabolism,Molecular Biology,nosource,protein,Proteins,regulation,Review,Schizosaccharomyces,Schizosaccharomyces pombe Proteins,Support,SYSTEM,SYSTEMS,Telomerase,Telomere,yeast} } % == BibTeX quality report for bianchiHowTelomeraseReaches2008: % ? unused Journal abbr (“Mol Cell”)

@article{bidouNonsensemediatedDecayMutants2000, title = {Nonsense-Mediated Decay Mutants Do Not Affect Programmed -1 Frameshifting}, author = {Bidou, L. and Stahl, G. and Hatin, I. and Namy, O. and Rousset, J.P. and Farabaugh, P.J.}, year = 2000, month = jul, journal = {RNA}, volume = {6}, number = {7}, pages = {952–961}, doi = {10.1017/S1355838200000443}, abstract = {Sequences in certain mRNAs program the ribosome to undergo a noncanonical translation event, translational frameshifting, translational hopping, or termination readthrough. These sequences are termed recoding sites, because they cause the ribosome to change temporarily its coding rules. Cis and trans-acting factors sensitively modulate the efficiency of recoding events. In an attempt to quantitate the effect of these factors we have developed a dual-reporter vector using the lacZ and luc genes to directly measure recoding efficiency. We were able to confirm the effect of several factors that modulate frameshift or readthrough efficiency at a variety of sites. Surprisingly, we were not able to confirm that the complex of factors termed the surveillance complex regulates translational frameshifting. This complex regulates degradation of nonsense codon-containing mRNAs and we confirm that it also affects the efficiency of nonsense suppression. Our data suggest that the surveillance complex is not a general regulator of translational accuracy, but that its role is closely tied to the translational termination and initiation processes}, keywords = {accuracy,Amino Acid Sequence,Base Sequence,Codon,COMPLEX,COMPLEXES,DECAY,degradation,efficiency,Escherichia coli,frameshift,Frameshift Mutation,Frameshifting,gene,Genes,GenesReporter,genetics,hopping,initiation,metabolism,Molecular Sequence Data,mRNA,Mutation,nonsense suppression,nonsense-mediated decay,nosource,Plasmids,readthrough,recoding,ribosome,RULES,Saccharomyces cerevisiae,sequence,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,suppression,termination,Trans-Activation (Genetics),translation,TranslationGenetic,vector} }

@article{bielingPeptideBondFormation2006, title = {Peptide Bond Formation Does Not Involve Acid-Base Catalysis by Ribosomal Residues}, author = {Bieling, P. and Beringer, M. and Adio, S. and Rodnina, M.V.}, year = 2006, month = may, journal = {Nature Structural & Molecular Biology}, volume = {13}, number = {5}, pages = {423–428}, publisher = {Nature Publishing Group}, doi = {10.1038/nsmb1091}, url = {http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb1091.html}, abstract = {Ribosomes catalyze the formation of peptide bonds between aminoacyl esters of transfer RNAs within a catalytic center composed of ribosomal RNA only. Here we show that the reaction of P-site formylmethionine (fMet)-tRNA(fMet) with a modified A-site tRNA substrate, Phelac-tRNA(Phe), in which the nucleophilic amino group is replaced with a hydroxyl group, does not show the pH dependence observed with small substrate analogs such as puromycin and hydroxypuromycin. This indicates that acid-base catalysis by ribosomal residues is not important in the reaction with the full-size substrate. Rather, the ribosome catalyzes peptide bond formation by positioning the tRNAs, or their 3’ termini, through interactions with rRNA that induce and/or stabilize a pH-insensitive conformation of the active site and provide a preorganized environment facilitating the reaction. The rate of peptide bond formation with unmodified Phe-tRNA(Phe) is estimated to be {\(>\)}300 s(-1)}, keywords = {0,3,A SITE,A-SITE,ACID,ACIDS,ACTIVE-SITE,Alkalies,Biochemistry,BOND FORMATION,Catalysis,chemistry,CONFORMATION,genetics,Germany,Hydrogen-Ion Concentration,Kinetics,La,metabolism,nosource,P SITE,P-SITE,peptide bond formation,Peptides,peptidyl transferase,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,Protein Biosynthesis,Puromycin,Research SupportNon-U.S.Gov’t,RESIDUES,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNATransfer,rRNA,SITE,Substrate Specificity,Transfer RNA Aminoacylation,TRANSFER-RNA,Transferases,tRNA} } % == BibTeX quality report for bielingPeptideBondFormation2006: % ? unused Journal abbr (“Nat.Struct.Mol.Biol.”)

@article{bishopRetroviruses1978, title = {Retroviruses}, author = {Bishop, J.M.}, year = 1978, journal = {Annu.Rev.Biochem.}, volume = {47}, pages = {35–88}, doi = {10.1146/annurev.bi.47.070178.000343}, keywords = {nosource,oncogenes,Review,virus} } % == BibTeX quality report for bishopRetroviruses1978: % ? Possibly abbreviated journal title Annu.Rev.Biochem.

@article{biswasHumanImmunodeficiencyVirus2004, title = {The Human Immunodeficiency Virus Type 1 Ribosomal Frameshifting Site Is an Invariant Sequence Determinant and an Important Target for Antiviral Therapy}, author = {Biswas, P. and Jiang, X. and Pacchia, A.L. and Dougherty, J.P. and Peltz, S.W.}, year = 2004, month = feb, journal = {J. Virol.}, volume = {78}, number = {4}, pages = {2082–2087}, publisher = {Am Soc Microbiol}, doi = {10.1128/JVI.78.4.2082-2087.2004}, url = {http://jvi.asm.org/cgi/content/abstract/78/4/2082}, abstract = {Human immunodeficiency virus type 1 (HIV-1) utilizes a distinctive form of gene regulation as part of its life cycle, termed programmed -1 ribosomal frameshifting, to produce the required ratio of the Gag and Gag-Pol polyproteins. We carried out a sequence comparison of 1,000 HIV-1 sequences at the slippery site (UUUUUUA) and found that the site is invariant, which is somewhat surprising for a virus known for its variability. This prompted us to prepare a series of mutations to examine their effect upon frameshifting and viral infectivity. Among the series of mutations were changes of the HIV-1 slippery site to those effectively utilized by other viruses, because such mutations would be anticipated to have a relatively mild effect upon frameshifting. The results demonstrate that any change to the slippery site reduced frameshifting levels and also dramatically inhibited infectivity. Because ribosomal frameshifting is essential for HIV-1 replication and it is surprisingly resistant to mutation, modulation of HIV-1 frameshifting efficiency potentially represents an important target for the development of novel antiviral therapeutics}, keywords = {antiviral,development,efficiency,FORM,Frameshifting,Gag,Gag-pol,Gag/Gag-pol ratio,gene,gene regulation,Genetic,genetics,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,immunology,La,microbiology,MOLECULAR-GENETICS,Mutation,MUTATIONS,nosource,POLYPROTEIN,Polyproteins,regulation,REPLICATION,RESISTANT,ribosomal frameshifting,sequence,SEQUENCES,SERIES,SITE,slippery site,TARGET,therapy,TYPE-1,VIRAL INFECTIVITY,virus} } % == BibTeX quality report for biswasHumanImmunodeficiencyVirus2004: % ? Possibly abbreviated journal title J. Virol.

@article{bjorkTransferRnaModification1987, title = {Transfer-{{Rna Modification}}}, author = {Bjork, G.R. and Ericson, J.U. and Gustafsson, C.E.D. and Hagervall, T.G. and Jonsson, Y.H. and Wikstrom, P.M.}, year = 1987, journal = {Annual Review of Biochemistry}, volume = {56}, number = {1}, pages = {263–287}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, doi = {10.1146/annurev.bi.56.070187.001403}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.bi.56.070187.001403}, keywords = {modification,nosource,Review,TRANSFER-RNA} } % == BibTeX quality report for bjorkTransferRnaModification1987: % ? Title looks like it was stored in title-case in Zotero

@article{blackburnGenomewideScreeningSaccharomyces2003, title = {Genome-Wide Screening of {{Saccharomyces}} Cerevisiae to Identify Genes Required for Antibiotic Insusceptibility of Eukaryotes}, author = {Blackburn, A.S. and Avery, S.V.}, year = 2003, month = feb, journal = {Antimicrobial agents and chemotherapy}, volume = {47}, number = {2}, pages = {676–681}, publisher = {Am Soc Microbiol}, doi = {10.1128/AAC.47.2.676-681.2003}, url = {http://aac.asm.org/cgi/content/abstract/47/2/676}, abstract = {The adverse reactions provoked by many antibiotics in humans are well documented but are generally poorly understood at the molecular level. To elucidate potential genetic defects that could give rise to susceptibility to prokaryote-specific antibiotics in eukaryotes, we undertook genome-wide screens using the yeast Saccharomyces cerevisiae as a model of eukaryotes; our previous work with a small number of yeast mutants revealed some specific gene functions required for oxytetracycline resistance. Here, the complete yeast deletion strain collection was tested for growth in the presence of a range of antibiotics. The sensitivities of mutants revealed by these screens were validated in independent tests. None of the approximately 4,800 defined deletion strains tested were found to be sensitive to amoxicillin, penicillin G, rifampin, or vancomycin. However, two of the yeast mutants were tetracycline sensitive and four were oxytetracycline sensitive; encompassed among the latter were mutants carrying deletions in the same genes that we had characterized previously. Seventeen deletion strains were found to exhibit growth defects in the presence of gentamicin, with MICs for the strains being as low as 32 micro g ml(-1) (the wild type exhibited no growth defects at any gentamicin concentration tested up to 512 micro g ml(-1)). Strikingly, 11 of the strains that were most sensitive to gentamicin carried deletions in genes whose products are all involved in various aspects of vacuolar and Golgi complex (or endoplasmic reticulum) function. Therefore, these and analogous organelles, which are also the principal sites of gentamicin localization in human cells, appear to be essential for normal resistance to gentamicin in eukaryotes. The approach and data described here offer a new route to gaining insight into the potential genetic bases of antibiotic insusceptibilities in eukaryotes}, keywords = {0,antibiotic,antibiotics,BASE,BASES,CELLS,CEREVISIAE,COMPLEX,COMPLEXES,drug effects,Drug Resistance,Endoplasmic Reticulum,ENDOPLASMIC-RETICULUM,Eukaryotic Cells,gene,Genes,Genetic,genetics,Genome,Gentamicins,GROWTH,growth & development,human,Humans,IDENTIFY,La,LOCALIZATION,Microbial Sensitivity Tests,MODEL,MUTANTS,nosource,Organelles,pharmacology,PRODUCT,PRODUCTS,RESISTANCE,Rifampin,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SITE,SITES,Support,Tetracycline,Tetracyclines,WILD-TYPE,yeast} } % == BibTeX quality report for blackburnGenomewideScreeningSaccharomyces2003: % ? unused Journal abbr (“Antimicrob.Agents Chemother.”)

@article{blackburnTelomeresTelomerasePath2006, title = {Telomeres and Telomerase: The Path from Maize, {{Tetrahymena}} and Yeast to Human Cancer and Aging}, author = {Blackburn, E.H. and Greider, C.W. and Szostak, J.W.}, year = 2006, month = oct, journal = {Nature Medicine}, volume = {12}, number = {10}, pages = {1133–1138}, publisher = {Nature Publishing Group}, doi = {10.1038/nm1006-1133}, url = {http://www.nature.com/nm/journal/v12/n10/full/nm1006-1133.html}, keywords = {0,Aging,Animals,Base Sequence,Biochemistry,Biophysics,cancer,DNA Fragmentation,enzymology,Fungal Proteins,genetics,human,Humans,La,metabolism,ModelsBiological,Molecular Sequence Data,Neoplasms,nosource,physiology,protein,Proteins,Publications,Telomerase,Telomere,Tetrahymena,ultrastructure,yeast,Zea mays} } % == BibTeX quality report for blackburnTelomeresTelomerasePath2006: % ? unused Journal abbr (“Nat.Med.”)

@article{blahaMutationsOutsideAnisomycinbinding2008, title = {Mutations Outside the Anisomycin-Binding Site Can Make Ribosomes Drug-Resistant}, author = {Blaha, G. and Gurel, G. and Schroeder, S.J. and Moore, P.B. and Steitz, T.A.}, year = 2008, month = jun, journal = {Journal of molecular biology}, volume = {379}, number = {3}, pages = {505–519}, publisher = {Elsevier}, doi = {10.1016/j.jmb.2008.03.075}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283608004142}, abstract = {Eleven mutations that make Haloarcula marismortui resistant to anisomycin, an antibiotic that competes with the amino acid side chains of aminoacyl tRNAs for binding to the A-site cleft of the large ribosomal unit, have been identified in 23S rRNA. The correlation observed between the sensitivity of H. marismortui to anisomycin and the affinity of its large ribosomal subunits for the drug indicates that its response to anisomycin is determined primarily by the binding of the drug to its large ribosomal subunit. The structures of large ribosomal subunits containing resistance mutations show that these mutations can be divided into two classes: (1) those that interfere with specific drug-ribosome interactions and (2) those that stabilize the apo conformation of the A-site cleft of the ribosome relative to its drug-bound conformation. The conformational effects of some mutations of the second kind propagate through the ribosome for considerable distances and are reversed when A-site substrates bind to the ribosome}, keywords = {A SITE,A-SITE,ACID,AMINO-ACID,anisomycin,antibiotic,BINDING,Biochemistry,Biophysics,CONFORMATION,Haloarcula,Haloarcula marismortui,La,Mutation,MUTATIONS,nosource,RESISTANCE,RESISTANCE MUTATIONS,RESISTANT,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,rRNA,SITE,structure,SUBUNIT,SUBUNITS,Support,tRNA} } % == BibTeX quality report for blahaMutationsOutsideAnisomycinbinding2008: % ? unused Journal abbr (“J.Mol Biol”)

@article{blancCoatProteinYeast1992a, title = {The Coat Protein of the Yeast Double-Stranded {{RNA}} Virus {{L-A}} Attaches Covalently to the Cap Structure of Eukaryotic {{mRNA}}.}, author = {Blanc, A. and Goyer, C. and Sonnenberg, N.}, year = 1992, journal = {Mol.Cell.Biol.}, volume = {12}, pages = {3390–3398}, keywords = {BINDING,Cap binding,Gag,His154,L-A,La,mRNA,Multiple DOI,nonfile,nosource,protein,Rna,structure,virus,yeast} } % == BibTeX quality report for blancCoatProteinYeast1992a: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{blanchardSolutionStructureLoop2001, title = {Solution Structure of the {{A}} Loop of {{23S}} Ribosomal {{RNA}}}, author = {Blanchard, S.C. and Puglisi, J.D.}, year = 2001, month = mar, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {7}, pages = {3720–3725}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.051608498}, url = {http://www.pnas.org/content/98/7/3720.short}, abstract = {The A loop is an essential RNA component of the ribosome peptidyltransferase center that directly interacts with aminoacyl (A)-site tRNA. The A loop is highly conserved and contains a ubiquitous 2’-O-methyl ribose modification at position U2552. Here, we present the solution structure of a modified and unmodified A-loop RNA to define both the A-loop fold and the structural impact of the U2552 modification. Solution data reveal that the A-loop RNA has a compact structure that includes a noncanonical base pair between C2556 and U2552. NMR evidence is presented that the N3 position of C2556 has a shifted pKa and that protonation at C2556-N3 changes the C-U pair geometry. Our data indicate that U2552 methylation modifies the A-loop fold, in particular the dynamics and position of residues C2556 and U2555. We compare our structural data with the structure of the A loop observed in a recent 50S crystal structure [Ban, N., Nissen, P., Hansen, J., Moore, P, B. 8 Steitz, T. A. (2000) Science 289, 905-920; Nissen, P,, Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. (2000) Science 289, 920-930]. The solution and crystal structures of the A loop are dramatically different, suggesting that a structural rearrangement of the A loop must occur on docking into the peptidyltransferase center. Possible roles of this docking event, the shifted pKa of C2556 and the U2552 2’-O-methylation in the mechanism of translation, are discussed}, keywords = {A-SITE,AMINOACYL-TRANSFER-RNA,COMPONENT,crystal structure,CRYSTAL-STRUCTURE,FUNCTIONAL TRANSFER-RNAS,LOOP,MECHANISM,Methylation,modification,NMR-SPECTROSCOPY,nosource,Nucleotides,PEPTIDYL TRANSFERASE CENTER,Peptidyltransferase,RESIDUES,Ribose,RIBOSOMAL-RNA,ribosome,Rna,SELECTION,Structural,structure,SUBUNIT,translation,tRNA} }

@article{blinkowaProgrammedRibosomalFrameshifting1990, title = {Programmed Ribosomal Frameshifting Generates the {{Escherichia}} Coli {{DNA}} Polymerase {{III}} Gamma Subunit from within the Tau Subunit Reading Frame}, author = {Blinkowa, A.L. and Walker, J.R.}, year = 1990, month = apr, journal = {Nucleic Acids Research}, volume = {18}, number = {7}, pages = {1725–1729}, doi = {10.1093/nar/18.7.1725}, keywords = {0,Amino Acid Sequence,Bacterial,Base Sequence,Codon,Codon/ge [Genetics],Dna,DNA Polymerase III/ge [Genetics],DNA Polymerases/ge [Genetics],Escherichia coli,Escherichia coli/en [Enzymology],Escherichia coli/ge [Genetics],ESCHERICHIA-COLI,frameshift,Frameshifting,GAMMA-SUBUNIT,gene,Genes,Genetic,In Vitro,IN-VITRO,IN-VIVO,Macromolecular Systems,microbiology,Molecular Sequence Data,Mutagenesis,Mutation,Non-U.S.Gov’t,nosource,Nucleic Acid Conformation,Nucleotides,Oligonucleotide Probes,P.H.S.,polymerase,protein,Recombinant/me [Metabolism],RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,Ribosomes/me [Metabolism],sequence,SIGNAL,Structural,Support,termination,translation,U.S.Gov’t} }

@article{bloeminkPhosphorylationRibosomalProtein1999, title = {Phosphorylation of Ribosomal Protein {{L18}} Is Required for Its Folding and Binding to {{5S rRNA}}.}, author = {Bloemink, M.J. and Moore, P.B.}, year = 1999, month = oct, journal = {Biochemistry}, volume = {38}, number = {40}, pages = {13385–13390}, publisher = {ACS Publications}, doi = {10.1021/bi9914816}, url = {http://pubs.acs.org/doi/abs/10.1021/bi9914816}, abstract = {Ribosomal protein L18 from Bacillus stearothermophilus (bL18) includes a previously unreported phosphoserine residue. The folded conformation of the protein is stabilized by the dianionic form of the phosphate group of that residue. In the absence of Mg(2+), the pK(a) of the phosphate group is so high that the protein is not fully folded at pH 7. In the presence of Mg(2+), its pK(a) drops significantly, and consequently the native conformation of bL18 becomes stable at pH 7 and the protein is able to bind to 5S rRNA. Dephosphorylated bL18 does not bind to 5S rRNA at neutral pH}, keywords = {5S rRNA,99459289,Bacillus stearothermophilus,BINDING,chemistry,nosource,Phosphorylation,protein,rRNA} }

@article{bocchetta23SRRNAPositions1998, title = {{{23S rRNA}} Positions Essential for {{tRNA}} Binding in Ribosomal Functional Sites}, author = {Bocchetta, M. and Xiong, L. and Mankin, A.S.}, year = 1998, month = mar, journal = {Proc.Natl.Acad.Sci.U.S.A}, volume = {95}, number = {7}, pages = {3525–3530}, doi = {10.1073/pnas.95.7.3525}, abstract = {rRNA plays an important role in function of peptidyl transferase, the catalytic center of the ribosome responsible for the peptide bond formation. Proper placement of the peptidyl transferase substrates, peptidyl-tRNA and aminoacyl-tRNA, is essential for catalysis of the transpeptidation reaction and protein synthesis. In this report, we define a small set of rRNA nucleotides that are most likely directly involved in binding of tRNA in the functional sites of the large ribosomal subunit. By binding biotinylated tRNA substrates to randomly modified large ribosomal subunits from Escherichia coli and capturing resulting complexes on the avidin resin, we identified four nucleotides in the large ribosomal subunit rRNA (positions G2252, A2451, U2506, and U2585) whose modifications prevent binding of a peptidyl-tRNA analog in the P site and one residue (U2555) whose modification interferes with transfer of peptidyl moiety to puromycin. These nucleotides represent a subset of positions protected by tRNA analogs from chemical modification and significantly narrow the number of 23S rRNA nucleotides that may be directly involved in tRNA binding in the ribosomal functional sites}, keywords = {98188236,BINDING,Binding Sites,Catalysis,chemistry,COMPLEX,COMPLEXES,Escherichia coli,ESCHERICHIA-COLI,metabolism,modification,nosource,Nucleotides,peptidyl transferase,protein,protein synthesis,PROTEIN-SYNTHESIS,Puromycin,ribosome,Ribosomes,RNARibosomal23S,RNATransfer,rRNA,supportu.s.gov’tp.h.s.,TranslationGenetic,tRNA} } % == BibTeX quality report for bocchetta23SRRNAPositions1998: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.U.S.A

@article{boddekerCharacterizationNovelAntibacterial2002, title = {Characterization of a Novel Antibacterial Agent That Inhibits Bacterial Translation.}, author = {Boddeker, N. and Bahador, G. and Gibbs, C. and Mabery, E. and Wolf, J. and Xu, L.H. and Watson, J.}, year = 2002, journal = {Rna-A Publication of the Rna Society}, volume = {8}, number = {9}, pages = {1120–1128}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838202024020}, url = {http://rnajournal.cshlp.org/content/8/9/1120.short ISI:000178024100005}, abstract = {Bacterial protein synthesis is the target for several classes of established antibiotics. This report describes the characterization of a novel translation inhibitor produced by the soil bacterium Flexibacter. The dipeptide antibiotic TAN1057 A/B was synthesized and designated GS71128. As reported previously, TAN1057 inhibits protein synthesis in both Escherichia coli and Staphylococcus aureus, leaving transcription unaffected. Cell-free translation systems from E. coli were used to further dissect the mechanism of translational inhibition. Binding of mRNA to ribosomes was unaffected by the drug, whereas the initiation reaction was reduced. Elongation of translation was completely inhibited by GS7128. Detailed analysis showed that the peptidyl transferase reaction was strongly inhibited, whereas tRNA binding to both A- and P-site was unaffected. Selection and analysis of drug-resistant mutants of S. aureus suggests that drug uptake may be mediated by a dipeptide transport mechanism}, keywords = {0,23S RIBOSOMAL-RNA,A-SITE,analysis,ANGSTROM RESOLUTION,antibiotic,antibiotics,Bacteria,Bacterial,BINDING,elongation,Escherichia coli,ESCHERICHIA-COLI,INHIBITION,initiation,MECHANISM,mRNA,MRSA,nosource,OXAZOLIDINONES,P-SITE,peptidyl transferase,protein,protein synthesis,PROTEIN-SYNTHESIS,ribosome,Ribosomes,STAPHYLOCOCCUS-AUREUS,STRUCTURAL BASIS,transcription,TRANSFER-RNA BINDING,translation,tRNA} }

@article{boekePositiveSelectionMutants1984a, title = {A Positive Selection for Mutants Lacking Orotidine-5’-Phosphate Decarboxylase Activity in Yeast: 5-Fluoro-Orotic Acid Resistance}, author = {Boeke, J.D. and LaCroute, F. and Fink, G.R.}, year = 1984, journal = {Mol Gen.Genet.}, volume = {197}, number = {2}, pages = {345–346}, doi = {10.1007/BF00330984}, url = {⬚PM:6394957 ⬚}, abstract = {Mutations at the URA3 locus of Saccharomyces cerevisiae can be obtained by a positive selection. Wild-type strains of yeast (or ura3 mutant strains containing a plasmid-borne URA3+ gene) are unable to grow on medium containing the pyrimidine analog 5-fluoro-orotic acid, whereas ura3- mutants grow normally. This selection, based on the loss of orotidine-5’-phosphate decarboxylase activity seems applicable to a variety of eucaryotic and procaryotic cells}, keywords = {0,5-FOA,ACID,analogs & derivatives,Carboxy-Lyases,Carboxy-Lyases: genetics,CELLS,CEREVISIAE,drug effects,Drug Resistance,Drug ResistanceMicrobial,enzymology,Fungal Proteins,Fungal Proteins: genetics,gene,genetics,La,media,Microbial,Microbiological Techniques,MUTANTS,Mutation,MUTATIONS,nosource,Orotic Acid,Orotic Acid: analogs & derivatives,Orotic Acid: pharmacology,Orotidine-5’-Phosphate Decarboxylase,Orotidine-5’-Phosphate Decarboxylase: genetics,pharmacology,protein,Proteins,RESISTANCE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae: drug effects,Saccharomyces cerevisiae: enzymology,Saccharomyces cerevisiae: genetics,SACCHAROMYCES-CEREVISIAE,SELECTION,WILD-TYPE,yeast} } % == BibTeX quality report for boekePositiveSelectionMutants1984a: % ? Possibly abbreviated journal title Mol Gen.Genet.

@article{boekeGeneralMethodChromosomal1988, title = {A General Method for the Chromosomal Amplification of Genes into Yeast.}, author = {Boeke, J.D. and Xu, H. and Fink, G.R.}, year = 1988, journal = {Science}, volume = {239}, pages = {280–282}, doi = {10.1126/science.2827308}, keywords = {gene,Genes,Methods,nosource,pJEF1105,Plasmids,Ty1,yeast} }

@article{bogdanovStructureFunction5S1995, title = {Structure and Function of {{5S rRNA}} in the Ribosome}, author = {Bogdanov, A.A. and Dontsova, O.A. and Dokudovskaya, S.S. and Lavrik, I.N.}, year = 1995, month = nov, journal = {Biochemistry and cell biology}, volume = {73}, number = {11-12}, pages = {869–876}, publisher = {NATIONAL RESEARCH COUNCIL CANADA}, doi = {10.1139/o95-094}, url = {http://www.nrcresearchpress.com/doi/abs/10.1139/o95-094}, abstract = {5S rRNA is a small RNA molecule that is a component of a ribosome from almost all living organisms. In this review, we discuss the biogenesis of 5S rRNA and its properties as an independent structural domain of a ribosome as well as the current concepts concerning the higher order structure of 5S rRNA in free state and in its complexes with ribosomal proteins and its folding in the ribosome. Special attention is paid to recent experimental approaches that have been useful in 5S rRNA studies. Our own data on topography of 5S rRNA in the ribosomes are discussed in detail. The hypothesis describing the possible functional role of 5S rRNA for ribosome functioning is discussed}, keywords = {0,5S rRNA,Base Sequence,chemistry,COMPLEX,COMPLEXES,COMPONENT,DOMAIN,genetics,La,Molecular Sequence Data,nosource,Nucleic Acid Conformation,protein,Proteins,Research SupportNon-U.S.Gov’t,Review,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNARibosomal5S,rRNA,Structural,structure,Structure-Activity Relationship,supportnon-u.s.gov’t} } % == BibTeX quality report for bogdanovStructureFunction5S1995: % ? unused Journal abbr (“Biochem.Cell Biol.”)

@article{bogdanovStructureFunction5S1995b, title = {[{{Structure}} and Function of {{5S rRNA}} in Ribosomes]}, author = {Bogdanov, A.A. and Lavrik, I.N. and Dokudovskaia, S.S. and Dontsova, O.A.}, year = 1995, month = nov, journal = {Mol.Biol.(Mosk)}, volume = {29}, number = {6}, pages = {1218–1227}, keywords = {5S rRNA,96139881,Base Sequence,chemistry,metabolism,Molecular Sequence Data,No DOI found,nosource,Nucleic Acid Conformation,Protein StructureSecondary,Protein StructureTertiary,Ribosomes,RNARibosomal5S,rRNA,Structure-Activity Relationship,supportnon-u.s.gov’t,TranslationGenetic} } % == BibTeX quality report for bogdanovStructureFunction5S1995b: % ? Possibly abbreviated journal title Mol.Biol.(Mosk)

@article{bogdanovaDirectedCleavage16S1995a, title = {[{{Directed}} Cleavage of the {{16S rRNA}} Molecule at a Single Internucleotide Bond]}, author = {Bogdanova, S.L. and Degtiarev, A.I. and Baranov, P.V. and Dokudovskaia, S.S. and Lavrik, I.N. and Dontsova, O.A. and Oretskaia, T.S. and Krynetskaia, I.F. and Shabarova, Z.A. and Bogdanov, A.A.}, year = 1995, month = feb, journal = {Biokhimii͡a (Moscow, Russia)}, volume = {60}, number = {2}, eprint = {7718670}, eprinttype = {pubmed}, pages = {297–307}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7718670}, abstract = {Cleavage of 16S ribosomal RNA (rRNA) from E. coli “hammerhead” type ribozymes as well as by RNAase iI in the presence of “hymeric” (2’- deoxy-F-thymidine containing) oligonucleotides has been studied. The conditions for the cleavage of a desired single internucleotide bond have been found for a large molecule with a very complicated secondary and three-dimensional structure}, keywords = {0,Base Sequence,chemistry,Chimera,Escherichia coli,genetics,Hydrolysis,La,metabolism,Molecular Sequence Data,No DOI found,nosource,Nucleic Acid Conformation,Oligonucleotides,Ribonuclease HCalf Thymus,ribozyme,Rna,RNARibosomal16S,rRNA,structure} } % == BibTeX quality report for bogdanovaDirectedCleavage16S1995a: % ? unused Journal abbr (“Biokhimiia.”)

@article{boldoghArp23Complex2001, title = {Arp2/3 Complex and Actin Dynamics Are Required for Actin-Based Mitochondrial Motility in Yeast}, author = {Boldogh, I.R. and Yang, H.C. and Nowakowski, W.D. and Karmon, S.L. and Hays, L.G. and Yates, J.R. and Pon, L.A.}, year = 2001, month = mar, journal = {Proceedings of the National Academy of Sciences}, volume = {98}, number = {6}, pages = {3162–3167}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.051494698}, url = {http://www.pnas.org/content/98/6/3162.short}, abstract = {The Arp2/3 complex is implicated in actin polymerization-driven movement of Listeria monocytogenes. Here, we find that Arp2p and Arc15p, two subunits of this complex, show tight, actin-independent association with isolated yeast mitochondria. Arp2p colocalizes with mitochondria. Consistent with this result, we detect Arp2p-dependent formation of actin clouds around mitochondria in intact yeast. Cells bearing mutations in ARP2 or ARC15 genes show decreased velocities of mitochondrial movement, loss of all directed movement and defects in mitochondrial morphology. Finally, we observe a decrease in the velocity and extent of mitochondrial movement in yeast in which actin dynamics are reduced but actin cytoskeletal structure is intact. These results support the idea that the movement of mitochondria in yeast is actin polymerization driven and that this movement requires Arp2/3 complex}, keywords = {0,3,Actins,ASSOCIATION,BIOLOGY,CELLS,COMPLEX,COMPLEXES,Cytoskeletal Proteins,drug effects,DYNAMICS,Fungal Proteins,gene,Genes,La,Membrane Proteins,metabolism,mitochondria,Movement,Mutation,MUTATIONS,nosource,pharmacology,physiology,Potassium,Potassium Chloride,protein,Proteins,REQUIRES,Saccharomyces cerevisiae,structure,SUBUNIT,SUBUNITS,Support,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,yeast} } % == BibTeX quality report for boldoghArp23Complex2001: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{bondAbsenceDbp2pAlters2001b, title = {Absence of {{Dbp2p}} Alters Both Nonsense-Mediated {{mRNA}} Decay and {{rRNA}} Processing}, author = {Bond, A.T. and Mangus, D.A. and He, F. and Jacobson, A.}, year = 2001, month = nov, journal = {Molecular and Cellular Biology}, volume = {21}, number = {21}, pages = {7366–7379}, doi = {10.1128/MCB.21.21.7366-7379.2001}, url = {ISI:000171486900023}, abstract = {Dbp2p, a member of the large family of DEAD-box proteins and a yeast homolog of human p68, was shown to interact with Upf1p, an essential component of the nonsense-mediated mRNA decay pathway. Dbp2p:Upf1p interaction occurs within a large conserved region in the middle of Upf1p that is largely distinct from its Nmd2p and Sup35/45p interaction domains. Deletion of DBP2, or point mutations within its highly conserved DEAD-box motifs, increased the abundance of nonsense-containing transcripts, leading us to conclude that Dbp2p also functions in the nonsense-mediated mRNA decay pathway. Dbp2p, like Upf1p, acts before or at decapping, is predominantly cytoplasmic, and associates with polyribosomes. Interestingly, Dbp2p also plays an important role in rRNA processing. In dbp2 Delta cells, polyribosome profiles are deficient in free 60S subunits and the mature 25S rRNA is greatly reduced. The ribosome biogenesis phenotype, but not the mRNA decay function, of dbp2 Delta cells can be complemented by the human p68 gene. We propose a unifying model in which Dbp2p affects both nonsense-mediated mRNA decay and rRNA processing by altering rRNA structure, allowing specific processing events in one instance and facilitating dissociation of the translation termination complex in the other}, keywords = {0,60S subunit,BlottingNorthern,Canavanine,Cell Nucleus,CELLS,CEREVISIAE,COMPLEX,COMPLEXES,COMPONENT,Conserved Sequence,Cycloheximide,DEAD-BOX PROTEINS,DECAY,DECAY PATHWAY,DOMAIN,DOMAINS,Dose-Response RelationshipDrug,EUKARYOTIC TRANSLATION,FAMILY,gene,Gene Deletion,Genetic,genetics,Helicase,homolog,human,IDENTIFICATION,INHIBITOR,kinase,La,MESSENGER-RNA DECAY,metabolism,microbiology,MODEL,ModelsBiological,MOLECULAR-GENETICS,MOTIFS,mRNA,mRNA decay,Mutation,MUTATIONS,nonsense-mediated mRNA decay,nosource,Oligonucleotides,Paromomycin,PATHWAY,pharmacology,Phenotype,PHENOTYPIC SUPPRESSION,physiology,PLASMID,Plasmids,Point Mutation,Polyribosomes,protein,Protein Binding,Protein Kinases,Protein StructureTertiary,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-KINASE,PROTEIN-SYNTHESIS,Proteins,REGION,ribosome,ribosome biogenesis,Ribosomes,Rna,RNA HELICASE,RNA Helicases,RNAMessenger,RNARibosomal,rRNA,S,S-CEREVISIAE,SACCHAROMYCES-CEREVISIAE,structure,Subcellular Fractions,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYNTHESIS INHIBITORS,termination,Time Factors,TRANSCRIPT,translation,TRANSLATION INITIATION FACTOR-4A,TRANSLATION TERMINATION,TranslationGenetic,Two-Hybrid System Techniques,Upf1,UPF1 PROTEIN,yeast,YEAST-CELLS} }

@article{bondensgaardGlobalConformationHammerhead2002, title = {The Global Conformation of the Hammerhead Ribozyme Determined Using Residual Dipolar Couplings}, author = {Bondensgaard, K. and Mollova, E.T. and Pardi, A.}, year = 2002, month = oct, journal = {Biochemistry}, volume = {41}, number = {39}, pages = {11532–11542}, publisher = {ACS Publications}, doi = {10.1021/bi012167q}, url = {http://pubs.acs.org/doi/abs/10.1021/bi012167q}, abstract = {The global structure of the hammerhead ribozyme was determined in the absence of Mg(2+) by solution NMR experiments. The hammerhead ribozyme motif forms a branched structure consisting of three helical stems connected to a catalytic core. The (1)H-(15)N and (1)H-(13)C residual dipolar couplings were measured in a set of differentially (15)N/(13)C-labeled ribozymes complexed with an unlabeled noncleavable substrate. The residual dipolar couplings provide orientation information on both the local and the global structure of the molecule. Analysis of the residual dipolar couplings demonstrated that the local structure of the three helical stems in solution is well modeled by an A-form conformation. However, the global structure of the hammerhead in solution in the absence of Mg(2+) is not consistent with the Y-shaped conformation observed in crystal structures of the hammerhead. The residual dipolar couplings for the helical stems were combined with standard NOE and J coupling constant NMR data from the catalytic core. The NOE data show formation of sheared G-A base pairs in domain 2. These NMR data were used to determine the global orientation of the three helical stems in the hammerhead. The hammerhead forms a rather extended structure under these conditions with a large angle between stems I and II ( approximately 153 degrees ), a smaller angle between stems II and III ( approximately 100 degrees ), and the smallest angle between stems I and III ( approximately 77 degrees ). The residual dipolar coupling data also contain information on the dynamics of the molecule and were used here to provide qualitative information on the flexibility of the helical domains in the hammerhead ribozyme-substrate complex}, keywords = {0,analysis,Bacterial,BASE,BASE-PAIR,Catalytic Domain,chemistry,COMPLEX,COMPLEXES,CONFORMATION,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,DOMAIN,DOMAINS,DYNAMICS,Fluorescence Resonance Energy Transfer,FORM,HAMMERHEAD RIBOZYME,La,ModelsChemical,ModelsMolecular,NMR,nosource,Nuclear Magnetic ResonanceBiomolecular,Nucleic Acid Conformation,ribozyme,Rna,RNABacterial,RNACatalytic,Solutions,structure,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Thermodynamics} }

@article{bonettiEfficiencyTranslationTermination1995a, title = {The Efficiency of Translation Termination Is Determined by a Synergistic Interplay between Upstream and Downstream Sequences in {{Saccharomyces}} Cerevisiae}, author = {Bonetti, B. and Fu, L. and Moon, J. and Bedwell, D.M.}, year = 1995, journal = {J.Mol.Biol.}, volume = {251}, number = {3}, pages = {334–345}, doi = {10.1006/jmbi.1995.0438}, url = {PM:7650736}, abstract = {In a recent study we found that the efficiency of translation termination could be decreased several hundred fold by altering the local sequence context surrounding stop codons in the yeast Saccharomyces cerevisiae. Suppression of termination was shown to be mediated by near-cognate tRNA mispairing with the termination codon. We have now examined in greater detail how the local sequence context affects the efficiency of translation termination in this organism. Our results indicate that the sequence immediately upstream of the termination codon plays a significant role in determining the efficiency of translation termination. An extended termination sequence (containing the stop codon and the following three nucleotides) was also found to be a major determinant of termination efficiency, with effects attributable to the fourth nucleotide being largely independent of the termination codon. For the UGA and UAA stop codons, the influence of the fourth position on termination efficiency (from most efficient to least efficient termination) was found to be G {\(>\)} U,A {\(>\)} C, while for the UAG codon it was U,A {\(>\)} C {\(>\)} G. These sequence-specific effects on the efficiency of translation termination suggest that polypeptide chain release factor (or another molecule that may play a role in translation termination, such as rRNA) recognizes an extended termination sequence in yeast. A previous study found a statistically significant bias toward certain tetranucleotide sequences (containing the stop codon and the first distal nucleotide) in several organisms. We found that tetranucleotide sequences most frequently used in yeast are among the most efficient at mediating translation termination, while rare tetranucleotide sequences mediate much less efficient termination. Taken together, our results indicate that upstream and downstream components of an extended sequence context act synergistically to determine the overall efficiency of translation termination in yeast}, keywords = {0,Amino Acid Sequence,Base Sequence,beta-Galactosidase,biosynthesis,CEREVISIAE,Codon,CODONS,CodonTerminator,COMPONENT,COMPONENTS,Dna,DNARecombinant,DOWNSTREAM,efficiency,genetics,La,microbiology,Molecular Sequence Data,nosource,Nucleotides,Peptide Chain TerminationTranslational,POLYPEPTIDE,POLYPEPTIDE-CHAIN,POSITION,Regulatory SequencesNucleic Acid,RELEASE,release factor,Research SupportU.S.Gov’tP.H.S.,Rna,RNAFungal,RNAMessenger,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,STOP CODON,suppression,SuppressionGenetic,termination,TERMINATION CODON,TERMINATION EFFICIENCY,TERMINATION-CODON,translation,TRANSLATION TERMINATION,tRNA,UAA,UPSTREAM,yeast} } % == BibTeX quality report for bonettiEfficiencyTranslationTermination1995a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{bonnerotFunctionalRedundancySpb1p2003, title = {Functional Redundancy of {{Spb1p}} and a {{snR52-dependent}} Mechanism for the 2 ’-{{O-ribose}} Methylation of a Conserved {{rRNA}} Position in Yeast}, author = {Bonnerot, C. and Pintard, L. and Lutfalla, G.}, year = 2003, month = nov, journal = {Molecular Cell}, volume = {12}, number = {5}, pages = {1309–1315}, publisher = {Elsevier}, doi = {10.1016/S1097-2765(03)00435-0}, url = {http://linkinghub.elsevier.com/retrieve/pii/s1097276503004350}, abstract = {In yeast, guide snoRNAs have been assigned to 51 of the 55 rRNA ribose methylation sites. LSU-Um(2918) is one of the four remaining positions. This residue is highly conserved and located in the peptidyl transferase center of the ribosome. The equivalent position on the E. coli 23S rRNA is methylated by FtsJ/RrmJ which has three yeast homologs: Spb1, involved in biogenesis of LSU; Trm7, a tRNA methyltransferase; and Mrm2, a mitochondrial 21S rRNA methyltransferase. We demonstrate that a point mutation in the AdoMet binding site of Spb1p affects cell growth but does not abolish methylation Of U-2918. When this mutation is combined with disruption of snR52 (a snoRNA C/D), cell growth is severely impaired and U-2918 is no longer methylated. In vitro, Spb1p is able to methylate U-2918 on 60S subunits. Our results reveal the importance of this methylation for which two mechanisms coexist: a site-specific methyltransferase (Spb1p) and a snoRNA-dependent mechanism}, keywords = {60S subunit,BINDING,BINDING-SITE,BIOGENESIS,cloning,DISRUPTION,E,ESCHERICHIA-COLI,gene,GROWTH,homolog,In Vitro,IN-VITRO,MECHANISM,MECHANISMS,Methylation,METHYLTRANSFERASE,Mutation,nosource,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Point Mutation,POSITION,POSITIONS,protein,purification,RECONSTITUTION,Ribose,ribosome,rRNA,SACCHAROMYCES-CEREVISIAE,SITE,site specific,SITES,SUBUNIT,SUBUNITS,TRANSFERASE CENTER,tRNA,yeast} }

@article{borkSpermeggBindingProtein1996a, title = {Sperm-Egg Binding Protein or Proto-Oncogene? [Letter; Comment]}, author = {Bork, P.}, year = 1996, month = mar, journal = {Science}, volume = {271}, number = {5254}, pages = {1431-2; discussion 1434-5}, doi = {10.1126/science.271.5254.1431}, keywords = {BINDING,Frameshifting,genomic,nosource,protein,regulation} }

@article{borowskiTruncatedElongationFactor1996a, title = {Truncated Elongation Factor {{G}} Lacking the {{G}} Domain Promotes Translocation of the 3’ End but Not of the Anticodon Domain of Peptidyl- {{tRNA}}}, author = {Borowski, C. and Rodnina, M.V. and Wintermeyer, W.}, year = 1996, month = apr, journal = {Proceedings of the National Academy of Sciences}, volume = {93}, number = {9}, pages = {4202–4206}, doi = {10.1073/pnas.93.9.4202}, abstract = {The mechanism by which elongation factor G (EF-G) catalyzes the translocation of tRNAs and mRNA on the ribosome is not known. The reaction requires GTP, which is hydrolyzed to GDP. Here we show that EF- G from Escherichia coli lacking the G domain still catalyzed partial translocation in that it promoted the transfer of the 3’ end of peptidyl-tRNA to the P site on the 50S ribosomal subunit into a puromycin-reactive state in a slow-turnover reaction. In contrast, it did not bring about translocation on the 30S subunit, since (i) deacylated tRNA was not released from the P site and (ii) the A site remained blocked for aminoacyl-tRNA binding during and after partial translocation. The reaction probably represents the first EF-G- dependent step of translocation that follows the spontaneous formation of the A/P state that is not puromycin-reactive [Moazed, D. & Noller, H. F. (1989) Nature (London) 342, 142-148]. In the complete system– i.e., with intact EF-G and GTP–the 50S phase of translocation is rapidly followed by the 30S phase during which the tRNAs together with the mRNA are shifted on the small ribosomal subunit, and GTP is hydrolyzed. As to the mechanism of EF-G function, the results show that the G domain has an important role, presumably exerted through interactions with other domains of EF-G, in the promotion of translocation on the small ribosomal subunit. The G domain’s intramolecular interactions are likely to be modulated by GTP binding and hydrolysis}, keywords = {96210618,A-SITE,Anticodon,BINDING,biosynthesis,elongation,Escherichia coli,ESCHERICHIA-COLI,GTP,Hydrolysis,Kinetics,MECHANISM,metabolism,mRNA,MutagenesisSite-Directed,nosource,P-SITE,Peptide Elongation Factors,Poly U,Polymerase Chain Reaction,proofreading,Puromycin,Recombinant Proteins,ribosome,Ribosomes,RNAMessenger,RNATransferAmino Acyl,RNATransferPhe,Sequence Deletion,supportnon-u.s.gov’t,translocation,tRNA} } % == BibTeX quality report for borowskiTruncatedElongationFactor1996a: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{boschRevisedBacterialPolypeptide1996, title = {A Revised Bacterial Polypeptide Chain Elongation Cycle with a Stepwise Increase in Restriction of Unwanted Ternary Complexes by the Ribosome}, author = {Bosch, L. and Vijgenboom, E. and Zeef, L.A.}, year = 1996, month = oct, journal = {Biochemistry}, volume = {35}, number = {39}, pages = {12647–12651}, doi = {10.1021/bi952925a}, keywords = {Bacterial,chemistry,COMPLEX,COMPLEXES,elongation,models,nosource,ribosome} }

@article{boslingResistancePeptidylTransferase2003, title = {Resistance to the Peptidyl Transferase Inhibitor Tiamulin Caused by Mutation of Ribosomal Protein {{L3}}}, author = {Bosling, J. and Poulsen, S.M. and Vester, B. and Long, K.S.}, year = 2003, journal = {Antimicrobial agents and chemotherapy}, volume = {47}, number = {9}, pages = {2892–2896}, publisher = {Am Soc Microbiol}, doi = {10.1128/AAC.47.9.2892-2896.2003}, url = {http://aac.asm.org/cgi/content/abstract/47/9/2892}, abstract = {The antibiotic tiamulin targets the 50S subunit of the bacterial ribosome and interacts at the peptidyl transferase center. Tiamulin-resistant Escherichia coli mutants were isolated in order to elucidate mechanisms of resistance to the drug. No mutations in the rRNA were selected as resistance determinants using a strain expressing only a plasmid-encoded rRNA operon. Selection in a strain with all seven chromosomal rRNA operons yielded a mutant with an A445G mutation in the gene coding for ribosomal protein L3, resulting in an Asn149Asp alteration. Complementation experiments and sequencing of transductants demonstrate that the mutation is responsible for the resistance phenotype. Chemical footprinting experiments show a reduced binding of tiamulin to mutant ribosomes. It is inferred that the L3 mutation, which points into the peptidyl transferase cleft, causes tiamulin resistance by alteration of the drug-binding site. This is the first report of a mechanism of resistance to tiamulin unveiled in molecular detail}, keywords = {antagonists &,antibiotic,antibiotics,Bacterial,BINDING,BIOLOGY,Chromosome Mapping,Diterpenes,DNA Footprinting,drugs,ESCHERICHIA-COLI,gene,Genetic Complementation Test,genetics,INHIBITOR,inhibitors,L3,Lac Operon,MECHANISM,MECHANISMS,metabolism,ModelsBiological,Molecular Conformation,MUTANTS,Mutation,MUTATIONS,nosource,Operon,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Peptidyltransferase,pharmacology,Phenotype,Plasmids,protein,RESISTANCE,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,RNARibosomal,rRNA,rRNA Operon,SELECTION,SITE,SUBUNIT,supportnon-u.s.gov’t,TARGET,tiamulin,TRANSFERASE CENTER} } % == BibTeX quality report for boslingResistancePeptidylTransferase2003: % ? unused Journal abbr (“Antimicrob.Agents Chemother.”)

@article{bouadlounCodonspecificMissenseErrors1983, title = {Codon-Specific Missense Errors in Vivo.}, author = {Bouadloun, F. and Donner, D. and Kurland, C.G.}, year = 1983, journal = {The EMBO journal}, volume = {2}, number = {8}, pages = {1351–1356}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1983.tb01591.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC555282/}, abstract = {We have developed a simple method for measuring the missense substitution of amino acids at specified positions in proteins synthesized in vivo. We find that the frequency of cysteine substitution for the single arginine in Escherichia coli ribosomal protein L7/L12 is close to 10(-3) for wild-type bacteria, decreases to 4 x 10(-4) in streptomycin-resistant bacteria containing mutant S12 (rpsL), and is virtually unchanged in Ram bacteria containing mutant S4 (rpsD). We have also found that the frequency of the cysteine substitution for the single tryptophan in E. coli ribosomal protein S6 is 3-4 x 10(-3) for wild-type bacteria, decreases to 6 x 10(-4) in streptomycin-resistant bacteria and is elevated to nearly 10(-2) in Ram bacteria}, keywords = {0,ACID,ACIDS,Amino Acid Substitution,Amino Acids,AMINO-ACID,AMINO-ACIDS,Arginine,Bacteria,BIOLOGY,Codon,Cysteine,E,ERRORS,Escherichia coli,ESCHERICHIA-COLI,genetics,IN-VIVO,La,Molecular Biology,MutationMissense,nosource,POSITION,POSITIONS,protein,PROTEIN L7/L12,Proteins,ram,Ribosomal Proteins,RIBOSOMAL-PROTEIN,Support,Tryptophan,WILD-TYPE} } % == BibTeX quality report for bouadlounCodonspecificMissenseErrors1983: % ? unused Journal abbr (“EMBO J.”)

@article{boulantUnusualMultipleRecoding2003, title = {Unusual Multiple Recoding Events Leading to Alternative Forms of Hepatitis {{C}} Virus Core Protein from Genotype 1b}, author = {Boulant, S. and Becchi, M. and Penin, F. and Lavergne, J.P.}, year = 2003, month = nov, journal = {Journal of Biological Chemistry}, volume = {278}, number = {46}, pages = {45785–45792}, publisher = {ASBMB}, doi = {10.1074/jbc.M307174200}, url = {http://www.jbc.org/content/278/46/45785.short}, abstract = {In addition to its involvement in the formation of the capsid shell of the virus particles, the core protein of hepatitis C virus (HCV) is believed to play an important role in the pathogenesis and/or establishment of persistent infection. We describe here alternative forms of genotype 1b HCV core protein identified after purification of various products of core protein segment 1-169 expressed in Escherichia coli and their analysis by proteolysis, mass spectrometry, and amino acid sequencing. These proteins all result from a +1 frameshift at codon 42 (a different position than that previously reported in genotype 1a) and, for some of them, from a rephasing in the normal open reading frame at the termination codon 144 in the +1 open reading frame. To test the relevance of these recoding events in a eukaryotic translational context, the nucleotide sequences surrounding the two shift sites were cloned in the three reading frames into expression vectors, allowing the production of a C-terminally fused green fluorescent protein, and expressed both in a reticulocyte lysate transcription/translation assay and in culture cells. Both recoding events were confirmed in these expression systems, strengthening the hypothesis that they might occur in HCV-infected cells. Moreover, sera from HCV-positive patients of genotype 1a or 1b were shown to react differently against synthetic peptides encoded in the +1 open reading frame. Together, these results indicate the occurrence of distinct recoding events in genotypes 1a and 1b, pointing out genotype-dependent specific features for F protein}, keywords = {ACID,AMINO-ACID,analysis,Capsid,CELLS,Codon,Escherichia coli,ESCHERICHIA-COLI,expression,FORM,FRAME,frameshift,Genotype,GREEN FLUORESCENT PROTEIN,HEPATITIS-C,INFECTION,La,lysate,nosource,NUCLEOTIDE-SEQUENCE,OPEN READING FRAME,PARTICLES,Peptides,POSITION,PRODUCT,PRODUCTS,protein,Proteins,PROTEOLYSIS,purification,READING FRAME,Reading Frames,recoding,sequence,SEQUENCES,SITE,SITES,SYSTEM,SYSTEMS,termination,TERMINATION CODON,TERMINATION-CODON,vector,vectors,virus} } % == BibTeX quality report for boulantUnusualMultipleRecoding2003: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{bourneGTPaseSuperfamilyConserved1991, title = {The {{GTPase}} Superfamily: Conserved Structure and Molecular Mechanism.}, author = {Bourne, H.R. and Sanders, D.A. and McCormick, F.}, year = 1991, journal = {Nature}, volume = {349}, pages = {117–127}, publisher = {Nature Publishing Group}, doi = {10.1038/349117a0}, url = {http://www.nature.com/nature/journal/v349/n6305/abs/349117a0.html}, keywords = {EF-1,EF-2,GTPase,MECHANISM,nosource,Review,review article,structure} }

@article{boursnellCompletionSequenceGenome1987, title = {Completion of the Sequence of the Genome of the Coronavirus Avian Infectious Bronchitis Virus}, author = {Boursnell, M.E. and Brown, T.D. and Foulds, I.J. and Green, P.F. and Tomley, F.M. and Binns, M.M.}, year = 1987, month = jan, journal = {Journal of General Virology}, volume = {68 ( Pt 1)}, number = {1}, pages = {57–77}, publisher = {Soc General Microbiol}, url = {http://vir.sgmjournals.org/cgi/content/abstract/68/1/57}, abstract = {The nucleotide sequence determination of the genome of the Beaudette strain of the coronavirus avian infectious bronchitis virus (IBV) has been completed. The complete sequence has been obtained from 17 overlapping cDNA clones, the 5’-most of which contains the leader sequence (as determined by direct sequencing of the genome) and the 3’-most of which contains the poly(A) tail. Approximately 8 kilobases at the 3’ end of this sequence have already been published. These contain the sequences of mRNAs A to E within which are the genes for the spike, the membrane and the nucleocapsid polypeptides: the main structural components of the virion. The remainder of the sequence, equivalent to the ‘unique’ region of mRNA F, is some 20 kilobases in length and is thought to code for a polymerase or polymerases which are involved in the replication of the genome and the production of the subgenomic messenger RNAs. This sequence contains two large open reading frames, potentially coding for polypeptides of molecular weights 441,000 and 300,000. Unlike other large open reading frames in the virus, the 300,000 open reading frame appears to have no subgenomic RNA associated with it which would allow it to be at the 5’ end of an mRNA species. Because of this, and because of the characteristics of the sequence in the region immediately upstream of its start codon, other mechanisms of translation, such as ribosome slippage, must be postulated}, keywords = {0,3,Amino Acid Sequence,analysis,Base Sequence,CloningMolecular,Codon,COMPONENT,COMPONENTS,Coronaviridae,Coronavirus,Dna,E,FRAME,gene,Genes,GenesViral,genetics,Genome,Infectious bronchitis virus,La,MECHANISM,MECHANISMS,MESSENGER-RNA,MESSENGER-RNAS,Microcomputers,Molecular Weight,mRNA,No DOI found,nosource,NUCLEOTIDE-SEQUENCE,OPEN READING FRAME,Open Reading Frames,poly(A),POLY(A) TAIL,polymerase,POLYPEPTIDE,POLYPEPTIDES,READING FRAME,Reading Frames,REGION,REPLICATION,ribosome,Rna,RNAMessenger,sequence,Sequence HomologyNucleic Acid,SEQUENCES,SLIPPAGE,Software,START CODON,Structural,translation,UPSTREAM,Virion,virus} } % == BibTeX quality report for boursnellCompletionSequenceGenome1987: % ? unused Journal abbr (“J.Gen.Virol.”)

@article{brachmannDesignerDeletionStrains1998, title = {Designer Deletion Strains Derived from {{Saccharomyces}} Cerevisiae {{S288C}}: A Useful Set of Strains and Plasmids for {{PCR-mediated}} Gene Disruption and Other Applications}, author = {Brachmann, C.B. and Davies, A. and Cost, G.J. and Caputo, E. and Li, J. and Hieter, P. and Boeke, J.D.}, year = 1998, month = jan, journal = {YEAST-CHICHESTER-}, volume = {14}, number = {2}, pages = {115–132}, publisher = {Wiley}, doi = {10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2}, url = {http://www.turbobiotech.com/maps/Brachmann et al. (1998).pdf}, abstract = {A set of yeast strains based on Saccharomyces cerevisiae S288C in which commonly used selectable marker genes are deleted by design based on the yeast genome sequence has been constructed and analysed. These strains minimize or eliminate the homology to the corresponding marker genes in commonly used vectors without significantly affecting adjacent gene expression. Because the homology between commonly used auxotrophic marker gene segments and genomic sequences has been largely or completely abolished, these strains will also reduce plasmid integration events which can interfere with a wide variety of molecular genetic applications. We also report the construction of new members of the pRS400 series of vectors, containing the kanMX, ADE2 and MET15 genes}, keywords = {0,Alleles,BIOLOGY,BlottingNorthern,BlottingSouthern,CEREVISIAE,chemistry,DISRUPTION,Dna,DNA Primers,expression,gene,Gene Deletion,Gene Expression,GENE-EXPRESSION,Genes,Genetic,Genetic Markers,genetics,Genome,GenomeFungal,genomic,La,MARKER,Mutation,nosource,physiology,PLASMID,Plasmids,Polymerase Chain Reaction,ResGen,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,SERIES,supportu.s.gov’tp.h.s.,vector,vectors,yeast} }

@article{bradshawNTerminalProcessingMethionine1998, title = {N-{{Terminal}} Processing: The Methionine Aminopeptidase and {{N}} [Alpha]-Acetyl Transferase Families}, author = {Bradshaw, R.A. and Brickey, W.W. and Walker, K.W.}, year = 1998, month = jul, journal = {Trends in biochemical sciences}, volume = {23}, number = {7}, pages = {263–267}, publisher = {Elsevier}, doi = {10.1016/S0968-0004(98)01227-4}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000498012274}, abstract = {Removal of the initiator methionine and/or acetylation of the alpha-amino group are among the earliest possible chemical modifications that occur during protein synthesis in eukaryotes. These events are catalyzed by methionine aminopeptidase and N alpha-acetyltransferase, respectively. Recent advances in the isolation and characterization of these enzymes indicate that they exist as isoforms that vary in cellular location, function, and evolutionary origins}, keywords = {Acetylation,Acetyltransferases,Aminopeptidases,Animals,CHEMICAL MODIFICATION,chemistry,enzyme,Enzymes,EvolutionMolecular,FAMILY,genetics,Humans,La,LOCATION,metabolism,Methionine,ModelsMolecular,modification,nosource,physiology,protein,Protein Conformation,Protein ProcessingPost-Translational,protein synthesis,PROTEIN-SYNTHESIS,Research SupportU.S.Gov’tP.H.S.,Review} } % == BibTeX quality report for bradshawNTerminalProcessingMethionine1998: % ? unused Journal abbr (“Trends Biochem.Sci.”)

@article{brandPseudouridylationYeastRibosomal1979, title = {Pseudouridylation of Yeast Ribosomal Precursor {{RNA}}}, author = {Brand, R.C. and Klootwijk, J. and Sibum, C.P. and Planta, R.J.}, year = 1979, journal = {Nucleic Acids Research}, volume = {7}, number = {1}, pages = {121–134}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/7.1.121}, url = {http://nar.oxfordjournals.org/content/7/1/121.short}, abstract = {The pseudouridylation of ribosomal RNA of Saccharomyces carlsbergensis was investigated with respect to its timing during the maturation of rRNA and its sequence specificity. Analysis of 37-S RNA, the common precursor to 17-S, 5.8-S and 26-S rRNA and most probably the primary ribosomal transcript, shows that this RNA molecule contains already most if not all of the 36-37 pseudouridine residues found in the mature rRNAs. Thus pseudouridylation is, like 2’-0-ribosemethylation, an early event in the maturation of rRNA, taking place immediately after, or even during, transcription. The data presented show that the non-conserved sequences of 37-S precursor rRNA contain very few pseudouridine residues if any. The pseudouridine residues within the rRNA sequences are apparently clustered to a certain degree as can inferred from the occurrence of a single oligonucleotide containing 3 pseudouridines, which was obtained by digestion of 26-S rRNA with ribonuclease T1}, keywords = {0,3,analogs & derivatives,analysis,Base Sequence,biosynthesis,La,MATURATION,metabolism,Molecular Weight,nosource,Oligoribonucleotides,PRECURSOR,Pseudouridine,pseudouridylation,RESIDUES,ribonuclease t1,ribosomal RNA,RIBOSOMAL-RNA,Rna,RNARibosomal,rRNA,Saccharomyces,sequence,SEQUENCES,SPECIFICITY,TRANSCRIPT,transcription,TranscriptionGenetic,Uridine,yeast} } % == BibTeX quality report for brandPseudouridylationYeastRibosomal1979: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{brandenburgerCardiacHypertrophyVivo2003, title = {Cardiac Hypertrophy in Vivo Is Associated with Increased Expression of the Ribosomal Gene Transcription Factor {{UBF}}}, author = {Brandenburger, Y. and Arthur, J.F. and Woodcock, E.A. and Du, X.J. and Gao, X.M. and Autelitano, D.J. and Rothblum, L.I. and Hannan, R.D.}, year = 2003, month = jul, journal = {FEBS letters}, volume = {548}, number = {1-3}, pages = {79–84}, publisher = {Elsevier}, doi = {10.1016/S0014-5793(03)00744-0}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579303007440}, abstract = {The ribosomal DNA transcription-specific factor, UBF, is a key target for the regulation of ribosomal RNA synthesis and hypertrophic growth of isolated neonatal cardiomyocytes. In this study, we have examined whether UBF expression is also an important determinant of cardiac growth rates in vivo. We show that rDNA transcription, rRNA synthesis and UBF expression in left ventricular myocytes isolated from mice 1-6 weeks following transverse aortic constriction were significantly increased (2.5-3.5-fold) compared to the levels in myocytes from the left ventricle of sham-operated mice}, keywords = {0,analysis,Animals,Atrial Natriuretic Factor,biosynthesis,Cardiomegaly,COMPLEX,COMPLEXES,Dna,etiology,expression,gene,GENE-TRANSCRIPTION,genetics,GROWTH,heart,Heart Ventricles,HypertrophyLeft Ventricular,IN-VIVO,initiation,La,Mice,Muscle Cells,nosource,pathology,physiology,Pol1 Transcription Initiation Complex Proteins,protein,Proteins,rDNA,RDNA TRANSCRIPTION,regulation,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tNon-P.H.S.,ribosomal RNA,RIBOSOMAL-RNA,Rna,RNAMessenger,RNARibosomal,rRNA,TARGET,transcription,TRANSCRIPTION FACTOR,TranscriptionGenetic,Up-Regulation} } % == BibTeX quality report for brandenburgerCardiacHypertrophyVivo2003: % ? unused Journal abbr (“FEBS Lett.”)

@article{brandtTransposableElementsSource2005, title = {Transposable Elements as a Source of Genetic Innovation: Expression and Evolution of a Family of Retrotransposon-Derived Neogenes in Mammals}, author = {Brandt, J. and Schrauth, S. and Veith, A.M. and Froschauer, A. and Haneke, T. and Schultheis, C. and Gessler, M. and Leimeister, C. and Volff, J.N.}, year = 2005, month = jan, journal = {Gene}, volume = {345}, number = {1}, pages = {101–111}, publisher = {Elsevier}, doi = {10.1016/j.gene.2004.11.022}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0378111904006900}, abstract = {A family of functional neogenes called Mart, related to the gag gene of Sushi-like long terminal repeat retrotransposons from fish and amphibians, is present in the genome of human (11 genes) and other primates, as well as in mouse (11 genes), rat, dog (12 genes), cat, and cow. Mart genes have lost their capacity of retrotransposition through non-functionalizing rearrangements having principally affected long terminal repeats and pol open reading frame. Most Mart genes are located on the X chromosome in different mammals. Sequence database analysis suggested that Mart genes are present in opossum (marsupial), but absent from the genome of chicken. Hence, the Mart gene family might have been formed from Sushi-like retrotransposon(s) after the split of birds and mammals (310 myr ago), but before the divergence between placental mammals and marsupials (170 myr ago). RT-PCR analysis showed that at least six Mart genes are expressed during mouse embryonic development, with in situ hybridization analysis revealing rather ubiquitous expression patterns. Mart expression was also detected in adult mice, with some genes being expressed in all tissues tested, while others showed a much more restricted expression pattern. Although additional analysis will be required to establish the function of the retrotransposon-derived Mart neogenes, these observations support the evolutionary importance of retrotransposable elements as a source of genetic novelty}, keywords = {0,Adult,Amino Acid Sequence,analysis,Animals,Comparative Study,DATABASE,development,ELEMENTS,Embryo,Evolution,EvolutionMolecular,expression,FAMILY,Female,FRAME,Frameshifting,Gag,gene,Gene Expression RegulationDevelopmental,Gene Productsgag,Gene Rearrangement,GENE-PRODUCT,Genes,Genetic,genetics,Genome,genomic,human,Humans,in situ hybridization,La,Male,Mammals,metabolism,Mice,Molecular Sequence Data,nosource,OPEN READING FRAME,PATTERNS,Phylogeny,pol,PRODUCT,PRODUCTS,rat,READING FRAME,Research SupportNon-U.S.Gov’t,Retroelements,RETROTRANSPOSITION,retrotransposon,Retroviridae,Reverse Transcriptase Polymerase Chain Reaction,sequence,Sequence Alignment,Sequence HomologyAmino Acid,Support} }

@article{braySmallElementMasonPfizer1994a, title = {A Small Element from the {{Mason-Pfizer}} Monkey Virus Genome Makes Human Immunodeficiency Virus Type 1 Expression and Replication {{Rev-independent}}}, author = {Bray, M. and Prasad, S. and Dubay, J.W. and Hunter, E. and Jeang, K.T. and Rekosh, D. and Hammarskjold, M.L.}, year = 1994, month = feb, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {4}, pages = {1256–1260}, doi = {10.1073/pnas.91.4.1256}, keywords = {development,expression,HIV,human,mRNA,nosource,protein,Proteins,Rna,sequence,virus} }

@article{breinigKre1pPlasmaMembrane2002, title = {Kre1p, the Plasma Membrane Receptor for the Yeast {{K1}} Viral Toxin}, author = {Breinig, F. and Tipper, D.J. and Schmitt, M.J.}, year = 2002, month = feb, journal = {Cell}, volume = {108}, number = {3}, pages = {395–405}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(02)00634-7}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867402006347}, abstract = {Saccharomyces cerevisiae K1 killer strains are infected by the M1 double-stranded RNA virus encoding a secreted protein toxin that kills sensitive cells by disrupting cytoplasmic membrane function. Toxin binding to spheroplasts is mediated by Kre1p, a cell wall protein initially attached to the plasma membrane by its C-terminal GPI anchor. Kre1p binds toxin directly. Both cells and spheroplasts of Deltakre1 mutants are completely toxin resistant; binding to cell walls and spheroplasts is reduced to 10% and {\(<\)} 0.5%, respectively. Expression of K28-Kre1p, an inactive C-terminal fragment of Kre1p retaining its toxin affinity and membrane anchor, fully restored toxin binding and sensitivity to spheroplasts, while intact cells remained resistant. Kre1p is apparently the toxin membrane receptor required for subsequent lethal ion channel formation}, keywords = {0,BINDING,CELLS,CEREVISIAE,DOUBLE-STRANDED-RNA,expression,Fungal Proteins,Gene Deletion,genetics,Ion Channels,killer,La,M1,Membrane Glycoproteins,metabolism,MUTANTS,Mycotoxins,nosource,protein,Proteins,ReceptorsCell Surface,RESISTANT,Rna,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Spheroplasts,supportnon-u.s.gov’t,toxin,virology,virus,yeast} }

@article{breviarioCarbonSourceRegulation1986, title = {Carbon Source Regulation of {{RAS1}} Expression in {{Saccharomyces}} Cerevisiae and the Phenotypes of Ras2- Cells}, author = {Breviario, D. and Hinnebusch, A. and Cannon, J. and Tatchell, K. and Dhar, R.}, year = 1986, month = jun, journal = {Proceedings of the National Academy of Sciences}, volume = {83}, number = {12}, pages = {4152–4156}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.83.12.4152}, url = {http://www.pnas.org/content/83/12/4152.short}, abstract = {Transcriptional analysis of the yeast RAS genes in different culture conditions suggests that the inability of ras2 mutants to grow in nonfermentable carbon sources results from the regulation of RAS1 mRNA expression. The amount of RAS1 mRNA is significantly repressed in cultures grown on the nonfermentable carbon sources ethanol and acetate. As a result, low RAS function should be expressed under these conditions in a ras2 mutant. This can explain the inability of ras2- cells to grow on nonfermentable carbon sources. This interpretation is supported by the finding that an extragenic suppressor of ras2- (sra6- 15), which restores growth on ethanol or acetate, also leads to an increase in the amount of RAS1 mRNA under these conditions. The sra6-15 mutation does not alter the level of RAS1 mRNA in cells grown on glucose. The pattern of transcriptional regulation described for the RAS1 gene is not shared by RAS2, indicating differential control of the functionally homologous yeast RAS genes at the level of gene expression}, keywords = {analysis,Carbon,carbon source,expression,Fungal Proteins,gene,Gene Expression,Gene Expression Regulation,GENE-EXPRESSION,Genes,genetics,growth & development,metabolism,mRNA,Mutation,nosource,Phenotype,Proto-Oncogene Proteins,ras,regulation,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SuppressionGenetic,TranscriptionGenetic,yeast} } % == BibTeX quality report for breviarioCarbonSourceRegulation1986: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A.”)

@article{breviarioMultipleRegulatoryMechanisms1988, title = {Multiple Regulatory Mechanisms Control the Expression of the {{RAS1}} and {{RAS2}} Genes of {{Saccharomyces}} Cerevisiae.}, author = {Breviario, D. and Hinnebusch, A.G. and Dhar, R.}, year = 1988, month = jun, journal = {The EMBO Journal}, volume = {7}, number = {6}, pages = {1805–1813}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1988.tb03012.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC457172/}, abstract = {Expression of the RAS1 and RAS2 genes of Saccharomyces cerevisiae has been examined at the transcriptional and translational levels. When dextrose is the carbon source, the steady-state amount of RAS1 mRNA and the rate of RAS1 protein synthesis are reduced in parallel as cells approach the mid-exponential phase of growth. RAS1 mRNA levels and protein synthesis are very low at all stages of growth when ethanol rather than dextrose is provided as the sole carbon source. The rate of RAS2 protein synthesis is regulated differently. In cells cultured on dextrose, it is lowest in the early exponential phase, increases approximately 10-fold and remains nearly constant as cells approach stationary phase. By contrast, RAS2 mRNA is found at uniformly high levels at all phases of exponential growth, suggesting that the translational efficiency of RAS2 mRNA is repressed during the early exponential phase. This repression is not observed when ethanol is the sole carbon source. Nutrient starvation, resulting in G1 arrest and sporulation in diploids, leads to greatly decreased amounts of RAS2 mRNA, accomplished in part by selective repression of RAS2 transcripts with particular 5’ ends. However, this reduction in RAS2 mRNA levels has little effect on the rate of RAS2 protein synthesis, suggesting that the translational efficiency of RAS2 mRNA is stimulated by nutrient starvation. The combination of transcriptional and translational controls which regulate yeast RAS gene expression seems to ensure that one or the other RAS proteins will be produced over a wide range of physiological states}, keywords = {biosynthesis,cancer,Carbon,carbon source,cell cycle,Comparative Study,Culture Media,efficiency,Ethanol,expression,Fungal Proteins,gene,Gene Expression,Gene Expression Regulation,GENE-EXPRESSION,Genes,GenesFungal,genetics,Glucose,Kinetics,MECHANISM,metabolism,Molecular Weight,mRNA,Nitrogen,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,ras,Saccharomyces,Saccharomyces cerevisiae,SporesFungal,Sulfur,TranscriptionGenetic,TranslationGenetic,virology,yeast} } % == BibTeX quality report for breviarioMultipleRegulatoryMechanisms1988: % ? unused Journal abbr (“EMBO J.”)

@article{brewerRNASequenceElements2004a, title = {{{RNA}} Sequence Elements Required for High Affinity Binding by the Zinc Finger Domain of Tristetraprolin: Conformational Changes Coupled to the Bipartite Nature of {{Au-rich MRNA-destabilizing}} Motifs}, author = {Brewer, B.Y. and Malicka, J. and Blackshear, P.J. and Wilson, G.M.}, year = 2004, month = jul, journal = {J.Biol Chem.}, volume = {279}, number = {27}, pages = {27870–27877}, doi = {10.1074/jbc.M402551200}, url = {PM:15117938}, abstract = {Tristetraprolin (TTP) binds AU-rich elements (AREs) encoded within selected labile mRNAs and targets these transcripts for rapid cytoplasmic decay. RNA binding by TTP is mediated by an approximately 70-amino acid domain containing two tandemly arrayed CCCH zinc fingers. Here we show that a 73-amino acid peptide spanning the TTP zinc finger domain, denoted TTP73, forms a dynamic, equimolar RNA.peptide complex with a 13-nucleotide fragment of the ARE from tumor necrosis factor alpha mRNA, which includes small but significant contributions from ionic interactions. Association of TTP73 with high affinity RNA substrates is accompanied by a large negative change in heat capacity without substantial modification of RNA structure, consistent with conformational changes in the peptide moiety during RNA binding. Analyses using mutant ARE substrates indicate that two adenylate residues located 3-6 bases apart within a uridylate-rich sequence are sufficient for high affinity recognition by TTP73 (K(d) {\(<\)}20 nm), with optimal affinity observed for RNA substrates containing AUUUA or AUUUUA. Linkage of conformational changes and binding affinity to the presence and spacing of these adenylate residues provides a thermodynamic basis for the RNA substrate specificity of TTP}, keywords = {0,ACID,Amino Acid Motifs,Amino Acid Sequence,anisotropy,ASSOCIATION,AU-RICH ELEMENTS,BASE,BASES,BINDING,Biochemistry,BIOLOGY,Biophysics,chemistry,COMPLEX,COMPLEXES,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,DECAY,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,DOMAIN,Dose-Response RelationshipDrug,ELEMENTS,Fluorescence,Fluorescence Resonance Energy Transfer,FORM,Heat,human,Humans,Immediate-Early Proteins,Ions,Kinetics,La,metabolism,ModelsBiological,ModelsStatistical,modification,Molecular Biology,Molecular Sequence Data,MOTIFS,mRNA,Mutation,nosource,Nucleic Acid Conformation,Peptides,protein,Protein Binding,Protein Conformation,Protein StructureTertiary,Proteins,RECOGNITION,RESIDUES,Rna,RNAMessenger,sequence,SPECIFICITY,SpectrometryFluorescence,SPECTROSCOPY,structure,Substrate Specificity,SUBSTRATE-SPECIFICITY,Support,TARGET,Temperature,Thermodynamics,Time Factors,TRANSCRIPT,Tristetraprolin,Tumor Necrosis Factor-alpha,Zinc,Zinc Fingers} } % == BibTeX quality report for brewerRNASequenceElements2004a: % ? Possibly abbreviated journal title J.Biol Chem.

@article{brewerCharacterizationCmycMRNA1998a, title = {Characterization of C-Myc 3’ to 5’ {{mRNA}} Decay Activities in an in Vitro System}, author = {Brewer, G.}, year = 1998, month = dec, journal = {J.Biol Chem.}, volume = {273}, number = {52}, pages = {34770–34774}, doi = {10.1074/jbc.273.52.34770}, url = {PM:9857001}, abstract = {The levels of mRNA and protein encoded by the c-myc protooncogene set the balance between proliferation and differentiation of mammalian cells. Thus, it is essential for the cell to tightly control c-myc expression. Indeed, cells utilize many mechanisms to control c-myc expression, including transcription, RNA processing, translation, and protein stability. We have focused on turnover of c-myc mRNA as a key modulator of the timing and level of c-myc expression. c-myc mRNA is labile in cells, and its half-life is controlled by multiple instability elements located within both the coding region and the 3’-untranslated region (3’-UTR). Much work has focused on the protein factors that bind the instability elements, yet little is known about the enzymatic activities that effect the degradation of c-myc mRNA. Here I have utilized a novel cell-free mRNA decay system to characterize the c-myc mRNA decay machinery. This machinery consists of 3’ to 5’ mRNA decay activities that are Mg2+-dependent, require neither exogenous ATP/GTP nor an ATP-regenerating system, and act independently of a 7mG(5’)ppp(5’)G cap structure to deadenylate an exogenous mRNA substrate in a c-myc 3’-UTR-dependent fashion. Following deadenylation, nucleolytic decay of the 3’-UTR occurs generating 3’ decay intermediates via a ribonucleolytic activity that can assemble on the c-myc 3’-UTR in a poly(A)-independent manner}, keywords = {0,3,3’ UNTRANSLATED REGION,3’ Untranslated Regions,3’ UTR,3’-UNTRANSLATED REGION,3’-UTR,biosynthesis,Cap,CAP STRUCTURE,Cell-Free System,CELLS,CODING REGION,DEADENYLATION,DECAY,degradation,ELEMENTS,expression,FUSION PROTEIN,Gene Expression RegulationNeoplastic,genetics,Globin,Globins,Half-Life,Humans,immunology,In Vitro,IN-VITRO,INTERMEDIATE,La,MAMMALIAN-CELLS,MECHANISM,MECHANISMS,metabolism,microbiology,mRNA,mRNA decay,nosource,Polyribosomes,PROLIFERATION,protein,Proteins,Proto-Oncogene Proteins,Proto-Oncogene Proteins c-myc,Recombinant Fusion Proteins,REGION,ribonucleolytic activity,Rna,RNAMessenger,RNANeoplasm,stability,structure,Support,SYSTEM,transcription,translation,turnover,Untranslated Regions} } % == BibTeX quality report for brewerCharacterizationCmycMRNA1998a: % ? Possibly abbreviated journal title J.Biol Chem.

@article{brierleyEfficientRibosomalFrameshifting1987, title = {An Efficient Ribosomal Frame-Shifting Signal in the Polymerase-Encoding Region of the Coronavirus {{IBV}}.}, author = {Brierley, I. and Boursnell, M.E. and Binns, M.M. and Bilimoria, B. and Blok, V.C. and Brown, T.D. and Inglis, S.C.}, year = 1987, month = dec, journal = {The EMBO Journal}, volume = {6}, number = {12}, pages = {3779–3785}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1987.tb02713.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC553849/}, abstract = {The polymerase-encoding region of the genomic RNA of the coronavirus infectious bronchitis virus (IBV) contains two very large, briefly overlapping open reading frames (ORF), F1 and F2, and it has been suggested on the basis of sequence analysis that expression of the downstream ORF, F2, might be mediated through ribosomal frame-shifting. To examine this possibility a cDNA fragment containing the F1/F2 overlap region was cloned within a marker gene and placed under the control of the bacteriophage SP6 promoter in a recombinant plasmid. Messenger RNA transcribed from this plasmid, when translated in cell-free systems, specified the synthesis of polypeptides whose size was entirely consistent with the products predicted by an efficient ribosomal frame-shifting event within the overlap region. The nature of the products was confirmed by their reactivity with antisera raised against defined portions of the flanking marker gene. This is the first non-retroviral example of ribosomal frame-shifting in higher eukaryotes}, keywords = {0,Amino Acid Sequence,analysis,Animals,Base Sequence,Cell-Free System,Coronaviridae,Coronavirus,CORONAVIRUS-IBV,DNA-Directed RNA Polymerase,DNA-Directed RNA Polymerases,DOWNSTREAM,enzymology,expression,FRAME,Frameshifting,gene,Genes,GenesViral,Genetic Vectors,genetics,genomic,GENOMIC RNA,Infectious bronchitis virus,La,MARKER,MESSENGER-RNA,metabolism,Mice,Molecular Sequence Data,nosource,Nucleic Acid Conformation,OPEN READING FRAME,Open Reading Frames,pathology,PLASMID,polymerase,POLYPEPTIDE,POLYPEPTIDES,PRODUCT,PRODUCTS,PROMOTER,Promoter Regions (Genetics),Protein Biosynthesis,READING FRAME,Reading Frames,REGION,ribosomal frameshifting,RIBOSOMAL FRAMESHIFTING SIGNAL,Ribosomes,Rna,RNA-POLYMERASE,RNAMessenger,RnaViral,sequence,Sequence Analysis,SEQUENCE-ANALYSIS,SIGNAL,Support,SYSTEM,SYSTEMS,TranscriptionGenetic,virus} } % == BibTeX quality report for brierleyEfficientRibosomalFrameshifting1987: % ? unused Journal abbr (“EMBO J.”)

@article{brierleyRibosomalFrameshiftingViral1995, title = {Ribosomal Frameshifting on Viral {{RNAs}}.}, author = {Brierley, I.}, year = 1995, month = aug, journal = {Journal of General Virology}, volume = {76}, number = {8}, pages = {1885–1892}, publisher = {Soc General Microbiol}, issn = {0022-1317}, doi = {10.1099/0022-1317-76-8-1885}, url = {http://vir.sgmjournals.org/content/76/8/1885.short http://vir.sgmjournals.org/cgi/content/abstract/76/8/1885}, keywords = {Animals,Base Sequence,Frameshifting,Humans,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Protein Biosynthesis,Reading Frames,Review,ribosomal frameshifting,Ribosomes,Rna,RNA Viruses,RNA- Viral} } % == BibTeX quality report for brierleyRibosomalFrameshiftingViral1995: % ? unused Journal abbr (“J.Gen.Virol.”)

@article{brierleyExpressionCoronavirusRibosomal1997a, title = {Expression of a Coronavirus Ribosomal Frameshift Signal in {{Escherichia}} Coli: Influence of {{tRNA}} Anticodon Modification on Frameshifting}, author = {Brierley, I. and Meredith, M.R. and Bloys, A.J. and Hagervall, T.G.}, year = 1997, month = jul, journal = {Journal of Molecular Biology}, volume = {270}, number = {3}, pages = {360–373}, doi = {10.1006/jmbi.1997.1134}, keywords = {A-SITE,Anticodon,biosynthesis,Codon,COMPLEX,COMPLEXES,efficiency,Escherichia coli,Escherichia coli/ge [Genetics],ESCHERICHIA-COLI,expression,frameshift,Frameshifting,modification,nosource,pseudoknot,RIBOSOMAL FRAMESHIFT,ribosome,Ribosomes,Rna,RNA PSEUDOKNOT,sequence,SIGNAL,structure,Support,translation,tRNA} }

@article{brierleyCharacterizationEfficientCoronavirus1989, title = {Characterization of an Efficient Coronavirus Ribosomal Frameshifting Signal: Requirement for an {{RNA}} Pseudoknot.}, author = {Brierley, I.A. and Dingard, P. and Inglis, S.C.}, year = 1989, journal = {Cell}, volume = {57}, number = {4}, pages = {537–547}, publisher = {Elsevier}, doi = {10.1016/0092-8674(89)90124-4}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867489901244}, keywords = {Frameshifting,nosource,pseudoknot,ribosomal frameshifting,RIBOSOMAL FRAMESHIFTING SIGNAL,Rna,RNA PSEUDOKNOT,SIGNAL} }

@article{brionesConformationalChangesInduced2000, title = {Conformational Changes Induced in the {{Saccharomyces}} Cerevisiae {{GTPase-associated rRNA}} by Ribosomal Stalk Components and a Translocation Inhibitor}, author = {Briones, C. and Ballesta, J.P.}, year = 2000, month = nov, journal = {Nucleic acids research}, volume = {28}, number = {22}, pages = {4497–4505}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/28.22.4497}, url = {http://nar.oxfordjournals.org/content/28/22/4497.short}, abstract = {The yeast ribosomal GTPase associated center is made of parts of the 26S rRNA domains II and VI, and a number of proteins including P0, P1alpha, P1beta, P2alpha, P2beta and L12. Mapping of the rRNA neighborhood of the proteins was performed by footprinting in ribosomes from yeast strains lacking different GTPase components. The absence of protein P0 dramatically increases the sensitivity of the defective ribosome to degradation hampering the RNA footprinting. In ribosomes lacking the P1/P2 complex, protection of a number of nucleotides is detected around positions 840, 880, 1100, 1220-1280 and 1350 in domain II as well as in several positions in the domain VI alpha-sarcin region. The protection pattern resembles the one reported for the interaction of elongation factors in bacterial systems. The results exclude a direct interaction of these proteins with the rRNA and are compatible with an increase in the ribosome affinity for EF-2 in the absence of the acidic P proteins. Interestingly, a sordarin derivative inhibitor of EF-2 causes an opposite effect, increasing the reactivity in positions protected by the absence of P1/P2. Similarly, a deficiency in protein L12 exposes nucleotides G1235, G1242, A1262, A1269, A1270 and A1272 to chemical modification, thus situating the protein binding site in the most conserved part of the 26S rRNA, equivalent to the bacterial protein L11 binding site}, keywords = {0,ALPHA-SARCIN,antibiotic,antibiotics,AntibioticsAntifungal,Aspergillus,Bacterial,Base Sequence,BINDING,Binding Sites,BINDING-SITE,BindingCompetitive,CEREVISIAE,CHEMICAL MODIFICATION,chemistry,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,deficiency,degradation,DOMAIN,DOMAIN-II,DOMAINS,drug effects,EF-2,elongation,elongation factors,ELONGATION-FACTORS,Endoribonucleases,Fungal Proteins,genetics,GTP,GTP Phosphohydrolase,GTP Phosphohydrolases,GTPase,INHIBITOR,inhibitors,La,mapping,metabolism,modification,Molecular Sequence Data,Molecular Structure,Mutagenesis,Mutation,NEIGHBORHOOD,nosource,Nucleic Acid Conformation,Nucleotides,pharmacology,POSITION,POSITIONS,PROTECTION,protein,Protein Binding,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,Proteins,REGION,Ribosomal Proteins,ribosome,ribosome-inactivating protein,Ribosomes,Rna,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SITE,sordarin,supportnon-u.s.gov’t,SYNTHESIS INHIBITORS,SYSTEM,SYSTEMS,translocation,yeast} } % == BibTeX quality report for brionesConformationalChangesInduced2000: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{broachTransformationYeastDevelopment1979a, title = {Transformation in Yeast: Development of a Hybrid Cloning Vector and Isolation of the ⬚{{CAN1}}⬚ Gene.}, author = {Broach, J.R. and Strathern, J.N. and Hicks, J.B.}, year = 1979, journal = {Gene}, volume = {8}, pages = {121–133}, doi = {10.1016/0378-1119(79)90012-X}, keywords = {cloning,development,gene,nosource,ras,vector,vectors,yeast} }

@article{brodersenAtomicStructures30S2001a, title = {Atomic Structures of the {{30S}} Subunit and Its Complexes with Ligands and Antibiotics}, author = {Brodersen, D.E. and Carter, A.P. and Clemons, W.M. and {Morgan-Warren}, R.J. and Murphy, F.V. and Ogle, J.M. and Tarry, M.J. and Wimberly, B.T. and Ramakrishnan, V.}, year = 2001, journal = {Cold Spring Harb.Symp.Quant.Biol.}, volume = {66}, pages = {17–32}, doi = {10.1101/sqb.2001.66.17}, url = {PM:12762005}, keywords = {0,16S,Anti-Bacterial Agents,antibiotic,antibiotics,Bacterial,Base Sequence,Binding Sites,BIOLOGY,chemistry,COMPLEX,COMPLEXES,genetics,La,Ligands,Molecular Biology,Molecular Sequence Data,Molecular Weight,nosource,Nucleic Acid Conformation,protein,Protein Conformation,Proteins,Review,Ribosomal Proteins,RIBOSOMAL-PROTEIN,Rna,RNABacterial,RNARibosomal,RNARibosomal16S,structure,SUBUNIT,Support,Thermus thermophilus} } % == BibTeX quality report for brodersenAtomicStructures30S2001a: % ? Possibly abbreviated journal title Cold Spring Harb.Symp.Quant.Biol.

@article{brodersenCrystalStructure302002a, title = {Crystal Structure of the 30 {{S}} Ribosomal Subunit from {{Thermus}} Thermophilus: {{Structure}} of the Proteins and Their Interactions with 16 {{S RNA}}}, author = {Brodersen, D.E. and Clemons, W.M. and Carter, A.P. and Wimberly, B.T. and Ramakrishnan, V.}, year = 2002, month = feb, journal = {Journal of Molecular Biology}, volume = {316}, number = {3}, pages = {725–768}, doi = {10.1006/jmbi.2001.5359}, url = {ISI:000174216400024}, abstract = {We present a detailed analysis of the protein structures in the 30 S ribosomal subunit from Thermus thermophilus, and their interactions with 16 S RNA based on a crystal structure at 3.05 Angstrom resolution. With 20 different polypeptide chains, the 30 S subunit adds significantly to our data base of RNA structure and protein-RNA interactions. In addition to globular domains, many of the proteins have long, extended regions, either in the termini or in internal loops, which make extensive contact to the RNA component and are involved in stabilizing RNA tertiary structure. Many ribosomal proteins share similar alpha + beta sandwich folds, but we show that the topology of this domain varies considerably, as do the ways in which the proteins interact with RNA. Analysis of the protein-RNA interactions in the context of ribosomal assembly shows that the primary binders are globular proteins that bind at RNA multihelix junctions, whereas proteins with long extensions assemble later. We attempt to correlate the structure with a large body of biochemical and genetic data on the 30 S subunit. (C) 2002 Elsevier Science Ltd}, keywords = {16 S RNA,16S-RIBOSOMAL RNA,3’ MAJOR DOMAIN,30 S,AMINO-ACID REPLACEMENTS,analysis,ANGSTROM RESOLUTION,assembly,BACILLUS-STEAROTHERMOPHILUS,COMPONENT,CROSS-LINKING,DSRNA-BINDING DOMAIN,ESCHERICHIA-COLI RIBOSOME,Genetic,INDUCED CONFORMATIONAL-CHANGES,MESSENGER-RNA,nosource,protein,protein-RNA interactions,Proteins,Review,Ribosomal Proteins,ribosome,Rna,structure,SUBUNIT,Thermus,Thermus thermophilus,THX} }

@article{broekDifferentialActiviationYeast1985, title = {Differential Activiation of Yeast Adenylate Cyclase by Wild-Type and Mutant {{Ras}} Proteins.}, author = {Broek, D. and Samiy, N. and Fasano, O. and Fujiyama, S. and Ysmsnoi, R. and Northup, J. and Wigler, M.}, year = 1985, journal = {Cell}, volume = {41}, pages = {763–769}, doi = {10.1016/S0092-8674(85)80057-X}, keywords = {nosource,protein,Proteins,ras,yeast} }

@article{brognaRibosomeComponentsAre2002a, title = {Ribosome Components Are Associated with Sites of Transcription - {{Vol}} 10, Pg 93, 2002}, author = {Brogna, S. and Sato, T.A. and Rosbash, M.}, year = 2002, month = oct, journal = {Molecular Cell}, volume = {10}, number = {4}, pages = {959-+}, doi = {10.1016/S1097-2765(02)00643-3}, url = {ISI:000178889000031}, abstract = {It is generally believed that eukaryotic ribosomes first associate with mRNA in the cytoplasm. However, we show with chromosomal immunostaining and in situ hybridization that ribosomal subunits are present at transcription sites of Drosophila salivary gland chromosomes. Immunostaining was carried out with antibodies specific for 27 ribosomal proteins, two translation factors and one that specifically recognizes rRNA. In situ hybridization was with several probes specific for both rRNA subunits. The kinetics of recruitment following transcription initiation suggest that the association is with newly transcribed pol II transcripts. These data indicate that ribosome components associate with nascent RNP complexes within the nucleus}, keywords = {0,Antibodies,antibody,ASSOCIATION,Chromosomes,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,Cytoplasm,CYTOPLASMIC MESSENGER-RNA,Drosophila,DROSOPHILA-MELANOGASTER,EARLY PUFF,ECDYSONE-INDUCIBLE GENE,ENDOPLASMIC-RETICULUM,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,initiation,Kinetics,M,mRNA,NONSENSE MUTATIONS,nosource,OPEN READING FRAME,pol,protein,PROTEIN-SYNTHESIS,Proteins,QUALITY-CONTROL,RECRUITMENT,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,RNA-POLYMERASE-II,rRNA,SITE,SITES,SUBUNIT,TRANSCRIPT,transcription,transcription site,translation} }

@article{browModulationYeast5S1987, title = {Modulation of Yeast {{5S rRNA}} Synthesis⬚ in Vitro⬚ by Ribosomal Protein {{YL3}}.}, author = {Brow, D.A. and Geiduschek, E.P.}, year = 1987, journal = {J.Biol.Chem.}, volume = {262}, pages = {13953–13958}, doi = {10.1016/S0021-9258(18)47887-8}, keywords = {5S rRNA,In Vitro,IN-VITRO,nosource,protein,rRNA,yeast} } % == BibTeX quality report for browModulationYeast5S1987: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{brownYeastAntiviralProteins2000, title = {The Yeast Antiviral Proteins {{Ski2p}}, {{Ski3p}}, and {{Ski8p}} Exist as a Complex in Vivo.}, author = {Brown, J.T. and Bai, X. and Johnson, A.W.}, year = 2000, month = mar, journal = {RNA}, volume = {6}, number = {3}, pages = {449–457}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838200991787}, url = {http://rnajournal.cshlp.org/content/6/3/449.short}, abstract = {The yeast superkiller (SKI) genes were originally identified from mutations allowing increased production of killer toxin encoded by M “killer” virus, a satellite of the dsRNA virus L-A. XRN1 (SKI1) encodes a cytoplasmic 5’-exoribonuclease responsible for the majority of cytoplasmic RNA turnover, whereas SKI2, SKI3, and SKI8 are required for normal 3’-degradation of mRNA and for repression of translation of poly(A) minus RNA. Ski2p is a putative RNA helicase, Ski3p is a tetratricopeptide repeat (TPR) protein, and Ski8p contains five WD-40 (beta-transducin) repeats. An xrn1 mutation in combination with a ski2, ski3, or ski8 mutation is lethal, suggesting redundancy of function. Using functional epitope-tagged Ski2, Ski3, and Ski8 proteins, we show that Ski2p, Ski3p, and Ski8p can be coimmunoprecipitated as an apparent heterotrimeric complex. With epitope-tagged Ski2p, there was a 1:1:1 stoichiometry of the proteins in the complex. Ski2p did not associate with Ski3p in the absence of Ski8p, nor did Ski2p associate with Ski8p in the absence of Ski3p. However, the Ski3p/Ski8p interaction did not require Ski2p. In addition, ski6-2 or ski4-1 mutations or deletion of SKI7 did not affect complex formation. The identification of a complex composed of Ski2p, Ski3p, and Ski8p explains previous results showing phenotypic similarity between mutations in SKI2, SKI3, and SKI8. Indirect immunofluorescence of Ski3p and subcellular fractionation of Ski2p and Ski3p suggest that Ski2p and Ski3p are cytoplasmic. These data support the idea that Ski2p, Ski3p, and Ski8p function in the cytoplasm in a 3’-mRNA degradation pathway}, keywords = {0,a,antiviral,Antiviral Agents,beta-transducin repeat,BIOLOGY,CEREVISIAE,chemistry,COMPLEX,COMPLEX-FORMATION,COMPLEXES,Cytoplasm,degradation,DSRNA,dsRNA virus,ENCODES,Fungal Proteins,gene,Genes,Genetic,genetics,Helicase,IDENTIFICATION,IN-VIVO,isolation & purification,killer,killer toxin,L-A,La,M,Macromolecular Substances,metabolism,microbiology,MOLECULAR-GENETICS,mRNA,mrna degradation,Mutation,MUTATIONS,nosource,Nuclear Proteins,PATHWAY,poly,poly(A),protein,Proteins,repeat,Repetitive Sequences-Amino Acid,Repetitive SequencesAmino Acid,repression,Research Support-U.S.Gov’t-P.H.S.,Research SupportU.S.Gov’tP.H.S.,Rna,rna helicase,RNA HELICASE,RNA-Messenger,Rna-Viral,RNAMessenger,RnaViral,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SKI,SKI2,superkiller,Support,tetratricopeptide,toxin,tpr,translation,turnover,virus,wd-40,XRN1,yeast} }

@article{bruennEndsYeastKiller1976a, title = {The 5’ Ends of Yeast Killer Factor {{RNAs}} Are {{pppGp}}}, author = {Bruenn, J. and Keitz, B.}, year = 1976, month = oct, journal = {Nucleic Acids Research}, volume = {3}, number = {10}, pages = {2427–2436}, doi = {10.1093/nar/3.10.2427}, keywords = {animal,Bacterial,Cap,Electrophoresis,nosource,Nucleotides,poly(A),Rna,RNAse,yeast} }

@article{bruennViruslikeParticleYeast1980, title = {Virus-like Particle of Yeast.}, author = {Bruenn, J.A.}, year = 1980, journal = {Annu.Rev.Microbiol.}, volume = {34}, pages = {49–68}, doi = {10.1146/annurev.mi.34.100180.000405}, keywords = {Gag,L-A,La,nosource,yeast} } % == BibTeX quality report for bruennViruslikeParticleYeast1980: % ? Possibly abbreviated journal title Annu.Rev.Microbiol.

@article{brunelleInteractionC75TRNA2006, title = {The Interaction between {{C75}} of {{tRNA}} and the {{A}} Loop of the Ribosome Stimulates Peptidyl Transferase Activity}, author = {Brunelle, J.L. and Youngman, E.M. and Sharma, D. and Green, R.}, year = 2006, month = jan, journal = {RNA.}, volume = {12}, number = {1}, pages = {33–39}, publisher = {Cold Spring Harbor Lab}, doi = {10.1261/rna.2256706}, url = {http://rnajournal.cshlp.org/content/12/1/33.short}, abstract = {Ribosomal variants carrying mutations in active site nucleotides are severely compromised in their ability to catalyze peptide bond formation (PT) with minimal aminoacyl tRNA substrates such as puromycin. However, catalysis of PT by these same ribosomes with intact aminoacyl tRNA substrates is uncompromised. These data suggest that these active site nucleotides play an important role in the positioning of minimal aminoacyl tRNA substrates but are not essential for catalysis per se when aminoacyl tRNAs are positioned by more remote interactions with the ribosome. Previously reported biochemical studies and atomic resolution X-ray structures identified a direct Watson-Crick interaction between C75 of the A-site substrate and G2553 of the 23S rRNA. Here we show that the addition of this single cytidine residue (the C75 equivalent) to puromycin is sufficient to suppress the deficiencies of active site ribosomal variants, thus restoring “tRNA-like” behavior to this minimal substrate. Studies of the binding parameters and the pH-dependence of catalysis with this minimal substrate indicate that the interaction between C75 and the ribosomal A loop is an essential feature for robust catalysis and further suggest that the observed effects of C75 on peptidyl transfer activity reflect previously reported conformational rearrangements in this active site}, keywords = {0,a loop,A SITE,A-SITE,ACTIVE-SITE,BINDING,Binding Sites,BIOLOGY,BOND FORMATION,Catalysis,chemistry,Comparative Study,deficiency,enzymology,Genetic,genetics,Hydrogen-Ion Concentration,La,LOOP,metabolism,Molecular Biology,Mutation,MUTATIONS,nosource,Nucleotides,peptide bond formation,peptidyl transfer,peptidyl transferase,Peptidyl Transferases,peptidyl-transfer,PEPTIDYL-TRANSFERASE,ph-rate profile,pharmacokinetics,Puromycin,RESOLUTION,ribosome,Ribosomes,Rna,RNARibosomal,rRNA,SITE,structure,Support,Transferases,trna,tRNA} } % == BibTeX quality report for brunelleInteractionC75TRNA2006: % ? Possibly abbreviated journal title RNA.

@article{brunelleExpressionHumanImmunodeficiency1999, title = {Expression of the Human Immunodeficiency Virus Frameshift Signal in a Bacterial Cell-Free System: Influence of an Interaction between the Ribosome and a Stem-Loop Structure Downstream from the Slippery Site}, author = {Brunelle, M.N. and Payant, C. and Lemay, G. and {Brakier-Gingras}, L.}, year = 1999, month = dec, journal = {Nucleic Acids Research}, volume = {27}, number = {24}, pages = {4783–4791}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/27.24.4783}, url = {http://nar.oxfordjournals.org/content/27/24/4783.short}, abstract = {A -1 frameshift event is required for expression of the pol gene when ribosomes translate the mRNA of human immunodeficiency virus type-1 (HIV-1). In this study, we inserted the frameshift region of HIV-1 (a slippery heptanucleotide motif followed by a stem-loop) in a reporter gene coding for firefly luciferase. The ability of the corresponding mRNA, generated by in vitro transcription, to be translated in an Escherichia coli cell-free extract is the first demonstration that the HIV-1 frameshift can be reproduced in a bacterial cell-free extract, providing a powerful approach for analysis of the frameshift mechanism. The responses of the frameshift signal to chloramphenicol, an inhibitor of peptide bond formation, and spectinomycin, an inhibitor of translocation, suggest that the frameshift complies with the same rules found in eukaryotic translation systems. Furthermore, when translation was performed in the presence of streptomycin and neamine, two error-inducing antibiotics, or with hyperaccurate ribosomes mutated in S12, the frameshift efficiency was increased or decreased, respectively, but only in the presence of the stem-loop, suggesting that the stem-loop can influence the frameshift through a functional interaction with the ribosomes}, keywords = {analysis,antibiotic,antibiotics,Bacterial,BOND FORMATION,Cell-Free System,Chloramphenicol,DOWNSTREAM,efficiency,Escherichia coli,ESCHERICHIA-COLI,EUKARYOTIC TRANSLATION,expression,FIREFLY LUCIFERASE,frameshift,GAG-POL REGION,gene,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,In Vitro,in vitro transcription,IN-VITRO,INHIBITOR,luciferase,MAMMALIAN-CELLS,MAMMARY-TUMOR VIRUS,MECHANISM,MESSENGER-RNA,mRNA,nosource,OVEREXPRESSION,pol,REGION,ribosome,Ribosomes,RNA PSEUDOKNOT,RULES,sequence,SIGNAL,SITE,slippery site,Spectinomycin,STEM-LOOP,Streptomycin,structure,SYSTEM,SYSTEMS,transcription,translation,translocation,TYPE-1,virus} }

@article{brungerCrystallographyNMRSystem1998, title = {Crystallography & {{NMR}} System: {{A}} New Software Suite for Macromolecular Structure Determination}, author = {Brunger, A.T. and Adams, P.D. and Clore, G.M. and DeLano, W.L. and Gros, P. and {Grosse-Kunstleve}, R.W. and Jiang, J.S. and Kuszewski, J. and Nilges, M. and Pannu, N.S. and Read, R.J. and Rice, L.M. and Simonson, T. and Warren, G.L.}, year = 1998, journal = {Acta Crystallographica Section D: Biological Crystallography}, volume = {54 ( Pt 5)}, number = {5}, pages = {905–921}, publisher = {International Union of Crystallography}, doi = {10.1107/S0907444998003254}, url = {http://scripts.iucr.org/cgi-bin/paper?S0907444998003254}, abstract = {A new software suite, called Crystallography & NMR System (CNS), has been developed for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing structure-determination programs, the architecture of CNS is highly flexible, allowing for extension to other structure-determination methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic structure-determination language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data structures, such as structure factors, electron-density maps, and atomic properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of macromolecular structure determination by X-ray crystallography and solution NMR}, keywords = {Algorithms,Computer Simulation,Crystallography,CrystallographyX-Ray,ELECTRON-MICROSCOPY,interface,La,Likelihood Functions,Magnetic Resonance Spectroscopy,Methods,modification,Molecular Structure,NMR,NMR-SPECTROSCOPY,nosource,nuclear magnetic resonance,NUCLEAR-MAGNETIC-RESONANCE,Software,SPECTROSCOPY,structure,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,SYSTEM} } % == BibTeX quality report for brungerCrystallographyNMRSystem1998: % ? unused Journal abbr (“Acta Crystallogr.D.Biol.Crystallogr.”)

@article{buchmanConnectionsTranscriptionalActivators1988, title = {Connections between Transcriptional Activators, Silencers, and Telomeres as Revealed by Functional Analysis of a Yeast {{DNA-binding}} Protein.}, author = {Buchman, A.R. and Lue, N.F. and Kornberg, R.D.}, year = 1988, month = dec, journal = {Molecular and cellular biology}, volume = {8}, number = {12}, pages = {5086–5099}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/8/12/5086}, abstract = {General regulatory factor I (GRFI) is a yeast protein that binds in vitro to specific DNA sequences at diverse genetic elements. A strategy was pursued to test whether GRFI functions in vivo at the sequences bound by the factor in vitro. Matches to a consensus sequence for GRFI binding were found in a variety of locations: upstream activating sequences (UASs), silencers, telomeres, and transcribed regions. All occurrences of the consensus sequence bound both crude and purified GRFI in vitro. All binding sites for GRFI, regardless of origin, provided UAS function in test plasmids. Also, GRFI binding sites specifically stimulated transcription in a yeast in vitro system, indicating that GRFI can function as a positive transcription factor. The stimulatory effect of GRFI binding sites at UASs for the PYK1 and ENO1 genes is significantly enhanced by flanking DNA elements. By contrast, regulatory sequences that flank the GRFI binding site at HMR E convert this region to a transcriptional silencer}, keywords = {89218968,analysis,Base Sequence,BINDING,Binding Sites,Chromosomes,Dna,DNA Probes,DNA-Binding Proteins,DNAFungal,Fungal Proteins,gene,Genes,GenesFungal,Genetic,genetics,In Vitro,IN-VITRO,IN-VIVO,isolation & purification,metabolism,Molecular Sequence Data,Multiple DOI,nonfile,nosource,Oligonucleotide Probes,physiology,Plasmids,protein,Saccharomyces cerevisiae,sequence,supportu.s.gov’tp.h.s.,Telomere,transcription,TranscriptionGenetic,yeast} } % == BibTeX quality report for buchmanConnectionsTranscriptionalActivators1988: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{buchmanYeastARSbindingProtein1990, title = {A Yeast {{ARS-binding}} Protein Activates Transcription Synergistically in Combination with Other Weak Activating Factors}, author = {Buchman, A.R. and Kornberg, R.D.}, year = 1990, month = mar, journal = {Mol.Cell Biol.}, volume = {10}, number = {3}, pages = {887–897}, abstract = {ABFI (ARS-binding protein I) is a yeast protein that binds specific DNA sequences associated with several autonomously replicating sequences (ARSs). ABFI also binds sequences located in promoter regions of some yeast genes, including DED1, an essential gene of unknown function that is transcribed constitutively at a high level. ABFI was purified by specific binding to the DED1 upstream activating sequence (UAS) and was found to recognize related sequences at several other promoters, at an ARS (ARS1), and at a transcriptional silencer (HMR E). All ABFI-binding sites, regardless of origin, provided weak UAS function in vivo when examined in test plasmids. UAS function was abolished by point mutations that reduced ABFI binding in vitro. Analysis of the DED1 promoter showed that two ABFI-binding sites combine synergistically with an adjacent T-rich sequence to form a strong constitutive activator. The DED1 T-rich element acted synergistically with all other ABFI-binding sites and with binding sites for other multifunctional yeast activators. An examination of the properties of sequences surrounding ARS1 left open the possibility that ABFI enhances the initiation of DNA replication at ARS1 by transcriptional activation}, keywords = {90158603,activation,analysis,Base Sequence,BINDING,Binding Sites,Dna,DNA Replication,DNA-Binding Proteins,Fungal Proteins,gene,Gene Expression RegulationFungal,Genes,genetics,In Vitro,IN-VITRO,IN-VIVO,initiation,isolation & purification,metabolism,Molecular Sequence Data,Multiple DOI,Mutation,nonfile,nosource,physiology,Plasmids,protein,Regulatory SequencesNucleic Acid,Saccharomyces cerevisiae,sequence,supportu.s.gov’tp.h.s.,transcription,Transcription Factors,TranscriptionGenetic,yeast} } % == BibTeX quality report for buchmanYeastARSbindingProtein1990: % ? Possibly abbreviated journal title Mol.Cell Biol.

@article{budkevichFeatures80SMammalian2008, title = {Features of {{80S}} Mammalian Ribosome and Its Subunits}, author = {Budkevich, T.V. and El’skaya, A.V. and Nierhaus, K.H.}, year = 2008, journal = {Nucleic Acids Research}, volume = {36}, number = {14}, pages = {4736–4744}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkn424}, url = {http://nar.oxfordjournals.org/content/36/14/4736.short}, abstract = {It is generally believed that basic features of ribosomal functions are universally valid, but a systematic test still stands out for higher eukaryotic 80S ribosomes. Here we report: (i) differences in tRNA and mRNA binding capabilities of eukaryotic and bacterial ribosomes and their subunits. Eukaryotic 40S subunits bind mRNA exclusively in the presence of cognate tRNA, whereas bacterial 30S do bind mRNA already in the absence of tRNA. 80S ribosomes bind mRNA efficiently in the absence of tRNA. In contrast, bacterial 70S interact with mRNA more productively in the presence rather than in the absence of tRNA. (ii) States of initiation (P(i)), pre-translocation (PRE) and post-translocation (POST) of the ribosome were checked and no significant functional differences to the prokaryotic counterpart were observed including the reciprocal linkage between A and E sites. (iii) Eukaryotic ribosomes bind tetracycline with an affinity 15 times lower than that of bacterial ribosomes (K(d) 30 microM and 1-2 microM, respectively). The drug does not effect enzymatic A-site occupation of 80S ribosomes in contrast to non-enzymatic tRNA binding to the A-site. Both observations explain the relative resistance of eukaryotic ribosomes to this antibiotic}, keywords = {0,A SITE,A-SITE,Allosteric Regulation,Animals,Anti-Bacterial Agents,antibiotic,Bacteria,Bacterial,BINDING,chemistry,Comparative Study,drug effects,E,E site,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,genetics,Germany,initiation,La,metabolism,mRNA,nosource,Peptide Chain Initiation-Translational,Peptide Chain InitiationTranslational,pharmacology,Protein Biosynthesis,Rabbits,RESISTANCE,ribosome,Ribosome Subunits-Large-Eukaryotic,Ribosome Subunits-Small-Bacterial,Ribosome Subunits-Small-Eukaryotic,Ribosome SubunitsLargeEukaryotic,Ribosome SubunitsSmallBacterial,Ribosome SubunitsSmallEukaryotic,Ribosomes,Rna,RNA-Messenger,RNA-Transfer,RNAMessenger,RNATransfer,SITE,SITES,SUBUNIT,SUBUNITS,Support,Tetracycline,tRNA,tRNA binding} } % == BibTeX quality report for budkevichFeatures80SMammalian2008: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{buhlerIntranuclearDegradationNonsense2002, title = {Intranuclear Degradation of Nonsense Codon-Containing {{mRNA}}}, author = {Buhler, M. and Wilkinson, M.F. and Muhlemann, O.}, year = 2002, month = jul, journal = {EMBO reports}, volume = {3}, number = {7}, pages = {646–651}, publisher = {Nature Publishing Group}, doi = {10.1093/embo-reports/kvf129}, url = {http://www.nature.com/embor/journal/v3/n7/abs/embor129.html PM:12101097}, abstract = {Most vertebrate mRNAs with premature termination codons (PTCs) are specifically recognized and degraded by a process referred to as nonsense-mediated mRNA decay (NMD) while still associated with the nucleus. However, it is still a matter of debate whether PTCs can be identified by intranuclear scanning or only by ribosomes on the cytoplasmic side of the nuclear envelope. Here we show that inhibition of mRNA export by two independent approaches does not affect the downregulation of PTC-containing T-cell receptor beta transcripts in the nuclear fraction of mammalian cells, providing strong evidence for intranuclear NMD. Our results are fully consistent with recently reported evidence for nuclear translation and suggest that an important biological role for nuclear ribosomes is the early elimination of nonsense mRNA during a pioneer round of translation}, keywords = {0,Active TransportCell Nucleus,Animals,BIOLOGY,Cell Fractionation,Cell Nucleus,CELLS,chemistry,Codon,CodonNonsense,CODONS,DECAY,degradation,FUSION PROTEIN,genetics,GREEN FLUORESCENT PROTEIN,Green Fluorescent Proteins,Hela Cells,Humans,In Situ HybridizationFluorescence,INHIBITION,La,Luminescent Proteins,M,MAMMALIAN-CELLS,metabolism,mRNA,mRNA decay,NMD,NONSENSE,nonsense-mediated mRNA decay,nosource,Oocytes,physiology,PREMATURE TERMINATION CODON,protein,Protein Biosynthesis,Proteins,Recombinant Fusion Proteins,ribosome,Ribosomes,Rna,RNAMessenger,scanning,Support,termination,TERMINATION CODON,TERMINATION-CODON,TRANSCRIPT,translation,Viral Matrix Proteins,virus,Xenopus laevis} } % == BibTeX quality report for buhlerIntranuclearDegradationNonsense2002: % ? unused Journal abbr (“EMBO Rep.”)

@article{burchANTIGENICVARIATIONNEISSERIA1997, title = {{{ANTIGENIC VARIATION IN NEISSERIA GONORRHOEAE}} - {{PRODUCTION OF MULTIPLE LIPOOLIGOSACCHARIDES}}}, author = {Burch, C.L. and Danaher, R.J. and Stein, D.C.}, year = 1997, month = feb, journal = {Journal of Bacteriology}, volume = {179}, number = {3}, pages = {982–986}, publisher = {Am Soc Microbiol}, doi = {10.1128/jb.179.3.982-986.1997}, url = {http://jb.asm.org/cgi/content/abstract/179/3/982}, keywords = {analysis,Antibodies,antibody,COMPONENT,Dna,DNA Replication,expression,frameshift,Frameshifting,gene,Genetic,mapping,Mutagenesis,nosource,Phenotype,protein,sequence,structure,transcription,translation} } % == BibTeX quality report for burchANTIGENICVARIATIONNEISSERIA1997: % ? Title looks like it was stored in title-case in Zotero

@article{burckTranslationalSuppressorsAntisuppressors1999b, title = {Translational Suppressors and Antisuppressors Alter the Eficiency of the ⬚{{Ty1}}⬚ Programmed Translational Frameshift.}, author = {Burck, C.L. and Chernoff, Y.O. and Liu, R. and Farabaugh, P.J. and Liebman, S.W.}, year = 1999, journal = {RNA}, volume = {5}, pages = {1451–1457}, doi = {10.1017/S1355838299990490}, keywords = {frameshift,nosource,RDN1,rDNA,retrotransposon,Ty1,yeast} }

@article{burgessBeatClockParadigms1993a, title = {Beat the Clock: Paradigms for {{NTPases}} in the Maintenance of Biological Fidelity.}, author = {Burgess, S.M. and Guthrie, C.}, year = 1993, journal = {Trends in biochemical sciences}, volume = {18}, number = {10}, eprint = {8256287}, eprinttype = {pubmed}, pages = {381–384}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8256287}, keywords = {Fidelity,No DOI found,nosource,proofreading,Review} }

@article{bushellHijackingTranslationApparatus2002, title = {Hijacking the Translation Apparatus by {{RNA}} Viruses}, author = {Bushell, M. and Sarnow, P.}, year = 2002, journal = {The Journal of cell biology}, volume = {158}, number = {3}, pages = {395–399}, publisher = {Rockefeller Univ Press}, doi = {10.1083/jcb.200205044}, url = {http://jcb.rupress.org/content/158/3/395.abstract}, abstract = {As invading viruses do not harbor functional ribosomes in their virions, successful amplification of the viral genomes requires that viral mRNAs compete with cellular mRNAs for the host cell translation apparatus. Several RNA viruses have evolved remarkable strategies to recruit the host translation initiation factors required for the first steps in translation initiation by host cell mRNAs. This review describes the ways that three families of RNA viruses effectively usurp limiting translation initiation factors from the host}, keywords = {BINDING-PROTEIN,CELL PROTEIN-SYNTHESIS,CLEAVAGE,cricket paralysis-like virus,Genome,IN-VITRO,INHIBITION,initiation,INITIATION-FACTOR EIF4G,mRNA,nosource,picornavirus,POLIOVIRUS INFECTION,POLY(A)-BINDING PROTEIN,PROTEOLYSIS,Review,ribosome,RIBOSOME ENTRY SITES,Ribosomes,Rna,RNA Viruses,rotavirus,start codon selection,translation,TRANSLATION INITIATION,Virion} }

@article{busseyK1KillerToxin1991, title = {K1 Killer Toxin, a Pore-Forming Protein from Yeast.}, author = {Bussey, H.}, year = 1991, journal = {Molecular microbiology}, volume = {5}, number = {10}, pages = {2339–2343}, publisher = {Wiley Online Library}, doi = {10.1111/j.1365-2958.1991.tb02079.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.1991.tb02079.x/pdf}, keywords = {killer toxin,M1,nosource,protein,Review,toxin,yeast} } % == BibTeX quality report for busseyK1KillerToxin1991: % ? unused Journal abbr (“Mol.Microbiol.”)

@article{buzinaInfrequentTranslationNonsense1999, title = {Infrequent Translation of a Nonsense Codon Is Sufficient to Decrease {{mRNA}} Level}, author = {Buzina, A. and Shulman, M.J.}, year = 1999, month = mar, journal = {Molecular biology of the cell}, volume = {10}, number = {3}, pages = {515–524}, publisher = {Am Soc Cell Biol}, doi = {10.1091/mbc.10.3.515}, url = {http://www.molbiolcell.org/cgi/content/abstract/10/3/515}, abstract = {In many organisms nonsense mutations decrease the level of mRNA. In the case of mammalian cells, it is still controversial whether translation is required for this nonsense-mediated RNA decrease (NMD). Although previous analyzes have shown that conditions that impede translation termination at nonsense codons also prevent NMD, the residual level of termination was unknown in these experiments. Moreover, the conditions used to impede termination might also have interfered with NMD in other ways. Because of these uncertainties, we have tested the effects of limiting translation of a nonsense codon in a different way, using two mutations in the immunoglobulin mu heavy chain gene. For this purpose we exploited an exceptional nonsense mutation at codon 3, which efficiently terminates translation but nonetheless maintains a high level of mu mRNA. We have shown 1) that translation of Ter462 in the double mutant occurs at only approximately 4% the normal frequency, and 2) that Ter462 in cis with Ter3 can induce NMD. That is, translation of Ter462 at this low (4%) frequency is sufficient to induce NMD}, keywords = {0,analysis,animal,Codon,CodonNonsense,CodonTerminator,Frameshift Mutation,gene,Genetic,genetics,Hybridomas,Immunoglobulinsmu-Chain,immunology,La,metabolism,Mice,mRNA,Mutation,NMD,nosource,Rna,RNAMessenger,supportnon-u.s.gov’t,termination,translation,TranslationGenetic} } % == BibTeX quality report for buzinaInfrequentTranslationNonsense1999: % ? unused Journal abbr (“Mol.Biol.Cell”)

@article{camierOnlyEssentialFunction1995, title = {The Only Essential Function of {{TFIIIA}} in Yeast Is the Transcription of {{5S rRNA}} Genes}, author = {Camier, S. and Dechampesme, A.M. and Sentenac, A.}, year = 1995, journal = {Proceedings of the National Academy of Sciences}, volume = {92}, number = {20}, pages = {9338–9342}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.92.20.9338}, url = {http://www.pnas.org/content/92/20/9338.short}, abstract = {We have developed a system to transcribe the yeast 5S rRNA gene in the absence of the transcription factor TFIIIA. A long transcript was synthesized both in vitro and in vivo from a hybrid gene in which the tRNA-like promoter sequence of the RPR1 gene was fused to the yeast 5S RNA gene. No internal initiation directed by the endogenous 5S rDNA promoter or any processing of the hybrid transcript was observed in vitro. Yeast cells devoid of transcription factor TFIIIA, which, therefore, could not synthesize any 5S rRNA from the endogenous chromosomal copies of 5S rDNA, could survive if they carried the hybrid RPR1-5S construct on a multicopy plasmid. In this case, the only source of 5S rRNA was the precursor RPR1-5S transcript that gave rise to two RNA species slightly larger than wild-type 5S rRNA. This establishes that the only essential function of TFIIIA is to promote the synthesis of 5S rRNA. However, cells devoid of TFIIIA and surviving with these two RNAs grew more slowly at 30 degrees C compared with wild-type cells and were thermosensitive at 37 degrees C}, keywords = {5S rRNA,96016165,Base Sequence,biosynthesis,DNA-Binding Proteins,DNARibosomal,gene,Gene Expression,Genes,GenesFungal,Genetic Complementation Test,genetics,growth & development,In Vitro,IN-VITRO,IN-VIVO,initiation,Kinetics,metabolism,Molecular Sequence Data,nosource,Plasmids,rDNA,Restriction Mapping,Rna,RNARibosomal5S,rRNA,Saccharomyces cerevisiae,sequence,supportnon-u.s.gov’t,TFIIIA,transcription,Transcription Factors,TranscriptionGenetic,yeast} } % == BibTeX quality report for camierOnlyEssentialFunction1995: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{cannonCharacterizationSaccharomycesCerevisiae1987a, title = {Characterization of ⬚{{Saccharomyces}} Cerevisiae⬚ Genes Encoding Subunits of Cyclic {{AMP-dependent}} Protein Kinase.}, author = {Cannon, J.F. and Tatchell, K.}, year = 1987, journal = {Mol.Cell.Biol.}, volume = {7}, pages = {2653–2663}, keywords = {gene,Genes,kinase,Multiple DOI,nonfile,nosource,protein,ras,Saccharomyces,Saccharomyces cerevisiae,SUBUNIT,yeast} } % == BibTeX quality report for cannonCharacterizationSaccharomycesCerevisiae1987a: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{canoAnisomycinActivatedProteinKinaseP451994, title = {Anisomycin-{{Activated Protein Kinase-P45}} and {{Kinase-P55 But Not Mitogen-Activated Protein Kinase-Erk-1}} and {{Kinase-Erk-2 Are Implicated}} in the {{Induction}} of {{C-Fos}} and {{C-Jun}}}, author = {Cano, E. and Hazzalin, C.A. and Mahadevan, L.C.}, year = 1994, month = nov, journal = {Molecular and Cellular Biology}, volume = {14}, number = {11}, pages = {7352–7362}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Anisomycin-Activated+Protein+Kinase-P45+and+Kinase-P55+But+Not+Mitogen-Activated+Protein+Kinase-Erk-1+and+Kinase-Erk-2+Are+Implicated+in+the+Induction+of+C-Fos+and+C-Jun#0}, abstract = {Independent of its ability to block translation, anisomycin intrinsically initiates intracellular signals and immediate-early gene induction [L. C. Mahadevan and D. R. Edwards, Nature (London) 349:747-749, 1991]. Here, we characterize further its action as a potent, selective signalling agonist. In-gel kinase assays show that epidermal growth factor (EGF) transiently activates five kinases: the mitogen-activated protein (MAP) kinases ERK-1 and -2, and three others, p45, p55, and p80. Anisomycin, at inhibitory and subinhibitory concentrations, does not activate ERK-1 and -2 but elicits strong sustained activation of p45 and p55, which are unique in being serine kinases whose detection is enhanced with poly-Glu/Tyr or poly-Glu/Phe copolymerized in these gels. Translational arrest using emetine or puromycin does not activate p45 and p55 but does prolong EGF-stimulated ERK-1 and -2 activation. Rapamycin, which blocks anisomycin-stimulated p70/85(S6k) activation without affecting nuclear responses, has no effect on p45 or p55 kinase. p45 and p55 are activable by okadaic acid or UV irradiation, and both kinases phosphorylate the c-Jun NH2-terminal peptide 1-79, putatively placing them within c-Jun NH2-terminal kinase/stress-activated protein kinase (JNK/SAPK) subfamily of MAP kinases. Thus, the EGF- and anisomycin-activated kinases p35 and p55 are strongly implicated in signalling to c-fos and c-jun, whereas the MAP kinases ERK-1 and -2 are not essential for this process}, keywords = {ACID,activation,anisomycin,assays,D,DISTINCT MECHANISMS,Emetine,Gels,gene,GROWTH,GROWTH-FACTOR,GROWTH-FACTORS,kinase,MAP KINASE,MICROTUBULE-ASSOCIATED PROTEIN-2,MOUSE FIBROBLASTS,Multiple DOI,nonfile,nosource,OKADAIC ACID,PHORBOL ESTERS,protein,PROTEIN-KINASE,Puromycin,Serine,SIGNAL,SIGNAL-TRANSDUCTION,SYNTHESIS INHIBITORS,TRANSCRIPTIONAL ACTIVATION,translation} } % == BibTeX quality report for canoAnisomycinActivatedProteinKinaseP451994: % ? Title looks like it was stored in title-case in Zotero

@article{canoIdentificationAnisomycinactivatedKinases1996a, title = {Identification of Anisomycin-Activated Kinases P45 and P55 in Murine Cells as {{MAPKAP}} Kinase-2.}, author = {Cano, E. and Doza, Y.N. and Cohen, P. and Mahadevan, L.C.}, year = 1996, journal = {Oncogene}, volume = {12}, number = {4}, eprint = {8632902}, eprinttype = {pubmed}, pages = {805–812}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8632902}, keywords = {anisomycin,IDENTIFICATION,kinase,No DOI found,nosource,p38,stress activated} }

@article{caoComputationalModelingEukaryotic2001a, title = {Computational Modeling of Eukaryotic {{mRNA}} Turnover}, author = {Cao, D. and Parker, R.}, year = 2001, journal = {RNA}, volume = {7}, number = {9}, pages = {1192–1212}, doi = {10.1017/S1355838201010330}, abstract = {The process of eukaryotic gene expression involves a diverse number of steps including transcription, RNA processing, transport, translation, and mRNA turnover. A critical step in understanding this process will be the development of mathematical models that quantitatively describe and predict the behavior of this complex system. We have simulated eukaryotic mRNA turnover in a linear multicomponent model based on the known mRNA decay pathways in yeast. Using rate constants based on experimental data for the yeast unstable MFA2 and stable PGK1 transcripts, the computational modeling reproduces experimental observations after minor adjustments. Subsequent analysis and a series of in silico experiments led to several conclusions. First, we demonstrate that mRNA half-life as commonly measured underestimates the average life span of an mRNA. Second, due to the properties of the pathways, the measurement of a half-life can predominantly measure different steps in the decay network. A corollary of this fact is that different mRNAs will be affected differentially by changes in specific rate constants. Third, the way to obtain the largest change of levels of mRNA for the smallest changes in rate is by changing the rate of deadenylation, where a large amount of regulation of mRNA decay occurs. Fourth, the 3’-to-5’ degradation of mRNA shows mRNA-specific rates of degradation that are dependent on the 5’ structure of the mRNA. These programs can be run over the Web, are adaptable to other eukaryotes, and provide outputs as graphs and virtual northern gels, which can be directly compared to experimental data. Therefore, this model constitutes a useful tool for the quantitative analysis of the process and control of mRNA degradation in eukaryotic cells}, keywords = {analysis,Biological Transport,COMPLEX,COMPLEXES,Computer Simulation,DECAY,degradation,development,Eukaryotic Cells,Exodeoxyribonucleases,expression,Fungal Proteins,Gels,gene,Gene Expression,GENE-EXPRESSION,genetics,Half-Life,IN-SILICO,metabolism,models,ModelsGenetic,mRNA,mRNA decay,nosource,regulation,Rna,Rna Caps,RNAFungal,RNAMessenger,Software,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,transcription,translation,turnover,yeast} }

@article{caoPredictingRNAPseudoknot2006, title = {Predicting {{RNA}} Pseudoknot Folding Thermodynamics}, author = {Cao, S. and Chen, S.J.}, year = 2006, journal = {Nucleic acids research}, volume = {34}, number = {9}, pages = {2634–2652}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkl346}, url = {http://nar.oxfordjournals.org/content/34/9/2634.short}, abstract = {Based on the experimentally determined atomic coordinates for RNA helices and the self-avoiding walks of the P (phosphate) and C4 (carbon) atoms in the diamond lattice for the polynucleotide loop conformations, we derive a set of conformational entropy parameters for RNA pseudoknots. Based on the entropy parameters, we develop a folding thermodynamics model that enables us to compute the sequence-specific RNA pseudoknot folding free energy landscape and thermodynamics. The model is validated through extensive experimental tests both for the native structures and for the folding thermodynamics. The model predicts strong sequence-dependent helix-loop competitions in the pseudoknot stability and the resultant conformational switches between different hairpin and pseudoknot structures. For instance, for the pseudoknot domain of human telomerase RNA, a native-like and a misfolded hairpin intermediates are found to coexist on the (equilibrium) folding pathways, and the interplay between the stabilities of these intermediates causes the conformational switch that may underlie a human telomerase disease}, keywords = {0,Animals,Base Pairing,Base Sequence,Carbon,chemistry,CONFORMATION,disease,DOMAIN,Entropy,enzymology,FrameshiftingRibosomal,genetics,HIV,HIV Reverse Transcriptase,human,Humans,INTERMEDIATE,La,LOOP,metabolism,MODEL,ModelsMolecular,ModelsStatistical,Molecular Sequence Data,Mutation,nosource,Nucleic Acid Conformation,PATHWAY,pseudoknot,pseudoknot structure,pseudoknots,REVERSE-TRANSCRIPTASE,Rna,RNA PSEUDOKNOT,RnaViral,stability,structure,Support,Telomerase,Tetrahymena thermophila,Thermodynamics,Tobacco Mosaic Virus,Tymovirus} } % == BibTeX quality report for caoPredictingRNAPseudoknot2006: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{caponigroMechanismsControlMRNA1996b, title = {Mechanisms and Control of {{mRNA}} Turnover in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Caponigro, G. and Parker, R.}, year = 1996, journal = {Microbiol.Rev.}, volume = {60}, pages = {233–249}, doi = {10.1128/mr.60.1.233-249.1996}, keywords = {MECHANISM,MECHANISMS,mRNA,NMD,nosource,Review,review article,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,turnover} } % == BibTeX quality report for caponigroMechanismsControlMRNA1996b: % ? Possibly abbreviated journal title Microbiol.Rev.

@article{caputiNonsenseMutationFibrillin12002a, title = {A Nonsense Mutation in the Fibrillin-1 Gene of a {{Marfan}} Syndrome Patient Induces {{NMD}} and Disrupts an Exonic Splicing Enhancer}, author = {Caputi, M. and Kendzior, R.J. and Beemon, K.L.}, year = 2002, month = jul, journal = {Genes & Development}, volume = {16}, number = {14}, pages = {1754–1759}, doi = {10.1101/gad.997502}, url = {ISI:000176974300003}, abstract = {A nonsense mutation in the fibrillin-1 (FBN1) gene of a Marfan syndrome (MFS) patient induces in-frame exon skipping of FBN1 exon 51. We present evidence, based on both in vivo and in vitro experiments, that the skipping of this exon is due to the disruption of an SC35-dependent splicing enhancer within exon 51. In addition, this nonsense mutation induces nonsense-mediated decay (NMD), which degrades the normally spliced mRNA in the patient’s cells. In contrast to NMD, skipping of FBN1 exon 51 does not require translation}, keywords = {CODONS,DECAY,disease,ESE,EXON,exon skipping,FAMILY,FBN1,gene,In Vitro,IN-VITRO,IN-VIVO,Marfan syndrome,MECHANISM,MESSAGE,mRNA,Mutation,NMD,nonsense-mediated decay,nosource,Rna,SEQUENCES,SITE SELECTION,splicing,SR proteins,SR-PROTEINS,translation} }

@article{carlierCharacterizationBiosynthesisWoodchuck1994a, title = {Characterization and Biosynthesis of the Woodchuck Hepatitis Virus e Antigen}, author = {Carlier, D. and {Jean-Jean}, O. and Rossignol, J.M.}, year = 1994, month = jan, journal = {Journal of general}, volume = {75 ( Pt 1)}, pages = {171–175}, url = {http://jgv.sgmjournals.org/cgi/content/abstract/75/1/171}, abstract = {The biosynthesis of the secretory core gene product of the woodchuck hepatitis virus (WHV) was studied in human cells. We have shown that the WHV e antigen was a N-glycosylated (most likely a diglycosylated) protein, with an apparent M(r) of 24K. To demonstrate that the WHV precore protein was correctly processed in human cells, we engineered chimeric proteins in which signal peptides or arginine-rich domains of WHV and hepatitis B virus (HBV) precore proteins were exchanged. Our results showed that both the signal peptide and the arginine-rich region of WHV precore protein were cleaved off during the secretion pathway, as previously reported for precore protein of human HBV and duck HBV. These observations demonstrate that the maturation process of the e antigen is conserved in hepadnaviruses. In addition, on the basis of inhibition experiments, we suggest that the cleavage of the carboxy terminus of the WHV precore protein occurred in a post-endoplasmic reticulum compartment, most likely beyond the medial Golgi, and that this cleavage was catalysed by an aspartyl protease}, keywords = {0,Amino Acid Sequence,ANTIGEN,ASPARTYL PROTEASE,biosynthesis,Cell Line,CELLS,chemistry,Chimeric Proteins,CLEAVAGE,DOMAIN,DOMAINS,E,gene,GENE-PRODUCT,Glycosylation,Hepatitis B e Antigens,Hepatitis B VirusWoodchuck,human,Humans,immunology,INHIBITION,La,MATURATION,Molecular Sequence Data,No DOI found,nosource,PATHWAY,Peptides,PRODUCT,protein,Protein ProcessingPost-Translational,Proteins,REGION,Research SupportNon-U.S.Gov’t,SIGNAL,Signal Peptides,virus} } % == BibTeX quality report for carlierCharacterizationBiosynthesisWoodchuck1994a: % ? unused Journal abbr (“J.Gen.Virol.”)

@article{carlsonTransferRNAModification1999a, title = {Transfer {{RNA}} Modification Status Influences Retroviral Ribosomal Frameshifting}, author = {Carlson, B.A. and Kwon, S.Y. and Chamorro, M. and Oroszlan, S. and Hatfield, D.L. and Lee, B.J.}, year = 1999, month = mar, journal = {Virology}, volume = {255}, number = {1}, pages = {2–8}, doi = {10.1006/viro.1998.9569}, url = {PM:10049815}, abstract = {The possibility of whether tRNAs with and without a highly modified base in their anticodon loop may influence the level of retroviral ribosomal frameshifting was examined. Rabbit reticulocyte lysates were programmed with mRNA encoding UUU or AAC at the frameshift site and the corresponding Phe tRNA with or without the highly modified wyebutoxine (Y) base on the 3’ side of its anticodon or Asn tRNA with or without the highly modified queuine (Q) base in the wobble position of its anticodon added. Phe and Asn tRNAs without the Y or Q base, respectively, stimulated the level of frameshifting, suggesting that the frameshift event is influenced by tRNA modification status. In addition, when AAU occurred immediately upstream of UUU as the penultimate frameshift site codon, addition of tRNAAsn without the Q base reduced the stimulatory effect of tRNAPhe without the Y base, whereas addition of tRNAAsn with the Q base did not alter the stimulatory effect. The addition of tRNAAsn without the Q base and tRNAPhe with the Y base inhibited frameshifting. The latter studies suggest an interplay between the tRNAs decoded at the penulimate frameshift and frameshift site codons that is also influenced by tRNA modification status. These data may be intrepreted as indicating that a hypomodified isoacceptor modulates frameshifting in an upward manner when utilized at the frameshift site codon, but modulates frameshifting in a downward manner when utilized at the penultimate frameshift site codon}, keywords = {0,3,Animals,Anticodon,ANTICODON LOOP,BASE,cancer,Codon,CODONS,frameshift,Frameshift Mutation,Frameshifting,genetics,La,LOOP,lysate,Mammary Tumor VirusMouse,Mice,modification,mRNA,nosource,POSITION,Q-base,Rabbits,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,ribosomal frameshifting,Ribosomes,Rna,RNATransferAsn,RNATransferPhe,SITE,TRANSFER-RNA,tRNA,UPSTREAM} }

@article{carlsonYeastAsparagineAsn2000a, title = {Yeast Asparagine ({{Asn}}) {{tRNA}} without {{Q}} Base Promotes Eukaryotic Frameshifting More Efficiently than Mammalian {{Asn tRNAs}} with or without {{Q}} Base}, author = {Carlson, B.A. and Kwon, S.Y. and Lee, B.J. and Hatfield, D.}, year = 2000, month = feb, journal = {Molecules and Cells}, volume = {10}, number = {1}, pages = {113–118}, doi = {10.1007/s10059-000-0113-6}, url = {http://www.springerlink.com/index/HP6K341R5L82U76Q.pdf}, abstract = {In this study, we compare the efficiency of Asn tRNA from mammalian sources with and without the highly modified queuosine (Q) base in the wobble position of its anticodon and Asn tRNA from yeast, which naturally lacks Q base, to promote frameshifting. Interestingly, no differences in the ability of the two mammalian Asn tRNAs to promote frameshifting were observed, while yeast tRNA(ASn)(-Q) promoted frameshifting more efficiently than its mammalian counterparts in both rabbit reticulocyte lysates and wheat germ extracts. The shiftability of yeast Asn tRNA is therefore not due, or at least not completely, to the lack of Q base and most likely the shiftiness resides in structural differences elsewhere in the molecule. However, we cannot absolutely rule out a role of Q base in frameshifting as wheat germ extracts and a lysate depleted of most of its tRNA and supplemented with calf liver tRNA contain both Asn tRNA with or without Q base}, keywords = {0,Animals,Anticodon,Asparagine,BASE,Base Sequence,BIOLOGY,cancer,Cell-Free System,Comparative Study,efficiency,Eukaryotic Cells,EXTRACTS,Frameshifting,genetics,La,Liver,lysate,Mammals,Molecular Sequence Data,Mutation,nosource,Nucleoside Q,POSITION,Protein Biosynthesis,Q-base,Research SupportNon-U.S.Gov’t,Rna,RNATransferAsn,Saccharomyces cerevisiae,Selenium,Sequence HomologyNucleic Acid,Structural,tRNA,Wheat,yeast} } % == BibTeX quality report for carlsonYeastAsparagineAsn2000a: % ? unused Journal abbr (“Mol.Cells”)

@article{carr-schmidMutationsGTPbindingMotif1999, title = {Mutations in a {{GTP-binding}} Motif of Eukaryotic Elongation Factor {{1A}} Reduce Both Translational Fidelity and the Requirement for Nucleotide Exchange}, author = {{Carr-Schmid}, A. and Durko, N. and Cavallius, J. and Merrick, W.C. and Kinzy, T.G.}, year = 1999, month = oct, journal = {Journal of Biological Chemistry}, volume = {274}, number = {42}, pages = {30297–30302}, publisher = {ASBMB}, doi = {10.1074/jbc.274.42.30297}, url = {http://www.jbc.org/content/274/42/30297.short}, abstract = {A series of mutations in the highly conserved N(153)KMD(156)GTP-binding motif of the Saccharomyces cerevisiae translation elongation factor 1A (eEF1A) affect the GTP-dependent functions of the protein and increase misincorporation of amino acids in vitro. Two critical regulatory processes of translation elongation, guanine nucleotide exchange and translational fidelity, were analyzed in strains with the N153T, D156N, and N153T/D156E mutations. These strains are omnipotent suppressors of nonsense mutations, indicating reduced A site fidelity, which correlates with changes either in total translation rates in vivo or in GTPase activity in vitro. All three mutant proteins also show an increase in the K(m) for GTP. An in vivo system lacking the guanine nucleotide exchange factor eukaryotic elongation factor 1Balpha (eEF1Balpha) and supported for growth by excess eEF1A was used to show the two mutations with the highest K(m) for GTP restore most but not all growth defects found in these eEF1Balpha deficient-strains to near wild type. An increase in K(m) alone, however, is not sufficient for suppression and may indicate eEF1Balpha performs additional functions. Additionally, eEF1A mutations that suppress the requirement for guanine nucleotide exchange may not effectively perform all the functions of eEF1A in vivo}, keywords = {99445598,A-SITE,Amino Acids,Binding Sites,chemistry,elongation,Fidelity,Genetic,genetics,growth & development,GTP,GTPase,Guanine Nucleotide Exchange Factors,GUANINE-NUCLEOTIDE-EXCHANGE,Guanosine Triphosphate,In Vitro,IN-VITRO,IN-VIVO,metabolism,Mutation,MUTATIONS,nosource,Peptide Elongation Factor 1,Plasmids,protein,Proteins,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,suppression,SYSTEM,translation,TranslationGenetic} } % == BibTeX quality report for carr-schmidMutationsGTPbindingMotif1999: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{carr-schmidMutationsElongationFactor1999, title = {Mutations in Elongation Factor 1beta, a Guanine Nucleotide Exchange Factor, Enhance Translational Fidelity}, author = {{Carr-Schmid}, A. and Valente, L. and Loik, V.I. and Williams, T. and Starita, L.M. and Kinzy, T.G.}, year = 1999, journal = {Molecular and cellular biology}, volume = {19}, number = {8}, pages = {5257–5266}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.19.8.5257}, url = {http://mcb.asm.org/cgi/content/abstract/19/8/5257}, abstract = {Translation elongation factor 1beta (EF-1beta) is a member of the family of guanine nucleotide exchange factors, proteins whose activities are important for the regulation of G proteins critical to many cellular processes. EF-1beta is a highly conserved protein that catalyzes the exchange of bound GDP for GTP on EF-1alpha, a required step to ensure continued protein synthesis. In this work, we demonstrate that the highly conserved C-terminal region of Saccharomyces cerevisiae EF-1beta is sufficient for normal cell growth. This region of yeast and metazoan EF-1beta and the metazoan EF-1beta- like protein EF-1delta is highly conserved. Human EF-1beta, but not human EF-1delta, is functional in place of yeast EF-1beta, even though both EF-1beta and EF-1delta have previously been shown to have guanine nucleotide exchange activity in vitro. Based on the sequence and functional homology, mutagenesis of two C-terminal residues identical in all EF-1beta protein sequences was performed, resulting in mutants with growth defects and sensitivity to translation inhibitors. These mutants also enhance translational fidelity at nonsense codons, which correlates with a reduction in total protein synthesis. These results indicate the critical function of EF-1beta in regulating EF-1alpha activity, cell growth, translation rates, and translational fidelity}, keywords = {0,Alleles,Amino Acid Sequence,Codon,CodonTerminator,Comparative Study,elongation,Fidelity,Frameshift Mutation,Fungal Proteins,Genetic,Genetic Complementation Test,genetics,GTP,Guanine Nucleotide Exchange Factors,GUANINE-NUCLEOTIDE-EXCHANGE,Guanosine Diphosphate,Guanosine Triphosphate,human,In Vitro,IN-VITRO,La,metabolism,microbiology,Molecular Sequence Data,Mutagenesis,Mutation,MUTATIONS,nosource,Peptide Chain Elongation,Peptide Elongation Factor 1,Peptide Elongation Factors,physiology,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,regulation,Rna,RNAFungal,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence Alignment,Sequence HomologyAmino Acid,Species Specificity,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,translation,TranslationGenetic,yeast} } % == BibTeX quality report for carr-schmidMutationsElongationFactor1999: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{carr-schmidNovelGproteinComplex2002, title = {Novel {{G-protein}} Complex Whose Requirement Is Linked to the Translational Status of the Cell}, author = {{Carr-Schmid}, A. and Pfund, C. and Craig, E.A. and Kinzy, T.G.}, year = 2002, month = apr, journal = {Molecular and Cellular Biology}, volume = {22}, number = {8}, pages = {2564–2574}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.22.8.2564-2574.2002}, url = {http://mcb.asm.org/cgi/content/abstract/22/8/2564}, abstract = {G proteins, which bind and hydrolyze GTP, are involved in regulating a variety of critical cellular processes, including the process of protein synthesis. Many members of the subfamily of elongation factor class G proteins interact with the ribosome and function to regulate discrete steps during the process of protein synthesis. Despite sequence similarity to factors involved in translation, a role for the yeast Hbs1 protein has not been defined. In this work we have identified a genetic relationship between genes encoding components of the translational apparatus and HBS1. HBS1, while not essential for viability, is important for efficient growth and protein synthesis under conditions of limiting translation initiation. The identification of an Hbs1p-interacting factor, Dom34p, which shares a similar genetic relationship with components of the translational apparatus, suggests that Hbs1p and Dom34p may function as part of a complex that facilitates gene expression. Dom34p contains an RNA binding motif present in several ribosomal proteins and factors that regulate translation of specific mRNAs. Thus, Hbs1p and Dom34p may function together to help directly or indirectly facilitate the expression either of specific mRNAs or under certain cellular conditions}, keywords = {BINDING,BINDING MOTIF,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,elongation,ELONGATION-FACTOR TU,expression,gene,Gene Expression,GENE-EXPRESSION,Genes,Genetic,GROWTH,GTP,Guanosine Diphosphate,IDENTIFICATION,IN-VIVO,initiation,KINASE GCN2,MESSENGER-RNA,MOLECULAR-GENETICS,mRNA,nosource,NUCLEOTIDE EXCHANGE,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Ribosomal Proteins,RIBOSOMAL-SUBUNITS,ribosome,Rna,SACCHAROMYCES-CEREVISIAE,sequence,T,TRANSFER-RNA-BINDING,translation,TRANSLATION INITIATION,yeast} }

@article{carrascoTricoderminGroupAntibiotics1973a, title = {The Tricodermin Group of Antibiotics, Inhibitors of Peptide Bond Formation by Eukaryotic Ribosomes.}, author = {Carrasco, L. and Barbacid, M. and Vazquez, D.}, year = 1973, journal = {Biochim.et Biophys.Acta.}, volume = {312}, pages = {368–376}, doi = {10.1016/0005-2787(73)90381-X}, keywords = {anisomycin,antibiotic,antibiotics,codon:anticodon,initiation,nosource,ribosome,Ribosomes,termination,translocation} } % == BibTeX quality report for carrascoTricoderminGroupAntibiotics1973a: % ? Possibly abbreviated journal title Biochim.et Biophys.Acta.

@article{carrollTranslationDsRNAPropagation1995, title = {Translation and {{M}}⬚1⬚ {{dsRNA}} Propagation: ⬚{{MAK18}} = {{RPL41B}}⬚ and Cycloheximide Curing.}, author = {Carroll, K. and Wickner, R.B.}, year = 1995, journal = {J.Bacteriol.}, volume = {177}, pages = {2887–2891}, doi = {10.1128/jb.177.10.2887-2891.1995}, keywords = {curing,Cycloheximide,M1,MAK,nosource,translation} } % == BibTeX quality report for carrollTranslationDsRNAPropagation1995: % ? Possibly abbreviated journal title J.Bacteriol.

@article{carterFunctionalInsightsStructure2000, title = {Functional Insights from the Structure of the {{30S}} Ribosomal Subunit and Its Interactions with Antibiotics.}, author = {Carter, A.P. and Clemons, W.M. and Brodersen, D.E. and {Morgan-Warren}, R.J. and Wimberly, B.T. and Ramakrishnan, V.}, year = 2000, month = sep, journal = {Nature}, volume = {407}, number = {6802}, pages = {340–348}, publisher = {Nature Publishing Group}, issn = {0028-0836}, doi = {10.1038/35030019}, url = {http://www.nature.com/nature/journal/v407/n6802/abs/407327a0.html http://www.nature.com/nature/journal/v407/n6802/abs/407340a0.html}, abstract = {The 30S ribosomal subunit has two primary functions in protein synthesis. It discriminates against aminoacyl transfer RNAs that do not match the codon of messenger RNA, thereby ensuring accuracy in translation of the genetic message in a process called decoding. Also, it works with the 50S subunit to move the tRNAs and associated mRNA by precisely one codon, in a process called translocation. Here we describe the functional implications of the high-resolution 30S crystal structure presented in the accompanying paper, and infer details of the interactions between the 30S subunit and its tRNA and mRNA ligands. We also describe the crystal structure of the 30S subunit complexed with the antibiotics paromomycin, streptomycin and spectinomycin, which interfere with decoding and translocation. This work reveals the structural basis for the action of these antibiotics, and leads to a model for the role of the universally conserved 16S RNA residues A1492 and A1493 in the decoding process.}, pmid = {11014183}, keywords = {16S,16S: chemistry,20466111,accuracy,Anti-Bacterial Agents,Anti-Bacterial Agents: chemistry,Anti-Bacterial Agents: pharmacology,antibiotic,antibiotics,Bacterial,Bacterial: chemistry,Bacterial: physiology,Binding Sites,chemistry,Codon,Crystallography,CrystallographyX-Ray,decoding,drug effects,Genetic,Genetic Code,Macromolecular Substances,Macromolecular Systems,Messenger,MESSENGER-RNA,Messenger: metabolism,metabolism,Models,ModelsMolecular,Molecular,Molecular Mimicry,mRNA,nosource,Nucleic Acid Conformation,Paromomycin,Paromomycin: chemistry,Paromomycin: pharmacology,pharmacology,physiology,protein,Protein Conformation,protein synthesis,PROTEIN-SYNTHESIS,Ribosomal,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: physiology,Ribosomal: chemistry,Ribosomal: physiology,Ribosomes,Ribosomes: chemistry,Ribosomes: drug effects,Ribosomes: metabolism,Rna,RNA,RNABacterial,RNAMessenger,RNARibosomal,RNARibosomal16S,RNATransfer,Spectinomycin,Spectinomycin: chemistry,Spectinomycin: pharmacology,Streptomycin,Streptomycin: chemistry,Streptomycin: pharmacology,Structural,STRUCTURAL BASIS,structure,Structure-Activity Relationship,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Thermus thermophilus,Transfer,Transfer: metabolism,translation,translocation,tRNA,X-Ray} }

@article{carterCrystalStructureInitiation2001, title = {Crystal Structure of an Initiation Factor Bound to the {{30S}} Ribosomal Subunit}, author = {Carter, A.P. and Clemons, W.M. and Brodersen, D.E. and {Morgan-Warren}, R.J. and Hartsch, T. and Wimberly, B.T. and Ramakrishnan, V.}, year = 2001, month = jan, journal = {Science}, volume = {291}, number = {5503}, pages = {498–501}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1057766}, url = {http://www.sciencemag.org/content/291/5503/498.short}, abstract = {Initiation of translation at the correct position on messenger RNA is essential for accurate protein synthesis. In prokaryotes, this process requires three initiation factors: IF1, IF2, and IF3, Here we report the crystal structure of a complex of IF1 and the 30S ribosomal subunit, Binding of IF1 occludes the ribosomal A site and flips out the functionally important bases A1492 and A1493 from helix 44 of 16S RNA, burying them in pockets in IF1. The binding of IF1 causes long-range changes in the conformation of H44 and Leads to movement of the domains of 30S with respect to each other. The structure explains how localized changes at the ribosomal A site lead to global alterations in the conformation of the 30S subunit}, keywords = {A-SITE,ACIDS,BINDING,BINDING MOTIF,COMPLEX,COMPLEXES,CONFORMATION,crystal structure,CRYSTAL-STRUCTURE,DOMAINS,ESCHERICHIA-COLI,FACTOR IF1,initiation,MECHANISM,MESSENGER-RNA,Movement,nosource,PROKARYOTES,protein,protein synthesis,PROTEIN-BIOSYNTHESIS,PROTEIN-SYNTHESIS,REQUIRES,RIBOSOMAL-SUBUNIT,Rna,SITE,structure,SUBUNIT,TRANSFER-RNA,translation,TRANSLATIONAL INITIATION} }

@article{caseroTargetingPolyamineMetabolism2007, title = {Targeting Polyamine Metabolism and Function in Cancer and Other Hyperproliferative Diseases}, author = {Casero, R.A. and Marton, L.J.}, year = 2007, month = may, journal = {Nature Reviews Drug Discovery}, volume = {6}, number = {5}, pages = {373–390}, publisher = {Nature Publishing Group}, doi = {10.1038/nrd2243}, url = {http://www.nature.com/nrd/journal/v6/n5/abs/nrd2243.html}, abstract = {The polyamines spermidine and spermine and their diamine precursor putrescine are naturally occurring, polycationic alkylamines that are essential for eukaryotic cell growth. The requirement for and the metabolism of polyamines are frequently dysregulated in cancer and other hyperproliferative diseases, thus making polyamine function and metabolism attractive targets for therapeutic intervention. Recent advances in our understanding of polyamine function, metabolic regulation, and differences between normal cells and tumour cells with respect to polyamine biology, have reinforced the interest in this target-rich pathway for drug development}, keywords = {0,Animals,antagonists & inhibitors,Antineoplastic Agents,Biogenic Polyamines,BIOLOGY,biosynthesis,cancer,CELLS,development,disease,drug therapy,enzyme,Enzyme Inhibitors,enzymology,GROWTH,Humans,INHIBITOR,inhibitors,La,metabolism,Neoplasms,nosource,PATHWAY,pharmacology,polyamine,Polyamines,PRECURSOR,Putrescine,regulation,Review,Spermidine,Spermine,Support,TARGET,therapeutic use} } % == BibTeX quality report for caseroTargetingPolyamineMetabolism2007: % ? unused Journal abbr (“Nat.Rev.Drug Discov.”)

@article{cassanTranslationalFrameshiftingGagpol1994, title = {Translational Frameshifting at the Gag-Pol Junction of Human Immunodeficiency Virus Type 1 Is Not Increased in Infected {{T-lymphoid}} Cells.}, author = {Cassan, M. and Delaunay, N. and Vaquero, C. and Rousset, J.P.}, year = 1994, month = mar, journal = {Journal of virology}, volume = {68}, number = {3}, pages = {1501–1508}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.68.3.1501-1508.1994}, url = {http://jvi.asm.org/cgi/content/abstract/68/3/1501}, abstract = {A frameshift event is necessary for expression of the products of the pol gene in a number of retroviruses, including human immunodeficiency virus type 1 (HIV-1). The basic signals necessary for frameshifting consist of a shifty sequence in which the ribosome slips and a downstream stimulatory structure which can be either a stem-loop or a pseudoknot. In HIV-1, much attention has been paid to the frameshift site itself, and only recently has the role of the downstream structure been examined. Here we used a luciferase-based experimental system to analyze in vivo the cis and trans factors potentially involved in controlling frameshifting efficiency at the gag-pol junction of HIV-1. We demonstrated that high-level frameshifting is dependent on the presence of a palindromic region located downstream of the site where the frameshift event takes place. Frameshifting efficiencies were found to be identical in mouse fibroblasts and the natural host cells of the virus, i.e., CD4+ human lymphoid cells. Furthermore, no increase in frameshifting was observed upon virus infection. Previous observations have shown that viral infection leads to specific alteration of tRNAs involved in translation of shifty sites (D. Hatfield, Y.-X. Feng, B.J. Lee, A. Rein, J.G. Levin, and S. Oroszlan, Virology 173:736-742, 1989). The results presented here strongly suggest that these modifications do not affect frameshifting efficiency}, keywords = {0,Animals,Base Sequence,CD4-Positive T-Lymphocytes,Cell Line,CELLS,Child,D,Dna,DNARecombinant,DOWNSTREAM,efficiency,enzymology,expression,frameshift,Frameshifting,Gag-pol,gene,Gene Expression RegulationViral,Genesgag,Genespol,genetics,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,Humans,IMMUNODEFICIENCY-VIRUS,IN-VIVO,INFECTION,Insects,La,luciferase,Luciferases,microbiology,modification,Molecular Sequence Data,MOUSE FIBROBLASTS,nosource,Nucleic Acid Conformation,pol,POL GENE,PRODUCT,PRODUCTS,Protein Biosynthesis,pseudoknot,Reading Frames,REGION,Research SupportNon-U.S.Gov’t,RETROVIRUSES,ribosome,S,sequence,SIGNAL,SITE,SITES,STEM-LOOP,structure,SYSTEM,Transfection,translation,TRANSLATIONAL FRAMESHIFTING,tRNA,TYPE-1,virology,virus} } % == BibTeX quality report for cassanTranslationalFrameshiftingGagpol1994: % ? unused Journal abbr (“J.Virol.”)

@article{castellanoCardiacBetaadrenoceptormediatedSignaling1997a, title = {The Cardiac Beta-Adrenoceptor-Mediated Signaling Pathway and Its Alterations in Hypertensive Heart Disease. [{{Review}}] [52 Refs]}, author = {Castellano, M. and Bohm, M.}, year = 1997, month = mar, journal = {Hypertension}, volume = {29}, number = {3}, pages = {715–722}, doi = {10.1161/01.HYP.29.3.715}, keywords = {activation,development,disease,expression,Genetic,heart,kinase,MECHANISM,MECHANISMS,models,nosource,protein,Proteins,rat,SIGNAL,Signal Transduction} }

@article{castilho-valviciusGeneticCharacterizationSaccharomyces1990a, title = {Genetic Characterization of the ⬚{{Saccharomyces}} Cerevisiae⬚ Translational Initiation Suppressors ⬚sui1⬚, ⬚sui2⬚ and ⬚{{SUI3}}⬚ and Their Effects on ⬚{{HIS4}}⬚ Expression.}, author = {{Castilho-Valvicius}, B. and Yoon, H. and Donahue, T.F.}, year = 1990, journal = {Genetics}, volume = {124}, pages = {483–495}, doi = {10.1093/genetics/124.3.483}, keywords = {expression,gene,Genetic,initiation,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sui,sui1,translation,yeast} }

@incollection{castonStructuralAspectsCapsid1995, title = {Structural Aspects of the Capsid of {{L-A dsRNA}} Virus of Yeast.}, booktitle = {Proceedings of the {{XIV International Phage}}/{{Virus Assembly Coneference}}.}, author = {Caston, J.R. and Trus, B.L. and Booy, F.P. and Dinman, J.D. and Wickner, R.B. and Steven, A.C.}, year = 1995, pages = {6}, collaborator = {Givosen, U. and Hendrix, R. and Russel, M.}, keywords = {assembly,L-A,La,nosource,Structural,virus,yeast} } % == BibTeX quality report for castonStructuralAspectsCapsid1995: % Missing required field ‘publisher’

@article{castonStructureVirusSpecialized1997a, title = {Structure of {{L-A}} Virus: A Specialized Compartment for the Transcription and Replication of Double-Stranded {{RNA}}.}, author = {Caston, J.R. and Trus, B.L. and Booy, F.P. and Wickner, R.B. and Wall, J.S. and Steven, A.C.}, year = 1997, journal = {J.Cell Biol.}, volume = {138}, pages = {975–985}, doi = {10.1083/jcb.138.5.975}, keywords = {EMS,L-A,La,morphogenesis,nosource,Rna,structure,transcription,viral particle,virus} } % == BibTeX quality report for castonStructureVirusSpecialized1997a: % ? Possibly abbreviated journal title J.Cell Biol.

@article{cateXrayCrystalStructures1999, title = {X-Ray Crystal Structures of {{70S}} Ribosome Functional Complexes.}, author = {Cate, J.H. and Yusupov, M.M. and Yusupova, G.Z. and Earnest, T.N. and Noller, H.F.}, year = 1999, journal = {Science}, volume = {285}, number = {5436}, pages = {2095–2104}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.285.5436.2095}, abstract = {Structures of 70S ribosome complexes containing messenger RNA and transfer RNA (tRNA), or tRNA analogs, have been solved by x-ray crystallography at up to 7.8 angstrom resolution. Many details of the interactions between tRNA and the ribosome, and of the packing arrangements of ribosomal RNA (rRNA) helices in and between the ribosomal subunits, can be seen. Numerous contacts are made between the 30S subunit and the P-tRNA anticodon stem-loop; in contrast, the anticodon region of A-tRNA is much more exposed. A complex network of molecular interactions suggestive of a functional relay is centered around the long penultimate stem of 16S rRNA at the subunit interface, including interactions involving the “switch” helix and decoding site of 16S rRNA, and RNA bridges from the 50S subunit}, keywords = {99428678,ANGSTROM RESOLUTION,Anticodon,Bacterial Proteins,Base Pairing,Binding Sites,chemistry,COMPLEX,COMPLEXES,Crystallization,Crystallography,CrystallographyX-Ray,decoding,Fourier Analysis,MESSENGER-RNA,metabolism,ModelsMolecular,nosource,Nucleic Acid Conformation,Peptide Elongation Factors,physiology,Protein Conformation,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNABacterial,RNAMessenger,RNARibosomal,RNARibosomal16S,RNARibosomal23S,RNATransfer,rRNA,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Thermus thermophilus,TranslationGenetic,tRNA,ultrastructure} }

@article{cavalliusSitedirectedMutagenesisYeast1998a, title = {Site-Directed Mutagenesis of Yeast {{eEF1A}}. {{Viable}} Mutants with Altered Nucleotide Specificity}, author = {Cavallius, J. and Merrick, W.C.}, year = 1998, month = oct, journal = {J.Biol.Chem.}, volume = {273}, number = {44}, pages = {28752–28758}, doi = {10.1074/jbc.273.44.28752}, url = {PM:9786872}, abstract = {Site-directed mutants of eEF1A (formerly eEF-1alpha) were generated using a modification of a highly versatile yeast shuttle vector (Cavallius, J., Popkie, A. P., and Merrick, W. C. (1997) Biochim. Biophys. Acta 1350, 345-358). The nucleotide specificity sequence NKMD (residues number 153-156) was targeted for mutagenesis, and the following mutants were obtained: N153D (DKMD), N153T (TKMD), D156N (NKMN), D156W (NKMW), and the double mutant N153T,D156E (TKNE). All of the yeast strains containing the mutant eEF1As as the sole source of eEF1A were viable except for the N153D mutant. Most of the purified mutant eEF1As had specific activities in the poly(U)-directed synthesis of polyphenylalanine similar to wild type, although with a Km for GTP increased by 1-2 orders of magnitude. The mutants showed a reduced rate of GTP hydrolysis, and most displayed misincorporation rates greater than wild type. The mutant NKMW eEF1A showed unusual properties. The yeast strain was temperature sensitive for growth, although the purified protein was not. Second, this form of eEF1A was 10-fold more accurate in protein synthesis, and its rate of GTP hydrolysis was about 20% of wild type. In total, the wild-type protein contains the most optimal nucleotide specificity sequence, NKMD, and even subtle changes in this sequence have drastic consequences on eEF1A function in vitro or yeast viability}, keywords = {0,Base Sequence,Dna,DNA Primers,Eif-1,eIF1,genetics,GTP,Guanosine,Guanosine Triphosphate,Hydrolysis,In Vitro,IN-VITRO,La,metabolism,modification,Mutagenesis,MutagenesisSite-Directed,nosource,protein,Protein Binding,protein synthesis,PROTEIN-SYNTHESIS,Saccharomyces cerevisiae,sequence,supportu.s.gov’tp.h.s.,Temperature,vector,yeast} } % == BibTeX quality report for cavalliusSitedirectedMutagenesisYeast1998a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{cawthonTelomereLengthMeasurement2009, title = {Telomere Length Measurement by a Novel Monochrome Multiplex Quantitative {{PCR}} Method}, author = {Cawthon, R.M.}, year = 2009, month = feb, journal = {Nucleic Acids Research}, volume = {37}, number = {3}, pages = {e21}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkn1027}, url = {http://nar.oxfordjournals.org/content/37/3/e21.short}, abstract = {The current quantitative polymerase chain reaction (QPCR) assay of telomere length measures telomere (T) signals in experimental DNA samples in one set of reaction wells, and single copy gene (S) signals in separate wells, in comparison to a reference DNA, to yield relative T/S ratios that are proportional to average telomere length. Multiplexing this assay is desirable, because variation in the amount of DNA pipetted would no longer contribute to variation in T/S, since T and S would be collected within each reaction, from the same input DNA. Multiplexing also increases throughput and lowers costs, since half as many reactions are needed. Here, we present the first multiplexed QPCR method for telomere length measurement. Remarkably, a single fluorescent DNA-intercalating dye is sufficient in this system, because T signals can be collected in early cycles, before S signals rise above baseline, and S signals can be collected at a temperature that fully melts the telomere product, sending its signal to baseline. The correlation of T/S ratios with Terminal Restriction Fragment (TRF) lengths measured by Southern blot was stronger with this monochrome multiplex QPCR method (R(2) = 0.844) than with our original singleplex method (R(2) = 0.677). Multiplex T/S results from independent runs on different days were highly reproducible (R(2) = 0.91)}, keywords = {0,Albumins,beta-Globins,chemistry,Dna,DNA Primers,gene,Gene Dosage,Genetic,genetics,human,Humans,La,Methods,nosource,PCR,polymerase,Polymerase Chain Reaction,PRODUCT,Reference Standards,Reproducibility of Results,S,SIGNAL,standards,Support,SYSTEM,T,Tandem Repeat Sequences,Telomere,Temperature} } % == BibTeX quality report for cawthonTelomereLengthMeasurement2009: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{celmaSubstrateAntibioticBinding1971a, title = {Substrate and Antibiotic Binding Sites at the Peptidyl Transferase Centre of {{E}}. Coli Ribosomes: {{Binding}} of {{UACCA-Leu}} to 50 {{S}} Subunits.}, author = {Celma, M.L. and Monro, R.E. and Vazquez, D.}, year = 1971, month = mar, journal = {FEBS letters}, volume = {13}, number = {4}, eprint = {11945678}, eprinttype = {pubmed}, pages = {247–251}, doi = {10.1016/0014-5793(71)80546-X}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11945678}, keywords = {antibiotic,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,E,La,nosource,peptidyl transferase,PEPTIDYL-TRANSFERASE,ribosome,Ribosomes,S,SITE,SITES,SUBUNIT,SUBUNITS} } % == BibTeX quality report for celmaSubstrateAntibioticBinding1971a: % ? unused Journal abbr (“FEBS Lett.”)

@article{cetinEnacyloxinIIaInhibitor1996, title = {Enacyloxin {{IIa}}, an Inhibitor of Protein Biosynthesis That Acts on Elongation Factor {{Tu}} and the Ribosome.}, author = {Cetin, r. and Krab, I.M. and Amborgh, P.H. and Cool, R.H. and Watenabe, T. and Sugiyama, T. and Izaki, K. and Parmeggiani, A.}, year = 1996, journal = {The EMBO journal}, volume = {15}, number = {10}, pages = {2604–2611}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1996.tb00618.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC450193/}, keywords = {antibiotic,antibiotics,biosynthesis,EF-1 alpha,elongation,nosource,protein,ribosome} } % == BibTeX quality report for cetinEnacyloxinIIaInhibitor1996: % ? unused Journal abbr (“EMBO J.”)

@article{chadaPosttranscriptionalRegulationGlutathione1989a, title = {Post-Transcriptional Regulation of Glutathione Peroxidase Gene Expression by Selenium in the {{HL-60}} Human Myeloid Cell Line⬚⬚ ⬚⬚}, author = {Chada, S. and Whitney, C. and Newburger, P.E.}, year = 1989, month = nov, journal = {Blood}, volume = {74}, number = {7}, pages = {2535–2541}, abstract = {We have used a cloned cDNA for the major human selenoprotein, glutathione peroxidase (GPx), to assess the mode of regulation of human GPx gene (GPX-1) expression by selenium. When the HL-60 human myeloid cell line is grown in a selenium-deficient medium, GPx enzymatic activity decreases 30-fold compared with selenium-replete cells. Upon return to a medium containing selenium in the form of selenite, GPx activity in the cells starts to increase within 48 hours and reaches maximal (selenium-replete) levels at 7 days. Steady-state immunoreactive protein levels correlate with enzymatic activity. Cycloheximide inhibits the rise in GPx activity that accompanies selenium replenishment, indicating that protein synthesis is required for the increase. However, GPx mRNA levels and the rate of transcription of the human GPx gene change very little and thus appear to be independent of the selenium supply. Thus the human GPx gene appears to be regulated post-transcriptionally, probably cotranslationally, in response to selenium availability}, keywords = {90028799,BlottingWestern,Cell Differentiation,Cell Line,Cell Nucleus,Cycloheximide,drug effects,enzymology,expression,gene,Gene Expression,Gene Expression RegulationLeukemic,GENE-EXPRESSION,genetics,Glutathione Peroxidase,human,In Vitro,LeukemiaMyeloid,media,metabolism,mRNA,Multiple DOI,NMD,nonfile,nosource,pathology,pharmacology,physiology,post-transcriptional regulation,protein,protein synthesis,PROTEIN-SYNTHESIS,regulation,RNAMessenger,Selenium,supportu.s.gov’tp.h.s.,transcription,TranscriptionGenetic,TranslationGenetic,Tumor CellsCultured} }

@article{chakrabartiLinkStreptomycinRifampicin1975a, title = {A Link between Streptomycin and Rifampicin Mutation}, author = {Chakrabarti, S.L. and Gorini, L.}, year = 1975, month = jun, journal = {Proc.Natl.Acad.Sci.U.S.A}, volume = {72}, number = {6}, pages = {2084–2087}, doi = {10.1073/pnas.72.6.2084}, url = {PM:1094452}, abstract = {Introduction of str A mutations frequently make “male” strains of Escherichia coli permissive to bacteriophage T7; certain rif mutations reverse the permissive effect of strA mutation. Permissiveness of the strA mutation is accompanied by enhanced transcription of bacteriophage T7 genome. Introduction of the nonpermissive rif allele to the permissive strA strain reduces or abolishes the transcription of T7 genome. Thus, a link is implied in the functioning of the ribosome and the RNA polymerase (RNA nucleotidyltransferase, EC 2.7.7.6)}, keywords = {0,Bacteriophage T7,biosynthesis,Carbon,Carbon Radioisotopes,Coliphages,drug effects,Drug ResistanceMicrobial,Escherichia coli,ESCHERICHIA-COLI,GeneticsMicrobial,Genome,Isotope Labeling,Kinetics,La,metabolism,Mutation,MUTATIONS,nosource,pharmacology,polymerase,radiation effects,ribosome,Rifampin,Rna,RNA-POLYMERASE,RnaViral,Streptomycin,Support,Time Factors,transcription,TranscriptionGenetic,ultraviolet rays,Uracil} } % == BibTeX quality report for chakrabartiLinkStreptomycinRifampicin1975a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.U.S.A

@article{chalfieGreenFluorescentProtein1994, title = {Green Fluorescent Protein as a Marker for Gene Expression}, author = {Chalfie, M. and Tu, Y. and Euskirchen, G. and Ward, W.W. and Prasher, D.C.}, year = 1994, month = feb, journal = {Science}, volume = {263}, number = {5148}, pages = {802–805}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.8303295}, url = {http://www.sciencemag.org/content/263/5148/802.short}, keywords = {Dna,Escherichia coli,ESCHERICHIA-COLI,expression,gene,Gene Expression,GENE-EXPRESSION,gfp,nosource,protein} }

@article{chamaryEvidenceSelectionSynonymous2005, title = {Evidence for Selection on Synonymous Mutations Affecting Stability of {{mRNA}} Secondary Structure in Mammals}, author = {Chamary, J.V. and Hurst, L.D.}, year = 2005, journal = {Genome biology}, volume = {6}, number = {9}, pages = {R75}, publisher = {BioMed Central Ltd}, doi = {10.1186/gb-2005-6-9-r75}, url = {http://www.biomedcentral.com/1465-6906/6/R75}, abstract = {BACKGROUND: In mammals, contrary to what is usually assumed, recent evidence suggests that synonymous mutations may not be selectively neutral. This position has proven contentious, not least because of the absence of a viable mechanism. Here we test whether synonymous mutations might be under selection owing to their effects on the thermodynamic stability of mRNA, mediated by changes in secondary structure. RESULTS: We provide numerous lines of evidence that are all consistent with the above hypothesis. Most notably, by simulating evolution and reallocating the substitutions observed in the mouse lineage, we show that the location of synonymous mutations is non-random with respect to stability. Importantly, the preference for cytosine at 4-fold degenerate sites, diagnostic of selection, can be explained by its effect on mRNA stability. Likewise, by interchanging synonymous codons, we find naturally occurring mRNAs to be more stable than simulant transcripts. Housekeeping genes, whose proteins are under strong purifying selection, are also under the greatest pressure to maintain stability. CONCLUSION: Taken together, our results provide evidence that, in mammals, synonymous sites do not evolve neutrally, at least in part owing to selection on mRNA stability. This has implications for the application of synonymous divergence in estimating the mutation rate}, keywords = {0,ACID,ACIDS,Amino Acid Substitution,Amino Acids,AMINO-ACID,AMINO-ACIDS,Animals,Base Composition,Base Pairing,Biochemistry,BIOLOGY,chemistry,Codon,CODONS,Cricetinae,Cytosine,Evolution,gene,Genes,genetics,La,LINE,LOCATION,Mammals,MECHANISM,Mice,mRNA,mRNA stability,Mutation,MUTATIONS,nosource,POSITION,protein,Proteins,Rats,Research SupportNon-U.S.Gov’t,Rna,RNA Stability,RNAMessenger,SECONDARY STRUCTURE,SELECTION,Selection (Genetics),SITE,SITES,stability,structure,thermodynamic stability,TRANSCRIPT} } % == BibTeX quality report for chamaryEvidenceSelectionSynonymous2005: % ? unused Journal abbr (“Genome Biol.”)

@article{chambersRasResponsiveGenes1993, title = {Ras Responsive Genes and Tumor Metastasis.}, author = {Chambers, A.F. and Tuck, A.B.}, year = 1993, journal = {Critical reviews in oncogenesis}, volume = {4}, number = {2}, eprint = {8420573}, eprinttype = {pubmed}, pages = {95–114}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8420573}, keywords = {gene,Genes,No DOI found,nosource,ras,Review} } % == BibTeX quality report for chambersRasResponsiveGenes1993: % ? unused Journal abbr (“Crit.Rev.Oncogenesis.”)

@article{chamorroRNAPseudoknotOptimal1992, title = {An {{RNA}} Pseudoknot and an Optimal Heptameric Shift Site Are Required for Highly Efficient Ribosomal Frameshifting on a Retroviral Messenger {{RNA}}.}, author = {Chamorro, M. and Parkin, N. and Varmus, H.E.}, year = 1992, journal = {Proceedings of the National Academy of Sciences}, volume = {89}, number = {2}, pages = {713–717}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.89.2.713}, url = {http://www.pnas.org/content/89/2/713.short}, keywords = {efficiency,Frameshifting,MESSENGER-RNA,nosource,pseudoknot,ribosomal frameshifting,Rna,RNA PSEUDOKNOT} } % == BibTeX quality report for chamorroRNAPseudoknotOptimal1992: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.USA”)

@article{chanPhenotypeMutationsBasepair2000a, title = {The Phenotype of Mutations of the Base-Pair {{C2658}} Center Dot {{G2663}} That Closes the Tetraloop in the Sarcin/Ricin Domain of {{Escherichia}} Coli 23 {{S}} Ribosomal {{RNA}}}, author = {Chan, Y.L. and Sitikov, A.S. and Wool, I.G.}, year = 2000, month = may, journal = {Journal of Molecular Biology}, volume = {298}, number = {5}, pages = {795–805}, doi = {10.1006/jmbi.2000.3720}, url = {ISI:000087980500006}, abstract = {The sarcin/ricin domain (SRD) in Escherichia coli 23 S rRNA is a part of the site for the association of elongation factors with ribosomes and for that reason is critical for the binding of aminoacyl-tRNA and for translocation during the reiterative elongation reactions of protein synthesis. The SRD has a GAGA tetraloop that is shut off by a Watson-Crick C2658.G2663 pair. The contribution of this pair to the function of the ribosome has been evaluated by constructing mutations in the nucleotides and determining their phenotype. Constitutive expression of a plasmid-encoded rrnB operon with a G2663C transversion mutation that disrupts the Watson-Crick pair was lethal. Double transversion mutations, C2658G.G2663C and C2658A.G2663U, that reverse the polarity of the pyrimidine and the purine but restore the potential to form a canonical pair, were also lethal. Induction of transcription of 23 S rRNA with the same mutations, but encoded in a plasmid with a lambda P-L promoter and expressed at a lower level, retarded growth. The sedimentation profiles of ribosomes with transversion mutations in C2658 and/or G2663 are altered; the ratio of 50 S subunits to 30 S particles is changed and polysomes are reduced. Ribosomes with a G2663C, a C2658G.G2663C, or a C2658A.G2663U mutation in 23 S rRNA were not active in protein synthesis, indeed, they appeared to inhibit the activity of ribosomes with wild-type 23 S rRNA. Transversion mutations in the analogs of C2658 and G2663 decreased binding of EF-G to SRD oligoribonucleotides; the same mutations in 23 S rRNA decreased binding of the factor to intact ribosomes. The most severe phenotype, in growth, in protein synthesis, and in the binding of EF-G, was associated with a C2658G.G2663C mutation; it is surprising that this was more severe than an analogous C2658A.G2663U mutation. A double transition mutation, C2658U.G2663A, which is not known to have occurred in nature, had no effect on the growth of cells or on the function of ribosomes. The lethal phenotype of transversion mutations in C2658 and G2663 appears to derive from a loss of the capacity of ribosomes to bind EF-G and by indirection the EF-Tu ternary complex. (C) 2000 Academic Press}, keywords = {30 S,ALPHA-SARCIN,ANGSTROM-RESOLUTION,BINDING,C2658 center dot G2663 mutations,CLEAVAGE SITE,COMPLEX,COMPLEXES,CONSERVED LOOP,CRYSTAL-STRUCTURE,EF-G,EFTu,elongation,elongation factors,ELONGATION-FACTORS,Escherichia coli,Escherichia coli ribosomes,ESCHERICHIA-COLI,EUKARYOTIC RIBOSOMES,expression,Mutation,MUTATIONS,N-GLYCOSIDASE ACTIVITY,nosource,Nucleotides,Oligoribonucleotides,Operon,Phenotype,PLASMID,polysomes,PROMOTER,protein,protein synthesis,PROTEIN-SYNTHESIS,RIBONUCLEIC-ACID,RIBOSOMAL-RNA,ribosome,Ribosomes,RICIN A-CHAIN,Rna,rRNA,sarcin/ricin domain,sarcin/ricin domain in 23 S rRNA,SITE,SUBUNIT,transcription,translocation} }

@article{chanLocationSignificanceCrosslink2004, title = {The Location and the Significance of a Cross-Link between the Sarcin/Ricin Domain of Ribosomal {{RNA}} and the Elongation Factor-{{G}}}, author = {Chan, Y.L. and Correll, C.C. and Wool, I.G.}, year = 2004, month = mar, journal = {Journal of molecular biology}, volume = {337}, number = {2}, pages = {263–272}, publisher = {Elsevier}, doi = {10.1016/j.jmb.2004.01.020}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283604000786}, abstract = {During translocation peptidyl-tRNA moves from the A-site to the P-site and mRNA is displaced by three nucleotides in the 3’ direction. This reaction is catalyzed by elongation factor-G (EF-G) and is associated with ribosome-dependent hydrolysis of GTP. The molecular basis of translocation is the most important unsolved problem with respect to ribosome function. A critical question, one that might provide a clue to the mechanism of translocation, is the precise identity of the contacts between EF-G and ribosome components. To make the identification, a covalent bond was formed, by ultraviolet irradiation, between EF-G and a sarcin/ricin domain (SRD) oligoribonucleotide containing 5-iodouridine. The cross-link was established, by mass spectroscopy and by Edman degradation, to be between a tryptophan at position 127 in the G domain in EF-G and either one of two 5-iodouridine nucleotides in the sequence UAG2655U in the SRD. G2655 is a critical identity element for the recognition of the factor’s ribosomal binding site. The site of the cross-link provides the first direct evidence that the SRD is in close proximity to the EF-G catalytic center. The proximity suggests that the SRD RNA has a role in the activation of GTP hydrolysis that leads to a transition in the conformation of the factor and to its release from the ribosome}, keywords = {0,3,A SITE,A-SITE,activation,Amino Acid Sequence,Bacterial,Bacterial Proteins,Base Sequence,BINDING,Binding Sites,BINDING-SITE,BIOLOGY,chemistry,COMPONENT,COMPONENTS,CONFORMATION,CROSS-LINKING,Cross-Linking Reagents,CROSSLINKING,degradation,DOMAIN,EF-G,elongation,ELONGATION-FACTOR-G,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,genetics,GTP,Hydrolysis,IDENTIFICATION,La,LOCATION,Macromolecular Systems,mass spectroscopy,MECHANISM,metabolism,ModelsMolecular,MOF,Molecular Sequence Data,mRNA,nosource,Nucleic Acid Conformation,Nucleotides,P SITE,P-SITE,Peptide Elongation Factor G,POSITION,protein,Proteins,RECOGNITION,RELEASE,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Ricin,Rna,RNABacterial,RNARibosomal,sarcin/ricin domain,sequence,Sequence HomologyAmino Acid,SITE,SPECTROSCOPY,supportu.s.gov’tp.h.s.,SYSTEM,SYSTEMS,Thermus thermophilus,translocation,Tryptophan,ultraviolet rays} } % == BibTeX quality report for chanLocationSignificanceCrosslink2004: % ? unused Journal abbr (“J.Mol.Biol.”)

@article{chandlerTranslationalFrameshiftingControl1993, title = {Translational Frameshifting in the Control of Transposition in Bacteria.}, author = {Chandler, M. and Fayet, O.}, year = 1993, month = feb, journal = {Molecular Microbiology}, volume = {7}, number = {4}, pages = {497–503}, publisher = {Wiley Online Library}, doi = {10.1111/j.1365-2958.1993.tb01140.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.1993.tb01140.x/abstract}, abstract = {The expression of an increasing number of genes of both prokaryotic and eukaryotic origin has been shown to be regulated at the translational level by programmed (sequence-specific) ribosomal frameshifting. Among these are the bacterial insertion sequences IS1 and two members of the widely distributed IS3-family, IS150 and IS911. Frameshifting provides a means of specifying several proteins with different functions using a minimum of genetic information. In this review, we survey present understanding of the way in which frameshifting is integrated into the overall control of transposition activity in these elements}, keywords = {Bacteria,Bacterial,BINDING,ELEMENT IS1,ELEMENTS,expression,Frameshifting,gene,Genes,Genetic,INITIATION FACTOR-IF3,INSA,INSERTION SEQUENCES,IS1 TRANSPOSITION,M,nosource,ORGANIZATION,PROMOTERS,protein,Proteins,Review,review article,ribosomal frameshifting,sequence,SEQUENCES,transoposon} } % == BibTeX quality report for chandlerTranslationalFrameshiftingControl1993: % ? unused Journal abbr (“Mol.Microbiol.”)

@article{chardinHumanSOSGuanine1993, title = {Human {{SOS}}: A Guanine Nucleotide Exchange Factor for {{Ras}} That Binds to {{GRB2}}.}, author = {Chardin, P. and Camonis, J.H. and Gale, N.W. and Van Aelst, L. and Schlessinger, J. and Wigler, M.H. and {Bar-Sagi}, D.}, year = 1993, journal = {Science}, volume = {260}, pages = {1338–1343}, doi = {10.1126/science.8493579}, keywords = {GUANINE-NUCLEOTIDE-EXCHANGE,human,nosource,ras} }

@article{charettePseudouridineRNAWhat2000, title = {Pseudouridine in {{RNA}}: What, Where, How, and Why}, author = {Charette, M. and Gray, M.W.}, year = 2000, month = may, journal = {IUBMB.Life}, volume = {49}, number = {5}, pages = {341–351}, publisher = {Wiley Online Library}, url = {http://onlinelibrary.wiley.com/doi/10.1080/152165400410182/pdf}, abstract = {Pseudouridine (5-ribosyluracil) is a ubiquitous yet enigmatic constituent of structural RNAs (transfer, ribosomal, small nuclear, and small nucleolar). Although pseudouridine (psi) was the first modified nucleoside to be discovered in RNA, and is the most abundant, its biosynthesis and biological roles have remained poorly understood since its identification as a “fifth nucleoside” in RNA. Recently, a combination of biochemical, biophysical, and genetic approaches has helped to illuminate the structural consequences of psi in polyribonucleotides, the biochemical mechanism of U–{\(>\)}psi isomerization in RNA, and the role of modification enzymes (psi synthases) and box H/ACA snoRNAs, a class of eukaryotic small nucleolar RNAs, in the site-specific biosynthesis of psi. Through its unique ability to coordinate a structural water molecule via its free N1-H, psi exerts a subtle but significant “rigidifying” influence on the nearby sugar-phosphate backbone and also enhances base stacking. These effects may underlie the biological role of most (but perhaps not all) of the psi residues in RNA. Certain genetic mutants lacking specific psi residues in tRNA or rRNA exhibit difficulties in translation, display slow growth rates, and fail to compete effectively with wild-type strains in mixed culture. In particular, normal growth is severely compromised in an Escherichia coli mutant deficient in a pseudouridine synthase responsible for the formation of three closely spaced psi residues in the mRNA decoding region of the 23S rRNA. Such studies demonstrate that pseudouridylation of RNA confers an important selective advantage in a natural biological context}, keywords = {0,Animals,BASE,Biochemistry,BIOLOGY,biosynthesis,chemistry,decoding,DECODING REGION,enzyme,Enzymes,enzymology,Escherichia coli,ESCHERICHIA-COLI,Genetic,genetics,GROWTH,Humans,Hydro-Lyases,Hydrogen Bonding,IDENTIFICATION,Isomerism,La,MECHANISM,metabolism,ModelsMolecular,modification,Molecular Biology,mRNA,MUTANTS,No DOI found,nosource,Nucleic Acid Conformation,physiology,Pseudouridine,PSEUDOURIDINE SYNTHASE,pseudouridylation,psi,REGION,RESIDUES,Review,Rna,RNARibosomal,RNASmall Nuclear,RNATransfer,rRNA,site specific,SMALL NUCLEOLAR RNAS,Structural,Support,translation,tRNA,Uridine,Water,WILD-TYPE} } % == BibTeX quality report for charettePseudouridineRNAWhat2000: % ? Possibly abbreviated journal title IUBMB.Life

@article{chastainPolyRABinds1992, title = {Poly ({{rA}}) Binds Poly ({{rG}}). Poly ({{rC}}) to Form a Triple Helix.}, author = {Chastain, M. and Tinoco, {I.Jr}.}, year = 1992, month = jan, journal = {Nucleic acids research}, volume = {20}, number = {2}, pages = {315–318}, publisher = {Oxford University Press}, doi = {10.1093/nar/20.2.315}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC310372/}, abstract = {Poly(rA) binds poly(rG).poly(rC) to form a triple helix. Evidence for this structure includes ultraviolet absorbance mixing curves and melting curves, and circular dichroism spectroscopy. The formation of the triple helix depends on the length of the poly(rC) strand. Triple helix forms when the average length is around 100 nucleotides but does not form when the average length is about 500 nucleotides}, keywords = {0,chemistry,Circular Dichroism,La,Macromolecular Systems,metabolism,nosource,Nucleic Acid Conformation,Nucleotides,Poly A,Poly C,Poly G,Spectrophotometry,structure,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,SYSTEM,Temperature} } % == BibTeX quality report for chastainPolyRABinds1992: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{chaudhuriHumanRibosomalProtein2007, title = {Human Ribosomal Protein {{L13a}} Is Dispensable for Canonical Ribosome Function but Indispensable for Efficient {{rRNA}} Methylation}, author = {Chaudhuri, S. and Vyas, K. and Kapasi, P. and Komar, A.A. and Dinman, J.D. and Barik, S. and Mazumder, B.}, year = 2007, month = dec, journal = {RNA.}, volume = {13}, number = {12}, pages = {2224–2237}, publisher = {Cold Spring Harbor Lab}, issn = {1469-9001}, doi = {10.1261/rna.694007}, url = {http://rnajournal.cshlp.org/content/13/12/2224.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2080596&tool=pmcentrez&rendertype=abstract}, abstract = {Previously, we demonstrated that treatment of monocytic cells with IFN-gamma causes release of ribosomal protein L13a from the 60S ribosome and subsequent translational silencing of Ceruloplasmin (Cp) mRNA. Here, evidence using cultured cells demonstrates that Cp mRNA silencing is dependent on L13a and that L13a-deficient ribosomes are competent for global translational activity. Human monocytic U937 cells were stably transfected with two different shRNA sequences for L13a and clonally selected for more than 98% abrogation of total L13a expression. Metabolic labeling of these cells showed rescue of Cp translation from the IFN-gamma mediated translational silencing activity. Depletion of L13a caused significant reduction of methylation of ribosomal RNA and of cap-independent translation mediated by Internal Ribosome Entry Site (IRES) elements derived from p27, p53, and SNAT2 mRNAs. However, no significant differences in the ribosomal RNA processing, polysome formation, global translational activity, translational fidelity, and cell proliferation were observed between L13a-deficient and wild-type control cells. These results support the notion that ribosome can serve as a depot for releasable translation-regulatory factors unrelated to its basal polypeptide synthetic function. Unlike mammalian cells, the L13a homolog in yeast is indispensable for growth. Thus, L13a may have evolved from an essential ribosomal protein in lower eukaryotes to having a role as a dispensable extra-ribosomal function in higher eukaryotes}, pmid = {17921318}, keywords = {0,CAP-INDEPENDENT TRANSLATION,Cell Line,Cell Line-Tumor,Cell LineTumor,Cell Proliferation,CELLS,Ceruloplasmin,ELEMENTS,expression,Fidelity,Gene Expression Regulation,Gene Expression Regulation-Neoplastic,Gene Expression RegulationNeoplastic,Genetic Vectors,genetics,GROWTH,homolog,human,Humans,INTERNAL RIBOSOME ENTRY,La,Lentivirus,Lentivirus: genetics,MAMMALIAN-CELLS,metabolism,Methylation,METHYLTRANSFERASE,mRNA,Neoplasm,Neoplasm: genetics,Neoplastic,nosource,p53,physiology,POLYPEPTIDE,PROLIFERATION,protein,Proteins,Recombinant Proteins,Recombinant Proteins: metabolism,RELEASE,Ribosomal,Ribosomal Proteins,Ribosomal Proteins: genetics,Ribosomal Proteins: metabolism,ribosomal RNA,RIBOSOMAL-PROTEIN,RIBOSOMAL-RNA,Ribosomal: metabolism,ribosome,RIBOSOME ENTRY SITE,Ribosomes,Ribosomes: physiology,Rna,RNA Interference,RNA-Neoplasm,RNA-Ribosomal,RNANeoplasm,RNARibosomal,rRNA,sequence,SEQUENCES,SITE,Support,Transfection,translation,translational fidelity,tRNA,tRNA Methyltransferases,tRNA Methyltransferases: metabolism,Tumor,U937 Cells,WILD-TYPE,yeast} } % == BibTeX quality report for chaudhuriHumanRibosomalProtein2007: % ? Possibly abbreviated journal title RNA.

@article{checovichFluorescencePolarizationNew1995, title = {Fluorescence Polarization–a New Tool for Cell and Molecular Biology}, author = {Checovich, W.J. and Bolger, R.E. and Burke, T.}, year = 1995, month = may, journal = {Nature}, volume = {375}, number = {6528}, pages = {254–256}, doi = {10.1038/375254a0}, url = {http://adsabs.harvard.edu/abs/1995Natur.375..254C}, abstract = {Fluorescence polarization (FP) equilibrium binding assays differ from other types of binding studies in one important regard: they require no steps to separate free from bound tracer and are therefore fast, simple and accurate}, keywords = {0,assays,BINDING,BIOLOGY,Dna,enzyme,Enzymes,Fluorescence,Fluorescence Polarization,La,metabolism,Methods,Molecular Biology,nosource,protein,Proteins} }

@article{chemalyRapidDiagnosisHistoplasma2001a, title = {Rapid Diagnosis of {{Histoplasma}} Capsulatum Endocarditis Using the {{AccuProbe}} on an Excised Valve}, author = {Chemaly, R.F. and Tomford, J.W. and Hall, G.S. and Sholtis, M. and Chua, J.D. and Procop, G.W.}, year = 2001, month = jul, journal = {J.Clin.Microbiol.}, volume = {39}, number = {7}, pages = {2640–2641}, doi = {10.1128/JCM.39.7.2640-2641.2001}, url = {PM:11427583}, abstract = {Histoplasma capsulatum is an infrequent but serious cause of endocarditis. The definitive diagnosis requires culture, which may require a long incubation. We demonstrated the ability of the Histoplasma capsulatum AccuProbe to accurately identify this organism when applied directly on an excised valve that contained abundant yeast forms consistent with H. capsulatum}, keywords = {0,analysis,Aortic Valve,classification,diagnosis,Dna,DNA Probes,DNARibosomal,Endocarditis,FORM,genetics,Heart Valve Prosthesis,Histoplasma,Histoplasmosis,Humans,IDENTIFY,isolation & purification,La,Male,microbiology,Middle Aged,nosource,pathology,Reagent KitsDiagnostic,REQUIRES,Rna,RNARibosomal,surgery,yeast} } % == BibTeX quality report for chemalyRapidDiagnosisHistoplasma2001a: % ? Possibly abbreviated journal title J.Clin.Microbiol.

@article{chenCharacterizationRNAElements2003, title = {Characterization of {{RNA}} Elements That Regulate Gag-Pol Ribosomal Frameshifting in Equine Infectious Anemia Virus}, author = {Chen, C. and Montelaro, R.C.}, year = 2003, month = oct, journal = {Journal of virology}, volume = {77}, number = {19}, pages = {10280–10287}, publisher = {Am Soc Microbiol}, doi = {10.1128/JVI.77.19.10280-10287.2003}, url = {http://jvi.asm.org/cgi/content/abstract/77/19/10280}, abstract = {Synthesis of Gag-Pol polyproteins of retroviruses requires ribosomes to shift translational reading frame once or twice in a -1 direction to read through the stop codon in the gag reading frame. It is generally believed that a slippery sequence and a downstream RNA structure are required for the programmed -1 ribosomal frameshifting. However, the mechanism regulating the Gag-Pol frameshifting remains poorly understood. In this report, we have defined specific mRNA elements required for sufficient ribosomal frameshifting in equine anemia infectious virus (EIAV) by using full-length provirus replication and Gag/Gag-Pol expression systems. The results of these studies revealed that frameshifting efficiency and viral replication were dependent on a characteristic slippery sequence, a five-base-paired GC stretch, and a pseudoknot structure. Heterologous slippery sequences from human immunodeficiency virus type 1 and visna virus were able to substitute for the EIAV slippery sequence in supporting EIAV replication. Disruption of the GC-paired stretch abolished the frameshifting required for viral replication, and disruption of the pseudoknot reduced the frameshifting efficiency by 60%. Our data indicated that maintenance of the essential RNA signals (slippery sequences and structural elements) in this region of the genomic mRNA was critical for sufficient ribosomal frameshifting and EIAV replication, while concomitant alterations in the amino acids translated from the same region of the mRNA could be tolerated during replication. The data further indicated that proviral mutations that reduced frameshifting efficiency by as much as 50% continued to sustain viral replication and that greater reductions in frameshifting efficiency lead to replication defects. These studies define for the first time the RNA sequence and structural determinants of Gag-Pol frameshifting necessary for EIAV replication, reveal novel aspects relative to frameshifting elements described for other retroviruses, and provide new genetic determinants that can be evaluated as potential antiviral targets}, keywords = {0,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,animal,antiviral,Base Sequence,chemistry,Codon,DISRUPTION,DOWNSTREAM,efficiency,ELEMENTS,expression,FRAME,Frameshifting,FrameshiftingRibosomal,FUSION PROTEIN,Fusion Proteinsgag-pol,Gag,Gag-pol,Genetic,genetics,genomic,Horses,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,Infectious Anemia VirusEquine,La,MECHANISM,Molecular Sequence Data,MOLECULAR-GENETICS,mRNA,Mutation,MUTATIONS,nosource,physiology,POLYPROTEIN,Polyproteins,protein,Proteins,pseudoknot,pseudoknot structure,READ-THROUGH,READING FRAME,REGION,REPLICATION,REQUIRES,RETROVIRUSES,ribosomal frameshifting,ribosome,Ribosomes,Rna,RnaViral,sequence,SEQUENCES,SIGNAL,STOP CODON,Structural,structure,supportu.s.gov’tp.h.s.,SYSTEM,SYSTEMS,TARGET,TYPE-1,virus} } % == BibTeX quality report for chenCharacterizationRNAElements2003: % ? unused Journal abbr (“J.Virol.”)

@article{chenInitiationProteinSynthesis1995, title = {Initiation of Protein Synthesis by the Eukaryotic Translational Apparatus on Circular {{RNAs}}}, author = {Chen, C.Y. and Sarnow, P.}, year = 1995, journal = {Science}, volume = {268}, number = {5209}, pages = {415–417}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.7536344}, url = {http://www.sciencemag.org/content/268/5209/415.short}, keywords = {Amino Acids,ANGSTROM RESOLUTION,BINDING,Binding Sites,COMPLEX,COMPLEXES,COMPONENT,Crystallography,EFTu,elongation,GTP,Guanosine,Guanosine Triphosphate,initiation,MECHANISM,MESSENGER-RNA,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,ribosome,Rna,sequence,structure,Thermus,translocation,yeast} }

@article{chenStructuralFunctionalStudies1995, title = {Structural and Functional Studies of Retroviral {{RNA}} Pseudoknots Involved in Ribosomal Frameshifting: Nucleotides at the Junction of the Two Stems Are Important for Efficient Ribosomal Frameshifting.}, author = {Chen, X. and Chamorro, M. and Lee, S.I. and Shen, L.X. and Hines, J.V. and Tinoco, {I.Jr}. and Varmus, H.E.}, year = 1995, journal = {The EMBO journal}, volume = {14}, number = {4}, pages = {842–852}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1995.tb07062.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC398151/}, keywords = {efficiency,Frameshifting,nosource,Nucleotides,pseudoknot,ribosomal frameshifting,Rna,RNA PSEUDOKNOT,Structural} } % == BibTeX quality report for chenStructuralFunctionalStudies1995: % ? unused Journal abbr (“EMBO J.”)

@article{chenCharacteristicBentConformation1996, title = {A Characteristic Bent Conformation of {{RNA}} Pseudoknots Promotes -1 Frameshifting during Translation of Retroviral {{RNA}}}, author = {Chen, X. and Kang, H. and Shen, L.X. and Chamorro, M. and Varmus, H.E. and Tinoco, I.}, year = 1996, month = jul, journal = {J.Mol.Biol.}, volume = {260}, number = {4}, pages = {479–483}, doi = {10.1006/jmbi.1996.0415}, url = {PM:8759314}, abstract = {The structures of four different RNA pseudoknots that provide one of the signals required for ribosomal frameshifting in mouse mammary tumor virus have been determined by NMR. The RNA pseudoknots have similar sequences and assume similar secondary structures, but show significantly different frameshifting efficiencies. The three-dimensional structures of one frameshifting and one non-frameshifting RNA pseudoknot had been determined previously by our group. Here we determine the structures of two new RNA pseudoknots, and relate the structures of all four pseudoknots to their frameshifting abilities. The two efficient frameshifting pseudoknots adopt characteristic bent conformations with stem 1 bending towards the major groove of stem 2. In contrast, the two poor frameshifting pseudoknots have structures very different from each other and from the efficient frameshifters. One has linear, coaxially stacked stems, the other has stems twisted and bent, but in the opposite direction to the efficient frameshifters. Changes in loop size that favor bending (shorter loops) increase frameshifting efficiency; longer loops that allow linear arrangement of the stems decrease frameshifting. Frameshifting pseudoknots in feline immunodeficiency virus and simian retrovirus have different loop sequences, but the sequences at their stem junctions imply the same bent conformation as in the mouse mammary tumor viral RNA. The requirement for a precise pseudoknot conformation for efficient frameshifting strongly implies that a specific interaction occurs between the viral RNA pseudoknot and the host protein-synthesizing machinery}, keywords = {0,ARRANGEMENT,Base Sequence,chemistry,CONFORMATION,efficiency,Frameshifting,genetics,IMMUNODEFICIENCY-VIRUS,La,LOOP,Magnetic Resonance Spectroscopy,Mammary Tumor VirusMouse,ModelsMolecular,Molecular Sequence Data,Mutation,NMR,nosource,Nucleic Acid Conformation,Protein Biosynthesis,pseudoknot,pseudoknots,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,RETROVIRAL RNA,retrovirus,RetrovirusesSimian,ribosomal frameshifting,Rna,RNA PSEUDOKNOT,RnaViral,SECONDARY STRUCTURE,sequence,SEQUENCES,SIGNAL,structure,translation,VIRAL-RNA,virus} } % == BibTeX quality report for chenCharacteristicBentConformation1996: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{chengFungalVirusCapsids1994a, title = {Fungal Virus Capsids, Cytoplasmic Compartments for the Replication of Double-Stranded {{RNA}}, Formed as Icosahedral Shells of Asymmetric {{Gag}} Dimers.}, author = {Cheng, R.H. and Caston, J.R. and Wang.G. and Gu, F. and Smith, T.J. and Baker, T.S. and Bozarth, R.F. and Trus, B.L. and Cheng, B.N. and Wickner, R.B. and Steven, A.C.}, year = 1994, journal = {J.Mol.Biol.}, number = {224}, pages = {255–258}, doi = {10.1006/jmbi.1994.1726}, keywords = {Gag,Gag-pol dimer,L-A,La,nosource,Rna,viral particle,virus} } % == BibTeX quality report for chengFungalVirusCapsids1994a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{chernoffMutationsEukaryotic18S1994, title = {Mutations in Eukaryotic {{18S}} Ribosomal {{RNA}} Affect Translational Fidelity and Resistance to Aminoglycoside Antibiotics.}, author = {Chernoff, Y.O. and Vincent, A. and Liebman, S.W.}, year = 1994, journal = {The EMBO journal}, volume = {13}, number = {4}, pages = {906–913}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1994.tb06334.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC394890/}, keywords = {antibiotic,antibiotics,Fidelity,Mutation,MUTATIONS,nosource,Plasmids,RDN1,Rna,rRNA,yeast} } % == BibTeX quality report for chernoffMutationsEukaryotic18S1994: % ? unused Journal abbr (“EMBO J.”)

@article{chernoffTranslationalFunctionNucleotide1996, title = {The Translational Function of Nucleotide {{C1054}} in the Small Subunit {{rRNA}} Is Conserved throughout Evolution: Genetic Evidence in Yeast}, author = {Chernoff, Y.O. and Newnam, G.P. and Liebman, S.W.}, year = 1996, month = mar, journal = {Proceedings of the National Academy of Sciences}, volume = {93}, number = {6}, pages = {2517–2522}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.93.6.2517}, url = {http://www.pnas.org/content/93/6/2517.short}, abstract = {Mutations at position C1054 of 16S rRNA have previously been shown to cause translational suppression in Escherichia coli. To examine the effects of similar mutations in a eukaryote, all three possible base substitutions and a base deletion were generated at the position of Saccharomyces cerevisiae 18S rRNA corresponding to E. coli C1054. In yeast, as in E. coli, both C1054A (rdn-1A) and C1054G (rdn-1G) caused dominant nonsense suppression. Yeast C1054U (rdn-1T) was a recessive antisuppressor, while yeast C1054-delta (rdn-1delta) led to recessive lethality. Both C1054U and two previously described yeast 18S rRNA antisuppressor mutations, G517A (rdn-2) and U912C (rdn-4), inhibited codon-nonspecific suppression caused by mutations in eukaryotic release factors, sup45 and sup35. However, among these only C1054U inhibited UAA-specific suppressions caused by a UAA-decoding mutant tRNA-Gln (SLT3). Our data implicate eukaryotic C1054 in translational termination, thus suggesting that its function is conserved throughout evolution despite the divergence of nearby nucleotide sequences}, keywords = {0,16S,BASE,Base Sequence,BIOLOGY,CEREVISIAE,chemistry,Dna,DNA Primers,E,Escherichia coli,ESCHERICHIA-COLI,Evolution,GenesSuppressor,Genetic,genetics,La,Molecular Biology,Molecular Sequence Data,Mutation,MUTATIONS,NONSENSE,nonsense suppression,nosource,NUCLEOTIDE-SEQUENCE,POSITION,Protein Biosynthesis,RELEASE,release factor,RELEASE FACTORS,Rna,RNAFungal,RNAMessenger,RNARibosomal18S,RNATransferGln,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,Structure-Activity Relationship,SUBUNIT,sup35,sup45,Support,suppression,termination,TRANSLATIONAL SUPPRESSION,TRANSLATIONAL TERMINATION,yeast} } % == BibTeX quality report for chernoffTranslationalFunctionNucleotide1996: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{cheungMakingReadingMicroarrays1999a, title = {Making and Reading Microarrays}, author = {Cheung, V.G. and Morley, M. and Aguilar, F. and Massimi, A. and Kucherlapati, R. and Childs, G.}, year = 1999, month = jan, journal = {Nature genetics}, volume = {21}, number = {1 Suppl}, pages = {15–19}, url = {http://www.rose-hulman.edu/~ahmed/making and reading cdna microarrays.pdf}, abstract = {There are a variety of options for making microarrays and obtaining microarray data. Here, we describe the building and use of two microarray facilities in academic settings. In addition to specifying technical detail, we comment on the advantages and disadvantages of components and approaches, and provide a protocol for hybridization. The fact that we are now making and using microarrays to answer biological questions demonstrates that the technology can be implemented in a university environment}, keywords = {chemistry,COMPONENT,Dna,Glass,instrumentation,Lasers,metabolism,Methods,No DOI found,nosource,Oligonucleotide Array Sequence Analysis,Review,Robotics} } % == BibTeX quality report for cheungMakingReadingMicroarrays1999a: % ? unused Journal abbr (“Nat.Genet.”)

@article{chiAnalysisPhosphorylationSites2007, title = {Analysis of Phosphorylation Sites on Proteins from {{Saccharomyces}} Cerevisiae by Electron Transfer Dissociation ({{ETD}}) Mass Spectrometry}, author = {Chi, A. and Huttenhower, C. and Geer, L.Y. and Coon, J.J. and Syka, J.E. and Bai, D.L. and Shabanowitz, J. and Burke, D.J. and Troyanskaya, O.G. and Hunt, D.F.}, year = 2007, month = feb, journal = {Proceedings of the National Academy of Sciences}, volume = {104}, number = {7}, pages = {2193–2198}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.0607084104}, url = {http://www.pnas.org/content/104/7/2193.short}, abstract = {We present a strategy for the analysis of the yeast phosphoproteome that uses endo-Lys C as the proteolytic enzyme, immobilized metal affinity chromatography for phosphopeptide enrichment, a 90-min nanoflow-HPLC/electrospray-ionization MS/MS experiment for phosphopeptide fractionation and detection, gas phase ion/ion chemistry, electron transfer dissociation for peptide fragmentation, and the Open Mass Spectrometry Search Algorithm for phosphoprotein identification and assignment of phosphorylation sites. From a 30-microg (approximately 600 pmol) sample of total yeast protein, we identify 1,252 phosphorylation sites on 629 proteins. Identified phosphoproteins have expression levels that range from {\(<\)}50 to 1,200,000 copies per cell and are encoded by genes involved in a wide variety of cellular processes. We identify a consensus site that likely represents a motif for one or more uncharacterized kinases and show that yeast kinases, themselves, contain a disproportionately large number of phosphorylation sites. Detection of a pHis containing peptide from the yeast protein, Cdc10, suggests an unexpected role for histidine phosphorylation in septin biology. From diverse functional genomics data, we show that phosphoproteins have a higher number of interactions than an average protein and interact with each other more than with a random protein. They are also likely to be conserved across large evolutionary distances}, keywords = {0,analysis,ASSIGNMENT,Binding Sites,BIOLOGY,CEREVISIAE,chemistry,Chromatography,enzyme,expression,functional genomics,gene,Genes,genomic,Genomics,Histidine,IDENTIFICATION,IDENTIFY,kinase,La,metabolism,Methods,nosource,phosphoprotein,Phosphoproteins,Phosphorylation,Phosphotransferases,protein,Protein Binding,Proteins,Proteomics,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,search,SITE,SITES,Support,Tandem Mass Spectrometry,yeast} } % == BibTeX quality report for chiAnalysisPhosphorylationSites2007: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{chienTwohybridSystemMethod1991a, title = {The Two-Hybrid System: {{A}} Method to Identify and Clone Genes for Proteins That Inteact with a Protein of Interest.}, author = {Chien, C.-T. and Bartel, P.L. and Sternglanz, R. and Fields, S.}, year = 1991, journal = {Proc.Natl.Acad.Sci.USA}, volume = {88}, number = {9578}, pages = {9582}, keywords = {2-hybrid system,gene,Genes,mehtods,No DOI found,nosource,protein,Proteins,SYSTEM,yeast} } % == BibTeX quality report for chienTwohybridSystemMethod1991a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{chiocchettiRibosomalProteinsRpl102007, title = {Ribosomal Proteins {{Rpl10}} and {{Rps6}} Are Potent Regulators of Yeast Replicative Life Span}, author = {Chiocchetti, A. and Zhou, J. and Zhu, H. and Karl, T. and Haubenreisser, O. and Rinnerthaler, M. and Heeren, G. and Oender, K. and Bauer, J. and Hintner, H. and Breitenbach, M. and {Breitenbach-Koller}, L.}, year = 2007, month = apr, journal = {Exp.Gerontol.}, volume = {42}, number = {4}, pages = {275–286}, doi = {10.1016/j.exger.2006.11.002}, url = {PM:17174052}, abstract = {The yeast ribosome is composed of two subunits, the large 60S subunit (LSU) and the small 40S subunit (SSU) and harbors 78 ribosomal proteins (RPs), 59 of which are encoded by duplicate genes. Recently, deletions of the LSU paralogs RPL31A and RPL6B were found to increase significantly yeast replicative life span (RLS). RPs Rpl10 and Rps6 are known translational regulators. Here, we report that heterozygosity for rpl10Delta but not for rpl25Delta, both LSU single copy RP genes, increased RLS by 24%. Deletion of the SSU RPS6B paralog, but not of the RPS6A paralog increased replicative life span robustly by 45%, while deletion of both the SSU RPS18A, and RPS18B paralogs increased RLS moderately, but significantly by 15%. Altering the gene dosage of RPL10 reduced the translating ribosome population, whereas deletion of the RPS6A, RPS6B, RPS18A, and RPS18B paralogs produced a large shift in free ribosomal subunit stoichiometry. We observed a reduction in growth rate in all deletion strains and reduced cell size in the SSU RPS6B, RPS6A, and RPS18B deletion strains. Thus, reduction of gene dosage of RP genes belonging to both the 60S and the 40S subunit affect lifespan, possibly altering the aging process by modulation of translation}, keywords = {0,60S subunit,BIOLOGY,Cell Count,Cell Division,cell size,CEREVISIAE,gene,Gene Deletion,Gene Dosage,Gene Expression RegulationFungal,Genes,GenesFungal,genetics,GROWTH,growth & development,Heterozygote,La,ModelsGenetic,nosource,protein,Protein Biosynthesis,Proteins,Ribosomal Protein S6,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SUBUNIT,SUBUNITS,Support,translation,yeast} } % == BibTeX quality report for chiocchettiRibosomalProteinsRpl102007: % ? Possibly abbreviated journal title Exp.Gerontol.

@article{chiuRadioprotectionCellularChromatin1998, title = {Radioprotection of Cellular Chromatin by the Polyamines Spermine and Putrescine: Preferential Action against Formation of {{DNA-protein}} Crosslinks}, author = {Chiu, S. and Oleinick, N.L.}, year = 1998, month = jun, journal = {Radiation research}, volume = {149}, number = {6}, pages = {543–549}, publisher = {Radiation Research Society}, doi = {10.2307/3579900}, url = {http://www.rrjournal.org/doi/pdf/10.2307/3579900}, abstract = {Spermine is an efficient radioprotector of plasmid or viral DNA and of viral minichromosomes by a mechanism involving radical scavenging and the induction of compaction and aggregation of DNA. Based on radioprotection of SV40 minichromosomes at a lower spermine concentration than needed for SV40 DNA, Newton et al. (Radiat. Res. 145, 776-780, 1996) proposed that the differential concentration dependence could account for the greater radiosensitivity of open regions of cellular chromatin compared to bulk inactive chromatin at physiological levels of spermine. However, we recently reported that, whereas the effects of spermine on the formation of DNA double-strand breaks (DSBs) in dehistonized V79 cell DNA (nucleoids) were consistent with spermine-induced DNA compaction, spermine provided no radioprotection of native chromatin and only modest radioprotection of histone H1-depleted chromatin (Chiu and Oleinick, Radiat. Res. 148, 188-192, 1997). To further characterize the radioprotection of cellular chromatin by spermine, radiation-induced DNA-protein crosslinks (DPCs) were investigated, because of evidence that these lesions occur preferentially at or near the sites of anchorage of chromosomes to the nuclear matrix. In contrast to the relatively inefficient radioprotection of V79 cell chromatin against the formation of DSBs, low concentrations ({\(<\)}0.1 mM) of spermine or putrescine provided partial radioprotection against the formation of DPCs in both native and H1-depleted chromatin. Whereas all DPCs generated by the irradiation of chromatin, above the level generated in intact cells, could be blocked by 5 mM spermine, less than half could be blocked by 5 mM putrescine. The difference in efficiency of radioprotection of native chromatin by the two polyamines can be accounted for by assuming that the binding of spermine is 10 times as efficient as the binding of putrescine. The results suggest that (a) both spermine and putrescine bind preferentially and with high affinity at matrix-associated sites of formation of DPCs, disrupting the associations between DNA and protein that are essential for formation of DPCs and/or scavenging hydroxyl radicals at these sites; (b) a smaller fraction of the sites are susceptible to putrescine than to spermine; and (c) endogenous spermine is a major radioprotector of cells against the formation of DPCs, either because of specific features of the lesion or because of the site of lesion formation at the nuclear matrix}, keywords = {0,Animals,ASSOCIATION,BINDING,CELLS,CellsCultured,Chromatin,Chromosomes,Cricetinae,Dna,efficiency,Hydroxyl Radical,La,MECHANISM,metabolism,nosource,pharmacology,PLASMID,polyamine,Polyamines,protein,Proteins,Putrescine,radiation effects,Radiation-Protective Agents,REGION,S,SITE,SITES,Spermine,Support} } % == BibTeX quality report for chiuRadioprotectionCellularChromatin1998: % ? unused Journal abbr (“Radiat.Res.”)

@article{chiuCharacterizationHumanSmg52003, title = {Characterization of Human {{Smg5}}/7a: {{A}} Protein with Similarities to {{Caenorhabditis}} Elegans {{SMG5}} and {{SMG7}} That Functions in the Dephosphorylation of {{Upf1}}}, author = {Chiu, S.Y. and Serin, G. and Ohara, O. and Maquat, L.E.}, year = 2003, month = jan, journal = {Rna-A Publication of the Rna Society}, volume = {9}, number = {1}, pages = {77–87}, publisher = {Cold Spring Harbor Lab}, doi = {10.1261/rna.2137903}, url = {http://rnajournal.cshlp.org/content/9/1/77.short}, abstract = {Nonsense-mediated mRNA decay (NMD) in mammalian cells depends on phosphorylation of Upf1, an RNA-dependent ATPase and 5’-to-3’ helicase. Upf1 phosphorylation is mediated by Smg1, a phosphoinositol 3-kinase-related protein kinase. Here, we describe a human protein, which we call hSmg5/7a, that manifests similarity to Caenorhabditis elegans NMD factors CeSMG5 and CeSMG7, as well as two Drosophila melanogaster proteins that are also similar to the C elegans NMD factors. Results indicate that hSmg5/7a functions in the dephosphorylation of Upf1. Furthermore, hSmg5/7a copurifies with Upf1, Upf2, Upf3X, Smg1, and the catalytic subunit of protein phosphatase 2A. We also demonstrate that Upf2, another factor involved in NMD, is a phosphoprotein. However, hSmg5/7a plays no role in the dephosphorylation of Upf2. These data indicate that hSmg5/7a targets protein phosphatase 2A to Upf1 but not Upf2. Results of Western blotting reveal that hSmg5/7a is mostly cytoplasmic in HEK293T cells}, keywords = {ATPase,Caenorhabditis,Caenorhabditis elegans,CAENORHABDITIS-ELEGANS,CELLS,COMPLEX,CYTOPLASMIC TRANSLATION,DECAY,Dna,Drosophila,Drosophila melanogaster,DROSOPHILA-MELANOGASTER,E,EXON-EXON JUNCTIONS,gene,Helicase,human,human Smg5/7 protein,INTRON,kinase,MAMMALIAN-CELLS,MESSENGER-RNA SURVEILLANCE,mRNA,mRNA decay,NMD,nonsense-mediated decay,nonsense-mediated mRNA decay,nosource,PHOSPHATASE,PHOSPHATASE 2A,phosphoprotein,Phosphorylation,protein,protein phosphatase 2A,PROTEIN-KINASE,Proteins,SUBUNIT,TARGET,TERMINATION-CODON,Upf1,Upf1 dephosphorylation} }

@article{christiansonMultifunctionalYeastHighcopynumber1992, title = {Multifunctional Yeast High-Copy-Number Shuttle Vectors.}, author = {Christianson, T.W. and Sikorski, R.S. and Dante, M. and Shero, J.H. and Hieter, P.}, year = 1992, month = jan, journal = {Yeast}, volume = {110}, number = {1}, pages = {119–122}, publisher = {Elsevier}, issn = {0378-1119}, url = {http://linkinghub.elsevier.com/retrieve/pii/037811199290454w}, abstract = {A set of four yeast shuttle vectors that incorporate sequences from the Saccharomyces cerevisiae 2 mu endogenous plasmid has been constructed. These yeast episomal plasmid (YEp)-type vectors (pRS420 series) differ only in their yeast selectable markers, HIS3, TRP1, LEU2 or URA3. The pRS420 plasmids are based on the backbone of a multifunctional phagemid, pBluescript II SK+, and share its useful properties for growth in Escherichia coli and manipulation in vitro. The pRS420 plasmids have a copy number of about 20 per cell, equivalent to that of YEp24. During non-selective yeast growth, pRS420 plasmids are lost through mitotic segregation at rates similar to other YEp vectors and yeast centromeric plasmid (YCp) vectors, in the range of 1.5-5% of progeny per doubling. The pRS420 series provides high-copy-number counterparts to the current pRS vectors [Sikorski and Hieter, Genetics 122 (1989) 19-27].}, pmid = {1544568}, keywords = {Cloning,DNA,DNA Replication,Fungal,Fungal: isolation & purification,Gene Amplification,Genetic Vectors,Molecular,No DOI found,nosource,Plasmids,Replicon,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,vector,vectors,yeast} }

@article{chuTranscriptionalProgramSporulation1998a, title = {The Transcriptional Program of Sporulation in Budding Yeast [Published Erratum Appears in {{Science}} 1998 {{Nov}} 20; 282 (5393): 1421]}, author = {Chu, S. and DeRisi, J. and Eisen, M. and Mulholland, J. and Botstein, D. and Brown, P.O. and Herskowitz, I.}, year = 1998, month = oct, journal = {Science}, volume = {282}, number = {5389}, pages = {699–705}, doi = {10.1126/science.282.5389.699}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:The+transcriptional+program+of+sporulation+in+budding+yeast+[published+erratum+appears+in+Science+1998+Nov+20;282(5393):1421]#0}, abstract = {Diploid cells of budding yeast produce haploid cells through the developmental program of sporulation, which consists of meiosis and spore morphogenesis. DNA microarrays containing nearly every yeast gene were used to assay changes in gene expression during sporulation. At least seven distinct temporal patterns of induction were observed. The transcription factor Ndt80 appeared to be important for induction of a large group of genes at the end of meiotic prophase. Consensus sequences known or proposed to be responsible for temporal regulation could be identified solely from analysis of sequences of coordinately expressed genes. The temporal expression pattern provided clues to potential functions of hundreds of previously uncharacterized genes, some of which have vertebrate homologs that may function during gametogenesis}, keywords = {99000795,analysis,animal,ChromosomesFungal,Dna,expression,Fungal Proteins,gene,Gene Expression,Gene Expression RegulationFungal,GENE-EXPRESSION,Genes,GenesFungal,genetics,GenomeFungal,homolog,human,Meiosis,metabolism,morphogenesis,nosource,Organelles,physiology,regulation,Saccharomyces cerevisiae,sequence,SporesFungal,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,transcription,Transcription Factors,TranscriptionGenetic,ultrastructure,yeast} }

@article{ciganYeastTranslationInitiation1989a, title = {Yeast Translation Initiation Suppressor ⬚sui2 ⬚encodes the `a Subunit of Eukaryotic Initiation Factor 2 and Shares Sequence Identity with the Human `a Subunit.}, author = {Cigan, A.M. and Pabich, E.K. and Feng, L. and Donahue, T.F.}, year = 1989, journal = {Proc.Natl.Acad.Sci.USA}, volume = {86}, pages = {2784–2788}, doi = {10.1073/pnas.86.8.2784}, keywords = {cloning,human,initiation,nosource,sequence,SUBUNIT,sui,SUI2,translation,TRANSLATION INITIATION,yeast} } % == BibTeX quality report for ciganYeastTranslationInitiation1989a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{clareNucleotideSequenceYeast1985, title = {Nucleotide Sequence of a Yeast {{Ty}} Element: Evidence for an Unusual Mechanism of Gene Expression}, author = {Clare, J. and Farabaugh, P.}, year = 1985, month = may, journal = {Proceedings of the National Academy of Sciences}, volume = {82}, number = {9}, pages = {2829–2833}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.82.9.2829}, url = {http://www.pnas.org/content/82/9/2829.short}, abstract = {We have determined the DNA sequence of the transposable element Ty912 of yeast. The 5918-base-pair element encodes two genes, tya912 and tyb912, which specify proteins similar to sequence-specific DNA-binding proteins of Escherichia coli and retroviral reverse transcriptases, respectively. The tyb912 gene is atypical of eukaryotic genes since (i) it begins 1336 nucleotides into the Ty912 mRNA (i.e., downstream of the tya912 gene) and (ii) the first in-frame AUG is 921 nucleotides into the coding frame. Protein blot analysis of Ty-lacZ fusions shows that the tyb912 gene is translated starting at the 5’ end of the tya912 gene and that the primary translational product is a tya912::tyb912 fusion protein. We have shown that synthesis of this fusion protein probably does not occur by RNA splicing. The data are consistent with a mechanism of translational frameshifting occurring within the region of overlap between the 3’ end of tya912 and the 5’ end of tyb912}, keywords = {0,3,Amino Acid Sequence,analysis,AUG,Base Sequence,Dna,DNA sequence,DNA Transposable Elements,DNA-BINDING,DNA-Binding Proteins,DNAFungal,DOWNSTREAM,ELEMENTS,ENCODES,Escherichia coli,ESCHERICHIA-COLI,EUKARYOTIC GENES,expression,FRAME,Frameshifting,Fungal Proteins,FUSION PROTEIN,gene,Gene Expression,Gene Expression Regulation,GENE-EXPRESSION,Genes,GenesFungal,genetics,La,MECHANISM,mRNA,nosource,NUCLEOTIDE-SEQUENCE,Nucleotides,polymerase,PRODUCT,protein,Protein Biosynthesis,Proteins,REGION,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,Retroviridae,REVERSE-TRANSCRIPTASE,Rna,RNA Splicing,RNA-Directed DNA Polymerase,Saccharomyces cerevisiae,sequence,Species Specificity,splicing,TRANSLATIONAL FRAMESHIFTING,Ty,yeast} } % == BibTeX quality report for clareNucleotideSequenceYeast1985: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{clarkeProteinIsoprenylationMethylation1992, title = {Protein Isoprenylation and Methylation at Carboxy-Terminal Cysteine Residues.}, author = {Clarke, S.}, year = 1992, journal = {Annu.Rev.Biochem.}, volume = {61}, pages = {355–386}, doi = {10.1146/annurev.bi.61.070192.002035}, keywords = {modification,nosource,protein,ras,Review,yeast} } % == BibTeX quality report for clarkeProteinIsoprenylationMethylation1992: % ? Possibly abbreviated journal title Annu.Rev.Biochem.

@article{cleggFluorescenceResonanceEnergy1992a, title = {Fluorescence Resonance Energy Transfer and Nucleic Acids}, author = {Clegg, R.M.}, year = 1992, journal = {Methods in enzymology}, volume = {211}, pages = {353–388}, doi = {10.1016/0076-6879(92)11020-J}, url = {http://cat.inist.fr/?aModele=afficheN&cpsidt=4480808}, keywords = {0,ACID,ACIDS,BIOLOGY,chemistry,Energy Transfer,Fluorescence,Fluorescence Resonance Energy Transfer,Germany,La,Molecular Biology,nosource,Nucleic Acids,Review,SpectrometryFluorescence} } % == BibTeX quality report for cleggFluorescenceResonanceEnergy1992a: % ? unused Journal abbr (“Methods Enzymol.”)

@article{clemonsStructureBacterial30S1999a, title = {Structure of a Bacterial {{30S}} Ribosomal Subunit at 5.5 {{A}} Resolution.}, author = {Clemons, W.M. and May, J.L. and Wimberly, B.T. and McCutcheon, J.P. and Capel, M.S. and Ramakrishnan, V.}, year = 1999, journal = {Nature}, volume = {400}, number = {6747}, pages = {833–840}, doi = {10.1038/23631}, abstract = {The 30S ribosomal subunit binds messenger RNA and the anticodon stem- loop of transfer RNA during protein synthesis. A crystallographic analysis of the structure of the subunit from the bacterium Thermus thermophilus is presented. At a resolution of 5.5 A, the phosphate backbone of the ribosomal RNA is visible, as are the alpha-helices of the ribosomal proteins, enabling double-helical regions of RNA to be identified throughout the subunit, all seven of the small-subunit proteins of known crystal structure to be positioned in the electron density map, and the fold of the entire central domain of the small- subunit ribosomal RNA to be determined}, keywords = {99404610,analysis,Anticodon,Bacteria,Bacterial,Bacterial Proteins,chemistry,CrystallographyX-Ray,MESSENGER-RNA,ModelsMolecular,nosource,Nucleic Acid Conformation,protein,Protein Conformation,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Ribosomal Proteins,Ribosomes,Rna,RNABacterial,RNARibosomal,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Thermus,Thermus thermophilus,ultrastructure} }

@article{clevelandMultipleElementsMRNA1989a, title = {Multiple Elements of {{mRNA}} Stability}, author = {Cleveland, D.W. and Yen, T.J.}, year = 1989, journal = {The New Biol.}, volume = {1}, pages = {121–126}, keywords = {ELEMENTS,mRNA,No DOI found,nosource,stability,turnover} } % == BibTeX quality report for clevelandMultipleElementsMRNA1989a: % ? Possibly abbreviated journal title The New Biol.

@article{cloteStructuralRNAHas2005, title = {Structural {{RNA}} Has Lower Folding Energy than Random {{RNA}} of the Same Dinucleotide Frequency}, author = {Clote, P. and Ferre, F. and Kranakis, E. and Krizanc, D.}, year = 2005, month = may, journal = {RNA}, volume = {11}, number = {5}, pages = {578–591}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, doi = {10.1261/rna.7220505}, url = {http://rnajournal.cshlp.org/content/11/5/578.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1370746&tool=pmcentrez&rendertype=abstract}, abstract = {We present results of computer experiments that indicate that several RNAs for which the native state (minimum free energy secondary structure) is functionally important (type III hammerhead ribozymes, signal recognition particle RNAs, U2 small nucleolar spliceosomal RNAs, certain riboswitches, etc.) all have lower folding energy than random RNAs of the same length and dinucleotide frequency. Additionally, we find that whole mRNA as well as 5’-UTR, 3’-UTR, and cds regions of mRNA have folding energies comparable to that of random RNA, although there may be a statistically insignificant trace signal in 3’-UTR and cds regions. Various authors have used nucleotide (approximate) pattern matching and the computation of minimum free energy as filters to detect potential RNAs in ESTs and genomes. We introduce a new concept of the asymptotic Z-score and describe a fast, whole-genome scanning algorithm to compute asymptotic minimum free energy Z-scores of moving-window contents. Asymptotic Z-score computations offer another filter, to be used along with nucleotide pattern matching and minimum free energy computations, to detect potential functional RNAs in ESTs and genomic regions.}, pmid = {15840812}, keywords = {0,3,3’ Untranslated Regions,3’ Untranslated Regions: chemistry,3’ Untranslated Regions: genetics,3’ Untranslated Regions: metabolism,3’ UTR,3’-UTR,5’ Untranslated Regions,5’ Untranslated Regions: chemistry,5’ Untranslated Regions: genetics,5’ Untranslated Regions: metabolism,5’-UTR,Algorithms,analysis,asymptotic z-score,Base Composition,Base Sequence,BIOLOGY,chemistry,Computational Biology,computer,Computer Simulation,EST,Expressed Sequence Tags,folding energy,genetics,Genome,genomic,HAMMERHEAD RIBOZYME,La,Markov Chains,metabolism,mRNA,nosource,Nucleic Acid Conformation,Nucleotides,Nucleotides: analysis,Nucleotides: chemistry,Nucleotides: genetics,Nucleotides: metabolism,RECOGNITION,REGION,Research SupportNon-U.S.Gov’t,riboswitch,ribozyme,Rna,RNA,rna secondary structure,RNA: chemistry,RNA: genetics,RNA: metabolism,scanning,SECONDARY STRUCTURE,SIGNAL,SIGNAL RECOGNITION PARTICLE,Structural,structural rna,structure,Thermodynamics,trna,Untranslated Regions} }

@article{cobucci-ponzanoIdentificationArchaealAlphaLfucosidase2003a, title = {Identification of an Archaeal Alpha-{{L-fucosidase}} Encoded by an Interrupted Gene. {{Production}} of a Functional Enzyme by Mutations Mimicking Programmed -1 Frameshifting}, author = {{Cobucci-Ponzano}, B. and Trincone, A. and Giordano, A. and Rossi, M. and Moracci, M.}, year = 2003, month = apr, journal = {The Journal of biological chemistry}, volume = {278}, number = {17}, pages = {14622–14631}, doi = {10.1074/jbc.M211834200}, url = {PM:12569098}, abstract = {The analysis of the complete genome of the thermoacidophilic Archaeon Sulfolobus solfataricus revealed two open reading frames (ORF), named SSO11867 and SSO3060, interrupted by a -1 frameshift and encoding for the N- and the C-terminal fragments, respectively, of an alpha-l-fucosidase. We report here that these ORFs are actively transcribed in vivo, and we confirm the presence of the -1 frameshift between them at the cDNA level, explaining why we could not find alpha-fucosidase activity in S. solfataricus extracts. Detailed analysis of the region of overlap between the two ORFs revealed the presence of the consensus sequence for a programmed -1 frameshifting. Two specific mutations, mimicking this regulative frameshifting event, allow the expression, in Escherichia coli, of a fully active thermophilic and thermostable alpha-l-fucosidase (EC ) with micromolar substrate specificity and showing transfucosylating activity. The analysis of the fucosylated products of this enzyme allows, for the first time, assigning a retaining reaction mechanism to family 29 of glycosyl hydrolases. The presence of an alpha-fucosidase putatively regulated by programmed -1 frameshifting is intriguing both with respect to the regulation of gene expression and, in post-genomic era, for the definition of gene function in Archaea}, keywords = {0,alpha-L-Fucosidase,analysis,Archaea,Base Sequence,Consensus Sequence,Dna,DNAComplementary,enzyme,Enzyme Stability,enzymology,Escherichia coli,ESCHERICHIA-COLI,expression,EXTRACTS,FAMILY,FRAME,frameshift,Frameshift Mutation,Frameshifting,gene,Gene Expression,GENE-EXPRESSION,genetics,Genome,GenomeBacterial,IDENTIFICATION,IN-VIVO,Kinetics,La,MECHANISM,metabolism,Molecular Sequence Data,Mutation,MUTATIONS,nosource,OPEN READING FRAME,Open Reading Frames,PRODUCT,PRODUCTS,protein,READING FRAME,Reading Frames,REGION,regulation,Research SupportNon-U.S.Gov’t,S,sequence,Sequence Alignment,SPECIFICITY,Substrate Specificity,SUBSTRATE-SPECIFICITY,Sulfolobus,TranscriptionGenetic} } % == BibTeX quality report for cobucci-ponzanoIdentificationArchaealAlphaLfucosidase2003a: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{cobucci-ponzanoRecodingArchaea2005, title = {Recoding in Archaea}, author = {{Cobucci-Ponzano}, B. and Rossi, M. and Moracci, M.}, year = 2005, month = jan, journal = {Molecular Microbiology}, volume = {55}, number = {2}, pages = {339–348}, publisher = {Wiley Online Library}, issn = {0950-382X}, doi = {10.1111/j.1365-2958.2004.04400.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2004.04400.x/full}, abstract = {Standard decoding of the genetic information into polypeptides is performed by one of the most sophisticated cell machineries, the translating ribosome, which, by following the genetic code, ensures the correspondence between the mature mRNA and the protein sequence. However, the expression of a minority of genes requires programmed deviations from the standard decoding rules, globally named recoding. This includes ribosome programmed -/+1 frameshifting, ribosome hopping, and stop codon readthrough. Recoding in Archaea was unequivocally demonstrated only for the translation of the UGA stop codon into the amino acid selenocysteine. However, a new recoding event leading to the 22nd amino acid pyrrolysine and the preliminary reports on a gene regulated by programmed -1 frameshifting have been recently described in Archaea. Therefore, it appears that the study of this phenomenon in Archaea is still at its dawn and that most of the genes whose expression is regulated by recoding are still uncharacterized.}, keywords = {0,ACID,AMINO-ACID,analogs & derivatives,Archaea,chemistry,Codon,Codon Terminator,CodonTerminator,decoding,expression,Frameshifting,Frameshifting Ribosomal,FrameshiftingRibosomal,gene,Genes,Genetic,Genetic Code,GENETIC-CODE,genetics,hopping,INFORMATION,La,Lysine,metabolism,mRNA,nosource,POLYPEPTIDE,POLYPEPTIDES,protein,Protein Biosynthesis,readthrough,recoding,REQUIRES,Research SupportNon-U.S.Gov’t,Review,ribosome,RULES,Selenocysteine,sequence,STOP CODON,translation} } % == BibTeX quality report for cobucci-ponzanoRecodingArchaea2005: % ? unused Journal abbr (“Mol.Microbiol.”) % ? unused Library catalog (“NCBI PubMed”)

@article{cochellaFidelityProteinSynthesis2005a, title = {Fidelity in Protein Synthesis.}, author = {Cochella, L. and Green, R.}, year = 2005, month = jul, journal = {Current biology: CB}, volume = {15}, number = {14}, pages = {R536-R540}, doi = {10.1016/j.cub.2005.07.018}, url = {http://ukpmc.ac.uk/abstract/MED/16051156}, keywords = {0,ACID,ACIDS,Amino Acids,Amino Acyl-tRNA Synthetases,AMINO-ACID,AMINO-ACIDS,BIOLOGY,chemistry,Codon,Dna,DNA-Directed DNA Polymerase,EvolutionMolecular,Fidelity,Genetic,genetics,Kinetics,La,metabolism,ModelsGenetic,Molecular Biology,nosource,Nucleotides,polymerase,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,Review,RNA Editing} } % == BibTeX quality report for cochellaFidelityProteinSynthesis2005a: % ? unused Journal abbr (“Curr.Biol”)

@article{cochellaMutationalAnalysisReveals2007, title = {Mutational Analysis Reveals Two Independent Molecular Requirements during Transfer {{RNA}} Selection on the Ribosome}, author = {Cochella, L. and Brunelle, J.L. and Green, R.}, year = 2007, month = jan, journal = {Nat.Struct.Mol.Biol}, volume = {14}, number = {1}, pages = {30–36}, publisher = {Nature Publishing Group}, doi = {10.1038/nsmb1183}, url = {PM:17159993 http://www.nature.com/nsmb/journal/v14/n1/abs/nsmb1183.html http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb1183.html}, abstract = {Accurate discrimination between cognate and near-cognate aminoacyl-tRNAs during translation relies on the specific acceleration of forward rate constants for cognate tRNAs. Such specific rate enhancement correlates with conformational changes in the tRNA and small ribosomal subunit that depend on an RNA-specific type of interaction, the A-minor motif, between universally conserved 16S ribosomal RNA nucleotides and the cognate codon-anticodon helix. We show that perturbations of these two components of the A-minor motif, the conserved rRNA bases and the codon-anticodon helix, result in distinct outcomes. Although both cause decreases in the rates of tRNA selection that are rescued by aminoglycoside antibiotics, only disruption of the codon-anticodon helix is overcome by a miscoding tRNA variant. On this basis, we propose that two independent molecular requirements must be met to allow tRNAs to proceed through the selection pathway, providing a mechanism for exquisite control of fidelity during this step in gene expression}, keywords = {0,16S,AMINOGLYCOSIDE ANTIBIOTICS,Aminoglycosides,analysis,antibiotic,antibiotics,Anticodon,Bacterial,BASE,BASES,BIOLOGY,chemistry,Codon,COMPONENT,COMPONENTS,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,CONSTANTS,DISRUPTION,Escherichia coli,expression,Fidelity,gene,Gene Expression,GENE-EXPRESSION,Genetic,genetics,La,MECHANISM,metabolism,Molecular Biology,Mutagenesis,MUTATIONAL ANALYSIS,nosource,Nucleic Acid Conformation,Nucleotides,PATHWAY,ribosomal RNA,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNA-Bacterial,RNA-Ribosomal-16S,RNA-Transfer,RNA-Transfer-Amino Acyl,RNABacterial,RNARibosomal16S,RNATransfer,RNATransferAmino Acyl,rRNA,SELECTION,SUBUNIT,Support,TRANSFER-RNA,translation,tRNA} } % == BibTeX quality report for cochellaMutationalAnalysisReveals2007: % ? Possibly abbreviated journal title Nat.Struct.Mol.Biol

@article{coelhoNovelMitochondrialProtein2002a, title = {A Novel Mitochondrial Protein, {{Tar1p}}, Is Encoded on the Antisense Strand of the Nuclear {{25S rDNA}}}, author = {Coelho, P.S. and Bryan, A.C. and Kumar, A. and Shadel, G.S. and Snyder, M.}, year = 2002, month = nov, journal = {Genes Dev.}, volume = {16}, number = {21}, pages = {2755–2760}, doi = {10.1101/gad.1035002}, abstract = {In eukaryotes, it is widely assumed that genes coding for proteins and structural RNAs do not overlap. Using a transposon-tagging strategy to globally analyze the Saccharomyces cerevisiae genome for expressed genes, we identified multiple insertions in an open reading frame that is contained fully within and transcribed antisense to the 25S rRNA gene in the nuclear rDNA repeat region on Chromosome XII. Expression of this gene, TAR1 (Transcript Antisense to Ribosomal RNA), can be detected at the RNA and protein levels, and the primary sequence of the corresponding 124-amino-acid protein is conserved in several yeast species. Tar1p was found to localize to mitochondria, and overexpression of the protein suppresses the respiration-deficient petite phenotype of a point mutation in mitochondrial RNA polymerase that affects mitochondrial gene expression and mtDNA stability. These findings indicate that coding information for protein and structural RNAs can overlap, raising issues regarding the coevolution of such complex genes, and also suggest that rDNA transcription and mitochondrial function are coordinately regulated in eukaryotic cells}, keywords = {Amino Acid Sequence,antisense,COMPLEX,COMPLEXES,DNARibosomal,Eukaryotic Cells,expression,gene,Gene Expression,GENE-EXPRESSION,Genes,genetics,Genome,GenomeFungal,mitochondria,Mitochondrial Proteins,Molecular Sequence Data,Mutation,nosource,Phenotype,Point Mutation,polymerase,protein,Proteins,rDNA,RDNA TRANSCRIPTION,RIBOSOMAL-RNA,Rna,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,Sequence Alignment,stability,Structural,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,transcription,yeast} } % == BibTeX quality report for coelhoNovelMitochondrialProtein2002a: % ? Possibly abbreviated journal title Genes Dev.

@article{coffinHIVPopulationDynamics1995a, title = {{{HIV}} Population Dynamics in Vivo: Implications for Genetic Variation, Pathogenesis, and Therapy [See Comments]}, author = {Coffin, J.M.}, year = 1995, month = jan, journal = {Science}, volume = {267}, number = {5197}, pages = {483–489}, doi = {10.1126/science.7824947}, keywords = {antiviral,development,drugs,Genetic,HIV,human,IN-VIVO,Mutation,MUTATIONS,nosource,turnover,virus} }

@article{cohlbergReconstitutionBacillusStearothermophilus1976a, title = {Reconstitution of {{Bacillus}} Stearothermophilus 50 {{S}} Ribosomal Subunits from Purified Molecular Components}, author = {Cohlberg, J.A. and Nomura, M.}, year = 1976, month = jan, journal = {Journal of Biological Chemistry}, volume = {251}, number = {1}, pages = {209–221}, doi = {10.1016/S0021-9258(17)33947-9}, url = {http://www.jbc.org/cgi/content/abstract/251/1/209}, keywords = {Bacillus stearothermophilus,BACILLUS-STEAROTHERMOPHILUS,COMPONENT,COMPONENTS,nonfile,nosource,RECONSTITUTION,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,S,SUBUNIT,SUBUNITS} }

@article{cohnSpermidineSpermineRequirement1978, title = {Spermidine or Spermine Requirement for Killer Double-Stranded {{RNA}} Plasmid Replication in Yeast.}, author = {Cohn, M.S. and Tabor, C.W. and Tabor, H. and Wickner, R.B.}, year = 1978, journal = {Journal of Biological Chemistry}, volume = {253}, number = {15}, pages = {5225–5227}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(17)30351-4}, url = {http://www.jbc.org/content/253/15/5225.short}, keywords = {DOUBLE-STRANDED-RNA,killer,M,nosource,PLASMID,REPLICATION,S,Spermidine,yeast} }

@article{coleConvergenceRRNAMRNA2009, title = {A Convergence of {{rRNA}} and {{mRNA}} Quality Control Pathways Revealed by Mechanistic Analysis of Nonfunctional {{rRNA}} Decay}, author = {Cole, S.E. and LaRiviere, F.J. and Merrikh, C.N. and Moore, M.J.}, year = 2009, month = may, journal = {Mol.Cell}, volume = {34}, number = {4}, pages = {440–450}, doi = {10.1016/j.molcel.2009.04.017}, url = {PM:19481524}, abstract = {Eukaryotes possess numerous quality control systems that monitor both the synthesis of RNA and the integrity of the finished products. We previously demonstrated that Saccharomyces cerevisiae possesses a quality control mechanism, nonfunctional rRNA decay (NRD), capable of detecting and eliminating translationally defective rRNAs. Here we show that NRD can be divided into two mechanistically distinct pathways: one that eliminates rRNAs with deleterious mutations in the decoding site (18S NRD) and one that eliminates rRNAs containing deleterious mutations in the peptidyl transferase center (25S NRD). 18S NRD is dependent on translation elongation and utilizes the same proteins as those participating in no-go mRNA decay (NGD). In cells that accumulate 18S NRD and NGD decay intermediates, both RNA types can be seen in P-bodies. We propose that 18S NRD and NGD are different observable outcomes of the same initiating event: a ribosome stalled inappropriately at a sense codon during translation elongation}, keywords = {0,adaptor,Adaptor ProteinsSignal Transducing,analysis,Animals,Biochemistry,Biological Markers,Cell Nucleus,CELLS,CEREVISIAE,Codon,DECAY,decoding,elongation,elongation factors,ELONGATION-FACTORS,Exoribonucleases,genetics,GTP-Binding Proteins,heat shock proteins,HEAT-SHOCK,HEAT-SHOCK PROTEIN,HEAT-SHOCK PROTEINS,HSP70 Heat-Shock Proteins,Humans,In Situ HybridizationFluorescence,INTERMEDIATE,La,MARKER,MECHANISM,metabolism,mRNA,mRNA decay,Mutation,MUTATIONS,nosource,PATHWAY,Peptide Elongation Factors,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,PRODUCT,PRODUCTS,protein,Proteins,Quality Control,QUALITY-CONTROL,ribosome,Rna,RNA Stability,RNAMessenger,RNARibosomal,RNARibosomal18S,rRNA,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SIGNAL,SITE,Support,SYSTEM,SYSTEMS,TRANSFERASE CENTER,translation} } % == BibTeX quality report for coleConvergenceRRNAMRNA2009: % ? Possibly abbreviated journal title Mol.Cell

@article{colganMechanismRegulationMRNA1997a, title = {Mechanism and Regulation of {{mRNA}} Polyadenylation. [{{Review}}] [106 Refs]}, author = {Colgan, D.F. and Manley, J.L.}, year = 1997, month = nov, journal = {Genes & Development}, volume = {11}, number = {21}, pages = {2755–2766}, doi = {10.1101/gad.11.21.2755}, keywords = {MECHANISM,mRNA,nosource,regulation} }

@article{conrad-webbPolymeraseSwitchSynthesis1995a, title = {A Polymerase Switch in the Synthesis of {{rRNA}} in {{Saccharomyces}} Cerevisiae}, author = {{Conrad-Webb}, H. and Butow, R.A.}, year = 1995, month = may, journal = {Mol.Cell Biol}, volume = {15}, number = {5}, pages = {2420–2428}, doi = {10.1128/MCB.15.5.2420}, url = {PM:7739526}, abstract = {Transcription of ribosomal DNA by RNA polymerase I is believed to be the sole source of the 25S, 18S, and 5.8S rRNAs in wild-type cells of Saccharomyces cerevisiae. Here we present evidence for a switch from RNA polymerase I to RNA polymerase II in the synthesis of a substantial fraction of those rRNAs in respiratory-deficient (petite) cells. The templates for the RNA polymerase II transcripts are largely, if not exclusively, episomal copies of ribosomal DNA arising from homologous recombination events within the ribosomal DNA repeat on chromosome XII. Ribosomal DNA contains a cryptic RNA polymerase II promoter that is activated in petites; it overlaps the RNA polymerase I promoter and produces a transcript equivalent to the 35S precursor rRNA made by RNA polymerase I. Yeast cells that lack RNA polymerase I activity, because of a disruption of the RPA135 gene that encodes subunit II of the enzyme, can survive by using the RNA polymerase II promoter in ribosomal DNA to direct the synthesis of the 35S rRNA precursor. This polymerase switch could provide cells with a mechanism to synthesize rRNA independent of the controls of RNA polymerase I transcription}, keywords = {0,Base Sequence,beta-Galactosidase,Biochemistry,biosynthesis,CELLS,CEREVISIAE,CloningMolecular,DISRUPTION,Dna,DNA Primers,DNA-Directed RNA Polymerase,DNA-Directed RNA Polymerases,DNAFungal,DNARibosomal,ENCODES,enzyme,gene,GenesFungal,genetics,HOMOLOGOUS RECOMBINATION,La,Lac Operon,MECHANISM,metabolism,Molecular Sequence Data,nosource,polymerase,PRECURSOR,PROMOTER,Promoter Regions (Genetics),RECOMBINATION,Repetitive SequencesNucleic Acid,Rna,RNA Polymerase I,RNA Polymerase II,RNA-POLYMERASE,RNA-POLYMERASE-I,RNA-POLYMERASE-II,RNAFungal,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUBUNIT,SUBUNIT-II,Support,Tata Box,TEMPLATE,Templates,TRANSCRIPT,transcription,WILD-TYPE,yeast,YEAST-CELLS} } % == BibTeX quality report for conrad-webbPolymeraseSwitchSynthesis1995a: % ? Possibly abbreviated journal title Mol.Cell Biol

@article{cormackFACSoptimizedMutantsGreen1996, title = {{{FACS-optimized}} Mutants of the Green Fluorescent Protein ({{GFP}})}, author = {Cormack, B.P. and Valdivia, R.H. and Falkow, S.}, year = 1996, journal = {Gene}, volume = {173}, number = {1 Spec No}, pages = {33–38}, publisher = {Elsevier}, doi = {10.1016/0378-1119(95)00685-0}, url = {http://linkinghub.elsevier.com/retrieve/pii/0378111995006850}, keywords = {analysis,Escherichia coli,ESCHERICHIA-COLI,gene,Genes,gfp,nosource,protein,Proteins,sequence} }

@article{cornishSpontaneousIntersubunitRotation2008, title = {Spontaneous Intersubunit Rotation in Single Ribosomes}, author = {Cornish, P.V. and Ermolenko, D.N. and Noller, H.F. and Ha, T.}, year = 2008, month = jun, journal = {Mol. Cell}, volume = {30}, number = {5}, pages = {578–588}, publisher = {Elsevier}, doi = {10.1016/j.molcel.2008.05.004}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276508003341 http://www.sciencedirect.com/science/article/pii/S1097276508003341}, abstract = {During the elongation cycle, tRNA and mRNA undergo coupled translocation through the ribosome catalyzed by elongation factor G (EF-G). Cryo-EM reconstructions of certain EF-G-containing complexes led to the proposal that the mechanism of translocation involves rotational movement between the two ribosomal subunits. Here, using single-molecule FRET, we observe that pretranslocation ribosomes undergo spontaneous intersubunit rotational movement in the absence of EF-G, fluctuating between two conformations corresponding to the classical and hybrid states of the translocational cycle. In contrast, posttranslocation ribosomes are fixed predominantly in the classical, nonrotated state. Movement of the acceptor stem of deacylated tRNA into the 50S E site and EF-G binding to the ribosome both contribute to stabilization of the rotated, hybrid state. Furthermore, the acylation state of P site tRNA has a dramatic effect on the frequency of intersubunit rotation. Our results provide direct evidence that the intersubunit rotation that underlies ribosomal translocation is thermally driven}, keywords = {0,Acylation,Bacterial,BINDING,chemistry,COMPLEX,COMPLEXES,CONFORMATION,E,E site,EF-G,elongation,ELONGATION CYCLE,ELONGATION-FACTOR-G,enzymology,Escherichia coli,Fluorescence Resonance Energy Transfer,genetics,Kinetics,La,MECHANISM,metabolism,Movement,mRNA,nosource,P SITE,P-SITE,Peptide Elongation Factor G,protein,Protein Binding,Protein Biosynthesis,Protein Subunits,Protein Transport,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNABacterial,RNAMessenger,RNATransfer,Rotation,SITE,SUBUNIT,SUBUNITS,Support,Transfer RNA Aminoacylation,translocation,tRNA} } % == BibTeX quality report for cornishSpontaneousIntersubunitRotation2008: % ? Possibly abbreviated journal title Mol. Cell

@article{correllCrystalStructureRibosomal1998, title = {Crystal Structure of the Ribosomal {{RNA}} Domain Essential for Binding Elongation Factors}, author = {Correll, C.C. and Munishkin, A. and Chan, Y.L. and Ren, Z. and Wool, I.G. and Steitz, T.A.}, year = 1998, month = nov, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {23}, pages = {13436–13441}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.95.23.13436}, url = {http://www.pnas.org/content/95/23/13436.short}, abstract = {The structure of a 29-nucleotide RNA containing the sarcin/ricin loop (SRL) of rat 28 S rRNA has been determined at 2.1 Angstrom resolution. Recognition of the SRL by elongation factors and by the ribotoxins, sarcin and ricin, requires a nearly universal dodecamer sequence that folds into a G-bulged cross-strand A stack and a GAGA tetraloop, The juxtaposition of these two motifs forms a distorted hairpin structure that allows direct recognition of bases in both grooves as well as recognition of nonhelical backbone geometry and two 5’-unstacked purines. Comparisons with other RNA crystal structures establish the cross-strand A stack and the GNRA tetraloop as defined and modular RNA structural elements. The conserved region at the top is connected to the base of the domain by a region presumed to be flexible because of the sparsity of stabilizing contacts. Although the conformation of the SRL RNA previously determined by NMR spectroscopy is similar to the structure determined by x-ray. crystallography, significant differences are observed in the “flexible” region and to a lesser extent in the G-bulged cross-strand A stack}, keywords = {3-DIMENSIONAL STRUCTURE,A-CHAIN,ALPHA-SARCIN,ANGSTROM RESOLUTION,BINDING,CONFORMATION,CRYSTAL-STRUCTURE,Crystallography,EF-G,ELEMENTS,elongation,EUKARYOTIC RIBOSOMES,HAMMERHEAD RIBOZYME,MECHANISM,nosource,PHENYLALANINE TRANSFER-RNA,Purines,rat,RECOGNITION,RIBOSOMAL-RNA,Ricin,Rna,rRNA,SARCIN RICIN LOOP,sequence,Structural,structure} }

@article{correllTwoFacesEscherichia1999a, title = {The Two Faces of the {{Escherichia}} Coli 23 {{S rRNA}} Sarcin/Ricin Domain: {{The}} Structure at 1.11 Angstrom Resolution}, author = {Correll, C.C. and Wool, I.G. and Munishkin, A.}, year = 1999, journal = {Journal of Molecular Biology}, volume = {292}, number = {2}, pages = {275–287}, doi = {10.1006/jmbi.1999.3072}, url = {ISI:000082597400008}, abstract = {The sarcin/ricin domain of 23 S - 28 S ribosomal RNA is essential for protein synthesis because it forms a critical part of the binding site for elongation factors. A crystal structure of an RNA of 27 nucleotides that mimics the domain in Escherichia coli 23 S rRNA was determined at 1.11 Angstrom resolution. The domain folds into a hairpin distorted by four noncanonical base-pairs and one base triple. The fold is stabilized by cross-strand and intra-stand stacking; no intramolecular stabilizing metal ions are observed. This is the first structure to reveal in great detail the geometry and the hydration of two common motifs that are conserved in this rRNA domain, a GAGA tetraloop and a G-bulged cross-strand A stack. Differences in the region connecting these motifs to the stem in the E. coli and in the rat sarcin/ricin domains may contribute to the species-specific binding of elongation factors. Correlation of nucleotide protection data with the structure indicates that the domain has two surfaces. One surface is accessible, lies primarily in the major groove, and is likely to bind the elongation factors. The second lies primarily in the minor groove, and is likely to be buried in the ribosome. This minor groove surface includes the Watson-Crick faces of the cytosine bases in the unusual A2654 C2666 and U2653.C2667 water-mediated base-pairs. (C) 1999 Academic Press}, keywords = {28S RIBOSOMAL-RNA,ALPHA-SARCIN,ANGSTROM RESOLUTION,BINDING,crystal structure,CRYSTAL-STRUCTURE,Cytosine,EF-G,elongation,elongation factors,ELONGATION-FACTORS,Escherichia coli,ESCHERICHIA-COLI,EUKARYOTIC RIBOSOMES,HAMMERHEAD RIBOZYME,Ions,LOOP,nosource,Nucleotides,protein,protein synthesis,PROTEIN-SYNTHESIS,rat,REGION,RIBONUCLEIC-ACID,RIBOSOMAL-RNA,ribosome,Ribosomes,RICIN A-CHAIN,Rna,RNA recognition,rRNA,sarcin/ricin domain,SITE,structure} }

@article{costantinoTRNAMRNAMimicry2008a, title = {{{tRNA}} – {{mRNA}} Mimicry Drives Translation Initiation from a Viral {{IRES}}}, author = {Costantino, D.A. and Pfingsten, J.S. and Rambo, R.P. and Kieft, J.S.}, year = 2008, month = jan, journal = {Nat.Struct.Mol Biol}, volume = {15}, number = {1}, pages = {57–64}, doi = {10.1038/nsmb1351}, url = {PM:18157151}, abstract = {Internal ribosome entry site (IRES) RNAs initiate protein synthesis in eukaryotic cells by a noncanonical cap-independent mechanism. IRESes are critical for many pathogenic viruses, but efforts to understand their function are complicated by the diversity of IRES sequences as well as by limited high-resolution structural information. The intergenic region (IGR) IRESes of the Dicistroviridae viruses are powerful model systems to begin to understand IRES function. Here we present the crystal structure of a Dicistroviridae IGR IRES domain that interacts with the ribosome’s decoding groove. We find that this RNA domain precisely mimics the transfer RNA anticodon-messenger RNA codon interaction, and its modeled orientation on the ribosome helps explain translocation without peptide bond formation. When combined with a previous structure, this work completes the first high-resolution description of an IRES RNA and provides insight into how RNAs can manipulate complex biological machines}, keywords = {0,Anticodon,Binding Sites,Biochemistry,BOND FORMATION,CELLS,chemistry,Codon,COMPLEX,COMPLEXES,crystal structure,CRYSTAL-STRUCTURE,decoding,DIVERSITY,DOMAIN,Eukaryotic Cells,Genetic,genetics,Hepacivirus,INFORMATION,initiation,INTERNAL RIBOSOME ENTRY,La,MECHANISM,metabolism,MODEL,ModelsGenetic,ModelsMolecular,MOLECULAR-GENETICS,nosource,Nucleic Acid Conformation,peptide bond formation,physiology,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,REGION,ribosome,RIBOSOME ENTRY SITE,Ribosomes,Rna,RNAMessenger,RNATransfer,RnaViral,sequence,SEQUENCES,SITE,Structural,structure,Support,SYSTEM,SYSTEMS,TRANSFER-RNA,translation,TRANSLATION INITIATION,translocation,Viruses} } % == BibTeX quality report for costantinoTRNAMRNAMimicry2008a: % ? Possibly abbreviated journal title Nat.Struct.Mol Biol

@article{counterCatalyticSubunitYeast1997, title = {The Catalytic Subunit of Yeast Telomerase.}, author = {Counter, C.M. and Meyerson, M. and Eaton, E.N. and Weinberg, R.A.}, year = 1997, month = aug, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {94}, number = {17}, eprint = {22193961}, eprinttype = {pubmed}, pages = {9202–9207}, publisher = {National Acad Sciences}, issn = {0027-8424}, doi = {10.1073/pnas.94.17.9202}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22193961 http://www.pnas.org/content/94/17/9202.short}, abstract = {Telomerase is an RNA-directed DNA polymerase, composed of RNA and protein subunits, that replicates the telomere ends of linear eukaryotic chromosomes. Using a genetic strategy described here, we identify the product of the EST2 gene, Est2p, as a subunit of telomerase in the yeast Saccharomyces cerevisiae. Est2p is required for enzyme catalysis, as mutations in EST2 were found to result in the absence of telomerase activity. Immunochemical experiments show that Est2p is an integral subunit of the telomerase enzyme. Critical catalytic residues present in RNA-directed DNA polymerases are conserved in Est2p; mutation of one such residue abolishes telomerase activity, suggesting a direct catalytic role for Est2p.}, pmid = {9256460}, keywords = {Amino Acid Sequence,Base Sequence,Binding Sites,BIOLOGY,Catalysis,CEREVISIAE,chemistry,Chromosomes,Dna,enzyme,enzymology,EST2,gene,Genetic,genetics,IDENTIFY,La,metabolism,Molecular Sequence Data,Mutagenesis,MutagenesisSite-Directed,Mutation,MUTATIONS,nosource,polymerase,PRODUCT,protein,Protein Subunits,RESIDUES,Rna,RNA-Directed DNA Polymerase,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae: enzymology,SACCHAROMYCES-CEREVISIAE,Site-Directed,SUBUNIT,SUBUNITS,Support,Telomerase,Telomerase: chemistry,Telomerase: genetics,Telomerase: metabolism,Telomere,yeast} } % == BibTeX quality report for counterCatalyticSubunitYeast1997: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{coureyTranscriptionalRepressionLong2001, title = {Transcriptional Repression: The Long and the Short of It}, author = {Courey, A.J. and Jia, S.}, year = 2001, month = nov, journal = {Genes & development}, volume = {15}, number = {21}, pages = {2786–2796}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.939601}, url = {http://genesdev.cshlp.org/content/15/21/2786.short}, keywords = {0,Amino Acid Motifs,animal,chemistry,DNA-Binding Proteins,Fungal Proteins,Gene Expression Regulation,Gene Silencing,Histone Deacetylase,La,metabolism,ModelsBiological,nosource,Peptides,polymerase,protein,Proteins,Repressor Proteins,Review,Rna,RNA Polymerase II,Trans-Activators,TranscriptionGenetic} } % == BibTeX quality report for coureyTranscriptionalRepressionLong2001: % ? unused Journal abbr (“Genes Dev.”)

@article{cowleyGillassociatedVirusPenaeus2000, title = {Gill-Associated Virus of {{Penaeus}} Monodon Prawns: An Invertebrate Virus with {{ORF1a}} and {{ORF1b}} Genes Related to Arteri- and Coronaviruses}, author = {Cowley, J.A. and Dimmock, C.M. and Spann, K.M. and Walker, P.J.}, year = 2000, month = jun, journal = {Journal of General Virology}, volume = {81}, number = {6}, pages = {1473–1484}, publisher = {Soc General Microbiol}, doi = {10.1099/0022-1317-81-6-1473}, url = {http://vir.sgmjournals.org/cgi/content/abstract/81/6/1473}, abstract = {A 20089 nucleotide (nt) sequence was determined for the 5’ end of the (+)-ssRNA genome of gill-associated virus (GAV), a yellow head-like virus infecting Penaeus monodon prawns. Clones were generated from a similar to 22 kb dsRNA purified from lymphoid organ total RNA of GAV-infected prawns. The region contains a single gene comprising two long overlapping open reading frames, ORF1a and ORF1b, of 4060 and 2646 amino acids, respectively. The ORFs are structurally related to the ORF1a and ORF1ab polyproteins of coronaviruses and arteriviruses. The 99 nt overlap between ORF1a and ORF1b contains a putative AAAUUUU ‘slippery’ sequence associated with -1 ribosomal frameshifting. A 131 nt stem-loop with the potential to form a complex pseudoknot resides 3 nt downstream of this sequence. Although different to the G/UUUAAAC frameshift sites and ‘H-type’ pseudoknots of nidoviruses, in vitro transcription/translation analysis demonstrated that the GAV element also facilitates read-through of the ORF1a/1b junction. As in coronaviruses, GAV ORF la encodes a 3C-like cysteine protease domain located between two hydrophobic regions. However, its sequence suggests some structural relationship to the chymotrypsin-like serine proteases of arteriviruses. ORF1b encodes homologues of the ‘SDD’ polymerase, which among (+)-RNA viruses is unique to nidoviruses, as well as metal-ion-binding and helicase domains. The presence of a dsRNA replicative intermediate and ORF1a and ORF1ab polyproteins translated by a - 1 frameshift suggests that GAV represents the first invertebrate member of the Order Nidovirales}, keywords = {3,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,BERNE VIRUS,COMPLEX,COMPLEXES,DOMAIN,DOMAINS,DOWNSTREAM,DSRNA,ENCODES,EPHEMERAL FEVER RHABDOVIRUS,FORM,FRAME,frameshift,Frameshifting,gene,Genes,Genome,Helicase,In Vitro,IN-VITRO,INTERMEDIATE,La,MESSENGER-RNAS,MOUSE HEPATITIS-VIRUS,nosource,NUCLEOTIDE-SEQUENCE,OPEN READING FRAME,Open Reading Frames,polymerase,POLYPROTEIN,pseudoknot,pseudoknots,READ-THROUGH,READING FRAME,Reading Frames,readthrough,REGION,REVERSE-TRANSCRIPTASE,ribosomal frameshifting,RIBOSOMAL FRAMESHIFTING SIGNAL,Rna,RNA-POLYMERASE,sequence,Serine,SERINE PROTEASES,SITE,SITES,STEM-LOOP,Structural,virus,YELLOW-HEAD VIRUS} }

@article{coxPsiFactorYeastProblem1988, title = {The {{Psi-Factor}} of {{Yeast}} - {{A Problem}} in {{Inheritance}}}, author = {Cox, B.S. and Tuite, M.F. and Mclaughlin, C.S.}, year = 1988, journal = {Yeast}, volume = {4}, number = {3}, pages = {159–178}, doi = {10.1002/yea.320040302}, url = {ISI:A1988P979000001}, keywords = {0,nosource,S,yeast} } % == BibTeX quality report for coxPsiFactorYeastProblem1988: % ? Title looks like it was stored in title-case in Zotero

@article{coxHistoricalOverviewSearching2001, title = {Historical Overview: Searching for Replication Help in All of the Rec Places}, author = {Cox, M.M.}, year = 2001, month = jul, journal = {Proceedings of the National Academy of Sciences}, volume = {98}, number = {15}, pages = {8173–8180}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.131004998}, url = {http://www.pnas.org/content/98/15/8173.short}, abstract = {For several decades, research into the mechanisms of genetic recombination proceeded without a complete understanding of its cellular function or its place in DNA metabolism. Many lines of research recently have coalesced to reveal a thorough integration of most aspects of DNA metabolism, including recombination. In bacteria, the primary function of homologous genetic recombination is the repair of stalled or collapsed replication forks. Recombinational DNA repair of replication forks is a surprisingly common process, even under normal growth conditions. The new results feature multiple pathways for repair and the involvement of many enzymatic systems. The long- recognized integration of replication and recombination in the DNA metabolism of bacteriophage T4 has moved into the spotlight with its clear mechanistic precedents. In eukaryotes, a similar integration of replication and recombination is seen in meiotic recombination as well as in the repair of replication forks and double-strand breaks generated by environmental abuse. Basic mechanisms for replication fork repair can now inform continued research into other aspects of recombination. This overview attempts to trace the history of the search for recombination function in bacteria and their bacteriophages, as well as some of the parallel paths taken in eukaryotic recombination research}, keywords = {0,animal,Bacteria,Bacteriophage T4,Bacteriophages,Dna,DNA Nucleotidyltransferases,DNA Repair,DNA Replication,DnaViral,Eukaryotic Cells,GenesBacterial,Genetic,genetics,La,MECHANISM,MECHANISMS,metabolism,ModelsGenetic,nosource,Prokaryotic Cells,protein,Rec A Protein,RecombinationGenetic,Review,search,SOS Response (Genetics),supportu.s.gov’tp.h.s.,SYSTEM} } % == BibTeX quality report for coxHistoricalOverviewSearching2001: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{craigRibosometetheredMolecularChaperones2003, title = {Ribosome-Tethered Molecular Chaperones: The First Line of Defense against Protein Misfolding?}, author = {Craig, E.A. and Eisenman, H.C. and Hundley, H.A.}, year = 2003, month = apr, journal = {Current Opinion in Microbiology}, volume = {6}, number = {2}, pages = {157–162}, publisher = {Elsevier}, doi = {10.1016/S1369-5274(03)00030-4}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1369527403000304}, abstract = {Folding of many cellular proteins is facilitated by molecular chaperones. Analysis of both prokaryotic and lower eukaryotic model systems has revealed the presence of ribosome-associated molecular chaperones, thought to be the first line of defense against protein aggregation as translating polypeptides emerge from the ribosome. However, structurally unrelated chaperones have evolved to carry out these functions in different microbes. In the yeast Saccharomyces cerevisiae, an unusual complex of Hsp70 and J-type chaperones associates with ribosome-bound nascent chains, whereas in Escherichia coli the ribosome-associated peptidyl-prolyl-cis-trans isomerase, trigger factor, plays a predominant role}, keywords = {0,analysis,Animals,CEREVISIAE,classification,COMPLEX,COMPLEXES,E,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,genetics,HEAT-SHOCK,HEAT-SHOCK PROTEINS,Heat-Shock Proteins 70,La,LINE,metabolism,MODEL,ModelsBiological,Molecular Chaperones,nosource,Peptidylprolyl Isomerase,POLYPEPTIDE,POLYPEPTIDES,protein,Protein Folding,Proteins,Review,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SYSTEM,SYSTEMS,yeast} } % == BibTeX quality report for craigRibosometetheredMolecularChaperones2003: % ? unused Journal abbr (“Curr.Opin.Microbiol.”)

@article{craigenBacterialPeptideChain1985, title = {Bacterial Peptide Chain Release Factors: Conserved Primary Structure and Possible Frameshift Regulation of Release Factor 2}, author = {Craigen, W.J. and Cook, R.G. and Tate, W.P. and Caskey, C.T.}, year = 1985, month = jun, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {82}, number = {June}, pages = {3616–3620}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.82.11.3616}, url = {http://www.pnas.org/content/82/11/3616.abstract}, abstract = {Escherichia coli peptide chain release factors are proteins that direct the termination of translation in response to specific peptide chain termination codons. The mechanisms of codon recognition and peptidyl-tRNA hydrolysis are unknown. We have characterized the genes encoding release factor 1 (RF-1) and release factor 2 (RF-2) to study the structure-function relationships of the proteins and their regulation in the bacterium. In this report, we present the gene structure of RF-1 and RF-2, and a partial peptide sequence of RF-2. RF-1 and RF-2 are highly homologous in their primary structure. In addition, an in-frame premature opal (UGA) termination codon is located within the RF-2 coding region at amino acid position 26. This region of the protein was sequenced by automated Edman degradation to confirm the predicted reading frame, and a second independent isolate of the RF-2 gene was identified and sequenced to confirm the DNA sequence. These results imply that a frameshift occurs prior to the premature termination codon, thus allowing for translation of RF-2 to be completed. This may represent a mechanism of translational control of RF-2 expression. An alternative possible means of translational regulation is discussed.}, keywords = {+1 frameshifting,Bacteria,Bacterial,Codon,degradation,Dna,Escherichia coli,ESCHERICHIA-COLI,expression,frameshift,gene,Genes,Hydrolysis,MECHANISM,MECHANISMS,nosource,protein,Proteins,regulation,sequence,structure,termination,translation} }

@article{craigenExpressionPeptideChain1986, title = {Expression of Peptide Chain Release Factor 2 Requires High- Efficiency Frameshift}, author = {Craigen, W.J. and Caskey, C.T.}, year = 1986, month = jul, journal = {Nature}, volume = {322}, number = {6076}, pages = {273–275}, publisher = {Nature Publishing Group}, doi = {10.1038/322273a0}, url = {http://www.nature.com/nature/journal/v322/n6076/abs/322273a0.html}, keywords = {+1 frameshifting,biosynthesis,Codon,Dna,efficiency,Escherichia coli,ESCHERICHIA-COLI,expression,frameshift,Frameshifting,gene,Genes,In Vitro,IN-VITRO,MECHANISM,nosource,protein,Proteins,regulation,sequence,STOP CODON,termination,translation} }

@article{crickCodonAnticodonPairingWobble1966, title = {Codon-{{Anticodon Pairing}} - {{Wobble Hypothesis}}}, author = {Crick, F.H.C.}, year = 1966, journal = {Journal of Molecular Biology}, volume = {19}, number = {2}, pages = {548-&}, doi = {10.1016/S0022-2836(66)80022-0}, url = {ISI:A19668268700022}, keywords = {nosource} } % == BibTeX quality report for crickCodonAnticodonPairingWobble1966: % ? Title looks like it was stored in title-case in Zotero

@article{cubertsonFrameshiftSuppressionSaccharomyces1980, title = {Frameshift Suppression in ⬚{{Saccharomyces}} Cerevisiae⬚. {{II}}. {{Genetic}} Properties of Group {{II}} Suppressors.}, author = {Cubertson, M.R. and Underbrink, K.M. and Fink, G.R.}, year = 1980, journal = {Genetics}, volume = {95}, pages = {833–853}, doi = {10.1093/genetics/95.4.833}, keywords = {frameshift,Genetic,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUF1,SUP mutants,suppression,yeast} }

@article{cuiIdentificationCharacterizationGenes1995, title = {Identification and Characterization of Genes That Are Required for the Accelerated Degradation of {{mRNAs}} Containing a Premature Translational Termination Codon.}, author = {Cui, Y. and Hagan, K.W. and Zhang, S. and Peltz, S.W.}, year = 1995, journal = {Genes & Development}, volume = {9}, number = {4}, pages = {423–436}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.9.4.423}, url = {http://genesdev.cshlp.org/content/9/4/423.short}, keywords = {cloning,Codon,degradation,gene,Genes,IDENTIFICATION,mRNA,nonsense-mediated decay,nosource,termination,UPF} } % == BibTeX quality report for cuiIdentificationCharacterizationGenes1995: % ? unused Journal abbr (“Genes & Dev.”)

@article{cuiMof2Sui1Protein1998, title = {The {{Mof2}}/{{Sui1}} Protein Is a General Monitor of Translational Accuracy.}, author = {Cui, Y. and Dinman, J.D. and Kinzy, T.G. and Peltz, S.W.}, year = 1998, journal = {Mol.Cell.Biol.}, volume = {18}, pages = {1506–1516}, doi = {10.1128/MCB.18.3.1506}, keywords = {accuracy,Gag/Gag-pol ratio,mof2,mRNA,nosource,protein,sui1,translation,turnover} } % == BibTeX quality report for cuiMof2Sui1Protein1998: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{cuiMutationsMOF2SUI11998a, title = {Mutations in the ⬚{{MOF2}}/{{SUI1}}⬚ Gene Affect Both Translation and Nonsense-Mediated {{mRNA}} Decay.}, author = {Cui, Y. and Kinzy, T.G. and Dinman, J.D. and Peltz, S.W.}, year = 1998, journal = {RNA}, volume = {5}, pages = {794–804}, doi = {10.1017/S1355838299982055}, keywords = {DECAY,Frameshifting,Gag/Gag-pol ratio,gene,Genes,MOF,mRNA,mRNA decay,Mutation,MUTATIONS,nosource,sui,sui1,translation} }

@article{cukrasMultipleEffectsS132005, title = {Multiple Effects of {{S13}} in Modulating the Strength of Intersubunit Interactions in the Ribosome during Translation}, author = {Cukras, A.R. and Green, R.}, year = 2005, month = may, journal = {Journal of molecular biology}, volume = {349}, number = {1}, pages = {47–59}, publisher = {Elsevier}, doi = {10.1016/j.jmb.2005.03.075}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283605003773}, abstract = {The ribosomal protein S13 is found in the head region of the small subunit, where it interacts with the central protuberance of the large ribosomal subunit and with the P site-bound tRNA through its extended C terminus. The bridging interactions between the large and small subunits are dynamic, and are thought to be critical in orchestrating the molecular motions of the translation cycle. S13 provides a direct link between the tRNA-binding site and the movements in the head of the small subunit seen during translocation, thereby providing a possible pathway of signal transduction. We have created and characterized an rpsM(S13)-deficient strain of Escherichia coli and have found significant defects in subunit association, initiation and translocation through in vitro assays of S13-deficient ribosomes. Targeted mutagenesis of specific bridge and tRNA contact elements in S13 provides evidence that these two interaction domains play critical roles in maintaining the fidelity of translation. This ribosomal protein thus appears to play a non-essential, yet important role by modulating subunit interactions in multiple steps of the translation cycle}, keywords = {0,assays,ASSOCIATION,beta-Galactosidase,Biological Assay,BIOLOGY,C-TERMINUS,DOMAIN,DOMAINS,ELEMENTS,Escherichia coli,ESCHERICHIA-COLI,Fidelity,Genetic,genetics,human,In Vitro,IN-VITRO,initiation,La,metabolism,Molecular Biology,Movement,Mutagenesis,Mutation,nosource,PATHWAY,physiology,Polyribosomes,protein,Protein Biosynthesis,Proteins,REGION,Research SupportN.I.H.Extramural,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,SIGNAL,Signal Transduction,SIGNAL-TRANSDUCTION,SITE,SUBUNIT,subunit association,SUBUNITS,translation,translocation,tRNA,tRNA binding} } % == BibTeX quality report for cukrasMultipleEffectsS132005: % ? unused Journal abbr (“J.Mol.Biol.”)

@article{culottiGeneticControlCell1971a, title = {Genetic Control of the Cell Division Cycle in Yeast. 3. {{Seven}} Genes Controlling Nuclear Division}, author = {Culotti, J. and Hartwell, L.H.}, year = 1971, journal = {Exp.Cell Res.}, volume = {67}, number = {2}, pages = {389–401}, doi = {10.1016/0014-4827(71)90424-1}, url = {PM:5097524}, keywords = {0,3,biosynthesis,Carbon,Carbon Isotopes,Cell Division,Cell Nucleus,CellsCultured,Dna,DNA Replication,gene,Genes,Genetic,GeneticsMicrobial,growth & development,La,metabolism,Mutation,nosource,Photomicrography,Saccharomyces,Temperature,Time Factors,Uracil,yeast} } % == BibTeX quality report for culottiGeneticControlCell1971a: % ? Possibly abbreviated journal title Exp.Cell Res.

@article{culverIdentificationRNAproteinBridge1999, title = {Identification of an {{RNA-protein}} Bridge Spanning the Ribosomal Subunit Interface}, author = {Culver, G.M. and Cate, J.H. and Yusupova, G.Z. and Yusupov, M.M. and Noller, H.F.}, year = 1999, journal = {Science}, volume = {285}, number = {5436}, pages = {2133–2135}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.285.5436.2133}, url = {http://www.sciencemag.org/content/285/5436/2133.short}, abstract = {The 7.8 angstrom crystal structure of the 70S ribosome reveals a discrete double-helical bridge (B4) that projects from the 50S subunit, making contact with the 30S subunit. Preliminary modeling studies Localized its contact site, near the bottom of the platform, to the binding site for ribosomal protein S15. Directed hydroxyl radical probing from iron(II) tethered to S15 specifically cleaved nucleotides in the 715 Loop of domain II of 23S ribosomal RNA, one of the known sites in 23S ribosomal RNA that are footprinted by the 30S subunit. Reconstitution studies show that protection of the 715 Loop, but none of the other 30S-dependent protections, is correlated with the presence of S15 in the 30S subunit. The 715 loop is specifically protected by binding free S15 to 50S subunits. Moreover, the previously determined structure of a homologous stem-loop from U2 small nuclear RNA fits closely to the electron density of the bridge}, keywords = {16S,30-S,70S RIBOSOME,ACID,ASSOCIATION,BINDING,BINDING-SITE,CHEMICAL MODIFICATION,crystal structure,CRYSTAL-STRUCTURE,DOMAIN-II,ESCHERICHIA-COLI RIBOSOME,FE(II),IDENTIFICATION,interface,LOOP,NEIGHBORHOOD,nosource,Nucleotides,PROTECTION,protein,ribosomal RNA,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Rna,SITE,SITES,structure,SUBUNIT} }

@article{cunninghamGenomicsProteomicsNew2000, title = {Genomics and Proteomics:: {{The}} New Millennium of Drug Discovery and Development}, author = {Cunningham, M.J.}, year = 2000, month = jul, journal = {Journal of pharmacological and toxicological methods}, volume = {44}, number = {1}, pages = {291–300}, publisher = {Elsevier}, doi = {10.1016/S1056-8719(00)00111-8}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1056871900001118}, abstract = {One of the most pressing issues facing the pharmaceutical and biotechnology industry is the tremendous dropout rate of lead drug candidates. Over the last two decades, several new genomic technologies have been developed in hopes of addressing the issues of target identification and lead candidate optimization. Gene expression microarray is one of these technologies and this review describes the four main formats, which are currently available: (a) cDNA; (b) oligonucleotide; (c) electrokinetic; and (d) fiberoptic. Many of these formats have been developed with the goal of screening large numbers of genes. Recently, a high-throughput array format has been developed where a large number of samples can be assayed using arrays in parallel. In addition, focusing on gene expression may be only one avenue in preventing lead candidate failure. Proteomics or the study of protein expression may also play a role. Two-dimensional polyacrylamide gel electrophoresis (2-DE) coupled with mass spectroscopy has been the most widely accepted format to study protein expression. However, protein microarrays are now being developed and modified to a high- throughput screening format. Examples of several gene and protein expression studies as they apply to drug discovery and development are reviewed. These studies often result in large data sets. Examples of how several statistical methods (principal components analysis [PCA], clustering methods, Shannon entropy, etc.) have been applied to these data sets are also described. These newer genomic and proteomic technologies and their analysis and visualization methods have the potential to make the drug discovery and development process less costly and more efficient by aiding to select better target and lead candidates}, keywords = {analysis,COMPONENT,development,Electrophoresis,expression,gene,Gene Expression,GENE-EXPRESSION,Genes,genomic,IDENTIFICATION,La,mass spectroscopy,Methods,nosource,protein,Review} } % == BibTeX quality report for cunninghamGenomicsProteomicsNew2000: % ? unused Journal abbr (“J.Pharmacol.Toxicol.Methods”)

@article{curcioSinglestepSelectionTy1991, title = {Single-Step Selection for {{Ty}}⬚1⬚ Element Retrotransposition.}, author = {Curcio, M.J. and Garfinkel, D.J.}, year = 1991, journal = {Proc.Natl.Acad.Sci.USA}, volume = {88}, pages = {936–940}, doi = {10.1073/pnas.88.3.936}, keywords = {nosource,pTY1HIS3AI,Ty1,vector} } % == BibTeX quality report for curcioSinglestepSelectionTy1991: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{czaplinskiPurificationCharacterizationUpf1p1995a, title = {Purification and Characterization of the {{Upf1p}}: A Factor Involved in Translation and {{mRNA}} Degradation.}, author = {Czaplinski, K. and Weng, Y. and Hagan, K. and Peltz, S.W.}, year = 1995, journal = {RNA}, volume = {1}, pages = {610–623}, keywords = {ATPase assays,degradation,mRNA,No DOI found,nosource,purification,translation,Upf1} }

@article{czaplinskiMtt1Upf1likeHelicase2000, title = {Mtt1 Is a {{Upf1-like}} Helicase That Interacts with the Translation Termination Factors and Whose Overexpression Can Modulate Termination Efficiency.}, author = {Czaplinski, K. and Majlesi, N. and Banerjee, T. and Peltz, S.W.}, year = 2000, month = may, journal = {Rna-A Publication of the Rna Society}, volume = {6}, number = {5}, pages = {730–743}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838200992392}, url = {http://journals.cambridge.org/abstract_S1355838200992392 http://rnajournal.cshlp.org/content/6/5/730.short}, abstract = {Translation termination is the final step that completes the synthesis of a polypeptide. Premature translation termination by introduction of a nonsense mutation leads to the synthesis of a truncated protein. We report the identification and characterization of the product of the MTT1 gene, a helicase belonging to the Upf1-like family of helicases that is involved in modulating translation termination. MTT1 is homologous to UPF1, a factor previously shown to function in both mRNA turnover and translation termination. Overexpression of MTT1 induced a nonsense suppression phenotype in a wild-type yeast strain. Nonsense suppression is apparently not due to induction of [PSI+], even though cooverexpression of HSP104 alleviated the nonsense suppression phenotype observed in cells overexpressing MTT1, suggesting a more direct role of Hsp104p in the translation termination process. The MTT1 gene product was shown to interact with translation termination factors and is localized to polysomes. Taken together, these results indicate that at least two members of a family of RNA helicases modulate translation termination efficiency in cells}, keywords = {AMINOGLYCOSIDE ANTIBIOTICS,CELLS,CHAIN RELEASE FACTORS,DNA-POLYMERASE ALPHA,efficiency,FAMILY,gene,Helicase,HUMAN HOMOLOG,IDENTIFICATION,MESSENGER-RNA TURNOVER,mRNA,mRNA turnover,Mutation,NONSENSE,nonsense suppression,nonsense-mediated mRNA decay,nosource,OMNIPOTENT SUPPRESSORS,Phenotype,PHENOTYPIC SUPPRESSION,polysomes,PRION-LIKE FACTOR,protein,release factor,Rna,RNA Helicases,S,suppression,termination,TERMINATION EFFICIENCY,translation,TRANSLATION TERMINATION,turnover,Upf1,UPF1 PROTEIN,yeast,YEAST SACCHAROMYCES-CEREVISIAE} }

@article{czworkowskiCrystalStructureElongation1994a, title = {The Crystal Structure of Elongation Factor {{G}} Complexed with {{GDP}}, at 2.7 {{A}} Resolution}, author = {Czworkowski, J. and Wang, J. and Steitz, T.A. and Moore, P.B.}, year = 1994, journal = {EMBO J.}, volume = {13}, number = {16}, pages = {3661–3668}, doi = {10.1002/j.1460-2075.1994.tb06675.x}, url = {PM:8070396}, abstract = {Elongation factor G (EF-G) catalyzes the translocation step of protein synthesis in bacteria, and like the other bacterial elongation factor, EF-Tu–whose structure is already known–it is a member of the GTPase superfamily. We have determined the crystal structure of EF-G–GDP from Thermus thermophilus. It is an elongated molecule whose large, N- terminal domain resembles the G domain of EF-Tu, except for a 90 residue insert, which covers a surface that is involved in nucleotide exchange in EF-Tu and other G proteins. The tertiary structures of the second domains of EF-G and EF-Tu are nearly identical, but the relative placement of the first two domains in EF-G–GDP resembles that seen in EF-Tu–GTP, not EF-Tu–GDP. The remaining three domains of EF-G look like RNA binding domains, and have no counterparts in EF-Tu}, keywords = {0,Amino Acid Sequence,Bacteria,Bacterial,BINDING,Binding Sites,chemistry,Comparative Study,CrystallographyX-Ray,EFTu,elongation,enzymology,GTP,GTP Phosphohydrolase-Linked Elongation Factors,GTPase,Guanosine,Guanosine Diphosphate,La,metabolism,ModelsMolecular,Molecular Sequence Data,nosource,Peptide Chain Elongation,Peptide Elongation Factor G,Peptide Elongation Factor Tu,Peptide Elongation Factors,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Rna,structure,supportu.s.gov’tp.h.s.,Thermus,Thermus thermophilus,translocation} } % == BibTeX quality report for czworkowskiCrystalStructureElongation1994a: % ? Possibly abbreviated journal title EMBO J.

@article{dsouzaNMRStructure101nucleotide2004a, title = {{{NMR}} Structure of the 101-Nucleotide Core Encapsidation Signal of the {{Moloney}} Murine Leukemia Virus}, author = {D’Souza, V. and Dey, A. and Habib, D. and Summers, M.F.}, year = 2004, month = mar, journal = {J.Mol.Biol.}, volume = {337}, number = {2}, pages = {427–442}, doi = {10.1016/j.jmb.2004.01.037}, url = {PM:15003457}, abstract = {The full length, positive-strand genome of the Moloney Murine Leukemia Virus contains a “core encapsidation signal” that is essential for efficient genome packaging during virus assembly. We have determined the structure of a 101-nucleotide RNA that contains this signal (called mPsi) using a novel isotope-edited NMR approach. The method is robust and should be generally applicable to larger RNAs. mPsi folds into three stem loops, two of which (SL-C and SL-D) co-stack to form an extended helix. The third stem loop (SL-B) is connected to SL-C by a flexible, four-nucleotide linker. The structure contains five mismatched base-pairs, an unusual C.CG base-triple platform, and a novel “A-minor K-turn,” in which unpaired adenosine bases A340 and A341 of a GGAA bulge pack in the minor groove of a proximal stem, and a bulged distal uridine (U319) forms a hydrogen bond with the phosphodiester of A341. Phylogenetic analyses indicate that these essential structural elements are conserved among the murine C-type retroviruses}, keywords = {0,Adenosine,Animals,assembly,BASE,Base Sequence,BASE-PAIR,BASES,chemistry,Comparative Study,ELEMENTS,ENCAPSIDATION,FORM,genetics,Genome,Hydrogen,La,LEUKEMIA,LOOP,Mice,ModelsMolecular,Molecular Sequence Data,Molecular Structure,Moloney murine leukemia virus,NMR,nosource,Nuclear Magnetic ResonanceBiomolecular,Nucleic Acid Conformation,packaging,Phylogeny,physiology,RETROVIRUSES,Rna,RnaViral,Sequence HomologyNucleic Acid,SIGNAL,STEM-LOOP,Structural,structure,supportu.s.gov’tp.h.s.,Uridine,virus,Virus Assembly} } % == BibTeX quality report for dsouzaNMRStructure101nucleotide2004a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{dabevaYeastRibosomalProtein1987, title = {The Yeast Ribosomal Protein {{L32}} and Its Gene.}, author = {Dabeva, M.D. and Warner, J.R.}, year = 1987, month = nov, journal = {Journal of Biological Chemistry}, volume = {262}, number = {33}, pages = {16055–16059}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(18)47695-8}, url = {http://www.jbc.org/content/262/33/16055.short}, abstract = {The yeast ribosomal protein gene RPL32 of Saccharomyces cerevisiae is of particular interest for two reasons: 1) it is adjacent to another ribosomal protein gene, RP29, whose divergent transcription may be driven from the same control sequences, and 2) it appears that the splicing of its transcript is regulated by the product of the gene, ribosomal protein in L32. RPL32 has been analyzed in detail. It is essential for cell growth. Its sequence predicts L32 to be a protein of 105 amino acids, somewhat basic near the NH2 terminus, rather acidic near the COOH terminus, and homologous to ribosomal protein L30 of mammals. The reading frame has been confirmed by partial NH2-terminal analysis of L32. The nucleotide sequence also predicts an intron of 230 nucleotides, which begins with the unusual sequence GTCAGT and ends 40 nucleotides downstream of the consensus sequence TAC-TAAC. The intron has been confirmed by determination of the sequence of a cDNA clone. Transcription initiates 58 nucleotides upstream of the AUG initiation codon, and the polyadenylation site occurs 100 nucleotides downstream of the termination codon. Regulation of the transcription of ribosomal protein genes has been linked to two related consensus sequences. Analysis of the intergenic region between RP29 and RPL32 reveals three copies of these sequences. A deletion removing all three sequences reduces synthesis of a L32-LacZ fusion protein by more than 90%. Some residual activity, however, remains}, keywords = {88058966,Amino Acid Sequence,Amino Acids,analysis,Base Sequence,Codon,gene,Genes,GenesFungal,GenesStructural,genetics,initiation,Mammals,Molecular Sequence Data,nosource,Nucleotides,Plasmids,protein,regulation,Ribosomal Proteins,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,splicing,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,termination,transcription,yeast} } % == BibTeX quality report for dabevaYeastRibosomalProtein1987: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{dabrowskiInteractionTransferRNAsRibosome1995a, title = {Interaction of {{Transfer-RNAs}} with the {{Ribosome}} at the {{A-Site}} and {{P-Site}}}, author = {Dabrowski, M. and Spahn, C.M.T. and Nierhaus, K.H.}, year = 1995, month = oct, journal = {EMBO Journal}, volume = {14}, number = {19}, pages = {4872–4882}, doi = {10.1002/j.1460-2075.1995.tb00168.x}, url = {ISI:A1995TA21600023}, abstract = {In vitro transcribed tRNA(Phe) analogues from Escherichia coli containing up to four randomly distributed A, G, U or C phosphorothioated nucleotides were used to investigate contact patterns with the ribosome in the A and P sites. The tRNAs were biologically active. Molecular iodine (I-2) can trigger a break in the sugar-phosphate backbone at phosphorothioated positions of the ribosomal bound tRNAs if contacts with ribosomal components do not prevent access of the iodine, Highly differentiated protection patterns were found which were strikingly different in the A and P sites, respectively. Strong protections accumulated in the T Psi C loop and no protection was seen in the extra-arm region in both sites, whereas the phosphates in the anticodon loop are more strongly protected in the A site. Strong common protections in both the A and P sites were found neighbouring universally or semiuniversally conserved bases in prominent regions of the tertiary structure of tRNAs: Y11, Y32, U33, Psi 55, C56, A58 and Y60, These bases are therefore candidates for ‘identity elements’ in ribosomal tRNA recognition, The data further indicate that tRNAs change their conformations upon binding to either ribosomal site}, keywords = {A SITE,A-SITE,AMINOACYL-TRANSFER RNA,Anticodon,BASE,BASES,BINDING,CODON-ANTICODON INTERACTION,COMPONENT,COMPONENTS,CONFORMATION,CONFORMATIONAL CHANGES,ELEMENTS,Escherichia coli,ESCHERICHIA-COLI,In Vitro,IN-VITRO,Iodine,LOOP,nosource,Nucleotides,P SITE,P-SITE,P-SITES,PHENYLALANINE TRANSFER-RNA,Phosphates,PHOSPHOROTHIOATED,POSITIONS,psi,RECOGNITION,REGION,RIBOSOMAL TRANSFER-RNA RECOGNITION,ribosome,SITE,SITES,structure,TRANSCRIBED INVITRO,TRANSFER-RNA,tRNA} } % == BibTeX quality report for dabrowskiInteractionTransferRNAsRibosome1995a: % ? Title looks like it was stored in title-case in Zotero

@article{dabrowskiPhosphateSitesRNAligands1996, title = {[{{Phosphate}} Sites of {{RNA-ligands}} Interacting with Ribosome at Different Stages of Translation. {{Thiophosphate}} Method of Analysis]}, author = {Dabrowski, M. and Junemann, R. and Schafer, M.A. and Spahn, C.M. and Nierhaus, K.H. and Alekseeva, E.V. and Dontsova, O.A. and Shpanchenko, O.V. and Bogdanov, A.A.}, year = 1996, month = nov, journal = {Biokhimiia.}, volume = {61}, number = {11}, pages = {1971–1983}, url = {PM:9004858}, abstract = {A novel footprinting method was recently developed which identifies phosphate groups of RNA involved in strong RNA-RNA and RNA-protein interactions. The method is based on iodine-dependent RNA cleavage at phosphothioate groups as long as these groups are not protected from iodine. Our recent studies of mRNA and tRNA regions protected in active ribosomes are summarized; initiation state of ribosomes as well as two elongation states in pre- and post-translocational states were analyzed. Only one phosphate group of mRNA, which was two positions upstream of the decoding codons, was weakly protected in longation complexes, whereas this group and the phosphate groups in the Shine- Dalgarno sequence were protected in the initiation complex. No protection was observed downstream of the decoding codons. On the contrary, numerous phosphate residues of tRNA were protected by the ribosome. The tRNA protection patterns significantly varied between two tRNAs simultaneously bound to the ribosome. The protection pattern of an individual tRNA was not significantly affected by translocation. The data indicate that both tRNA molecules are tightly bound to the ribosome, whereas mRNA is fixed predominantly by two tRNAs via codon- anticodon interaction. A possible translocation mechanism is suggested}, keywords = {0,Anticodon,Base Sequence,CLEAVAGE,Codon,COMPLEX,COMPLEXES,decoding,elongation,Genetic Techniques,initiation,Iodine,La,Ligands,MECHANISM,metabolism,Molecular Sequence Data,mRNA,No DOI found,nosource,Peptide Chain Elongation,Review,ribosome,Ribosomes,Rna,sequence,translation,TranslationGenetic,translocation,tRNA} } % == BibTeX quality report for dabrowskiPhosphateSitesRNAligands1996: % ? Possibly abbreviated journal title Biokhimiia.

@article{dahlbergFunctionalRoleRibosomal1989, title = {The Functional Role of Ribosomal {{RNA}} in Protein Synthesis}, author = {Dahlberg, A.E.}, year = 1989, month = may, journal = {Cell}, volume = {57}, number = {4}, pages = {525–529}, publisher = {Cell Press}, doi = {10.1016/0092-8674(89)90122-0}, url = {http://cat.inist.fr/?aModele=afficheN&cpsidt=7289263}, keywords = {89249317,Bacterial Proteins,biosynthesis,Escherichia coli,genetics,metabolism,Mutagens,nosource,Peptide Chain Elongation,Peptide Chain Termination,Peptidyltransferase,pharmacology,physiology,protein,protein synthesis,PROTEIN-SYNTHESIS,Review,RIBOSOMAL-RNA,Rna,RNAMessenger,RNARibosomal,RNARibosomal16S,RNARibosomal23S,TranscriptionGenetic,Translocation (Genetics)} }

@article{daiFeedbackRegulationCMyc2007a, title = {Feedback Regulation of C-{{Myc}} by Ribosomal Protein {{L11}}}, author = {Dai, M.S. and Sears, R. and Lu, H.}, year = 2007, month = nov, journal = {Cell Cycle}, volume = {6}, number = {22}, pages = {2735–2741}, doi = {10.4161/cc.6.22.4895}, url = {PM:18032916}, abstract = {Several ribosomal proteins including L11 have been shown to activate p53 by inhibiting oncoprotein MDM2, leading to inhibition of cell cycle progression. Our recent study showed that L11 also inhibits oncoprotein c-Myc. Overexpression of L11 inhibits c-Myc-induced transcription and cell proliferation, while reduction of endogenous L11 increases these c-Myc activities. Interestingly, L11 is a transcriptional target of c-Myc, thus forming a negative feedback loop. We further showed that L11 competes with coactivator TRRAP for binding to c-Myc through the Myc box II (MB II) and reduces histone H4 acetylation at c-Myc target gene promoters. In addition, L11 appears to regulate c-Myc levels. Knocking down L11 markedly increases the mRNA and protein levels of endogenous c-Myc. These results suggest that L11 also inhibits cell cycle progression by regulating the c-Myc pathway. Here we further discuss the implications of this regulation and questions that this finding raises}, keywords = {0,Acetylation,Animals,antagonists & inhibitors,BINDING,Biochemistry,BIOLOGY,cell cycle,Cell Proliferation,Feedback,FeedbackBiochemical,gene,Gene Expression RegulationNeoplastic,genetics,GROWTH,Growth Inhibitors,Humans,INHIBITION,INHIBITOR,inhibitors,La,LOOP,metabolism,Molecular Biology,mRNA,nosource,OVEREXPRESSION,p53,PATHWAY,physiology,PROLIFERATION,PROMOTER,PROMOTERS,protein,Protein Binding,Proteins,Proto-Oncogene Proteins,Proto-Oncogene Proteins c-myc,regulation,Review,Ribosomal Proteins,RIBOSOMAL-PROTEIN,Support,TARGET,transcription} }

@article{daiAgingCheck2006, title = {Aging in Check}, author = {Dai, W. and Wang, X.}, year = 2006, month = mar, journal = {Sci.Aging Knowledge.Environ.}, volume = {2006}, number = {7}, pages = {e9}, doi = {10.1126/sageke.2006.7.pe9}, url = {PM:16600919}, abstract = {The spindle checkpoint monitors the interaction between spindle microtubules and kinetochores to prevent precocious entry into anaphase, delaying this stage of mitosis until all condensed chromosomes have been attached to the mitotic spindle in a bi-oriented manner (so that the two kinetochores associated with a pair of sister chromatids are oriented toward opposite poles of the spindle). In addition to conserved Bub and Mad family members, which are known to function in the spindle checkpoint pathway in organisms ranging from yeast to mammals, two mRNA transport genes, Rae1 and Nup9, are also involved in the spindle checkpoint function in mammals. Biochemically, activated spindle checkpoint components have been shown to suppress the activity of the anaphase promoting complex/cyclosome. It is generally thought that decreased activity of the checkpoint components predisposes cells to chromosomal instability, aneuploidy, and malignant transformation. Interestingly, a recent study has shed light on a new function of the spindle checkpoint components Bub3 and Rae1 in the regulation of aging. Mice with haploinsufficiency of Bub3 and Rae1 have a short life span that is associated with the early onset of aging-related features. The progeroid phenotypes caused by deficiency of Bub3 and Rae1 are tightly linked to precocious activation of cellular senescence, but not apoptotic, programs. Therefore, premature aging, rather than neoplastic transformation, may be the major manifestation of a compromised spindle checkpoint in vivo}, keywords = {0,activation,Aging,AgingPremature,Aneuploidy,Animals,Cell Aging,cell cycle,Cell Cycle Proteins,CELLS,Chromosomal Instability,Chromosomes,COMPONENT,COMPONENTS,deficiency,FAMILY,gene,Genes,Genescdc,Genesp53,genetics,human,Humans,IN-VIVO,La,Light,Mammals,Mice,Microtubules,Mitosis,mRNA,nosource,Nuclear Matrix-Associated Proteins,Nucleocytoplasmic Transport Proteins,PATHWAY,Phenotype,physiology,protein,Proteins,regulation,Review,TRANSFORMATION,TRANSPORT,yeast} } % == BibTeX quality report for daiAgingCheck2006: % ? Possibly abbreviated journal title Sci.Aging Knowledge.Environ.

@article{darnellInactivationCoronavirusThat2004, title = {Inactivation of the Coronavirus That Induces Severe Acute Respiratory Syndrome, {{SARS-CoV}}}, author = {Darnell, M.E. and Subbarao, K. and Feinstone, S.M. and Taylor, D.R.}, year = 2004, month = oct, journal = {Journal of virological methods}, volume = {121}, number = {1}, pages = {85–91}, publisher = {Elsevier}, doi = {10.1016/j.jviromet.2004.06.006}, url = {http://linkinghub.elsevier.com/retrieve/pii/S016609340400179X}, abstract = {Severe acute respiratory syndrome (SARS) is a life-threatening disease caused by a novel coronavirus termed SARS-CoV. Due to the severity of this disease, the World Health Organization (WHO) recommends that manipulation of active viral cultures of SARS-CoV be performed in containment laboratories at biosafety level 3 (BSL3). The virus was inactivated by ultraviolet light (UV) at 254 nm, heat treatment of 65 degrees C or greater, alkaline (pH {\(>\)} 12) or acidic (pH {\(<\)} 3) conditions, formalin and glutaraldehyde treatments. We describe the kinetics of these efficient viral inactivation methods, which will allow research with SARS-CoV containing materials, that are rendered non-infectious, to be conducted at reduced safety levels}, keywords = {3,Coronavirus,disease,Heat,Kinetics,La,Methods,nosource,ORGANIZATION,SARS,Severe Acute Respiratory Syndrome,virus,WORLD,World Health,World Health Organization} } % == BibTeX quality report for darnellInactivationCoronavirusThat2004: % ? unused Journal abbr (“J.Virol.Methods”)

@article{dasSV40PromotersTheir1985, title = {{{SV40}} Promoters and Their Regulation}, author = {Das, G.C. and Niyogi, S.K. and Salzman, N.P.}, year = 1985, journal = {Progress in nucleic acid research and molecular biology}, volume = {32}, pages = {217–236}, publisher = {Elsevier}, doi = {10.1016/S0079-6603(08)60349-9}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0079660308603499}, keywords = {86121782,AntigensPolyomavirus Transforming,AntigensViralTumor,DNA Restriction Enzymes,DnaViral,enhancer elements (genetics),GenesRegulator,GenesViral,genetics,immunology,nosource,Oncogene ProteinsViral,Polyomavirus macacae,Promoter Regions (Genetics),Protein Binding,regulation,supportu.s.gov’tnon-p.h.s.,TranscriptionGenetic} } % == BibTeX quality report for dasSV40PromotersTheir1985: % ? unused Journal abbr (“Prog.Nucleic Acid Res.Mol.Biol.”)

@article{daumDiverseEffectsHeparin1997a, title = {Diverse Effects of Heparin on Mitogen-Activated Protein Kinase- Dependent Signal Transduction in Vascular Smooth Muscle Cells}, author = {Daum, G. and Hedin, U. and Wang, Y. and Wang, T. and Clowes, A.W.}, year = 1997, month = jul, journal = {Circulation Research}, volume = {81}, number = {1}, pages = {17–23}, doi = {10.1161/01.RES.81.1.17}, keywords = {activation,Dna,heart,In Vitro,IN-VITRO,IN-VIVO,kinase,MECHANISM,nosource,protein,SIGNAL,Signal Transduction,Support} }

@article{davidovichInducedfitTightensPleuromutilins2007, title = {Induced-Fit Tightens Pleuromutilins Binding to Ribosomes and Remote Interactions Enable Their Selectivity}, author = {Davidovich, C. and Bashan, A. and {Auerbach-Nevo}, T. and Yaggie, R.D. and Gontarek, R.R. and Yonath, A.}, year = 2007, month = mar, journal = {Proceedings of the National Academy of Sciences}, volume = {104}, number = {11}, pages = {4291–4296}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.0700041104}, url = {http://www.pnas.org/content/104/11/4291.short}, abstract = {New insights into functional flexibility at the peptidyl transferase center (PTC) and its vicinity were obtained by analysis of pleuromutilins binding modes to the ribosome. The crystal structures of Deinococcus radiodurans large ribosomal subunit complexed with each of three pleuromutilin derivatives: retapamulin (SB-275833), SB-280080, and SB-571519, show that all bind to the PTC with their core oriented similarly at the A-site and their C14 extensions pointing toward the P-site. Except for an H-bond network with a single nucleotide, G2061, which involves the essential keto group of all three compounds, only minor hydrophobic contacts are formed between the pleuromutilin C14 extensions and any ribosomal component, consistent with the PTC tolerance to amino acid diversity. Efficient drug binding mode is attained by a mechanism based on induced-fit motions exploiting the ribosomal intrinsic functional flexibility and resulting in conformational rearrangements that seal the pleuromutilin-binding pocket and tightens it up. Comparative studies identified a network of remote interactions around the PTC, indicating that pleuromutilins selectivity is acquired by nonconserved nucleotides residing in the PTC vicinity, in a fashion resembling allosterism. Likewise, pleuromutilin resistant mechanisms involve nucleotides residing in the environs of the binding pocket, consistent with their slow resistance-development rates}, keywords = {0,A SITE,A-SITE,ACID,Allosteric Site,Amino Acid Sequence,AMINO-ACID,analysis,Anti-Bacterial Agents,Bicyclo CompoundsHeterocyclic,BINDING,BIOLOGY,chemistry,Comparative Study,COMPONENT,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,CrystallographyX-Ray,Deinococcus,derivatives,Diterpenes,DIVERSITY,Escherichia coli,Kinetics,La,MECHANISM,MECHANISMS,metabolism,ModelsChemical,ModelsMolecular,Molecular Sequence Data,Motion,nosource,Nucleotides,P SITE,P-SITE,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Protein Binding,Protein StructureTertiary,RESISTANT,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Structural,structure,SUBUNIT,Support,TRANSFERASE CENTER} } % == BibTeX quality report for davidovichInducedfitTightensPleuromutilins2007: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{daviterMolecularBiologyRenewed2005, title = {Molecular Biology. {{A}} Renewed Focus on Transfer {{RNA}}.}, author = {Daviter, T. and Murphy, F.V. and Ramakrishnan, V.}, year = 2005, month = may, journal = {Science (New York, N.Y.)}, volume = {308}, number = {5725}, eprint = {15905389}, eprinttype = {pubmed}, pages = {1123–1124}, issn = {1095-9203}, doi = {10.1126/science.1113415}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15905389}, pmid = {15905389}, keywords = {Amino Acyl,Amino Acyl: chemistry,Amino Acyl: metabolism,Anticodon,Base Pairing,BIOLOGY,Codon,GTP Phosphohydrolases,GTP Phosphohydrolases: metabolism,Guanosine Triphosphate,Guanosine Triphosphate: metabolism,La,Mutation,nosource,Nucleic Acid Conformation,Peptide Elongation Factor Tu,Peptide Elongation Factor Tu: metabolism,Protein Biosynthesis,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,Rna,RNA,Transfer,TRANSFER-RNA,Transfer: chemistry,Transfer: genetics,Transfer: metabolism} } % == BibTeX quality report for daviterMolecularBiologyRenewed2005: % ? Possibly abbreviated journal title Science (New York, N.Y.)

@article{daviterRibosomesResponseCodonanticodon2006, title = {The Ribosome’s Response to Codon-Anticodon Mismatches}, author = {Daviter, T. and Gromadski, K.B. and Rodnina, M.V.}, year = 2006, journal = {Biochimie}, volume = {88}, number = {8}, pages = {1001–1011}, publisher = {Elsevier}, doi = {10.1016/j.biochi.2006.04.013}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0300908406000630}, abstract = {The ribosome is a molecular machine that synthesizes polypeptides from aminoacyl-tRNAs according to the sequence of the mRNA template. Codon reading by the anticodon of tRNA is controlled by a network of ribosome contacts that are specific for each position of the codon-anticodon duplex and involve A-minor RNA interactions. Rapid and accurate tRNA selection is accomplished by switching the conformation of the decoding site between accepting and rejecting mode, regardless of the thermodynamic stability of the respective codon-anticodon complexes or their interactions at the decoding site. The forward reactions are particularly sensitive to mismatches and determine the variations in the extent of misreading of near-cognate codons, both during initial selection and proofreading. This review emphasizes the progress made in understanding the mechanisms that determine recognition and selection of tRNA by the translational machinery}, keywords = {0,Anticodon,Base Pair Mismatch,Biochemistry,chemistry,Codon,CODONS,COMPLEX,COMPLEXES,CONFORMATION,decoding,genetics,Germany,GTP,GTP Phosphohydrolase,GTP Phosphohydrolases,La,MECHANISM,MECHANISMS,metabolism,mRNA,nosource,Nucleic Acid Conformation,POLYPEPTIDE,POLYPEPTIDES,POSITION,proofreading,Protein Biosynthesis,RECOGNITION,Review,ribosome,Ribosomes,Rna,RNATransfer,SELECTION,sequence,SITE,stability,Support,TEMPLATE,thermodynamic stability,tRNA} }

@article{delaPrimaryEffectsYeast1980, title = {Primary Effects of Yeast Killer Toxin}, author = {{}{de la}, Pena P. and Barros, F. and Gascon, S. and Ramos, S. and Lazo, P.S.}, year = 1980, journal = {Biochemical and Biophysical Research Communications}, volume = {96}, number = {2}, pages = {544–550}, publisher = {Elsevier}, doi = {10.1016/0006-291X(80)91390-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/0006291X8091390X}, keywords = {81038761,Biological Transport,Cell Membrane,Electrochemistry,killer,killer toxin,Leucine,metabolism,Mycotoxins,nosource,physiology,Protons,Saccharomyces cerevisiae,toxin,yeast} } % == BibTeX quality report for delaPrimaryEffectsYeast1980: % ? unused Journal abbr (“Biochem.Biophys.Res.Commun.”)

@article{delaEffectYeastKiller1981, title = {Effect of Yeast Killer Toxin on Sensitive Cells of {{Saccharomyces}} Cerevisiae.}, author = {{}{de la}, Pena P. and Barros, F. and Gascon, S. and Lazo, P.S. and Ramos, S.}, year = 1981, month = oct, journal = {Journal of Biological Chemistry}, volume = {256}, number = {20}, pages = {10420–10425}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(19)68636-9}, url = {http://www.jbc.org/content/256/20/10420.short}, abstract = {Killer toxin from Saccharomyces cerevisiae inhibited the pumping of protons into the medium by metabolically active sensitive cells. Such inhibition coincided with that of the uptake of potassium ions which are thought to be accumulated by yeast cells in order to neutralize the membrane potential created because of the extrusion of protons. The consumption of glucose, however, was identical in killer-treated and untreated cells. These alterations can be explained by the ability of the toxin to reduce the chemical proton gradient across the plasma membrane as measured by the accumulation of the weak permeable [14C]propionic acid. With this method, an internal pH of 6.42 was calculated from normal cells (the external pH was 4.6) while that of toxin-treated cells was decreased as a function of time. The proton concentration gradient was reduced from 66- to 17-fold. It is shown that the toxin-induced alteration of the proton gradient is due to an enhanced proton permeability of the yeast plasma membrane upon binding of the toxin. It is suggested that killer toxin acts as a macromolecular proton conductor similar in some respects to the known proton conductors 2,4-dinitrophenol and carbonyl cyanide m-chlorophenylhydrazone, since all the described effects are also observed with these substances}, keywords = {82030807,BINDING,Biological Transport,Carbonyl Cyanide m-Chlorophenyl Hydrazone,Cell Membrane,Cell Membrane Permeability,drug effects,Glucose,Hydrogen-Ion Concentration,INHIBITION,Ions,killer,killer toxin,Kinetics,media,Membrane Potentials,metabolism,Mycotoxins,nosource,pharmacology,physiology,Potassium,Protons,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportnon-u.s.gov’t,toxin,yeast} } % == BibTeX quality report for delaEffectYeastKiller1981: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{decaturRRNAModificationsRibosome2002, title = {{{rRNA}} Modifications and Ribosome Function}, author = {Decatur, W.A. and Fournier, M.J.}, year = 2002, month = jul, journal = {Trends in biochemical sciences}, volume = {27}, number = {7}, pages = {344–351}, publisher = {Elsevier}, doi = {10.1016/S0968-0004(02)02109-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000402021096}, abstract = {The development of three-dimensional maps of the modified nucleotides in the ribosomes of Escherichia coli and yeast has revealed that most ( approximately 95% in E. coli and 60% in yeast) occur in functionally important regions. These include the peptidyl transferase centre, the A, P and E sites of tRNA- and mRNA binding, the polypeptide exit tunnel, and sites of subunit-subunit interaction. The correlations suggest that many ribosome functions benefit from nucleotide modification}, keywords = {BINDING,development,Escherichia coli,ESCHERICHIA-COLI,La,modification,mRNA,nosource,Nucleotides,peptidyl transferase,ribosome,Ribosomes,rRNA,tRNA,yeast} } % == BibTeX quality report for decaturRRNAModificationsRibosome2002: % ? unused Journal abbr (“Trends Biochem.Sci.”)

@article{decaturDifferentMechanismsPseudouridine2008a, title = {Different Mechanisms for Pseudouridine Formation in Yeast {{5S}} and 5.{{8S rRNAs}}}, author = {Decatur, W.A. and Schnare, M.N.}, year = 2008, month = may, journal = {Mol.Cell Biol.}, volume = {28}, number = {10}, pages = {3089–3100}, doi = {10.1128/MCB.01574-07}, url = {PM:18332121}, abstract = {The selection of sites for pseudouridylation in eukaryotic cytoplasmic rRNA occurs by the base pairing of the rRNA with specific guide sequences within the RNA components of box H/ACA small nucleolar ribonucleoproteins (snoRNPs). Forty-four of the 46 pseudouridines (Psis) in the cytoplasmic rRNA of Saccharomyces cerevisiae have been assigned to guide snoRNAs. Here, we examine the mechanism of Psi formation in 5S and 5.8S rRNA in which the unassigned Psis occur. We show that while the formation of the Psi in 5.8S rRNA is associated with snoRNP activity, the pseudouridylation of 5S rRNA is not. The position of the Psi in 5.8S rRNA is guided by snoRNA snR43 by using conserved sequence elements that also function to guide pseudouridylation elsewhere in the large-subunit rRNA; an internal stem-loop that is not part of typical yeast snoRNAs also is conserved in snR43. The multisubstrate synthase Pus7 catalyzes the formation of the Psi in 5S rRNA at a site that conforms to the 7-nucleotide consensus sequence present in other substrates of Pus7. The different mechanisms involved in 5S and 5.8S rRNA pseudouridylation, as well as the multiple specificities of the individual trans factors concerned, suggest possible roles in linking ribosome production to other processes, such as splicing and tRNA synthesis}, keywords = {0,5S rRNA,A SITE,A-SITE,Ascomycota,BASE,Base Pairing,Base Sequence,Biochemistry,BIOLOGY,CBF5,CEREVISIAE,chemistry,COMPONENT,COMPONENTS,Consensus Sequence,Conserved Sequence,Dna,DNA Primers,ELEMENTS,Gene Deletion,GenesFungal,Genetic Complementation Test,genetics,Hydro-Lyases,La,MECHANISM,MECHANISMS,metabolism,Microtubule-Associated Proteins,Molecular Biology,Molecular Sequence Data,nosource,Nucleic Acid Conformation,POSITION,protein,Proteins,Pseudouridine,pseudouridylation,psi,RIBONUCLEOPROTEIN,Ribonucleoproteins,RibonucleoproteinsSmall Nuclear,ribosome,Rna,RNAFungal,RNARibosomal5.8S,RNARibosomal5S,RNASmall Nucleolar,rRNA,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SELECTION,sequence,Sequence HomologyNucleic Acid,SEQUENCES,SITE,SITES,SPECIFICITY,Spliceosomes,splicing,STEM-LOOP,Support,tRNA,yeast} } % == BibTeX quality report for decaturDifferentMechanismsPseudouridine2008a: % ? Possibly abbreviated journal title Mol.Cell Biol.

@article{dechampesmeAssembly5SRibosomal1999, title = {Assembly of {{5S}} Ribosomal {{RNA}} Is Required at a Specific Step of the Pre- {{rRNA}} Processing Pathway}, author = {Dechampesme, A.M. and Koroleva, O. and {Leger-Silvestre}, I. and Gas, N. and Camier, S.}, year = 1999, month = jun, journal = {The Journal of cell biology}, volume = {145}, number = {7}, pages = {1369–1380}, publisher = {Rockefeller Univ Press}, doi = {10.1083/jcb.145.7.1369}, url = {http://jcb.rupress.org/content/145/7/1369.abstract}, abstract = {A collection of yeast strains surviving with mutant 5S RNA has been constructed. The mutant strains presented alterations of the nucleolar structure, with less granular component, and a delocalization of the 25S rRNA throughout the nucleoplasm. The 5S RNA mutations affected helix I and resulted in decreased amounts of stable 5S RNA and of the ribosomal 60S subunits. The shortage of 60S subunits was due to a specific defect in the processing of the 27SB precursor RNA that gives rise to the mature 25S and 5.8S rRNA. The processing rate of the 27SB pre-rRNA was specifically delayed, whereas the 27SA and 20S pre-rRNA were processed at a normal rate. The defect was partially corrected by increasing the amount of mutant 5S RNA. We propose that the 5S RNA is recruited by the pre-60S particle and that its recruitment is necessary for the efficient processing of the 27SB RNA precursor. Such a mechanism could ensure that all newly formed mature 60S subunits contain stoichiometric amounts of the three rRNA components}, keywords = {60S subunit,99315907,assembly,Cell Nucleolus,Cell Nucleus,chemistry,COMPONENT,Cytoplasm,Fungal Proteins,Gene Expression,GenesFungal,genetics,growth & development,Kinetics,MECHANISM,metabolism,Molecular Weight,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Ribosomal Proteins,RIBOSOMAL-RNA,Ribosomes,Rna,RNA Precursors,RNA ProcessingPost-Transcriptional,RNA-Binding Proteins,RNAFungal,RNARibosomal,RNARibosomal5S,rRNA,Saccharomyces cerevisiae,structure,SUBUNIT,supportnon-u.s.gov’t,yeast} } % == BibTeX quality report for dechampesmeAssembly5SRibosomal1999: % ? unused Journal abbr (“J.Cell Biol.”)

@article{decottigniesCompleteInventoryYeast1997, title = {Complete Inventory of the Yeast {{ABC}} Proteins}, author = {Decottignies, A. and Goffeau, A.}, year = 1997, month = feb, journal = {Nature genetics}, volume = {15}, number = {2}, pages = {137–145}, publisher = {Nature Publishing Group}, doi = {10.1038/ng0297-137}, url = {http://www.nature.com/ng/journal/v15/n2/abs/ng0297-137.html}, abstract = {The complete sequence of the yeast genome predicts the existence of 29 proteins belonging to the ubiquitous ATP-binding cassette (ABC) superfamily. Using binary comparison, phylogenetic classification and detection of conserved amino acid residues, the yeast ABC proteins have been classified in a total of six clusters, including ten subclusters of distinct predicted topology and presumed distinct function. Study of the yeast ABC proteins provides insight into the physiological function and biochemical mechanisms of their human homologues, such as those involved in cystic fibrosis, adrenoleukodystrophy, Zellweger syndrome, multidrug resistance and the antiviral activity of interferons}, keywords = {0,ACID,Adenosine,Adenosine Triphosphate,Amino Acid Sequence,AMINO-ACID,antiviral,ATP-Binding Cassette Transporters,Binding Sites,Biological TransportActive,chemistry,classification,Comparative Study,enzymology,Fungal Proteins,GenesFungal,genetics,Genome,human,human homologue,Humans,La,MECHANISM,MECHANISMS,metabolism,Molecular Sequence Data,Multigene Family,nosource,PDR5,Phylogeny,protein,Protein Conformation,Proteins,RESIDUES,RESISTANCE,Review,Saccharomyces cerevisiae,sequence,Sequence Alignment,Sequence HomologyAmino Acid,Species Specificity,SUPERFAMILY,Support,Syndrome,yeast} } % == BibTeX quality report for decottigniesCompleteInventoryYeast1997: % ? unused Journal abbr (“Nat.Genet.”)

@article{delabreRPL29CodesNonessential2002, title = {{{RPL29}} Codes for a Non-Essential Protein of the {{60S}} Ribosomal Subunit in {{Saccharomyces}} Cerevisiae and Exhibits Synthetic Lethality with Mutations in Genes for Proteins Required for Subunit Coupling}, author = {DeLabre, M.L. and Kessl, J. and Karamanou, S. and Trumpower, B.L.}, year = 2002, month = apr, journal = {Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression}, volume = {1574}, number = {3}, pages = {255–261}, publisher = {Elsevier}, doi = {10.1016/S0167-4781(01)00372-4}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0167478101003724}, abstract = {RPL29 (YFR032c-a) is a non-essential gene that codes for a 60S ribosomal subunit protein in Saccharomyces cerevisiae. Deletion of RPL29 leads to a moderate accumulation of half-mer polysomes with little or no change in the amounts of free 60S subunits. In vitro translation and the growth rate are also delayed in the Deltarpl29 strain. Such a phenotype is characteristic of mutants defective in 60S to 40S subunit joining. The Deltarpl29 strain exhibits synthetic lethality with mutations in RPL10, the gene encoding an essential 60S ribosomal subunit protein that is required for 60S to 40S subunit joining. The Deltarpl29 strain also exhibits synthetic lethality with RSA1, a gene encoding a nucleoplasmic protein required for the loading of Rpl10p onto the 60S subunit. Over-expression of RPL10 suppresses the half-mer phenotype of the Deltarpl29 strain, but does not correct the growth defect of the deletion strain. We conclude that absence of Rpl29p impairs proper assembly of proteins onto the 60S subunit and that this retards subunit joining and additionally retards protein synthesis subsequent to subunit joining}, keywords = {0,60S subunit,assembly,Biochemistry,biosynthesis,Cell-Free System,CEREVISIAE,Fungal Proteins,gene,Gene Deletion,Genes,GenesFungal,GenesLethal,genetics,GROWTH,growth & development,In Vitro,in vitro translation,IN-VITRO,La,MUTANTS,Mutation,MUTATIONS,nosource,OVEREXPRESSION,Phenotype,polysomes,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUBUNIT,SUBUNITS,Support,translation} } % == BibTeX quality report for delabreRPL29CodesNonessential2002: % ? unused Journal abbr (“Biochim.Biophys.Acta”)

@article{delaglioNMRPipeMultidimensionalSpectral1995a, title = {{{NMRPipe}}: A Multidimensional Spectral Processing System Based on {{UNIX}} Pipes}, author = {Delaglio, F. and Grzesiek, S. and Vuister, G.W. and Zhu, G. and Pfeifer, J. and Bax, A.}, year = 1995, month = nov, journal = {J.Biomol.NMR}, volume = {6}, number = {3}, pages = {277–293}, url = {PM:8520220}, abstract = {The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks}, keywords = {analysis,COMPONENT,computer,development,disease,instrumentation,Kidney,La,Magnetic Resonance Spectroscopy,No DOI found,nosource,PREDICTION,Software,supportnon-u.s.gov’t,SYSTEM,TRANSFORMATION} } % == BibTeX quality report for delaglioNMRPipeMultidimensionalSpectral1995a: % ? Possibly abbreviated journal title J.Biomol.NMR

@misc{delanoPyMOLMolecularGraphics2006, title = {The {{PyMOL Molecular Graphics System}}}, author = {DeLano, W.L.}, year = 2006, journal = {http://www.pymol.org}, url = {⬚http://www.pymol.org⬚⬚⬚ ⬚⬚}, keywords = {nosource,SYSTEM} } % == BibTeX quality report for delanoPyMOLMolecularGraphics2006: % ? Possibly abbreviated journal title http://www.pymol.org % ? Title looks like it was stored in title-case in Zotero

@article{dellaABF1FactorTranscriptional1990, title = {The {{ABF1}} Factor Is the Transcriptional Activator of the {{L2}} Ribosomal Protein Genes in {{Saccharomyces}} Cerevisiae.}, author = {Della, Seta F. and Ciafre, S.A. and Marck, C. and Santoro, B. and Presutti, C. and Sentenac, A. and Bozzoni, I.}, year = 1990, month = may, journal = {Molecular and cellular biology}, volume = {10}, number = {5}, pages = {2437–2441}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/10/5/2437}, abstract = {The same factor, ABF1, binds to the promoters of the two gene copies (L2A and L2B) coding for the ribosomal protein L2 in Saccharomyces cerevisiae. In vitro binding experiments and in vivo functional analysis showed that the different affinities of the L2A and L2B promoters for the ABF1 factor are responsible for the differential transcriptional activities of the two gene copies. The presence of ABF1-binding sites in front of many housekeeping genes suggests a general role for ABF1 in the regulation of gene activity}, keywords = {90220633,analysis,Base Sequence,BINDING,DNAFungal,Fungal Proteins,gene,Gene Expression RegulationFungal,Genes,genetics,In Vitro,IN-VITRO,IN-VIVO,L2,Molecular Sequence Data,Multiple DOI,nonfile,nosource,physiology,Promoter Regions (Genetics),protein,regulation,Regulatory SequencesNucleic Acid,Restriction Mapping,Ribosomal Proteins,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportnon-u.s.gov’t,Transcription Factors,TranscriptionGenetic} } % == BibTeX quality report for dellaABF1FactorTranscriptional1990: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{demeshkinaNovelActivityEukaryotic2007, title = {Novel Activity of Eukaryotic Translocase, {{eEF2}}: Dissociation of the {{80S}} Ribosome into Subunits with {{ATP}} but Not with {{GTP}}}, author = {Demeshkina, N. and Hirokawa, G. and Kaji, A. and Kaji, H.}, year = 2007, journal = {Nucleic Acids Research}, volume = {35}, number = {14}, pages = {4597–4607}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkm468}, url = {http://nar.oxfordjournals.org/content/35/14/4597.short}, abstract = {Ribosomes must dissociate into subunits in order to begin protein biosynthesis. The enzymes that catalyze this fundamental process in eukaryotes remained unknown. Here, we demonstrate that eukaryotic translocase, eEF2, which catalyzes peptide elongation in the presence of GTP, dissociates yeast 80S ribosomes into subunits in the presence of ATP but not GTP or other nucleoside triphosphates. Dissociation was detected by light scattering or ultracentrifugation after the split subunits were stabilized. ATP was hydrolyzed during the eEF2-dependent dissociation, while a non-hydrolyzable analog of ATP was inactive in ribosome splitting by eEF2. GTP inhibited not only ATP hydrolysis but also dissociation. Sordarin, a fungal eEF2 inhibitor, averted the splitting but stimulated ATP hydrolysis. Another elongation inhibitor, cycloheximide, also prevented eEF2/ATP-dependent splitting, while the inhibitory effect of fusidic acid on the splitting was nominal. Upon dissociation of the 80S ribosome, eEF2 was found on the subunits. We propose that the dissociation activity of eEF2/ATP plays a role in mobilizing 80S ribosomes for protein synthesis during the shift up of physiological conditions}, keywords = {0,ACID,Adenosine,Adenosine Triphosphate,ATP,ATP HYDROLYSIS,Biochemistry,BIOLOGY,biosynthesis,CentrifugationDensity Gradient,Cycloheximide,elongation,enzyme,Enzymes,Fusidic Acid,GTP,Guanosine,Guanosine Triphosphate,Hydrolysis,INHIBITOR,initiation,INITIATION-FACTOR,La,Light,metabolism,Molecular Biology,nosource,Peptide Elongation Factor 2,Peptide Initiation Factors,protein,Protein Biosynthesis,protein synthesis,PROTEIN-BIOSYNTHESIS,PROTEIN-SYNTHESIS,ribosome,Ribosomes,ScatteringRadiation,sordarin,SUBUNIT,SUBUNITS,Support,Ultracentrifugation,yeast} } % == BibTeX quality report for demeshkinaNovelActivityEukaryotic2007: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{denboonEquineArteritisVirus1991, title = {Equine Arteritis Virus Is Not a Togavirus but Belongs to the Coronaviruslike Superfamily.}, author = {Den Boon, J.A. and Snijder, E.J. and Chirnside, E.D. and {}{de Vries}, A.A. and Horzinek, M.C. and Spaan, W.J.}, year = 1991, month = jun, journal = {Journal of virology}, volume = {65}, number = {6}, pages = {2910–2920}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.65.6.2910-2920.1991}, url = {http://jvi.asm.org/cgi/content/abstract/65/6/2910}, abstract = {The nucleotide sequence of the genome of equine arteritis virus (EAV) was determined from a set of overlapping cDNA clones and was found to contain eight open reading frames (ORFs). ORFs 2 through 7 are expressed from six 3’-coterminal subgenomic mRNAs, which are transcribed from the 3’-terminal quarter of the viral genome. A number of these ORFs are predicted to encode structural EAV proteins. The organization and expression of the 3’ part of the EAV genome are remarkably similar to those of coronaviruses and toroviruses. The 5’-terminal three-quarters of the genome contain the putative EAV polymerase gene, which also shares a number of features with the corresponding gene of corona- and toroviruses. The gene contains two large ORFs, ORF1a and ORF1b, with an overlap region of 19 nucleotides. The presence of a “shifty” heptanucleotide sequence in this region and a downstream RNA pseudoknot structure indicate that ORF1b is probably expressed by ribosomal frameshifting. The frameshift-directing potential of the ORF1a/ORF1b overlap region was demonstrated by using a reporter gene. Moreover, the predicted ORF1b product was found to contain four domains which have been identified in the same relative positions in coronavirus and torovirus ORF1b products. The sequences of the EAV and coronavirus ORF1a proteins were found to be much more diverged. The EAV ORF1a product contains a putative trypsinlike serine protease motif. Our data indicate that EAV, presently considered a togavirus, is evolutionarily related to viruses from the coronaviruslike superfamily}, keywords = {0,3,Amino Acid Sequence,Arteritis VirusEquine,Base Sequence,biosynthesis,chemistry,Coronaviridae,Coronavirus,Dna,DNA-Directed RNA Polymerase,DNA-Directed RNA Polymerases,DnaViral,DOMAIN,DOMAINS,DOWNSTREAM,Endopeptidases,Evolution,expression,FRAME,Frameshifting,gene,Gene Expression,genetics,Genome,growth & development,Hela Cells,Humans,La,metabolism,microbiology,Molecular Sequence Data,mRNA,nosource,NUCLEOTIDE-SEQUENCE,Nucleotides,OPEN READING FRAME,Open Reading Frames,ORGANIZATION,polymerase,POSITION,POSITIONS,PRODUCT,PRODUCTS,protein,Proteins,pseudoknot,pseudoknot structure,READING FRAME,Reading Frames,REGION,Research SupportNon-U.S.Gov’t,ribosomal frameshifting,Ribosomes,Rna,RNA PSEUDOKNOT,RNA-POLYMERASE,RNAMessenger,sequence,SEQUENCES,Serine,Serine Endopeptidases,Structural,structure,SUPERFAMILY,Togaviridae,Virion,virology,virus,Virus Replication,Viruses} } % == BibTeX quality report for denboonEquineArteritisVirus1991: % ? unused Journal abbr (“J.Virol.”)

@article{dengIdentificationMajorCoreceptor1996a, title = {Identification of a Major Co-Receptor for Primary Isolates of {{HIV-1}}}, author = {Deng, H. and Liu, R. and Ellmeier, W. and Choe, S. and Unutmaz, D. and Burkhart, M. and Di Marzio, P. and Marmon, S. and Sutton, R.E. and Hill, C.M. and Davis, C.B. and Peiper, S.C. and Schall, T.J. and Littman, D.R. and Landau, N.R.}, year = 1996, month = jun, journal = {Nature}, volume = {381}, number = {6584}, pages = {661–666}, doi = {10.1038/381661a0}, url = {http://www.nature.com/nature/journal/v381/n6584/abs/381661a0.html http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Identification+of+a+major+co-receptor+for+primary+isolates+of+HIV-1#9 pm:8649511}, abstract = {Entry of HIV-1 into target cells requires cell-surface CD4 and additional host cell cofactors. A cofactor required for infection with virus adapted for growth in transformed T-cell lines was recently identified and named fusin. However, fusin does not promote entry of macrophage-tropic viruses, which are believed to be the key pathogenic strains in vivo. The principal cofactor for entry mediated by the envelope glycoproteins of primary macrophage-tropic strains of HIV-1 is CC-CKR-5, a receptor for the beta-chemokines RANTES, MIP-1alpha and MIP-1beta}, keywords = {0,3T3 Cells,Animals,ANTIGEN,AntigensCD4,Cell Line,CELLS,Chemokines,Dna,gene,Gene Productsenv,GENE-PRODUCT,genetics,GROWTH,Hela Cells,HIV,Hiv-1,Humans,IDENTIFICATION,immunology,IN-VIVO,INFECTION,La,LINE,Macrophages,Membrane Fusion,Membrane Proteins,metabolism,Mice,Molecular Sequence Data,nosource,physiology,PRODUCT,PRODUCTS,protein,Proteins,ReceptorsCCR5,ReceptorsCXCR4,ReceptorsCytokine,ReceptorsHIV,Recombinant Proteins,REQUIRES,Support,T-Lymphocytes,TARGET,virology,virus,Virus Replication,Viruses} }

@article{denhardtSignaltransducingProteinPhosphorylation1996, title = {Signal-Transducing Protein Phosphorylation Cascades Mediated by {{Ras}}/{{Rho}} Proteins in the Mammalian Cell: The Potential for Multiplex Signalling. [{{Review}}] [228 Refs]}, author = {Denhardt, D.T.}, year = 1996, month = sep, journal = {Biochemical Journal}, volume = {318}, number = {Pt 3}, pages = {729–747}, keywords = {activation,Ca2+,COMPLEX,COMPLEXES,COMPONENT,Cytokines,Dna,GAMMA-SUBUNIT,Hormones,kinase,No DOI found,nosource,Phosphorylation,protein,PROTEIN COMPLEX,Proteins,ras,SIGNAL,structure,SUBUNIT,transcription} }

@article{dennisAncientCiphersTranslation1997a, title = {Ancient Ciphers: Translation in {{Archaea}}.}, author = {Dennis, P.P.}, year = 1997, month = jun, journal = {Cell}, volume = {89}, number = {7}, eprint = {9215623}, eprinttype = {pubmed}, pages = {1007–1010}, doi = {10.1016/S0092-8674(00)80288-3}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9215623}, keywords = {97358527,Archaea,Base Sequence,Consensus Sequence,genetics,nosource,RNABacterial,translation,TranslationGenetic} }

@article{derrigoRNAproteinInteractionsControl2000a, title = {{{RNA-protein}} Interactions in the Control of Stability and Localization of Messenger {{RNA}} (Review).}, author = {Derrigo, M. and Cestelli, A. and Savettieri, G. and Di, Liegro}, year = 2000, month = feb, journal = {International journal of molecular medicine}, volume = {5}, number = {2}, eprint = {10639588}, eprinttype = {pubmed}, pages = {111–123}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10639588}, abstract = {Growing evidence demonstrates the importance of regulating mRNA localization, stability and translation, in the control of gene expression, both in development and in differentiated cells. The signals responsible for specific regulation of mRNA metabolism reside in the RNA message itself: both 5’ and 3’ to the coding region, all transcripts contain variable lengths of untranslated sequences (5’-UTR and 3’-UTR) which contain the binding sites for a number of RNA-binding proteins (RBPs). Most RBPs assemble on the message at the moment of transcription, thus determining the future fate of the transcript from the very beginning. We discuss possible mechanisms through which mRNA, leaving from the nucleus as an RNA-protein complex, might reach its final intracellular destinations and how its access to the translational apparatus might be regulated in time and space. We also focus on a few known examples of aberrant RNA-protein interactions associated with human diseases, including cancer}, keywords = {3’ Untranslated Regions,3’ UTR,5’ Untranslated Regions,Amino Acid Sequence,animal,BINDING,Binding Sites,cancer,Cell Nucleus,COMPLEX,COMPLEXES,development,disease,expression,gene,Gene Expression,GENE-EXPRESSION,human,MECHANISM,MECHANISMS,MESSENGER-RNA,metabolism,Molecular Sequence Data,mRNA,No DOI found,nosource,Nucleic Acid Conformation,protein,Proteins,regulation,Review,Rna,RNA Stability,RNA-Binding Proteins,RNAMessenger,sequence,SIGNAL,stability,transcription,translation,TranslationGenetic} } % == BibTeX quality report for derrigoRNAproteinInteractionsControl2000a: % ? unused Journal abbr (“Int.J.Mol.Med.”)

@article{deshmukhYeastRibosomalProtein1993, title = {Yeast Ribosomal Protein {{L1}} Is Required for the Stability of Newly Synthesized {{5S rRNA}} and the Assembly of {{60S}} Ribosomal Subunits.}, author = {Deshmukh, M. and Tsay, Y.F. and Paulovich, A.G. and Woolford, J.L.}, year = 1993, month = may, journal = {Molecular and cellular biology}, volume = {13}, number = {5}, pages = {2835–2845}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/13/5/2835}, keywords = {5S rRNA,assembly,gene,IN-VIVO,L1,Multiple DOI,nonfile,nosource,protein,ribosome,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,stability,SUBUNIT,transcription,yeast} }

@article{deshmukhMultipleRegionsYeast1995, title = {Multiple Regions of Yeast Ribosomal Protein {{L1}} Are Important for Its Interaction with 5 {{S rRNA}} and Assembly into Ribosomes}, author = {Deshmukh, M. and Stark, J. and Yeh, L.C. and Lee, J.C. and Woolford, J.L.}, year = 1995, month = dec, journal = {Journal of Biological Chemistry}, volume = {270}, number = {50}, pages = {30148–30156}, publisher = {ASBMB}, doi = {10.1074/jbc.270.50.30148}, url = {http://www.jbc.org/content/270/50/30148.short}, keywords = {5S rRNA,Alleles,Amino Acids,antibody,assembly,BINDING,gene,In Vitro,IN-VITRO,IN-VIVO,L1,Mutagenesis,Mutation,MUTATIONS,nosource,protein,ribosome,Ribosomes,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUBUNIT,yeast} }

@article{deusserRibosomalProteinsXVI1970a, title = {Ribosomal Proteins. {{XVI}}. {{Altered S4}} Proteins in {{Escherichia}} Coli Revertants from Streptomycin Dependence to Independence}, author = {Deusser, E. and Stoffler, G. and Wittmann, H.G.}, year = 1970, journal = {Mol.Gen.Genet.}, volume = {109}, number = {4}, pages = {298–302}, doi = {10.1007/BF00267699}, url = {PM:4925044}, keywords = {0,Acrylates,Amides,analysis,Bacterial,Bacterial Proteins,Electrophoresis,Escherichia coli,ESCHERICHIA-COLI,Gels,GeneticsMicrobial,La,Mutation,nosource,Phenotype,protein,Proteins,Ribosomal Proteins,Ribosomes,S4-PROTEIN,Streptomycin} } % == BibTeX quality report for deusserRibosomalProteinsXVI1970a: % ? Possibly abbreviated journal title Mol.Gen.Genet.

@article{diTranslationalFrameshiftingBarley1993, title = {Translational Frameshifting by Barley Yellow Dwarf Virus {{RNA}} ({{PAV}} Serotype) in {{Escherichia}} Coli and in Eukaryotic Cell-Free Extracts}, author = {Di, R. and {Dinesh-Kumar}, S.P. and Miller, W.A.}, year = 1993, month = jul, journal = {MOLECULAR PLANT MICROBE INTERACTIONS}, volume = {6}, number = {4}, pages = {444–452}, publisher = {APS PRESS}, doi = {10.1094/MPMI-6-444}, url = {http://www.apsnet.org/publications/mpmi/backissues/Documents/1993Articles/Microbe06_444.pdf}, abstract = {The open reading frame (39K ORF) at the 5’ end of the genome of barley yellow dwarf virus, PAV serotype (BYDV-PAV), overlaps with a 60K ORF by 13 nucleotides. Several approaches were used to show that the 60K ORF (putative polymerase gene) is translated by a low-frequency frameshift event in which some ribosomes shift into the 60K ORF rather than terminate at the 39K ORF stop codon. A sequence encompassing this region of overlap induced minus one (-1) translational frameshifting in heterologous and native contexts. In Escherichia coli, with the alpha subunit of lacZ used as a reporter gene, the rate of frameshifting caused by the BYDV-PAV sequence was approximately 3%. Amino acid sequencing of the transframe protein confirmed that ribosomes slip into the -1 frame in the overlapping region which includes a consensus shifty heptanucleotide: GGGUUUU. In a wheat germ translation system, BYDV-PAV genomic RNA from virions frameshifted about twice as efficiently as full-length transcripts from a cDNA clone. Frameshifting in rabbit reticulocyte lysates was much lower for either template. The identity of the 99-kDa wheat germ translation product was verified as the transframe protein by immunoprecipitation with antibody specific for the 60K ORF. These results support our previous observations of frameshifting in protoplasts and illustrate a subtle molecular control mechanism between this pathogen and its host cells}, keywords = {0,ACID,Amino Acid Sequence,AMINO-ACID,Animals,Antibodies,antibody,Base Sequence,Cell-Free System,CELLS,Cereals,CloningMolecular,Codon,Dna,DNA Primers,Escherichia coli,ESCHERICHIA-COLI,EXTRACTS,FRAME,frameshift,Frameshift Mutation,Frameshifting,gene,genetics,Genome,genomic,GENOMIC RNA,La,Luteovirus,lysate,MECHANISM,Molecular Sequence Data,nosource,Nucleotides,OPEN READING FRAME,Open Reading Frames,pathology,polymerase,Precipitin Tests,PRODUCT,protein,Protein Biosynthesis,PROTOPLASTS,Rabbits,READING FRAME,REGION,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tNon-P.H.S.,ribosome,Ribosomes,Rna,RnaViral,sequence,STOP CODON,SUBUNIT,Support,SYSTEM,TEMPLATE,TRANSCRIPT,translation,TRANSLATIONAL FRAMESHIFTING,Triticum,Virion,VIRIONS,virus,VIRUS-RNA,Wheat,YELLOW DWARF VIRUS} } % == BibTeX quality report for diTranslationalFrameshiftingBarley1993: % ? unused Journal abbr (“Mol.Plant Microbe Interact.”)

@article{diExpressionTruncatedForm2005, title = {Expression of a Truncated Form of Ribosomal Protein {{L3}} Confers Resistance to Pokeweed Antiviral Protein and the {{Fusarium}} Mycotoxin Deoxynivalenol}, author = {Di, R. and Tumer, N.E.}, year = 2005, journal = {Molecular plant-microbe interactions}, volume = {18}, number = {8}, pages = {762–770}, publisher = {Am Phytopath Society}, doi = {10.1094/MPMI-18-0762}, url = {http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-18-0762}, abstract = {The contamination of important agricultural products such as wheat, barley, or maize with the trichothecene mycotoxin deoxynivalenol (DON) due to infection with Fusarium species is a worldwide problem. Trichothecenes inhibit protein synthesis by targeting ribosomal protein L3. Pokeweed antiviral protein (PAP), a ribosome-inactivating protein binds to L3 to depurinate the alpha-sarcin/loop of the large rRNA. Plants transformed with the wild-type PAP show lesions and express very low levels of PAP because PAP autoregulates its expression by destabilizing its own mRNA. We show here that transgenic tobacco plants expressing both the wild-type PAP and a truncated form of yeast L3 (L3delta) are phenotypically normal. PAP mRNA and protein levels are very high in these plants, indicating that L3delta suppresses the autoregulation of PAP mRNA expression. Ribosomes are not depurinated in the transgenic plants expressing PAP and L3delta, even though PAP is associated with ribosomes. The expression of the endogenous tobacco ribosomal protein L3 is up-regulated in these plants and they are resistant to the Fusarium mycotoxin DON. These results demonstrate that expression of an N-terminal fragment of yeast L3 leads to trans-dominant resistance to PAP and the trichothecene mycotoxin DON, providing evidence that both toxins target L3 by a common mechanism}, keywords = {antiviral,expression,FORM,INFECTION,L3,La,MECHANISM,mRNA,nosource,PAP,Plants,Pokeweed antiviral protein,PRODUCT,PRODUCTS,protein,protein synthesis,PROTEIN-SYNTHESIS,RESISTANCE,RESISTANT,ribosome,ribosome-inactivating protein,Ribosomes,rRNA,TARGET,Tobacco,toxin,Wheat,WILD-TYPE,yeast} } % == BibTeX quality report for diExpressionTruncatedForm2005: % ? unused Journal abbr (“Mol.Plant Microbe Interact.”)

@article{diamondOverlappingGenesYeast1989, title = {Overlapping Genes in a Yeast Double-Stranded {{RNA}} Virus.}, author = {Diamond, M.E. and Dowhanick, J.J. and Nemeroff, M.E. and Pietras, D.F. and Tu, C.L. and Bruenn, J.A.}, year = 1989, journal = {Journal of Virology}, volume = {63}, number = {9}, pages = {3983–3990}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.63.9.3983-3990.1989}, url = {http://jvi.asm.org/cgi/content/abstract/63/9/3983}, keywords = {DOUBLE-STRANDED-RNA,gene,Genes,nosource,virus,yeast} }

@article{diedrichRibosomalProteinL22000, title = {Ribosomal Protein {{L2}} Is Involved in the Association of the Ribosomal Subunits, {{tRNA}} Binding to {{A}} and {{P}} Sites and Peptidyl Transfer}, author = {Diedrich, G. and Spahn, C.M. and Stelzl, U. and Schafer, M.A. and Wooten, T. and Bochkariov, D.E. and Cooperman, B.S. and Traut, R.R. and Nierhaus, K.H.}, year = 2000, month = oct, journal = {The EMBO Journal}, volume = {19}, number = {19}, pages = {5241–5250}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/19.19.5241}, url = {http://www.nature.com/emboj/journal/v19/n19/abs/7593338a.html}, abstract = {Ribosomal proteins L2, L3 and L4, together with the 23S RNA, are the main candidates for catalyzing peptide bond formation on the 50S subunit. That L2 is evolutionarily highly conserved led us to perform a thorough functional analysis with reconstituted 50S particles either lacking L2 or harboring a mutated L2. L2 does not play a dominant role in the assembly of the 50S subunit or in the fixation of the 3’-ends of the tRNAs at the peptidyl-transferase center. However, it is absolutely required for the association of 30S and 50S subunits and is strongly involved in tRNA binding to both A and P sites, possibly at the elbow region of the tRNAs. Furthermore, while the conserved histidyl residue 229 is extremely important for peptidyl-transferase activity, it is apparently not involved in other measured functions. None of the other mutagenized amino acids (H14, D83, S177, D228, H231) showed this strong and exclusive participation in peptide bond formation. These results are used to examine critically the proposed direct involvement of His229 in catalysis of peptide synthesis}, keywords = {20515642,Amino Acid Sequence,Amino Acids,analysis,assembly,BINDING,Binding Sites,Catalysis,Catalytic Domain,chemistry,Escherichia coli,genetics,Histidine,L2,L3,metabolism,Molecular Sequence Data,Mutation,nosource,P-SITE,Peptide Synthesis,peptidyl transferase,peptidyl-transfer,Peptidyltransferase,protein,Proteins,Ribosomal Proteins,Ribosomes,Rna,RNATransfer,Sequence Alignment,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,TranslationGenetic,tRNA} } % == BibTeX quality report for diedrichRibosomalProteinL22000: % ? unused Journal abbr (“EMBO J.”)

@article{dingleyDirectObservationHydrogen1998, title = {Direct Observation of Hydrogen Bonds in Nucleic Acid Base Pairs by Internucleotide (2){{J}}({{NN}}) Couplings}, author = {Dingley, A.J. and Grzesiek, S.}, year = 1998, journal = {Journal of the American Chemical Society}, volume = {120}, number = {33}, pages = {8293–8297}, publisher = {ACS Publications}, doi = {10.1021/ja981513x}, url = {http://pubs.acs.org/doi/abs/10.1021/ja981513x}, abstract = {Hydrogen bonds play a key role in the stabilization of protein and nucleic acid secondary structure. Currently, most of the experimental evidence for the interaction of hydrogen bond donor and acceptor atoms is indirect. Here we show that scaler couplings across the hydrogen bond are observable for Watson-Crick base pairs in N-15-labeled RNA. These scalar couplings correlate the imino donor N-15 nucleus and the corresponding acceptor N-15 nucleus on the complementary base. The two-bond J(NN) couplings between the N3 of uridine and the N1 of adenosine, and between the N1 of guanosine and the N3 of cytidine, have values of approximately 7 Hz as determined by a novel quantitative J-correlation experiment for the 69-nucleotide TI domain of the potato spindle tuber viroid. In contrast, for non-Watson-Crick base pairs the hydrogen bond acceptor is usually nota nitrogen, but an oxygen atom, and thus, the two-bond J(NN) couplings are not observed}, keywords = {ACID,Adenosine,BASE,BASE-PAIR,CHEMICAL-SHIFT ANISOTROPY,Deuterium,DOMAIN,Guanosine,Hydrogen,MAGNETIC-RESONANCE SPECTROSCOPY,N-15-ENRICHED PROTEINS,Nitrogen,NMR-SPECTROSCOPY,nosource,Nucleotides,protein,PROTON,QUANTITATIVE MEASUREMENT,RELAXATION INTERFERENCE,Rna,S,SECONDARY STRUCTURE,structure,Uridine} }

@article{dinmanRibosomalFrameshiftingEfficiency1992b, title = {Ribosomal Frameshifting Efficiency and {{Gag}}/{{Gag-pol}} Ratio Are Critical for Yeast {{M}}⬚1⬚ Double-Stranded {{RNA}} Virus Propagation.}, author = {Dinman, J.D. and Wickner, R.B.}, year = 1992, journal = {J.Virology}, volume = {66}, pages = {3669–3676}, doi = {10.1128/jvi.66.6.3669-3676.1992}, keywords = {efficiency,frameshift,Frameshifting,Gag/Gag-pol ratio,M1,nosource,ribosomal frameshifting,Rna,virus,yeast} } % == BibTeX quality report for dinmanRibosomalFrameshiftingEfficiency1992b: % ? Possibly abbreviated journal title J.Virology

@article{dinmanTranslationalMaintenanceFrame1994a, title = {Translational Maintenance of Frame: Mutants of ⬚{{Saccharomyces}} Cerevisiae⬚ with Altered -1 Ribosomal Frameshifting Efficiencies.}, author = {Dinman, J.D. and Wickner, R.B.}, year = 1994, journal = {Genetics}, volume = {136}, pages = {75–86}, doi = {10.1093/genetics/136.1.75}, keywords = {efficiency,Frameshifting,Gag/Gag-pol ratio,L-A,M1,MOF,nosource,ribosomal frameshifting,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE} }

@article{dinman5SRRNAInvolved1995, title = {{{5S rRNA}} Is Involved in Fidelity of Translational Reading Frame.}, author = {Dinman, J. D. and Wickner, R. B.}, year = 1995, journal = {Genetics}, volume = {141}, pages = {95–105}, keywords = {5S rRNA,Fidelity,MOF,nosource,ribosomal frameshifting,rRNA} }

@article{dinmanRibosomalFrameshiftingYeast1995, title = {Ribosomal Frameshifting in Yeast Viruses.}, author = {Dinman, J.D.}, year = 1995, journal = {Yeast}, volume = {11}, number = {12}, pages = {1115–1127}, publisher = {Wiley Online Library}, doi = {10.1002/yea.320111202}, url = {http://onlinelibrary.wiley.com/doi/10.1002/yea.320111202/abstract}, keywords = {Frameshifting,Gag/Gag-pol ratio,L-A,M1,nosource,Review,review article,ribosomal frameshifting,Ty,yeast} }

@article{dinmanTranslationalMisreadingMutations1997a, title = {Translational Misreading: {{Mutations}} in Translation Elongation Factor 1`a Differentially Affect Programmed Ribosomal Frameshifting and Drug Sensitivity.}, author = {Dinman, J.D. and Kinzy, T.G.}, year = 1997, journal = {RNA}, volume = {3}, pages = {870–881}, keywords = {drugs,elongation,Frameshifting,Gag/Gag-pol ratio,Mutation,MUTATIONS,No DOI found,nosource,ribosomal frameshifting,translation} }

@article{dinmanPeptidylTransferaseInhibitors1997, title = {Peptidyl Transferase Inhibitors Have Antiviral Properties by Altering Programmed -1 Ribosomal Frameshifting Efficiencies: Development of Model Systems.}, author = {Dinman, J.D. and {Ruiz-Echevarria}, M.J. and Czaplinski, K. and Peltz, S.W.}, year = 1997, journal = {Proceedings of the National Academy of Sciences}, volume = {94}, number = {13}, pages = {6606–6611}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.94.13.6606}, url = {http://www.pnas.org/content/94/13/6606.short}, keywords = {anisomycin,antiviral,development,efficiency,Frameshifting,Gag/Gag-pol ratio,mRNA decay,nosource,peptidyl transferase,ribosomal frameshifting,sparsomycin,SYSTEM} } % == BibTeX quality report for dinmanPeptidylTransferaseInhibitors1997: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.USA”)

@article{dinmanTranslatingOldDrugs1998a, title = {Translating Old Drugs into New Treatments: {{Identifying}} Compounds That Modulate Programmed -1 Ribosomal Frameshifting and Function as Potential Antiviral Agents.}, author = {Dinman, J.D. and {Ruiz-Echevarria}, M.J. and Peltz, S.W.}, year = 1998, journal = {Trends in Biotech.}, volume = {16}, pages = {190–196}, doi = {10.1016/S0167-7799(97)01167-0}, keywords = {anisomycin,antiviral,Antiviral Agents,drugs,Frameshifting,Gag/Gag-pol ratio,nosource,Review,ribosomal frameshifting,sparsomycin} } % == BibTeX quality report for dinmanTranslatingOldDrugs1998a: % ? Possibly abbreviated journal title Trends in Biotech.

@article{dinmanCaseInvolvementUpf3p2000, title = {The Case for the Involvement of the {{Upf3p}} in Programmed -1 Ribosomal Frameshifting.}, author = {Dinman, J.D. and {Ruiz-Echevarria}, M.J. and Wang, W and Peltz, S.W.}, year = 2000, journal = {RNA}, volume = {6}, number = {12}, pages = {1685–1686}, publisher = {Cambridge Univ Press}, doi = {10.1017/S1355838200001886}, url = {http://journals.cambridge.org/abstract_S1355838200001886}, keywords = {Frameshifting,Gag/Gag-pol ratio,NMD,nosource,ribosomal frameshifting,UPF} }

@incollection{dinmanRegulationTerminationRecoding2006, title = {Regulation of {{Termination}} and {{Recoding}}.}, booktitle = {Translational {{Control}} in {{Biology}} and {{Medicine}}.}, author = {Dinman, J.D. and Berry, M.J.}, year = 2006, series = {Cold {{Spring Harbor Monograph Series}} 48}, volume = {3⬚ ⬚}, publisher = {Cold Spring Harbor Press}, address = {Cold Spring Harbor, NY}, collaborator = {Mathews, M.B. and Sonenberg, N. and Hershey, J.W.B.}, isbn = {ISBN 0-87969-767-9}, keywords = {BIOLOGY,Cold,nosource,recoding,regulation,Review,SERIES,termination} } % == BibTeX quality report for dinmanRegulationTerminationRecoding2006: % ? Title looks like it was stored in title-case in Zotero

@article{dinmanProgrammedRibosomalFrameshifting2006a, title = {Programmed {{Ribosomal Frameshifting Goes Beyond Viruses}}: {{Organisms}} from All Three Kingdoms Use Frameshifting to Regulate Gene Expression, Perhaps Signaling a Paradigm Shift}, author = {Dinman, J.D.}, year = 2006, month = nov, journal = {Microbe Wash.DC.}, volume = {1}, number = {11}, pages = {521–527}, url = {PM:17541450}, keywords = {BIOLOGY,expression,Frameshifting,gene,Gene Expression,GENE-EXPRESSION,Genetic,genetics,La,MOLECULAR-GENETICS,No DOI found,nosource,paradigm shift,Review,ribosomal frameshifting,Viruses} } % == BibTeX quality report for dinmanProgrammedRibosomalFrameshifting2006a: % ? Possibly abbreviated journal title Microbe Wash.DC.

@article{dinmanEukaryoticRibosomeCurrent2009, title = {The Eukaryotic Ribosome: Current Status and Challenges.}, author = {Dinman, J.D.}, year = 2009, month = may, journal = {The Journal of biological chemistry}, volume = {284}, number = {18}, pages = {11761–11765}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.R800074200}, url = {http://www.jbc.org/content/284/18/11761.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2673243&tool=pmcentrez&rendertype=abstract}, abstract = {Despite having been identified first, their greater degree of complexity has resulted in our understanding of eukaryotic ribosomes lagging behind that of their bacterial and archaeal counterparts. A much more complicated biogenesis program results in ribosomes that are structurally, biochemically, and functionally more complex. However, recent advances in molecular genetics and structural biology are helping to reveal the intricacies of the eukaryotic ribosome and to address many longstanding questions regarding its many roles in the regulation of gene expression.}, pmid = {19117941}, keywords = {Animals,Bacterial,BIOGENESIS,BIOLOGY,chemistry,COMPLEX,COMPLEXES,Eukaryotic Cells,Eukaryotic Cells: metabolism,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,expression,gene,Gene Expression,Gene Expression Regulation,Gene Expression Regulation: physiology,GENE-EXPRESSION,Genetic,genetics,Humans,La,metabolism,MOLECULAR-GENETICS,nosource,physiology,regulation,Review,ribosome,Ribosomes,Ribosomes: chemistry,Ribosomes: genetics,Ribosomes: metabolism,Structural,Structure-Activity Relationship,Support} } % == BibTeX quality report for dinmanEukaryoticRibosomeCurrent2009: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{dinmanExpandingRibosomalUniverse2009, title = {Expanding the Ribosomal Universe}, author = {Dinman, J.D. and Kinzy, T.G.}, year = 2009, month = dec, journal = {Structure}, volume = {17}, number = {12}, pages = {1547–1548}, publisher = {Elsevier Ltd}, issn = {0969-2126}, doi = {10.1016/j.str.2009.11.003}, url = {http://dx.doi.org/10.1016/j.str.2009.11.003 http://www.sciencedirect.com/science/article/pii/S0969212609004250 http://linkinghub.elsevier.com/retrieve/pii/S0969212609004250 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2801869&tool=pmcentrez&r}, abstract = {In this issue of Structure, Taylor et al. (2009) present the most complete model of an eukaryotic ribosome to date. This achievement represents a critical milestone along the path to structurally defining the unique aspects of the eukaryotic protein synthetic machinery.}, pmid = {20004156}, keywords = {Biological,BIOLOGY,Cryoelectron Microscopy,EUKARYOTIC RIBOSOME,Genetic,genetics,Humans,La,MODEL,Models,MOLECULAR-GENETICS,nosource,protein,ribosome,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,Ribosomes: ultrastructure,structure} }

@article{dinosDissectingRibosomalInhibition2004, title = {Dissecting the Ribosomal Inhibition Mechanisms of Edeine and Pactamycin: The Universally Conserved Residues {{G693}} and {{C795}} Regulate {{P-site RNA}} Binding}, author = {Dinos, G. and Wilson, D.N. and Teraoka, Y. and Szaflarski, W. and Fucini, P. and Kalpaxis, D. and Nierhaus, K.H.}, year = 2004, month = jan, journal = {Molecular cell}, volume = {13}, number = {1}, pages = {113–124}, publisher = {Elsevier}, doi = {10.1016/S1097-2765(04)00002-4}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276504000024}, abstract = {The crystal structures of the universal translation-initiation inhibitors edeine and pactamycin bound to ribosomal 30S subunit have revealed that edeine induces base pairing of G693:C795, residues that constitute the pactamycin binding site. Here, we show that base pair formation by addition of edeine inhibits tRNA binding to the P site by preventing codon-anticodon interaction and that addition of pactamycin, which rebreaks the base pair, can relieve this inhibition. In addition, edeine induces translational misreading in the A site, at levels comparable to those induced by the classic misreading antibiotic streptomycin. Binding of pactamycin between residues G693 and C795 strongly inhibits translocation with a surprising tRNA specificity but has no effect on translation initiation, suggesting that reclassification of this antibiotic is necessary. Collectively, these results suggest that the universally conserved G693:C795 residues regulate tRNA binding at the P site of the ribosome and influence translocation efficiency}, keywords = {0,A SITE,A-SITE,ACID,antibiotic,Anticodon,BASE,Base Pairing,BASE-PAIR,BINDING,Binding Sites,BINDING-SITE,Codon,CODON-ANTICODON INTERACTION,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,Cytosine,drug effects,Edeine,efficiency,Escherichia coli,GREEN FLUORESCENT PROTEIN,Guanine,INHIBITION,INHIBITOR,inhibitors,initiation,La,Luminescent Proteins,MECHANISM,MECHANISMS,metabolism,ModelsBiological,ModelsMolecular,nosource,Nucleic Acid Synthesis Inhibitors,P SITE,P-SITE,Pactamycin,pharmacology,protein,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,Proteins,RESIDUES,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNARibosomal,RNATransfer,SITE,SPECIFICITY,Streptomycin,structure,SUBUNIT,supportnon-u.s.gov’t,SYNTHESIS INHIBITORS,translation,TRANSLATION INITIATION,TranslationGenetic,translocation,tRNA,tRNA binding} } % == BibTeX quality report for dinosDissectingRibosomalInhibition2004: % ? unused Journal abbr (“Mol.Cell”)

@article{dmitrievConversion48STranslation2003, title = {Conversion of {{48S}} Translation Preinitiation Complexes into {{80S}} Initiation Complexes as Revealed by Toeprinting}, author = {Dmitriev, S.E. and Pisarev, A.V. and Rubtsova, M.P. and Dunaevsky, Y.E. and Shatsky, I.N.}, year = 2003, month = jan, journal = {FEBS letters}, volume = {533}, number = {1-3}, pages = {99–104}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579302037766}, abstract = {A method of analysis of translation initiation complexes by toeprinting has recently acquired a wide application to investigate molecular mechanisms of translation initiation in eukaryotes. So far, this very fruitful approach was used when researchers did not aim to discriminate between patterns of toeprints for 48S and 80S translation initiation complexes. Here, using cap-dependent and internal ribosomal entry site (IRES)-dependent mRNAs, we show that the toeprint patterns for 48S and 80S complexes are distinct whether the complexes are assembled in rabbit reticulocyte lysate or from fully purified individual components. This observation allowed us to demonstrate for the first time a delay in the conversion of the 48S complex into the 80S complex for beta-globin and encephalomyocarditis virus (EMCV) RNAs, and to assess the potential of some 80S antibiotics to block polypeptide elongation. Besides, additional selection of the authentic initiation codon among three consecutive AUGs that follow the EMCV IRES was revealed at steps subsequent to the location of the initiation codon by the 40S ribosomal subunit}, keywords = {0,analysis,Animals,antibiotic,antibiotics,AUG,Base Sequence,BIOLOGY,Cap,chemistry,Codon,CodonInitiator,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,Dna,DNAComplementary,elongation,ENCEPHALOMYOCARDITIS VIRUS,Eukaryotic Initiation Factors,Genetic Techniques,genetics,Globin,Globins,In Vitro,initiation,INITIATION-FACTOR,INTERNAL RIBOSOMAL ENTRY,internal ribosomal entry site,La,LOCATION,lysate,Macromolecular Systems,MECHANISM,MECHANISMS,metabolism,MOLECULAR MECHANISMS,Molecular Weight,mRNA,No DOI found,nosource,PATTERNS,POLYPEPTIDE,Rabbits,Reticulocytes,RIBOSOMAL-SUBUNIT,Rna,Rna Caps,RNAMessenger,RnaViral,SELECTION,SITE,SUBUNIT,supportnon-u.s.gov’t,SYSTEM,SYSTEMS,toeprinting,translation,TRANSLATION INITIATION,virus} } % == BibTeX quality report for dmitrievConversion48STranslation2003: % ? unused Journal abbr (“FEBS Lett.”)

@article{dohmeRole5SRNA1976, title = {Role of {{5S RNA}} in Assembly and Function of the {{50S}} Subunit from {{Escherichia}} Coli}, author = {Dohme, F. and Nierhaus, K.H.}, year = 1976, month = jul, journal = {Proceedings of the National Academy of Sciences}, volume = {73}, number = {7}, pages = {2221–2225}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.73.7.2221}, url = {http://www.pnas.org/content/73/7/2221.short}, abstract = {Total reconstitution experiments performed under various conditions revealed that 5S RNA plays an important role during the last assembly step in vitro leading to an active 50S particle. For the preceding steps this RNA species is dispensable. However, 50S RNA can be integrated efficiently during any of the assembly steps in vitro. The 47S particle, reconstituted in two steps and lacking 5S RNA, shows low but significant activity in many functional tests. High activity could be obtained by incubating this particle with 5S RNA alone, demonstrating the importance of the 5S RNA in generating an active ribosomal conformation. In particular, the activity of the peptidyltransferase (peptidyl-tRNA:aminoacyl-tRNA N- peptidyltransferase; EC 2.3.2.12) center is drastically influenced by 5S RNA. No significant factor-dependent tRNA binding to the A-site was observed with the 47S particle, in contrast to the corresponding P-site binding. The elongation factor G dependent GTPase activity was not affected by the lack of 5S RNA}, keywords = {5S rRNA,76244497,A-SITE,assembly,BINDING,Binding Sites,Cell-Free System,elongation,Escherichia coli,ESCHERICHIA-COLI,GTP Phosphohydrolase,GTPase,In Vitro,IN-VITRO,metabolism,nosource,P-SITE,Peptide Elongation Factors,Peptidyltransferase,physiology,Ribosomal Proteins,Ribosomes,Rna,RNABacterial,RNARibosomal,RNATransfer,Structure-Activity Relationship,SUBUNIT,tRNA,ultrastructure} } % == BibTeX quality report for dohmeRole5SRNA1976: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A.”)

@article{dokalDyskeratosisCongenitaAll2000, title = {Dyskeratosis Congenita in All Its Forms}, author = {Dokal, I.}, year = 2000, month = jul, journal = {British journal of haematology}, volume = {110}, number = {4}, pages = {768–779}, publisher = {Wiley Online Library}, doi = {10.1046/j.1365-2141.2000.02109.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2141.2000.02109.x/full}, abstract = {Dyskeratosis congenita (DC) is a rare inherited multi-system disorder. Although DC is classically characterized by mucocutaneous features, the vast majority of patients develop hematologic abnormalities, and in its occult form the disease can present as aplastic anemia. The gene responsible for the X-linked form of the disease encodes a protein involved in ribosome biogenesis and in stabilizing the telomerase complex, while the autosomal dominant form is caused by mutations in the core RNA component of telomerase. It has been suggested that DC is primarily a disease of defective telomere maintenance. Premature shortening of telomeres resulting in a limited proliferative potential of stem cells would explain the pathology observed in DC, as the affected tissues are those that require constant renewal}, keywords = {0,AnemiaAplastic,cell cycle,Cell Cycle Proteins,Consanguinity,diagnosis,Dyskeratosis Congenita,Female,FORM,Gene Therapy,GenesRecessive,genetics,human,Humans,La,Linkage (Genetics),Male,Mutation,nosource,Nuclear Proteins,protein,Proteins,Registries,Review,Support,therapy,trends,X Chromosome} } % == BibTeX quality report for dokalDyskeratosisCongenitaAll2000: % ? unused Journal abbr (“Br.J.Haematol.”)

@article{dokudovskayaLoopIV5S1996, title = {Loop {{IV}} of {{5S}} Ribosomal {{RNA}} Has Contacts Both to Domain {{II}} and to Domain {{V}} of the {{23S RNA}}.}, author = {Dokudovskaya, S. and Dontsova, O. and Shpanchenko, O. and Bogdanov, A. and Brimacombe, R.}, year = 1996, month = feb, journal = {RNA.}, volume = {2}, number = {2}, pages = {146–152}, publisher = {Cold Spring Harbor Lab}, url = {http://rnajournal.cshlp.org/content/2/2/146.short}, abstract = {An analogue of 5S rRNA, containing a random distribution of thiouridine residues in place of normal uridine, was prepared by T7 transcription from a suitable DNA template. The modified RNA molecule was reconstituted into 50S or 70S ribosomes, and the thiouridine residues were activated by irradiation at 350 nm. Crosslinks generated between the 5S and 23S RNA were analyzed by our standard procedures. Two crosslink sites were identified, one to residue A-960 at the loop-end of helix 39 in Domain II, and the other to C-2475 at the loop-end of helix 89 in Domain V of the 23S RNA. Both crosslinks involved residue U- 89 of the 5S RNA, that in Domain V corresponding to the principal crosslink found in a previously published series of experiments. The relative intensities of the two crosslink sites were found to be highly dependent on individual preparations of 50S ribosomal proteins and 23S RNA. The results are discussed in terms of the three-dimensional folding and dynamics of the 23S RNA within the 50S subunit}, keywords = {0,23S RNA,5S RNA,5S rRNA,70S RIBOSOME,Binding Sites,chemistry,Dna,DOMAIN,DOMAIN-II,DOMAIN-V,DYNAMICS,La,LOOP,metabolism,Molecular Structure,No DOI found,nosource,Nucleic Acid Conformation,protein,Proteins,Research SupportNon-U.S.Gov’t,RESIDUES,Ribosomal Proteins,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNARibosomal23S,RNARibosomal5S,rRNA,Sequence Analysis,SERIES,SITE,SITES,SUBUNIT,supportnon-u.s.gov’t,TEMPLATE,Thiouridine,transcription,Uridine} } % == BibTeX quality report for dokudovskayaLoopIV5S1996: % ? Possibly abbreviated journal title RNA.

@article{dokudovskayaMRNAribosomeInteractions1993, title = {{{mRNA-ribosome}} Interactions}, author = {Dokudovskaya, S.S. and Dontsova, O.A. and Bogdanova, S.L. and Bogdanov, A.A. and Brimacombe, R.}, year = 1993, month = oct, journal = {Biotechnology and applied biochemistry}, volume = {18 ( Pt 2)}, number = {2}, pages = {149–155}, publisher = {Wiley Online Library}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1470-8744.1993.tb00261.x/abstract}, abstract = {Synthetic mRNA analogues were constructed with sequences related to the Cro-protein mRNA from lambda-phage and prepared by T7 transcription. Each mRNA contained several thiouridine (thio-U) residues. The regions upstream from the AUG initiator codon of the mRNA were the same in all the messages, whereas in the downstream part the thio-U residues were placed in selected positions. These positions covered the region from +4 to +16 (A in the initiator AUG codon being defined as +1). After binding to the ribosome in the presence of initiator tRNA the thio-U residues were activated by u.v. irradiation and the resulting sites of cross-linking to 16 S rRNA and ribosomal proteins were analysed. Cross- links to several ribosomal proteins were identified in different types of complex. Changes in the conformation of the small ribosomal subunit in different initiation and elongation complexes are discussed}, keywords = {0,Bacteriophage lambda,Base Sequence,BINDING,biosynthesis,chemical synthesis,chemistry,Codon,COMPLEX,COMPLEXES,CROSS-LINKING,Cross-Linking Reagents,elongation,genetics,initiation,La,metabolism,Molecular Sequence Data,mRNA,No DOI found,nosource,protein,Proteins,Repressor Proteins,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNAMessenger,RNARibosomal16S,rRNA,sequence,SUBUNIT,Thiouridine,transcription,Transcription Factors,tRNA} } % == BibTeX quality report for dokudovskayaMRNAribosomeInteractions1993: % ? unused Journal abbr (“Biotechnol.Appl.Biochem.”)

@article{dokudovskayaTelomeraseUnusualRNAcontaining1997a, title = {Telomerase Is an Unusual {{RNA-containing}} Enzyme. {{A}} Review.}, author = {Dokudovskaya, S.S. and Petrov, A.V. and Dontsova, O.A. and Bogdanov, A.A.}, year = 1997, month = nov, journal = {Biochemistry (Mosc.)}, volume = {62}, number = {11}, eprint = {9467844}, eprinttype = {pubmed}, pages = {1206–1215}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9467844}, abstract = {Telomeres, the natural ends of linear eukaryotic chromosomes, are essential for protecting chromosomes from degradation and fusion. The synthesis of telomere DNA repeats in most eukaryotes is performed by a special enzyme, telomerase. Telomerase, a ribonucleoprotein enzyme, is a specialized reverse transcriptase utilizing its RNA moiety as a template for synthesis of telomeric DNA. Enzymatic properties and results of comparative analysis of telomerase RNA and protein structures from different eukaryotic systems are discussed in this review}, keywords = {analysis,animal,Base Sequence,chemistry,Chromosomes,degradation,Dna,DNA Replication,La,metabolism,No DOI found,nosource,Nucleic Acid Conformation,physiology,protein,Repetitive SequencesNucleic Acid,Review,Rna,structure,Substrate Specificity,SYSTEM,Telomerase,Telomere} } % == BibTeX quality report for dokudovskayaTelomeraseUnusualRNAcontaining1997a: % ? Possibly abbreviated journal title Biochemistry (Mosc.)

@article{dolinskiExpandingYeastKnowledge1998, title = {Expanding Yeast Knowledge Online}, author = {Dolinski, K. and Ball, C.A. and Chervitz, S.A. and Dwight, S.S. and Harris, M.A. and Roberts, S. and Roe, T. and Cherry, J.M. and Botstein, D.}, year = 1998, month = dec, journal = {Yeast (Chichester, England)}, volume = {14}, number = {16}, pages = {1453–1469}, publisher = {NIH Public Access}, doi = {10.1002/(SICI)1097-0061(199812)14:16<1453::AID-YEA348>3.0.CO;2-G}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037831/}, abstract = {The completion of the Saccharomyces cerevisiae genome sequencing project(11) and the continued development of improved technology for large-scale genome analysis have led to tremendous growth in the amount of new yeast genetics and molecular biology data. Efficient organization, presentation, and dissemination of this information are essential if researchers are to exploit this knowledge. In addition, the development of tools that provide efficient analysis of this information and link it with pertinent information from other systems is becoming increasingly important at a time when the complete genome sequences of other organisms are becoming available. The aim of this review is to familiarize biologists with the type of data resources currently available on the World Wide Web (WWW). (C) 1998 John Wiley & Sons, Ltd}, keywords = {analysis,DATA-BANK,development,Genetic,genetics,Genome,Munich Information Center for Protein Sequences,nosource,protein,Review,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces Genome Database,SACCHAROMYCES-CEREVISIAE,sequence,SGD,SYSTEM,World Wide Web,yeast,yeast protein database} }

@article{dominguezIdentificationElongationFactor1998, title = {Identification of Elongation Factor 2 as the Essential Protein Targeted by Sordarins in {{Candida}} Albicans}, author = {Dominguez, J.M. and Martin, J.J.}, year = 1998, journal = {Antimicrobial agents and chemotherapy}, volume = {42}, number = {9}, pages = {2279–2283}, publisher = {Am Soc Microbiol}, doi = {10.1128/AAC.42.9.2279}, url = {http://aac.asm.org/cgi/content/full/42/9/2279?view=full&pmid=9736549}, abstract = {The target for sordarins in Candida albicans has been elucidated. Kinetic experiments of sordarin inhibition as well as displacement experiments showed that the formation of a sordarin-target complex follows a reversible mechanism. Binding of tritiated drug to the target is enhanced in the presence of ribosomes. Isolation of the target by classical protein purification methods has allowed us to identify it as elongation factor 2. This is in agreement with the nature of sordarin derivatives as specific inhibitors of the elongation cycle within protein synthesis in yeasts}, keywords = {98409717,Amino Acid Sequence,AntibioticsAntifungal,BINDING,Candida albicans,Carrier Proteins,COMPLEX,COMPLEXES,drug effects,elongation,IDENTIFICATION,INHIBITION,isolation & purification,MECHANISM,metabolism,Methods,Molecular Sequence Data,nosource,Peptide Elongation Factors,pharmacology,protein,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,purification,ribosome,Ribosomes,yeast,Yeasts} } % == BibTeX quality report for dominguezIdentificationElongationFactor1998: % ? unused Journal abbr (“Antimicrob.Agents Chemother.”)

@article{dominguezSordarinInhibitsFungal1999, title = {Sordarin Inhibits Fungal Protein Synthesis by Blocking Translocation Differently to Fusidic Acid}, author = {Dominguez, J.M. and {Gomez-Lorenzo}, M.G. and Martin, J.J.}, year = 1999, journal = {J.Biol.Chem.}, volume = {274}, number = {32}, pages = {22423–22427}, doi = {10.1074/jbc.274.32.22423}, abstract = {Sordarin derivatives are selective inhibitors of fungal protein synthesis, which specifically impair elongation factor 2 (EF-2) function. We have studied the effect of sordarin on the ribosome-dependent GTPase activity of EF-2 from Candida albicans in the absence of any other component of the translation system. The effect of sordarin turned out to be dependent both on the ratio of ribosomes to EF-2 and on the nature of the ribosomes. When the amount of EF-2 exceeded that of ribosomes sordarin inhibited the GTPase activity following an inverted bell-shaped dose-response curve, whereas when EF-2 and ribosomes were in equimolar concentrations sordarin yielded a typical sigmoidal dose-dependent inhibition. However, when ricin-treated ribosomes were used, sordarin stimulated the hydrolysis of GTP. These results were compared with those obtained with fusidic acid, showing that both drugs act in a different manner. All these data are consistent with sordarin blocking the elongation cycle at the initial steps of translocation, prior to GTP hydrolysis. In agreement with this conclusion, sordarin prevented the formation of peptidyl-[(3)H]puromycin on polysomes from Candida albicans}, keywords = {99357771,AntibioticsAntifungal,Candida albicans,Comparative Study,COMPONENT,Dose-Response RelationshipDrug,drug effects,drugs,EF-2,elongation,Fusidic Acid,GTP,GTP Phosphohydrolase-Linked Elongation Factors,GTPase,Guanosine Triphosphate,Hydrolysis,INHIBITION,metabolism,ModelsBiological,nosource,Peptide Chain Elongation,Peptide Elongation Factors,pharmacology,polysomes,protein,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,Puromycin,ribosome,Ribosomes,Ricin,SYSTEM,translation,translocation} } % == BibTeX quality report for dominguezSordarinInhibitsFungal1999: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{donahueMutationsZnII1988a, title = {Mutations at a {{Zn}}({{II}}) Finger Motif in the Yeast {{eIF2'a}} Gene Alter Ribosomal Start-Site Selection during the Scanning Process.}, author = {Donahue, T.F. and Cigan, A.M. and Pabich, E.K. and {Castilho-Vavavicius}, B.}, year = 1988, journal = {Cell}, volume = {54}, pages = {621–632}, doi = {10.1016/S0092-8674(88)80006-0}, keywords = {gene,Mutation,MUTATIONS,nosource,sui,yeast} }

@article{donahueGeneticSelectionMutations1988a, title = {Genetic Selection for Mutations That Reduce or Abolish Ribosomal Recognition of the ⬚{{HIS4}}⬚ Translational Initiator Region.}, author = {Donahue, T.F. and Cigan, A.M.}, year = 1988, journal = {Mol.Cell.Biol.}, volume = {8}, pages = {2955–2963}, keywords = {Genetic,IDENTIFICATION,Multiple DOI,Mutation,MUTATIONS,nonfile,nosource,sui,sui1,yeast} } % == BibTeX quality report for donahueGeneticSelectionMutations1988a: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@incollection{donahueGeneticApproachesTranslation2000a, title = {Genetic Approaches to Translation Initiation in ⬚{{Saccharomyces}} Cerevisiae⬚.}, booktitle = {Translational Control of Gene Expression}, author = {Donahue, T.F.}, year = 2000, pages = {487–502}, publisher = {Cold Spring Harbor Press}, address = {Cold Spring Harbor, NY}, collaborator = {Sonnenberg, N. and Hershey, J.W.B. and Mathews, M.B.}, keywords = {CEREVISIAE,expression,gene,Gene Expression,GENE-EXPRESSION,Genetic,initiation,nosource,review article,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,translation,TRANSLATION INITIATION} }

@article{dongGeneticIdentificationYeast2008a, title = {Genetic Identification of Yeast {{18S rRNA}} Residues Required for Efficient Recruitment of Initiator {{tRNA}}({{Met}}) and {{AUG}} Selection}, author = {Dong, J. and Nanda, J.S. and Rahman, H. and Pruitt, M.R. and Shin, B.S. and Wong, C.M. and Lorsch, J.R. and Hinnebusch, A.G.}, year = 2008, journal = {Genes Dev.}, volume = {22}, number = {16}, pages = {2242–2255}, doi = {10.1101/gad.1696608}, url = {PM:18708582}, abstract = {High-resolution structures of bacterial 70S ribosomes have provided atomic details about mRNA and tRNA binding to the decoding center during elongation, but such information is lacking for preinitiation complexes (PICs). We identified residues in yeast 18S rRNA critical in vivo for recruiting methionyl tRNA(i)(Met) to 40S subunits during initiation by isolating mutations that derepress GCN4 mRNA translation. Several such Gcd(-) mutations alter the A928:U1389 base pair in helix 28 (h28) and allow PICs to scan through the start codons of upstream ORFs that normally repress GCN4 translation. The A928U substitution also impairs TC binding to PICs in a reconstituted system in vitro. Mutation of the bulge G926 in h28 and certain other residues corresponding to direct contacts with the P-site codon or tRNA in bacterial 70S complexes confer Gcd(-) phenotypes that (like A928 substitutions) are suppressed by overexpressing tRNA(i)(Met). Hence, the nonconserved 928:1389 base pair in h28, plus conserved 18S rRNA residues corresponding to P-site contacts in bacterial ribosomes, are critical for efficient Met-tRNA(i)(Met) binding and AUG selection in eukaryotes}, keywords = {0,70S RIBOSOME,Amino Acid Substitution,AUG,Bacterial,BASE,BASE-PAIR,BINDING,CEREVISIAE,Child,Codon,CodonInitiator,CODONS,COMPLEX,COMPLEXES,decoding,development,elongation,Eukaryotic Initiation Factor-2B,GCN4,gene,gene regulation,Genetic,genetics,human,IDENTIFICATION,In Vitro,IN-VITRO,IN-VIVO,INFORMATION,initiation,La,metabolism,mRNA,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Open Reading Frames,P SITE,P-SITE,Peptide Chain InitiationTranslational,Phenotype,protein,Proteins,RECRUITMENT,regulation,RESIDUES,ribosome,Ribosomes,Rna,RNAFungal,RNARibosomal18S,RNATransferMet,rRNA,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SELECTION,START CODON,structure,SUBUNIT,SUBUNITS,Support,SYSTEM,translation,tRNA,tRNA binding,UPSTREAM,yeast} } % == BibTeX quality report for dongGeneticIdentificationYeast2008a: % ? Possibly abbreviated journal title Genes Dev.

@article{donlyFrameshiftAutoregulationGene1990, title = {Frameshift Autoregulation in the Gene for {{Escherichia}} Coli Release Factor 2: Partly Functional Mutants Result in Frameshift Enhancement}, author = {Donly, B.C. and Edgar, C.D. and Adamski, F.M. and Tate, W.P.}, year = 1990, month = nov, journal = {Nucleic Acids Research}, volume = {18}, number = {22}, pages = {6517–6522}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/18.22.6517}, url = {http://nar.oxfordjournals.org/content/18/22/6517.short}, keywords = {assays,BINDING,Chimeric Proteins,efficiency,Escherichia coli,ESCHERICHIA-COLI,expression,frameshift,Frameshifting,gene,Genes,Hydrolysis,In Vitro,IN-VITRO,IN-VIVO,nosource,pausing,protein,Proteins,regulation,ribosome,termination,translation} }

@article{donlyTightlyControlledExpression1990a, title = {Tightly Controlled Expression Systems for the Production and Purification of {{Escherichia}} Coli Release Factor 1.}, author = {Donly, B.C. and Edgar, C.D. and Williams, J.M. and Tate, W.P.}, year = 1990, journal = {Biochemistry International}, volume = {20}, number = {3}, eprint = {2189411}, eprinttype = {pubmed}, pages = {437–443}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2189411}, keywords = {Escherichia coli,ESCHERICHIA-COLI,expression,gene,Genes,No DOI found,nosource,Plasmids,protein,purification,SYSTEM} }

@article{donovanTranscriptionalRegulationRibosomal1986, title = {Transcriptional Regulation of Ribosomal Proteins during a Nutritional Upshift in {{Saccharomyces}} Cerevisiae.}, author = {Donovan, D.M. and Pearson, N.J.}, year = 1986, month = jul, journal = {Molecular and cellular biology}, volume = {6}, number = {7}, pages = {2429–2435}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/6/7/2429}, abstract = {The relative rates of synthesis of Saccharomyces cerevisiae ribosomal proteins increase coordinately during a nutritional upshift. We constructed a gene fusion which contained 528 base pairs of sequence upstream from and including the TATA box of ribosomal protein gene rp55-1 (S16A-1) fused to a CYC1-lacZ fusion. This fusion was integrated in single copy at the rp55-1 locus in the yeast genome. During a nutritional upshift, in which glucose was added to cells growing in an ethanol-based medium, we found that the increase in the relative rate of synthesis of the beta-galactosidase protein product followed the same kinetics as the change in relative rates of synthesis of several ribosomal proteins measured in the same experiment. This demonstrates that the nontranscribed sequences upstream from the rp55-1 gene, which are present in the fusion, are sufficient to mediate the change in rates of synthesis characteristic of ribosomal proteins under these conditions. The results also suggest that a change in transcription rates is mainly responsible for the increase in relative rates of synthesis of ribosomal proteins during a nutritional upshift in S. cerevisiae}, keywords = {87064540,Base Sequence,beta-Galactosidase,Chromosome Mapping,Endonucleases,Ethanol,gene,genetics,Genome,Glucose,Kinetics,media,metabolism,Multiple DOI,nonfile,nosource,pharmacology,Plasmids,protein,Proteins,regulation,Ribosomal Proteins,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,transcription,TranscriptionGenetic,yeast} } % == BibTeX quality report for donovanTranscriptionalRegulationRibosomal1986: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{dontsovaStemloopIV5S1994, title = {Stem-Loop {{IV}} of {{5S rRNA}} Lies Close to the Peptidyltransferase Center}, author = {Dontsova, O. and Tishkov, V. and Dokudovskaya, S. and Bogdanov, A. and Doring, T. and {Rinke-Appel}, J. and Thamm, S. and Greuer, B. and Brimacombe, R.}, year = 1994, month = may, journal = {Proceedings of the National Academy of Sciences}, volume = {91}, number = {10}, pages = {4125–4129}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.91.10.4125}, url = {http://www.pnas.org/content/91/10/4125.short}, abstract = {A DNA fragment containing the Escherichia coli 5S rDNA sequence linked to a T7 promoter was prepared by PCR from an M13 clone carrying the 5S- complementary sequence. The DNA was transcribed with T7 polymerase using a mixture of [alpha-32P]UTP and 4-thio-UTP, yielding a transcript in which approximately 18% of the uridine residues were randomly replaced by thiouridine. This modified 5S RNA could be reconstituted efficiently into 50S ribosomal subunits or 70S functional complexes. The reconstituted particles were irradiated at wavelengths above 300 nm, and the crosslinked ribosomal components were identified. A crosslink in high yield was reproducibly observed between the modified 5S RNA and 23S RNA, involving residue U-89 of the 5S RNA (at the loop end of helix IV) linked to nucleotide 2477 of the 23S RNA in the loop end of helix 89, immediately adjacent to the peptidyltransferase “ring.” On the basis of this result, and in combination with earlier immunoelectron microscopic data, we propose a model for the orientation of the 5S RNA in the 50S subunit}, keywords = {5S rRNA,94240090,Base Sequence,biosynthesis,chemistry,COMPLEX,COMPLEXES,COMPONENT,Dna,DNA Primers,DNARibosomal,enzymology,Escherichia coli,ESCHERICHIA-COLI,genetics,metabolism,ModelsStructural,Molecular Sequence Data,nosource,Nucleic Acid Conformation,PCR,Peptidyltransferase,polymerase,Polymerase Chain Reaction,rDNA,Ribonuclease HCalf Thymus,Ribosomes,Rna,RNA-Directed DNA Polymerase,RNARibosomal5S,rRNA,sequence,SUBUNIT,supportnon-u.s.gov’t,Thiouridine,TranscriptionGenetic,Uridine,Uridine Triphosphate} } % == BibTeX quality report for dontsovaStemloopIV5S1994: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A.”)

@article{dontsovaSynthesisColiCells1989, title = {[{{Synthesis}} in {{E}}. Coli Cells of Short {{RNA}} Encoded in Plasmids]}, author = {Dontsova, O.A. and Bogdanova, S.L. and Kopylov, A.M.}, year = 1989, month = may, journal = {Biokhimiia.}, volume = {54}, number = {5}, pages = {870–876}, abstract = {The synthesis of 5S rRNA and 4.5S RNA in E. coli HB 101 cells harbouring plasmids pKK 5-1 and pKK 247-2 was studied. The plasmids were derived from pBK 322 and contained genes coding for 5S rRNA and 4.5S RNA with regulatory elements of an rRNA transcription operon rrn B. When the cells were grown on enriched or minimal media (2 and 0.3 duplications per hour), the synthesis of both 5S rRNA and 4.5S RNA was proportional to the gene dosage and was greater in the plasmid than in the host strain. Such RNA accumulation did not change the cell growth parameters and was thus not toxic for the cells. At high growth rates, the RNA synthesis in the cells became excessive, and the processing system was upset with the accumulation of RNA precursors. The fact confirms the hypothesis, according to which the whole rRNA operon is essential for its own feedback regulation}, keywords = {5S rRNA,89335861,biosynthesis,ELEMENTS,Escherichia coli,Feedback,gene,Gene Dosage,Genes,genetics,media,No DOI found,nosource,Operon,Plasmids,Promoter Regions (Genetics),regulation,Rna,RNA Precursors,RNARibosomal,RNARibosomal5S,rRNA,rRNA Operon,SYSTEM,transcription,TranscriptionGenetic} } % == BibTeX quality report for dontsovaSynthesisColiCells1989: % ? Possibly abbreviated journal title Biokhimiia.

@article{dontsovaPhotoaffinityModificationSmall1990, title = {[{{Photoaffinity}} Modification of Small Ribosomal Subunits of {{Escherichia}} Coli with 5’-Diaziryl Derivatives of {{mRNA}}]}, author = {Dontsova, O.A. and Bogdanova, S.L. and Rozen, K.V. and Skriabin, G.A. and Skripkin, E.A. and Kopylov, A.M. and Bogdanov, A.A.}, year = 1990, journal = {Dokl.Akad.Nauk SSSR}, volume = {313}, number = {3}, pages = {730–733}, url = {PM:1701378}, keywords = {0,Affinity Labels,Azirines,Bacterial,Base Sequence,ChromatographyHigh Pressure Liquid,Codon,drug effects,Escherichia coli,ESCHERICHIA-COLI,genetics,La,metabolism,ModelsMolecular,modification,Molecular Sequence Data,No DOI found,nosource,Photochemistry,Plasmids,protein,Proteins,Ribosomal Proteins,Ribosomes,Rna,RNABacterial,RNAMessenger,SUBUNIT,TranslationGenetic} } % == BibTeX quality report for dontsovaPhotoaffinityModificationSmall1990: % ? Possibly abbreviated journal title Dokl.Akad.Nauk SSSR

@article{dontsova5SRRNAproteinComplex1990, title = {[{{The 5S rRNA-protein}} Complex of {{Escherichia}} Coli Studied by Carbodiimide Modification]}, author = {Dontsova, O.A. and Efimov, A.V. and Kopylov, A.M.}, year = 1990, journal = {Nauchnye.Doki.Vyss.Shkoly.Biol.Nauki}, number = {2}, pages = {22–30}, url = {PM:1693861}, abstract = {5S rRNA-protein complex has been reconstituted from 5S rRNA and total protein of large (L) ribosomal subunit of Escherichia coli. The complex consists of 5S rRNA and 3 proteins only: L5, L18, L25. A water-soluble carbodiimide [N-cyclohexyl-N’-(2-morpholinoethyl)-carbodiimide-methyl-p- toluolsulp honate] cross-links L18 to 5S rRNA at pH 7.2 and L25 to 5S rRNA at pH 7.7. This pH-dependence of cross-linked proteins is a consequence of the difference in stability of the initial complex: the complex has all three proteins at pH 7.7 but L18 mainly at pH 7.2. It has been shown that L18 stimulates the chemical modification of U87 and U89 residues of 5S rRNA by carbodiimide. A model of L18-5S rRNA complex has been proposed}, keywords = {0,5S rRNA,analysis,Bacterial,Bacterial Proteins,Base Sequence,Binding Sites,Carbodiimides,COMPLEX,COMPLEXES,CROSS-LINKING,Cross-Linking Reagents,drug effects,Escherichia coli,ESCHERICHIA-COLI,genetics,Hydrogen-Ion Concentration,isolation & purification,La,ModelsMolecular,modification,Molecular Sequence Data,No DOI found,nosource,Nucleic Acid Conformation,pharmacology,protein,Protein Conformation,Proteins,Rna,RNABacterial,RNARibosomal,RNARibosomal5S,rRNA,stability,SUBUNIT} } % == BibTeX quality report for dontsova5SRRNAproteinComplex1990: % ? Possibly abbreviated journal title Nauchnye.Doki.Vyss.Shkoly.Biol.Nauki

@article{dontsovaIdentificationEscherichiaColi1992a, title = {Identification of the {{Escherichia}} Coli {{30S}} Ribosomal Subunit Protein Neighboring {{mRNA}} during Initiation of Translation}, author = {Dontsova, O.A. and Rosen, K.V. and Bogdanova, S.L. and Skripkin, E.A. and Kopylov, A.M. and Bogdanov, A.A.}, year = 1992, month = apr, journal = {Biochimie}, volume = {74}, number = {4}, pages = {363–371}, doi = {10.1016/0300-9084(92)90114-T}, url = {PM:1379079}, abstract = {To identify the proteins of the 30S ribosomal subunit of E coli that neighbor mRNA in the ternary initiation complex (mRNA30S subunittRNA(fMet), we used an affinity cross-linking approach in which photoactivated groups were attached to different positions along the mRNA chain. A series of mini-genes originating from the 5’-end region of the cro gene of lambda bacteriophage were constructed as templates for mini-mRNA synthesis. Two strategies were used to introduce photo- reactive agents into the message. According to the first, two transcripts were isolated from E coli and chemically derivatized at their 5’-ends with a photoinducible diaziril group. One of these messages allowed for localization of the 5’-end of the Shine-Dalgarno sequence while the other one allowed for labeling of the ribosome at the 5’-end side of the initiation AUG codon in the P site. According to the second approach, 5-azidouridine (5N3U) was randomly incorporated into mRNA transcripts during a T7 RNA polymerase catalyzed reaction by using a mixture of 5N3UTP and UTP. A message that had U residues at either -4, -3, -1, +2 and +14, +19, +20 positions was used (A from cro AUG is +1). Whereas cross-links with the 5N3U transcripts were essentially ‘zero-length’, the 5’-derivatized transcripts were covalently attached to ribosomal components about 14 A from the 5’-end. We found that proteins S1, S7, S5, S3 and S4 compose, or were close to, the ribosomal mRNA-binding site.(ABSTRACT TRUNCATED AT 250 WORDS)}, keywords = {0,Affinity Labels,analogs & derivatives,Azides,Bacterial,Bacterial Proteins,Base Sequence,chemistry,Codon,COMPLEX,COMPLEXES,COMPONENT,CROSS-LINKING,Cross-Linking Reagents,Escherichia coli,ESCHERICHIA-COLI,gene,genetics,IDENTIFICATION,initiation,La,Molecular Sequence Data,mRNA,nosource,P-SITE,Peptide Chain Initiation,polymerase,protein,Proteins,Ribosomal Proteins,ribosome,Rna,RNABacterial,RNAMessenger,sequence,SUBUNIT,Templates,translation,Uridine,Uridine Triphosphate} }

@article{dontsova5SRRNAStructure2005, title = {{{5S rRNA}}: Structure and Function from Head to Toe.}, author = {Dontsova, O.A. and Dinman, J.D.}, year = 2005, journal = {Int.J.Biomed.Sci.}, volume = {1⬚ ⬚}, number = {1}, pages = {2–7}, abstract = {5S rRNA is uniquely positioned so as to link together all of the functional centers of the ribosome. Previous studies have supported the hypothesis that 5S rRNA acts as a physical transducer of information, facilitating communication between the different functional centers and coordinating of the multiple events catalyzed by the ribosome. Here, we present a synthesis of both structural and genetic information to construct a more detailed picture of how 5S rRNA may act to transmit and coordinate all of the functional centers of the ribosome.}, keywords = {5S rRNA,Frameshifting,Genetic,INFORMATION,No DOI found,nosource,ribosome,rRNA,Structural,structure} } % == BibTeX quality report for dontsova5SRRNAStructure2005: % ? Possibly abbreviated journal title Int.J.Biomed.Sci.

@article{dornerMolecularAspectsRibosomal2002a, title = {Molecular Aspects of the Ribosomal Peptidyl Transferase}, author = {Dorner, S. and Polacek, N. and Schulmeister, U. and Panuschka, C. and Barta, A.}, year = 2002, month = nov, journal = {Biochem.Soc.Trans.}, volume = {30}, number = {Pt 6}, pages = {1131–1136}, abstract = {The proteins in a living cell are synthesized on a large bipartite ribonucleoprotein complex termed the ribosome. The peptidyl transferase, which polymerizes amino acids to yield peptides, is localized on the large subunit. Biochemical investigations over the past 35 years have led to the hypothesis that rRNA has a major role in all ribosomal functions. The recent high resolution X-ray structures of the ribosomal subunits clearly demonstrated that peptidyl transfer is an RNA-mediated process. As all ribosomal activities are dependent on bivalent metal ions, as is the case for most ribozymes, we investigated metal-ion-binding sites in rRNA by metal-ion-cleavage reactions. Some cleavage sites are near active sites and are evolutionarily highly conserved. The structure of the active site is flexible and undergoes changes during translocation and activation of the ribosome. Using modified P-site substrates, we showed that the 2’-OH group of the terminal adenosine is important for peptidyl transfer. These substrates were also used to investigate the metal ion dependency of the peptidyl transferase reaction}, keywords = {ACID,ACIDS,activation,Adenosine,Amino Acids,AMINO-ACID,AMINO-ACIDS,Base Sequence,chemistry,ChromatographyThin Layer,CLEAVAGE,CLEAVAGE SITE,CLEAVAGE SITES,COMPLEX,COMPLEXES,genetics,Ions,metabolism,ModelsChemical,Molecular Sequence Data,No DOI found,nosource,Nucleic Acid Conformation,P SITE,P-SITE,Peptides,peptidyl transferase,peptidyl-transfer,PEPTIDYL-TRANSFERASE,Peptidyltransferase,protein,Proteins,RESOLUTION,Review,RIBONUCLEOPROTEIN,RIBOSOMAL PEPTIDYL TRANSFERASE,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,ribozyme,RNARibosomal23S,rRNA,S,SITE,SITES,structure,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,translocation} } % == BibTeX quality report for dornerMolecularAspectsRibosomal2002a: % ? Possibly abbreviated journal title Biochem.Soc.Trans.

@article{dorsmanARSSilencerBinding1989, title = {An {{ARS}}/Silencer Binding Factor Also Activates Two Ribosomal Protein Genes in Yeast.}, author = {Dorsman, J.C. and Doorenbosch, M.M. and Maurer, C.T.C. and {deWinde}, J.H. and Mager, W.H. and Planta, R.J. and Grivell, L.A.}, year = 1989, journal = {Nucleic acids research}, volume = {17}, number = {13}, pages = {4917–4923}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/17.13.4917}, url = {http://nar.oxfordjournals.org/content/17/13/4917.short}, keywords = {BINDING,gene,Genes,L3,nosource,protein,transcription,yeast} } % == BibTeX quality report for dorsmanARSSilencerBinding1989: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{doudnaStructureFunctionEukaryotic2002a, title = {Structure and Function of the Eukaryotic Ribosome: The next Frontier}, author = {Doudna, J.A. and Rath, V.L.}, year = 2002, month = apr, journal = {Cell}, volume = {109}, number = {2}, pages = {153–156}, doi = {10.1016/S0092-8674(02)00725-0}, url = {PM:12007402}, abstract = {As the catalytic and regulatory centers of protein synthesis in cells, ribosomes are central to many aspects of cell and structural biology. Recent work highlights the unique properties and complexity of eukaryotic ribosomes and their component rRNAs and proteins}, keywords = {0,animal,biosynthesis,Catalytic Domain,COMPONENT,enzymology,Eukaryotic Cells,genetics,human,Intracellular Membranes,La,metabolism,Molecular Structure,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Review,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNARibosomal,rRNA,Structural,structure,TranslationGenetic,ultrastructure,Viral Physiology} }

@article{doyonNovelGagPolFrameshift1998, title = {Novel {{Gag-Pol}} Frameshift Site in Human Immunodeficiency Virus Type 1 Variants Resistant to Protease Inhibitors}, author = {Doyon, L. and Payant, C. and {Brakier-Gingras}, L. and Lamarre, D.}, year = 1998, month = jul, journal = {Journal of virology}, volume = {72}, number = {7}, pages = {6146–6150}, publisher = {Am Soc Microbiol}, doi = {10.1128/JVI.72.7.6146-6150.1998}, url = {http://jvi.asm.org/cgi/content/abstract/72/7/6146}, abstract = {Human immunodeficiency virus type 1 (HIV-1) variants resistant to protease inhibitors have been shown to contain a mutation in the p1/p6 Gag precursor cleavage site. At the messenger RNA level, this mutation generates a U UUU UUU sequence that is reminiscent of the U UUU UUA sequence required for ribosomal frameshifting and Gag-Pol synthesis. To test whether the p1/p6 cleavage site mutation was generating a novel frameshift site, HIV sequences were inserted in translation vectors containing a chloramphenicol acetyltransferase (CAT) reporter gene requiring -1 frameshifting for expression. All sequences containing the original HIV frameshift site supported the synthesis of CAT but expression was increas}, keywords = {0,Amino Acid Sequence,Base Sequence,Chloramphenicol,CLEAVAGE,drug effects,Drug ResistanceMicrobial,expression,frameshift,Frameshift Mutation,Frameshifting,Fusion Proteinsgag-pol,Gag,Gag-pol,gene,genetics,HIV,HIV Protease Inhibitors,Hiv-1,human,La,MESSENGER-RNA,Molecular Sequence Data,Mutation,nosource,pharmacology,protein,Proteins,ribosomal frameshifting,Rna,sequence,supportnon-u.s.gov’t,translation,vector,vectors,virus} } % == BibTeX quality report for doyonNovelGagPolFrameshift1998: % ? unused Journal abbr (“J.Virol.”)

@article{dragicHIV1EntryCD41996, title = {{{HIV-1}} Entry into {{CD4}}+ Cells Is Mediated by the Chemokine Receptor {{CC-CKR-5}}}, author = {Dragic, T. and Litwin, V. and Allaway, G.P. and Martin, S.R. and Huang, Y. and Nagashima, K.A. and Cayanan, C. and Maddon, P.J. and Koup, R.A. and Moore, J.P. and Paxton, W.A.}, year = 1996, month = jun, journal = {Nature}, volume = {381}, number = {6584}, pages = {667–673}, publisher = {Nature Publishing Group}, doi = {10.1038/381667a0}, url = {PM:8649512 http://www.nature.com/nature/journal/v381/n6584/abs/381667a0.html}, abstract = {The beta-chemokines MIP-1alpha, MIP-1beta and RANTES inhibit infection of CD4+ T cells by primary, non-syncytium-inducing (NSI) HIV-1 strains at the virus entry stage, and also block env-mediated cell-cell membrane fusion. CD4+ T cells from some HIV-1-exposed uninfected individuals cannot fuse with NSI HIV-1 strains and secrete high levels of beta-chemokines. Expression of the beta-chemokine receptor CC-CKR-5 in CD4+, non-permissive human and non-human cells renders them susceptible to infection by NSI strains, and allows env-mediated membrane fusion. CC-CKR-5 is a second receptor for NSI primary viruses}, keywords = {0,AIDS,Base Sequence,CCR5,CD4-Positive T-Lymphocytes,Cell Line,CELLS,CellsCultured,Chemokine CCL3,Chemokine CCL4,Chemokine CCL5,Dna,DNA Primers,expression,gene,Gene Productsenv,GENE-PRODUCT,genetics,Hela Cells,HIV Infections,Hiv-1,human,Humans,INFECTION,La,Macrophage Inflammatory Proteins,Macrophages,Membrane Fusion,metabolism,Molecular Sequence Data,Monokines,nosource,pathogenicity,pharmacology,physiology,PRODUCT,PRODUCTS,protein,Proteins,Rantes,ReceptorsCCR5,ReceptorsCytokine,ReceptorsVirus,Recombinant Proteins,Support,T,virology,virus,Virus Replication,Viruses} }

@article{dragonLargeNucleolarU32002a, title = {A Large Nucleolar {{U3}} Ribonucleoprotein Required for {{18S}} Ribosomal {{RNA}} Biogenesis}, author = {Dragon, F. and Gallagher, J.E. and {Compagnone-Post}, P.A. and Mitchell, B.M. and Porwancher, K.A. and Wehner, K.A. and Wormsley, S. and Settlage, R.E. and Shabanowitz, J. and Osheim, Y. and Beyer, A.L. and Hunt, D.F. and Baserga, S.J.}, year = 2002, month = jul, journal = {Nature}, volume = {417}, number = {6892}, pages = {967–970}, doi = {10.1038/nature00769}, url = {PM:12068309}, abstract = {Although the U3 small nucleolar RNA (snoRNA), a member of the box C/D class of snoRNAs, was identified with the spliceosomal small nuclear RNAs (snRNAs) over 30 years ago, its function and its associated protein components have remained more elusive. The U3 snoRNA is ubiquitous in eukaryotes and is required for nucleolar processing of pre-18S ribosomal RNA in all organisms where it has been tested. Biochemical and genetic analyses suggest that U3 pre-rRNA base-pairing interactions mediate endonucleolytic pre-rRNA cleavages. Here we have purified a large ribonucleoprotein (RNP) complex from Saccharomyces cerevisiae that contains the U3 snoRNA and 28 proteins. Seventeen new proteins (Utp1 17) and Rrp5 were present, as were ten known components. The Utp proteins are nucleolar and specifically associated with the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. On the basis of its large size (80S; calculated relative molecular mass of at least 2,200,000) and function, this complex may correspond to the terminal knobs present at the 5’ ends of nascent pre- rRNAs. We have termed this large RNP the small subunit (SSU) processome}, keywords = {Base Pairing,CLEAVAGE,COMPLEX,COMPLEXES,COMPONENT,Genetic,La,nosource,protein,Proteins,RIBOSOMAL-RNA,Rna,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUBUNIT} }

@article{draperHowProteinsRecognize1989, title = {How Do Proteins Recognize Specific {{RNA}} Sites? {{New}} Clues from Autogenously Regulated Ribosomal Proteins.}, author = {Draper, D.}, year = 1989, journal = {Trends in biochemical sciences}, volume = {14}, number = {8}, pages = {335–338}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0968000489901679}, keywords = {BINDING,Binding Sites,expression,mRNA,No DOI found,nosource,protein,Proteins,Review,Ribosomal Proteins,ribosome,Rna,rRNA,sequence,structure} }

@article{draperGuideIonsRNA2004a, title = {A Guide to Ions and {{RNA}} Structure}, author = {Draper, D.E.}, year = 2004, month = mar, journal = {RNA}, volume = {10}, number = {3}, pages = {335–343}, doi = {10.1261/rna.5205404}, url = {PM:14970378}, abstract = {RNA folding into stable tertiary structures is remarkably sensitive to the concentrations and types of cations present; an understanding of the physical basis of ion-RNA interactions is therefore a prerequisite for a quantitative accounting of RNA stability. This article summarizes the energetic factors that must be considered when ions interact with two different RNA environments. “Diffuse ions” accumulate near the RNA because of the RNA electrostatic field and remain largely hydrated. A “chelated” ion directly contacts a specific location on the RNA surface and is held in place by electrostatic forces. Energetic costs of ion chelation include displacement of some of the waters of hydration by the RNA surface and repulsion of diffuse ions. Methods are discussed for computing both the free energy of the set of diffuse ions associated with an RNA and the binding free energies of individual chelated ions. Such calculations quantitatively account for the effects of Mg(2+) on RNA stability where experimental data are available. An important conclusion is that diffuse ions are a major factor in the stabilization of RNA tertiary structures}, keywords = {0,Animals,BINDING,Cations,chemistry,human,Ions,La,LOCATION,Magnesium,metabolism,Methods,nosource,Nucleic Acid Conformation,Potassium,Review,Rna,RNA folding,RNA Stability,stability,structure,supportu.s.gov’tp.h.s.,Water} }

@article{dresiosYeastRibosomalProtein2000, title = {Yeast Ribosomal Protein {{L24}} Affects the Kinetics of Protein Synthesis and Ribosomal Protein {{L39}} Improves Translational Accuracy, While Mutants Lacking Both Remain Viable}, author = {Dresios, J. and Derkatch, I.L. and Liebman, S.W. and Synetos, D.}, year = 2000, month = jun, journal = {Biochemistry}, volume = {39}, number = {24}, pages = {7236–7244}, publisher = {ACS Publications}, doi = {10.1021/bi9925266}, url = {http://pubs.acs.org/doi/abs/10.1021/bi9925266}, abstract = {Four mutant strains from Saccharomyces cerevisiae were used to study ribosome structure and function. They included a strain carrying deletions of the two genes encoding ribosomal protein L24, a strain carrying a mutation spb2 in the gene for ribosomal protein L39, a strain carrying a deletion of the gene for L39, and a mutant lacking both L24 and L39. The mutant lacking only L24 showed just 25% of the normal polyphenylalanine-synthesizing activity followed by a decrease in P-site binding, suggesting the possibility that protein L24 is involved in the kinetics of translation. Each of the two L39 mutants displayed a 4-fold increase of their error frequencies over the wild type. This was accompanied by a substantial increase in A-site binding, typical of error-prone mutants. The absence of L39 also increased sensitivity to paromomycin, decreased the ribosomal subunit ratio, and caused a cold-sensitive phenotype. Mutant cells lacking both ribosomal proteins remained viable. Their ribosomes showed reduced initial rates caused by the absence of L24 but a normal extent of polyphenylalanine synthesis and a substantial in vivo reduction in the amount of 80S ribosomes compared to wild type. Moreover, this mutant displayed decreased translational accuracy, hypersensitivity to the antibiotic paromomycin, and a cold-sensitive phenotype, all caused mainly by the deletion of L39. Protein L39 is the first protein of the 60S ribosomal subunit implicated in translational accuracy}, keywords = {0,A SITE,A-SITE,accuracy,antibiotic,BINDING,Cell Division,CELLS,CEREVISIAE,chemistry,Cold,drug effects,Fungal Proteins,gene,Genes,genetics,IN-VIVO,Kinetics,La,metabolism,MUTANTS,Mutation,nosource,P SITE,P-SITE,Paromomycin,Peptides,pharmacology,Phenotype,Poly U,Polyribosomes,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,structure,SUBUNIT,supportnon-u.s.gov’t,translation,TranslationGenetic,WILD-TYPE,yeast} }

@article{dresiosYeastRibosomalProtein2001a, title = {Yeast Ribosomal Protein Deletion Mutants Possess Altered Peptidyltransferase Activity and Different Sensitivity to Cycloheximide}, author = {Dresios, J. and Panopoulos, P. and Frantziou, C.P. and Synetos, D.}, year = 2001, month = jul, journal = {Biochemistry}, volume = {40}, number = {27}, pages = {8101–8108}, doi = {10.1021/bi0025722}, url = {ISI:000169833400017}, abstract = {The major function of the ribosome is its ability to catalyze formation of peptide bonds, and it is carried out by the ribosomal peptidyltransferase. Recent evidence suggests that the catalyst of peptide bond formation is the 23S rRNA of the large ribosomal subunit. We have developed an in vitro system for the determination of peptidyltransferase activity in yeast ribosomes. Using this system, a kinetic analysis of a model reaction for peptidyltransferase is described with Ac-Phe-tRNA as the peptidyl donor and puromycin as the acceptor. The Ac-Phe-tRNA-poly(U)-80S ribosome complex (complex C) was isolated and then reacted with excess puromycin to give Ac-Phe-puromycin. This reaction (puromycin reaction) followed first-order kinetics. At saturating concentrations of puromycin, the first-order rate constant (k(3)) is identical to the catalytic rate constant (k(cat)) of peptidyltransferase. This k(cat) from wild-type yeast strains was equal to 2.18 min(-1) at 30 degreesC. We now present for the first time kinetic evidence that yeast ribosomes lacking a particular protein of the 60S subunit may possess significantly altered peptide bond-forming ability. The k(cat) of peptidyltransferase from mutants lacking ribosomal protein L24 was decreased 3-fold to 0.69 min(-1), whereas the k(cat) from mutants lacking L39 was slightly increased to 3.05 min(-1) and that from mutants lacking both proteins was 1.07 min(-1). These results suggest that the presence of ribosomal proteins L24 and, to a lesser extent, L39 is required for exhibition of the normal catalytic activity of the ribosome, Finally, the L24 or L39 mutants did not affect the rate or the extent of the translocation phase of protein synthesis. However, the absence of L24 caused increased resistance to cycloheximide, a translocation inhibitor. Translocation of Ac-Phe-tRNA from the A- to P-site was inhibited by 50% at 1.4 muM cycloheximide for the L24 mutant compared to 0.7 muM for the wild type}, keywords = {0,60S subunit,accuracy,analysis,COMPLEX,COMPLEXES,Cycloheximide,In Vitro,IN-VITRO,Kinetics,MUTATIONS,nosource,P-SITE,PEPTIDE-BOND FORMATION,Peptidyltransferase,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Puromycin,Ribosomal Proteins,ribosome,Ribosomes,rRNA,SUBUNIT,SYSTEM,translation,translocation,yeast} }

@article{dresiosIdentificationAminoAcids2002a, title = {Identification of the Amino Acids in Yeast Ribosomal Protein {{YL37a}} for Binding to Ribosomal {{RNA}} and the Role of the Zinc Finger Motif}, author = {Dresios, J. and Chan, Y.L. and Wool, I.G.}, year = 2002, month = mar, journal = {Faseb Journal}, volume = {16}, number = {4}, pages = {A163-A164}, url = {ISI:000174533600911}, keywords = {0,ACID,Amino Acids,BINDING,IDENTIFICATION,No DOI found,nosource,protein,RIBOSOMAL-RNA,Rna,yeast} }

@article{dresiosDispensableYeastRibosomal2003, title = {A Dispensable Yeast Ribosomal Protein Optimizes Peptidyltransferase Activity and Affects Translocation}, author = {Dresios, J. and Panopoulos, P. and Suzuki, K. and Synetos, D.}, year = 2003, month = jan, journal = {Journal of Biological Chemistry}, volume = {278}, number = {5}, pages = {3314–3322}, doi = {10.1074/jbc.M207533200}, url = {ISI:000180915000070}, abstract = {Yeast ribosomal protein L41 is dispensable in the yeast. Its absence had no effect on polyphenylalanine synthesis activity, and a limited effect on growth, translational accuracy, or the resistance toward the antibiotic paromomycin. Removal of L41 did not affect the 60:40 S ratio, but it reduced the amount of 80 S, suggesting that L41 is involved in ribosomal subunit association. However, the two most important effects of L41 were on peptidyltransferase activity and translocation. Peptidyltransferase activity was measured as a second-order rate constant (k(cat)/K-s) corresponding to the rate of peptide bond formation; this k(cat)/K-s was lowered 3-fold to 1.15 min(-1) mM(-1) in the L41 mutant compared with 3.46 min(-1) mM(-1) in the wild type. Translocation was also affected by L41. Elongation factor 2 (EF2)-dependent (enzymatic) translocation of Ac-Phe-tRNA from the A- to P-site was more efficient in the absence of L41, because 50% translocation was achieved at only 0.004 muM EF2 compared with 0.02 muM for the wild type. Furthermore, the EF2-dependent translocation was inhibited by 50% at 2.5 muM of the translocation inhibitor cycloheximide in the L41 mutant compared with 1.2 muM in the wild type. Finally, the rate of EF2-independent (spontaneous) translocation was increased in the absence of L41}, keywords = {0,accuracy,ACCURACY CENTER,ANGSTROM RESOLUTION,antibiotic,Cycloheximide,elongation,ESCHERICHIA-COLI,L41,MUTATIONS,nosource,P-SITE,Paromomycin,PEPTIDYL TRANSFERASE CENTER,Peptidyltransferase,protein,SACCHAROMYCES-CEREVISIAE,SUBUNIT,TRANSFER-RNA BINDING,translocation,yeast} }

@article{dresiosEukaryoticRibosomalProteins2006, title = {Eukaryotic Ribosomal Proteins Lacking a Eubacterial Counterpart: Important Players in Ribosomal Function}, author = {Dresios, J. and Panopoulos, P. and Synetos, D.}, year = 2006, month = mar, journal = {Molecular microbiology}, volume = {59}, number = {6}, pages = {1651–1663}, publisher = {Wiley Online Library}, doi = {10.1111/j.1365-2958.2006.05054.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2006.05054.x/full}, abstract = {The ribosome is a macromolecular machine responsible for protein synthesis in all organisms. Despite the enormous progress in studies on the structure and function of prokaryotic ribosomes, the respective molecular details of the mechanism by which the eukaryotic ribosome and associated factors construct a polypeptide accurately and rapidly still remain largely unexplored. Eukaryotic ribosomes possess more RNA and a higher number of proteins than eubacterial ribosomes. As the tertiary structure and basic function of the ribosomes are conserved, what is the contribution of these additional elements? Elucidation of the role of these components should provide clues to the mechanisms of translation in eukaryotes and help unravel the molecular mechanisms underlying the differences between eukaryotic and eubacterial ribosomes. This article focuses on a class of eukaryotic ribosomal proteins that do not have a eubacterial homologue. These proteins play substantial roles in ribosomal structure and function, and in mRNA binding and nascent peptide folding. The role of these proteins in human diseases and viral expression, as well as their potential use as targets for antiviral agents is discussed}, keywords = {0,Animals,antiviral,Antiviral Agents,BINDING,CEREVISIAE,chemistry,COMPONENT,COMPONENTS,disease,Drug Design,ELEMENTS,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,expression,human,Humans,La,MECHANISM,MECHANISMS,metabolism,MOLECULAR MECHANISMS,mRNA,NASCENT-PEPTIDE,Neoplasms,nosource,POLYPEPTIDE,protein,Protein Conformation,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Research SupportNon-U.S.Gov’t,Review,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Rna,RNAMessenger,RNARibosomal,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,structure,TARGET,translation,ultrastructure,Viral Physiology} } % == BibTeX quality report for dresiosEukaryoticRibosomalProteins2006: % ? unused Journal abbr (“Mol.Microbiol.”)

@article{dreyfussHnRNPProteinsBiogenesis1993a, title = {{{hnRNP}} Proteins and the Biogenesis of {{mRNA}}.}, author = {Dreyfuss, G. and Matunis, M.J. and {Pinol-Roma}, S. and Burd, C.G.}, year = 1993, journal = {Annual Review of Biochemistry}, volume = {62}, pages = {289–321}, doi = {10.1146/annurev.bi.62.070193.001445}, keywords = {mRNA,nosource,protein,Proteins} }

@article{drosopoulosIncreasedPolymeraseFidelity1996a, title = {Increased Polymerase Fidelity of {{E89G}}, a Nucleoside Analog- Resistant Variant of Human Immunodeficiency Virus Type 1 Reverse Transcriptase}, author = {Drosopoulos, W.C. and Prasad, V.R.}, year = 1996, month = jul, journal = {Journal of Virology}, volume = {70}, number = {7}, pages = {4834–4838}, doi = {10.1128/jvi.70.7.4834-4838.1996}, keywords = {efficiency,Fidelity,human,In Vitro,IN-VITRO,Mutation,MUTATIONS,nosource,polymerase,virus} }

@article{drozdowskiChickenCDNAOrnithine1998a, title = {The Chicken {{cDNA}} for Ornithine Decarboxylase Antizyme}, author = {Drozdowski, B. and Gong, T.W. and Lomax, M.I.}, year = 1998, journal = {Biochim.Biophys.Acta}, volume = {1396}, number = {1}, pages = {21–26}, doi = {10.1016/S0167-4781(97)00162-0}, keywords = {Amino Acid Sequence,Amino Acids,animal,antagonists & inhibitors,antizyme,Base Sequence,chickens,CloningMolecular,cochlea,DNAComplementary,Frameshifting,genetics,isolation & purification,Molecular Sequence Data,mRNA,nosource,Ornithine Decarboxylase,ORNITHINE DECARBOXYLASE ANTIZYME,poly(A),Polymerase Chain Reaction,protein,Proteins,sequence,Sequence HomologyAmino Acid,Sequence HomologyNucleic Acid,SIGNAL,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Xenopus} } % == BibTeX quality report for drozdowskiChickenCDNAOrnithine1998a: % ? Possibly abbreviated journal title Biochim.Biophys.Acta

@article{duStructureAutoregulatoryPseudoknot1996a, title = {Structure of the Autoregulatory Pseudoknot within the Gene 32 Messenger {{RNA}} of Bacteriophages {{T2}} and {{T6}}: A Model for a Possible Family of Structurally Related {{RNA}} Pseudoknots}, author = {Du, Z. and Giedroc, D.P. and Hoffman, D.W.}, year = 1996, journal = {Biochemistry}, volume = {35}, number = {13}, pages = {4187–4198}, doi = {10.1021/bi9527350}, keywords = {analysis,Bacteriophages,Base Sequence,biosynthesis,chemistry,Comparative Study,Frameshifting,gene,Genes,GenesViral,genetics,Hydrogen Bonding,isolation & purification,MESSENGER-RNA,metabolism,Methods,models,ModelsMolecular,Molecular Sequence Data,mRNA,myoviridae,nosource,nuclear magnetic resonance,Nucleic Acid Conformation,pseudoknot,readthrough,Rna,RNA PSEUDOKNOT,RNAMessenger,RnaViral,sequence,stability,Structural,structure,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Temperature,Thermodynamics} }

@article{duBasepairingsRNAPseudoknot1997, title = {Base-Pairings within the {{RNA}} Pseudoknot Associated with the Simian Retrovirus-1 Gag-pro Frameshift Site.}, author = {Du, Z. and Holland, J.A. and Hansen, M.R. and Giedroc, D.P. and Hoffman, D.W.}, year = 1997, month = jul, journal = {Journal of Molecular Biology}, volume = {270}, number = {3}, eprint = {9237911}, eprinttype = {pubmed}, pages = {464–470}, publisher = {Elsevier}, issn = {0022-2836}, doi = {10.1006/jmbi.1997.1127}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9237911 http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(97)91127-x}, abstract = {Frameshift and readthrough sites within retroviral messenger RNAs are often followed by nucleotide sequences that have the potential to form pseudoknot structures. In the work presented here, NMR methods were used to characterize the base-pairings and structural features of the RNA pseudoknot downstream of the gag-pro frameshift site of simian retrovirus type-1 (SRV-1) and a functional mutant of the SRV-1 pseudoknot. Evidence is presented that these pseudoknots contain two A-form helical stems of six base-pairs each, connected by two loops, in a classic H-type pseudoknot topology. A particularly interesting feature is that the shorter of the two connecting loops, loop 1, consists of only a single adenosine nucleotide that spans the major groove of stem 2. In this respect, the frameshift-associated pseudoknots are structurally similar to the pseudoknot within the gene 32 mRNA of bacteriophage T2, previously characterized by NMR methods. Despite having similar nucleotide sequences, the solvent exchange rates of the imino protons at the junction of the helical stems in the wild-type and mutant frameshifting pseudoknots differ from each other and from the bacteriophage T2 pseudoknot. The implications of this finding are discussed.}, pmid = {9237911}, keywords = {Base Pairing,frameshift,Frameshifting,gag,Gag,gag: genetics,gene,Genes,Magnetic Resonance Spectroscopy,Magnetic Resonance Spectroscopy: methods,MESSENGER-RNA,Methods,mRNA,Mutation,Myoviridae,Myoviridae: chemistry,nosource,Nucleic Acid Conformation,pol,pol: genetics,Protons,pseudoknot,readthrough,Retroviruses,Ribosomal,Ribosomal: genetics,Rna,RNA,RNA PSEUDOKNOT,sequence,Simian,Simian: chemistry,Structural,structure,Viral,Viral: chemistry,Viral: genetics} }

@article{duNMRMutationalStudy1997, title = {An {{NMR}} and Mutational Study of the Pseudoknot within the Gene 32 {{mRNA}} of Bacteriophage {{T2}} - Insights into a Family of Structurally Related {{RNA}} Pseudoknots.}, author = {Du, Z.H. and Hoffman, D.W.}, year = 1997, month = mar, journal = {Nucleic Acids Research}, volume = {25}, number = {6}, pages = {1130–1135}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/25.6.1130}, url = {http://nar.oxfordjournals.org/content/25/6/1130.short}, keywords = {frameshift,gene,Genes,MESSENGER-RNA,Methods,mRNA,nosource,pseudoknot,readthrough,Rna,RNA PSEUDOKNOT,sequence,Structural,structure,Support} }

@article{dubridgeAnalysisMutationHuman1987, title = {Analysis of Mutation in Human Cells by Using an {{Epstein-Barr}} Virus Shuttle System.}, author = {DuBridge, R.B. and Tang, P. and Hsia, H.C. and Leong, P.M. and Miller, J.H. and Calos, M.P.}, year = 1987, month = jan, journal = {Molecular and cellular biology}, volume = {7}, number = {1}, pages = {379–387}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/7/1/379}, keywords = {analysis,Bacterial,cancer,Cell Line,cell lines,Dna,Escherichia coli,ESCHERICHIA-COLI,gene,human,Multiple DOI,Mutation,MUTATIONS,nonfile,nosource,sequence,Support,SYSTEM,vector,vectors,virus} }

@article{duludeCharacterizationFrameshiftStimulatory2002a, title = {Characterization of the Frameshift Stimulatory Signal Controlling a Programmed -1 Ribosomal Frameshift in the Human Immunodeficiency Virus Type 1}, author = {Dulude, D. and Baril, M. and {Brakier-Gingras}, L.}, year = 2002, month = dec, journal = {Nucleic Acids Research}, volume = {30}, number = {23}, pages = {5094–5102}, doi = {10.1093/nar/gkf657}, abstract = {Synthesis of the Gag-Pol protein of the human immunodeficiency virus type 1 (HIV-1) requires a programmed -1 ribosomal frameshifting when ribosomes translate the unspliced viral messenger RNA. This frameshift occurs at a slippery sequence followed by an RNA structure motif that stimulates frameshifting. This motif is commonly assumed to be a simple stem-loop for HIV-1. In this study, we show that the frameshift stimulatory signal is more complex than believed and consists of a two-stem helix. The upper stem-loop corresponds to the classic stem-loop, and the lower stem is formed by pairing the spacer region following the slippery sequence and preceding this classic stem-loop with a segment downstream of this stem-loop. A three-purine bulge interrupts the two stems. This structure was suggested by enzymatic probing with nuclease V1 of an RNA fragment corresponding to the gag/pol frameshift region of HIV-1. The involvement of the novel lower stem in frameshifting was supported by site-directed mutagenesis. A fragment encompassing the gag/pol frameshift region of HIV-1 was inserted in the beginning of the coding sequence of a reporter gene coding for the firefly luciferase, such that expression of luciferase requires a -1 frameshift. When the reporter was expressed in COS cells, mutations that disrupt the capacity to form the lower stem reduced frameshifting, whereas compensatory changes that allow re-formation of this stem restored the frameshift efficiency near wild-type level. The two-stem structure that we propose for the frameshift stimulatory signal of HIV-1 differs from the RNA triple helix structure recently proposed}, keywords = {animal,Base Sequence,chemistry,COMPLEX,COMPLEXES,Conserved Sequence,Cos Cells,efficiency,expression,frameshift,Frameshifting,FrameshiftingRibosomal,Fusion Proteinsgag-pol,Gag-pol,gene,Gene Expression RegulationViral,GenesReporter,genetics,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,isolation &,luciferase,MESSENGER-RNA,Molecular Sequence Data,Mutagenesis,MutagenesisSite-Directed,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,protein,pseudoknot,purification,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,ribosome,Ribosomes,Rna,RnaViral,sequence,SIGNAL,structure,virus} } % == BibTeX quality report for duludeCharacterizationFrameshiftStimulatory2002a: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{duludeDecreasingFrameshiftEfficiency2006, title = {Decreasing the Frameshift Efficiency Translates into an Equivalent Reduction of the Replication of the Human Immunodeficiency Virus Type 1}, author = {Dulude, D. and Berchiche, Y.A. and Gendron, K. and {Brakier-Gingras}, L. and Heveker, N.}, year = 2006, month = feb, journal = {Virology}, volume = {345}, number = {1}, pages = {127–136}, publisher = {Elsevier}, doi = {10.1016/j.virol.2005.08.048}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0042682205006288}, abstract = {The Gag-Pol polyprotein of the human immunodeficiency virus type 1 (HIV-1) is the precursor of the virus enzymatic activities and is produced via a programmed -1 translational frameshift. In this study, we altered the frameshift efficiency by introducing mutations within the slippery sequence and the frameshift stimulatory signal, the two elements that control the frameshift. These mutations decreased the frameshift efficiency to different degrees, ranging from approximately 0.3% to 70% of the wild-type efficiency. These values were mirrored by a reduced incorporation of Gag-Pol into virus-like particles, as assessed by a decrease in the reverse transcriptase activity associated to these particles. Analysis of Gag processing in infectious mutant virions revealed processing defects to various extents, with no clear correlation with frameshift decrease. Nevertheless, the observed frameshift reductions translated into equivalently reduced viral infectivity and replication kinetics. Our results show that even moderate variations in frameshift efficiency, as obtained with mutations in the frameshift stimulatory signal, reduce viral replication. Therapeutic targeting of this structure may therefore result in the attenuation of virus replication and in clinical benefit}, keywords = {analysis,efficiency,ELEMENTS,frameshift,Gag,Gag-pol,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,Kinetics,La,Mutation,MUTATIONS,nosource,PARTICLES,POLYPROTEIN,PRECURSOR,REPLICATION,REVERSE-TRANSCRIPTASE,sequence,SIGNAL,structure,TYPE-1,VIRAL INFECTIVITY,Virion,VIRIONS,virus,Virus Replication,VIRUS-LIKE PARTICLES,WILD-TYPE} }

@article{dunbarMpp10pU3Small1997, title = {Mpp10p, a {{U3}} Small Nucleolar Ribonucleoprotein Component Required for Pre-{{18S rRNA}} Processing in Yeast}, author = {Dunbar, D.A. and Wormsley, S. and Agentis, T.M. and Baserga, S.J.}, year = 1997, month = oct, journal = {Molecular and cellular biology}, volume = {17}, number = {10}, pages = {5803–5812}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.17.10.5803}, url = {http://mcb.asm.org/cgi/content/abstract/17/10/5803}, abstract = {We have isolated and characterized Mpp10p, a novel protein component of the U3 small nucleolar ribonucleoprotein (snoRNP) from the yeast Saccharomyces cerevisiae. The MPP10 protein was first identified in human cells by its reactivity with an antibody that recognizes specific sites of mitotic phosphorylation. To study the functional role of MPP10 in pre-rRNA processing, we identified the yeast protein by performing a GenBank search. The yeast Mpp10p homolog is 30% identical to the human protein over its length. Antibodies to the purified yeast protein recognize a 110-kDa polypeptide in yeast extracts and immunoprecipitate the U3 snoRNA, indicating that Mpp10p is a specific protein component of the U3 snoRNP in yeast. As a first step in the genetic analysis of Mpp10p function, diploid S. cerevisiae cells were transformed with a null allele. Sporulation and tetrad analysis indicate that MPP10 is an essential gene. A strain was constructed where Mpp10p is expressed from a galactose-inducible, glucose- repressible promoter. After depletion of Mpp10p by growth in glucose, cell growth is arrested and levels of 18S and its 20S precursor are reduced or absent while the 23S and 35S precursors accumulate. This pattern of accumulation of rRNA precursors suggests that Mpp10p is required for cleavage at sites A0, A1, and A2. Pulse-chase analysis of newly synthesized pre-rRNAs in Mpp10p-depleted yeast confirms that little mature 18S rRNA formed. These results reveal a novel protein essential for ribosome biogenesis and further elucidate the composition of the U3 snoRNP}, keywords = {0,Amino Acid Sequence,analysis,animal,Antibodies,antibody,chemistry,CLEAVAGE,CloningMolecular,COMPONENT,Escherichia coli,gene,GenesFungal,Genetic,genetics,Glucose,homolog,human,La,metabolism,Mice,Molecular Sequence Data,Molecular Weight,nosource,Phosphoproteins,Phosphorylation,physiology,protein,Proteins,Recombinant Fusion Proteins,Ribonucleoproteins,RibonucleoproteinsSmall Nuclear,ribosome,Rna,RNA Precursors,RNA ProcessingPost-Transcriptional,RNARibosomal,RNARibosomal18S,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,search,Sequence HomologyAmino Acid,SporesFungal,yeast} } % == BibTeX quality report for dunbarMpp10pU3Small1997: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{dunbarNucleolarProteinRelated2000a, title = {A Nucleolar Protein Related to Ribosomal Protein {{L7}} Is Required for an Early Step in Large Ribosomal Subunit Biogenesis}, author = {Dunbar, D.A. and Dragon, F. and Lee, S.J. and Baserga, S.J.}, year = 2000, month = nov, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {24}, pages = {13027–13032}, doi = {10.1073/pnas.97.24.13027}, url = {ISI:000165476300026}, abstract = {The Saccharomyces cerevisiae R1p7 protein has extensive identity and similarity to the large ribosomal subunit L7 proteins and shares an RNA-binding domain with them. R1p7p is not a ribosomal protein; however, it is encoded by an essential gene and therefore must perform a function essential for cell growth. In this report, we show that R1p7p is a nucleolar protein that plays a critical role in processing of precursors to the large ribosomal subunit RNAs. Pulse-chase labeling experiments with R1p7p-depleted cells reveal that neither 5.8S(s). 5.8S(L), nor 25S is produced, indicating that both the major and minor processing pathways are affected. Analysis of processing intermediates by primer extension indicates that R1pT7p-depleted cells accumulate the 27SA(3) precursor RNA, which is normally the major substrate (85%) used to produce the 5.85 and 25S rRNAs, and the ratio of 27SB(L) to 27SB(S) precursors changes from approximately 1:8 to 8:1 (depleted cells). Because 27SA(3) is the direct precursor to 27SB(S), we conclude that R1p7p is specifically required for the 5’ to 3’ exonucleolytic trimming of the 27SA(3) into the 27SB(S) precursor. As it is essential for processing in both the major and minor pathways, we propose that R1p7p may act as a specificity factor that binds precursor rRNAs and tethers the enzymes that carry out the early 5’ to 3’ exonucleolytic reactions that generate the mature rRNAs. R1p7p may also be required for the endonucleolytic cleavage in internal transcribed spacer 2 that separates the 5.8S rRNA from the 25S rRNA}, keywords = {ACID,analysis,BINDING DOMAINS,CLEAVAGE,COMPONENTS,enzyme,gene,NOP1,nosource,primer extension,protein,Proteins,RAT1P,RIBONUCLEOPROTEIN,RIBOSOMAL-SUBUNIT,Rna,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUBUNIT,yeast} }

@book{durbinBiologicalSequenceAnalysis1998a, title = {Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids.}, author = {Durbin, R.}, year = 1998, journal = {Arxiv preprint math/0304372}, eprint = {math/0304372}, publisher = {Cambridge University Press}, address = {Cambridge UK, New York}, url = {http://books.google.com/books?hl=en&lr=&id=R5P2GlJvigQC&oi=fnd&pg=PA1&dq=Biological+sequence+analysis:+probabilistic+models+of+proteins+and+nucleic+acids.&ots=hpuRjGmibA&sig=M0H1c-RdoRP0LjGsyzPiyg32hhY http://arxiv.org/abs/math/0304372 http://books.google.com/books?hl=en&lr=&id=R5P2GlJvigQC&oi=fnd&pg=PA1&dq=Biological+sequence+analysis:+Probabilistic+models+of+proteins+and+nucleic+acids&ots=hpxKhJlk3A&sig=MKVVqMw0ds0YPhT3D5EcDNfXFJU}, archiveprefix = {arXiv}, keywords = {ACID,ACIDS,analysis,MODEL,models,nosource,Nucleic Acids,protein,Proteins,sequence,Sequence Analysis,SEQUENCE-ANALYSIS} }

@article{easterwoodOrientationsTransferRnaRibosomal1994, title = {Orientations of {{Transfer-Rna}} in the {{Ribosomal A-Site}} and {{P-Site}}}, author = {Easterwood, T.R. and Major, F. and Malhotra, A. and Harvey, S.C.}, year = 1994, journal = {Nucleic Acids Research}, volume = {22}, number = {18}, pages = {3779–3786}, doi = {10.1093/nar/22.18.3779}, url = {ISI:A1994PJ87400019}, abstract = {In protein synthesis, peptide bond formation requires that the tRNA carrying the amino acid (A site tRNA) contact the tRNA carrying the growing peptide chain (P site tRNA) at their 3’ termini. Two models have been proposed for the orientations of two tRNAs as they would be bound to the mRNA in the ribosome. Viewing the tRNA as an upside down L, anticodon loop pointing down, acceptor stem pointing right, and calling this the front view, the R (Rich) model would have the back of the P site tRNA facing the front of the A site tRNA. In the S (Sundaralingam) model the front of the P site tRNA faces the back of the A site tRNA. Models of two tRNAs bound to mRNA as they would be positioned in the ribosomal A and P sites have been created using MC-SYM, a constraint satisfaction search program designed to build nucleic acid structures. The models incorporate information from fluorescence energy transfer experiments and chemical crosslinks. The models that best answer the constraints are of the S variety, with no R conformations produced consistent with the constraints}, keywords = {2 TRANSFER-RNAS,3-DIMENSIONAL STRUCTURE,A SITE,A-SITE,ACID,Anticodon,ANTICODON LOOP,ARRANGEMENT,BOND FORMATION,CONFORMATION,CROSS-LINKING,CROSSLINKING,Fluorescence,IDENTIFICATION,LOOP,MESSENGER-RNA,MODEL,models,mRNA,nosource,P SITE,P-SITE,P-SITES,protein,protein synthesis,PROTEIN-SYNTHESIS,REQUIRES,ribosome,search,SITE,SITES,structure,TRANSFER-RNA,translocation,tRNA} } % == BibTeX quality report for easterwoodOrientationsTransferRnaRibosomal1994: % ? Title looks like it was stored in title-case in Zotero

@article{eckerPseudoHalfKnotFormation1992, title = {Pseudo {{Half-Knot Formation}} with {{Rna}}}, author = {Ecker, D.J. and Vickers, T.A. and Bruice, T.W. and Freier, S.M. and Jenison, R.D. and Manoharan, M. and Zounes, M.}, year = 1992, journal = {Science}, volume = {257}, number = {5072}, pages = {958–961}, doi = {10.1126/science.1502560}, url = {ISI:A1992JH82700033}, abstract = {A pseudo-half-knot can be formed by binding an oligonucleotide asymmetrically to an RNA hairpin loop. This binding motif was used to target the human immunodeficiency virus TAR element, an important viral RNA structure that is the receptor for Tat, the major viral transactivator protein. Oligonucleotides complementary to different halves of the TAR structure bound with greater affinity than molecules designed to bind symmetrically around the hairpin. The pseudo-half-knot-forming oligonucleotides altered the TAR structure so that specific recognition and binding of a Tat-derived peptide was disrupted. This general binding motif may be used to disrupt the structure of regulatory RNA hairpins}, keywords = {BINDING,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,nosource,Oligonucleotides,protein,pseudoknot,Rna,sequence,structure,TAR RNA,virus} } % == BibTeX quality report for eckerPseudoHalfKnotFormation1992: % ? Title looks like it was stored in title-case in Zotero

@article{edskesMak21pSaccharomycesCerevisiae1998, title = {Mak21p of {{Saccharomyces}} Cerevisiae, a Homolog of Human {{CAATT-binding}} Protein, Is Essential for 60 {{S}} Ribosomal Subunit Biogenesis}, author = {Edskes, H.K. and Ohtake, Y. and Wickner, R.B.}, year = 1998, month = oct, journal = {Journal of Biological Chemistry}, volume = {273}, number = {44}, pages = {28912–28920}, publisher = {ASBMB}, doi = {10.1074/jbc.273.44.28912}, url = {http://www.jbc.org/content/273/44/28912.short}, abstract = {Mak21-1 mutants are unable to propagate M1 double-stranded RNA, a satellite of the L-A double-stranded RNA virus, encoding a secreted protein toxin lethal to yeast strains that do not carry M1. We cloned MAK21 using its map location and found that Mak21p is homologous to a human and mouse CAATT-binding protein and open reading frames in Schizosaccharomyces pombe and Caenorhabditis elegans. Although the human protein regulates Hsp70 production, Mak21p is essential for growth and necessary for 60 S ribosomal subunit biogenesis. mak21-1 mutants have decreased levels of L-A coat protein and L-A double- stranded RNA. Electroporation with reporter mRNAs shows that mak21-1 cells cannot optimally express mRNAs which, like L-A viral mRNA, lack 3’-poly(A) or 5’-cap structures but can normally express mRNA with both cap and poly(A). The virus propagation phenotype of mak21-1 is suppressed by ski2 or ski6 mutations, each of which derepresses translation of non-poly(A) mRNA}, keywords = {99003241,Amino Acid Sequence,animal,Base Sequence,Cap,CloningMolecular,DNA-Binding Proteins,Genetic,genetics,homolog,human,L-A,La,M1,metabolism,Mice,Molecular Sequence Data,mRNA,Mutation,MUTATIONS,nosource,Open Reading Frames,Phenotype,poly(A),protein,Ribosomes,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Sequence Deletion,Sequence HomologyAmino Acid,structure,SUBUNIT,toxin,Transcription Factors,translation,virus,yeast} } % == BibTeX quality report for edskesMak21pSaccharomycesCerevisiae1998: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{egertonVCPMammalianHomolog1992a, title = {{{VCP}}, the Mammalian Homolog of ⬚cdc48,⬚ Is Tyrosine Phosphorylated in Response to {{T-cell}} Antigen Receptor Activation.}, author = {Egerton, M. and Ashe, O.R. and Chen, D. and Druker, B.J. and Burgess, W.H. and Samelson, L.E.}, year = 1992, journal = {EMBO J.}, volume = {11}, pages = {3533–3540}, doi = {10.1002/j.1460-2075.1992.tb05436.x}, keywords = {activation,CDC48,homolog,MOF6,nosource} } % == BibTeX quality report for egertonVCPMammalianHomolog1992a: % ? Possibly abbreviated journal title EMBO J.

@article{egliMetalIonsFlexibility2002, title = {Metal Ions and Flexibility in a Viral {{RNA}} Pseudoknot at Atomic Resolution}, author = {Egli, M. and Minasov, G. and Su, L. and Rich, A.}, year = 2002, month = apr, journal = {Proceedings of the National Academy of Sciences}, volume = {99}, number = {7}, pages = {4302–4307}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.062055599}, url = {http://www.pnas.org/content/99/7/4302.short}, abstract = {Many pathogenic viruses use programmed -1 ribosomal frameshifting to regulate translation of their structural and enzymatic proteins from polycistronic mRNAs. Frameshifting is commonly stimulated by a pseudoknot located downstream from a slippery sequence, the latter positioned at the ribosomal A and P sites. We report here the structures of two crystal forms of the frameshifting RNA pseudoknot from beet western yellow virus at resolutions of 1.25 and 2.85 A. Because of the very high resolution of 1.25 A, ten mono- and divalent metal ions per asymmetric unit could be identified, giving insight into potential roles of metal ions in stabilizing the pseudoknot. A magnesium ion located at the junction of the two pseudoknot stems appears to play a crucial role in stabilizing the structure. Because the two crystal forms exhibit mostly unrelated packing interactions and local crystallographic disorder in the high-resolution form was resolvable, the two structures offer the most detailed view yet of the conformational preference and flexibility of an RNA pseudoknot}, keywords = {0,chemistry,Crystallization,Frameshifting,genetics,Ions,La,Luteovirus,Magnesium,metabolism,mRNA,nosource,Nucleic Acid Conformation,P-SITE,Potassium,protein,Proteins,pseudoknot,ribosomal frameshifting,Ribosomes,Rna,RNA PSEUDOKNOT,RnaViral,sequence,Structural,structure,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,translation,virus} } % == BibTeX quality report for egliMetalIonsFlexibility2002: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{egnerGeneticSeparationFK5061998, title = {Genetic Separation of {{FK506}} Susceptibility and Drug Transport in the Yeast {{Pdr5 ATP-binding}} Cassette Multidrug Resistance Transporter}, author = {Egner, R. and Rosenthal, F.E. and Kralli, A. and Sanglard, D. and Kuchler, K.}, year = 1998, month = feb, journal = {Molecular biology of the cell}, volume = {9}, number = {2}, pages = {523–543}, publisher = {Am Soc Cell Biol}, doi = {10.1091/mbc.9.2.523}, url = {http://www.molbiolcell.org/cgi/content/abstract/9/2/523}, abstract = {Overexpression of the yeast Pdr5 ATP-binding cassette transporter leads to pleiotropic drug resistance to a variety of structurally unrelated cytotoxic compounds. To identify Pdr5 residues involved in substrate recognition and/or drug transport, we used a combination of random in vitro mutagenesis and phenotypic screening to isolate novel mutant Pdr5 transporters with altered substrate specificity. A plasmid library containing randomly mutagenized PDR5 genes was transformed into appropriate drug-sensitive yeast cells followed by phenotypic selection of Pdr5 mutants. Selected mutant Pdr5 transporters were analyzed with respect to their expression levels, subcellular localization, drug resistance profiles to cycloheximide, rhodamines, antifungal azoles, steroids, and sensitivity to the inhibitor FK506. DNA sequencing of six PDR5 mutant genes identified amino acids important for substrate recognition, drug transport, and specific inhibition of the Pdr5 transporter. Mutations were found in each nucleotide-binding domain, the transmembrane domain 10, and, most surprisingly, even in predicted extracellular hydrophilic loops. At least some point mutations identified appear to influence folding of Pdr5, suggesting that the folded structure is a major substrate specificity determinant. Surprisingly, a S1360F exchange in transmembrane domain 10 not only caused limited substrate specificity, but also abolished Pdr5 susceptibility to inhibition by the immunosuppressant FK506. This is the first report of a mutation in a yeast ATP-binding cassette transporter that allows for the functional separation of substrate transport and inhibitor susceptibility}, keywords = {0,ACID,ACIDS,Amino Acid Sequence,Amino Acid Substitution,Amino Acids,AMINO-ACID,AMINO-ACIDS,antagonists & inhibitors,antibiotic,antibiotics,AntibioticsAntifungal,ATP-Binding Cassette Transporters,BINDING,BINDING PROTEIN,BINDING-PROTEIN,Biological Transport,Carrier Proteins,Cell Membrane,CELLS,CEREVISIAE,chemistry,CloningMolecular,Cycloheximide,Dexamethasone,Dna,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,DOMAIN,drug effects,Drug Resistance,Drug ResistanceMicrobial,Drug ResistanceMultiple,Estradiol,expression,gene,Gene Expression,Genes,Genetic,genetics,heat shock proteins,HEAT-SHOCK,HEAT-SHOCK PROTEIN,HEAT-SHOCK PROTEINS,IDENTIFY,In Vitro,IN-VITRO,INHIBITION,INHIBITOR,La,library,LOCALIZATION,LOOP,Membrane Proteins,metabolism,Molecular Sequence Data,MOLECULAR-GENETICS,Mutagenesis,MUTANTS,Mutation,MUTATIONS,nosource,OVEREXPRESSION,PDR5,pharmacology,physiology,PLASMID,Point Mutation,protein,Proteins,RECOGNITION,RESIDUES,RESISTANCE,Rhodamine 123,Rhodamines,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SELECTION,Sequence Alignment,SPECIFICITY,structure,SUBCELLULAR-LOCALIZATION,Substrate Specificity,SUBSTRATE-SPECIFICITY,Support,Tacrolimus,Tacrolimus Binding Proteins,TRANSPORT,yeast,YEAST-CELLS} } % == BibTeX quality report for egnerGeneticSeparationFK5061998: % ? unused Journal abbr (“Mol Biol Cell”)

@article{eisenClusterAnalysisDisplay1998, title = {Cluster Analysis and Display of Genome-Wide Expression Patterns}, author = {Eisen, M.B. and Spellman, P.T. and Brown, P.O. and Botstein, D.}, year = 1998, month = dec, journal = {Proceedings of the National Academy of Sciences}, volume = {95}, number = {25}, pages = {14863–14868}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.95.25.14863}, url = {http://www.pnas.org/content/95/25/14863.short}, abstract = {A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression. The output is displayed graphically, conveying the clustering and the underlying expression data simultaneously in a form intuitive for biologists. We have found in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function, and we find a similar tendency in human data. Thus patterns seen in genome-wide expression experiments can be interpreted as indications of the status of cellular processes. Also, coexpression of genes of known function with poorly characterized or novel genes may provide a simple means of gaining leads to the functions of many genes for which information is not available currently}, keywords = {99061959,analysis,Cluster Analysis,Dna,expression,gene,Gene Expression,GENE-EXPRESSION,Genes,Genetic,genetics,GenomeFungal,GenomeHuman,human,Multigene Family,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportu.s.gov’tp.h.s.,SYSTEM,yeast} } % == BibTeX quality report for eisenClusterAnalysisDisplay1998: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{eisingerSQT1WhichEncodes1997, title = {{{SQT1}}, Which Encodes an Essential {{WD}} Domain Protein of {{Saccharomyces}} Cerevisiae, Suppresses Dominant-Negative Mutations of the Ribosomal Protein Gene {{QSR1}}}, author = {Eisinger, D.P. and Dick, F.A. and Denke, E. and Trumpower, B.L.}, year = 1997, journal = {Molecular and cellular biology}, volume = {17}, number = {9}, pages = {5146–5155}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.17.9.5146}, url = {http://mcb.asm.org/cgi/content/abstract/17/9/5146}, abstract = {QSR1 is an essential Saccharomyces cerevisiae gene, which encodes a 60S ribosomal subunit protein required for joining of 40S and 60S subunits. Truncations of QSR1 predicted to encode C-terminally truncated forms of Qsr1p do not substitute for QSR1 but do act as dominant negative mutations, inhibiting the growth of yeast when expressed from an inducible promoter. The dominant negative mutants exhibit a polysome profile characterized by ‘half-mer’ polysomes, indicative of a subunit joining defect like that seen in other qsr1 mutants (D. P. Eisinger, F. A. Dick, and B. L. Trumpower, Mol. Cell. Biol. 17:5136-5145, 1997.) By screening a high-copy yeast genomic library, we isolated several clones containing overlapping inserts of a novel gene that rescues the slow- growth phenotype of the dominant negative qsr1 truncations. The suppressor of qsr1 truncation mutants, SQT1, is an essential gene, which encodes a 47.1-kDa protein containing multiple WD repeats and which interacts strongly with Qsr1p in a yeast two-hybrid system. SQT1 restores growth and the “half-mer” polysome profile of the dominant negative qsr1 mutants to normal, but it does not rescue temperature- sensitive qsr1 mutants or the original qsr1-1 missense allele. In yeast cell lysates, Sqt1p fractionates as part of an oligomeric protein complex that is loosely associated with ribosomes but is distinct from known eukaryotic initiation factor complexes. Loss of SQT1 function by down regulation from an inducible promoter results in formation of half- mer polyribosomes and decreased Qsr1p levels on free 60S subunits. Sqt1p thus appears to be involved in a late step of 60S subunit assembly or modification in the cytoplasm}, keywords = {60S subunit,97415593,Amino Acid Sequence,assembly,Binding Sites,COMPLEX,COMPLEXES,Cytoplasm,Cytosol,Dna,Fungal Proteins,gene,GenesFungal,genetics,genomic,initiation,library,metabolism,modification,Molecular Sequence Data,Mutagenesis,Mutation,MUTATIONS,nosource,Phenotype,Polyribosomes,polysomes,protein,PROTEIN COMPLEX,regulation,Ribosomal Proteins,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUBUNIT,supportnon-u.s.gov’t,SuppressionGenetic,SYSTEM,Temperature,TranslationGenetic,yeast} } % == BibTeX quality report for eisingerSQT1WhichEncodes1997: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{eisingerQsr1p60SRibosomal1997, title = {Qsr1p, a {{60S}} Ribosomal Subunit Protein, Is Required for Joining of {{40S}} and {{60S}} Subunits}, author = {Eisinger, D.P. and Dick, F.A. and Trumpower, B.L.}, year = 1997, journal = {Mol. Cell. Biol.}, volume = {17}, number = {9}, pages = {5136–5145}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.17.9.5136}, url = {http://mcb.asm.org/cgi/content/abstract/17/9/5136}, abstract = {QSR1 is a recently discovered, essential Saccharomyces cerevisiae gene, which encodes a 60S ribosomal subunit protein. Thirty-one unique temperature-sensitive alleles of QSR1 were generated by regional codon randomization within a conserved 20-amino-acid sequence of the QSR1-encoded protein. The temperature-sensitive mutants arrest as viable, large, unbudded cells 24 to 48 h after a shift to 37 degrees C. Polysome and ribosomal subunit analysis by velocity gradient centrifugation of lysates from temperature-sensitive qsr1 mutants and from cells in which Qsr1p was depleted by down regulation of an inducible promoter revealed the presence of half-mer polysomes and a large pool of free 60S subunits that lack Qsr1p. In vitro subunit-joining assays and analysis of a mutant conditional for the synthesis of Qsr1p demonstrate that 60S subunits devoid of Qsr1p are unable to join with 40S subunits whereas 60S subunits that contain either wild-type or mutant forms of the protein are capable of subunit joining. The defective 60S subunits result from a reduced association of mutant Qsr1p with 60S subunits. These results indicate that Qsr1p is required for ribosomal subunit joining}, keywords = {0,60S subunit,Alleles,analysis,assays,ASSOCIATION,biosynthesis,Cell Survival,CELLS,CEREVISIAE,Codon,Down-Regulation,ENCODES,FORM,Fungal Proteins,gene,genetics,In Vitro,IN-VITRO,La,lysate,metabolism,Mutagenesis,MUTANTS,nosource,Polyribosomes,polysomes,PROMOTER,Promoter Regions (Genetics),protein,Proteins,regulation,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,Temperature,WILD-TYPE} } % == BibTeX quality report for eisingerQsr1p60SRibosomal1997: % ? Possibly abbreviated journal title Mol. Cell. Biol.

@article{eleouetCompleteSequence201995, title = {Complete Sequence (20 Kilobases) of the Polyprotein-Encoding Gene 1 of Transmissible Gastroenteritis Virus}, author = {Eleouet, J.F. and Rasschaert, D. and Lambert, P. and Levy, L. and Vende, P. and Laude, H.}, year = 1995, month = feb, journal = {Virology}, volume = {206}, number = {2}, pages = {817–822}, publisher = {Elsevier}, doi = {10.1006/viro.1995.1004}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0042682285710045}, abstract = {The entire nucleotide sequence of cloned cDNAs containing the 5’-untranslated region and gene 1 of Purdue-115 strain of transmissible gastroenteritis virus (TGEV) was determined. This completes the sequence of the TGEV genome, which is 28,579 nucleotides long. The gene 1 is composed of two large open reading frames, ORF1a and ORF1b, which contain 4017 and 2698 codons, respectively (stop excluded). A brief, three-codon-long ORF is present upstream of ORF1a. ORF1b overlaps ORF1a by 43 bases in the (-1) reading frame. In vitro experiments indicated that translation of the ORF1a/b polyprotein involves an efficient ribosomal frameshifting activity, as previously shown for other coronaviruses. Analysis of the predicted ORF1a and ORF1b translation products revealed that the putative functional domains identified in infectious bronchitis virus (IBV), mouse hepatitis virus (MHV) and human coronavirus 229E (HCV 229E) are all present in TGEV. The amino-terminal half of the ORF1a product exhibits greater divergence than the carboxyl-terminal half, including within the TGEV/HCV229E pair. The ORF1b protein is overall highly conserved among the above four coronaviruses, except a divergent region situated near the carboxy terminus}, keywords = {0,Amino Acid Sequence,analysis,Animals,BASE,Base Sequence,BASES,biosynthesis,CloningMolecular,Codon,CODONS,Comparative Study,Conserved Sequence,Coronaviridae,Coronavirus,Dna,DNA Primers,DNAComplementary,DOMAIN,DOMAINS,FRAME,Frameshifting,gene,GenesViral,genetics,Genome,human,In Vitro,IN-VITRO,Infectious bronchitis virus,La,metabolism,Mice,Molecular Sequence Data,Murine hepatitis virus,nosource,NUCLEOTIDE-SEQUENCE,Nucleotides,OPEN READING FRAME,Open Reading Frames,Polymerase Chain Reaction,POLYPROTEIN,PRODUCT,PRODUCTS,protein,Proteins,READING FRAME,Reading Frames,REGION,Restriction Mapping,ribosomal frameshifting,Ribosomes,sequence,Sequence HomologyAmino Acid,translation,Transmissible gastroenteritis virus,UPSTREAM,Viral Proteins,virus} }

@article{ellisDiamondBlackfanAnemia2006, title = {Diamond {{Blackfan}} Anemia: {{A}} Paradigm for a Ribosome-Based Disease}, author = {Ellis, S.R. and Massey, A.T.}, year = 2006, journal = {Med.Hypotheses}, volume = {66}, number = {3}, pages = {643–648}, doi = {10.1016/j.mehy.2005.09.010}, url = {PM:16239073}, abstract = {Diamond Blackfan anemia is characterized by a severe hypoplastic anemia and a heterogeneous collection of other clinical features. Approximately 25% of Diamond Blackfan anemia cases are associated with mutations in the gene encoding ribosomal protein S19. The hypothesis presented here ties together molecular and clinical features of the disease, and establishes a conceptual framework for understanding many of the unusual characteristics of a growing number of diseases linked to factors involved in ribosome synthesis. The hypothesis states that ribosomal proteins are expressed in amounts that differ relative to one another in a tissue-specific manner, and that haploinsufficiency for a particular protein may make that protein limiting for ribosome assembly in some tissues, while other tissues remain unaffected. Further, polymorphisms in factors controlling the expression of a particular ribosomal protein gene may alter its expression and expand or contract the number of tissues affected from individual to individual. Support for the hypothesis comes from the observation that promoters in ribosomal protein genes exhibit little conservation and transcription profiling indicates that the absolute amounts of mRNAs for individual ribosomal proteins can vary dramatically relative to one another. Balanced expression of ribosomal proteins is achieved post-translationally, where excess proteins not assembled into ribosomal subunits are often rapidly degraded. The number of ribosomes per cell is therefore determined by the factors that limit assembly. In principle, any essential ribosomal protein could become limiting for assembly if its level of expression falls below a critical threshold. Whether an inactivating mutation in ribosomal protein gene would affect protein synthetic capacity of a tissue would depend on the ratio of the ribosomal protein relative to other ribosomal proteins in that tissue. If the ratio were high, the tissue may not be affected as the level of functional protein may not fall to a point where it becomes limiting for subunit assembly. In contrast, if the ratio were low, an inactivating mutation could make the protein limiting for subunit assembly resulting in a clinical phenotype. Polymorphisms in the myriad of cis- and trans-acting factors, which govern the expression of ribosomal proteins in response to developmental and physiological signals, could act to increase or decrease ribosomal protein expression and thereby impact the profile and severity of clinical phenotypes. Therefore, these factors represent targets for the development of new therapies to treat Diamond Blackfan anemia and other ribosome based diseases}, keywords = {0,Anemia,AnemiaDiamond-Blackfan,assembly,Biochemistry,BIOLOGY,development,diagnosis,disease,expression,gene,Genes,genetics,Humans,La,metabolism,ModelsBiological,ModelsTheoretical,Molecular Biology,mRNA,Mutation,MUTATIONS,nosource,pathology,Phenotype,physiology,PolymorphismGenetic,PROMOTER,PROMOTERS,protein,Proteins,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,RIBOSOME SYNTHESIS,Ribosomes,SIGNAL,SUBUNIT,SUBUNITS,Support,TARGET,therapy,TRANS-ACTING FACTORS,Trans-Activation (Genetics),transcription} } % == BibTeX quality report for ellisDiamondBlackfanAnemia2006: % ? Possibly abbreviated journal title Med.Hypotheses

@article{endoSiteActionSix1988, title = {The Site of Action of Six Different Ribosome-Inactivating Proteins from Plants on Eukaryotic Ribosomes: The {{RNA N-glycosidase}} Activity of the Proteins}, author = {Endo, Y. and Tsurugi, K. and Lambert, J.M.}, year = 1988, month = feb, journal = {Biochemical and biophysical research communications}, volume = {150}, number = {3}, pages = {1032–1036}, publisher = {Elsevier}, doi = {10.1016/0006-291X(88)90733-4}, url = {http://linkinghub.elsevier.com/retrieve/pii/0006291X88907334}, abstract = {The site of action of six different ribosome-inactivating proteins from plants on eukaryotic ribosomes was studied. Treatment of ribosomes with any one of these proteins caused the 28S rRNA extracted from the inactivated ribosomes to become sensitive to treatment with aniline. A fragment containing about 450 nucleotides was released from the 28S rRNA. Further analysis of the nucleotide sequences of the 450-nucleotide fragments revealed that the aniline-sensitive phosphodiester bond was between A-4324 and G-4325 of the 28S rRNA. These results indicate that all six ribosome-inactivating proteins damage eukaryotic ribosomes by cleaving the N-glycosidic bond at A-4324 of the 28S rRNA of the ribosomes, as does ricin A-chain}, keywords = {analysis,nosource,Nucleotides,PAP,protein,Proteins,ribosome,Ribosomes,Ricin,Rna,rRNA,sequence} }

@article{engelberg-kulkaRegulatoryImplicationsTranslational1994, title = {Regulatory Implications of Translational Frameshifting in Cellular Gene Expression}, author = {{Engelberg-Kulka}, H. and {Schoulaker-Schwarz}, R.}, year = 1994, month = jan, journal = {Molecular microbiology}, volume = {11}, number = {1}, pages = {3–8}, publisher = {Wiley Online Library}, doi = {10.1111/j.1365-2958.1994.tb00283.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.1994.tb00283.x/abstract}, abstract = {The genetic code, once thought to be rigid, has been found to be quite flexible, permitting several different reading alternatives. One of these is translational frameshifting, a process programmed in the mRNA sequence and which enables a +1 or -1 shift from the reading frame of the initiation codon. So far, the involvement of translational frameshifting in gene expression has been described mainly in viruses (particularly retroviruses), retrotransposons, and bacterial insertion elements. In this MicroReview, we present a survey of the cellular genes, mostly in Escherichia coli, which have been found to be expressed through a translational frameshifting process, as well as a discussion of the regulatory implications of this process}, keywords = {0,Bacterial,Base Sequence,BIOLOGY,Codon,ELEMENTS,Escherichia coli,ESCHERICHIA-COLI,expression,FRAME,Frameshifting,gene,Gene Expression,Gene Expression RegulationBacterial,GENE-EXPRESSION,Genes,GenesBacterial,Genetic,Genetic Code,GENETIC-CODE,genetics,initiation,INSERTION ELEMENT,La,Molecular Sequence Data,mRNA,nosource,physiology,Protein Biosynthesis,READING FRAME,Research SupportNon-U.S.Gov’t,retrotransposon,RETROVIRUSES,Review,sequence,TRANSLATIONAL FRAMESHIFTING,Viruses} } % == BibTeX quality report for engelberg-kulkaRegulatoryImplicationsTranslational1994: % ? unused Journal abbr (“Mol.Microbiol.”)

@article{ennifarStructurebasedApproachTargeting2007a, title = {A Structure-Based Approach for Targeting the {{HIV-1}} Genomic {{RNA}} Dimerization Initiation Site}, author = {Ennifar, E. and Paillart, J.C. and Bernacchi, S. and Walter, P. and Pale, P. and Decout, J.L. and Marquet, R. and Dumas, P.}, year = 2007, month = oct, journal = {Biochimie}, volume = {89}, number = {10}, pages = {1195–1203}, doi = {10.1016/j.biochi.2007.03.003}, url = {PM:17434658}, abstract = {Dimerization of the genomic RNA is an important step of the HIV-1 replication cycle. The Dimerization Initiation Site (DIS) promotes dimerization of the viral genome by forming a loop-loop complex between two DIS hairpins. Crystal structures of the DIS loop-loop complex revealed an unexpected and strong similitude with the bacterial 16S ribosomal aminoacyl-tRNA site (A site), which is the target of aminoglycoside antibiotics. As a consequence of these structural and sequence similarities, the HIV-1 DIS also binds some aminoglycosides, not only in vitro, but also ex vivo, in lymphoid cells and in viral particles. Crystal structures of the DIS loop-loop in complex with several aminoglycoside antibiotics provide a detailed-view of the DIS/drug interaction and reveal some hints about possible modifications to increase the drug affinity and/or specificity}, keywords = {16S,A SITE,A-SITE,AMINOGLYCOSIDE ANTIBIOTICS,Aminoglycosides,antibiotic,antibiotics,Bacterial,CELLS,COMPLEX,COMPLEXES,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,Dimerization,Genome,genomic,GENOMIC RNA,HAIRPINS,Hiv-1,In Vitro,IN-VITRO,initiation,INITIATION SITE,La,modification,nosource,PARTICLES,REPLICATION,Review,Rna,sequence,SITE,SPECIFICITY,Structural,structure,Support,TARGET,viral particle,VIRAL PARTICLES} }

@article{ericksonDirectCloningYeast1993, title = {Direct Cloning of Yeast Genes from an Ordered Set of Lambda Clones in {{Saccharomyces}} Cerevisiae by Recombination in Vivo}, author = {Erickson, J.R. and Johnston, M.}, year = 1993, month = may, journal = {Genetics}, volume = {134}, number = {1}, pages = {151–157}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/134.1.151}, url = {http://www.genetics.org/content/134/1/151.short}, abstract = {We describe a technique that facilitates the isolation of yeast genes that are difficult to clone. This technique utilizes a plasmid vector that rescues lambda clones as yeast centromere plasmids. The source of these lambda clones is a set of clones whose location in the yeast genome has been determined by L. Riles et al. in 1993. The Escherichia coli-yeast shuttle plasmid carries URA3, ARS4 and CEN6, and contains DNA fragments from the lambda vector that flank the cloned yeast insert. When yeast is cotransformed with linearized plasmid and lambda clone DNA, Ura+ transformants are obtained by a recombination event between the lambda clone and the plasmid vector that generates an autonomously replicating plasmid containing the cloned yeast DNA sequences. Genes whose genetic map positions are known can easily be identified and recovered in this plasmid by testing only those lambda clones that map to the relevant region of the yeast genome for their ability to complement the mutant phenotype. This technique facilitates the isolation of yeast genes that resist cloning either because (1) they are underrepresented in yeast genomic libraries amplified in E. coli, (2) they provide phenotypes that are too marginal to allow selection of the gene by genetic complementation or (3) they provide phenotypes that are laborious to score. We demonstrate the utility of this technique by isolating three genes, GAL83, SSN2 and MAK7, each of which presents one of these problems for cloning}, keywords = {0,Bacteriophage lambda,Base Sequence,Chromosome Mapping,cloning,CloningMolecular,Dna,DNAFungal,DNARecombinant,Escherichia coli,gene,Genes,GenesFungal,Genetic,Genetic Vectors,genetics,Genome,genomic,Genomic Library,IN-VIVO,La,library,Molecular Sequence Data,nosource,Phenotype,Plasmids,RecombinationGenetic,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,supportu.s.gov’tp.h.s.,TransformationGenetic,vector,vectors,yeast} }

@article{erlacherEfficientRibosomalPeptidyl2006, title = {Efficient Ribosomal Peptidyl Transfer Critically Relies on the Presence of the Ribose 2’-{{OH}} at {{A2451}} of {{23S rRNA}}}, author = {Erlacher, M.D. and Lang, K. and Wotzel, B. and Rieder, R. and Micura, R. and Polacek, N.}, year = 2006, month = apr, journal = {Journal of the American Chemical Society}, volume = {128}, number = {13}, pages = {4453–4459}, publisher = {ACS Publications}, doi = {10.1021/ja0588454}, url = {http://pubs.acs.org/doi/abs/10.1021/ja0588454}, abstract = {The ribosomal peptidyl transferase center is a ribozyme catalyzing peptide bond synthesis in all organisms. We applied a novel modified nucleoside interference approach to identify functional groups at 9 universally conserved active site residues. Owing to their immediate proximity to the chemical center, the 23S rRNA nucleosides A2451, U2506 and U2585 were of particular interest. Our study ruled out U2506 and U2585 as contributors of vital chemical groups for transpeptidation. In contrast the ribose 2’-OH of A2451 was identified as the prime ribosomal group with potential functional importance. This 2’-OH renders almost full catalytic power to the ribosome even when embedded into an active site of six neighboring 2’-deoxyribose nucleosides. These data highlight the unique functional role of the A2451 2’-OH for peptide bond synthesis among all other functional groups at the ribosomal peptidyl transferase active site}, keywords = {0,ACTIVE-SITE,Base Sequence,Binding Sites,chemistry,enzymology,genomic,Genomics,IDENTIFY,La,metabolism,ModelsMolecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleosides,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,Peptidyl Transferases,peptidyl-transfer,PEPTIDYL-TRANSFERASE,RESIDUES,Ribose,RIBOSOMAL PEPTIDYL TRANSFERASE,ribosome,Ribosomes,ribozyme,Rna,RNARibosomal23S,rRNA,SITE,Structure-Activity Relationship,Support,TRANSFERASE CENTER,Transferases} } % == BibTeX quality report for erlacherEfficientRibosomalPeptidyl2006: % ? unused Journal abbr (“J.Am.Chem.Soc.”)

@article{ermolenkoAntibioticViomycinTraps2007, title = {The Antibiotic Viomycin Traps the Ribosome in an Intermediate State of Translocation}, author = {Ermolenko, D.N. and Spiegel, P.C. and Majumdar, Z.K. and Hickerson, R.P. and Clegg, R.M. and Noller, H.F.}, year = 2007, month = jun, journal = {Nature structural & molecular biology}, volume = {14}, number = {6}, pages = {493–497}, publisher = {Nature Publishing Group}, doi = {10.1038/nsmb1243}, url = {http://www.nature.com/nsmb/journal/v14/n6/abs/nsmb1243.html}, abstract = {During protein synthesis, transfer RNA and messenger RNA undergo coupled translocation through the ribosome’s A, P and E sites, a process catalyzed by elongation factor EF-G. Viomycin blocks translocation on bacterial ribosomes and is believed to bind at the subunit interface. Using fluorescent resonance energy transfer and chemical footprinting, we show that viomycin traps the ribosome in an intermediate state of translocation. Changes in FRET efficiency show that viomycin causes relative movement of the two ribosomal subunits indistinguishable from that induced by binding of EF-G with GDPNP. Chemical probing experiments indicate that viomycin induces formation of a hybrid-state translocation intermediate. Thus, viomycin inhibits translation through a unique mechanism, locking ribosomes in the hybrid state; the EF-G-induced ‘ratcheted’ state observed by cryo-EM is identical to the hybrid state; and, since translation is viomycin sensitive, the hybrid state may be present in vivo}, keywords = {antibiotic,Bacterial,BINDING,BIOLOGY,E,E site,EF-G,efficiency,elongation,Energy Transfer,IN-VIVO,interface,INTERMEDIATE,La,MECHANISM,MESSENGER-RNA,Molecular Biology,Movement,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,SITE,SITES,SUBUNIT,SUBUNITS,Support,TRANSFER-RNA,translation,translocation,Viomycin} } % == BibTeX quality report for ermolenkoAntibioticViomycinTraps2007: % ? unused Journal abbr (“Nat.Struct.Mol.Biol”)

@article{ernstStructuredRetroviralRNA1997a, title = {A Structured Retroviral {{RNA}} Element That Mediates Nucleocytoplasmic Export of Intron-Containing {{RNA}}}, author = {Ernst, R.K. and Bray, M. and Rekosh, D. and Hammarskjold, M.L.}, year = 1997, month = jan, journal = {Molecular & Cellular Biology}, volume = {17}, number = {1}, pages = {135–144}, doi = {10.1128/MCB.17.1.135}, keywords = {COMPLEX,COMPLEXES,Cytoplasm,ELEMENTS,expression,gene,Gene Expression,GENE-EXPRESSION,Genome,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,nosource,protein,Proteins,Rna,SIGNAL,virus} }

@article{estebanThreeDifferentM11986a, title = {Three Different {{M}}⬚1⬚ {{RNA-containing}} Viruslike Particle Types in ⬚{{Saccharomyces}} Cerevisiae⬚: ⬚in Vitro⬚ {{M}}⬚1⬚ Double-Stranded {{RNA}} Synthesis.}, author = {Esteban, R. and Wickner, R.B.}, year = 1986, journal = {Mol.Cell.Biol.}, volume = {6}, pages = {1552–1561}, keywords = {Gag,In Vitro,IN-VITRO,L-A,La,M1,Multiple DOI,nonfile,nosource,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,virus} } % == BibTeX quality report for estebanThreeDifferentM11986a: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{estebanNewNonMendelianGenetic1987, title = {A {{New Non-Mendelian Genetic Element}} of {{Yeast That Increases Cytopathology Produced}} by {{M1 Double-Stranded-Rna}} in {{Ski Strains}}}, author = {Esteban, R. and Wickner, R.B.}, year = 1987, month = nov, journal = {Genetics}, volume = {117}, number = {3}, pages = {399–408}, doi = {10.1093/genetics/117.3.399}, url = {ISI:A1987K677500005}, keywords = {DOUBLE-STRANDED-RNA,Genetic,M1,nosource,SKI,yeast} } % == BibTeX quality report for estebanNewNonMendelianGenetic1987: % ? Title looks like it was stored in title-case in Zotero

@article{estebanSiteSpecificBindingViral1988, title = {Site-{{Specific Binding}} of {{Viral Plus Single-Stranded Rna}} to {{Replicase-Containing Open Virus-Like Particles}} of {{Yeast}}}, author = {Esteban, R. and Fujimura, T. and Wickner, R.B.}, year = 1988, month = jun, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {85}, number = {12}, pages = {4411–4415}, doi = {10.1073/pnas.85.12.4411}, url = {ISI:A1988N986900064}, keywords = {BINDING,nosource,PARTICLES,Rna,site specific,yeast} } % == BibTeX quality report for estebanSiteSpecificBindingViral1988: % ? Title looks like it was stored in title-case in Zotero

@article{estebanInternalTerminalCisActing1989a, title = {Internal and {{Terminal Cis-Acting Sites Are Necessary}} for {{Invitro Replication}} of the {{L-A Double-Stranded-Rna Virus}} of {{Yeast}}}, author = {Esteban, R. and Fujimura, T. and Wickner, R.B.}, year = 1989, month = mar, journal = {EMBO Journal}, volume = {8}, number = {3}, pages = {947–954}, doi = {10.1002/j.1460-2075.1989.tb03456.x}, url = {ISI:A1989T691000036}, keywords = {DOUBLE-STRANDED-RNA,INVITRO,L-A,La,nosource,REPLICATION,SITE,SITES,virus,yeast} } % == BibTeX quality report for estebanInternalTerminalCisActing1989a: % ? Title looks like it was stored in title-case in Zotero

@article{estebanLaunchingYeast23S2003, title = {Launching the Yeast {{23S RNA Narnavirus}} Shows 5’ and 3’ Cis-Acting Signals for Replication}, author = {Esteban, R. and Fujimura, T.}, year = 2003, month = mar, journal = {Proceedings of the National Academy of Sciences}, volume = {100}, number = {5}, pages = {2568–2573}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.0530167100}, url = {http://www.pnas.org/content/100/5/2568.short}, abstract = {Narnavirus 23S RNA is a persistent positive-stranded RNA virus found in yeast Saccharomyces cerevisiae. The viral genome (2.9 kb) only encodes its RNA-dependent RNA polymerase, p104. Here we report the generation of 23S RNA virus, with high frequency, from a vector containing the entire viral cDNA sequence. When the conserved GDD (Gly-Asp-Asp) motif of RNA-dependent RNA polymerase was modified, the vector failed to generate the virus, indicating that an active p104 is essential for replication. Successful launching required transcripts having the proper viral 3’ terminus generated in vivo. This was accomplished through in vivo processing of the primary transcripts by the hepatitis delta virus antigenomic ribozyme directly fused to the 3’ terminus of the 23S RNA genome. Although the primary transcripts also contained extra nucleotides at their 5’ ends derived from the vector, the launched virus possessed the authentic 5’ terminus of the viral genome without these extra nucleotides. Modifications of the genome sequence at the 5’ and 3’ termini abolished viral generation, indicating that the viral genome has cis-acting signals for replication at both termini. The great ease to generate the virus will facilitate the identification of these cis-acting signals. Furthermore, the virus, once generated, can be transmitted to daughter cells indefinitely without the vector or any selection, which makes the 23S RNA virus-launching system particularly useful for investigating the basis for RNA virus persistence}, keywords = {0,23S RNA,3,Amino Acid Motifs,BlottingNorthern,CELLS,CEREVISIAE,Dna,DNAComplementary,ENCODES,Genetic,Genetic Vectors,genetics,Genome,Hepatitis Delta Virus,IDENTIFICATION,IN-VIVO,La,metabolism,modification,Mutation,nosource,Nucleotides,PLASMID,Plasmids,polymerase,Protein StructureTertiary,REPLICATION,ribozyme,Rna,RNA Viruses,RNA-DEPENDENT RNA POLYMERASE,RNA-POLYMERASE,RNAMessenger,RNARibosomal23S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SELECTION,sequence,SIGNAL,supportnon-u.s.gov’t,SYSTEM,TRANSCRIPT,vector,vectors,virus,Virus Replication,yeast} } % == BibTeX quality report for estebanLaunchingYeast23S2003: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{eusticeFidelityEukaryoticCodonanticodon1984, title = {Fidelity of the Eukaryotic Codon-Anticodon Interaction: Interference by Aminoglycoside Antibiotics}, author = {Eustice, D.C. and Wilhelm, J.M.}, year = 1984, month = mar, journal = {Biochemistry}, volume = {23}, number = {7}, pages = {1462–1467}, publisher = {ACS Publications}, doi = {10.1021/bi00302a019}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00302a019}, abstract = {A homologous in vitro method was developed from Tetrahymena for ribosomal A-site binding of aminoacyl-tRNA to poly(uridylic acid)-programmed ribosomes with very low error frequency. The reaction mixture pH was the crucial factor in the stable A-site association of aminoacyl-tRNA with high fidelity. At a pH greater than 7.1, endogenous activity translocated A-site-bound aminoacyl-tRNA to the P site. If translocation was allowed to occur, a near-cognate amino-acyl-tRNA, Leu-tRNA, could stably bind to the ribosome by translocation to the ribosomal P site. Near-cognate aminoacyl-tRNA did not stably bind to either site when translocation was blocked. Misreading antibiotics stimulated the stable association of near-cognate aminoacyl-tRNA to the ribosomal A site, thereby increasing the error frequency by several orders of magnitude. Ribosome binding of total aminoacyl-tRNA near equilibrium was not inhibited by misreading antibiotics; however, initial rate kinetics of the binding reaction were dramatically altered such that a 6-fold rate increase was observed with paromomycin or hygromycin B. The rate increase was evident with both cognate and near-cognate aminoacyl-tRNAs. Several antibiotics were tested for misreading potency by the ribosome binding method. We found gentamicin G418 greater than paromomycin greater than neomycin greater than hygromycin B greater than streptomycin in the potentiation of misreading. Tetracycline group antibiotics effectively inhibited A-site aminoacyl-tRNA binding without promoting misreading}, keywords = {0,A SITE,A-SITE,AMINOGLYCOSIDE ANTIBIOTICS,Animals,Anti-Bacterial Agents,antibiotic,antibiotics,Anticodon,ASSOCIATION,BINDING,Binding Sites,Codon,CODON-ANTICODON INTERACTION,drug effects,elongation,elongation factors,ELONGATION-FACTORS,Fidelity,Hydrogen-Ion Concentration,Hygromycin B,In Vitro,IN-VITRO,Kinetics,La,metabolism,Neomycin,nosource,P SITE,P-SITE,Paromomycin,Peptide Elongation Factors,pharmacology,Protein Biosynthesis,ribosome,RIBOSOME BINDING,Ribosomes,SITE,Streptomycin,Structure-Activity Relationship,Support,Tetracycline,Tetrahymena,Transfer RNA Aminoacylation,translocation} }

@article{everettRNADeliverySaccharomyces1992, title = {{{RNA}} Delivery in {{Saccharomyces}} Cerevisiae Using Electroporation}, author = {Everett, J.G. and Gallie, D.R.}, year = 1992, month = dec, journal = {Yeast}, volume = {8}, number = {12}, pages = {1007–1014}, publisher = {Wiley Online Library}, doi = {10.1002/yea.320081203}, url = {http://onlinelibrary.wiley.com/doi/10.1002/yea.320081203/abstract}, abstract = {An efficient delivery method for introducing in vitro synthesized RNA into yeast has been developed using electroporation. Spheroplast preparation, electroporation, and subsequent expression analysis can be accomplished within a single day. The use of introduced mRNA constructs avoids any complications due to nuclear regulation and is particularly suited for cytoplasmic regulatory studies. Moreover, this technique is useful for introducing those RNAs that cannot be made in vivo, such as poly(A)- mRNAs or RNAs with base modifications. We demonstrate that the Escherichia coli GUS gene and the firefly Luc gene are both excellent reporter genes for RNA electroporation}, keywords = {0,analysis,animal,BASE,Beetles,biosynthesis,Cap,CEREVISIAE,Drug Carriers,enzymology,Escherichia coli,ESCHERICHIA-COLI,expression,gene,Genes,genetics,Glucuronidase,In Vitro,IN-VITRO,IN-VIVO,La,luciferase,metabolism,Methods,modification,mRNA,nosource,pharmacology,Poly A,poly(A),regulation,Rna,Rna Caps,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Spheroplasts,supportnon-u.s.gov’t,Transfection,TranslationGenetic,yeast} }

@article{fabijanskiIdentificationProteinsPeptidyltRNA1981, title = {Identification of Proteins at the Peptidyl-{{tRNA}} Binding Site of Rat Liver Ribosomes}, author = {Fabijanski, S. and Pellegrini, M.}, year = 1981, journal = {Molecular and General Genetics MGG}, volume = {184}, number = {3}, pages = {551–556}, publisher = {Springer}, doi = {10.1007/BF00352539}, url = {http://www.springerlink.com/index/T3T37056P6537566.pdf}, abstract = {We have identified proteins involved in the peptidyl-tRNA-binding site of rat liver ribosomes, using an affinity label designed specifically to probe the P-site in eukaryotic peptidyl transferase. The label is a 3’-terminal pentanucleotide fragment of N-acetylleucyl-tRNA in which mercury atoms have been added at the C-5 position of the three cytosine residues. This mercurated fragment can bind to rat liver peptidyl transferase and function as a donor of N-acetylleucine to puromycin. Concomitant with this binding, the mercury atoms present in the fragment can form a covalent linkage with a small number of ribosomal proteins. The major proteins labeled by this reagent are L5 and L36A. Four protein spots are found labeled to a lesser extent: L10, L7/7a, L3/4 and L25/31. Each of these proteins, therefore, is implicated in the binding of the 3’-terminus of peptidyl-tRNA. The results presented here are correlated with other investigations of the structure-function aspects of rat liver peptidyl transferase. Using these data, we have constructed a model for the arrangement of proteins within this active site}, keywords = {0,Affinity Labels,animal,Base Sequence,BINDING,Binding Sites,Cytosine,IDENTIFICATION,L5,La,Liver,Mercury,metabolism,nosource,P-SITE,Peptides,peptidyl transferase,Peptidyltransferase,protein,Protein Binding,Proteins,Puromycin,rat,Rats,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNATransfer,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,tRNA} } % == BibTeX quality report for fabijanskiIdentificationProteinsPeptidyltRNA1981: % ? unused Journal abbr (“Mol.Gen.Genet.”)

@article{fahlmanUniformBindingAminoacylated2004, title = {Uniform Binding of Aminoacylated Transfer {{RNAs}} to the Ribosomal {{A}} and {{P}} Sites}, author = {Fahlman, R.P. and Dale, T. and Uhlenbeck, O.C.}, year = 2004, month = dec, journal = {Molecular cell}, volume = {16}, number = {5}, pages = {799–805}, publisher = {Elsevier}, doi = {10.1016/j.molcel.2004.10.030}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276504006550}, abstract = {The association and dissociation rate constants of eight different E. coli aminoacyl-tRNAs (aa-tRNAs) for E. coli ribosomes programmed with mRNAs of defined sequences were determined. Identical association and dissociation rate constants were observed for all eight aa-tRNAs in both the ribosomal A and P sites despite substantial differences in tRNA sequence, the type of esterified amino acid, and posttranscriptional modifications. These results indicate that the overall binding of all aa-tRNAs to the ribosome is uniform. However, when either the esterified amino acid or the tRNA modifications were removed, binding was no longer uniform. These results suggest that differences in tRNA sequences and tRNA modifications have evolved to offset differential thermodynamic contributions of the esterified amino acid and the codon-anticodon interaction so that ribosomal binding of all aa-tRNAs remains uniform}, keywords = {ACID,AMINO-ACID,ASSOCIATION,BINDING,BIOLOGY,CODON-ANTICODON INTERACTION,E,La,modification,mRNA,nosource,P SITE,P-SITE,P-SITES,posttranscriptional modification,ribosome,Ribosomes,Rna,sequence,SEQUENCES,SITE,SITES,TRANSFER-RNA,tRNA} } % == BibTeX quality report for fahlmanUniformBindingAminoacylated2004: % ? unused Journal abbr (“Mol.Cell”)

@article{fahnestockEvidenceInvolvement50S1975, title = {Evidence of the Involvement of a {{50S}} Ribosomal Protein in Several Active Sites}, author = {Fahnestock, S.R.}, year = 1975, month = dec, journal = {Biochemistry}, volume = {14}, number = {24}, pages = {5321–5327}, publisher = {ACS Publications}, doi = {10.1021/bi00695a016}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00695a016}, abstract = {The functional role of the Bacillus stearothermophilus 50S ribosomal protein B-L3 (probably homologous to the Escherichia coli protein L2) was examined by chemical modification. The complex [B-L3-23S RNA] was photooxidized in the presence of rose bengal and the modified protein incorporated by reconstitution into 50S ribosomal subunits containing all other unmodified components. Particles containing photooxidized B- L3 are defective in several functional assays, including (1) poly(U)- directed poly(Phe) synthesis, (2) peptidyltransferase activity, (3) ability to associate with a [30S-poly(U)-Phe-tRNA] complex, and (4) binding of elongation factor G and GTP. The rates of loss of the partial functional activities during photooxidation of B-L3 indicate that at least two independent inactivating events are occurring, a faster one, involving oxidation of one or more histidine residues, affecting peptidyltransferase and subunit association activities and a slower one affecting EF-G binding. Therefore the protein B-L3 has one or more histidine residues which are essential for peptidyltransferase and subunit association, and another residue which is essential for EF- G-GTP binding. B-L3 may be the ribosomal peptidyltransferase protein, or a part of the active site, and may contribute functional groups to the other active sites as well}, keywords = {0,assays,Bacillus stearothermophilus,BACILLUS-STEAROTHERMOPHILUS,BINDING,Binding Sites,COMPLEX,COMPLEXES,COMPONENT,elongation,Escherichia coli,ESCHERICHIA-COLI,GTP,Histidine,Hydrogen-Ion Concentration,Kinetics,L2,L3,La,Macromolecular Systems,metabolism,modification,nosource,Oxidation-Reduction,Peptidyltransferase,Photochemistry,protein,Protein Binding,Proteins,Ribosomal Proteins,Ribosomes,SUBUNIT,supportu.s.gov’tp.h.s.,SYSTEM} }

@article{fan-minogueEukaryoticRibosomalRNA2008, title = {Eukaryotic Ribosomal {{RNA}} Determinants of Aminoglycoside Resistance and Their Role in Translational Fidelity}, author = {{Fan-Minogue}, H. and Bedwell, D.M.}, year = 2008, month = jan, journal = {RNA.}, volume = {14}, number = {1}, pages = {148–157}, publisher = {Cold Spring Harbor Lab}, doi = {10.1261/rna.805208}, url = {http://rnajournal.cshlp.org/content/14/1/148.short}, abstract = {Recent studies of prokaryotic ribosomes have dramatically increased our knowledge of ribosomal RNA (rRNA) structure, functional centers, and their interactions with antibiotics. However, much less is known about how rRNA function differs between prokaryotic and eukaryotic ribosomes. The core decoding sites are identical in yeast and human 18S rRNAs, suggesting that insights obtained in studies with yeast rRNA mutants can provide information about ribosome function in both species. In this study, we examined the importance of key nucleotides of the 18S rRNA decoding site on ribosome function and aminoglycoside susceptibility in Saccharomyces cerevisiae cells expressing homogeneous populations of mutant ribosomes. We found that residues G577, A1755, and A1756 (corresponding to Escherichia coli residues G530, A1492, and A1493, respectively) are essential for cell viability. We also found that residue G1645 (A1408 in E. coli) and A1754 (G1491 in E. coli) both make significant and distinct contributions to aminoglycoside resistance. Furthermore, we found that mutations at these residues do not alter the basal level of translational accuracy, but influence both paromomycin-induced misreading of sense codons and readthrough of stop codons. This study represents the most comprehensive mutational analysis of the eukaryotic decoding site to date, and suggests that many fundamental features of decoding site function are conserved between prokaryotes and eukaryotes}, keywords = {0,18s rrna,accuracy,aminoglycosides,Aminoglycosides,analysis,antibiotic,antibiotics,BIOLOGY,CELLS,CEREVISIAE,Codon,CODONS,decoding,decoding site,drug effects,Drug ResistanceMicrobial,E,elongation fidelity,Escherichia coli,ESCHERICHIA-COLI,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,Fidelity,genetics,human,INFORMATION,La,Microbial Sensitivity Tests,MUTANTS,Mutation,MUTATIONAL ANALYSIS,MUTATIONS,nosource,Nucleotides,pharmacology,PROKARYOTES,Protein Biosynthesis,readthrough,RESIDUES,RESISTANCE,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNAFungal,RNARibosomal18S,rRNA,rRNA mutants,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SITE,SITES,STOP CODON,structure,Support,translation termination,translational fidelity,yeast} } % == BibTeX quality report for fan-minogueEukaryoticRibosomalRNA2008: % ? Possibly abbreviated journal title RNA.

@article{fanGlobalAnalysisStressregulated2002, title = {Global Analysis of Stress-Regulated {{mRNA}} Turnover by Using {{cDNA}} Arrays}, author = {Fan, J. and Yang, X. and {wang}, w. and Wood, W.H. and Becker, K.G. and Gorospe, M.}, year = 2002, journal = {Proceedings of the National Academy of Sciences}, volume = {99}, number = {16}, pages = {10611–10616}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.162212399}, url = {http://www.pnas.org/content/99/16/10611.short}, abstract = {cDNA array technology has proven to be a powerful way to monitor global changes in gene expression patterns. Here, we present an approach that extends the current utility of cDNA arrays to allow the evaluation of the relative roles of transcription and mRNA turnover in governing gene expression on a global basis, compared with current individual gene-by-gene analyses. This method, which involves comparison of large-scale hybridization patterns generated with steady-state mRNA versus newly transcribed (nuclear run-on) RNA, was used to demonstrate the importance of mRNA turnover in regulating gene expression following several conditions of stress}, keywords = {0,analysis,ARRAYS,BIOLOGY,CarcinomaNon-Small-Cell Lung,Dna,expression,gene,Gene Expression,GENE-EXPRESSION,genetics,Heat-Shock Response,human,La,Lung Neoplasms,mRNA,mRNA turnover,nosource,Oligonucleotide Array Sequence Analysis,PATTERNS,pharmacology,Prostaglandins A,Rna,RNAMessenger,Stress,transcription,Tumor CellsCultured,turnover,ultraviolet rays} } % == BibTeX quality report for fanGlobalAnalysisStressregulated2002: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{fangEvolutionarilyConservedFeatures2000, title = {Evolutionarily Conserved Features of the Arginine Attenuator Peptide Provide the Necessary Requirements for Its Function in Translational Regulation}, author = {Fang, P. and Wang, Z. and Sachs, M.S.}, year = 2000, journal = {Journal of Biological Chemistry}, volume = {275}, number = {35}, pages = {26710–26719}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(19)61434-1}, url = {http://www.jbc.org/content/275/35/26710.short}, abstract = {Neurospora crassa arg-2 mRNA contains an evolutionarily conserved upstream open reading frame (uORF) encoding the Arg attenuator peptide (AAP) that confers negative translational regulation in response to Arg. We examined the regulatory role of the AAP and the RNA encoding it using an N. crassa cell-free translation system. AAPs encoded by uORFs in four fungal mRNAs each conferred negative regulation in response to Arg by causing ribosome stalling at the uORF termination codon. Deleting the AAP non-conserved N terminus did not impair regulation, but deletions extending into the conserved region eliminated it. Introducing many silent mutations into a functional AAP coding region did not eliminate regulation, but a single additional nucleotide change altering the conserved AAP sequence abolished regulation. Therefore, the conserved peptide sequence, but not the mRNA sequence, appeared responsible for regulation. AAP extension at its C terminus resulted in Arg-mediated ribosomal stalling during translational elongation within the extended region and during termination. Comparison of Arg-mediated stalling at a rare or common codon revealed more stalling at the rare codon, These data indicate that the highly evolutionarily conserved peptide core functions within the ribosome to cause stalling; translational events at a potential stall site can influence the extent of stalling there}, keywords = {AMINO-ACID AVAILABILITY,Arginine,CARBAMOYL-PHOSPHATE SYNTHETASE,Codon,elongation,expression,FRAME,gene,IN-VITRO TRANSLATION,LEADER PEPTIDE,M,MESSENGER-RNA,mRNA,Mutation,MUTATIONS,NEUROSPORA-CRASSA,nosource,OPEN READING FRAME,REGION,regulation,ribosome,Rna,S,S-ADENOSYLMETHIONINE DECARBOXYLASE,sequence,SITE,SYSTEM,termination,TERMINATION CODON,translation,UPSTREAM} }

@article{farabaughNovelProgrammedFrameshift1993, title = {A {{Novel Programmed Frameshift Expresses}} the {{Pol3 Gene}} of {{Retrotransposon-Ty3}} of {{Yeast}} - {{Frameshifting Without Transfer-Rna Slippage}}}, author = {Farabaugh, P.J. and Zhao, H. and Vimaladithan, A.}, year = 1993, month = jul, journal = {Cell}, volume = {74}, number = {1}, pages = {93–103}, doi = {10.1016/0092-8674(93)90297-4}, url = {ISI:A1993LN62500010}, abstract = {Most retroviruses and retrotransposons express their pol gene as a translational fusion to the upstream gag gene, often involving translational frameshifting. We describe here an unusual translational frameshift event occurring between the GAG3 and POL3 genes of the retrotransposon Ty3 of yeast. A + 1 frameshift occurs within the sequence GCG AGU U (shown as codons of GAG3), encoding alanine-valine (GCG A GUU). Unlike other programed translational frameshifts described, this event does not require tRNA slippage between cognate or near-cognate codons in the mRNA. Two features distal to the GCG codon stimulate frameshifting. The low availability of the tRNA specific for the ‘’hungry’’ serine codon, AGU, induces a translational pause required for frameshifting. A sequence of 12 nt distal to the AGU codon (termed the Ty3 ‘’context’’) also stimulates the event}, keywords = {BASE-PAIR,Codon,CODONS,ELONGATION-FACTOR-TU,ESCHERICHIA-COLI,frameshift,Frameshifting,Gag,gene,Genes,mRNA,nosource,pol,RELEASE FACTOR-II,retrotransposon,Ribosomes,SACCHAROMYCES-CEREVISIAE,sequence,Serine,SLIPPAGE,suppression,SYNONYMOUS CODONS DIFFER,TRANSFER-RNA,translation,tRNA,TY3,UPSTREAM,yeast} } % == BibTeX quality report for farabaughNovelProgrammedFrameshift1993: % ? Title looks like it was stored in title-case in Zotero

@article{farabaughPosttranscriptionalRegulationTransposition1995a, title = {Post-Transcriptional Regulation of Transposition by {{Ty}} Retrotransposons of ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Farabaugh, P.J.}, year = 1995, journal = {J.Biol.Chem.}, volume = {270}, pages = {10361–10364}, doi = {10.1074/jbc.270.18.10361}, keywords = {Frameshifting,nosource,post-transcriptional regulation,regulation,retrotransposon,Review,review article,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Ty} } % == BibTeX quality report for farabaughPosttranscriptionalRegulationTransposition1995a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{farabaughEffectFrameshiftinductingMutants1998a, title = {Effect of Frameshift-Inducting Mutants of Elongation Factor 1`a on Programmed +1 Frameshifting in Yeast.}, author = {Farabaugh, P.J. and Vimaladithan, A.}, year = 1998, journal = {RNA}, volume = {4}, pages = {38–46}, keywords = {+1 frameshifting,EF-1 alpha,elongation,Frameshifting,No DOI found,nosource,pausing,proofreading,ribosomal frameshifting,Ty1,yeast} }

@article{fathAssociationYeastRNA2000, title = {Association of Yeast {{RNA}} Polymerase {{I}} with a Nucleolar Substructure Active in {{rRNA}} Synthesis and Processing}, author = {Fath, S. and Milkereit, P. and Podtelejnikov, A.V. and Bischler, N. and Schultz, P. and Bier, M. and Mann, M. and Tschochner, H.}, year = 2000, month = may, journal = {The Journal of Cell Biology}, volume = {149}, number = {3}, pages = {575–589}, publisher = {Rockefeller Univ Press}, doi = {10.1083/jcb.149.3.575}, url = {http://jcb.rupress.org/content/149/3/575.abstract}, abstract = {A novel ribonucleoprotein complex enriched in nucleolar proteins was purified from yeast extracts and constituents were identified by mass spectrometry. When isolated from rapidly growing cells, the assembly contained ribonucleic acid (RNA) polymerase (pol) I, and some of its transcription factors like TATA-binding protein (TBP), Rrn3p, Rrn5p, Rm7p, and Reb1p along with rRNA processing factors, like Nop1p, Cbf5p, Nhp2p, and Rrp5p. The small nucleolar RNAs (snoRNAs) U3, U14, and MRP were also found to be associated with the complex, which supports accurate transcription, termination, and pseudouridylation of rRNA. Formation of the complex did not depend on pol I, and the complex could efficiently recruit exogenous pol I into active ribosomal DNA (rDNA) transcription units. Visualization of the complex by electron microscopy and immunogold labeling revealed a characteristic cluster-forming network of nonuniform size containing nucleolar proteins like Nop1p and Fpr3p and attached pol I. Our results support the idea that a functional nucleolar subdomain formed independently of the state of rDNA transcription may serve as a scaffold for coordinated rRNA synthesis and processing}, keywords = {assembly,BASAL TRANSCRIPTION,COMPLEX,COMPLEXES,desorption ionization (MALDI) mass spectrometry,Dna,GENE-TRANSCRIPTION,in vitro transcription,matrix assisted laser,nosource,nucleolus,pol,polymerase,PRE-RIBOSOMAL-RNA,PRENUCLEOLAR BODIES,protein,Proteins,PSEUDOURIDINE SYNTHASE,rDNA,RDNA TRANSCRIPTION,ribosome biogenesis,Rna,RNA Polymerase I,rRNA,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Support,TATA-BINDING PROTEIN,termination,transcription,TRANSCRIPTION FACTOR,Transcription Factors,UPSTREAM ACTIVATION FACTOR,yeast} }

@article{faticaMakingRibosomes2002, title = {Making Ribosomes}, author = {Fatica, A. and Tollervey, D.}, year = 2002, month = jun, journal = {Current opinion in cell biology}, volume = {14}, number = {3}, pages = {313–318}, publisher = {Elsevier}, doi = {10.1016/S0955-0674(02)00336-8}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0955067402003368}, abstract = {The past year has seen dramatic changes in our understanding of ribosome synthesis, fuelled largely by advances in proteomic analysis. It is now possible to outline the pathway of ribosome assembly, which is highly dynamic and involves a remarkable separation of the factors involved in the synthesis of the 40S and 60S ribosomal subunits. Around 140 identified, non-ribosomal proteins are currently implicated in post-transcriptional ribosome synthesis in yeast}, keywords = {0,Active TransportCell Nucleus,analysis,assembly,BIOLOGY,genetics,human,La,Macromolecular Systems,metabolism,ModelsBiological,nosource,PATHWAY,protein,Proteins,Review,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,RIBOSOME SYNTHESIS,Ribosomes,Rna,RNA ProcessingPost-Transcriptional,RNARibosomal,Saccharomyces cerevisiae,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,SYSTEM,SYSTEMS,yeast} } % == BibTeX quality report for faticaMakingRibosomes2002: % ? unused Journal abbr (“Curr.Opin.Cell Biol.”)

@article{fehrmannIntracisternalAtypeParticles1997, title = {Intracisternal {{A-type}} Particles Express Their Proteinase in a Separate Reading Frame by Translational Frameshifting, Similar to {{D-type}} Retroviruses}, author = {Fehrmann, F. and Welker, R. and Krausslich, H.G.}, year = 1997, month = sep, journal = {Virology}, volume = {235}, number = {2}, pages = {352–359}, publisher = {Elsevier}, doi = {10.1006/viro.1997.8708}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0042682297987080}, keywords = {analysis,efficiency,expression,frameshift,Frameshifting,Gag,Genome,In Vitro,IN-VITRO,nosource,pol,pseudoknot,sequence,Sequence Analysis,SIGNAL,structure,translation} }

@article{felsensteinExpressionGagpolFusion1988a, title = {Expression of the ⬚gag-Pol⬚ Fusion Protein of Moloney Murine Leukemia Virus without ⬚gag⬚ Protein Does Not Induce Viron Formation or Proteolytic Processing.}, author = {Felsenstein, K.M. and Goff, S.P.}, year = 1988, journal = {J.Virol.}, volume = {62}, pages = {2179–2182}, doi = {10.1128/jvi.62.6.2179-2182.1988}, keywords = {expression,Frameshifting,Gag,Gag-pol,Gag/Gag-pol ratio,nosource,protein,virus} } % == BibTeX quality report for felsensteinExpressionGagpolFusion1988a: % ? Possibly abbreviated journal title J.Virol.

@article{felsensteinMutationalAnalysisGagpol1992, title = {Mutational Analysis of the Gag-Pol Junction of {{Moloney}} Murine Leukemia Virus: Requirements for Expression of the Gag-Pol Fusion Protein.}, author = {Felsenstein, K.M. and Goff, S.P.}, year = 1992, month = nov, journal = {Journal of virology}, volume = {66}, number = {11}, pages = {6601–6608}, publisher = {Am Soc Microbiol}, issn = {0022-538X}, doi = {10.1128/jvi.66.11.6601-6608.1992}, url = {http://jvi.asm.org/content/66/11/6601.short papers2://publication/uuid/2F1FEFD1-7D43-491A-8421-65FB5E4AF2A8}, abstract = {The gag-pol polyprotein of the murine and feline leukemia viruses is expressed by translational readthrough of a UAG terminator codon at the 3’ end of the gag gene. To explore the cis-acting sequence requirements for the readthrough event in vivo, we generated a library of mutants of the Moloney murine leukemia virus with point mutations near the terminator codon and tested the mutant viral DNAs for the ability to direct synthesis of the gag-pol fusion protein and formation of infectious virus. The analysis showed that sequences 3’ to the terminator are necessary and sufficient for the process. The results do not support a role for one proposed stem-loop structure that includes the terminator but are consistent with the involvement of another stem-loop 3’ to the terminator. One mutant, containing two compensatory changes in this stem structure, was temperature sensitive for replication and for formation of the gag-pol protein. The results suggest that RNA sequence and structure are critical determinants of translational readthrough in vivo.}, isbn = {0022-538X (Print)}, pmid = {1404606}, keywords = {93021388,analysis,animal,biosynthesis,Cell Line,Codon,Comparative Study,Dna,expression,Gag,Gag-pol,Gag/Gag-pol ratio,gene,Gene Productsgag,Gene Productspol,Genesgag,Genespol,genetics,IN-VIVO,library,Mice,Moloney Leukemia Virus,Mutagenesis,Mutation,MUTATIONAL ANALYSIS,MUTATIONS,nosource,Nucleic Acid Conformation,Point Mutation,protein,Proviruses,Rats,readthrough,Rna,sequence,structure,Support,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Temperature,Terminator Regions (Genetics),virus} } % == BibTeX quality report for felsensteinMutationalAnalysisGagpol1992: % ? unused Journal abbr (“J.Virol.”)

@article{feroMurineGeneP27Kip11998, title = {The Murine Gene {{p27Kip1}} Is Haplo-Insufficient for Tumour Suppression}, author = {Fero, M.L. and Randel, E. and Gurley, K.E. and Roberts, J.M. and Kemp, C.J.}, year = 1998, month = nov, journal = {Nature}, volume = {396}, number = {6707}, pages = {177–180}, publisher = {Nature Publishing Group}, doi = {10.1038/24179}, url = {http://www.nature.com/nature/journal/v396/n6707/abs/396177a0.html}, abstract = {p27Kip is a candidate human tumour-suppressor protein, because it is able to inhibit cyclin-dependent kinases and block cell proliferation. Abnormally low levels of the p27 protein are frequently found in human carcinomas, and these low levels correlate directly with both histological aggressiveness and patient mortality. However, it has not been possible to establish a causal link between p27 and tumour suppression, because only rare instances of homozygous inactivating mutations of the p27 gene have been found in human tumours. Thus, p27Kip1 does not fulfil Knudson’s ‘two-mutation’ criterion for a tumour-suppressor gene. Here we show that both p27 nullizygous and p27 heterozygous mice are predisposed to tumours in multiple tissues when challenged with gamma-irradiation or a chemical carcinogen. Therefore p27 is a multiple-tissue tumour suppressor in mice. Molecular analyses of tumours in p27 heterozygous mice show that the remaining wild-type allele is neither mutated nor silenced. Hence, p27 is haplo-insufficient for tumour suppression. The assumption that null mutations in tumour-suppressor genes are recessive excludes those genes that exhibit haplo-insufficiency}, keywords = {0,Animals,cancer,cell cycle,Cell Cycle Proteins,Cell Proliferation,Cyclin-Dependent Kinase Inhibitor p27,Ethylnitrosourea,Female,Gamma Rays,gene,Genes,GenesTumor Suppressor,genetics,Haplotypes,Heterozygote,human,INHIBITOR,kinase,La,Male,Mice,MiceInbred C57BL,Microtubule-Associated Proteins,Mutation,MUTATIONS,NeoplasmsExperimental,nosource,PROLIFERATION,protein,Proteins,Support,suppression,Tumor Suppressor Proteins,WILD-TYPE} }

@article{ferre-damareCrystalStructureHepatitis1998a, title = {Crystal Structure of a Hepatitis Delta Virus Ribozyme}, author = {{Ferre-D’Amare}, A.R. and Zhou, K. and Doudna, J.A.}, year = 1998, month = oct, journal = {Nature}, volume = {395}, number = {6702}, pages = {567–574}, publisher = {[London: Macmillan Journals], 1869-}, doi = {10.1038/26912}, url = {http://cmgm.stanford.edu/biochem201/Papers/doudna.pdf PM:9783582}, abstract = {The self-cleaving ribozyme of the hepatitis delta virus (HDV) is the only catalytic RNA known to be required for the viability of a human pathogen. We obtained crystals of a 72-nucleotide, self-cleaved form of the genomic HDV ribozyme that diffract X-rays to 2.3 A resolution by engineering the RNA to bind a small, basic protein without affecting ribozyme activity. The co-crystal structure shows that the compact catalytic core comprises five helical segments connected as an intricate nested double pseudoknot. The 5’-hydroxyl leaving group resulting from the self-scission reaction is buried deep within an active-site cleft produced by juxtaposition of the helices and five strand-crossovers, and is surrounded by biochemically important backbone and base functional groups in a manner reminiscent of protein enzymes}, keywords = {0,BASE,Base Sequence,Binding Sites,Catalysis,chemistry,CloningMolecular,Computer Graphics,crystal structure,CRYSTAL-STRUCTURE,CrystallographyX-Ray,enzyme,enzymology,Escherichia coli,FORM,genetics,genomic,Hepatitis Delta Virus,human,La,ModelsMolecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,protein,pseudoknot,RESOLUTION,RIBONUCLEOPROTEIN,RibonucleoproteinU1 Small Nuclear,ribozyme,Rna,RNACatalytic,RnaViral,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,virus} }

@article{ferreira-cercaRolesEukaryoticRibosomal2005, title = {Roles of Eukaryotic Ribosomal Proteins in Maturation and Transport of Pre-{{18S rRNA}} and Ribosome Function}, author = {{Ferreira-Cerca}, S. and Poll, G. and Gleizes, P.E. and Tschochner, H. and Milkereit, P.}, year = 2005, month = oct, journal = {Molecular cell}, volume = {20}, number = {2}, pages = {263–275}, publisher = {Elsevier}, doi = {10.1016/j.molcel.2005.09.005}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276505016059 http://www.sciencedirect.com/science/article/pii/S1097276505016059}, abstract = {Despite the rising knowledge about ribosome function and structure and how ribosomal subunits assemble in vitro in bacteria, the in vivo role of many ribosomal proteins remains obscure both in pro- and eukaryotes. Our systematic analysis of yeast ribosomal proteins (r-proteins) of the small subunit revealed that most eukaryotic r-proteins fulfill different roles in ribosome biogenesis, making them indispensable for growth. Different r-proteins control distinct steps of nuclear and cytoplasmic pre-18S rRNA processing and, thus, ensure that only properly assembled ribosomes become engaged in translation. Comparative analysis of dynamic and steady-state maturation assays revealed that several r-proteins are required for efficient nuclear export of pre-18S rRNA, suggesting that they form an interaction platform with the export machinery. In contrast, the presence of other r-proteins is mainly required before nuclear export is initiated. Our studies draw a correlation between the in vitro assembly, structural localization, and in vivo function of r-proteins}, keywords = {0,analysis,assays,assembly,Bacteria,BIOGENESIS,CEREVISIAE,chemistry,Eukaryotic Cells,FORM,genetics,Germany,GROWTH,In Vitro,IN-VITRO,IN-VIVO,La,LOCALIZATION,MATURATION,metabolism,nosource,protein,Proteins,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,ribosome biogenesis,Ribosomes,Rna,RNARibosomal18S,rRNA,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Structural,structure,SUBUNIT,SUBUNITS,Support,translation,TRANSPORT,yeast} } % == BibTeX quality report for ferreira-cercaRolesEukaryoticRibosomal2005: % ? unused Journal abbr (“Mol.Cell”)

@book{fershtStructureMechanismProtein1998, title = {Structure and Mechanism in Protein Science}, author = {Fersht, A.}, year = 1998, publisher = {{W.H. Freeman and Co.}}, address = {New York⬚ ⬚}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Structure+and+mechanism+in+protein+science#0}, keywords = {Kinetics,MECHANISM,nosource,protein,structure} }

@article{fewellRibosomalProteinS141999a, title = {Ribosomal Protein {{S14}} of {{Saccharomyces}} Cerevisiae Regulates Its Expression by Binding to {{RPS14B}} Pre-{{mRNA}} and to {{18S rRNA}}}, author = {Fewell, S.W. and Woolford, J.L.}, year = 1999, month = jan, journal = {Mol.Cell Biol.}, volume = {19}, number = {1}, pages = {826–834}, doi = {10.1128/MCB.19.1.826}, abstract = {Production of ribosomal protein S14 in Saccharomyces cerevisiae is coordinated with the rate of ribosome assembly by a feedback mechanism that represses expression of RPS14B. Three-hybrid assays in vivo and filter binding assays in vitro demonstrate that rpS14 directly binds to an RNA stem-loop structure in RPS14B pre-mRNA that is necessary for RPS14B regulation. Moreover, rpS14 binds to a conserved helix in 18S rRNA with approximately five- to sixfold-greater affinity. These results support the model that RPS14B regulation is mediated by direct binding of rpS14 either to its pre-mRNA or to rRNA. Investigation of these interactions with the three-hybrid system reveals two regions of rpS14 that are involved in RNA recognition. D52G and E55G mutations in rpS14 alter the specificity of rpS14 for RNA, as indicated by increased affinity for RPS14B RNA but reduced affinity for the rRNA target. Deletion of the C terminus of rpS14, where multiple antibiotic resistance mutations map, prevents binding of rpS14 to RNA and production of functional 40S subunits. The emetine-resistant protein, rpS14-EmRR, which contains two mutations near the C terminus of rpS14, does not bind either RNA target in the three-hybrid or in vitro assays. This is the first direct demonstration that an antibiotic resistance mutation alters binding of an r protein to rRNA and is consistent with the hypothesis that antibiotic resistance mutations can result from local alterations in rRNA structure}, keywords = {99078019,Alkaloids,Amino Acid Sequence,antibiotic,assays,assembly,Base Sequence,BINDING,chemistry,drug effects,Drug ResistanceMicrobial,Emetine,expression,Feedback,Gene Expression RegulationFungal,genetics,In Vitro,IN-VITRO,IN-VIVO,MECHANISM,metabolism,Molecular Sequence Data,Mutagenesis,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Nucleic Acid Hybridization,pharmacology,protein,regulation,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNA Precursors,RNAFungal,RNARibosomal18S,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,structure,Structure-Activity Relationship,SUBUNIT,Support,supportu.s.gov’tp.h.s.,SYSTEM} } % == BibTeX quality report for fewellRibosomalProteinS141999a: % ? Possibly abbreviated journal title Mol.Cell Biol.

@article{fialaTransverseRelaxationOptimized2000, title = {Transverse Relaxation Optimized Triple-Resonance {{NMR}} Experiments for Nucleic Acids}, author = {Fiala, R. and Czernek, J. and Sklenar, V.}, year = 2000, month = apr, journal = {Journal of Biomolecular NMR}, volume = {16}, number = {4}, pages = {291–302}, publisher = {Springer}, doi = {10.1023/A:1008388400601}, url = {http://www.springerlink.com/index/TUVM0GMN63115234.pdf}, abstract = {Triple resonance HCN and HCNCH experiments are reliable methods of establishing sugar-to-base connectivity in the NMR spectra of isotopicaly labeled oligonucleotides. However, with larger molecules the sensitivity of the experiments is drastically reduced due to relaxation processes. Since the polarization transfer between 13C and 15N nuclei relies on rather small heteronuclear coupling constants (11-12 Hz), the long evolution periods (up to 30-40 ms) in the pulse sequences cannot be avoided. Therefore any effort to enhance sensitivity has to concentrate on manipulating the spin system in such a way that the spin-spin relaxation rates would be minimized. In the present paper we analyze the efficiency of the two known approaches of relaxation rate control, namely the use of multiple-quantum coherence (MQ) and of the relaxation interference between chemical shift anisotropy and dipolar relaxation - TROSY. Both theoretical calculations and experimental results suggest that for the sugar moiety (H1’-C1’-N1/9) the MQ approach is clearly preferable. For the base moiety (H6/8-C6/8-N1/9), however, the TROSY shows results superior to the MQ suppression of the dipole-dipole relaxation at moderate magnetic fields (500 MHz) and the sensitivity improvement becomes dramatically more pronounced at very high fields (800 MHz). The pulse schemes of the triple-resonance HCN experiments with sensitivity optimized performance for unambiguous assignments of intra-residual sugar-to-base connectivities combining both approaches are presented}, keywords = {0,ACID,ACIDS,anisotropy,ASSIGNMENT,BASE,chemical synthesis,chemistry,COUPLING-CONSTANTS,DYNAMICS,efficiency,Evolution,La,Magnetics,Methods,NMR,nosource,Nuclear Magnetic ResonanceBiomolecular,Nucleic Acids,Nucleosides,Oligonucleotides,Quantum Theory,Rna,sequence,SEQUENCES,structure,supportnon-u.s.gov’t,suppression,SYSTEM} } % == BibTeX quality report for fialaTransverseRelaxationOptimized2000: % ? unused Journal abbr (“J.Biomol.NMR”)

@article{fieldsExpressedSequenceTags1994a, title = {Expressed Sequence Tags Identify a Human Isolog of the ⬚{{SUI1}}⬚ Translation Initiation Factor.}, author = {Fields, C. and Adams, M.D.}, year = 1994, journal = {Biochem.Biophys.Res.Comm.}, volume = {198}, pages = {288–291}, doi = {10.1006/bbrc.1994.1040}, keywords = {homolog,human,initiation,mof2,nosource,sequence,sui1,translation,TRANSLATION INITIATION} } % == BibTeX quality report for fieldsExpressedSequenceTags1994a: % ? Possibly abbreviated journal title Biochem.Biophys.Res.Comm.

@article{fieldsNovelGeneticSystem1989a, title = {A Novel Genetic System to Detect Protein-Protein Interactions.}, author = {Fields, S. and Song, O.}, year = 1989, journal = {Nature}, volume = {340}, pages = {245–246}, doi = {10.1038/340245a0}, keywords = {2-hybrid system,Genetic,Methods,nosource,SYSTEM,yeast} }

@article{fieldsTwohybridSystemAssay1994, title = {The Two-Hybrid System: An Assay for Protein-Protein Interactions}, author = {Fields, S. and Sternglanz, R.}, year = 1994, journal = {Trends in Genetics}, volume = {10}, number = {8}, pages = {286–292}, publisher = {Elsevier}, doi = {10.1016/0168-9525(90)90012-U}, url = {http://linkinghub.elsevier.com/retrieve/pii/016895259090012U}, abstract = {The two-hybrid system is a yeast-based genetic assay for detecting protein-protein interactions. It can be used to identify proteins that bind to a protein of interest, or to delineate domains or residues critical for an interaction. Variations on this methodology have been developed to clone genes that encode DNA-binding proteins, to identify, peptides that bind to a protein and, potentially, to screen for drugs}, keywords = {0,2 hybrid,2-hybrid,2-hybrid system,BINDING,cloning,COMPLEX,DNA-BINDING,DNA-Binding Proteins,DOMAIN,DOMAINS,drugs,gene,Genes,Genetic,genetics,IDENTIFICATION,IDENTIFY,La,metabolism,microbiology,MOLECULAR-GENETICS,nosource,Peptides,PHOSPHATASE,protein,Protein Binding,Proteins,ras,RESIDUES,Review,S,supportu.s.gov’tp.h.s.,SYSTEM,TRANSCRIPTION FACTOR,yeast} } % == BibTeX quality report for fieldsTwohybridSystemAssay1994: % ? unused Journal abbr (“Trends Genet.”)

@article{fillibenProbabilityPlotCorrelation1975a, title = {Probability {{Plot Correlation Coefficient Test}} for {{Normality}}.}, author = {Filliben, J.J.}, year = 1975, journal = {Technometrics}, volume = {17}, pages = {111–117}, doi = {10.1080/00401706.1975.10489279}, keywords = {nosource} } % == BibTeX quality report for fillibenProbabilityPlotCorrelation1975a: % ? Title looks like it was stored in title-case in Zotero

@article{firePotentSpecificGenetic1998, title = {Potent and Specific Genetic Interference by Double-Stranded {{RNA}} in {{Caenorhabditis}} Elegans}, author = {Fire, A. and Xu, S. and Montgomery, M.K. and Kostas, S.A. and Driver, S.E. and Mello, C.C.}, year = 1998, month = feb, journal = {Nature}, volume = {391}, number = {6669}, pages = {806–811}, publisher = {Nature Publishing Group}, doi = {10.1038/35888}, url = {http://www.nature.com/nature/journal/v391/n6669/abs/391806a0.html}, abstract = {Experimental introduction of RNA into cells can be used in certain biological systems to interfere with the function of an endogenous gene. Such effects have been proposed to result from a simple antisense mechanism that depends on hybridization between the injected RNA and endogenous messenger RNA transcripts. RNA interference has been used in the nematode Caenorhabditis elegans to manipulate gene expression. Here we investigate the requirements for structure and delivery of the interfering RNA. To our surprise, we found that double-stranded RNA was substantially more effective at producing interference than was either strand individually. After injection into adult animals, purified single strands had at most a modest effect, whereas double-stranded mixtures caused potent and specific interference. The effects of this interference were evident in both the injected animals and their progeny. Only a few molecules of injected double-stranded RNA were required per affected cell, arguing against stochiometric interference with endogenous mRNA and suggesting that there could be a catalytic or amplification component in the interference process}, keywords = {0,Adult,animal,Animals,antisense,Caenorhabditis,Caenorhabditis elegans,Caenorhabditis elegans Proteins,CAENORHABDITIS-ELEGANS,Calmodulin-Binding Proteins,CELLS,COMPONENT,DOUBLE-STRANDED-RNA,drug effects,ELEGANS,embryology,expression,gene,Gene Expression,Gene Expression Regulation,GENE-EXPRESSION,GenesHelminth,Genetic,genetics,Helminth Proteins,La,MECHANISM,MESSENGER-RNA,mRNA,Muscle Proteins,nosource,pharmacology,Phenotype,protein,Proteins,Rna,RNA Interference,RNAAntisense,RNADouble-Stranded,structure,Support,SYSTEM,SYSTEMS,TRANSCRIPT} }

@article{firthDetectingOverlappingCoding2006, title = {Detecting Overlapping Coding Sequences in Virus Genomes}, author = {Firth, A.E. and Brown, C.M.}, year = 2006, journal = {BMC.Bioinformatics.}, volume = {7}, number = {1}, pages = {75}, publisher = {BioMed Central Ltd}, doi = {doi:10.1186/1471-2105-7-75}, url = {http://www.biomedcentral.com/1471-2105/7/75}, abstract = {BACKGROUND: Detecting new coding sequences (CDSs) in viral genomes can be difficult for several reasons. The typically compact genomes often contain a number of overlapping coding and non-coding functional elements, which can result in unusual patterns of codon usage; conservation between related sequences can be difficult to interpret–especially within overlapping genes; and viruses often employ non-canonical translational mechanisms–e.g. frameshifting, stop codon read-through, leaky-scanning and internal ribosome entry sites–which can conceal potentially coding open reading frames (ORFs). RESULTS: In a previous paper we introduced a new statistic–MLOGD (Maximum Likelihood Overlapping Gene Detector)–for detecting and analysing overlapping CDSs. Here we present (a) an improved MLOGD statistic, (b) a greatly extended suite of software using MLOGD, (c) a database of results for 640 virus sequence alignments, and (d) a web-interface to the software and database. Tests show that, from an alignment with just 20 mutations, MLOGD can discriminate non-overlapping CDSs from non-coding ORFs with a typical accuracy of up to 98%, and can detect CDSs overlapping known CDSs with a typical accuracy of 90%. In addition, the software produces a variety of statistics and graphics, useful for analysing an input multiple sequence alignment. CONCLUSION: MLOGD is an easy-to-use tool for virus genome annotation, detecting new CDSs–in particular overlapping or short CDSs–and for analysing overlapping CDSs following frameshift sites. The software, web-server, database and supplementary material are available at http://guinevere.otago.ac.nz/mlogd.html}, keywords = {0,accuracy,Algorithms,alignment,Binding Sites,Biochemistry,coding sequence,Codon,Codon-Terminator,CodonTerminator,Computational Biology,Conserved Sequence,D,DATABASE,Databases as Topic,ELEMENTS,FRAME,frameshift,Frameshift Mutation,Frameshifting,gene,Genes,Genes-Overlapping,Genes-Viral,GenesOverlapping,GenesViral,Genome,Genome-Viral,GenomeViral,INTERNAL RIBOSOME ENTRY,La,Likelihood Functions,Methods,Models-Statistical,ModelsStatistical,Mutation,MUTATIONS,nosource,OPEN READING FRAME,Open Reading Frames,PATTERNS,Protein Biosynthesis,READ-THROUGH,READING FRAME,Reading Frames,readthrough,ribosome,sequence,Sequence Alignment,Sequence Analysis-DNA,Sequence AnalysisDNA,SEQUENCES,SITE,SITES,Software,Statistics,STOP CODON,Support,virus,Viruses} } % == BibTeX quality report for firthDetectingOverlappingCoding2006: % ? Possibly abbreviated journal title BMC.Bioinformatics.

@article{fisherDominantInterferingFas1995a, title = {Dominant Interfering {{Fas}} Gene Mutations Impair Apoptosis in Human Autoimmune Lynphoproliferative Syndrome.}, author = {Fisher, G.H. and Rosenberg, F.J. and Straus, S.E. and Dale, J.K. and Middelton, L.A. and Lin, A.Y. and Strober, W. and Lenardo, M.J. and Puck, J.M.}, year = 1995, journal = {Cell}, volume = {81}, pages = {935–946}, doi = {10.1016/0092-8674(95)90013-6}, keywords = {frameshift,gene,human,Mutation,MUTATIONS,nosource} }

@article{fletcherStructureInteractionsTranslation1999, title = {Structure and Interactions of the Translation Initiation Factor {{eIF1}}}, author = {Fletcher, C.M. and Pestova, T.V. and Hellen, C.U. and Wagner, G.}, year = 1999, month = may, journal = {EMBO J.}, volume = {18}, number = {9}, pages = {2631–2637}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/18.9.2631}, url = {http://www.nature.com/emboj/journal/v18/n9/abs/7591684a.html}, abstract = {eIF1 is a universally conserved translation factor that is necessary for scanning and involved in initiation site selection. We have determined the solution structure of human eIF1 with an N-terminal His tag using NMR spectroscopy. Residues 29-113 of the native sequence form a tightly packed domain with two alpha-helices on one side of a five- stranded parallel and antiparallel beta-sheet. The fold is new but similar to that of several ribosomal proteins and RNA-binding domains. A likely binding site is indicated by yeast mutations and conserved residues located together on the surface. No interaction with recombinant eIF5 or the initiation site RNA GCCACAAUGGCA was detected by NMR, but GST pull-down experiments show that eIF1 binds specifically to the p110 subunit of eIF3. This interaction explains how eIF1 is recruited to the 40S ribosomal subunit}, keywords = {99246285,Amino Acid Sequence,BINDING,Binding Sites,chemistry,Conserved Sequence,Eif-1,eIF1,eIF3,EIF5,human,initiation,metabolism,ModelsMolecular,Molecular Sequence Data,Mutation,MUTATIONS,nosource,Nuclear Magnetic ResonanceBiomolecular,Peptide Chain Initiation,Peptide Initiation Factors,pharmacology,protein,Protein Folding,Protein StructureSecondary,Proteins,Ribosomal Proteins,Ribosomes,Rna,RNA-Binding Proteins,sequence,structure,SUBUNIT,sui1,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,translation,TRANSLATION INITIATION,yeast} } % == BibTeX quality report for fletcherStructureInteractionsTranslation1999: % ? Possibly abbreviated journal title EMBO J.

@article{flowerTranscriptionalOrganizationEscherichia1991a, title = {Transcriptional Organization of The⬚ {{Escherichia}} Coli {{dnaX}}⬚ Gene}, author = {Flower, A.M. and McHenry, C.S.}, year = 1991, month = aug, journal = {Journal of Molecular Biology}, volume = {220}, number = {3}, pages = {649–658}, doi = {10.1016/0022-2836(91)90107-H}, keywords = {+1 frameshifting,0,Bacterial,Base Sequence,Codon,Codon/ge [Genetics],Dna,DNA Polymerase III/ge [Genetics],DNA Probes,Escherichia coli,Escherichia coli/en [Enzymology],Escherichia coli/ge [Genetics],ESCHERICHIA-COLI,expression,Frameshifting,gene,Genes,Genetic,genetics,Macromolecular Systems,mapping,MECHANISM,Messenger/ge [Genetics],Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleotides,Operon,P.H.S.,polymerase,primer extension,Promoter Regions (Genetics),protein,Restriction Mapping,Rna,Structural,SUBUNIT,SYSTEM,transcription,U.S.Gov’t,vector} }

@article{flygareHumanRPS19Gene2007, title = {Human {{RPS19}}, the Gene Mutated in {{Diamond-Blackfan}} Anemia, Encodes a Ribosomal Protein Required for the Maturation of {{40S}} Ribosomal Subunits}, author = {Flygare, J. and Aspesi, A. and Bailey, J.C. and Miyake, K. and Caffrey, J.M. and Karlsson, S. and Ellis, S.R.}, year = 2007, month = feb, journal = {Blood}, volume = {109}, number = {3}, pages = {980–986}, doi = {10.1182/blood-2006-07-038232}, url = {PM:16990592}, abstract = {Diamond-Blackfan anemia (DBA) typically presents with red blood cell aplasia that usually manifests in the first year of life. The only gene currently known to be mutated in DBA encodes ribosomal protein S19 (RPS19). Previous studies have shown that the yeast RPS19 protein is required for a specific step in the maturation of 40S ribosomal subunits. Our objective here was to determine whether the human RPS19 protein functions at a similar step in 40S subunit maturation. Studies where RPS19 expression is reduced by siRNA in the hematopoietic cell line, TF-1, show that human RPS19 is also required for a specific step in the maturation of 40S ribosomal subunits. This maturation defect can be monitored by studying rRNA-processing intermediates along the ribosome synthesis pathway. Analysis of these intermediates in}, keywords = {0,analysis,Anemia,AnemiaDiamond-Blackfan,blood,Bone Marrow Cells,Cell Line,cytology,ENCODES,expression,gene,Gene Therapy,genetics,Hematopoietic Stem Cells,human,Humans,INTERMEDIATE,La,LINE,MATURATION,metabolism,Mutation,nosource,PATHWAY,pharmacology,physiology,PRECURSOR,protein,Proteins,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,RIBOSOME SYNTHESIS,Ribosomes,Rna,RNA Precursors,RNASmall Interfering,SUBUNIT,SUBUNITS,Support,therapy,yeast} }

@article{foianiGCD2TranslationalRepressor1991, title = {{{GCD2}}, a Translational Repressor of the {{GCN4}} Gene, Has a General Function in the Initiation of Protein Synthesis in {{Saccharomyces}} Cerevisiae.}, author = {Foiani, M. and Cigan, A.M. and Paddon, C.J. and Harashima, S. and Hinnebusch, A.G.}, year = 1991, month = jun, journal = {Molecular and Cellular Biology}, volume = {11}, number = {6}, pages = {3203–3216}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/11/6/3203}, abstract = {The GCD2 protein is a translational repressor of GCN4, the transcriptional activator of multiple amino acid biosynthetic genes in Saccharomyces cerevisiae. We present evidence that GCD2 has a general function in the initiation of protein synthesis in addition to its gene-specific role in translational control of GCN4 expression. Two temperature-sensitive lethal gcd2 mutations result in sensitivity to inhibitors of protein synthesis at the permissive temperature, and the gcd2-503 mutation leads to reduced incorporation of labeled leucine into total protein following a shift to the restrictive temperature of 36 degrees C. The gcd2-503 mutation also results in polysome runoff, accumulation of inactive 80S ribosomal couples, and accumulation of at least one of the subunits of the general translation initiation factor 2 (eIF-2 alpha) in 43S-48S particles following a shift to the restrictive temperature. The gcd2-502 mutation causes accumulation of 40S subunits in polysomes, known as halfmers, that are indicative of reduced 40S-60S subunit joining at the initiation codon. These phenotypes suggest that GCD2 functions in the translation initiation pathway at a step following the binding of eIF-2.GTP.Met-tRNA(iMet) to 40S ribosomal subunits. consistent with this hypothesis, we found that inhibiting 40S-60S subunit joining by deleting one copy (RPL16B) of the duplicated gene encoding the 60S ribosomal protein L16 qualitatively mimics the phenotype of gcd2 mutations in causing derepression of GCN4 expression under nonstarvation conditions. However, deletion of RPL16B also prevents efficient derepression of GCN4 under starvation conditions, indicating that lowering the concentration of 60S subunits and reducing GCD2 function affect translation initiation at GCN4 in different ways. This distinction is in accord with a recently proposed model for GCN4 translational control in which ribosomal reinitiation at short upstream open reading frames in the leader of GCN4 mRNA is suppressed under amino acid starvation conditions to allow for increased reinitiation at the GCN4 start codon}, keywords = {0,60S subunit,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,BINDING,biosynthesis,CEREVISIAE,Child,Codon,development,Eif-2,Eukaryotic Initiation Factor-2,Eukaryotic Initiation Factor-2B,expression,FRAME,Fungal Proteins,GCN4,gene,Genes,GenesFungal,Genetic,genetics,Genotype,human,INHIBITOR,inhibitors,initiation,INITIATION-FACTOR,Kinetics,La,Leucine,metabolism,MODEL,MOLECULAR-GENETICS,mRNA,Multiple DOI,Mutation,MUTATIONS,nonfile,nosource,OPEN READING FRAME,Open Reading Frames,PARTICLES,PATHWAY,Peptide Chain InitiationTranslational,Phenotype,Plasmids,Polyribosomes,polysomes,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,Proteins,READING FRAME,Reading Frames,REPRESSOR,Repressor Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,Ribosomes,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,START CODON,SUBUNIT,SUBUNITS,Temperature,translation,TRANSLATION INITIATION,UPSTREAM} } % == BibTeX quality report for foianiGCD2TranslationalRepressor1991: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{fordPolyATailInhibits1997, title = {The Poly({{A}}) Tail Inhibits the Assembly of a 3’-to-5’ Exonuclease in an in Vitro {{RNA}} Stability System}, author = {Ford, L.P. and Bagga, P.S. and Wilusz, J.}, year = 1997, month = jan, journal = {Molecular and cellular biology}, volume = {17}, number = {1}, pages = {398–406}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.17.1.398}, url = {http://mcb.asm.org/cgi/content/abstract/17/1/398}, abstract = {We have developed an in vitro system which faithfully reproduces several aspects of general mRNA stability. Poly(A)- RNAs were rapidly and efficiently degraded in this system with no detectable intermediates by a highly processive 3’-to-5’ exonuclease activity. The addition of a poly(A) tail of at least 30 bases, or a 3’ histone stem-loop element, specifically stabilized these transcripts. Stabilization by poly(A) required the interaction of proteins with the poly(A) tail but did not apparently require a 3’ OH or interaction with the 5’ cap structure. Finally, movement of the poly(A) tract internal to the 3’ end caused a loss of its ability to stabilize transcripts incubated in the system but did not affect its ability to interact with poly(A) binding proteins. The requirement for the poly(A) tail to be proximal to the 3’ end indicates that it mediates RNA stability by blocking the assembly, but not the action, of an exonuclease involved in RNA degradation in vitro}, keywords = {0,3,assembly,BASE,BASES,BINDING,BINDING PROTEIN,BINDING-PROTEIN,Cap,CAP STRUCTURE,degradation,Exoribonucleases,Genesmyc,Genetic,genetics,human,In Vitro,IN-VITRO,INTERMEDIATE,La,metabolism,microbiology,MOLECULAR-GENETICS,Movement,mRNA,mRNA stability,nosource,Poly A,poly(A),POLY(A) TAIL,POLY(A)-BINDING PROTEIN,Poly(A)-Binding Proteins,protein,Proteins,Rna,RNA Stability,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAMessenger,RnaViral,Simian virus 40,stability,STEM-LOOP,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,TRANSCRIPT} } % == BibTeX quality report for fordPolyATailInhibits1997: % ? unused Journal abbr (“Mol Cell Biol.”)

@article{fordDifferentSequences5S1973, title = {Different Sequences for {{5S RNA}} in Kidney Cells and Ovaries of {{Xenopus}} Laevis.}, author = {Ford, P.J. and Southern, E.M.}, year = 1973, month = jan, journal = {Nat.New Biol.}, volume = {241⬚ ⬚}, number = {105}, pages = {7–12}, publisher = {Nature Publishing Group}, doi = {10.1038/newbio241007a0}, url = {http://www.nature.com/nature-newbio/journal/v241/n105/abs/newbio241007a0.html}, keywords = {0,5S RNA,analysis,Animals,Base Sequence,biosynthesis,CELLS,ChromatographyGel,Electrophoresis,Female,GenesStructural,Genetic Code,Hela Cells,Kidney,La,metabolism,No DOI found,nosource,Nucleotides,Ovary,Phosphorus Isotopes,Ribonucleases,Rna,RNANeoplasm,RNARibosomal,sequence,SEQUENCES,TranscriptionGenetic,Xenopus,Xenopus laevis,XENOPUS-LAEVIS} } % == BibTeX quality report for fordDifferentSequences5S1973: % ? Possibly abbreviated journal title Nat.New Biol.

@article{fordControl5SRNA1976, title = {Control of {{5S RNA}} Synthesis in {{Xenopus}} Laevis}, author = {Ford, P.J. and Mathieson, T.}, year = 1976, month = jun, journal = {Nature}, volume = {261}, number = {5559}, pages = {433–435}, publisher = {Nature Publishing Group}, doi = {10.1038/261433a0}, url = {http://www.nature.com/nature/journal/v261/n5559/abs/261433a0.html}, keywords = {0,5S RNA,Animals,Base Sequence,biosynthesis,CellsCultured,Female,GenesStructural,Kidney,Kinetics,La,Liver,metabolism,Molecular Weight,nosource,Oocytes,Rna,RNARibosomal,TranscriptionGenetic,Xenopus,Xenopus laevis,XENOPUS-LAEVIS} }

@article{fouillotTranslationHepatitisVirus1993, title = {Translation of the Hepatitis {{B}} Virus {{P}} Gene by Ribosomal Scanning as an Alternative to Internal Initiation.}, author = {Fouillot, N. and Tlouzeau, S. and Rossignol, J.M. and {Jean-Jean}, O.}, year = 1993, journal = {Journal of virology}, volume = {67}, number = {8}, pages = {4886–4895}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.67.8.4886-4895.1993}, url = {http://jvi.asm.org/cgi/content/abstract/67/8/4886}, abstract = {The hepatitis B virus (HBV) P gene which encodes the reverse transcriptase and other proteins required for replication is expressed on the bicistronic mRNA pregenome which also encodes the capsid protein in its first cistron. Recent results have suggested that the hepadnaviral P gene is translated by internal entry of ribosomes upstream from the P gene, in the overlapping C gene. Using a reporter gene fused to the HBV C or P gene, we demonstrate that the C sequence does not allow internal initiation of translation. Alternatively, our results support a model in which the HBV P gene is translated by ribosomes which scan from the capped extremity of the bicistronic mRNA pregenome. The mechanism by which the ribosomes scan past four AUGs before they initiate translation at the P AUG was analyzed. Our results show that these AUGs are skipped via two mechanisms: leaky scanning on AUGs in a weak or suboptimal initiation context and translation of an out-of-C-frame minicistron followed by reinitiation at P AUG. The minicistron translation allows ribosomes to bypass an AUG in a favorable context that would otherwise be used as a start codon for translation of a truncated capsid protein. Our results suggest that this elaborated scanning mechanism permits the coordinate expression of the HBV C and P genes on the viral bicistronic mRNA pregenome}, keywords = {0,AUG,Base Sequence,beta-Galactosidase,bicistronic,biosynthesis,Capsid,capsid protein,Cell LineTransformed,Chloramphenicol,Chloramphenicol O-Acetyltransferase,CloningMolecular,Codon,Comparative Study,Dna,ENCODES,Escherichia coli,expression,gene,Gene Deletion,Genes,GenesStructuralBacterial,GenesStructuralViral,genetics,GenomeViral,Hepatitis B virus,Humans,initiation,La,MECHANISM,MECHANISMS,metabolism,MODEL,Molecular Sequence Data,mRNA,nosource,Peptide Chain InitiationTranslational,PLASMID,Plasmids,polymerase,protein,Protein Biosynthesis,Proteins,Recombinant Proteins,REPLICATION,Research SupportNon-U.S.Gov’t,Restriction Mapping,REVERSE-TRANSCRIPTASE,ribosome,Ribosomes,Rna,RNA-Directed DNA Polymerase,RNAMessenger,scanning,sequence,Sequence HomologyNucleic Acid,START CODON,Support,translation,UPSTREAM,virus} } % == BibTeX quality report for fouillotTranslationHepatitisVirus1993: % ? unused Journal abbr (“J.Virol.”)

@article{fourmyStructureSiteEscherichia1996a, title = {Structure of the {{A}} Site of ⬚{{Escherichia}} Coli⬚ {{16S}} Ribosomal {{RNA}} Complexed with an Aminoglycoside Antibiotic.}, author = {Fourmy, D. and Recht., M.I. and Blanchard, S.C. and Puglisi, J.D.}, year = 1996, journal = {Science}, volume = {274}, pages = {1367–1371}, doi = {10.1126/science.274.5291.1367}, keywords = {A-SITE,antibiotic,antibiotics,Escherichia coli,ESCHERICHIA-COLI,nosource,Paromomycin,RIBOSOMAL-RNA,Rna,structure} }

@misc{fraenkelRasFunctionYeast1985, title = {On ⬚ras⬚ Function in Yeast}, author = {Fraenkel, D.G.}, year = 1985, keywords = {Carbon,carbon source,Glucose,nosource,ras,yeast} }

@article{franceschiRibosomalProteinL201988, title = {Ribosomal Protein {{L20}} Can Replace the Assembly-Initiator Protein {{L24}} at Low Temperatures}, author = {Franceschi, F.J. and Nierhaus, K.H.}, year = 1988, journal = {Biochemistry}, volume = {27}, number = {18}, pages = {7056–7059}, publisher = {ACS Publications}, doi = {10.1021/bi00418a058}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00418a058}, abstract = {The assembly of the 50S subunit from Escherichia coli ribosomes is initiated by two ribosomal proteins, L24 and L3. A mutant lacking the assembly-initiator protein L24 shows distinct phenotypic features (temperature sensitivity, growth rate reduced by a factor of 6 at permissive temperatures below 34 degrees C, underproduction of 50S subunits), which could be traced back to assembly effects caused by lack of L24 [Herold, M., Nowotny, V., Dabbs, E. R., & Nierhaus, K. H. (1986) Mol. Gen. Genet. 203, 281-287]. As expected, only one assembly protein was effective during in vitro assembly at nonpermissive temperatures, whereas surprisingly the restoration of active particle formation at permissive temperatures was paralleled by the reappearance of two initiator proteins. Here we analyze the initiation of assembly at permissive temperatures in the absence of L24. We demonstrate in a series of reconstitution experiments with purified proteins that the two initiator proteins are L20 and L3. Thus, L20 can replace L24 for the initiation of assembly at permissive temperatures}, keywords = {0,assembly,Bacterial,Binding Sites,E,Escherichia coli,Escherichia coli ribosomes,ESCHERICHIA-COLI,genetics,GROWTH,In Vitro,IN-VITRO,initiation,L3,La,M,metabolism,Mutation,nosource,PARTICLE FORMATION,protein,Proteins,RECONSTITUTION,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNABacterial,RNARibosomal23S,SERIES,SUBUNIT,SUBUNITS,Temperature} }

@article{franceschiRibosomalProteinsL151990, title = {Ribosomal Proteins {{L15}} and {{L16}} Are Mere Late Assembly Proteins of the Large Ribosomal Subunit. {{Analysis}} of an {{Escherichia}} Coli Mutant Lacking {{L15}}.}, author = {Franceschi, F.J. and Nierhaus, K.H.}, year = 1990, journal = {Journal of Biological Chemistry}, volume = {265}, number = {27}, pages = {16676–16682}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(17)46274-0}, url = {http://www.jbc.org/content/265/27/16676.short}, abstract = {The (minus L15) character from the Escherichia coli strain AM16.98 was transduced to an RNase-deficient strain in order to enable a reconstitution analysis. The following results were obtained. 1) The strain lacking L15 showed a 2-3-fold prolonged generation time and the 70 S ribosomes a reduced tendency toward dissociation. 2) Active particles could not be reconstituted unless L15 was added. Addition of L15 regained activity, even if L15 was added after the two-step procedure during a third incubation. However, a modification of the standard two-step reconstitution procedure (lowering NH4+ from 400 to 240 mM and the incubation temperature of the second step from 50 to 47 degrees C) yielded 100% active particles in the absence of L15. Active particles could be formed which even lacked L15, L16, and L30. Addition of either L15 or L16 accelerated the formation of active particles in the second step by a factor of five, and both proteins together by a factor of more than 20. 3) The activation energy of the rate-limiting step of the second incubation was surprisingly reduced for about 20 kcal/mol in the absence of L15, although the corresponding rates were two to five times slower. We conclude 1) that L15 and L16 are late assembly proteins which accelerate the formation of active particles during the late assembly but are neither needed for the early assembly nor essential for ribosomal functions; 2) that some routes of the late assembly (e.g. incorporation of L16) are changing their significance depending on the NH4+ concentration and the absence and presence of L15; and 3) that different reactions are rate limiting during the second step incubation in the presence and absence of L15, respectively, and that the corresponding reaction rates exhibit a different temperature dependence}, keywords = {0,3,activation,analysis,assembly,CHARACTER,Chromosome Deletion,ElectrophoresisGelTwo-Dimensional,Escherichia coli,ESCHERICHIA-COLI,genetics,Germany,isolation & purification,Kinetics,L15,La,metabolism,ModelsGenetic,modification,Mutation,nosource,PARTICLES,protein,Proteins,RECONSTITUTION,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,S,SUBUNIT,Temperature,TransductionGenetic} } % == BibTeX quality report for franceschiRibosomalProteinsL151990: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{frankAnimationDynamicalEvents1999, title = {Animation of the Dynamical Events of the Elongation Cycle Based on Cryoelectron Microscopy of Functional Complexes of the Ribosome}, author = {Frank, J. and Heagle, A.B. and Agrawal, R.K.}, year = 1999, month = dec, journal = {Journal of Structural Biology}, volume = {128}, number = {1}, pages = {15–18}, publisher = {Elsevier}, doi = {10.1006/jsbi.1999.4138}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1047847799941382}, abstract = {Using three-dimensional cryoelectron microscopy, the binding positions of tRNA and elongation factors EF-G and EF-Tu (the latter complexed with aminoacyl tRNA and GTP) on the ribosome were determined in previous studies. On the basis of these studies, the dynamical events that take place in the course of the elongation cycle of protein synthesis have been animated. The resulting 3-min movie is accessible on the website of this journal (http://www. idealibrary.com). The following article provides a brief annotation of those frames of the movie for which experimental support is available}, keywords = {0,BINDING,chemistry,COMPLEX,COMPLEXES,Computer Simulation,Cryoelectron Microscopy,EF-G,EFTu,elongation,ELONGATION CYCLE,elongation factors,ELONGATION-FACTOR-G,ELONGATION-FACTOR-TU,ELONGATION-FACTORS,Escherichia coli,FACTOR TU,FRAME,GTP,Internet,La,ModelsMolecular,nosource,Peptide Elongation Factor G,Peptide Elongation Factor Tu,POSITION,POSITIONS,protein,protein synthesis,PROTEIN-SYNTHESIS,ribosome,Ribosomes,Rna,RNAMessenger,RNATransferMet,Software,Support,supportu.s.gov’tp.h.s.,tRNA} } % == BibTeX quality report for frankAnimationDynamicalEvents1999: % ? unused Journal abbr (“J.Struct.Biol.”)

@article{frankRatchetlikeIntersubunitReorganization2000, title = {A Ratchet-like Inter-Subunit Reorganization of the Ribosome during Translocation}, author = {Frank, J. and Agrawal, R.K.}, year = 2000, month = jul, journal = {Nature}, volume = {406}, number = {6793}, pages = {318–322}, doi = {10.1038/35018597}, abstract = {The ribosome is a macromolecular assembly that is responsible for protein biosynthesis following genetic instructions in all organisms. It is composed of two unequal subunits: the smaller subunit binds messenger RNA and the anticodon end of transfer RNAs, and helps to decode the mRNA; and the larger subunit interacts with the amino-acid-carrying end of tRNAs and catalyses the formation of the peptide bonds. After peptide-bond formation, elongation factor G (EF-G) binds to the ribosome, triggering the translocation of peptidyl-tRNA from its aminoacyl site to the peptidyl site, and movement of mRNA by one codon. Here we analyse three-dimensional cryo-electron microscopy maps of the Escherichia coli 70S ribosome in various functional states, and show that both EF-G binding and subsequent GTP hydrolysis lead to ratchet-like rotations of the small 30S subunit relative to the large 50S subunit. Furthermore, our finding indicates a two-step mechanism of translocation: first, relative rotation of the subunits and opening of the mRNA channel following binding of GTP to EF-G; and second, advance of the mRNA/(tRNA)2 complex in the direction of the rotation of the 30S subunit, following GTP hydrolysis}, keywords = {20372203,Anticodon,assembly,BINDING,Biological Transport,biosynthesis,chemistry,Codon,COMPLEX,COMPLEXES,Cryoelectron Microscopy,elongation,Escherichia coli,ESCHERICHIA-COLI,Genetic,GTP,Guanosine Triphosphate,Hydrolysis,Macromolecular Systems,MECHANISM,MESSENGER-RNA,metabolism,ModelsMolecular,Molecular Conformation,Movement,mRNA,nosource,Peptide Elongation Factor G,PEPTIDE-BOND FORMATION,protein,ribosome,Ribosomes,Rna,RNAMessenger,RNATransfer,SUBUNIT,supportu.s.gov’tp.h.s.,translocation,tRNA,ultrastructure} }

@article{frankElectronMicroscopyFunctional2003, title = {Electron Microscopy of Functional Ribosome Complexes}, author = {Frank, J.}, year = 2003, month = feb, journal = {Biopolymers}, volume = {68}, number = {2}, pages = {223–233}, publisher = {Wiley Online Library}, doi = {10.1002/bip.10210}, url = {http://onlinelibrary.wiley.com/doi/10.1002/bip.10210/full}, abstract = {Cryoelectron microscopy has made a number of significant contributions to our understanding of the translation process. The method of single-particle reconstruction is particularly well suited for the study of the dynamics of ribosome-ligand interactions. This review follows the events of the functional cycle and discusses the findings in the context provided by the recently published x-ray structures}, keywords = {Binding Sites,COMPLEX,COMPLEXES,Cryoelectron Microscopy,DYNAMICS,ELECTRON-MICROSCOPY,Image ProcessingComputer-Assisted,nosource,Review,ribosome,Ribosomes,RNARibosomal16S,RNATransfer,RNATransferMet,structure,supportu.s.gov’tp.h.s.,translation,ultrastructure} }

@article{frankSingleparticleReconstrutionBiological2009, title = {Single-Particle Reconstrution of Biological Macromolecules in Electron Microscopy - 30 Years.}, author = {Frank, J.}, year = 2009, journal = {Quarterly Reviews of Biophysics}, volume = {(in press)⬚ ⬚}, keywords = {ELECTRON-MICROSCOPY,No DOI found,nosource} }

@article{frankHumanHomologueYeast1996a, title = {The Human Homologue of the Yeast ⬚{{CHL1}}⬚ Gene Is a Novel Keratinocyte Growth Factor-Regulated Gene}, author = {Frank, S. and Werner, S.}, year = 1996, month = oct, journal = {J.Biol.Chem.}, volume = {271}, number = {40}, pages = {24337–24340}, doi = {10.1074/jbc.271.40.24337}, keywords = {analysis,cell cycle,cloning,Cytokines,differential display,gene,Genes,Helicase,human,human homologue,MECHANISM,MECHANISMS,Multigene Family,nosource,polymerase,Polymerase Chain Reaction,protein,transcription,yeast} } % == BibTeX quality report for frankHumanHomologueYeast1996a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{fredrickAccurateTranslocationMRNA2002a, title = {Accurate {{Translocation}} of {{mRNA}} by the {{Ribosome Requires}} a {{Peptidyl Group}} or {{Its Analog}} on the {{tRNA Moving}} into the {{30S P Site}}}, author = {Fredrick, K. and Noller, H.F.}, year = 2002, month = may, journal = {Mol.Cell}, volume = {9}, number = {5}, pages = {1125–1131}, doi = {10.1016/S1097-2765(02)00523-3}, url = {PM:12049747}, abstract = {The ribosome must accurately translocate mRNA to maintain the reading frame. Here, we monitor the position of mRNA within the ribosome before and after EF-G-catalyzed translocation near the initiation site. When a deacylated tRNA that is translocated to the 30S P site recognizes other nearby codons, movement of tRNA and mRNA often becomes uncoupled. Instead of moving in the 5’ direction by 3 nucleotides, the mRNA slips backward, repositioning the tRNA on an out-of-frame codon more optimally spaced from the Shine-Dalgarno sequence. In contrast, when peptidyl-tRNA or its analog (N-acetyl-aminoacyl-tRNA) is translocated in the same context, translocation of mRNA is highly accurate. If aminoacyl-tRNA is translocated, an intermediate level of translocational accuracy is observed. Thus, translocational accuracy depends on the acylation state of the tRNA entering the 30S P site}, keywords = {accuracy,Codon,initiation,La,Movement,mRNA,nosource,Nucleotides,P-SITE,ribosome,Rna,sequence,translocation,tRNA} } % == BibTeX quality report for fredrickAccurateTranslocationMRNA2002a: % ? Possibly abbreviated journal title Mol.Cell % ? Title looks like it was stored in title-case in Zotero

@article{fredrickCatalysisRibosomalTranslocation2003, title = {Catalysis of Ribosomal Translocation by Sparsomycin}, author = {Fredrick, K. and Noller, H.F.}, year = 2003, month = may, journal = {Science}, volume = {300}, number = {5622}, pages = {1159–1162}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1084571}, url = {http://www.sciencemag.org/content/300/5622/1159.short}, abstract = {During protein synthesis, transfer RNAs (tRNAs) are translocated from the aminoacyl to peptidyl to exit sites of the ribosome, coupled to the movement of messenger RNA ( mRNA), in a reaction catalyzed by elongation factor G (EF-G) and guanosine triphosphate (GTP). Here, we show that the peptidyl transferase inhibitor sparsomycin triggers accurate translocation in vitro in the absence of EF-G and GTP. Our results provide evidence that translocation is a function inherent to the ribosome and that the energy to drive this process is stored in the tRNA-mRNA-ribosome complex after peptide-bond formation. These findings directly implicate the peptidyl transferase center of the 50S subunit in the mechanism of translocation, a process involving large-scale movement of tRNA and mRNA in the 30S subunit, some 70 angstroms away}, keywords = {0,ANGSTROM RESOLUTION,ANTITUMOR ANTIBIOTIC SPARSOMYCIN,BINDING,Catalysis,COMPLEX,COMPLEXES,EF-G,elongation,ESCHERICHIA-COLI,GTP,Guanosine,Guanosine Triphosphate,In Vitro,IN-VITRO,INHIBITOR,INTERMEDIATE,MECHANISM,MESSENGER-RNA,Movement,mRNA,nosource,P-SITE,PEPTIDE-BOND FORMATION,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,protein,protein synthesis,PROTEIN-SYNTHESIS,ribosome,Rna,SITE,SITES,sparsomycin,STRUCTURAL BASIS,SUBUNIT,TRANSFER-RNA,TRANSFERASE CENTER,translocation,tRNA} }

@article{freneauxGlutaricAcidemiaType1992, title = {Glutaric Acidemia Type {{II}}. {{Heterogeneity}} in Beta-Oxidation Flux, Polypeptide Synthesis, and Complementary {{DNA}} Mutations in the Alpha Subunit of Electron Transfer Flavoprotein in Eight Patients.}, author = {Freneaux, E. and Sheffield, V.C. and Molin, L. and Shires, A. and Rhead, W.J.}, year = 1992, month = nov, journal = {Journal of Clinical Investigation}, volume = {90}, number = {5}, pages = {1679–1686}, publisher = {American Society for Clinical Investigation}, doi = {10.1172/JCI116040}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC443224/}, keywords = {analysis,Codon,deficiency,disease,Dna,Frameshifting,Genetic,human,Mutation,MUTATIONS,nosource,Phenotype,sequence,SUBUNIT} }

@article{friedElectronMicroscopicHeteroduplex1978, title = {Electron Microscopic Heteroduplex Analysis of “Killer” Double-Stranded {{RNA}} Species from Yeast.}, author = {Fried, H.M. and Fink, G.R.}, year = 1978, journal = {Proceedings of the National Academy of Sciences}, volume = {75}, number = {9}, pages = {4224–4228}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.75.9.4224}, url = {http://www.pnas.org/content/75/9/4224.short}, keywords = {analysis,L-A,M1,nosource,Rna,yeast} } % == BibTeX quality report for friedElectronMicroscopicHeteroduplex1978: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.USA”)

@article{friedCloningYeastGene1981, title = {Cloning of Yeast Gene for Trichodermin Resistance and Ribosomal Protein {{L3}}.}, author = {Fried, H.M. and Warner, J.R.}, year = 1981, journal = {Proceedings of the National Academy of Sciences}, volume = {78}, number = {1}, pages = {238–242}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.78.1.238}, url = {http://www.pnas.org/content/78/1/238.short}, keywords = {antibiotics,cloning,drugs,gene,L3,nosource,Peptidyltransferase,protein,ribosome,yeast} } % == BibTeX quality report for friedCloningYeastGene1981: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.USA”)

@article{friedMolecularCloningAnalysis1982, title = {Molecular Cloning and Analysis of Yeast Gene for Cycloheximide Resistance and Ribosomal Protein {{L29}}.}, author = {Fried, H.M. and Warner, J.R.}, year = 1982, journal = {Nucleic acids research}, volume = {10}, number = {10}, pages = {3133–3148}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/10.10.3133}, url = {http://nar.oxfordjournals.org/content/10/10/3133.short}, keywords = {analysis,cloning,Cycloheximide,gene,L29,nosource,protein,ribosome,yeast} } % == BibTeX quality report for friedMolecularCloningAnalysis1982: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{friedCharacterizationYeastStrains1985, title = {Characterization of Yeast Strains with Conditionally Expressed Variants of Ribosomal Protein Genes Tcm1 and Cyh2.}, author = {Fried, H.M. and Nam, H.G. and Loechel, S. and Teem, J.}, year = 1985, journal = {Molecular and Cellular Biology}, volume = {5}, number = {1}, pages = {99–108}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/5/1/99}, keywords = {CYH2,gene,Genes,M,Multiple DOI,nonfile,nosource,TCM1,yeast} }

@article{friesNovelConservedNuclear2007a, title = {A Novel Conserved Nuclear Localization Signal Is Recognized by a Group of Yeast Importins}, author = {Fries, T. and Betz, C. and Sohn, K. and Caesar, S. and Schlenstedt, G. and Bailer, S.M.}, year = 2007, month = may, journal = {J.Biol Chem.}, url = {PM:17485461}, abstract = {Nucleo-cytoplasmic transport of proteins is mostly mediated by specific interaction between transport receptors of the importin beta-family and signal sequences present in their cargo. While several signal sequences, in particular the classical nuclear localization signal (NLS) recognized by the heterodimeric importin alpha / beta complex are well known, the signals recognized by other importin beta-like transport receptors remain to be characterized in detail. Here we present the systematic analysis of the nuclear import of Saccharomyces cerevisiae Asr1p, a nonessential alcohol-responsive Ring/PHD finger protein that shuttles between nucleus and cytoplasm but accumulates in the nucleus upon alcohol stress. Nuclear import of Asr1p is constitutive and mediated by its C-terminal domain. A short sequence comprising residues}, keywords = {analysis,CEREVISIAE,COMPLEX,COMPLEXES,Cytoplasm,DOMAIN,La,LOCALIZATION,No DOI found,nosource,Nuclear Localization Signal,protein,Proteins,RESIDUES,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,SIGNAL,Stress,TRANSPORT,yeast} } % == BibTeX quality report for friesNovelConservedNuclear2007a: % ? Possibly abbreviated journal title J.Biol Chem.

@article{frischmeyerMRNASurveillanceMechanism2002, title = {An {{mRNA}} Surveillance Mechanism That Eliminates Transcripts Lacking Termination Codons}, author = {Frischmeyer, P.A. and {}{van Hoof}, A. and O’Donnell, K. and Guerrerio, A.L. and Parker, R. and Dietz, H.C.}, year = 2002, month = mar, journal = {Science}, volume = {295}, number = {5563}, pages = {2258–2261}, publisher = {American Association for the Advancement of Science}, issn = {1095-9203}, doi = {10.1126/science.1067338}, url = {http://www.sciencemag.org/content/295/5563/2258.short http://www.ncbi.nlm.nih.gov/pubmed/11910109 http://www.sciencemag.org/cgi/doi/10.1126/science.1067338}, abstract = {Translation is an important mechanism to monitor the quality of messenger RNAs (mRNAs), as exemplified by the translation-dependent recognition and degradation of transcripts harboring premature termination codons (PTCs) by the nonsense-mediated mRNA decay (NMD) pathway. We demonstrate in yeast that mRNAs lacking all termination codons are as labile as nonsense transcripts. Decay of “nonstop” transcripts in yeast requires translation but is mechanistically distinguished from NMD and the major mRNA turnover pathway that requires deadenylation, decapping, and 5’-to-3’ exonucleolytic decay. These data suggest that nonstop decay is initiated when the ribosome reaches the 3’ terminus of the message. We demonstrate multiple physiologic sources of nonstop transcripts and conservation of their accelerated decay in mammalian cells. This process regulates the stability and expression of mRNAs that fail to signal translational termination}, pmid = {11910109}, keywords = {0,3,3’ Untranslated Regions,3’ Untranslated Regions: chemistry,3’ Untranslated Regions: genetics,3’ Untranslated Regions: metabolism,Base Sequence,Cell Line,CELLS,chemistry,Codon,CODONS,CodonTerminator,Databases,DatabasesGenetic,DEADENYLATION,DECAY,degradation,expression,Fungal,Fungal: genetics,Genes,GenesFungal,Genetic,genetics,Glucuronidase,Glucuronidase: genetics,Half-Life,Humans,La,MAMMALIAN-CELLS,MECHANISM,MESSAGE,Messenger,MESSENGER-RNA,MESSENGER-RNAS,Messenger: chemistry,Messenger: genetics,Messenger: metabolism,metabolism,mRNA,mRNA decay,mRNA turnover,NMD,NONSENSE,nonsense-mediated mRNA decay,nosource,PATHWAY,Polyadenylation,Post-Transcriptional,PREMATURE TERMINATION CODON,Protein Biosynthesis,RECOGNITION,REGION,REQUIRES,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,ribosome,Rna,RNA,RNA 3’ End Processing,RNA Processing,RNA ProcessingPost-Transcriptional,RNA Stability,RNAMessenger,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Sequence Deletion,Sequence Deletion: genetics,SIGNAL,stability,SURVEILLANCE,termination,TERMINATION CODON,TERMINATION-CODON,Terminator,Terminator: genetics,TRANSCRIPT,translation,TRANSLATIONAL TERMINATION,turnover,Untranslated Regions,yeast} }

@article{frohlichYeastCellCycle1991a, title = {Yeast Cell Cycle Protein ⬚{{CDC48}}⬚ Shows Full-Length Homology to the Mammalian Protein {{VCP}} and Is a Member of a Protein Family Involved in Secretion, Peroxisome Formation, and Gene Expression.}, author = {Frohlich, K.U. and Fries, H.W. and Rudiger, M. and Erdmann, R. and Botstein, D. and Mecke, D.}, year = 1991, journal = {J.Cell.Biol.}, volume = {114}, pages = {443–453}, doi = {10.1083/jcb.114.3.443}, keywords = {CDC48,cell cycle,expression,gene,Gene Expression,GENE-EXPRESSION,MOF6,nosource,protein,yeast} } % == BibTeX quality report for frohlichYeastCellCycle1991a: % ? Possibly abbreviated journal title J.Cell.Biol.

@article{fromont-racineRibosomeAssemblyEukaryotes2003, title = {Ribosome Assembly in Eukaryotes}, author = {{Fromont-Racine}, M. and Senger, B. and Saveanu, C. and Fasiolo, F.}, year = 2003, journal = {Gene}, volume = {313}, pages = {17–42}, publisher = {Elsevier}, doi = {10.1016/S0378-1119(03)00629-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0378111903006292}, abstract = {Ribosome synthesis is a highly complex and coordinated process that occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells. Based on the protein composition of several ribosomal subunit precursors recently characterized in yeast, a total of more than 170 factors are predicted to participate in ribosome biogenesis and the list is still growing. So far the majority of ribosomal factors have been implicated in RNA maturation (nucleotide modification and processing). Recent advances gave insight into the process of ribosome export and assembly. Proteomic approaches have provided the first indications for a ribosome assembly pathway in eukaryotes and confirmed the dynamic character of the whole process}, keywords = {0,Animals,assembly,BIOGENESIS,Cell Nucleolus,CELLS,CHARACTER,COMPLEX,COMPLEXES,Cytoplasm,Eukaryotic Cells,genetics,La,MATURATION,metabolism,modification,nosource,nucleolus,PATHWAY,PRECURSOR,protein,Proteins,Review,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,ribosome biogenesis,RIBOSOME SYNTHESIS,Ribosomes,Rna,RNARibosomal,Saccharomyces cerevisiae,SUBUNIT,yeast} }

@article{fujimuraInvitroDoubleStrandedRnaSynthesis1986, title = {Invitro {{L-A Double-Stranded-Rna Synthesis}} in {{Virus-Like Particles}} from {{Saccharomyces-Cerevisiae}}}, author = {Fujimura, T. and Esteban, R. and Wickner, R.B.}, year = 1986, month = jun, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {83}, number = {12}, pages = {4433–4437}, doi = {10.1073/pnas.83.12.4433}, url = {ISI:A1986C835000068}, keywords = {DOUBLE-STRANDED-RNA,INVITRO,L-A,La,nosource,PARTICLES,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,T} } % == BibTeX quality report for fujimuraInvitroDoubleStrandedRnaSynthesis1986: % ? Title looks like it was stored in title-case in Zotero

@article{fujimuraThermolabileViruslikeParticles1986a, title = {Thermolabile {{L-A}} Virus-like Particles from Pet18 Mutants of {{Saccharomyces}} Cerevisiae}, author = {Fujimura, T. and Wickner, R.B.}, year = 1986, month = feb, journal = {Mol.Cell Biol.}, volume = {6}, number = {2}, pages = {404–410}, url = {PM:3537688}, abstract = {pet18 mutations in Saccharomyces cerevisiae confer on the cell the inability to maintain either L-A or M double-stranded RNAs (dsRNAs) at the nonpermissive temperature. In in vitro experiments, we examined the effects of pet18 mutations on the RNA-dependent RNA polymerase activity associated with virus-like particles (VLPs). pet18 mutations caused thermolabile RNA polymerase activity of L-A VLPs, and this thermolability was found to be due to the instability of the L-A VLP structure. The pet18 mutations did not affect RNA polymerase activity of M VLPs. Furthermore, the temperature sensitivity of wild-type L-A RNA polymerase differed substantially from that of M RNA polymerase. From these results, and from other genetic and biochemical lines of evidence which suggest that replication of M dsRNA requires the presence of L-A dsRNA, we propose that the primary effect of the pet18 mutation is on the L-A VLP structure and that the inability of pet18 mutants to maintain M dsRNA comes from the loss of L-A dsRNA}, keywords = {0,CEREVISIAE,DOUBLE-STRANDED-RNA,Drug Stability,DSRNA,Genetic,genetics,Genotype,Heat,In Vitro,IN-VITRO,isolation & purification,Kinetics,L-A,La,LINE,M,Multiple DOI,MUTANTS,Mutation,MUTATIONS,nonfile,nosource,Nucleic Acid Hybridization,PARTICLES,polymerase,POLYMERASE ACTIVITY,REPLICATION,REQUIRES,Rna,RNA Viruses,RNA-DEPENDENT RNA POLYMERASE,RNA-POLYMERASE,RNADouble-Stranded,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,structure,Temperature,VIRUS-LIKE PARTICLES,WILD-TYPE} } % == BibTeX quality report for fujimuraThermolabileViruslikeParticles1986a: % ? Possibly abbreviated journal title Mol.Cell Biol.

@article{fujimuraDoubleStrandedRnaVirusLikeParticle1987, title = {L-{{A Double-Stranded-Rna Virus-Like Particle Replication Cycle}} in {{Saccharomyces-Cerevisiae}} - {{Particle Maturation Invitro}} and {{Effects}} of {{Mak10}} and {{Pet18 Mutations}}}, author = {Fujimura, T. and Wickner, R.B.}, year = 1987, month = jan, journal = {Molecular and Cellular Biology}, volume = {7}, number = {1}, pages = {420–426}, url = {ISI:A1987F500500051}, keywords = {DOUBLE-STRANDED-RNA,INVITRO,L-A,La,MATURATION,Multiple DOI,Mutation,MUTATIONS,nonfile,nosource,REPLICATION,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,T} } % == BibTeX quality report for fujimuraDoubleStrandedRnaVirusLikeParticle1987: % ? Title looks like it was stored in title-case in Zotero

@article{fujimuraGeneOverlapResults1988a, title = {Gene Overlap Results in a Viral Protein Having an {{RNA}} Bnding Domain and a Major Coat Protein Domain.}, author = {Fujimura, T. and Wickner, R.B.}, year = 1988, journal = {Cell}, volume = {55}, pages = {663–671}, doi = {10.1016/0092-8674(88)90225-5}, keywords = {Gag,Gag-pol,gene,L-A,nosource,protein,Rna,virus} }

@article{fujimuraReplicaseVirusLikeParticles1988, title = {Replicase of {{L-A Virus-Like Particles}} of {{Saccharomyces-Cerevisiae}} - {{Invitro Conversion}} of {{Exogenous L-A}} and {{M1 Single-Stranded Rnas}} to {{Double-Stranded Form}}}, author = {Fujimura, T. and Wickner, R.B.}, year = 1988, month = jan, journal = {Journal of Biological Chemistry}, volume = {263}, number = {1}, pages = {454–460}, doi = {10.1016/S0021-9258(19)57414-2}, url = {ISI:A1988L504700070}, keywords = {INVITRO,L-A,La,M1,nosource,PARTICLES,Rna,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,T} } % == BibTeX quality report for fujimuraReplicaseVirusLikeParticles1988: % ? Title looks like it was stored in title-case in Zotero

@article{fujimuraReconstitutionTemplateDependentInvitro1989, title = {Reconstitution of {{Template-Dependent Invitro Transcriptase Activity}} of {{A Yeast Double-Stranded-Rna Virus}}}, author = {Fujimura, T. and Wickner, R.B.}, year = 1989, month = jun, journal = {Journal of Biological Chemistry}, volume = {264}, number = {18}, pages = {10872–10877}, doi = {10.1016/S0021-9258(18)81701-X}, url = {ISI:A1989AB64300082}, keywords = {DOUBLE-STRANDED-RNA,INVITRO,nosource,T,virus,yeast} } % == BibTeX quality report for fujimuraReconstitutionTemplateDependentInvitro1989: % ? Title looks like it was stored in title-case in Zotero

@article{fujimuraPortableEncapsidationSignal1990a, title = {Portable {{Encapsidation Signal}} of the {{L-A Double-Stranded-Rna Virus}} of {{Saccharomyces-Cerevisiae}}}, author = {Fujimura, T. and Esteban, R. and Esteban, L.M. and Wickner, R.B.}, year = 1990, journal = {Cell}, volume = {62}, number = {4}, pages = {819–828}, doi = {10.1016/0092-8674(90)90125-X}, url = {ISI:A1990DW30600020}, keywords = {DOUBLE-STRANDED-RNA,L-A,La,nosource,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SIGNAL,T,virus} } % == BibTeX quality report for fujimuraPortableEncapsidationSignal1990a: % ? Title looks like it was stored in title-case in Zotero

@article{fujimuraInteractionTwoCis1992a, title = {Interaction of Two ⬚cis⬚ Sites with the {{RNA}} Replicase of the Yeast {{L-A}} Virus.}, author = {Fujimura, T. and Wickner, R.B.}, year = 1992, journal = {J.Biol.Chem.}, volume = {267}, pages = {2708–2713}, doi = {10.1016/S0021-9258(18)45937-6}, keywords = {L-A,La,nosource,packaging,Rna,virus,yeast} } % == BibTeX quality report for fujimuraInteractionTwoCis1992a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{fujimuraPolGagPolFusion1992, title = {Pol of {{Gag-Pol Fusion Protein Required}} for {{Encapsidation}} of {{Viral-Rna}} of {{Yeast L-A-Virus}}}, author = {Fujimura, T. and Ribas, J.C. and Makhov, A.M. and Wickner, R.B.}, year = 1992, month = oct, journal = {Nature}, volume = {359}, number = {6397}, pages = {746–749}, doi = {10.1038/359746a0}, url = {ISI:A1992JU65000062}, abstract = {DOUBLE-STRANDED RNA viruses have an RNA-dependent RNA polymerase activity associated with the viral particles which is indispensable for their replication cycle. Using the yeast L-A double-stranded RNA virus we have investigated the mechanism by which the virus encapsidates its genomic RNA and RNA polymerase. The L-A gag gene encodes the principal viral coat protein and the overlapping pol gene is expressed as a gag-pol fusion protein which is formed by a -1 ribosomal frameshift1-3. Here we show that Gag alone is sufficient for virus particle formation, but that it fails to package the viral single-stranded RNA genome. Encapsidation of the viral RNA requires only a part of the Pol region (the N-terminal quarter), which is presumably distinct from the RNA polymerase domain. Given that the Pol region has single-stranded RNA-binding activity, these results are consistent with our LA virus encapsidation model1: the Pol region of the fusion protein binds specifically to the viral genome (+) strand, and the N-terminal gag-encoded region primes polymerization of Gag to form the capsid, thus ensuring the packaging of both the viral genome and the RNA polymerase}, keywords = {Capsid,COAT PROTEIN,DOMAIN,DOUBLE-STRANDED-RNA,ENCAPSIDATION,Gag,Gag-pol,gene,Genome,genomic,GENOMIC RNA,HEPATITIS-B VIRUS,INVITRO,L-A,L-A-VIRUS,La,MATURATION,MECHANISM,nosource,packaging,PARTICLES,pol,polymerase,protein,REGION,REPLICATION,REQUIRES,Rna,RNA Viruses,RNA-POLYMERASE,SACCHAROMYCES-CEREVISIAE,T,transcription,viral particle,VIRAL-RNA,virus,yeast} } % == BibTeX quality report for fujimuraPolGagPolFusion1992: % ? Title looks like it was stored in title-case in Zotero

@article{fujimuraRecognitionRNAEncapsidation2000a, title = {Recognition of {{RNA}} Encapsidation Signal by the Yeast {{L-A}} Double-Stranded {{RNA}} Virus}, author = {Fujimura, T. and Esteban, R.}, year = 2000, month = nov, journal = {J.Biol.Chem.}, volume = {275}, number = {47}, pages = {37118–37126}, doi = {10.1074/jbc.M005245200}, url = {PM:10954712}, abstract = {The encapsidation signal of the yeast L-A virus contains a 24-nucleotide stem-loop structure with a 5-nucleotide loop and an A bulged at the 5’ side of the stem. The Pol part of the Gag-Pol fusion protein is responsible for encapsidation of viral RNA. Opened empty viral particles containing Gag-Pol specifically bind to this encapsidation signal in vitro. We found that binding to empty particles protected the bulged A and the flanking-two nucleotides from cleavage by Fe(II)-EDTA-generated hydroxyl radicals. The five nucleotides of the loop sequence ((4190)GAUCC(4194)) were not protected. However, T1 RNase protection and in vitro mutagenesis experiments indicated that G(4190) is essential for binding. Although the sequence of the other four nucleotides of the loop is not essential, data from RNase protection and chemical modification experiments suggested that C(4194) was also directly involved in binding to empty particles rather than indirectly through its potential base pairing with G(4190). These results suggest that the Pol domain of Gag-Pol contacts the encapsidation signal at two sites: one, the bulged A, and the other, G and C bases at the opening of the loop. These two sites are conserved in the encapsidation signal of M1, a satellite RNA of the L-A virus}, keywords = {0,ACID,BASE,Base Pairing,Base Sequence,BASES,BINDING,Capsid,CHEMICAL MODIFICATION,CLEAVAGE,Consensus Sequence,DOMAIN,DOUBLE-STRANDED-RNA,ENCAPSIDATION,FUSION PROTEIN,Fusion Proteinsgag-pol,Gag-pol,In Vitro,IN-VITRO,L-A,L-A-VIRUS,La,LOOP,M1,metabolism,modification,Molecular Sequence Data,Mutagenesis,nosource,Nucleic Acid Conformation,Nucleotides,PARTICLES,pharmacology,physiology,pol,PROTECTION,protein,Proteins,RECOGNITION,Ribonucleases,Rna,RNAse,RNAse protection,sequence,SIGNAL,SITE,SITES,STEM-LOOP,structure,Structure-Activity Relationship,Sulfuric Acid Esters,supportnon-u.s.gov’t,TranscriptionGenetic,viral particle,VIRAL PARTICLES,VIRAL-RNA,virus,yeast} } % == BibTeX quality report for fujimuraRecognitionRNAEncapsidation2000a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{funariStructureFreeThermus2000, title = {Structure of Free {{Thermus}} Flavus 5 {{S rRNA}} at 1.3 Nm Resolution from Synchrotron {{X-ray}} Solution Scattering}, author = {Funari, S.S. and Rapp, G. and Perbandt, M. and Dierks, K. and Vallazza, M. and Betzel, C. and Erdmann, V.A. and Svergun, D.I.}, year = 2000, month = oct, journal = {Journal of Biological Chemistry}, volume = {275}, number = {40}, pages = {31283–31288}, publisher = {ASBMB}, doi = {10.1074/jbc.M004974200}, url = {http://www.jbc.org/content/275/40/31283.short}, abstract = {The shape of free Thermus flavus 5 S rRNA in solution at 1.3 nm resolution is restored from synchrotron x-ray scattering data using an ab initio simulated annealing algorithm. The free 5 S rRNA is a bent elongated molecule displaying a compact central region and two projecting arms, similar to those of the tRNA. The atomic models of the 5 S rRNA domains A-D-E and B-C in the form of elongated helices can be well accommodated within the shape, yielding a tentative model of the structure of the free 5 S rRNA in solution. Its comparison with the recent protein-RNA map in the ribosome (Svergun, D. I., and Nierhaus, K. H. (2000) J. Biol. Chem. 275, 14432-14439) indicates that the 5 S rRNA becomes essentially more compact upon complex formation with specific ribosomal proteins. A conceivable conformational change involves rotation of the B-C domain toward the A-D-E domain. The model of free 5 S rRNA displays no interactions between domains E and C, but such interactions are possible in the bound molecule}, keywords = {0,5 S rRNA,Algorithms,chemistry,COMPLEX,COMPLEX-FORMATION,COMPLEXES,CONFORMATIONAL CHANGE,CONFORMATIONAL-CHANGE,D,DOMAIN,DOMAINS,Dose-Response RelationshipDrug,E,Escherichia coli,FORM,genetics,La,metabolism,MODEL,models,ModelsMolecular,nosource,Nucleic Acid Conformation,protein,Protein Conformation,Protein StructureSecondary,Protein StructureTertiary,Proteins,REGION,Research SupportNon-U.S.Gov’t,RESOLUTION,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNARibosomal5S,Rotation,rRNA,S,ScatteringRadiation,Software,structure,Thermus,tRNA,X-Rays} } % == BibTeX quality report for funariStructureFreeThermus2000: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{funatsuRibosomalProteins331972a, title = {Ribosomal Proteins. 33. {{Location}} of Amino-Acid Replacements in Protein {{S12}} Isolated from {{Escherichia}} Coli Mutants Resistant to Streptomycin.}, author = {Funatsu, G. and Wittmann, H.G.}, year = 1972, month = jul, journal = {Journal of molecular biology}, volume = {68}, number = {3}, eprint = {4560854}, eprinttype = {pubmed}, pages = {547–550}, doi = {10.1016/0022-2836(72)90108-8}, url = {http://www.ncbi.nlm.nih.gov/pubmed/4560854/}, keywords = {0,ACID,ACIDS,Alleles,Amino Acids,AMINO-ACID,AMINO-ACID REPLACEMENTS,AMINO-ACIDS,analysis,Bacterial,Bacterial Proteins,Drug ResistanceMicrobial,Escherichia coli,ESCHERICHIA-COLI,Genetic Code,La,LOCATION,Lysine,MUTANTS,Mutation,nosource,Peptides,pharmacology,protein,PROTEIN-S12,Proteins,RESISTANT,Ribosomal Proteins,Ribosomes,Streptomycin,Trypsin} } % == BibTeX quality report for funatsuRibosomalProteins331972a: % ? unused Journal abbr (“J.Mol.Biol.”)

@article{furfineSingleStrandedRnaCopy1989, title = {A {{Single-Stranded Rna Copy}} of the {{Giardia-Lamblia Virus Double-Stranded-Rna Genome Is Present}} in the {{Infected Giardia-Lamblia}}}, author = {Furfine, E.S. and White, T.C. and Wang, A.L. and Wang, C.C.}, year = 1989, journal = {Nucleic Acids Research}, volume = {17}, number = {18}, pages = {7453–7467}, doi = {10.1093/nar/17.18.7453}, url = {ISI:A1989AR73300030}, keywords = {DOUBLE-STRANDED-RNA,Genome,nosource,Rna,virus} } % == BibTeX quality report for furfineSingleStrandedRnaCopy1989: % ? Title looks like it was stored in title-case in Zotero

@article{furfineTransfectionGiardiaLamblia1990, title = {Transfection of the {{Giardia}} Lamblia Double-Stranded {{RNA}} Virus into Giardia Lamblia by Electroporation of a Single-Stranded {{RNA}} Copy of the Viral Genome.}, author = {Furfine, E.S. and Wang, C.C.}, year = 1990, month = jul, journal = {Molecular and Cellular Biology}, volume = {10}, number = {7}, pages = {3659–3663}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/10/7/3659}, keywords = {DOUBLE-STRANDED-RNA,Genome,Multiple DOI,nonfile,nosource,Rna,Transfection,virus} }

@article{gabaPhysicalEvidenceDistinct2001, title = {Physical Evidence for Distinct Mechanisms of Translational Control by Upstream Open Reading Frames}, author = {Gaba, A. and Wang, Z. and Krishnamoorthy, T. and Hinnebusch, A.G. and Sachs, M.S.}, year = 2001, month = nov, journal = {The EMBO Journal}, volume = {20}, number = {22}, pages = {6453–6463}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/20.22.6453}, url = {http://www.nature.com/emboj/journal/v20/n22/abs/7594135a.html}, abstract = {The Saccharomyces cerevisiae GCN4 mRNA 5’-leader contains four upstream open reading frames (uORFS) and the CPA1 leader contains a single uORF. To determine how these uORFs control translation, we examined mRNAs containing these leaders in cell-free translation extracts to determine where ribosomes were loaded first and where they were loaded during steady-state translation. Ribosomes predominantly loaded first at GCN4 uORF1. Following its translation, but not the translation of uORF4, they efficiently reinitiated protein synthesis at Gcn4p. Adding purified eIF2 increased reinitiation at uORFs 3 or 4 and reduced reinitiation at Gcn4p. This indicates that eIF2 affects the site of reinitiation following translation of GCN4 uORF1 in vitro. In contrast, for mRNA containing the CPA1 uORF, ribosomes reached the downstream start codon by scanning past the uORF. Addition of arginine caused ribosomes that had synthesized the uORF polypeptide to stall at its termination codon, reducing loading at the downstream start codon, apparently by blocking scanning ribosomes, and not by affecting reinitiation. The GCN4 and CPA1 uORFs thus control translation in fundamentally different ways}, keywords = {3,Arginine,Codon,FRAME,GCN4,gene,GENE-EXPRESSION,In Vitro,IN-VITRO,INHIBITION,LEADER PEPTIDE,M,MECHANISM,MECHANISMS,MESSENGER-RNA,mRNA,NASCENT-PEPTIDE,Neurospora,NEUROSPORA-CRASSA,nosource,OPEN READING FRAME,Open Reading Frames,protein,protein synthesis,PROTEIN-SYNTHESIS,ribosome,ribosome reinitiation,ribosome scanning,Ribosomes,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SITE,termination,TERMINATION CODON,translation,uORF,UPSTREAM,yeast} }

@article{gabashviliMajorRearrangements70S1999, title = {Major Rearrangements in the {{70S}} Ribosomal {{3D}} Structure Caused by a Conformational Switch in {{16S}} Ribosomal {{RNA}}.}, author = {Gabashvili, I.S. and Agrawal, R.K. and Grassucci, R. and Squires, C.L. and Dahlberg, A.E. and Frank, J.}, year = 1999, month = nov, journal = {The EMBO Journal}, volume = {18}, number = {22}, pages = {6501–6507}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/18.22.6501}, url = {http://www.nature.com/emboj/journal/v18/n22/abs/7592051a.html}, abstract = {Dynamic changes in secondary structure of the 16S rRNA during the decoding of mRNA are visualized by three-dimensional cryo-electron microscopy of the 70S ribosome. Thermodynamically unstable base pairing of the 912-910 (CUC) nucleotides of the 16S RNA with two adjacent complementary regions at nucleotides 885-887 (GGG) and 888-890 (GAG) was stabilized in either of the two states by point mutations at positions 912 (C912G) and 885 (G885U). A wave of rearrangements can be traced arising from the switch in the three base pairs and involving functionally important regions in both subunits of the ribosome. This significantly affects the topography of the A-site tRNA-binding region on the 30S subunit and thereby explains changes in tRNA affinity for the ribosome and fidelity of decoding mRNA}, keywords = {20031661,A-SITE,Base Pairing,Cryoelectron Microscopy,decoding,Fidelity,Gag,mRNA,Mutation,MUTATIONS,nosource,Nucleotides,Point Mutation,RIBOSOMAL-RNA,ribosome,Rna,rRNA,structure,SUBUNIT,tRNA} } % == BibTeX quality report for gabashviliMajorRearrangements70S1999: % ? unused Journal abbr (“EMBO J.”)

@article{gabashviliSolutionStructureColi2000, title = {Solution Structure of the {{E}}. Coli {{70S}} Ribosome at 11.5 {{A}} Resolution}, author = {Gabashvili, I.S. and Agrawal, R.K. and Spahn, C.M. and Grassucci, R.A. and Svergun, D.I. and Frank, J. and Penczek, P.}, year = 2000, month = mar, journal = {Cell}, volume = {100}, number = {5}, pages = {537–549}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(00)80690-X}, url = {http://www.sciencedirect.com/science/article/pii/S009286740080690X http://linkinghub.elsevier.com/retrieve/pii/S009286740080690X}, abstract = {Over 73,000 projections of the E. coli ribosome bound with formyl- methionyl initiator tRNAf(Met) were used to obtain an 11.5 A cryo- electron microscopy map of the complex. This map allows identification of RNA helices, peripheral proteins, and intersubunit bridges. Comparison of double-stranded RNA regions and positions of proteins identified in both cryo-EM and X-ray maps indicates good overall agreement but points to rearrangements of ribosomal components required for the subunit association. Fitting of known components of the 50S stalk base region into the map defines the architecture of the GTPase- associated center and reveals a major change in the orientation of the alpha-sarcin-ricin loop. Analysis of the bridging connections between the subunits provides insight into the dynamic signaling mechanism between the ribosomal subunits}, keywords = {0,analysis,Bacterial,Bacterial Proteins,COMPLEX,COMPLEXES,COMPONENT,Cryoelectron Microscopy,elongation,Escherichia coli,GTP,GTP Phosphohydrolase,GTP Phosphohydrolases,GTPase,IDENTIFICATION,Image Processing-Computer-Assisted,Image ProcessingComputer-Assisted,La,Macromolecular Systems,MECHANISM,nosource,Peptide Elongation Factor G,protein,Proteins,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNA-Bacterial,RNA-Ribosomal,RNA-Transfer-Met,RNABacterial,RNARibosomal,RNATransferMet,Solutions,structure,SUBUNIT,support-u.s.gov’t-non-p.h.s.,support-u.s.gov’t-p.h.s.,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,SYSTEM,tRNA,ultrastructure} }

@article{gadalNuclearExport60s2001, title = {Nuclear Export of 60s Ribosomal Subunits Depends on {{Xpo1p}} and Requires a Nuclear Export Sequence-Containing Factor, {{Nmd3p}}, That Associates with the Large Subunit Protein {{Rpl10p}}}, author = {Gadal, O. and Strauss, D. and Kessl, J. and Trumpower, B. and Tollervey, D. and Hurt, E.}, year = 2001, month = may, journal = {Molecular and cellular biology}, volume = {21}, number = {10}, pages = {3405–3415}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.21.10.3405-3415.2001}, url = {http://mcb.asm.org/cgi/content/abstract/21/10/3405}, abstract = {Nuclear export of ribosomes requires a subset of nucleoporins and the Ran system, but specific transport factors have not been identified. Using a large subunit reporter (Rpl25p-eGFP), we have isolated several temperature-sensitive ribosomal export (rix) mutants. One of these corresponds to the ribosomal protein Rpl10p, which interacts directly with Nmd3p, a conserved and essential protein associated with 60S subunits. We find that thermosensitive nmd3 mutants are impaired in large subunit export. Strikingly, Nmd3p shuttles between the nucleus and cytoplasm and is exported by the nuclear export receptor Xpo1p. Moreover, we show that export of 60S subunits is Xpo1p dependent. We conclude that nuclear export of 60S subunits requires the nuclear export sequence-containing nonribosomal protein Nmd3p, which directly binds to the large subunit protein Rpl10p}, keywords = {60S subunit,Carrier Proteins,Cytoplasm,Fungal Proteins,Gene Expression RegulationFungal,genetics,metabolism,Mutation,nosource,Nuclear Proteins,protein,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Saccharomyces cerevisiae,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM} } % == BibTeX quality report for gadalNuclearExport60s2001: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{gafnerDeltaSequences51983, title = {Delta Sequences in the 5’ Non-Coding Region of Yeast {{tRNA}} Genes.}, author = {Gafner, J. and De Robertis, E.M. and Phillippsen, P.}, year = 1983, journal = {The EMBO journal}, volume = {2}, number = {4}, pages = {583–591}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1983.tb01467.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC555065/}, keywords = {gene,Genes,nosource,sequence,tRNA,yeast} } % == BibTeX quality report for gafnerDeltaSequences51983: % ? unused Journal abbr (“EMBO J.”)

@article{galaktionovCDC25PhosphatasesPotential1995, title = {{{CDC25}} Phosphatases as Potential Human Oncogenes.}, author = {Galaktionov, K. and Lee, A.K. and Eckstein, J. and Draetta, G. and Meckler, J. and Loda, M. and Beach, D.}, year = 1995, journal = {Science}, volume = {268}, number = {5230}, pages = {1575–1577}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.7667636}, url = {http://www.sciencemag.org/content/269/5230/1575.short}, keywords = {cdc25,human,nosource,oncogenes} }

@article{galeTranslationalControlViral2000, title = {Translational Control of Viral Gene Expression in Eukaryotes}, author = {Gale, M. and Tan, S.L. and Katze, M.G.}, year = 2000, month = jun, journal = {Microbiology and Molecular Biology Reviews}, volume = {64}, number = {2}, pages = {239-+}, publisher = {Am Soc Microbiol}, doi = {10.1128/MMBR.64.2.239-280.2000}, url = {http://mmbr.asm.org/cgi/content/abstract/64/2/239 ISI:000087486200001}, abstract = {As obligate intracellular parasites, viruses rely exclusively on the translational machinery of the host cell for the synthesis of viral proteins. This relationship has imposed numerous challenges on both the infecting virus and the host cell. Importantly, viruses must compete with the endogenous transcripts of the host cell for the translation of viral mRNA. Eukaryotic viruses have thus evolved diverse mechanisms to ensure translational efficiency of viral mRNA above and beyond that of cellular mRNA. Mechanisms that facilitate the efficient and selective translation of viral mRNA may be inherent in the structure of the viral nucleic acid itself and can involve the recruitment and/or modification of specific host factors. These processes serve to redirect the translation apparatus to favor viral transcripts and they often come at the expense of the host cell. Accordingly, eukaryotic cells have developed antiviral countermeasures to target the translational machinery and disrupt protein synthesis during the course of virus infection. Not to be outdone many viruses have answered these countermeasures with their own mechanisms to disrupt cellular antiviral pathways, thereby ensuring the uncompromised translation of virion proteins Here we review the varied and complex translational programs employed by eukaryotic viruses. We discuss how these translational strategies have been incorporated into the virus life cycle and examine how such programming contributes to the pathogenesis of the host cell}, keywords = {antiviral,COMPLEX,COMPLEXES,DEPENDENT PROTEIN-KINASE,DOUBLE-STRANDED-RNA,efficiency,Eukaryotic Cells,expression,gene,Gene Expression,GENE-EXPRESSION,HEPATITIS-C VIRUS,HERPES-SIMPLEX VIRUS,HUMAN-IMMUNODEFICIENCY-VIRUS,INITIATION-FACTOR 4E,INTERNAL RIBOSOMAL ENTRY,MECHANISM,MECHANISMS,modification,mRNA,MURINE LEUKEMIA-VIRUS,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Review,structure,TRACT-BINDING-PROTEIN,translation,Viral Proteins,Virion,VIRION HOST SHUTOFF,virus} }

@article{galkinRolesNegativelyCharged2007, title = {Roles of the Negatively Charged {{N-terminal}} Extension of {{Saccharomyces}} Cerevisiae Ribosomal Protein {{S5}} Revealed by Characterization of a Yeast Strain Containing Human Ribosomal Protein {{S5}}}, author = {Galkin, O. and Bentley, A.A. and Gupta, S. and Compton, B.A. and Mazumder, B. and Kinzy, T.G. and Merrick, W.C. and Hatzoglou, M. and Pestova, T.V. and Hellen, C.U. and Komar, A.A.}, year = 2007, month = dec, journal = {RNA.}, volume = {13}, number = {12}, pages = {2116–28}, publisher = {Cold Spring Harbor Lab}, issn = {1469-9001}, doi = {10.1261/rna.688207}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2080588&tool=pmcentrez&rendertype=abstract http://rnajournal.cshlp.org/content/13/12/2116.short}, abstract = {Ribosomal protein (rp) S5 belongs to a family of ribosomal proteins that includes bacterial rpS7. rpS5 forms part of the exit (E) site on the 40S ribosomal subunit and is essential for yeast viability. Human rpS5 is 67% identical and 79% similar to Saccharomyces cerevisiae rpS5 but lacks a negatively charged (pI approximately 3.27) 21 amino acid long N-terminal extension that is present in fungi. Here we report that replacement of yeast rpS5 with its human homolog yielded a viable yeast strain with a 20%-25% decrease in growth rate. This replacement also resulted in a moderate increase in the heavy polyribosomal components in the mutant strain, suggesting either translation elongation or termination defects, and in a reduction in the polyribosomal association of the elongation factors eEF3 and eEF1A. In addition, the mutant strain was characterized by moderate increases in +1 and -1 programmed frameshifting and hyperaccurate recognition of the UAA stop codon. The activities of the cricket paralysis virus (CrPV) IRES and two mammalian cellular IRESs (CAT-1 and SNAT-2) were also increased in the mutant strain. Consistently, the rpS5 replacement led to enhanced direct interaction between the CrPV IRES and the mutant yeast ribosomes. Taken together, these data indicate that rpS5 plays an important role in maintaining the accuracy of translation in eukaryotes and suggest that the negatively charged N-terminal extension of yeast rpS5 might affect the ribosomal recruitment of specific mRNAs.}, pmid = {17901157}, keywords = {accuracy,ACID,AMINO-ACID,ASSOCIATION,Bacterial,Base Sequence,CEREVISIAE,Codon,COMPONENT,COMPONENTS,Cricket paralysis virus,E,elongation,elongation factors,ELONGATION-FACTORS,FAMILY,FORM,Frameshifting,Fungal,Fungal: genetics,Fungal: metabolism,Fungi,GROWTH,homolog,human,HUMAN HOMOLOG,Humans,La,Messenger,Messenger: genetics,Messenger: metabolism,Models,Molecular,Molecular Sequence Data,mRNA,Mutagenesis,nosource,Nucleic Acid Conformation,programmed frameshifting,protein,Proteins,RECOGNITION,RECRUITMENT,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: genetics,Ribosomal Proteins: metabolism,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Ribosomes: metabolism,RNA,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: chemistry,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: genetics,SACCHAROMYCES-CEREVISIAE,SITE,STOP CODON,SUBUNIT,termination,termination defect,Transfection,translation,UAA,virus,yeast} } % == BibTeX quality report for galkinRolesNegativelyCharged2007: % ? Possibly abbreviated journal title RNA.

@article{gallantRibosomeFrameshiftingHungry1993a, title = {Ribosome {{Frameshifting}} at {{Hungry Codons}} - {{Sequence Rules}}, {{Directional Specificity}} and {{Possible Relationship}} to {{Mobile Element Behavior}}}, author = {Gallant, J. and Lindsley, D.}, year = 1993, month = nov, journal = {Biochemical Society Transactions}, volume = {21}, number = {4}, pages = {817–821}, doi = {10.1042/bst0210817}, url = {ISI:A1993MN41200002}, keywords = {CELLS,Codon,CODONS,DIRECTIONAL SPECIFICITY,ESCHERICHIA-COLI,Frameshifting,GAMMA-SUBUNIT,gene,HUNGRY CODON,HUNGRY CODONS,MECHANISM,nosource,POLYMERASE-III HOLOENZYME,ribosome,RULES,sequence} } % == BibTeX quality report for gallantRibosomeFrameshiftingHungry1993a: % ? Title looks like it was stored in title-case in Zotero

@article{gallantLeftwardRibosomeFrameshifting1992a, title = {Leftward {{Ribosome Frameshifting}} at {{A Hungry Codon}}}, author = {Gallant, J.A. and Lindsley, D.}, year = 1992, month = jan, journal = {Journal of Molecular Biology}, volume = {223}, number = {1}, pages = {31–40}, doi = {10.1016/0022-2836(92)90713-T}, url = {ISI:A1992GZ96400006}, keywords = {CELLS,Codon,Frameshifting,HUNGRY CODON,nosource,ribosome,translation} } % == BibTeX quality report for gallantLeftwardRibosomeFrameshifting1992a: % ? Title looks like it was stored in title-case in Zotero

@article{galliePosttranscriptionalRegulationHigher1991, title = {Post-Transcriptional Regulation in Higher Eukaryotes: The Role of the Reporter Gene in Controlling Expression.}, author = {Gallie, D.R. and Feder, J.N. and Schimke, R.T. and Walbot, V.}, year = 1991, journal = {Molecular and General Genetics MGG}, volume = {288}, number = {1}, pages = {258–265}, publisher = {Springer}, doi = {10.1007/BF00282474}, url = {http://www.springerlink.com/index/L406410243T45V3G.pdf}, keywords = {expression,gene,in vitro translation,luciferase,mRNA,nosource,post-transcriptional regulation,regulation} } % == BibTeX quality report for galliePosttranscriptionalRegulationHigher1991: % ? unused Journal abbr (“Mol.Gen.Genet.”)

@article{gallieCapPolyTail1991, title = {The Cap and Poly ({{A}}) Tail Function Synergistically to Regulate {{mRNA}} Translational Efficiency.}, author = {Gallie, D.R.}, year = 1991, month = nov, journal = {Genes & development}, volume = {5}, number = {11}, pages = {2108–2116}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.5.11.2108}, url = {http://genesdev.cshlp.org/content/5/11/2108.short}, abstract = {The cap structure and the poly(A) tail are important regulatory determinants in establishing the translational efficiency of a messenger RNA. Although the mechanism by which either determinant functions remains poorly characterized, the interaction between the poly(A) tail-poly(A)-binding protein complex and events occurring at the 5’ terminus during translation initiation has been an intriguing possibility. In this report, the mutual dependence of the cap and the poly(A) tail was studied. Poly(A)+ and poly(A)- luciferase (Luc) mRNAs generated in vitro containing or lacking a cap were translated in vivo in tobacco protoplasts, Chinese hamster ovary cells, and yeast following delivery by electroporation. The poly(A) tail-mediated regulation of translational efficiency was wholly dependent on the cap for function. Moreover, cap function was enhanced over an order of magnitude by the presence of a poly(A) tail. The relative differences in stability between the mRNAs could not account for the synergism. The synergism between the cap and poly(A) tail was not observed in yeast cells in which active translation had been disrupted. In addition, the synergism was not observed in in vitro translation lysates. These data demonstrate that the cap and the poly(A) tail are interdependent for optimal function in vivo and suggest that communication between the two regulatory determinants may be important in establishing efficient translation}, keywords = {0,animal,Cap,CAP STRUCTURE,CELLS,Cho Cells,COMPLEX,COMPLEXES,efficiency,EFFICIENT TRANSLATION,Gene Expression Regulation,genetics,Hamsters,In Vitro,in vitro translation,IN-VITRO,IN-VIVO,initiation,Kinetics,La,luciferase,lysate,MECHANISM,MESSENGER-RNA,metabolism,mRNA,nosource,PlantsToxic,PLASMID,Plasmids,Poly A,poly(A),POLY(A) TAIL,protein,PROTEIN COMPLEX,PROTOPLASTS,regulation,Rna,Rna Caps,RNAMessenger,Saccharomyces cerevisiae,stability,structure,Tobacco,translation,TRANSLATION INITIATION,TranslationGenetic,yeast,YEAST-CELLS} } % == BibTeX quality report for gallieCapPolyTail1991: % ? unused Journal abbr (“Genes Dev.”)

@article{gallieTaleTwoTermini1998a, title = {A Tale of Two Termini: A Functional Interaction between the Termini of an {{mRNA}} Is a Prerequisite for Efficient Translation Initiation}, author = {Gallie, D.R.}, year = 1998, journal = {Gene}, volume = {216}, number = {1}, pages = {1–11}, doi = {10.1016/S0378-1119(98)00318-7}, url = {PM:9714706}, abstract = {A quarter of century following the prediction that mRNAs are translated in a circular form, recent biochemical and genetic evidence has accumulated to support the idea that communication between the termini of an mRNA is necessary to promote translation initiation. The poly(A)-binding protein (PABP) interacts with the cap-associated eukaryotic initiation factor (eIF) 4G (in yeast and plants) and eIF4B (in plants), a functional consequence of which is to increase the affinity of PABP for poly(A) and to increase the affinity of the cap-binding complex, eIF4F (of which eIF4G is a subunit) for the 5’ cap structure. In mammals, PABP interacts with a novel PABP-interacting protein that also binds eIF4A. The interaction between PABP and those initiation factors associated with the 5’ terminus of an mRNA may also explain the role of PABP during mRNA turnover, as it protects the 5’ cap from attack by Dcp1p, the decapping enzyme. Several of those mRNAs that have evolved functional equivalents to a cap or a poly(A) tail nevertheless require a functional interaction between terminal regulatory elements similar to that observed between the 5’ cap and poly(A) tail, suggesting that efficient translation is predicated on communication between largely-separated regulatory elements within an mRNA}, keywords = {0,animal,Cap,Cap binding,CAP STRUCTURE,CAP-BINDING COMPLEX,chemistry,COMPLEX,COMPLEXES,DECAPPING ENZYME,EFFICIENT TRANSLATION,ELEMENTS,enzyme,FORM,Genetic,genetics,initiation,INITIATION-FACTOR,La,Mammals,metabolism,mRNA,mRNA turnover,nosource,Nucleic Acid Conformation,Peptide Initiation Factors,Plants,poly(A),POLY(A) TAIL,POLY(A)-BINDING PROTEIN,Poly(A)-Binding Proteins,PREDICTION,protein,Protein Binding,Proteins,Review,Rna,Rna Caps,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAMessenger,structure,SUBUNIT,Support,supportu.s.gov’tnon-p.h.s.,translation,TRANSLATION INITIATION,TranslationGenetic,turnover,yeast} }

@article{gaoEvidenceThatUncharged1995a, title = {Evidence That Uncharged {{tRNA}} Can Inhibit a Programmed Translational Frameshift in {{Escherichia}} Coli}, author = {Gao, W. and Jakubowski, H. and Goldman, E.}, year = 1995, journal = {J.Mol Biol.}, volume = {251}, number = {2}, pages = {210–216}, doi = {10.1006/jmbi.1995.0428}, url = {PM:7643397}, abstract = {In the modified release factor 2 (RF2) programmed translational frameshift (with a sense codon replacing the wild-type in-frame UGA codon at the shift site), ribosomes shift +1 into the reading frame for an out-of-frame reporter fused to the frameshift sequence. Partitioning of ribosomes between the out-of-frame shift and in-frame reading depends on the codon at the shift site and on the levels of tRNA decoding the in-frame codon. Overexpression of a tRNA species cognate to the in-frame codon at the shift site significantly reduces the frequency of frame-shifting, presumably by facilitating in-frame reading, which would reduce production of the out-of-frame reporter. However, since overexpression of a tRNA increases levels of both charged and uncharged tRNA, it is possible that uncharged cognate tRNA might be able to reduce the frequency of the frameshift, by entering the A site on the ribosome. To test this, we manipulated charged and uncharged tRNA levels in vivo, using the tryptophan analog tryptophan hydroxamate, which increases the proportion of uncharged tRNA(Trp) by competing with cognate amino acid tryptophan for tryptophanyl-tRNA synthetase, thereby reducing protein synthesis. We report here that a slight but reproducible reduction in the relative frequency of the frameshift is observed when tryptophan hydroxamate is added to cells containing the modified RF2 shift with UGG (Trp codon) at the shift site. When tRNA(Trp) is overexpressed from another plasmid, the shift frequency drops three- to fourfold, as expected, however, this reduction is still seen in the presence of the analog. Thus, under conditions when most of the tRNA(Trp) is apparently uncharged, excess tRNA(Trp) still causes a significant reduction in the frameshift when UGG is at the shift site, providing evidence that uncharged cognate tRNA also can inhibit this frameshift}, keywords = {0,A SITE,A-SITE,ACID,Amino Acyl-tRNA Ligases,AMINO-ACID,analogs & derivatives,CELLS,Codon,decoding,drug effects,Escherichia coli,ESCHERICHIA-COLI,FRAME,frameshift,Frameshift Mutation,Frameshifting,Genetic,genetics,IN-VIVO,La,Ligases,metabolism,microbiology,MOLECULAR-GENETICS,Mutagenesis,nosource,OVEREXPRESSION,pharmacology,PLASMID,protein,protein synthesis,PROTEIN-SYNTHESIS,READING FRAME,RELEASE,release factor,ribosome,Ribosomes,Rna,RNATransferTrp,sequence,SITE,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,TranslationGenetic,tRNA,Tryptophan,WILD-TYPE} } % == BibTeX quality report for gaoEvidenceThatUncharged1995a: % ? Possibly abbreviated journal title J.Mol Biol.

@article{garciaDifferentialResponseFrameshift1993, title = {Differential {{Response}} to {{Frameshift Signals}} in {{Eukaryotic}} and {{Prokaryotic Translational Systems}}}, author = {Garcia, A. and Vanduin, J. and Pleij, C.W.A.}, year = 1993, month = feb, journal = {Nucleic Acids Research}, volume = {21}, number = {3}, pages = {401–406}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/21.3.401}, url = {http://nar.oxfordjournals.org/content/21/3/401.short}, abstract = {The genomic RNA of beet western yellows virus (BWYV) contains a potential translational frameshift signal in the overlap region of open reading frames ORF2 and ORF3. The signal, composed of a heptanucleotide slippery sequence and a downstream pseudoknot, is similar in appearance to those identified in retroviral RNAs. We have examined whether the proposed BWYV signal functions in frameshifting in three translational systems, i.c. in vitro in a reticulocyte lysate or a wheat germ extract and in vivo in E.coli. The efficiency of the signal in the eukaryotic system is low but significant, as it responds strongly to changes in either the slip sequence or the pseudoknot. In contrast, in E.coli there is hardly any response to the same changes. Replacing the slip sequence to the typical prokaryotic signal AAAAAAG yields more than 5% frameshift in E.coli. In this organism the frameshifting is highly sensitive to changes in the slip sequence but only slightly to disruption of the pseudoknot. The eukaryotic assay systems are barely sensitive to changes in either AAAAAAG or in the pseudoknot structure in this construct. We conclude that eukaryotic frameshift signals are not recognized by prokaryotes. On the other hand the typical prokaryotic slip sequence AAAAAAG does not lead to significant frameshifting in the eukaryote. In contrast to recent reports on the closely related potato leaf roll virus (PLRV) we show that the frameshifting in BWYV is pseudoknot-dependent}, keywords = {DISRUPTION,DOWNSTREAM,E.coli,efficiency,ESCHERICHIA-COLI,expression,FRAME,frameshift,Frameshifting,Gag,GAMMA-SUBUNIT,genomic,GENOMIC RNA,In Vitro,IN-VITRO,IN-VIVO,lysate,MAMMARY-TUMOR VIRUS,nosource,OPEN READING FRAME,Open Reading Frames,pol,POLYMERASE-III HOLOENZYME,PROKARYOTES,pseudoknot,pseudoknot structure,READING FRAME,Reading Frames,REGION,RETROVIRAL RNA,Rna,RNA PSEUDOKNOT,sequence,SIGNAL,structure,SYSTEM,SYSTEMS,virus,Wheat} } % == BibTeX quality report for garciaDifferentialResponseFrameshift1993: % ? Title looks like it was stored in title-case in Zotero

@article{gardonyiStreptomycesRubiginosusXylose2003b, title = {The ⬚{{Streptomyces}} Rubiginosus⬚ Xylose Isomerase Is Misfolded When Expressed in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Gardonyi, M. and {Hahn-Hagerdal}, B.}, year = 2003, journal = {Enzyme Microbial Technology}, volume = {32⬚ ⬚}, pages = {252–259}, doi = {10.1016/S0141-0229(02)00285-5}, keywords = {CEREVISIAE,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Streptomyces,Xylose} }

@article{garfinkelTransposonTaggingUsing1988, title = {Transposon Tagging Using {{Ty}} Elements in Yeast.}, author = {Garfinkel, D.J. and Mastrangelo, M.F. and Sanders, N.J. and Shafer, B.K. and Strathern, J.N.}, year = 1988, journal = {Genetics}, volume = {120}, number = {1}, pages = {95–108}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/120.1.95}, url = {http://www.genetics.org/content/120/1/95.short}, keywords = {ELEMENTS,nosource,Ty,yeast} }

@article{garfinkelProteolyticProcessingPolTYB1991, title = {Proteolytic Processing of Pol-{{TYB}} Proteins from the Yeast Retrotransposon {{Ty1}}.}, author = {Garfinkel, D.J. and Hedge, A.M. and Youngren, S.D. and Copeland, T.D.}, year = 1991, journal = {Journal of virology}, volume = {65}, number = {9}, pages = {4573–4581}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.65.9.4573-4581.1991}, url = {http://jvi.asm.org/cgi/content/abstract/65/9/4573}, abstract = {Using antibodies directed against the TYB1 protein of the transpositionally competent retrotransposon Ty1-H3, we have identified three mature proteins of 23, 60, and 90 kDa and processing intermediates of 140 and 160 kDa that are derived from the 190-kDa TYA1-TYB1 polyprotein. Mature proteins and variable amounts of the precursors cofractionate with Ty viruslike particles. The map locations and precursor-product relationships of mature TYB1 polypeptides suggest that p23 is Ty1 protease, p90 is integrase, and p60 contains reverse transcriptase and RNase H. Immunoprecipitation and immunoblot analyses of Ty1 proteins show that p190 is cleaved to form p160. The p160 intermediate is cleaved to form p23 and p140, and p140 is cleaved to form p90 and p60. Processing of TYB1 proteins is dependent on Ty1 protease. Immunoblot analysis of TYB proteins from different Ty1 isolates reveal that correct processing of TYB1 proteins is a characteristic of functional Ty1 elements, whereas aberrant processing is a common defect found in transposition-incompetent elements}, keywords = {91332996,Amino Acid Sequence,analysis,Antibodies,antibody,cancer,chemistry,CloningMolecular,development,DNA Nucleotidyltransferases,DNA Transposable Elements,ELEMENTS,Endopeptidases,Endoribonucleases,GenesStructuralFungal,genetics,Immunologic Techniques,immunology,metabolism,Molecular Sequence Data,Molecular Weight,nosource,Peptides,protein,Protein ProcessingPost-Translational,Proteins,Recombinant Fusion Proteins,retrotransposon,RNA-Directed DNA Polymerase,RNAse,Saccharomyces cerevisiae,supportu.s.gov’tp.h.s.,Ty,Ty1,yeast} } % == BibTeX quality report for garfinkelProteolyticProcessingPolTYB1991: % ? unused Journal abbr (“J.Virol.”)

@article{garlapatiIdentificationNovelInternal2004, title = {Identification of a Novel Internal Ribosome Entry Site in Giardiavirus That Extends to Both Sides of the Initiation Codon}, author = {Garlapati, S. and Wang, C.C.}, year = 2004, month = jan, journal = {Journal of Biological Chemistry}, volume = {279}, number = {5}, pages = {3389–3397}, publisher = {ASBMB}, doi = {10.1074/jbc.M307565200}, url = {http://www.jbc.org/content/279/5/3389.short}, abstract = {In Giardia lamblia, enhanced translation of luciferase mRNA, flanked between the 5’-untranslated region (UTR) and 3 ‘-end of giardiavirus transcript, requires the presence of the initial 264-nucleotide (nt) viral capsid-coding region. By introducing the transcripts of dicistronic viral constructs into Giardia, we demonstrated that the 264-nt downstream region alone is insufficient to function as an internal ribosome entry site (IRES) without including a portion of the 5’-UTR as well. Deletion analysis showed that efficient internal initiation requires the last 253 nts (nts 114-367) of the 5 ‘-UTR in combination with the downstream 264 nts. Specific mutations that disrupted the predicted secondary structural elements in either the 5’-UTR or the 264-nt capsid-coding region completely abolished the IRES-mediated translation of downstream cistron, suggesting that the IRES activity requires the presence of these structures in both regions. Mutations that abolished translation of the first cistron did not, however, affect the IRES-mediated translation of the second cistron, indicating that this IRES-mediated translation is independent of the translation of the upstream cistron. This is, to our knowledge, the first reported identification of a viral IRES with an estimated size of 517 nts that extends to both sides of the initiation site}, keywords = {0,3,5’ Untranslated Regions,analysis,Base Sequence,Binding Sites,BlottingNorthern,chemistry,Codon,CodonInitiator,Dna,DNAComplementary,DOWNSTREAM,ELEMENTS,Gene Deletion,Genetic,Genetic Vectors,genetics,GIARDIA-LAMBLIA,Giardiavirus,IDENTIFICATION,initiation,INITIATION SITE,INTERNAL RIBOSOME ENTRY,La,LAMBLIA,luciferase,metabolism,ModelsGenetic,Molecular Sequence Data,mRNA,MutagenesisSite-Directed,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,PLASMID,Plasmids,REGION,REQUIRES,ribosome,RIBOSOME ENTRY SITE,Ribosomes,Rna,RNAMessenger,SITE,Structural,structure,supportu.s.gov’tp.h.s.,TRANSCRIPT,TranscriptionGenetic,Transfection,translation,TranslationGenetic,Untranslated Regions,UPSTREAM,vector,vectors} } % == BibTeX quality report for garlapatiIdentificationNovelInternal2004: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{garrodIncidenceAlkaptonuriaStudy1902, title = {The Incidence of Alkaptonuria: {{A}} Study in Clinical Individuality.}, author = {Garrod, A.E.}, year = 1902, journal = {Lancet}, volume = {2}, pages = {1616–1620}, doi = {10.1016/S0140-6736(01)41972-6}, keywords = {enzyme,gene,genetics,nosource,protein} }

@article{gasparTranslationInitiationFactor1994, title = {Translation Initiation Factor {{eIF-2}}. {{Cloning}} and Expression of the Human {{cDNA}} Encoding the Gamma-Subunit.}, author = {Gaspar, N.J. and Kinzy, T.G. and Scherer, B.J. and Humbelin, M. and Hershey, J.W. and Merrick, W.C.}, year = 1994, month = feb, journal = {Journal of Biological Chemistry}, volume = {269}, number = {5}, pages = {3415–3422}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(17)41878-3}, url = {http://www.jbc.org/content/269/5/3415.short}, keywords = {Antibodies,antibody,BINDING,BINDING-PROTEIN,cloning,COMPLEX,COMPLEXES,CROSS-LINKING,Dna,EFTu,ELEMENTS,expression,GAMMA-SUBUNIT,GTP,homolog,human,initiation,library,nosource,protein,Proteins,RIBOSOMAL-SUBUNIT,sequence,SUBUNIT,Transfection,translation,TRANSLATION INITIATION,yeast} }

@article{gaudinStructureRNASignal2005, title = {Structure of the {{RNA}} Signal Essential for Translational Frameshifting in {{HIV-1}}}, author = {Gaudin, C. and Mazauric, M.H. and Traikia, M. and Guittet, E. and Yoshizawa, S. and Fourmy, D.}, year = 2005, month = jun, journal = {Journal of molecular biology}, volume = {349}, number = {5}, pages = {1024–1035}, publisher = {Elsevier}, doi = {10.1016/j.jmb.2005.04.045}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283605004663}, abstract = {Many pathogenic viruses use a programmed -1 translational frameshifting mechanism to regulate synthesis of their structural and enzymatic proteins. Frameshifting is vital for viral replication. A slippery sequence bound at the ribosomal A and P sites as well as a downstream stimulatory RNA structure are essential for frameshifting. Conflicting data have been reported concerning the structure of the downstream RNA signal in human immunodeficiency virus type 1 (HIV-1). Here, the solution structure of the HIV-1 frameshifting RNA signal was solved by heteronuclear NMR spectroscopy. This structure reveals a long hairpin fold with an internal three-nucleotide bulge. The internal loop introduces a bend between the lower and upper helical regions, a structural feature often seen in frameshifting pseudoknots. The NMR structure correlates with chemical probing data. The upper stem rich in conserved G-C Watson-Crick base-pairs is highly stable, whereas the bulge region and the lower stem are more flexible}, keywords = {0,Base Composition,Base Sequence,BASE-PAIR,chemistry,DOWNSTREAM,Frameshifting,FrameshiftingRibosomal,genetics,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,Humans,IMMUNODEFICIENCY-VIRUS,La,LOOP,MECHANISM,Molecular Sequence Data,NMR,NMR-SPECTROSCOPY,nosource,Nuclear Magnetic ResonanceBiomolecular,Nucleic Acid Conformation,P SITE,P-SITE,P-SITES,protein,Protein Biosynthesis,Proteins,pseudoknot,pseudoknots,REGION,REPLICATION,Research SupportNon-U.S.Gov’t,Ribosomes,Rna,RnaViral,sequence,SIGNAL,SITE,SITES,SPECTROSCOPY,Structural,structure,TRANSLATIONAL FRAMESHIFTING,TYPE-1,virus,Viruses} } % == BibTeX quality report for gaudinStructureRNASignal2005: % ? unused Journal abbr (“J.Mol.Biol.”)

@article{gaurenteYeastPromotersLacZ1983, title = {Yeast Promoters and ⬚{{lacZ}}⬚ Fusions Designed to Study Expression of Cloned Genes in Yeast.}, author = {Gaurente, L.}, year = 1983, journal = {Met.Enzymol.}, volume = {101}, pages = {181–191}, doi = {10.1016/0076-6879(83)01013-7}, keywords = {expression,gene,Genes,nosource,yeast} } % == BibTeX quality report for gaurenteYeastPromotersLacZ1983: % ? Possibly abbreviated journal title Met.Enzymol.

@article{gautschiRACStableRibosomeassociated2001, title = {{{RAC}}, a Stable Ribosome-Associated Complex in Yeast Formed by the {{DnaK-DnaJ}} Homologs {{Ssz1p}} and Zuotin}, author = {Gautschi, M. and Lilie, H. and Funfschilling, U. and Mun, A. and Ross, S. and Lithgow, T. and Rucknagel, P. and Rospert, S.}, year = 2001, month = mar, journal = {Proceedings of the National Academy of Sciences}, volume = {98}, number = {7}, pages = {3762–3767}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.071057198}, url = {http://www.pnas.org/content/98/7/3762.short}, abstract = {The yeast cytosol contains multiple homologs of the DnaK and DnaJ chaperone family. Our current understanding of which homologs functionally interact is incomplete. Zuotin is a DnaJ homolog bound to the yeast ribosome. We have now identified the DnaK homolog Ssz1p/Pdr13p as zuotin’s partner chaperone. Zuotin and Ssz1p form a ribosome-associated complex (RAC) that is bound to the ribosome via the zuotin subunit. RAC is unique among the eukaryotic DnaK-DnaJ systems, as the 1:1 complex is stable, even in the presence of ATP or ADP. In vitro, RAC stimulates the translocation of a ribosome-bound mitochondrial precursor protein into mitochondria, providing evidence for its chaperone-like effect on nascent chains. In agreement with the existence of a functional complex, deletion of each RAC subunit resulted in a similar phenotype in vivo. However, overexpression of zuotin partly rescued the growth defect of the Delta ssz1 strain, whereas overexpression of Ssz1p did not affect the Delta zuo1 strain, suggesting a pivotal function for the DnaJ homolog}, keywords = {0,analysis,ATP,CEREVISIAE,chemistry,COMPLEX,COMPLEXES,Cytosol,Dimerization,DNA-BINDING,DNA-Binding Proteins,DNAJ HOMOLOG,E,enzymology,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,FAMILY,FORM,Fungal Proteins,GROWTH,HEAT-SHOCK,HEAT-SHOCK PROTEINS,Heat-Shock Proteins 70,homolog,In Vitro,IN-VITRO,IN-VIVO,isolation & purification,La,mitochondria,Molecular Chaperones,nosource,OVEREXPRESSION,Phenotype,physiology,PRECURSOR,PRECURSOR PROTEIN,protein,Protein Folding,Proteins,Research SupportNon-U.S.Gov’t,ribosome,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SUBUNIT,SYSTEM,SYSTEMS,translocation,yeast} } % == BibTeX quality report for gautschiRACStableRibosomeassociated2001: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{gautschiFunctionalChaperoneTriad2002, title = {A Functional Chaperone Triad on the Yeast Ribosome}, author = {Gautschi, M. and Mun, A. and Ross, S. and Rospert, S.}, year = 2002, month = apr, journal = {Proc.Natl.Acad.Sci.U.S.A}, volume = {99}, number = {7}, pages = {4209–4214}, doi = {10.1073/pnas.062048599}, url = {PM:11929994}, abstract = {The chaperones RAC (ribosome-associated complex), consisting of Ssz1p and zuotin, and Ssb1/2p are associated with ribosomes of yeast. Ssb1/2p was previously shown to form a crosslink product to polypeptides trapped in ribosome-nascent chain complexes (RNCs) in vitro. Here we show that an efficient crosslink of the nascent chain to Ssb1/2p depends on the presence of functional RAC. The crosslink to Ssb1/2p was significantly diminished if (i) RAC was removed from RNCs: a process reversed by addition of purified RAC; (ii) RAC carried a mutation in the J-domain of zuotin, leading to its inactivation in vivo; (iii) RAC’s Ssz1p subunit was absent because RNCs were generated in a Deltassz1-derived translation extract. In vivo the same specific set of growth defects caused by the absence of any of the three chaperones was also displayed by a Deltassb1/2Deltassz1Deltazuo1 strain. The combination of in vitro and in vivo data supports a model in which Ssb1/2p, Ssz1p, and zuotin act in concert on nascent chains while they are being synthesized}, keywords = {0,CEREVISIAE,chemistry,COMPLEX,COMPLEXES,DNA-BINDING,DNA-Binding Proteins,enzymology,FORM,Fungal Proteins,genetics,GROWTH,HEAT-SHOCK,HEAT-SHOCK PROTEINS,Heat-Shock Proteins 70,In Vitro,IN-VITRO,IN-VIVO,La,metabolism,MODEL,Molecular Chaperones,Mutation,nosource,physiology,POLYPEPTIDE,POLYPEPTIDES,PRODUCT,protein,Protein Folding,Proteins,Research SupportNon-U.S.Gov’t,ribosome,Ribosomes,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Schizosaccharomyces,Schizosaccharomyces pombe Proteins,SUBUNIT,Support,translation,yeast} } % == BibTeX quality report for gautschiFunctionalChaperoneTriad2002: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.U.S.A

@article{gavinFunctionalOrganizationYeast2002, title = {Functional Organization of the Yeast Proteome by Systematic Analysis of Protein Complexes}, author = {Gavin, A.C. and Bosche, M. and Krause, R. and Grandi, P. and Marzioch, M. and Bauer, A. and Schultz, J. and Rick, J.M. and Michon, A.M. and Cruciat, C.M. and Remor, M. and Hofert, C. and Schelder, M. and Brajenovic, M. and Ruffner, H. and Merino, A. and Klein, K. and Hudak, M. and Dickson, D. and Rudi, T. and Gnau, V. and Bauch, A. and Bastuck, S. and Huhse, B. and Leutwein, C. and Heurtier, M.A. and Copley, R.R. and Edelmann, A. and Querfurth, E. and Rybin, V. and Drewes, G. and Raida, M. and Bouwmeester, T. and Bork, P. and Seraphin, B. and Kuster, B. and Neubauer, G. and {Superti-Furga}, G.}, year = 2002, month = jan, journal = {Nature}, volume = {415}, number = {6868}, pages = {141–147}, publisher = {Nature Publishing Group}, doi = {10.1038/415141a}, url = {http://www.nature.com/nature/journal/v415/n6868/full/415141a.html?free=2}, abstract = {Most cellular processes are carried out by multiprotein complexes. The identification and analysis of their components provides insight into how the ensemble of expressed proteins (proteome) is organized into functional units. We used tandem-affinity purification (TAP) and mass spectrometry in a large-scale approach to characterize multiprotein complexes in Saccharomyces cerevisiae. We processed 1,739 genes, including 1,143 human orthologues of relevance to human biology, and purified 589 protein assemblies. Bioinformatic analysis of these assemblies defined 232 distinct multiprotein complexes and proposed new cellular roles for 344 proteins, including 231 proteins with no previous functional annotation. Comparison of yeast and human complexes showed that conservation across species extends from single proteins to their molecular environment. Our analysis provides an outline of the eukaryotic proteome as a network of protein complexes at a level of organization beyond binary interactions. This higher-order map contains fundamental biological information and offers the context for a more reasoned and informed approach to drug discovery}, keywords = {0,analysis,assembly,BIOLOGY,CellsCultured,CEREVISIAE,chemistry,ChromatographyAffinity,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,DISCOVERY,FUSION PROTEIN,gene,Gene Targeting,Genes,genetics,Germany,human,Humans,IDENTIFICATION,INFORMATION,isolation & purification,La,Macromolecular Substances,Multiprotein Complexes,nosource,ORGANIZATION,physiology,protein,PROTEIN COMPLEX,Proteins,Proteome,purification,Recombinant Fusion Proteins,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Sensitivity and Specificity,Species Specificity,SpectrometryMassMatrix-Assisted Laser Desorption-Ionization,UNITS,yeast} }

@article{geiduschekTranscriptionRNAPolymerase1988, title = {Transcription by {{RNA}} Polymerase {{III}}}, author = {Geiduschek, E.P. and {Tocchini-Valentini}, G.P.}, year = 1988, journal = {Annual review of biochemistry}, volume = {57:873-914}, number = {1}, pages = {873–914}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, doi = {10.1146/annurev.bi.57.070188.004301}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.bi.57.070188.004301}, keywords = {89024592,animal,DNA-Directed RNA Polymerase,genetics,La,nosource,polymerase,Rna,RNA Polymerase III,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,transcription,TranscriptionGenetic} } % == BibTeX quality report for geiduschekTranscriptionRNAPolymerase1988: % ? unused Journal abbr (“Annu.Rev.Biochem.”)

@article{gendronVirionassociatedGagPolDecreased2005, title = {The Virion-Associated {{Gag-Pol}} Is Decreased in Chimeric {{Moloney}} Murine Leukemia Viruses in Which the Readthrough Region Is Replaced by the Frameshift Region of the Human Immunodeficiency Virus Type 1}, author = {Gendron, K. and Dulude, D. and Lemay, G. and Ferbeyre, G. and {Brakier-Gingras}, L.}, year = 2005, month = apr, journal = {Virology}, volume = {334}, number = {2}, pages = {342–352}, publisher = {Elsevier}, doi = {10.1016/j.virol.2005.01.044}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0042-6822(05)00094-2}, abstract = {The human immunodeficiency virus type 1 (HIV-1) requires a programmed -1 translational frameshift event to synthesize the precursor of its enzymes, Gag-Pol, when ribosomes from the infected cells translate the full-length viral messenger RNA. Translation of the same RNA according to conventional translational rules produces Gag, the precursor of the structural proteins of the virus. The efficiency of the frameshift controls the ratio of Gag-Pol to Gag, which is critical for viral infectivity. The Moloney murine leukemia virus (MoMuLV) uses a different strategy, the programmed readthrough of a stop codon, to synthesize Gag-Pol. In this study, we investigated whether different forms of the HIV-1 frameshift region can functionally replace the readthrough signal in MoMuLV. Chimeric proviral DNAs were obtained by inserting into the MoMuLV genome the HIV-1 frameshift region encompassing the slippery sequence where the frameshift occurs, followed by the frameshift stimulatory signal. The inserted signal was either a simple stem-loop, previously considered as the stimulatory signal, or a longer bulged helix, now shown to be the complete stimulatory signal, or a mutated version of the complete signal with a three-nucleotide deletion. Although the three chimeric viruses can propagate essentially as the wild-type virus in NIH 3T3 cells, single-round infectivity assays revealed that the infectivity of the chimeric virions is about three to fivefold lower than that of the wild-type virions, depending upon the nature of the frameshift signal. It was also observed that the Gag-Pol to Gag ratio was decreased about two to threefold in chimeric virions. Comparison of the readthrough efficiency of MoMuLV to the HIV-1 frameshift efficiency, by monitoring the expression of a luciferase reporter in cultured cells, revealed that the frameshift efficiencies were only 30-60% of the readthrough efficiency. Altogether, these observations indicate that replacement of the readthrough region of MoMuLV with the frameshift region of HIV-1 results in virions that are replication competent, although less infectious than wild-type MoMuLV. This type of chimera could provide an interesting tool for in vivo studies of novel drugs targeted against the HIV-1 frameshift event}, keywords = {0,3T3 Cells,Animals,assays,Base Sequence,Cell Line,CELLS,chemistry,Chimera,Chimeric Proteins,Codon,Dna,drugs,efficiency,enzyme,Enzymes,expression,FORM,frameshift,FrameshiftingRibosomal,FUSION PROTEIN,Fusion Proteinsgag-pol,Gag,Gag-pol,Gene Expression RegulationViral,Genesgag,Genespol,genetics,Genome,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,Humans,IMMUNODEFICIENCY-VIRUS,IN-VIVO,INFECTED CELLS,INFECTED-CELLS,La,LEUKEMIA,luciferase,MESSENGER-RNA,metabolism,Mice,Molecular Sequence Data,Moloney murine leukemia virus,Nih 3T3 Cells,nosource,pathogenicity,PRECURSOR,protein,Proteins,readthrough,REGION,REPLICATION,REQUIRES,Research SupportNon-U.S.Gov’t,ribosome,Ribosomes,Rna,RULES,sequence,SIGNAL,STEM-LOOP,STOP CODON,Structural,translation,TYPE-1,VIRAL INFECTIVITY,Virion,VIRIONS,virus,Virus Replication,Viruses,WILD-TYPE} }

@article{gentryStepwiseExposureStaphylococcus2007, title = {Stepwise Exposure of {{Staphylococcus}} Aureus to Pleuromutilins Is Associated with Stepwise Acquisition of Mutations in {{rplC}} and Minimally Affects Susceptibility to Retapamulin}, author = {Gentry, D.R. and Rittenhouse, S.F. and McCloskey, L. and Holmes, D.J.}, year = 2007, month = jun, journal = {Antimicrob.Agents Chemother.}, volume = {51}, number = {6}, pages = {2048–2052}, doi = {10.1128/AAC.01066-06}, url = {PM:17404009}, abstract = {To assess their effects on susceptibility to retapamulin in Staphylococcus aureus, first-, second-, and third-step mutants with elevated MICs to tiamulin and other investigational pleuromutilin compounds were isolated and characterized through exposure to high drug concentrations. All first- and second-step mutations were in rplC, encoding ribosomal protein L3. Most third-step mutants acquired a third mutation in rplC. While first- and second-step mutations did cause an elevation in tiamulin and retapamulin MICs, a significant decrease in activity was not seen until a third mutation was acquired. All third-step mutants exhibited severe growth defects, and faster-growing variants arose at a high frequency from most isolates. These faster-growing variants were found to be more susceptible to pleuromutilins. In the case of a mutant with three alterations in rplC, the fast-growing variants acquired an additional mutation in rplC. In the case of fast-growing variants of isolates with two mutations in rplC and at least one mutation at an unmapped locus, one of the two rplC mutations reverted to wild type. These data indicate that mutations in rplC that lead to pleuromutilin resistance have a direct, negative effect on fitness. While reduction in activity of retapamulin against S. aureus can be seen through mutations in rplC, it is likely that target-specific resistance to retapamulin will be slow to emerge due to the need for three mutations for a significant effect on activity and the fitness cost of each mutational step}, keywords = {GROWTH,L3,La,MUTANTS,Mutation,MUTATIONS,nosource,protein,RESISTANCE,RIBOSOMAL-PROTEIN,S,STAPHYLOCOCCUS-AUREUS,tiamulin,WILD-TYPE} } % == BibTeX quality report for gentryStepwiseExposureStaphylococcus2007: % ? Possibly abbreviated journal title Antimicrob.Agents Chemother.

@article{gerbasiMyotonicDystrophyType2007, title = {The Myotonic Dystrophy Type 2 Protein {{ZNF9}} Is Part of an {{ITAF}} Complex That Promotes Cap-Independent Translation}, author = {Gerbasi, V.R. and Link, A.J.}, year = 2007, month = jun, journal = {Mol Cell Proteomics.}, volume = {6}, number = {6}, pages = {1049–1058}, doi = {10.1074/mcp.M600384-MCP200}, url = {PM:17327219}, abstract = {The 5’-untranslated region of the ornithine decarboxylase (ODC) mRNA contains an internal ribosomal entry site (IRES). Mutational analysis of the ODC IRES has led to the identification of sequences necessary for cap-independent translation of the ODC mRNA. To discover novel IRES trans-acting factors (ITAFs), we performed a proteomics screen for proteins that regulate ODC translation using the wild-type ODC mRNA and a mutant version with an inactive IRES. We identified two RNA-binding proteins that associate with the wild-type ODC IRES but not the mutant IRES. One of these RNA-binding proteins, PCBP2, is an established activator of viral and cellular IRESs. The second protein, ZNF9 (myotonic dystrophy type 2 protein), has not been shown previously to bind IRES-like elements. Using a series of biochemical assays, we validated the interaction of these proteins with ODC mRNA. Interestingly ZNF9 and PCBP2 biochemically associated with each other and appeared to function as part of a larger holo-ITAF ribonucleoprotein complex. Our functional studies showed that PCBP2 and ZNF9 stimulate translation of the ODC IRES. Importantly these results may provide insight into the normal role of ZNF9 and why ZNF9 mutations cause myotonic dystrophy}, keywords = {0,ACID,analysis,assays,biosynthesis,Cap,CAP-INDEPENDENT TRANSLATION,Cell Line,CentrifugationDensity Gradient,COMPLEX,COMPLEXES,ELEMENTS,genetics,human,Humans,IDENTIFICATION,immunology,INTERNAL RIBOSOMAL ENTRY,internal ribosomal entry site,isolation & purification,La,metabolism,microbiology,mRNA,Multiprotein Complexes,Mutation,MUTATIONAL ANALYSIS,MUTATIONS,nosource,Ornithine Decarboxylase,protein,Protein Binding,Protein Biosynthesis,Protein Transport,Proteins,Proteomics,REGION,Regulatory SequencesRibonucleic Acid,RIBONUCLEIC-ACID,RIBONUCLEOPROTEIN,Ribonucleoproteins,Ribosomes,Rna,Rna Caps,RNA-Binding Proteins,RNA-BINDING-PROTEIN,sequence,SEQUENCES,SERIES,SITE,Support,TRANS-ACTING FACTORS,translation,WILD-TYPE} } % == BibTeX quality report for gerbasiMyotonicDystrophyType2007: % ? Possibly abbreviated journal title Mol Cell Proteomics.

@incollection{gerbiExpansionSegmentRegions1996, title = {Expansion Segment: Regions of Variable Size That Interrupt the Universal Core Secondary Structure of Ribosomal {{RNA}}.}, booktitle = {Ribosomal {{RNA}}: Structure, Evolution, Processing, and Function in Protein Synthesis.}, author = {Gerbi, S.A.}, year = 1996, pages = {71–87}, publisher = {CRC Press}, address = {New York}, collaborator = {Zimmermann, R.A. and Dahlberg, A.E.}, keywords = {Evolution,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,RIBOSOMAL-RNA,Rna,structure} }

@article{gerlandForceinducedDenaturationRNA2001, title = {Force-Induced Denaturation of {{RNA}}}, author = {Gerland, U. and Bundschuh, R. and Hwa, T.}, year = 2001, journal = {Biophysical Journal}, volume = {81}, number = {3}, pages = {1324–1332}, publisher = {Elsevier}, doi = {10.1016/S0006-3495(01)75789-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/S000634950175789X}, abstract = {We quantitatively describe an RNA molecule under the influence of an external force exerted at its two ends as in a typical single-molecule experiment. Our calculation incorporates the interactions between nucleotides by using the experimentally determined free energy rules for RNA secondary structure and models the polymeric properties of the exterior single-stranded regions explicitly as elastic freely jointed chains. We find that despite complicated secondary structures, force-extension curves are typically smooth in quasi-equilibrium. We identify and characterize two sequence/structure-dependent mechanisms that, in addition to the sequence-independent entropic elasticity of the exterior single-stranded regions, are responsible for the smoothness. These involve compensation between different structural elements on which the external force acts simultaneously and contribution of suboptimal structures, respectively. We estimate how many features a force-extension curve recorded in nonequilibrium, where the pulling proceeds faster than rearrangements in the secondary structure of the molecule, could show in principle. Our software is available to the public through an “RNA-pulling server.”}, keywords = {Biomechanics,Biopolymers,chemistry,Computer Simulation,elasticity,ELEMENTS,La,MECHANISM,MECHANISMS,metabolism,models,ModelsChemical,nosource,Nucleic Acid Conformation,Nucleic Acid Denaturation,Nucleotides,Rna,RULES,Software,Structural,structure,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,Thermodynamics} } % == BibTeX quality report for gerlandForceinducedDenaturationRNA2001: % ? unused Journal abbr (“Biophys.J.”)

@article{gersaLabileProteinsPlay1992, title = {Labile Proteins Play a Dual Role in the Control of Endothelial Leukocyte Adhesion Molecule-1 ({{ELAM-1}}) Gene Regulation.}, author = {Gersa, P. and {Hooft van Huijsduijnen}, R. and Whelan, J. and DeLamarter, J.F.}, year = 1992, journal = {Journal of Biological Chemistry}, volume = {267}, number = {27}, pages = {19226–19232}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(18)41765-6}, url = {http://www.jbc.org/content/267/27/19226.short}, keywords = {anisomycin,gene,mRNA,nosource,protein,Proteins,regulation} } % == BibTeX quality report for gersaLabileProteinsPlay1992: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{gestelandRecodingDynamicReprogramming1996, title = {Recoding: {{Dynamic}} Reprogramming of Translation.}, author = {Gesteland, R.F. and Atkins, J.F.}, year = 1996, month = jan, journal = {Annual review of biochemistry}, volume = {65}, number = {1}, eprint = {8811194}, eprinttype = {pubmed}, pages = {741–768}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, issn = {0066-4154/96/0701-0741}, doi = {10.1146/annurev.bi.65.070196.003521}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8811194 http://www.annualreviews.org/doi/abs/10.1146/annurev.bi.65.070196.003521}, abstract = {A minority of genes in probably all organisms rely on “recoding” for translation of their mRNAs. In these cases, the rules for decoding are temporarily altered through the action of specific signals built into the mRNA sequences. Three classes are described. 1. Frameshifting at a particular site allows expression of a protein from an mRNA with overlapping open reading frames, often giving two protein products from one mRNA. 2. The meanings of code words are altered: specific stop codons can be redirected to encode selenocysteine, tryptophan, or glutamine. 3. Ribosomes can translate over coding gaps in mRNA. These novel mechanisms expand the repertoire of the genetic code and are at the heart of several regulatory schemes.}, pmid = {8811194}, keywords = {Animals,Biological Evolution,Codon,Frameshifting,Messenger,Messenger: genetics,nosource,Protein Biosynthesis,recoding,Review,RNA,translation} } % == BibTeX quality report for gestelandRecodingDynamicReprogramming1996: % ? unused Journal abbr (“Annu.Rev.Biochem.”)

@article{ghaemmaghamiGlobalAnalysisProtein2003a, title = {Global Analysis of Protein Expression in Yeast}, author = {Ghaemmaghami, S. and Huh, W.K. and Bower, K. and Howson, R.W. and Belle, A. and Dephoure, N. and O’Shea, E.K. and Weissman, J.S.}, year = 2003, month = oct, journal = {Nature}, volume = {425}, number = {6959}, pages = {737–741}, doi = {10.1038/nature02046}, url = {http://biotecnologie.unipr.it/didattica/att/b9ef.file.pdf PM:14562106}, abstract = {The availability of complete genomic sequences and technologies that allow comprehensive analysis of global expression profiles of messenger RNA have greatly expanded our ability to monitor the internal state of a cell. Yet biological systems ultimately need to be explained in terms of the activity, regulation and modification of proteins–and the ubiquitous occurrence of post-transcriptional regulation makes mRNA an imperfect proxy for such information. To facilitate global protein analyses, we have created a Saccharomyces cerevisiae fusion library where each open reading frame is tagged with a high-affinity epitope and expressed from its natural chromosomal location. Through immunodetection of the common tag, we obtain a census of proteins expressed during log-phase growth and measurements of their absolute levels. We find that about 80% of the proteome is expressed during normal growth conditions, and, using additional sequence information, we systematically identify misannotated genes. The abundance of proteins ranges from fewer than 50 to more than 10(6) molecules per cell. Many of these molecules, including essential proteins and most transcription factors, are present at levels that are not readily detectable by other proteomic techniques nor predictable by mRNA levels or codon bias measurements}, keywords = {0,analysis,BlottingWestern,CEREVISIAE,chemistry,Codon,Computational Biology,epitope,Epitopes,expression,FRAME,FUSION PROTEIN,gene,Gene Expression Profiling,Genes,genetics,GenomeFungal,genomic,GROWTH,growth & development,IDENTIFY,INFORMATION,La,library,LOCATION,MESSENGER-RNA,metabolism,modification,mRNA,nosource,OPEN READING FRAME,Open Reading Frames,post-transcriptional regulation,POSTTRANSCRIPTIONAL REGULATION,protein,Proteins,Proteome,Proteomics,READING FRAME,Recombinant Fusion Proteins,regulation,Rna,RNAFungal,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,Support,SYSTEM,SYSTEMS,techniques,transcription,TRANSCRIPTION FACTOR,Transcription Factors,yeast} }

@article{ghoshNonbridgingPhosphateOxygens2005, title = {Nonbridging Phosphate Oxygens in {{16S rRNA}} Important for {{30S}} Subunit Assembly and Association with the {{50S}} Ribosomal Subunit}, author = {Ghosh, S. and Joseph, S.}, year = 2005, month = may, journal = {RNA.}, volume = {11}, number = {5}, pages = {657–667}, publisher = {Cold Spring Harbor Lab}, doi = {10.1261/rna.7224305}, url = {http://rnajournal.cshlp.org/content/11/5/657.short}, abstract = {Ribosomes are composed of RNA and protein molecules that associate together to form a supramolecular machine responsible for protein biosynthesis. Detailed information about the structure of the ribosome has come from the recent X-ray crystal structures of the ribosome and the ribosomal subunits. However, the molecular interactions between the rRNAs and the r-proteins that occur during the intermediate steps of ribosome assembly are poorly understood. Here we describe a modification-interference approach to identify nonbridging phosphate oxygens within 16S rRNA that are important for the in vitro assembly of the Escherichia coli 30S small ribosomal subunit and for its association with the 50S large ribosomal subunit. The 30S small subunit was reconstituted from phosphorothioate-substituted 16S rRNA and small subunit proteins. Active 30S subunits were selected by their ability to bind to the 50S large subunit and form 70S ribosomes. Analysis of the selected population shows that phosphate oxygens at specific positions in the 16S rRNA are important for either subunit assembly or for binding to the 50S subunit. The X-ray crystallographic structures of the 30S subunit suggest that some of these phosphate oxygens participate in r-protein binding, coordination of metal ions, or for the formation of intersubunit bridges in the mature 30S subunit. Interestingly, however, several of the phosphate oxygens identified in this study do not participate in any interaction in the mature 30S subunit, suggesting that they play a role in the early steps of the 30S subunit assembly}, keywords = {0,16S,16s rrna,30s subunit,70S RIBOSOME,analysis,assembly,ASSOCIATION,Bacterial,BINDING,Biochemistry,biosynthesis,chemistry,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,ElectrophoresisGelTwo-Dimensional,Escherichia coli,ESCHERICHIA-COLI,FORM,genetics,IDENTIFY,In Vitro,IN-VITRO,INFORMATION,INTERMEDIATE,Ions,La,metabolism,ModelsMolecular,nosource,Nucleic Acid Conformation,Phosphates,phosphorothioate,POSITION,POSITIONS,protein,Protein Binding,Protein Biosynthesis,Protein Subunits,PROTEIN-BIOSYNTHESIS,Proteins,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNABacterial,RNARibosomal16S,RNATransfer,rRNA,structure,SUBUNIT,SUBUNITS,Support} } % == BibTeX quality report for ghoshNonbridgingPhosphateOxygens2005: % ? Possibly abbreviated journal title RNA.

@article{giaeverFunctionalProfilingSaccharomyces2002, title = {Functional Profiling of the {{Saccharomyces}} Cerevisiae Genome}, author = {Giaever, G. and Chu, A.M. and Ni, L. and Connelly, C. and Riles, L. and Veronneau, S. and Dow, S. and {Lucau-Danila}, A. and Anderson, K. and Andre, B. and Arkin, A.P. and Astromoff, A. and El Bakkoury, M. and Bangham, R. and Benito, R. and Brachat, S. and Campanaro, S. and Curtiss, M. and Davis, K. and Deutschbauer, A. and Entian, K.D. and Flaherty, P. and Foury, F. and Garfinkel, D.J. and Gerstein, M. and Gotte, D. and Guldener, U. and Hegemann, J.H. and Hempel, S. and Herman, Z. and Jaramillo, D.F. and Kelly, D.E. and Kelly, S.L. and Kotter, P. and LaBonte, D. and Lamb, D.C. and Lan, N. and Liang, H. and Liao, H. and Liu, L. and Luo, C. and Lussier, M. and Mao, R. and Menard, P. and Ooi, S.L. and Revuelta, J.L. and Roberts, C.J. and Rose, M. and {Ross-Macdonald}, P. and Scherens, B. and Schimmack, G. and Shafer, B. and Shoemaker, D.D. and {Sookhai-Mahadeo}, S. and Storms, R.K. and Strathern, J.N. and Valle, G. and Voet, M. and Volckaert, G. and Wang, C.Y. and Ward, T.R. and Wilhelmy, J. and Winzeler, E.A. and Yang, Y. and Yen, G. and Youngman, E. and Yu, K. and Bussey, H. and Boeke, J.D. and Snyder, M. and Philippsen, P. and Davis, R.W. and Johnston, M.}, year = 2002, month = jul, journal = {Nature}, volume = {418}, number = {6896}, pages = {387–391}, publisher = {Nature Publishing Group}, doi = {10.1038/nature00935}, url = {http://www.nature.com/nature/journal/v418/n6896/abs/nature00935.html}, abstract = {Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed ‘molecular bar codes’ uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics}, keywords = {0,ARRAYS,cell size,CEREVISIAE,Cluster Analysis,Culture Media,Dna,DNA sequence,drug effects,expression,FRAME,functional genomics,Galactose,gene,Gene Deletion,Gene Expression Profiling,Genes,GenesFungal,Genetic,genetics,Genome,GenomeFungal,genomic,Genomics,GROWTH,growth & development,Hydrogen-Ion Concentration,IDENTIFY,La,media,MESSENGER-RNA,metabolism,MUTANTS,nosource,Nystatin,OPEN READING FRAME,Open Reading Frames,Osmolar Concentration,pharmacology,Phenotype,protein,Proteins,Proteome,READING FRAME,Reading Frames,Rna,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Selection (Genetics),sequence,SEQUENCES,Sorbitol,Support,yeast} }

@article{gibsonOnestepAssemblyYeast2008, title = {One-Step Assembly in Yeast of 25 Overlapping {{DNA}} Fragments to Form a Complete Synthetic {{Mycoplasma}} Genitalium Genome}, author = {Gibson, D.G. and Benders, G.A. and Axelrod, K.C. and Zaveri, J. and Algire, M.A. and Moodie, M. and Montague, M.G. and Venter, J.C. and Smith, H.O. and Hutchison, C.A.}, year = 2008, month = dec, journal = {Proceedings of the National Academy of Sciences}, volume = {105}, number = {51}, pages = {20404–20409}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.0811011106}, url = {http://www.pnas.org/content/105/51/20404.short}, abstract = {We previously reported assembly and cloning of the synthetic Mycoplasma genitalium JCVI-1.0 genome in the yeast Saccharomyces cerevisiae by recombination of six overlapping DNA fragments to produce a 592-kb circle. Here we extend this approach by demonstrating assembly of the synthetic genome from 25 overlapping fragments in a single step. The use of yeast recombination greatly simplifies the assembly of large DNA molecules from both synthetic and natural fragments}, keywords = {0,assembly,BIOLOGY,biosynthesis,CEREVISIAE,cloning,CloningMolecular,Dna,FORM,genetics,Genome,GenomeBacterial,La,metabolism,Methods,Mycoplasma genitalium,nosource,Oligodeoxyribonucleotides,RECOMBINATION,RecombinationGenetic,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Support,yeast,Yeasts} } % == BibTeX quality report for gibsonOnestepAssemblyYeast2008: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{giedrocStructureStabilityFunction2000a, title = {Structure, Stability and Function of {{RNA}} Pseudoknots Involved in Stimulating Ribosomal Frameshifting}, author = {Giedroc, D.P. and Theimer, C.A. and Nixon, P.L.}, year = 2000, month = apr, journal = {J.Mol.Biol.}, volume = {298}, number = {2}, pages = {167–185}, doi = {10.1006/jmbi.2000.3668}, url = {PM:10764589}, abstract = {Programmed -1 ribosomal frameshifting has become the subject of increasing interest over the last several years, due in part to the ubiquitous nature of this translational recoding mechanism in pathogenic animal and plant viruses. All cis-acting frameshift signals encoded in mRNAs are minimally composed of two functional elements: a heptanucleotide “slippery sequence” conforming to the general form X XXY YYZ, followed by an RNA structural element, usually an H-type RNA pseudoknot, positioned an optimal number of nucleotides (5 to 9) downstream. The slippery sequence itself promotes a low level ( approximately 1 %) of frameshifting; however, downstream pseudoknots stimulate this process significantly, in some cases up to 30 to 50 %. Although the precise molecular mechanism of stimulation of frameshifting remains poorly understood, significant advances have been made in our knowledge of the three-dimensional structures, thermodynamics of folding, and functional determinants of stimulatory RNA pseudoknots derived from the study of several well-characterized frameshift signals. These studies are summarized here and provide new insights into the structural requirements and mechanism of programmed - 1 ribosomal frameshifting}, keywords = {0,animal,Base Sequence,Cations,chemistry,drug effects,ELEMENTS,frameshift,Frameshifting,FrameshiftingRibosomal,genetics,Infectious bronchitis virus,La,Luteovirus,Mammary Tumor VirusMouse,MECHANISM,metabolism,ModelsGenetic,mRNA,nosource,Nucleic Acid Conformation,Nucleotides,pharmacology,pseudoknot,recoding,RetrovirusesSimian,Review,ribosomal frameshifting,Rna,RNA PSEUDOKNOT,RNA Stability,RNAMessenger,RnaViral,sequence,SIGNAL,stability,Structural,structure,supportu.s.gov’tp.h.s.,Thermodynamics} } % == BibTeX quality report for giedrocStructureStabilityFunction2000a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{giedrocDetectionScalarCouplings2003, title = {Detection of Scalar Couplings Involving 2 ’-Hydroxyl Protons across Hydrogen Bonds in a Frameshifting {{mRNA}} Pseudoknot}, author = {Giedroc, D.P. and Cornish, P.V. and Hennig, M.}, year = 2003, month = apr, journal = {Journal of the American Chemical Society}, volume = {125}, number = {16}, pages = {4676–4677}, publisher = {ACS Publications}, doi = {10.1021/ja029286t}, url = {http://pubs.acs.org/doi/abs/10.1021/ja029286t}, keywords = {ASSIGNMENT,BASE,D,Frameshifting,Hydrogen,La,mRNA,NMR,nosource,PROTON,Protons,pseudoknot,Rna} }

@article{gilbertReconfigurationYeast40S2007, title = {Reconfiguration of Yeast {{40S}} Ribosomal Subunit Domains by the Translation Initiation Multifactor Complex}, author = {Gilbert, R.J. and Gordiyenko, Y. and {}{von der}, Haar T. and Sonnen, A.F. and Hofmann, G. and Nardelli, M. and Stuart, D.I. and McCarthy, J.E.}, year = 2007, month = apr, journal = {Proceedings of the National Academy of Sciences}, volume = {104}, number = {14}, pages = {5788–5793}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.0606880104}, url = {http://www.pnas.org/content/104/14/5788.short}, abstract = {In the process of protein synthesis, the small (40S) subunit of the eukaryotic ribosome is recruited to the capped 5’ end of the mRNA, from which point it scans along the 5’ untranslated region in search of a start codon. However, the 40S subunit alone is not capable of functional association with cellular mRNA species; it has to be prepared for the recruitment and scanning steps by interactions with a group of eukaryotic initiation factors (eIFs). In budding yeast, an important subset of these factors (1, 2, 3, and 5) can form a multifactor complex (MFC). Here, we describe cryo-EM reconstructions of the 40S subunit, of the MFC, and of 40S complexes with MFC factors plus eIF1A. These studies reveal the positioning of the core MFC on the 40S subunit, and show how eIF-binding induces mobility in the head and platform and reconfigures the head-platform-body relationship. This is expected to increase the accessibility of the mRNA channel, thus enabling the 40S subunit to convert to a recruitment-competent state}, keywords = {0,3,5’ Untranslated Regions,ASSOCIATION,BIOLOGY,chemistry,Codon,CodonInitiator,COMPLEX,COMPLEXES,Cryoelectron Microscopy,DOMAIN,DOMAINS,eIF1A,Eukaryotic Initiation Factor-1,Eukaryotic Initiation Factor-2,Eukaryotic Initiation Factor-3,Eukaryotic Initiation Factor-5,Eukaryotic Initiation Factors,EUKARYOTIC RIBOSOME,FORM,Genetic,genetics,human,initiation,INITIATION-FACTOR,La,metabolism,ModelsChemical,ModelsMolecular,mRNA,nosource,protein,Protein Binding,Protein Biosynthesis,Protein StructureSecondary,Protein Subunits,protein synthesis,PROTEIN-SYNTHESIS,RECRUITMENT,REGION,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNAFungal,RNAMessenger,Saccharomyces cerevisiae,scanning,search,START CODON,Structural,SUBUNIT,SUBUNITS,Support,translation,TRANSLATION INITIATION,ultrastructure,Untranslated Regions,yeast} } % == BibTeX quality report for gilbertReconfigurationYeast40S2007: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{gilbertCapindependentTranslationRequired2007, title = {Cap-Independent Translation Is Required for Starvation-Induced Differentiation in Yeast}, author = {Gilbert, W.V. and Zhou, K. and Butler, T.K. and Doudna, J.A.}, year = 2007, month = aug, journal = {Science}, volume = {317}, number = {5842}, eprint = {17761883}, eprinttype = {pubmed}, pages = {1224–1227}, publisher = {American Association for the Advancement of Science}, issn = {1095-9203}, doi = {10.1126/science.1144467}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17761883 http://www.sciencemag.org/content/317/5842/1224.short}, abstract = {Cellular internal ribosome entry sites (IRESs) are untranslated segments of mRNA transcripts thought to initiate protein synthesis in response to environmental stresses that prevent canonical 5’ cap-dependent translation. Although numerous cellular mRNAs are proposed to have IRESs, none has a demonstrated physiological function or molecular mechanism. Here we show that seven yeast genes required for invasive growth, a developmental pathway induced by nutrient limitation, contain potent IRESs that require the initiation factor eIF4G for cap-independent translation. In contrast to the RNA structure-based activity of viral IRESs, we show that an unstructured A-rich element mediates internal initiation via recruitment of the poly(A) binding protein (Pab1) to the 5’ untranslated region (UTR) of invasive growth messages. A 5’UTR mutation that impairs IRES activity compromises invasive growth, which indicates that cap-independent translation is required for physiological adaptation to stress}, pmid = {17761883}, keywords = {0,5’ Untranslated Regions,5’ Untranslated Regions: genetics,5’ Untranslated Regions: metabolism,Adaptation,AdaptationPhysiological,BINDING,BINDING PROTEIN,BINDING-PROTEIN,BIOLOGY,biosynthesis,Cap,CAP-INDEPENDENT TRANSLATION,CEREVISIAE,chemistry,Eukaryotic Initiation Factor-4G,Eukaryotic Initiation Factor-4G: genetics,Eukaryotic Initiation Factor-4G: metabolism,FACTOR 4G,Fungal,Fungal: chemistry,Fungal: genetics,Fungal: metabolism,gene,Genes,GenesFungal,genetics,Glucose,Glucose: metabolism,GROWTH,growth & development,initiation,INITIATION-FACTOR,INTERNAL RIBOSOME ENTRY,La,MECHANISM,MESSAGE,Messenger,Messenger: chemistry,Messenger: genetics,Messenger: metabolism,metabolism,mRNA,Mutation,nosource,Nuclear Proteins,Nuclear Proteins: biosynthesis,Nuclear Proteins: genetics,Nuclear Proteins: metabolism,Nucleic Acid Conformation,PATHWAY,Peptide Chain Initiation,Peptide Chain InitiationTranslational,Physiological,Poly A,Poly A: metabolism,poly(A),POLY(A)-BINDING PROTEIN,Poly(A)-Binding Proteins,Poly(A)-Binding Proteins: metabolism,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,Proteins,RECRUITMENT,REGION,ribosome,RIBOSOME ENTRY SITE,RIBOSOME ENTRY SITES,Rna,RNA,Rna Caps,RNA Caps,RNA Caps: metabolism,RNAFungal,RNAMessenger,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: biosynthesis,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: growth & development,Saccharomyces cerevisiae: metabolism,SACCHAROMYCES-CEREVISIAE,SITE,SITES,Stress,Support,Trans-Activators,Trans-Activators: biosynthesis,Trans-Activators: genetics,Trans-Activators: metabolism,TRANSCRIPT,translation,Translational,Untranslated Regions,yeast} }

@article{gluckRibosomalRNAIdentity1994, title = {The Ribosomal {{RNA}} Identity Elements for Ricin and for Alpha-Sarcin: Mutations in the Putative {{CG}} Pair That Closes a {{GAGA}} Tetraloop}, author = {Gluck, A. and Endo, Y. and Wool, I.G.}, year = 1994, month = feb, journal = {Nucleic Acids Res.}, volume = {22}, number = {3}, pages = {321–324}, doi = {10.1093/nar/22.3.321}, abstract = {alpha-Sarcin is a ribonuclease that cleaves the phosphodiester bond on the 3’ side of G4325 in 28S rRNA; ricin A-chain is a RNA N-glycosidase that depurinates the 5’ adjacent A4324. These single covalent modifications inactivate the ribosome. An oligoribonucleotide that reproduces the structure of the sarcin/ricin domain in 28S rRNA was synthesized and mutations were constructed in the 5’ C and the 3’ G that surround a GAGA tetrad that has the sites of toxin action. Covalent modification of the RNA by ricin, but not by alpha-sarcin, requires a Watson-Crick pair to shut off a putative GAGA tetraloop. Either the recognition elements for the two toxins are different despite their catalyzing covalent modification of adjacent nucleotides in 28S rRNA or there are transitions in the conformation of the alpha- sarcin/ricin domain in 28S rRNA and one conformer is recognized by alpha-sarcin and the other by ricin A-chain}, keywords = {94173678,Base Sequence,Binding Sites,chemistry,ELEMENTS,Fungal Proteins,Hydrogen Bonding,In Vitro,Kinetics,modification,Molecular Sequence Data,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Nucleotides,RIBOSOMAL-RNA,ribosome,Ricin,Rna,RNARibosomal28S,rRNA,structure,Substrate Specificity,supportu.s.gov’tp.h.s.,toxin} } % == BibTeX quality report for gluckRibosomalRNAIdentity1994: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{gluckAnalysisSystematicDeletion2002, title = {Analysis by Systematic Deletion of Amino Acids of the Action of the Ribotoxin Restrictocin}, author = {Gluck, A. and Wool, I.G.}, year = 2002, month = jan, journal = {Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology}, volume = {1594}, number = {1}, pages = {115–126}, publisher = {Elsevier}, doi = {10.1016/S0167-4838(01)00290-4}, url = {ISI:000173826100012 http://linkinghub.elsevier.com/retrieve/pii/S0167483801002904}, abstract = {A series of contiguous deletions were made in a cDNA encoding the ribonuclease restrictocin with the purpose of identifying the amino acids that are essential for the cleavage of the phosphodiester bond on the 3’ side of G4325 in the alpha-sarcin/ricin domain of mammalian (rat) 28S rRNA. In all 93 of 149 amino acids, 62% of the residues in restrictocin, were not essential for the action of the toxin. Of the five residues that have been proposed to constitute the active site, three could be deleted without loss of activity if they were part of a deletion of three or five amino acids but not if they were removed singly. It is likely that the loss of these three residues is compensated for by a neighboring residue that occupies the structural space created by the larger amino acid deletions. This was demonstrated to be the case for the active site residue Glu95 which in the deletion mutant Delta91-95 is replaced by Asp90. Systematic deletion of amino acids is a rapid, cost effective method for identifying the residues in a protein likely to contribute directly to function and, hence, deserving of closer scrutiny. Moreover, a semiquantitative estimate of the contribution of the residue to function can be made. For this reason the method may be useful for functional proteomics. (C) 2002 Elsevier Science B.V. All rights reserved}, keywords = {ACID,ALPHA-SARCIN,Amino Acids,analysis,CLEAVAGE,CRYSTAL-STRUCTURE,EF-G,ELONGATION-FACTORS,EUKARYOTIC RIBOSOMES,FUNGAL RIBOTOXIN,HETEROLOGOUS EXPRESSION,nosource,protein,rat,RESIDUES,restrictocin,RIBOSOMAL RIBONUCLEIC-ACID,ribosome,ribotoxin,RICIN-A-CHAIN,rRNA,SARCIN CLEAVAGE SITE,SITE,Structural,systematic deletion of amino acids,toxin} }

@article{gnirkeTRNABindingSites1986, title = {{{tRNA}} Binding Sites on the Subunits of {{Escherichia}} Coli Ribosomes.}, author = {Gnirke, A. and Nierhaus, K.H.}, year = 1986, month = nov, journal = {Journal of Biological Chemistry}, volume = {261}, number = {31}, pages = {14506–14514}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(18)66898-X}, url = {http://www.jbc.org/content/261/31/14506.short}, abstract = {Programmed 30 S subunits expose only one binding site, to which the different classes of tRNA (deacylated tRNAPhe, Phe-tRNAPhe, and N-acetylphenylalanyl (AcPhe)-tRNAPhe) bind with about the same affinity. Elongation factor Tu within the ternary complex does not contribute to the binding of Phe-tRNA. Binding of acylated or deacylated tRNA to 30 S depends on the cognate codon; nonprogrammed 30 S subunits do not bind tRNA to any significant extent. The existence of only one binding site/30 S subunit (and not, for example, two sites in 50% of the subunits) could be shown with Phe-tRNAPhe as well as deacylated tRNAPhe pursuing different strategies. Upon 50 S association the 30 S-bound tRNA appears in the P site (except the ternary complex which is found at the A site). Inhibition experiments with tetracycline demonstrated that the 30 S inhibition pattern is identical to that of the P site but differs from that of the A site of 70 S ribosomes. In contrast to 30 S subunits the 50 S subunit exclusively binds up to 0.2 and 0.4 molecules of deacylated tRNAPhe/50 S subunit in the absence and presence of poly(U), respectively, but neither Phe-tRNA nor AcPhe-tRNA. Noncognate poly(A) did not stimulate the binding indicating codon-anticodon interaction at the 50 S site. The exclusive binding of deacylated tRNA and its dependence on the presence of cognate mRNA is reminiscent of the characteristics of the E site on 70 S ribosomes. 30 and 50 S subunits in one test tube expose one binding site more than the sum of binding capacities of the individual subunits. The results suggest that the small subunit contains the prospective P site and the large subunit the prospective E site, thus implying that the A site is generated upon 30 S-50 S association}, keywords = {0,30 S,30-S,A SITE,A-SITE,ASSOCIATION,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,Carbon,Carbon Radioisotopes,Codon,CODON-ANTICODON INTERACTION,COMPLEX,COMPLEXES,E,E site,elongation,ELONGATION-FACTOR-TU,Escherichia coli,Escherichia coli ribosomes,ESCHERICHIA-COLI,FACTOR TU,Guanosine,Guanosine Triphosphate,INHIBITION,Kinetics,La,metabolism,mRNA,nosource,P SITE,P-SITE,Peptide Elongation Factor Tu,Phenylalanine,poly(A),ribosome,Ribosomes,Rna,RNATransfer,RNATransferAmino Acyl,S,SITE,SITES,SUBUNIT,SUBUNITS,Tetracycline,Tritium,tRNA,tRNA binding,TU} } % == BibTeX quality report for gnirkeTRNABindingSites1986: % ? unused Journal abbr (“J.Biol Chem.”)

@article{goddardStructuresFunctionsTransfer1977a, title = {The Structures and Functions of Transfer {{RNA}}.}, author = {Goddard, J.P.}, year = 1977, journal = {Progress in biophysics and molecular biology}, volume = {32}, number = {3}, eprint = {339274}, eprinttype = {pubmed}, pages = {233–308}, url = {http://www.ncbi.nlm.nih.gov/pubmed/339274}, keywords = {0,Amino Acyl-tRNA Ligases,analysis,Base Sequence,biosynthesis,Hydrogen Bonding,La,Ligases,metabolism,ModelsMolecular,No DOI found,nosource,Nucleic Acid Conformation,Nucleic Acid Hybridization,Phenylalanine,protein,Proteins,Review,Ribonucleotides,Ribosomes,Rna,RNATransfer,Saccharomyces cerevisiae,Species Specificity,structure,TranscriptionGenetic,TranslationGenetic} } % == BibTeX quality report for goddardStructuresFunctionsTransfer1977a: % ? unused Journal abbr (“Prog.Biophys.Mol.Biol.”)

@article{godenyCompleteGenomicSequence1993, title = {Complete {{Genomic Sequence}} and {{Phylogenetic Analysis}} of the {{Lactate Dehydrogenase-Elevating Virus}} ({{Ldv}})}, author = {Godeny, E.K. and Chen, L. and Kumar, S.N. and Methven, S.L. and Koonin, E.V. and Brinton, M.A.}, year = 1993, month = jun, journal = {Virology}, volume = {194}, number = {2}, pages = {585–596}, publisher = {Elsevier}, doi = {10.1006/viro.1993.1298}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0042682283712985}, keywords = {analysis,CORONAVIRUS-IBV,CYSTEINE PROTEASES,genomic,IDENTIFICATION,nosource,polymerase,protein,RECOMBINATION,REPLICATION,sequence,SERINE PROTEASES,STRAND RNA VIRUSES,SUPERFAMILY,virus} } % == BibTeX quality report for godenyCompleteGenomicSequence1993: % ? Title looks like it was stored in title-case in Zotero

@article{goebelCisactingGenomicReplication2004a, title = {The 3’ Cis-Acting Genomic Replication Element of the Severe Acute Respiratory Syndrome Coronavirus Can Function in the Murine Coronavirus Genome}, author = {Goebel, S.J. and Taylor, J. and Masters, P.S.}, year = 2004, month = jul, journal = {J.Virol.}, volume = {78}, number = {14}, pages = {7846–7851}, doi = {10.1128/JVI.78.14.7846-7851.2004}, url = {PM:15220462}, abstract = {The 3’ untranslated region (3’ UTR) of the genome of the severe acute respiratory syndrome coronavirus can functionally replace its counterpart in the prototype group 2 coronavirus mouse hepatitis virus (MHV). By contrast, the 3’ UTRs of representative group 1 or group 3 coronaviruses cannot operate as substitutes for the MHV 3’ UTR}, keywords = {0,3,3’ Untranslated Regions,Animals,Base Sequence,Coronavirus,enhancer elements (genetics),genetics,Genome,GenomeViral,genomic,human,La,Mice,Molecular Sequence Data,Murine hepatitis virus,nosource,RecombinationGenetic,REGION,REPLICATION,Sars Virus,Severe Acute Respiratory Syndrome,supportu.s.gov’tp.h.s.,Untranslated Regions,virus,Virus Replication} } % == BibTeX quality report for goebelCisactingGenomicReplication2004a: % ? Possibly abbreviated journal title J.Virol.

@article{goebelCharacterizationRNAComponents2004, title = {Characterization of the {{RNA}} Components of a Putative Molecular Switch in the 3’ Untranslated Region of the Murine Coronavirus Genome}, author = {Goebel, S.J. and Hsue, B. and Dombrowski, T.F. and Masters, P.S.}, year = 2004, month = jan, journal = {Journal of virology}, volume = {78}, number = {2}, pages = {669–682}, publisher = {Am Soc Microbiol}, doi = {10.1128/JVI.78.2.669-682.2004}, url = {http://jvi.asm.org/cgi/content/abstract/78/2/669}, abstract = {RNA virus genomes contain cis-acting sequence and structural elements that participate in viral replication. We previously identified a bulged stem-loop secondary structure at the upstream end of the 3’ untranslated region (3’ UTR) of the genome of the coronavirus mouse hepatitis virus (MHV). This element, beginning immediately downstream of the nucleocapsid gene stop codon, was shown to be essential for virus replication. Other investigators discovered an adjacent downstream pseudoknot in the 3’ UTR of the closely related bovine coronavirus (BCoV). This pseudoknot was also shown to be essential for replication, and it has a conserved counterpart in every group 1 and group 2 coronavirus. In MHV and BCoV, the bulged stem-loop and pseudoknot are, in part, mutually exclusive, because of the overlap of the last segment of the stem-loop and stem 1 of the pseudoknot. This led us to hypothesize that they form a molecular switch, possibly regulating a transition occurring during viral RNA synthesis. We have now performed an extensive genetic analysis of the two components of this proposed switch. Our results define essential and nonessential components of these structures and establish the limits to which essential parts of each element can be destabilized prior to loss of function. Most notably, we have confirmed the interrelationship of the two putative switch elements. Additionally, we have identified a pseudoknot loop insertion mutation that appears to point to a genetic interaction between the pseudoknot and a distant region of the genome}, keywords = {0,3,3’ Untranslated Regions,analysis,Animals,Base Sequence,chemistry,Codon,COMPONENT,COMPONENTS,Coronavirus,DOWNSTREAM,ELEMENTS,enhancer elements (genetics),FORM,gene,Genetic,genetics,Genome,IMMEDIATELY DOWNSTREAM,La,LOOP,metabolism,Mice,Molecular Sequence Data,Murine hepatitis virus,Mutation,nosource,Nucleic Acid Conformation,physiology,pseudoknot,RecombinationGenetic,REGION,REPLICATION,Rna,RnaViral,SECONDARY STRUCTURE,sequence,STEM-LOOP,STOP CODON,Structural,structure,supportu.s.gov’tp.h.s.,Untranslated Regions,UPSTREAM,VIRAL-RNA,virus,Virus Replication} } % == BibTeX quality report for goebelCharacterizationRNAComponents2004: % ? unused Journal abbr (“J.Virol.”)

@article{goffGeneticReprogrammingRetroviruses2004, title = {Genetic Reprogramming by Retroviruses: Enhanced Suppression of Translational Termination}, author = {Goff, S.P.}, year = 2004, month = feb, journal = {Cell Cycle}, volume = {3}, number = {February}, pages = {123–125}, url = {http://www.landesbioscience.com/journals/6/article/653/}, abstract = {Viruses often exploit or subvert host machinery for their own purposes during replication. A search for proteins interacting with the murine leukemia virus reverse transcriptase (RT) recently provided a new example of such exploitation. RT was found to bind the eukaryotic translational release factor 1 (eRF1), the protein that recognizes stop codons and, in complex with eRF3, causes termination and polypeptide release from the ribosome. RT is derived from a large Gag-Pol polyprotein, and its synthesis requires a translational readthrough, a suppression of termination, at a stop codon at the end of the gag gene. The binding of eRF1 by RT was found to inhibit eRF1 action, enhance the efficiency of readthrough, and thus cause higher levels of RT synthesis. The observations suggest that retroviruses manipulate the translational machinery in sophisticated ways to fine-tune their own gene expression}, keywords = {0,a search for proteins,bind the eukary-,BINDING,CHAIN TERMINATION,Codon,CODONS,CodonTerminator,COMPLEX,COMPLEXES,Dna,efficiency,example of such exploitation,expression,FUSION PROTEIN,Fusion Proteinsgag-pol,Gag,Gag-pol,gene,Gene Expression,GENE-EXPRESSION,Genetic,genetics,interacting with the murine,La,LEUKEMIA,leukemia virus reverse transcriptase,metabolism,No DOI found,nosource,Peptide Chain Termination,Peptide Chain TerminationTranslational,Peptide Termination Factors,physiology,polymerase,POLYPEPTIDE,POLYPROTEIN,protein,Protein Biosynthesis,Proteins,readthrough,recently provided a new,RELEASE,release factor,replication,REPLICATION,REQUIRES,Retroviridae,RETROVIRUSES,REVERSE-TRANSCRIPTASE,Review,ribosome,Ribosomes,Rna,RNA-Directed DNA Polymerase,RNATransfer,rt,rt was found to,search,STOP CODON,subvert host machinery for,suppression,SuppressionGenetic,termination,Terminator Regions (Genetics),their own purposes during,TRANSLATIONAL READTHROUGH,TRANSLATIONAL TERMINATION,virus,Viruses,viruses often exploit or} }

@article{gomez-lorenzoThreedimensionalCryoelectronMicroscopy2000a, title = {Three-Dimensional Cryo-Electron Microscopy Localization of {{EF2}} in the {{Saccharomyces}} Cerevisiae {{80S}} Ribosome at 17.5 {{A}} Resolution}, author = {{Gomez-Lorenzo}, M.G. and Spahn, C.M. and Agrawal, R.K. and Grassucci, R.A. and Penczek, P. and Chakraburtty, K. and Ballesta, J.P. and Lavandera, J.L. and {Garcia-Bustos}, J.F. and Frank, J.}, year = 2000, month = jun, journal = {EMBO J.}, volume = {19}, number = {11}, pages = {2710–2718}, doi = {10.1093/emboj/19.11.2710}, abstract = {Using a sordarin derivative, an antifungal drug, it was possible to determine the structure of a eukaryotic ribosome small middle dotEF2 complex at 17.5 A resolution by three-dimensional (3D) cryo-electron microscopy. EF2 is directly visible in the 3D map and the overall arrangement of the complex from Saccharomyces cerevisiae corresponds to that previously seen in Escherichia coli. However, pronounced differences were found in two prominent regions. First, in the yeast system the interaction between the elongation factor and the stalk region of the large subunit is much more extensive. Secondly, domain IV of EF2 contains additional mass that appears to interact with the head of the 40S subunit and the region of the main bridge of the 60S subunit. The shape and position of domain IV of EF2 suggest that it might interact directly with P-site-bound tRNA}, keywords = {20296695,60S subunit,analysis,chemistry,COMPLEX,COMPLEXES,Cryoelectron Microscopy,elongation,Escherichia coli,ESCHERICHIA-COLI,Fungal Proteins,Macromolecular Systems,metabolism,ModelsMolecular,nosource,Nucleic Acid Conformation,Peptide Elongation Factor 2,Protein Conformation,Protein StructureTertiary,ribosome,Ribosomes,RNAFungal,RNATransfer,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,tRNA,ultrastructure,yeast} } % == BibTeX quality report for gomez-lorenzoThreedimensionalCryoelectronMicroscopy2000a: % ? Possibly abbreviated journal title EMBO J.

@article{goncalvesTranscriptionActivationYeast1995, title = {Transcription Activation of Yeast Ribosomal Protein Genes Requires Additional Elements Apart from Binding Sites for {{Abf1p}} or {{Rap1p}}}, author = {Goncalves, P.M. and Griffioen, G. and Minnee, R. and Bosma, M. and Kraakman, L.S. and Mager, W.H. and Planta, R.J.}, year = 1995, month = may, journal = {Nucleic acids research}, volume = {23}, number = {9}, pages = {1475–1480}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/23.9.1475}, url = {http://nar.oxfordjournals.org/content/23/9/1475.short}, abstract = {All ribosomal protein (rp) gene promoters from Saccharomyces cerevisiae studied so far contain either (usually two) binding sites for the global gene regulator Rap1p or one binding site for another global factor, Abf1p. Previous analysis of the rpS33 and rpL45 gene promoters suggested that apart from the Abf1 binding site, additional cis-acting elements play a part in transcription activation of these genes. We designed a promoter reconstruction system based on the beta-glucuronidase reporter gene to examine the role of the Abf1 binding site and other putative cis-acting elements in promoting transcription. An isolated Abf1 binding site turned out to be a weak activating element. A T-rich sequence derived from the rpS33 proximal promoter was found to be stronger, but full transcription activation was only achieved by a combination of these elements. Both in the natural rpL45 promoter and in the reconstituted promoter, a Rap1 binding site could functionally replace the Abf1 binding site. Characteristic rp gene nutritional control of transcription, evoked by a carbon source upshift or by nitrogen re-feeding to nitrogen starved cells, could only be mediated by the combined Abf1 (or Rap1) binding site and T-rich element and not by the individual elements. These results demonstrate that Abf1p and Rap1p do not activate rp genes in a prototypical fashion, but rather may serve to potentiate transcription activation through the T-rich element}, keywords = {95303628,activation,analysis,Base Sequence,BINDING,Binding Sites,Carbon,carbon source,DNA-Binding Proteins,ELEMENTS,gene,Genes,genetics,GTP-Binding Proteins,metabolism,Molecular Sequence Data,Nitrogen,nosource,Plasmids,protein,Ribosomal Proteins,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,supportnon-u.s.gov’t,SYSTEM,Trans-Activation (Genetics),transcription,Transcription Factors,yeast} } % == BibTeX quality report for goncalvesTranscriptionActivationYeast1995: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{gongadzeRibosomalProteinsTL41993, title = {Ribosomal Proteins, {{TL4}} and {{TL5}}, from {{Thermus}} Thermophilus Form Hybrid Complexes with 5 {{S}} Ribosomal {{RNA}} from Different Microorganisms}, author = {Gongadze, G.M. and Tishchenko, S.V. and Sedelnikova, S.E. and Garber, M.B.}, year = 1993, journal = {FEBS letters}, volume = {330}, number = {1}, pages = {46–48}, publisher = {Elsevier}, doi = {10.1016/0014-5793(93)80916-I}, url = {http://linkinghub.elsevier.com/retrieve/pii/001457939380916I}, abstract = {Hybrid complexes of the ribosomal proteins, TL4 and TL5, from Thermus thermophilus with 5 S ribosomal RNA from Escherichia coli and Bacillus stearothermophilus have been prepared. There was no competition between the two proteins for the binding sites. Stoichiometry of 5 S RNA binding for both proteins was 1:1 (protein/RNA). The TL4 protein competed with the E. coli ribosomal L5 protein, and the TL5 protein competed with the E. coli ribosomal proteins, L18 and L25, for binding with 5 S RNA}, keywords = {0,Bacillus stearothermophilus,BACILLUS-STEAROTHERMOPHILUS,BINDING,Binding Sites,COMPLEX,COMPLEXES,Escherichia coli,ESCHERICHIA-COLI,L5,La,metabolism,nosource,protein,Proteins,Ribosomal Proteins,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNARibosomal5S,structure,Thermus,Thermus thermophilus} } % == BibTeX quality report for gongadzeRibosomalProteinsTL41993: % ? unused Journal abbr (“FEBS Lett.”)

@article{gonzalezNonsensemediatedMRNADecay2001a, title = {Nonsense-Mediated {{mRNA}} Decay in {{Saccharomyces}} Cerevisiae: A Quality Control Mechanism That Degrades Transcripts Harboring Premature Termination Codons.}, author = {Gonzalez, C.I. and Wang, W and Peltz, S.W.}, year = 2001, month = jan, journal = {Cold Spring Harbor Symposia on Quantitative Biology}, volume = {66:321-8.}, pages = {321–328}, issn = {0091-7451}, doi = {10.1101/sqb.2001.66.321}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2685090&tool=pmcentrez&rendertype=abstract}, pmid = {12762034}, keywords = {chemistry,Codon,CodonNonsense,DECAY,Fungal,Fungal: genetics,Genetic,Genetic: genetics,genetics,Kinetics,MECHANISM,Messenger,Messenger: genetics,metabolism,mRNA,mRNA decay,Nonsense,Nonsense: genetics,nosource,Peptide Chain Termination,Protein Conformation,Quality Control,RNA,RNA-Binding Proteins,RNA-Binding Proteins: chemistry,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,SACCHAROMYCES-CEREVISIAE,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,termination,Terminator Regions,Terminator Regions (Genetics),Transcription,TranscriptionGenetic,Translational,Translational: genetics} } % == BibTeX quality report for gonzalezNonsensemediatedMRNADecay2001a: % ? unused Journal abbr (“Cold Spring Harb.Symp.Quant.Biol.”)

@article{gonzalezSolutionStructureThermodynamics1999a, title = {Solution Structure and Thermodynamics of a Divalent Metal Ion Binding Site in an {{RNA}} Pseudoknot}, author = {Gonzalez, R.L. and Tinoco, {I.Jr}.}, year = 1999, month = jun, journal = {J.Mol.Biol.}, volume = {289}, number = {5}, pages = {1267–1282}, doi = {10.1006/jmbi.1999.2841}, abstract = {Identification and characterization of a metal ion binding site in an RNA pseudoknot was accomplished using cobalt (III) hexammine, Co(NH3)63+, as a probe for magnesium (II) hexahydrate, Mg(H2O)62+, in nuclear magnetic resonance (NMR) structural studies. The pseudoknot causes efficient -1 ribosomal frameshifting in mouse mammary tumor virus. Divalent metal ions, such as Mg2+, are critical for RNA structure and function; Mg2+preferentially stabilizes the pseudoknot relative to its constituent hairpins. The use of Co(NH3)63+as a substitute for Mg2+was investigated by ultraviolet absorbance melting curves, NMR titrations of the imino protons, and analysis of NMR spectra in the presence of Mg2+or Co (NH3)63+. The structure of the pseudoknot-Co(NH3)63+complex reveals an ion-binding pocket formed by a short, two-nucleotide loop and the major groove of a stem. Co(NH3)63+stabilizes the sharp loop-to-stem turn and reduces the electrostatic repulsion of the phosphates in three proximal strands. Hydrogen bonds are identified between the Co(NH3)63+protons and non- bridging phosphate oxygen atoms, 2’ hydroxyl groups, and nitrogen and oxygen acceptors on the bases. The binding site is significantly different from that previously characterized in the major groove surface of tandem G.U base-pairs, but is similar to those observed in crystal structures of a fragment of the 5 S rRNA and the P5c helix of the Tetrahymena thermophila group I intron. Changes in chemical shifts occurred at the same pseudoknot protons on addition of Mg2+as on addition of Co(NH3)63+, indicating that both ions bind at the same site. Ion binding dissociation constants of approximately 0.6 mM and 5 mM (in 200 mM Na+and a temperature of 15 degrees C) were obtained for Co(NH3)63+and Mg2+, respectively, from the change in chemical shift as a function of metal ion concentration. An extensive array of non- sequence-specific hydrogen bond acceptors coupled with conserved structural elements within the binding pocket suggest a general mode of divalent metal ion stabilization of this type of frameshifter pseudoknot. These results provide new thermodynamic and structural insights into the role divalent metal ions play in stabilizing RNA tertiary structural motifs such as pseudoknots. Copyright 1999 Academic Press}, keywords = {99303695,analysis,BINDING,Binding Sites,CationsDivalent,chemistry,Cobalt,ELEMENTS,Frameshifting,IDENTIFICATION,Ions,Magnesium,metabolism,Nitrogen,nosource,nuclear magnetic resonance,Nuclear Magnetic ResonanceBiomolecular,Nucleic Acid Conformation,Phosphates,Protons,pseudoknot,ribosomal frameshifting,Rna,RNA PSEUDOKNOT,rRNA,Solutions,Structural,structure,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Temperature,Tetrahymena,Thermodynamics,ultraviolet rays,virus} } % == BibTeX quality report for gonzalezSolutionStructureThermodynamics1999a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{goringerEffectTRNABinding1984, title = {The Effect of {{tRNA}} Binding on the Structure of 5 {{S RNA}} in {{Escherichia}} Coli. {{A}} Chemical Modification Study.}, author = {Goringer, H.U. and Bertram, S. and Wagner, R.}, year = 1984, month = jan, journal = {Journal of Biological Chemistry}, volume = {259}, number = {1}, pages = {491–496}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(17)43688-X}, url = {http://www.jbc.org/content/259/1/491.short}, abstract = {The structure of 5 S RNA within the 70 S ribosome from Escherichia coli was studied using the chemical reagent kethoxal (alpha-keto-beta- ethoxybutyraldehyde) to modify accessible guanosines. The modification pattern of 5 S RNA from free 70 S ribosomes was compared with that of poly(U) programmed ribosomes where tRNA had been bound to both the A- and P-sites. Binding to the ribosomal A-site was achieved enzymatically using the elongation factor Tu and GTP in the presence of deacylated tRNA which blocks the ribosomal P-site. Modified guanosines were identified after partial RNase T1 hydrolysis and separation of the hydrolysis products on sequencing gels. Binding of tRNA to the ribosome leads to a strong protection of 5 S RNA guanosine G-41 and to some degree G-44 from kethoxal modification. The limited RNase T1 hydrolysis pattern provides evidence for the existence of a 5 S RNA conformation different from the known 5 S RNA A- and B-forms which are characterized by their gel electrophoretic mobility. The importance of 5 S RNA for the binding of tRNA to the ribosome is discussed}, keywords = {5S rRNA,84161955,A-SITE,analysis,Base Sequence,BINDING,elongation,Escherichia coli,ESCHERICHIA-COLI,Gels,genetics,GTP,Guanosine,Hydrolysis,metabolism,modification,nosource,Nucleic Acid Conformation,P-SITE,ribonuclease t1,ribosome,Ribosomes,Rna,RNABacterial,RNAse,RNATransfer,structure,supportnon-u.s.gov’t,tRNA} } % == BibTeX quality report for goringerEffectTRNABinding1984: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{gotodaNewlyIdentifiedNull1992a, title = {A Newly Identified Null Allelic Mutation in the Human Lipoprotein Lipase ({{LPL}}) Gene of a Compound Heterozygote with Familial {{LPL}} Deficiency}, author = {Gotoda, T. and Yamada, N. and Murase, T. and Miyake, S. and Murakami, R. and Kawamura, M. and Kozaki, K. and Mori, N. and Shimano, H. and Shimada, M. and {}{et al.}}, year = 1992, month = apr, journal = {Biochimica et Biophysica Acta}, volume = {1138}, number = {4}, pages = {353–356}, doi = {10.1016/0925-4439(92)90015-F}, keywords = {deficiency,disease,Dna,Frameshifting,gene,Genes,human,Mutation,nosource} }

@article{gottesfeldAssemblyTranscriptionallyActive1982, title = {Assembly of Transcriptionally Active {{5S RNA}} Gene Chromatin in Vitro}, author = {Gottesfeld, J. and Bloomer, L.S.}, year = 1982, month = apr, journal = {Cell}, volume = {28}, number = {4}, pages = {781–791}, publisher = {Elsevier}, doi = {10.1016/0092-8674(82)90057-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867482900575}, abstract = {We have studied the requirements for the in vitro assembly of transcriptionally active 5S RNA gene chromatin from cloned Xenopus laevis 5S plasmid DNA. Both plasmid DNA and DNA assembled into chromatin with Xenopus oocyte extracts are transcribed efficiently in vitro. Chromatin prepared by NaCl reconstitution with purified histones in the absence of any cellular factors, however, is transcriptionally inert. A transcriptionally active template is formed if plasmid DNA is incubated in an ovary extract prior to, but not after, NaCl reconstitution. The cellular component responsible for this effect is the 5S RNA transcription factor TFIIIA. Both chromatographically purified TFIIIA and TFIIIA derived from 7S RNP particles can complex with 5S DNA to yield an active chromatin template upon reconstitution with histones. This effect is specific for 5S RNA genes, since TFIIIA will not form an active template when incubated with a cloned Bombyx mori alanine tRNA gene}, keywords = {5S rRNA,82233697,assembly,Chromatin,COMPLEX,COMPLEXES,COMPONENT,Dna,Female,gene,Genes,genetics,Histones,human,In Vitro,IN-VITRO,metabolism,nosource,Nucleosomes,Oocytes,Ovum,physiology,Rna,RNARibosomal,rRNA,supportu.s.gov’tp.h.s.,TFIIIA,transcription,TRANSCRIPTION FACTOR,TranscriptionGenetic,tRNA,Xenopus,Xenopus laevis} }

@article{gottesmanProteinQualityControl1997, title = {Protein Quality Control: Triage by Chaperones and Proteases.}, author = {Gottesman and Wickner, S. and Maurizi, M.R.}, year = 1997, journal = {Genes & development}, volume = {11}, number = {7}, pages = {815–823}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.11.7.815}, url = {http://genesdev.cshlp.org/content/11/7/815.short}, keywords = {nosource,protein,Quality Control} } % == BibTeX quality report for gottesmanProteinQualityControl1997: % ? unused Journal abbr (“Genes & Dev.”)

@article{graackMitochondrialRibosomesYeast1988, title = {Mitochondrial Ribosomes of Yeast: Isolation of Individual Proteins and {{N-terminal}} Sequencing.}, author = {Graack, H.-R. and Grohmann, L. and Choli, T.}, year = 1988, journal = {FEBS letters}, volume = {242}, number = {1}, pages = {4–8}, publisher = {Elsevier}, doi = {10.1016/0014-5793(88)80975-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/001457938880975X}, keywords = {L3,Methods,mitochondria,mrpl9,nosource,protein,Proteins,ribosome,Ribosomes,yeast} } % == BibTeX quality report for graackMitochondrialRibosomesYeast1988: % ? unused Journal abbr (“FEBS Letts.”)

@article{graackYmL9NucleusencodedMitochondrial1992, title = {{{YmL9}}, a Nucleus-Encoded Mitochondrial Ribosomal Protein of Yeast, Is Homologous to {{L3}} Ribosomal Proteins from All Natural Kingdoms and Photosynthetic Organelles.}, author = {Graack, H.-R. and Grohmann, L. and Kitakawa, M. and Schafer, K.-L. and Kruft, V.}, year = 1992, journal = {European Journal of Biochemistry}, volume = {206}, number = {2}, pages = {373–380}, publisher = {Wiley Online Library}, doi = {10.1111/j.1432-1033.1992.tb16937.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1992.tb16937.x/full}, keywords = {L3,mof1,mrpl9,nosource,Organelles,protein,Proteins,Ribosomal Proteins,sequence,yeast} } % == BibTeX quality report for graackYmL9NucleusencodedMitochondrial1992: % ? unused Journal abbr (“Eur.J.Biochem.”)

@article{grabarekPropertiesTroponinAcetylated1995, title = {Properties of Troponin {{C}} Acetylated at Lysine Residues}, author = {Grabarek, Z. and Mabuchi, Y. and Gergely, J.}, year = 1995, journal = {Biochemistry}, volume = {34}, number = {37}, pages = {11872–11881}, publisher = {ACS Publications}, doi = {10.1021/bi00037a027}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00037a027}, abstract = {We have studied the properties of rabbit skeletal troponin C (TnC) fully acetylated at its lysine residues (AcTnC). Acetylation causes a decrease in thermal stability of both domains of TnC in the absence of Ca2+. At 25 degrees C, the acetylated C-terminal domain of TnC is almost completely unfolded and the melting temperature of the N-terminal domain monitored by far-UV circular dichroism is decreased by 16.3 degrees C. In the presence of 1 mM CaCl2, no cooperative unfolding can be detected up to 90 degrees C for either TnC or AcTnC. At 25 degrees C, CD spectra show that AcTnC has a slightly lower alpha-helix content in the absence of Ca2+, but higher in the presence of Ca2+ as compared to unmodified TnC. Acetylation causes a 3.5-fold increase in affinity for Ca2+ at the low-affinity sites and a 2-fold decrease at the high-affinity sites. Polyacrylamide gel electrophoresis under nondissociating conditions (no SDS, no urea, pH 8.6) indicates that acetylation has little effect on the apparent affinity of TnC for troponin I; however, the binding of the acetylated peptides corresponding to the N-terminal domain of TnC to troponin I is significantly stronger than that of the unmodified peptides. Troponin T binding to AcTnC is significantly enhanced, the altered properties of the N-terminal domain being predominantly responsible for the increase. Titration of the ATPase activity of TnC-depleted myofibrils with AcTnC or native TnC indicates that acetylation increases TnC’s affinity for myofibrils in the presence of Ca2+ approximately 6 times; at saturation the ATPase activity is the same for the two forms of TnC. The Ca2+ dependence of the ATPase activity of myofibrils containing AcTnC is shifted to lower Ca2+ concentrations, consistent with the higher Ca2+ affinity of AcTnC at the low-affinity sites. These data indicate that positively charged lysine side chains, especially those located in the N-terminal domain, modulate TnC’s structural stability and interactions with Ca2+ and other troponin components}, keywords = {0,Acetylation,Adenosine,Adenosine Triphosphatases,Animals,ATPase,BINDING,Binding Sites,Ca2+,Calcium,chemistry,Circular Dichroism,COMPONENT,COMPONENTS,DOMAIN,DOMAINS,Drug Stability,Electrochemistry,Electrophoresis,FORM,GEL-ELECTROPHORESIS,In Vitro,IN-VITRO,Kinetics,La,Lysine,metabolism,MuscleSkeletal,nosource,Peptide Fragments,Peptides,POLYACRYLAMIDE-GEL-ELECTROPHORESIS,Protein Folding,Protein StructureSecondary,Rabbits,RESIDUES,SITE,SITES,SPECTRA,stability,Structural,Support,T,Temperature,Thermodynamics,Troponin,Troponin C,Troponin I,Troponin T,Urea} }

@article{graberProbabilisticPredictionSaccharomyces2002a, title = {Probabilistic Prediction of {{Saccharomyces}} Cerevisiae {{mRNA}} 3’-Processing Sites}, author = {Graber, J.H. and McAllister, G.D. and Smith, T.F.}, year = 2002, month = apr, journal = {Nucleic Acids Res.}, volume = {30}, number = {8}, pages = {1851–1858}, doi = {10.1093/nar/30.8.1851}, abstract = {We present a tool for the prediction of mRNA 3’-processing (cleavage and polyadenylation) sites in the yeast Saccharomyces cerevisiae, based on a discrete state-space model or hidden Markov model. Comparison of predicted sites with experimentally verified 3’-processing sites indicates good agreement. All predicted or known yeast genes were analyzed to find probable 3’-processing sites. Known alternative 3’-processing sites, both within the 3’-untranslated region and within the protein coding sequence were successfully identified, leading to the possibility of prediction of previously unknown alternative sites. The lack of an apparent 3’-processing site calls into question the validity of some predicted genes. This is specifically investigated for predicted genes with overlapping coding sequences}, keywords = {3’ Untranslated Regions,analysis,Base Sequence,CLEAVAGE,Comparative Study,gene,Genes,GenesFungal,genetics,Markov Chains,metabolism,mRNA,nosource,protein,RNA 3’ End Processing,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Sensitivity and Specificity,sequence,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,yeast} } % == BibTeX quality report for graberProbabilisticPredictionSaccharomyces2002a: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{gramstatNucleicAcidbindingZinc1994, title = {The Nucleic Acid-Binding Zinc Finger Protein of Potato Virus {{M}} Is Translated by Internal Initiation as Well as by Ribosomal Frameshifting Involving a Shifty Stop Codon and a Novel Mechanism of {{P-site}} Slippage.}, author = {Gramstat, A. and Prufer, D. and Rohde, W.}, year = 1994, journal = {Nucleic Acids Research}, volume = {22}, number = {19}, pages = {3911–3917}, publisher = {Oxford University Press}, doi = {10.1093/nar/22.19.3911}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308388/}, abstract = {The genes for the capsid protein CP and the nucleic acid-binding 12K protein (pr12) of potato virus M (PVM) constitute the 3’ terminal gene cluster of the PVM RNA genome. Both proteins are presumably translated from a single subgenomic RNA. We have identified two translational strategies operating in pr12 gene expression. Internal initiation at the first and the second AUG codon of the pr12 coding sequence results in the synthesis of the 12K protein. In addition the protein is produced as a CP/12K transframe protein by ribosomal frameshifting. For these studies parts of the CP and pr12 coding sequences including the putative frameshift region were introduced into an internal position of the beta-glucuronidase gene. Mutational analyses in conjunction with in vitro translation experiments identified a homopolymeric string of four adenosine nucleotides which together with a 3’ flanking UGA stop codon were required for efficient frameshifting. The signal AAAAUGA is the first frameshift signal with a shifty stop codon to be analyzed in the eukaryotic system. Substitution of the four consecutive adenosine nucleotides by UUUU increased the efficiency of frameshifting, while substitution by GGGG or CCCC dramatically reduced the synthesis of the transframe protein. Also, UAA and UAG could replace the opal stop codon without effect on the frameshifting event, but mutation of UGA to the sense codon UGG inhibited transframe protein formation. These findings suggest that the mechanism of ribosomal frameshifting at the PVM signal is different from the one described by the ‘simultaneous slippage’ model in that only the string of four adenosine nucleotides represents the slippery sequence involved in a -1 P-site slippage}, keywords = {3,Adenosine,Capsid,COAT PROTEIN,Codon,efficiency,ESCHERICHIA-COLI,expression,frameshift,Frameshifting,gene,Gene Expression,GENE-EXPRESSION,Genes,Genome,GENOME ORGANIZATION,IDENTIFICATION,In Vitro,in vitro translation,IN-VITRO,initiation,INVITRO,M,MECHANISM,MODEL,MOSAIC-VIRUS,Mutation,nosource,Nucleotides,P SITE,P-SITE,protein,Proteins,REGION,ribosomal frameshifting,Rna,RNA-POLYMERASE,sequence,SEQUENCES,SIGNAL,SLIPPAGE,STOP CODON,SYSTEM,TOBACCO STREAK VIRUS,translation,virus} }

@article{grannemanRibosomeBiogenesisKnobs2004, title = {Ribosome Biogenesis: Of Knobs and {{RNA}} Processing}, author = {Granneman, S. and Baserga, S.J.}, year = 2004, month = may, journal = {Exp. Cell. Res.}, volume = {296}, number = {1}, pages = {43–50}, publisher = {Elsevier}, doi = {10.1016/j.yexcr.2004.03.016}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014482704001284}, abstract = {The synthesis of ribosomes in eukaryotes involves processing of pre-ribosomal RNA (pre-rRNA) and sequential assembly of a large number of ribosomal proteins on the rRNAs. Although we have gained tremendous insights into the processing of pre-rRNA intermediates in the last three decades, little was known about the dynamic nature of ribosome biogenesis. Only recently the development of efficient affinity-purification procedures and mass-spectrometry techniques has allowed the isolation of large pre-ribosomal complexes, which led to the identification of several ribosome assembly intermediates and a large number of novel ribosome assembly factors. In this mini-review, we summarize some of the discoveries that have been made in the field of ribosome biogenesis in the past 30 years and highlight some key aspects about what remains to be learned}, keywords = {0,assembly,Biochemistry,BIOGENESIS,Biophysics,COMPLEX,COMPLEXES,development,DISCOVERY,IDENTIFICATION,INTERMEDIATE,La,Macromolecular Substances,metabolism,nosource,Nuclear Proteins,physiology,PRE-RIBOSOMAL-RNA,PRECURSOR,protein,Proteins,Review,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,ribosome biogenesis,Ribosomes,Rna,RNA Precursors,rRNA,Support,techniques,ultrastructure,Yeasts} } % == BibTeX quality report for grannemanRibosomeBiogenesisKnobs2004: % ? Possibly abbreviated journal title Exp. Cell. Res.

@article{grannemanBuildingRibosomesEven2007, title = {Building Ribosomes: Even More Expensive than Expected?}, author = {Granneman, S. and Tollervey, D.}, year = 2007, month = jun, journal = {Current biology}, volume = {17}, number = {11}, pages = {R415-R417}, publisher = {Elsevier}, doi = {10.1016/j.cub.2007.04.011}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982207012511}, abstract = {Recent quantitative analyses of ribosomal protein trafficking in HeLa cells have revealed a prominent and unexpected role for the proteasome in regulating the availability of ribosomal proteins for subunit assembly}, keywords = {assembly,BIOLOGY,CELLS,Hela Cells,HELA-CELLS,La,nosource,protein,Proteins,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,SUBUNIT} } % == BibTeX quality report for grannemanBuildingRibosomesEven2007: % ? unused Journal abbr (“Curr.Biol”)

@article{grantMappingTrichoderminResistence1976, title = {Mapping of Trichodermin Resistence in ⬚{{Saccharomyces}} Cerevisiae⬚: A Genetic Locus for a Component of the {{60S}} Ribosomal Subunit.}, author = {Grant, P.G. and Schindler, D. and Davies, J.E.}, year = 1976, journal = {Genetics}, volume = {83}, pages = {667–673}, doi = {10.1093/genetics/83.4.667}, abstract = {Resistance to the protein synthesis inhibitor trichodermin in Saccharomyces cerevisiae has been studied. A single recessive nuclear gene was responsible for resistance. The resistance locus, tcm1 was found to be closely linked (1 centi-morgan) to the locus pet 17 on the right arm of chromosome XV. The mutation to trichodermin resistance conferred resistance to other 12,13-epoxytrichothecenes and to the structurally unrelated antibiotic anisomycin.}, keywords = {anisomycin,antibiotic,antibiotics,COMPONENT,drugs,gene,Genetic,L3,mapping,Mutation,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,RIBOSOMAL-SUBUNIT,ribosome,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUBUNIT,TCM1,trichodermin,yeast} }

@article{grayControlTranslationInitiation1998, title = {Control of Translation Initiation in Animals}, author = {Gray, N.K. and Wickens, M.}, year = 1998, month = jan, journal = {Annual review of cell and developmental }, volume = {14}, number = {1}, pages = {399–458}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, issn = {1081-0706}, doi = {10.1146/annurev.cellbio.14.1.399}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.cellbio.14.1.399 http://www.ncbi.nlm.nih.gov/pubmed/9891789}, abstract = {Regulation of translation initiation is a central control point in animal cells. We review our current understanding of the mechanisms of regulation, drawing particularly on examples in which the biological consequences of the regulation are clear. Specific mRNAs can be controlled via sequences in their 5’ and 3’ untranslated regions (UTRs) and by alterations in the translation machinery. The 5’UTR sequence can determine which initiation pathway is used to bring the ribosome to the initiation codon, how efficiently initiation occurs, and which initiation site is selected. 5’UTR-mediated control can also be accomplished via sequence-specific mRNA-binding proteins. Sequences in the 3’ untranslated region and the poly(A) tail can have dramatic effects on initiation frequency, with particularly profound effects in oogenesis and early development. The mechanism by which 3’UTRs and poly(A) regulate initiation may involve contacts between proteins bound to these regions and the basal translation apparatus. mRNA localization signals in the 3’UTR can also dramatically influence translational activation and repression. Modulations of the initiation machinery, including phosphorylation of initiation factors and their regulated association with other proteins, can regulate both specific mRNAs and overall translation rates and thereby affect cell growth and phenotype}, pmid = {9891789}, keywords = {0,3,3’ Untranslated Regions,3’ Untranslated Regions: genetics,5’ Untranslated Regions,5’ Untranslated Regions: genetics,activation,animal,Animals,ASSOCIATION,CELLS,Codon,development,Gene Expression Regulation,genetics,GROWTH,human,Humans,initiation,initiation factors,INITIATION SITE,INITIATION-FACTOR,interactions,La,LOCALIZATION,maternal mrnas,MECHANISM,MECHANISMS,Messenger,Messenger: genetics,mRNA,nosource,PATHWAY,Peptide Chain Initiation,Phenotype,Phosphorylation,poly(A),POLY(A) TAIL,polyadenylation,protein,Protein Biosynthesis,Proteins,REGION,regulation,repression,Review,ribosome,Rna,RNA,rna-protein,RNAMessenger,sequence,SEQUENCES,SIGNAL,SITE,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,translation,TRANSLATION INITIATION,Translational,TranslationGenetic,untranslated regions,Untranslated Regions,utrs} } % == BibTeX quality report for grayControlTranslationInitiation1998: % ? unused Journal abbr (“Annu.Rev.Cell Dev.Biol.”)

@article{greenIdentificationNovelVertebrate1996a, title = {Identification of a Novel Vertebrate Circadian Clock-Regulated Gene Encoding the Protein Nocturnin [See Comments]}, author = {Green, C.B. and Besharse, J.C.}, year = 1996, month = dec, journal = {Proc.Natl.Acad.Sci.USA}, volume = {93}, number = {25}, pages = {14884–14888}, doi = {10.1073/pnas.93.25.14884}, keywords = {analysis,cloning,COMPONENT,differential display,gene,IDENTIFICATION,Leucine,mRNA,nosource,protein,sequence,SYSTEM,transcription,TRANSCRIPTION FACTOR,Xenopus,Xenopus laevis,yeast} } % == BibTeX quality report for greenIdentificationNovelVertebrate1996a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{greenMutationsNucleotidesG22511997a, title = {Mutations at Nucleotides {{G2251}} and {{U2585}} of 23 {{S rRNA}} Perturb the Peptidyl Transferase Center of the Ribosome}, author = {Green, R. and Samaha, R.R. and Noller, H.F.}, year = 1997, month = feb, journal = {J.Mol Biol.}, volume = {266}, number = {1}, pages = {40–50}, doi = {10.1006/jmbi.1996.0780}, url = {ISI:A1997WH76800006}, abstract = {Previous experiments have shown that the phylogenetically conserved G2252 of 23 S rRNA forms a Watson-Crick base-pair with C74 of peptidyl-tRNA. In the studies presented here, site-directed mutations were introduced at two other conserved positions in 23 S rRNA, G2251 and U2585, that were previously implicated in interaction of the CCA acceptor end of tRNA with the 50 S subunit P site. The mutant 23 S rRNAs were characterized by determining (1) the in vivo phenotypes, (2) the ability of mutant ribosomes to bind tRNA oligonucleotide fragments in vitro, using footprinting with allele-specific primer extension and (3) the ability of mutant ribosomes to catalyze peptide bond formation using a chimeric reconstitution approach. Mutations at either position confer a dominant lethal phenotype when the mutant 23 S rRNA is coexpressed with the endogenous wild-type 23 S rRNA. Mutations at 2585 disrupt binding of the wild-type (CCA) tRNA oligonucleotide fragment and cause a modest decrease in the peptidyl transferase activity of reconstituted ribosomes. By contrast, mutations at 2251 abolish both binding of the wild-type (CCA) tRNA fragment and peptidyl transferase activity using the wild-type tRNA fragment. In neither case was the loss of binding or peptidyl transferase activity suppressed by mutations in the tRNA oligonucleotide fragment. Chemical modification analysis revealed that mutations at 2251 perturb the reactivity of bases 2584 to 2586, providing further evidence that the 2250 loop of 23 S rRNA interacts, either directly or indirectly, with the 2585 region in the central loop of domain V of 23 S rRNA. (C) 1997 Academic Press Limited}, keywords = {analysis,BASES,BINDING,chimeric reconstitution,COMPLEX,Dna,DOMAIN-V,ESCHERICHIA-COLI,IDENTIFICATION,In Vitro,IN-VITRO,IN-VIVO,LOOP,MODEL,modification,Mutation,MUTATIONS,nosource,Nucleotides,P-SITE,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Phenotype,polymerase,primer extension,REGION,ribosome,Ribosomes,rRNA,rRNA mutants,SITE,SUBUNIT,TRANSFER-RNA,tRNA,tRNA binding} } % == BibTeX quality report for greenMutationsNucleotidesG22511997a: % ? Possibly abbreviated journal title J.Mol Biol.

@article{greenRibosomecatalyzedPeptidebondFormation1998, title = {Ribosome-Catalyzed Peptide-Bond Formation with an {{A-site}} Substrate Covalently Linked to {{23S}} Ribosomal {{RNA}}}, author = {Green, R. and Switzer, C. and Noller, H.F.}, year = 1998, month = apr, journal = {Science}, volume = {280}, number = {5361}, pages = {286–289}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.280.5361.286}, url = {http://www.sciencemag.org/content/280/5361/286.short}, abstract = {In the ribosome, the aminoacyl-transfer RNA (tRNA) analog 4-thio-dT-p-C-p-puromycin crosslinks photochemically with G2553 of 23S ribosomal RNA (rRNA). This covalently linked substrate reacts with a peptidyl-tRNA analog to form a peptide bond in a peptidyl transferase-catalyzed reaction. This result places the conserved 2555 loop of 23S rRNA at the peptidyl transferase A site and suggests that peptide bond formation can occur uncoupled from movement of the A-site tRNA. Crosslink formation depends on occupancy of the P site by a tRNA carrying an intact CCA acceptor end, indicating that peptidyl-tRNA, directly or indirectly, helps to create the peptidyl transferase A site}, keywords = {16S RNA,A SITE,A-SITE,AMINOACYL-TRANSFER-RNA,COMPLEXES,DIRECTED CROSS-LINKING,DOMAIN-V,ESCHERICHIA-COLI RIBOSOMES,IDENTIFICATION,LOOP,Movement,nosource,P-SITE,P-SITES,peptide bond formation,PEPTIDE-BOND FORMATION,peptidyl transferase,PEPTIDYL-TRANSFERASE,POSITIONS,REGION,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Rna,rRNA,SITE,TRANSFERASE CENTER,tRNA} }

@article{greenfieldTropomyosinRequiresIntact2002, title = {Tropomyosin Requires an Intact {{N-terminal}} Coiled Coil to Interact with Tropomodulin}, author = {Greenfield, N.J. and Fowler, V.M.}, year = 2002, month = may, journal = {Biophysical journal}, volume = {82}, number = {5}, pages = {2580–2591}, publisher = {Elsevier}, doi = {10.1016/S0006-3495(02)75600-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006349502756002}, abstract = {Tropomodulins (Tmods) are tropomyosin (TM) binding proteins that bind to the pointed end of actin filaments and modulate thin filament dynamics. They bind to the N termini of both “long” TMs (with the N terminus encoded by exon 1a of the alpha-TM gene) and “short” nonmuscle TMs (with the N terminus encoded by exon 1b). In this present study, circular dichroism was used to study the interaction of two designed chimeric proteins, AcTM1aZip and AcTM1bZip, containing the N terminus of a long or a short TM, respectively, with protein fragments containing residues 1 to 130 of erythrocyte or skeletal muscle Tmod. The binding of either TMZip causes similar conformational changes in both Tmod fragments promoting increases in both alpha-helix and beta-structure, although they differ in binding affinity. The circular dichroism changes in the Tmod upon binding and modeling of the Tmod sequences suggest that the interface between TM and Tmod includes a three- or four-stranded coiled coil. An intact coiled coil at the N terminus of the TMs is essential for Tmod binding, as modifications that disrupt the N-terminal helix, such as removal of the N-terminal acetyl group from AcTM1aZip or striated muscle alpha-TM, or introduction of a mutation that causes nemaline myopathy, Met-8-Arg, into AcTM1aZip destroyed Tmod binding}, keywords = {0,Acetylation,Actins,Amino Acid Sequence,BINDING,BINDING PROTEIN,Binding Sites,BINDING-PROTEIN,Carrier Proteins,chemistry,Chimeric Proteins,Circular Dichroism,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,DYNAMICS,EXON,FUSION PROTEIN,gene,genetics,human,Humans,interface,Kinetics,La,metabolism,Microfilament Proteins,ModelsMolecular,modification,Molecular Sequence Data,Mutation,MyopathiesNemaline,nosource,pathology,Peptide Fragments,protein,Protein Conformation,Protein Denaturation,Proteins,Recombinant Fusion Proteins,REQUIRES,RESIDUES,sequence,Sequence Alignment,Sequence HomologyAmino Acid,SEQUENCES,Support,Thermodynamics,Tropomodulin,Tropomyosin} } % == BibTeX quality report for greenfieldTropomyosinRequiresIntact2002: % ? unused Journal abbr (“Biophys.J.”)

@article{gregoryMolecularBasisDiamondBlackfan2007, title = {Molecular Basis of {{Diamond-Blackfan}} Anemia: Structure and Function Analysis of {{RPS19}}}, author = {Gregory, L.A. and {Aguissa-Toure}, A.H. and Pinaud, N. and Legrand, P. and Gleizes, P.E. and Fribourg, S.}, year = 2007, journal = {Nucleic Acids Res.}, volume = {35}, number = {17}, pages = {5913–5921}, doi = {10.1093/nar/gkm626}, url = {PM:17726054}, abstract = {Diamond-Blackfan anemia (DBA) is a rare congenital disease linked to mutations in the ribosomal protein genes rps19, rps24 and rps17. It belongs to the emerging class of ribosomal disorders. To understand the impact of DBA mutations on RPS19 function, we have solved the crystal structure of RPS19 from Pyrococcus abyssi. The protein forms a five alpha-helix bundle organized around a central amphipathic alpha-helix, which corresponds to the DBA mutation hot spot. From the structure, we classify DBA mutations relative to their respective impact on protein folding (class I) or on surface properties (class II). Class II mutations cluster into two conserved basic patches. In vivo analysis in yeast demonstrates an essential role for class II residues in the incorporation into pre-40S ribosomal particles. This data indicate that missense mutations in DBA primarily affect the capacity of the protein to be incorporated into pre-ribosomes, thus blocking maturation of the pre-40S particles}, keywords = {0,Amino Acid Sequence,analysis,Anemia,AnemiaDiamond-Blackfan,Archaeal Proteins,chemistry,crystal structure,CRYSTAL-STRUCTURE,disease,FORM,gene,Genes,genetics,Humans,IN-VIVO,La,MATURATION,metabolism,ModelsMolecular,Molecular Sequence Data,Mutation,MutationMissense,MUTATIONS,nosource,PARTICLES,protein,Protein Folding,Proteins,Pyrococcus abyssi,RESIDUES,Ribosomal Proteins,RIBOSOMAL-PROTEIN,Ribosomes,Sequence Alignment,structure,Support,Surface Properties,yeast} } % == BibTeX quality report for gregoryMolecularBasisDiamondBlackfan2007: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{gregoryMutationsConservedLoop1999a, title = {Mutations in the Conserved {{P}} Loop Perturb the Conformation of Two Structural Elements in the Peptidyl Transferase Center of 23 {{S}} Ribosomal {{RNA}}}, author = {Gregory, S.T. and Dahlberg, A.E.}, year = 1999, month = jan, journal = {Journal of Molecular Biology}, volume = {285}, number = {4}, pages = {1475–1483}, doi = {10.1006/jmbi.1998.2410}, url = {ISI:000078447300014}, abstract = {Evidence is presented for the participation of the P loop (nucleotides G2250-C2254) of 23 S rRNA in establishing the tertiary structure of the peptidyl transferase center. Single base substitutions were introduced into the P loop, which participates in peptide bond formation through direct interaction with the CCA end of P site-bound tRNA. These mutations altered the pattern of reactivity of RNA to chemical probes in a structural subdomain encompassing the P loop and extending roughly from G2238 to A2433. Most of the effects on chemical modification in the P loop subdomain occurred near sites of tertiary interactions inferred from comparative sequence analysis, indicating that these mutations perturb the tertiary structure of this region of RNA. Changes in chemical modification were also seen in a subdomain composed of the 2530 loop (nucleotides G2529-A2534) and the A loop (nucleotides U2552-C2556), the latter a site of interaction with the CCA end of A site-bound tRNA. Mutations in the P loop induced effects on chemical modification that were commensurate with the severity of their characterized functional defects in peptide bond formation, tRNA binding and translational fidelity. These results indicate that, in addition to its direct role in peptide bond formation, the P loop contributes to the tertiary structure of the peptidyl transferase center and influences the conformation of both the acceptor and peptidyl tRNA binding sites. (C) 1999 Academic Press}, keywords = {A-SITE,analysis,BASE,BINDING,Binding Sites,BINDING-SITE,BOND FORMATION,CONFORMATION,ELEMENTS,ESCHERICHIA-COLI,Fidelity,HAIRPINS,LOOP,modification,MOTIFS,Mutation,MUTATIONS,nosource,Nucleotides,P and A sites,P loop,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,REGION,ribosomal RNA,RIBOSOMAL-RNA,ribozyme,Rna,RNA conformation,rRNA,sequence,Sequence Analysis,SITE,SITES,stability,Structural,structure,TRANSFERASE CENTER,translational fidelity,tRNA,tRNA binding} }

@article{grens53untranslatedRegions1990, title = {The 5’- and 3’-Untranslated Regions of Ornithine Decarboxylase {{mRNA}} Affect the Translational Efficiency}, author = {Grens, A. and Scheffler, I.E.}, year = 1990, month = jul, journal = {Journal of Biological Chemistry}, volume = {265}, number = {20}, pages = {11810–11816}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(19)38470-4}, url = {http://www.jbc.org/content/265/20/11810.short}, abstract = {We have determined the roles of the 5’- and 3’-untranslated regions (UTR) of ornithine decarboxylase (ODC) mRNA in the post-transcriptional regulation of this enzyme. A series of expression vectors were constructed in which portions of the ODC 5’ and/or 3’ UTRs were placed flanking a reporter gene coding sequence, either firefly luciferase or chloramphenicol acetyltransferase, so as to generate a hybrid transcript. Translation of these chimeric genes in transient expression assays in wild type and ODC-deficient hamster cells was examined in the presence of normal or depleted polyamine pools. The ODC 5’ UTR suppresses translation of the coding sequence it precedes irrespective of polyamine levels, and this effect is shown to be due to the GC-rich 5’ segment of the UTR. The same effect is observed in vivo and in a rabbit reticulocyte in vitro translation system. The GC-rich region has the potential to form a very stable hairpin structure and inhibits translation in a position-dependent but orientation-independent manner. Insertion of the 3’ UTR of ODC downstream of the translation termination codon of the reporter gene but prior to the polyadenylation signal partially relieves the suppression of translation imposed by the 5’ UTR; the overall translatability of the message improves 30-50-fold}, keywords = {0,3,3’ UNTRANSLATED REGION,3’ Untranslated Regions,3’-UNTRANSLATED REGION,Animals,assays,Base Sequence,BIOLOGY,BlottingNorthern,Cell Line,CELLS,Chloramphenicol,CHLORAMPHENICOL ACETYLTRANSFERASE,Chloramphenicol O-Acetyltransferase,coding sequence,Codon,DOWNSTREAM,efficiency,enzyme,expression,FIREFLY LUCIFERASE,FORM,gene,Genes,Genetic Vectors,genetics,In Vitro,in vitro translation,IN-VITRO,IN-VIVO,La,luciferase,Luciferases,MESSAGE,Molecular Sequence Data,mRNA,Mutation,nosource,Nucleic Acid Conformation,Nucleic Acid Hybridization,Ornithine Decarboxylase,Polyadenylation,polyamine,post-transcriptional regulation,POSTTRANSCRIPTIONAL REGULATION,Protein Biosynthesis,REGION,regulation,Rna,RNA ProcessingPost-Transcriptional,RNAMessenger,sequence,SERIES,SIGNAL,structure,Support,suppression,SYSTEM,termination,TERMINATION CODON,TERMINATION-CODON,TRANSCRIPT,Transfection,translation,TRANSLATION TERMINATION,vector,vectors,WILD-TYPE} } % == BibTeX quality report for grens53untranslatedRegions1990: % ? unused Journal abbr (“J.Biol Chem.”)

@article{grollmanInhibitorsProteinBiosynthesis1967, title = {Inhibitors of Protein Biosynthesis. {{II}}. {{Mode}} of Action of Anisomycin.}, author = {Grollman, A.P.}, year = 1967, month = jul, journal = {Journal of Biological Chemistry}, volume = {242}, number = {13}, pages = {3226–3233}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1016/S0021-9258(18)95953-3}, url = {http://www.jbc.org/content/242/13/3226.short http://www.ncbi.nlm.nih.gov/pubmed/6027796}, pmid = {6027796}, keywords = {Animals,anisomycin,Anti-Bacterial Agents,Anti-Bacterial Agents: pharmacology,Antimetabolites,Antimetabolites: pharmacology,biosynthesis,Blood Proteins,Blood Proteins: biosynthesis,Centrifugation,Density Gradient,DNA,drugs,Experimental,HeLa Cells,Hemoglobins,Hemoglobins: biosynthesis,Neoplasm,Neoplasm Proteins,Neoplasm Proteins: biosynthesis,Neoplasm: biosynthesis,Neoplasms,nosource,Peptide Biosynthesis,protein,Protein Biosynthesis,Pyrrolidines,Pyrrolidines: pharmacology,Rabbits,Reticulocytes,Reticulocytes: cytology,Reticulocytes: metabolism,ribosome,Ribosomes,Ribosomes: drug effects,Ribosomes: metabolism,RNA,Saccharomyces,Saccharomyces: cytology,Saccharomyces: metabolism,Transfer,Transfer: metabolism} } % == BibTeX quality report for grollmanInhibitorsProteinBiosynthesis1967: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{gromadskiUniformResponseMismatches2006a, title = {A Uniform Response to Mismatches in Codon-Anticodon Complexes Ensures Ribosomal Fidelity}, author = {Gromadski, K.B. and Daviter, T. and Rodnina, M.V.}, year = 2006, month = feb, journal = {Mol.Cell}, volume = {21}, number = {3}, pages = {369–377}, doi = {10.1016/j.molcel.2005.12.018}, url = {PM:16455492}, abstract = {Ribosomes take an active part in aminoacyl-tRNA selection by distinguishing correct and incorrect codon-anticodon pairs. Correct codon-anticodon complexes are recognized by a network of ribosome contacts that are specific for each position of the codon-anticodon duplex and involve A-minor RNA interactions. Here, we show by kinetic analysis that single mismatches at any position of the codon-anticodon complex result in slower forward reactions and a uniformly 1000-fold faster dissociation of the tRNA from the ribosome. This suggests that high-fidelity tRNA selection is achieved by a conformational switch of the decoding site between accepting and rejecting modes, regardless of the thermodynamic stability of the respective codon-anticodon complexes or their docking partners at the decoding site. The forward reactions on mismatched codons were particularly sensitive to the disruption of the A-minor interactions with 16S rRNA and determined the variations in the misreading efficiency of near-cognate codons}, keywords = {16S,analysis,Codon,CODONS,COMPLEX,COMPLEXES,decoding,DISRUPTION,efficiency,Fidelity,La,nosource,POSITION,ribosome,Ribosomes,Rna,rRNA,SELECTION,SITE,stability,thermodynamic stability,tRNA} } % == BibTeX quality report for gromadskiUniformResponseMismatches2006a: % ? Possibly abbreviated journal title Mol.Cell

@article{gubserStructurePolyadenylationRegulatory1996, title = {Structure of the Polyadenylation Regulatory Element of the Human {{U1A}} Pre-{{mRNA}} 3’-Untranslated Region and Interaction with the {{U1A}} Protein}, author = {Gubser, C.C. and Varani, G.}, year = 1996, month = feb, journal = {Biochemistry}, volume = {35}, number = {7}, pages = {2253–2267}, publisher = {ACS Publications}, doi = {10.1021/bi952319f}, url = {http://pubs.acs.org/doi/abs/10.1021/bi952319f}, keywords = {3’ UTR,BINDING,COMPLEX,COMPLEXES,human,nosource,poly(A),protein,Protein Binding,Rna,sequence,Structural,structure} }

@article{guddatProteinmediatedNuclearExport1990, title = {Protein-Mediated Nuclear Export of {{RNA}}: {{5S rRNA}} Containing Small {{RNPs}} in Xenopus Oocytes}, author = {Guddat, U. and Bakken, A.H. and Pieler, T.}, year = 1990, month = feb, journal = {Cell}, volume = {60}, number = {4}, pages = {619–628}, publisher = {Elsevier}, doi = {10.1016/0092-8674(90)90665-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867490906652}, abstract = {We have analyzed RNP formation and nucleocytoplasmic migration of 5S RNA and 5S RNA variants transcribed from microinjected genes in Xenopus oocytes. Using antisera against three different proteins we find that newly transcribed nuclear 5S rRNA transiently interacts with La antigen. The La protein is then replaced by either ribosomal protein L5 or the 5S gene-specific transcription factor IIIA (TFIIIA), and each of these two RNPs migrates out of the nucleus and accumulates in the cytoplasm. RNA molecules that are impaired in their ability to interact with L5 and TFIIIA are retained in the nucleus. Thus, L5 and TFIIIA define a new functional class of proteins involved in the nuclear export of RNA. In addition, we show that RNP migration depletes the nucleus of TFIIIA, resulting in a loss of transcription competence for newly injected 5S rRNA genes}, keywords = {0,5S RNA,5S rRNA,animal,ANTIGEN,Cell Nucleus,Cytoplasm,Dna,Female,gene,Genes,genetics,L5,La,metabolism,Microinjections,nosource,Oocytes,protein,Proteins,RIBONUCLEOPROTEIN,Ribonucleoproteins,RibonucleoproteinsSmall Nuclear,Ribosomal Proteins,Rna,RNA ProcessingPost-Transcriptional,RNARibosomal,RNARibosomal5S,RNASmall Nuclear,rRNA,rRNA genes,supportnon-u.s.gov’t,TFIIIA,transcription,TRANSCRIPTION FACTOR,Transcription Factor TFIIIA,Transcription Factors,TranscriptionGenetic,Xenopus,Xenopus laevis,Xenopus oocyte} }

@article{guhaniyogiRegulationMRNAStability2001, title = {Regulation of {{mRNA}} Stability in Mammalian Cells}, author = {Guhaniyogi, J. and Brewer, G.}, year = 2001, month = mar, journal = {Gene}, volume = {265}, number = {1-2}, pages = {11–23}, publisher = {Elsevier}, doi = {10.1016/S0378-1119(01)00350-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/S037811190100350X http://www.sciencedirect.com/science/article/pii/S037811190100350X}, abstract = {The regulation of mRNA decay is a major control point in gene expression. The stability of a particular mRNA is controlled by specific interactions between its structural elements and RNA-binding proteins that can be general or mRNA-specific. Regulated mRNA stability is achieved through fluctuations in half-lives in response to developmental or environmental stimuli like nutrient levels, cytokines, hormones and temperature shifts as well as environmental stresses like hypoxia, hypocalcemia, viral infection, and tissue injury. Furthermore, in specific disorders like some forms of neoplasia, thalassemia and Alzheimer’s disease, deregulated mRNA stability can lead to the aberrant accumulation of mRNAs and the proteins they encode. This review presents a discussion of some recently identified examples of regulated and deregulated mRNA stability in order to illustrate the diversity of genes regulated by alterations in the degradation rates of their mRNAs. (C) 2001 Elsevier Science B.V. All rights reserved}, keywords = {3 ‘-untranslated region,3’-UNTRANSLATED REGION,AU-RICH ELEMENTS,BINDING-PROTEIN,CHOLESTEROL 7-ALPHA-HYDROXYLASE,Cytokines,DECAY,decay pathways,degradation,disease,ELEMENTS,expression,gene,Gene Expression,GENE-EXPRESSION,Genes,GROWTH-FACTOR,hormonal regulation of mRNA turnover deregulated d,hormonal regulation of mRNA turnover deregulated decay,Hormones,MAMMALIAN-CELLS,MESSENGER-RNA STABILITY,mRNA,mRNA decay,mRNA stability,nosource,POLY(A) TAIL,POSTTRANSCRIPTIONAL REGULATION,protein,PROTEIN-CODING REGION,Proteins,regulation,Review,RNA-Binding Proteins,stability,Structural,Temperature} }

@article{guillierTranslationalFeedbackRegulation2002, title = {Translational Feedback Regulation of the Gene for {{L35}} in {{Escherichia}} Coli Requires Binding of Ribosomal Protein {{L20}} to Two Sites in Its Leader {{mRNA}}: A Possible Case of Ribosomal {{RNA-messenger RNA}} Molecular Mimicry.}, author = {Guillier, M. and Allemand, F. and Raibaud, S. and Dardel, F. and Springer, M. and Chiaruttini, C.}, year = 2002, month = jul, journal = {RNA.}, volume = {8}, number = {7}, pages = {878–889}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838202029084}, url = {http://rnajournal.cshlp.org/content/8/7/878.short}, abstract = {In addition to being a component of the large ribosomal subunit, ribosomal protein L20 of Escherichia coli also acts as a translational repressor. L20 is synthesized from the IF3 operon that contains three cistrons coding for IF3, and ribosomal proteins L35 and L20. L20 directly represses the expression of the gene encoding L35 and the expression of its own gene by translational coupling. All of the cis- acting sequences required for repression by L20, called the operator, are found on an mRNA segment extending from the middle of the IF3 gene to the start of the L35 gene. L20-mediated repression requires a long- range base-pairing interaction between nucleotide residues within the IF3 gene and residues just upstream of the L35 gene. This interaction results in the formation of a pseudoknot. Here we show that L20 causes protection of nucleotide residues in two regions of the operator in vitro. The first region is the pseudoknot itself and the second lies in an irregular stem located upstream of the L35 gene. By primer extension analysis, we show that L20 specifically induces reverse transcriptase stops in both regions. Therefore, these two regions define two L20- binding sites in the operator. Using mutations and deletions of rpml’- ‘lacZ fusions, we show that both sites are essential for repression in vivo. However L20 can bind to each site independently in vitro. One site is similar to the L20-binding site on 23S rRNA. Here we propose that L20 recognizes its mRNA and its rRNA in similar way}, keywords = {0,5’ Untranslated Regions,analysis,Bacterial,Base Pairing,Base Sequence,BINDING,Binding Sites,chemistry,COMPONENT,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,expression,Feedback,gene,GenesBacterial,genetics,In Vitro,IN-VITRO,IN-VIVO,La,metabolism,Molecular Mimicry,Molecular Sequence Data,mRNA,MutagenesisSite-Directed,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Operon,Plant Proteins,primer extension,protein,Proteins,pseudoknot,regulation,Repressor Proteins,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,Rna,RNABacterial,RNARibosomal,RNARibosomal23S,rRNA,sequence,Sequence Deletion,SUBUNIT,supportnon-u.s.gov’t,TranslationGenetic,Untranslated Regions} } % == BibTeX quality report for guillierTranslationalFeedbackRegulation2002: % ? Possibly abbreviated journal title RNA.

@article{gundersonInvolvementCarboxylTerminus1997, title = {Involvement of the Carboxyl Terminus of Vertebrate Poly ({{A}}) Polymerase in {{U1A}} Autoregulation and in the Coupling of Splicing and Polyadenylation.}, author = {Gunderson, S.I. and Vagner, S. and {Polycarpou-Schwarz}, M. and Mattaj, I.W.}, year = 1997, month = mar, journal = {Genes & Development}, volume = {11}, number = {6}, pages = {761–773}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.11.6.761}, url = {http://genesdev.cshlp.org/content/11/6/761.short}, keywords = {Amino Acids,analysis,CLEAVAGE,COMPLEX,COMPLEXES,efficiency,enzyme,In Vitro,IN-VITRO,INHIBITION,MUTATIONAL ANALYSIS,nosource,PAP,poly(A),polymerase,protein,PROTEIN COMPLEX,Rna,splicing,structure,yeast} }

@article{guoBasepairingUntranslatedRegions2001, title = {Base-Pairing between Untranslated Regions Facilitates Translation of Uncapped, Nonpolyadenylated Viral {{RNA}}}, author = {Guo, L. and Allen, E.M. and Miller, W.A.}, year = 2001, month = may, journal = {Molecular Cell}, volume = {7}, number = {5}, pages = {1103–1109}, publisher = {Elsevier}, doi = {10.1016/S1097-2765(01)00252-0}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276501002520}, abstract = {Translationally competent mRNAs form a closed loop via interaction of initiation factors with the 5 ’ cap and poly(A) tail. However, many viral mRNAs lack a cap and/or a poly(A) tail. We show that an uncapped, nonpolyadenylated plant viral mRNA forms a closed loop by direct base-pairing (kissing) of a stem loop in the 3 ’ untranslated region (UTR) with a stem loop in the 5 ’ UTR. This allows a sequence in the 3 ’ UTR to confer translation initiation at the 5 ’ -proximal AUG. This base-pairing is also required for replication. Unlike other cap-independent translation mechanisms, the ribosome enters at the 5 ’ end of the mRNA. This remarkably long-distance base-pairing reveals a novel mechanism of cap-independent translation and means by which mRNA UTRs can communicate}, keywords = {3’-END,3’-UNTRANSLATED REGION,Base Pairing,Cap,CAP-INDEPENDENT TRANSLATION,initiation,LOOP,MECHANISM,MECHANISMS,MESSENGER-RNA,mRNA,nosource,poly(A),REGION,REPLICATION,REQUIRES,ribosome,Rna,sequence,SUBGENOMIC RNAS,translation,TRANSLATION INITIATION,Untranslated Regions,virus} }

@article{guo3endformingSignalsYeast1996, title = {3’-End-Forming Signals of Yeast {{mRNA}}}, author = {Guo, Z. and Sherman, F.}, year = 1996, month = dec, journal = {Trends in biochemical sciences}, volume = {21}, number = {12}, pages = {477–481}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000496100578}, abstract = {The signals required for forming 3’-ends of mRNAs from the yeast Saccharomyces cerevisiae differ from the corresponding signals of higher eukaryotes. Yeast signals consist of three elements: (1) the efficiency element, which enhances the efficiency of downstream positioning elements; (2) the positioning element, which positions the poly(A) site; and (3) the actual poly(A) site. These three elements are not only necessary, but also sufficient for mRNA 3’-end formation in yeast}, keywords = {0,animal,efficiency,ELEMENTS,genetics,La,Mammals,metabolism,mRNA,nosource,Poly A,poly(A),Review,Rna,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SIGNAL,supportu.s.gov’tp.h.s.,yeast} }

@article{guschlbauerFourstrandedNucleicAcid1990a, title = {Four-Stranded Nucleic Acid Structures 25 Years Later: From Guanosine Gels to Telomer {{DNA}}.}, author = {Guschlbauer, W. and Chantot, J.F. and Thiele, D.}, year = 1990, month = dec, journal = {Journal of biomolecular structure & dynamics}, volume = {8}, number = {3}, eprint = {2100515}, eprinttype = {pubmed}, pages = {491–511}, doi = {10.1080/07391102.1990.10507825}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2100515}, abstract = {The subject of four-stranded nucleic acid structures is reviewed. Studies on gels formed by guanosine and its analogues have provided appropriate models for the structures of poly(I) and poly(G). The stabilizing influence of certain cations, in particular K+, on Guo-5’-P gels and poly(I) is discussed in the light of recent data on selective K+ stabilization of telomeric DNA structures. The topological possibilities these dG containing sequences could adopt are discussed. In particular the role of the glycosidic linkage (anti/syn), the polarity of the strands and the orientation of the G-tetrad stacks is highlighted}, keywords = {0,Base Sequence,Cations,chemistry,Dna,Gels,Guanosine,La,Magnetic Resonance Spectroscopy,models,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Poly G,Poly I,Polynucleotides,Potassium,Review,sequence,structure} } % == BibTeX quality report for guschlbauerFourstrandedNucleicAcid1990a: % ? unused Journal abbr (“J.Biomol.Struct.Dyn.”)

@article{haenniBehaviourAcetylphenylalanylSoluble1966a, title = {The Behaviour of Acetylphenylalanyl Soluble Ribonucleic Acid in Polyphenylalanine Synthesis⬚⬚ ⬚⬚}, author = {Haenni, A.L. and Chapeville, F.}, year = 1966, month = jan, journal = {Biochim.Biophys.Acta}, volume = {114}, number = {1}, pages = {135–148}, doi = {10.1016/0005-2787(66)90261-9}, keywords = {66141274,Acetates,Acetylation,biosynthesis,cytology,Escherichia coli,In Vitro,Kinetics,metabolism,nosource,Peptides,Phenylalanine,Polynucleotides,Ribosomes,RNATransfer,tRNA,Uracil Nucleotides} } % == BibTeX quality report for haenniBehaviourAcetylphenylalanylSoluble1966a: % ? Possibly abbreviated journal title Biochim.Biophys.Acta

@article{haganCharacterizationCisActing1995, title = {Characterization of ⬚cis⬚-Acting Sequences and Decay Intermediates Involved in Nonsense-Mediated {{mRNA}} Turnover.}, author = {Hagan, K.W. and {Ruiz-Echevarria}, M.J. and Quan, Y. and Peltz, S.W.}, year = 1995, journal = {Mol.Cell.Biol.}, volume = {15}, pages = {809–823}, doi = {10.1128/MCB.15.2.809}, keywords = {DECAY,downstream element,mRNA,nonsense-mediated decay,nosource,sequence,turnover} } % == BibTeX quality report for haganCharacterizationCisActing1995: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{hageSurfeitFactorsWhy2004a, title = {A Surfeit of Factors: Why Is Ribosome Assembly so Much More Complicated in Eukrayotes than Bacteria?}, author = {Hage, A.E. and Tollervey, D.}, year = 2004, journal = {RNA Biology}, volume = {1}, number = {1}, pages = {45–50}, doi = {10.4161/rna.1.1.932}, url = {⬚http://www.landesbioscience.com/journals/rnabiology/rnabiologypdf/a11820916767671121y00gf30471010/elhageRNA1-1.pdf⬚⬚⬚ ⬚⬚}, abstract = {Recent years have seen a dramatic increase in the number of ribosome synthesis factors identified in the yeast ⬚Saccharomyces cerevisiae⬚. Most of these are not predicted to directly catalyze either RNA processing or modification, and they are therefore predicted to function in some sense as assembly factors, promoting the assembly and/or disassembly of the processing and modification machinery, binding of the ribosomal proteins and correct folding of the pre-rRNAs and rRNAs. In contrast, ribosome synthesis in ⬚E.coli⬚, which has also been extensively analyzed, appears to involve a very small number of potential assembly factors. Here we will consider the differences between eukaryotic and bacterial ribosome synthesis that may underlie this distinction.}, keywords = {assembly,Bacteria,Bacterial,BINDING,CEREVISIAE,E.coli,modification,nosource,protein,Proteins,Ribosomal Proteins,ribosome,RIBOSOME SYNTHESIS,Rna,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,yeast} }

@misc{hagstromOverviewIntegratedGenomic1992, title = {Overview of the {{Integrated Genomic Data System}} ({{IGD}}).}, author = {Hagstrom, R. and Michalls, G. and Overbeek, R. and Price, M. and Taylor, R.}, year = 1992, month = oct, publisher = {Argonne National Laboratory}, keywords = {genomic,nosource,SYSTEM} } % == BibTeX quality report for hagstromOverviewIntegratedGenomic1992: % ? Title looks like it was stored in title-case in Zotero

@article{hagstromOverviewGRACEDatabase1993, title = {Overview of {{GRACE–A}} Database System for Analysis of Multiple Genomes.}, author = {Hagstrom, R. and Michaels, G. and Overbeek, R. and Price, M. and Taylor, R.}, year = 1993, journal = {Proc.23rd (1993) Hawaiian Intl.Conf.on System Sci.}, keywords = {analysis,DATABASE,Genome,No DOI found,nosource,SYSTEM} } % == BibTeX quality report for hagstromOverviewGRACEDatabase1993: % ? Possibly abbreviated journal title Proc.23rd (1993) Hawaiian Intl.Conf.on System Sci.

@article{haitElongationFactor2Kinase1996a, title = {Elongation Factor-2 Kinase: Immunological Evidence for the Existence of Tissur-Specific Isoforms,}, author = {Hait, W.N. and Ward and Trakht, I.N. and Ryazanov, A.G.}, year = 1996, journal = {FEBS Lett.}, volume = {397}, pages = {55–60}, doi = {10.1016/S0014-5793(96)01140-4}, keywords = {cancer,Cell Line,cell lines,EF-2,EF-2 kinase,elongation,kinase,nosource} } % == BibTeX quality report for haitElongationFactor2Kinase1996a: % ? Possibly abbreviated journal title FEBS Lett.

@article{halbeisenAffinityPurificationRibosomes2009, title = {Affinity Purification of Ribosomes to Access the Translatome}, author = {Halbeisen, R.E. and Scherrer, T. and Gerber, A.P.}, year = 2009, month = jul, journal = {Methods}, volume = {48}, number = {3}, pages = {306–310}, publisher = {Elsevier}, doi = {10.1016/j.ymeth.2009.04.003}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1046202309000863}, abstract = {We describe ribosome affinity purification (RAP), a method that allows rapid purification of ribosomes and associated messages from the yeast Saccharomyces cerevisiae. The method relies on the expression of protein A tagged versions of the ribosomal protein Rpl16, which is used to efficiently recover endogenously formed ribosomes and polysomes from cellular extracts with IgG-coupled spherical microbeads. This approach can be applied to profile reactions of the translatome, which refers to all messages associated with ribosomes, with those of the transcriptome using DNA microarrays. In addition, ribosomal proteins, their modifications, and/or other associated proteins can be mapped with mass spectrometry. Finally, application of this method in other organisms provides a valuable tool to decipher cell-type specific gene expression patterns}, keywords = {0,Cell Fractionation,CEREVISIAE,chemistry,ChromatographyAffinity,Dna,DNA MICROARRAYS,expression,EXTRACTS,gene,Gene Expression,GENE-EXPRESSION,genetics,isolation & purification,La,Mass Spectrometry,MESSAGE,Methods,modification,nosource,PATTERNS,polysomes,protein,Protein Array Analysis,Proteins,purification,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,RNA-Binding Proteins,RNA-BINDING-PROTEIN,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Support,yeast} }

@article{hallSequenceComplementarityT2DNA1961, title = {Sequence Complementarity of {{T2-DNA}} and {{T2-specific RNA}}.}, author = {Hall, B.D.and Spiegleman}, year = 1961, journal = {Proceedings of the National Academy of Sciences}, volume = {47}, number = {2}, pages = {137–146}, publisher = {National Academy of Sciences}, doi = {10.1073/pnas.47.2.137}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC221635/}, keywords = {history,mRNA,nosource,Rna,sequence,virus} } % == BibTeX quality report for hallSequenceComplementarityT2DNA1961: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.SA”)

@article{hallstromRegulationTranscriptionFactor1998, title = {Regulation of Transcription Factor {{Pdr1p}} Function by an {{Hsp70}} Protein in {{Saccharomyces}} Cerevisiae}, author = {Hallstrom, T.C. and Katzmann, D.J. and Torres, R.J. and Sharp, W.J. and {Moye-Rowley}, W.S.}, year = 1998, month = mar, journal = {Molecular and cellular biology}, volume = {18}, number = {3}, pages = {1147–1155}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.18.3.1147}, url = {http://mcb.asm.org/cgi/content/abstract/18/3/1147}, abstract = {Multiple or pleiotropic drug resistance in the yeast Saccharomyces cerevisiae requires the expression of several ATP binding cassette transporter-encoding genes under the control of the zinc finger-containing transcription factor Pdrlp. The ATP binding cassette transporter-encoding genes regulated by Pdrlp include PDR5 and YOR1, which are required for normal cycloheximide and oligomycin tolerances, respectively. We have isolated a new member of the PDR gene family that encodes a member of the Hsp70 family of proteins found in this organism. This gene has been designated PDR13 and is required for normal growth. Overexpression of Pdr13p leads to an increase in both the expression of PDR5 and YOR1 and a corresponding enhancement in drug resistance. Pdr13p requires the presence of both the PDR1 structural gene and the Pdr1p binding sites in target promoters to mediate its effect on drug resistance and gene expression. A dominant, gain-of-function mutant allele of PDR13 was isolated and shown to have the same phenotypic effects as when the gene is present on a 2microm plasmid. Genetic and Western blotting experiments indicated that Pdr13p exerts its effect on Pdr1p at a posttranslational step. These data support the view that Pdr13p influences pleiotropic drug resistance by enhancing the function of the transcriptional regulatory protein Pdr1p}, keywords = {0,Animals,ATP,ATP-Binding Cassette Transporters,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,biosynthesis,CEREVISIAE,Cycloheximide,DNA-BINDING,DNA-Binding Proteins,drug effects,Drug Resistance,Drug ResistanceMicrobial,ENCODES,expression,FAMILY,Fungal Proteins,FUSION PROTEIN,gene,Gene Deletion,Gene Dosage,Gene Expression,GENE-EXPRESSION,Genes,GenesFungal,Genetic,genetics,GROWTH,growth & development,HEAT-SHOCK,HEAT-SHOCK PROTEINS,Heat-Shock Proteins 70,La,Membrane Proteins,metabolism,Molecular Chaperones,nosource,OVEREXPRESSION,pharmacology,physiology,PLASMID,PROMOTER,PROMOTERS,protein,Protein ProcessingPost-Translational,Proteins,Recombinant Fusion Proteins,regulation,REQUIRES,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,RESISTANCE,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SITE,SITES,Structural,Support,TARGET,Trans-Activators,transcription,TRANSCRIPTION FACTOR,Transcription Factors,yeast,Zinc Fingers} } % == BibTeX quality report for hallstromRegulationTranscriptionFactor1998: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{hamaguchiIdentificationRibosomalProtein2002, title = {Identification of Ribosomal Protein {{S3a}} as a Candidate for a Novel {{PI}} 3-Kinase Target in the Nucleus}, author = {Hamaguchi, N. and Ohdaira, T. and Shinohara, A. and Iwamatsu, A. and Ihara, S. and Fukui, Y.}, year = 2002, month = nov, journal = {Cytotechnology}, volume = {40}, number = {1-3}, pages = {85–92}, publisher = {Springer}, url = {http://www.springerlink.com/index/U52672674JP4816L.pdf}, abstract = {Phosphatidylinositol 3,4,5-trisphosphate (PIP(3)) is an important lipid second messenger that mediates various cell responses. We have searched for the nuclear PIP(3) binding proteins using PIP(3) analogue beads. A 33 kD protein was detected in this method, which was identified as ribosomal protein S3a by the mass spectrometric analysis. The recombinant S3a protein bound specifically to PIP(3). S3a localized not only in the cytosol but also in the nucleus. Interestingly, not cytosolic but nuclear S3a bound to PIP(3), suggesting different roles of S3a in the cytosol and the nucleus}, keywords = {analysis,BINDING,BINDING PROTEIN,BINDING-PROTEIN,chemistry,Cytosol,IDENTIFICATION,La,No DOI found,nosource,protein,Proteins,RIBOSOMAL-PROTEIN,TARGET} }

@article{hamilConstitutiveTranscriptionYeast1988a, title = {Constitutive Transcription of Yeast Ribosomal Protein Gene ⬚{{TCM1}}⬚ Is Promoted by Uncommon ⬚cis-⬚ and ⬚trans⬚-Acting Elements.}, author = {Hamil, K.G. and Nam, H.G. and Fried, H.M.}, year = 1988, journal = {Mol.Cell.Biol.}, volume = {8}, pages = {4328–4341}, keywords = {antibiotics,ELEMENTS,gene,L3,Multiple DOI,nonfile,nosource,protein,TCM1,transcription,translation,yeast} } % == BibTeX quality report for hamilConstitutiveTranscriptionYeast1988a: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@phdthesis{hammellRibosomalProteinL32000a, title = {Ribosomal Protein {{L3}}: Autoregulation, Translational Fidelity, and Virus Propagation.}, author = {Hammell, A.B.}, year = 2000, keywords = {Fidelity,L3,nosource,PROPAGATION,protein,RIBOSOMAL-PROTEIN,translational fidelity,virus} } % == BibTeX quality report for hammellRibosomalProteinL32000a: % Missing required field ‘school’

@article{hamplRibosomalComponentsEscherichia1981, title = {Ribosomal Components from {{Escherichia}} Coli 50 {{S}} Subunits Involved in the Reconstitution of Peptidyltransferase Activity.}, author = {Hampl, H. and Schulze, H. and Nierhaus, K.H.}, year = 1981, month = mar, journal = {Journal of Biological Chemistry}, volume = {256}, number = {5}, pages = {2284–2288}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(19)69775-9}, url = {http://www.jbc.org/content/256/5/2284.short}, keywords = {0,Acyltransferases,COMPONENT,enzymology,Escherichia coli,ESCHERICHIA-COLI,isolation & purification,Kinetics,La,Macromolecular Systems,metabolism,Molecular Weight,nosource,Peptidyltransferase,protein,Proteins,Ribosomal Proteins,Ribosomes,SUBUNIT,SYSTEM} } % == BibTeX quality report for hamplRibosomalComponentsEscherichia1981: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{hampseyExtragenicSuppressorsTranslation1991, title = {Extragenic Suppressors of a Translation Initiation Defect in the Cyc1 Gene of {{Saccharomyces}} Cerevisiae}, author = {Hampsey, M. and Na, J.G. and Pinto, I. and Ware, D.E. and Berroteran, R.W.}, year = 1991, month = dec, journal = {Biochimie}, volume = {73}, number = {12}, pages = {1445–1455}, publisher = {Elsevier}, doi = {10.1016/0300-9084(91)90177-3}, url = {http://linkinghub.elsevier.com/retrieve/pii/0300908491901773}, abstract = {The cycl-362 allele contains a point mutation that generates an aberrant AUG codon upstream of the normal CYC1 translation initiation codon. Mutants containing this allele express only about 2% of normal iso-1-cytochrome c, presumably due to translation initiation at the upstream AUG, termination at a UAA sequence six codons downstream, and failure to reinitiate at the normal AUG codon two nucleotides later. Both intragenic and extragenic revertants of cycl-362, expressing elevated levels of iso-1-cytochrome c, have been isolated simply by selecting for growth on lactate medium. Here we describe an improved method for isolating and readily distinguishing cis- from trans-acting suppressors of the upstream AUG. Eight different genes, designated sua1-sua8, are represented in our current collection of extragenic suppressors; all are recessive and enhance iso-1-cytochrome c levels to 10-60% of normal. None of the sua genes is allelic to SUI2 or sui3, which encode eIF-2 alpha and eIF-2 beta, respectively, or to SUI1. Many of the suppressors exhibit pleiotropic phenotypes, including slow growth, cold (16 degrees C) and heat (37 degrees C) sensitivity. These phenotypes have been exploited to clone the SUA5, SUA7 and SUA8 genes, which are presently being characterized. The structure of cyc1-362 and the number of sua genes already uncovered suggest that the SUA genes are likely to encode factors affecting several different cellular processes, including translation initiation, mRNA stability and possibly transcription start site selection}, keywords = {0,Alleles,AUG,Base Sequence,BIOLOGY,CEREVISIAE,Codon,CODONS,Cold,Cytochrome c,DOWNSTREAM,Eif-2,gene,Gene Expression RegulationFungal,Genes,genetics,Genotype,GROWTH,Heat,initiation,La,media,metabolism,Molecular Sequence Data,mRNA,mRNA stability,MUTANTS,Mutation,nosource,Nucleotides,Phenotype,Point Mutation,protein,Rna,RNAMessenger,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SELECTION,sequence,SITE,SITE SELECTION,stability,structure,SUA genes,sui1,SUI2,SUI3,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SuppressionGenetic,termination,transcription,TranscriptionGenetic,translation,TRANSLATION INITIATION,TranslationGenetic,UAA,UPSTREAM} }

@article{hampseyReviewPhenotypesSaccharomyces1997, title = {A Review of Phenotypes in {{Saccharomyces}} Cerevisiae}, author = {Hampsey, M.}, year = 1997, journal = {Yeast}, volume = {13}, number = {12}, pages = {1099–1133}, doi = {10.1002/(SICI)1097-0061(19970930)13:12<1099::AID-YEA177>3.0.CO;2-7}, abstract = {A summary of previously defined phenotypes in the yeast Saccharomyces cerevisiae is presented. The purpose of this review is to provide a compendium of phenotypes that can be readily screened to identify pleiotropic phenotypes associated with primary or suppressor mutations. Many of these phenotypes provide a convenient alternative to the primary phenotype for following a gene, or as a marker for cloning a gene by genetic complementation. In many cases a particular phenotype or set of phenotypes can suggest a function for the product of the mutated gene}, keywords = {cell cycle,cloning,drug effects,gene,Genetic,genetics,metabolism,Mutation,MUTATIONS,Nitrogen,nosource,Phenotype,physiology,Review,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,yeast} }

@article{hanPSEUDOVIEWER2VisualizationRNA2003, title = {{{PSEUDOVIEWER2}}: {{Visualization}} of {{RNA}} Pseudoknots of Any Type}, author = {Han, K. and Byun, Y.}, year = 2003, month = jul, journal = {Nucleic Acids Research}, volume = {31}, number = {13}, pages = {3432–3440}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkg539}, url = {http://nar.oxfordjournals.org/content/31/13/3432.short}, abstract = {Visualizing RNA pseudoknot structures is computationally more difficult than depicting RNA secondary structures, because a drawing of a pseudoknot structure is a graph (and possibly a nonplanar graph) with inner cycles within the pseudoknot, and possibly outer cycles formed between the pseudoknot and other structural elements. We previously developed PSEUDOVIEWER for visualizing H-type pseudoknots. PSEUDOVIEWER2 improves on the first version in many ways: (i) PSEUDOVIEWER2 is more general because it can visualize a pseudoknot of any type, including H-type pseudoknots, as a planar graph; (ii) PSEUDOVIEWER2 computes a drawing of RNA structures much more efficiently and is an order of magnitude faster in actual running time; and (iii) PSEUDOVIEWER2 is a web-based application program. Experimental results demonstrate that PSEUDOVIEWER2 generates an aesthetically pleasing drawing of pseudoknots of any type and that the new representation offered by PSEUDOVIEWER2 ensures uniform and clear drawings, with no edge crossing, for all types of pseudoknots. The PSEUDOVIEWER2 algorithm is the first developed for the automatic drawing of RNA secondary structures, including pseudoknots of any type. PSEUDOVIEWER2 is accessible at http://wilab.inha.ac.kr/pseudoviewer2/}, keywords = {Algorithms,chemistry,computer,Computer Graphics,ELEMENTS,Internet,La,ModelsMolecular,nosource,Nucleic Acid Conformation,pseudoknot,pseudoknot structure,pseudoknots,Rna,RNA PSEUDOKNOT,RNA SECONDARY STRUCTURE,SECONDARY STRUCTURE,Software,Structural,structure,Support,VISUALIZATION} } % == BibTeX quality report for hanPSEUDOVIEWER2VisualizationRNA2003: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{hanfreyDualUpstreamOpen2005, title = {A Dual Upstream Open Reading Frame-Based Autoregulatory Circuit Controlling Polyamine-Responsive Translation}, author = {Hanfrey, C. and Elliott, K. A. and Franceschetti, M. and Mayer, M. J. and Illingworth, C. and Michael, A. J.}, year = 2005, month = nov, journal = {Journal of Biological Chemistry}, volume = {280}, number = {47}, pages = {39229}, publisher = {ASBMB}, url = {http://www.jbc.org/content/280/47/39229.short}, abstract = {A novel form of translational regulation is described for the key polyamine biosynthetic enzyme S-adenosylmethionine decarboxylase (AdoMetDC). Plant AdoMetDC mRNA 5’ leaders contain two highly conserved overlapping upstream open reading frames (uORFs): the 5’ tiny and 3’ small uORFs. We demonstrate that the small uORF-encoded peptide is responsible for constitutively repressing downstream translation of the AdoMetDC proenzyme ORF in the absence of increased polyamine levels. This first example of a sequence-dependent uORF to be described in plants is also functional in Saccharomyces cerevisiae. The tiny uORF is required for normal polyamine-responsive AdoMetDC mRNA translation, and we propose that this is achieved by control of ribosomal recognition of the occluded small uORF, either by ribosomal leaky scanning or by programmed -1 frameshifting. In vitro expression demonstrated that both the tiny and the small uORFs are translated. This tiny/small uORF configuration is highly conserved from moss to Arabidopsis thaliana, and a more diverged tiny/small uORF arrangement is found in the AdoMetDC mRNA 5’ leader of the single-celled green alga Chlamydomonas reinhardtii, indicating an ancient origin for the uORFs}, keywords = {3,ARRANGEMENT,CEREVISIAE,DOWNSTREAM,enzyme,expression,FORM,FRAME,Frameshifting,In Vitro,IN-VITRO,La,mRNA,nosource,OPEN READING FRAME,Open Reading Frames,Plants,polyamine,READING FRAME,Reading Frames,RECOGNITION,regulation,S-Adenosylmethionine,S-ADENOSYLMETHIONINE DECARBOXYLASE,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,scanning,translation,uORF,UPSTREAM} }

@article{haniTRNAGenesRetroelements1998, title = {{{tRNA}} Genes and Retroelements in the Yeast Genome}, author = {Hani, J. and Feldmann, H.}, year = 1998, month = feb, journal = {Nucleic acids research}, volume = {26}, number = {3}, pages = {689–696}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/26.3.689}, url = {http://nar.oxfordjournals.org/content/26/3/689.short}, abstract = {A survey of tRNA genes and retroelements (Ty) in the genome of the yeast Saccharomyces cerevisiae is presented. Aspects of genomic organization and evolution of these genetic entities and their interplay are discussed. Attention is also given to the relationship between tRNA gene multiplicity and codon selection in yeast and the role of Ty elements}, keywords = {0,CEREVISIAE,Chromosome Mapping,Codon,ELEMENTS,Evolution,EvolutionMolecular,gene,Gene Dosage,Genes,GenesFungal,Genetic,genetics,Genome,GenomeFungal,genomic,Germany,INFORMATION,Introns,La,nosource,ORGANIZATION,protein,Retroelements,Rna,RNAFungal,RNATransfer,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SELECTION,sequence,SEQUENCES,Support,tRNA,Ty,yeast} } % == BibTeX quality report for haniTRNAGenesRetroelements1998: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{hannanCardiacHypertrophyMatter2003, title = {Cardiac Hypertrophy: A Matter of Translation}, author = {Hannan, R.D. and Jenkins, A. and Jenkins, A.K. and Brandenburger, Y.}, year = 2003, journal = {Clinical and experimental pharmacology and physiology}, volume = {30}, number = {8}, pages = {517–527}, publisher = {Wiley Online Library}, doi = {10.1046/j.1440-1681.2003.03873.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1440-1681.2003.03873.x/full}, abstract = {1. Left ventricular hypertrophy (LVH) of the heart is an adaptive response to sustained increases in blood pressure and hormone imbalances. Left ventricular hypertrophy is associated with programmed responses at the molecular and biochemical level in different subsets of cardiac cells, including the cardiac muscle cells (cardiomyocytes), fibroblasts, conductive tissue and coronary vasculature. 2. Regardless of the initiating cause, the actual increase in chamber enlargement is, in each case, due to an increase in size of a pre-existing cardiomyocyte population, with little or no change in their number; a process referred to as cellular hypertrophy. 3. An accelerated rate of global protein synthesis is the primary mechanism by which protein accumulation increases during cardiomyocyte hypertrophy. In turn, increased rates of synthesis are a result of increased translational rates of existing ribosomes (translational efficiency) and/or synthesis and recruitment of additional ribosomes (translational capacity). 4. The present review examines the relative importance of translational capacity and translational efficiency in the response of myocytes to acute and chronic demands for increased protein synthesis and the role of these mechanisms in the development of LVH}, keywords = {0,3,Animals,biosynthesis,blood,Cardiomegaly,CELLS,development,efficiency,gene,GENE-TRANSCRIPTION,genetics,heart,Humans,HypertrophyLeft Ventricular,La,MECHANISM,MECHANISMS,Muscle Proteins,Myocardium,nosource,pathology,physiology,physiopathology,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,Proteins,RECRUITMENT,Review,ribosome,Ribosomes,transcription,translation} } % == BibTeX quality report for hannanCardiacHypertrophyMatter2003: % ? unused Journal abbr (“Clin.Exp.Pharmacol.Physiol”)

@article{hannigGCD11NegativeRegulator1993, title = {{{GCD11}}, a Negative Regulator of {{GCN4}} Expression, Encodes the Gamma Subunit of {{eIF-2}} in {{Saccharomyces}} Cerevisiae.}, author = {Hannig, E.M. and Cigan, A.M. and Freeman, B.A. and Kinzy, T.G.}, year = 1993, month = jan, journal = {Molecular and Cellular Biology}, volume = {13}, number = {1}, pages = {506–520}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/13/1/506}, keywords = {Amino Acid Sequence,Antibodies,antibody,BINDING,Codon,efficiency,EFTu,ELEMENTS,elongation,expression,GAMMA-SUBUNIT,GCN4,gene,Genes,initiation,Multiple DOI,Mutation,MUTATIONS,nonfile,nosource,Peptides,Phenotype,protein,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SUBUNIT,translation,TRANSLATION INITIATION,yeast} }

@article{hansenStructuralInsightsPeptide2002, title = {Structural Insights into Peptide Bond Formation}, author = {Hansen, J.L. and Schmeing, T.M. and Moore, P.B. and Steitz, T.A.}, year = 2002, journal = {Proceedings of the National Academy of Sciences}, volume = {99}, number = {18}, pages = {11670–11675}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.172404099}, url = {http://www.pnas.org/content/99/18/11670.short}, abstract = {The large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-RNA fragments of tRNA. We have refined at 3-A resolution the structures of both A and P site substrate and product analogues, as well as an intermediate analogue, bound to the Haloarcula marismortui 50S ribosomal subunit. A P site substrate, CCA-Phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the P site. The CCA portions of these analogues are bound identically by either the A or P loop of the 23S rRNA. Combining the separate P and A site substrate complexes into one model reveals interactions that may occur when both are present simultaneously. The alpha-NH(2) group of an aminoacylated fragment in the A site forms one hydrogen bond with the N3 of A2486 (2451) and may form a second hydrogen bond either with the 2’ OH of the A-76 ribose in the P site or with the 2’ OH of A2486 (2451). These interactions position the alpha amino group adjacent to the carbonyl carbon of esterified P site substrate in an orientation suitable for a nucleophilic attack}, keywords = {0,A-SITE,Carbon,chemistry,COMPLEX,COMPLEXES,Crystallization,CrystallographyX-Ray,Haloarcula,Haloarcula marismortui,La,ModelsMolecular,nosource,P-SITE,Peptides,Protein Conformation,Ribose,RIBOSOMAL-SUBUNIT,rRNA,sparsomycin,Structural,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,tRNA} } % == BibTeX quality report for hansenStructuralInsightsPeptide2002: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{hansenTy3YeastRetrotransposon1988, title = {Ty3, a Yeast Retrotransposon Associated with {{tRNA}} Genes, Has Homology to Animal Retroviruses.}, author = {Hansen, L.J. and Chalker, D.L. and Sandmeyer, S.B.}, year = 1988, month = dec, journal = {Molecular and cellular biology}, volume = {8}, number = {12}, pages = {5245–5256}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/8/12/5245}, abstract = {Ty3, a retrotransposon of Saccharomyces cerevisiae, is found within 20 base pairs (bp) of the 5’ ends of different tRNA genes. Determination of the complete nucleotide sequence of one Ty3 retrotransposon (Ty3-2) shows that the element is composed of an internal domain 4,748 bp long flanked by long terminal repeats of the 340-bp sigma element. Three open reading frames (ORFs) longer than 100 codons are present in the sense strand. The first ORF, TYA3, encodes a protein with a motif found in the nucleic acid-binding protein of retroviruses. The second ORF, TYB3, has homology to retroviral pol genes. The deduced amino acid sequence of the reverse transcriptase domain shows the greatest similarity to Drosophila retrotransposon 17.6, with 43% identical residues. The inferred order of functional domains within TYB3–protease, reverse transcriptase, and endonuclease–resembles the order in Drosophila element 17.6 and in animal retroviruses but is different from that found in yeast elements Ty1 and Ty2. A second Ty3 element (Ty3-1) from a standard laboratory strain was overexpressed and shown to transpose}, keywords = {0,ACID,Amino Acid Sequence,AMINO-ACID,animal,BASE,Base Sequence,BASE-PAIR,CEREVISIAE,Codon,CODONS,Comparative Study,Dna,DNA Transposable Elements,DOMAIN,DOMAINS,Drosophila,ELEMENTS,ENCODES,FRAME,gene,Genes,GenesFungal,GenesStructural,GenesViral,Genetic,genetics,La,microbiology,Molecular Sequence Data,MOLECULAR-GENETICS,Multiple DOI,nonfile,nosource,NUCLEOTIDE-SEQUENCE,OPEN READING FRAME,Open Reading Frames,pol,POL GENE,protein,Proteins,READING FRAME,Reading Frames,Research SupportU.S.Gov’tP.H.S.,RESIDUES,Restriction Mapping,retrotransposon,Retroviridae,Retroviridae Proteins,RETROVIRUSES,REVERSE-TRANSCRIPTASE,Rna,RNATransfer,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence HomologyNucleic Acid,tRNA,Ty1,TY3,yeast} } % == BibTeX quality report for hansenTy3YeastRetrotransposon1988: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{hansenTunableAlignmentMacromolecules1998, title = {Tunable Alignment of Macromolecules by Filamentous Phage Yields Dipolar Coupling Interactions}, author = {Hansen, M.R. and Mueller, L. and Pardi, A.}, year = 1998, month = dec, journal = {Nature Structural & Molecular Biology}, volume = {5}, number = {12}, pages = {1065–1074}, publisher = {Nature Publishing Group}, doi = {10.1038/4176}, url = {http://www.nature.com/nsmb/journal/v5/n12/abs/nsb1298_1065.html}, abstract = {Dipolar coupling interactions represent an extremely valuable source of long-range distance and angle information that was previously not available for solution structure determinations of macromolecules. This is because observation of these dipolar coupling data requires creating an anisotropic environment for the macromolecule. Here we introduce a new method for generating tunable degrees of alignment of macromolecules by addition of magnetically aligned Pf1 filamentous bacteriophage as a cosolute. This phage-induced alignment technique has been used to study 1H-1H, 1H-13C, and 1H-15N dipolar coupling interactions in a DNA duplex, an RNA hairpin and several proteins including thioredoxin and apo-calmodulin. The phage allow alignment of macromolecules over a wide range of temperature and solution conditions and thus represent a stable versatile method for generating partially aligned macromolecules in solution}, keywords = {0,alignment,Calmodulin,chemistry,Dna,Inovirus,La,Macromolecular Systems,Magnetic Resonance Spectroscopy,metabolism,ModelsMolecular,nosource,Nucleic Acid Conformation,protein,Protein Conformation,Proteins,REQUIRES,Rna,Solutions,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,SYSTEMS,Temperature,Thioredoxin} } % == BibTeX quality report for hansenTunableAlignmentMacromolecules1998: % ? unused Journal abbr (“Nat.Struct.Biol.”)

@article{hansenFilamentousBacteriophageAligning2000a, title = {Filamentous Bacteriophage for Aligning {{RNA}}, {{DNA}}, and Proteins for Measurement of Nuclear Magnetic Resonance Dipolar Coupling Interactions.}, author = {Hansen, M.R. and Hanson, P. and Pardi, A.}, year = 2000, journal = {Methods in enzymology}, volume = {317}, pages = {220–240}, doi = {10.1016/S0076-6879(00)17017-X}, url = {http://ukpmc.ac.uk/abstract/MED/10829283}, keywords = {0,chemistry,Dna,Inovirus,La,Magnetic Resonance Spectroscopy,nosource,nuclear magnetic resonance,NUCLEAR-MAGNETIC-RESONANCE,protein,Proteins,Review,Rna,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for hansenFilamentousBacteriophageAligning2000a: % ? unused Journal abbr (“Methods Enzymol.”)

@article{hansenMaintenanceCorrectOpen2003, title = {Maintenance of the Correct Open Reading Frame by the Ribosome}, author = {Hansen, T.M. and Baranov, P.V. and Ivanov, I.P. and Gesteland, R.F. and Atkins, J.F.}, year = 2003, month = may, journal = {Embo Reports}, volume = {4}, number = {5}, pages = {499–504}, publisher = {Nature Publishing Group}, doi = {10.1038/sj.embor.embor825}, url = {http://www.nature.com/embor/journal/v4/n5/abs/embor825.html}, abstract = {During translation, a string of non-overlapping triplet codons in messenger RNA is decoded into protein. The ability of a ribosome to decode mRNA without shifting between reading frames is a strict requirement for accurate protein biosynthesis. Despite enormous progress in understanding the mechanism of transfer RNA selection, the mechanism by which the correct reading frame is maintained remains unclear. In this report, evidence is presented that supports the idea that the translational frame is controlled mainly by the stability of codon - anticodon interactions at the P site. The relative instability of such interactions may lead to dissociation of the P-site tRNA from its codon, and formation of a complex with an overlapping codon, the process known as P-site tRNA slippage. We propose that this process is central to all known cases of +1 ribosomal frameshifting, including that required for the decoding of the yeast transposable element Ty3. An earlier model for the decoding of this element proposed ‘out-of-frame’ binding of A-site tRNA without preceding P-site tRNA slippage}, keywords = {0,A-SITE,ANGSTROM RESOLUTION,Anticodon,BINDING,biosynthesis,Codon,COMPLEX,COMPLEXES,decoding,ESCHERICHIA-COLI,Frameshifting,gene,human,MECHANISM,MESSENGER-RNA,mRNA,nosource,P-SITE,protein,RELEASE FACTOR-II,ribosomal frameshifting,ribosome,Rna,SLIPPAGE,stability,SUBUNIT,Support,TRANSFER-RNA,translation,tRNA,yeast} }

@article{hansenCorrelationMechanicalStrength2007, title = {Correlation between Mechanical Strength of Messenger {{RNA}} Pseudoknots and Ribosomal Frameshifting}, author = {Hansen, T.M. and Reihani, S.N. and Oddershede, L.B. and Sorensen, M.A.}, year = 2007, month = apr, journal = {Proceedings of the National Academy of Sciences}, volume = {104}, number = {14}, pages = {5830–5835}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.0608668104}, url = {http://www.pnas.org/content/104/14/5830.short}, abstract = {Programmed ribosomal frameshifting is often used by viral pathogens including HIV. Slippery sequences present in some mRNAs cause the ribosome to shift reading frame. The resulting protein is thus encoded by one reading frame upstream from the slippery sequence and by another reading frame downstream from the slippery sequence. Although the mechanism is not well understood, frameshifting is known to be stimulated by an mRNA structure such as a pseudoknot. Here, we show that the efficiency of frameshifting relates to the mechanical strength of the pseudoknot. Two pseudoknots derived from the Infectious Bronchitis Virus were used, differing by one base pair in the first stem. In Escherichia coli, these two pseudoknots caused frameshifting frequencies that differed by a factor of two. We used optical tweezers to unfold the pseudoknots. The pseudoknot giving rise to the highest degree of frameshifting required a nearly 2-fold larger unfolding force than the other. The observed energy difference cannot be accounted for by any existing model. We propose that the degree of ribosomal frameshifting is related to the mechanical strength of RNA pseudoknots. Our observations support the “9 A model” that predicts some physical barrier is needed to force the ribosome into the -1 frame. Also, our findings support the recent observation made by cryoelectron microscopy that mechanical interaction between a ribosome and a pseudoknot causes a deformation of the A-site tRNA. The result has implications for the understanding of genetic regulation, reading frame maintenance, tRNA movement, and unwinding of mRNA secondary structures by ribosomes}, keywords = {0,A SITE,A-SITE,BASE,Base Sequence,BASE-PAIR,BIOLOGY,Biomechanics,chemistry,Computer Simulation,Cryoelectron Microscopy,DOWNSTREAM,efficiency,Escherichia coli,ESCHERICHIA-COLI,FRAME,FRAME MAINTENANCE,Frameshift Mutation,Frameshifting,Frameshifting-Ribosomal,FrameshiftingRibosomal,Genetic,genetics,HIV,Infectious bronchitis virus,La,MECHANISM,MESSENGER-RNA,metabolism,MODEL,Models-Biological,ModelsBiological,Molecular Biology,Molecular Sequence Data,Movement,mRNA,nosource,Nucleic Acid Conformation,Optical Tweezers,Plasmids,protein,Protein Biosynthesis,pseudoknot,pseudoknots,READING FRAME,regulation,ribosomal frameshifting,ribosome,Ribosomes,Rna,RNA PSEUDOKNOT,RNA-Messenger,Rna-Viral,RNAMessenger,RnaViral,SECONDARY STRUCTURE,sequence,SEQUENCES,structure,Support,Thermodynamics,tRNA,UPSTREAM,virus} } % == BibTeX quality report for hansenCorrelationMechanicalStrength2007: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{hansonTetracyclineaptamermediatedTranslationalRegulation2003, title = {Tetracycline-Aptamer-Mediated Translational Regulation in Yeast}, author = {Hanson, S. and Berthelot, K. and Fink, B. and McCarthy, J.E. and Suess, B.}, year = 2003, journal = {Molecular microbiology}, volume = {49}, number = {6}, pages = {1627–1637}, publisher = {Wiley Online Library}, doi = {10.1046/j.1365-2958.2003.03656.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2003.03656.x/full}, abstract = {We describe post-transcriptional gene regulation in yeast based on direct RNA-ligand interaction. Tetracycline-dependent translational regulation could be imposed via specific aptamers inserted at two different positions in the 5’ untranslated region (5’UTR). Translation in vivo was suppressed up to ninefold upon addition of tetracycline. Repression via an aptamer located near the start codon (cap-distal) in the 5’UTR was more effective than repression via a cap-proximal position. On the other hand, suppression in a cell-free system reached maximally 50-fold and was most effective via a cap-proximal aptamer. Examination of the kinetics of tetracycline-dependent translational inhibition in vitro revealed that preincubation of tetracycline and mRNA before starting translation led not only to the fastest onset of inhibition but also the most effective repression. The differences between the behaviour of the regulatory system in vivo and in vitro are likely to be related to distinct properties of mRNP structure and mRNA accessibility in intact cells as opposed to cell-extracts. Tetracycline-dependent regulation was also observed after insertion of an uORF sequence upstream of the aptamer, indicating that our system also targets reinitiating ribosomes. Polysomal gradient analyses provided insight into the mechanism of regulation. Cap-proximal insertion inhibits binding of the 43S complex to the cap structure whereas start-codon-proximal aptamers interfere with formation of the 80S ribosome, probably by blocking the scanning preinitiation complex}, keywords = {0,5’ Untranslated Regions,Base Sequence,BINDING,BlottingNorthern,Cap,CAP STRUCTURE,Cell Extracts,Cell-Free System,CELLS,Codon,COMPLEX,COMPLEXES,drug effects,gene,Gene Expression RegulationFungal,gene regulation,GenesReporter,genetics,In Vitro,IN-VITRO,IN-VIVO,INHIBITION,Kinetics,La,Luminescent Proteins,MECHANISM,metabolism,Molecular Sequence Data,mRNA,nosource,Oligoribonucleotides,pharmacology,PLASMID,Plasmids,Polyribosomes,POSITION,POSITIONS,protein,Proteins,REGION,regulation,repression,ribosome,Ribosomes,Rna,RNAFungal,RNAMessenger,Saccharomyces cerevisiae,scanning,sequence,START CODON,structure,supportnon-u.s.gov’t,suppression,SYSTEM,TARGET,Tetracycline,TransformationGenetic,translation,TranslationGenetic,Untranslated Regions,uORF,UPSTREAM,yeast} } % == BibTeX quality report for hansonTetracyclineaptamermediatedTranslationalRegulation2003: % ? unused Journal abbr (“Mol.Microbiol.”)

@article{haoudiDevelopmentalExpressionAnalysis1997, title = {Developmental Expression Analysis of the 1731 Retrotransposon Reveals an Enhancement of {{Gag-Pol}} Frameshifting in Males of {{Drosophila}} Melanogaster}, author = {Haoudi, A. and Rachidi, M. and Kim, M.H. and Champion, S. and {Best-Belpomme}, M. and Maisonhaute and C.}, year = 1997, month = sep, journal = {Gene}, volume = {196}, number = {1-2}, pages = {83–93}, publisher = {Elsevier}, doi = {10.1016/S0378-1119(97)00203-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0378111997002035}, keywords = {analysis,Antibodies,antibody,development,Drosophila,expression,Frameshifting,Gag,Gag-pol,Male,mRNA,nosource,pol,protein,Proteins,regulation,retrotransposon,SYSTEM,transcription,translation} }

@article{haradaIdentificationSitedirectedMutagenesis1998, title = {Identification by Site-Directed Mutagenesis of Amino Acid Residues in Ribosomal Protein {{L2}} That Are Essential for Binding to {{23S}} Ribosomal {{RNA}}}, author = {Harada, N. and Maemura, K. and Yamasaki, N. and Kimura, M.}, year = 1998, month = dec, journal = {Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology}, volume = {1429}, number = {1}, pages = {176–186}, publisher = {Elsevier}, doi = {10.1016/S0167-4838(98)00230-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0167483898002301}, abstract = {The ribosomal protein L2 (BstL2) from Bacillus stearothermophilus is a primary 23S rRNA binding protein. We made use of site-directed mutagenesis to identify essential basic and aromatic amino acid residues for 23S rRNA binding. Four mutants, R68Q, K70Q, R86Q, and R155Q, in which Arg-68, Lys-70, Arg-86, and Arg-155, respectively, are replaced by the Gln residue. showed reduced binding affinities as compared with that of the wild type BstL2 (a binding constant K=8.93 microM(-1)): K values of these mutants range between 0.24 and 1.86 microM(-1). As for aromatic amino acids, replacements of Phe-66, Tyr-95 or Tyr-102 by alanine significantly abolished the binding affinities. CD analysis of the mutant proteins indicated that the mutations of four basic residues (Arg-68, Lys-70, Arg-86 and Arg-155) did not affect protein structure, whereas those of aromatic residues (Phe-66, Tyr-95, and Tyr-102) appeared to cause slight structural perturbations. These results, together with sequence comparison of L2 family proteins, suggest that Arg-86 and Arg-155 in BstL2 may act as positively charged recognition groups for negatively charged phosphate backbone of the 23S rRNA, and that Phe-66, Tyr-95, and Tyr-102 may be candidate residues which stabilize the BstL2-23S rRNA interaction through intramolecular interactions}, keywords = {Alanine,Amino Acid Sequence,Amino Acids,analysis,Arginine,Bacillus stearothermophilus,BACILLUS-STEAROTHERMOPHILUS,BINDING,BINDING-PROTEIN,biosynthesis,chemistry,CloningMolecular,genetics,Glycine,IDENTIFICATION,L2,Lysine,metabolism,Molecular Sequence Data,Mutagenesis,MutagenesisSite-Directed,Mutation,MUTATIONS,nosource,Plasmids,Polymerase Chain Reaction,protein,Proteins,Ribosomal Proteins,RIBOSOMAL-RNA,Rna,RNARibosomal23S,rRNA,sequence,Sequence Alignment,Structural,structure} } % == BibTeX quality report for haradaIdentificationSitedirectedMutagenesis1998: % ? unused Journal abbr (“Biochim.Biophys.Acta”)

@article{harfordTranslationtargetedTherapeuticsViral1995a, title = {Translation-Targeted Therapeutics for Viral Diseases.}, author = {Harford, J.B.}, year = 1995, journal = {Gene Expression}, volume = {4}, number = {6}, eprint = {7549467}, eprinttype = {pubmed}, pages = {357–367}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7549467}, keywords = {antibiotic,antibiotics,antiviral,disease,enzyme,Frameshifting,kinase,MECHANISM,MECHANISMS,mRNA,No DOI found,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,ribosomal frameshifting,ribosome,RIBOSOME ENTRY SITES,Rna,translation,Viral Proteins} }

@article{hargerTy1RetrotranspositionProgrammed2001a, title = {Ty1 Retrotransposition and Programmed +1 Ribosomal Frameshifting Require the Integrity of the Protein Synthetic Translocation Step.}, author = {Harger, J.W. and Meskauskas, A. and Nielsen, N. and Justice, M.C. and Dinman, J.D.}, year = 2001, journal = {Virology}, volume = {286}, pages = {216–224}, doi = {10.1006/viro.2001.0997}, keywords = {drug effects,drugs,Frameshifting,nosource,protein,ribosomal frameshifting,translocation,Ty1} }

@article{hargerIntegratedModelProgrammed2002b, title = {An ‘integrated Model’ of Programmed Ribosomal Frameshifting and Post-Transcriptional Surveillance.}, author = {Harger, J.W. and Meskauskas, A. and Dinman, J.D.}, year = 2002, journal = {TIBS}, volume = {27}, pages = {448–454}, abstract = {Many viral mRNAs, including those of HIV-1, can make translating ribosomes change reading frame. Altering the efficiencies of programmed ribosomal frameshift (PRF) inhibits viral propagation. As a new target for potential antiviral agents, it is therefore important to understand how PRF is controlled. Incorporation of the current models describing PRF into the context of the translation elongation cycle leads us to propose an ‘integrated model’ of PRF both as a guide towards further characterization of PRF at the molecular and biochemical levels, and for the identification of new targets for antiviral therapeutics.}, keywords = {antiviral,Antiviral Agents,EF-1,EF-2,efficiency,elongation,frameshift,Frameshifting,Gag/Gag-pol ratio,Hiv-1,IDENTIFICATION,killer,L-A,M1,models,mRNA,No DOI found,nosource,peptidyl-transfer,Review,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,ribosome,Ribosomes,translation,tRNA,Ty,viral propagation,virus} }

@article{hargerEvidenceDirectRole2004, title = {Evidence against a Direct Role for the {{Upf}} Proteins in Frameshfiting or Nonsense Codon Readthrough.}, author = {Harger, J.W. and Dinman, J.D.}, year = {In press 2004}, journal = {RNA}, volume = {10}, pages = {1721–1729}, doi = {10.1261/rna.7120504}, url = {http://rnajournal.cshlp.org/content/10/11/1721.short}, abstract = {The Upf proteins are essential for nonsense-mediated mRNA decay (NMD). They have also been implicated in the modulation of translational fidelity at viral frameshift signals and premature termination codons. How these factors function in both mRNA turnover and translational control remains unclear. In this study, mono- and bicistronic reporter systems were used in the yeast ⬚Saccharomyces cerevisae⬚ to differentiate between effects at the levels of mRNA turnover and those at the level of translation . We confirm that ⬚upf?⬚ mutants do not affect programmed frameshifting, and show that this is also true for mutant forms of eIF1/Sui1p. Further, bicistronic reporters did not detect defects in translational readthrough due to deletion of the ⬚UPF⬚ genes, suggesting that their function in termination is not as general a phenomenon as was previously believed. The demonstration that ⬚upf sui1⬚ double mutants are synthetically lethal demonstrates an important functional interaction between the NMD and translation initiation pathway.}, keywords = {bicistronic,Codon,CODONS,DECAY,Fidelity,FORM,frameshift,frameshifting,Frameshifting,gene,Genes,initiation,mRNA,mRNA decay,mrna surveillance,mRNA turnover,MUTANTS,NMD,NONSENSE,nonsense-mediated mRNA decay,nosource,PATHWAY,PREMATURE TERMINATION CODON,programmed frameshifting,protein,Proteins,readthrough,Saccharomyces,SIGNAL,sui1,synthetic lethality,SYSTEM,SYSTEMS,termination,TERMINATION CODON,TERMINATION-CODON,translation,TRANSLATION INITIATION,translational fidelity,TRANSLATIONAL READTHROUGH,turnover,UPF,yeast} }

@article{harmsHighResolutionStructure2001, title = {High Resolution Structure of the Large Ribosomal Subunit from a Mesophilic Eubacterium}, author = {Harms, J. and Schluenzen, F. and Zarivach, R. and Bashan, A. and Gat, S. and Agmon, I. and Bartels, H. and Franceschi, F. and Yonath, A.}, year = 2001, month = nov, journal = {Cell}, volume = {107}, number = {5}, pages = {679–688}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(01)00546-3}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867401005463}, abstract = {We describe the high resolution structure of the large ribosomal subunit from Deinococcus radiodurans (D50S), a gram-positive mesophile suitable for binding of antibiotics and functionally relevant ligands. The over-all structure of D50S is similar to that from the archae bacterium Haloarcula marismortui (H50S); however, a detailed comparison revealed significant differences, for example, in the orientation of nucleotides in peptidyl transferase center and in the structures of many ribosomal proteins. Analysis of ribosomal features involved in dynamic aspects of protein biosynthesis that are partially or fully disordered in H50S revealed the conformations of intersubunit bridges in unbound subunits, suggesting how they may change upon subunit association and how movements of the L1-stalk may facilitate the exit of tRNA}, keywords = {0,analysis,antibiotic,antibiotics,Bacteria,Bacterial,Bacterial Proteins,BINDING,biosynthesis,chemistry,CrystallographyX-Ray,Gram-Positive Cocci,Haloarcula,Haloarcula marismortui,La,Ligands,Macromolecular Systems,metabolism,ModelsMolecular,Molecular Structure,Movement,nosource,Nucleic Acid Conformation,Nucleotides,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,protein,Protein Conformation,Protein StructureSecondary,Protein StructureTertiary,Proteins,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,Ribosomes,Rna,RNABacterial,RNARibosomal,RNATransfer,structure,SUBUNIT,SYSTEM,tRNA,ultrastructure} }

@article{harmsTranslationalRegulationL112008, title = {Translational Regulation via {{L11}}: Molecular Switches on the Ribosome Turned on and off by Thiostrepton and Micrococcin}, author = {Harms, J.M. and Wilson, D.N. and Schluenzen, F. and Connell, S.R. and Stachelhaus, T. and Zaborowska, Z. and Spahn, C.M. and Fucini, P.}, year = 2008, month = apr, journal = {Molecular cell}, volume = {30}, number = {1}, pages = {26–38}, publisher = {Elsevier}, doi = {10.1016/j.molcel.2008.01.009}, url = {http://www.sciencedirect.com/science/article/pii/S1097276508000440 http://linkinghub.elsevier.com/retrieve/pii/S1097276508000440}, abstract = {The thiopeptide class of antibiotics targets the GTPase-associated center (GAC) of the ribosome to inhibit translation factor function. Using X-ray crystallography, we have determined the binding sites of thiostrepton (Thio), nosiheptide (Nosi), and micrococcin (Micro), on the Deinococcus radiodurans large ribosomal subunit. The thiopeptides, by binding within a cleft located between the ribosomal protein L11 and helices 43 and 44 of the 23S rRNA, overlap with the position of domain V of EF-G, thus explaining how this class of drugs perturbs translation factor binding to the ribosome. The presence of Micro leads to additional density for the C-terminal domain (CTD) of L7, adjacent to and interacting with L11. The results suggest that L11 acts as a molecular switch to control L7 binding and plays a pivotal role in positioning one L7-CTD monomer on the G’ subdomain of EF-G to regulate EF-G turnover during protein synthesis}, keywords = {0,Anti-Bacterial Agents,antibiotic,antibiotics,Bacterial,Bacterial Proteins,Bacteriocins,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,chemistry,COMPLEX,COMPLEXES,Crystallography,Crystallography-X-Ray,CrystallographyX-Ray,Deinococcus,DOMAIN,DOMAIN-V,drugs,EF-G,Gene Expression Regulation,genetics,Germany,La,metabolism,Models-Molecular,ModelsMolecular,Molecular Sequence Data,Molecular Structure,nosource,Peptides,POSITION,protein,Protein Biosynthesis,Protein Structure-Tertiary,Protein StructureTertiary,protein synthesis,PROTEIN-SYNTHESIS,Proteins,regulation,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,rRNA,SITE,SITES,SUBUNIT,Support,TARGET,Thiazoles,Thiostrepton,translation,turnover} } % == BibTeX quality report for harmsTranslationalRegulationL112008: % ? unused Journal abbr (“Mol Cell”)

@article{harnpicharnchaiCompositionFunctionalCharacterization2001, title = {Composition and Functional Characterization of Yeast {{66S}} Ribosome Assembly Intermediates}, author = {Harnpicharnchai, P. and Jakovljevic, J. and Horsey, E. and Miles, T. and Roman, J. and Rout, M. and Meagher, D. and Imai, B. and Guo, Y.R. and Brame, C.J. and Shabanowitz, J. and Hunt, D.F. and Woolford, J.L.}, year = 2001, journal = {Molecular Cell}, volume = {8}, number = {3}, pages = {505–515}, publisher = {Elsevier}, doi = {10.1016/S1097-2765(01)00344-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276501003446}, abstract = {The pathway and complete collection of factors that orchestrate ribosome assembly are not clear. To address these problems, we affinity purified yeast preribosomal particles containing the nucleolar protein Nop7p and developed means to separate their components. Nop7p is associated primarily with 66S preribosomes containing either 27SB or 25.5S plus 7S pre-rRNAs. Copurifying proteins identified by mass spectrometry include ribosomal proteins, nonribosomal proteins previously implicated in 60S ribosome biogenesis, and proteins not known to be involved in ribosome production. Analysis of strains mutant for eight of these proteins not previously implicated in ribosome biogenesis showed that they do participate in this pathway. These results demonstrate that proteomic approaches in concert with genetic tools provide powerful means to purify and characterize ribosome assembly intermediates}, keywords = {analysis,assembly,ASSOCIATION,COMPONENT,COMPONENTS,FUNCTIONAL-CHARACTERIZATION,Gene Deletion,Genetic,homolog,INTERMEDIATE,MATURATION,MUTATIONS,nosource,PARTICLES,PATHWAY,PRECURSOR PARTICLES,protein,PROTEIN COMPLEX,Proteins,Ribosomal Proteins,ribosome,ribosome biogenesis,RNA HELICASE,SACCHAROMYCES-CEREVISIAE,SUBUNIT BIOGENESIS,yeast} }

@article{harrisStudiesFormationTransfer1973a, title = {Studies on the Formation of Transfer Ribonucleic Acid-Ribosome Complexes. {{XXIV}}. {{Effects}} of Antibiotics on Binding of Aminoacyl-Oligonucleotides to Ribosomes}, author = {Harris, R. and Pestka, S.}, year = 1973, month = feb, journal = {J.Biol.Chem.}, volume = {248}, number = {4}, pages = {1168–1174}, doi = {10.1016/S0021-9258(19)44277-4}, keywords = {Adenine Nucleotides,Amides,Amino Acids,Amino Sugars,antibiotic,antibiotics,BINDING,Binding Sites,Carbon Isotopes,COMPLEX,COMPLEXES,cytology,Cytosine,Cytosine Nucleotides,drug effects,Escherichia coli,Glycosides,Kinetics,Lactones,Leucomycins,Lincomycin,Mathematics,metabolism,nosource,Nucleosides,Nucleotides,Oligonucleotides,pharmacology,Phenylalanine,Puromycin,Pyrimidines,ribosome,Ribosomes,RNATransfer,sparsomycin,tRNA} } % == BibTeX quality report for harrisStudiesFormationTransfer1973a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{harrisonSmallReservoirDisabled2002, title = {A Small Reservoir of Disabled {{ORFs}} in the Yeast Genome and Its Implications for the Dynamics of Proteome Evolution}, author = {Harrison, P. and Kumar, A. and Lan, N. and Echols, N. and Snyder, M. and Gerstein, M.}, year = 2002, month = feb, journal = {J.Mol.Biol.}, volume = {316}, number = {3}, pages = {409–419}, doi = {10.1006/jmbi.2001.5343}, url = {PM:11866506}, abstract = {We surveyed the sequenced Saccharomyces cerevisiae genome (strain S288C) comprehensively for open reading frames (ORFs) that could encode full-length proteins but contain obvious mid-sequence disablements (frameshifts or premature stop codons). These pseudogenic features are termed disabled ORFs (dORFs). Using homology to annotated yeast ORFs and non-yeast proteins plus a simple region extension procedure, we have found 183 dORFs. Combined with the 38 existing annotations for potential dORFs, we have a total pool of up to 221 dORFs, corresponding to less than approximately 3% of the proteome. Additionally, we found 20 pairs of annotated ORFs for yeast that could be merged into a single ORF (termed a mORF) by read-through of the intervening stop codon, and may comprise a complete ORF in other yeast strains. Focussing on a core pool of 98 dORFs with a verifying protein homology, we find that most dORFs are substantially decayed, with approximately 90% having two or more disablements, and approximately 60% having four or more. dORFs are much more yeast-proteome specific than live yeast genes (having about half the chance that they are related to a non-yeast protein). They show a dramatically increased density at the telomeres of chromosomes, relative to genes. A microarray study shows that some dORFs are expressed even though they carry multiple disablements, and thus may be more resistant to nonsense-mediated decay. Many of the dORFs may be involved in responding to environmental stresses, as the largest functional groups include growth inhibition, flocculation, and the SRP/TIP1 family. Our results have important implications for proteome evolution. The characteristics of the dORF population suggest the sorts of genes that are likely to fall in and out of usage (and vary in copy number) in a strain-specific way and highlight the role of subtelomeric regions in engendering this diversity. Our results also have important implications for the effects of the [PSI+] prion. The dORFs disabled by only a single stop and the mORFs (together totalling 35) provide an estimate for the extent of the sequence population that can be resurrected readily through the demonstrated ability of the [PSI+] prion to cause nonsense-codon read-through. Also, the dORFs and mORFs that we find have properties (e.g. growth inhibition, flocculation, vanadate resistance, stress response) that are potentially related to the ability of [PSI+] to engender substantial phenotypic variation in yeast strains under different environmental conditions. (See genecensus.org/pseudogene for further information.)}, keywords = {0,Biochemistry,CEREVISIAE,Chromosomes,ChromosomesFungal,Codon,CODONS,CodonTerminator,Computational Biology,DECAY,DIVERSITY,DYNAMICS,Evolution,EvolutionMolecular,FAMILY,FRAME,frameshift,Frameshift Mutation,gene,Genes,GenesFungal,genetics,Genome,GenomeFungal,GROWTH,INFORMATION,INHIBITION,La,nonsense-mediated decay,nosource,OPEN READING FRAME,Open Reading Frames,prion,Prions,protein,Proteins,Proteome,Pseudogenes,READ-THROUGH,READING FRAME,Reading Frames,readthrough,REGION,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,RESISTANCE,RESISTANT,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Species Specificity,STOP CODON,Stress,stress response,Telomere,yeast} } % == BibTeX quality report for harrisonSmallReservoirDisabled2002: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{hartleySinglechainRibosomeInactivating1991, title = {Single-Chain Ribosome Inactivating Proteins from Plants Depurinate ⬚{{Escherichia}} Coli ⬚{{23S}} Ribosomal {{RNA}}}, author = {Hartley, M.R. and Legname, G. and Osborn, R. and Chen, Z. and Lord, J.M.}, year = 1991, journal = {FEBS Letters.}, volume = {290}, number = {1-2}, pages = {65–68}, publisher = {Elsevier}, doi = {10.1016/0014-5793(91)81227-Y}, url = {http://linkinghub.elsevier.com/retrieve/pii/001457939181227Y}, abstract = {The rRNA N-glycosidase activities of the catalytically active A chains of the heterodimeric ribosome inactivating proteins (RIPs) ricin and abrin, the single-chain RIPs dianthin 30, dianthin 32, and the leaf and seed forms of pokeweed antiviral protein (PAP) were assayed on E. coli ribosomes. All of the single-chain RIPs were active on E. coli ribosomes as judged by the release of a 243 nucleotide fragment from the 3’ end of 23S rRNA following aniline treatment of the RNA. In contrast, E. coli ribosomes were refractory to the A chains of ricin and abrin. The position of the modification of 23S rRNA by dianthin 32 was determined by primer extension and found to be A2660, which lies in a sequence that is highly conserved in all species}, keywords = {Abrin,antiviral,Escherichia coli,ESCHERICHIA-COLI,modification,nosource,PAP,Pokeweed antiviral protein,primer extension,protein,Proteins,RIBOSOMAL-RNA,ribosome,Ribosomes,Ricin,Rna,rRNA,sequence} } % == BibTeX quality report for hartleySinglechainRibosomeInactivating1991: % ? Possibly abbreviated journal title FEBS Letters.

@article{hartmanPrinciplesBufferingGenetic2001, title = {Principles for the Buffering of Genetic Variation}, author = {Hartman, J.L. and Garvik, B. and Hartwell, L.}, year = 2001, month = feb, journal = {Science}, volume = {291}, number = {5506}, pages = {1001–1004}, publisher = {American Association for the Advancement of Science}, url = {http://www.sciencemag.org/content/291/5506/1001.short}, keywords = {Alleles,animal,cancer,EpistasisGenetic,Evolution,Genes,Genetic,genetics,Genotype,human,La,Multiple DOI,Mutation,nonfile,nosource,Phenotype,physiology,Quantitative Trait,Review,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Variation (Genetics),Yeasts} }

@article{hassigHistoneDeacetylaseActivity1997, title = {Histone Deacetylase Activity Is Required for Full Transcriptional Repression by {{mSin3A}}}, author = {Hassig, C.A. and Fleischer, T.C. and Billin, A.N. and Schreiber, S.L. and Ayer, D.E.}, year = 1997, month = may, journal = {Cell}, volume = {89}, number = {3}, pages = {341–347}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(00)80214-7}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867400802147}, abstract = {Members of the Mad family of bHLH-Zip proteins heterodimerize with Max to repress transcription in a sequence-specific manner. Transcriptional repression by Mad:Max heterodimers is mediated by ternary complex formation with either of the corepressors mSin3A or mSin3B. We report here that mSin3A is an in vivo component of large, heterogeneous multiprotein complexes and is tightly and specifically associated with at least seven polypeptides. Two of the mSin3A-associated proteins, p50 and p55, are highly related to the histone deacetylase HDAC1. The mSin3A immunocomplexes possess histone deacetylase activity that is sensitive to the specific deacetylase inhibitor trapoxin. mSin3A- targeted repression of a reporter gene is reduced by trapoxin treatment, suggesting that histone deacetylation mediates transcriptional repression through Mad-Max-mSin3A multimeric complexes}, keywords = {97294377,Acetylation,animal,antagonists & inhibitors,AntibioticsPeptide,Carrier Proteins,CellsCultured,chemistry,COMPLEX,COMPLEXES,COMPONENT,DNA-Binding Proteins,drug effects,Enzyme Inhibitors,enzymology,gene,Gene Expression RegulationEnzymologic,genetics,Histone Deacetylase,IN-VIVO,metabolism,Multienzyme Complexes,nosource,Nuclear Proteins,pharmacology,physiology,protein,Proteins,Rabbits,Repressor Proteins,Retinoblastoma,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,transcription,Transcription Factors,TranscriptionGenetic} }

@article{hatfieldChromatographicAnalysisAminoacylTransfer1989a, title = {Chromatographic {{Analysis}} of the {{Aminoacyl-Transfer Rnas Which Are Required}} for {{Translation}} of {{Codons}} at and {{Around}} the {{Ribosomal Frameshift Sites}} of {{Hiv}}, {{Htlv-1}}, and {{Blv}}}, author = {Hatfield, D. and Feng, Y.X. and Lee, B.J. and Rein, A. and Levin, J.G. and Oroszlan, S.}, year = 1989, month = dec, journal = {Virology}, volume = {173}, number = {2}, pages = {736–742}, doi = {10.1016/0042-6822(89)90589-8}, url = {ISI:A1989CD81900042}, keywords = {AMINOACYL-TRANSFER RNA,AMINOACYL-TRANSFER-RNA,analysis,Codon,CODONS,D,frameshift,HIV,nosource,RIBOSOMAL FRAMESHIFT,Rna,SITE,SITES,translation} } % == BibTeX quality report for hatfieldChromatographicAnalysisAminoacylTransfer1989a: % ? Title looks like it was stored in title-case in Zotero

@article{hatfieldTranslationalSuppressionRetroviral1992, title = {Translational Suppression in Retroviral Gene Expression.}, author = {Hatfield, D. and Levin, J.G. and Rein, A. and Oroszlan, S.}, year = 1992, journal = {Advances in Virus Research}, volume = {41}, pages = {193–239}, publisher = {Elsevier}, doi = {10.1016/S0065-3527(08)60037-8}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0065352708600378}, keywords = {expression,Frameshifting,gene,Gene Expression,GENE-EXPRESSION,nosource,Review,review article,suppression,virus} } % == BibTeX quality report for hatfieldTranslationalSuppressionRetroviral1992: % ? unused Journal abbr (“Adv.Virus Res.”)

@book{hauglandGuideFluorescentProbes2005, title = {A Guide to Fluorescent Probes and Labeling Technologies.}, author = {Haugland, R.P.}, year = 2005, publisher = {Invitrogen}, address = {Carlsbad, CA⬚ ⬚}, keywords = {nosource} }

@article{hayashiRapidRegulatedDegradation1995, title = {Rapid and Regulated Degradation of Ornithine Decarboxylase.}, author = {Hayashi, S.-I. and Murakami, Y.}, year = 1995, journal = {Biochemical Journal}, volume = {306}, number = {Pt 1}, pages = {1–10}, publisher = {Portland Press Ltd}, doi = {10.1042/bj3060001}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1136473/}, keywords = {+1 frameshifting,degradation,Frameshifting,Mammals,nosource,Ornithine Decarboxylase,polyamine,ribosomal frameshifting} } % == BibTeX quality report for hayashiRapidRegulatedDegradation1995: % ? unused Journal abbr (“Biochem.J.”)

@article{hazzalinP38RKEssential1996a, title = {P38/{{RK}} Is Essential for the Stress-Induced Nuclear Responses: {{JNK}}/{{SAPKs}} and c-{{Jun}}/{{ATF-2}} Phosphorylation Are Insufficient.}, author = {Hazzalin, C.A. and Cano, E. and Cuenda, A. and Barratt, M.J. and Cohen, P. and Mahadevan, L.C.}, year = 1996, journal = {Curr.Biol.}, number = {6}, pages = {1028–1031}, doi = {10.1016/S0960-9822(02)00649-8}, keywords = {anisomycin,nosource,Phosphorylation,stress activated} } % == BibTeX quality report for hazzalinP38RKEssential1996a: % ? Possibly abbreviated journal title Curr.Biol.

@article{heStabilizationRibosomeAssociation1993b, title = {Stabilization and Ribosome Association of Unspliced Pre-{{mRNAs}} in a Yeast ⬚upf1⬚-⬚⬚ Mutant.}, author = {He, F. and Peltz, S.W. and Donahue, J.L. and Rsobash, M. and Jacobson, A.}, year = 1993, journal = {Proc.Natl.Acad.Sci.USA}, volume = {90}, pages = {7034–7038}, doi = {10.1073/pnas.90.15.7034}, keywords = {nonsense-mediated decay,nosource,ribosome,UPF,Upf1,yeast} } % == BibTeX quality report for heStabilizationRibosomeAssociation1993b: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{heIdentificationNovelComponent1995a, title = {Identification of a Novel Component of the Nonsense-Mediated {{mRNA}} Decay Pathway Using an Interacting Protein Screen.}, author = {He, F. and Jacobson, A.J.}, year = 1995, journal = {Genes & Dev.}, volume = {9}, pages = {437–454}, doi = {10.1101/gad.9.4.437}, keywords = {2 hybrid,COMPONENT,DECAY,IDENTIFICATION,mRNA,mRNA decay,nosource,protein,UPF3} } % == BibTeX quality report for heIdentificationNovelComponent1995a: % ? Possibly abbreviated journal title Genes & Dev.

@article{heFunctionsLsmProteins2000, title = {Functions of {{Lsm}} Proteins in {{mRNA}} Degradation and Splicing}, author = {He, W. and Parker, R.}, year = 2000, month = jun, journal = {Current Opinion in Cell Biology}, volume = {12}, number = {3}, pages = {346–350}, publisher = {Elsevier}, doi = {10.1016/S0955-0674(00)00098-3}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0955067400000983}, abstract = {Recent results have identified a family of Lsm (Like Sm) proteins that are related to the Sm protein family. Seven Lsm proteins form a complex, which interacts with the U6 snRNA and functions in splicing. In addition, a different complex of Lsm proteins interacts with cytoplasmic mRNA and promotes its turnover. These diverse functions of Lsm proteins suggest that they are important modulators of RNA biogenesis and function}, keywords = {20263563,chemistry,COMPLEX,COMPLEXES,degradasome,degradation,human,metabolism,ModelsBiological,mRNA,nosource,protein,Proteins,RibonucleoproteinsSmall Nuclear,Rna,Rna Caps,RNA Splicing,RNAFungal,RNAMessenger,RNASmall Nuclear,Saccharomyces cerevisiae,splicing,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,turnover} } % == BibTeX quality report for heFunctionsLsmProteins2000: % ? unused Journal abbr (“Curr.Opin.Cell Biol.”)

@article{heYeastCytoplasmicLsmI2001, title = {The Yeast Cytoplasmic {{LsmI}}/{{Pat1p}} Complex Protects {{mRNA}} 3’ Termini from Partial Degradation}, author = {He, W. and Parker, R.}, year = 2001, journal = {Genetics}, volume = {158}, number = {4}, pages = {1445–1455}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/158.4.1445}, url = {http://www.genetics.org/content/158/4/1445.short}, abstract = {A key aspect of understanding eukaryotic gene regulation will be the identification and analysis of proteins that bind mRNAs and control their function. Recently, a complex of seven Lsm proteins and the Pat1p have been shown to interact with yeast mRNAs and promote mRNA decapping. In this study we present several observations to indicate that the LsmI/Pat1 complex has a second distinct function in protecting the 3’-UTR of mRNAs from trimming. First, mutations in the LSM1 to LSM7, as well as PAT1, genes led to the accumulation of MFA2pG and PGK1pG transcripts that had been shortened by 10-20 nucleotides at their 3’ ends (referred to as trimming). Second, the trimming of these mRNAs was more severe at the high temperature, correlating with the inability of these mutant strains to grow at high temperature. In contrast, trimming did not occur in a dcp1 Delta strain, wherein the decapping enzyme is lacking. This indicates that trimming is not simply a consequence of the inhibition of mRNA decapping. Third, the temperature-sensitive growth of lsm and pat1 mutants was suppressed by mutations in the exosome or the functionally related Ski proteins, which are required for efficient 3’ to 5’ mRNA degradation of mRNA. Moreover, in lsm ski double mutants, higher levels of the trimmed mRNAs accumulated, indicating that exosome function is not required for mRNA trimming but that the exosome does degrade the trimmed mRNAs. These results raise the possibility that the temperature-sensitive growth of the lsm1-7 and pat1 mutants is at least partially due to mRNA trimming, which either inactivates the function of the mRNAs or makes them available for premature 3’ to 5’ degradation by the exosome}, keywords = {0,3,3’ Untranslated Regions,3’ UTR,3’-UTR,analysis,BIOLOGY,BlottingNorthern,Cap,Cell Division,CEREVISIAE,COMPLEX,COMPLEXES,Cytoplasm,DECAPPING ENZYME,degradation,DNA-BINDING,DNA-Binding Proteins,enzyme,exosome,Fungal Proteins,Fungi,gene,gene regulation,Genes,genetics,GROWTH,IDENTIFICATION,INHIBITION,La,metabolism,ModelsGenetic,mRNA,MUTANTS,Mutation,MUTATIONS,nosource,Nucleotides,Phenotype,physiology,PLASMID,Plasmids,protein,Protein Binding,Proteins,Proto-Oncogene Proteins,REGION,regulation,Rna,Rna Caps,RNAMessenger,S,S-CEREVISIAE,SKI,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Temperature,TRANSCRIPT,Untranslated Regions,yeast} }

@article{heatonAnalysisChimericMRNAs1992, title = {Analysis of Chimeric {{mRNAs}} Derived from the {{STE3 mRNA}} Identifies Multiple Regions within Yeast {{mRNAs}} That Modulate {{mRNA}} Decay.}, author = {Heaton, B. and Decker, C. and Muhlrad, D. and Donahue, J. and Jacobson, A. and Parker, R.}, year = 1992, month = oct, journal = {Nucleic acids research}, volume = {20}, number = {20}, pages = {5365–5373}, publisher = {Oxford University Press}, doi = {10.1093/nar/20.20.5365}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC334343/}, abstract = {In the yeast Saccharomyces cerevisiae unstable mRNAs decay 10-20 fold more rapidly than stable mRNAs. In order to examine the basis for the differences in decay rate of the unstable STE3 mRNA and the stable PGK1 and ACT1 mRNAs we have constructed and measured the decay rates of numerous chimeric mRNAs. These experiments indicate that multiple regions within yeast mRNAs are involved in modulating mRNA decay rates. Our results suggest that at least two regions within the STE3 mRNA are involved in stimulating rapid decay. One region is located within the coding region and requires sequences between codons 13 and 179. In addition, the STE3 3’ UT can also function to stimulate decay. Surprisingly, the STE3 3’ UT is not sufficient to accelerate the turnover of the stable PGK1 transcript unless portions of the PGK1 coding region are first deleted. These results not only identify sequences that function within yeast to stimulate mRNA turnover but also have important implications for an understanding of the basis of differences in eukaryotic mRNA decay rates}, keywords = {93065203,analysis,Base Sequence,BlottingNorthern,Chimeric Proteins,Codon,DECAY,Fungal Proteins,genetics,metabolism,Molecular Sequence Data,mRNA,mRNA decay,nosource,Oligodeoxyribonucleotides,Plasmids,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,turnover,yeast} } % == BibTeX quality report for heatonAnalysisChimericMRNAs1992: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{hebertPhosphorylationVitroVivo1977a, title = {Phosphorylation in Vitro and in Vivo of Ribosomal Proteins from {{Saccharomyces}} Cerevisia}, author = {Hebert, J. and Pierre, M. and Loeb, J.E.}, year = 1977, month = jan, journal = {Eur.J.Biochem.}, volume = {72}, number = {1}, pages = {167–174}, doi = {10.1111/j.1432-1033.1977.tb11236.x}, url = {PM:318998}, abstract = {Crude ribosomes from Saccharomyces cerevisiae cultures were phosphorylated in vitro when incubated in the presence of [gamma-32P]ATP. Analysis of the ribosomal proteins with two-dimensional electrophoresis revealed that of the 29 proteins identified in the small subunit, only protein S6 was phosphorylated. Of the 37 proteins identified in the large subunit, one was highly phosphorylated (L3) and two only slightly phosphorylated (L11 and L14). The protein kinase activity associated with the ribosomes was extracted with 1 M KCl and was not dependent on adenosine 3’:5’-monophosphate; it preferentially phosphorylated casein and phosvitin, but was less active on histones. Structural ribosomal proteins were also phosphorylated in vivo when the yeast cultures were incubated with [32P]orthophosphate; the radioactivity resistant to hydrolysis by hot perchloric acid was incorporated into the proteins of the two subunits. Radioactive phosphoserine was found by subjecting hydrolysates of ribosomal proteins to high-voltage electrophoresis. After two-dimensional electrophoresis, one poorly phosphorylated protein (S10) was identified in the small subunit. In the large subunit, one protein (L3) was highly labelled, and two proteins (L11 and L24) only slightly labelled}, keywords = {0,ACID,ACIDS,Adenosine,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,biosynthesis,CEREVISIAE,Electrophoresis,enzymology,Histones,Hydrolysis,In Vitro,IN-VITRO,IN-VIVO,kinase,L3,La,M,metabolism,nosource,phosphoprotein,Phosphoproteins,Phosphorylation,Phosphoserine,protein,Protein Kinases,PROTEIN-KINASE,Proteins,RESISTANT,Ribosomal Proteins,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Structural,SUBUNIT,SUBUNITS,yeast} } % == BibTeX quality report for hebertPhosphorylationVitroVivo1977a: % ? Possibly abbreviated journal title Eur.J.Biochem.

@article{heintzRegulationHumanHistone1983, title = {Regulation of Human Histone Gene Expression: Kinetics of Accumulation and Changes in the Rate of Synthesis and in the Half-Lives of Individual Histone {{mRNAs}} during the {{HeLa}} Cell Cycle.}, author = {Heintz, N. and Sive, H.L. and Roeder, R.G.}, year = 1983, month = apr, journal = {Molecular and Cellular Biology}, volume = {3}, number = {4}, pages = {539–550}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/3/4/539}, abstract = {We have analyzed the kinetics of accumulation of each of the individual core histone mRNAs throughout the HeLa cell cycle in cells synchronized by sequential thymidine and aphidicolin treatments. These analyses showed that during the S phase there was a 15-fold increase in the levels of histone mRNAs and that this resulted from both an increased rate of synthesis and a lengthening of the half-life of histone mRNAs. A comparison of the kinetics of accumulation of histone mRNA in the total cellular and nuclear RNA populations suggested an increased transcription rate through the S phase. Within 30 min after the inhibition of DNA synthesis in mid-S phase, the steady-state concentration and the rate of synthesis of histone mRNA each declined to their non-S-phase levels. Reactivation of histone mRNA accumulation could occur even after an extended mid-S-phase block in DNA synthesis. These results suggest that the mechanisms responsible for histone mRNA synthesis are not restricted to the G1/S boundary of the HeLa cell cycle, but can operate whenever DNA synthesis is occurring}, keywords = {0,Aphidicolin,cell cycle,CELLS,Diterpenes,Dna,DNA Replication,drug effects,expression,gene,Gene Expression,Gene Expression Regulation,GENE-EXPRESSION,genetics,Half-Life,Hela Cells,Histones,human,Humans,INHIBITION,Kinetics,La,MECHANISM,MECHANISMS,metabolism,mRNA,Multiple DOI,nonfile,nosource,pharmacology,regulation,Rna,RNA ProcessingPost-Transcriptional,RNAMessenger,S,S Phase,Support,transcription,TranscriptionGenetic} } % == BibTeX quality report for heintzRegulationHumanHistone1983: % ? unused Journal abbr (“Mol Cell Biol”)

@article{heldReconstitutionEscherichiaColi1973a, title = {Reconstitution of {{Escherichia}} Coli 30 {{S Ribosomal Subunits}} from {{Purified Molecular Components}}}, author = {Held, W.A. and Mizushima, S. and Nomura, M.}, year = 1973, journal = {Journal of Biological Chemistry}, volume = {248}, number = {16}, pages = {5720–5730}, doi = {10.1016/S0021-9258(19)43564-3}, url = {⬚http://www.jbc.org/cgi/content/abstract/248/16/5720 ⬚}, abstract = {Reconstitution of 30 S ribosomal subunits from 16 S RNA and a mixture of purified individual 30 S ribosomal proteins has been studied.Proteins from the 30 S ribosomal subunit of Escherichia coli were purified by a combination of phosphocellulose and DEAE-chromatography, and Sephadex gel filtration. The proteins purified correspond to the 21 proteins generally accepted as 30 S proteins, with the exception of two proteins, P3b and P3c, which correspond to the protein S6 studied by other workers. P3b and P3c are closely related, and one is probably a derivative of the other.Using a mixture of these purified proteins, reconstitution of functionally active 30 S subunits has been demonstrated. Reconstituted particles had higher activities in poly(U)-directed polyphenylalanine synthesis than reference 30 S particles in several experiments. The functional activity of reconstituted particles was also examined in several other assays; these included natural messenger RNA-directed polypeptide synthesis, poly(U)-directed Phe-tRNA binding, AUG-directed fMet-puromycin formation, AUG-directed fMet-tRNA binding, and the binding of termination codon UAA in the presence of chain termination factors. In all cases, activities comparable to reference 30 S subunits were observed. The sedimentation properties and the protein composition of reconstituted particles were also similar to 30 S ribosomal subunits. The kinetics of reconstitution using purified protein mixtures was essentially identical with those of reconstitution using unfractionated 30 S proteins. These results strongly suggest that 21 purified 30 S proteins together with 16 S RNA are sufficient to reconstitute 30 S subunits, and that no essential 30 S components were lost during the fractionation and purification of the 30 S proteins.Single component omission experiments indicated that all purified proteins, except P1(S1) and P3b,c(S6), are required for full functional activity. A requirement for P9a(S16) has been shown in some, but not all, experiments. P3b,c(S6) and P9a(S16) have been shown to be involved in the reconstitution reaction in other experiments (Mizushima, S., and Nomura, M. (1970) Nature 226, 1214; Nomura, M. (1973) Science 179, 864) and therefore are 30 S components. It is still not clear whether P1(S1) should be considered a “true” 30 S protein or a ribosomal-associated “factor.”}, keywords = {16 S RNA,30 S,30-S,assays,BINDING,CHAIN TERMINATION,Codon,COMPONENT,COMPONENTS,Escherichia coli,ESCHERICHIA-COLI,Kinetics,M,nosource,PARTICLES,POLYPEPTIDE,protein,Proteins,purification,RECONSTITUTION,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,Rna,S,SUBUNIT,SUBUNITS,termination,TERMINATION CODON,TERMINATION-CODON,UAA} }

@article{heldAssemblyMapping301974, title = {Assembly {{Mapping}} of 30 {{S Ribosomal Proteins}} from {{Escherichia}} Coli. {{FURTHER STUDIES}}}, author = {Held, W.A. and Ballou, B. and Mizushima, S. and Nomura, M.}, year = 1974, month = may, journal = {Journal of Biological Chemistry}, volume = {249}, number = {10}, pages = {3103–3111}, doi = {10.1016/S0021-9258(19)42644-6}, url = {⬚http://www.jbc.org/cgi/content/abstract/249/10/3103 ⬚}, abstract = {Further studies were performed on the sequence of addition of proteins to 16 S RNA during the in vitro reconstitution of 30 S ribosomal subunits from Escherichia coli. Direct binding of protein S17 to 16 S RNA was studied in detail, and the following results were obtained: (a) under reconstitution conditions, a maximum of approximately 1 mole of S17 is bound per mole of 16 S RNA, either alone, or in the presence of all other 30 S proteins; (b) S17 binds only to 16 S RNA and not to 23 S RNA; and (c) radioactive S17-16 S RNA complexes are directly converted (without dissociation) to 30 S subunits by the addition of excess unlabeled total 30 S proteins. From these results, we conclude that the binding of S17 to 16 S RNA is specific. We have also determined the positions of S15, S16, S17, and S12 in the assembly map and have clarified subsequent interactions depending on these proteins. A revised assembly map is presented which incorporates the additional information obtained from these experimental results}, keywords = {16 S RNA,30 S,30-S,assembly,BINDING,COMPLEX,COMPLEXES,Escherichia coli,ESCHERICHIA-COLI,In Vitro,IN-VITRO,mapping,nosource,POSITION,POSITIONS,protein,Proteins,RECONSTITUTION,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,Rna,S,sequence,SUBUNIT,SUBUNITS} }

@article{heldEscherichiaColi301975, title = {Escherichia Coli 30 {{S}} Ribosomal Proteins Uniquely Required for Assembly}, author = {Held, W.A. and Nomura, M.}, year = 1975, month = apr, journal = {Journal of Biological Chemistry}, volume = {250}, number = {8}, pages = {3179–3184}, doi = {10.1016/S0021-9258(19)41608-6}, url = {http://www.jbc.org/cgi/content/abstract/250/8/3179}, keywords = {30 S,30-S,assembly,Escherichia coli,ESCHERICHIA-COLI,nonfile,nosource,protein,Proteins,Ribosomal Proteins,S} }

@article{hellerCellularControlOrnithine1981, title = {Cellular Control of Ornithine Decarboxylase Activity by Its Antizyme}, author = {Heller, J.S. and Canellakis, E.S.}, year = 1981, month = may, journal = {Journal of Cellular Physiology}, volume = {107}, number = {2}, pages = {209–217}, publisher = {Wiley Online Library}, doi = {10.1002/jcp.1041070206}, url = {http://onlinelibrary.wiley.com/doi/10.1002/jcp.1041070206/abstract}, abstract = {Conditions have been established under which the antizyme of ornithine decarboxylase (E.C. 4.1.1.17, L-ornithine carboxy-lyase, ODC) a non-competitive protein inhibitor of ODC, can be detected in cells in response to as little as 10(-7) M putrescine. The maintenance of intracellular antizyme activity depends upon the continued presence of putrescine in the medium. Removal of putrescine results in a rapid decline of antizyme activity. These phenomena are unaffected by the presence of cycloheximide and are comparable to the requirement of L-asparagine for the maintenance of ODC activity. The extent to which the antizyme level is increased is inversely related to the preexisting level of intracellular ODC at the time of addition of putrescine. The time of appearance of free antizyme is delayed in cells that have high levels of ODC; the amount of free antizyme that can be assayed for in these cells, at any particular time is correspondingly less. The converse is also true. In cells that have high levels of antizyme, the delay in appearance of ODC is greater and the amount of ODC that can be assayed for is correspondingly less than in cells with low levels of antizyme. These experiments, as well as others, indicate that the ODC antizyme and ODC interact in vivo with each other to modify their respective activities}, keywords = {0,Animals,antagonists & inhibitors,antizyme,Asparagine,Carboxy-Lyases,Cell Line,CELLS,Cycloheximide,IN-VIVO,INHIBITOR,La,M,media,metabolism,Mice,Neuroblastoma,nosource,Ornithine Decarboxylase,ORNITHINE DECARBOXYLASE ANTIZYME,pharmacology,protein,Proteins,Putrescine,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.} } % == BibTeX quality report for hellerCellularControlOrnithine1981: % ? unused Journal abbr (“J.Cell Physiol”)

@article{helmPosttranscriptionalNucleotideModification2006, title = {Post-Transcriptional Nucleotide Modification and Alternative Folding of {{RNA}}}, author = {Helm, M.}, year = 2006, journal = {Nucleic acids research}, volume = {34}, number = {2}, pages = {721–733}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkj471}, url = {http://nar.oxfordjournals.org/content/34/2/721.short}, abstract = {Alternative foldings are an inherent property of RNA and a ubiquitous problem in scientific investigations. To a living organism, alternative foldings can be a blessing or a problem, and so nature has found both, ways to harness this property and ways to avoid the drawbacks. A simple and effective method employed by nature to avoid unwanted folding is the modulation of conformation space through post-transcriptional base modification. Modified nucleotides occur in almost all classes of natural RNAs in great chemical diversity. There are about 100 different base modifications known, which may perform a plethora of functions. The presumably most ancient and simple nucleotide modifications, such as methylations and uridine isomerization, are able to perform structural tasks on the most basic level, namely by blocking or reinforcing single base-pairs or even single hydrogen bonds in RNA. In this paper, functional, genomic and structural evidence on cases of folding space alteration by post-transcriptional modifications in native RNA are reviewed}, keywords = {0,BASE,Base Sequence,BASE-PAIR,chemistry,CONFORMATION,DIVERSITY,genomic,Germany,Hydrogen,La,metabolism,Methylation,modification,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleotides,posttranscriptional modification,Review,Rna,RNA ProcessingPost-Transcriptional,RNATransfer,Structural,Support,Uridine} } % == BibTeX quality report for helmPosttranscriptionalNucleotideModification2006: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{hendrickYeastFrameshiftSuppressor2001, title = {Yeast Frameshift Suppressor Mutations in the Genes Coding for Transcription Factor {{Mbf1p}} and Ribosomal Protein {{S3}}: {{Evidence}} for Autoregulation of {{S3}} Synthesis}, author = {Hendrick, J.L. and Wilson, P.G. and Edelman, I.I. and Sandbaken, M.G. and Ursic, D. and Culbertson, M.R.}, year = 2001, month = mar, journal = {Genetics}, volume = {157}, number = {3}, pages = {1141–1158}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/157.3.1141}, url = {http://www.genetics.org/content/157/3/1141.short}, abstract = {The SUF13 and SUF14 genes were identified among extragenic suppressors of +1 frameshift mutations. SUF13 is synonymous with MBF1, a single-copy nonessential gene coding for a POLII transcription factor. The suf13-1 mutation is a two-nucleotide deletion in the SUE13/MBF1 coding region. A suf13::TRP1 null mutant suppresses +1 frameshift mutations, indicating that suppression is caused by loss of SUF13 function. The suf13-1 suppressor alters sensitivity to aminoglycoside antibiotics and reduces the accumulation of his4-713 mRNA, suggesting that suppression is mediated at the translational level. The SUF14 gene is synonymous with RPS3 a single-copy essential gene that codes for the ribosomal protein S3. The suf14-1 mutation is a missense substitution in the coding region. Increased expression of S3 limits the accumulation of SUF14 mRNA, suggesting that expression is autoregulated. A frameshift mutation in SUF14 that prevents full-length translation eliminated regulation, indicating that S3 is required for regulation. Using CUP1-SUF14 and SUF14-lacZ fusions, run-on transcription assays, and estimates of mRNA half-life, our results show that transcription plays a minor role if any in regulation and that the 5’-UTR is necessary but not sufficient for regulation. A change in mRNA decay rate may be the primary mechanism for regulation}, keywords = {0,5’-UTR,AMINOGLYCOSIDE ANTIBIOTICS,antibiotic,antibiotics,assays,BINDING PROTEIN,DECAY,ELONGATION-FACTOR EF-1-ALPHA,ESCHERICHIA-COLI,expression,frameshift,Frameshift Mutation,gene,Genes,Half-Life,IDENTIFICATION,M,MECHANISM,MESSENGER-RNA DECAY,mRNA,mRNA decay,Mutation,MUTATIONS,nosource,NUCLEOTIDE-SEQUENCE,PHENOTYPIC SUPPRESSION,POLYPEPTIDE-CHAIN,protein,REGION,regulation,SACCHAROMYCES-CEREVISIAE,SHUTTLE VECTORS,suppression,transcription,TRANSCRIPTION FACTOR,translation,yeast} }

@article{henniganFunctionalMappingTranslationdependent1996, title = {Functional Mapping of the Translation-Dependent Instability Element of Yeast {{MATalpha1 mRNA}}}, author = {Hennigan, A.N. and Jacobson, A.}, year = 1996, month = jul, journal = {Molecular and cellular biology}, volume = {16}, number = {7}, pages = {3833–3843}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.16.7.3833}, url = {http://mcb.asm.org/cgi/content/abstract/16/7/3833}, abstract = {The determinants of mRNA stability include specific cis-acting destabilizing sequences located within mRNA coding and noncoding regions. We have developed an approach for mapping coding-region instability sequences in unstable yeast mRNAs that exploits the link between mRNA translation and turnover and the dependence of nonsense-mediated mRNA decay on the activity of the UPF1 gene product. This approach, which involves the systematic insertion of in-frame translational termination codons into the coding sequence of a gene of interest in a upf1delta strain, differs significantly from conventional methods for mapping cis-acting elements in that it causes minimal perturbations to overall mRNA structure. Using the previously characterized MATalpha1 mRNA as a model, we have accurately localized its 65-nucleotide instability element (IE) within the protein coding region. Termination of translation 5’ to this element stabilized the MATalpha1 mRNA two- to threefold relative to wild-type transcripts. Translation through the element was sufficient to restore an unstable decay phenotype, while internal termination resulted in different extents of mRNA stabilization dependent on the precise location of ribosome stalling. Detailed mutagenesis of the element’s rare-codon/AU-rich sequence boundary revealed that the destabilizing activity of the MATalpha1 IE is observed when the terminal codon of the element’s rare-codon interval is translated. This region of stability transition corresponds precisely to a MATalpha1 IE sequence previously shown to be complementary to 18S rRNA. Deletion of three nucleotides 3’ to this sequence shifted the stability boundary one codon 5’ to its wild-type location. Conversely, constructs containing an additional three nucleotides at this same location shifted the transition downstream by an equivalent sequence distance. Our results suggest a model in which the triggering of MATalpha1 mRNA destabilization results from establishment of an interaction between translating ribosomes and a downstream sequence element. Furthermore, our data provide direct molecular evidence for a relationship between mRNA turnover and mRNA translation}, keywords = {0,3,Alleles,Base Sequence,CODING REGION,coding sequence,Codon,CODONS,DECAY,DOWNSTREAM,ELEMENTS,Fungal Proteins,gene,GENE-PRODUCT,GenesFungal,Genetic,genetics,La,LOCATION,mapping,metabolism,Methods,microbiology,MODEL,Molecular Sequence Data,MOLECULAR-GENETICS,mRNA,mRNA decay,mRNA stability,mRNA turnover,Mutagenesis,MutagenesisSite-Directed,nonsense-mediated mRNA decay,nosource,Nucleotides,Oligodeoxyribonucleotides,Peptide Chain Termination,Peptide Synthesis,Peptides,Phenotype,Pheromones,PLASMID,Plasmids,PRODUCT,protein,Proteins,Recombinant Proteins,REGION,ribosome,Ribosomes,Rna,RNAMessenger,rRNA,Saccharomyces cerevisiae,sequence,SEQUENCES,stability,structure,supportu.s.gov’tp.h.s.,termination,TERMINATION CODON,TERMINATION-CODON,TRANSCRIPT,TranscriptionGenetic,translation,TRANSLATIONAL TERMINATION,TranslationGenetic,turnover,Upf1,UPF1 PROTEIN,WILD-TYPE,yeast} } % == BibTeX quality report for henniganFunctionalMappingTranslationdependent1996: % ? unused Journal abbr (“Mol Cell Biol.”)

@article{henrasCbf5pPutativePseudouridine2004, title = {Cbf5p, the Putative Pseudouridine Synthase of {{H}}/{{ACA-type snoRNPs}}, Can Form a Complex with {{Gar1p}} and {{Nop10p}} in Absence of {{Nhp2p}} and Box {{H}}/{{ACA snoRNAs}}}, author = {Henras, A.K. and Capeyrou, R. and Henry, Y. and {Caizergues-Ferrer}, M.}, year = 2004, month = nov, journal = {RNA.}, volume = {10}, number = {11}, pages = {1704–1712}, publisher = {Cold Spring Harbor Lab}, doi = {10.1261/rna.7770604}, url = {http://rnajournal.cshlp.org/content/10/11/1704.short}, abstract = {Box C/D and box H/ACA small ribonucleoprotein particles (sRNPs) are found from archaea to humans, and some of these play key roles during the biogenesis of ribosomes or components of the splicing apparatus. The protein composition of the core of both types of particles is well established and the assembly pathway of box C/D sRNPs has been extensively investigated both in archaeal and eukaryotic systems. In contrast, knowledge concerning the mode of assembly and final structure of box H/ACA sRNPs is much more limited. In the present study, we have investigated the protein/protein interactions taking place between the four protein components of yeast box H/ACA small nucleolar RNPs (snoRNPs), Cbf5p, Gar1p, Nhp2p, and Nop10p. We provide evidence that Cbf5p, Gar1p, and Nop10p can form a complex devoid of Nhp2p and small nucleolar RNA (snoRNA) components of the particles and that Cbf5p and Nop10p can directly bind to each other. We also show that the absence of any component necessary for assembly of box H/ACA snoRNPs inhibits accumulation of Cbf5p, Gar1p, or Nop10p, whereas Nhp2p levels are little affected}, keywords = {0,Archaea,assembly,BIOGENESIS,BlottingWestern,CBF5,CEREVISIAE,chemistry,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,Dose-Response RelationshipDrug,drug effects,FORM,Fungal Proteins,growth & development,human,Humans,Hydro-Lyases,La,Magnesium,Magnesium Chloride,metabolism,Microtubule-Associated Proteins,nosource,Nuclear Proteins,PARTICLES,PATHWAY,pharmacology,Potassium,Potassium Chloride,PRECURSOR,protein,Protein StructureTertiary,Proteins,Pseudouridine,PSEUDOURIDINE SYNTHASE,Recombinant Proteins,RIBONUCLEOPROTEIN,Ribonucleoproteins,RibonucleoproteinsSmall Nuclear,RibonucleoproteinsSmall Nucleolar,ribosome,Ribosomes,Rna,RNA Precursors,RNA ProcessingPost-Transcriptional,RNA-Binding Proteins,RNA-BINDING-PROTEIN,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,splicing,structure,Support,SYSTEM,SYSTEMS,yeast} } % == BibTeX quality report for henrasCbf5pPutativePseudouridine2004: % ? Possibly abbreviated journal title RNA.

@article{hernerStabilizationNacetylphenylalanylTransfer1969, title = {Stabilization of {{N-acetylphenylalanyl}} Transfer Ribonucleic Acid Binding to Ribosomes by Sparsomycin.}, author = {Herner, A.E. and Goldberg, I.H. and Cohen, L.B.}, year = 1969, journal = {Biochemistry}, volume = {8}, number = {4}, pages = {1335–1344}, publisher = {ACS Publications}, doi = {10.1021/bi00832a006}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00832a006}, keywords = {BINDING,COMPLEX,COMPLEXES,nosource,ribosome,Ribosomes,sparsomycin} }

@article{heroldElaboratedPseudoknotRequired1993, title = {An ‘elaborated’ Pseudoknot Is Required for High Frequency Frameshifting during Translation of {{HCV 229E}} Polymerase {{mRNA}}}, author = {Herold, J. and Siddell, S.G.}, year = 1993, month = dec, journal = {Nucleic acids research}, volume = {21}, number = {25}, pages = {5838–5842}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/21.25.5838}, url = {http://nar.oxfordjournals.org/content/21/25/5838.short PM:8290341}, abstract = {The RNA polymerase gene (gene 1) of the human coronavirus 229E is approximately 20 kb in length and is located at the 5’ end of the positive-strand genomic RNA. The coding sequence of gene 1 is divided into two large open reading frames, ORF1a and ORF1b, that overlap by 43 nucleotides. In the region of the ORF1a/ORF1b overlap, the genomic RNA displays two elements that are known to mediate (-1) ribosomal frameshifting. These are the slippery sequence, UUUAAAC, and a 3’ pseudoknot structure. By introducing site-specific mutations into synthetic mRNAs, we have analysed the predicted structure of the HCV 229E pseudoknot and shown that besides the well-known stem structures, S1 and S2, a third stem structure, S3, is required for a high frequency of frameshifting. The requirement for an S3 stem is independent of the length of loop 2}, keywords = {0,3,Amino Acid Sequence,Base Composition,Base Sequence,chemical synthesis,chemistry,coding sequence,Coronavirus,Coronavirus 229EHuman,Dna,DNA-Directed RNA Polymerase,DNA-Directed RNA Polymerases,ELEMENTS,FRAME,Frameshift Mutation,Frameshifting,gene,genetics,genomic,GENOMIC RNA,human,La,LOOP,metabolism,Molecular Sequence Data,mRNA,MutagenesisSite-Directed,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Nucleotides,OPEN READING FRAME,Open Reading Frames,polymerase,pseudoknot,pseudoknot structure,READING FRAME,Reading Frames,REGION,ribosomal frameshifting,Rna,RNA-POLYMERASE,RnaViral,sequence,site specific,structure,supportnon-u.s.gov’t,translation,TranslationGenetic,virology} } % == BibTeX quality report for heroldElaboratedPseudoknotRequired1993: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{herrMutationsWhichAlter1999, title = {Mutations Which Alter the Elbow Region of {{tRNA2Gly}} Reduce {{T4}} Gene 60 Translational Bypassing Efficiency}, author = {Herr, A.J. and Atkins, J.F. and Gesteland, R.F.}, year = 1999, month = may, journal = {The EMBO Journal}, volume = {18}, number = {10}, pages = {2886–2896}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/18.10.2886}, url = {http://www.nature.com/emboj/journal/v18/n10/abs/7591709a.html}, abstract = {Translating ribosomes bypass a 50 nucleotide coding gap in bacteriophage T4 gene 60 mRNA between codons 46 and 47 in order to synthesize the full-length protein. Bypassing of the coding gap requires peptidyl-tRNA2Gly detachment from a GGA codon (codon 46) followed by re-pairing at a matching GGA codon just before codon 47. Using negative selection, based on the sacB gene from Bacillus subtilis, Escherichia coli mutants were isolated which reduce bypassing efficiency. All of the mutations are in the gene for tRNA2Gly. Most of the mutations disrupt the hydrogen bonding interactions between the D- and T-loops (G18psi55 and G19C56) which stabilize the elbow region in nearly all tRNAs. The lone mutation not in the elbow region destabilizes the anticodon stem at position 40. Previously described Salmonella typhimurium mutants of tRNA2Gly, which reduce the stability of the T-loop, were also tested and found to decrease bypassing efficiency. Each tRNA2Gly mutant is functional in translation (tRNA2Gly is essential), but has a decoding efficiency 10- to 20-fold lower than wild-type. This suggests that rigidity of the elbow region and the anticodon stem is critical for both codon-anticodon stability and bypassing}, keywords = {0,Anticodon,Bacteriophage T4,Base Pairing,Base Sequence,Codon,CODONS,D,decoding,E,efficiency,Escherichia coli,ESCHERICHIA-COLI,gene,GenesViral,Genetic,genetics,human,Hydrogen Bonding,La,Molecular Sequence Data,mRNA,MUTANTS,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,POSITION,protein,Proteins,REGION,REQUIRES,ribosome,Ribosomes,Rna,RNAMessenger,RNATransferGly,Salmonella typhimurium,SELECTION,stability,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,translation,TranslationGenetic,tRNA,Viral Proteins,WILD-TYPE} } % == BibTeX quality report for herrMutationsWhichAlter1999: % ? unused Journal abbr (“EMBO J.”)

@article{herrCouplingOpenReading2000, title = {Coupling of Open Reading Frames by Translational Bypassing.}, author = {Herr, A.J. and Atkins, J.F. and Gesteland, R.F.}, year = 2000, journal = {Annual review of biochemistry}, volume = {69:343-72}, number = {1}, pages = {343–372}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, doi = {10.1146/annurev.biochem.69.1.343}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.biochem.69.1.343}, keywords = {20439991,Genetic,genetics,human,nosource,Open Reading Frames} } % == BibTeX quality report for herrCouplingOpenReading2000: % ? unused Journal abbr (“Annu.Rev.Biochem.”)

@article{herrOneProteinTwo2000, title = {One Protein from Two Open Reading Frames: Mechanism of a 50 Nt Translational Bypass}, author = {Herr, A.J. and Gesteland, R.F. and Atkins, J.F.}, year = 2000, month = jun, journal = {The EMBO journal}, volume = {19}, number = {11}, pages = {2671–2680}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/19.11.2671}, url = {http://www.nature.com/emboj/journal/v19/n11/abs/7593090a.html}, abstract = {Translating ribosomes bypass a 50 nt coding gap in order to fuse the information found in the two open reading frames (ORFs) of bacteriophage T4 gene 60. This study investigates the underlying mechanism by focusing on the competition between initiation of bypassing and termination at the end of the first ORF. While nearly all ribosomes initiate bypassing, no more than 50% resume translation in the second ORF. Two previously described cis-acting stimulatory signals are critical for favoring initiation of bypassing over termination. Genetic analysis of these signals supports a working model in which the first (a stem-loop structure at the junction between the first ORF and the coding gap) interferes with decoding in the A-site, and the second (a stretch of amino acids in the nascent peptide encoded by the first ORF) destabilizes peptidyl-tRNA-mRNA pairing}, keywords = {20296691,A-SITE,Amino Acid Sequence,Amino Acids,analysis,Bacteriophage T4,Base Sequence,Codon,decoding,gene,Genetic,genetics,human,initiation,MECHANISM,metabolism,Molecular Sequence Data,nosource,Open Reading Frames,physiology,protein,ribosome,Ribosomes,RNATransferGly,SIGNAL,Signal Peptides,structure,Support,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,termination,translation,translational bypass,TranslationGenetic} } % == BibTeX quality report for herrOneProteinTwo2000: % ? unused Journal abbr (“EMBO J.”)

@article{herrickCodingRegionSegment1992, title = {A Coding Region Segment Is Necessary, but Not Sufficient for Rapid Decay of the {{HIS3 mRNA}} in Yeast}, author = {Herrick, D. and Jacobson, A.}, year = 1992, month = may, journal = {Gene}, volume = {114}, number = {1}, pages = {35–41}, doi = {10.1016/0378-1119(92)90704-S}, abstract = {In Saccharomyces cerevisiae, the HIS3 (encoding imidazoleglycerolphosphate dehydratase) mRNA is unstable (t1/2 = 7 min), whereas the ACT1 (encoding actin) mRNA is more stable (t1/2 = 30 min). To define determinants responsible for rapid mRNA decay, hybrid genes comprised of various regions of these two mRNAs were constructed, transformed into yeast on centromere-containing vectors, and the half-lives of the resultant chimeric mRNAs were measured. To examine whether the 3’-untranslated region (3’-UTR) of HIS3 can confer instability to the ACT1 mRNA, DNA encoding the 3’-UTR of ACT1 was replaced with the corresponding region of HIS3. The hybrid mRNA containing the HIS3 3’-UTR decayed at a rate similar to the endogenous ACT1 mRNA. The mRNA containing the HIS3 5’-UTR and most of the HIS3 coding region fused to an ACT1 3’-fragment was unstable, indicating that HIS3 instability determinants are located within the HIS3 5’-UTR or coding sequence. Deleting 411 nucleotides (nt) from the coding region of either HIS3 or the 5’-HIS3-ACT1-3’ chimeric gene resulted in a three- to fourfold stabilization of the respective mRNAs. However, insertion of this 411-nt fragment in-frame into the entire ACT1 gene had no destabilizing effect on the resultant hybrid mRNA. We conclude that the instability determinants of HIS3 mRNA are complex, involving a coding region segment and, possibly, the 5’-UTR}, keywords = {3’ UTR,92267382,Actins,COMPLEX,COMPLEXES,DECAY,Dna,DNA Mutational Analysis,enzymology,Fungal Proteins,gene,Gene Expression RegulationFungal,Genes,Genetic,genetics,Hydro-Lyases,metabolism,microbiology,mRNA,mRNA decay,nosource,Nucleotides,Recombinant Fusion Proteins,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,supportu.s.gov’tp.h.s.,TranscriptionGenetic,vector,vectors,yeast} }

@article{herruerExtendedPromoterGene1989, title = {The Extended Promoter of the Gene Encoding Ribosomal Protein {{S33}} in Yeast Consists of Multiple Protein Binding Elements}, author = {Herruer, M.H. and Mager, W.H. and Doorenbosch, T.M. and Wessels, P.L. and Wassenaar, T.M. and Planta, R.J.}, year = 1989, journal = {Nucleic acids research}, volume = {17}, number = {18}, pages = {7427–7439}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/17.18.7427}, url = {http://nar.oxfordjournals.org/content/17/18/7427.short}, abstract = {At least 4 different, protein binding cis-acting elements are present in the upstream region of the S33-gene. The major protein binding site is situated between positions -148 and -163 relative to the ATG start codon. It binds a trans-acting factor designated SUF (S33 Upstream Factor). When yeast cells are growing on glucose, deletion of this site results in a decrease of transcription of 50%. Using ethanol as a carbon-source, deletion of the SUF-responsive site lowers the transcription as much as 80%. A second protein binding site is found between positions -85 and -105. Only extracts from glucose-grown cells contain a factor that is able to bind to this site in vitro. A third protein binding site was found using a protein extract from ethanol-grown cells. This site, which is located quite close to the transcriptional start site, is probably responsible for the 20% residual transcription when the SUF binding site is removed. Finally, a site far upstream was found, which binds a protein from both glucose-grown and ethanol-grown cells. This site may function as an upstream repression site which is only functional when a non-fermentable carbon-source is used. Taking these findings into account, we present a model for the carbon-source dependent transcription activation of the gene encoding S33}, keywords = {90016803,A-SITE,activation,Base Sequence,BINDING,Binding Sites,Carbon,carbon source,Chromosome Mapping,Codon,DNA Mutational Analysis,DNA-Binding Proteins,ELEMENTS,Ethanol,gene,Gene Expression RegulationFungal,GenesStructuralFungal,genetics,Glucose,In Vitro,IN-VITRO,metabolism,nosource,Oligonucleotide Probes,physiology,Promoter Regions (Genetics),protein,Protein Binding,Ribosomal Proteins,Saccharomyces cerevisiae,supportnon-u.s.gov’t,transcription,Transcription Factors,TranscriptionGenetic,yeast} } % == BibTeX quality report for herruerExtendedPromoterGene1989: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{hersheyIndependentFunctionsViral1952a, title = {Independent Functions of Viral Protein and Nucleic Acid in Growth of Bacteriophage.}, author = {Hershey, A.D. and Chase, M.}, year = 1952, journal = {The Journal of general physiology}, volume = {36}, pages = {29–56}, doi = {10.1085/jgp.36.1.39}, url = {http://jgp.rupress.org/content/36/1/39.short}, keywords = {Dna,Genetic,nosource,protein,virus} } % == BibTeX quality report for hersheyIndependentFunctionsViral1952a: % ? unused Journal abbr (“J.Gen.Physiol.”)

@article{hersheyTranslationalControlMammalian1991, title = {Translational Control in Mammalian Cells.}, author = {Hershey, J.W.B.}, year = 1991, journal = {Annual review of biochemistry}, volume = {60}, number = {1}, pages = {717–755}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, doi = {10.1146/annurev.bi.60.070191.003441}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.bi.60.070191.003441}, keywords = {nosource,Review,translation} } % == BibTeX quality report for hersheyTranslationalControlMammalian1991: % ? unused Journal abbr (“Annu.Rev.Biochem.”)

@incollection{hersheyPathwayMechanismInitiation2000, title = {The Pathway and Mechanism of Initiation of Protein Synthesis}, booktitle = {Translational {{Control}} of {{Gene Expression}}}, author = {Hershey, J.W.B. and Merrick, W.C.}, year = 2000, pages = {33–88}, publisher = {Cold Spring Harbor Press}, address = {Cold Spring Harbor, NY}, collaborator = {Sonnenberg, N. and Hershey, J.W.B. and Mathews, M.B}, isbn = {0-87969-568-4}, keywords = {expression,gene,Gene Expression,GENE-EXPRESSION,initiation,MECHANISM,nosource,PATHWAY,protein,protein synthesis,PROTEIN-SYNTHESIS,review article} }

@article{hillDifferentialRegulationRat1992, title = {Differential Regulation of Rat Liver Selenoprotein {{mRNAs}} in Selenium Deficiency}, author = {Hill, K.E. and Lyons, P.R. and Burk, R.F.}, year = 1992, month = may, journal = {Biochemical and biophysical research communications}, volume = {185}, number = {1}, pages = {260–263}, publisher = {Elsevier}, doi = {10.1016/S0006-291X(05)80984-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006291X05809842}, abstract = {Selenium deficiency causes a fall in the concentrations of selenoproteins but selenoprotein P and type I iodothyronine 5’- deiodinase (5’-deiodinase) are more resistant to this effect than is glutathione peroxidase. To investigate the differential regulation of these selenoproteins, a selenium-deficient diet was fed to weanling rats for 14.5 weeks and their hepatic mRNAs were measured by Northern analysis. Levels of all 3 mRNAs fell progressively with time. Selenoprotein P and 5’-deiodinase mRNAs remained higher at all time points relative to control than glutathione peroxidase mRNA. mRNA decreases were mirrored by decreases in glutathione peroxidase activity and selenoprotein P concentration. However, the decreases in the protein levels were greater than the decreases in their mRNAs, suggesting that synthesis of both proteins was limited to a similar extent at the translational level by the availability of selenium. In addition to this apparently unregulated translational effect, these results point to a pretranslational regulation, affecting mRNA levels, which could account for the differential effect of selenium deficiency on glutathione peroxidase and the other selenoproteins. This regulation might serve to direct selenium to selenoprotein P and 5’-deiodinase when limited amounts of the element are available}, keywords = {0,analysis,animal,deficiency,Diet,Gene Expression Regulation,Glutathione Peroxidase,Iodide Peroxidase,La,Liver,Male,metabolism,mRNA,nosource,protein,Proteins,rat,Rats,RatsInbred Strains,regulation,Rna,RNAMessenger,Selenium,supportu.s.gov’tp.h.s.,Weaning} } % == BibTeX quality report for hillDifferentialRegulationRat1992: % ? unused Journal abbr (“Biochem.Biophys.Res.Commun.”)

@article{hillGagPolSuppliedTrans2001, title = {Gag-{{Pol}} Supplied in Trans Is Efficiently Packaged and Supports Viral Function in Human Immunodeficiency Virus Type 1}, author = {Hill, M.K. and Hooker, C.W. and Harrich, D. and Crowe, S.M. and Mak, J.}, year = 2001, journal = {Journal of Virology}, volume = {75}, number = {15}, pages = {6835–6840}, publisher = {Am Soc Microbiol}, doi = {10.1128/JVI.75.15.6835-6840.2001}, url = {http://jvi.asm.org/cgi/content/abstract/75/15/6835}, abstract = {The intracellular trafficking and subsequent incorporation of Gag-Pol into human immunodeficiency virus type 1 (HIV-1) remains poorly defined. Gag-Pol is encoded by the same mRNA as Gag and is generated by ribosomal frameshifting. The multimerization of Gag and Gag-Pol is an essential step in the formation of infectious viral particles. In this study, we examined whether the interaction between Gag and Gag-Pol is initiated during protein translation in order to facilitate the trafficking and subsequent packaging of Gag-Pol into the virion. A conditional cotransfection system was developed in which virion formation required the coexpression of two HIV-1-based plasmids, one that produces both Gag and Gag-Pol and one that only produces Gag-Pol. The Gag-Pol proteins were either immunotagged with a His epitope or functionally tagged with a mutation (K65R) in reverse transcriptase that is associated with drug resistance. Gag-Pol packaging was assessed to determine whether the Gag-Pol incorporated into the virion was preferentially packaged from the plasmid that expressed both Gag and Gag-Pol or whether it could be packaged from either plasmid. Our data show that translation of Gag and Gag-Pol from the same mRNA is not critical for virion packaging of the Gag-Pol polyprotein or for viral function}, keywords = {AIDS,ASSEMBLY INTERMEDIATE COMPLEXES,CELLS,Drug Resistance,epitope,Frameshifting,Gag,Gag-pol,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,IN-VITRO,MAK,mRNA,Mutation,nosource,packaging,PARTICLES,PLASMID,Plasmids,POLYPROTEIN,PRECURSOR PROTEIN,protein,Proteins,REGION,RESISTANCE,REVERSE-TRANSCRIPTASE,ribosomal frameshifting,Support,SYSTEM,translation,viral particle,VIRAL PARTICLES,Virion,VIRIONS,virus,WILD-TYPE} }

@incollection{hinnebuschProteinSynthesisTranslational1991a, title = {Protein Synthesis and Translational Control in ⬚{{Saccharomyces}} Cerevisiae⬚.}, booktitle = {The {{Molecular}} and {{Cellular Biologh}} of the {{Yeast}} ⬚{{Saccharomyces}}⬚.}, author = {Hinnebusch, A.G. and Leibman, S.W.}, year = 1991, series = {Genome {{Dynamics}}, {{Protein Synthesis}}, and {{Energetics}}.}, volume = {IV}, pages = {627–736}, publisher = {Cold Spring Harbor Laboratory Press.}, address = {Cold Spring Harbor, New York}, collaborator = {Broach, J.R. and Pringle, J.R. and Jones, E.W.}, keywords = {Genome,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Review,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,yeast}, annotation = {2; 1} }

@article{hinnebuschUnleashingYeastGenetics2001, title = {Unleashing Yeast Genetics on a Factor-Independent Mechanism of Internal Translation Initiation}, author = {Hinnebusch, A.G.}, year = 2001, month = nov, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {23}, pages = {12866–12868}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.241517998}, url = {http://www.pnas.org/content/98/23/12866.short}, keywords = {0,CELLS,CODONS,COMPLEXES,expression,gene,Genetic,genetics,initiation,MECHANISM,nosource,POLIOVIRUS RNA,PROTEIN-SYNTHESIS,RIBOSOME ENTRY SITE,translation,TRANSLATION INITIATION,virus,yeast} }

@article{hinnebuschStudyTranslationalControl2004, title = {Study of Translational Control of Eukaryotic Gene Expression Using Yeast}, author = {Hinnebusch, A.G. and Asano, K. and Olsen, D.S. and Phan, L. and Nielsen, K.H. and Valasek, L.}, year = 2004, month = dec, journal = {Annals of the New York Academy of Sciences}, volume = {1038}, number = {1}, pages = {60–74}, publisher = {Wiley Online Library}, doi = {10.1196/annals.1315.012}, url = {http://onlinelibrary.wiley.com/doi/10.1196/annals.1315.012/pdf}, abstract = {Eukaryotic cells respond to starvation by decreasing the rate of general protein synthesis while inducing translation of specific mRNAs encoding transcription factors GCN4 (yeast) or ATF4 (humans). Both responses are elicited by phosphorylation of translation initiation factor 2 (eIF2) and the attendant inhibition of its nucleotide exchange factor eIF2B-decreasing the binding to 40S ribosomes of methionyl initiator tRNA in the ternary complex (TC) with eIF2 and GTP. The reduction in TC levels enables scanning ribosomes to bypass the start codons of upstream open reading frames in the GCN4 mRNA leader and initiate translation at the authentic GCN4 start codon. We exploited the fact that GCN4 translation is a sensitive reporter of defects in TC recruitment to identify the catalytic and regulatory subunits of eIF2B. More recently, we implicated the C-terminal domain of eIF1A in 40S-binding of TC in vivo. Interestingly, we found that TC resides in a multifactor complex (MFC) with eIF3, eIF1, and the GTPase-activating protein for eIF2, known as eIF5. Our biochemical and genetic analyses indicate that physical interactions between MFC components enhance TC binding to 40S subunits and are required for wild-type translational control of GCN4. MFC integrity and eIF3 function also contribute to post-assembly steps in the initiation pathway that impact GCN4 expression. Thus, apart from its critical role in the starvation response, GCN4 regulation is a valuable tool for dissecting the contributions of multiple translation factors in the eukaryotic initiation pathway}, keywords = {0,BINDING,CELLS,CEREVISIAE,Codon,CODONS,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,development,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,DOMAIN,eIF1,eIF1A,eIF3,EIF5,Eukaryotic Cells,Eukaryotic Initiation Factor-1,Eukaryotic Initiation Factor-2,Eukaryotic Initiation Factor-2B,expression,FRAME,GCN4,gene,Gene Expression,Gene Expression RegulationFungal,gene regulation,GENE-EXPRESSION,Genetic,genetics,GTP,human,Humans,IDENTIFY,IN-VIVO,INHIBITION,initiation,INITIATION-FACTOR,kinase,La,Macromolecular Substances,metabolism,ModelsMolecular,mRNA,nosource,NUCLEOTIDE EXCHANGE,OPEN READING FRAME,Open Reading Frames,PATHWAY,Phosphorylation,protein,Protein Binding,Protein Biosynthesis,Protein Kinases,Protein StructureTertiary,protein synthesis,PROTEIN-KINASE,PROTEIN-SYNTHESIS,Proteins,READING FRAME,Reading Frames,RECRUITMENT,regulation,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,scanning,START CODON,SUBUNIT,SUBUNITS,transcription,TRANSCRIPTION FACTOR,Transcription Factors,translation,TRANSLATION INITIATION,tRNA,UPSTREAM,WILD-TYPE,yeast} } % == BibTeX quality report for hinnebuschStudyTranslationalControl2004: % ? unused Journal abbr (“Ann.N.Y.Acad.Sci.”)

@article{hirabayashiConservedLoopSequence2006, title = {Conserved Loop Sequence of Helix 69 in {{Escherichia}} Coli 23 {{S rRNA}} Is Involved in {{A-site tRNA}} Binding and Translational Fidelity}, author = {Hirabayashi, N. and Sato, N.S. and Suzuki, T.}, year = 2006, month = jun, journal = {Journal of Biological Chemistry}, volume = {281}, number = {25}, pages = {17203–17211}, publisher = {ASBMB}, doi = {10.1074/jbc.M511728200}, url = {http://www.jbc.org/content/281/25/17203.short}, abstract = {Ribosomal (r) RNAs play a crucial role in the fundamental structure and function of the ribosome. Helix 69 (H69) (position 1906-1924), a highly conserved stem-loop in domain IV of the 23 S rRNA of bacterial 50 S subunits, is located on the surface for intersubunit association with the 30 S subunit by connecting with helix 44 of 16 S rRNA with the bridge B2a. H69 directly interacts with A/T-, A-, and P-site tRNAs during each translation step. To investigate the functional importance of the highly conserved loop sequence (1912-1918) of H69, we employed a genetic method that we named SSER (systematic selection of functional sequences by enforced replacement). This method allowed us to identify and select from the randomized loop sequences of H69 in Escherichia coli 23 S rRNA functional sequences that are absolutely required for ribosomal function. From a library consisting of 16,384 sequence variations, 13 functional variants were obtained. A1912 and U(Psi)1917 were selected as essential residues in all variants. An E. coli strain having 23 S rRNA with a U to A mutation at position 1915 showed a severe growth phenotype and low translational fidelity. The result could be explained by the fact that the A1915-ribosome variant has weak subunit association, weak A-site tRNA binding, and decreased translational activity. This study proposes that H69 plays an important role in the control of translational fidelity by modulating A-site tRNA binding during the decoding process}, keywords = {0,30 S,30-S,A SITE,A-SITE,ASSOCIATION,Bacterial,Base Sequence,BINDING,chemistry,CONSERVED LOOP,decoding,DOMAIN,E,Escherichia coli,ESCHERICHIA-COLI,Fidelity,Gene Library,Genetic,genetics,GROWTH,IDENTIFY,La,library,LOOP,metabolism,ModelsMolecular,Molecular Sequence Data,Mutation,nosource,Nucleic Acid Conformation,P SITE,P-SITE,Peptides,Phenotype,Phylogeny,POSITION,Protein Binding,Protein Biosynthesis,Protein StructureTertiary,Research SupportNon-U.S.Gov’t,RESIDUES,ribosome,Rna,RNARibosomal23S,RNATransfer,rRNA,S,SELECTION,sequence,SEQUENCES,STEM-LOOP,structure,SUBUNIT,subunit association,SUBUNITS,translation,translational fidelity,tRNA,tRNA binding} } % == BibTeX quality report for hirabayashiConservedLoopSequence2006: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{hiragaCloningCharacterizationElongation1993, title = {Cloning and Characterization of the Elongation Factor {{EF-1}} [Beta] Homologue of {{Saccharomyces}} Cerevisiae:: {{EF-1}} [Beta] Is Essential for Growth}, author = {Hiraga, K. and Suzuki, K. and Tsuchiya, E. and Miyakawa, T.}, year = 1993, month = jan, journal = {FEBS letters}, volume = {316}, number = {2}, pages = {165–169}, publisher = {Elsevier}, doi = {10.1016/0014-5793(93)81208-H}, url = {http://linkinghub.elsevier.com/retrieve/pii/001457939381208H}, abstract = {A Saccharomyces cerevisiae cDNA homologue of the elongation factor EF-1 beta was found among the clones obtained by immunoscreening of a yeast cDNA expression library with an antibody against calmodulin affinity-purified proteins. The cDNA encoded a protein of 206 amino acids which was highly homologous (about 70% homology) with Artemia salina and human EF-1 beta. A protein with an apparent molecular mass of 33,000, significantly larger than that expected from the gene, was identified by Western blotting. Gene disruption experiments indicated that EF-1 beta is essential for growth}, keywords = {0,ACID,ACIDS,Amino Acid Sequence,Amino Acids,AMINO-ACID,AMINO-ACIDS,Antibodies,antibody,Base Sequence,BlottingSouthern,BlottingWestern,Calmodulin,CEREVISIAE,cloning,CloningMolecular,DISRUPTION,Dna,DNAFungal,EF-1,elongation,elongation factors,ELONGATION-FACTORS,expression,Fermentation,gene,GenesFungal,genetics,GROWTH,growth & development,human,Humans,La,library,Molecular Sequence Data,nosource,Peptide Elongation Factor 1,Peptide Elongation Factors,protein,Proteins,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Sequence HomologyAmino Acid,yeast} } % == BibTeX quality report for hiragaCloningCharacterizationElongation1993: % ? unused Journal abbr (“FEBS Lett.”)

@article{hiranoInteractionRibosomalProtein1995, title = {Interaction of the Ribosomal Protein, {{L5}}, with Protein Phosphatase Type 1}, author = {Hirano, K. and Ito, M. and Hartshorne, D.J.}, year = 1995, journal = {Journal of Biological Chemistry}, volume = {270}, number = {34}, pages = {19786–19790}, publisher = {ASBMB}, doi = {10.1074/jbc.270.34.19786}, url = {http://www.jbc.org/content/270/34/19786.short}, abstract = {The two-hybrid system was used to screen for binding proteins of type 1 protein phosphatase. Two plasmids were constructed, one containing the cDNA of the delta isoform of the type 1 catalytic subunit and the other containing a chicken gizzard cDNA library. Yeast (Y190) were transformed with the plasmids and screened for interacting species. 35 positive clones were categorized into 19 gene groups. Most of these were not identified. One clone, however, contained a sequence identical to the C-terminal portion of the chicken ribosomal protein L5 and corresponded to nucleotide residues 606-975. L5 was isolated from rat liver ribosomes as the L5.5 S RNA complex. This activated phosphatase activity of a myosin-bound phosphatase and the isolated type 1 catalytic subunit using phosphorylated myosin light chains and phosphorylase alpha as substrates. In addition, it was found that phosphatase sedimented with ribosomal subunits containing L5 but did not sediment with those deficient in L5. These data indicate that L5 binds to the catalytic subunit of the type 1 protein phosphatase and may act as a target molecule for phosphatase in ribosomal function or other cell mechanisms}, keywords = {5S rRNA,95378222,Amino Acid Sequence,animal,Base Sequence,BINDING,BINDING-PROTEIN,chickens,CloningMolecular,Comparative Study,COMPLEX,COMPLEXES,DNA Primers,DNAComplementary,gene,genetics,human,In Vitro,L5,L5/L1,library,Liver,MECHANISM,MECHANISMS,metabolism,Molecular Sequence Data,nosource,Phosphoprotein Phosphatase,Plasmids,protein,Protein Binding,Proteins,rat,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,Saccharomyces cerevisiae,sequence,Sequence HomologyAmino Acid,Sequence HomologyNucleic Acid,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,yeast} } % == BibTeX quality report for hiranoInteractionRibosomalProtein1995: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{hiziCharacterizationMouseMammary1987, title = {Characterization of Mouse Mammary Tumor Virus Gag-pro Gene Products and the Ribosomal Frameshift Site by Protein Sequencing}, author = {Hizi, A. and Henderson, L.E. and Copeland, T.D. and Sowder, R.C. and Hixson, C.V. and Oroszlan, S.}, year = 1987, month = oct, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {84}, number = {20}, pages = {7041–7045}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.84.20.7041}, url = {http://www.pnas.org/content/84/20/7041.short}, keywords = {Amino Acid Sequence,analysis,Codon,Dna,elongation,enzyme,frameshift,Gag,gene,IN-VIVO,MECHANISM,MECHANISMS,MMTV,mRNA,nosource,pol,polymerase,protein,Proteins,readthrough,RIBOSOMAL FRAMESHIFT,sequence,Sequence Analysis,suppression,termination,tRNA,virus} }

@article{hiziAnalysisGagProteins1989, title = {Analysis of Gag Proteins from Mouse Mammary Tumor Virus.}, author = {Hizi, A. and Henderson, L.E. and Copeland, T.D. and Sowder, R.C. and Krutzsch, H.C. and Oroszlan and S.}, year = 1989, month = jun, journal = {Journal of Virology}, volume = {63}, number = {6}, pages = {2543–2549}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.63.6.2543-2549.1989}, url = {http://jvi.asm.org/cgi/content/abstract/63/6/2543}, keywords = {Amino Acid Sequence,Amino Acids,analysis,Capsid,Chromatography,CLEAVAGE,Codon,Dna,Gag,gene,Glycine,MMTV,nosource,protein,Proteins,sequence,Structural,virus} }

@article{hoNMD3EncodesEssential1999, title = {{{NMD3}} Encodes an Essential Cytoplasmic Protein Required for Stable {{60S}} Ribosomal Subunits in {{Saccharomyces}} Cerevisiae}, author = {Ho, J.H. and Johnson, A.W.}, year = 1999, month = mar, journal = {Molecular and cellular biology}, volume = {19}, number = {3}, pages = {2389–2399}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.19.3.2389}, url = {http://mcb.asm.org/cgi/content/abstract/19/3/2389}, abstract = {A mutation in NMD3 was found to be lethal in the absence of XRN1, which encodes the major cytoplasmic exoribonuclease responsible for mRNA turnover. Molecular genetic analysis of NMD3 revealed that it is an essential gene required for stable 60S ribosomal subunits. Cells bearing a temperature-sensitive allele of NMD3 had decreased levels of 60S subunits at the nonpermissive temperature which resulted in the formation of half-mer polysomes. Pulse-chase analysis of rRNA biogenesis indicated that 25S rRNA was made and processed with kinetics similar to wild-type kinetics. However, the mature RNA was rapidly degraded, with a half-life of 4 min. Nmd3p fractionated as a cytoplasmic protein and sedimented in the position of free 60S subunits in sucrose gradients. These results suggest that Nmd3p is a cytoplasmic factor required for a late cytoplasmic assembly step of the 60S subunit but is not a ribosomal protein. Putative orthologs of Nmd3p exist in Drosophila, in nematodes, and in archaebacteria but not in eubacteria. The Nmd3 protein sequence does not contain readily recognizable motifs of known function. However, these proteins all have an amino-terminal domain containing four repeats of Cx2C, reminiscent of zinc-binding proteins, implicated in nucleic acid binding or protein oligomerization}, keywords = {0,60S subunit,ACID,Amino Acid Sequence,analysis,Animals,assembly,BINDING,BIOLOGY,Caenorhabditis elegans,Cell Fractionation,CELLS,CEREVISIAE,Cycloheximide,Cytoplasm,DOMAIN,Drosophila,Drosophila melanogaster,ENCODES,Eubacterium,Exoribonucleases,Fungal Proteins,gene,GenesFungal,Genetic,genetics,Half-Life,Hygromycin B,INHIBITOR,inhibitors,Kinetics,La,metabolism,microbiology,Molecular Sequence Data,MOTIFS,mRNA,mRNA turnover,Mutation,nosource,Paromomycin,pharmacology,Polyribosomes,polysomes,POSITION,protein,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,Ribosomes,Rna,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAFungal,RNAMessenger,RNARibosomal,rRNA,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,Sequence AnalysisDNA,Sequence HomologyAmino Acid,SUBUNIT,SUBUNITS,supportu.s.gov’tp.h.s.,SYNTHESIS INHIBITORS,Temperature,TranslationGenetic,turnover,WILD-TYPE,XRN1} } % == BibTeX quality report for hoNMD3EncodesEssential1999: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{hoNascent60SRibosomal2000, title = {Nascent {{60S}} Ribosomal Subunits Enter the Free Pool Bound by {{Nmd3p}}}, author = {Ho, J.H. and Kallstrom, G. and Johnson, A.W.}, year = 2000, month = nov, journal = {RNA}, volume = {6}, number = {11}, pages = {1625–1634}, publisher = {Cambridge Univ Press}, doi = {10.1017/S1355838200001291}, url = {PM:11105761}, abstract = {Nmd3p from yeast is required for the export of the large (60S) ribosomal subunit from the nucleus (Ho et al., 2000). Here, we show that Nmd3p forms a stable complex with free 60S subunits. Using an epitope-tagged Nmd3p, we show that free 60S subunits can be coimmunoprecipitated with Nmd3p. The interaction was specific for 60S subunits; 40S subunits were not coimmunoprecipitated. Using this coprecipitation technique and pulse-chase labeling of ribosomal subunit proteins we showed that Nmd3p bound nascent subunits, consistent with its role in export. However, under conditions in which ribosome biogenesis was inhibited (e.g., inhibition of transcription with thiolutin, inhibition of transcription of ribosomal protein and RNA genes in a sly1-1 mutant at nonpermissive temperature, and inhibition of translation in a conditional prt1 mutant), Nmd3p remained associated with 60S subunits. In addition, Nmd3delta120, a truncated protein that lacked a nuclear localization signal, retained 60S binding. These results suggest that Nmd3p recruits nascent 60S subunits into the pool of free 60S subunits and exchanges on 60S subunits as they recycle during translation}, keywords = {0,60S subunit,Base Sequence,BINDING,Binding Sites,BIOLOGY,Carrier Proteins,Cell Nucleus,CEREVISIAE,COMPLEX,COMPLEXES,FORM,Fungal Proteins,gene,Genes,Genetic,genetics,INHIBITION,isolation & purification,La,LOCALIZATION,metabolism,Methionine,microbiology,Molecular Sequence Data,MOLECULAR-GENETICS,MutagenesisInsertional,nosource,Nuclear Localization Signal,Oligodeoxyribonucleotides,physiology,protein,Proteins,PRT1,Recombinant Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,ribosome biogenesis,Ribosomes,Rna,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAFungal,RNARibosomal,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SIGNAL,SUBUNIT,SUBUNITS,supportu.s.gov’tp.h.s.,Temperature,transcription,TranscriptionGenetic,translation,TranslationGenetic,yeast} }

@article{hoNmd3pCrm1pdependentAdapter2000, title = {Nmd3p Is a {{Crm1p-dependent}} Adapter Protein for Nuclear Export of the Large Ribosomal Subunit}, author = {Ho, J.H. and Kallstrom, G. and Johnson, A.W.}, year = 2000, month = nov, journal = {The Journal of cell biology}, volume = {151}, number = {5}, pages = {1057–1066}, publisher = {Rockefeller Univ Press}, doi = {10.1083/jcb.151.5.1057}, url = {http://jcb.rupress.org/content/151/5/1057.abstract}, abstract = {In eukaryotic cells, nuclear export of nascent ribosomal subunits through the nuclear pore complex depends on the small GTPase Ran. However, neither the nuclear export signals (NESs) for the ribosomal subunits nor the receptor proteins, which recognize the NESs and mediate export of the subunits, have been identified. We showed previously that Nmd3p is an essential protein from yeast that is required for a late step in biogenesis of the large (60S) ribosomal subunit. Here, we show that Nmd3p shuttles and that deletion of the NES from Nmd3p leads to nuclear accumulation of the mutant protein, inhibition of the 60S subunit biogenesis, and inhibition of the nuclear export of 60S subunits. Moreover, the 60S subunits that accumulate in the nucleus can be coimmunoprecipitated with the NES-deficient Nmd3p. 60S subunit biogenesis and export of truncated Nmd3p were restored by the addition of an exogenous NES. To identify the export receptor for Nmd3p we show that Nmd3p shuttling and 60S export is blocked by the Crm1p-specific inhibitor leptomycin B. These results identify Crm1p as the receptor for Nmd3p export. Thus, export of the 60S subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway}, keywords = {0,60S subunit,Active TransportCell Nucleus,analysis,BIOLOGY,Carrier Proteins,Cell Nucleus,CELLS,CEREVISIAE,chemistry,COMPLEX,COMPLEXES,Eukaryotic Cells,Fungal Proteins,GenesDominant,Genetic,genetics,GTPase,IDENTIFY,INHIBITION,INHIBITOR,Karyopherins,La,metabolism,microbiology,MOLECULAR-GENETICS,Mutation,nosource,PATHWAY,physiology,Precipitin Tests,protein,Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,Ribosomes,RNA-Binding Proteins,RNA-BINDING-PROTEIN,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SIGNAL,SUBUNIT,SUBUNIT BIOGENESIS,SUBUNITS,supportu.s.gov’tp.h.s.,yeast} } % == BibTeX quality report for hoNmd3pCrm1pdependentAdapter2000: % ? unused Journal abbr (“J.Cell Biol.”)

@article{hoSitedirectedMutagenesisOverlap1989, title = {Site-Directed Mutagenesis by Overlap Extension Using the Polymerase Chain Reaction}, author = {Ho, S.N. and Hunt, H.D. and Horton, R.M. and Pullen, J.K. and Pease, L.R.}, year = 1989, month = apr, journal = {Gene}, volume = {77}, number = {1}, pages = {51–59}, publisher = {Elsevier}, doi = {10.1016/0378-1119(89)90358-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/0378111989903582}, keywords = {COMPLEX,COMPLEXES,Dna,efficiency,gene,Genetic,Methods,Mutagenesis,Mutation,MUTATIONS,nosource,PCR,polymerase,Polymerase Chain Reaction,sequence,techniques} }

@article{hobbieGeneticModelInvestigate2006a, title = {A Genetic Model to Investigate Drug-Target Interactions at the Ribosomal Decoding Site}, author = {Hobbie, S.N. and Bruell, C. and Kalapala, S. and Akshay, S. and Schmidt, S. and Pfister, P. and Bottger, E.C.}, year = 2006, journal = {Biochimie}, volume = {88}, number = {8}, pages = {1033–1043}, doi = {10.1016/j.biochi.2006.04.008}, url = {PM:16690195}, abstract = {Recent advances in X-ray crystallography have greatly contributed to the understanding of the structural interactions between aminoglycosides and the ribosomal decoding site. Efforts to genetically probe the functional relevance of proposed drug-nucleotide contacts have in part been hampered by the presence of multiple rRNA operons in most bacteria. A derivative of the Gram-positive Mycobacterium smegmatis was rendered single rRNA operon allelic by means of gene inactivation techniques. In this system, genetic manipulation of the single chromosomal rRNA operon results in cells carrying homogeneous populations of mutant ribosomes. An exhaustive mutagenesis study of the ribosomal A site has been performed to define the importance of individual drug-nucleotide contacts. Mutational alterations in the M. smegmatis decoding site are discussed here, comparing the results with those obtained in other organisms. Implications for the selectivity of antimicrobial agents and for the fitness cost of resistance mutations are addressed}, keywords = {0,16S,A SITE,A-SITE,aminoglycoside,Aminoglycosides,Anti-Bacterial Agents,Bacteria,Bacterial,Binding Sites,CELLS,chemistry,Crystallography,decoding,gene,Genetic,genetics,La,M,metabolism,MODEL,Models-Genetic,Models-Molecular,ModelsGenetic,ModelsMolecular,Molecular Structure,mutagenesis,Mutagenesis,Mutation,MUTATIONS,nosource,Operon,pharmacology,resistance,RESISTANCE,RESISTANCE MUTATIONS,Review,ribosome,Ribosomes,Rna,RNA-Bacterial,RNA-Ribosomal-16S,RNABacterial,RNARibosomal16S,rRNA,rRNA Operon,SITE,Structural,structure,Support,SYSTEM,techniques} }

@article{hoferMutationalAnalysisRibosomal2007, title = {Mutational Analysis of the Ribosomal Protein {{RPL10}} from Yeast}, author = {Hofer, A. and Bussiere, C. and Johnson, A.W.}, year = 2007, month = nov, journal = {J. Biol. Chem.}, volume = {282}, number = {45}, pages = {32630–9}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.M705057200}, url = {http://www.jbc.org/content/282/45/32630.short}, abstract = {Yeast Rpl10 belongs to the L10e family of ribosomal proteins. In the large (60S) subunit, Rpl10 is positioned in a cleft between the central protuberance and the GTPase activating center. It is loaded into the 60S subunit at a late step in maturation. We have shown previously that Rpl10 is required for the release of the Crm1-dependent nuclear export adapter Nmd3, an event that also requires the cytoplasmic GTPase Lsg1. Here we have carried out an extensive mutational analysis of Rpl10 to identify mutations that would allow us to map activities to distinct domains of the protein to begin to understand the molecular interaction between Rpl10 and Nmd3. We found that mutations in a central loop (amino acids 102-112) had a significant impact on release of Nmd3. This loop is unstructured in the crystal and solution structures of prokaryotic Rpl10 orthologs. Thus, the loop is not necessary for stable interaction of Rpl10 with the ribosome, suggesting that it plays a dynamic role in ribosome function or regulating the association of other factors. We also found that mutant Rpl10 proteins that were engineered to be unable to bind to the ribosome accumulated in the nucleus. This was unexpected and may suggest a nuclear role for Rpl10}, pmid = {17761675}, keywords = {60S subunit,ACID,ACIDS,Amino Acid Sequence,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,Animals,ASSOCIATION,Centrifugation,Conserved Sequence,Density Gradient,DOMAIN,DOMAINS,FAMILY,Genetic,genetics,GTPase,Humans,IDENTIFY,La,LOOP,MATURATION,microbiology,Models,Molecular,Molecular Sequence Data,MOLECULAR-GENETICS,Mutation,Mutation: genetics,MUTATIONAL ANALYSIS,MUTATIONS,nosource,Phenotype,protein,Protein Binding,Protein Structure,Proteins,RELEASE,REQUIRES,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: genetics,Ribosomal Proteins: metabolism,RIBOSOMAL-PROTEIN,ribosome,Saccharomyces cerevisiae,Saccharomyces cerevisiae: chemistry,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Sequence Alignment,structure,SUBUNIT,Tertiary,yeast} } % == BibTeX quality report for hoferMutationalAnalysisRibosomal2007: % ? Possibly abbreviated journal title J. Biol. Chem.

@article{hofsConcentrationSequenceDependent1994a, title = {Concentration and Sequence Dependent Synergism of Ehtyldeshydroxy-Sparsomycin in Combination with Antitumor Agents.}, author = {Hofs, H.P. and Wagener, D.J. and {}{de Valk-Bakker}, V. and Ottenheijm, H.C. and De Grip, W.J.}, year = 1994, journal = {Anti-Cancer Drugs.}, volume = {1}, pages = {35–42}, doi = {10.1097/00001813-199402000-00006}, keywords = {antitumor,nosource,sequence,sparsomycin} } % == BibTeX quality report for hofsConcentrationSequenceDependent1994a: % ? Possibly abbreviated journal title Anti-Cancer Drugs.

@article{hofsAntitumorActivityTerinotoxicity1995a, title = {Antitumor Activity and Terinotoxicity of Ethyldeshydroxy-Sparsomycin in Mice.}, author = {Hofs, H.P. and Wagener, D.J. and De Vos, D. and Ottenheijm, H.C. and Winkens, H.J. and Bovee, P.H. and De Grip, W.J.}, year = 1995, journal = {Eur.J.Cancer.}, volume = {31A}, pages = {1526–1530}, doi = {10.1016/0959-8049(95)00246-F}, keywords = {antitumor,cancer,Mice,nosource,sparsomycin} } % == BibTeX quality report for hofsAntitumorActivityTerinotoxicity1995a: % ? Possibly abbreviated journal title Eur.J.Cancer.

@article{hofsScheduledependentEnhancementAntitumor1995a, title = {Schedule-Dependent Enhancement of Antitumor Activity of Ethyldeshydroxy-Sparsomycin in Combination with Classical Antineoplastic Agents.}, author = {Hofs, H.P. and Wagener, D.J. and {}{van Rennes}, H. and De Vos, D. and Doesburg, W.H. and Ottenheijm, H.C. and De Grip, W.J.}, year = 1995, journal = {Anti.Cancer Drugs}, volume = {6}, number = {2}, pages = {277–284}, doi = {10.1097/00001813-199504000-00012}, url = {http://journals.lww.com/anti-cancerdrugs/Abstract/1995/04000/Schedule_dependent_enhancement_of_antitumor.12.aspx}, keywords = {antitumor,nosource,sparsomycin} } % == BibTeX quality report for hofsScheduledependentEnhancementAntitumor1995a: % ? Possibly abbreviated journal title Anti.Cancer Drugs

@article{hokeMurineHIPL291998, title = {Murine {{HIP}}/{{L29}} Is a Heparin-Binding Protein with a Restricted Pattern of Expression in Adult Tissues}, author = {Hoke, D.E. and Regisford, E.G. and Julian, J. and Amin, A. and {Begue-Kirn}, C. and Carson, D.D.}, year = 1998, journal = {Journal of Biological Chemistry}, volume = {273}, number = {39}, pages = {25148–25157}, publisher = {ASBMB}, doi = {10.1074/jbc.273.39.25148}, url = {http://www.jbc.org/content/273/39/25148.short}, abstract = {Heparin/heparan sulfate (Hp/HS)-binding proteins are implicated in a variety of cell biological processes including cell adhesion, modulation of blood coagulation, and cytokine/growth factor action. Hp/HS-interacting protein (HIP) has been identified in various adult tissues in humans. HIP supports high affinity, selective binding to Hp/HS, promotes cell adhesion, and modulates blood coagulation activities via Hp/HS-dependent mechanisms. Herein, a murine ortholog of human HIP is described that is 78.8% identical to human HIP and 99.8% identical at the cDNA level and identical at the amino acid level to a previously described murine ribosomal protein, L29. Western blot analyses and immunohistological staining with affinity-purified antibodies generated against two distinct peptide sequences of murine HIP/L29 indicate that HIP/L29 is differentially expressed in adult murine tissues and cell types. In the normal murine mammary epithelial cell line, NMuMG, HIP/L29 is enriched in the 100,000 x g particulate fraction. HIP/L29 can be solubilized from the 100,000 x g particulate fraction with 0.8 M NaCl, suggesting that it is a peripheral membrane protein. HIP/L29 directly binds 125I-Hp in gel overlay assays and requires 0.75 M NaCl for elution from Hp-agarose. In addition, recombinant murine HIP expressed in Escherichia coli binds Hp in a saturable and highly selective manner, compared with other glycosaminoglycans including dermatan sulfate, chondroitin sulfate, keratan sulfate, and hyaluronic acid. Collectively, these data indicate that murine HIP/L29, like its human ortholog, is a Hp-binding protein expressed in a restricted manner in adult tissues}, keywords = {0,ACID,Adult,Amino Acid Sequence,AMINO-ACID,Animals,Antibodies,antibody,assays,Base Sequence,BINDING,Biochemistry,BIOLOGY,blood,BlottingNorthern,BlottingWestern,cancer,Cell Line,D,Dna,DNAComplementary,Escherichia coli,ESCHERICHIA-COLI,expression,genetics,Heparin,human,Humans,L29,La,LINE,M,MECHANISM,MECHANISMS,metabolism,Mice,Molecular Biology,Molecular Sequence Data,nosource,protein,Protein Binding,Proteins,Recombinant Proteins,REQUIRES,Ribosomal Proteins,RIBOSOMAL-PROTEIN,sequence,Sequence HomologyAmino Acid,SEQUENCES,Staining,Subcellular Fractions,Support} } % == BibTeX quality report for hokeMurineHIPL291998: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{holbrookInternalRibosomeEntry2006, title = {Internal Ribosome Entry Sequence-Mediated Translation Initiation Triggers Nonsense-Mediated Decay}, author = {Holbrook, J.A. and {Neu-Yilik}, G. and Gehring, N.H. and Kulozik, A.E. and Hentze, M.W.}, year = 2006, month = jul, journal = {EMBO Reports}, volume = {7}, number = {7}, pages = {722–726}, publisher = {Nature Publishing Group}, doi = {10.1038/sj.embor.7400721}, url = {http://www.nature.com/embor/journal/v7/n7/abs/7400721.html}, abstract = {In eukaryotes, a surveillance pathway known as nonsense-mediated decay (NMD) regulates the abundance of messenger RNAs containing premature termination codons (PTCs). In mammalian cells, it has been asserted that the NMD-relevant first round of translation is special and involves initiation by a specific protein heterodimer, the nuclear cap-binding complex (CBC). Arguing against a requirement for CBC-mediated translation initiation, we show that ribosomal recruitment by the internal ribosomal entry sequence of the encephalomyocarditis virus triggers NMD of a PTC-containing transcript under conditions in which ribosome entry from the cap is prohibited. These data generalize the previous model and suggest that translation per se, irrespective of how it is initiated, can mediate NMD}, keywords = {0,10,1038,1967,1979,1999,2002,2005,2006,699,7,703,722,726,7400721,7400732,BIOLOGY,Cap,Cap binding,CAP-BINDING COMPLEX,CELLS,Codon,CodonNonsense,CODONS,COMPLEX,COMPLEXES,DECAY,doi,eif4e,embo reports,embor,ENCEPHALOMYOCARDITIS VIRUS,fragment reaction,genetics,Germany,Globin,Globins,Hela Cells,Humans,initiation,INTERNAL RIBOSOMAL ENTRY,INTERNAL RIBOSOME ENTRY,internal ribosome entry sequence,krayevsky,kukhanova,La,MAMMALIAN-CELLS,MESSENGER-RNA,MESSENGER-RNAS,metabolism,MODEL,Molecular Biology,monro,NMD,NONSENSE,nonsense-mediated decay,nosource,nuclear cap-binding complex,okuda et al,PATHWAY,premature termination codon,PREMATURE TERMINATION CODON,protein,Protein Biosynthesis,rapid kinetics,RECRUITMENT,Research SupportNon-U.S.Gov’t,ribosome,ribosomes,Ribosomes,ribozymes,Rna,RNA Interference,RNAMessenger,RNASmall Interfering,RnaViral,sardesai et al,schmeing et al,sequence,sj,SURVEILLANCE,termination,TERMINATION CODON,TERMINATION-CODON,TRANSCRIPT,translation,TRANSLATION INITIATION,virus} } % == BibTeX quality report for holbrookInternalRibosomeEntry2006: % ? unused Journal abbr (“EMBO Rep.”)

@article{holmesSARSCoronavirusNew2003, title = {{{SARS}} Coronavirus: A New Challenge for Prevention and Therapy}, author = {Holmes, K.V.}, year = 2003, month = jun, journal = {Journal of Clinical Investigation}, volume = {111}, number = {11}, pages = {1605–1609}, publisher = {Am Soc Clin Investig}, doi = {10.1172/JCI18819}, url = {http://www.jci.org/cgi/content/abstract/111/11/1605}, keywords = {Animals,genetics,human,Infection Control,La,microbiology,ModelsBiological,nosource,pathogenicity,Phylogeny,physiology,prevention & control,Review,SARS,Sars Virus,Severe Acute Respiratory Syndrome,therapy} } % == BibTeX quality report for holmesSARSCoronavirusNew2003: % ? unused Journal abbr (“J.Clin.Invest”)

@article{hondaRNASignalsTranslation1995a, title = {{{RNA}} Signals for Translation Frameshift: Influence of Stem Size and Slippery Sequence}, author = {Honda, A. and Nakamura, T. and Nishimura, S.}, year = 1995, month = aug, journal = {Biochem.Biophys.Res.Comm.}, volume = {213}, number = {2}, pages = {575–582}, doi = {10.1006/bbrc.1995.2170}, keywords = {Codon,efficiency,frameshift,Frameshifting,Gag,Gag-pol,gene,Hiv-1,In Vitro,in vitro translation,IN-VITRO,initiation,luciferase,nosource,pol,protein,ribosomal frameshifting,Rna,sequence,SIGNAL,structure,translation} } % == BibTeX quality report for hondaRNASignalsTranslation1995a: % ? Possibly abbreviated journal title Biochem.Biophys.Res.Comm.

@article{hongTemperatureSensitiveNop22001, title = {Temperature Sensitive Nop2 Alleles Defective in Synthesis of {{25S rRNA}} and Large Ribosomal Subunits in {{Saccharomyces}} Cerevisiae}, author = {Hong, B. and Wu, K. and Brockenbrough, J.S. and Wu, P. and Aris, J.P.}, year = 2001, month = jul, journal = {Nucleic Acids Research}, volume = {29}, number = {14}, pages = {2927–2937}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/29.14.2927}, url = {http://nar.oxfordjournals.org/content/29/14/2927.short}, abstract = {Using molecular genetic techniques, we have generated and characterized six temperature sensitive (ts) alleles of nop2. All failed to support growth at 37 degreesC and one was also formamide sensitive (fs) and failed to grow on media containing 3% formamide. Conditional lethality is not due to rapid turnover of mutant Nop2p proteins at 37 degreesC. Each allele contains between seven and 14 amino acid substitutions and one possesses a nonsense mutation near the C-terminus. Mapping experiments with one allele, nop2-4, revealed that a subset of the amino acid substitutions conferred the ts phenotype and that these mutations have an additive effect. All six mutants exhibited dramatic reductions in levels of 60S ribosome subunits under non-permissive conditions as well as some reduction at permissive temperature. Processing of 27S pre-rRNA to mature 25S rRNA was defective in all six mutants grown under nonpermissive conditions. Levels of the 40S ribosomal subunit and 18S rRNA were not significantly affected. Amino acid substitutions in nop2 conditional alleles are discussed in the context of the hypothesis that Nop2p functions both as an RNA methyltransferase and a trans-acting factor in rRNA processing and large ribosomal subunit biogenesis}, keywords = {ACID,Alleles,Amino Acid Substitution,DIMETHYLASE DIM1P,Dna,ESCHERICHIA-COLI,ESSENTIAL NUCLEOLAR PROTEIN,Genes,Genetic,Genetic Techniques,GROWTH,IDENTIFICATION,mapping,media,Methylation,MUTANTS,Mutation,MUTATIONS,nosource,Phenotype,protein,Proteins,RIBOSOMAL-SUBUNIT,ribosome,Rna,RNA M(5)C967 METHYLTRANSFERASE,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SHUTTLE VECTORS,SUBUNIT,Support,techniques,Temperature,turnover,yeast} }

@article{honigmanTranslationEfficiencyHuman1995, title = {Translation {{Efficiency}} of the {{Human T-Cell Leukemia-Virus}} ({{Htlv-2}}) {{Gag Gene Modulates}} the {{Frequency}} of {{Ribosomal Frameshifting}}}, author = {Honigman, A. and Falk, H. and Mador, N. and Rosental, T. and Panet, A.}, year = 1995, month = apr, journal = {Virology}, volume = {208}, number = {1}, pages = {312–318}, publisher = {Elsevier}, doi = {10.1006/viro.1995.1154}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0042682285711543}, abstract = {The regulation of ribosomal frameshifting during translation of the polycistronic mRNA of human T-cell leukemia virus (HTLV) was studied in a cell-free system. Translation inhibitors such as cycloheximide and puromycin antibiotics were much more effective in blocking the synthesis of the frameshift polypeptide Gag-Pro than the synthesis of the Gag product. The preferential inhibition of the frameshift polypeptide Gag-Pro by the two antibiotics was not a reflection of the different sizes of the two gene products, but rather a consequence of the effect of the inhibitors on ribosomal translation efficiencies. To further analyze the effect of translation efficiencies on ribosomal frameshifting, we compared the translation of 5’-capped RNA to noncapped RNA. The translation of 5’-capped RNA was higher, as expected. Consequently, ribosomal frameshifting producing the Gag-Pro polypeptide was enhanced when compared to the translation of noncapped RNA. Taken together these results indicate that efficiencies of translation, in conjunction with the cis regulatory genetic elements at the frameshift sites, determine the ratio of the polypeptides Gag, Gag-Pro, and Gag-Pro-Pol produced in the HTLV-infected cell. Thus, physiological changes which affect the cellular translation machinery may alter the optimal ratio of these three polyprotein products needed for virus maturation. (C) 1995 Academic Press, Inc}, keywords = {antibiotic,antibiotics,Cell-Free System,Cycloheximide,efficiency,ELEMENTS,ELONGATION-FACTOR-TU,expression,frameshift,Frameshifting,Gag,gene,Genetic,human,INHIBITION,INHIBITOR,LEUKEMIA,MAMMALIAN-CELLS,MATURATION,mRNA,nosource,POLYPEPTIDE,POLYPEPTIDES,POLYPROTEIN,PRODUCTS,pseudoknot,Puromycin,READING FRAME,readthrough,regulation,ribosomal frameshifting,Rna,sequence,SITE,SITES,SYSTEM,translation,translocation,virus} } % == BibTeX quality report for honigmanTranslationEfficiencyHuman1995: % ? Title looks like it was stored in title-case in Zotero

@article{hopfieldKineticProofreadingNew1974, title = {Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity}, author = {Hopfield, J.J.}, year = 1974, month = oct, journal = {Proceedings of the National Academy of Sciences}, volume = {71}, number = {10}, pages = {4135–4139}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.71.10.4135}, url = {http://www.pnas.org/content/71/10/4135.short}, keywords = {0,ACID,ACIDS,Amino Acid Sequence,Amino Acids,AMINO-ACID,AMINO-ACIDS,biosynthesis,DNA Replication,ERRORS,Genetic Code,Kinetics,La,MECHANISM,metabolism,ModelsBiological,nosource,proofreading,protein,Proteins,Rna,RNATransfer,SPECIFICITY} } % == BibTeX quality report for hopfieldKineticProofreadingNew1974: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{hopkinsSimultaneousDNABinding2004a, title = {Simultaneous {{DNA}} Binding, Bending, and Base Flipping: Evidence for a Novel {{M}}.{{EcoRI}} Methyltransferase-{{DNA}} Complex}, author = {Hopkins, B.B. and Reich, N.O.}, year = 2004, journal = {J.Biol Chem.}, volume = {279}, number = {35}, pages = {37049–37060}, doi = {10.1074/jbc.M404573200}, url = {PM:15210696}, abstract = {We measured the kinetics of DNA bending by M.EcoRI using DNA labeled at both 5’-ends and observed changes in fluorescence resonance energy transfer. Although known to bend its cognate DNA site, energy transfer is decreased upon enzyme binding. This unanticipated effect is shown to be robust because we observe the identical decrease with different dye pairs, when the dye pairs are placed on the respective 3’-ends, the effect is cofactor- and protein-dependent, and the effect is observed with duplexes ranging from 14 through 17 base pairs. The same labeled DNA shows the anticipated increased energy transfer with EcoRV endonuclease, which also bends this sequence, and no change in energy transfer with EcoRI endonuclease, which leaves this sequence unbent. We interpret these results as evidence for an increased end-to-end distance resulting from M.EcoRI binding, mediated by a mechanism novel for DNA methyltransferases, combining DNA bending and an overall expansion of the DNA duplex. The M.EcoRI protein sequence is poorly accommodated into well defined classes of DNA methyltransferases, both at the level of individual motifs and overall alignment. Interestingly, M.EcoRI has an intercalation motif observed in the FPG DNA glycosylase family of repair enzymes. Enzyme-dependent changes in anisotropy and fluorescence resonance energy transfer have similar rate constants, which are similar to the previously determined rate constant for base flipping; thus, the three processes are nearly coincidental. Similar fluorescence resonance energy transfer experiments following AdoMet-dependent catalysis show that the unbending transition determines the steady state product release kinetics}, keywords = {3’-END,alignment,Amino Acid Motifs,anisotropy,BASE,BASE-PAIR,BINDING,Biochemistry,Catalysis,chemistry,COMPLEX,COMPLEXES,CONSTANTS,Dna,DNA Glycosylases,DNA-BINDING,Endonucleases,Energy Transfer,enzyme,Enzymes,Escherichia coli,FAMILY,Fluorescence,Fluorescence Resonance Energy Transfer,Kinetics,La,MECHANISM,metabolism,METHYLTRANSFERASE,ModelsChemical,ModelsStatistical,modification,MOTIFS,nosource,Nucleic Acid Conformation,PRODUCT,protein,RELEASE,sequence,SITE,site specific,Site-Specific DNA-Methyltransferase (Adenine-Specific),Support,Time Factors} } % == BibTeX quality report for hopkinsSimultaneousDNABinding2004a: % ? Possibly abbreviated journal title J.Biol Chem.

@article{hopperTranslationLspeciesDsRNA1977a, title = {Translation of the {{L-species dsRNA}} Genome of the Killer-Associated Virus-like Particles of ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Hopper, J.E. and Bostian, K.A. and Rowe, L.B. and Tipper, D.J.}, year = 1977, journal = {J.Biol.Chem.}, volume = {252}, pages = {9010–9017}, doi = {10.1016/S0021-9258(17)38338-2}, keywords = {Genome,L-A,nosource,packaging,polymerase,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,translation,virus} } % == BibTeX quality report for hopperTranslationLspeciesDsRNA1977a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{horanIntersubunitMovementRequired2007, title = {Intersubunit Movement Is Required for Ribosomal Translocation}, author = {Horan, L.H. and Noller, H.F.}, year = 2007, month = mar, journal = {Proceedings of the National Academy of Sciences}, volume = {104}, number = {12}, pages = {4881–4885}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.0700762104}, url = {http://www.pnas.org/content/104/12/4881.short}, abstract = {Translocation of tRNA and mRNA during protein synthesis is believed to be coupled to structural changes in the ribosome. The “ratchet model,” based on cryo-EM reconstructions of ribosome complexes, invokes relative movement of the 30S and 50S ribosomal subunits in this process; however, evidence that directly demonstrates a requirement for intersubunit movement during translocation is lacking. To address this problem, we created an intersubunit disulfide cross-link to restrict potential movement. The cross-linked ribosomes were unable to carry out polypeptide synthesis; this inhibition was completely reversed upon reduction of the disulfide bridge. In vitro assays showed that the cross-linked ribosomes were specifically blocked in elongation factor G-dependent translocation. These findings show that intersubunit movement is required for ribosomal translocation, accounting for the universal two-subunit architecture of ribosomes}, keywords = {0,assays,Base Sequence,BIOLOGY,COMPLEX,COMPLEXES,CROSS-LINKING,Cross-Linking Reagents,CROSSLINKING,Disulfides,drug effects,elongation,ELONGATION-FACTOR-G,Escherichia coli,genetics,In Vitro,IN-VITRO,INHIBITION,La,metabolism,Models-Molecular,ModelsMolecular,Molecular Biology,Molecular Sequence Data,Movement,mRNA,nosource,Peptide Elongation Factor G,pharmacology,POLYPEPTIDE,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNA-Messenger,RNAMessenger,Structural,SUBUNIT,SUBUNITS,Support,translocation,tRNA} } % == BibTeX quality report for horanIntersubunitMovementRequired2007: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{hosokawaReconstitutionFunctionallyActive1966, title = {Reconstitution of Functionally Active Ribosomes from Inactive Subparticles and Proteins.}, author = {Hosokawa, K. and Fujimura, R.K. and Nomura, M.}, year = 1966, month = jan, journal = {Proc.Natl.Acad.Sci.U.S.A}, volume = {55}, number = {1}, pages = {198–204}, publisher = {National Academy of Sciences}, doi = {10.1073/pnas.55.1.198}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC285776/}, keywords = {0,Bacterial,Bacterial Proteins,cytology,Escherichia coli,In Vitro,IN-VITRO,La,nosource,protein,Proteins,RECONSTITUTION,ribosome,Ribosomes,Ultracentrifugation} } % == BibTeX quality report for hosokawaReconstitutionFunctionallyActive1966: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.U.S.A

@article{hovhannisyanAffinityChromatographyUsing2009, title = {Affinity Chromatography Using 2’ Fluoro-Substituted {{RNAs}} for Detection of {{RNA-protein}} Interactions in {{RNase-rich}} or {{RNase-treated}} Extracts.}, author = {Hovhannisyan, R.H. and Carstens, R.P.}, year = 2009, journal = {Biotechniques}, volume = {46}, number = {2}, pages = {95–98}, doi = {10.2144/000113067}, keywords = {binding proteins that interact,Chromatography,chromatography is commonly used,compli-,EXTRACTS,in post-transcriptional gene regulation,nosource,Rna,rna affinity purification,rna-protein interactions,that function,these purifications can be,to identify rna,use of rna affinity,with specific rna cis-elements} }

@article{howardCellCultureAnalysis2001, title = {Cell Culture Analysis of the Regulatory Frameshift Event Required for the Expression of Mammalian Antizymes}, author = {Howard, M.T. and Shirts, B.H. and Zhou, J. and Carlson, C.L. and Matsufuji, S. and Gesteland, R.F. and Weeks, R.S. and Atkins, J.F.}, year = 2001, month = nov, journal = {Genes to Cells}, volume = {6}, number = {11}, pages = {931–941}, publisher = {Wiley Online Library}, doi = {10.1046/j.1365-2443.2001.00477.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2443.2001.00477.x/full}, abstract = {BACKGROUND: Antizyme is a critical regulator of cellular polyamine levels due to its effect on polyamine transport and its ability to target ornithine decarboxylase for degradation. Antizyme expression is autoregulatory, through dependence on an unusual +1 translational frameshift mechanism that responds to polyamine levels. RESULTS: HEK293 cells were depleted of polyamines by treatment with an ornithine decarboxylase inhibitor, difluoromethylornithine (DFMO), and grown in the presence or absence of exogenous polyamines prior to the analysis of ribosomal frameshifting levels. Results obtained using an optimized dual luciferase assay system reveal a 10-fold dynamic range of frameshifting, which correlates positively with polyamine addition. Polyamine addition to cells, which have not been pre-treated with DFMO, also resulted in an increase in antizyme frameshifting but to a lesser degree (1.3 to 1.5-fold). In addition, the constructs with the 3’ deletion were more responsive to stimulation by polyamine addition than those with the 5’ deletion. CONCLUSIONS: The observed regulation of antizyme frameshifting demonstrates the efficiency of a polyamine homeostatic mechanism, and illustrates the utility of a quantifiable cell-based assay for the analysis of polyamines or their analogues on translational frameshifting}, keywords = {0,3,analysis,Animals,antagonists & inhibitors,antizyme,Base Sequence,Biogenic Polyamines,Cell Culture Techniques,Cell Line,CELLS,degradation,Dna,E,efficiency,Eflornithine,expression,frameshift,Frameshift Mutation,Frameshifting,Gene Expression RegulationEnzymologic,Genetic,genetics,human,Humans,INHIBITOR,La,luciferase,MECHANISM,metabolism,Molecular Sequence Data,nosource,Ornithine Decarboxylase,ORNITHINE DECARBOXYLASE ANTIZYME,pharmacology,polyamine,Polyamines,protein,Proteins,regulation,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,ribosomal frameshifting,SYSTEM,TARGET,TRANSLATIONAL FRAMESHIFTING,TRANSPORT} } % == BibTeX quality report for howardCellCultureAnalysis2001: % ? unused Journal abbr (“Genes Cells”)

@article{hsiehRecognitionSilencingRepeated2000, title = {Recognition and Silencing of Repeated {{DNA}}}, author = {Hsieh, J. and Fire, A.}, year = 2000, journal = {Annual Review of Genetics}, volume = {34}, number = {1}, pages = {187–204}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, doi = {10.1146/annurev.genet.34.1.187}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.genet.34.1.187}, abstract = {Mechanisms for repetition of DNA pose both opportunities and challenges to a functional genome: opportunities for increasing gene expression by amplification of useful sequences, and challenges of controlling amplification by unwanted sequences such as transposons and viruses. Experiments in numerous organisms have suggested the likely existence of a general mechanism for recognition of repeated character in DNA. This review focuses (a) on the nature of these recognition mechanisms, and (b) on types of chromatin modification and gene silencing that are used to control repeated DNA}, keywords = {0,Animals,CHARACTER,Chromatin,Dna,embryology,expression,gene,Gene Expression,Gene Silencing,GENE-EXPRESSION,genetics,Genome,La,MECHANISM,MECHANISMS,modification,nosource,physiology,protein,Proteins,RECOGNITION,Repetitive SequencesNucleic Acid,Review,sequence,SEQUENCES,Support,Viruses} } % == BibTeX quality report for hsiehRecognitionSilencingRepeated2000: % ? unused Journal abbr (“Annu.Rev.Genet.”)

@article{hsuYeastCellsLacking1993a, title = {Yeast Cells Lacking 5’–{\(>\)}3’ Exoribonuclease 1 Contain {{mRNA}} Species That Are Poly({{A}}) Deficient and Partially Lack the 5’ Cap Structure}, author = {Hsu, C.L. and Stevens, A.}, year = 1993, month = aug, journal = {Molecular & Cellular Biology}, volume = {13}, number = {8}, pages = {4826–4835}, keywords = {analysis,Cap,DEADENYLATION,enzyme,Hydrolysis,mRNA,Multiple DOI,nonfile,nosource,poly(A),primer extension,protein,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SKI,structure,turnover,XRN1,yeast} }

@article{htunSingleStrandsTriple1988, title = {Single Strands, Triple Strands, and Kinks in {{H-DNA}}}, author = {Htun, H. and Dahlberg, J.E.}, year = 1988, journal = {Science}, volume = {241}, number = {4874}, pages = {1791–1796}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.3175620}, url = {http://www.sciencemag.org/content/241/4874/1791.short}, abstract = {A naturally occurring (dT-dC)18:(dA-dG)18 repeat in the H conformation of DNA was shown to contain single-stranded nucleotides in the center of the TC18 repeat and on one half of the AG18 repeat. These results support the model that H-DNA is a structure containing both triple- stranded and single-stranded regions. The stability of this structure was affected by both pH and the degree of negative supercoiling: at pH 7.6 to 7.7, a high level of supercoiling was needed to keep about half of the molecules in the H conformation; at pH 6 and pH 5, normal levels of supercoiling supported H-DNA; and at pH 4, no supercoiling was required. At mildly alkaline pH, the TC/AG18 repeat assumed a novel conformation called J-DNA that differed from both the B and H forms. A three-dimensional model for the structure of H-DNA is proposed that accounts both for the single-strandedness of the nucleotides and for the influence of supercoiling on H-DNA formation. This model predicts and evidence is presented that H-DNA introduces a sharp kink in the DNA. Moreover, the angle of this kink appears not to be fixed, so that H-DNA is also a hinged-DNA}, keywords = {0,Base Sequence,chemistry,Dna,DNASingle-Stranded,DNASuperhelical,Hydrogen Bonding,Hydrogen-Ion Concentration,La,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleotides,stability,structure,Support,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,ultrastructure} }

@article{htunTopologyFormationTriplestranded1989, title = {Topology and Formation of Triple-Stranded {{H-DNA}}}, author = {Htun, H. and Dahlberg, J.E.}, year = 1989, month = mar, journal = {Science}, volume = {243}, number = {4898}, pages = {1571–1576}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.2648571}, url = {http://www.sciencemag.org/content/243/4898/1571.short}, abstract = {Repeating copolymers of (dT-dC)n.(dA-dG)n sequences (TC.AGn) can assume a hinged DNA structure (H-DNA) which is composed of triple-stranded and single-stranded regions. A model for the formation of H-DNA is proposed, based on two-dimensional gel electrophoretic analysis of DNA’s with different lengths of (TC.AG)n copolymers. In this model, H- DNA formation is initiated at a small denaturation bubble in the interior of the copolymer, which allows the duplexes on either side to rotate slightly and to fold back, in order to make the first base triplet. This nucleation establishes which of several nonequivalent H- DNA conformations is to be assumed by any DNA molecule, thereby trapping each molecule in one of several metastable conformers that are not freely interconvertible. Subsequently, the acceptor region spools up single-stranded polypyrimidines as they are released by progressive denaturation of the donor region; both the spooling and the denaturation result in relaxation of negative supercoils in the rest of the DNA molecule. From the model, it can be predicted that the levels of supercoiling of the DNA determine which half of the (dT-dC)n repeat is to become the donated third strand}, keywords = {0,analysis,chemistry,Dna,DNASingle-Stranded,DNASuperhelical,La,nosource,Nucleic Acid Conformation,Review,sequence,structure,Structure-Activity Relationship,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,ultrastructure} }

@article{huangOrganizationExpressionDoublestranded1996, title = {Organization and Expression of the Double-Stranded {{RNA}} Genome of {{Helminthosporium}} Victoriae {{190S}} Virus, a Totivirus Infecting a Plant Pathogenic Filamentous Fungus}, author = {Huang, S. and Ghabrial, S.A.}, year = 1996, month = oct, journal = {Proceedings of the National Academy of Sciences}, volume = {93}, number = {22}, pages = {12541–12546}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.93.22.12541}, url = {http://www.pnas.org/content/93/22/12541.short}, abstract = {The complete nucleotide sequence, 5178 bp, of the totivirus Helminthosporium vicotoriae 190S virus (Hv190SV) double-stranded RNA, was determined. Computer-assisted sequence analysis revealed the presence of two large overlapping ORFs; the 5’-proximal large ORF (ORF1) codes for the coat protein (CP) with a predicted molecular mass of 81 kDa, and the 3’-proximal ORF (ORF2), which is in the -1 frame relative to ORF1, codes for an RNA-dependent RNA polymerase (RDRP). Unlike many other totiviruses, the overlap region between ORF1 and ORF2 lacks known structural information required for translational frameshifting. Using an antiserum to a C-terminal fragment of the RDRP, the product of ORF2 was identified as a minor virion-associated polypeptide of estimated molecular mass of 92 kDa. No CP-RDRP fusion protein with calculated molecular mass of 165 kDa was detected. The predicted start codon of the RDRP ORF (2605-AUG-2607) overlaps with the stop codon (2606-UGA-2608) of the CP ORF, suggesting RDRP is expressed by an internal initiation mechanism. Hv190SV is associated with a debilitating disease of its phytopathogenic fungal host. Knowledge of its genome organization and expression will be valuable for understanding its role in pathogenesis and for potential exploitation in the development of biocontrol measures}, keywords = {0,Amino Acid Sequence,analysis,Base Sequence,Capsid,capsid protein,chemistry,CloningMolecular,COAT PROTEIN,Codon,development,disease,DNA Mutational Analysis,DOUBLE-STRANDED-RNA,expression,FRAME,Frameshifting,FUSION PROTEIN,genetics,Genome,GENOME ORGANIZATION,Helminthosporium,initiation,La,MECHANISM,Molecular Sequence Data,nosource,Nucleic Acid Conformation,NUCLEOTIDE-SEQUENCE,Open Reading Frames,ORGANIZATION,pathology,polymerase,POLYPEPTIDE,PRODUCT,protein,REGION,REPLICASE,Rna,RNA Replicase,RNA-DEPENDENT RNA POLYMERASE,RNA-POLYMERASE,RNADouble-Stranded,RnaViral,sequence,Sequence Analysis,SEQUENCE-ANALYSIS,START CODON,STOP CODON,Structural,TRANSLATIONAL FRAMESHIFTING,virus} } % == BibTeX quality report for huangOrganizationExpressionDoublestranded1996: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{huangBuildingEfficientFactory2002a, title = {Building an Efficient Factory: Where Is Pre-{{rRNA}} Synthesized in the Nucleolus?}, author = {Huang, S.}, year = 2002, month = may, journal = {Journal of Cell Biology}, volume = {157}, number = {5}, pages = {739–741}, doi = {10.1083/jcb.200204159}, url = {ISI:000176427100001}, keywords = {Br-U labeling,CELLS,Christmas tree,dense fibrillar components,E,nosource,nucleolus,RIBOSOMAL-RNA,S,sites of DNA transcription,TRANSCRIPTION SITES} }

@article{huberStructureHelixIII2001a, title = {The Structure of Helix {{III}} in {{Xenopus}} Oocyte 5 {{S rRNA}}: An {{RNA}} Stem Containing a Two-Nucleotide Bulge}, author = {Huber, P.W. and Rife, J.P. and Moore, P.B.}, year = 2001, journal = {J.Mol.Biol.}, volume = {312}, number = {4}, pages = {823–832}, doi = {10.1006/jmbi.2001.4966}, url = {PM:11575935}, abstract = {The solution structure of an oligonucleotide containing the helix III sequence from Xenopus oocyte 5 S rRNA has been determined by NMR spectroscopy. Helix III includes two unpaired adenosine residues, flanked on either side by G:C base-pairs, that are required for binding of ribosomal protein L5. The consensus conformation of helix III in the context provided by this oligonucleotide has the two adenosine residues located in the minor groove and stacked upon the 3’ flanking guanosine residue, consistent with biochemical studies of free 5 S rRNA in solution. A distinct break in stacking that occurs between the first adenosine residue of the bulge and the flanking 5’ guanosine residue exposes the base of the adenosine residue in the minor groove and the base of the guanosine residue in the major groove. The major groove of the helix is widened at the site of the unpaired nucleotides and the helix is substantially bent; nonetheless, the G:C base-pairs flanking the bulge are intact. The data indicate that there may be conformational heterogeneity centered in the bulge region. The corresponding adenosine residues in the Haloarcula marismortui 50 S ribosomal subunit form a dinucleotide platform, which is quite different from the motif seen in solution. Thus, the conformation of helix III probably changes when 5 S rRNA is incorporated into the ribosome}, keywords = {0,3,5 S rRNA,Adenosine,Animals,BASE,Base Sequence,BASE-PAIR,BINDING,chemistry,CONFORMATION,FORM,genetics,Guanosine,Haloarcula,Haloarcula marismortui,L5,La,metabolism,ModelsMolecular,NMR,NMR-SPECTROSCOPY,nosource,Nuclear Magnetic ResonanceBiomolecular,Nucleic Acid Conformation,Nucleotides,Oligoribonucleotides,Oocytes,protein,PROTON,Protons,REGION,Research SupportU.S.Gov’tP.H.S.,RESIDUES,RIBOSOMAL-SUBUNIT,ribosome,Rna,RNARibosomal5S,rRNA,S,sequence,SITE,SPECTROSCOPY,structure,SUBUNIT,Xenopus,Xenopus laevis,Xenopus oocyte} } % == BibTeX quality report for huberStructureHelixIII2001a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{hudakNovelMechanismInhibition2000a, title = {A Novel Mechanism for Inhibition of Translation by Pokeweed Antiviral Protein: Depurination of the Capped {{RNA}} Template}, author = {Hudak, K.A. and Wang, P. and Tumer, N.E.}, year = 2000, month = mar, journal = {RNA.}, volume = {6}, number = {3}, pages = {369–380}, doi = {10.1017/S1355838200991337}, abstract = {Pokeweed antiviral protein (PAP) is known to inactivate ribosomes by removal of a specific adenine from the sarcin/ricin (S/R) loop of the large rRNA, thereby inhibiting translation. We demonstrate here that in addition to the previously identified adenine (A4324), PAP removes another adenine (A4321) and a guanine (G4323) from the eukaryotic large rRNA. Recent results indicate that the antiviral activity of PAP may not be due to depurination of host ribosomes. Using PAP mutants that do not depurinate either tobacco or reticulocyte lysate rRNA, we show that PAP inhibits translation of brome mosaic virus (BMV) and potato virus X (PVX) RNAs without depurinating ribosomes. Furthermore, translation of only capped, but not uncapped, luciferase transcripts is inhibited by PAP, providing evidence that PAP and PAP mutants are able to distinguish between capped and uncapped transcripts. Translation inhibition of BMV RNAs is overcome by treatment with PAP in the presence of increasing concentrations of the cap analog m7GpppG, but not GpppG or GTP, indicating that PAP recognizes the cap structure. Incubation of BMV RNAs or the capped luciferase transcripts with PAP results in depurination of either RNA. In contrast, uncapped luciferase transcripts are not depurinated after incubation with identical concentrations of PAP. These results demonstrate for the first time that PAP can inhibit translation by a mechanism other than ribosome depurination, by recognizing the cap structure and specifically depurinating the capped RNAs}, keywords = {20205888,animal,antiviral,Antiviral Agents,Cap,Cell-Free System,chemistry,genetics,GTP,INHIBITION,luciferase,lysate,MECHANISM,metabolism,Mutation,nosource,PAP,pathology,pharmacology,physiology,Plant Proteins,Pokeweed antiviral protein,protein,Purines,Rabbits,Reticulocytes,ribosome,Ribosomes,Rna,Rna Caps,RNA ProcessingPost-Transcriptional,RNAMessenger,RnaPlant,RnaViral,rRNA,structure,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,Templates,Tobacco,translation,TranslationGenetic,virus} } % == BibTeX quality report for hudakNovelMechanismInhibition2000a: % ? Possibly abbreviated journal title RNA.

@article{hudakCTerminalDeletionMutant2001, title = {A {{C-Terminal Deletion Mutant}} of {{Pokeweed Antiviral Protein Inhibits Programmed}} +1 {{Ribosomal Frameshifting}} and {{Ty1 Retrotransposition}} without {{Depurinating}} the {{Sarcin}}/{{Ricin Loop}} of {{rRNA}}}, author = {Hudak, K.A. and Hammell, A.B. and Yasenchak, J. and Tumer, N.E. and Dinman, J.D.}, year = 2001, month = jan, journal = {Virology}, volume = {279}, number = {1}, pages = {292–301}, doi = {10.1006/viro.2000.0647}, abstract = {Pokeweed antiviral protein (PAP) is a ribosome-inactivating protein characterized by its ability to depurinate the sarcin/ricin (S/R) loop of the large rRNA of prokaryotic and eukaryotic ribosomes. Here, a series of PAP mutants were used to examine the relationship between depurination of the S/R loop and inhibition of +1 programmed ribosomal frameshifting (PRF) and to define PAP sequences critical for inhibition of +1 PRF and Ty1 retrotransposition in the yeast Saccharomyces cerevisiae. Using three different classes of mutants we present evidence that strong binding of a C-terminal PAP mutant (PAPc) to ribosomes is sufficient to inhibit +1 PRF and Ty1 retrotransposition in the absence of S/R loop depurination. PAPc did not affect the totivirus ScV-L-A and HIV-1-directed -1 PRF efficiencies or the ability of cells to maintain the M(1)-dependent killer phenotype, demonstrating the specificity of the effect of PAPc on +1 PRF. Copyright 2001 Academic Press}, keywords = {antiviral,BINDING,efficiency,Frameshifting,Gag/Gag-pol ratio,INHIBITION,killer,nosource,PAP,pathology,Phenotype,Pokeweed antiviral protein,protein,ribosomal frameshifting,ribosome,Ribosomes,rRNA,S/R loop,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Ty1,yeast} } % == BibTeX quality report for hudakCTerminalDeletionMutant2001: % ? Title looks like it was stored in title-case in Zotero

@article{hudakPokeweedAntiviralProtein2002, title = {Pokeweed Antiviral Protein Binds to the Cap Structure of Eukaryotic {{mRNA}} and Depurinates the {{mRNA}} Downstream of the Cap.}, author = {Hudak, K.A. and Bauman, J.D. and Tumer, N.E.}, year = 2002, journal = {RNA.}, volume = {8}, number = {9}, pages = {1148–1159}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838202026638}, url = {http://rnajournal.cshlp.org/content/8/9/1148.short}, abstract = {Several cap-binding proteins from both the nucleus and cytosol have been identified that mediate processes such as pre-mRNA splicing, translation initiation, and mRNA turnover. Here we describe a novel cap- binding protein, pokeweed antiviral protein (PAP), a 29-kDa type I ribosome-inactivating protein (RIP) isolated from Phytolacca americana. In addition to depurinating the sarcin/ricin loop of the large rRNA, an activity common to all RIPs, we have reported recently that PAP depurinates capped, but not uncapped RNAs in vitro. Here we characterize this activity further and, using affinity chromatography, show that PAP binds to the m7Gppp cap structure. PAP UV-crosslinks to m7GpppG-capped luciferase mRNA more efficiently than GpppG-capped luciferase mRNA, indicating specificity for the methylated guanosine. We present evidence that PAP does not remove the cap structure or depurinate the m7Gppp as shown by primer extension of capped and uncapped luciferase transcripts incubated with PAP. Modeling studies of cap interaction with PAP predict that the cap structure would bind to the active site of PAP in a similar manner to guanine. We map the depurination sites on the capped luciferase RNA and illustrate that depurination occurs at specific adenine and guanine residues throughout the RNA sequence. Incubation of isolated ribosomes with PAP and increasing molar concentrations of m7GpppG relative to PAP resulted in a decrease in the level of rRNA depurination. Therefore, at elevated concentrations, the methylated cap structure competes with the adenine or guanine for binding to PAP, even though the affinity of PAP for capped message is almost fourfold lower than for rRNA. These results demonstrate that the activity of PAP is not limited to rRNA depurination, but that PAP binds to the cap structure and depurinates mRNAs downstream of the cap in vitro. These findings may have implications for understanding PAP activity in vivo}, keywords = {Adenine,antiviral,BINDING,BINDING-PROTEIN,Cap,Cap binding,Chromatography,Cytosol,Guanine,Guanosine,In Vitro,IN-VITRO,IN-VIVO,initiation,La,luciferase,mRNA,nosource,PAP,pathology,Pokeweed antiviral protein,primer extension,protein,Proteins,ribosome,Ribosomes,Rna,rRNA,sequence,splicing,structure,translation,TRANSLATION INITIATION,turnover} } % == BibTeX quality report for hudakPokeweedAntiviralProtein2002: % ? Possibly abbreviated journal title RNA.

@article{hudsonIdentificationNewLocalized1996a, title = {Identification of New Localized {{RNAs}} in the ⬚{{Xenopus}}⬚ Oocyte by Differential Display {{PCR}}}, author = {Hudson, J.W. and Alarcon, V.B. and Elinson, R.P.}, year = 1996, journal = {Dev.Genetics}, volume = {19}, number = {3}, pages = {190–198}, doi = {10.1002/(SICI)1520-6408(1996)19:3<190::AID-DVG2>3.0.CO;2-4}, keywords = {animal,cell cycle,Cell Division,development,differential display,expression,human,IDENTIFICATION,nosource,Oocytes,PCR,protein,Rna,sequence,Xenopus,yeast} } % == BibTeX quality report for hudsonIdentificationNewLocalized1996a: % ? Possibly abbreviated journal title Dev.Genetics

@article{huetRNAPolymeraseIII1996a, title = {{{RNA}} Polymerase {{III}} and Class {{III}} Transcription Factors from {{Saccharomyces}} Cerevisiae}, author = {Huet, J. and Manaud, N. and Dieci, G. and Peyroche, G. and Conesa, C. and Lefebvre, O. and Ruet, A. and Riva, M. and Sentenac, A.}, year = 1996, journal = {Methods Enzymology}, volume = {273:249-67}, pages = {249–267}, doi = {10.1016/S0076-6879(96)73024-0}, keywords = {5S rRNA,96383457,Chromatography,classification,DNA-Binding Proteins,Fungal Proteins,isolation & purification,metabolism,nosource,polymerase,Precipitation,Recombinant Fusion Proteins,Review,Rna,RNA Polymerase III,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportnon-u.s.gov’t,TFIIIA,transcription,TRANSCRIPTION FACTOR,Transcription Factors} } % == BibTeX quality report for huetRNAPolymeraseIII1996a: % ? unused Journal abbr (“Methods Enzymol.”)

@article{hughesMutantsElongationFactor1987, title = {Mutants of Elongation Factor {{Tu}} Promote Ribosomal Frameshifting and Nonsense Readthrough.}, author = {Hughes, D. and Atkins, J.F. and Thompson, S.}, year = 1987, month = dec, journal = {The EMBO Journal}, volume = {6}, number = {13}, pages = {4235–4239}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1987.tb02772.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC553909/}, abstract = {This is the first report of ribosomal frameshifting promoted by mutants of the elongation factor Tu (EF-Tu). EF-Tu mutants can suppress both -1 and +1 frameshift mutations. The level of nonsense readthrough is also increased at some UGA (this paper) and UAG (Hughes, 1987) sites by these mutants. Suppression occurs when a mutant tuf allele is paired with a wild-type copy of the other tuf gene but is most efficient when both tuf genes are mutant. Frameshifting mediated by the tuf alleles studied, tufA8 and tufB103, is not general; indeed most frameshift mutations are not suppressed. Several possible mechanisms by which mutant EF-Tu may cause frameshifting are discussed}, keywords = {0,Alleles,Base Sequence,Codon,EFTu,elongation,ELONGATION-FACTOR-TU,Escherichia coli,FACTOR TU,frameshift,Frameshift Mutation,Frameshifting,gene,Genes,GenesBacterial,GenesStructural,Genetic,genetics,La,MECHANISM,MECHANISMS,metabolism,Molecular Sequence Data,MUTANTS,Mutation,MUTATIONS,NONSENSE,nosource,Operon,Peptide Elongation Factor Tu,readthrough,ribosomal frameshifting,Ribosomes,Salmonella Phages,Salmonella typhimurium,SITE,SITES,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,suppression,WILD-TYPE} } % == BibTeX quality report for hughesMutantsElongationFactor1987: % ? unused Journal abbr (“EMBO J.”)

@article{hughesRoleESTGenes1997, title = {The Role of the {{EST}} Genes in Yeast Telomere Replication}, author = {Hughes, T.R. and Morris, D.K. and Salinger, A. and Walcott, N. and Nugent, C.I. and Lundblad, V.}, year = 1997, journal = {Ciba Found.Symp.}, volume = {211}, pages = {41–47}, url = {PM:9524750}, abstract = {We have recently completed a large mutant screen designed to identify new mutants of Saccharomyces cerevisiae with a telomerase-like defect. From this screen; 22 mutants were identified that mapped to three genes, called EST1, EST2 and EST3, as well as a novel EST-like mutation in a fourth gene, previously identified as CDC13. Mutations in each of these genes give rise to phenotypes that are indistinguishable from those observed when TLC1, encoding the yeast telomerase RNA, is deleted. In addition, genetic analysis indicates that all four genes function in the same pathway for telomere replication as defined by TLC1, the one known component of telomerase. This indicates that these genes encode factors that are essential in vivo for telomerase function. Genetic and biochemical analyses have shown that EST1 and CDC13 encode single-stranded telomeric DNA-binding proteins, suggesting that these two proteins may function to mediate access of telomerase to the end of the telomere}, keywords = {0,analysis,CEREVISIAE,COMPONENT,DNA Replication,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,EST,gene,Genes,GenesFungal,Genetic,Genetic Code,Genetic Screening,genetics,human,IDENTIFY,IN-VIVO,La,MUTANTS,Mutation,MUTATIONS,No DOI found,nosource,PATHWAY,Phenotype,protein,Proteins,REPLICATION,Review,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Support,Telomerase,Telomere,yeast} } % == BibTeX quality report for hughesRoleESTGenes1997: % ? Possibly abbreviated journal title Ciba Found.Symp.

@article{hummel23SRibosomalRNA1987, title = {{{23S}} Ribosomal {{RNA}} Mutations in Halobacteria Conferring Resistance to the Anti-{{80S}} Ribosome Targeted Antibiotic Anisomycin}, author = {Hummel, H. and Bo{}{"u}ck, A.}, year = 1987, month = mar, journal = {Nucleic acids research}, volume = {15}, number = {6}, pages = {2431}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/15/6/2431.short}, abstract = {Halobacterium (H.) halobium and H. cutirubrum mutants resistant to the anti-80S ribosome targeted inhibitor anisomycin were isolated. Three classes of mutants were obtained: Class I displayed a minimal inhibitory concentration (MIC) to anisomycin of 10 micrograms/ml, class II of 25 micrograms/ml and class III of at least 400 micrograms/ml. In vitro polyphenylalanine synthesis assays demonstrated that in those cases tested resistance was a property of the large ribosomal subunit. By primer extension analysis, each mutation class could be correlated with a distinct base change within the peptidyltransferase loop of 235 rRNA. In class I A2472 was changed to C, in class II G2466 was changed to C and in the high-level resistant class III C2471 was replaced by U. A. double mutant - obtained by selection of a class I mutant for high- level anisomycin resistance - acquired the C2471 to U replacement of class III in addition to the class I mutation. The results provide information on the action of a eukaryotic protein synthesis inhibitor on archaebacterial ribosomes and demonstrate the suitability of organisms with a single rRNA transcriptional unit on the chromosome for direct selection of mutations in ribosomal RNA}, keywords = {0,analysis,anisomycin,antibiotic,assays,Base Sequence,CloningMolecular,Dna,drug effects,Drug ResistanceMicrobial,genetics,Halobacterium,In Vitro,IN-VITRO,Kinetics,La,metabolism,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Peptidyltransferase,pharmacology,Poly U,primer extension,protein,protein synthesis,PROTEIN-SYNTHESIS,Pyrrolidines,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNARibosomal,rRNA,SUBUNIT,supportnon-u.s.gov’t,TranslationGenetic} }

@article{hundleyHumanMpp11Protein2005, title = {Human {{Mpp11 J Protein}}: {{Ribosome-Tethered Molecular Chaperones Are Ubiquitous}}}, author = {Hundley, H.A. and Walter, W. and Bairstow, S. and Craig, E.A.}, year = 2005, month = mar, journal = {Science}, volume = {308}, number = {5724}, pages = {1032}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1109247}, url = {http://www.sciencemag.org/content/308/5724/1032.short}, abstract = {The existence of specialized molecular chaperones that interact directly with ribosomes is well-established in microorganisms. Such proteins bind polypeptides exiting the ribosomal tunnel and provide a physical link between translation and protein folding. We report that ribosome-associated molecular chaperones have been maintained throughout eukaryotic evolution, as illustrated by Mpp11, the human ortholog of the yeast ribosome-associated J-protein Zuo. When expressed in yeast, Mpp11 partially substituted for Zuo by partnering with the multi-purpose Hsp70 Ssa, the homolog of mammalian Hsc70. We propose that in metazoans, ribosome-associated Mpp11 recruits the multi-functional soluble Hsc70 to nascent polypeptide chains as they exit the ribosome}, keywords = {chemistry,Evolution,homolog,human,La,No DOI found,nosource,POLYPEPTIDE,POLYPEPTIDE-CHAIN,POLYPEPTIDES,protein,Protein Folding,Proteins,ribosome,Ribosomes,translation,yeast} } % == BibTeX quality report for hundleyHumanMpp11Protein2005: % ? Title looks like it was stored in title-case in Zotero

@article{hungImportanceRibosomalFrameshifting1998a, title = {Importance of Ribosomal Frameshifting for Human Immumodeficiency Virus Type 1 Assembly and Replication.}, author = {Hung, M. and Patel, P. and Davis, S. and Green, S.R.}, year = 1998, journal = {J.Virol.}, volume = {72}, pages = {4819–4824}, doi = {10.1128/JVI.72.6.4819-4824.1998}, keywords = {analysis,anisomycin,assembly,drugs,efficiency,frameshift,Frameshifting,Gag-pol,Gag/Gag-pol ratio,HIV,Hiv-1,human,INHIBITION,nosource,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,SIGNAL,sparsomycin,viral particle assembly,viral propagation,virus} } % == BibTeX quality report for hungImportanceRibosomalFrameshifting1998a: % ? Possibly abbreviated journal title J.Virol.

@article{hurIsolationCharacterizationPokeweed1995a, title = {Isolation and Characterization of Pokeweed Antiviral Protein Mutations in ⬚{{Saccharomyces}} Cerevisiae⬚: {{Identification}} of Residues Important for Toxicity.}, author = {Hur, Y. and Hwang, D.-J. and Zoubenko, O. and Coetzer, C. and Uckun, R.M. and Tumer, N.E.}, year = 1995, journal = {Proc.Natl.Acad.Sci.USA}, volume = {92}, pages = {8448–8452}, doi = {10.1073/pnas.92.18.8448}, keywords = {antiviral,IDENTIFICATION,Mutation,MUTATIONS,nosource,Pokeweed antiviral protein,protein,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,translation,translocation} } % == BibTeX quality report for hurIsolationCharacterizationPokeweed1995a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{hurwitzDifferentialActivationYeast1995a, title = {Differential Activation of Yeast Adenyl Cyclase by {{Ras1}} and {{Ras2}} Depends on the Conserved {{N-terminus}}.}, author = {Hurwitz, N. and Segal, M. and Marbach, I. and Levitzki, A.}, year = 1995, journal = {Proc.Natl.Acad.Sci.USA}, volume = {92}, pages = {11009–11013}, doi = {10.1073/pnas.92.24.11009}, keywords = {activation,nosource,ras,yeast} } % == BibTeX quality report for hurwitzDifferentialActivationYeast1995a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{hussainTranslationHomologousHeterologous1986, title = {Translation of Homologous and Heterologous Messenger {{RNAs}} in a Yeast Cell-Free System}, author = {Hussain, I. and Leibowitz, M.J.}, year = 1986, journal = {Gene}, volume = {46}, number = {1}, pages = {13–23}, publisher = {Elsevier}, doi = {10.1016/0378-1119(86)90162-9}, url = {http://linkinghub.elsevier.com/retrieve/pii/0378111986901629}, abstract = {A stable mRNA-dependent cell-free translation system from Saccharomyces cerevisiae, prepared by a modification of the method of Hofbauer et al. [Eur. J. Biochem. 122 (1982) 199-203] was active in translation of exogenous homologous and heterologous mRNAs. Optimal translational activity required the addition of polyamines and yeast tRNA. The m transcript of the M segment of double-stranded RNA, synthesized in vitro using the killer virus-associated RNA polymerase, directed the synthesis of preprotoxin polypeptide (M-p32), which was immunologically identified using antitoxin antibody. Sindbis virus capsid protein and rabbit globin were also translated from their mRNAs. Translation was inhibited by puromycin, sparsomycin and anisomycin. Analogues of the 5’- terminal caps present on most eukaryotic mRNA molecules inhibited translation of added mRNAs, including capped mRNAs and the uncapped killer virus mRNA}, keywords = {anisomycin,Antibodies,antibody,Cap,Capsid,Cell-Free System,DOUBLE-STRANDED-RNA,drug effects,genetics,Globin,In Vitro,IN-VITRO,killer,Kinetics,Magnesium,MESSENGER-RNA,modification,mRNA,nosource,pharmacology,Poly A,polyamine,Polyamines,polymerase,Potassium,protein,Puromycin,Rna,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Sindbis Virus,sparsomycin,Spermidine,supportu.s.gov’tp.h.s.,SYSTEM,translation,TranslationGenetic,tRNA,virus,yeast} }

@article{iborraCoupledTranscriptionTranslation2001, title = {Coupled Transcription and Translation within Nuclei of Mammalian Cells}, author = {Iborra, F.J. and Jackson, D.A. and Cook, P.R.}, year = 2001, journal = {Science}, volume = {293}, number = {5532}, pages = {1139–1142}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1061216}, url = {http://www.sciencemag.org/content/293/5532/1139.short}, abstract = {It is widely assumed that the vital processes of transcription and translation are spatially separated in eukaryotes and that no translation occurs in nuclei. We localized translation sites by incubating permeabilized mammalian cells with [3H]lysine or lysyl- transfer RNA tagged with biotin or BODIPY; although most nascent polypeptides were cytoplasmic, some were found in discrete nuclear sites known as transcription “factories.” Some of this nuclear translation also depends on concurrent transcription by RNA polymerase II. This coupling is simply explained if nuclear ribosomes translate nascent transcripts as those transcripts emerge from still-engaged RNA polymerases, much as they do in bacteria}, keywords = {0,animal,Autoradiography,Bacteria,biosynthesis,Biotin,Boron Compounds,Cell Fractionation,Cell Membrane Permeability,Cell Nucleus,Cos Cells,Cycloheximide,Cytoplasm,Fluorescence,genetics,Hela Cells,human,Immunohistochemistry,La,Lysine,metabolism,mitochondria,nosource,pathology,pharmacology,polymerase,protein,protein synthesis,Protein Synthesis Inhibitors,Protein Transport,PROTEIN-SYNTHESIS,Proteins,ribosome,Ribosomes,Rna,RNA Polymerase II,RNATransferAmino Acyl,supportnon-u.s.gov’t,transcription,TranscriptionGenetic,TRANSFER-RNA,translation,TranslationGenetic,tRNA,Tumor CellsCultured} }

@article{ichibaNucleotideSequenceOrnithine1995, title = {Nucleotide Sequence of Ornithine Decarboxylase Antizyme {{cDNA}} from {{Xenopus}} Laevis}, author = {Ichiba, T. and Matsufuji, S. and Miyazaki, Y. and Hayashi, S.}, year = 1995, month = may, journal = {Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression}, volume = {1262}, number = {1}, pages = {83–86}, publisher = {Elsevier}, doi = {10.1016/0167-4781(95)00062-L}, url = {http://linkinghub.elsevier.com/retrieve/pii/016747819500062L}, keywords = {antizyme,frameshift,Frameshifting,Liver,mRNA,nosource,Open Reading Frames,Ornithine Decarboxylase,ORNITHINE DECARBOXYLASE ANTIZYME,pseudoknot,rat,ribosomal frameshifting,sequence,translation,Xenopus,Xenopus laevis} }

@article{ichoMAK11ProteinEssential1988a, title = {The ⬚{{MAK11}}⬚ Protein Is Essential for Cell Growth and Replication of {{M}} Double-Stranded {{RNA}} and Is Apparently a Membrane-Associated Protein.}, author = {Icho, T. and Wickner, R.B.}, year = 1988, journal = {J.Biol.Chem.}, volume = {263}, pages = {1467–1475}, doi = {10.1016/S0021-9258(19)57326-4}, keywords = {DOUBLE-STRANDED-RNA,L-A,M1,MAK,nosource,protein,Rna} } % == BibTeX quality report for ichoMAK11ProteinEssential1988a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{iizukaCapdependentCapindependentTranslation1994, title = {Cap-Dependent and Cap-Independent Translation by Internal Initaition of {{mRNAs}} in Cell Extracts Prepared from ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Iizuka, N. and Najita, L. and Franzusorr, A. and Sarnow, P.}, year = 1994, journal = {Mol.Cell.Biol.}, volume = {14}, pages = {7322–7330}, keywords = {In Vitro,in vitro translation,IN-VITRO,mRNA,Multiple DOI,nonfile,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,translation,yeast} } % == BibTeX quality report for iizukaCapdependentCapindependentTranslation1994: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{ikemuraCorrelationAbundanceYeast1982a, title = {Correlation between the Abundance of Yeast Transfer {{RNAs}} and the Occurrence of the Respective Codons in Protein Genes. {{Differences}} in Synonymous Codon Choice Patterns of Yeast and {{Escherichia}} Coli with Reference to the Abundance of Isoaccepting Transfer {{RNAs}}}, author = {Ikemura, T.}, year = 1982, month = jul, journal = {J.Mol.Biol}, volume = {158}, number = {4}, pages = {573–597}, doi = {10.1016/0022-2836(82)90250-9}, url = {PM:6750137}, keywords = {0,Codon,CODONS,Escherichia coli,ESCHERICHIA-COLI,gene,Genes,genetics,La,metabolism,nosource,PATTERNS,protein,Protein Biosynthesis,Rna,RNAMessenger,RNATransfer,Saccharomyces cerevisiae,Support,TRANSFER-RNA,yeast} } % == BibTeX quality report for ikemuraCorrelationAbundanceYeast1982a: % ? Possibly abbreviated journal title J.Mol.Biol

@article{inadaOnestepAffinityPurification2002, title = {One-Step Affinity Purification of the Yeast Ribosome and Its Associated Proteins and {{mRNAs}}.}, author = {Inada, T. and Winstall, E. and Tarun, S.Z. and Yates, J.R. and Schieltz, D. and Sachs, A.B.}, year = 2002, month = jul, journal = {RNA.}, volume = {8}, number = {7}, pages = {948–958}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838202026018}, url = {http://rnajournal.cshlp.org/content/8/7/948.short}, abstract = {We describe a one-step affinity method for purifying ribosomes from the budding yeast Saccharomyces cerevisiae. Extracts from yeast strains expressing only C-terminally tagged Rpl25 protein or overexpressing this protein in the presence of endogenous Rpl25p were used as the starling materials. The purification was specific for tagged 60S subunits, and resulted in the copurification of 80S subunits and polysomes, as well as ribosome-associated proteins and mRNAs. Two of these associated proteins, Mpt4p and Asc1p, were nearly stoichiometrically bound to the ribosome. In addition, the degree of mRNA association with the purified ribosomes was found to reflect the mRNA’s translational status within the cell. The one-step purification of ribosome and its associated components from a crude extract should provide an important tool for future structural and biochemical studies of the ribosome, as well as for expression profiling of translated mRNAs}, keywords = {0,60S subunit,Base Sequence,Cell Fractionation,chemistry,ChromatographyAffinity,COMPONENT,expression,genetics,isolation & purification,La,Methods,mRNA,nosource,Plasmids,polysomes,protein,Proteins,purification,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Structural,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,yeast} } % == BibTeX quality report for inadaOnestepAffinityPurification2002: % ? Possibly abbreviated journal title RNA.

@article{ingoliaGenomewideAnalysisVivo2009, title = {Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling.}, author = {Ingolia, N.T. and Ghaemmaghami, S. and Newman, J.R. and Weissman, J.S.}, year = 2009, month = apr, journal = {Science}, volume = {324}, number = {5924}, pages = {218–223}, issn = {1095-9203}, doi = {10.1126/science.1168978}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2746483&tool=pmcentrez&rendertype=abstract http://www.ncbi.nlm.nih.gov/pubmed/19213877}, abstract = {Techniques for systematically monitoring protein translation have lagged far behind methods for measuring messenger RNA (mRNA) levels. Here, we present a ribosome-profiling strategy that is based on the deep sequencing of ribosome-protected mRNA fragments and enables genome-wide investigation of translation with subcodon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. These studies defined the protein sequences being translated and found extensive translational control in both determining absolute protein abundance and responding to environmental stress. We also observed distinct phases during translation that involve a large decrease in ribosome density going from early to late peptide elongation as well as widespread regulated initiation at non-adenine-uracil-guanine (AUG) codons. Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible.}, pmid = {19213877}, keywords = {0,5’ Untranslated Regions,analysis,AUG,biosynthesis,CEREVISIAE,Codon,CODONS,DNA,elongation,Fungal,Fungal: genetics,Fungal: metabolism,Gene Library,genetics,Genome,GenomeFungal,IN-VIVO,initiation,Introns,La,Messenger,MESSENGER-RNA,Messenger: genetics,Messenger: metabolism,metabolism,Methods,mRNA,nosource,NUCLEOTIDE RESOLUTION,Peptide Chain Elongation,Peptide Chain ElongationTranslational,Peptide Chain Initiation,Peptide Chain InitiationTranslational,pharmacology,physiology,protein,Protein Biosynthesis,Proteins,REGION,RESOLUTION,ribosome,Ribosomes,Ribosomes: metabolism,Rna,RNA,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: biosynthesis,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Saccharomyces cerevisiae: physiology,SACCHAROMYCES-CEREVISIAE,sequence,Sequence Analysis,Sequence AnalysisDNA,SEQUENCES,Stress,Support,techniques,translation,Translational,Untranslated Regions,yeast} }

@article{inoueHighEfficiencyTransformation1990, title = {High Efficiency Transformation of {{Escherichia}} Coli with Plasmids}, author = {Inoue, H. and Nojima, H. and Okayama, H.}, year = 1990, month = nov, journal = {Gene}, volume = {96}, number = {1}, pages = {23–28}, publisher = {Elsevier}, doi = {10.1016/0378-1119(90)90336-P}, url = {http://linkinghub.elsevier.com/retrieve/pii/037811199090336P}, abstract = {We have re-evaluated the conditions for preparing competent Escherichia coli cells and established a simple and efficient method (SEM) for plasmid transfection. Cells (DH5, JM109 and HB101) prepared by SEM are extremely competent for transformation (1-3 x 10(9) cfu/microgram of pBR322 DNA), and can be stored in liquid nitrogen for at least 40 days without loss of competence. Unlike electroporation, transformation using these competent cells is affected minimally by salts in DNA preparation. These competent cells are particularly useful for construction of high-complexity cDNA libraries with a minimum expenditure of mRNA}, keywords = {0,Bacterial,Buffers,CELLS,Dna,DNABacterial,efficiency,enzyme,Escherichia coli,ESCHERICHIA-COLI,Freezing,GenesBacterial,genetics,Hydrogen-Ion Concentration,La,library,mRNA,Nitrogen,nosource,PLASMID,Plasmids,Temperature,Transfection,TRANSFORMATION,TransformationBacterial} }

@article{inoueIntermolecularExonLigation1985, title = {Intermolecular Exon Ligation of the {{rRNA}} Precursor of {{Tetrahymena}}: Oligonucleotides Can Function as 5’ Exons}, author = {Inoue, T. and Sullivan, F.X. and Cech, T.R.}, year = 1985, month = dec, journal = {Cell}, volume = {43}, number = {2 Pt 1}, pages = {431–437}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867485901734}, abstract = {The dinucleotide CpUOH, when incubated with self-splicing Tetrahymena pre-rRNA in the absence of GTP, functions as a 5’ exon. It cleaves the precursor exactly at the 3’ splice site and becomes covalently ligated to the 3’ exon. Other oligonucleotides with sequences that resemble CUCUCU, the sequence at the 3’ end of the 5’ exon, can add to the 3’ exon in this reaction. Such splicing in trans is most readily explained by a site within the intervening sequence that binds the last few nucleotides of the 5’ exon. This binding site functions in splice site recognition and is also part of the active site of the ribozyme. The mechanism by which 5’ splice sites are selected in Tetrahymena rRNA and group I mitochondrial RNA splicing is like that used in nuclear mRNA splicing, in that it involves specific pairing of bases adjacent to the splice site with a complementary RNA sequence}, keywords = {86079525,A-SITE,animal,Base Sequence,BINDING,Binding Sites,biosynthesis,GTP,MECHANISM,metabolism,mRNA,No DOI found,nosource,Nucleotides,Oligonucleotides,ribozyme,Rna,RNA Splicing,RNARibosomal,rRNA,sequence,splicing,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Tetrahymena} }

@article{ioannouKineticsInhibitionRabbit1998, title = {Kinetics of Inhibition of Rabbit Reticulocyte Peptidyltransferase by Anisomycin and Sparsomycin}, author = {Ioannou, M. and Coutsogeorgopoulos, C. and Synetos, D.}, year = 1998, month = jun, journal = {Molecular pharmacology}, volume = {53}, number = {6}, pages = {1089–1096}, publisher = {ASPET}, url = {http://molpharm.aspetjournals.org/content/53/6/1089.short}, abstract = {A detailed kinetic study was carried out on the inhibitory mechanisms of two eukaryotic peptidyltransferase drugs (I), anisomycin and sparsomycin. In an in vitro system from rabbit reticulocytes, AcPhe-puromycin is produced in a pseudo-first-order reaction from the preformed AcPhe-tRNA/poly(U)/80S ribosome complex (complex C) and excess puromycin (S). This reaction is inhibited by anisomycin and sparsomycin through different mechanisms. Anisomycin acts as a mixed noncompetitive inhibitor. The product, AcPhe-puromycin, is derived only from C according to the puromycin reaction. On the other hand, sparsomycin reacts with complex C in a two-step reaction, [REACTION; SEE TEXT] An initial rapid binding of the drug produces the encounter complex CI. During this step and before conversion of CI to CI, sparsomycin behaves as a competitive inhibitor. The rapidly produced CI is isomerized slowly to a conformationally altered species CI in which I is bound more tightly. The rate constants of this step are k6 = 2.1 min-1 and k7 = 0.095 min-1. Moreover, the low value of the association rate constant k7/Ki’ (2 x 10(5) M-1 sec-1), provides insight into the rates of possible conformational changes occurring during protein synthesis and supports the proposal that sparsomycin is the first example of a slow-binding inhibitor of eukaryotic peptidyltransferase. When complex C is preincubated with concentrations of sparsomycin of {\(>\)}8 Ki and then reacts with a mixture of puromycin and sparsomycin, the inhibition becomes linear mixed noncompetitive and involves C*I instead of CI. During this phase, AcPhe-puromycin is produced from a new, modified ribosomal complex with a lower catalytic rate constant. Thus, sparsomycin also acts as a modifier of eukaryotic peptidyltransferase activity}, keywords = {0,animal,anisomycin,antagonists & inhibitors,ASSOCIATION,BINDING,COMPLEX,COMPLEXES,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,drugs,enzymology,In Vitro,IN-VITRO,INHIBITION,INHIBITOR,Kinetics,La,M1,MECHANISM,MECHANISMS,metabolism,No DOI found,nosource,Peptidyltransferase,pharmacology,PRODUCT,protein,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,Puromycin,Rabbits,Reticulocytes,ribosome,S,sparsomycin,Support,supportnon-u.s.gov’t,SYNTHESIS INHIBITORS,SYSTEM} } % == BibTeX quality report for ioannouKineticsInhibitionRabbit1998: % ? unused Journal abbr (“Mol Pharmacol.”)

@article{iordanovRibotoxicStressResponse1997, title = {Ribotoxic Stress Response: Activation of the Stress-Activated Protein Kinase {{JNK1}} by Inhibitors of the Peptidyl Transferase Reaction and by Sequence-Specific {{RNA}} Damage to the Alpha-Sarcin/Ricin Loop in the {{28S rRNA}}}, author = {Iordanov, M.S. and Pribnow, D. and Magun, J.L. and Dinh, T.H. and Pearson, J.A. and Chen, S.L. and Magun, B.E.}, year = 1997, month = jun, journal = {Molecular and cellular biology}, volume = {17}, number = {6}, pages = {3373–3381}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.17.6.3373}, url = {http://mcb.asm.org/cgi/content/abstract/17/6/3373}, abstract = {Inhibition of protein synthesis per se does not potentiate the stress- activated protein kinases (SAPKs; also known as cJun NH2-terminal kinases [JNKs]). The protein synthesis inhibitor anisomycin, however, is a potent activator of SAPKs/JNKs. The mechanism of this activation is unknown. We provide evidence that in order to activate SAPK/JNK1, anisomycin requires ribosomes that are translationally active at the time of contact with the drug, suggesting a ribosomal origin of the anisomycin-induced signaling to SAPK/JNK1. In support of this notion, we have found that aminohexose pyrimidine nucleoside antibiotics, which bind to the same region in the 28S rRNA that is the target site for anisomycin, are also potent activators of SAPK/JNK1. Binding of an antibiotic to the 28S rRNA interferes with the functioning of the molecule by altering the structural interactions of critical regions. We hypothesized, therefore, that such alterations in the 28S rRNA may act as recognition signals to activate SAPK/JNK1. To test this hypothesis, we made use of two ribotoxic enzymes, ricin A chain and alpha-sarcin, both of which catalyze sequence-specific RNA damage in the 28S rRNA. Consistent with our hypothesis, ricin A chain and alpha- sarcin were strong agonists of SAPK/JNK1 and of its activator SEK1/MKK4 and induced the expression of the immediate-early genes c-fos and c- jun. As in the case of anisomycin, ribosomes that were active at the time of exposure to ricin A chain or alpha-sarcin were able to initiate signal transduction from the damaged 28S rRNA to SAPK/JNK1 while inactive ribosomes were not}, keywords = {97299687,activation,animal,anisomycin,antagonists & inhibitors,antibiotic,antibiotics,Base Sequence,BINDING,Binding Sites,Ca(2+)-Calmodulin Dependent Protein Kinase,chemistry,Endoribonucleases,enzyme,Enzyme Activation,Enzyme Inhibitors,expression,gene,Genes,INHIBITION,kinase,MECHANISM,metabolism,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleosides,peptidyl transferase,Peptidyltransferase,pharmacology,protein,Protein Kinases,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,Proto-Oncogene Proteins c-fos,Proto-Oncogene Proteins c-jun,Rats,ribosome,Ribosomes,Ricin,Rna,RNARibosomal28S,rRNA,SIGNAL,Signal Transduction,stress activated,stress response,Structural,Support,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for iordanovRibotoxicStressResponse1997: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{ioukRrb1pYeastNuclear2001, title = {Rrb1p, a Yeast Nuclear {{WD-repeat}} Protein Involved in the Regulation of Ribosome Biosynthesis}, author = {Iouk, T.L. and Aitchison, J.D. and Maguire, S. and Wozniak, R.W.}, year = 2001, month = feb, journal = {Molecular and Cellular Biology}, volume = {21}, number = {4}, pages = {1260–1271}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.21.4.1260-1271.2001}, url = {http://mcb.asm.org/cgi/content/abstract/21/4/1260}, abstract = {Ribosome biogenesis is regulated by environmental cues that coordinately modulate the synthesis of ribosomal components and their assembly into functional subunits. We have identified an essential yeast WD-repeat-containing protein, termed Rrb1p, that has a role in both the assembly of the 60S ribosomal subunits and the transcriptional regulation of ribosomal protein (RP) genes. Rrb1p is located in the nucleus and is concentrated in the nucleolus. Its presence is required to maintain normal cellular levels of 60S subunits, 80S ribosomes, and polyribosomes. The function of Rrb1p in ribosome biogenesis appears to be linked to its association with the ribosomal protein rpL3. Immunoprecipitation of Rrb1p from nuclear extracts revealed that it physically interacts with rpL3. Moreover, the overproduction of Rrb1p led to increases in cellular levels of free rpL3 that accumulated in the nucleus together with Rrb1p. The concentration of these proteins within the nucleus was dependent on ongoing protein translation. We also showed that overexpression of RRB1 led to an increase in the expression of RPL3 while all other examined RP genes were unaffected. In contrast, depletion of RRB1 caused an increase in the expression of all RP genes examined except RPL3. These results suggest that Rrb1p regulates RPL3 expression and uncouples it from the coordinated expression of other RP genes}, keywords = {0,60S subunit,Alleles,assembly,biosynthesis,COMPONENT,expression,Fungal Proteins,gene,Gene Expression,Genes,GenesFungal,genetics,L3,La,metabolism,nosource,Nuclear Proteins,nucleolus,Polyribosomes,protein,Proteins,Recombinant Fusion Proteins,regulation,Repetitive SequencesAmino Acid,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,ribosome biogenesis,Ribosomes,Rna,RNAFungal,RNAMessenger,RRB1,Saccharomyces cerevisiae,SUBUNIT,supportnon-u.s.gov’t,translation,TranslationGenetic,yeast} } % == BibTeX quality report for ioukRrb1pYeastNuclear2001: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{irvinPokeweedAntiviralProtein1992, title = {Pokeweed Antiviral Protein: Ribosome Inactivation and Therapeutic Applications}, author = {Irvin, J.D. and Uckun, F.M.}, year = 1992, journal = {Pharmacology & therapeutics}, volume = {55}, number = {3}, pages = {279–302}, publisher = {Elsevier}, doi = {10.1016/0163-7258(92)90053-3}, url = {http://linkinghub.elsevier.com/retrieve/pii/0163725892900533}, abstract = {Pokeweed antiviral protein (PAP) is a ribosome-inactivating protein (RIP) that inactivates ribosomes by the removal of a single adenine from ribosomal RNA. The studies summarized in our review concern the nature and application of this novel therapeutic agent. We describe how researchers continue to elucidate the structure and biologic activity of RIPs. Pokeweed antiviral protein is among the RIPs that have been conjugated to selective monoclonal antibodies for the treatment of several human cancers and viral diseases. Clinical trials using PAP immunotoxins for the treatment of leukemia have been particularly encouraging}, keywords = {0,Adenine,adverse effects,Amino Acid Sequence,Animals,Antibodies,antibody,Antineoplastic AgentsPhytogenic,antiviral,Antiviral Agents,cancer,chemistry,disease,drug effects,drug therapy,HIV,human,Humans,Immunotoxins,La,LEUKEMIA,Molecular Sequence Data,N-Glycosyl Hydrolases,nosource,PAP,Plant Proteins,Pokeweed antiviral protein,protein,Proteins,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,Review,ribosomal RNA,RIBOSOMAL-RNA,ribosome,ribosome-inactivating protein,Ribosomes,Rna,RNARibosomal28S,structure,Structure-Activity Relationship,therapeutic use} } % == BibTeX quality report for irvinPokeweedAntiviralProtein1992: % ? unused Journal abbr (“Pharmacol.Ther.”)

@article{itoTransformationIntactYeast1983, title = {Transformation of Intact Yeast Cells Treated with Alkali Cations.}, author = {Ito, H. and Fukuda, Y. and Murata, K. and Kimura, A.}, year = 1983, journal = {J. Bacteriol.}, volume = {153}, number = {1}, pages = {163–168}, publisher = {Am Soc Microbiol}, doi = {10.1128/jb.153.1.163-168.1983}, keywords = {Cations,Methods,nosource,yeast} } % == BibTeX quality report for itoTransformationIntactYeast1983: % ? Possibly abbreviated journal title J. Bacteriol.

@article{ivanovDrosophilaGeneAntizyme1998a, title = {The ⬚{{Drosophila}}⬚ Gene for Antizyme Requires Ribosomal Frameshifting for Expression and Contains an Intronic Gene for {{snRNA Sm D3}} on the Opposite Strand.}, author = {Ivanov, I.P. and Simin, K. and Letsou, A. and Atkins, J.F. and Gesteland, R.F.}, year = 1998, journal = {Mol.Cell.Biol.}, volume = {18}, pages = {1553–1561}, doi = {10.1128/MCB.18.3.1553}, keywords = {+1 frameshifting,antizyme,Drosophila,expression,Frameshifting,gene,nosource,ribosomal frameshifting} } % == BibTeX quality report for ivanovDrosophilaGeneAntizyme1998a: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{ivanovSecondMammalianAntizyme1998, title = {A Second Mammalian Antizyme: Conservation of Programmed Ribosomal Frameshifting.}, author = {Ivanov, I.P. and Gesteland, R.F. and Atkins, J.F.}, year = 1998, journal = {Genomics}, volume = {52}, number = {2}, pages = {119–129}, doi = {10.1006/geno.1998.5434}, abstract = {A second mammalian ornithine decarboxylase antizyme was discovered. The deduced protein sequence of the human antizyme2 is 54% identical and 67% similar to human antizyme1 but 99.5% identical to mouse antizyme2. Polyamine-regulated programmed ribosomal frameshifting is used in decoding antizyme2 mRNA as it is for antizyme1 mRNA. The mRNA signals for the programmed frameshifting are similar in the mRNAs for the two antizymes. However, in the stimulatory pseudoknot 3’ of the shift site, while the sequences of the stems are highly conserved, the sequences of the loops are divergent. Functional distinctions between antizymes seem likely, but no distinction in the tissue distribution of human antizyme1 and 2 mRNAs was distinguished, though antizyme2 mRNA is 16- fold less abundant than its antizyme1 counterpart. In addition to the previously characterized human antizyme1 mRNA, a second antizyme1 mRNA with an additional 160 nucleotides at its 3’ end was identified, and it has a tissue distribution different from that of the shorter antizyme1 mRNA. Copyright 1998 Academic Press}, keywords = {antizyme,decoding,Frameshifting,Genetic,genetics,human,mRNA,nosource,Nucleotides,Ornithine Decarboxylase,ORNITHINE DECARBOXYLASE ANTIZYME,programmed frameshifting,protein,pseudoknot,ribosomal frameshifting,sequence,SIGNAL} }

@article{ivanovDiscoverySpermatogenesisStagespecific2000, title = {Discovery of a Spermatogenesis Stage-Specific Ornithine Decarboxylase Antizyme: Antizyme 3}, author = {Ivanov, I.P. and Rohrwasser, A. and Terreros, D.A. and Gesteland, R.F. and Atkins, J.F.}, year = 2000, month = apr, journal = {Proceedings of the National Academy of Sciences}, volume = {97}, number = {9}, pages = {4808–4813}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.070055897}, url = {http://www.pnas.org/content/97/9/4808.short}, abstract = {Previous studies with mice overproducing ornithine decarboxylase have demonstrated the importance of polyamine homeostasis for normal mammalian spermatogenesis. The present study introduces a likely key player in the maintenance of proper polyamine homeostasis during spermatogenesis. Antizyme 3 is a paralog of mammalian ornithine decarboxylase antizymes. Like its previously described counterparts, antizymes 1 and 2, it inhibits ornithine decarboxylase, which catalyzes the synthesis of putrescine. Earlier work has shown that the coding sequences for antizymes 1 and 2 are in two different, partially overlapping reading frames. Ribosomes translate the first reading frame, and just before the stop codon for that frame, they shift to the second reading frame to synthesize a trans-frame product. The efficiency of this frameshifting depends on polyamine concentration, creating an autoregulatory circuit. Antizyme 3 cDNA has the same arrangement of reading frames and a potential shift site with definite, although limited, homology to its evolutionarily distant antizyme 1 and 2 counterparts. In contrast to antizymes 1 and 2, which are widely expressed throughout the body, antizyme 3 transcription is restricted to testis germ cells. Expression starts early in spermiogenesis and finishes in the late spermatid phase. The potential significance of antizyme 3 expression during spermatogenesis is discussed in this paper}, keywords = {0,3,Adult,Amino Acid Sequence,animal,antagonists & inhibitors,antizyme,ARRANGEMENT,BODIES,CELLS,chemistry,chickens,coding sequence,Codon,DISCOVERY,Drosophila melanogaster,efficiency,enzyme,Enzyme Inhibitors,expression,FRAME,Frameshifting,Genetic,genetics,human,in situ hybridization,INHIBITOR,La,Male,metabolism,Mice,Molecular Sequence Data,nosource,Open Reading Frames,Ornithine Decarboxylase,ORNITHINE DECARBOXYLASE ANTIZYME,pharmacology,Phylogeny,physiology,polyamine,PRODUCT,protein,Proteins,READING FRAME,Reading Frames,ribosome,Ribosomes,Seminiferous Tubules,sequence,Sequence Alignment,Sequence HomologyAmino Acid,SEQUENCES,Sertoli Cells,SITE,Spermatogenesis,STOP CODON,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Testis,transcription,Xenopus laevis} } % == BibTeX quality report for ivanovDiscoverySpermatogenesisStagespecific2000: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{ivanovIdentificationNewAntizyme2004, title = {Identification of a New Antizyme {{mRNA}} +1 Frameshifting Stimulatory Pseudoknot in a Subset of Diverse Invertebrates and Its Apparent Absence in Intermediate Species}, author = {Ivanov, I.P. and Anderson, C.B. and Gesteland, R.F. and Atkins, J.F.}, year = 2004, month = jun, journal = {Journal of molecular biology}, volume = {339}, number = {3}, pages = {495–504}, publisher = {Elsevier}, doi = {10.1016/j.jmb.2004.03.082}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283604004681}, abstract = {The expression of eukaryotic antizyme genes requires +1 translational frameshifting. The frameshift in decoding most vertebrate antizyme mRNAs is stimulated by an RNA pseudoknot 3’ of the frameshift site. Although the frameshifting event itself is conserved in a wide variety of organisms from yeast to mammals, until recently no corresponding 3’ RNA pseudoknot was known in invertebrate antizyme mRNAs. A pseudoknot, different in structure and origin from its vertebrate counterparts, is now shown to be encoded by the antizyme genes of distantly related invertebrates. Identification of the 3’ frameshifting stimulator in intermediate species or other invertebrates remains unresolved}, keywords = {+1 frameshifting,0,3,analysis,Animals,antizyme,Base Sequence,Cell Line,chemistry,decoding,enzymology,expression,frameshift,Frameshift Mutation,Frameshifting,gene,Genes,Genetic,genetics,human,Humans,IDENTIFICATION,INTERMEDIATE,Invertebrates,La,Mammals,Molecular Sequence Data,mRNA,MutagenesisSite-Directed,nosource,Nucleic Acid Conformation,Ornithine Decarboxylase,ORNITHINE DECARBOXYLASE ANTIZYME,Phylogeny,protein,Proteins,pseudoknot,REQUIRES,Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,Rna,RNA PSEUDOKNOT,RNAMessenger,Sequence HomologyNucleic Acid,SITE,structure,TRANSLATIONAL FRAMESHIFTING,yeast} } % == BibTeX quality report for ivanovIdentificationNewAntizyme2004: % ? unused Journal abbr (“J.Mol.Biol.”)

@article{jacksTwoEfficientRibosomal1987, title = {Two Efficient Ribosomal Frameshifting Events Are Required for Synthesis of Mouse Mammary Tumor Virus Gag-Related Polyproteins}, author = {Jacks, T. and Townsley, K. and Varmus, H.E. and Majors, J.}, year = 1987, month = jun, journal = {Proceedings of the National Academy of Sciences}, volume = {84}, number = {12}, pages = {4298–4302}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.84.12.4298}, url = {http://www.pnas.org/content/84/12/4298.short}, abstract = {The primary translation products of retroviral pol genes are polyproteins initiated in an upstream gene (gag). To investigate the manner in which the gag-initiated polyproteins of the mouse mammary tumor virus are produced, we determined the nucleotide sequence of a 1.8-kilobase DNA fragment that spans the region between gag and pol in the C3H strain of mouse mammary tumor virus. The sequence reveals three overlapping open reading frames: the first encodes products of gag (p27gag and p14gag); the second encodes a protein domain of unknown function (termed X) that is highly related to a similarly positioned sequence in simian type D retroviruses and the viral protease (pro); and the third encodes the reverse transcriptase. The reading frames are organized to permit uninterrupted readthrough from gag to pol if ribosomal frameshifts occur in the -1 direction within each of the two overlapping regions, one of which is 16 nucleotides in length and the other 13 nucleotides. Cell-free translation of RNA containing these overlap regions shows that fusion of the reading frames by ribosomal frameshifting occurs efficiently: about one-fourth of the ribosomes traversing the gag-X/pro overlap and one-tenth traversing the X/pro-pol overlap shift frames, generating gag-related polyproteins in ratios similar to those observed in vivo. Synthetic oligonucleotides containing either of the overlap regions inserted into novel contexts do not induce frameshifting; hence the overlapping portions of the reading frames are not sufficient to induce a frameshift event, and a larger sequence context or secondary structure may be implicated}, keywords = {0,Amino Acid Sequence,Animals,Base Sequence,biosynthesis,Cell Line,CELL-FREE TRANSLATION,D,Dna,DNA Restriction Enzymes,DOMAIN,ENCODES,enzyme,Enzymes,FRAME,frameshift,Frameshifting,Gag,gene,Gene Productsgag,GENE-PRODUCT,Genes,GenesStructural,GenesViral,genetics,IN-VIVO,La,Mammary Tumor VirusMouse,metabolism,Mice,MiceInbred C3H,nosource,Nucleic Acid Conformation,NUCLEOTIDE-SEQUENCE,Nucleotides,Oligonucleotides,OPEN READING FRAME,Open Reading Frames,pol,POL GENE,POLYPROTEIN,Polyproteins,PRODUCT,PRODUCTS,protein,Protein Biosynthesis,Proteins,Rats,READING FRAME,Reading Frames,readthrough,REGION,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,Retroviridae,Retroviridae Proteins,RETROVIRUSES,REVERSE-TRANSCRIPTASE,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,ribosome,Ribosomes,Rna,SECONDARY STRUCTURE,sequence,structure,translation,UPSTREAM,virus} } % == BibTeX quality report for jacksTwoEfficientRibosomal1987: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{jacksCharacterizationRibosomalFrameshifting1988a, title = {Characterization of Ribosomal Frameshifting in {{HIV-1}} ⬚gag-Pol⬚ Expression.}, author = {Jacks, T. and Power, M.D. and Masiarz, F.R. and Luciw, {PA}. and Barr, P.J. and Varmus, H.E.}, year = 1988, journal = {Nature}, volume = {331}, pages = {280–283}, doi = {10.1038/331280a0}, keywords = {expression,Frameshifting,Gag-pol,HIV,Hiv-1,nosource,ribosomal frameshifting} }

@article{jacksTranslationalSuppressionGene1990a, title = {Translational Suppression in Gene Expression in Retroviruses and Retrotransposons.}, author = {Jacks, T.}, year = 1990, journal = {Current topics in microbiology and immunology}, volume = {157}, eprint = {2168307}, eprinttype = {pubmed}, pages = {93–124}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2168307}, keywords = {expression,Frameshifting,gene,Gene Expression,GENE-EXPRESSION,No DOI found,nosource,retrotransposon,Review,review article,suppression} } % == BibTeX quality report for jacksTranslationalSuppressionGene1990a: % ? unused Journal abbr (“Curr.Top.Microbiol.Immunol.”)

@article{jacksonDevelopmentTRNAdependentVitro2001, title = {Development of a {{tRNA-dependent}} in Vitro Translation System.}, author = {Jackson, R.J. and Napthine, S. and Brierley, I.}, year = 2001, month = may, journal = {RNA}, volume = {7}, number = {5}, pages = {765–773}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838201002539}, url = {http://rnajournal.cshlp.org/content/7/5/765.short}, abstract = {A method is described for depleting rabbit reticulocyte lysates and wheat germ extracts of endogenous tRNAs by affinity chromatography using a matrix generated by coupling ethanolamine to epoxy-activated Sepharose 6B. Greater than 90% depletion of tRNA is achieved with the result that translation becomes in effect absolutely dependent on added tRNA. This depletion procedure should prove very useful for studying the influence of tRNA concentration, and the spectrum of the tRNA population, on recoding events such as programmed frameshifting and readthrough of termination codons}, keywords = {0,animal,Chromatography,Codon,CODONS,development,EXTRACTS,Frameshifting,genetics,In Vitro,in vitro translation,IN-VITRO,isolation & purification,La,lysate,nosource,programmed frameshifting,Rabbits,readthrough,recoding,Reticulocytes,Rna,RNAMessenger,RNATransfer,supportnon-u.s.gov’t,SYSTEM,termination,TERMINATION CODON,TERMINATION-CODON,translation,TranslationGenetic,Triticum,tRNA,Wheat} }

@article{jacobGeneticRegulatoryMechanisms1961, title = {Genetic Regulatory Mechanisms in the Synthesis of Proteins.}, author = {Jacob, F. and Monod, J.}, year = 1961, month = jan, journal = {J.Mol.Biol.}, volume = {3}, pages = {318–356}, doi = {10.1016/S0022-2836(61)80072-7}, keywords = {Genetic,history,MECHANISM,MECHANISMS,mRNA,nosource,protein,Proteins} } % == BibTeX quality report for jacobGeneticRegulatoryMechanisms1961: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{jagadishGeneticControlCell1977, title = {Genetic Control of Cell Division in Yeast Cultured at Different Growth Rates.}, author = {Jagadish, M.N. and Carter, B.L.A.}, year = 1977, journal = {Nature}, volume = {269}, pages = {145–147}, publisher = {Nature Publishing Group}, doi = {10.1038/269145a0}, url = {http://www.nature.com/nature/journal/v269/n5624/abs/269145a0.html}, keywords = {cell cycle,Cell Division,drugs,Genetic,nosource,ras,yeast} }

@article{jamesonQuantificationProteinproteinInteractions1999, title = {Quantification of Protein-Protein Interactions Using Fluorescence Polarization}, author = {Jameson, D.M. and Seifried, S.E.}, year = 1999, month = oct, journal = {Methods}, volume = {19}, number = {2}, pages = {222–233}, publisher = {Elsevier}, doi = {10.1006/meth.1999.0853}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1046202399908538}, abstract = {Quantitative determinations of the dissociation constants of biomolecular interactions, in particular protein-protein interactions, are essential for a detailed understanding of the molecular basis of their specificities. Fluorescence spectroscopy is particularly well suited for such studies. This article highlights the theoretical and practical aspects of fluorescence polarization and its application to the study of protein-protein interactions. Consideration is given to the nature of the different types of fluorescence probes available and the probe characteristics appropriate for the system under investigation. Several examples from the literature are discussed that illustrate different practical aspects of the technique applied to diverse systems}, keywords = {0,Bacterial,Bacterial Proteins,BIOLOGY,chemistry,Citrate (si)-Synthase,CONSTANTS,DEHYDROGENASE,enzymology,Fluorescence,Fluorescence Polarization,Genetic,genetics,instrumentation,La,Malate Dehydrogenase,metabolism,Methods,mitochondria,Molecular Biology,nosource,protein,Protein Conformation,Proteins,Ribosomal Proteins,RIBOSOMAL-PROTEIN,SPECIFICITY,SPECTROSCOPY,Support,SYSTEM,SYSTEMS} }

@article{janInitiatorMettRNAindependentTranslation2001a, title = {Initiator {{Met-tRNA-independent}} Translation Mediated by an Internal Ribosome Entry Site Element in Cricket Paralysis Virus-like Insect Viruses}, author = {Jan, E. and Thompson, S.R. and Wilson, J.E. and Pestova, T.V. and Hellen, C.U. and Sarnow, P.}, year = 2001, journal = {Cold Spring Harb.Symp.Quant.Biol}, volume = {66}, pages = {285–292}, doi = {10.1101/sqb.2001.66.285}, url = {PM:12762030}, keywords = {0,Animals,Base Sequence,chemistry,Eukaryotic Initiation Factor-2,genetics,Gryllidae,Guanosine,Guanosine Triphosphate,immunology,initiation,Insect Viruses,INTERNAL RIBOSOME ENTRY,La,metabolism,microbiology,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Protein Biosynthesis,Review,ribosome,RIBOSOME ENTRY SITE,Ribosomes,Rna,RNARibosomal,Saccharomyces cerevisiae,SITE,Support,translation,virology,Viruses} } % == BibTeX quality report for janInitiatorMettRNAindependentTranslation2001a: % ? Possibly abbreviated journal title Cold Spring Harb.Symp.Quant.Biol

@article{janFactorlessRibosomeAssembly2002, title = {Factorless Ribosome Assembly on the Internal Ribosome Entry Site of Cricket Paralysis Virus}, author = {Jan, E. and Sarnow, P.}, year = 2002, month = dec, journal = {Journal of molecular biology}, volume = {324}, number = {5}, pages = {889–902}, publisher = {Elsevier}, doi = {10.1016/S0022-2836(02)01099-9}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283602010999}, abstract = {The cricket paralysis virus (CrPV), a member of the CrPV-like virus family, contains a single positive-stranded RNA genome that encodes two non-overlapping open reading frames separated by a short intergenic region (IGR). The CrPV IGR contains an internal ribosomal entry site (IRES) that directs the expression of structural proteins. Unlike previously described IRESs, the IGR IRES initiates translation by recruiting 80S ribosomes in the absence of initiator Met-tRNA(i) or any canonical initiation factors, from a GCU alanine codon located in the A-site of the ribosome. Here, we have shown that a variety of mutations, designed to disrupt individually three pseudoknot (PK) structures and alter highly conserved nucleotides among the CrPV-like viruses, inhibit IGR IRES-mediated translation. By separating the steps of translational initiation into ribosomal recruitment, ribosomal positioning and ribosomal translocation, we found that the mutated IRES elements could be grouped into two classes. One class, represented by mutations in PKII and PKIII, bound 40S subunits with significantly reduced affinity, suggesting that PKIII and PKII are involved in the initial recruitment of the ribosome. A second class of mutations, exemplified by alterations in PKI, did not affect 40S binding but altered the positioning of the ribosome on the IRES, indicating that PKI is involved in the correct positioning of IRES-associated ribosomes. These results suggest that the IGR IRES has distinct pseudoknot-like structures that make multiple contacts with the ribosome resulting in initiation factor-independent recruitment and correct positioning of the ribosome on the mRNA}, keywords = {0,A SITE,A-SITE,Alanine,Animals,assembly,Base Sequence,BINDING,chemistry,Codon,conserved nucleotide,Cricket paralysis virus,Electrophoretic Mobility Shift Assay,ELEMENTS,ENCODES,expression,FAMILY,FRAME,genetics,Genome,Gryllidae,immunology,initiation,INITIATION-FACTOR,Insect Viruses,INTERNAL RIBOSOMAL ENTRY,internal ribosomal entry site,INTERNAL RIBOSOME ENTRY,La,metabolism,microbiology,Molecular Sequence Data,mRNA,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Nucleotides,OPEN READING FRAME,Open Reading Frames,protein,Protein Biosynthesis,Protein Subunits,Proteins,pseudoknot,READING FRAME,Reading Frames,RECRUITMENT,REGION,Regulatory SequencesNucleic Acid,ribonuclease t1,ribosome,RIBOSOME ENTRY SITE,Ribosomes,Rna,RNA Viruses,RnaViral,SITE,Structural,structure,SUBUNIT,SUBUNITS,Support,translation,TRANSLATIONAL INITIATION,translocation,virology,virus,Viruses} } % == BibTeX quality report for janFactorlessRibosomeAssembly2002: % ? unused Journal abbr (“J.Mol Biol”)

@article{jansenTranslationalControlGene1995, title = {Translational Control of Gene Expression.}, author = {Jansen, M. and {}{de Moor}, C.H. and Sussenbach, J.S. and {}{van den Brande}, J.L.}, year = 1995, month = jun, journal = {Pediatric Research}, volume = {37}, number = {6}, pages = {681–686}, doi = {10.1203/00006450-199506000-00001}, keywords = {antisense,development,drugs,efficiency,expression,gene,Gene Expression,GENE-EXPRESSION,Genes,initiation,MECHANISM,MECHANISMS,mRNA,nosource,protein,Proteins,regulation,Review,Structural,translation} }

@article{janssenKineticStudiesRole1988, title = {Kinetic Studies on the Role of Elongation Factors 1 Beta and 1 Gamma in Protein Synthesis.}, author = {Janssen, G.M. and Moller, W.}, year = 1988, month = feb, journal = {Journal of Biological Chemistry}, volume = {263}, number = {4}, pages = {1773–1778}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(19)77943-5}, url = {http://www.jbc.org/content/263/4/1773.short}, abstract = {An equilibrium isotope exchange technique was used to measure in an Artemia system the catalytic influence of elongation factor (EF) 1 beta gamma on the dissociation of GDP from the complex of elongation factor 1 alpha.[3H] GDP in the presence of an excess of free GDP. The kinetic data demonstrate that, in analogy to procaryotes, dissociation of GDP occurs via the formation of a transient ternary complex of EF-1 alpha.GDP.EF-1 beta gamma. The rate constants for the dissociation of GDP from EF-1 alpha.GDP and from the ternary complex EF-1 alpha.GDP.EF-1 beta gamma were found to be 0.7 x 10(-3) and greater than or equal to 0.7 s-1, respectively. The equilibrium association constants of GDP to EF-1 alpha.EF-1 beta gamma and of EF-1 beta gamma to EF-1 alpha.GDP were found to be 2.3 x 10(5) and 4.2 x 10(5) M-1, respectively. Judged from the known elongation rate in vivo and kinetic constants of nucleotide exchange, it was estimated that the recycling of EF-1 alpha may be a rate-controlling step in eucaryotic translation. As a model for GTP exchange, the formation of the ternary EF-1 alpha.guanylyl (beta gamma-methylene)diphosphonate.EF-1 beta gamma complex was also studied. It was observed that both an increase of the level of aminoacyl-tRNA and of temperature favored the dissociation of this complex, thereby enabling EF-1 beta gamma to recycle as a catalyst. This behavior would explain the frequent occurrence of a heavy form of elongation factor 1 in extracts of the eucaryotic cell}, keywords = {0,Algorithms,Animals,Artemia,ASSOCIATION,chemistry,COMPLEX,COMPLEXES,CONSTANTS,EF-1,EF-1 alpha,EF-1-ALPHA,elongation,elongation factors,ELONGATION-FACTORS,EXTRACTS,FORM,GTP,Guanosine,Guanosine Diphosphate,Guanosine Triphosphate,IN-VIVO,Kinetics,La,M1,metabolism,MODEL,nosource,NUCLEOTIDE EXCHANGE,Peptide Elongation Factor 1,Peptide Elongation Factors,physiology,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,SYSTEM,Temperature,translation} } % == BibTeX quality report for janssenKineticStudiesRole1988: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{jayaramanLocalizationSparsomycinAction1968, title = {Localization of Sparsomycin Action to the Peptide-Bond-Forming Step.}, author = {Jayaraman, J. and Goldberg, I.H.}, year = 1968, journal = {Biochemistry}, volume = {7}, number = {1}, pages = {418–421}, publisher = {ACS Publications}, doi = {10.1021/bi00841a053}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00841a053}, keywords = {drugs,nosource,protein,ribosome,sparsomycin} }

@article{jeanteurPartialSequenceAnalysis1968a, title = {Partial Sequence Analysis of Ribosomal {{RNA}} from {{HeLa}} Cells. {{II}}. {{Evidence}} for Sequences of Non-Ribosmal Type in 45 and 32 s Ribosomal {{RNA}} Precursors}, author = {Jeanteur, P. and Amaldi, F. and Attardi, G.}, year = 1968, month = may, journal = {J.Mol.Biol.}, volume = {33}, number = {3}, pages = {757–775}, doi = {10.1016/0022-2836(68)90318-5}, url = {PM:5700421}, keywords = {0,Adenosine,Adenosine Triphosphate,analysis,biosynthesis,Cell Nucleolus,CELLS,Cytosine,Cytosine Nucleotides,Guanine,Guanine Nucleotides,GUANINE-NUCLEOTIDE,Hela Cells,HELA-CELLS,La,nosource,Nucleic Acid Denaturation,Nucleotides,Phosphorus Isotopes,PRECURSOR,Ribonucleases,ribosomal RNA,RIBOSOMAL-RNA,Ribosomes,Rna,RNA Precursors,S,sequence,Sequence Analysis,SEQUENCE-ANALYSIS,SEQUENCES,Tritium,Ultracentrifugation,Uracil,Uracil Nucleotides} } % == BibTeX quality report for jeanteurPartialSequenceAnalysis1968a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{jeffriesUtilizationXyloseBacteria1983, title = {Utilization of Xylose by Bacteria, Yeasts, and Fungi}, author = {Jeffries, T.W.}, year = 1983, journal = {Adv.Biochem.Eng Biotechnol.}, volume = {27}, pages = {1–32}, publisher = {Springer}, url = {http://www.springerlink.com/index/p3q6g365l54n7217.pdf}, keywords = {0,Bacteria,Cellulose,Chemical Engineering,Comparative Study,Fungi,La,Lignin,metabolism,No DOI found,nosource,Polysaccharides,Review,Xylose,yeast,Yeasts} } % == BibTeX quality report for jeffriesUtilizationXyloseBacteria1983: % ? Possibly abbreviated journal title Adv.Biochem.Eng Biotechnol.

@article{jelencNucleosideTriphosphateRegeneration1979, title = {Nucleoside {{Triphosphate Regeneration Decreases}} the {{Frequency}} of {{Translation Errors}}}, author = {Jelenc, P.C. and Kurland, C.G.}, year = 1979, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {76}, number = {7}, pages = {3174–3178}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.76.7.3174}, url = {http://www.pnas.org/content/76/7/3174.short}, keywords = {nosource,translation} } % == BibTeX quality report for jelencNucleosideTriphosphateRegeneration1979: % ? Title looks like it was stored in title-case in Zotero

@article{jemioloUGASuppressionMutant1995, title = {{{UGA}} Suppression by a Mutant {{RNA}} of the Large Ribosomal Subunit}, author = {Jemiolo, D.K. and Pagel, F.T. and Murgola, E.J.}, year = 1995, month = dec, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {92}, number = {26}, pages = {12309–12313}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.92.26.12309}, url = {http://www.pnas.org/content/92/26/12309.short}, abstract = {A role for rRNA in peptide chain termination ,vas indicated several years ago by isolation of a 16S rRNA (small subunit) mutant of Escherichia coli that suppressed UGA mutations,In this paper, we describe another interesting rRNA mutant, selected as a translational suppressor of the chain-terminating mutant trpA(UGA211) of E. coli, The finding that it suppresses UGA at two positions in trpA and does not suppress the other two termination codons, UAA and UAG, at the same codon positions (or several missense mutations, including UGG, available at one of the two positions) suggests a defect in UGA-specific termination, The suppressor mutation was mapped by plasmid fragment exchanges and in vivo suppression to domain II of the 23S rRNA gene of the rrnB operon, Sequence analysis revealed a single base change of G to A at residue 1093, an almost universally conserved base in a highly conserved region known to have specific interactions with ribosomal proteins, elongation factor G, tRNA in the A-site, and the peptidyltransferase region of 23S rRNA, Several avenues of action of the suppressor mutation are suggested, including altered interactions with release factors, ribosomal protein L11, or 16S rRNA, Regardless of the mechanism, the results indicate that a particular residue in 23S rRNA affects peptide chain termination, specifically in decoding of the UGA termination codon}, keywords = {23S RNA,23S rRNAdomain II,A-SITE,analysis,BINDING-SITE,Codon,CODONS,conserved nucleotide,decoding,DIRECTED CROSS-LINKING,elongation,Escherichia coli,ESCHERICHIA-COLI,ESCHERICHIA-COLI RIBOSOME,gene,IN-VIVO,MECHANISM,MESSENGER-RNA,MITOCHONDRIAL OCHRE MUTATIONS,Mutation,MUTATIONS,nonsense suppression,nosource,Operon,Peptide Chain Termination,Peptidyltransferase,PLASMID,PLASMID COPY NUMBER,POLYPEPTIDE-CHAIN TERMINATION,protein,Proteins,REGION,RELEASE FACTOR-II,RELEASE FACTORS,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,Rna,rRNA,sequence,Sequence Analysis,SUBUNIT,suppression,termination,TERMINATION CODON,termination defect,tRNA} }

@article{jennerMessengerRNAConformations2007, title = {Messenger {{RNA}} Conformations in the Ribosomal {{E}} Site Revealed by {{X-ray}} Crystallography}, author = {Jenner, L. and Rees, B. and Yusupov, M. and Yusupova, G.}, year = 2007, journal = {EMBO reports}, volume = {8}, number = {9}, pages = {846–850}, publisher = {Nature Publishing Group}, doi = {10.1038/sj.embor.7401044}, url = {http://www.nature.com/embor/journal/vaop/ncurrent/full/7401044.html}, abstract = {A comparison of messenger RNA in X-ray crystal structures of 70S ribosomal complexes in the initiation, post-initiation and elongation states of translation shows distinct conformational differences in the exit (E) codon. Here, we present structural evidence indicating that, after the initiation event, the E codon nucleotides relax and form a classical A-helical conformation. This conformation is similar to that of the P and A codons, and is favourable for establishing Watson-Crick interactions with the anticodon of E-site transfer RNA}, keywords = {0,10,1038,2007,7401044,8,846,850,Anticodon,Base Sequence,chemistry,Codon,CODONS,COMPLEX,COMPLEXES,CONFORMATION,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,Crystallography,CrystallographyX-Ray,doi,E,E site,e-codon,elongation,embo reports,embor,FORM,initiation,La,MESSENGER-RNA,Molecular Sequence Data,mrna,nosource,Nucleic Acid Conformation,Nucleotides,Peptide Chain InitiationTranslational,ribosome,Ribosomes,Rna,RNA conformation,RNA CONFORMATIONS,RNAMessenger,SITE,sj,Structural,structure,Support,Thermus thermophilus,TRANSFER-RNA,translation,trna} } % == BibTeX quality report for jennerMessengerRNAConformations2007: % ? unused Journal abbr (“EMBO Rep.”)

@article{jeonIntegrationHumanPapillomavirus1995b, title = {Integration of Human Papillomavirus Type16 {{DNA}} into the Human Genome Leads to Increased Stability of {{E6}} and {{E7 mRNAs}}: Implictions for Cervical Carcinogenesis.}, author = {Jeon, S. and Lambert, J.M.}, year = 1995, journal = {Proc.Natl.Acad.Sci.SA}, volume = {92}, pages = {1654–1658}, doi = {10.1073/pnas.92.5.1654}, keywords = {Dna,Genome,human,mRNA,nosource,stability} } % == BibTeX quality report for jeonIntegrationHumanPapillomavirus1995b: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.SA

@article{jeoungEffectsTumorNecrosis1995, title = {Effects of Tumor Necrosis Factor-Alpha on Antimitogenicity and Cell Cycle-Related Proteins in {{MCF-7}} Cells.}, author = {Jeoung, D.I. and Tang, B. and Sonenberg, M.}, year = 1995, journal = {Journal of Biological Chemistry}, volume = {270}, pages = {18367–18373}, doi = {10.1074/jbc.270.31.18367}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Effects+of+tumor+necrosis+factor-alpha+on+antimitogenicity+and+cell+cycle-related+proteins+in+MCF-7+cells.#2}, keywords = {cancer,cdk2,cell lines,nosource,protein,Proteins,Rb} } % == BibTeX quality report for jeoungEffectsTumorNecrosis1995: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{jeppesenCrystalStructureGlutathione2003a, title = {The Crystal Structure of the Glutathione {{S-transferase-like}} Domain of Elongation Factor {{1Bgamma}} from {{Saccharomyces}} Cerevisiae}, author = {Jeppesen, M.G. and Ortiz, P. and Shepard, W. and Kinzy, T.G. and Nyborg, J. and Andersen, G.R.}, year = 2003, month = nov, journal = {J.Biol.Chem.}, volume = {278}, number = {47}, pages = {47190–47198}, doi = {10.1074/jbc.M306630200}, url = {PM:12972429}, abstract = {The crystal structure of the N-terminal 219 residues (domain 1) of the conserved eukaryotic translation elongation factor 1Bgamma (eEF1Bgamma), encoded by the TEF3 gene in Saccharomyces cerevisiae, has been determined at 3.0 A resolution by the single wavelength anomalous dispersion technique. The structure is overall very similar to the glutathione S-transferase proteins and contains a pocket with architecture highly homologous to what is observed in glutathione S-transferase enzymes. The TEF3-encoded form of eEF1Bgamma has no obvious catalytic residue. However, the second form of eEF1Bgamma encoded by the TEF4 gene contains serine 11, which may act catalytically. Based on the x-ray structure and gel filtration studies, we suggest that the yeast eEF1 complex is organized as an [eEF1A.eEF1Balpha.eEF1Bgamma]2 complex. A 23-residue sequence in the middle of eEF1Bgamma is essential for the stable dimerization of eEF1Bgamma and the quaternary structure of the eEF1 complex}, keywords = {0,Amino Acid Sequence,BIOLOGY,CEREVISIAE,chemistry,COMPLEX,COMPLEXES,crystal structure,CRYSTAL-STRUCTURE,CrystallographyX-Ray,Dimerization,DOMAIN,elongation,enzyme,Enzymes,EUKARYOTIC TRANSLATION,FORM,gene,Glutathione,GLUTATHIONE S-TRANSFERASE,Glutathione Transferase,La,Molecular Biology,Molecular Structure,nosource,Peptide Elongation Factor 1,protein,Protein StructureQuaternary,Protein StructureTertiary,Proteins,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,RESIDUES,RESOLUTION,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,Serine,structure,translation,yeast} } % == BibTeX quality report for jeppesenCrystalStructureGlutathione2003a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{jerinicConformationalChangesRibosome2000, title = {Conformational Changes in the Ribosome Induced by Translational Miscoding Agents}, author = {Jerinic, O. and Joseph, S.}, year = 2000, month = dec, journal = {Journal of Molecular Biology}, volume = {304}, number = {5}, pages = {707–713}, publisher = {Academic Press}, doi = {10.1006/jmbi.2000.4269}, url = {http://www.ingentaconnect.com/content/ap/mb/2000/00000304/00000005/art04269}, abstract = {Ribosomes are dynamic complexes responsible for translating the genetic information encoded in mRNAs to proteins. The accuracy of this process is vital to the survival of an organism, and is often compromised by translational miscoding agents. Aminoglycosides are a group of miscoding agents that bind to the ribosome and reduce the fidelity of translation. Previous studies have shown that aminoglycosides alter the higher order structure of the ribosome. Here, we used a toeprinting assay to how that streptomycin, neomycin, kanamycin, gentamycin, and hygromycin B trigger conformational changes within Escherichia coli ribosome. Miscoding agents viomycin and 30% ethanol also cause similar structural changes within the ribosome. In contrast, antibiotics that do not cause miscoding, such as tetracycline, chloramphenicol, erythromycin, fusidic acid and spectinomycin, do not induce the conformational changes triggered by miscoding agents. Furthermore, ribosomes isolated from strains that are either streptomycin resistant or dependent for growth do not show these conformational changes in the presence of streptomycin. These results correlate structural changes in the ribosome induced by miscoding agents in vitro with their in vivo phenotype}, keywords = {0,accuracy,antibiotic,antibiotics,Bacterial,Base Sequence,chemistry,Chloramphenicol,COMPLEX,COMPLEXES,drug effects,Drug ResistanceMicrobial,Erythromycin,Escherichia coli,ESCHERICHIA-COLI,Ethanol,Fidelity,Fusidic Acid,GenesBacterial,Genetic,genetics,In Vitro,IN-VITRO,IN-VIVO,Kanamycin,La,metabolism,mRNA,Mutation,Neomycin,nosource,pharmacology,Phenotype,protein,Protein Conformation,Protein Footprinting,Proteins,ribosome,Ribosomes,Rna,RNABacterial,RNAMessenger,RNATransfer,Spectinomycin,Streptomycin,Structural,structure,supportnon-u.s.gov’t,Tetracycline,toeprinting,translation,TranslationGenetic,Viomycin} } % == BibTeX quality report for jerinicConformationalChangesRibosome2000: % ? unused Journal abbr (“J.Mol.Biol”)

@article{jiYeastEst2pAffects2008, title = {Yeast {{Est2p}} Affects Telomere Length by Influencing Association of {{Rap1p}} with Telomeric Chromatin}, author = {Ji, H. and Adkins, C.J. and Cartwright, B.R. and Friedman, K.L.}, year = 2008, month = apr, journal = {Molecular and Cellular Biology}, volume = {28}, number = {7}, pages = {2380–2390}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.01648-07}, url = {http://mcb.asm.org/cgi/content/abstract/28/7/2380}, abstract = {In Saccharomyces cerevisiae, the sequence-specific binding of the negative regulator Rap1p provides a mechanism to measure telomere length: as the telomere length increases, the binding of additional Rap1p inhibits telomerase activity in cis. We provide evidence that the association of Rap1p with telomeric DNA in vivo occurs in part by sequence-independent mechanisms. Specific mutations in EST2 (est2-LT) reduce the association of Rap1p with telomeric DNA in vivo. As a result, telomeres are abnormally long yet bind an amount of Rap1p equivalent to that observed at wild-type telomeres. This behavior contrasts with that of a second mutation in EST2 (est2-up34) that increases bound Rap1p as expected for a strain with long telomeres. Telomere sequences are subtly altered in est2-LT strains, but similar changes in est2-up34 telomeres suggest that sequence abnormalities are a consequence, not a cause, of overelongation. Indeed, est2-LT telomeres bind Rap1p indistinguishably from the wild type in vitro. Taken together, these results suggest that Est2p can directly or indirectly influence the binding of Rap1p to telomeric DNA, implicating telomerase in roles both upstream and downstream of Rap1p in telomere length homeostasis}, keywords = {0,ASSOCIATION,BINDING,Carrier Proteins,CEREVISIAE,Chromatin,ChromosomesFungal,Comparative Study,cytology,deficiency,Dna,DNA Helicases,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,DNAFungal,DOWNSTREAM,FUSION PROTEIN,Gene Silencing,genetics,Helicase,In Vitro,IN-VITRO,IN-VIVO,La,MECHANISM,MECHANISMS,metabolism,Mutation,MutationMissense,MUTATIONS,nosource,physiology,protein,Protein Binding,Proteins,Recombinant Fusion Proteins,REPRESSOR,Repressor Proteins,Rna,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,Support,Telomerase,Telomere,Telomere-Binding Proteins,transcription,TRANSCRIPTION FACTOR,Transcription Factors,ultrastructure,UPSTREAM,WILD-TYPE,yeast} } % == BibTeX quality report for jiYeastEst2pAffects2008: % ? unused Journal abbr (“Mol Cell Biol”)

@article{jiangEssentialYeastProtein1993, title = {An Essential Yeast Protein, {{CBF5p}}, Binds in Vitro to Centromeres and Microtubules.}, author = {Jiang, W. and Middleton, K. and Yoon, H.J. and Fouquet, C. and Carbon, J.}, year = 1993, journal = {Molecular and cellular biology}, volume = {13}, number = {8}, pages = {4884–4893}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/13/8/4884}, abstract = {Yeast centromere DNA (CEN) affinity column chromatography has been used to purify several putative centromere and kinetochore proteins from yeast chromatin extracts. The single yeast gene (CBF5) specifying one of the major low-affinity centromere-binding proteins (p64’/CBF5p) has been cloned and shown to be essential for viability of Saccharomyces cerevisiae. CBF5 specifies a 55-kDa highly charged protein that contains a repeating KKD/E sequence domain near the C terminus, similar to known microtubule-binding domains in microtubule-associated proteins 1A and 1B, CBF5p, obtained by overexpression in bacterial cells, binds microtubules in vitro, whereas C-terminal deleted proteins lacking the (KKD/E)n domain do not. Dividing yeast cells containing a C-terminal truncated CBF5 gene, producing CBF5p containing only three copies of the KKD/E repeat, delay with replicated genomes at the G2/M phase of the cell cycle, while depletion of CBF5p arrests most cells in G1/S. Overproduction of CBF5p in S. cerevisiae complements a temperature sensitivity mutation in the gene (CBF2) specifying the 110-kDa subunit of the high-affinity CEN DNA-binding factor CBF3, suggesting in vivo interaction of CBF5p and CBF3. A second low-affinity centromere-binding factor has been identified as topoisomerase II}, keywords = {0,Bacterial,Base Sequence,C-TERMINUS,CBF5,cell cycle,Cell Division,CELLS,Centromere,CEREVISIAE,chemistry,Chromatin,Chromatography,Chromosome Mapping,CloningMolecular,Dna,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,DOMAIN,DOMAINS,EXTRACTS,Fungal Proteins,gene,GenesFungal,genetics,Genome,Hydro-Lyases,In Vitro,IN-VITRO,IN-VIVO,La,Macromolecular Substances,metabolism,Microtubule-Associated Proteins,Microtubules,Molecular Sequence Data,Multiple DOI,Mutation,nonfile,nosource,Oligonucleotides,OVEREXPRESSION,protein,Proteins,RIBONUCLEOPROTEIN,Ribonucleoproteins,RibonucleoproteinsSmall Nuclear,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,Sequence HomologyAmino Acid,Structure-Activity Relationship,SUBUNIT,Support,Temperature,yeast,YEAST-CELLS} } % == BibTeX quality report for jiangEssentialYeastProtein1993: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{jimenezSimultaneousRibosomalResistance1975a, title = {Simultaneous Ribosomal Resistance to Trichodermin and Anisomycin in ⬚{{Saccharomyces}} Cerevisiae⬚ Mutants.}, author = {Jimenez, A. and Sanchez, L. and Vazquez, D.}, year = 1975, journal = {Biochim.Biophys.Acta}, volume = {383}, pages = {427–434}, doi = {10.1016/0005-2787(75)90312-3}, abstract = {A spontaneous mutant of Saccharomyces cerevisiae resistant to trichodermin has been isolated. It displays cross resistance both in vivo and in vitro to a number of sesquiterpene antibiotics (fusarenon X, trichothecin and verrucarin A) and to the chemically unrelated antibiotic anisomycin. The mutation conferring resistance to anisomycin and trichodermin is expressed in the 60-S subunit of the yeast 80-S ribosome. Mutant ribosomes bind [-14C]trichodermin much less efficiently than wild type ribosomes, suggesting that resistance may be due, at least in part, to this property. However, both types of ribosomes bind [-3H] anisomycin equally. These results suggest that anisomycin and trichodermin have different binding sites on the 60-S subunit of eukaryotic ribosomes, even though previous results have shown that both antibiotics bind to mutually exclusive sites.}, keywords = {60S subunit,anisomycin,antibiotic,antibiotics,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,CEREVISIAE,drugs,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,In Vitro,IN-VITRO,IN-VIVO,L3,Mutation,nosource,RESISTANCE,RESISTANT,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SITE,SITES,SUBUNIT,trichodermin,WILD-TYPE,yeast} } % == BibTeX quality report for jimenezSimultaneousRibosomalResistance1975a: % ? Possibly abbreviated journal title Biochim.Biophys.Acta

@article{jimenezQuantitativeBindingAntibiotics1975, title = {Quantitative Binding of Antibiotics to Ribosomes from a Yeast Mutant Altered on the Peptidyl-Transferase Center}, author = {Jimenez, A. and Vazquez, D.}, year = 1975, month = jun, journal = {European Journal of Biochemistry}, volume = {54}, number = {2}, pages = {483–492}, publisher = {Wiley Online Library}, doi = {10.1111/j.1432-1033.1975.tb04160.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1975.tb04160.x/full}, abstract = {Quantitative binding studies of [G-3H]anisomycin and [acetyl-14C]trichodermin to sensitive and resistant 80-S ribosomes from yeasts are described in this work. A single mutation, most probably affecting the ribosome peptidyl transferase centre, appears to have pleiotropic effects on the ribosome leading to resistance to trichodermin and anisomycin and to an increased sensitivity to sparsomycin. Resistance to trichodermin is due to a reduced affinity of ribosomes from the mutant for the antibiotic. Ribosomes from the sensitive strain (Y 1661 bind [acetyl-14C]trichodermin with a dissociation constant of 0.99 muM while those from the resistant one (TR1) bind [acetyl-14C]trichodermin with a dissociation constant of 15.4 muM. Similar results are obtained when the binding of [acetyl-14C]trichodermin to Y 166 and TR1 60-S subunits is studied. The mutant TR1 is also resistant to anisomycin. Although trichodermin and anisomycin bind to the ribosome at mutually exclusive sites, the higher affinity binding of [G-3H]anisomycin that is responsible for the inhibition of the peptidyl transferase center is practically identical for Y 166 and TR1 ribosomes. Therefore, the mutation in the ribosome leading to resistance to trichodermin and anisomycin decreases the affinity for trichodermin but not for anisomycin. Trichodermin, trichothecin and fusarenon X inhibit the binding of [G-3H]anisomycin to TR1 ribosomes to a lower extent than to Y 166 ribosomes, suggesting that the resistance of TR1 ribosomes to the effects of trichothecin and fusarenon X is caused by a decrease in the affinity of the ribosomes for these drugs, as was seen with trichodermin. On the other hand, verrucarin A inhibits [G-3H]anisomycin binding to Y 166 and TR1 ribosomes to a similar extent and therefore its affinity for the ribosome does not appear to be affected by the mutation leading to resistance. Trichothecin, trichodermin and fusarenon X appear to have a common binding site on the 60-S ribosomal subunits, which overlaps or is closely linked to the binding sites of anisomycin and verrucarin A}, keywords = {0,60S subunit,Acyltransferases,anisomycin,Anti-Bacterial Agents,antibiotic,antibiotics,AntibioticsAntifungal,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,drugs,Fungal Proteins,INHIBITION,Kinetics,La,metabolism,Mutation,nosource,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,Phenylalanine,protein,Protein Binding,Proteins,ReceptorsDrug,RESISTANCE,RESISTANT,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNAMessenger,Saccharomyces cerevisiae,SITE,SITES,sparsomycin,SUBUNIT,SUBUNITS,TRANSFERASE CENTER,trichodermin,yeast,Yeasts} } % == BibTeX quality report for jimenezQuantitativeBindingAntibiotics1975: % ? unused Journal abbr (“Eur.J.Biochem.”)

@article{johnsonNuclearExportLarge2001a, title = {Nuclear Export of the Large Ribosomal Subunit}, author = {Johnson, A.W. and Ho, J.H. and Kallstrom, G. and Trotta, C. and Lund, E. and Kahan, L. and Dahlberg, J. and Hedges, J.}, year = 2001, journal = {Cold Spring Harb.Symp.Quant.Biol.}, volume = {66}, pages = {599–605}, doi = {10.1101/sqb.2001.66.599}, url = {http://symposium.cshlp.org/content/66/599.short}, keywords = {0,Active TransportCell Nucleus,Archaea,BIOLOGY,chemistry,Genetic,genetics,La,metabolism,microbiology,MOLECULAR-GENETICS,nosource,protein,Proteins,Review,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,Ribosomes,Rna,RNARibosomal,Saccharomyces cerevisiae,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for johnsonNuclearExportLarge2001a: % ? Possibly abbreviated journal title Cold Spring Harb.Symp.Quant.Biol.

@article{johnsonNuclearExportRibosomal2002a, title = {Nuclear Export of Ribosomal Subunits}, author = {Johnson, A.W. and Lund, E. and Dahlberg, J.}, year = 2002, month = nov, journal = {Trends Biochem.Sci.}, volume = {27}, number = {11}, pages = {580–585}, doi = {10.1016/S0968-0004(02)02208-9}, url = {PM:12417134}, abstract = {The partitioning of cells by a nuclear envelope ensures that precursors of ribosomes do not interact prematurely with other components of the translation machinery. Ribosomal subunits are assembled in nucleoli and exported to the cytoplasm in a CRM1/Ran-GTP-dependent fashion. Export of the large (60S) subunit requires a shuttling adaptor protein, NMD3, which binds to mature, correctly folded subunits. Immature or defective particles do not bind NMD3 and thus are excluded from the export pathway. This structural proofreading is extended into the cytoplasm, where it is believed that several energy-requiring steps release shuttling factors from the subunit, allowing it to function in translation}, keywords = {0,Active TransportCell Nucleus,adaptor,BIOLOGY,Cell Nucleus,CELLS,CEREVISIAE,COMPONENT,COMPONENTS,Conserved Sequence,Cytoplasm,Fungal Proteins,Genetic,genetics,Karyopherins,La,metabolism,microbiology,MOLECULAR-GENETICS,Mutation,nosource,PARTICLES,PATHWAY,physiology,PRECURSOR,proofreading,protein,Protein StructureTertiary,Protein Subunits,Proteins,ran GTP-Binding Protein,RELEASE,REQUIRES,Review,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,RNA-Binding Proteins,RNA-BINDING-PROTEIN,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Structural,SUBUNIT,SUBUNITS,supportu.s.gov’tp.h.s.,translation} } % == BibTeX quality report for johnsonNuclearExportRibosomal2002a: % ? Possibly abbreviated journal title Trends Biochem.Sci.

@article{johnsonNMRViewComputerProgram1994, title = {{{NMRView}}: {{A}} Computer Program for the Visualization and Analysis of {{NMR}} Data.}, author = {Johnson, B.A. and Blevins, R.A.}, year = 1994, journal = {J.Biomolecular NMR}, volume = {4⬚ ⬚}, pages = {630–614}, keywords = {analysis,computer,NMR,No DOI found,nosource} } % == BibTeX quality report for johnsonNMRViewComputerProgram1994: % ? Possibly abbreviated journal title J.Biomolecular NMR

@article{johnsonCoordinationGrowthCell1977a, title = {Coordination of Growth with Cell Division in the Yeast ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Johnson, G.C. and Pringle, J.R. and Hartwell, L.H.}, year = 1977, journal = {Exp.Cell.Res.}, volume = {105}, pages = {79–89}, doi = {10.1016/0014-4827(77)90154-9}, keywords = {cell cycle,Cell Division,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,yeast} } % == BibTeX quality report for johnsonCoordinationGrowthCell1977a: % ? Possibly abbreviated journal title Exp.Cell.Res.

@article{johnsonRegulationCellSize1979, title = {Regulation of Cell Size in the Yeast ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Johnson, G.C. and Eharhardt, C.W. and Lorincz, A. and Carter, B.L.A.}, year = 1979, journal = {J.Bacteriol.}, volume = {137}, pages = {1–5}, doi = {10.1128/jb.137.1.1-5.1979}, keywords = {cell cycle,Cell Division,cell size,nosource,ras,regulation,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,yeast} } % == BibTeX quality report for johnsonRegulationCellSize1979: % ? Possibly abbreviated journal title J.Bacteriol.

@article{jonesEffectSpecificMutations1989a, title = {The {{Effect}} of {{Specific Mutations}} at and {{Around}} the {{Gag-Pol Gene Junction}} of {{Moloney Murine Leukemia-Virus}}}, author = {Jones, D.S. and Nemoto, F. and Kuchino, Y. and Masuda, M. and Yoshikura, H. and Nishimura, S.}, year = 1989, journal = {Nucleic Acids Research}, volume = {17}, number = {15}, pages = {5933–5945}, doi = {10.1093/nar/17.15.5933}, url = {ISI:A1989AK53100005}, keywords = {Gag-pol,gene,MURINE LEUKEMIA-VIRUS,Mutation,MUTATIONS,nosource} } % == BibTeX quality report for jonesEffectSpecificMutations1989a: % ? Title looks like it was stored in title-case in Zotero

@article{jonesCharacterizationFunctionalOrdering1995, title = {Characterization and Functional Ordering of {{Slu7p}} and {{Prp17p}} during the Second Step of Pre-{{mRNA}} Splicing in Yeast}, author = {Jones, M.H. and Frank, D.N. and Guthrie, C.}, year = 1995, month = oct, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {92}, number = {21}, pages = {9687–9691}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.92.21.9687}, url = {http://www.pnas.org/content/92/21/9687.short}, keywords = {Alleles,ATP,ATPase,COMPLEX,COMPLEXES,gene,Genes,In Vitro,IN-VITRO,IN-VIVO,nosource,prp17,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,splicing,suppression,yeast} }

@article{josephEFGcatalyzedTranslocationAnticodon1998a, title = {{{EF-G-catalyzed}} Translocation of Anticodon Stem-Loop Analogs of Transfer {{RNA}} in the Ribosome}, author = {Joseph, S. and Noller, H.F.}, year = 1998, month = jun, journal = {EMBO J.}, volume = {17}, number = {12}, pages = {3478–3483}, doi = {10.1093/emboj/17.12.3478}, url = {PM:9628883}, abstract = {Translocation, catalyzed by elongation factor EF-G, is the precise movement of the tRNA-mRNA complex within the ribosome following peptide bond formation. Here we examine the structural requirement for A- and P-site tRNAs in EF-G-catalyzed translocation by substituting anticodon stem-loop (ASL) analogs for the respective tRNAs. Translocation of mRNA and tRNA was monitored independently; mRNA movement was assayed by toeprinting, while tRNA and ASL movement was monitored by hydroxyl radical probing by Fe(II) tethered to the ASLs and by chemical footprinting. Translocation depends on occupancy of both A and P sites by tRNA bound in a mRNA-dependent fashion. The requirement for an A-site tRNA can be satisfied by a 15 nucleotide ASL analog comprising only a 4 base pair (bp) stem and a 7 nucleotide anticodon loop. Translocation of the ASL is both EF-G- and GTP-dependent, and is inhibited by the translocational inhibitor thiostrepton. These findings show that the D, T and acceptor stem regions of A-site tRNA are not essential for EF-G-dependent translocation. In contrast, no translocation occurs if the P-site tRNA is substituted with an ASL, indicating that other elements of P-site tRNA structure are required for translocation. We also tested the effect of increasing the A-site ASL stem length from 4 to 33 bp on translocation from A to P site. Translocation efficiency decreases as the ASL stem extends beyond 22 bp, corresponding approximately to the maximum dimension of tRNA along the anticodon-D arm axis. This result suggests that a structural feature of the ribosome between the A and P sites, interferes with movement of tRNA analogs that exceed the normal dimensions of the coaxial tRNA anticodon-D arm}, keywords = {0,A SITE,A-SITE,Anticodon,ANTICODON LOOP,BASE,BASE-PAIR,BIOLOGY,BOND FORMATION,COMPLEX,COMPLEXES,D,EF-G,efficiency,ELEMENTS,elongation,elongation factors,ELONGATION-FACTOR-G,ELONGATION-FACTORS,Escherichia coli,FE(II),genetics,Hydroxyl Radical,INHIBITOR,La,LOOP,metabolism,Movement,mRNA,nosource,P SITE,P-SITE,P-SITES,peptide bond formation,Peptide Elongation Factor G,Peptide Elongation Factors,REGION,ribosome,Ribosomes,Rna,RNATransfer,SITE,SITES,STEM-LOOP,Structural,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,T,Thiostrepton,toeprinting,TRANSFER-RNA,translocation,tRNA} } % == BibTeX quality report for josephEFGcatalyzedTranslocationAnticodon1998a: % ? Possibly abbreviated journal title EMBO J.

@article{jungGuanidineHydrochlorideInhibits2001, title = {Guanidine Hydrochloride Inhibits {{Hsp104}} Activity in Vivo: A Possible Explanation for Its Effect in Curing Yeast Prions}, author = {Jung, G. and Masison, d.C.}, year = 2001, month = jul, journal = {Current microbiology}, volume = {43}, number = {1}, pages = {7–10}, publisher = {Springer}, doi = {10.1007/s002840010251}, url = {http://www.springerlink.com/index/UQR6JDA0V14H8ETU.pdf}, abstract = {The presence of millimolar concentrations of guanidine hydrochloride (Gdn-HCl) in growth media causes efficient loss of the normally stable [PSI+] element from yeast cells. Although it has become common practice to include 5 mm Gdn-HCl in growth media to cure [PSI+] and other prions of yeast, the biochemical mechanism by which it cures is unknown. We find that 5 mm Gdn-HCl significantly reduces Hsp104-mediated basal and acquired thermotolerance. Gdn-HCl also reduced the ability of Hsp104 to restore activity of thermally denatured luciferase in vivo. The abundance of Hsp104 was not reduced in cells grown in the presence of Gdn-HCl, ruling out negative effects on expression or stability of Hsp104. We therefore conclude that Gdn-HCl inhibits Hsp104 activity in vivo. Since replication of yeast prions is dependent on Hsp104, our results suggest that Gdn-HCl cures prions by inhibiting Hsp104 activity}, keywords = {0,antagonists & inhibitors,Biochemistry,biosynthesis,CELLS,CEREVISIAE,Colony CountMicrobial,curing,disease,drug effects,Enzyme Activation,expression,Fungal Proteins,Genetic,genetics,GROWTH,growth & development,Guanidine,Heat,heat shock proteins,HEAT-SHOCK,HEAT-SHOCK PROTEIN,HEAT-SHOCK PROTEINS,IN-VIVO,Kidney,La,luciferase,Luciferases,MECHANISM,media,metabolism,nosource,pharmacology,physiology,prion,Prions,protein,Protein Denaturation,Proteins,REPLICATION,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,stability,sup35,yeast,YEAST-CELLS,Yeasts} } % == BibTeX quality report for jungGuanidineHydrochlorideInhibits2001: % ? unused Journal abbr (“Curr.Microbiol.”)

@article{justiceElongationFactor21998, title = {Elongation Factor 2 as a Novel Target for Selective Inhibition of Fungal Protein Synthesis}, author = {Justice, M.C. and Hsu, M.J. and Tse, B. and Ku, T. and Balkovec, J. and Schmatz, D. and Nielsen, J.}, year = 1998, month = feb, journal = {Journal of Biological Chemistry}, volume = {273}, number = {6}, pages = {3148–3151}, publisher = {ASBMB}, doi = {10.1074/jbc.273.6.3148}, url = {http://www.jbc.org/content/273/6/3148.short}, abstract = {Elongation factor 2 (EF2) is an essential protein catalyzing ribosomal translocation during protein synthesis and is highly conserved in all eukaryotes. It is largely interchangeable in translation systems reconstituted from such divergent organisms as human, wheat, and fungi. We have identified the sordarins as selective inhibitors of fungal protein synthesis acting via a specific interaction with EF2 despite the high degree of amino acid sequence homology exhibited by EF2s from various eukaryotes. In vitro reconstitution assays using purified components from human, yeast, and plant cells demonstrate that sordarin sensitivity is dependent on fungal EF2. Genetic analysis of sordarin- resistant mutants of Saccharomyces cerevisiae shows that resistance to the inhibitor is linked to the genes EFT1 and EFT2 that encode EF2. Sordarin blocks ribosomal translocation by stabilizing the fungal EF2- ribosome complex in a manner similar to that of fusidic acid. The fungal specificity of the sordarins, along with a detailed understanding of its mechanism of action, make EF2 an attractive antifungal target. These findings are of particular significance due to the need for new antifungal agents}, keywords = {98123075,Amino Acid Sequence,analysis,animal,antagonists & inhibitors,AntibioticsAntifungal,assays,biosynthesis,COMPLEX,COMPLEXES,COMPONENT,elongation,Fungal Proteins,Fungi,Fusidic Acid,gene,Genes,Genetic,human,In Vitro,IN-VITRO,INHIBITION,MECHANISM,metabolism,nosource,Peptide Elongation Factors,pharmacology,protein,protein synthesis,PROTEIN-SYNTHESIS,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SYSTEM,translation,translocation,Wheat,yeast} } % == BibTeX quality report for justiceElongationFactor21998: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{justiceMutationsRibosomalProtein1999, title = {Mutations in Ribosomal Protein {{L10e}} Confer Resistance to the Fungal- Specific Eukaryotic Elongation Factor 2 Inhibitor Sordarin}, author = {Justice, M.C. and Ku, T. and Hsu, M.J. and Carniol, K. and Schmatz, D. and Nielsen, J.}, year = 1999, month = feb, journal = {Journal of Biological Chemistry}, volume = {274}, number = {8}, pages = {4869–4875}, publisher = {ASBMB}, doi = {10.1074/jbc.274.8.4869}, url = {http://www.jbc.org/content/274/8/4869.short}, abstract = {The natural product sordarin, a tetracyclic diterpene glycoside, selectively inhibits fungal protein synthesis by impairing the function of eukaryotic elongation factor 2 (eEF2). Sordarin and its derivatives bind to the eEF2-ribosome-nucleotide complex in sensitive fungi, stabilizing the post-translocational GDP form. We have previously described a class of Saccharomyces cerevisiae mutants that exhibit resistance to varying levels of sordarin and have identified amino acid substitutions in yeast eEF2 that confer sordarin resistance. We now report on a second class of sordarin-resistant mutants. Biochemical and molecular genetic analysis of these mutants demonstrates that sordarin resistance is dependent on the essential large ribosomal subunit protein L10e in S. cerevisiae. Five unique L10e alleles were characterized and sequenced, and several nucleotide changes that differ from the wild-type sequence were identified. Changes that result in the resistance phenotype map to 4 amino acid substitutions and 1 amino acid deletion clustered in a conserved 10-amino acid region of L10e. Like the previously identified eEF2 mutations, the mutant ribosomes show reduced sordarin-conferred stabilization of the eEF2-nucleotide- ribosome complex. To our knowledge, this report provides the first description of ribosomal protein mutations affecting translocation. These results and our previous observations with eEF2 suggest a functional linkage between L10e and eEF2}, keywords = {99143148,Alleles,Amino Acid Sequence,Amino Acid Substitution,analysis,animal,antagonists & inhibitors,AntibioticsAntifungal,Base Sequence,CloningMolecular,COMPLEX,COMPLEXES,DNAFungal,drug effects,Drug ResistanceMicrobial,Eif-2,elongation,Fungi,Genetic,genetics,Molecular Sequence Data,Mutation,MUTATIONS,nosource,pharmacology,Phenotype,Phosphoproteins,protein,protein synthesis,PROTEIN-SYNTHESIS,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SUBUNIT,translocation,yeast} } % == BibTeX quality report for justiceMutationsRibosomalProtein1999: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{kadoshHistoneDeacetylaseActivity1998, title = {Histone Deacetylase Activity of {{Rpd3}} Is Important for Transcriptional Repression in Vivo}, author = {Kadosh, D. and Struhl, K.}, year = 1998, month = mar, journal = {Genes & development}, volume = {12}, number = {6}, pages = {797–805}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.12.6.797}, url = {http://genesdev.cshlp.org/content/12/6/797.short}, abstract = {Eukaryotic organisms from yeast to human contain a multiprotein complex that includes Rpd3 histone deacetylase and Sin3 corepressor. The Sin3- Rpd3 complex, when recruited to promoters by specific DNA-binding proteins, can direct transcriptional repression of specific classes of target genes. It has been proposed that the histone deacetylase activity of Rpd3 is important for repression, but direct evidence is lacking. Here, we describe four Rpd3 derivatives with mutations in evolutionarily invariant histidine residues in a putative deacetylation motif. These Rpd3 mutants lack detectable histone deacetylase activity in vitro, but interact normally with Sin3 in vivo. In yeast cells, these catalytically inactive mutants are defective for transcriptional repression. They retain some residual Rpd3 function in vivo, however, suggesting that repression by the Sin3-Rpd3 complex may not be attributable exclusively to its intrinsic histone deacetylase activity. Finally, we show that a human Rpd3 homolog can interact with yeast Sin3 and repress transcription when artificially recruited to a promoter. These results suggest that the histone deacetylase activity of Rpd3 is important, but perhaps not absolutely required, for transcriptional repression in vivo}, keywords = {98180982,Acetylation,Amino Acid Sequence,Binding Sites,Catalysis,chemistry,COMPLEX,COMPLEXES,DNA-Binding Proteins,enzymology,Fungal Proteins,gene,Gene Expression RegulationFungal,Genes,genetics,Histidine,Histone Deacetylase,homolog,human,In Vitro,IN-VITRO,IN-VIVO,metabolism,Molecular Sequence Data,Mutation,MUTATIONS,nosource,pharmacology,physiology,protein,Proteins,Saccharomyces cerevisiae,Sequence HomologyAmino Acid,supportu.s.gov’tp.h.s.,transcription,Transcription Factors,TranscriptionGenetic,yeast} } % == BibTeX quality report for kadoshHistoneDeacetylaseActivity1998: % ? unused Journal abbr (“Genes Dev.”)

@article{kambourisCloningGeneticCharacterization1993a, title = {Cloning and Genetic Characterization of a Calcium- and Phospholipid-Binding Protein from {{Saccharomyces}} Cerevisiae That Is Homologous to Translation Elongation Factor-1 Gamma}, author = {Kambouris, N.G. and Burke, D.J. and Creutz, C.E.}, year = 1993, month = feb, journal = {Yeast}, volume = {9}, number = {2}, pages = {151–163}, doi = {10.1002/yea.320090206}, url = {PM:8465602}, abstract = {We have isolated a gene (CAM1) from the yeast Saccharomyces cerevisiae that encodes a protein homologous to the translational cofactor elongation factor-1 gamma (EF-1 gamma) first identified in the brine shrimp Artemia salina. The predicted Cam1 amino acid sequence consists of 415 residues that share 32% identity with the Artemia protein, increasing to 72% when conservative substitutions are included. The calculated M(r) of Cam1p (47,092 Da) is in close agreement with that of EF-1 gamma (M(r) = 49,200 Da), and hydropathy plots of each protein exhibit strikingly similar profiles. Disruption of the CAM1 locus yields four viable meiotic progeny, indicating that under normal growth conditions the Cam1 protein is non-essential. Attempts to elicit a translational phenotype have been unsuccessful. Since EF-1 gamma participates in the regulation of a GTP-binding protein (EF-1 alpha), double mutants with cam1 disruptions and various mutant alleles of known GTP-binding proteins were constructed and examined. No evidence was found for an interaction of CAM1 with TEF1, TEF2, SEC4, YPT1, RAS1, RAS2, CDC6, ARF1, ARF2 or CIN4. The possibility that Cam1p may play a redundant role in the regulation of protein synthesis or another GTP-dependent process is discussed}, keywords = {0,ACID,Alleles,Amino Acid Sequence,AMINO-ACID,Base Sequence,Calcium,Cell Division,CEREVISIAE,Chromosome Mapping,cloning,CloningMolecular,CrossesGenetic,DISRUPTION,DISRUPTIONS,Dna,DNA Probes,drug effects,EF-1,EF-1 alpha,EF-1-ALPHA,elongation,elongation factors,ELONGATION-FACTORS,ENCODES,Fungal Proteins,gene,GenesFungal,Genetic,GENETIC-CHARACTERIZATION,genetics,GROWTH,GTP-Binding Proteins,Guanosine,Guanosine Triphosphate,Hygromycin B,La,metabolism,Molecular Sequence Data,Mutagenesis,MUTANTS,nosource,Peptide Elongation Factor 1,Peptide Elongation Factors,pharmacology,Phenotype,Phospholipids,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,Proteins,regulation,Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,RESIDUES,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,Sequence AnalysisDNA,Sequence HomologyAmino Acid,translation,yeast} }

@article{kanekoAlterationValylsRNASporulation1966, title = {Alteration of Valyl-{{sRNA}} during Sporulation of Bacillus Subtilis.}, author = {Kaneko, I. and Doi, R.H.}, year = 1966, month = mar, journal = {Proceedings of the National Academy of Sciences}, volume = {55}, number = {3}, pages = {564–571}, publisher = {National Academy of Sciences}, doi = {10.1073/pnas.55.3.564}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC224188/}, keywords = {0,Bacillus subtilis,Bacterial,Chromatography,Genetic Code,In Vitro,La,Ligases,metabolism,Molecular Biology,nosource,Rna,RNABacterial,RNATransfer,Spores,SPORULATION,Valine} } % == BibTeX quality report for kanekoAlterationValylsRNASporulation1966: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{kangMutantRNAPseudoknot1997a, title = {A Mutant {{RNA}} Pseudoknot That Promotes Ribosomal Frameshifting in Mouse Mammary Tumor Virus}, author = {Kang, H. and Tinoco, I.}, year = 1997, month = may, journal = {Nucleic Acids Res.}, volume = {25}, number = {10}, pages = {1943–1949}, doi = {10.1093/nar/25.10.1943}, url = {PM:9115361}, abstract = {A single A–{\(>\)}G mutation that changes a potential A.U base pair to a G.U pair at the junction of the stems and loops of a non-frameshifting pseudoknot dramatically increases its frameshifting efficiency in mouse mammary tumor virus. The structure of the non-frameshifting pseudoknot APK has been found to be very different from that of pseudoknots that cause efficient frameshifting [Kang,H., Hines,J.V. and Tinoco,I. (1995) J. Mol. Biol. , 259, 135-147]. The 3-dimensional structure of the mutant pseudoknot was determined by restrained molecular dynamics based on NMR-derived interproton distance and torsion angle constraints. One striking feature of the mutant pseudoknot compared with the parent pseudoknot is that a G.U base pair forms at the top of stem 2, thus leaving only 1 nt at the junction of the two stems. The conformation is very different from that of the previously determined non-frameshifting parent pseudoknot, which lacks the A.U base pair at the top of the stem and has 2 nt between the stems. However, the conformation is quite similar to that of efficient frameshifting pseudoknots whose structures were previously determined by NMR. A single adenylate residue intervenes between the two stems and interrupts their coaxial stacking. This unpaired nucleotide produces a bent structure. The structural similarity among the efficient frameshifting pseudoknots indicates that a specific conformation is required for ribosomal frameshifting, further implying a specific interaction of the pseudoknot with the ribosome}, keywords = {0,3-DIMENSIONAL STRUCTURE,Adenine,animal,BASE,Base Composition,Base Sequence,BASE-PAIR,chemistry,Comparative Study,Computer Simulation,CONFORMATION,DYNAMICS,efficiency,FORM,Frameshifting,FrameshiftingRibosomal,genetics,Guanine,La,LOOP,Magnetic Resonance Spectroscopy,Mammary Tumor VirusMouse,Mice,ModelsMolecular,Molecular Sequence Data,Mutation,NMR,nosource,Nucleic Acid Conformation,Point Mutation,pseudoknot,pseudoknots,ribosomal frameshifting,ribosome,Rna,RNA PSEUDOKNOT,RnaViral,Structural,structure,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Thermodynamics,Uracil,virus} } % == BibTeX quality report for kangMutantRNAPseudoknot1997a: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{kankareStructureOrganizationExpression1997, title = {Structure, Organization and Expression of the Mouse Ornithine Decarboxylase Antizyme Gene.}, author = {Kankare, K. and {Uusi-Oukari}, M. and Janne, O.A.}, year = 1997, month = jun, journal = {Biochemical Journal}, volume = {324}, number = {Pt 3}, pages = {807–813}, publisher = {Portland Press Ltd}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1218496/}, keywords = {Antibodies,antibody,antizyme,Cell Line,cell lines,Culture Media,Escherichia coli,ESCHERICHIA-COLI,expression,Frameshifting,gene,Genes,genomic,media,Methods,mRNA,No DOI found,nosource,Ornithine Decarboxylase,ORNITHINE DECARBOXYLASE ANTIZYME,polyamine,protein,Rabbits,rat,regulation,sequence,Spermidine,structure,transcription,Transfection,translation} }

@article{kaplanNonparametricEstimationIncomplete1958, title = {Nonparametric Estimation from Incomplete Observations.}, author = {Kaplan, E.L. and Meier, P.}, year = 1958, journal = {Journal of the American Statistical Association}, volume = {53⬚ ⬚}, number = {282}, eprint = {2281868}, eprinttype = {jstor}, pages = {457–481}, publisher = {JSTOR}, doi = {10.1080/01621459.1958.10501452}, url = {http://www.jstor.org/stable/2281868}, keywords = {nosource,Statistics} }

@article{kappMolecularMechanicsEukaryotic2004, title = {The Molecular Mechanics of Eukaryotic Translation.}, author = {Kapp, L.D. and Lorsch, J.R.}, year = 2004, journal = {Annual review of biochemistry}, volume = {73}, number = {1}, pages = {657–704}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, doi = {10.1146/annurev.biochem.73.030403.080419}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.biochem.73.030403.080419}, abstract = {Great advances have been made in understanding the molecular mechanisc underlying protein sysntesis in bacteria in the past three decades, but our understanding of the correspoinding events in eukaryotic organisms is only beginning to catch up. In this review we describe the current state of our knowledge and ignorance of the molecular mechanics underling eukaryotic translation. We discuss the mechanisms conserved across the three kingdoms of lifs as well as the important divergences that have taken place in the pathway.}, keywords = {Bacteria,EUKARYOTIC TRANSLATION,MECHANISM,MECHANISMS,nosource,PATHWAY,protein,Review,translation} } % == BibTeX quality report for kappMolecularMechanicsEukaryotic2004: % ? unused Journal abbr (“Annu.Rev.Biochem.”)

@article{karacostasOverexpressionHIV1Gagpol1993, title = {Overexpression of the {{HIV-1}} Gag-Pol Polyprotein Results in Intracellular Activation of {{HIV-1}} Protease and Inhibition of Assembly and Budding of Virus-like Particles}, author = {Karacostas, V. and Wolffe, E.J. and Nagashima, K. and Gonda, M.A. and Moss, B.}, year = 1993, month = apr, journal = {Virology}, volume = {193}, number = {2}, pages = {661–671}, publisher = {Elsevier}, doi = {10.1006/viro.1993.1174}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0042-6822(83)71174-8}, keywords = {activation,assembly,efficiency,expression,frameshift,Gag,Gag-pol,Gag/Gag-pol ratio,gene,Genes,Hiv-1,Immunoblotting,INHIBITION,lysate,MECHANISM,Mutagenesis,nosource,pol,protein,Proteins,structure,translation,vector,vectors,virus} }

@article{kardalinouAnisomycinRapamycinDefine1994, title = {Anisomycin and {{Rapamycin Define An Area Upstream}} of {{P70}}/85({{S6K}}) {{Containing A Bifurcation}} to {{Histone H3-Hmg-Like Protein-Phosphorylation}} and {{C-Fos C-Jun Induction}}}, author = {Kardalinou, E. and Zhelev, N. and Hazzalin, C.A. and Mahadevan, L.C.}, year = 1994, month = feb, journal = {Molecular and Cellular Biology}, volume = {14}, number = {2}, pages = {1066–1074}, url = {ISI:A1994NK73400022}, abstract = {Anisomycin, a translational inhibitor, synergizes with growth factors and phorbol esters to superinduce c-fos and c-jun by a number mechanisms, one of which is its ability to act as a potent signalling agonist, producing strong, prolonged activation of the same nuclear responses as epidermal growth factor or tetradecanoyl phorbol acetate. These responses include the phosphorylation of pp33, which exists in complexed and chromatin-associated forms, and of histone H3 and an HMG-like protein. By peptide mapping and microsequencing, we show here that pp33 is the phosphoprotein S6, present in ribosomes and in preribosomes in the nucleolus. Ablation of epidermal growth factor-, tetradecanoyl phorbol acetate-, or anisomycin-stimulated S6 phosphorylation by using the p70/85(S6k) inhibitor rapamycin has no effect on histone H3 and HMG-like protein phosphorylation or on the induction and superinduction of c-fos and c-jun. Further, [S-35]methionine-labelling and immunoprecipitation studies show that the ablation of S6 phosphorylation has no discernible effect on translation in general or translation of newly induced c-fos transcripts. Finally, we show that anisomycin augments and prolongs S6 phosphorylation not by blocking S6 phosphatases but by sustained activation of p70/85(S6k). These results suggest the possible use of anisomycin and rapamycin to define upstream and downstream boundaries of an area of signalling above p70/85(S6k) which contains a bifurcation that produced histone H3-HMG-like protein phosphorylation and c-fos-c-jun induction in the nucleus}, keywords = {activation,anisomycin,COMPLEX-FORMATION,DISTINCT MECHANISMS,DOWNSTREAM,FORM,GEL-ELECTROPHORESIS,GROWTH,GROWTH-FACTOR,INHIBITOR,KINASE-C,MAP2 KINASE,mapping,MECHANISM,MECHANISMS,Multiple DOI,nonfile,nosource,nucleolus,Peptide Mapping,PHOSPHATASE,phosphoprotein,Phosphorylation,protein,RIBOSOMAL PROTEIN-S6,ribosome,Ribosomes,S6 PROTEIN,Signal Transduction,SYNTHESIS INHIBITORS,TRANSCRIPT,TRANSCRIPTIONAL ACTIVATION,translation,UPSTREAM} } % == BibTeX quality report for kardalinouAnisomycinRapamycinDefine1994: % ? Title looks like it was stored in title-case in Zotero

@article{kargelStudiesInteraction51987, title = {Studies on Interaction of 5 {{S RNA}} with Ribosomal Proteins}, author = {Kargel, H.J. and Stahl, J. and Gross, B. and Knespel, S. and Bielka, H. and Saarma, M.}, year = 1987, month = aug, journal = {FEBS Letters}, volume = {220}, number = {1}, pages = {126–128}, publisher = {Elsevier}, doi = {10.1016/0014-5793(87)80889-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/001457938780889X}, keywords = {5S rRNA,BINDING,Electrophoresis,L3,Liver,nosource,protein,Proteins,rat,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Rna,SUBUNIT} }

@article{karimiDissociationRateCognate1994, title = {Dissociation Rate of Cognate Peptidyl-{{tRNA}} from the {{A-site}} of Hyper-Accurate and Error-Prone Ribosomes}, author = {Karimi, R. and Ehrenberg, M.}, year = 1994, month = dec, journal = {European Journal of Biochemistry}, volume = {226}, number = {2}, pages = {355–360}, publisher = {Wiley Online Library}, doi = {10.1111/j.1432-1033.1994.tb20059.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1994.tb20059.x/pdf}, keywords = {A-SITE,accuracy,BINDING,COMPLEX,COMPLEXES,Neomycin,nosource,Phenotype,proofreading,ram,ribosome,Ribosomes,stability,Streptomycin} }

@article{karimiDissociationRatesPeptidyltRNA1996, title = {Dissociation Rates of Peptidyl-{{tRNA}} from the {{P-site}} of {{E}}. Coli Ribosomes.}, author = {Karimi, R. and Ehrenberg, M.}, year = 1996, month = mar, journal = {The EMBO Journal}, volume = {15}, number = {5}, pages = {1149–1154}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1996.tb00453.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC450013/}, keywords = {A-SITE,BINDING,E.coli,Escherichia coli,ESCHERICHIA-COLI,IN-VIVO,Neomycin,nosource,P-SITE,ram,ribosome,Ribosomes,rRNA,Streptomycin,structure} }

@article{karinPrimaryStructureTranscription1984a, title = {Primary Structure and Transcription of an Amplified Genetic Locus: The ⬚{{CUP1}}⬚ Locus of Yeast.}, author = {Karin, M. and Najarian, R. and Haslinger, A. and Valenzuela, P. and Uelch, J. and Fogel, S.}, year = 1984, journal = {Proc.Natl.Acad.Sci.USA}, volume = {81}, pages = {337–341}, doi = {10.1073/pnas.81.2.337}, keywords = {CUP1,Genetic,nosource,sequence,structure,transcription,yeast} } % == BibTeX quality report for karinPrimaryStructureTranscription1984a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{kasperaitisAminoAcidSequence1995, title = {The Amino Acid Sequence of Eukaryotic Translation Initiation Factor 1 and Its Similarity to Yeast Initiation Factor {{SUI1}}.}, author = {Kasperaitis, M.A.M. and Voorma, H.O. and Thomal, A.A.M.}, year = 1995, journal = {FEBS letters}, volume = {365}, number = {1}, pages = {47–50}, publisher = {Elsevier}, doi = {10.1016/0014-5793(95)00427-B}, url = {http://linkinghub.elsevier.com/retrieve/pii/001457939500427B}, keywords = {Amino Acid Sequence,human,human homologue,initiation,nosource,sequence,sui,sui1,translation,TRANSLATION INITIATION,yeast} } % == BibTeX quality report for kasperaitisAminoAcidSequence1995: % ? unused Journal abbr (“FEBS Lett.”)

@article{kastenLargeProteinComplex1997a, title = {A Large Protein Complex Containing the Yeast {{Sin3p}} and {{Rpd3p}} Transcriptional Regulators}, author = {Kasten, M.M. and Dorland, S. and Stillman, D.J.}, year = 1997, journal = {Mol.Cell Biol.}, volume = {17}, number = {8}, pages = {4852–4858}, doi = {10.1128/MCB.17.8.4852}, abstract = {The SIN3 gene is required for the transcriptional repression of diverse genes in Saccharomyces cerevisiae. Sin3p does not bind directly to DNA but is thought to be targeted to promoters by interacting with sequence- specific DNA-binding proteins. We show here that Sin3p is present in a large multiprotein complex with an apparent molecular mass, estimated by gel filtration chromatography, of greater than 2 million Da. Genetic studies have shown that the yeast RPD3 gene has a function similar to that of SIN3 in transcriptional regulation, as SIN3 and RPD3 negatively regulate the same set of genes. The SIN3 and RPD3 genes are conserved from yeasts to mammals, and recent work suggests that RPD3 may encode a histone deacetylase. We show that Rpd3p is present in the Sin3p complex and that an rpd3 mutation eliminates SIN3-dependent repression. Thus, Sin3p may function as a bridge to recruit the Rpd3p histone deacetylase to specific promoters}, keywords = {97378060,analysis,Bacterial Proteins,cancer,chemistry,Chromatography,ChromatographyGel,COMPLEX,COMPLEXES,Dna,DNA-Binding Proteins,Fungal Proteins,gene,Genes,GenesFungal,Genetic,genetics,Histone Deacetylase,Macromolecular Systems,Mammals,metabolism,Methods,Molecular Weight,Mutation,nosource,protein,PROTEIN COMPLEX,Proteins,Recombinant Fusion Proteins,regulation,Repressor Proteins,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Serine Proteinases,supportu.s.gov’tp.h.s.,Transcription Factors,TranscriptionGenetic,yeast,Yeasts} } % == BibTeX quality report for kastenLargeProteinComplex1997a: % ? Possibly abbreviated journal title Mol.Cell Biol.

@article{kastenmayerFunctionalGenomicsGenes2006a, title = {Functional Genomics of Genes with Small Open Reading Frames ({{sORFs}}) in {{S}}. Cerevisiae}, author = {Kastenmayer, J.P. and Ni, L. and Chu, A. and Kitchen, L.E. and Au, W.C. and Yang, H. and Carter, C.D. and Wheeler, D. and Davis, R.W. and Boeke, J.D. and Snyder, M.A. and Basrai, M.A.}, year = 2006, month = mar, journal = {Genome Res.}, volume = {16}, number = {3}, pages = {365–373}, doi = {10.1101/gr.4355406}, url = {http://genome.cshlp.org/content/16/3/365.short}, abstract = {Genes with small open reading frames (sORFs; {\(<\)}100 amino acids) represent an untapped source of important biology. sORFs largely escaped analysis because they were difficult to predict computationally and less likely to be targeted by genetic screens. Thus, the substantial number of sORFs and their potential importance have only recently become clear. To investigate sORF function, we undertook the first functional studies of sORFs in any system, using the model eukaryote Saccharomyces cerevisiae. Based on independent experimental approaches and computational analyses, evidence exists for 299 sORFs in the S. cerevisiae genome, representing approximately 5% of the annotated ORFs. We determined that a similar percentage of sORFs are annotated in other eukaryotes, including humans, and 184 of the S. cerevisiae sORFs exhibit similarity with ORFs in other organisms. To investigate sORF function, we constructed a collection of gene-deletion mutants of 140 newly identified sORFs, each of which contains a strain-specific “molecular barcode,” bringing the total number of sORF deletion strains to 247. Phenotypic analyses of the new gene-deletion strains identified 22 sORFs required for haploid growth, growth at high temperature, growth in the presence of a nonfermentable carbon source, or growth in the presence of DNA damage and replication-arrest agents. We provide a collection of sORF deletion strains that can be integrated into the existing deletion collection as a resource for the yeast community for elucidating gene function. Moreover, our analyses of the S. cerevisiae sORFs establish that sORFs are conserved across eukaryotes and have important biological functions}, keywords = {ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,BIOLOGY,cancer,Carbon,carbon source,CEREVISIAE,Conserved Sequence,Dna,DNA Damage,EvolutionMolecular,FRAME,functional genomics,gene,Gene Deletion,Gene Expression Profiling,Gene Expression Regulation,Genes,Genetic,genetics,Genome,GenomeFungal,genomic,Genomics,GROWTH,Haploidy,human,Humans,La,MODEL,MUTANTS,nosource,OPEN READING FRAME,Open Reading Frames,Phenotype,READING FRAME,Reading Frames,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Support,SYSTEM,Temperature,yeast} } % == BibTeX quality report for kastenmayerFunctionalGenomicsGenes2006a: % ? Possibly abbreviated journal title Genome Res.

@article{katzWidespreadSelectionLocal2003, title = {Widespread Selection for Local {{RNA}} Secondary Structure in Coding Regions of Bacterial Genes.}, author = {Katz, L. and Burge, C.B.}, year = 2003, month = sep, journal = {Genome Research}, volume = {13}, number = {9}, pages = {2042–2051}, publisher = {Cold Spring Harbor Lab}, issn = {1088-9051}, doi = {10.1101/gr.1257503}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=403678&tool=pmcentrez&rendertype=abstract http://genome.cshlp.org/content/13/9/2042.short}, abstract = {Redundancy of the genetic code dictates that a given protein can be encoded by a large collection of distinct mRNA species, potentially allowing mRNAs to simultaneously optimize desirable RNA structural features in addition to their protein-coding function. To determine whether natural mRNAs exhibit biases related to local RNA secondary structure, a new randomization procedure was developed, DicodonShuffle, which randomizes mRNA sequences while preserving the same encoded protein sequence, the same codon usage, and the same dinucleotide composition as the native message. Genes from 10 of 14 eubacterial species studied and one eukaryote, the yeast Saccharomyces cerevisiae, exhibited statistically significant biases in favor of local RNA structure as measured by folding free energy. Several significant associations suggest functional roles for mRNA structure, including stronger secondary structure bias in the coding regions of intron-containing yeast genes than in intronless genes, and significantly higher folding potential in polycistronic messages than in monocistronic messages in Escherichia coli. Potential secondary structure generally increased in genes from the 5’ to the 3’ end of E. coli operons, and secondary structure potential was conserved in homologous Salmonella typhi operons. These results are interpreted in terms of possible roles of RNA structures in RNA processing, regulation of mRNA stability, and translational control.}, pmid = {12952875}, keywords = {0,3,ASSOCIATION,Bacterial,Bacterial: biosynthesis,Bacterial: chemistry,Bacterial: genetics,BIOLOGY,biosynthesis,CEREVISIAE,chemistry,CODING REGION,Codon,Comparative Study,Computational Biology,Computational Biology: methods,Computational Biology: statistics & numerical data,E,Escherichia coli,ESCHERICHIA-COLI,Fungal,gene,Gene Expression Regulation,Gene Expression RegulationBacterial,Gene Expression RegulationFungal,Genes,GenesStructuralBacterial,GenesStructuralFungal,Genetic,Genetic Code,GENETIC-CODE,genetics,Introns,Introns: genetics,La,MESSAGE,Messenger,Messenger: chemistry,Messenger: genetics,Messenger: metabolism,metabolism,Methods,mRNA,mRNA stability,nosource,Nucleic Acid Conformation,Open Reading Frames,Operon,Operon: genetics,protein,REGION,regulation,Rna,RNA,RNA SECONDARY STRUCTURE,RNA Stability,RNA Stability: genetics,RNA: chemistry,RNA: genetics,RNA: metabolism,RNABacterial,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,SACCHAROMYCES-CEREVISIAE,SECONDARY STRUCTURE,SELECTION,sequence,SEQUENCES,stability,statistics & numerical data,Structural,STRUCTURAL FEATURES,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Thermodynamics,yeast} } % == BibTeX quality report for katzWidespreadSelectionLocal2003: % ? unused Journal abbr (“Genome Res.”)

@article{kavranStructureBaseL72007, title = {Structure of the {{Base}} of the {{L7}}/{{L12 Stalk}} of the {{Haloarcula}} Marismortui {{Large Ribosomal Subunit}}: {{Analysis}} of {{L11 Movements}}}, author = {Kavran, J.M. and Steitz, T.A.}, year = 2007, month = jun, journal = {J. Mol. Biol.}, volume = {371}, number = {4}, pages = {1047–1059}, publisher = {Elsevier}, url = {PM:17599351}, abstract = {Initiation factors, elongation factors, and release factors all interact with the L7/L12 stalk of the large ribosomal subunit during their respective GTP-dependent cycles on the ribosome. Electron density corresponding to the stalk is not present in previous crystal structures of either 50 S subunits or 70 S ribosomes. We have now discovered conditions that result in a more ordered factor-binding center in the Haloarcula marismortui (H.ma) large ribosomal subunit crystals and consequently allows the visualization of the full-length L11, the N-terminal domain (NTD) of L10 and helices 43 and 44 of 23 S rRNA. The resulting model is currently the most complete reported structure of a L7/L12 stalk in the context of a ribosome. This region contains a series of intermolecular interfaces that are smaller than those typically seen in other ribonucleoprotein interactions within the 50 S subunit. Comparisons of the L11 NTD position between the current structure, which is has an NTD splayed out with respect to previous structures, and other structures of ribosomes in different functional states demonstrates a dynamic range of L11 NTD movements. We propose that the L11 NTD moves through three different relative positions during the translational cycle: apo-ribosome, factor-bound pre-GTP hydrolysis and post-GTP hydrolysis. These positions outline a pathway for L11 NTD movements that are dependent on the specific nucleotide state of the bound ligand. These three states are represented by the orientations of the L11 NTD relative to the ribosome and suggest that L11 may play a more specialized role in the factor binding cycle than previously appreciated}, keywords = {analysis,BASE,BINDING,Biochemistry,Biophysics,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,DOMAIN,elongation,elongation factors,ELONGATION-FACTORS,Haloarcula,Haloarcula marismortui,Hydrolysis,initiation,INITIATION-FACTOR,interface,L10,La,MODEL,MOF,Movement,No DOI found,nosource,PATHWAY,POSITION,POSITIONS,REGION,RELEASE,release factor,RELEASE FACTORS,RIBONUCLEOPROTEIN,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,rRNA,S,SERIES,structure,SUBUNIT,SUBUNITS,VISUALIZATION} } % == BibTeX quality report for kavranStructureBaseL72007: % ? Possibly abbreviated journal title J. Mol. Biol.

@article{kawakamiRareTRNAArgCCU1993, title = {A Rare {{tRNA-Arg}}({{CCU}}) That Regulates {{Ty1}} Element Ribosomal Frameshifting Is Essential for {{Ty1}} Retrotransposition in {{Saccharomyces}} Cerevisiae.}, author = {Kawakami, K. and Paned, S. and Faioa, B. and Moore, D.P. and Boeke, J.D. and Farabaugh, P.J. and Strathern, J.N. and Nakamura, Y. and Garfinkel, D.J.}, year = 1993, journal = {Genetics}, volume = {135}, pages = {309–320}, doi = {10.1093/genetics/135.2.309}, keywords = {Frameshifting,Gag/Gag-pol ratio,nosource,ribosomal frameshifting,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Ty1} }

@article{kawasakiRasdependentRasindependentActivation1996, title = {Ras-Dependent and {{Ras-independent}} Activation Pathways for the Stress-Activated-Protein-Kinase Cascade.}, author = {Kawasaki, H. and Moriguchi, T. and Matsuda, S. and Li, H.Z. and Nakamura, S. and Shimohama, S. and Kimura, J. and Gotoh, Y. and Nishida, E.}, year = 1996, journal = {European Journal of Biochemistry}, volume = {241}, number = {2}, pages = {315–321}, publisher = {Wiley Online Library}, doi = {10.1111/j.1432-1033.1996.00315.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1996.00315.x/full}, keywords = {activation,anisomycin,nosource,stress activation} } % == BibTeX quality report for kawasakiRasdependentRasindependentActivation1996: % ? unused Journal abbr (“Eur.J.Biochem.”)

@article{kawashimaStructureEscherichiaColi1996a, title = {The Structure of the {{Escherichia}} Coli {{EF-Tu}}.{{EF-Ts}} Complex at 2.5 {{A}} Resolution [See Comments] [Published Erratum Appears in {{Nature}} 1996 {{May}} 9;381(6578):172]}, author = {Kawashima, T. and {Berthet-Colominas}, C. and Wulff, M. and Cusack, S. and Leberman, R.}, year = 1996, month = feb, journal = {Nature}, volume = {379}, number = {6565}, pages = {511–518}, doi = {10.1038/379511a0}, keywords = {BINDING,COMPLEX,COMPLEXES,EFTu,elongation,Escherichia coli,ESCHERICHIA-COLI,Guanine,nosource,Nucleotides,structure,SUBUNIT} }

@article{kazemieBindingAminoacyltRNAReconstituted1976, title = {Binding of Aminoacyl-{{tRNA}} to Reconstituted Subparticles of {{Escherichia}} Coli Large Ribosomal Subunits}, author = {Kazemie, M.}, year = 1976, journal = {European Journal of Biochemistry}, volume = {67}, number = {2}, pages = {373–378}, publisher = {Wiley Online Library}, doi = {10.1111/j.1432-1033.1976.tb10701.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1976.tb10701.x/abstract}, abstract = {The activity of 50-S subunits to stimulate the binding of aminoacyl- tRNA to the 30-S subunits was lost when the particles were washed with LiCl concentrations higher than 1.0 M [Kazemie, M. (1975) Eur. J. Biochem. 58,501-510]. The particles could regain this activity when they were incubated with the corresponding LiCl washes. This effect of LiCl washes was used as an assay for identification of 50-S subunit proteins which are essential for binding of aminoacyl-tRNA. A protein mixture containing mainly Ll, Lll and L16 can reactivate 50-S “core” particles, consisting of 10 proteins and 23-S RNA, to bind aminoacyl- tRNAs in the presence of 30-S subunits. Besides 5-S RNA, protein L24 has a stimulatory effect on the binding of aminoacyl-tRNA. Proteins L2, L20 and L23 are possibly required for maintaining the 50-S subunits in the correct conformation for binding of aminoacyl-tRNAs}, keywords = {30 S,5S rRNA,77003036,BINDING,Binding Sites,drug effects,Escherichia coli,ESCHERICHIA-COLI,IDENTIFICATION,L2,Lithium,metabolism,nosource,pharmacology,Phenylalanine,protein,Protein Binding,Proteins,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,Ribosomes,Rna,RNATransfer,SUBUNIT,tRNA,ultrastructure} } % == BibTeX quality report for kazemieBindingAminoacyltRNAReconstituted1976: % ? unused Journal abbr (“Eur.J.Biochem.”)

@article{kelleherAutisticNeuronTroubled2008, title = {The Autistic Neuron: Troubled Translation?}, author = {Kelleher, R.J. and Bear, M.F.}, year = 2008, month = oct, journal = {Cell}, volume = {135}, number = {3}, pages = {401–406}, publisher = {Elsevier}, doi = {10.1016/j.cell.2008.10.017}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867408013081 pm:18984149 http://www.sciencedirect.com/science/article/pii/S0092867408013081}, abstract = {Autism is a complex genetic disorder, but single-gene disorders with a high prevalence of autism offer insight into its pathogenesis. Recent evidence suggests that some molecular defects in autism may interfere with the mechanisms of synaptic protein synthesis. We propose that aberrant synaptic protein synthesis may represent one possible pathway leading to autistic phenotypes, including cognitive impairment and savant abilities}, keywords = {COMPLEX,COMPLEXES,Genetic,genetics,genomic,Genomics,human,La,MECHANISM,MECHANISMS,nosource,PATHWAY,Phenotype,protein,protein synthesis,PROTEIN-SYNTHESIS,translation} }

@article{kellerComparisonMammalianYeast1997, title = {A Comparison of Mammalian and Yeast Pre-{{mRNA}} 3’-End Processing. [{{Review}}] [52 Refs]}, author = {Keller, W. and {Minvielle-Sebastia}, L.}, year = 1997, month = jun, journal = {Current Opinion in Cell Biology}, volume = {9}, number = {3}, pages = {329–336}, doi = {10.1016/S0955-0674(97)80004-X}, keywords = {Amino Acid Sequence,COMPLEX,COMPLEXES,COMPONENT,gene,Genes,history,nosource,Rna,sequence,SUBUNIT,yeast} }

@article{kervestinStopCodonRecognition2001, title = {Stop Codon Recognition in Ciliates: {{Euplotes}} Release Factor Does Not Respond to Reassigned {{UGA}} Codon}, author = {Kervestin, S. and Frolova, L. and Kisselev, L. and {Jean-Jean}, O.}, year = 2001, journal = {EMBO reports}, volume = {2}, number = {8}, pages = {680–684}, publisher = {Nature Publishing Group}, doi = {10.1093/embo-reports/kve156}, url = {http://www.nature.com/embor/journal/v2/n8/abs/embor364.html}, abstract = {In eukaryotes, the polypeptide release factor 1 (eRF1) is involved in translation termination at all three stop codons. However, the mechanism for decoding stop codons remains unknown. A direct interaction of eRF1 with the stop codons has been postulated. Recent studies focus on eRF1 from ciliates in which some stop codons are reassigned to sense codons. Using an in vitro assay based on mammalian ribosomes, we show that eRF1 from the ciliate Euplotes aediculatus responds to UAA and UAG as stop codons and lacks the capacity to decipher the UGA codon, which encodes cysteine in this organism. This result strongly suggests that in ciliates with variant genetic codes eRF1 does not recognize the reassigned codons. Recent hypotheses describing stop codon discrimination by eRF1 are not fully consistent with the set of eRF1 sequences available so far and require direct experimental testing}, keywords = {0,Amino Acid Sequence,Animals,CHAIN TERMINATION,chemistry,Codon,CODON RECOGNITION,CODONS,CodonTerminator,Cysteine,cytology,decoding,ENCODES,Euplotes,Genetic,Genetic Code,GENETIC-CODE,genetics,human,Humans,In Vitro,IN-VITRO,isolation & purification,La,MECHANISM,metabolism,Molecular Sequence Data,MutagenesisSite-Directed,nosource,Peptide Chain Termination,Peptide Termination Factors,POLYPEPTIDE,protein,Protein Biosynthesis,Protein StructureTertiary,RECOGNITION,RELEASE,release factor,Research SupportNon-U.S.Gov’t,ribosome,Ribosomes,sequence,Sequence Alignment,SEQUENCES,STOP CODON,STOP CODON RECOGNITION,termination,translation,TRANSLATION TERMINATION,UAA} } % == BibTeX quality report for kervestinStopCodonRecognition2001: % ? unused Journal abbr (“EMBO Rep.”)

@article{keulenInitialAppearance184Ile1997, title = {Initial Appearance of the {{184Ile}} Variant in Lamivudine-Treated Patients Is Caused by the Mutational Bias of Human Immunodeficiency Virus Type 1 Reverse Transcriptase}, author = {Keulen, W. and Back, N.K. and {}{van Wijk}, A. and Boucher, C.A. and Berkhout, B.}, year = 1997, month = apr, journal = {Journal of Virology}, volume = {71}, number = {4}, pages = {3346–3350}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.71.4.3346-3350.1997}, url = {http://jvi.asm.org/cgi/content/abstract/71/4/3346}, keywords = {Codon,drugs,enzyme,gene,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,In Vitro,IN-VITRO,initiation,Mutation,nosource,virus} }

@article{kewSubunitselectiveMutagenesisGlu891994, title = {Subunit-Selective Mutagenesis of {{Glu-89}} Residue in Human Immunodeficiency Virus Reverse Transcriptase. {{Contribution}} of P66 and P51 Subunits to Nucleoside Analog Sensitivity, Divalent Cation Preference, and Steady State Kinetic Properties.}, author = {Kew, Y. and Qingbin, S. and Prasad, V.R.}, year = 1994, month = may, journal = {Journal of Biological Chemistry}, volume = {269}, number = {21}, pages = {15331–15336}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(17)36610-3}, url = {http://www.jbc.org/content/269/21/15331.short}, keywords = {analysis,enzyme,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,Magnesium,Mutagenesis,nosource,SUBUNIT,virus} }

@article{khaitovichEffectAntibioticsLarge1999a, title = {Effect of Antibiotics on Large Ribosomal Subunit Assembly Reveals Possible Function of 5 {{S rRNA}}}, author = {Khaitovich, P. and Mankin, A.S.}, year = 1999, journal = {J.Mol.Biol.}, volume = {291}, number = {5}, pages = {1025–1034}, doi = {10.1006/jmbi.1999.3030}, abstract = {Functional large ribosomal subunits of Thermus aquaticus can be reconstituted from ribosomal proteins and either natural or in vitro transcribed 23 S and 5 S rRNA. Omission of 5 S rRNA during subunit reconstitution results in dramatic decrease of the peptidyl transferase activity of the assembled subunits. However, the presence of some ribosome-targeted antibiotics of the macrolide, ketolide or streptogramin B groups during 50 S subunit reconstitution can partly restore the activity of ribosomal subunits assembled without 5 S rRNA. Among tested antibiotics, macrolide RU69874 was the most active: activity of the subunits assembled in the absence of 5 S rRNA was increased more than 30-fold if antibiotic was present during reconstitution procedure. Activity of the subunits assembled with 5 S rRNA was also slightly stimulated by RU69874, but to a much lesser extent, approximately 1.5-fold. Activity of the native T. aquaticus 50 S subunits incubated in the reconstitution conditions in the presence of RU69874 was, in contrast, slightly decreased. The presence of antibiotics was essential during the last incubation step of the in vitro assembly, indicating that drugs affect one of the last assembly steps. The 5 S rRNA was previously shown to form contacts with segments of domains II and V of 23 S rRNA. All the antibiotics which can functionally compensate for the lack of 5 S rRNA during subunit reconstitution interact simultaneously with the central loop in domain V (which is known to be a component of peptidyl transferase center) and a loop of the helix 35 in domain II of 23 S rRNA. It is proposed that simultaneous interaction of 5 S rRNA or of antibiotics with the two domains of 23 S rRNA is essential for the successful assembly of ribosomal peptidyl transferase center. Consequently, one of the functions of 5 S rRNA in the ribosome can be that of assisting the assembly of ribosomal peptidyl transferase by correctly positioning functionally important segments of domains II and V of 23 S rRNA}, keywords = {99448385,analysis,antibiotic,antibiotics,assembly,Bacterial Proteins,Binding Sites,Catalysis,Catalytic Domain,CentrifugationDensity Gradient,chemistry,COMPONENT,drug effects,Drug ResistanceMicrobial,drugs,ElectrophoresisGelTwo-Dimensional,enzymology,genetics,In Vitro,IN-VITRO,Macrolides,metabolism,Mutation,nosource,Nucleic Acid Conformation,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,Peptidyltransferase,pharmacology,protein,Proteins,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,RNABacterial,RNARibosomal23S,RNARibosomal5S,rRNA,SUBUNIT,supportu.s.gov’tp.h.s.,Thermus} } % == BibTeX quality report for khaitovichEffectAntibioticsLarge1999a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{khaitovichCharacterizationFunctionallyActive1999, title = {Characterization of Functionally Active Subribosomal Particles from {{Thermus}} Aquaticus}, author = {Khaitovich, P. and Mankin, A.S. and Green, R. and Lancaster, L. and Noller, H.F.}, year = 1999, month = jan, journal = {Proceedings of the National Academy of Sciences}, volume = {96}, number = {1}, pages = {85–90}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.96.1.85}, url = {http://www.pnas.org/content/96/1/85.short}, abstract = {Peptidyl transferase activity of Thermus aquaticus ribosomes is resistant to the removal of a significant number of ribosomal proteins by protease digestion, SDS, and phenol extraction. To define the upper limit for the number of macromolecular components required for peptidyl transferase, particles obtained by extraction of T. aquaticus large ribosomal subunits were isolated and their RNA and protein composition was characterized. Active subribosomal particles contained both 23S and 5S rRNA associated with notable amounts of eight ribosomal proteins. N- terminal sequencing of the proteins identified them as L2, L3, L13, L15, L17, L18, L21, and L22. Ribosomal protein L4, which previously was thought to be essential for the reconstitution of particles active in peptide bond formation, was not found. These findings, together with the results of previous reconstitution experiments, reduce the number of possible essential macromolecular components of the peptidyl transferase center to 23S rRNA and ribosomal proteins L2 and L3. Complete removal of ribosomal proteins from T. aquaticus rRNA resulted in loss of tertiary folding of the particles and inactivation of peptidyl transferase. The accessibility of proteins in active subribosomal particles to proteinase hydrolysis was increased significantly after RNase treatment. These results and the observation that 50S ribosomal subunits exhibited much higher resistance to SDS extraction than 30S subunits are compatible with a proposed structural organization of the 50S subunit involving an RNA “cage” surrounding a core of a subset of ribosomal proteins}, keywords = {0,5S rRNA,chemistry,COMPONENT,Hydrolysis,isolation & purification,L2,L3,La,metabolism,nosource,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,Peptidyltransferase,protein,Proteins,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNARibosomal23S,RNARibosomal5S,RNAse,rRNA,Sequence Analysis,Sequence HomologyAmino Acid,Structural,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Thermus} } % == BibTeX quality report for khaitovichCharacterizationFunctionallyActive1999: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{khaitovichPeptidylTransferaseActivity1999, title = {Peptidyl Transferase Activity Catalyzed by Protein-Free {{23S}} Ribosomal {{RNA}} Remains Elusive.}, author = {Khaitovich, P. and Tenson, T. and Mankin, A.S. and Green, R.}, year = 1999, month = may, journal = {RNA}, volume = {5}, number = {5}, pages = {605–608}, publisher = {Cold Spring Harbor Laboratory Press}, doi = {10.1017/S1355838299990295}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1369786/}, keywords = {BOND FORMATION,nosource,peptide bond formation,peptidyl transferase,PEPTIDYL-TRANSFERASE,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Rna,RNA catalysis,rRNA,S,SITES} }

@article{khajaviNonsensemediatedMRNADecay2006, title = {Nonsense-Mediated {{mRNA}} Decay Modulates Clinical Outcome of Genetic Disease}, author = {Khajavi, M. and Inoue, K. and Lupski, J.R.}, year = 2006, month = oct, journal = {European journal of human genetics}, volume = {14}, number = {10}, pages = {1074–1081}, publisher = {Nature Publishing Group}, doi = {10.1038/sj.ejhg.5201649}, url = {http://www.nature.com/ejhg/journal/v14/n10/abs/5201649a.html}, abstract = {The nonsense-mediated decay (NMD) pathway is an mRNA surveillance system that typically degrades transcripts containing premature termination codons (PTCs) in order to prevent translation of unnecessary or aberrant transcripts. Failure to eliminate these mRNAs with PTCs may result in the synthesis of abnormal proteins that can be toxic to cells through dominant-negative or gain-of-function effects. Recent studies have expanded our understanding of the mechanism by which nonsense transcripts are recognized and targeted for decay. Here, we review the physiological role of this surveillance pathway, its implications for human diseases, and why knowledge of NMD is important to an understanding of genotype-phenotype correlations in various genetic disorders.European Journal of Human Genetics (2006) 14, 1074-1081. doi:10.1038/sj.ejhg.5201649; published online 7 June 2006}, keywords = {CELLS,Codon,CODONS,DECAY,disease,Genetic,genetics,human,La,MECHANISM,mRNA,mRNA decay,NMD,NONSENSE,nonsense-mediated decay,nonsense-mediated mRNA decay,nosource,PATHWAY,PREMATURE TERMINATION CODON,protein,Proteins,Review,SURVEILLANCE,SYSTEM,termination,TERMINATION CODON,TERMINATION-CODON,TRANSCRIPT,translation} } % == BibTeX quality report for khajaviNonsensemediatedMRNADecay2006: % ? unused Journal abbr (“Eur.J.Hum.Genet.”)

@article{kieftMechanismRibosomeRecruitment2001, title = {Mechanism of Ribosome Recruitment by Hepatitis {{C IRES RNA}}.}, author = {Kieft, J.S. and Zhou, K. and Jubin, R. and Doudna, J.A.}, year = 2001, month = feb, journal = {RNA}, volume = {7}, number = {2}, pages = {194–206}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838201001790}, url = {http://rnajournal.cshlp.org/content/7/2/194.short}, abstract = {Many viruses and certain cellular mRNAs initiate protein synthesis from a highly structured RNA sequence in the 5’ untranslated region, called the internal ribosome entry site (IRES). In hepatitis C virus (HCV), the IRES RNA functionally replaces several large initiation factor proteins by directly recruiting the 43S particle. Using quantitative binding assays, modification interference of binding, and chemical and enzymatic footprinting experiments, we show that three independently folded tertiary structural domains in the IRES RNA make intimate contacts to two purified components of the 43S particle: the 40S ribosomal subunit and eukaryotic initiation factor 3 (eIF3). We measure the affinity and demonstrate the specificity of these interactions for the first time and show that the high affinity interaction of IRES RNA with the 40S subunit drives formation of the IRES RNA-40S-eIF3 ternary complex. Thus, the HCV IRES RNA recruits 43S particles in a mode distinct from both eukaryotic cap-dependent and prokaryotic ribosome recruitment strategies, and is architecturally and functionally unique from other large folded RNAs that have been characterized to date}, keywords = {0,ACID,analysis,Animals,assays,Base Sequence,BINDING,Catalytic Domain,chemistry,Codon,CodonInitiator,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,Dna,DNA Primers,DOMAIN,DOMAINS,eIF3,Eukaryotic Initiation Factor-3,genetics,Hepacivirus,HEPATITIS-C,initiation,INITIATION-FACTOR,INTERNAL RIBOSOME ENTRY,La,MECHANISM,metabolism,modification,Molecular Sequence Data,mRNA,nosource,Nucleic Acid Conformation,PARTICLES,Peptide Initiation Factors,Phosphates,Point Mutation,Polioviruses,Polymerase Chain Reaction,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Rabbits,RECRUITMENT,REGION,Reticulocytes,ribonuclease t1,RIBOSOMAL-SUBUNIT,ribosome,RIBOSOME ENTRY SITE,Ribosomes,Rna,RNAMessenger,RnaViral,sequence,SITE,SPECIFICITY,Structural,SUBUNIT,TranscriptionGenetic,Triple filter assay,virus,Viruses} }

@article{kiernanHIV1TatTranscriptional1999, title = {{{HIV-1}} Tat Transcriptional Activity Is Regulated by Acetylation.}, author = {Kiernan, R.E. and Vanhulle, C. and Schiltz, L. and Adam, E. and Xiao, H. and Maudoux, F. and Calomme, C. and Burny, A. and Nakatani, Y. and Jeang, K.T. and Benkirane, M. and Van Lint, C.}, year = 1999, month = nov, journal = {The EMBO journal}, volume = {18}, number = {21}, pages = {6106–6118}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/18.21.6106}, url = {http://www.nature.com/emboj/journal/v18/n21/abs/7592013a.html}, abstract = {The human immunodeficiency virus (HIV) trans- activator protein, Tat, stimulates transcription from the viral long-terminal repeats (LTR) through an RNA hairpin element, trans-activation responsive region (TAR). We and others have shown that trans-activator protein (Tat)- associated histone acetyltransferases (TAHs), p300 and p300/CBP- associating factor (PCAF), assist functionally in the activation of chromosomally integrated HIV-1 LTR. Here, we show that p300 and PCAF also directly acetylate Tat. We defined two sites of acetylation located in different functional domains of Tat. p300 acetylated Lys50 in the TAR RNA binding domain, while PCAF acetylated Lys28 in the activation domain of Tat. In support of a functional role for acetylation in vivo, histone deacetylase inhibitor (trichostatin A) synergized with Tat in transcriptional activation of the HIV-1 LTR. Synergism was TAR-dependent and required the intact presence of both Lys28 and Lys50. Mechanistically, acetylation at Lys28 by PCAF enhanced Tat binding to the Tat-associated kinase, CDK9/P-TEFb, while acetylation by p300 at Lys50 of Tat promoted the dissociation of Tat from TAR RNA that occurs during early transcription elongation. These data suggest that acetylation of Tat regulates two discrete and functionally critical steps in transcription, binding to an RNAP II CTD- kinase and release of Tat from TAR RNA}, keywords = {20012920,Acetylation,Acetyltransferases,activation,BINDING,elongation,gene,Histone Deacetylase,HIV,Hiv-1,HIV-1 TAT,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,IN-VIVO,kinase,nosource,protein,Rna,RPD3,Support,TAR RNA,transcription,virus} } % == BibTeX quality report for kiernanHIV1TatTranscriptional1999: % ? unused Journal abbr (“EMBO J.”)

@article{kiledjianPosttranscriptionalRegulationHuman1991, title = {Post-Transcriptional Regulation of the Human Liver/Bone/Kidney Alkaline Phosphatase Gene.}, author = {Kiledjian, M. and Kadesch, T.}, year = 1991, journal = {Journal of Biological Chemistry}, volume = {266}, number = {7}, pages = {4207–4213}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(20)64308-3}, url = {http://www.jbc.org/content/266/7/4207.short}, keywords = {gene,human,Methods,nosource,post-transcriptional regulation,regulation,RNAse,RNAse protection} } % == BibTeX quality report for kiledjianPosttranscriptionalRegulationHuman1991: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{kimBasepairing23SRRNA1999, title = {Base-Pairing between {{23S rRNA}} and {{tRNA}} in the Ribosomal {{A}} Site}, author = {Kim, D.F. and Green, R.}, year = 1999, month = nov, journal = {Molecular cell}, volume = {4}, number = {5}, pages = {859–864}, publisher = {Elsevier}, doi = {10.1016/S1097-2765(00)80395-0}, url = {http://linkinghub.elsevier.com/retrieve/pii/s1097-2765(00)80395-0}, abstract = {The aminoacyl (A site) tRNA analog 4-thio-dT-p-C-p-puromycin (s4TCPm) photochemically cross-links with high efficiency and specificity to G2553 of 23S rRNA and is peptidyl transferase reactive in its cross- linked state, establishing proximity between the highly conserved 2555 loop in domain V of 23S rRNA and the universally conserved CCA end of tRNA. To test for base-pairing interactions between 23S rRNA and aminoacyl tRNA, site-directed mutations were made at the universally conserved nucleotides U2552 and G2553 of 23S rRNA in both E. coli and B. stearothermophilus ribosomal RNA and incorporated into ribosomes. Mutations at G2553 resulted in dominant growth defects in E. coli and in decreased levels of peptidyl transferase activity in vitro. Genetic analysis in vitro of U2552 and G2553 mutant ribosomes and CCA end mutant tRNA substrates identified a base-pairing interaction between C75 of aminoacyl tRNA and G2553 of 23S rRNA}, keywords = {0,2-Aminopurine,A-SITE,analogs & derivatives,analysis,Bacillus stearothermophilus,Base Pairing,Binding Sites,chemistry,Conserved Sequence,efficiency,enzymology,Escherichia coli,GenesBacterial,Genetic,genetics,growth & development,Hydrogen Bonding,In Vitro,IN-VITRO,Kinetics,La,metabolism,MutagenesisSite-Directed,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Nucleotides,peptidyl transferase,Peptidyltransferase,Puromycin,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNARibosomal23S,RNATransferAmino Acyl,rRNA,supportnon-u.s.gov’t,SuppressionGenetic,tRNA} } % == BibTeX quality report for kimBasepairing23SRRNA1999: % ? unused Journal abbr (“Mol.Cell”)

@article{kimAnalysisActiveSite2001a, title = {Analysis of the Active Site of the Ribosome by Site-Directed Mutagenesis}, author = {Kim, D.F. and Semrad, K. and Green, R.}, year = 2001, journal = {Cold Spring Harb.Symp.Quant.Biol}, volume = {66}, pages = {119–126}, doi = {10.1101/sqb.2001.66.119}, url = {PM:12762014}, keywords = {0,ACTIVE-SITE,Amino Acid Substitution,analysis,Bacillus stearothermophilus,Bacterial,Bacterial Proteins,chemistry,CrystallographyX-Ray,enzymology,Escherichia coli,genetics,La,metabolism,Mutagenesis,MutagenesisSite-Directed,nosource,peptidyl transferase,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,protein,Proteins,Recombinant Proteins,Review,ribosome,Ribosomes,Rna,RNARibosomal23S,SITE,Support,Transferases} } % == BibTeX quality report for kimAnalysisActiveSite2001a: % ? Possibly abbreviated journal title Cold Spring Harb.Symp.Quant.Biol

@article{kimExpressionGenesEncoding2005a, title = {Expression of Genes Encoding Innate Host Defense Molecules in Normal Human Monocytes in Response to {{Candida}} Albicans}, author = {Kim, H.S. and Choi, E.H. and Khan, J. and Roilides, E. and Francesconi, A. and Kasai, M. and Sein, T. and Schaufele, R.L. and Sakurai, K. and Son, C.G. and Greer, B.T. and Chanock, S. and Lyman, C.A. and Walsh, T.J.}, year = 2005, month = jun, journal = {Infect.Immun.}, volume = {73}, number = {6}, pages = {3714–3724}, doi = {10.1128/IAI.73.6.3714-3724.2005}, url = {PM:15908401}, abstract = {Little is known about the regulation and coordinated expression of genes involved in the innate host response to Candida albicans. We therefore examined the kinetic profile of gene expression of innate host defense molecules in normal human monocytes infected with C. albicans using microarray technology. Freshly isolated peripheral blood monocytes from five healthy donors were incubated with C. albicans for 0 to 18 h in parallel with time-matched uninfected control cells. RNA from monocytes was extracted and amplified for microarray analysis, using a 42,421-gene cDNA chip. Expression of genes encoding proinflammatory cytokines, including tumor necrosis factor alpha, interleukin 1 (IL-1), IL-6, and leukemia inhibitory factor, was markedly enhanced during the first 6 h and coincided with an increase in phagocytosis. Expression of these genes returned to near baseline by 18 h. Genes encoding chemokines, including IL-8; macrophage inflammatory proteins 1, 3, and 4; and monocyte chemoattractant protein 1, also were strongly up-regulated, with peak expression at 4 to 6 h, as were genes encoding chemokine receptors CCR1, CCR5, CCR7, and CXCR5. Expression of genes whose products may protect monocyte viability, such as BCL2-related protein, metallothioneins, CD71, and SOCS3, was up-regulated at 4 to 6 h and remained elevated throughout the 18-h time course. On the other hand, expression of genes encoding T-cell-regulatory molecules (e.g., IL-12, gamma interferon, and transforming growth factor beta) was not significantly affected during the 18-h incubation. Moreover, genes encoding IL-15, the IL-13 receptor (IL-13Ra1), and CD14 were suppressed during the 18-h exposure to C. albicans. Thus, C. albicans is a potent inducer of a dynamic cascade of expression of genes whose products are related to the recruitment, activation, and protection of neutrophils and monocytes}, keywords = {0,3,activation,analysis,ANTIGEN,AntigensCD,AntigensCD31,AntigensDifferentiationB-Lymphocyte,blood,cancer,Candida albicans,CCR5,CELLS,Chemokines,Cytokines,expression,gene,Gene Expression,Gene Expression Profiling,GENE-EXPRESSION,Genes,genetics,GROWTH,GROWTH-FACTOR,human,Humans,immunology,Interleukin-12,Interleukin-15,Interleukin-23,Interleukin-23 Subunit p19,Interleukins,La,LEUKEMIA,metabolism,metallothionein,Monocytes,nosource,PRODUCT,PRODUCTS,PROTECTION,protein,Proteins,ReceptorsChemokine,ReceptorsTransferrin,RECRUITMENT,regulation,Rna,SUBUNIT,Transforming Growth Factor beta,Tumor Necrosis Factor-alpha} } % == BibTeX quality report for kimExpressionGenesEncoding2005a: % ? Possibly abbreviated journal title Infect.Immun.

@article{kimIdentificationAnalysisSite1994a, title = {Identification and {{Analysis}} of the {{Site}} of -1 {{Ribosomal Frameshifting}} in {{Red-Clover Necrotic Mosaic-Virus}}}, author = {Kim, K.H. and Lommel, S.A.}, year = 1994, month = may, journal = {Virology}, volume = {200}, number = {2}, pages = {574–582}, doi = {10.1006/viro.1994.1220}, url = {ISI:A1994NG52300025}, abstract = {The genomic RNA-1 of red clover necrotic mosaic dianthovirus (RCNMV) contains the heptanucleotide GGAUUUU that precedes the termination codon of the 5’ proximal p27 open reading frame (ORF). This heptanucleotide is followed by a sequence with the potential to form a stable, complex secondary structure. Translation of RNA-1 is postulated to utilize a -1 ribosomal frameshifting mechanism to express the 88-kDa viral RNA polymerase. Using site-directed mutagenesis together with cell-free translation to monitor frameshifting and a biological assay of the mutants in plants, we establish the role of the GGAUUUU as the site where -1 ribosomal frameshifting occurs. The frameshifting signal sequence conforms to the simultaneous slippage model. Stop codons flanking the shifty signal are not required for frameshifting but the p27 ORF termination codon is necessary for maintaining optimal infectivity of the virus. Mutations abolishing the RCNMV RNA-1 internal p57 ORF initiation codon did not affect infectivity of the virus, suggesting that this cistron is only expressed in vivo as an 88-kDa ribosomal frameshifting product. Shifty heptanucleotide signals from a number of animal retroviruses and RNA plant viruses facilitate RCNMV frameshifting in vitro. However, only a limited number of the heterologous shifty heptanucleotides were functional in plant cells. We suggest that specific shifty tRNA populations in the cell facilitate viral -1 ribosomal frameshifting. This analysis also suggests that the slippery sequence requirements are not identical in mammalian and in plant systems. (C) 1944 Academic Press, Inc}, keywords = {analysis,animal,BOVINE LEUKEMIA-VIRUS,CELL-FREE TRANSLATION,CELLS,Codon,CODONS,COMPLETE NUCLEOTIDE-SEQUENCE,COMPLEX,COMPLEXES,DROSOPHILA-MELANOGASTER,FORM,FRAME,Frameshifting,genomic,IDENTIFICATION,IMMUNODEFICIENCY-VIRUS,In Vitro,IN-VITRO,IN-VIVO,INFECTIOUS TRANSCRIPTS,initiation,MAMMARY-TUMOR VIRUS,MECHANISM,MODEL,MOSAIC-VIRUS,Mutagenesis,MUTANTS,Mutation,MUTATIONS,nosource,OPEN READING FRAME,Plants,polymerase,READING FRAME,RETROVIRUSES,REVERSE-TRANSCRIPTASE,ribosomal frameshifting,Rna,RNA PSEUDOKNOT,RNA-POLYMERASE,ROUS-SARCOMA VIRUS,SECONDARY STRUCTURE,sequence,SIGNAL,SITE,SLIPPAGE,STOP CODON,structure,SYNTHESIZED INVITRO,SYSTEM,SYSTEMS,termination,TERMINATION CODON,TERMINATION-CODON,translation,tRNA,VIRAL-RNA,virus} } % == BibTeX quality report for kimIdentificationAnalysisSite1994a: % ? Title looks like it was stored in title-case in Zotero

@article{kimSequenceElementRequired1998a, title = {Sequence {{Element Required}} for {{Efficient}} -1 {{Ribosomal Frameshifting}} in {{Red Clover Necrotic Mosaic Dianthovirus}}}, author = {Kim, K.H. and Lommel, S.A.}, year = 1998, month = oct, journal = {Virology}, volume = {250}, number = {1}, pages = {50–59}, doi = {10.1006/viro.1998.9358}, abstract = {The RNA-1 of the bipartite red clover necrotic mosaic dianthovirus (RCNMV) genome encodes the 88-kDa polymerase. The polymerase is translated from both 5’ proximal and internal open reading frames by a - 1 ribosomal frameshifting event. A shifty heptanucleotide conforming to the simultaneous slippage model is identified, and a downstream stem- loop structure and atypical pseudoknot are predicted. A beta- glucuronidase reporter assay identified a 118-nucleotide element containing both the shifty heptanucleotide and the predicted secondary structures that were required for efficient -1 ribosomal frameshift expression in vivo. A series of site-directed and compensatory mutations affecting the base-paired regions of the predicted secondary structure were introduced into a RCNMV RNA-1 cDNA clone from which infectious transcripts were derived. Mutations that destroyed the predicted pseudoknot had no effect on frameshifting efficiency in vitro or infectivity of the virus, whereas mutations destabilizing the stem- loop structure abolished both ribosomal frameshifting in vitro and biological activity. These results demonstrate the essential role of a predicted secondary structure that does not involve a pseudoknot in the expression of the RCNMV polymerase by ribosomal frameshifting. Copyright 1998 Academic Press}, keywords = {efficiency,expression,frameshift,Frameshifting,Genome,In Vitro,IN-VITRO,IN-VIVO,Mutation,MUTATIONS,nosource,Open Reading Frames,pathology,polymerase,pseudoknot,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,sequence,SLIPPAGE,structure,virus} } % == BibTeX quality report for kimSequenceElementRequired1998a: % ? Title looks like it was stored in title-case in Zotero

@article{kimRoleNonsensemediatedDecay2001, title = {Role of the Nonsense-Mediated Decay Factor {{hUpf3}} in the Splicing-Dependent Exon-Exon Junction Complex}, author = {Kim, V.N. and Kataoka, N. and Dreyfuss, G.}, year = 2001, journal = {Science}, volume = {293}, number = {5536}, pages = {1832–1836}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1062829}, url = {http://www.sciencemag.org/content/293/5536/1832.short}, abstract = {Nonsense-mediated messenger RNA (mRNA) decay, or NMD, is a critical process of selective degradation of mRNAs that contain premature stop codons. NMD depends on both pre-mRNA splicing and translation, and it requires recognition of the position of stop codons relative to exon-exon junctions. A key factor in NMD is hUpf3, a mostly nuclear protein that shuttles between the nucleus and cytoplasm and interacts specifically with spliced mRNAs. We found that hUpf3 interacts with Y14, a component of post-splicing mRNA-protein (mRNP) complexes, and that hUpf3 is enriched in Y14-containing mRNP complexes. The mRNA export factors Aly/REF and TAP are also associated with nuclear hUpf3, indicating that hUpf3 is in mRNP complexes that are poised for nuclear export. Like Y14 and Aly/REF, hUpf3 binds to spliced mRNAs specifically ( approximately 20 nucleotides) upstream of exon-exon junctions. The splicing-dependent binding of hUpf3 to mRNAs before export, as part of the complex that assembles near exon-exon junctions, allows it to serve as a link between splicing and NMD in the cytoplasm}, keywords = {0,3,3’ Untranslated Regions,Active TransportCell Nucleus,BINDING,BINDING MOTIF,Cell Line,CEREVISIAE,chemistry,Codon,CodonNonsense,CODONS,COMPLEX,COMPLEXES,COMPONENT,Cytoplasm,DECAY,degradation,DNA-BINDING,DNA-Binding Proteins,EXON-EXON JUNCTIONS,Exons,Fungal Proteins,FUSION PROTEIN,genetics,Globin,Globins,human,La,Macromolecular Systems,MESSENGER-RNA,metabolism,ModelsBiological,mRNA,NMD,NONSENSE,nonsense-mediated decay,nosource,Nucleotides,POSITION,Precipitin Tests,protein,Protein Binding,Proteins,RECOGNITION,Recombinant Fusion Proteins,REGION,REQUIRES,RIBONUCLEOPROTEIN,Ribonucleoproteins,Rna,RNA Splicing,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAMessenger,S,S-CEREVISIAE,splicing,STOP CODON,Substrate Specificity,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,SYSTEMS,translation,Untranslated Regions,UPF3,UPSTREAM} }

@article{kimTwoEvolutionarilyDivergent1990, title = {Two Evolutionarily Divergent Genes Encode a Cytoplasmic Ribosomal Protein of {{Arabidopsis}} Thaliana}, author = {Kim, Y. and Zhang, H. and Scholl, R.L.}, year = 1990, journal = {Gene}, volume = {93}, number = {2}, pages = {177–182}, publisher = {Elsevier}, doi = {10.1016/0378-1119(90)90222-D}, url = {http://linkinghub.elsevier.com/retrieve/pii/037811199090222D}, abstract = {Two clones of Arabidopsis thaliana possessing high sequence identity to the yeast gene encoding ribosomal (r) protein L3 were isolated by heterologous DNA hybridization. The coding regions of these two clones have approx. 63% amino acid (aa) sequence identity to the yeast L3 r-protein and 85% aa sequence identity to each other. Both genes are expressed in shoots. The presence of two divergent genes in A. thaliana raises the possibility that the gene products participate in the formation of functionally distinct ribosomes}, keywords = {Dna,gene,Genes,L3,nosource,PAP,protein,ribosome,Ribosomes,sequence,yeast} }

@article{kimSpecificMutationsViral1999, title = {Specific Mutations in a Viral {{RNA}} Pseudoknot Drastically Change Ribosomal Frameshifting Efficiency.}, author = {Kim, Y.G. and Su, L. and Maas, S. and O’Neill, A. and Rich, A.}, year = 1999, month = dec, journal = {Proceedings of the National Academy of Sciences}, volume = {96}, number = {25}, pages = {14234–14239}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.96.25.14234}, url = {http://www.pnas.org/content/96/25/14234.short}, abstract = {Many viruses regulate protein synthesis by -1 ribosomal frameshifting using an RNA pseudoknot. Frameshifting is vital for viral reproduction. Using the information gained from the recent high-resolution crystal structure of the beet western yellow virus pseudoknot, a systematic mutational analysis has been carried out in vitro and in vivo. We find that specific nucleotide tertiary interactions at the junction between the two stems of the pseudoknot are crucial. A triplex is found between stem 1 and loop 2, and triplex interactions are required for frameshifting function. For some mutations, loss of one hydrogen bond is sufficient to abolish frameshifting. Furthermore, mutations near the 5’ end of the pseudoknot can increase frameshifting by nearly 300%, possibly by modifying ribosomal contacts. It is likely that the selection of suitable mutations can thus allow viruses to adjust frameshifting efficiencies and thereby regulate protein synthesis in response to environmental change}, keywords = {20056228,analysis,CellsCultured,chemistry,efficiency,Frameshifting,Hydrogen Bonding,In Vitro,IN-VITRO,IN-VIVO,Mutation,MUTATIONAL ANALYSIS,MUTATIONS,nosource,Nucleic Acid Conformation,physiology,protein,protein synthesis,PROTEIN-SYNTHESIS,pseudoknot,ribosomal frameshifting,Ribosomes,Rna,RNA PSEUDOKNOT,RnaViral,structure,Structure-Activity Relationship,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,virus} } % == BibTeX quality report for kimSpecificMutationsViral1999: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.USA”)

@article{kimMutationalStudyReveals2000, title = {Mutational Study Reveals That Tertiary Interactions Are Conserved in Ribosomal Frameshifting Pseudoknots of Two Luteoviruses.}, author = {Kim, Y.G. and Maas, S. and Wang, S.C. and Rich, A.}, year = 2000, journal = {RNA.}, volume = {6}, number = {8}, pages = {1157–1165}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838200000510}, url = {http://rnajournal.cshlp.org/content/6/8/1157.short}, abstract = {Expression of the putative replicase of potato leafroll virus (PLRV) is regulated by -1 ribosomal frameshifting in which a primary viral transcript has two overlapping open reading frames (ORFs). A region of 39 nt at the junction of the two ORFs is essential for frameshifting to occur. It has been shown to harbor two signals, one active on the level of the primary structure, termed the slippery sequence, and one component that forms a secondary or tertiary level structure, described as either a pseudoknot or a stem-loop motif. We have performed extensive site-directed mutagenesis of the frameshifting region and analyzed individual mutants for their ability to promote -1 frameshifting in vitro. Detailed comparison of our results with analogous mutants in the frameshifting region of the evolutionarily related beet western yellow virus, for which a crystal structure is available, unequivocally argues for the pseudoknot to be the structural motif necessary for the frameshifting function in PLRV transcripts. Mutations in PLRV that affect putative pseudoknot-specific tertiary-base interactions drastically affect frameshifting activity. In addition, a specific deletion mutant was identified that displayed PLRV wild-type frameshifting activity with only 22 nt available for pseudoknot formation}, keywords = {Base Sequence,chemistry,COMPONENT,ElectrophoresisPolyacrylamide Gel,expression,Frameshifting,Gene Deletion,genetics,Glutathione Transferase,In Vitro,IN-VITRO,Luminescent Proteins,Luteovirus,metabolism,Molecular Sequence Data,Mutagenesis,MutagenesisSite-Directed,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Open Reading Frames,Plasmids,pseudoknot,ribosomal frameshifting,RnaViral,sequence,SIGNAL,Structural,structure,TranslationGenetic,virus} } % == BibTeX quality report for kimMutationalStudyReveals2000: % ? Possibly abbreviated journal title RNA.

@article{kimComparativeMutationalAnalysis2001, title = {Comparative Mutational Analysis of Cis-Acting {{RNA}} Signals for Translational Frameshifting in {{HIV-1}} and {{HTLV-2}}}, author = {Kim, Y.G. and Maas, S. and Rich, A.}, year = 2001, month = mar, journal = {Nucleic acids research}, volume = {29}, number = {5}, pages = {1125–1131}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/29.5.1125}, url = {http://nar.oxfordjournals.org/content/29/5/1125.short}, abstract = {Human immunodeficiency virus type 1 (HIV-1) and human T cell leukemia virus type II (HTLV-2) use a similar mechanism for -1 translational frameshifting to overcome the termination codon in viral RNA at the end of the gag gene. Previous studies have identified two important RNA signals for frameshifting, the slippery sequence and a downstream stem-loop structure. However, there have been somewhat conflicting reports concerning the individual contributions of these sequences. In this study we have performed a comprehensive mutational analysis of the cis-acting RNA sequences involved in HIV-1 gag-pol and HTLV-2 gag-pro frameshifting. Using an in vitro translation system we determined frameshifting efficiencies for shuffled HIV-1/HTLV-2 RNA elements in a background of HIV-1 or HTLV-2 sequences. We show that the ability of the slippery sequence and stem-loop to promote ribosomal frameshifting is influenced by the flanking upstream sequence and the nucleotides in the spacer element. A wide range of frameshift efficiency rates was observed for both viruses when shuffling single sequence elements. The results for HIV-1/HTLV-2 chimeric constructs represent strong evidence supporting the notion that the viral wild-type sequences are not designed for maximal frameshifting activity but are optimized to a level suited to efficient viral replication}, keywords = {0,analysis,Base Sequence,BIOLOGY,chemistry,Codon,Comparative Study,DOWNSTREAM,efficiency,ELEMENTS,frameshift,Frameshifting,FrameshiftingRibosomal,FUSION PROTEIN,Gag,Gag-pol,gene,genetics,Glutathione,Glutathione Transferase,GREEN FLUORESCENT PROTEIN,Green Fluorescent Proteins,Hiv-1,human,Human T-lymphotropic virus 2,HUMAN-IMMUNODEFICIENCY-VIRUS,Humans,IMMUNODEFICIENCY-VIRUS,In Vitro,in vitro translation,IN-VITRO,La,LEUKEMIA,Luminescent Proteins,MECHANISM,metabolism,Mutation,MUTATIONAL ANALYSIS,nosource,Nucleic Acid Conformation,Nucleotides,physiology,protein,Protein Biosynthesis,Proteins,Recombinant Fusion Proteins,REPLICATION,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,ribosomal frameshifting,Rna,RnaViral,sequence,SEQUENCES,SIGNAL,Signal Transduction,STEM-LOOP,structure,SYSTEM,T,termination,TERMINATION CODON,TERMINATION-CODON,translation,TRANSLATIONAL FRAMESHIFTING,TYPE-1,UPSTREAM,VIRAL-RNA,virus,Viruses,WILD-TYPE} } % == BibTeX quality report for kimComparativeMutationalAnalysis2001: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{kimMammalianStaufen1Recruits2005, title = {Mammalian {{Staufen1}} Recruits {{Upf1}} to Specific {{mRNA}} 3’{{UTRs}} so as to Elicit {{mRNA}} Decay}, author = {Kim, Y.K. and Furic, L. and Desgroseillers, L. and Maquat, L.E.}, year = 2005, month = jan, journal = {Cell}, volume = {120}, number = {2}, pages = {195–208}, publisher = {Elsevier}, doi = {10.1016/j.cell.2004.11.050}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867404011572}, abstract = {Mammalian Staufen (Stau)1 is an RNA binding protein that is thought to function in mRNA transport and translational control. Nonsense-mediated mRNA decay (NMD) degrades abnormal and natural mRNAs that terminate translation sufficiently upstream of a splicing-generated exon-exon junction. Here we describe an mRNA decay mechanism that involves Stau1, the NMD factor Upf1, and a termination codon. Unlike NMD, this mechanism does not involve pre-mRNA splicing and occurs when Upf2 or Upf3X is downregulated. Stau1 binds directly to Upf1 and elicits mRNA decay when tethered downstream of a termination codon. Stau1 also interacts with the 3’-untranslated region of ADP-ribosylation factor (Arf)1 mRNA. Accordingly, downregulating either Stau1 or Upf1 increases Arf1 mRNA stability. These findings suggest that Arf1 mRNA is a natural target for Stau1-mediated decay, and data indicate that other mRNAs are also natural targets. We discuss this pathway as a means for cells to downregulate the expression of Stau1 binding transcripts}, keywords = {0,3,3’ UNTRANSLATED REGION,3’ Untranslated Regions,3’-UNTRANSLATED REGION,ADP-Ribosylation Factor 1,Animals,BINDING,BINDING PROTEIN,BINDING-PROTEIN,Biochemistry,CELLS,Cells-Cultured,CellsCultured,Codon,Codon-Terminator,CodonTerminator,DECAY,DOWNSTREAM,Exons,expression,genetics,Hela Cells,human,Humans,La,MECHANISM,metabolism,Mice,mRNA,mRNA decay,mRNA stability,NMD,nonsense-mediated mRNA decay,nosource,PATHWAY,protein,Proteins,REGION,Research Support-Non-U.S.Gov’t,Research Support-U.S.Gov’t-P.H.S.,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,Rna,RNA Splicing,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNA-Messenger,RNA-Small Interfering,RNAMessenger,RNASmall Interfering,splicing,stability,TARGET,termination,TERMINATION CODON,TERMINATION-CODON,Trans-Activators,TRANSCRIPT,transcription,TRANSCRIPTION FACTOR,Transcription Factors,translation,TRANSPORT,Two-Hybrid System Techniques,Untranslated Regions,Upf1,UPSTREAM} }

@article{kingRibosomeStructureActivity2003, title = {Ribosome Structure and Activity Are Altered in Cells Lacking {{snoRNPs}} That Form Pseudouridines in the Peptidyl Transferase Center}, author = {King, T.H. and Liu, B. and McCully, R.R. and Fournier, M.J.}, year = 2003, month = feb, journal = {Molecular cell}, volume = {11}, number = {2}, pages = {425–435}, publisher = {Elsevier}, doi = {10.1016/S1097-2765(03)00040-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276503000406}, abstract = {One of the oldest questions in RNA science is the role of nucleotide modification. Here, the importance of pseudouridine formation (Psi) in the peptidyl transferase center of rRNA was examined by depleting yeast cells of 1-5 snoRNAs that guide a total of six Psi modifications. Translation was impaired substantially with loss of a conserved Psi in the A site of tRNA binding. Depletion of other Psis had subtle or no apparent effect on activity; however, synergistic effects were observed in some combinations. Pseudouridines are proposed to enhance ribosome activity by altering rRNA folding and interactions, with some Psis having greater effects than others. The possibility that modifying snoRNPs might affect ribosome structure in other ways is also discussed}, keywords = {A SITE,A-SITE,BINDING,CELLS,DNAJ HOMOLOG,ESCHERICHIA-COLI,FORM PSEUDOURIDINES,IN-VIVO,M,modification,nosource,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Pseudouridine,psi,ribosome,Rna,rRNA,SACCHAROMYCES-CEREVISIAE,sarcin/ricin domain,SITE,SMALL NUCLEAR-RNA,SMALL NUCLEOLAR RNAS,structure,TRANSFERASE CENTER,translation,translational fidelity,tRNA,tRNA binding,U2 SNRNA,yeast,YEAST-CELLS} } % == BibTeX quality report for kingRibosomeStructureActivity2003: % ? unused Journal abbr (“Mol.Cell”)

@article{kingstonTranscriptionControlOncogenes1985a, title = {Transcription Control by Oncogenes.}, author = {Kingston, R.E. and Baldwin, A.S. and Sharp, P.A.}, year = 1985, month = may, journal = {Cell}, volume = {41}, number = {1}, eprint = {2986847}, eprinttype = {pubmed}, pages = {3–5}, doi = {10.1016/0092-8674(85)90049-2}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2986847}, keywords = {85201680,Adenoviridae,animal,AntigensViralTumor,Cell Line,Cell TransformationNeoplastic,Cell TransformationViral,enhancer elements (genetics),Gene Expression Regulation,GenesViral,genetics,Herpesvirus 1Suid,Htlv-Blv Viruses,immunology,Mutation,nosource,oncogenes,physiology,Polyomavirus,Polyomavirus macacae,Promoter Regions (Genetics),Simplexvirus,transcription,TranscriptionGenetic,Transfection,Viral Proteins} }

@article{kinzyCharacterizationLimitedTrypsin1991, title = {Characterization of a Limited Trypsin Digestion Form of Eukaryotic Elongation Factor 1 Alpha.}, author = {Kinzy, T.G. and Merrick, W.C.}, year = 1991, month = mar, journal = {Journal of Biological Chemistry}, volume = {166}, number = {7}, pages = {4099–4105}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(20)64291-0}, url = {http://www.jbc.org/content/266/7/4099.short}, keywords = {Amino Acids,analysis,BINDING,Chromatography,CROSS-LINKING,Crystallography,EF-1,EF-1 alpha,EFTu,elongation,Escherichia coli,ESCHERICHIA-COLI,GTP,GTPase,Methods,modification,nosource,Peptides,Phenylalanine,protein,purification,ribosome,Ribosomes,Structural,techniques} } % == BibTeX quality report for kinzyCharacterizationLimitedTrypsin1991: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{kinzyModelAminoacyltRNABinding1992a, title = {A Model for the Aminoacyl-{{tRNA}} Binding Site of Eukaryotic Elongation Factor 1 Alpha}, author = {Kinzy, T.G. and Freeman, J.P. and Johnson, A.E. and Merrick, W.C.}, year = 1992, month = jan, journal = {Journal of Biological Chemistry}, volume = {267}, number = {3}, pages = {1623–1632}, doi = {10.1016/S0021-9258(18)45991-1}, keywords = {BINDING,Binding Sites,COMPLEX,COMPLEXES,CROSS-LINKING,Cross-Linking Reagents,EF-1,EF-1 alpha,EFTu,ELEMENTS,elongation,GTP,Histidine,mapping,nosource,Peptides,structure,tRNA} }

@article{kinzyMultipleGenesEncode1994a, title = {Multiple Genes Encode the Translation Elongation Factor {{EF-1}} Gamma in {{Saccharomyces}} Cerevisiae}, author = {Kinzy, T.G. and Ripmaster, T.L. and Woolford, J.L.}, year = 1994, month = jul, journal = {Nucleic Acids Research}, volume = {22}, number = {13}, pages = {2703–2707}, doi = {10.1093/nar/22.13.2703}, keywords = {analysis,assembly,CEREVISIAE,deficiency,DISRUPTION,DISRUPTIONS,EF-1,elongation,ENCODES,gene,Gene Dosage,Genes,genomic,GROWTH,INTRON,nosource,Phenotype,Polyribosomes,protein,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Spores,SUBUNIT,SUBUNITS,translation,yeast} }

@article{kinzyIncreasedExpressionSaccharomyces1995, title = {Increased {{Expression}} of {{Saccharomyces}} Cerevisiae {{Translation Elongation Factor}} 1 $$alpha$$ {{Bypasses}} the {{Lethality}} of a {{TEF5 Null Allele Encoding Elongation Factor}} 1 $$beta$$}, author = {Kinzy, T.G. and Woolford, J.L.}, year = 1995, month = oct, journal = {Genetics}, volume = {141}, number = {2}, pages = {481–489}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/141.2.481}, url = {http://www.genetics.org/cgi/content/abstract/141/2/481}, keywords = {Alleles,antibiotic,antibiotics,drugs,elongation,expression,frameshift,Frameshift Mutation,gene,GTP,Mutation,MUTATIONS,nosource,Phenotype,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,suppression,translation} }

@article{kinzyIncreasedExpessionSaccharomyces1996a, title = {Increased Expession of ⬚{{Saccharomyces}} Cerevisiae⬚ Translation Elongation Factor 1`a Bypasses the Lethality of a ⬚{{TEF5}}⬚ Null Allele Encoding {{EF-1'a}}.}, author = {Kinzy, T.G. and Woolford, J.L.}, year = {in press 1996}, journal = {Genetics}, keywords = {elongation,No DOI found,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,translation} }

@article{kinzyNewTargetsAntivirals2002, title = {New Targets for Antivirals: The Ribosomal {{A-site}} and the Factors That Interact with It.}, author = {Kinzy, T.G. and Harger, J.W. and {Carr-Schmid}, A. and Kwon, J. and Shastry, M. and Justice, M.C. and Dinman, J.D.}, year = 2002, month = aug, journal = {Virology}, volume = {300}, number = {1}, pages = {60–70}, issn = {00426822}, doi = {10.1006/viro.2002.1567}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0042682202915679}, abstract = {Many viruses use programmed -1 ribosomal frameshifting to ensure the correct ratio of viral structural to enzymatic proteins. Alteration of frameshift efficiencies changes these ratios, in turn inhibiting viral particle assembly and virus propagation. Previous studies determined that anisomycin, a peptidyltransferase inhibitor, specifically inhibited -1 frameshifting and the ability of yeast cells to propagate the L-A and M⬚1 dsRNA viruses (Dinman, et al., 1997). Here we show that preussin, a pyrollidine that is structurally similar to anisomycin (Schwartz, et al, 1988), also inhibits -1 programmed ribosomal frameshifting and virus propagation by acting at the same site or through the same mechanism as anisomycin. Since anisomycin is known to assert its effect at the ribosomal A-site, we undertook a pharmacogenetic analysis of mutants of ⬚trans⬚-acting eukaryotic Elongation Factors (eEFs) that function at this region of the ribosome. Among mutants of eEF1A, a correlation is observed between resistance/susceptibility profiles to preussin and anisomycin, and these in turn correlate with programmed -1 ribosomal frameshifting efficiencies and killer virus phenotypes. Among mutants of eEF2, the extent of resistance to preussin correlates with resistance to sordarin, an eEF2 inhibitor. These results suggest that structural features associated with the ribosomal A-site and with the ⬚trans⬚-acting factors that interact with it may present a new set of molecular targets for the rational design of antiviral compounds. ⬚}, keywords = {A-SITE,analysis,anisomycin,antiviral,assembly,drugs,efficiency,elongation,elongation factors,frameshift,frameshifting,Frameshifting,hiv,HIV,killer,L-A,La,M1,MECHANISM,nosource,Peptidyltransferase,Phenotype,protein,Proteins,ribosomal frameshifting,ribosome,sordarin,Structural,translation,viral particle,viral particle assembly,virus,yeast} }

@article{kiparisovStructuralFunctionalAnalysis2005a, title = {Structural and Functional Analysis of {{5S rRNA}}.}, author = {Kiparisov, S. and Petrov, A. and Meskauskas, A. and Sergiev, P.V. and Dontsova, O.A. and Dinman, J.D.}, year = 2005, journal = {Molecular Genetics and Genomics}, volume = {27}, pages = {235–247}, doi = {10.1007/s00438-005-0020-9}, abstract = {5S rRNA extends from the central protuberance of the large ribosomal subunit, through the A-site finger, and down to the GTPase-associated center. Here, we present a structure-function analysis of seven 5S rRNA alleles which are sufficient for viability in the yeast Saccharomyces cerevisiae when expressed in the absence of wild-type 5S rRNAs, and extend this analysis using a large bank of mutant alleles that show semi-dominant phenotypes in the presence of wild-type 5S rRNA. This analysis supports the hypothesis that 5S rRNA serves to link together several different functional centers of the ribosome. Data are also presented which suggest that in eukaryotic genomes selection has favored the maintenance of multiple alleles of 5S rRNA, and that these may provide cells with a mechanism to post-transcriptionally regulate gene expression.}, keywords = {5S rRNA,A SITE,A-SITE,Alleles,analysis,CELLS,CEREVISIAE,expression,functional analysis,gene,Gene Expression,GENE-EXPRESSION,Genome,MECHANISM,nosource,Phenotype,RIBOSOMAL-SUBUNIT,ribosome,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SELECTION,Structural,SUBUNIT,Support,WILD-TYPE,yeast} }

@article{kirillovPeptidylTransferaseAntibiotics1999, title = {Peptidyl Transferase Antibiotics Perturb the Relative Positioning of the 3’-Terminal Adenosine of {{P}}/{{P}}‘-Site-Bound {{tRNA}} and {{23S rRNA}} in the Ribosome.}, author = {Kirillov, S.V. and Porse, B.T. and Garrett, R.A.}, year = 1999, journal = {RNA.}, volume = {5}, number = {8}, pages = {1003–1013}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838299990568}, url = {http://rnajournal.cshlp.org/content/5/8/1003.short}, abstract = {A range of antibiotic inhibitors that act within the peptidyl transferase center of the ribosome were examined for their capacity to perturb the relative positioning of the 3’ end of P/P’-site-bound tRNA and the Escherichia coli ribosome. The 3’-terminal adenosines of deacylated tRNA and N-Ac-Phe-tRNA were derivatized at the 2 position with an azido group and the tRNAs were cross-linked to the ribosome on irradiation with ultraviolet light at 365 nm. The cross-links were localized on the rRNA within extended versions of three previously characterized 23S rRNA fragments F1’, F2’, and F4’ at nucleotides C2601/A2602, U2584/U2585 (F1’), U2506 (F2’), and A2062/C2063 (F4’). Each of these nucleotides lies within the peptidyl transferase loop region of the 23S rRNA. Cross-links were also formed with ribosomal proteins L27 (strong) and L33 (weak), as shown earlier. The antibiotics sparsomycin, chloramphenicol, the streptogramins pristinamycin IA and IIA, gougerotin, lincomycin, and spiramycin were tested for their capacity to alter the identities or yields of each of the cross-links. Although no new cross-links were detected, each of the drugs produced major changes in cross-linking yields, mainly decreases, at one or more rRNA sites but, with the exception of chloramphenicol, did not affect cross-linking to the ribosomal proteins. Moreover, the effects were closely similar for both deacylated and N-Ac-Phe-tRNAs, indicating that the drugs selectively perturb the 3’ terminus of the tRNA. The strongest decreases in the rRNA cross-links were observed with pristinamycin IIA and chloramphenicol, which correlates with their both producing complex chemical footprints on 23S rRNA within E. coli ribosomes. Furthermore, gougerotin and pristinamycin IA strongly increased the yields of fragments F2’ (U2506) and F4’ (U2062/C2063), respectively. The results obtained with an RNAse H approach correlate well with primer extension data implying that cross-linking occurs primarily to the bases. Both sets of data are also consistent with the results of earlier rRNA footprinting experiments on antibiotic-ribosome complexes. It is concluded that the antibiotics perturb the relative positioning of the 3’ end of the P/P’-site-bound tRNA and the peptidyl transferase loop region of 23S rRNA}, keywords = {Adenosine,antibiotic,antibiotics,AntibioticsAntineoplastic,AntibioticsPeptide,Autoradiography,Chloramphenicol,Comparative Study,COMPLEX,COMPLEXES,CROSS-LINKING,Cross-Linking Reagents,drug effects,drugs,enzymology,Escherichia coli,ESCHERICHIA-COLI,Lincomycin,metabolism,ModelsGenetic,nosource,Nucleotides,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,Peptidyltransferase,pharmacology,primer extension,protein,Protein Synthesis Inhibitors,Proteins,Radiation-Sensitizing Agents,regulation,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNARibosomal23S,RNAse,RNATransferPhe,rRNA,sparsomycin,supportnon-u.s.gov’t,tRNA,ultraviolet rays,Virginiamycin} } % == BibTeX quality report for kirillovPeptidylTransferaseAntibiotics1999: % ? Possibly abbreviated journal title RNA.

@article{kirn-safranCloningExpressionChromosome2000a, title = {Cloning, Expression, and Chromosome Mapping of the Murine {{Hip}}/{{Rpl29}} Gene}, author = {{Kirn-Safran}, C.B. and Dayal, S. and {Martin-DeLeon}, P.A. and Carson, D.D.}, year = 2000, journal = {Genomics}, volume = {68}, number = {2}, pages = {210–219}, doi = {10.1006/geno.2000.6283}, url = {PM:10964519}, abstract = {We previously have identified murine heparin/heparan sulfate-interacting protein (HIP) identical to mouse ribosomal protein L29 that is, like its human orthologue, distinctively expressed both on the cell surface and intracellularly in different adult tissues and cell types. In the present study, we show that mouse HIP/RPL29 is encoded by a single mRNA and that it is expressed to different extents in most of the tissues of the developing embryo without restriction to a specific cell type. We isolated the single-copy gene coding for murine Hip/Rpl29 among a large number of pseudogenes, established its structure, and assigned its location to distal chromosome 9. Similar to other ribosomal protein promoters, the promoter of Hip/Rpl29 is rich in polypyrimidine tracts, contains binding motifs for ubiquitously expressed transcription factors, and lacks a TATA box. Progressive 5’ deletion analyses identified a strong enhancer region that includes CT-rich sequences and a potential consensus binding site for NF-kappaB. These data will provide valuable tools to progress the understanding of HIP/RPL29 function as a ribosomal protein and/or as a regulator of growth and cell adhesion through interaction with heparan sulfate proteoglycans}, keywords = {0,Adult,Animals,Base Sequence,BINDING,BINDING MOTIF,BINDING-SITE,Cell Line,chemistry,Chromosome Banding,Chromosome Mapping,cloning,CloningMolecular,Dna,Embryo,expression,Female,FUSION PROTEIN,gene,Gene Expression,Gene Expression RegulationDevelopmental,Genes,genetics,GROWTH,human,in situ hybridization,In Situ HybridizationFluorescence,L29,La,LOCATION,luciferase,Luciferases,Male,mapping,metabolism,Mice,MiceInbred Strains,Molecular Sequence Data,MOTIFS,mRNA,nosource,PROMOTER,Promoter Regions (Genetics),PROMOTERS,protein,Proteins,Pseudogenes,Recombinant Fusion Proteins,REGION,Ribosomal Proteins,RIBOSOMAL-PROTEIN,Rna,RNAMessenger,sequence,Sequence AnalysisDNA,SEQUENCES,SITE,structure,Support,Tata Box,transcription,TRANSCRIPTION FACTOR,Transcription Factors} }

@article{kirn-safranGlobalGrowthDeficiencies2006, title = {Global Growth Deficiencies in Mice Lacking the Ribosomal Protein {{HIP}}/{{RPL29}}}, author = {{Kirn-Safran}, C.B. and Oristian, D.S. and Focht, R.J. and Parker, S.G. and Vivian, J.L. and Carson, D.D.}, year = 2006, month = dec, journal = {Developmental Dynamics}, volume = {236}, number = {2}, pages = {447–460}, publisher = {Wiley Online Library}, doi = {10.1002/dvdy.21046}, url = {PM:17195189 http://onlinelibrary.wiley.com/doi/10.1002/dvdy.21046/full}, abstract = {Because of their deleterious effects on developing organisms, ribosomal protein (RP) mutations have been poorly described in mammals, and only a few heterozygous mutations have been shown to be viable. This observation is believed to be due to the fact that each RP is an essential component in the assembly of a functional stable ribosome. Here, we created gene targeted mutant mice lacking HIP/RPL29, an RP associated with translationally active ribosomes in eukaryotes. In contrast to other RP mutants, HIP/RPL29 null mice are viable but are up to 50% smaller than their control littermates at weaning age. In null embryos, delayed global growth is first observed around mid-gestation, and postnatal lethality due to low birth weight results in distortion of the Mendelian ratio. Prenatal growth defects are not fully compensated for during adulthood, and null animals display proportionately smaller organs and stature, and reach sexual maturity considerably later when compared with their control siblings. Additionally, HIP/RPL29 null embryonic fibroblasts have decreased rates of proliferation and protein synthesis and exhibit reduced steady state levels of core RPs. Altogether, our findings provide conclusive genetic evidence that HIP/RPL29 functions as an important regulator of global growth by modulating the rate of protein synthesis. Developmental Dynamics 236:447-460, 2007. (c) 2006 Wiley-Liss, Inc}, keywords = {animal,Animals,assembly,COMPONENT,deficiency,DYNAMICS,Embryo,gene,Genetic,GROWTH,La,Mammals,Mice,MUTANTS,Mutation,MUTATIONS,nosource,PROLIFERATION,protein,protein synthesis,PROTEIN-SYNTHESIS,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Weaning} } % == BibTeX quality report for kirn-safranGlobalGrowthDeficiencies2006: % ? unused Journal abbr (“Dev.Dyn.”)

@article{kirschAminoAcidIncorporation1960a, title = {Amino Acid Incorporation in Vitro by Ribonucleoprotein Particles Detached from Guinea Pig Liver Microsomes.}, author = {KIRSCH, J.F. and SIEKEVITZ, P. and PALADE, G.E.}, year = 1960, month = may, journal = {J. Biol. Chem.}, volume = {235}, pages = {1419–1424}, doi = {10.1016/S0021-9258(18)69423-2}, url = {PM:14409376}, keywords = {0,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,chemistry,In Vitro,IN-VITRO,La,Liver,metabolism,nosource,Nucleoproteins,PARTICLES,RIBONUCLEOPROTEIN,Rna} } % == BibTeX quality report for kirschAminoAcidIncorporation1960a: % ? Possibly abbreviated journal title J. Biol. Chem.

@article{kirthiNovelSingleAmino2006, title = {A Novel Single Amino Acid Change in Small Subunit Ribosomal Protein {{S5}} Has Profound Effects on Translational Fidelity}, author = {Kirthi, N. and {Roy-Chaudhuri}, B. and Kelley, T. and Culver, G.M.}, year = 2006, month = dec, journal = {RNA.}, volume = {12}, number = {12}, pages = {2080–2091}, doi = {10.1261/rna.302006}, url = {PM:17053085}, abstract = {S5 is a small subunit ribosomal protein (r-protein) linked to the functional center of the 30S ribosomal subunit. In this study we have identified a unique amino acid mutation in Escherichia coli S5 that produces spectinomycin-resistance and cold sensitivity. This mutation significantly alters cell growth, folding of 16S ribosomal RNA, and translational fidelity. While translation initiation is not affected, both +1 and -1 frameshifting and nonsense suppression are greatly enhanced in the mutant strain. Interestingly, this S5 ribosome ambiguity-like mutation is spatially remote from previously identified S5 ribosome ambiguity (ram) mutations. This suggests that the mechanism responsible for ram phenotypes in the novel mutant strain is possibly distinct from those proposed for other known S5 (and S4) ram mutants. This study highlights the importance of S5 in ribosome function and cell physiology, and suggests that translational fidelity can be regulated in multiple ways}, keywords = {0,16S,30s ribosome,ACID,Amino Acid Sequence,Amino Acid Substitution,AMINO-ACID,Biochemistry,BIOLOGY,Biophysics,Cell Physiology,Cold,coli,Drug ResistanceBacterial,e,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,Fidelity,Frameshifting,genetics,Glycine,GROWTH,growth & development,initiation,La,MECHANISM,metabolism,Molecular Biology,Molecular Sequence Data,MUTANTS,Mutation,MUTATIONS,NONSENSE,nonsense suppression,nosource,pharmacology,Phenotype,physiology,protein,Protein Biosynthesis,Proteins,ram,ram mutant,Ribosomal Proteins,ribosomal RNA,RIBOSOMAL-PROTEIN,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNARibosomal16S,RNATransfer,s5 protein,Selection (Genetics),Spectinomycin,spectinomycin resistance,SUBUNIT,Support,suppression,translation,TRANSLATION INITIATION,translational fidelity} } % == BibTeX quality report for kirthiNovelSingleAmino2006: % ? Possibly abbreviated journal title RNA.

@article{kiss-laszloSitespecificRiboseMethylation1996, title = {Site-Specific Ribose Methylation of Preribosomal {{RNA}}: A Novel Function for Small Nucleolar {{RNAs}}}, author = {{Kiss-Laszlo}, Z. and Henry, Y. and Bachellerie, J.P. and {Caizergues-Ferrer}, M. and Kiss, T.}, year = 1996, month = jun, journal = {Cell}, volume = {85}, number = {7}, pages = {1077–1088}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(00)81308-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867400813082 PM:8674114}, abstract = {Eukaryotic cells contain many fibrillarin-associated small nucleolar RNAs (snoRNAs) that possess long complementarities to mature rRNAs. Characterization of 21 novel antisense snoRNAs from human cells followed by genetic depletion and reconstitution studies on yeast U24 snoRNA provides evidence that this class of snoRNAs is required for site-specific 2’-O-methylation of preribosomal RNA (pre-rRNA). Antisense sno-RNAs function through direct base-pairing interactions with pre-rRNA. The antisense element, together with the D or D’ box of the snoRNA, provide the information necessary to select the target nucleotide for the methyltransfer reaction. The conclusion that sno- RNAs function in covalent modification of the sugar moieties of ribonucleotides demonstrates that eukaryotic small nuclear RNAs have a more versatile cellular function than earlier anticipated}, keywords = {0,antisense,Base Pairing,Base Sequence,Chromosomal ProteinsNon-Histone,Consensus Sequence,Eukaryotic Cells,Genetic,genetics,Hela Cells,human,La,metabolism,Methylation,modification,Molecular Sequence Data,nosource,Nucleotides,physiology,protein,Proteins,Ribonucleoproteins,Ribonucleotides,Ribose,Rna,RNA Precursors,RNAAntisense,RNARibosomal,RNASmall Nuclear,rRNA,site specific,supportnon-u.s.gov’t,tRNA,tRNA Methyltransferases,yeast,Yeasts} }

@article{kitaharaFunctionalGeneticSelection2007, title = {Functional Genetic Selection of {{Helix}} 66 in {{Escherichia}} Coli {{23S rRNA}} Identified the Eukaryotic-Binding Sequence for Ribosomal Protein {{L2}}}, author = {Kitahara, K. and Kajiura, A. and Sato, N.S. and Suzuki, T.}, year = 2007, journal = {Nucleic Acids Research}, volume = {35}, number = {12}, pages = {4018–4029}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkm356}, url = {http://nar.oxfordjournals.org/content/35/12/4018.short}, abstract = {Ribosomal protein L2 is a highly conserved primary 23S rRNA-binding protein. L2 specifically recognizes the internal bulge sequence in Helix 66 (H66) of 23S rRNA and is localized to the intersubunit space through formation of bridge B7b with 16S rRNA. The L2-binding site in H66 is highly conserved in prokaryotic ribosomes, whereas the corresponding site in eukaryotic ribosomes has evolved into distinct classes of sequences. We performed a systematic genetic selection of randomized rRNA sequences in Escherichia coli, and isolated 20 functional variants of the L2-binding site. The isolated variants consisted of eukaryotic sequences, in addition to prokaryotic sequences. These results suggest that L2/L8e does not recognize a specific base sequence of H66, but rather a characteristic architecture of H66. The growth phenotype of the isolated variants correlated well with their ability of subunit association. Upon continuous cultivation of a deleterious variant, we isolated two spontaneous mutations within domain IV of 23S rRNA that compensated for its weak subunit association, and alleviated its growth defect, implying that functional interactions between intersubunit bridges compensate ribosomal function}, keywords = {0,16S,ASSOCIATION,Bacterial,BASE,Base Sequence,Binding Sites,chemistry,DOMAIN,Escherichia coli,ESCHERICHIA-COLI,Eukaryotic Cells,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,EvolutionMolecular,Genetic,genetics,GROWTH,L2,La,metabolism,ModelsMolecular,Molecular Sequence Data,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Phenotype,protein,Proteins,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Rna,RNABacterial,RNARibosomal23S,rRNA,SELECTION,sequence,Sequence AnalysisRNA,Sequence Deletion,SEQUENCES,SITE,SUBUNIT,subunit association,Support} } % == BibTeX quality report for kitaharaFunctionalGeneticSelection2007: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{kitakawaMitochondrialRibosomes1991, title = {The Mitochondrial Ribosomes}, author = {Kitakawa, M. and Isono, K.}, year = 1991, month = jun, journal = {Biochimie}, volume = {73}, number = {6}, pages = {813–825}, publisher = {Elsevier}, doi = {10.1016/0300-9084(91)90061-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/0300908491900615}, keywords = {92110447,Amino Acid Sequence,animal,Cell Nucleus,chemistry,Comparative Study,Fungi,genetics,mitochondria,Molecular Sequence Data,nosource,Plants,Protein ProcessingPost-Translational,Protozoa,Review,Ribosomal Proteins,ribosome,Ribosomes,RNARibosomal,Saccharomyces cerevisiae,Sequence HomologyNucleic Acid,supportnon-u.s.gov’t} }

@article{klauckMutationsRibosomalProtein2006, title = {Mutations in the Ribosomal Protein Gene {{RPL10}} Suggest a Novel Modulating Disease Mechanism for Autism}, author = {Klauck, S.M. and Felder, B. and {Kolb-Kokocinski}, A. and Schuster, C. and Chiocchetti, A. and Schupp, I. and Wellenreuther, R. and Schmotzer, G. and Poustka, F. and {Breitenbach-Koller}, L. and Poustka, A.}, year = 2006, journal = {Mol.Psychiatry}, volume = {11}, number = {12}, pages = {1073–1084}, publisher = {Nature Publishing Group}, doi = {10.1038/sj.mp.4001883}, url = {http://www.nature.com/mp/journal/v11/n12/abs/4001883a.html}, abstract = {Autism has a strong genetic background with a higher frequency of affected males suggesting involvement of X-linked genes and possibly also other factors causing the unbalanced sex ratio in the etiology of the disorder. We have identified two missense mutations in the ribosomal protein gene RPL10 located in Xq28 in two independent families with autism. We have obtained evidence that the amino-acid substitutions L206M and H213Q at the C-terminal end of RPL10 confer hypomorphism with respect to the regulation of the translation process while keeping the basic translation functions intact. This suggests the contribution of a novel, possibly modulating aberrant cellular function operative in autism. Previously, we detected high expression of RPL10 by RNA in situ hybridization in mouse hippocampus, a constituent of the brain limbic system known to be afflicted in autism. Based on these findings, we present a model for autistic disorder where a change in translational function is suggested to impact on those cognitive functions that are mediated through the limbic system.Molecular Psychiatry advance online publication, 29 August 2006; doi:10.1038/sj.mp.4001883}, keywords = {Amino Acid Substitution,AMINO-ACID,analysis,Brain,disease,etiology,expression,FAMILY,gene,Genes,Genetic,Genome,Germany,in situ hybridization,L10,La,Male,MECHANISM,MODEL,Mutation,MUTATIONS,nosource,protein,regulation,RIBOSOMAL-PROTEIN,Rna,SYSTEM,translation} } % == BibTeX quality report for klauckMutationsRibosomalProtein2006: % ? Possibly abbreviated journal title Mol.Psychiatry

@article{kleinRolesRibosomalProteins2004, title = {The Roles of Ribosomal Proteins in the Structure Assembly, and Evolution of the Large Ribosomal Subunit}, author = {Klein, D.J. and Moore, P.B. and Steitz, T.A.}, year = 2004, month = jun, journal = {Journal of molecular biology}, volume = {340}, number = {1}, pages = {141–177}, publisher = {Elsevier}, doi = {10.1016/j.jmb.2004.03.076}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022283604003845}, abstract = {The structures of ribosomal proteins and their interactions with RNA have been examined in the refined crystal structure of the Haloarcula marismortui large ribosomal subunit. The protein structures fall into six groups based on their topology. The 50S subunit proteins function primarily to stabilize inter-domain interactions that are necessary to maintain the subunit’s structural integrity. An extraordinary variety of protein-RNA interactions is observed. Electrostatic interactions between numerous arginine and lysine residues, particularly those in tail extensions, and the phosphate groups of the RNA backbone mediate many protein-RNA contacts. Base recognition occurs via both the minor groove and widened major groove of RNA helices, as well as through hydrophobic binding pockets that capture bulged nucleotides and through insertion of amino acid residues into hydrophobic crevices in the RNA. Primary binding sites on contiguous RNA are identified for 20 of the 50S ribosomal proteins, which along with few large protein-protein interfaces, suggest the order of assembly for some proteins and that the protein extensions fold cooperatively with RNA. The structure supports the hypothesis of co-transcriptional assembly, centered around L24 in domain I. Finally, comparing the structures and locations of the 50S ribosomal proteins from H.marismortui and D.radiodurans revealed striking examples of molecular mimicry. These comparisons illustrate that identical RNA structures can be stabilized by unrelated proteins}, keywords = {ACID,AMINO-ACID,Arginine,assembly,BASE,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,crystal structure,CRYSTAL-STRUCTURE,DOMAIN,Evolution,Haloarcula,Haloarcula marismortui,interface,La,LOCATION,Lysine,Molecular Mimicry,nosource,Nucleotides,protein,protein-RNA interaction,protein-RNA interactions,Proteins,RECOGNITION,RESIDUES,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,Rna,SITE,SITES,Structural,structure,SUBUNIT,Support} } % == BibTeX quality report for kleinRolesRibosomalProteins2004: % ? unused Journal abbr (“J.Mol.Biol.”)

@article{klobutcherShiftyCiliatesFrequent2002, title = {Shifty {{Ciliates}}:: {{Frequent Programmed Translational Frameshifting}} in {{Euplotids}}}, author = {Klobutcher, L.A. and Farabaugh, P.J.}, year = 2002, month = dec, journal = {Cell}, volume = {111}, number = {6}, pages = {763–766}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(02)01138-8}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867402011388}, abstract = {Recent work suggests that there is a high frequency of programmed +1 translational frameshifting in ciliates of the Euplotes genus. Frequent frameshifting may have been potentiated by stop codon reassignment, which is also a feature of this group}, keywords = {animal,Codon,CodonTerminator,Euplotes,Frameshift Mutation,Frameshifting,genetics,metabolism,ModelsBiological,ModelsGenetic,nosource,Review,RNAMessenger,STOP CODON,TranslationGenetic} } % == BibTeX quality report for klobutcherShiftyCiliatesFrequent2002: % ? Title looks like it was stored in title-case in Zotero

@article{knudsenKissingLoopsHide1997, title = {Kissing Loops Hide Premature Termination Codons in Pre-{{mRNA}} of Selenoprotein Genes and in Genes Containing Programmed Ribosomal Frameshifts.}, author = {Knudsen, S. and Brunak, S.}, year = 1997, month = jul, journal = {Rna-A Publication of the Rna Society}, volume = {3}, number = {7}, pages = {697–701}, publisher = {Cold Spring Harbor Laboratory Press}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1369517/}, keywords = {Codon,FRAME,frameshift,gene,Genes,MESSENGER-RNA,mRNA stability,No DOI found,nosource,nuclear scanning,RECOGNITION,RIBOSOMAL FRAMESHIFT,RNA SECONDARY STRUCTURE,selenoproteins,sequence,SEQUENCES,SITE,splicing,termination,translation} }

@article{kobayashiExpansionContractionRibosomal1998, title = {Expansion and Contraction of Ribosomal {{DNA}} Repeats in {{Saccharomyces}} Cerevisiae: Requirement of Replication Fork Blocking ({{Fob1}}) Protein and the Role of {{RNA}} Polymerase {{I}}}, author = {Kobayashi, T. and Heck, D.J. and Nomura, M. and Horiuchi, T.}, year = 1998, month = dec, journal = {Genes & development}, volume = {12}, number = {24}, pages = {3821–3830}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.12.24.3821}, url = {http://genesdev.cshlp.org/content/12/24/3821.short}, abstract = {Saccharomyces cerevisiae carries approximately 150 copies of rDNA in tandem repeats. It was found that the absence of an essential subunit of RNA polymerase I (Pol I) in rpa135 deletion mutants triggers a gradual decrease in rDNA repeat number to about one-half the normal level. Reintroduction of the missing RPA135 gene induced a gradual increase in repeat number back to the normal level. Gene FOB1 was shown to be essential for both the decrease and increase of rDNA repeats. FOB1 was shown previously to be required for replication fork blocking (RFB) activity at RFB site in rDNA and for recombination hot-spot (HOT1) activity. Thus, DNA replication fork blockage appears to stimulate recombination and play an essential role in rDNA expansion/contraction and sequence homogenization, and possibly, in the instability of repeated sequences in general. RNA Pol I, on the other hand, appears to control repeat numbers, perhaps by stabilizing rDNA with the normal repeat numbers as a stable nucleolar structure}, keywords = {99088032,BlottingSouthern,Cell Division,Chromosomes,Dna,DNA Replication,DNAFungal,DNARibosomal,ElectrophoresisGelPulsed-Field,Fungal Proteins,gene,Gene Amplification,Gene Dosage,Genetic Vectors,genetics,metabolism,ModelsGenetic,Molecular Weight,MutagenesisInsertional,nosource,physiology,pol,polymerase,protein,rDNA,RecombinationGenetic,Regulatory SequencesNucleic Acid,Rna,RNA Polymerase I,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Tandem Repeat Sequences} } % == BibTeX quality report for kobayashiExpansionContractionRibosomal1998: % ? unused Journal abbr (“Genes Dev.”)

@article{kobayashiIdentificationSaccharomycesCerevisiae2006, title = {Identification of {{Saccharomyces}} Cerevisiae Ribosomal Protein {{L3}} as a Target of Curvularol, a {{G}} 1-Specific Inhibitor of Mammalian Cells}, author = {Kobayashi, Y. and Mizunuma, M. and Osada, H. and Miyakawa, T.}, year = 2006, month = oct, journal = {Biosci.Biotechnol.Biochem.}, volume = {70}, number = {10}, pages = {2451–2459}, publisher = {J-STAGE}, doi = {10.1271/bbb.60186}, url = {http://joi.jlc.jst.go.jp/JST.JSTAGE/bbb/60186?from=Google}, abstract = {The cellular target of curvularol, a G1-specific cell-cycle inhibitor of mammalian cells, was identified by a genetic approach in Saccharomyces cerevisiae. Since the wild-type W303 strain was highly resistant to curvularol, a drug hypersensitive parental strain was constructed in which various genes implicated in general drug resistance had been disrupted. Curvularol resistant mutants were isolated, and strains that exhibited a semi-dominant, curvularol-specific resistance phenotype were selected. All five strains examined were classified into a single genetic complementation group designated YCR1. A mutant gene responsible for curvularol resistance was identified as an allele of the RPL3 gene encoding the ribosomal protein L3. Sequence analysis of the mutant genes revealed that Trp255Cys and Trp255Leu substitutions of Rpl3p are responsible for curvularol resistance. Rpl3p mutants in which Trp255 residue was replaced by other amino acids were constructed. All of these replacements led to varying degrees of increased resistance to curvularol and growth defects}, isbn = {8182424704}, keywords = {0,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,Animals,antagonists & inhibitors,cell cycle,CELLS,CEREVISIAE,curvularol-re-,drug effects,Drug Resistance,g 1 -specific inhibitor,G1 Phase,gene,Genes,Genetic,genetics,GROWTH,growth & development,Humans,IDENTIFICATION,INHIBITOR,L3,La,MAMMALIAN-CELLS,Mammals,MUTANTS,MutationMissense,nosource,pharmacology,Phenotype,protein,Proteins,RESISTANCE,RESISTANT,riboso-,Ribosomal Proteins,RIBOSOMAL-PROTEIN,Saccharomyces,saccharomyces cerevisiae,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,Sequence Analysis,SEQUENCE-ANALYSIS,sistant mutant,TARGET,Trichothecenes,WILD-TYPE} } % == BibTeX quality report for kobayashiIdentificationSaccharomycesCerevisiae2006: % ? Possibly abbreviated journal title Biosci.Biotechnol.Biochem.

@article{kobernaRibosomalGenesFocus2002a, title = {Ribosomal Genes in Focus: New Transcripts Label the Dense Fibrillar Components and Form Clusters Indicative of “{{Christmas}} Trees” in Situ}, author = {Koberna, K. and Malinsky, J. and Pliss, A. and Masata, M. and Vecerova, J. and Fialova, M. and Bednar, J. and Raska, I.}, year = 2002, month = may, journal = {Journal of Cell Biology}, volume = {157}, number = {5}, pages = {743–748}, doi = {10.1083/jcb.200202007}, url = {ISI:000176427100002}, abstract = {T he organization of transcriptionally active ribosomal genes in animal cell nucleoli is investigated in this study in order to address the long-standing controversy with regard to the intranucleolar localization of these genes. Detailed analyses of HeLa cell nucleoli include direct localization of ribosomal genes by in situ hybridization and their indirect localization via nascent ribosomal transcript mappings. On the light microscopy (LM) level, ribosomal genes map in 10-40 fluorescence foci per nucleus, and transcription activity is associated with most foci. We demonstrate that each nucleolar focus observed by LM corresponds, on the EM level, to an individual fibrillar center (FC) and surrounding dense fibrillar components (DFCs). The EM data identify the DFC as the nucleolar subcompartment in which rRNA synthesis takes place, consistent with detection of rDNA within the DFC. The highly sensitive method for mapping nascent transcripts in permeabilized cells on ultrastructural level provides intense and unambiguous clustered immunogold signal over the DFC, whereas very little to no label is detected over the FC. This signal is strongly indicative of nascent “Christmas trees” of rRNA associated with individual rDNA genes, sampled on the surface of thin sections. Stereological analysis of the clustered transcription signal further suggests that these Christmas trees may be contorted in space and exhibit a DNA compaction ratio on the order of 4-5.5}, keywords = {analysis,animal,Cell Nucleolus,CELLS,Christmas tree,COMPONENT,COMPONENTS,dense fibrillar components,Dna,Fluorescence,gene,Genes,IDENTIFY,Immunohistochemistry,in situ hybridization,LOCALIZATION,mapping,nosource,nucleolus,ORGANIZATION,rDNA,ribosomal RNA,Rna,rRNA,rRNA genes,SIGNAL,T,TRANSCRIPT,transcription,UNITS} }

@article{kohnoAminoAcidSequence1986, title = {Amino Acid Sequence of Mammalian Elongation Factor 2 Deduced from the {{cDNA}} Sequence: Homology with {{GTP-binding}} Proteins.}, author = {Kohno, K. and Uchida, T. and Ohkubo, H. and Nakanishi, S. and Nakanishi, T. and Fukui, T. and Ohtsuka, E. and Ikehara, M. and Okada, Y.}, year = 1986, journal = {Proceedings of the National Academy of Sciences}, volume = {83}, number = {14}, pages = {4979–4982}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.83.14.4978}, url = {http://www.pnas.org/content/83/14/4978.short}, keywords = {Amino Acid Sequence,EF-2,elongation,GTP-Binding Proteins,nosource,protein,Proteins,sequence} } % == BibTeX quality report for kohnoAminoAcidSequence1986: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.USA”)

@article{kolkNMRStructureClassical1998, title = {{{NMR}} Structure of a Classical Pseudoknot: Interplay of Single- and Double-Stranded {{RNA}}}, author = {Kolk, M.H. and {}{van der}, Graaf M. and Wijmenga, S.S. and Pleij, C.W. and Heus, H.A. and Hilbers, C.W.}, year = 1998, month = apr, journal = {Science}, volume = {280}, number = {5362}, pages = {434–438}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.280.5362.434}, url = {http://www.sciencemag.org/content/280/5362/434.short}, abstract = {Pseudoknot formation folds the 3’ ends of many plant viral genomic RNAs into structures that resemble transfer RNA in global folding and in their reactivity to transfer RNA-specific proteins. The solution structure of the pseudoknotted T arm and acceptor arm of the transfer RNA-like structure of turnip yellow mosaic virus (TYMV) was determined by nuclear magnetic resonance (NMR) spectroscopy. The molecule is stabilized by the hairpin formed by the 5’ end of the RNA, and by the intricate interactions related to the loops of the pseudoknot. Loop 1 spans the major groove of the helix with only two of its four nucleotides. Loop 2, which crosses the minor groove, interacts closely with its opposing helix, in particular through hydrogen bonds with a highly conserved adenine. The structure resulting from this interaction between the minor groove and single-stranded RNA at helical junctions displays internal mobility, which may be a general feature of RNA pseudoknots that regulates their interaction with proteins or other RNA molecules}, keywords = {0,3,Adenine,Amino Acyl-tRNA Synthetases,Binding Sites,chemistry,Diethyl Pyrocarbonate,DOUBLE-STRANDED-RNA,genetics,genomic,GENOMIC RNA,Hydrogen,Hydrogen Bonding,La,LOOP,Magnetic Resonance Spectroscopy,metabolism,ModelsMolecular,Molecular Structure,MOSAIC-VIRUS,Mutation,NMR,nosource,nuclear magnetic resonance,NUCLEAR-MAGNETIC-RESONANCE,Nucleic Acid Conformation,Nucleotides,protein,Proteins,pseudoknot,pseudoknots,Research SupportNon-U.S.Gov’t,Rna,RNA PSEUDOKNOT,RNADouble-Stranded,RNATransfer,RnaViral,SPECTROSCOPY,structure,T,TRANSFER-RNA,Tymovirus,virus} }

@article{kollmusSequencesDistanceTwo1994a, title = {The Sequences of and Distance between Two ⬚cis⬚-Acting Signals Determine the Efficiency of Ribosomal Frameshifting in Human Immunodeficiency Virus Type 1 and Human {{T-cell}} Leukemia Virus Type {{II}} ⬚in Vivo⬚.}, author = {Kollmus, H. and Honigman, A. and Panet, A. and Hauser, H.}, year = 1994, journal = {J.Virol.}, volume = {68}, pages = {6087–6091}, doi = {10.1128/jvi.68.9.6087-6091.1994}, keywords = {Chromosomes,efficiency,frameshift,Frameshifting,Gag,Gag-pol,HIV,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,IN-VIVO,nosource,ribosomal frameshifting,sequence,SIGNAL,virus} } % == BibTeX quality report for kollmusSequencesDistanceTwo1994a: % ? Possibly abbreviated journal title J.Virol.

@article{kollmusRegulatedRibosomalFrameshifting1996, title = {Regulated Ribosomal Frameshifting by an {{RNA-protein}} Interaction.}, author = {Kollmus, H. and Hentze, M.W. and Hauser, H.}, year = 1996, month = apr, journal = {RNA}, volume = {2}, number = {4}, pages = {316–323}, publisher = {Cold Spring Harbor Laboratory Press}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1369374/ http://www.ncbi.nlm.nih.gov/pmc/articles/pmc1369374/}, keywords = {BINDING,downstream element,ELEMENTS,frameshift,Frameshifting,Gag-pol,Hiv-1,MECHANISM,mRNA,No DOI found,nosource,programmed frameshifting,protein,Protein Binding,Proteins,ribosomal frameshifting,Rna,sequence,stability,structure,translation} }

@article{komarInternalInitiationDrives2003, title = {Internal Initiation Drives the Synthesis of {{Ure2}} Protein Lacking the Prion Domain and Affects [{{URE3}}] Propagation in Yeast Cells}, author = {Komar, A.A. and Lesnik, T. and Cullin, C. and Merrick, W.C. and Trachsel, H. and Altmann, M.}, year = 2003, month = mar, journal = {The EMBO Journal}, volume = {22}, number = {5}, pages = {1199–1209}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/cdg103}, url = {http://www.nature.com/emboj/journal/v22/n5/abs/7595013a.html}, abstract = {The [URE3] phenotype in Saccharomyces cerevisiae is caused by the inactive, altered (prion) form of the Ure2 protein (Ure2p), a regulator of nitrogen catabolism. Ure2p has two functional domains: an N-terminal domain necessary and sufficient for prion propagation and a C-terminal domain responsible for nitrogen regulation. We show here that the mRNA encoding Ure2p possesses an IRES (internal ribosome entry site). Internal initiation leads to the synthesis of an N-terminally truncated active form of the protein (amino acids 94-354) lacking the prion-forming domain. Expression of the truncated Ure2p form (94-354) mediated by the IRES element cures yeast cells of the [URE3] phenotype. We assume that the balance between the full-length and truncated (94-354) Ure2p forms plays an important role in yeast cell physiology and differentiation}, keywords = {0,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,animal,cell size,CELLS,CEREVISIAE,chemistry,Codon,CodonInitiator,cytology,DOMAIN,DOMAINS,expression,FORM,FUSION PROTEIN,GenesReporter,genetics,initiation,INTERNAL RIBOSOME ENTRY,La,metabolism,mRNA,Nitrogen,nosource,Peptide Chain Initiation,Phenotype,physiology,prion,Prions,Promoter Regions (Genetics),PROPAGATION,protein,Protein StructureTertiary,Proteins,Recombinant Fusion Proteins,REGION,regulation,ribosome,RIBOSOME ENTRY SITE,Rna,RNAMessenger,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SITE,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,TranslationGenetic,Untranslated Regions,yeast,YEAST-CELLS} } % == BibTeX quality report for komarInternalInitiationDrives2003: % ? unused Journal abbr (“EMBO J.”)

@article{komiliFunctionalSpecificityRibosomal2007, title = {Functional Specificity among Ribosomal Proteins Regulates Gene Expression}, author = {Komili, S. and Farny, N.G. and Roth, F.P. and Silver, P.A.}, year = 2007, month = nov, journal = {Cell}, volume = {131}, number = {3}, pages = {557–571}, publisher = {Elsevier}, doi = {10.1016/j.cell.2007.08.037}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867407011002}, abstract = {Duplicated genes escape gene loss by conferring a dosage benefit or evolving diverged functions. The yeast Saccharomyces cerevisiae contains many duplicated genes encoding ribosomal proteins. Prior studies have suggested that these duplicated proteins are functionally redundant and affect cellular processes in proportion to their expression. In contrast, through studies of ASH1 mRNA in yeast, we demonstrate paralog-specific requirements for the translation of localized mRNAs. Intriguingly, these paralog-specific effects are limited to a distinct subset of duplicated ribosomal proteins. Moreover, transcriptional and phenotypic profiling of cells lacking specific ribosomal proteins reveals differences between the functional roles of ribosomal protein paralogs that extend beyond effects on mRNA localization. Finally, we show that ribosomal protein paralogs exhibit differential requirements for assembly and localization. Together, our data indicate complex specialization of ribosomal proteins for specific cellular processes and support the existence of a ribosomal code}, keywords = {assembly,BIOLOGY,CELLS,CEREVISIAE,COMPLEX,COMPLEXES,expression,gene,Gene Expression,GENE-EXPRESSION,Genes,La,LOCALIZATION,mRNA,nosource,protein,Proteins,Ribosomal Proteins,RIBOSOMAL-PROTEIN,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SPECIFICITY,Support,SYSTEM,SYSTEMS,translation,yeast} }

@article{kondoTwoConformationalStates2006, title = {Two Conformational States in the Crystal Structure of the {{Homo}} Sapiens Cytoplasmic Ribosomal Decoding {{A}} Site}, author = {Kondo, J. and Urzhumtsev, A. and Westhof, E.}, year = 2006, journal = {Nucleic acids research}, volume = {34}, number = {2}, pages = {676–685}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkj467}, url = {http://nar.oxfordjournals.org/content/34/2/676.short}, abstract = {The decoding A site of the small ribosomal subunit is an RNA molecular switch, which monitors codon-anticodon interactions to guarantee translation fidelity. We have solved the crystal structure of an RNA fragment containing two Homo sapiens cytoplasmic A sites. Each of the two A sites presents a different conformational state. In one state, adenines A1492 and A1493 are fully bulged-out with C1409 forming a wobble-like pair to A1491. In the second state, adenines A1492 and A1493 form non-Watson-Crick pairs with C1409 and G1408, respectively while A1491 bulges out. The first state of the eukaryotic A site is, thus, basically the same as in the bacterial A site with bulging A1492 and A1493. It is the state used for recognition of the codon/anticodon complex. On the contrary, the second state of the H.sapiens cytoplasmic A site is drastically different from any of those observed for the bacterial A site without bulging A1492 and A1493}, keywords = {0,16S,A SITE,A-SITE,A-SITES,Adenine,analogs & derivatives,Animals,Bacterial,chemistry,CODON-ANTICODON INTERACTION,Comparative Study,COMPLEX,COMPLEXES,crystal structure,CRYSTAL-STRUCTURE,CrystallographyX-Ray,decoding,Fidelity,FORM,Genetic Code,genetics,human,Humans,La,ModelsMolecular,Nebramycin,nosource,Nucleic Acid Conformation,RECOGNITION,RIBOSOMAL-SUBUNIT,Ribosomes,Rna,RNABacterial,RNAProtozoan,RNARibosomal16S,RNARibosomal18S,SITE,SITES,structure,SUBUNIT,Support,Tetrahymena thermophila,translation} } % == BibTeX quality report for kondoTwoConformationalStates2006: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{konevegaSpontaneousReverseMovement2007, title = {Spontaneous Reverse Movement of {{mRNA-bound tRNA}} through the Ribosome}, author = {Konevega, A.L. and Fischer, N. and Semenkov, Y.P. and Stark, H. and Wintermeyer, W. and Rodnina, M.V.}, year = 2007, month = apr, journal = {Nature Structural & Molecular Biology}, volume = {14}, number = {4}, pages = {318–324}, publisher = {Nature Publishing Group}, doi = {10.1038/nsmb1221}, url = {http://www.nature.com/nsmb/journal/v14/n4/abs/nsmb1221.html}, abstract = {During the translocation step of protein synthesis, a complex of two transfer RNAs bound to messenger RNA (tRNA-mRNA) moves through the ribosome. The reaction is promoted by an elongation factor, called EF-G in bacteria, which, powered by GTP hydrolysis, induces an open, unlocked conformation of the ribosome that allows for spontaneous tRNA-mRNA movement. Here we show that, in the absence of EF-G, there is spontaneous backward movement, or retrotranslocation, of two tRNAs bound to mRNA. Retrotranslocation is driven by the gain in affinity when a cognate E-site tRNA moves into the P site, which compensates the affinity loss accompanying the movement of peptidyl-tRNA from the P to the A site. These results lend support to the diffusion model of tRNA movement during translocation. In the cell, tRNA movement is biased in the forward direction by EF-G, which acts as a Brownian ratchet and prevents backward movement}, keywords = {0,A SITE,A-SITE,Bacteria,Bacterial,Biochemistry,COMPLEX,COMPLEXES,CONFORMATION,Cryoelectron Microscopy,E site,EF-G,elongation,Escherichia coli,Germany,GTP,Hydrolysis,La,MESSENGER-RNA,metabolism,MODEL,ModelsMolecular,MOF,Movement,mRNA,nosource,P SITE,P-SITE,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,ribosome,Ribosomes,Rna,RNABacterial,RNAMessenger,RNATransfer,RNATransferAmino Acyl,SITE,Support,TRANSFER-RNA,translocation,tRNA,ultrastructure} } % == BibTeX quality report for konevegaSpontaneousReverseMovement2007: % ? unused Journal abbr (“Nat.Struct.Mol.Biol”)

@article{konstantinidisTranslationalFidelityMutations2006, title = {Translational {{Fidelity Mutations}} in {{18S rRNA Affect}} the {{Catalytic Activity}} of {{Ribosomes}} and the {{Oxidative Balance}} of {{Yeast Cells}}}, author = {Konstantinidis, T.C. and Patsoukis, N. and Georgiou, C.D. and Synetos, D.}, year = 2006, month = mar, journal = {Biochemistry}, volume = {45}, number = {11}, pages = {3525–3533}, publisher = {ACS Publications}, doi = {10.1021/bi052505d}, url = {http://pubs.acs.org/doi/abs/10.1021/bi052505d}, abstract = {The function of mutations rdn1A, rdn1T, and rdn2 in 18S rRNA of Saccharomyces cerevisiae is investigated. The mutations correspond to substitutions C1054A, C1054U in helix 34, and G517A in helix 18 of 16S rRNA in Escherichia coli, respectively, in which the first and third mutations caused nonsense suppression, while C1054U caused no suppression. In yeast, rdn1A caused phenotypic suppression at nonsense codons, whereas rdn1T and rdn2 caused antisuppression. We provide in vitro evidence that, in addition, rdn1A decreases translational accuracy at sense codons as well, by a factor of 8, accompanied by extreme sensitivity to paromomycin, compatible with its error-prone character. Mutations rdn1T andrdn2 exhibit hyperaccuracy and paromomycin resistance. Thus, mutations in conserved rRNA regions may affect the same functions in the various species but in opposite directions. Mutation rdn1A, but not rdn1T or rdn2, affected also the catalytic activity of the ribosome, a 60S subunit activity. The rate of peptide bond formation was reduced to half its normal value, indicating a communication between the two subunits. Moreover, error-prone mutation rdn1A was less susceptible to oxidative modifications than wild type, indicated by decreased lipid peroxidation and nonprotein/protein disulfides, as well as by increased protein thiols. In contrast, hyperaccurate mutations rdn1T and rdn2 displayed increased oxidative stress. Our results suggest that the cells may consume more energy to achieve hyperaccuracy leading to increased oxidative modifications}, keywords = {16S,60S subunit,accuracy,BIOLOGY,BOND FORMATION,CELLS,CEREVISIAE,CHARACTER,Codon,CODONS,Disulfides,Escherichia coli,ESCHERICHIA-COLI,Fidelity,In Vitro,IN-VITRO,La,modification,Mutation,MUTATIONS,NONSENSE,nonsense suppression,nosource,Paromomycin,PAROMOMYCIN-RESISTANCE,peptide bond formation,PHENOTYPIC SUPPRESSION,protein,REGION,RESISTANCE,ribosome,Ribosomes,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Stress,SUBUNIT,SUBUNITS,suppression,translational fidelity,WILD-TYPE,yeast,YEAST-CELLS} } % == BibTeX quality report for konstantinidisTranslationalFidelityMutations2006: % ? Title looks like it was stored in title-case in Zotero

@article{kooninNewGroupPutative1992, title = {A New Group of Putative {{RNA}} Helicases.}, author = {Koonin, E.V.}, year = 1992, journal = {TIBS}, volume = {17}, pages = {495–497}, keywords = {Helicase,No DOI found,nosource,Review,Rna,RNA Helicases,UPF} }

@article{kooshaAlterationsPeptidyltransferaseDecoding2000, title = {Alterations in the Peptidyltransferase and Decoding Domains of Ribosomal {{RNA}} Suppress Mutations in the Elongation Factor {{G}} Gene}, author = {Koosha, H. and Cameron, D. and Andrews, K. and Dahlberg, A.E. and March, P.E.}, year = 2000, journal = {RNA.}, volume = {6}, number = {8}, pages = {1166–1173}, publisher = {Cambridge Univ Press}, doi = {10.1017/S1355838200000534}, url = {http://journals.cambridge.org/abstract_S1355838200000534}, abstract = {The translocation stage of protein synthesis is a highly conserved process in all cells. Although the components necessary for translocation have been delineated, the mechanism of this activity has not been well defined. Ribosome movement on template mRNA must allow for displacement of tRNA-mRNA complexes from the ribosomal A to P sites and P to E sites, while ensuring rigid maintenance of the correct reading frame. In Escherichia coli, translocation of the ribosome is promoted by elongation factor G (EF-G). To examine the role of EF-G and rRNA in translocation we have characterized mutations in rRNA genes that can suppress a temperature-sensitive (ts) allele of fusA, the gene in E. coli that encodes EF-G. This analysis was performed using the ts E. coli strain PEM100, which contains a point mutation within fusA. The ts phenotype of PEM100 can be suppressed by either of two mutations in the decoding region of the 16S rRNA when present in combination with a mutation at position 2058 in the peptidyltransferase domain of the 23S rRNA. Communication between these ribosomal domains is essential for coordinating the events of the elongation cycle. We propose a model in which EF-G promotes translocation by modulating this communication, thereby increasing the efficiency of this fundamental process}, keywords = {analysis,BlottingWestern,chemistry,COMPLEX,COMPLEXES,COMPONENT,decoding,efficiency,elongation,Escherichia coli,ESCHERICHIA-COLI,Fidelity,gene,Genes,genetics,Hydroxylamine,immunology,MECHANISM,metabolism,microbiology,Movement,mRNA,Mutation,MutationMissense,MUTATIONS,nosource,P-SITE,Peptide Elongation Factor G,Peptidyltransferase,pharmacology,Phenotype,Plasmids,Point Mutation,protein,protein synthesis,PROTEIN-SYNTHESIS,RIBOSOMAL-RNA,ribosome,Rna,RNABacterial,RNARibosomal16S,RNARibosomal23S,rRNA,Temperature,translocation,Translocation (Genetics)} } % == BibTeX quality report for kooshaAlterationsPeptidyltransferaseDecoding2000: % ? Possibly abbreviated journal title RNA.

@article{kopeinaStepwiseFormationEukaryotic2008, title = {Step-Wise Formation of Eukaryotic Double-Row Polyribosomes and Circular Translation of Polysomal {{mRNA}}}, author = {Kopeina, G.S. and Afonina, Z.A. and Gromova, K.V. and Shirokov, V.A. and Vasiliev, V.D. and Spirin, A.S.}, year = 2008, month = may, journal = {Nucleic Acids Research}, volume = {36}, number = {8}, pages = {2476–2488}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkm1177}, url = {http://nar.oxfordjournals.org/content/36/8/2476.short}, abstract = {The time course of polysome formation was studied in a long-term wheat germ cell-free translation system using sedimentation and electron microscopy techniques. The polysomes were formed on uncapped luciferase mRNA with translation-enhancing 5’ and 3’ UTRs. The formation of fully loaded polysomes was found to be a long process that required many rounds of translation and proceeded via several phases. First, short linear polysomes containing no more than six ribosomes were formed. Next, folding of these polysomes into short double-row clusters occurred. Subsequent gradual elongation of the clusters gave rise to heavy-loaded double-row strings containing up to 30-40 ribosomes. The formation of the double-row polysomes was considered to be equivalent to circularization of polysomes, with antiparallel halves of the circle being laterally stuck together by ribosome interactions. A slow exchange with free ribosomes and free mRNA observed in the double-row type polysomes, as well as the resistance of translation in them to AMP-PNP, provided evidence that most polysomal ribosomes reinitiate translation within the circularized polysomes without scanning of 5’ UTR, while de novo initiation including 5’ UTR scanning proceeds at a much slower rate. Removal or replacements of 5’ and 3’ UTRs affected the initial phase of translation, but did not prevent the formation of the double-row polysomes during translation}, keywords = {0,3,3’ Untranslated Regions,5’ Untranslated Regions,Cell-Free System,CELL-FREE TRANSLATION,CentrifugationDensity Gradient,chemistry,ELECTRON-MICROSCOPY,elongation,genetics,initiation,Kinetics,La,luciferase,Luciferases,Luminescent Proteins,metabolism,mRNA,nosource,Polyribosomes,polysomes,protein,Protein Biosynthesis,Proteins,REGION,RESISTANCE,ribosome,Ribosomes,Rna,RNAMessenger,scanning,Support,SYSTEM,techniques,Tobacco Mosaic Virus,translation,Triticum,ultrastructure,Untranslated Regions,Wheat} } % == BibTeX quality report for kopeinaStepwiseFormationEukaryotic2008: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{koradiMOLMOLProgramDisplay1996, title = {{{MOLMOL}}: A Program for Display and Analysis of Macromolecular Structures}, author = {Koradi, R. and Billeter, M. and Wuthrich, K.}, year = 1996, month = feb, journal = {J.Mol.Graph.}, volume = {14}, number = {1}, pages = {51–32}, doi = {10.1016/0263-7855(96)00009-4}, url = {PM:8744573}, abstract = {MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids. MOLMOL has a graphical user interface with menus, dialog boxes, and on-line help. The display possibilities include conventional presentation, as well as novel schematic drawings, with the option of combining different presentations in one view of a molecule. Covalent molecular structures can be modified by addition or removal of individual atoms and bonds, and three-dimensional structures can be manipulated by interactive rotation about individual bonds. Special efforts were made to allow for appropriate display and analysis of the sets of typically 20-40 conformers that are conventionally used to represent the result of an NMR structure determination, using functions for superimposing sets of conformers, calculation of root mean square distance (RMSD) values, identification of hydrogen bonds, checking and displaying violations of NMR constraints, and identification and listing of short distances between pairs of hydrogen atoms}, keywords = {0,analysis,Aprotinin,chemistry,Computer Graphics,Computer Simulation,Glutathione,Homeodomain Proteins,IDENTIFICATION,La,Magnetic Resonance Spectroscopy,ModelsMolecular,Molecular Structure,nosource,nuclear magnetic resonance,Nucleic Acid Conformation,Nucleic Acids,Pheromones,protein,Protein StructureSecondary,Proteins,structure,supportnon-u.s.gov’t,Surface Properties,Time Factors,User-Computer Interface} } % == BibTeX quality report for koradiMOLMOLProgramDisplay1996: % ? Possibly abbreviated journal title J.Mol.Graph.

@article{kornbergTenCommandmentsEnzymology2003a, title = {Ten Commandments of Enzymology, Amended}, author = {Kornberg, A.}, year = 2003, month = oct, journal = {Trends in Biochemical Sciences}, volume = {28}, number = {10}, pages = {515–517}, publisher = {[Amsterdam]: Published for the International Union of Biochemistry by Elsevier, 1976-}, doi = {10.1016/j.tibs.2003.08.007}, url = {http://molbio.med.miami.edu/NewWebsite/Pdf-Files/Arthur Kornberg enzymology.pdf}, keywords = {enzymology,La,nosource} } % == BibTeX quality report for kornbergTenCommandmentsEnzymology2003a: % ? unused Journal abbr (“Trends Biochem.Sci.”)

@article{korostelevCrystalStructure70S2006, title = {Crystal Structure of a {{70S}} Ribosome-{{tRNA}} Complex Reveals Functional Interactions and Rearrangements}, author = {Korostelev, A. and Trakhanov, S. and Laurberg, M. and Noller, H.F.}, year = 2006, journal = {Cell}, volume = {126}, number = {6}, pages = {1065–1077}, publisher = {Elsevier}, doi = {10.1016/j.cell.2006.08.032}, url = {PM:16962654}, abstract = {Our understanding of the mechanism of protein synthesis has undergone rapid progress in recent years as a result of low-resolution X-ray and cryo-EM structures of ribosome functional complexes and high-resolution structures of ribosomal subunits and vacant ribosomes. Here, we present the crystal structure of the Thermus thermophilus 70S ribosome containing a model mRNA and two tRNAs at 3.7 A resolution. Many structural details of the interactions between the ribosome, tRNA, and mRNA in the P and E sites and the ways in which tRNA structure is distorted by its interactions with the ribosome are seen. Differences between the conformations of vacant and tRNA-bound 70S ribosomes suggest an induced fit of the ribosome structure in response to tRNA binding, including significant changes in the peptidyl-transferase catalytic site}, keywords = {70S RIBOSOME,BINDING,BIOLOGY,COMPLEX,COMPLEXES,CONFORMATION,crystal structure,CRYSTAL-STRUCTURE,E,E site,La,MECHANISM,MODEL,Molecular Biology,mRNA,nosource,peptidyl transferase,PEPTIDYL-TRANSFERASE,Peptidyltransferase,protein,protein synthesis,PROTEIN-SYNTHESIS,RESOLUTION,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,SITE,SITES,Structural,structure,SUBUNIT,SUBUNITS,Thermus,Thermus thermophilus,THERMUS-THERMOPHILUS,tRNA,tRNA binding} }

@article{korostelevStructuralDynamicsRibosome2008, title = {Structural Dynamics of the Ribosome}, author = {Korostelev, A. and Ermolenko, D.N. and Noller, H.F.}, year = 2008, month = oct, journal = {Current opinion in chemical biology}, volume = {12}, number = {6}, pages = {674–683}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1367593108001464}, abstract = {Protein synthesis is inherently a dynamic process, requiring both small-scale and large-scale movements of tRNA and mRNA. It has long been suspected that these movements might be coupled to conformational changes in the ribosome, and in its RNA moieties in particular. Recently, the nature of ribosome structural dynamics has begun to emerge from a combination of approaches, most notably cryo-EM, X-ray crystallography, and FRET. Ribosome movement occurs both on a grand scale, as in the intersubunit rotational movements that are coupled to tRNA-mRNA translocation, and in intricate localized rearrangements such as those that accompany codon-anticodon recognition and peptide bond formation. In spite of much progress, our understanding of the mechanics of translation is now beset with countless new questions, reflecting the vast molecular architecture of the ribosome itself}, keywords = {BIOLOGY,BOND FORMATION,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,Crystallography,DYNAMICS,La,Molecular Biology,Movement,mRNA,No DOI found,nosource,peptide bond formation,protein,protein synthesis,PROTEIN-SYNTHESIS,RECOGNITION,Review,ribosome,Rna,Structural,translation,translocation,tRNA} } % == BibTeX quality report for korostelevStructuralDynamicsRibosome2008: % ? unused Journal abbr (“Curr.Opin.Chem.Biol”)

@article{kosowska-shickSingleMultistepResistance2006, title = {Single- and Multistep Resistance Selection Studies on the Activity of Retapamulin Compared to Other Agents against {{Staphylococcus}} Aureus and {{Streptococcus}} Pyogenes}, author = {{Kosowska-Shick}, K. and Clark, C. and Credito, K. and McGhee, P. and Dewasse, B. and Bogdanovich, T. and Appelbaum, P.C.}, year = 2006, month = feb, journal = {Antimicrobial Agents and Chemotherapy}, volume = {50}, number = {2}, pages = {765–769}, publisher = {American Society for Microbiology (ASM)}, doi = {10.1128/AAC.50.2.765-769.2006}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1366917/}, abstract = {Retapamulin had the lowest rate of spontaneous mutations by single-step passaging and the lowest parent and selected mutant MICs by multistep passaging among all drugs tested for all Staphylococcus aureus strains and three Streptococcus pyogenes strains which yielded resistant clones. Retapamulin has a low potential for resistance selection in S. pyogenes, with a slow and gradual propensity for resistance development in S. aureus}, keywords = {0,Amino Acid Sequence,Anti-Bacterial Agents,Bicyclo CompoundsHeterocyclic,chemistry,Comparative Study,development,drug effects,Drug ResistanceBacterial,drugs,genetics,INHIBITOR,inhibitors,L3,La,Microbial Sensitivity Tests,Molecular Sequence Data,Mutation,MUTATIONS,nosource,pathology,pharmacology,protein,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,Proteins,RESISTANCE,RESISTANT,Ribosomal Proteins,RIBOSOMAL-PROTEIN,S,SELECTION,Staphylococcus aureus,STAPHYLOCOCCUS-AUREUS,Streptococcus pyogenes,Support,SYNTHESIS INHIBITORS} } % == BibTeX quality report for kosowska-shickSingleMultistepResistance2006: % ? unused Journal abbr (“Antimicrob.Agents Chemother.”)

@article{kotheSinglestepPurificationSpecific2006, title = {Single-Step Purification of Specific {{tRNAs}} by Hydrophobic Tagging}, author = {Kothe, U. and Paleskava, A. and Konevega, A.L. and Rodnina, M.V.}, year = 2006, journal = {Anal.Biochem.}, volume = {356}, number = {1}, pages = {148–150}, doi = {10.1016/j.ab.2006.04.038}, url = {PM:16750812}, keywords = {0,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,Bacterial,Biochemistry,chemistry,ChromatographyHigh Pressure Liquid,Escherichia coli,Fluorenes,Germany,Hydrophobicity,isolation & purification,La,Methods,nosource,purification,Research SupportNon-U.S.Gov’t,Rna,RNABacterial,RNATransfer,RNATransferAla,RNATransferAmino Acid-Specific,Selenocysteine,tRNA} } % == BibTeX quality report for kotheSinglestepPurificationSpecific2006: % ? Possibly abbreviated journal title Anal.Biochem.

@article{kouvelaChangesConformation5S2007, title = {Changes in the Conformation of {{5S rRNA}} Cause Alterations in Principal Functions of the Ribosomal Nanomachine}, author = {Kouvela, E.C. and Gerbanas, G.V. and Xaplanteri, M.A. and Petropoulos, A.D. and Dinos, G.P. and Kalpaxis, D.L.}, year = 2007, journal = {Nucleic acids research}, volume = {35}, number = {15}, pages = {5108–5119}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkm546}, url = {http://nar.oxfordjournals.org/content/35/15/5108.short}, abstract = {5S rRNA is an integral component of the large ribosomal subunit in virtually all living organisms. Polyamine binding to 5S rRNA was investigated by cross-linking of N1-azidobenzamidino (ABA)-spermine to naked 5S rRNA or 50S ribosomal subunits and whole ribosomes from Escherichia coli cells. ABA-spermine cross-linking sites were kinetically measured and their positions in 5S rRNA were localized by primer extension analysis. Helices III and V, and loops A, C, D and E in naked 5S rRNA were found to be preferred polyamine binding sites. When 50S ribosomal subunits or poly(U)-programmed 70S ribosomes bearing tRNA(Phe) at the E-site and AcPhe-tRNA at the P-site were targeted, the susceptibility of 5S rRNA to ABA-spermine was greatly reduced. Regardless of 5S rRNA assembly status, binding of spermine induced significant changes in the 5S rRNA conformation; loop A adopted an apparent ‘loosening’ of its structure, while loops C, D, E and helices III and V achieved a more compact folding. Poly(U)-programmed 70S ribosomes possessing 5S rRNA cross-linked with spermine were more efficient than control ribosomes in tRNA binding, peptidyl transferase activity and translocation. Our results support the notion that 5S rRNA serves as a signal transducer between regions of 23S rRNA responsible for principal ribosomal functions}, keywords = {0,5S rRNA,70S RIBOSOME,analogs & derivatives,analysis,assembly,Azides,Bacterial,Base Sequence,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,Biochemistry,CELLS,chemistry,COMPONENT,CONFORMATION,CROSS-LINKING,CROSSLINKING,D,E,E site,enzymology,Escherichia coli,ESCHERICHIA-COLI,genetics,Kinetics,La,LOOP,metabolism,ModelsMolecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,P SITE,P-SITE,peptidyl transferase,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,Photoaffinity Labels,Poly U,polyamine,POSITION,POSITIONS,primer extension,REGION,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNABacterial,RNARibosomal5S,RNATransferAmino Acyl,rRNA,SIGNAL,SITE,SITES,Spermine,structure,SUBUNIT,SUBUNITS,Support,Transferases,translocation,tRNA,tRNA binding} } % == BibTeX quality report for kouvelaChangesConformation5S2007: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{kowalczukTotalNumberCoding1999a, title = {Total Number of Coding Open Reading Frames in the Yeast Genome}, author = {Kowalczuk, M. and Mackiewicz, P. and Gierlik, A. and Dudek, M.R. and Cebrat, S.}, year = 1999, journal = {Yeast}, volume = {15}, number = {11}, pages = {1031–1034}, doi = {10.1002/(SICI)1097-0061(199908)15:11<1031::AID-YEA431>3.0.CO;2-G}, url = {http://www.smorfland.uni.wroc.pl/uploads/Main/Yeast 15.pdf}, abstract = {At the end of 1996 we approximated the total number of protein coding ORFs in the Saccharomyces cerevisiae genome, based on their properties, as 4700-4800. The number is much smaller than the 5800 which is widely accepted. According to our calculations, there remain about 200-300 orphans-ORFs without known function or homology to already discovered genes, which is only about 5% of the total number of genes. Our results would be questionable if the analysed set of known genes was not a statistically representative sample of the whole set of protein coding genes in the S. cerevisiae genome. Therefore, we repeated our estimation using recently updated databases. In the course of the last 18 months, previously unknown functions of about 500 genes have been found. We have used these to check our method, former results and conclusions. Our previous estimation of the total number of coding ORFs was confirmed. Copyright (C) 1999 John Wiley & Sons, Ltd}, keywords = {CEREVISIAE,coding sequence,COMPLETE DNA-SEQUENCE,DATABASE,Databases,FRAME,gene,gene number,Genes,Genome,genome coding capacity,nosource,OPEN READING FRAME,Open Reading Frames,protein,READING FRAME,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,yeast} }

@article{kozakScanningModelTranslation1989, title = {The Scanning Model for Translation: An Update.}, author = {Kozak, M.}, year = 1989, month = feb, journal = {The Journal of Cell Biology}, volume = {108}, number = {2}, pages = {229–241}, publisher = {Rockefeller Univ Press}, doi = {10.1083/jcb.108.2.229}, url = {http://jcb.rupress.org/content/108/2/229.abstract}, abstract = {The small (40S) subunit of eukaryotic ribosomes is believed to bind initially at the capped 5’-end of messenger RNA and then migrate, stopping at the first AUG codon in a favorable context for initiating translation. The first-AUG rule is not absolute, but there are rules for breaking the rule. Some anomalous observations that seemed to contradict the scanning mechanism now appear to be artifacts. A few genuine anomalies remain unexplained}, keywords = {0,animal,AUG,Codon,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,GenesFungal,GenesViral,human,La,MECHANISM,MESSENGER-RNA,metabolism,Methionine,MODEL,ModelsBiological,nosource,Regulatory SequencesNucleic Acid,Review,ribosome,Ribosomes,Rna,RNAMessenger,RNATransferAmino Acyl,RULES,scanning,SUBUNIT,supportu.s.gov’tp.h.s.,translation,TranslationGenetic} } % == BibTeX quality report for kozakScanningModelTranslation1989: % ? unused Journal abbr (“J.Cell Biol.”)

@article{kozakRegulationTranslationEukaryotic1992, title = {Regulation of Translation in Eukaryotic Systems.}, author = {Kozak, M.}, year = 1992, journal = {Annual review of cell biology}, volume = {8}, number = {1}, pages = {197–225}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, doi = {10.1146/annurev.cb.08.110192.001213}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.cb.08.110192.001213}, keywords = {accuracy,GTP,nosource,regulation,Review,SYSTEM,translation} } % == BibTeX quality report for kozakRegulationTranslationEukaryotic1992: % ? unused Journal abbr (“Annu.Rev.Cell Biol.”)

@article{kozakPrimerExtensionAnalysis1998, title = {Primer Extension Analysis of Eukaryotic Ribosome-{{mRNA}} Complexes}, author = {Kozak, M.}, year = 1998, month = nov, journal = {Nucleic acids research}, volume = {26}, number = {21}, pages = {4853–4859}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/26.21.4853}, url = {http://nar.oxfordjournals.org/content/26/21/4853.short}, abstract = {Conditions are described for using a primer extension inhibition (toeprinting) assay to study the initiation step of protein synthesis in rabbit reticulocyte lysates. These studies revealed that chloramphenicol acetyltransferase mRNA, which is widely used as a reporter, forms unusually labile initiation complexes. This and other unexpected problems were solved by adjustments in pH and temperature during the reverse transcriptase step. Complications that may occur during the ribosome binding step were also examined, including the possibility of rapid mRNA degradation. The suitability of inhibitors commonly used to block the elongation phase of translation was studied. The refined toeprinting assay was used to confirm context-dependent selection of the AUG start codon. Absence of the m7G cap did not subvert the process wherein initiation is restricted to the first AUG codon. The fidelity of initiation was impaired, however, when NaF was introduced during the ribosome binding step. In a preliminary assessment of the processivity of scanning, no dissociation of 40S ribosomal subunits was detected as the distance from the cap to the AUG codon was increased to nearly 300 bases. With an mRNA that contains a pseudoknot upstream from the AUG codon, the toeprinting assay revealed 40S ribosomal subunits trapped behind the base paired structure. Thus the assay is usable for mapping some intermediates as well as for detecting conventional 80S initiation complexes}, keywords = {0,analysis,animal,Base Sequence,BINDING,Cap,chemistry,Chloramphenicol,Chloramphenicol O-Acetyltransferase,Codon,CodonInitiator,COMPLEX,COMPLEXES,degradation,elongation,Fidelity,GenesReporter,Genetic Techniques,genetics,In Vitro,INHIBITION,initiation,La,lysate,mapping,metabolism,Molecular Sequence Data,mRNA,nosource,Nucleic Acid Conformation,Peptide Chain Initiation,primer extension,protein,protein synthesis,PROTEIN-SYNTHESIS,pseudoknot,Rabbits,Reticulocytes,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNAMessenger,structure,SUBUNIT,Temperature,toeprinting,translation} } % == BibTeX quality report for kozakPrimerExtensionAnalysis1998: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{kozakNewWaysInitiating2001a, title = {New Ways of Initiating Translation in Eukaryotes? {{Author}}’s Reply}, author = {Kozak, M.}, year = 2001, month = dec, journal = {Molecular and Cellular Biology}, volume = {21}, number = {23}, pages = {8241–8246}, url = {ISI:000172059100035}, keywords = {BINDING-PROTEIN,expression,FACTOR 4G,FUNCTIONAL-CHARACTERIZATION,INTERNAL RIBOSOME ENTRY,LA AUTOANTIGEN,M,MESSENGER-RNA SEQUENCES,MOSAIC-VIRUS,No DOI found,nosource,PROTEIN-SYNTHESIS,SITE IRES,translation} }

@article{kraakmanFunctionalAnalysisPromoter1991, title = {Functional Analysis of the Promoter of the Gene Encoding the Acidic Ribosomal Protein {{L45}} in Yeast}, author = {Kraakman, L.S. and Mager, W.H. and Grootjans, J.J. and Planta, R.J.}, year = 1991, month = oct, journal = {Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression}, volume = {1090}, number = {2}, pages = {204–210}, publisher = {Elsevier}, doi = {10.1016/0167-4781(91)90102-R}, url = {http://linkinghub.elsevier.com/retrieve/pii/016747819190102R}, abstract = {The gene encoding the acidic ribosomal protein L45 in yeast is expressed coordinately with other rp-genes. The promoter region of this gene harbours binding sites for CP1 and ABF1. We demonstrate that the CP1-site is not involved in the transcription activation of the L45-gene. Rather, the ABF1-site, through deviating from the consensus sequence (RTARY3N3ACG), appears to be essential for efficient transcription. Replacement of this site by a consensus RAP1-binding site (an RPG box) did not alter the transcriptional yield of the L45-gene. An additional transcription activating region is present downstream of the ABF1-site. The relevant nucleotide sequence, which is repeated in the L45-gene promoter, gives rise to complex formation with a yeast protein extract in a bandshift assay. The results indicate that the L45-gene promoter has a complex architecture}, keywords = {92031692,activation,analysis,Base Sequence,BINDING,Binding Sites,COMPLEX,COMPLEXES,Consensus Sequence,DNA-Binding Proteins,Fungal Proteins,gene,GenesFungal,genetics,metabolism,Molecular Sequence Data,nosource,Promoter Regions (Genetics),protein,Ribosomal Proteins,Saccharomyces cerevisiae,sequence,supportnon-u.s.gov’t,transcription,TranscriptionGenetic,yeast} } % == BibTeX quality report for kraakmanFunctionalAnalysisPromoter1991: % ? unused Journal abbr (“Biochim.Biophys.Acta”)

@article{kramerRibosomalGeneTranscription1985, title = {5 {{S}} Ribosomal Gene Transcription during {{Xenopus}} Oogenesis.}, author = {Kramer, A. and Kr{"a}mer, A.}, year = 1985, journal = {Developmental biology (New York, NY: 1985)}, volume = {1}, eprint = {3917205}, eprinttype = {pubmed}, pages = {431–451}, url = {http://www.ncbi.nlm.nih.gov/pubmed/3917205}, keywords = {Animals,BIOLOGY,biosynthesis,cancer,gene,GENE-TRANSCRIPTION,genetics,No DOI found,nosource,Oogenesis,physiology,RNARibosomal,RNARibosomal5S,S,transcription,Transcription Factor TFIIIA,Transcription Factors,TranscriptionGenetic,Xenopus} }

@article{kramerFrequencyTranslationalMisreading2007, title = {The Frequency of Translational Misreading Errors in {{E}}. Coli Is Largely Determined by {{tRNA}} Competition}, author = {Kramer, E.B. and Farabaugh, P.J.}, year = 2007, month = jan, journal = {RNA.}, volume = {13}, number = {1}, pages = {87–96}, publisher = {Cold Spring Harbor Lab}, doi = {10.1261/rna.294907}, url = {http://rnajournal.cshlp.org/content/13/1/87.short}, abstract = {Estimates of missense error rates (misreading) during protein synthesis vary from 10(-3) to 10(-4) per codon. The experiments reporting these rates have measured several distinct errors using several methods and reporter systems. Variation in reported rates may reflect real differences in rates among the errors tested or in sensitivity of the reporter systems. To develop a more accurate understanding of the range of error rates, we developed a system to quantify the frequency of every possible misreading error at a defined codon in Escherichia coli. This system uses an essential lysine in the active site of firefly luciferase. Mutations in Lys529 result in up to a 1600-fold reduction in activity, but the phenotype varies with amino acid. We hypothesized that residual activity of some of the mutant genes might result from misreading of the mutant codons by tRNA(Lys) (UUUU), the cognate tRNA for the lysine codons, AAA and AAG. Our data validate this hypothesis and reveal details about relative missense error rates of near-cognate codons. The error rates in E. coli do, in fact, vary widely. One source of variation is the effect of competition by cognate tRNAs for the mutant codons; higher error frequencies result from lower competition from low-abundance tRNAs. We also used the system to study the effect of ribosomal protein mutations known to affect error rates and the effect of error-inducing antibiotics, finding that they affect misreading on only a subset of near-cognate codons and that their effect may be less general than previously thought}, keywords = {0,accuracy,ACID,ACTIVE-SITE,AMINO-ACID,analysis,antibiotic,antibiotics,Binding Sites,BIOLOGY,chemistry,Codon,CODONS,drug effects,E,ERRORS,Escherichia coli,ESCHERICHIA-COLI,FIREFLY LUCIFERASE,gene,Genes,genetics,La,luciferase,Luciferases,LuciferasesFirefly,Lysine,metabolism,Methods,misreading errors,Mutation,MutationMissense,MUTATIONS,nosource,paromomycin,Paromomycin,pharmacology,Phenotype,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,RIBOSOMAL-PROTEIN,Rna,RNA Editing,RNATransfer,SITE,streptomycin,Streptomycin,Support,SYSTEM,SYSTEMS,tRNA} } % == BibTeX quality report for kramerFrequencyTranslationalMisreading2007: % ? Possibly abbreviated journal title RNA.

@article{krokowskiElevatedCopyNumber2007a, title = {Elevated Copy Number of {{L-A}} Virus in Yeast Mutant Strains Defective in Ribosomal Stalk}, author = {Krokowski, D. and Tchorzewski, M. and Boguszewska, A. and McKay, A.R. and Maslen, S.L. and Robinson, C.V. and Grankowski, N.}, year = 2007, month = apr, journal = {Biochem.Biophys.Res.Commun.}, volume = {355}, number = {2}, pages = {575–580}, doi = {10.1016/j.bbrc.2007.02.024}, url = {PM:17307145}, abstract = {The eukaryotic ribosomal stalk, composed of the P-proteins, is a part of the GTPase-associated-center which is directly responsible for stimulation of translation-factor-dependent GTP hydrolysis. Here we report that yeast mutant strains lacking P1/P2-proteins show high propagation of the yeast L-A virus. Affinity-capture-MS analysis of a protein complex isolated from a yeast mutant strain lacking the P1A/P2B proteins using anti-P0 antibodies showed that the Gag protein, the major coat protein of the L-A capsid, is associated with the ribosomal stalk. Proteomic analysis revealed that the elongation factor eEF1A was also present in the isolated complex. Additionally, yeast strains lacking the P1/P2-proteins are hypersensitive to paromomycin and hygromycin B, underscoring the fact that structural perturbations in the stalk strongly influence the ribosome function, especially at the level of elongation}, keywords = {0,analysis,Antibodies,antibody,BIOLOGY,Capsid,capsid protein,Capsid Proteins,ChromatographyAffinity,COAT PROTEIN,COMPLEX,COMPLEXES,ElectrophoresisPolyacrylamide Gel,elongation,Gag,genetics,GTP,Hydrolysis,Hygromycin B,L-A,L-A-VIRUS,La,metabolism,Molecular Biology,Mutation,nosource,Paromomycin,pharmacology,PROPAGATION,protein,PROTEIN COMPLEX,Proteins,Proteome,ribosome,Ribosomes,Saccharomyces cerevisiae,Structural,Support,Tandem Mass Spectrometry,virology,virus,yeast} } % == BibTeX quality report for krokowskiElevatedCopyNumber2007a: % ? Possibly abbreviated journal title Biochem.Biophys.Res.Commun.

@article{ksiazekNovelCoronavirusAssociated2003, title = {A Novel Coronavirus Associated with Severe Acute Respiratory Syndrome}, author = {Ksiazek, T.G. and Erdman, D. and Goldsmith, C.S. and Zaki, S.R. and Peret, T. and Emery, S. and Tong, S. and Urbani, C. and Comer, J.A. and Lim, W. and Rollin, P.E. and Dowell, S.F. and Ling, A.E. and Humphrey, C.D. and Shieh, W.J. and Guarner, J. and Paddock, C.D. and Rota, P. and Fields, B. and DeRisi, J. and Yang, J.Y. and Cox, N. and Hughes, J.M. and LeDuc, J.W. and Bellini, W.J. and Anderson, L.J.}, year = 2003, month = may, journal = {N.Engl.J.Med.}, volume = {348}, number = {20}, pages = {1953–1966}, doi = {10.1056/NEJMoa030781}, url = {PM:12690092}, abstract = {BACKGROUND: A worldwide outbreak of severe acute respiratory syndrome (SARS) has been associated with exposures originating from a single ill health care worker from Guangdong Province, China. We conducted studies to identify the etiologic agent of this outbreak. METHODS: We received clinical specimens from patients in seven countries and tested them, using virus-isolation techniques, electron-microscopical and histologic studies, and molecular and serologic assays, in an attempt to identify a wide range of potential pathogens. RESULTS: None of the previously described respiratory pathogens were consistently identified. However, a novel coronavirus was isolated from patients who met the case definition of SARS. Cytopathological features were noted in Vero E6 cells inoculated with a throat-swab specimen. Electron-microscopical examination revealed ultrastructural features characteristic of coronaviruses. Immunohistochemical and immunofluorescence staining revealed reactivity with group I coronavirus polyclonal antibodies. Consensus coronavirus primers designed to amplify a fragment of the polymerase gene by reverse transcription-polymerase chain reaction (RT-PCR) were used to obtain a sequence that clearly identified the isolate as a unique coronavirus only distantly related to previously sequenced coronaviruses. With specific diagnostic RT-PCR primers we identified several identical nucleotide sequences in 12 patients from several locations, a finding consistent with a point-source outbreak. Indirect fluorescence antibody tests and enzyme-linked immunosorbent assays made with the new isolate have been used to demonstrate a virus-specific serologic response. This virus may never before have circulated in the U.S. population. CONCLUSIONS: A novel coronavirus is associated with this outbreak, and the evidence indicates that this virus has an etiologic role in SARS. Because of the death of Dr. Carlo Urbani, we propose that our first isolate be named the Urbani strain of SARS-associated coronavirus}, keywords = {0,Adult,analysis,Animals,Antibodies,antibody,assays,Bronchoalveolar Lavage Fluid,Cell Line,CELLS,classification,Coronavirus,disease,Disease Outbreaks,epidemiology,Female,Fluorescence,gene,genetics,human,IDENTIFY,isolation & purification,La,LOCATION,Lung,Male,Methods,MicroscopyElectron,Middle Aged,nosource,NUCLEOTIDE-SEQUENCE,Oropharynx,pathology,Phylogeny,polymerase,Polymerase Chain Reaction,Rna,RnaViral,SARS,Sars Virus,sequence,SEQUENCES,Severe Acute Respiratory Syndrome,Staining,techniques,ultrastructure,virology,virus} } % == BibTeX quality report for ksiazekNovelCoronavirusAssociated2003: % ? Possibly abbreviated journal title N.Engl.J.Med.

@article{kuaiPolyadenylationRRNASaccharomyces2004, title = {Polyadenylation of {{rRNA}} in {{Saccharomyces}} Cerevisiae}, author = {Kuai, L. and Fang, F. and Butler, J.S. and Sherman, F.}, year = 2004, month = jun, journal = {Proceedings of the National Academy of Sciences}, volume = {101}, number = {23}, pages = {8581–8586}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.0402888101}, url = {http://www.pnas.org/content/101/23/8581.short}, abstract = {In contrast to mRNAs, rRNAs are transcribed by RNA polymerase I or III and are not believed to be polyadenylated. Here we show that in Saccharomyces cerevisiae, at least a small fraction of rRNAs do have a poly(A) tail. The levels of polyadenylated rRNAs are dramatically increased in strains lacking the degradation function of Rrp6p, a component of the nuclear exosome. Pap1p, the poly(A) polymerase, is responsible for adenylating the rRNAs despite the fact that the rRNAs do not have a canonical polyadenylation signal. Polyadenylated rRNAs reside mainly within the nucleus and are in turn degraded. For at least one rRNA type, the polyadenylation preferentially occurs on the precursor rather than the mature product. The existence of polyadenylated rRNAs may reflect a quality-control mechanism of rRNA biogenesis}, keywords = {0,Base Sequence,Biochemistry,BIOGENESIS,Biophysics,Cell Nucleus,CEREVISIAE,chemistry,COMPONENT,degradation,Exoribonucleases,exosome,GenesFungal,genetics,In Situ HybridizationFluorescence,La,MECHANISM,metabolism,mRNA,nosource,Poly A,poly(A),POLY(A) TAIL,Polyadenylation,polymerase,Polynucleotide Adenylyltransferase,PRECURSOR,PRODUCT,protein,Proteins,Quality Control,QUALITY-CONTROL,Reverse Transcriptase Polymerase Chain Reaction,ribosomal RNA,RIBOSOMAL-RNA,Rna,RNA Polymerase I,RNA-POLYMERASE,RNA-POLYMERASE-I,RNAFungal,RNARibosomal,rRNA,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SIGNAL,Support} } % == BibTeX quality report for kuaiPolyadenylationRRNASaccharomyces2004: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{kudlickiRibosomalProteinSubstrate1976, title = {Ribosomal Protein as Substrate for a {{GTP-dependent}} Protein Kinase from Yeast}, author = {Kudlicki, W. and Grankowski, N. and Gasior, E.}, year = 1976, month = nov, journal = {Molecular biology reports}, volume = {3}, number = {2}, pages = {121–129}, publisher = {Springer}, doi = {10.1007/BF00423225}, url = {http://www.springerlink.com/index/M2671680332U7G05.pdf}, abstract = {A protein kinase specific for casein and acidic ribosomal proteins was isolated and partly characterized. It was found that the enzyme utilizes GTP and ATP as phosphoryl donors. Its affinity for ATP was considerably higher than for GTP with the km values of 7.6 X 10(-6)M and 5.5 X 10(-5)M, respectively. Two-dimensional acrylamide gel electrophoresis revealed the phosphorylation of the same ribosomal proteins with either of the [gamma-32P] nucleotides used. It was also shown that one acidic protein (S1 or S2) of 40 S and two acidic proteins (L2 and L3) of 60 S ribosomal subunits were predominantly phosphorylated in vitro. The phosphorylated proteins: L2 and L3 seem to correspond to the proteins of L7 and L12 of E. coli ribosomes. The isolated kinase phosphorylated several basic ribosomal proteins though to a lower extent than the acidic ones}, keywords = {0,ATP,E,Electrophoresis,enzyme,enzymology,GEL-ELECTROPHORESIS,GTP,Guanosine,Guanosine Triphosphate,In Vitro,IN-VITRO,kinase,Kinetics,L2,L3,La,Magnesium,metabolism,nosource,Nucleotides,pharmacology,Phosphorylation,protein,Protein Kinases,PROTEIN-KINASE,Proteins,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,S,Saccharomyces cerevisiae,SUBUNIT,SUBUNITS,yeast} } % == BibTeX quality report for kudlickiRibosomalProteinSubstrate1976: % ? unused Journal abbr (“Mol.Biol.Rep.”)

@article{kudlickiEvidenceHighlySpecific1980, title = {Evidence for a Highly Specific Protein Kinase Phosphorylating Two Strongly Acidic Proteins of Yeast 60 {{S}} Ribosomal Subunit}, author = {Kudlicki, W. and Szyszka, R. and Palen, E. and Gasior, E.}, year = 1980, month = dec, journal = {Biochimica et Biophysica Acta (BBA)-General Subjects}, volume = {633}, number = {3}, pages = {376–385}, publisher = {Elsevier}, doi = {10.1016/0304-4165(80)90196-8}, url = {http://linkinghub.elsevier.com/retrieve/pii/0304416580901968}, abstract = {Two distinct, cyclic AMP-independent protein kinase (ATP : protein photransferase, EC 2.7.1.37) from yeast have been isolated and highly purified. The first of the enzymes, protein kinase 1 A, phosphorylates casein and phosvitin, and its cellular protein substrate is unknown. The second enzyme, protein kinase 1 B, phosphorylates two strongly acidic proteins, L44 and L45, of the 60 S ribosomal subunit}, keywords = {0,Adenosine,Adenosine Triphosphate,ATP,classification,Comparative Study,enzyme,Enzymes,kinase,Kinetics,L2,L3,La,Magnesium,metabolism,nosource,pharmacology,Phosphorylation,protein,Protein Kinases,PROTEIN-KINASE,Proteins,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,Ribosomes,S,Saccharomyces cerevisiae,Substrate Specificity,SUBUNIT,Support,yeast} } % == BibTeX quality report for kudlickiEvidenceHighlySpecific1980: % ? unused Journal abbr (“Biochim.Biophys.Acta”)

@article{kujawaStructuralRequirementsEfficient1993, title = {Structural Requirements for Efficient Translational Frameshifting in the Synthesis of the Putative Viral {{RNA-dependent RNA}} Polymerase of Potato Leafroll Virus.}, author = {Kujawa, A.B. and Drugeon, G. and Hulanicka, D. and Haenni, A.-L.}, year = 1993, journal = {Nucleic acids research}, volume = {21}, number = {9}, pages = {2165–2171}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/21.9.2165}, url = {http://nar.oxfordjournals.org/content/21/9/2165.short}, keywords = {efficiency,Frameshifting,nosource,polymerase,pseudoknot,Rna,Structural,virus} } % == BibTeX quality report for kujawaStructuralRequirementsEfficient1993: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{kumarTRIPLESDatabaseGene2000, title = {{{TRIPLES}}: A Database of Gene Function in {{Saccharomyces}} Cerevisiae}, author = {Kumar, A. and Cheung, K.H. and {Ross-Macdonald}, P. and Coelho, P.S. and Miller, P. and Snyder, M.}, year = 2000, month = jan, journal = {Nucleic acids research}, volume = {28}, number = {1}, pages = {81–84}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/28.1.81}, url = {http://nar.oxfordjournals.org/content/28/1/81.short}, abstract = {Using a novel multipurpose mini-transposon, we have generated a collection of defined mutant alleles for the analysis of disruption phenotypes, protein localization, and gene expression in Saccharomyces cerevisiae. To catalog this unique data set, we have developed TRIPLES, a Web-accessible database of TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces. Encompassing over 250 000 data points, TRIPLES provides convenient access to information from nearly 7800 transposon-mutagenized yeast strains; within TRIPLES, complete data reports of each strain may be viewed in table format, or if desired, downloaded as tab-delimited text files. Each report contains external links to corresponding entries within the Saccharomyces Genome Database and International Nucleic Acid Sequence Data Library (GenBank). Unlike other yeast databases, TRIPLES also provides on-line order forms linked to each clone report; users may immediately request any desired strain free-of-charge by submitting a completed form. In addition to presenting a wealth of information for over 2300 open reading frames, TRIPLES constitutes an important medium for the distribution of useful reagents throughout the yeast scientific community. Maintained by the Yale Genome Analysis Center, TRIPLES may be accessed at http://ycmi.med.yale.edu/ygac/triples.htm}, keywords = {20063221,Alleles,analysis,DATABASE,DatabasesFactual,DNA Transposable Elements,expression,gene,Gene Expression,GENE-EXPRESSION,GenesFungal,genetics,Genome,library,media,nosource,Open Reading Frames,Phenotype,protein,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces Genome Database,SACCHAROMYCES-CEREVISIAE,sequence,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,yeast} } % == BibTeX quality report for kumarTRIPLESDatabaseGene2000: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{kumarInsertionalMutagenesisTransposoninsertion2002, title = {Insertional Mutagenesis: {{Transposon-insertion}} Libraries as Mutagens in Yeast}, author = {Kumar, A. and Vidan, S. and Snyder, M.}, year = 2002, journal = {Guide to Yeast Genetics and Molecular and Cell Biology, Pt B}, volume = {350}, pages = {219–229}, publisher = {Elsevier}, doi = {10.1016/S0076-6879(02)50965-4}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0076687902509654}, keywords = {0,DISRUPTION,GENE-EXPRESSION,Genome,LARGE-SCALE ANALYSIS,library,Mutagenesis,Mutagens,nosource,PROTEIN LOCALIZATION,Review,SACCHAROMYCES-CEREVISIAE,SEQUENCES,SYSTEM,yeast} }

@article{kunkelRapidEfficientSitespecific1985a, title = {Rapid and Efficient Site-Specific Mutagenesis without Phenotype Selection.}, author = {Kunkel, T.}, year = 1985, journal = {Proc.Natl.Acad.Sci.USA}, volume = {82}, pages = {488–492}, doi = {10.1073/pnas.82.2.488}, keywords = {Mutagenesis,nosource,Phenotype,site specific} } % == BibTeX quality report for kunkelRapidEfficientSitespecific1985a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{kuntzelConsensusStructureEvolution1983, title = {Consensus Structure and Evolution of {{5S rRNA}}}, author = {Kuntzel, H. and Piechulla, B. and Hahn, U.}, year = 1983, month = feb, journal = {Nucleic Acids Research}, volume = {11}, number = {3}, pages = {893–900}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/11.3.893}, url = {http://nar.oxfordjournals.org/content/11/3/893.short}, abstract = {A consensus structure model of 5S rRNA presenting all conserved nucleotides in fixed positions has been deduced from the primary and secondary structure of 71 eubacterial, archaebacterial, eukaryotic cytosolic and organellar molecules. Phylogenetically related groups of molecules are characterized by nucleotide deletions in helices III, IV and V, and by potential base pair interactions in helix IV. The group-specific deletions are correlated with the early branching pattern of a dendrogram calculated from nucleotide substitution data: the first major division separates the group of eubacterial and organellar molecules from a second group containing the common ancestors of archaebacterial and eukaryotic/cytosolic molecules. The earliest diverging branch of the eubacterial/organellar group includes molecules from Thermus thermophilus, T. aquaticus, Rhodospirillum rubrum, Paracoccus denitrificans and wheat mitochondria}, keywords = {5S rRNA,83168909,Bacteria,Base Sequence,Comparative Study,Evolution,genetics,mitochondria,ModelsGenetic,nosource,Nucleic Acid Conformation,Nucleotides,RNARibosomal,rRNA,Species Specificity,structure,Thermus,Thermus thermophilus,Wheat} } % == BibTeX quality report for kuntzelConsensusStructureEvolution1983: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{kurlandAllostericMechanismCodonDependent1975a, title = {Allosteric {{Mechanism}} for {{Codon-Dependent Transfer-RNA Selection}} on {{Ribosomes}}}, author = {Kurland, C.G. and Rigler, R. and Ehrenberg, M. and Blomberg, C.}, year = 1975, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {72}, number = {11}, pages = {4248–4251}, doi = {10.1073/pnas.72.11.4248}, url = {ISI:A1975AX56700016}, keywords = {MECHANISM,nosource,ribosome,Ribosomes,SELECTION,TRANSFER-RNA} } % == BibTeX quality report for kurlandAllostericMechanismCodonDependent1975a: % ? Title looks like it was stored in title-case in Zotero

@article{kurlandTranslationalAccuracyVitro1982a, title = {Translational {{Accuracy In}} Vitro}, author = {Kurland, C.G.}, year = 1982, journal = {Cell}, volume = {28}, number = {2}, pages = {201–202}, doi = {10.1016/0092-8674(82)90336-1}, url = {http://cat.inist.fr/?aModele=afficheN&cpsidt=9351775}, keywords = {accuracy,In Vitro,IN-VITRO,nosource,Review} }

@article{kurlandTranslationalAccuracyFitness1992a, title = {Translational Accuracy and the Fitness of Bacteria.}, author = {Kurland, C.G.}, year = 1992, journal = {Annu.Rev.Genet.}, volume = {26}, pages = {29–50}, doi = {10.1146/annurev.ge.26.120192.000333}, keywords = {accuracy,Bacteria,Fidelity,nosource,translation} } % == BibTeX quality report for kurlandTranslationalAccuracyFitness1992a: % ? Possibly abbreviated journal title Annu.Rev.Genet.

@article{kuyperHighlevelFunctionalExpression2003, title = {High-Level Functional Expression of a Fungal Xylose Isomerase: The Key to Efficient Ethanolic Fermentation of Xylose by {{Saccharomyces}} Cerevisiae?}, author = {Kuyper, M. and Harhangi, H.R. and Stave, A.K. and Winkler, A.A. and Jetten, M.S. and {}{de Laat}, W.T. and {}{den Ridder}, J.J. and {Op den Camp}, H.J. and {}{van Dijken}, J.P. and Pronk, J.T.}, year = 2003, month = oct, journal = {FEMS yeast research}, volume = {4}, number = {1}, pages = {69–78}, publisher = {Wiley Online Library}, doi = {10.1016/S1567-1356(03)00141-7}, url = {http://onlinelibrary.wiley.com/doi/10.1016/S1567-1356(03)00141-7/full}, abstract = {Evidence is presented that xylose metabolism in the anaerobic cellulolytic fungus Piromyces sp. E2 proceeds via a xylose isomerase rather than via the xylose reductase/xylitol-dehydrogenase pathway found in xylose-metabolising yeasts. The XylA gene encoding the Piromyces xylose isomerase was functionally expressed in Saccharomyces cerevisiae. Heterologous isomerase activities in cell extracts, assayed at 30 degrees C, were 0.3-1.1 micromol min(-1) (mg protein)(-1), with a Km for xylose of 20 mM. The engineered S. cerevisiae strain grew very slowly on xylose. It co-consumed xylose in aerobic and anaerobic glucose-limited chemostat cultures at rates of 0.33 and 0.73 mmol (g biomass)(-1) h(-1), respectively}, keywords = {0,Aldose-Ketose Isomerases,Anaerobiosis,Cell Extracts,CEREVISIAE,enzymology,Ethanol,expression,EXTRACTS,Fermentation,gene,Gene Expression,genetics,La,metabolism,nosource,PATHWAY,Piromyces,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Support,Xylose,yeast,Yeasts} } % == BibTeX quality report for kuyperHighlevelFunctionalExpression2003: % ? unused Journal abbr (“FEMS Yeast Res.”)

@article{laalamiMessengerRNATranslation1996, title = {Messenger {{RNA}} Translation in Prokaryotes: {{GTPase}} Centers Associated with Translational Factors}, author = {Laalami, S. and Grentzmann, G. and Bremaud, L. and Cenatiempo, Y.}, year = 1996, journal = {Biochimie}, volume = {78}, number = {7}, pages = {577–589}, publisher = {Elsevier}, doi = {10.1016/S0300-9084(96)80004-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0300-9084(96)80004-6}, abstract = {During the decoding of messenger RNA, each step of the translational cycle requires the intervention of protein factors and the hydrolysis of one or more GTP molecule(s). Of the prokaryotic translational factors, IF2, EF-Tu, SELB, EF-G and RF3 are GTP-binding proteins. In this review we summarize the latest findings on the structures and the roles of these GTPases in the translational process}, keywords = {0,Amidohydrolases,Amino Acid Sequence,Bacterial,Bacterial Proteins,chemistry,decoding,EFTu,elongation,GTP,GTP Phosphohydrolase-Linked Elongation Factors,GTP-Binding Proteins,GTPase,Hydrolysis,initiation,La,MESSENGER-RNA,metabolism,Molecular Sequence Data,nosource,Peptide Chain Elongation,Peptide Elongation Factor G,Peptide Elongation Factor Tu,Peptide Elongation Factors,Peptide Initiation Factors,protein,Proteins,Review,Rna,RNAMessenger,Sequence Alignment,structure,translation} }

@article{laemmliCleavageStructuralProteins1970, title = {Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage {{T4}}}, author = {Laemmli, U.K.}, year = 1970, month = aug, journal = {Nature}, volume = {227}, number = {5259}, pages = {680–685}, publisher = {London)}, url = {http://bioinfcpcri.org/misc/nature.pdf}, keywords = {assembly,Autoradiography,Bacteriophage T4,Carbon Isotopes,CLEAVAGE,Coliphages/me [Metabolism],Disc,Electrophoresis,Genes,genetics,Kinetics,Microbial,No DOI found,nosource,protein,Proteins,SDS-PAGE,Structural,Viral Proteins/me [Metabolism]} }

@article{lafontaineBoxACASnoRNAs1998, title = {The Box {{H}} + {{ACA snoRNAs}} Carry {{Cbf5p}}, the Putative {{rRNA}} Pseudouridine Synthase}, author = {Lafontaine, D.L. and {Bousquet-Antonelli}, C. and Henry, Y. and {Caizergues-Ferrer}, M. and Tollervey, D.}, year = 1998, month = feb, journal = {Genes & development}, volume = {12}, number = {4}, pages = {527–537}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.12.4.527}, url = {http://genesdev.cshlp.org/content/12/4/527.short}, abstract = {Many or all of the sites of pseudouridine (Psi) formation in eukaryotic rRNA are selected by site-specific base-pairing with members of the box H + ACA class of small nucleolar RNAs (snoRNAs). Database searches previously identified strong homology between the rat nucleolar protein Nap57p, its yeast homolog Cbf5p, and the Escherichia coli Psi synthase truB/P35. We therefore tested whether Cbf5p is required for synthesis of Psi in the yeast rRNA. After genetic depletion of Cbf5p, formation of Psi in the pre-rRNA is dramatically inhibited, resulting in accumulation of the unmodified rRNA. Protein A-tagged Cbf5p coprecipitates all tested members of the box H + ACA snoRNAs but not box C + D snoRNAs or other RNA species. Genetic depletion of Cbf5p leads to depletion of all box H + ACA snoRNAs. These include snR30, which is required for pre-rRNA processing. Depletion of Cbf5p also results in a pre-rRNA processing defect similar to that seen on depletion of snR30. We conclude that Cbf5p is likely to be the rRNA Psi synthase and is an integral component of the box H + ACA class of snoRNPs, which function to target the enzyme to its site of action}, keywords = {0,Base Pairing,BIOLOGY,biosynthesis,CBF5,Cell Nucleolus,CEREVISIAE,classification,COMPONENT,D,DATABASE,enzyme,enzymology,Escherichia coli,ESCHERICHIA-COLI,GenesLethal,Genetic,genetics,homolog,Hydro-Lyases,La,metabolism,Microtubule-Associated Proteins,Molecular Biology,nosource,Nuclear Proteins,PRECURSOR,protein,Protein Binding,Proteins,Pseudouridine,PSEUDOURIDINE SYNTHASE,psi,rat,RIBONUCLEOPROTEIN,Ribonucleoproteins,RibonucleoproteinsSmall Nuclear,Rna,RNA Precursors,RNA ProcessingPost-Transcriptional,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNARibosomal,RNASmall Nuclear,rRNA,S,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,search,SITE,site specific,SITES,SMALL NUCLEOLAR RNAS,Support,TARGET,yeast} } % == BibTeX quality report for lafontaineBoxACASnoRNAs1998: % ? unused Journal abbr (“Genes Dev.”)

@article{lageABCtransportersImplicationsDrug2003a, title = {{{ABC-transporters}}: Implications on Drug Resistance from Microorganisms to Human Cancers}, author = {Lage, H.}, year = 2003, journal = {Int.J.Antimicrob.Agents}, volume = {22}, number = {3}, pages = {188–199}, doi = {10.1016/S0924-8579(03)00203-6}, url = {PM:13678820}, abstract = {Resistance to chemotherapy is a common clinical problem in patients with infectious diseases as well as in patients with cancer. During treatment of infections or malignant tumors, the drug targets of prokaryotic or eukaryotic microorganisms and neoplastic cells are often found to be refractory to a variety of drugs that have different structures and functions. This phenomenon has been termed multidrug resistance (MDR). The mechanisms leading to MDR are frequently caused by trans-membrane xenobiotic transport molecules belonging to the superfamily of ATP-binding cassette (ABC) transporters. There is an urgent need to understand the structure-function relationships of these efflux pumps that underlie their transport mechanism and drug selectivity. This knowledge may allow the rational design of new drugs that can inhibit or circumvent the activity of these MDR transport molecules. Furthermore, the development of such chemosensitizing agents would help us learn more about the physiological functions and substrates of these pump proteins. This review will discuss the current state of knowledge of the functional and structural similarities among ABC-transporters in prokaryotic and eukaryotic cells and their impact on MDR}, keywords = {0,Animals,ATP-Binding Cassette Transporters,Bacteria,cancer,CELLS,chemistry,CHEMOTHERAPY,Communicable Diseases,development,disease,drug effects,Drug Resistance,Drug ResistanceMicrobial,Drug ResistanceMultiple,Drug ResistanceNeoplasm,drug therapy,drugs,Eukaryotic Cells,Fungi,Germany,human,Humans,INFECTION,La,MECHANISM,MECHANISMS,metabolism,ModelsMolecular,Neoplasms,nosource,pathology,protein,Proteins,Protozoa,RESISTANCE,Review,Structural,structure,SUPERFAMILY,Support,TARGET,TRANSPORT} } % == BibTeX quality report for lageABCtransportersImplicationsDrug2003a: % ? Possibly abbreviated journal title Int.J.Antimicrob.Agents

@article{lagrandeurCisActingSequences1999, title = {The Cis Acting Sequences Responsible for the Differential Decay of the Unstable {{MFA2}} and Stable {{PGK1}} Transcripts in Yeast Include the Context of the Translational Start Codon.}, author = {LaGrandeur, T. and Parker, R.}, year = 1999, month = mar, journal = {RNA.}, volume = {5}, number = {3}, pages = {420–433}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838299981748}, url = {http://rnajournal.cshlp.org/content/5/3/420.short}, abstract = {A general pathway of mRNA turnover has been described for yeast in which the 3’ poly(A) tail is first deadenylated to an oligo(A) length, leading to decapping and subsequent 5’-3’ exonucleolytic decay. The unstable MFA2 mRNA and the stable PGK1 mRNAs both decay through this pathway, albeit at different rates of deadenylation and decapping. To determine the regions of the mRNAs that are responsible for these differences, we examined the decay of chimeric mRNAs derived from the 5’ untranslated, coding, and 3’ untranslated regions of these two mRNAs. These experiments have led to the identification of the features of these mRNAs that lead to their different stabilities. The MFA2 mRNA is unstable solely because its 3’ UTR promotes the rates of deadenylation and decapping; all other features of this mRNA are neutral with respect to mRNA decay rates. The PGK1 mRNA is stable because the sequence context of the PGK1 translation start codon and the coding region function together to stabilize the transcript, whereas the PGK13’ UTR is neutral with respect to decay. Importantly, changes in the PGK1 start codon context that destabilized the transcript also reduced its translational efficiency. This observation suggests that the nature of the translation initiation complex modulates the rates of mRNA decapping and decay}, keywords = {3’ Untranslated Regions,5’ Untranslated Regions,99192123,Base Sequence,Codon,CodonInitiator,COMPLEX,COMPLEXES,DEADENYLATION,DECAY,efficiency,GenesFungal,genetics,IDENTIFICATION,initiation,metabolism,Molecular Sequence Data,mRNA,mRNA decay,nosource,Plasmids,poly(A),Polyribosomes,Rna,Rna Caps,RNAFungal,RNAMessenger,sequence,stability,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,TranscriptionGenetic,translation,TRANSLATION INITIATION,TranslationGenetic,turnover,Untranslated Regions,yeast} } % == BibTeX quality report for lagrandeurCisActingSequences1999: % ? Possibly abbreviated journal title RNA.

@article{lagrandeurIsolationCharacterizationDcp1p1998, title = {Isolation and Characterization of {{Dcp1p}}, the Yeast {{mRNA}} Decapping Enzyme}, author = {LaGrandeur, T.E. and Parker, R.}, year = 1998, month = mar, journal = {The EMBO journal}, volume = {17}, number = {5}, pages = {1487–1496}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/17.5.1487}, url = {http://www.nature.com/emboj/journal/v17/n5/abs/7590863a.html}, abstract = {A major mechanism of mRNA decay occurs by the process of deadenylation, decapping and 5’ –{\(>\)} 3’ exonucleolytic degradation. Recently, the product of the DCP1 gene has been shown to be required for decapping mRNAs in vivo and co-purifies with decapping activity in vitro. We have purified Dcp1p to homogeneity and shown that it is sufficient for decapping, thereby indicating that Dcp1p is the decapping enzyme. Characterization of Dcp1p activity in vitro indicated that the 7-methyl group of the cap structure contributes to the enzyme’s substrate specificity. In addition, Dcp1p was effectively inhibited by uncapped mRNAs, and the enzyme efficiently cleaved substrates that were {\(>\)}/=25 nucleotides in length, with a preference for longer mRNA substrates. These properties suggest that Dcp1p recognizes the mRNA substrate by interactions with both the cap and the RNA moiety. The Dcp1p is also a phosphoprotein, suggesting its activity may be regulated by post-transcriptional modification}, keywords = {0,3,BIOLOGY,Cap,CAP STRUCTURE,CEREVISIAE,DEADENYLATION,decapping activity,DECAPPING ENZYME,DECAY,degradation,Endoribonucleases,enzyme,enzymology,Fungal Proteins,FUSION PROTEIN,gene,genetics,In Vitro,IN-VITRO,IN-VIVO,isolation & purification,kinase,La,MECHANISM,metabolism,modification,mRNA,mRNA decay,nosource,Nucleotides,Phosphoglycerate Kinase,phosphoprotein,Phosphorylation,physiology,posttranscriptional modification,PRODUCT,protein,Proteins,Recombinant Fusion Proteins,Rna,Rna Caps,RNA ProcessingPost-Transcriptional,RNAFungal,S,S-CEREVISIAE,Saccharomyces cerevisiae,SPECIFICITY,structure,Substrate Specificity,SUBSTRATE-SPECIFICITY,supportnon-u.s.gov’t,yeast} } % == BibTeX quality report for lagrandeurIsolationCharacterizationDcp1p1998: % ? unused Journal abbr (“EMBO J.”)

@article{laiSARSVirusBeginning2003, title = {{{SARS}} Virus: The Beginning of the Unraveling of a New Coronavirus}, author = {Lai, M.M.}, year = 2003, month = nov, journal = {Journal of biomedical science}, volume = {10}, number = {6 Pt 2}, pages = {664–675}, publisher = {Springer}, url = {http://www.springerlink.com/index/Y146871U12R30760.pdf}, abstract = {Severe acute respiratory syndrome (SARS) virus caused a severe outbreak in several regions of the world in 2003. The virus is a novel coronavirus, which may have an origin in wild animals such as civet cats in southern China. Its genome structure, gene expression pattern and protein profiles are similar to those of other coronaviruses. However, distinct patterns of several open reading frames in the SARS virus genome may contribute to its severe virulence. The potential mutability of the coronavirus genome may pose problems in the control of future SARS outbreaks. The mechanism of SARS pathogenesis may involve both direct viral cytocidal effects on the target cells and immune-mediated mechanisms. The life cycle of the SARS virus is largely unknown; however, based on the analogy with other coronaviruses, several potential targets for antiviral development are identified. Vaccines offer an important preventive measure for possible future recurrences of SARS, but the prospect for their development is still unknown because of the uncertainty regarding the role of immune responses in SARS virus pathogenesis. The comparative studies of other coronaviruses offer insights into the understanding of SARS virus}, keywords = {0,animal,Animals,antiviral,CELLS,Chromosome Mapping,classification,Comparative Study,development,expression,FRAME,gene,Gene Expression,GENE-EXPRESSION,genetics,Genome,immunology,La,MECHANISM,MECHANISMS,microbiology,No DOI found,nosource,OPEN READING FRAME,Open Reading Frames,PATTERNS,physiology,prevention & control,protein,Proteins,READING FRAME,Reading Frames,REGION,Review,SARS,Sars Virus,Severe Acute Respiratory Syndrome,Structural,structure,TARGET,transmission,Viral Structural Proteins,virology,virus,WORLD} } % == BibTeX quality report for laiSARSVirusBeginning2003: % ? unused Journal abbr (“J.Biomed.Sci.”)

@book{lakowiczPrinciplesFluorescenceSpectroscopy1999a, title = {Principles of {{Fluorescence Spectroscopy}}.}, author = {Lakowicz, J.R.}, year = 1999, publisher = {L;iwere Academic/Plenum}, address = {New York}, keywords = {Fluorescence,nosource,SPECTROSCOPY} } % == BibTeX quality report for lakowiczPrinciplesFluorescenceSpectroscopy1999a: % ? Title looks like it was stored in title-case in Zotero

@article{lamAnalysisNucleolarProtein2007, title = {Analysis of Nucleolar Protein Dynamics Reveals the Nuclear Degradation of Ribosomal Proteins}, author = {Lam, Y.W. and Lamond, A.I. and Mann, M. and Andersen, J.S.}, year = 2007, month = may, journal = {Current biology}, volume = {17}, number = {9}, pages = {749–760}, publisher = {Elsevier}, doi = {10.1016/j.cub.2007.03.064}, url = {http://www.sciencedirect.com/science/article/pii/S096098220701202X http://linkinghub.elsevier.com/retrieve/pii/S096098220701202X}, abstract = {BACKGROUND: The nucleolus is a subnuclear organelle in which rRNAs are transcribed, processed, and assembled with ribosomal proteins into ribosome subunits. Mass spectrometry combined with pulsed incorporation of stable isotopes of arginine and lysine was used to perform a quantitative and unbiased global analysis of the rates at which newly synthesized, endogenous proteins appear within mammalian nucleoli. RESULTS: Newly synthesized ribosomal proteins accumulated in nucleoli more quickly than other nucleolar components. Studies involving time-lapse fluorescence microscopy of stable HeLa cell lines expressing fluorescent-protein-tagged nucleolar factors also showed that ribosomal proteins accumulate more quickly than other components. Photobleaching and mass-spectrometry experiments suggest that only a subset of newly synthesized ribosomal proteins are assembled into ribosomes and exported to the cytoplasm. Inhibition of the proteasome caused an accumulation of ribosomal proteins in the nucleus but not in the cytoplasm. Inhibition of rRNA transcription prior to proteasomal inhibition further increased the accumulation of ribosomal proteins in the nucleoplasm. CONCLUSIONS: Ribosomal proteins are expressed at high levels beyond that required for the typical rate of ribosome-subunit production and accumulate in the nucleolus more quickly than all other nucleolar components. This is balanced by continual degradation of unassembled ribosomal proteins in the nucleoplasm, thereby providing a mechanism for mammalian cells to ensure that ribosomal protein levels are never rate limiting for the efficient assembly of ribosome subunits. The dual time-lapse strategy used in this study, combining proteomics and imaging, provides a powerful approach for the quantitative analysis of the flux of newly synthesized proteins through a cell organelle}, keywords = {0,analysis,Arginine,assembly,biosynthesis,Cell Line,cell lines,Cell Nucleolus,CELLS,Comparative Study,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,Cytoplasm,degradation,DYNAMICS,expression,Fluorescence,Fluorescence Recovery After Photobleaching,FUSION PROTEIN,gene,gene regulation,Hela Cells,Humans,INHIBITION,La,LINE,Lysine,MAMMALIAN-CELLS,Mass Spectrometry,MECHANISM,metabolism,Methods,Microscopy-Fluorescence,MicroscopyFluorescence,nosource,nucleolus,physiology,Proteasome Endopeptidase Complex,protein,Protein Transport,Proteins,Proteomics,Recombinant Fusion Proteins,regulation,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Rna,RNA-Ribosomal,RNARibosomal,rRNA,SUBUNIT,SUBUNITS,Support,transcription} } % == BibTeX quality report for lamAnalysisNucleolarProtein2007: % ? unused Journal abbr (“Curr.Biol”)

@article{lancasterSarcinricinLoop23S2008, title = {The Sarcin-Ricin Loop of {{23S rRNA}} Is Essential for Assembly of the Functional Core of the {{50S}} Ribosomal Subunit}, author = {Lancaster, L. and Lambert, N.J. and Maklan, E.J. and Horan, L.H. and Noller, H.F.}, year = 2008, journal = {RNA.}, pages = {1999–2012}, doi = {10.1261/rna.1202108}, url = {http://rnajournalcshlp.needshape.com/content/14/10/1999.short}, abstract = {The sarcin-ricin loop (SRL) of 23S rRNA in the large ribosomal subunit is a factor-binding site that is essential for GTP-catalyzed steps in translation, but its precise functional role is thus far unknown. Here, we replaced the 15-nucleotide SRL with a GAAA tetraloop and affinity purified the mutant 50S subunits for functional and structural analysis in vitro. The SRL deletion caused defects in elongation-factor-dependent steps of translation and, unexpectedly, loss of EF-Tu-independent A-site tRNA binding. Detailed chemical probing analysis showed disruption of a network of rRNA tertiary interactions that hold together the 23S rRNA elements of the functional core of the 50S subunit, accompanied by loss of ribosomal protein L16. Our results reveal an influence of the SRL on the higher-order structure of the 50S subunit, with implications for its role in translation}, keywords = {23s rrna,a site,A SITE,A-SITE,analysis,assembly,BINDING,BIOLOGY,DISRUPTION,ELEMENTS,In Vitro,IN-VITRO,La,LOOP,Molecular Biology,nosource,protein,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome assembly,ricin loop,Rna,rRNA,sarcin,SARCIN RICIN LOOP,SITE,Structural,structure,SUBUNIT,SUBUNITS,translation,tRNA,tRNA binding} } % == BibTeX quality report for lancasterSarcinricinLoop23S2008: % ? Possibly abbreviated journal title RNA.

@article{larderHumanImmunodeficiencyVirus1996, title = {Human Immunodeficiency Virus Type 1 Drug Susceptibility during Zidovudine ({{AZT}}) Monotherapy Compared with {{AZT}} plus 2’, 3’-Dideoxyinosine or {{AZT}} plus 2’, 3’-Dideoxycytidine Combination Therapy. {{The}} Protocol 34,225-02 {{Collaborative Group}}}, author = {Larder, B.A. and Kohli, A. and Bloor, S. and Kemp, S.D. and Harrigan, P.R. and Schooley, R.T. and Lange, J.M. and Pennington, K.N. and St.Clair, M.H.}, year = 1996, month = sep, journal = {Journal of Virology}, volume = {70}, number = {9}, pages = {5922–5929}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.70.9.5922-5929.1996}, url = {http://jvi.asm.org/cgi/content/abstract/70/9/5922}, keywords = {assays,Codon,development,Dna,drugs,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,Mutation,nosource,virus} }

@article{lariviereLateactingQualityControl2006a, title = {A Late-Acting Quality Control Process for Mature Eukaryotic {{rRNAs}}}, author = {LaRiviere, F.J. and Cole, S.E. and Ferullo, D.J. and Moore, M.J.}, year = 2006, month = nov, journal = {Mol.Cell}, volume = {24}, number = {4}, pages = {619–626}, doi = {10.1016/j.molcel.2006.10.008}, url = {PM:17188037}, abstract = {Ribosome biogenesis is a multifaceted process involving a host of trans-acting factors mediating numerous chemical reactions, RNA conformational changes, and RNA-protein associations. Given this high degree of complexity, tight quality control is likely crucial to ensure structural and functional integrity of the end products. We demonstrate that ribosomal RNAs (rRNAs) containing individual point mutations, in either the 25S peptidyl transferase center or 18S decoding site, that adversely affect ribosome function are strongly downregulated in Saccharomyces cerevisiae. This downregulation occurs via decreased stability of the mature rRNA contained in fully assembled ribosomes and ribosomal subunits. Thus, eukaryotes possess a quality-control mechanism, nonfunctional rRNA decay (NRD), capable of detecting and eliminating the rRNA component of mature ribosomes}, keywords = {0,ASSOCIATION,BIOGENESIS,CEREVISIAE,COMPONENT,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,DECAY,decoding,Down-Regulation,genetics,La,MECHANISM,metabolism,Mutation,MUTATIONS,nosource,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,physiology,Point Mutation,PRODUCT,PRODUCTS,protein,Proteins,Quality Control,QUALITY-CONTROL,ribosomal RNA,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,ribosome biogenesis,Ribosomes,Rna,RNA,RNA ProcessingPost-Transcriptional,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SITE,stability,Structural,SUBUNIT,SUBUNITS,Support,TRANS-ACTING FACTORS,TRANSFERASE CENTER} } % == BibTeX quality report for lariviereLateactingQualityControl2006a: % ? Possibly abbreviated journal title Mol.Cell

@article{larsenRRNAmRNABasePairing1994a, title = {{{rRNA-mRNA}} Base Pairing Stimulates a Programmed -1 Ribosomal Frameshift}, author = {Larsen, B. and Wills, N.M. and Gesteland, R.F. and Atkins, J.F.}, year = 1994, month = nov, journal = {J.Bacteriol.}, volume = {176}, number = {22}, pages = {6842–6851}, doi = {10.1128/jb.176.22.6842-6851.1994}, url = {PM:7961443}, abstract = {Base pairing between the 3’ end of 16S rRNA and mRNA is shown to be important for the programmed -1 frameshifting utilized in decoding the Escherichia coli dnaX gene. This pairing is the same as the Shine-Dalgarno pairing used by prokaryotic ribosomes in selection of translation initiators, but for frameshifting the interaction occurs within elongating ribosomes. For dnaX -1 frameshifting, the 3’ base of the Shine-Dalgarno sequence is 10 nucleotides 5’ of the shift site. Previously, Shine-Dalgarno rRNA-mRNA pairing was shown to stimulate the +1 frameshifting necessary for decoding the release factor 2 gene. However, in the release factor 2 gene, the Shine-Dalgarno sequence is located 3 nucleotides 5’ of the shift site. When the Shine-Dalgarno sequence is moved to the same position relative to the dnaX shift site, it is inhibitory rather than stimulatory. Shine-Dalgarno interactions by elongating ribosomes are likely to be used in stimulating -1 frameshifting in the decoding of a variety of genes}, keywords = {+1 frameshifting,0,16S,3,BASE,Base Composition,Base Pairing,Base Sequence,Binding Sites,biosynthesis,CHAIN TERMINATION,Comparative Study,decoding,Dna,DNA Mutational Analysis,DNA Polymerase III,dnaX,DNAX GENE,enzymology,Escherichia coli,ESCHERICHIA-COLI,frameshift,Frameshifting,FUSION PROTEIN,gene,Genes,genetics,La,metabolism,Molecular Sequence Data,mRNA,nosource,Nucleotides,Peptide Chain Termination,Peptide Termination Factors,polymerase,POLYMERASE-III,POSITION,protein,Protein Biosynthesis,Proteins,Recombinant Fusion Proteins,RELEASE,release factor,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,RIBOSOMAL FRAMESHIFT,ribosome,Ribosomes,Rna,RNADouble-Stranded,RNAMessenger,RNARibosomal16S,rRNA,SELECTION,sequence,Sequence Deletion,SITE,Structure-Activity Relationship,termination,translation} } % == BibTeX quality report for larsenRRNAmRNABasePairing1994a: % ? Possibly abbreviated journal title J.Bacteriol.

@article{larsenNonlinearityGeneticDecoding2000, title = {Nonlinearity in Genetic Decoding: {{Homologous DNA}} Replicase Genes Use Alternatives of Transcriptional Slippage or Translational Frameshifting}, author = {Larsen, B. and Wills, N.M. and Nelson, C. and Atkins, J.F. and Gesteland, R.F.}, year = 2000, month = feb, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {4}, pages = {1683–1688}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.97.4.1683}, url = {http://www.pnas.org/content/97/4/1683.short}, abstract = {The tau and gamma subunits of DNA polymerase III are both encoded by a single gene in Escherichia coli and Thermus thermophilus. gamma is two-thirds the size of tau and shares virtually all its amino acid sequence with tau, E. coli and T. thermophilus have evolved very different mechanisms for setting the approximate 1:1 ratio between tau and gamma, Both mechanisms put ribosomes into alternate reading frames so that stop codons in the new frame serve to make the smaller gamma protein. In E, coli, approximate to 50% of initiating ribosomes translate the dnaX mRNA conventionally to give tau, but the other 50% shift into the -1 reading frame at a specific site (A AAA AAG) in the mRNA to produce gamma. In T. thermophilus ribosomal frameshifting is not required: the dnaX mRNA is a heterogeneous population of molecules with different numbers of A residues arising from transcriptional slippage on a run of nine T residues in the DNA template. Translation of the subpopulation containing nine As (or +/- multiples of three As) yields tau. The rest of the population of mRNAs (containing nine +/- nonmultiples of three As) puts ribosomes into the alternate reading frames to produce the gamma protein(s). It is surprising that two rather similar dnaX sequences in E. coli and T. thermophilus lead to very different mechanisms of expression}, keywords = {ACID,Adenine,Amino Acid Sequence,AMINO-ACID,Codon,CODONS,decoding,Dna,dnaX,E,elongation,Escherichia coli,ESCHERICHIA-COLI,expression,FRAME,Frameshifting,GAMMA-SUBUNIT,gene,Genes,Genetic,human,IDENTIFICATION,M,MECHANISM,MECHANISMS,MESSENGER-RNA,mRNA,nosource,polymerase,POLYMERASE-III,POLYMERASE-III HOLOENZYME,protein,READING FRAME,Reading Frames,READING-FRAME RESTORATION,RESIDUES,ribosomal frameshifting,ribosome,Ribosomes,sequence,SEQUENCES,SITE,SLIPPAGE,STOP CODON,SUBUNIT,T,TEMPLATE,THERMOPHILIC BACTERIUM,Thermus,Thermus thermophilus,THERMUS-THERMOPHILUS,translation,TRANSLATIONAL FRAMESHIFTING} }

@article{launAgedMotherCells2001, title = {Aged Mother Cells of {{Saccharomyces}} Cerevisiae Show Markers of Oxidative Stress and Apoptosis}, author = {Laun, P. and Pichova, A. and Madeo, F. and Fuchs, J. and Ellinger, A. and Kohlwein, S. and Dawes, I. and Frohlich, K.U. and Breitenbach, M.}, year = 2001, month = mar, journal = {Molecular microbiology}, volume = {39}, number = {5}, pages = {1166–1173}, publisher = {Wiley Online Library}, doi = {10.1111/j.1365-2958.2001.02317.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2001.02317.x/full}, abstract = {Recently, we and others have shown that genetic and environmental changes that increase the load of yeast cells with reactive oxygen species (ROS) lead to a shortening of the life span of yeast mother cells. Deletions of yeast genes coding for the superoxide dismutases or the catalases, as well as changes in atmospheric oxygen concentration, considerably shortened the life span. The presence of the physiological antioxidant glutathione, on the other hand, increased the life span of yeast cells. Taken together, these results pointed to a role for oxygen in the yeast ageing process. Here, we show by staining with dihydrorhodamine that old yeast mother cells isolated by elutriation, but not young cells, contain ROS that are localized in the mitochondria. A relatively large proportion of the old mother cells shows phenotypic markers of yeast apoptosis, i.e. TUNEL (TdT-mediated dUTP nick end labelling) and annexin V staining. Although it has been shown previously that apoptosis in yeast can be induced by a cdc48 allele, by expressing pro-apoptotic human cDNAs or by stressing the cells with hydrogen peroxide, we are now showing a physiological role for apoptosis in unstressed but aged wild-type yeast mother cells}, keywords = {0,analysis,Apoptosis,Biological Markers,CDC48,CELLS,CEREVISIAE,Culture Media,gene,Genes,Genetic,genetics,Glutathione,human,Hydrogen,In Situ Nick-End Labeling,isolation & purification,La,MARKER,media,metabolism,Methods,Microbiological Techniques,MicroscopyConfocal,MicroscopyFluorescence,mitochondria,nosource,Oxidative Stress,physiology,Reactive Oxygen Species,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Staining,Staining and Labeling,Stress,Support,WILD-TYPE,yeast,YEAST-CELLS} } % == BibTeX quality report for launAgedMotherCells2001: % ? unused Journal abbr (“Mol Microbiol.”)

@article{laurbergStructuralBasisTranslation2008, title = {Structural Basis for Translation Termination on the {{70S}} Ribosome}, author = {Laurberg, M. and Asahara, H. and Korostelev, A. and Zhu, J. and Trakhanov, S. and Noller, H.F.}, year = 2008, journal = {Nature}, volume = {454}, number = {7206}, pages = {852–857}, publisher = {Nature Publishing Group}, doi = {10.1038/nature07115}, url = {http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07115.html}, abstract = {At termination of protein synthesis, type I release factors promote hydrolysis of the peptidyl-transfer RNA linkage in response to recognition of a stop codon. Here we describe the crystal structure of the Thermus thermophilus 70S ribosome in complex with the release factor RF1, tRNA and a messenger RNA containing a UAA stop codon, at 3.2 A resolution. The stop codon is recognized in a pocket formed by conserved elements of RF1, including its PxT recognition motif, and 16S ribosomal RNA. The codon and the 30S subunit A site undergo an induced fit that results in stabilization of a conformation of RF1 that promotes its interaction with the peptidyl transferase centre. Unexpectedly, the main-chain amide group of Gln 230 in the universally conserved GGQ motif of the factor is positioned to contribute directly to peptidyl-tRNA hydrolysis}, keywords = {16S,70S RIBOSOME,A SITE,A-SITE,BIOLOGY,Codon,COMPLEX,COMPLEXES,CONFORMATION,crystal structure,CRYSTAL-STRUCTURE,ELEMENTS,Hydrolysis,La,MESSENGER-RNA,Molecular Biology,nosource,peptidyl transferase,peptidyl-transfer,PEPTIDYL-TRANSFER-RNA,PEPTIDYL-TRANSFERASE,protein,protein synthesis,PROTEIN-SYNTHESIS,RECOGNITION,RELEASE,release factor,RELEASE FACTORS,RESOLUTION,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Rna,SITE,STOP CODON,Structural,STRUCTURAL BASIS,structure,SUBUNIT,Support,termination,Thermus,Thermus thermophilus,THERMUS-THERMOPHILUS,translation,TRANSLATION TERMINATION,tRNA,UAA} }

@article{lawlerFrameshiftSignalTransplantation2001, title = {Frameshift Signal Transplantation and the Unambiguous Analysis of Mutations in the Yeast Retrotransposon {{Ty1 Gag-Pol}} Overlap Region}, author = {Lawler, J.F. and Merkulov, G.V. and Boeke, J.D.}, year = 2001, journal = {Journal of Virology}, volume = {75}, number = {15}, pages = {6769–6775}, publisher = {Am Soc Microbiol}, doi = {10.1128/JVI.75.15.6769-6775.2001}, url = {ISI:000169870700004 http://jvi.asm.org/cgi/content/abstract/75/15/6769}, abstract = {The yeast retrotransposon Ty1 encodes a 7-nucleotide RNA sequence that directs a programmed, +1 ribosomal frameshifting event required for Gag-Pol translation and retrotransposition, We report mutations that block frameshifting, which can be suppressed in cis by “transplanting” the frameshift signal to a position upstream of its native location, These “frameshift transplant” mutants transpose with only a modest decrease in efficiency, suggesting that the location of the frameshift signal in a functional Ty1 element may vary. The genomic architecture of Ty1 is such that Gag, Ty1 PR (PR), and the Gag-derived p4 peptide share a common sequence. The functional independence of the movement of the frameshift signal to a new location within the Ty1 element is used to unambiguously attribute the effect of mutations deleterious to transposition in this region of overlapping coding sequences to effects on the Ty1 (PR). This work defines the amino terminus of the Ty1 PR and introduces a new technique for studying viral genome organization}, keywords = {3,analysis,C-TERMINUS,coding sequence,D,efficiency,ELEMENT TRANSPOSITION,ENCODES,frameshift,Frameshifting,Gag,Gag-pol,Genome,GENOME ORGANIZATION,genomic,HOMOLOGOUS RECOMBINATION,INTERMEDIATE,LOCATION,Movement,Mutagenesis,MUTANTS,Mutation,MUTATIONS,nosource,NUCLEAR-LOCALIZATION SIGNAL,ORGANIZATION,Proteins,REGION,RETROTRANSPOSITION,retrotransposon,ribosomal frameshifting,Rna,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,SIGNAL,SITE,translation,Ty1,UPSTREAM,VIRUS-LIKE PARTICLES,yeast} }

@incollection{lawrenceClassicalMutagenesisTechniques1991a, title = {Classical Mutagenesis Techniques.}, booktitle = {Guide to {{Yeast Genetics}} and {{Molecular Biology}}.}, author = {Lawrence, E.W.}, year = 1991, pages = {508–519}, publisher = {Academic Press}, address = {New York}, collaborator = {Guthrie, C. and Fink, G.R.}, keywords = {EMS,Genetic,genetics,Methods,Mutagenesis,nosource,techniques,yeast} }

@article{lawrenceChromatinTurnOns2004a, title = {Chromatin Turn Ons and Turn Offs of Ribosomal {{RNA}} Genes.}, author = {Lawrence, R.J. and Pikaard, C.S.}, year = 2004, month = jul, journal = {Cell cycle (Georgetown, Tex.)}, volume = {3}, number = {7}, eprint = {15190210}, eprinttype = {pubmed}, pages = {880}, doi = {10.4161/cc.3.7.983}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15190210}, abstract = {Eukaryotes have hundreds (sometimes thousands) of ribosomal RNA (rRNA) genes whose transcription by RNA polymerase I helps establish the proliferative ability of cells by dictating the pace of ribosome production and protein synthesis. Interestingly, only a subset of the total rRNA gene pool is active at any one time, making rRNA genes attractive for understanding the dynamic balance between gene silencing and activation. However, the fact that rRNA genes are essentially identical in sequence in a pure species has been an obstacle to telling apart the active and inactive genes. Nature has provided one solution to this conundrum in the form of the epigenetic phenomenon, nucleolar dominance: the transcriptional silencing of one parental set of rRNA genes in a genetic hybrid. Parental genes in hybrids typically differ in sequence as well as expression, allowing a definition of the chromatin modifications of rRNA genes in the on and off states in vivo. By exploiting nucleolar dominance in plants, we recently showed that concerted changes in DNA methylation and histone methylation comprise an epigenetic switch that turns rRNA genes on and off. Independent studies using mouse and human cells have led to similar conclusions, implicating chromatin modifications as important components of the regulatory networks that control the effective dosage of active rRNA genes}, keywords = {activation,BIOLOGY,CELLS,Chromatin,COMPONENT,COMPONENTS,Dna,expression,FORM,gene,Gene Silencing,Genes,Genetic,human,IN-VIVO,La,Methylation,modification,nosource,Plants,polymerase,protein,protein synthesis,PROTEIN-SYNTHESIS,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Rna,RNA Polymerase I,RNA-POLYMERASE,RNA-POLYMERASE-I,rRNA,rRNA genes,sequence,transcription,TURN-ON} } % == BibTeX quality report for lawrenceChromatinTurnOns2004a: % ? Possibly abbreviated journal title Cell cycle (Georgetown, Tex.) % ? unused Journal abbr (“Cell Cycle”)

@article{lehirExonexonJunctionComplex2001, title = {The Exon-Exon Junction Complex Provides a Binding Platform for Factors Involved in {{mRNA}} Export and Nonsense-Mediated {{mRNA}} Decay}, author = {Le Hir, H. and Gatfield, D. and Izaurralde, E. and Moore, M.J.}, year = 2001, journal = {EMBO J.}, volume = {20}, number = {17}, pages = {4987–4997}, doi = {10.1093/emboj/20.17.4987}, url = {PM:11532962}, abstract = {We recently reported that spliceosomes alter messenger ribonucleoprotein particle (mRNP) composition by depositing several proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. When assembled in vitro, this so-called ‘exon-exon junction complex’ (EJC) contains at least five proteins: SRm160, DEK, RNPS1, Y14 and REF. To better investigate its functional attributes, we now describe a method for generating spliced mRNAs both in vitro and in vivo that either do or do not carry the EJC. Analysis of these mRNAs in Xenopus laevis oocytes revealed that this complex is the species responsible for enhancing nucleocytoplasmic export of spliced mRNAs. It does so by providing a strong binding site for the mRNA export factors REF and TAP/p15. Moreover, by serving as an anchoring point for the factors Upf2 and Upf3, the EJC provides a direct link between splicing and nonsense-mediated mRNA decay. Finally, we show that the composition of the EJC is dynamic in vivo and is subject to significant evolution upon mRNA export to the cytoplasm}, keywords = {0,analysis,animal,BINDING,BINDING MOTIF,Binding Sites,BINDING-SITE,CloningMolecular,COMPLEX,COMPLEXES,Cytoplasm,DECAY,DNA-BINDING,DNA-Binding Proteins,Escherichia coli,Evolution,EXON-EXON JUNCTIONS,Exons,genetics,human,In Vitro,IN-VITRO,IN-VIVO,La,metabolism,ModelsGenetic,mRNA,mRNA decay,nonsense-mediated mRNA decay,nosource,Nuclear Proteins,Nucleotides,Oocytes,physiology,PRECURSOR,protein,Proteins,Recombinant Proteins,RIBONUCLEOPROTEIN,Rna,RNA Precursors,RNA Splicing,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAMessenger,SITE,Spliceosomes,splicing,UPF3,UPSTREAM,Xenopus,Xenopus laevis,XENOPUS-LAEVIS} } % == BibTeX quality report for lehirExonexonJunctionComplex2001: % ? Possibly abbreviated journal title EMBO J.

@article{leroyNewlyDiscoveredFunction2005, title = {A Newly Discovered Function for {{RNase L}} in Regulating Translation Termination}, author = {Le Roy, F. and Salehzada, T. and Bisbal, C. and Dougherty, J.P. and Peltz, S.W.}, year = 2005, month = jun, journal = {Nat.Struct.Mol Biol}, volume = {12}, number = {6}, pages = {505–512}, doi = {10.1038/nsmb944}, url = {PM:15908960}, abstract = {The antiviral and antiproliferative effects of interferons are mediated in part by the 2’-5’ oligoadenylate-RNase L RNA decay pathway. RNase L is an endoribonuclease that requires 2’-5’ oligoadenylates to cleave single-stranded RNA. In this report we present evidence demonstrating a role for RNase L in translation. We identify and characterize the human translation termination factor eRF3/GSPT1 as an interacting partner of RNase L. We show that interaction of eRF3 with RNase L leads to both increased translation readthrough efficiency at premature termination codons and increased +1 frameshift efficiency at the antizyme +1 frameshift site. On the basis of our results, we present a model describing how RNase L is involved in regulating gene expression by modulating the translation termination process}, keywords = {0,3,antiviral,antizyme,Carrier Proteins,Cell LineTumor,Codon,CODONS,DECAY,DECAY PATHWAY,efficiency,Endoribonucleases,expression,frameshift,Frameshift Mutation,gene,Gene Expression,GENE-EXPRESSION,GenesReporter,Genetic,genetics,human,Humans,IDENTIFY,immunology,La,luciferase,Luciferases,metabolism,microbiology,MODEL,MOLECULAR-GENETICS,nosource,PATHWAY,Peptide Chain TerminationTranslational,Peptide Termination Factors,PREMATURE TERMINATION CODON,protein,Protein Biosynthesis,Proteins,readthrough,REQUIRES,Rna,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAse,SITE,Support,termination,TERMINATION CODON,TERMINATION-CODON,translation,TRANSLATION TERMINATION} } % == BibTeX quality report for leroyNewlyDiscoveredFunction2005: % ? Possibly abbreviated journal title Nat.Struct.Mol Biol

@article{leLocalThermodynamicStability2001, title = {Local Thermodynamic Stability Scores Are Well Represented by a Non-Central Student’s t Distribution}, author = {Le, S.Y. and Liu, W.M. and Chen, J.H. and Maizel, J.V.}, year = 2001, month = jun, journal = {Journal of Theoretical Biology}, volume = {210}, number = {4}, pages = {411–423}, publisher = {Elsevier}, doi = {10.1006/jtbi.2001.2318}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022519301923185}, abstract = {Local folding in mRNAs is closely associated w ith biological functions. In this study, we reveal the whole distribution of local thermodynamic stability in the complete genome of the poliovirus P3/Leon/37 and the single-stranded RNA sequences that corresponds to the nucleotide sequence of the complete genome sequence (1 667 867 bp) of Helicobacter pylori (H. pylori) strain 26695. Local thermodynamic stability in the RNA sequences is measured by two standard z -scores, significance score and stability score. To estimate the distribution of thermodynamic stability, a model based on the non-central Student’s t distribution has been developed. Significant patterns of extremes that are either much more stable or unstable than expected by chance are detected. Our results indicate that the highly stable and statistically more significant folding regions are predominantly in non-coding sequences in the two genome sequences. Moreover, the highly unstable folding regions, on the contrary, are predominantly in the protein coding sequences of H. pylori. The observed differences across the complete genomic sequences are statistically very significant by a chi2-test. These extreme patterns may be useful in searching for target sequences for long-chain antisense RNA and for locating potential RNA functional elements involved in the regulation of gene expression including translation, mRNA localization and metabolism}, keywords = {0,Animals,antisense,BIOLOGY,cancer,Chi-Square Distribution,coding sequence,Computational Biology,ELEMENTS,expression,gene,Gene Expression,GENE-EXPRESSION,GenesBacterial,GenesViral,genetics,Genome,genomic,Helicobacter pylori,La,LOCALIZATION,metabolism,MODEL,ModelsStatistical,mRNA,nosource,NUCLEOTIDE-SEQUENCE,PATTERNS,Polioviruses,protein,REGION,regulation,Rna,RNAMessenger,sequence,SEQUENCES,stability,T,TARGET,thermodynamic stability,Thermodynamics,translation} } % == BibTeX quality report for leLocalThermodynamicStability2001: % ? unused Journal abbr (“J.Theor.Biol.”)

@article{learyRegulationRibosomeBiogenesis2001, title = {Regulation of Ribosome Biogenesis within the Nucleolus}, author = {Leary, D.J. and Huang, S.}, year = 2001, month = dec, journal = {FEBS letters}, volume = {509}, number = {2}, pages = {145–150}, publisher = {Elsevier}, doi = {10.1016/S0014-5793(01)03143-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0014-5793(01)03143-x}, abstract = {Ribosome biogenesis is both necessary for cellular adaptation, growth, and proliferation as well as a major energetic and biosynthetic demand upon cells. For these reasons, ribosome biogenesis requires precise regulation to balance supply and demand. The complexity of ribosome biogenesis gives rise to many steps and opportunities where regulation could take place. For trans-acting factors involved in ribosome biogenesis in the nucleolus, there may be a dynamic coordination, both spatially and temporally, that regulates their functions from the transcription of rDNA to the assembly and export of preribosomal particles. Here we summarize most of the described regulations on ribosome biogenesis in the nucleolus. However, these may represent only a small fraction of a larger picture. Further studies are required to determine the initial signals, signal transduction pathways utilized, and the specific targets of these regulatory modifications and how these are used to control ribosome biogenesis as a whole}, keywords = {0,assembly,Biological Transport,Cell Nucleolus,Gene Expression Regulation,La,metabolism,modification,nosource,nucleolus,rDNA,regulation,Review,ribosome,ribosome biogenesis,Ribosomes,Rna,RNA Precursors,RNA ProcessingPost-Transcriptional,RNARibosomal,SIGNAL,Signal Transduction,transcription,TranscriptionGenetic} } % == BibTeX quality report for learyRegulationRibosomeBiogenesis2001: % ? unused Journal abbr (“FEBS Lett.”)

@article{lecointeLackPseudouridine382002, title = {Lack of Pseudouridine 38/39 in the Anticodon Arm of Yeast Cytoplasmic {{tRNA}} Decreases in Vivo Recoding Efficiency}, author = {Lecointe, F. and Namy, O. and Hatin, I. and Simos, G. and Rousset, J.P. and Grosjean, H.}, year = 2002, journal = {Journal of Biological Chemistry}, volume = {277}, number = {34}, pages = {30445–30453}, publisher = {ASBMB}, doi = {10.1074/jbc.M203456200}, url = {http://www.jbc.org/content/277/34/30445.short}, abstract = {Many different modified nucleotides are found in naturally occurring tRNA, especially in the anticodon region. Their importance for the efficiency of the translational process begins to be well documented. Here we have analyzed the in vivo effect of deleting genes coding for yeast tRNA-modifying enzymes, namely Pus1p, Pus3p, Pus4p, or Trm4p, on termination readthrough and +1 frameshift events. To this end, we have transformed each of the yeast deletion strains with a lacZ-luc dual-reporter vector harboring selected programmed recoding sites. We have found that only deletion of the PUS3 gene, encoding the enzyme that introduces pseudouridines at position 38 or 39 in tRNA, has an effect on the efficiency of the translation process. In this mutant, we have observed a reduced readthrough efficiency of each stop codon by natural nonsense suppressor tRNAs. This effect is solely due to the absence of pseudouridine 38 or 39 in tRNA because the inactive mutant protein Pus3[D151A]p did not restore the level of natural readthrough. Our results also show that absence of pseudouridine 39 in the slippery tRNA(UAG)(Leu) reduces +1 frameshift efficiency. Therefore, the presence of pseudouridine 38 or 39 in the tRNA anticodon arm enhances misreading of certain codons by natural nonsense tRNAs as well as promotes frameshifting on slippery sequences in yeast}, keywords = {0,Anticodon,Codon,efficiency,enzyme,ESCHERICHIA-COLI,FRAME MAINTENANCE,frameshift,Frameshifting,gene,Genes,IN-VIVO,MESSENGER-RNA,nosource,Nucleotides,protein,Pseudouridine,readthrough,recoding,RIBOSOMAL-RNA,SACCHAROMYCES-CEREVISIAE,sequence,STOP CODON,SUBSTRATE-SPECIFICITY,SUPPRESSOR TRANSFER-RNAS,termination,TRANSFER-RNA GENES,translation,TRANSLATION TERMINATION,tRNA,vector,yeast} }

@article{leeIdentificationAdditionalGene1995, title = {Identification of an Additional Gene Required for Eukaryotic Nonsense {{mRNA}} Turnover.}, author = {Lee, B.S. and Culbertson, M.R.}, year = 1995, journal = {Proceedings of the National Academy of Sciences}, volume = {92}, number = {22}, pages = {10354–10358}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.92.22.10354}, url = {http://www.pnas.org/content/92/22/10354.short}, keywords = {gene,IDENTIFICATION,mRNA,nonsense suppression,nonsense-mediated decay,nosource,turnover} } % == BibTeX quality report for leeIdentificationAdditionalGene1995: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.USA”)

@article{leeInactivationCapbindingProteins1982a, title = {Inactivation of Cap-Binding Proteins Accompanies the Shut-off of Host Protein Synthesis in Poliovirus.}, author = {Lee, K. and Sonenberg, M.}, year = 1982, journal = {Proc.Natl.Acad.Sci.USA}, volume = {79}, pages = {3447–3451}, doi = {10.1073/pnas.79.11.3447}, keywords = {Cap binding,human,In Vitro,in vitro translation,IN-VITRO,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,SYSTEM,translation} } % == BibTeX quality report for leeInactivationCapbindingProteins1982a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{leeProteinThatShuttles1996, title = {A Protein That Shuttles between the Nucleus and the Cytoplasm Is an Important Mediator of {{RNA}} Export}, author = {Lee, M.S. and Henry, M. and Silver, P.A.}, year = 1996, month = may, journal = {Genes & Development}, volume = {10}, number = {10}, pages = {1233–1246}, doi = {10.1101/gad.10.10.1233}, keywords = {Cytoplasm,mRNA,Mutation,MUTATIONS,nosource,polymerase,protein,Rna,RNA Polymerase II,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Support,Temperature,transcription,yeast} }

@article{leeIdentificationRibosomalFrameshift1996a, title = {Identification of a Ribosomal Frameshift in {{Leishmania RNA}} Virus 1-4}, author = {Lee, S.E. and Suh, J.M. and Scheffter, S. and Patterson, J.L. and Chung, I.K.}, year = 1996, month = jul, journal = {Journal of Biochemistry}, volume = {120}, number = {1}, pages = {22–25}, url = {ISI:A1996UY25600004}, abstract = {Double-stranded Leishmania RNA virus 1-4 (LRV 1-4) has at least four open reading frames (ORFs), The two small ORFs located near its 5’ terminus, ORF1 and ORFx, could encode 34- and 60-amino acid polypeptides, respectively, ORF2 encodes an 82-kDa major capsid protein, and ORF3 encodes a 98-kDa polypeptide which contains the consensus sequence for RNA-dependent RNA polymerases of plus-strand and double-stranded RNA viruses, The complete sequence of LRV 1-4 shows that ORF2 and ORF3 overlap by 71 nucleotides, and that ORF3 lacks a potential translation initiation site, suggesting that the viral polymerase may be synthesized as a 180-kDa fusion protein with the virus capsid, In this report, we present evidence for the synthesis of a fusion protein through a ribosomal frameshift. In vitro-translation experimentation and immunostudies involving antiserum against the viral capsid protein demonstrated that the overlapping 71 nucleotides of ORF2 and ORF3 are contained in a region which promotes translational frameshifting. Computer analysis of the putative frameshift region revealed a potential pseudoknot structure! located within the overlapping 71 nucleotide sequence}, keywords = {3,ACID,analysis,Capsid,capsid protein,computer,computer analysis,Consensus Sequence,DOUBLE-STRANDED-RNA,ENCODES,expression,FRAME,frameshift,Frameshifting,Genome,GUYANENSIS,IDENTIFICATION,in vitro translation,initiation,INITIATION SITE,LEISHMANIA,Leishmania RNA virus,MESSENGER-RNAS,Multiple DOI,nonfile,nosource,NUCLEOTIDE-SEQUENCE,Nucleotides,OPEN READING FRAME,Open Reading Frames,polymerase,POLYMERASE ACTIVITY,POLYPEPTIDE,POLYPEPTIDES,protein,pseudoknot,pseudoknot structure,READING FRAME,Reading Frames,REGION,RIBOSOMAL FRAMESHIFT,Rna,RNA Viruses,RNA-dependent RNA polymerases,RNA-POLYMERASE,sequence,SEQUENCES,SITE,STRANDED-RNA,structure,translation,TRANSLATION INITIATION,TRANSLATIONAL FRAMESHIFTING,VIRAL PARTICLES,virus} }

@article{leeGeneticScreenIdentifies1995a, title = {A Genetic Screen Identifies Cellular Factors Involved in Retroviral -1 Frameshifting.}, author = {Lee, S.I. and Umen, J.G. and Varmus, H.E.}, year = 1995, journal = {Proc.Natl.Acad.Sci.USA}, volume = {92}, pages = {6587–6591}, doi = {10.1073/pnas.92.14.6587}, keywords = {Frameshifting,Genetic,MOF,nosource,UPF,yeast} } % == BibTeX quality report for leeGeneticScreenIdentifies1995a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{leeImp3pImp4pTwo1999, title = {Imp3p and {{Imp4p}}, Two Specific Components of the {{U3}} Small Nucleolar Ribonucleoprotein That Are Essential for Pre-{{18S rRNA}} Processing}, author = {Lee, S.J. and Baserga, S.J.}, year = 1999, journal = {Molecular and cellular biology}, volume = {19}, number = {8}, pages = {5441–5452}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.19.8.5441}, url = {http://mcb.asm.org/cgi/content/abstract/19/8/5441}, abstract = {The function of the U3 small nucleolar ribonucleoprotein (snoRNP) is central to the events surrounding pre-rRNA processing, as evidenced by the severe defects in cleavage of pre-18S rRNA precursors observed upon depletion of the U3 RNA and its unique protein components. Although the precise function of each component remains unclear, since U3 snoRNA levels remain unchanged upon genetic depletion of these proteins, it is likely that the proteins themselves have significant roles in the cleavage reactions. Here we report the identification of two previously undescribed protein components of the U3 snoRNP, representing the first snoRNP components identified by using the two-hybrid methodology. By screening for proteins that physically associate with the U3 snoRNP- specific protein, Mpp10p, we have identified Imp3p (22 kDa) and Imp4p (34 kDa) (named for interacting with Mpp10p). The genes encoding both proteins are essential in yeast. Genetic depletion reveals that both proteins are critical for U3 snoRNP function in pre-18S rRNA processing at the A0, A1, and A2 sites in the pre-rRNA. Both Imp proteins associate with Mpp10p in vivo, and both are complexed only with the U3 snoRNA. Conservation of RNA binding domains between Imp3p and the S4 family of ribosomal proteins suggests that it might associate with RNA directly. However, as with other U3 snoRNP-specific proteins, neither Imp3p nor Imp4p is required for maintenance of U3 snoRNA integrity. Imp3p and Imp4p are therefore novel protein components specific to the U3 snoRNP with critical roles in pre-rRNA cleavage events}, keywords = {0,Amino Acid Sequence,BINDING,chemistry,CLEAVAGE,Comparative Study,COMPONENT,gene,Genes,GenesReporter,Genetic,Genetic Techniques,Genetic Vectors,genetics,IDENTIFICATION,IN-VIVO,isolation & purification,La,Macromolecular Systems,metabolism,Molecular Sequence Data,nosource,Phosphoproteins,physiology,protein,Proteins,Recombinant Fusion Proteins,Ribonucleoproteins,RibonucleoproteinsSmall Nuclear,Ribosomal Proteins,Rna,RNA Precursors,RNAFungal,RNARibosomal18S,rRNA,Saccharomyces cerevisiae,Sequence Alignment,Sequence HomologyAmino Acid,supportu.s.gov’tp.h.s.,SYSTEM,vector,vectors,yeast} } % == BibTeX quality report for leeImp3pImp4pTwo1999: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{leeDirectMassSpectrometric2002, title = {Direct Mass Spectrometric Analysis of Intact Proteins of the Yeast Large Ribosomal Subunit Using Capillary {{LC}}/{{FTICR}}}, author = {Lee, S.W. and Berger, S.J. and Martinovic, S. and {Pasa-Tolic}, L. and Anderson, G.A. and Shen, Y. and Zhao, R. and Smith, R.D.}, year = 2002, month = apr, journal = {Proceedings of the National Academy of Sciences}, volume = {99}, number = {9}, pages = {5942–5947}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.082119899}, url = {http://www.pnas.org/content/99/9/5942.short}, abstract = {Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry coupled with capillary reverse-phase liquid chromatography was used to characterize intact proteins from the large subunit of the yeast ribosome. High mass measurement accuracy, achieved by “mass locking” with an internal standard from a dual electrospray ionization source, allowed identification of ribosomal proteins. Analyses of the intact proteins revealed information on cotranslational and posttranslational modifications of the ribosomal proteins that included loss of the initiating methionine, acetylation, methylation, and proteolytic maturation. High-resolution separations permitted differentiation of protein isoforms having high structural similarity as well as proteins from their modified forms, facilitating unequivocal assignments. The study identified 42 of the 43 core large ribosomal subunit proteins and 58 (of 64 possible) core large subunit protein isoforms having unique masses in a single analysis. These results demonstrate the basis for the high-throughput analyses of complex mixtures of intact proteins, which we believe will be an important complement to other approaches for defining protein modifications and their changes resulting from physiological processes or environmental perturbations}, keywords = {0,accuracy,Acetylation,analysis,ASSIGNMENT,chemistry,Chromatography,COMPLEX,COMPLEXES,DNA Methylation,FORM,IDENTIFICATION,INFORMATION,Ions,La,MATURATION,metabolism,Methionine,Methods,Methylation,modification,nosource,Phosphorylation,protein,Protein Isoforms,Protein ProcessingPost-Translational,Protein StructureTertiary,Proteins,Research SupportU.S.Gov’tNon-P.H.S.,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Saccharomyces cerevisiae,Software,SpectroscopyFourier Transform Infrared,Spectrum AnalysisMass,Structural,SUBUNIT,ultrastructure,yeast} } % == BibTeX quality report for leeDirectMassSpectrometric2002: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{leeActivationTransformingPotential1988, title = {Activation of Transforming Potential of the Human ⬚fos⬚ Proto-Oncogene Requires Message Stabilization and Results in Increased Amounts of Partially Modified Fos Protein.}, author = {Lee, W.M.F. and Lin, C. and Curran, T.}, year = 1988, journal = {Mol.Cell.Biol.}, volume = {8}, pages = {5521–5527}, keywords = {activation,fos,human,mRNA,Multiple DOI,nonfile,nosource,protein,stability} } % == BibTeX quality report for leeActivationTransformingPotential1988: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{leeMAK10GlucoserepressibleGene1992, title = {{{MAK10}}, a Glucose-Repressible Gene Necessary for Replication of a {{dsRNA}} Virus of {{Saccharomyces}} Cerevisiae, Has {{T}} Cell Recptor `a-Subunit Motifs.}, author = {Lee, Y. and Wickner, R. B.}, year = 1992, journal = {Genetics}, volume = {132}, pages = {87–96}, keywords = {gene,L-A,M1,MAK,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,virus,yeast} }

@article{leeTerminationFactorQuality1995, title = {Termination as a Factor in” Quality Control” during Ribosome Biogenesis}, author = {Lee, Y. and Melekhovets, Y.F. and Nazar, R.N.}, year = 1995, month = nov, journal = {Journal of Biological Chemistry}, volume = {270}, number = {47}, pages = {28003–28005}, publisher = {ASBMB}, doi = {10.1074/jbc.270.47.28003}, url = {http://www.jbc.org/content/270/47/28003.short}, abstract = {In eukaryotes, nascent rDNA and 5 S rRNA gene transcripts undergo 3’-end processing after termination. Mutations in which terminator sequences in these ribosomal RNA genes are deleted completely result in highly unstable transcripts, which are not properly processed and integrated into stable ribosome structure. Mutations that retard RNA processing by extending the 3’ external transcribed spacer or by introducing additional secondary structure in the spacers have a similar effect on stable transcript integration. The results indicate that proper termination coupled with efficient rRNA processing acts as a ‘’quality control’’ process, which helps to ensure that only normal rRNA precursors are effectively processed and assembled into active ribosomes}, keywords = {5 S rRNA,5S RNA,Drosophila,gene,Genes,MATURATION,MESSENGER-RNA STABILITY,Mutation,MUTATIONS,nosource,PRECURSOR,Quality Control,rDNA,RIBOSOMAL-RNA,ribosome,ribosome biogenesis,Ribosomes,Rna,rRNA,SACCHAROMYCES-CEREVISIAE,SECONDARY STRUCTURE,sequence,SEQUENCES,structure,termination,TRANSCRIPTION TERMINATION,yeast} }

@article{leeRibosomal5RRNA1997, title = {Ribosomal 5 {{S rRNA}} Maturation in {{Saccharomyces}} Cerevisiae}, author = {Lee, Y. and Nazar, R.N.}, year = 1997, month = jun, journal = {Journal of Biological Chemistry}, volume = {272}, number = {24}, pages = {15206–15212}, publisher = {ASBMB}, doi = {10.1074/jbc.272.24.15206}, url = {http://www.jbc.org/content/272/24/15206.short}, abstract = {The maturation of the ribosomal 5 S RNA in Saccharomyces cerevisiae is examined based on the expression of mutant 5 S rRNA genes, in vivo, and a parallel analysis of RNA processing, in vitro. Both types of analysis indicate that 5 S rRNA processing is not dependent on the nucleotide sequence of either the external transcribed spacer or the mature 5 S rRNA. The results further indicate the RNA is processed by an exonuclease activity which is limited primarily or entirely by helix I, the secondary structure formed between the mature and interacting termini. The 5 S RNA binding protein (YL3) also appears not to influence directly the maturation process, but rather to play a role in protecting the rRNA from further degradation by “housekeeping” nucleases. Taken together, the results continue to support a “quality control” function which helps to ensure that during maturation only normal precursors are processed and assembled into active ribosomes}, keywords = {97326092,analysis,BINDING,BINDING-PROTEIN,chemistry,degradation,expression,gene,Genes,Genetic,genetics,In Vitro,IN-VITRO,IN-VIVO,nosource,Nucleic Acid Conformation,protein,ribosome,Ribosomes,Rna,RNA ProcessingPost-Transcriptional,RNARibosomal5S,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,structure,Support,supportnon-u.s.gov’t} } % == BibTeX quality report for leeRibosomal5RRNA1997: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{leeVivoAnalysesUpstream1997a, title = {In Vivo Analyses of Upstream Promoter Sequence Elements in the 5 {{S rRNA}} Gene from {{Saccharomyces}} Cerevisiae}, author = {Lee, Y. and Wong, W.M. and Guyer, D. and Erkine, A.M. and Nazar, R.N.}, year = 1997, month = jun, journal = {Journal of Molecular Biology}, volume = {269}, number = {5}, pages = {676–683}, doi = {10.1006/jmbi.1997.1071}, url = {ISI:A1997XG93000003}, abstract = {Upstream promoter elements of the Saccharomyces cerevisiae 5S rRNA gene have been characterized by genomic DNase I ‘’footprinting’’ and by in vivo mutational analyses using base substitutions and deletions. A high copy shuttle-vectar was used to efficiently express the mutant 5S rRNA genes in vivo and a structural mutation in the 5S rRNA, which was previously shown to be functionally neutral but easily detected by gel electrophoresis, allowed for an accurate measure of gene expression. The results provide direct evidence for upstream regulatory elements which confirms a start site element (sse) from -1 to -8 and identifies a new independent upstream promoter element (upe) centered from about -17 to -20. In contrast to previous reports with reconstituted systems, both elements dramatically affect the efficiency of gene expression and suggest that the saturated conditions which are used in reconstituted studies mask sequence dependence; a dependency that could be physiologically significant and play a role in the regulation of 5S rRNA expression. The footprint analyses support an extended region of protein interaction as recently observed in reconstituted systems but again provide evidence of significant structural rearrangements when the upstream sequence is changed. (C) 1997 Academic Press Limited}, keywords = {5 S rRNA,5S rRNA,5S-RNA GENES,CONTROL REGION,DIRECTS SPECIFIC INITIATION,Dna,efficiency,Electrophoresis,ELEMENTS,expression,gene,Gene Expression,GENE-EXPRESSION,Genes,genomic,IN-VIVO,INVITRO TRANSCRIPTION,Mutation,nosource,NUCLEOTIDE-SEQUENCE,POLYMERASE-III,PROMOTER,protein,regulation,RIBOSOMAL-RNA GENES,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SITE,Structural,Support,SYSTEM,TATA-BINDING PROTEIN,UPSTREAM,yeast} }

@article{leedsProductYeastUPF11991b, title = {The Product of the Yeast⬚ {{UPF1}}⬚ Gene Is Required for Rapid Turnover on {{mRNAs}} Containing a Premature Translational Termination Codon.}, author = {Leeds, P. and Peltz, S.W. and Jacobson, A.J. and Culbertson, M.R.}, year = 1991, journal = {Genes & Dev.}, volume = {5}, pages = {2303–2314}, doi = {10.1101/gad.5.12a.2303}, keywords = {Codon,gene,mRNA,nonsense-mediated decay,nosource,termination,turnover,UPF,Upf1,yeast} } % == BibTeX quality report for leedsProductYeastUPF11991b: % ? Possibly abbreviated journal title Genes & Dev.

@article{leedsGeneProductsThat1992a, title = {Gene Products That Promote {{mRNA}} Turnover in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Leeds, P. and Wood, J.M. and Lee, B.-S. and Culbertson, M.R.}, year = 1992, journal = {Mol.Cell.Biol.}, volume = {12}, pages = {2165–2177}, keywords = {gene,mRNA,Multiple DOI,nonfile,nonsense-mediated decay,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,turnover,UPF} } % == BibTeX quality report for leedsGeneProductsThat1992a: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{leerPrimaryStructureGene1984a, title = {The Primary Structure of the Gene Encoding Yeast Ribosomal Protein {{L16}}}, author = {Leer, R.J. and {Raamsdonk-Duin}, M.M. and Mager, W.H. and Planta, R.J.}, year = 1984, month = oct, journal = {FEBS Lett.}, volume = {175}, number = {2}, pages = {371–376}, doi = {10.1016/0014-5793(84)80771-1}, url = {PM:6090215}, abstract = {As part of our studies on the molecular basis for the coordinate expression of ribosomal protein genes in yeast we analyzed the primary structure of the gene encoding protein L16 of the large ribosomal subunit including the flanking sequences. L16 turned out to be a ribosomal protein with a molecular mass of 22662 Da and a net charge of +12. Both the 5’- and the 3’-end of the L16 mRNA were mapped by primer extension and S1 nuclease analysis. In the DNA regions flanking the coding sequence several conserved elements are present that may be involved in transcription initiation or termination}, keywords = {0,3’-END,Amino Acid Sequence,analysis,Base Sequence,CloningMolecular,coding sequence,Dna,DNA Restriction Enzymes,DNARecombinant,ELEMENTS,enzyme,Enzymes,expression,gene,Genes,GenesFungal,genetics,initiation,La,Macromolecular Substances,metabolism,mRNA,nosource,Plasmids,primer extension,protein,Proteins,REGION,Research SupportNon-U.S.Gov’t,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,Saccharomyces cerevisiae,sequence,SEQUENCES,structure,SUBUNIT,termination,transcription,yeast} } % == BibTeX quality report for leerPrimaryStructureGene1984a: % ? Possibly abbreviated journal title FEBS Lett.

@article{leerGenesYeastRibosomal1985, title = {The Genes for Yeast Ribosomal Proteins {{S24}} and {{L46}} Are Adjacent and Divergently Transcribed}, author = {Leer, R.J. and {Raamsdonk-Duin}, M.M. and Kraakman, P. and Mager, W.H. and Planta, R.J.}, year = 1985, month = feb, journal = {Nucleic acids research}, volume = {13}, number = {3}, pages = {701–709}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/13.3.701}, url = {http://nar.oxfordjournals.org/content/13/3/701.short}, abstract = {Unlike most yeast ribosomal protein genes studied so far the genes coding for S24 and L46 are adjacent on the genome. Sequence analysis showed that the two genes are transcribed divergently, their initiation codons being 630 bp apart. Taking the respective ATG translation start sites as reference points, the 5’- end of L46 mRNA was mapped at position -26, while the S24 mRNA showed two major 5’-ends mapping at positions -13 and -16 respectively. Unlike most other yeast ribosomal protein genes, the gene for S24 does not contain an intron. Its coding region encompasses 390 nucleotides encoding a protein of 14762 D. The gene for L46 on the other hand is split by an intron of 386 nucleotides starting after its second codon. This gene encodes a small, very basic protein having a molecular weight of 6334 D. Yeast ribosomal proteins S24 and L46 show striking homologies with ribosomal proteins from other organisms. In particular, yeast L46 is clearly the evolutionary counterpart of rat liver L39. A search of the intergenic region for sequence elements previously identified as common to most yeast ribosomal protein genes, revealed the presence of a single conserved box (RPG-box) roughly equidistant from the transcription initiation sites of both genes. We suggest that this box acts as a regulatory signal in either orientation and thus influences the expression of both genes simultaneously}, keywords = {85215509,Amino Acid Sequence,analysis,animal,Base Sequence,Codon,Comparative Study,ELEMENTS,expression,gene,Genes,genetics,Genome,initiation,Liver,mapping,Molecular Weight,mRNA,nosource,Nucleotides,protein,Proteins,rat,Rats,Ribosomal Proteins,RNAMessenger,search,sequence,Sequence Analysis,SIGNAL,supportnon-u.s.gov’t,transcription,translation,yeast,Yeasts} } % == BibTeX quality report for leerGenesYeastRibosomal1985: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{leeuwenhoekObservationesAnthoniiLeeuwenhoek1678, title = {Observationes {{D}}. {{Anthonii Leeuwenhoek}}, de Natis e Semine Genitali Animalculis.}, author = {Leeuwenhoek, A.van}, year = 1678, journal = {Philos.Trans.Roy.Soc.London}, volume = {12}, pages = {1040–1043}, doi = {10.1098/rstl.1677.0068}, keywords = {nosource,Spermine} } % == BibTeX quality report for leeuwenhoekObservationesAnthoniiLeeuwenhoek1678: % ? Possibly abbreviated journal title Philos.Trans.Roy.Soc.London

@article{leger-silvestreRibosomalProteinRps15p2004, title = {The Ribosomal Protein {{Rps15p}} Is Required for Nuclear Exit of the {{40S}} Subunit Precursors in Yeast}, author = {{Leger-Silvestre}, I. and Milkereit, P. and {Ferreira-Cerca}, S. and Saveanu, C. and Rousselle, J.C. and Choesmel, V. and Guinefoleau, C. and Gas, N. and Gleizes, P.E.}, year = 2004, month = jun, journal = {The EMBO Journal}, volume = {23}, number = {12}, pages = {2336–2347}, publisher = {Nature Publishing Group}, doi = {10.1038/sj.emboj.7600252}, url = {PM:15167894 http://www.nature.com/emboj/journal/v23/n12/abs/7600252a.html}, abstract = {We have conducted a genetic screen in order to identify ribosomal proteins of Saccharomyces cerevisiae involved in nuclear export of the small subunit precursors. This has led us to distinguish Rps15p as a protein dispensable for maturation of the pre-40S particles, but whose assembly into the pre-ribosomes is a prerequisite to their nuclear exit. Upon depletion of Rps15p, 20S pre-rRNA is released from the nucleolus and retained in the nucleus, without alteration of the pre-rRNA early cleavages. In contrast, Rps18p, which contacts Rps15p in the small subunit, is required upstream for pre-rRNA processing at site A2. Most pre-40S specific factors are correctly associated with the intermediate particles accumulating in the nucleus upon Rps15p depletion, except the late-binding proteins Tsr1p and Rio2p. Here we show that these two proteins are dispensable for nuclear exit; instead, they participate in 20S pre-rRNA processing in the cytoplasm. We conclude that, during the final maturation steps in the nucleus, incorporation of the ribosomal protein Rps15p is specifically required to render the pre-40S particles competent for translocation to the cytoplasm}, keywords = {0,assembly,Cell Nucleus,CEREVISIAE,CLEAVAGE,Cytoplasm,Genetic,IDENTIFY,INTERMEDIATE,L15,L18,La,MATURATION,metabolism,nosource,Nuclear Proteins,nucleolus,PARTICLES,PRECURSOR,protein,Protein Transport,Proteins,Research SupportNon-U.S.Gov’t,Ribosomal Proteins,RIBOSOMAL-PROTEIN,Rna,RNA Precursors,RNARibosomal,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SITE,SUBUNIT,translocation,UPSTREAM,yeast} } % == BibTeX quality report for leger-silvestreRibosomalProteinRps15p2004: % ? unused Journal abbr (“EMBO J.”)

@article{legerReassessmentResponseBacterial2004, title = {A Reassessment of the Response of the Bacterial Ribosome to the Frameshift Stimulatory Signal of the Human Immunodeficiency Virus Type 1}, author = {Leger, M. and Sidani, S. and {Brakier-Gingras}, L.}, year = 2004, journal = {RNA}, volume = {10}, number = {8}, pages = {1225–1235}, doi = {10.1261/rna.7670704}, url = {PM:15247429}, abstract = {HIV-1 uses a programmed -1 ribosomal frameshift to produce the precursor of its enzymes. This frameshift occurs at a specific slippery sequence followed by a stimulatory signal, which was recently shown to be a two-stem helix, for which a three-purine bulge separates the upper and lower stems. In the present study, we investigated the response of the bacterial ribosome to this signal, using a translation system specialized for the expression of a firefly luciferase reporter. The HIV-1 frameshift region was inserted at the beginning of the coding sequence of the luciferase gene, such that its expression requires a -1 frameshift. Mutations that disrupt the upper or the lower stem of the frameshift stimulatory signal or replace the purine bulge with pyrimidines decreased the frameshift efficiency, whereas compensatory mutations that re-form both stems restored the frame-shift efficiency to near wild-type level. These mutations had the same effect in a eukaryotic translation system, which shows that the bacterial ribosome responds like the eukaryote ribosome to the HIV-1 frameshift stimulatory signal. Also, we observed, in contrast to a previous report, that a stop codon immediately 3’ to the slippery sequence does not decrease the frameshift efficiency, ruling out a proposal that the frameshift involves the deacylated-tRNA and the peptidyl-tRNA in the E and P sites of the ribosome, rather than the peptidyl-tRNA and the aminoacyl-tRNA in the P and A sites, as commonly assumed. Finally, mutations in 16S ribosomal RNA that facilitate the accommodation of the incoming aminoacyl-tRNA in the A site decreased the frameshift efficiency, which supports a previous suggestion that the frameshift occurs when the aminoacyl-tRNA occupies the A/T entry site}, keywords = {16S,3,A SITE,A-SITE,A-SITES,Bacterial,coding sequence,Codon,E,efficiency,enzyme,Enzymes,EUKARYOTIC TRANSLATION,expression,FIREFLY LUCIFERASE,frameshift,gene,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,La,luciferase,Mutation,MUTATIONS,nosource,P and A sites,P SITE,P-SITE,P-SITES,PRECURSOR,Pyrimidines,REGION,REQUIRES,RIBOSOMAL FRAMESHIFT,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Rna,sequence,SIGNAL,SITE,SITES,STOP CODON,Support,SYSTEM,translation,TYPE-1,virus,WILD-TYPE} }

@article{legerThreeTransferRNAs2007, title = {The Three Transfer {{RNAs}} Occupying the {{A}}, {{P}} and {{E}} Sites on the Ribosome Are Involved in Viral Programmed -1 Ribosomal Frameshift}, author = {Leger, M. and Dulude, D. and Steinberg, S.V. and {Brakier-Gingras}, L.}, year = 2007, journal = {Nucleic Acids Research}, volume = {35}, number = {16}, pages = {5581–5592}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkm578}, url = {PM:17704133 http://nar.oxfordjournals.org/content/35/16/5581.short}, abstract = {The -1 programmed ribosomal frameshifts (PRF), which are used by many viruses, occur at a heptanucleotide slippery sequence and are currently thought to involve the tRNAs interacting with the ribosomal P- and A-site codons. We investigated here whether the tRNA occupying the ribosomal E site that precedes a slippery site influences -1 PRF. Using the human immunodeficiency virus type 1 (HIV-1) frameshift region, we found that mutating the E-site codon altered the -1 PRF efficiency. When the HIV-1 slippery sequence was replaced with other viral slippery sequences, mutating the E-site codon also altered the -1 PRF efficiency. Because HIV-1 -1 PRF can be recapitulated in bacteria, we used a bacterial ribosome system to select, by random mutagenesis, 16S ribosomal RNA (rRNA) mutations that modify the expression of a reporter requiring HIV-1 -1 PRF. Three mutants were isolated, which are located in helices 21 and 22 of 16S rRNA, a region involved in translocation and E-site tRNA binding. We propose a novel model where -1 PRF is triggered by an incomplete translocation and depends not only on the tRNAs interacting with the P- and A-site codons, but also on the tRNA occupying the E site}, keywords = {0,16S,A SITE,A-SITE,Bacteria,Bacterial,BINDING,Cell Line,chemistry,Codon,CODONS,E,E site,efficiency,expression,frameshift,Frameshifting-Ribosomal,FrameshiftingRibosomal,Genes-Reporter,GenesReporter,genetics,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,Humans,IMMUNODEFICIENCY-VIRUS,La,metabolism,MODEL,Models-Genetic,ModelsGenetic,Mutagenesis,MUTANTS,Mutation,MUTATIONS,nosource,Nucleotides,REGION,RIBOSOMAL FRAMESHIFT,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNA-Messenger,RNA-Ribosomal-16S,RNA-Transfer,Rna-Viral,RNAMessenger,RNARibosomal16S,RNATransfer,RnaViral,rRNA,sequence,SEQUENCES,SITE,SITES,slippery site,Support,SYSTEM,TRANSFER-RNA,translocation,tRNA,tRNA binding,TYPE-1,virus,Viruses} } % == BibTeX quality report for legerThreeTransferRNAs2007: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{lehnerProteinInteractionFramework2004, title = {A Protein Interaction Framework for Human {{mRNA}} Degradation}, author = {Lehner, B. and Sanderson, C.M.}, year = 2004, month = jul, journal = {Genome Res.}, volume = {14}, number = {7}, pages = {1315–1323}, doi = {10.1101/gr.2122004}, url = {PM:15231747}, abstract = {The degradation of mRNA is an important regulatory step in the control of gene expression. However, mammalian RNA decay pathways remain poorly characterized. To provide a framework for studying mammalian RNA decay, a two-hybrid protein interaction map was generated using 54 constructs from 38 human proteins predicted to function in mRNA decay. The results provide evidence for interactions between many different proteins required for mRNA decay. Of particular interest are interactions between the poly(A) ribonuclease and the exosome and between the Lsm complex, decapping factors, and 5’–{\(>\)}3’ exonucleases. Moreover, multiple interactions connect 5’–{\(>\)}3’ and 3’–{\(>\)}5’ decay proteins to each other and to nonsense-mediated decay factors, providing the opportunity for coordination between decay pathways. The interaction network also predicts the internal organization of the exosome and Lsm complexes. Additional interactions connect mRNA decay factors to many novel proteins and to proteins required for other steps in gene expression. These results provide an experimental insight into the organization of proteins required for mRNA decay and their coupling to other cellular processes, and the physiological relevance of many of these interactions are supported by their evolutionary conservation. The interactions also provide a wealth of hypotheses to guide future research on mRNA degradation and demonstrate the power of exhaustive protein interaction mapping in aiding understanding of uncharacterized protein complexes and pathways}, keywords = {0,Carrier Proteins,CEREVISIAE,chemistry,Comparative Study,COMPLEX,COMPLEXES,Conserved Sequence,DECAY,DECAY PATHWAY,decay pathways,degradation,EvolutionMolecular,Exonucleases,Exoribonucleases,exosome,expression,gene,Gene Expression,GENE-EXPRESSION,genomic,Genomics,human,La,mapping,metabolism,Methods,mRNA,mRNA decay,Multienzyme Complexes,nonsense-mediated decay,nosource,Nuclear Proteins,ORGANIZATION,PATHWAY,physiology,poly(A),protein,PROTEIN COMPLEX,Protein Interaction Mapping,Protein Subunits,Proteins,Rna,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Structure-Activity Relationship,SUBUNIT,SUBUNITS,Two-Hybrid System Techniques} } % == BibTeX quality report for lehnerProteinInteractionFramework2004: % ? Possibly abbreviated journal title Genome Res.

@article{leibowitzRoleProteinSynthesisReplication1982, title = {Role of {{Protein-Synthesis}} in the {{Replication}} of the {{Killer Virus}} of {{Yeast}}}, author = {Leibowitz, M.J.}, year = 1982, journal = {Current Genetics}, volume = {5}, number = {2}, pages = {161–163}, publisher = {Springer}, doi = {10.1007/BF00365709}, url = {http://www.springerlink.com/index/K852G43419652538.pdf}, keywords = {3,killer,M,nosource,protein synthesis,PROTEIN-SYNTHESIS,REPLICATION,virus,yeast} } % == BibTeX quality report for leibowitzRoleProteinSynthesisReplication1982: % ? Title looks like it was stored in title-case in Zotero

@article{lempereurConformationYeast18S1985a, title = {Conformation of Yeast {{18S rRNA}}. {{Direct}} Chemical Probing of the 5’ Domain in Ribosomal Subunits and in Deproteinized {{RNA}} by Reverse Transcriptase Mapping of Dimethyl Sulfate-Accessible}, author = {Lempereur, L. and Nicoloso, M. and Riehl, N. and Ehresmann, C. and Ehresmann, B. and Bachellerie, J.P.}, year = 1985, month = dec, journal = {Nucleic Acids Res.}, volume = {13}, number = {23}, pages = {8339–8357}, doi = {10.1093/nar/13.23.8339}, abstract = {The structure of the 5’ domain of yeast 18S rRNA has been probed by dimethyl sulfate (DMS), either in “native” deproteinized molecules or in the 40S ribosomal subunits. DMS-reacted RNA has been used as a template for reverse transcription and a large number of reactive sites, corresponding to all types of bases have been mapped by a primer extension procedure, taking advantage of blocks in cDNA elongation immediately upstream from bases methylated at atom positions involved in the base-pair recognition of the template. Since the same atom positions are protected from DMS in base-paired nucleotides, the secondary structure status of each nucleotide can be directly assessed in this procedure, thus allowing to evaluate the potential contribution of proteins in modulating subunit rRNA conformation. While the DMS probing of deproteinized rRNA confirms a number of helical stems predicted by phylogenetic comparisons, it is remarkable that a few additional base-pairings, while proven by the comparative analysis, appear to require the presence of the bound ribosomal subunit proteins to be stabilized}, keywords = {analysis,Base Pairing,DMS,elongation,Hydrogen Bonding,mapping,metabolism,Methylation,nosource,Nucleic Acid Conformation,Nucleotides,primer extension,protein,Proteins,RIBOSOMAL-SUBUNIT,Ribosomes,Rna,RNA-Directed DNA Polymerase,RNAFungal,RNARibosomal,rRNA,Saccharomyces cerevisiae,structure,SUBUNIT,Sulfuric Acid Esters,supportnon-u.s.gov’t,transcription,ultrastructure,yeast} } % == BibTeX quality report for lempereurConformationYeast18S1985a: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{lendvaySenescenceMutantsSaccharomyces1996, title = {Senescence Mutants of {{Saccharomyces}} Cerevisiae with a Defect in Telomere Replication Identify Three Additional {{EST}} Genes}, author = {Lendvay, T.S. and Morris, D.K. and Sah, J. and Balasubramanian, B. and Lundblad, V.}, year = 1996, month = dec, journal = {Genetics}, volume = {144}, number = {4}, pages = {1399–1412}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/144.4.1399}, url = {http://www.genetics.org/content/144/4/1399.short}, abstract = {The primary determinant for telomere replication is the enzyme telomerase, responsible for elongating the G-rich strand of the telomere. The only component of this enzyme that has been identified in Saccharomyces cerevisiae is the TLC1 gene, encoding the telomerase RNA subunit. However, a yeast strain defective for the EST1 gene exhibits the same phenotypes (progressively shorter telomeres and a senescence phenotype) as a strain deleted for TLC1, suggesting that EST1 encodes either a component of telomerase or some other factor essential for telomerase function. We designed a multitiered screen that led to the isolation of 22 mutants that display the same phenotypes as est1 and tlc1 mutant strains. These mutations mapped to four complementation groups: the previously identified EST1 gene and three additional genes, called EST2, EST3 and EST4. Cloning of the EST2 gene demonstrated that it encodes a large, extremely basic novel protein with no motifs that provide clues as to function. Epistasis analysis indicated that the four EST genes function in the same pathway for telomere replication as defined by the TLC1 gene, suggesting that the EST genes encode either components of telomerase or factors that positively regulate telomerase activity}, keywords = {0,Amino Acid Sequence,analysis,CEREVISIAE,cloning,CloningMolecular,COMPONENT,COMPONENTS,Dna,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,DNAFungal,ENCODES,enzyme,EST,Fungal Proteins,gene,Gene Expression RegulationFungal,Genes,Genetic,genetics,human,IDENTIFY,La,Molecular Sequence Data,MOTIFS,MUTANTS,Mutation,MUTATIONS,nosource,PATHWAY,Phenotype,protein,Proteins,REPLICATION,Rna,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SUBUNIT,Support,Telomerase,Telomere,Telomere-Binding Proteins,yeast} }

@article{leonovDirectedIntroductionPhotoaffinity1999a, title = {[{{Directed}} Introduction of Photoaffinity Reagents in Internal Segments of {{RNA}}]}, author = {Leonov, A.A. and Sergiev, P.V. and Dontsova, O.A. and Bogdanov, A.A.}, year = 1999, month = nov, journal = {Molekuliarnaia biologiia}, volume = {33}, number = {6}, eprint = {10624698}, eprinttype = {pubmed}, pages = {1063–1073}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10624698}, keywords = {0,Base Sequence,chemistry,Dna,DNA-Directed DNA Polymerase,genetics,La,No DOI found,nosource,Nucleic Acid Conformation,Photoaffinity Labels,polymerase,Polynucleotide Adenylyltransferase,Rna,TranscriptionGenetic} } % == BibTeX quality report for leonovDirectedIntroductionPhotoaffinity1999a: % ? unused Journal abbr (“Mol.Biol.(Mosk)”)

@article{leonovAffinityPurificationRibosomes2003a, title = {Affinity Purification of Ribosomes with a Lethal {{G2655C}} Mutation in {{23S rRNA}} That Affects the Translocation}, author = {Leonov, A.A. and Sergiev, P.V. and Bogdanov, A.A. and Brimacombe, R. and Dontsova, O.A.}, year = 2003, month = may, journal = {J.Biol.Chem.}, volume = {278}, pages = {25664–26670}, doi = {10.1074/jbc.M302873200}, url = {PM:12730236}, abstract = {A method for preparation of E. coli ribosomes carrying lethal mutations in 23S rRNA was developed. The method is based on the site-directed incorporation of a streptavidin-binding tag into functionally neutral sites of the 23S rRNA and subsequent affinity chromatography. It was tested with ribosomes mutated at 23S rRNA position 2655 (the EF-G binding site). Ribosomes carrying the lethal G2655C mutation were purified and studied in vitro. It was found in particular that this mutation confers strong inhibition of the translocation process, but only moderately affects GTPase activity and binding of EF-G}, keywords = {0,BINDING,chemistry,Chromatography,GTPase,In Vitro,IN-VITRO,INHIBITION,La,Mutation,MUTATIONS,nosource,purification,ribosome,Ribosomes,rRNA,translocation} } % == BibTeX quality report for leonovAffinityPurificationRibosomes2003a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{leontis5SRRNALoop1998, title = {The {{5S rRNA}} Loop {{E}}: Chemical Probing and Phylogenetic Data versus Crystal Structure.}, author = {Leontis, N.B. and Westhof, E.}, year = 1998, journal = {RNA}, volume = {4}, number = {9}, pages = {1134–1153}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838298980566}, url = {http://rnajournal.cshlp.org/content/4/9/1134.short}, abstract = {A significant fraction of the bases in a folded, structured RNA molecule participate in noncanonical base pairing interactions, often in the context of internal loops or multi-helix junction loops. The appearance of each new high-resolution RNA structure provides welcome data to guide efforts to understand and predict RNA 3D structure, especially when the RNA in question is a functionally conserved molecule. The recent publication of the crystal structure of the “Loop E” region of bacterial 5S ribosomal RNA is such an event [Correll CC, Freeborn B, Moore PB, Steitz TA, 1997, Cell 91:705-712]. In addition to providing more examples of already established noncanonical base pairs, such as purine-purine sheared pairings, trans-Hoogsteen UA, and GU wobble pairs, the structure provides the first high-resolution views of two new purine-purine pairings and a new GU pairing. The goal of the present analysis is to expand the capabilities of both chemical probing and phylogenetic analysis to predict with greater accuracy the structures of RNA molecules. First, in light of existing chemical probing data, we investigate what lessons could be learned regarding the interpretation of this widely used method of RNA structure probing. Then we analyze the 3D structure with reference to molecular phylogeny data (assuming conservation of function) to discover what alternative base pairings are geometrically compatible with the structure. The comparisons between previous modeling efforts and crystal structures show that the intricate involvements of ions and water molecules in the maintenance of non-Watson-Crick pairs render the process of correctly identifying the interacting sites in such pairs treacherous, except in cases of trans-Hoogsteen A/U or sheared A/G pairs for the adenine N1 site. The phylogenetic analysis identifies A/A, A/C, A/U and C/A, C/C, and C/U pairings isosteric with sheared A/G, as well as A/A and A/C pairings isosteric with both G/U and G/G bifurcated pairings. Thus, each non-Watson-Crick pair could be characterized by a phylogenetic signature of variations between isosteric-like pairings. In addition to the conservative changes, which form a dictionary of pairings isosterically compatible with those observed in the crystal structure, concerted changes involving several base pairs also occur. The latter covariations may indicate transitions between related but distinctive motifs within the loop E of 5S ribosomal RNA}, keywords = {5S rRNA,98410847,accuracy,Adenine,analysis,Bacteria,Bacterial,Base Composition,Base Pairing,Base Sequence,chemistry,Comparative Study,CrystallographyX-Ray,Escherichia coli,genetics,Ions,ModelsMolecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Phylogeny,RIBOSOMAL-RNA,Rna,RNABacterial,RNAChloroplast,RNARibosomal5S,rRNA,Spinach,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Water} }

@article{lessardStudiesFormationTransfer1972a, title = {Studies on the Formation of Transfer Ribonucleic Acid-Ribosome Complexes. {{XXII}}. {{Binding}} of Aminoacyl-Oligonucleotides to Ribosomes}, author = {Lessard, J.L. and Pestka, S.}, year = 1972, month = nov, journal = {J.Biol.Chem.}, volume = {247}, number = {21}, pages = {6901–6908}, doi = {10.1016/S0021-9258(19)44670-X}, keywords = {Adenine Nucleotides,Alanine,Amino Acids,Amino Acyl-tRNA Ligases,Ammonium Chloride,BINDING,ChromatographyIon Exchange,COMPLEX,COMPLEXES,cytology,Cytosine Nucleotides,drug effects,ElectrophoresisPaper,Escherichia coli,Ethanol,Glutamates,Leucine,Lysine,Magnesium,metabolism,nosource,Oligonucleotides,pharmacology,Phenylalanine,Polynucleotides,Puromycin,ribosome,Ribosomes,Serine,Tritium} } % == BibTeX quality report for lessardStudiesFormationTransfer1972a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{levievRoleHighlyConserved1995a, title = {Role for the Highly Conserved Region of Domain {{IV}} of {{23S-like rRNA}} in Subunit-Subunit Interactions at the Peptidyl Transferase Centre.}, author = {Leviev, I. and Levieva, S. and Garrett, R.A.}, year = 1995, journal = {Nucleic Acids Res.}, volume = {23}, pages = {1512–1517}, doi = {10.1093/nar/23.9.1512}, keywords = {E.coli,nosource,peptidyl transferase,rRNA} } % == BibTeX quality report for levievRoleHighlyConserved1995a: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{levinProgrammedTranslationalFrameshift1993, title = {A Programmed Translational Frameshift Is Required for the Synthesis of a Bacteriophage Lambda Tail Assembly Protein}, author = {Levin, M.E. and Hendrix, R.W. and Casjens, S.R.}, year = 1993, month = nov, journal = {J.Mol.Biol.}, volume = {234}, number = {1}, pages = {124–139}, doi = {10.1006/jmbi.1993.1568}, abstract = {Two proteins, one of 31 kDa and one of 16 kDa, are encoded by a segment of the phage lambda tail gene region that contains two overlapping reading frames, neither of which is long enough to encode the larger protein. We show that the abundant 16-kDa protein (gpG) is encoded by the upstream open reading frame, gene G. The 31-kDa protein, gpG-T, is encoded jointly by gene G and the overlapping downstream T open reading frame. gpG-T is synthesized as the result of a translational frameshift that occurs when a ribosome translating the G gene slips back by one nucleotide at a position six codons from the C terminus of the gene and thereby bypasses the G termination codon to continue on in the T open reading frame. The resulting protein shares 135 residues of N-terminal amino acid sequence with gpG, followed by 144 amino acid residues of unique sequence. The frameshift event occurs with a frequency of approximately 4% at the sequence G GGA AAG, which encodes the dipeptide -Gly-Lys- in both the zero and -1 reading frames. The frameshift frequencies of point mutants in this “slippery sequence” argue that codon-anticodon interactions with both the glycyl and the lysyl-tRNA are important for frameshifting to occur. We find no clear evidence for a pausing mechanism to enhance frameshifting, as is seen in other well- characterized frameshifts. No simple secondary structure has been predicted for the region downstream from the slippery sequence, but this downstream sequence does contribute to the frameshifting rate. Our results together with those of Katsura and Kuhl show that the frameshift product, gpG-T, has an essential role in lambda tail assembly, acting prior to tail shaft assembly. The role of gpG in tail assembly is not known. We find that both gpG and the gpG-T are absent from mature virions}, keywords = {Amino Acid Sequence,assembly,Bacteriophage lambda,Base Sequence,chemistry,Codon,DnaViral,frameshift,Frameshifting,gene,Gene Expression RegulationViral,GenesStructuralViral,genetics,MECHANISM,Molecular Sequence Data,morphogenesis,nosource,pausing,protein,Proteins,ribosome,sequence,structure,supportu.s.gov’tp.h.s.,termination,TranslationGenetic,ultrastructure,Viral Tail Proteins,Virion,Virus Replication} } % == BibTeX quality report for levinProgrammedTranslationalFrameshift1993: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{levyPathogenesisHumanImmunodeficiency1993, title = {Pathogenesis of Human Immunodeficiency Virus Infection.}, author = {Levy, J.A.}, year = 1993, month = mar, journal = {Microbiology and Molecular Biology Reviews}, volume = {57}, number = {1}, pages = {183–289}, publisher = {Am Soc Microbiol}, doi = {10.1128/mr.57.1.183-289.1993}, url = {http://mmbr.asm.org/cgi/content/abstract/57/1/183}, keywords = {Antibodies,antibody,antiviral,development,expression,gene,Genes,Genetic,HIV,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,MECHANISM,MECHANISMS,nosource,sequence,virus} }

@article{lewTelomereLengthRegulation1998, title = {Telomere Length Regulation and Telomeric Chromatin Require the Nonsense- Mediated {{mRNA}} Decay Pathway}, author = {Lew, J.E. and Enomoto, S. and Berman, J.}, year = 1998, month = oct, journal = {Molecular and Cellular Biology}, volume = {18}, number = {10}, pages = {6121–6130}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.18.10.6121}, url = {http://mcb.asm.org/cgi/content/abstract/18/10/6121}, abstract = {Rap1p localization factor 4 (RLF4) is a Saccharomyces cerevisiae gene that was identified in a screen for mutants that affect telomere function and alter the localization of the telomere binding protein Rap1p. In rlf4 mutants, telomeric silencing is reduced and telomere DNA tracts are shorter, indicating that RLF4 is required for both the establishment and/or maintenance of telomeric chromatin and for the control of telomere length. In this paper, we demonstrate that RLF4 is allelic to NMD2/UPF2, a gene required for the nonsense-mediated mRNA decay (NMD) pathway (Y. Cui, K. W. Hagan, S. Zhang, and S. W. Peltz, Mol. Cell. Biol. 9:423-436, 1995, and F. He and A. Jacobson, Genes Dev. 9:437-454, 1995). The NMD pathway, which requires Nmd2p/Rlf4p together with two other proteins, (Upf1p and Upf3p), targets nonsense messages for degradation in the cytoplasm by the exoribonuclease Xrn1p. Deletion of UPF1 and UPF3 caused telomere-associated defects like those caused by rlf4 mutations, implying that the NMD pathway, rather than an NMD- independent function of Nmd2p/Rlf4p, is required for telomere functions. In addition, telomere length regulation required Xrn1p but not Rat1p, a nuclear exoribonuclease with functional similarity to Xrn1p (A. W. Johnson, Mol. Cell. Biol. 17:6122-6130, 1997). In contrast, telomere-associated defects were not observed in pan2, pan3, or pan2 pan3 strains, which are defective in the intrinsic deadenylation-dependent decay of normal (as opposed to nonsense) mRNAs. Thus, loss of the NMD pathway specifically causes defects at telomeres, demonstrating a physiological requirement for the NMD pathway in normal cell functions. We propose a model in which the NMD pathway regulates the levels of specific mRNAs that are important for telomere functions}, keywords = {98414628,BINDING,BINDING-PROTEIN,Chromatin,Cloning-Molecular,CloningMolecular,Cytoplasm,DECAY,degradation,Dna,DNA-Binding Proteins,Exoribonucleases,Fungal Proteins,gene,Genes,Genes-Fungal,GenesFungal,Genetic,genetics,metabolism,mRNA,mRNA decay,Mutagenesis,Mutation,MUTATIONS,NMD,nosource,protein,Proteins,regulation,RNA-Fungal,RNA-Messenger,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,support-u.s.gov’t-p.h.s.,supportu.s.gov’tp.h.s.,Telomere,Trans-Activators,Upf1,UPF3} } % == BibTeX quality report for lewTelomereLengthRegulation1998: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{lewisInfluenceEndStructures1995a, title = {The Influence of 5’ and 3’ End Structures on Pre-{{mRNA}} Metabolism}, author = {Lewis, J.D. and Gunderson, S.I. and Mattaj, I.W.}, year = 1995, journal = {Journal of cell science. Supplement}, volume = {19}, number = {6}, eprint = {8655642}, eprinttype = {pubmed}, pages = {13–19}, doi = {10.1242/jcs.1995.Supplement_19.2}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8655642}, abstract = {The 5’ cap structure of RNA polymerase II transcripts and the poly(A) tail found at the 3’ end of most mRNAs have been demonstrated to play multiple roles in gene expression and its regulation. In the first part of this review we will concentrate on the role played by the cap in pre-mRNA splicing and how it may contribute to efficient and specific substrate recognition. In the second half, we will discuss the roles that polyadenylation has been demonstrated to play in RNA metabolism and will concentrate in particular on an elegant mechanism where regulation of polyadenylation is used to control gene expression}, keywords = {96112715,animal,Cap,expression,gene,Gene Expression,Gene Expression Regulation,GENE-EXPRESSION,genetics,human,MECHANISM,metabolism,mRNA,nosource,physiology,Poly A,poly(A),polymerase,regulation,Review,RibonucleoproteinU1 Small Nuclear,Rna,Rna Caps,RNA Polymerase II,RNA Precursors,RNA ProcessingPost-Transcriptional,RNA Splicing,RNA-Binding Proteins,splicing,structure} } % == BibTeX quality report for lewisInfluenceEndStructures1995a: % ? Possibly abbreviated journal title Journal of cell science. Supplement % ? unused Journal abbr (“J.Cell Sci.Suppl”)

@article{lewisAttractsGettingRNA2000a, title = {Like Attracts like: {{Getting RNA}} Processing Together in the Nucleus}, author = {Lewis, J.D. and Tollervey, D.}, year = 2000, month = may, journal = {Science}, volume = {288}, number = {5470}, pages = {1385–1389}, doi = {10.1126/science.288.5470.1385}, url = {ISI:000087270900040}, abstract = {Structures visible within the eukaryotic nucleus have fascinated generations of biologists. Recent data show that these structures form in response to gene expression and are highly dynamic in Living cells. RNA processing and assembly require many factors but the nucleus apparently lacks any active transport system to deliver these to the RNAs. Instead, processing factors move by diffusion but are concentrated by transient association with functionally related components. At sites of high activity this gives rise to visible structures, with components in dynamic equilibrium with the surrounding nucleoplasm. Processing factors are recruited from this pool by cooperative binding to RNA substrates}, keywords = {assembly,ASSOCIATION,BINDING,CARBOXY-TERMINAL DOMAIN,CELLS,COILED BODIES,COMPONENT,COMPONENTS,D,DISEASE GENE-PRODUCT,expression,gene,Gene Expression,GENE-EXPRESSION,GREEN FLUORESCENT PROTEIN,nosource,POLYMERASE-II TRANSCRIPTION,PRE-MESSENGER-RNA,Review,Rna,SITE,SITES,SMALL NUCLEOLAR RNAS,SPLICING FACTORS,structure,SYSTEM,TRANSCRIPTION ELONGATION-FACTOR,TRANSPORT,U6 SPLICEOSOMAL RNA} }

@article{lewisStudiesAstrovirusSignal1997a, title = {Studies of the Astrovirus Signal That Induces (-1) Ribosomal Frameshifting.}, author = {Lewis, T.L. and Matsui, S.M.}, year = 1997, journal = {Advances in experimental medicine and biology}, volume = {412}, eprint = {9192037}, eprinttype = {pubmed}, pages = {323–330}, doi = {10.1007/978-1-4899-1828-4_53}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9192037}, keywords = {analysis,Antibodies,antibody,Cytoplasm,efficiency,expression,frameshift,Frameshifting,gene,human,MECHANISM,nosource,picornavirus,Plasmids,polymerase,protein,Proteins,pseudoknot,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,ribosome,Rna,rotavirus,sequence,SIGNAL,SYSTEM,transcription,translation,virus} }

@article{lhoestColdsensitiveRibosomeAssembly1981, title = {Cold-Sensitive Ribosome Assembly in an {{Escherichia}} Coli Mutant Lacking a Single Methyl Group in Ribosomal Protein {{L3}}}, author = {Lhoest, J. and Colson, C.}, year = 1981, month = dec, journal = {Eur.J.Biochem.}, volume = {121}, number = {1}, pages = {33–37}, doi = {10.1111/j.1432-1033.1981.tb06425.x}, abstract = {Ribosomal protein methylation has been well documented but its function remains unclear. We have examined this phenomenon using an Escherichia coli mutant (prmB2), which fails to methylate glutamine residue number 150 of ribosomal protein L3. This mutant exhibits a cold-sensitive phenotype: its growth rate at 22 degrees C is abnormally low in complete medium. In addition, strains with this mutation accumulate abnormal and unstable ribosomal particles; 50-S and 30-S subunits are formed, but at a lower rate. Once assembled, ribosomes with unmethylated L3 are fully active by several criteria. (a) Protein synthesis in vitro with purified 70-S prmB2 ribosomes is as active as wild-type using either a natural (R17) or an artificial [poly(U)] messenger. (b) The induction of beta-galactosidase in vivo exhibits normal kinetics and the enzyme has a normal rate of thermal denaturation. (c) These ribosomes are standard when exposed in vitro to a low magnesium concentration or increasing molarities of LiCl. Efficient methylation of L3 in vitro requires either unfolded ribosomes or a mixture of ribosomal protein and RNA. We suggest that the L3-specific methyltransferase may qualify as one of the postulated ‘assembly factors’ of the E. coli ribosome}, keywords = {30 S,assembly,beta-Galactosidase,biosynthesis,Cold,Drug Stability,enzyme,Escherichia coli,ESCHERICHIA-COLI,genetics,Glutamine,In Vitro,IN-VITRO,IN-VIVO,Kinetics,L3,Magnesium,media,metabolism,Methylation,Mutation,nosource,Phenotype,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Ribosomal Proteins,ribosome,Ribosomes,Rna,SUBUNIT,supportnon-u.s.gov’t} } % == BibTeX quality report for lhoestColdsensitiveRibosomeAssembly1981: % ? Possibly abbreviated journal title Eur.J.Biochem.

@article{liTranscriptionalElementsInvolved1999, title = {Transcriptional Elements Involved in the Repression of Ribosomal Protein Synthesis}, author = {Li, B. and Nierras, C.R. and Warner, J.R.}, year = 1999, journal = {Molecular and cellular biology}, volume = {19}, number = {8}, pages = {5393–5404}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.19.8.5393}, url = {http://mcb.asm.org/cgi/content/full/19/8/5393?view=full&pmid=10409730}, abstract = {The ribosomal proteins (RPs) of Saccharomyces cerevisiae are encoded by 137 genes that are among the most transcriptionally active in the genome. These genes are coordinately regulated: a shift up in temperature leads to a rapid, but temporary, decline in RP mRNA levels. A defect in any part of the secretory pathway leads to greatly reduced ribosome synthesis, including the rapid loss of RP mRNA. Here we demonstrate that the loss of RP mRNA is due to the rapid transcriptional silencing of the RP genes, coupled to the naturally short lifetime of their transcripts. The data suggest further that a global inhibition of polymerase II transcription leads to overestimates of the stability of individual mRNAs. The transcription of most RP genes is activated by two Rap1p binding sites, 250 to 400 bp upstream from the initiation of transcription. Rap1p is both an activator and a silencer of transcription. The swapping of promoters between RPL30 and ACT1 or GAL1 demonstrated that the Rap1p binding sites of RPL30 are sufficient to silence the transcription of ACT1 in response to a defect in the secretory pathway. Sir3p and Sir4p, implicated in the Rap1p- mediated repression of silent mating type genes and of telomere- proximal genes, do not influence such silencing of RP genes. Sir2p, implicated in the silencing both of the silent mating type genes and of genes within the ribosomal DNA locus, does not influence the repression of either RP or rRNA genes. Surprisingly, the 180-bp sequence of RPL30 that lies between the Rap1p sites and the transcription initiation site is also sufficient to silence the Gal4p-driven transcription in response to a defect in the secretory pathway, by a mechanism that requires the silencing region of Rap1p. We conclude that for Rap1p to activate the transcription of an RP gene it must bind to upstream sequences; yet for Rap1p to repress the transcription of an RP gene it need not bind to the gene directly. Thus, the cell has evolved a two- pronged approach to effect the rapid extinction of RP synthesis in response to the stress imposed by a heat shock or by a failure of the secretory pathway. Calculations based on recent transcriptome data and on the half-life of the RP mRNAs suggest that in a rapidly growing cell the transcription of RP mRNAs accounts for nearly 50% of the total transcriptional events initiated by RNA polymerase II. Thus, the sudden silencing of the RP genes must have a dramatic effect on the overall transcriptional economy of the cell}, keywords = {99340239,Base Sequence,BINDING,Binding Sites,biosynthesis,Dna,DNA-Binding Proteins,ELEMENTS,Fungal Proteins,gene,Gene Expression RegulationFungal,Genes,genetics,Genome,Half-Life,INHIBITION,initiation,MECHANISM,metabolism,Molecular Sequence Data,mRNA,nosource,physiology,polymerase,Promoter Regions (Genetics),protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Repressor Proteins,Ribosomal Proteins,ribosome,Rna,RNA Polymerase II,RNAFungal,RNAMessenger,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,stability,supportu.s.gov’tp.h.s.,Telomere,Temperature,Trans-Activators,transcription,TranscriptionGenetic} } % == BibTeX quality report for liTranscriptionalElementsInvolved1999: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{liMolecularGeneticAnalysis1996a, title = {Molecular Genetic Analysis of Plastocyanin Biosynthesis in ⬚{{Chlamydomonas}} Reinhardtii⬚.}, author = {Li, H.H. and Quinn, J. and Culler, D. and Girard, Bascou and Merchant, S.}, year = 1996, journal = {J.Biol.Chem.}, volume = {271}, pages = {31283–31289}, doi = {10.1074/jbc.271.49.31283}, keywords = {analysis,anisomycin,biosynthesis,Genetic,mRNA,nosource,stability} } % == BibTeX quality report for liMolecularGeneticAnalysis1996a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{liStructuralAnalysisThe12001, title = {Structural Analysis of The-1 Ribosomal Frameshift Elements in Giardiavirus {{mRNA}}}, author = {Li, L. and Wang, A.L. and Wang, C.C.}, year = 2001, month = nov, journal = {Journal of Virology}, volume = {75}, number = {22}, pages = {10612–10622}, publisher = {Am Soc Microbiol}, doi = {10.1128/JVI.75.22.10612-10622.2001}, url = {http://jvi.asm.org/cgi/content/abstract/75/22/10612}, abstract = {The RNA polymerase of giardiavirus (GLV) is synthesized as a fusion protein through a -1 ribosomal frameshift in a; region where gag and pol open reading frames (ORFs) overlap. A heptamer, CCCUUUA, and a potential pseudoknot found in the overlap were predicted to be required for the frameshift. A 68-nuelcotide (at) cDNA fragment containing these elements was inserted between the GLV 5’ 631-nt cDNA and the out-of-frame luciferase gene that required a -1 frameshift within the 68-nt fragment for expression. Giardia lamblia trophozoites transfected with the transcript of this construct showed a frameshift frequency at 1.7%, coinciding with the polymerase-to-capsid protein ratio in GLV. The heptamer is required for the frameshift but can be replaced with other sequences of the same motif, Mutations placing stop codons in the 0 or -1 frame, located directly before or after the heptamer, implicated the latter as the site for the -1 frameshift. Shortening or destroying the putative stem decreased the frameshift efficiency threefold; the efficiency was fully recovered by mutations to restore the stem. Deleting 18 nt from the 3’ end of the 68-nt fragment, which formed the second stem in the putative pseudoknot, had no effect on the frequency of the frameshift. Chemical probing of the RNA secondary structure in the frameshift region showed that bases resistant to chemical modification were clustered in the putative stem structures, thus confirming the presence of the postulated stem-loop, while all the bases in the loop, were chemically modified, thus ruling out their capability of forming a pseudoknot. These results confirmed the conclusion based, on data from the mutation study that there is but a simple stem-loop downstream from the heptamer. Together, they constitute the structural elements for a -1 ribosomal frameshift in the GLV transcript}, keywords = {0,3,analysis,BASE,BASES,CHEMICAL MODIFICATION,Codon,CODONS,DOWNSTREAM,efficiency,ELEMENTS,ESCHERICHIA-COLI,expression,FRAME,frameshift,Gag,gene,GIARDIA-LAMBLIA,IMMUNODEFICIENCY-VIRUS,LOOP,luciferase,MESSENGER-RNA,modification,mRNA,Mutation,MUTATIONAL ANALYSIS,MUTATIONS,nosource,OPEN READING FRAME,Open Reading Frames,pol,POL FUSION PROTEIN,polymerase,protein,pseudoknot,READING FRAME,Reading Frames,REGION,RESISTANT,RIBOSOMAL FRAMESHIFT,Rna,RNA SECONDARY STRUCTURE,RNA-POLYMERASE,ROUS-SARCOMA VIRUS,SACCHAROMYCES-CEREVISIAE,SECONDARY STRUCTURE,sequence,SEQUENCES,SITE,STEM-LOOP,STOP CODON,STRANDED-RNA VIRUS,Structural,structure,TRANSCRIPT,TRANSLATION FRAMESHIFT} }

@article{liFeedbackInhibitionYeast1995, title = {Feedback Inhibition of the Yeast Ribosomal Protein Gene {{CRY2}} Is Mediated by the Nucleotide Sequence and Secondary Structure of {{CRY2}} Pre-{{mRNA}}}, author = {Li, Z. and Paulovich, A.G. and Woolford, J.L.}, year = 1995, month = nov, journal = {Molecular and cellular biology}, volume = {15}, number = {11}, pages = {6454–6464}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.15.11.6454}, url = {http://mcb.asm.org/cgi/content/abstract/15/11/6454}, keywords = {analysis,assembly,Cytoplasm,degradation,ELEMENTS,expression,Feedback,gene,Gene Expression,GENE-EXPRESSION,Genes,INHIBITION,mRNA,Mutation,MUTATIONS,nosource,Nucleotides,Point Mutation,protein,regulation,ribosome,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,structure,Upf1,yeast} }

@article{liProgrammedFrameshiftingStimulated2001, title = {Programmed +1 Frameshifting Stimulated by Complementarity between a Downstream {{mRNA}} Sequence and an Error-Correcting Region of {{rRNA}}}, author = {Li, Z. and Stahl, G. and Farabaugh, P.J.}, year = 2001, month = feb, journal = {RNA}, volume = {7}, number = {2}, pages = {275–284}, doi = {10.1017/S135583820100190X}, abstract = {Like most retroviruses and retrotransposons, the retrotransposon Ty3 expresses its pol gene analog (POL3) as a translational fusion to the upstream gag analog (GAG3). The Gag3-Pol3 fusion occurs by frameshifting during translation of the mRNA that encodes the two separate but overlapping ORFs. We showed previously that the shift occurs by out-of-frame binding of a normal aminoacyl-tRNA in the ribosomal A site caused by an aberrant codonoanticodon interaction in the P site. This event is unlike all previously described programmed translational frameshifts because it does not require tRNA slippage between cognate or near-cognate codons in the mRNA. A sequence of 15 nt distal to the frameshift site stimulates frameshifting 7.5-fold. Here we show that the Ty3 stimulator acts as an unstructured region to stimulate frameshifting. Its function depends on strict spacing from the site of frameshifting. Finally, the stimulator increases frameshifting dependent on sense codon-induced pausing, but has no effect on frameshifting dependent on pauses induced by nonsense codons. Complementarity between the stimulator and a portion of the accuracy center of the ribosome, Helix 18, implies that the stimulator may directly disrupt error correction by the ribosome}, keywords = {+1 frameshifting,A-SITE,accuracy,ACCURACY CENTER,Amino Acid Sequence,Base Sequence,BINDING,chemistry,Codon,frameshift,Frameshifting,FrameshiftingRibosomal,Fusion Proteinsgag-pol,Gag,gene,genetics,metabolism,ModelsMolecular,Molecular Sequence Data,mRNA,MutationMissense,nosource,Nucleic Acid Conformation,P-SITE,pausing,physiology,Plasmids,pol,Retroelements,retrotransposon,ribosome,Ribosomes,RNA Viruses,RNAMessenger,RNARibosomal,rRNA,Saccharomyces cerevisiae,sequence,SLIPPAGE,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,translation,TranslationGenetic,tRNA} }

@article{liangGenomewideStudyDual2006a, title = {A Genome-Wide Study of Dual Coding Regions in Human Alternatively Spliced Genes}, author = {Liang, H. and Landweber, L.F.}, year = 2006, month = feb, journal = {Genome Res.}, volume = {16}, number = {2}, pages = {190–196}, doi = {10.1101/gr.4246506}, url = {PM:16365380}, abstract = {Alternative splicing is a major mechanism for gene product regulation in many multicellular organisms. By using different exon combinations, some coding regions can encode amino acids in multiple reading frames in different transcripts. Here we performed a systematic search through a set of high-quality human transcripts and show that approximately 7% of alternatively spliced genes contain dual (multiple) coding regions. By using a conservative criterion, we found that in these regions most secondary reading frames evolved recently in mammals, and a significant proportion of them may be specific to primates. Based on the presence of in-frame stop codons in orthologous sequences in other animals, we further classified ancestral and derived reading frames in these regions. Our results indicated that ancestral reading frames are usually under stronger selection than are derived reading frames. Ancestral reading frames mainly influence the coding properties of these dual coding regions. Compared with coding regions of the whole genome, ancestral reading frames largely maintain similar nucleotide composition at each codon position and amino acid usage, while derived reading frames are significantly different. Our results also indicated that prior to acquisition of a new reading frame, the suppression of in-frame stop codons in the ancestral state is mainly achieved by one-step transition substitutions at the first or second codon position. Finally, the selective forces imposed on these dual coding regions will also be discussed}, keywords = {0,ACID,ACIDS,Alternative Splicing,Amino Acids,AMINO-ACID,AMINO-ACIDS,animal,Animals,chemistry,CODING REGION,Codon,CODONS,CodonTerminator,Comparative Study,EvolutionMolecular,EXON,Exons,FRAME,gene,GENE-PRODUCT,Genes,genetics,Genome,GenomeHuman,human,Humans,La,Mammals,MECHANISM,nosource,Open Reading Frames,POSITION,PRODUCT,READING FRAME,Reading Frames,REGION,regulation,Research SupportN.I.H.Extramural,Research SupportU.S.Gov’tNon-P.H.S.,search,SELECTION,Selection (Genetics),sequence,SEQUENCES,splicing,STOP CODON,suppression,TRANSCRIPT} } % == BibTeX quality report for liangGenomewideStudyDual2006a: % ? Possibly abbreviated journal title Genome Res.

@article{liangDifferentialDisplayEukaryotic1992, title = {Differential Display of Eukaryotic Messenger {{RNA}} by Means of the Polymerase Chain Reaction.}, author = {Liang, P. and Pardee, A.B.}, year = 1992, journal = {Science}, volume = {257}, number = {5072}, pages = {967–971}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1354393}, url = {http://www.sciencemag.org/content/257/5072/967.short}, keywords = {differential display,MESSENGER-RNA,nosource,polymerase,Polymerase Chain Reaction,Rna} }

@article{liangDistributionCloningEukaryotic1993a, title = {Distribution and Cloning of Eukaryotic {{mRNAs}} by Means of Differential Display: Refinements and Optimazation.}, author = {Liang, P. and Averboukh, L. and Pardee, A.B.}, year = 1993, journal = {Nucleic Acids Res.}, volume = {21}, pages = {3269–3275}, doi = {10.1093/nar/21.14.3269}, keywords = {cloning,differential display,mRNA,nosource} } % == BibTeX quality report for liangDistributionCloningEukaryotic1993a: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{liaoNewKineticModel2008a, title = {A New Kinetic Model Reveals the Synergistic Effect of {{E-}}, {{P-}} and {{A-sites}} on +1 Ribosomal Frameshifting}, author = {Liao, P.Y. and Gupta, P. and Petrov, A.N. and Dinman, J.D. and Lee, K.H.}, year = 2008, month = mar, journal = {Nucleic Acids Res.}, url = {PM:18344525}, abstract = {Programmed ribosomal frameshifting (PRF) is a process by which ribosomes produce two different polypeptides from the same mRNA. In this study, we propose three different kinetic models of +1 PRF, incorporating the effects of the ribosomal E-, P- and A-sites toward promoting efficient +1 frameshifting in Escherichia coli. Specifically, the timing of E-site tRNA dissociation is discussed within the context of the kinetic proofreading mechanism of aminoacylated tRNA (aa-tRNA) selection. Mathematical modeling using previously determined kinetic rate constants reveals that destabilization of deacylated tRNA in the E-site, rearrangement of peptidyl-tRNA in the P-site, and availability of cognate aa-tRNA corresponding to the A-site act synergistically to promote efficient +1 PRF. The effect of E-site codon:anticodon interactions on +1 PRF was also experimentally examined with a dual fluorescence reporter construct. The combination of predictive modeling and empirical testing allowed the rate constant for P-site tRNA slippage (k(s)) to be estimated as k(s) approximately 1.9 s(-1) for the release factor 2 (RF2) frameshifting sequence. These analyses suggest that P-site tRNA slippage is the driving force for +1 ribosomal frameshifting while the presence of a ‘hungry codon’ in the A-site and destabilization in the E-site further enhance +1 PRF in E. coli}, keywords = {+1 frameshifting,A SITE,A-SITE,A-SITES,BIOLOGY,Chemical Engineering,Codon,codon:anticodon,CONSTANTS,E,E site,Escherichia coli,ESCHERICHIA-COLI,Fluorescence,Frameshifting,Genetic,genetics,HUNGRY CODON,La,MECHANISM,MODEL,models,MOLECULAR-GENETICS,mRNA,No DOI found,nosource,P and A sites,P SITE,P-SITE,POLYPEPTIDE,POLYPEPTIDES,proofreading,RELEASE,release factor,ribosomal frameshifting,ribosome,Ribosomes,SELECTION,sequence,SLIPPAGE,tRNA} } % == BibTeX quality report for liaoNewKineticModel2008a: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{liaoCharacterizationRecombinantSaccharomyces2005, title = {Characterization of Recombinant {{Saccharomyces}} Cerevisiae Telomerase Core Enzyme Purified from Yeast}, author = {Liao, X.H. and Zhang, M.L. and Yang, C.P. and Xu, L.X. and Zhou, J.Q.}, year = 2005, journal = {Biochemical Journal}, volume = {390}, number = {Pt 1}, pages = {169–176}, publisher = {Portland Press Ltd}, doi = {10.1042/BJ20050208}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Characterization+of+recombinant+Saccharomyces+cerevisiae+telomerase+core+enzyme+purified+from+yeast#0 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1184572/}, abstract = {Telomerase is a cellular reverse transcriptase that elongates the single-stranded chromosome ends and oligonucleotides in vivo and in vitro. In Saccharomyces cerevisiae, Est2p (telomerase catalytic subunit) and Tlc1 (telomerase RNA template subunit) constitute the telomerase core complex. We co-overexpressed GST (glutathione S-transferase)-Est2p and Tlc1 in S. cerevisiae, and reconstituted the telomerase activity. The GST-Est2p-Tlc1 complex was partially purified by ammonium sulphate fractionation and affinity chromatography on glutathione beads, and the partially purified telomerase did not contain the other two subunits of the telomerase holoenzyme, Est1p and Est3p. The purified recombinant GST-Est2p-Tlc1 telomerase core complex could specifically add nucleotides on to the single-stranded TG(1-3) primer in a processive manner, but could not translocate to synthesize more than one telomeric repeat. The purified telomerase core complex exhibited different activities when primers were paired with the Tlc1 template at different positions. The procedure of reconstitution and purification of telomerase core enzyme that we have developed now allows for further mechanistic studies of the functions of other subunits of the telomerase holoenzyme as well as other telomerase regulation proteins}, keywords = {0,Biochemistry,BIOLOGY,CEREVISIAE,chemistry,Chromatography,COMPLEX,COMPLEXES,enzyme,Enzyme Activation,enzymology,EST2,Gene Expression,Glutathione,Hydrogen-Ion Concentration,In Vitro,IN-VITRO,IN-VIVO,La,metabolism,Molecular Biology,nosource,Nucleotides,Oligonucleotides,OVEREXPRESSION,POSITION,POSITIONS,protein,Proteins,purification,Recombinant Proteins,RECONSTITUTION,regulation,REVERSE-TRANSCRIPTASE,Rna,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Sodium,Sodium Chloride,SUBUNIT,SUBUNITS,Support,Telomerase,TEMPLATE,yeast} } % == BibTeX quality report for liaoCharacterizationRecombinantSaccharomyces2005: % ? unused Journal abbr (“Biochem.J.”)

@article{liebermanRibosomecatalyzedPeptidebondFormation1995a, title = {Ribosome-Catalyzed Peptide-Bond Formation}, author = {Lieberman, K.R. and Dahlberg, A.E.}, year = 1995, journal = {Prog.Nucleic Acid Res.Mol.Biol.}, volume = {50:1-23}, pages = {1–23}, doi = {10.1016/S0079-6603(08)60809-0}, keywords = {95273600,Base Sequence,Escherichia coli,metabolism,Molecular Sequence Data,nosource,Peptide Chain Elongation,PEPTIDE-BOND FORMATION,Review,Ribosomes,RNAMessenger,RNARibosomal,RNATransfer,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for liebermanRibosomecatalyzedPeptidebondFormation1995a: % ? Possibly abbreviated journal title Prog.Nucleic Acid Res.Mol.Biol.

@article{liermannImprovedPurificationDoublestranded2000a, title = {Improved Purification of the Double-Stranded {{RNA}} from Killer Strains of Yeast.}, author = {Liermann, R.T. and Dinman, J.D. and Sylvers, L.A. and Jackson, J.C.}, year = 2000, month = jan, journal = {Biotechniques}, volume = {28}, number = {1}, pages = {64–65}, doi = {10.2144/00281bm12}, url = {http://ukpmc.ac.uk/abstract/MED/10649772}, keywords = {20114032,DOUBLE-STRANDED-RNA,killer,L-A,M1,Methods,nosource,purification,Rna,virus,yeast} }

@article{limVertebrateMicroRNAGenes2003, title = {Vertebrate {{microRNA}} Genes}, author = {Lim, L.P. and Glasner, M.E. and Yekta, S. and Burge, C.B. and Bartel, D.P.}, year = 2003, month = mar, journal = {Science}, volume = {299}, number = {5612}, pages = {1540}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1080372}, url = {http://www.sciencemag.org/content/299/5612/1540.short}, keywords = {0,Animals,BIOLOGY,Caenorhabditis,chemistry,Computational Biology,Conserved Sequence,gene,Genes,genetics,Genome,GenomeHuman,human,La,Likelihood Functions,MicroRNAs,nosource,Nucleic Acid Conformation,PRECURSOR,Rna,RNA Precursors,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Takifugu,Vertebrates,Zebrafish} }

@article{limMicroRNAsCaenorhabditisElegans2003, title = {The {{microRNAs}} of {{Caenorhabditis}} Elegans}, author = {Lim, L.P. and Lau, N.C. and Weinstein, E.G. and Abdelhakim, A. and Yekta, S. and Rhoades, M.W. and Burge, C.B. and Bartel, D.P.}, year = 2003, month = apr, journal = {Genes & Development}, volume = {17}, number = {8}, pages = {991–1008}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.1074403}, url = {http://genesdev.cshlp.org/content/17/8/991.short}, abstract = {MicroRNAs (miRNAs) are an abundant class of tiny RNAs thought to regulate the expression of protein-coding genes in plants and animals. In the present study, we describe a computational procedure to identify miRNA genes conserved in more than one genome. Applying this program, known as MiRscan, together with molecular identification and validation methods, we have identified most of the miRNA genes in the nematode Caenorhabditis elegans. The total number of validated miRNA genes stands at 88, with no more than 35 genes remaining to be detected or validated. These 88 miRNA genes represent 48 gene families; 46 of these families (comprising 86 of the 88 genes) are conserved in Caenorhabditis briggsae, and 22 families are conserved in humans. More than a third of the worm miRNAs, including newly identified members of the lin-4 and let-7 gene families, are differentially expressed during larval development, suggesting a role for these miRNAs in mediating larval developmental transitions. Most are present at very high steady-state levels-more than 1000 molecules per cell, with some exceeding 50,000 molecules per cell. Our census of the worm miRNAs and their expression patterns helps define this class of noncoding RNAs, lays the groundwork for functional studies, and provides the tools for more comprehensive analyses of miRNA genes in other species}, keywords = {0,animal,Animals,Base Sequence,BIOLOGY,BlottingNorthern,Caenorhabditis,Caenorhabditis elegans,CAENORHABDITIS-ELEGANS,chemistry,CloningMolecular,Comparative Study,Computational Biology,Conserved Sequence,development,ELEGANS,EvolutionMolecular,expression,FAMILY,gene,Gene Expression Regulation,Gene Expression RegulationDevelopmental,Gene Library,Genes,GenesHelminth,genetics,Genome,growth & development,human,IDENTIFICATION,IDENTIFY,La,metabolism,Methods,MicroRNAs,Molecular Sequence Data,nosource,Nucleic Acid Conformation,PATTERNS,Plants,Rna,RNAHelminth,RNAUntranslated,Sequence HomologyNucleic Acid,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Transcription Initiation Site} } % == BibTeX quality report for limMicroRNAsCaenorhabditisElegans2003: % ? unused Journal abbr (“Genes Dev.”)

@article{limAnalysisInteractionsCodonanticodon1997, title = {Analysis of Interactions between the Codon-Anticodon Duplexes within the Ribosome: Their Role in Translation}, author = {Lim, V.I.}, year = 1997, month = mar, journal = {Journal of Molecular Biology}, volume = {266}, number = {5}, pages = {877–890}, doi = {10.1006/jmbi.1996.0802}, keywords = {A-SITE,Adenine,analysis,Anticodon,Codon,COMPLEX,COMPLEXES,computer,Computer Graphics,efficiency,Frameshifting,Guanine,nosource,P-SITE,ribosome,translation,translocation,tRNA} }

@article{limRibosomalElongationCycle2005, title = {Ribosomal Elongation Cycle: Energetic, Kinetic and Stereochemical Aspects}, author = {Lim, V.I. and Curran, J.F. and Garber, M.B.}, year = 2005, journal = {Journal of molecular biology}, volume = {351}, number = {3}, pages = {470–480}, publisher = {Elsevier}, doi = {10.1016/j.jmb.2005.06.019}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283605006698}, abstract = {As a preface to an analysis of the ribosomal elongation cycle, we examine the energetics of macromolecular structural transformations. We show that the kinetic barriers and changes of the energetic levels during these transformations are essentially determined by disruption of hydrogen and cation-ligand bonds, and by uncompensated losses of these bonds (ULBs). The disruption of a hydrogen or cation-ligand bond increases the heights of kinetic barriers by the energy of these bonds. The association and dissociation of macromolecules, and conformational transitions within macromolecules, can change the numbers of ULBs but cannot completely eliminate them. Two important general conclusions are drawn from this analysis. First, occupation of enzyme active centers by substrates should be accompanied by a reduction in the number of ULBs. This reduction decreases the activation barriers in enzyme reactions, and is a major contributor to catalysis. Second, the enzymic reactions of the ribosomal cycle (structural changes caused by transpeptidation and by GTP hydrolyses in EF-Tu and EF-G) disrupt kinetic traps that prevent tRNAs from dissociating into solution during their motion within the ribosome and are necessary for progression of the cycle. These results are general purpose structural-functional blocks for building a molecular model of the ribosomal elongation cycle. Here, we demonstrate the utility of these blocks for analysis of acceptance of cognate tRNAs into the ribosomal elongation cycle}, keywords = {0,activation,analysis,ASSOCIATION,BIOLOGY,Catalysis,Cations,chemistry,Codon,DISRUPTION,EF-G,EFTu,elongation,ELONGATION CYCLE,energetics,enzyme,GTP,Hydrogen,Hydrogen Bonding,Kinetics,La,metabolism,MODEL,Molecular Biology,nosource,ribosome,Ribosomes,Rna,RNATransfer,Stereoisomerism,Structural,Support,TRANSFORMATION,tRNA} } % == BibTeX quality report for limRibosomalElongationCycle2005: % ? unused Journal abbr (“J.Mol.Biol”)

@article{lindstromMotherEnrichmentProgram2009, title = {The {{Mother Enrichment Program}}: {{A Genetic System}} for {{Facile Replicative Life Span Analysis}} in {{Saccharomyces}} Cerevisiae}, author = {Lindstrom, D.L. and Gottschling, D.E.}, year = 2009, journal = {Genetics}, volume = {183}, number = {2}, pages = {413–422}, publisher = {Genetics Soc America}, doi = {10.1534/genetics.109.106229}, url = {http://www.genetics.org/content/183/2/413.short}, abstract = {The replicative life span (RLS) of Saccharomyces cerevisiae has been established as a model for the genetic regulation of longevity despite the inherent difficulty of the RLS assay, which requires separation of mother and daughter cells by micromanipulation after every division. Here we present the Mother Enrichment Program (MEP): An inducible genetic system in which mother cells maintain a normal RLS - a median of 36 generations in the diploid MEP strain - while the proliferative potential of daughter cells is eliminated. Thus, the viability of a population over time becomes a function of RLS, and it displays features of a survival curve such as changes in hazard rate with age. We show that viability of mother cells in liquid culture is regulated by SIR2 and FOB1, two opposing regulators of RLS in yeast. We demonstrate that viability curves of these short- and long-lived strains can be easily distinguished from wild type using a colony formation assay. This provides a simplified screening method for identifying genetic or environmental factors that regulate RLS. Additionally, the MEP can provide a cohort of cells at any stage of their life span for the analysis of age-associated phenotypes. These capabilities effectively remove the hurdles presented by RLS analysis that have hindered S. cerevisiae aging studies since their inception 50 years ago.}, keywords = {Aging,analysis,cancer,CELLS,CEREVISIAE,Genetic,La,MODEL,nosource,Phenotype,regulation,REQUIRES,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SYSTEM,WILD-TYPE,yeast} }

@article{lingnerThreeEverShorter1997, title = {Three {{Ever Shorter Telomere}} ({{EST}}) Genes Are Dispensable for in Vitro Yeast Telomerase Activity}, author = {Lingner, J. and Cech, T.R. and Hughes, T.R. and Lundblad, V.}, year = 1997, month = oct, journal = {Proceedings of the National Academy of Sciences}, volume = {94}, number = {21}, pages = {11190–11195}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.94.21.11190}, url = {http://www.pnas.org/content/94/21/11190.short}, abstract = {Telomerase is a specialized reverse transcriptase consisting of both RNA and protein components. Previous characterization of yeast telomerase function in vivo identified four EST (for ever shorter telomeres) genes that, when mutated, result in the phenotypes expected for a defect in telomerase. Consistent with this genetic prediction, the EST2 gene has recently been shown to encode the catalytic component of telomerase. Using an in vitro assay, we show here that telomerase activity is present in extracts prepared from yeast strains carrying est1-Delta, est3-Delta, and cdc13-2(est) mutations. Therefore, while these three genes are necessary for telomerase function in vivo, they do not encode components essential for core catalytic activity. When Est2p, the one EST gene product found to be essential for catalytic activity, was immunoprecipitated from extracts, the telomerase RNA subunit was also specifically precipitated, supporting the conclusion that these two components are in a stable complex}, keywords = {0,Biochemistry,CentrifugationDensity Gradient,CEREVISIAE,chemistry,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,Cyclin B,enzymology,EST,EXTRACTS,Fungal Proteins,gene,GENE-PRODUCT,Genes,GenesFungal,Genetic,genetics,growth & development,In Vitro,IN-VITRO,IN-VIVO,isolation & purification,La,metabolism,Mutagenesis,Mutation,MUTATIONS,nosource,Phenotype,Polymerase Chain Reaction,PREDICTION,PRODUCT,protein,Proteins,REVERSE-TRANSCRIPTASE,Rna,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SUBUNIT,Support,Telomerase,Telomere,Telomere-Binding Proteins,yeast} } % == BibTeX quality report for lingnerThreeEverShorter1997: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{lingnerReverseTranscriptaseMotifs1997, title = {Reverse Transcriptase Motifs in the Catalytic Subunit of Telomerase}, author = {Lingner, J. and Hughes, T.R. and Shevchenko, A. and Mann, M. and Lundblad, V. and Cech, T.R.}, year = 1997, month = apr, journal = {Science}, volume = {276}, number = {5312}, pages = {561–567}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.276.5312.561}, url = {http://www.sciencemag.org/content/276/5312/561.short}, abstract = {Telomerase is a ribonucleoprotein enzyme essential for the replication of chromosome termini in most eukaryotes. Telomerase RNA components have been identified from many organisms, but no protein component has been demonstrated to catalyze telomeric DNA extension. Telomerase was purified from Euplotes aediculatus, a ciliated protozoan, and one of its proteins was partially sequenced by nanoelectrospray tandem mass spectrometry. Cloning and sequence analysis of the corresponding gene revealed that this 123-kilodalton protein (p123) contains reverse transcriptase motifs. A yeast (Saccharomyces cerevisiae) homolog was found and subsequently identified as EST2 (ever shorter telomeres), deletion of which had independently been shown to produce telomere defects. Introduction of single amino acid substitutions within the reverse transcriptase motifs of Est2 protein led to telomere shortening and senescence in yeast, indicating that these motifs are important for catalysis of telomere elongation in vivo. In vitro telomeric DNA extension occurred with extracts from wild-type yeast but not from est2 mutants or mutants deficient in telomerase RNA. Thus, the reverse transcriptase protein fold, previously known to be involved in retroviral replication and retrotransposition, is essential for normal chromosome telomere replication in diverse eukaryotes}, keywords = {0,ACID,Amino Acid Sequence,Amino Acid Substitution,AMINO-ACID,analysis,Animals,Binding Sites,Biochemistry,Catalysis,CEREVISIAE,chemistry,Chromosomes,cloning,COMPONENT,COMPONENTS,Dna,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,DNAFungal,elongation,enzyme,enzymology,Euplotes,EvolutionMolecular,EXTRACTS,Fungal Proteins,gene,GenesFungal,GenesProtozoan,genetics,homolog,In Vitro,IN-VITRO,IN-VIVO,isolation & purification,La,Mass Spectrometry,metabolism,Molecular Sequence Data,MOTIFS,MUTANTS,nosource,polymerase,protein,Protein Conformation,Proteins,REPLICATION,RETROTRANSPOSITION,REVERSE-TRANSCRIPTASE,RIBONUCLEOPROTEIN,Rna,RNA-Directed DNA Polymerase,RNAFungal,RNAProtozoan,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,Sequence Alignment,Sequence Analysis,SEQUENCE-ANALYSIS,SUBUNIT,Support,Tandem Mass Spectrometry,Telomerase,Telomere,TemplatesGenetic,WILD-TYPE,yeast} }

@article{lioPhylogenomicsBioinformaticsSARSCoV2004, title = {Phylogenomics and Bioinformatics of {{SARS-CoV}}}, author = {Lio, P. and Goldman, N.}, year = 2004, month = mar, journal = {Trends in microbiology}, volume = {12}, number = {3}, pages = {106–111}, publisher = {Elsevier}, doi = {10.1016/j.tim.2004.01.005}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0966842X04000216}, keywords = {Genome,La,nosource} } % == BibTeX quality report for lioPhylogenomicsBioinformaticsSARSCoV2004: % ? unused Journal abbr (“Trends Microbiol.”)

@article{liphardtEvidenceRNAPseudoknot1999a, title = {Evidence for an {{RNA}} Pseudoknot Loop-Helix Interaction Essential for Efficient -1 Ribosomal Frameshifting}, author = {Liphardt, J. and Napthine, S. and Kontos, H. and Brierley, I.}, year = 1999, month = may, journal = {J.Mol.Biol.}, volume = {288}, number = {3}, pages = {321–335}, doi = {10.1006/jmbi.1999.2689}, abstract = {RNA pseudoknots are structural elements that participate in a variety of biological processes. At -1 ribosomal frameshifting sites, several types of pseudoknot have been identified which differ in their organisation and functionality. The pseudoknot found in infectious bronchitis virus (IBV) is typical of those that possess a long stem 1 of 11-12 bp and a long loop 2 (30-164 nt). A second group of pseudoknots are distinguishable that contain stems of only 5 to 7 bp and shorter loops. The NMR structure of one such pseudoknot, that of mouse mammary tumor virus (MMTV), has revealed that it is kinked at the stem 1-stem 2 junction, and that this kinked conformation is essential for efficient frameshifting. We recently investigated the effect on frameshifting of modulating stem 1 length and stability in IBV-based pseudoknots, and found that a stem 1 with at least 11 bp was needed for efficient frameshifting. Here, we describe the sequence manipulations that are necessary to bypass the requirement for an 11 bp stem 1 and to convert a short non-functional IBV-derived pseudoknot into a highly efficient, kinked frameshifter pseudoknot. Simple insertion of an adenine residue at the stem 1-stem 2 junction (an essential feature of a kinked pseudoknot) was not sufficient to create a functional pseudoknot. An additional change was needed: efficient frameshifting was recovered only when the last nucleotide of loop 2 was changed from a G to an A. The requirement for an A at the end of loop 2 is consistent with a loop-helix contact similar to those described in other RNA tertiary structures. A mutational analysis of both partners of the proposed interaction, the loop 2 terminal adenine residue and two G.C pairs near the top of stem 1, revealed that the interaction was essential for efficient frameshifting. The specific requirement for a 3’-terminal A residue was lost when loop 2 was increased from 8 to 14 nt, suggesting that the loop-helix contact may be required only in those pseudoknots with a short loop 2. Copyright 1999 Academic Press}, keywords = {99262845,Adenine,analysis,Base Sequence,chemistry,ELEMENTS,Frameshifting,FrameshiftingRibosomal,genetics,Infectious bronchitis virus,Mammary Tumor VirusesMouse,metabolism,MMTV,ModelsMolecular,Molecular Sequence Data,MutagenesisSite-Directed,MUTATIONAL ANALYSIS,nosource,Nucleic Acid Conformation,pathology,pseudoknot,ribosomal frameshifting,Rna,RNA Probes,RNA PSEUDOKNOT,RnaViral,sequence,stability,Structural,structure,supportnon-u.s.gov’t,virology,virus} } % == BibTeX quality report for liphardtEvidenceRNAPseudoknot1999a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{lippensUseWaterFlipBack1995, title = {Use of {{A Water Flip-Back Pulse}} in the {{Homonuclear Noesy Experiment}}}, author = {Lippens, G. and Dhalluin, C. and Wieruszeski, J.M.}, year = 1995, month = apr, journal = {Journal of Biomolecular Nmr}, volume = {5}, number = {3}, pages = {327–331}, publisher = {Springer}, url = {http://www.springerlink.com/index/R717128568753189.pdf}, abstract = {A simple modification to the WATERGATE water suppression scheme [Piotto, M., Saudek, V. and Sklenar, V. (1992) J. Biomol. NMR, 2, 661-665] is proposed. Radiation damping is used as an active element during the mixing time of a NOESY experiment, in order to obtain a reproducable state of the water magnetization at the end of the mixing time. Through the use of a water flip-back pulse and a gradient-tailored excitation scheme, we obtain both an excellent water suppression and a water magnetization close to equilibrium at the beginning of the acquisition time. We show experimentally that this modification results in a 20% gain in intensity for all signals when using a relaxation delay of 1.5 s, and also that avoiding a semisaturated state for the water magnetization allows the amide protons as well as other proton resonances to relax to equilibrium with their proper relaxation time}, keywords = {AQUEOUS-SOLUTIONS,BASELINE DISTORTIONS,EXCHANGE RATES,M,modification,NMR,NMR-SPECTROSCOPY,No DOI found,NOE SPECTROSCOPY,nosource,Proteins,Protons,RELAXATION,RESONANCES,S,SIGNAL,SOLVENT-SATURATION-TRANSFER,SPECTRA,SPIN-DIFFUSION,suppression,Water,WATER FLIP-BACK,WATER SUPPRESSION} } % == BibTeX quality report for lippensUseWaterFlipBack1995: % ? Title looks like it was stored in title-case in Zotero

@article{listonRibosomalFrameshiftingTranslation1995a, title = {Ribosomal {{Frameshifting During Translation}} of {{Measles-Virus-P Protein Messenger-Rna Is Capable}} of {{Directing Synthesis}} of {{A Unique Protein}}}, author = {Liston, P. and Briedis, D.J.}, year = 1995, month = nov, journal = {Journal of Virology}, volume = {69}, number = {11}, pages = {6742–6750}, doi = {10.1128/jvi.69.11.6742-6750.1995}, url = {ISI:A1995RZ10000017}, abstract = {Members of the Paramyxoviridae family utilize a variety of different strategies to increase coding capacity within their P cistrons, Translation initiation at alternative 5’-proximal AUG codons is used by measles virus (MV) to express the virus-specific P and C proteins from overlapping reading frames on their mRNAs. Additional species of mRNAs are transcribed from the MV P cistron by the insertion of extra nontemplated G residues at a specific site within the P transcript. Addition of only a single nontemplated G residue results in the expression of the V protein, which contains a unique carboxyl terminus. We have used an Escherichia coli system to express MV P cistron-related mRNAs and proteins. We have found that ribosomal frameshifting on the MV P protein mRNA is capable of generating a previously unrecognized P cistron encoded protein that,pe have designated R. Some ribosomes which have initiated translation of the P protein mRNA use the sequence TCC CCG AG (24 nucleotides upstream of the V protein stop codon) to slip into the -1 reading frame, thus translating the sequence as TC CCC GAG. The resulting R protein terminates five codons downstream of the frameshift site at the V protein stop codon. We have gone on to use a chloramphenicol acetyltransferase reporter system to demonstrate that this MV-specific sequence is capable of directing frameshifting during in vivo translation in eukaryotic cells. Analysis of immunoprecipitated proteins from MV-infected cells by two-dimensional gel electrophoresis allowed detection of a protein species consistent with R protein in MV-infected cells. Quantitation of this protein species allowed a rough estimation of frameshift frequency of approximately 1.8%. Significant stimulation of ribosomal frameshift frequency at this locus of the MV P mRNA was mediated by a downstream stimulator element which, although not yet fully defined, appeared to be neither a conventional stem-loop nor an RNA pseudoknot structure}, keywords = {analysis,AUG,C-PROTEIN,CELLS,Chloramphenicol,Codon,CODONS,DISTEMPER VIRUS,DOWNSTREAM,Electrophoresis,Escherichia coli,ESCHERICHIA-COLI,Eukaryotic Cells,expression,FAMILY,FRAME,frameshift,Frameshifting,FUSION PROTEIN,G-RESIDUES,Gag,GENOME ENCODES,IN-VIVO,INFECTED-CELLS,initiation,MESSENGER-RNA,mRNA,nosource,NUCLEOCAPSID PROTEIN,Nucleotides,protein,Proteins,pseudoknot,pseudoknot structure,READING FRAME,Reading Frames,RESIDUES,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,ribosome,Ribosomes,Rna,RNA PSEUDOKNOT,sequence,SEQUENCE-ANALYSIS,SINGLE MESSENGER-RNA,SITE,STEM-LOOP,STOP CODON,structure,SYSTEM,TRANSCRIPT,translation,TRANSLATION INITIATION,UPSTREAM,V-PROTEIN,virus} } % == BibTeX quality report for listonRibosomalFrameshiftingTranslation1995a: % ? Title looks like it was stored in title-case in Zotero

@article{liuKineticQualityControl2007, title = {Kinetic Quality Control of Anticodon Recognition by a Eukaryotic Aminoacyl-{{tRNA}} Synthetase}, author = {Liu, C. and Gamper, H. and Shtivelband, S. and Hauenstein, S. and Perona, J.J. and Hou, Y.M.}, year = 2007, month = apr, journal = {Journal of molecular biology}, volume = {367}, number = {4}, pages = {1063–1078}, publisher = {Elsevier}, doi = {10.1016/j.jmb.2007.01.050}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283607001027}, abstract = {Aminoacyl-tRNA synthetases are an ancient class of enzymes responsible for the matching of amino acids with anticodon sequences of tRNAs. Eukaryotic tRNA synthetases are often larger than their bacterial counterparts, and several mammalian enzymes use the additional domains to facilitate assembly into a multi-synthetase complex. Human cysteinyl-tRNA synthetase (CysRS) does not associate with the multi-synthetase complex, yet contains a eukaryotic-specific C-terminal extension that follows the tRNA anticodon-binding domain. Here we show by mutational and kinetic analysis that the C-terminal extension of human CysRS is used to selectively improve recognition and binding of the anticodon sequence, such that the specificity of anticodon recognition by human CysRS is higher than that of its bacterial counterparts. However, the improved anticodon recognition is achieved at the expense of a significantly slower rate in the aminoacylation reaction, suggesting a previously unrecognized kinetic quality control mechanism. This kinetic quality control reflects an evolutionary adaptation of some tRNA synthetases to improve the anticodon specificity of tRNA aminoacylation from bacteria to humans, possibly to accommodate concomitant changes in codon usage}, keywords = {0,ACID,ACIDS,Amino Acid Sequence,Amino Acids,Amino Acyl-tRNA Synthetases,AMINO-ACID,AMINO-ACIDS,analysis,Anticodon,assembly,Bacteria,Bacterial,Base Sequence,BINDING,Biochemistry,BIOLOGY,chemistry,Codon,Comparative Study,COMPLEX,COMPLEXES,Dimerization,DOMAIN,DOMAINS,enzyme,Enzymes,enzymology,Eukaryotic Cells,human,Humans,La,MECHANISM,metabolism,ModelsMolecular,Molecular Biology,Molecular Sequence Data,Mutant Proteins,nosource,Nucleic Acid Conformation,protein,Protein Binding,Protein StructureTertiary,Proteins,Quality Control,QUALITY-CONTROL,RECOGNITION,Rna,RNATransferCys,sequence,Sequence HomologyAmino Acid,SEQUENCES,SPECIFICITY,Substrate Specificity,Support,Transfer RNA Aminoacylation,tRNA} } % == BibTeX quality report for liuKineticQualityControl2007: % ? unused Journal abbr (“J.Mol Biol”)

@article{liuRibosomesMarrowFailure2006, title = {Ribosomes and Marrow Failure: Coincidental Association or Molecular Paradigm?}, author = {Liu, J.M. and Ellis, S.R.}, year = 2006, month = jun, journal = {Blood}, volume = {107}, number = {12}, pages = {4583–4588}, doi = {10.1182/blood-2005-12-4831}, url = {PM:16507776}, abstract = {Gene products mutated in the inherited bone marrow failure syndromes dyskeratosis congenita (DC), cartilage-hair hypoplasia (CHH), Diamond-Blackfan anemia (DBA), and Shwachman-Diamond syndrome (SDS) are all predicted to be involved in different aspects of ribosome synthesis. At this moment, however, it is unclear whether this link indicates a causal relationship. Although defective ribosome synthesis may contribute to each of these bone marrow failure syndromes (and perhaps others), precisely which feature of each disease is a consequence of failure to produce adequate amounts of ribosomes is obscured by the tendency of each gene product to have extraribosomal functions. Delineation of the precise role of each gene product in ribosomal biogenesis and in hematopoietic development may have both therapeutic and prognostic importance and perhaps even direct the search for new bone marrow failure genes.}, pmid = {16507776}, keywords = {0,Anemia,Animals,ASSOCIATION,BIOGENESIS,Bone Marrow Diseases,development,disease,Dyskeratosis Congenita,gene,GENE-PRODUCT,Genes,GenesrRNA,Genetic DiseasesInborn,genetics,Hematopoiesis,Humans,La,metabolism,nosource,PRODUCT,PRODUCTS,protein,Proteins,Review,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,RIBOSOME SYNTHESIS,Ribosomes,search,Syndrome,therapy} }

@article{liuTranslationalFidelityMutation1996a, title = {A Translational Fidelity Mutation in the Universally Conserved Sarcin/Ricin Domain of {{25S}} Yeast Ribosomal {{RNA}}}, author = {Liu, R. and Liebman, S.W.}, year = 1996, month = mar, journal = {RNA}, volume = {2}, number = {3}, pages = {254–263}, url = {PM:8608449}, abstract = {Recent evidence suggests that ribosomal RNAs have functional roles in translation. We describe here a new ribosomal RNA mutation that causes translational suppression and antibiotic resistance in eukaryotic cells. Using random mutagenesis of the cloned ribosomal RNA gene and in vivo selection, we isolated a C –{\(>\)} U mutation in the universally conserved sarcin/ricin domain in Saccharomyces cerevisiae 25S ribosomal RNA. This mutation changes the putative CG pair, which closes the GAGA tetraloop in the sarcin/ricin domain, into a weaker UG pair without eliminating ribosomal sensitivity to ricin. We show that suppression of several UGA, UAG, and frameshift mutations is evident when a portion of the cellular ribosomal RNA contains the C –{\(>\)} U mutation. Cells that contain essentially all mutant ribosomal RNA grow only 10% slower than the wild-type, but show increased suppression as well as resistance to paramomycin, G418, and hygromycin, and sensitivity to cycloheximide. Our results provide genetic evidence for the participation of the sarcin/ricin loop in maintaining translational accuracy and are discussed in terms of a hypothesis that this ribosomal RNA region normally undergoes a conformational change during translation}, keywords = {0,accuracy,Anti-Bacterial Agents,antibiotic,Aspergillus,Base Sequence,BIOLOGY,CELLS,CEREVISIAE,chemistry,CONFORMATIONAL CHANGE,CONFORMATIONAL-CHANGE,Conserved Sequence,Cycloheximide,DOMAIN,drug effects,Drug ResistanceMicrobial,Endoribonucleases,Eukaryotic Cells,Fidelity,frameshift,Frameshift Mutation,Fungal Proteins,gene,Genetic,genetics,growth & development,IN-VIVO,La,LOOP,Molecular Sequence Data,Mutagenesis,Mutation,MUTATIONS,No DOI found,nosource,Nucleic Acid Conformation,pharmacology,physiology,Point Mutation,protein,Proteins,REGION,RESISTANCE,ribosomal RNA,RIBOSOMAL-RNA,ribosome-inactivating protein,Ricin,Rna,RNARibosomal,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sarcin/ricin domain,SELECTION,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,suppression,SuppressionGenetic,translation,translational fidelity,TRANSLATIONAL SUPPRESSION,TranslationGenetic,WILD-TYPE,yeast} }

@article{liuHomozygousDefectHIV11996, title = {Homozygous Defect in {{HIV-1}} Coreceptor Accounts for Resistance of Some Multiply-Exposed Individuals to {{HIV-1}} Infection}, author = {Liu, R. and Paxton, W.A. and Choe, S. and Ceradini, D. and Martin, S.R. and Horuk, R. and MacDonald, M.E. and Stuhlmann, H. and Koup, R.A. and Landau, N.R.}, year = 1996, journal = {Cell}, volume = {86}, number = {3}, pages = {367–377}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(00)80110-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867400801105}, abstract = {Rare individuals have been multiply exposed to HIV-1 but remain uninfected. The CD4+ T-cells of two of these individuals, designated EU2 and EU3, are highly resistant in vitro to the entry of primary macrophagetropic virus but are readily infectable with transformed T-cell line adapted viruses. We report here on the genetic basis of this resistance. We found that EU2 and EU3 have a homozygous defect in CKR-5, the gene encoding the recently described coreceptor for primary HIV-1 isolates. These individuals appear to have inherited a defective CKR-5 allele that contains an internal 32 base pair deletion. The encoded protein is severely truncated and cannot be detected at the cell surface. Surprisingly, this defect has no obvious phenotype in the affected individuals. Thus, a CKR-5 allele present in the human population appears to protect homozygous individuals from sexual transmission of HIV-1. Heterozygous individuals are quite common (approximately 20%) in some populations. These findings indicate the importance of CKR-5 in HIV-1 transmission and suggest that targeting the HIV-1-CKR-5 interaction may provide a means of preventing or slowing disease progression}, keywords = {0,AIDS,Alleles,Amino Acid Sequence,analysis,BASE,Base Sequence,BASE-PAIR,disease,Dna,DNAComplementary,DnaViral,gene,Genetic,genetics,HIV,HIV Infections,Hiv-1,Homozygote,human,Humans,ImmunityNatural,immunology,In Vitro,IN-VITRO,INFECTION,La,LINE,Molecular Sequence Data,nosource,Phenotype,protein,ReceptorsCCR5,ReceptorsCytokine,ReceptorsHIV,RESISTANCE,RESISTANT,Restriction Mapping,Sequence Deletion,Support,TranscriptionGenetic,transmission,virus,Virus Replication,Viruses} }

@article{liuOverproductionYeastViruslike1989, title = {Overproduction of Yeast Viruslike Particles by Strains Deficient in a Mitochondrial Nuclease.}, author = {Liu, Y.X. and Dieckmann, C.L.}, year = 1989, journal = {Molecular and cellular biology}, volume = {9}, number = {8}, pages = {3323–3331}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/9/8/3323}, abstract = {Saccharomyces cerevisiae strains are often host to several types of cytoplasmic double-stranded RNA (dsRNA) genomes, some of which are encapsidated by the L-A dsRNA product, an 86,000-dalton coat protein. Here we present the finding that nuclear recessive mutations in the NUC1 gene, which encodes the major nonspecific nuclease of yeast mitochondria, resulted in at least a 10-fold increase in amounts of the L-A dsRNA and its encoded coat protein. The effect of nuc1 mutations on L-A abundance was completely suppressed in strains that also hosted the killer-toxin-encoding M dsRNA. Both NUC1 and nuc1 strains containing the L-A genome exhibited an increase in coat protein abundance and a concomitant increase in L-A dsRNA when the cells were grown on a nonfermentable carbon source rather than on glucose, an effect independent of the increase in coat protein due to nuc1 mutations or to the absence of M. The increase in L-A expression in nuc1 strains was similar to that observed in strains with mutations in the nuclear gene encoding the most abundant outer mitochondrial membrane protein, porin. nuc1 mutations did not affect the level of porin in the mitochondrial outer membrane. Since the effect of mutations in nuc1 was to alter the copy number of the L-A coat protein genome rather than to change the level of the M toxin genome (as do mak and ski mutations), these mutations define a new class of nuclear genes affecting yeast dsRNA abundance}, keywords = {0,Amino Acid Sequence,Base Sequence,biosynthesis,Capsid,Carbon,carbon source,CELLS,CEREVISIAE,COAT PROTEIN,Cytochrome b,DNA Mutational Analysis,DOUBLE-STRANDED-RNA,DSRNA,ENCODES,Endonucleases,enzymology,expression,gene,Gene Expression Regulation,Genes,genetics,Genome,Glucose,L-A,La,M,MAK,Membrane Proteins,metabolism,mitochondria,Molecular Sequence Data,Multiple DOI,Mutation,MUTATIONS,nonfile,nosource,PARTICLES,Phenotype,physiology,PRODUCT,protein,Proteins,Rna,RNADouble-Stranded,RNAFungal,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SKI,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,toxin,yeast} } % == BibTeX quality report for liuOverproductionYeastViruslike1989: % ? unused Journal abbr (“Mol Cell Biol.”)

@article{livakAnalysisRelativeGene2001a, title = {Analysis of Relative Gene Expression Data Using Real-Time Quantitative {{PCR}} and the 2(-{{Delta Delta C}}({{T}})) {{Method}}}, author = {Livak, K.J. and Schmittgen, T.D.}, year = 2001, month = dec, journal = {Methods}, volume = {25}, number = {4}, pages = {402–408}, doi = {10.1006/meth.2001.1262}, url = {PM:11846609}, abstract = {The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data}, keywords = {0,Algorithms,analysis,Brain,Cell Line,Dna,DNAComplementary,expression,gene,Gene Expression,GENE-EXPRESSION,Humans,La,metabolism,Methods,nosource,PCR,Polymerase Chain Reaction,Reverse Transcriptase Polymerase Chain Reaction,SIGNAL,TARGET,Time Factors,TRANSCRIPT} }

@article{lodmellConformationalSwitchEscherichia1997, title = {A Conformational Switch in {{Escherichia}} Coli {{16S}} Ribosomal {{RNA}} during Decoding of Messenger {{RNA}}}, author = {Lodmell, J.S. and Dahlberg, A.E.}, year = 1997, journal = {Science}, volume = {277}, number = {5330}, pages = {1262–1267}, doi = {10.1126/science.277.5330.1262}, abstract = {Direct evidence is presented for a conformational switch in 16S ribosomal RNA (rRNA) that affects tRNA binding to the ribosome and decoding of messenger RNA (mRNA). These data support the hypothesis that dynamic changes in rRNA structure occur during translation. The switch involves two alternating base-paired arrangements apparently facilitated by ribosomal proteins S5 and S12, and produces significant changes in the rRNA structure. Chemical probing shows reciprocal enhancements or protections at sites in 16S rRNA that are at or very near sites that were previously crosslinked to mRNA. These data indicate that the switch affects codon-anticodon arrangement and proper selection of tRNA at the ribosomal A site, and that the switch is a fundamental mechanism in all ribosomes}, keywords = {97419247,A-SITE,Anticodon,Base Composition,BINDING,chemistry,Codon,decoding,Escherichia coli,ESCHERICHIA-COLI,genetics,growth & development,MECHANISM,MESSENGER-RNA,metabolism,mRNA,Mutation,nosource,Nucleic Acid Conformation,protein,Proteins,Ribosomal Proteins,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNABacterial,RNAMessenger,RNARibosomal16S,RNATransfer,rRNA,structure,Support,supportu.s.gov’tp.h.s.,translation,TranslationGenetic,tRNA} }

@article{loftfiel.rbFrequencyErrorsProteinBiosynthesis1972, title = {Frequency of {{Errors}} in {{Protein-Biosynthesis}}}, author = {LOFTFIEL.RB and VANDERJA.D}, year = 1972, journal = {Biochemical Journal}, volume = {128}, number = {5}, pages = {1353-&}, doi = {10.1042/bj1281353}, url = {ISI:A1972N183000044}, keywords = {nosource,PROTEIN-BIOSYNTHESIS} } % == BibTeX quality report for loftfiel.rbFrequencyErrorsProteinBiosynthesis1972: % ? Title looks like it was stored in title-case in Zotero

@article{logsdonSelective5Modification1992, title = {Selective 5’ Modification of {{T7 RNA}} Polymerase Transcripts}, author = {Logsdon, N. and Lee, C.G. and Harper, J.W.}, year = 1992, journal = {Analytical biochemistry}, volume = {205}, number = {1}, pages = {36–41}, publisher = {Elsevier}, doi = {10.1016/0003-2697(92)90575-R}, url = {http://linkinghub.elsevier.com/retrieve/pii/000326979290575R}, abstract = {We have developed two methods for selective 5’ modification of RNAs generated by enzymatic synthesis using T7 RNA polymerase. The first method involves a two-step procedure. Transcription reactions are performed under standard conditions except that GTP is replaced by GTP gamma S. Since the polymerase initiates transcription with GTP, every transcript contains a 5’ gamma-thiophosphate group which is modified with the thiol-specific reagent of choice (e.g., iodoacetyl dansyl derivative) in the second step. In an alternative method, transcription and modification reactions are carried out in a single step, using a mixture of dansylated GTP and GTP. Under the appropriate conditions, dansylated GTP effectively competes with GTP in the initiation reaction but does not substantially inhibit the elongation reaction. Yields of fluorescent 64-mer RNA ranging from 30 to 70% of the total transcription product have been obtained using these methods in combination with HPLC purification. This approach is amenable to large scale synthesis reactions and can be used to produce a wide variety of 5’-modified RNAs of virtually any size for structural or functional studies}, keywords = {0,Bacteriophage T7,Base Sequence,Biochemistry,chemistry,ChromatographyHigh Pressure Liquid,ChromatographyIon Exchange,DNA-Directed RNA Polymerase,DNA-Directed RNA Polymerases,ElectrophoresisAgar Gel,elongation,genetics,GTP,Guanosine,Guanosine 5’-O-(3-Thiotriphosphate),Guanosine Triphosphate,HIV Long Terminal Repeat,Hiv-1,initiation,La,metabolism,Methods,modification,Molecular Sequence Data,nosource,polymerase,PRODUCT,protein,Proteins,purification,Rna,RNA-POLYMERASE,RNAMessenger,S,Structural,Support,TRANSCRIPT,transcription,TranscriptionGenetic,Viral Proteins} } % == BibTeX quality report for logsdonSelective5Modification1992: % ? unused Journal abbr (“Anal.Biochem.”)

@article{longtineAdditionalModulesVersatile1998a, title = {Additional Modules for Versatile and Economical {{PCR-based}} Gene Deletion and Modification in {{Saccharomyces}} Cerevisiae}, author = {Longtine, M.S. and McKenzie, A. and Demarini, D.J. and Shah, N.G. and Wach, A. and Brachat, A. and Philippsen, P. and Pringle, J.R.}, year = 1998, month = jul, journal = {Yeast}, volume = {14}, number = {10}, pages = {953–961}, doi = {10.1002/(SICI)1097-0061(199807)14:10<953::AID-YEA293>3.0.CO;2-U}, url = {ISI:000075005100008}, abstract = {An important recent advance in the functional analysis of Saccharomyces cerevisiae genes is the development of the one-step PCR-mediated technique for deletion and modification of chromosomal genes. This method allows very rapid gene manipulations without requiring plasmid clones of the gene of interest. We describe here a new set of plasmids that serve as templates for the PCR synthesis of fragments that allow a variety of gene modifications. Using as selectable marker the S. cerevisiae TRP1 gene or modules containing the heterologous Schizosaccharomyces pombe his5(+) or Escherichia coli kan(r) gene, these plasmids allow gene deletion, gene overexpression (using the regulatable GAL1 promoter), C- or N-terminal protein tagging [with GFP(S65T), GST, or the 3HA or 13Myc epitope], and partial N- or C-terminal deletions (with or without concomitant protein tagging). Because of the modular nature of the plasmids, they allow efficient and economical use of a small number of PCR primers for a wide variety of gene manipulations. Thus, these plasmids should further facilitate the rapid analysis of gene function in S. cerevisiae. (C) 1998 John Wiley & Sons, Ltd}, keywords = {analysis,CEREVISIAE,CHROMOSOMAL GENES,development,DISRUPTIONS,Epitope tagging,Escherichia coli,ESCHERICHIA-COLI,expression,functional analysis,gene,Gene Deletion,gene truncation,Genes,GLUTATHIONE S-TRANSFERASE,GREEN FLUORESCENT PROTEIN,LOCALIZATION,M,MARKER,modification,nosource,OVEREXPRESSION,overexpression studies,PCR,PLASMID,Plasmids,Polymerase Chain Reaction,PRODUCT,PROMOTER,protein,purification,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Schizosaccharomyces,TEMPLATE,Templates,TRANSFORMATION,yeast} }

@article{lorenzCrystallizationEngineeredThermus2000, title = {Crystallization of Engineered {{Thermus}} Flavus {{5S rRNA}} under Earth and Microgravity Conditions}, author = {Lorenz, S. and Perbandt, M. and Lippmann, C. and Moore, K. and DeLucas, L.J. and Betzel, C. and Erdmann, V.A.}, year = 2000, month = apr, journal = {Acta Crystallographica Section D: Biological Crystallography}, volume = {56 ( Pt 4)}, number = {4}, pages = {498–500}, publisher = {International Union of Crystallography}, url = {http://scripts.iucr.org/cgi-bin/paper?VJ0024}, abstract = {Thermus flavus 5S rRNA with a molecular weight of about 40 kDa was modified at the 5’ and 3’ ends. Crystals were obtained under earth and microgravity conditions. The best crystals were obtained during NASA space mission STS 94. For the first time, it was possible to collect a complete data set from 5S rRNA crystals to 7.8 A resolution and to assign the space group as R32, with unit-cell parameters a = b = 110.3, c = 387.6 A, alpha = beta = 90, gamma = 120 degrees}, keywords = {0,3,5S rRNA,Bacterial,Base Sequence,chemistry,Crystallization,CrystallographyX-Ray,Genetic Engineering,genetics,Gravitation,isolation & purification,La,ModelsMolecular,Molecular Sequence Data,Molecular Weight,No DOI found,nosource,Nucleic Acid Conformation,Research SupportNon-U.S.Gov’t,RESOLUTION,Rna,RNABacterial,RNARibosomal5S,rRNA,S,Thermus,Weightlessness} } % == BibTeX quality report for lorenzCrystallizationEngineeredThermus2000: % ? unused Journal abbr (“Acta Crystallogr.D.Biol.Crystallogr.”)

@article{lorenziniCooperation531997, title = {Co-Operation of the 5’ and 3’ Untranslated Regions of Ornithine Decarboxylase {{mRNA}} and Inhibitory Role of Its 3’ Untranslated Region in Regulating the Translational Efficiency of Hybrid {{RNA}} Species via Cellular Factor}, author = {Lorenzini, E.C. and Scheffler, I.E.}, year = 1997, journal = {Biochemical Journal}, volume = {326 ( Pt 2)}, number = {Pt 2}, pages = {361–367}, publisher = {Portland Press Ltd}, doi = {10.1042/bj3260361}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1218679/}, abstract = {The 5’ untranslated region (UTR) has an inhibitory role in the translatability of ornithine decarboxylase (ODC) mRNA and of hybrid mRNA species, whereas the ODC 3’ UTR causes a partial release of this inhibition. We designed experiments to explore whether the co-operation between ODC 5’ UTR and 3’ UTR in the translational regulation is due to a direct interaction of those sequences or whether it is mediated by their interaction with cellular factor(s). We stably transfected Chinese hamster ovary (CHO)-K1 cells and transiently transfected COS-1 cells with expression vectors carrying different chimaeric DNAs having the luciferase (LUC) coding sequence as reporter gene, the ODC 5’ UTR or the ODC 3’ UTR, or both, in the appropriate positions. We compared the results obtained by assaying the LUC activities of both transfected cell lines with each chimaeric DNA with those observed by translating the hybrid RNAs in a translation system in vitro. When the ODC 3’ UTR was present, we observed a partial release of the translation inhibition owing to the ODC 5’ UTR only in vivo. The releasing effect was restored in vitro by the addition of cytoplasmic extracts from wild-type CHO-K1 or COS-1 cells, prepared 2 and 8 h after their release from serum starvation. We also observed a partial inhibition of the translatability of the hybrid RNA owing to the presence of the ODC 3’ UTR itself; the translational efficiency could be rescued by cell extract from 8 h serum-stimulated cells. The co-operation between the ODC-UTRs might be mediated by factors expressed by cells during particular phases of the cell cycle. Excess copies of the ODC-UTRs, expressed in trans, could compete in binding limited amounts of such regulatory factors and remove them from interaction with the endogenous ODC mRNA. This phenomenon should be reflected by modifications of the kinetics of ODC and/or LUC activities during serum stimulation. The overexpression of the ODC 3’ UTR determined an increase in both endogenous ODC activity and LUC activity. Moreover, in the transfectants expressing the hybrid RNA species bearing the ODC 3’ UTR the basal ODC activity is higher than that observed in control cells. We suggest that excess copies of the ODC 3’ UTR mis-regulate the endogenous ODC translatability, probably by tying up regulatory molecules expressed by cells in limited amounts and sequestering them from the ODC mRNA species they should interact with}, keywords = {0,3,Animals,BINDING,cell cycle,Cell Line,cell lines,CELLS,Cho Cells,coding sequence,Cos Cells,Cricetinae,Dna,efficiency,expression,EXTRACTS,gene,Genetic Complementation Test,genetics,In Vitro,IN-VITRO,IN-VIVO,INHIBITION,initiation,INITIATION-FACTOR,Kinetics,La,LINE,luciferase,Luciferases,metabolism,modification,mRNA,nosource,Ornithine Decarboxylase,Ovary,OVEREXPRESSION,pathology,Peptide Initiation Factors,physiology,Plasmids,POSITION,POSITIONS,Protein Biosynthesis,REGION,regulation,RELEASE,Rna,RNAMessenger,sequence,SEQUENCES,Support,SYSTEM,Transfection,translation,Untranslated Regions,vector,vectors,WILD-TYPE} } % == BibTeX quality report for lorenziniCooperation531997: % ? unused Journal abbr (“Biochem.J.”)

@article{lorschDEADBoxProtein1998, title = {The {{DEAD}} Box Protein {{eIF4A}}. 2. {{A}} Cycle of Nucleotide and {{RNA-dependent}} Conformational Changes}, author = {Lorsch, J.R. and Herschlag, D.}, year = 1998, month = feb, journal = {Biochemistry}, volume = {37}, number = {8}, pages = {2194–2206}, publisher = {ACS Publications}, doi = {10.1021/bi9724319}, url = {http://pubs.acs.org/doi/abs/10.1021/bi9724319 PM:9485364}, abstract = {Limited proteolysis experiments have been carried out with the DEAD box protein eIF4A. The results suggest that there is a substantial conformational change in eIF4A upon binding single-stranded RNA. Binding of ADP induces conformational changes in the free enzyme and the enzyme.RNA complex, and binding of the ATP analogue AMP-PNP induces a conformational change in the enzyme.RNA complex. The presence or absence of the gamma-phosphate on the bound nucleotide acts as a switch, presumably via the Walker motifs, that mediates changes in protein conformation and, as described in the preceding paper in this issue, also mediates changes in RNA affinity. Thus, these results suggest that there is a series of changes in conformation and substrate affinity throughout the ATP hydrolysis reaction cycle. A model is proposed in which eIF4A and the eIF4A-like domains of the DEAD box proteins act as ATP-driven conformational switches or motors that produce movements or structural rearrangements of attached protein domains or associated proteins. These movements could then be used to rearrange RNA structures or RNA.protein complexes}, keywords = {0,Adenine,Adenine Nucleotides,Adenosine,Adenosine Triphosphate,Adenosinetriphosphatase,Amino Acid Sequence,animal,ATP,BINDING,Binding Sites,Buffers,chemistry,COMPLEX,COMPLEXES,CONFORMATION,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,DOMAIN,DOMAINS,enzyme,Eukaryotic Initiation Factor-4A,genetics,Hydrolysis,In Vitro,initiation,INITIATION-FACTOR,Kinetics,La,Ligands,metabolism,Mice,MODEL,ModelsChemical,Molecular Sequence Data,MOTIFS,Movement,nosource,Nucleotides,Peptide Initiation Factors,protein,Protein Conformation,Proteins,PROTEOLYSIS,Recombinant Proteins,Rna,SERIES,Structural,structure,supportnon-u.s.gov’t,Thermodynamics,Trypsin} }

@article{lorschDEADBoxProtein1998a, title = {The {{DEAD}} Box Protein {{eIF4A}}. 1. {{A}} Minimal Kinetic and Thermodynamic Framework Reveals Coupled Binding of {{RNA}} and Nucleotide}, author = {Lorsch, J.R. and Herschlag, D.}, year = 1998, month = feb, journal = {Biochemistry}, volume = {37}, number = {8}, pages = {2180–2193}, doi = {10.1021/bi972430g}, url = {PM:9485364}, abstract = {eIF4A is the archetypal member of the DEAD box family of proteins and has been proposed to use the energy from ATP hydrolysis to unwind structures in the 5’-untranslated regions of eukaryotic mRNAs during translation initiation. As a step toward understanding the mechanism of action of this class of enzymes, a minimal kinetic and thermodynamic framework for the RNA-activated ATPase function has been established for eIF4A. The enzyme’s affinity for ssRNA is modulated by the binding of ATP.Mg2+ and ADP.Mg2+: the affinity of the E.ATP complex for ssRNA is approximately 40-fold higher than that of the E.ADP complex. The enzyme binds its substrates in a random manner; contrary to previous suggestions, neither ATP binding nor hydrolysis is required for binding of single-stranded RNA. The presence or absence of the gamma-phosphate on the bound nucleotide acts as a switch that modulates the enzyme’s structure and ssRNA affinity. The data presented in this and the following paper in this issue suggest that ATP binding and hydrolysis produce a cycle of conformational and RNA affinity changes in eIF4A. Such cycles may be used by DEAD box proteins to transduce the energy from ATP hydrolysis into physical work, thereby allowing each member of this family to rearrange its RNA or RNA.protein target}, keywords = {0,5’ Untranslated Regions,Adenine,Adenine Nucleotides,animal,ATP,ATPase,Base Sequence,BINDING,Binding Sites,chemistry,COMPLEX,COMPLEXES,CROSS-LINKING,Cross-Linking Reagents,CROSSLINKING,enzyme,Eukaryotic Initiation Factor-4A,FAMILY,genetics,human,Hydrolysis,In Vitro,initiation,INITIATION-FACTOR,Kinetics,La,MECHANISM,metabolism,Mice,Molecular Sequence Data,mRNA,nosource,Nucleotides,Peptide Initiation Factors,protein,Protein Conformation,Proteins,radiation effects,Recombinant Proteins,REGION,Rna,RNA Nucleotidyltransferases,RNADouble-Stranded,structure,Substrate Specificity,supportnon-u.s.gov’t,TARGET,Thermodynamics,translation,TRANSLATION INITIATION,ultraviolet rays} }

@article{lorschKineticDissectionFundamental1999, title = {Kinetic Dissection of Fundamental Processes of Eukaryotic Translation Initiation in Vitro}, author = {Lorsch, J.R. and Herschlag, D.}, year = 1999, month = dec, journal = {The EMBO journal}, volume = {18}, number = {23}, pages = {6705–6717}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/18.23.6705}, url = {http://www.nature.com/emboj/journal/v18/n23/abs/7592071a.html}, abstract = {Approaches have been developed for the kinetic dissection of eukaryotic translation initiation in vitro using rabbit reticulocyte ribosomes and a crude preparation of initiation factors. These new approaches have allowed the kinetics of formation of the 43S and 80S ribosomal complexes to be followed and have substantially improved the ability to follow formation of the first peptide bond. The results suggest the existence of a new step on the initiation pathway that appears to require at least one additional factor and the hydrolysis of GTP and may prepare the 80S complex for the formation of the first peptide bond. The initial kinetic framework and methods developed herein will allow the properties of individual species along the initiation pathway to be probed further and will facilitate dissection of the mechanistic roles of individual translation factors and their interplay with RNA structural elements}, keywords = {0,animal,COMPLEX,COMPLEXES,ELEMENTS,Escherichia coli,EUKARYOTIC TRANSLATION,GTP,Guanosine,Guanosine Triphosphate,Guanylyl Imidodiphosphate,Hydrolysis,In Vitro,IN-VITRO,initiation,INITIATION-FACTOR,Kinetics,La,metabolism,Methods,ModelsBiological,nosource,PATHWAY,Peptide Chain Initiation,physiology,Rabbits,Reticulocytes,ribosome,Ribosomes,Rna,RNAMessenger,RNATransferMet,Structural,supportnon-u.s.gov’t,Time Factors,translation,TRANSLATION INITIATION,TranslationGenetic} } % == BibTeX quality report for lorschKineticDissectionFundamental1999: % ? unused Journal abbr (“EMBO J.”)

@article{lovelessInfluenceAminoglycosideAntibiotics1984a, title = {The Influence of Aminoglycoside Antibiotics on the in Vitro Function of Rat Liver Ribosomes.}, author = {Loveless, M.O. and Kohlhepp, S.J. and Gilbert, D.N.}, year = 1984, month = feb, journal = {The Journal of laboratory and clinical medicine}, volume = {103}, number = {2}, eprint = {6693798}, eprinttype = {pubmed}, pages = {294–303}, url = {http://www.ncbi.nlm.nih.gov/pubmed/6693798}, abstract = {There are few studies of the influence of aminoglycoside antibiotics on the ribosomes of higher eukaryotic organisms. To this end, cytoplasmic ribosomes were prepared from rat liver. In vitro, poly(U)-directed ribosome protein synthesis was studied in the presence and absence of selected aminoglycosides. Misreading of poly(U) was also assessed. Consistent with earlier studies using different sources of ribosomes, paromomycin inhibited cell-free protein synthesis and caused poly(U) misreading. In contrast to the findings of other studies in cell-free ribosomes of eukaryotic organisms, netilmicin, tobramycin, and neomycin were most active in inhibiting protein synthesis, and gentamicin C2 and neomycin caused appreciable misreading. Thus the previous suggestion that a paromamine fragment (found in paromomycin) might be a structural requirement for in vitro inhibition of protein synthesis and misreading is not substantiated by the results in rat liver ribosomes. Commercial gentamicin C is a mixture of gentamicins C1, C1a, and C2. Despite nearly identical chemical structures, the three constituents displayed greatly different propensities for inducing poly(U) misreading. C2 was the most active, followed by C1a. In summary, selected aminoglycoside antibiotics caused inhibition and mistranslation of poly(U) messenger in an in vitro ribosome system prepared from rat liver. These effects were not limited to paromamine-containing aminoglycoside antibiotics. Gentamicin C2 caused much more poly(U) misreading than the other two constituents of the gentamicin C complex}, keywords = {0,AMINOGLYCOSIDE ANTIBIOTICS,Aminoglycosides,Animals,Anti-Bacterial Agents,antibiotic,antibiotics,biosynthesis,COMPLEX,COMPLEXES,drug effects,Gentamicins,In Vitro,IN-VITRO,INHIBITION,La,Leucine,Liver,Male,metabolism,Neomycin,No DOI found,nosource,Paromomycin,pharmacology,Phenylalanine,Poly U,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,rat,Rats,RatsInbred F344,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Structural,structure,Support,SYSTEM,Tobramycin} } % == BibTeX quality report for lovelessInfluenceAminoglycosideAntibiotics1984a: % ? unused Journal abbr (“J.Lab Clin.Med.”)

@article{lovkvist-wallstromRegulationMammalianOrnithine1995, title = {Regulation of Mammalian Ornithine Decarboxylase. {{Studies}} on the Induction of the Enzyme by Hypotonic Stress}, author = {{Lovkvist-Wallstrom}, E. and {Stjernborg-Ulvsback}, L. and Scheffler, I.E. and Persson, L.}, year = 1995, month = jul, journal = {Eur.J.Biochem.}, volume = {231}, number = {1}, pages = {40–44}, doi = {10.1111/j.1432-1033.1995.0040f.x}, url = {PM:7628482}, abstract = {One of the cellular responses to hypotonic stress is a marked induction of a key regulatory enzyme in the polyamine biosynthetic pathway, i.e. ornithine decarboxylase (ODC). This increase in ODC activity appears to be a physiological response since the elevated putrescine production seen after the hypotonic shock renders the cells less sensitive to the decrease in osmolarity. In the present study, we have investigated the mechanisms by which the hypotonicity may induce ODC activity. We provide support for a translational mechanism, closely related to the polyamine-mediated feedback regulation of ODC synthesis. In addition, we have examined whether the long G+C-rich 5’ untranslated region of the ODC mRNA, which has been demonstrated to negatively affect the translatability of the message, is of any importance for the induction of ODC by hypotonic stress. Chinese hamster ovary (CHO) cells expressing ODC mRNA, with or without the 5’ untranslated region, were isolated after transfecting ODC-deficient CHO cells with the appropriate constructs. Hypotonic treatment of the stable transfectants, however, revealed no major difference in ODC induction between the cells expressing a full-length ODC mRNA and those expressing an ODC mRNA deleted of its 5’ untranslated region, demonstrating that this part of the message was not essential for the osmotic effects on ODC expression}, keywords = {0,Animals,biosynthesis,Cell Line,CELLS,Cho Cells,Cricetinae,enzyme,Enzyme Induction,enzymology,expression,Feedback,genetics,La,Leukemia L1210,MECHANISM,MECHANISMS,MESSAGE,metabolism,mRNA,nosource,Ornithine,Ornithine Decarboxylase,Osmolar Concentration,Ovary,PATHWAY,physiology,polyamine,Protein Biosynthesis,Putrescine,REGION,regulation,Rna,RNAMessenger,Stress,Support,Tumor CellsCultured} } % == BibTeX quality report for lovkvist-wallstromRegulationMammalianOrnithine1995: % ? Possibly abbreviated journal title Eur.J.Biochem.

@article{lovkvistImportance3Untranslated2001, title = {Importance of the 3’ Untranslated Region of Ornithine Decarboxylase {{mRNA}} in the Translational Regulation of the Enzyme}, author = {Lovkvist, Wallstrom E. and Takao, K. and Wendt, A. and Vargiu, C. and Yin, H. and Persson, L.}, year = 2001, month = jun, journal = {Biochemical Journal}, volume = {356}, number = {Pt 2}, pages = {627–634}, publisher = {Portland Press Ltd}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1221878/ PM:11368794}, abstract = {Translational regulation of ornithine decarboxylase (ODC), which catalyses the first step in the biosynthesis of polyamines, appears to be an important mechanism in the strong feedback control as well as in the hypotonic induction of the enzyme. However, the exact mechanisms are not yet understood. The ODC mRNA has long 5’ and 3’ untranslated regions (UTRs) which may be involved in the translational control of the enzyme. In the present study we have used a series of stable transfectants of Chinese Hamster ovary cells expressing ODC mRNAs with various truncations in the 5’ and 3’ UTRs to investigate the importance of these regions. It is demonstrated that neither the 5’ UTR nor the 3’ UTR appears to be involved in the polyamine-mediated feedback control of ODC synthesis. The hypotonic induction of ODC, on the other hand, was shown to be highly dependent on the presence of the 3’ UTR, but not on the 5’ UTR, of ODC mRNA. Cells expressing ODC mRNAs lacking the 3’ UTR showed no, or only a very slight, induction of ODC whether the 5’ UTR was present or not, whereas the cell lines expressing ODC mRNAs containing the 3’ UTR (with or without the 5’ UTR) markedly induced ODC after a hypotonic shock. The present finding of a role for the ODC mRNA 3’ UTR in the hypotonic induction of ODC is the first demonstration of a specific effect of the 3’ UTR in the regulation of ODC}, keywords = {0,3,3’ Untranslated Regions,5’ Untranslated Regions,Animals,biosynthesis,Cell Line,cell lines,CELLS,Cho Cells,Cricetinae,Down-Regulation,drug effects,enzyme,Enzyme Induction,Feedback,genetics,Hypotonic Solutions,La,LINE,MECHANISM,MECHANISMS,metabolism,mRNA,No DOI found,nosource,Ornithine Decarboxylase,Ovary,pharmacology,polyamine,Polyamines,Protein Biosynthesis,Putrescine,REGION,regulation,Rna,RNAMessenger,SERIES,Solutions,Spermidine,Spermine,Support,Untranslated Regions} } % == BibTeX quality report for lovkvistImportance3Untranslated2001: % ? unused Journal abbr (“Biochem.J.”)

@article{loweComputationalScreenMethylation1999, title = {A Computational Screen for Methylation Guide {{snoRNAs}} in Yeast}, author = {Lowe, T.M. and Eddy, S.R.}, year = 1999, month = feb, journal = {Science}, volume = {283}, number = {5405}, pages = {1168–1171}, doi = {10.1126/science.283.5405.1168}, url = {PM:10024243}, abstract = {Small nucleolar RNAs (snoRNAs) are required for ribose 2’-O-methylation of eukaryotic ribosomal RNA. Many of the genes for this snoRNA family have remained unidentified in Saccharomyces cerevisiae, despite the availability of a complete genome sequence. Probabilistic modeling methods akin to those used in speech recognition and computational linguistics were used to computationally screen the yeast genome and identify 22 methylation guide snoRNAs, snR50 to snR71. Gene disruptions and other experimental characterization confirmed their methylation guide function. In total, 51 of the 55 ribose methylated sites in yeast ribosomal RNA were assigned to 41 different guide snoRNAs}, keywords = {0,Algorithms,analysis,Base Pairing,Cell Nucleolus,CEREVISIAE,chemistry,DISRUPTION,DISRUPTIONS,FAMILY,gene,Genes,Genetic,genetics,Genome,IDENTIFY,La,metabolism,Methods,Methylation,ModelsGenetic,ModelsStatistical,nosource,RECOGNITION,Ribose,ribosomal RNA,RIBOSOMAL-RNA,Rna,RNAFungal,RNARibosomal,RNASmall Nuclear,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SITE,SITES,SMALL NUCLEOLAR RNAS,Software,Support,yeast} }

@article{lucioliGeneDosageAlteration1988, title = {Gene Dosage Alteration of {{L2}} Ribosomal Protein Genes in {{Saccharomyces}} Cerevisiae: Effects on Ribosome Synthesis.}, author = {Lucioli, A. and Presutti, C. and Ciafre, S. and Caffarelli, E. and Fragapane, P. and Bozzoni, I.}, year = 1988, month = nov, journal = {Molecular and cellular biology}, volume = {8}, number = {11}, pages = {4792–4798}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/8/11/4792}, abstract = {In Saccharomyces cerevisiae, the genes coding for the ribosomal protein L2 are present in two copies per haploid genome. The two copies, which encode proteins differing in only a few amino acids, contribute unequally to the L2 mRNA pool: the L2A copy makes 72% of the mRNA, while the L2B copy makes only 28%. Disruption of the L2B gene (delta B strain) did not lead to any phenotypic alteration, whereas the inactivation of the L2A copy (delta A strain) produced a slow-growth phenotype associated with decreased accumulation of 60S subunits and ribosomes. No intergenic compensation occurred at the transcriptional level in the disrupted strains; in fact, delta A strains contained reduced levels of L2 mRNA, whereas delta B strains had almost normal levels. The wild-type phenotype was restored in the delta A strains by transformation with extra copies of the intact L2A or L2B gene. As already shown for other duplicated genes (Kim and Warner, J. Mol. Biol. 165:79-89, 1983; Leeret al., Curr. Genet. 9:273-277, 1985), the difference in expression of the two gene copies could be accounted for via differential transcription activity. Sequence comparison of the rpL2 promoter regions has shown the presence of canonical HOMOL1 boxes which are slightly different in the two genes}, keywords = {0,60S subunit,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,Base Sequence,CEREVISIAE,Comparative Study,DISRUPTION,E,expression,gene,Gene Dosage,Gene Expression Regulation,Genes,GenesFungal,genetics,Genome,L2,La,metabolism,Molecular Sequence Data,mRNA,Multigene Family,Multiple DOI,Mutation,nonfile,nosource,Phenotype,PROMOTER,Promoter Regions (Genetics),protein,Proteins,REGION,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,RIBOSOME SYNTHESIS,Ribosomes,Rna,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SUBUNIT,SUBUNITS,Support,transcription,TRANSFORMATION,WILD-TYPE} } % == BibTeX quality report for lucioliGeneDosageAlteration1988: % ? unused Journal abbr (“Mol Cell Biol”)

@article{lukavskyStructureHCVIRES2003, title = {Structure of {{HCV IRES}} Domain {{II}} Determined by {{NMR}}}, author = {Lukavsky, P.J. and Kim, I. and Otto, G.A. and Puglisi, J.D.}, year = 2003, month = dec, journal = {Nature Structural & Molecular Biology}, volume = {10}, number = {12}, pages = {1033–1038}, publisher = {Nature Publishing Group}, doi = {10.1038/nsb1004}, url = {http://www.nature.com/nsmb/journal/v10/n12/abs/nsb1004.html}, abstract = {Complex RNA structures regulate many biological processes, but are often too large for structure determination by NMR methods. The 5’ untranslated region (5’ UTR) of the hepatitis C viral (HCV) RNA genome contains an internal ribosome entry site (IRES) that binds to 40S ribosomal subunits with high affinity and specificity to control translation. Domain II of the HCV IRES forms a 25-kDa folded subdomain that may alter ribosome conformation. We report here the structure of domain II as determined using an NMR approach that combines short- and long-range structural data. Domain II adopts a distorted L-shape structure, and its overall shape in the free form is markedly similar to its 40S subunit-bound form; this suggests how domain II may modulate 40S subunit conformation. The results show how NMR can be used for structural analysis of large biological RNAs}, keywords = {0,5’ Untranslated Regions,analysis,Base Sequence,BIOLOGY,chemistry,COMPLEX,COMPLEXES,CONFORMATION,DOMAIN,DOMAIN-II,FORM,Genome,GenomeViral,Hepacivirus,HEPATITIS-C,INTERNAL RIBOSOME ENTRY,La,Magnetic Resonance Spectroscopy,Methods,ModelsMolecular,Molecular Sequence Data,NMR,nosource,Nucleic Acid Conformation,REGION,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,RIBOSOME ENTRY SITE,Rna,RnaViral,SITE,SPECIFICITY,Structural,structure,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,translation,Untranslated Regions} } % == BibTeX quality report for lukavskyStructureHCVIRES2003: % ? unused Journal abbr (“Nat.Struct.Biol.”)

@article{lundExpressionUrokinasetypePlasminogen1996a, title = {Expression of Urokinase-Type Plasminogen Activator, Its Receptor and Type-1 Plasminogen Activator Inhibitor Is Differentially Regulated by Inhibitors of Protein Synthesis in Human Cancer Cell Lines.}, author = {Lund, L.R.}, year = 1996, journal = {FEBS Letts.}, volume = {383}, pages = {139–144}, doi = {10.1016/0014-5793(96)00223-2}, keywords = {anisomycin,cancer,Cell Line,cell lines,expression,human,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS} } % == BibTeX quality report for lundExpressionUrokinasetypePlasminogen1996a: % ? Possibly abbreviated journal title FEBS Letts.

@article{lundbladProgrammedTranslationalFrameshifting1997, title = {Programmed Translational Frameshifting in a Gene Required for Yeast Telomere Replication.}, author = {Lundblad, V. and Morris, D.K.}, year = 1997, journal = {Current Biology}, volume = {7}, number = {12}, pages = {969–976}, publisher = {Elsevier}, doi = {10.1016/S0960-9822(06)00416-7}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0960-9822(06)00416-7 http://www.sciencedirect.com/science/article/pii/S0960982206004167}, keywords = {+1 frameshifting,expression,frameshift,Frameshifting,gene,Genes,nosource,RIBOSOMAL FRAMESHIFT,SIGNAL,Telomere,Ty1,yeast} }

@article{lutzInteractionU1SnRNPA1996, title = {Interaction between the {{U1 snRNP-A}} Protein and the 160-{{kD}} Subunit of Cleavage-Polyadenylation Specificity Factor Increases Polyadenylation Efficiency in Vitro.}, author = {Lutz, C.S. and Murthy, K.G. and Schek, N. and O’Connor, J.P. and Manley, J.L. and Alwine, J.C.}, year = 1996, month = feb, journal = {Genes & Development}, volume = {10}, number = {3}, pages = {325–337}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.10.3.325}, url = {http://genesdev.cshlp.org/content/10/3/325.short}, keywords = {BINDING,COMPLEX,COMPLEXES,COMPONENT,efficiency,ELEMENTS,In Vitro,IN-VITRO,microbiology,nosource,poly(A),polymerase,protein,Proteins,purification,Rna,SIGNAL,splicing,SUBUNIT} }

@article{luxHumanRetroviralGag2005a, title = {Human Retroviral Gag- and Gag-Pol-like Proteins Interact with the Transforming Growth Factor-Beta Receptor Activin Receptor-like Kinase 1}, author = {Lux, A. and Beil, C. and Majety, M. and Barron, S. and Gallione, C.J. and Kuhn, H.M. and Berg, J.N. and Kioschis, P. and Marchuk, D.A. and Hafner, M.}, year = 2005, month = mar, journal = {J.Biol.Chem.}, volume = {280}, number = {9}, pages = {8482–8493}, doi = {10.1074/jbc.M409197200}, url = {PM:15611116}, abstract = {Mutations in activin receptor-like kinase 1 (ALK1), a transforming growth factor (TGF)-beta type I receptor, lead to the vascular disorder hereditary hemorrhagic telangiectasia caused by abnormal vascular remodeling. The underlying molecular cause of this disease is not well understood. Identifying binding partners for ALK1 will help to understand its cellular function. Using the two-hybrid system, we identified an ALK1-binding protein encoded by an ancient retroviral/retrotransposon element integrated as a single copy gene known as PEG10 on human chromosome 7q21. PEG10 contains two overlapping reading frames from which two proteins, PEG10-RF1 and PEG10-RF1/2, are translated by a typical retroviral -1 ribosomal frameshift mechanism. Reverse transcription-PCR and Northern blot analysis showed a broad range of PEG10 expression in different tissues and cell types, i.e. human placenta, brain, kidney, endothelial cells, lymphoblasts, and HepG2 and HEK293 cells. However, endogenous PEG10-RF1 and PEG10-RF1/2 proteins were only detected in HepG2 and HEK293 cells. PEG10-RF1, which is the major PEG10 protein product, represents a gag-like protein, and PEG10-RF1/2 represents a gag-pol-like protein. PEG10-RF1 also interacts with different members of TGF-beta superfamily type I and II receptors. PEG10-RF1 binding to ALK1 is mediated by a 200-amino acid domain with no recognized motif. PEG10-RF1 inhibits ALK1 as well as ALK5 signaling. Co-expression of ALK1 and PEG10-RF1 in different cell types induced morphological changes reminiscent of neuronal cells or sprouting cells. This is the first report of a human retroviral-like protein interacting with members of the TGF-beta receptor family}, keywords = {0,ACID,Activin ReceptorsType I,Amino Acid Motifs,analysis,Animals,BINDING,BIOLOGY,BlottingNorthern,BlottingWestern,Cell Line,CELLS,Cho Cells,CloningMolecular,Cos Cells,Cytoplasm,disease,Dna,DNA Transposable Elements,DOMAIN,ELEMENTS,expression,FAMILY,FRAME,frameshift,FUSION PROTEIN,Fusion Proteinsgag-pol,Gag,Gag-pol,gene,Gene Library,Gene Productsgag,GENE-PRODUCT,GenesReporter,genetics,GROWTH,GROWTH-FACTOR,Hamsters,human,Humans,Immunoprecipitation,Kidney,kinase,La,luciferase,Luciferases,MECHANISM,metabolism,MicroscopyFluorescence,ModelsGenetic,Mutation,MUTATIONS,Neurons,nosource,Open Reading Frames,Polymerase Chain Reaction,PRODUCT,PRODUCTS,protein,Protein Binding,Protein StructureTertiary,Proteins,READING FRAME,Reading Frames,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,Retroviridae,Reverse Transcriptase Polymerase Chain Reaction,RIBOSOMAL FRAMESHIFT,Signal Transduction,SUPERFAMILY,SYSTEM,Tissue Distribution,Transfection,Transforming Growth Factor beta,Two-Hybrid System Techniques,U937 Cells} } % == BibTeX quality report for luxHumanRetroviralGag2005a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{lyamichevUnusualDNAStructure1989, title = {An Unusual {{DNA}} Structure Detected in a Telomeric Sequence under Superhelical Stress and at Low {{pH}}}, author = {Lyamichev, V.I. and Mirkin, S.M. and Danilevskaya, O.N. and Voloshin, O.N. and Balatskaya, S.V. and Dobrynin, V.N. and Filippov, S.A. and {Frank-Kamenetskii}, M.D.}, year = 1989, month = jun, journal = {Nature}, volume = {339}, number = {6226}, pages = {634–637}, doi = {10.1038/339634a0}, url = {PM:2733795}, abstract = {Telomeric sequences of DNA, which are found at the ends of linear chromosomes, have been attracting attention as potential sites for the formation of unusual DNA structures. They consist of (GnTm) or (GnATm) motifs (n greater than or equal to m) and, in the single-stranded state, form hairpins stabilized by non-canonical G.G pairs. In the duplex state and under superhelical stress they exhibit hypersensitivity to SI nuclease which by analogy with homopurine- homopyrimidine sequences may reflect the formation of an unusual structure. To determine whether this is the case we have inserted into a plasmid the Tetrahymena telomeric motif (G4T2).(A2C4) and probed it by two-dimensional gel electrophoresis, chemical modification and oligonucleotide binding. Our data demonstrate that, under superhelical stress and at low pH, the insert does indeed adopt a novel DNA conformation. We have concluded that in this structure the C-rich strand forms a hairpin stabilized by non-Watson-Crick base pairs C.C+ and A.A+, whereas the G-rich strand remains unstructured. We term this new DNA structure the (C,A)-hairpin}, keywords = {0,BINDING,Chromosomes,Dna,Electrophoresis,ElectrophoresisGelTwo-Dimensional,Genetic,genetics,Hydrogen-Ion Concentration,La,ModelsMolecular,modification,Molecular Structure,nosource,Plasmids,sequence,structure,Tetrahymena} }

@article{lydallHidingEndsYeast2003, title = {Hiding at the Ends of Yeast Chromosomes: Telomeres, Nucleases and Checkpoint Pathways}, author = {Lydall, D.}, year = 2003, month = oct, journal = {Journal of cell science}, volume = {116}, number = {Pt 20}, pages = {4057–4065}, publisher = {The Company of Biologists Ltd}, url = {http://jcs.biologists.org/content/116/20/4057.short}, abstract = {Telomeres stabilise DNA at the ends of chromosomes, preventing chromosome fusion and genetic instability. Telomeres differ from double strand breaks in that they activate neither DNA repair nor DNA damage checkpoint pathways. Paradoxically DNA repair and checkpoint genes play critical roles in telomere stability. Recent work has provided insights into the roles of DNA repair and DNA damage checkpoint pathways in the physiological maintenance of telomeres and in cellular responses when telomeres become uncapped. In budding yeast the Mre11p nuclease, along with other unidentified nucleases, plays critical roles in physiological telomere maintenance. However, when telomeres are uncapped, the 5’-to-3’ exonuclease, Exo1p, plays a critical role in generating single-stranded DNA and activating checkpoint pathways. Intriguingly Exo1p does not play an important role in normal telomere maintenance. Although checkpoint pathways are not normally activated by telomeres, at least four different types of telomere defect activate checkpoint pathways. Interestingly, each of these telomere defects depends on a different subset of checkpoint proteins to induce cell cycle arrest. A model for how a spectrum of telomeric states might interact with telomerase and checkpoint pathways is proposed}, keywords = {0,cell cycle,Cell Cycle Proteins,CEREVISIAE,Chromosomes,ChromosomesFungal,Deoxyribonucleases,Dna,DNA Damage,DNA Repair,DNA Replication,Endodeoxyribonucleases,Enzyme Induction,Exodeoxyribonucleases,gene,Genes,Genetic,La,metabolism,MODEL,ModelsMolecular,No DOI found,nosource,PATHWAY,physiology,protein,Proteins,Review,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Saccharomycetales,SPECTRA,stability,Support,Telomerase,Telomere,yeast} } % == BibTeX quality report for lydallHidingEndsYeast2003: % ? unused Journal abbr (“J.Cell Sci.”)

@article{lynchComparisonXrayCrystal2003, title = {Comparison of X-Ray Crystal Structure of the {{30S}} Subunit-Antibiotic Complex with {{NMR}} Structure of Decoding Site Oligonucleotide-Paromomycin Complex}, author = {Lynch, S.R. and Gonzalez, R.L. and Puglisi, J.D.}, year = 2003, month = jan, journal = {Structure}, volume = {11}, number = {1}, pages = {43–53}, publisher = {Elsevier}, doi = {10.1016/S0969-2126(02)00934-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0969212602009346}, abstract = {Aminoglycoside antibiotics that bind to 16S ribosomal RNA in the aminoacyl-tRNA site (A site) cause misreading of the genetic code and inhibit translocation. Structures of an A site RNA oligonucleotide free in solution and bound to the aminoglycosides paromomycin or gentamicin C1a have been determined by NMR. Recently, the X-ray crystal structure of the entire 30S subunit has been determined, free and bound to paromomycin. Distinct differences were observed in the crystal structure, particularly at A1493. Here, the NMR structure of the oligonucleotide-paromomycin complex was determined with higher precision and is compared with the X-ray crystal structure of the 30S subunit complex. The comparison shows the validity of both structures in identifying critical interactions that affect ribosome function}, keywords = {16S,16S RIBOSOMAL-RNA,A SITE,A-SITE,AMINOGLYCOSIDE ANTIBIOTICS,antibiotic,antibiotics,ASSIGNMENT,COMPLEX,COMPLEXES,CONFORMATION,crystal structure,CRYSTAL-STRUCTURE,D,decoding,ESCHERICHIA-COLI,Genetic,Genetic Code,H-1,nosource,Paromomycin,RECOGNITION,RESONANCES,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Rna,SITE,SPECIFICITY,SPECTROSCOPY,structure,SUBUNIT,translocation} }

@article{lyngsoRNAPseudoknotPrediction2000, title = {{{RNA}} Pseudoknot Prediction in Energy-Based Models.}, author = {Lyngso, R.B. and Pedersen, C.N.}, year = 2000, month = jan, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {7}, number = {3-4}, eprint = {11108471}, eprinttype = {pubmed}, pages = {409–427}, publisher = {Mary Ann Liebert, Inc.}, issn = {1066-5277}, doi = {10.1089/106652700750050862}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11108471 http://www.liebertonline.com/doi/abs/10.1089/106652700750050862 PM:11108471}, abstract = {RNA molecules are sequences of nucleotides that serve as more than mere intermediaries between DNA and proteins, e.g., as catalytic molecules. Computational prediction of RNA secondary structure is among the few structure prediction problems that can be solved satisfactorily in polynomial time. Most work has been done to predict structures that do not contain pseudoknots. Allowing pseudoknots introduces modeling and computational problems. In this paper we consider the problem of predicting RNA secondary structures with pseudoknots based on free energy minimization. We first give a brief comparison of energy-based methods for predicting RNA secondary structures with pseudoknots. We then prove that the general problem of predicting RNA secondary structures containing pseudoknots is NP complete for a large class of reasonable models of pseudoknots.}, pmid = {11108471}, keywords = {Algorithms,chemistry,Computational Biology,computer,Dna,La,Methods,MODEL,models,Models,ModelsMolecular,Molecular,nosource,Nucleic Acid Conformation,Nucleotides,PREDICTION,protein,Proteins,pseudoknot,pseudoknots,Research SupportNon-U.S.Gov’t,Rna,RNA,RNA PSEUDOKNOT,RNA SECONDARY STRUCTURE,RNA: chemistry,SECONDARY STRUCTURE,sequence,SEQUENCES,structure,Thermodynamics} } % == BibTeX quality report for lyngsoRNAPseudoknotPrediction2000: % ? unused Journal abbr (“J.Comput.Biol.”)

@article{lyonMutationDetectionUsing2001, title = {Mutation Detection Using Fluorescent Hybridization Probes and Melting Curve Analysis}, author = {Lyon, E.}, year = 2001, month = may, journal = {Expert review of molecular diagnostics}, volume = {1}, number = {1}, pages = {92–101}, publisher = {Expert Reviews}, doi = {10.1586/14737159.1.1.92}, url = {http://www.ingentaconnect.com/content/ftd/erm/2001/00000001/00000001/art00012}, abstract = {The LightCycler is a real-time PCR instrument that combines a thermocycler and a micro-volume fluorimeter. LightCycler technology is gaining popularity due to its ability to detect mutations quickly and accurately. Multiple base alterations are discriminated using hybridization probes and fluorescent melting curves. This review focuses on mutation detection and base discrimination by fluorescent hybridization probes. Assay designs for single base mutation detection and complex multiplex reactions are discussed. Types of mutations detected and reported applications are reviewed. Guidelines using melting curve analysis for the clinical laboratory are presented}, keywords = {0,analysis,BASE,chemistry,COMPLEX,COMPLEXES,diagnostic use,DNA Mutational Analysis,Factor V,Fluorescent Dyes,genetics,human,La,Molecular Diagnostic Techniques,Mutation,MUTATIONS,nosource,pathology,PCR,Polymerase Chain Reaction,Review,Temperature} } % == BibTeX quality report for lyonMutationDetectionUsing2001: % ? unused Journal abbr (“Expert.Rev.Mol.Diagn.”)

@article{maPseudouridylationYeastU22005, title = {Pseudouridylation of Yeast {{U2 snRNA}} Is Catalyzed by Either an {{RNA-guided}} or {{RNA-independent}} Mechanism}, author = {Ma, X. and Yang, C. and Alexandrov, A. and Grayhack, E.J. and {Behm-Ansmant}, I. and Yu, Y.T.}, year = 2005, month = jul, journal = {The EMBO Journal}, volume = {24}, number = {13}, pages = {2403–2413}, publisher = {Nature Publishing Group}, doi = {10.1038/sj.emboj.7600718}, url = {http://www.nature.com/emboj/journal/v24/n13/abs/7600718a.html}, abstract = {Yeast U2 small nuclear RNA (snRNA) contains three pseudouridines (Psi35, Psi42, and Psi44). Pus7p and Pus1p catalyze the formation of Psi35 and Psi44, respectively, but the mechanism of Psi42 formation remains unclear. Using a U2 substrate containing a single (32)P radiolabel at position 42, we screened a GST-ORF library for pseudouridylase activity. Surprisingly, we found a Psi42-specific pseudouridylase activity that coincided with Nhp2p, a protein component of a Box H/ACA sno/scaRNP (small nucleolar/Cajal body-specific ribonucleoprotein). When isolated by tandem affinity purification (TAP), the other protein components of the H/ACA sno/scaRNP also copurified with the pseudouridylase activity. Micrococcal nuclease-treated TAP preparations were devoid of pseudouridylase activity; however, activity was restored upon addition of RNAs from TAP preparations. Pseudouridylation reconstitution using RNAs from a Box H/ACA RNA library identified snR81, a snoRNA known to guide rRNA pseudouridylation, as the Psi42-specific guide RNA. Using the snR81-deletion strain, Nhp2p- or Cbf5p-conditional depletion strain, and a cbf5 mutation strain, we further demonstrated that the pseudouridylase activity is dependent on snR81 snoRNP in vivo. Our data indicate that snRNA pseudouridylation can be catalyzed by both RNA-dependent and RNA-independent mechanisms}, keywords = {0,Biochemistry,Biophysics,Catalysis,CBF5,CEREVISIAE,chemistry,COMPONENT,COMPONENTS,Gene Library,Hydro-Lyases,IN-VIVO,La,library,MECHANISM,MECHANISMS,metabolism,Microtubule-Associated Proteins,Mutation,nosource,Nuclear Proteins,POSITION,protein,Proteins,Pseudouridine,pseudouridylation,purification,RECONSTITUTION,RIBONUCLEOPROTEIN,Ribonucleoproteins,RibonucleoproteinsSmall Nuclear,RibonucleoproteinsSmall Nucleolar,Rna,RNAFungal,RNASmall Nuclear,RNASmall Nucleolar,rRNA,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Support,U2 SNRNA,yeast} } % == BibTeX quality report for maPseudouridylationYeastU22005: % ? unused Journal abbr (“EMBO J.”)

@article{maagCommunicationEukaryoticTranslation2003, title = {Communication between Eukaryotic Translation Initiation Factors 1 and {{1A}} on the Yeast Small Ribosomal Subunit}, author = {Maag, D. and Lorsch, J.R.}, year = 2003, month = jul, journal = {Journal of molecular biology}, volume = {330}, number = {5}, pages = {917–924}, publisher = {Elsevier}, doi = {10.1016/S0022-2836(03)00665-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/S002228360300665X}, abstract = {We have used expressed protein ligation to site-specifically label eukaryotic translation initiation factors (eIFs) 1 and 1A at their C termini with tetramethyl rhodamine. These fluorescent proteins were used in steady-state anisotropy-based binding experiments to measure the dissociation constants of the factors and the yeast small (40S) ribosomal subunit for the first time. These studies demonstrate that both eIF1 and eIF1A are capable of binding to the 40S subunit in the absence of any other initiation factors or mRNA, arguing against previous suggestions that eIF3 is required for recruitment of eIF1 to the small ribosomal subunit. Strikingly, the data also demonstrate that there is approximately ninefold thermodynamic coupling in the binding of the two factors to the 40S subunit. This indicates that eIF1 and eIF1A communicate with one another when bound to the 40S subunit. Communication between these two factors is likely to be important for coordinating their functions during the initiation process. The data presented here provide a foundation on which to build a quantitative understanding of the network of interactions between these essential factors and the rest of the initiation machinery}, keywords = {BINDING,chemistry,eIF1,eIF1A,eIF3,EUKARYOTIC TRANSLATION,initiation,INITIATION-FACTOR,La,mRNA,nosource,protein,Proteins,RECRUITMENT,RIBOSOMAL-SUBUNIT,SUBUNIT,translation,TRANSLATION INITIATION,yeast} } % == BibTeX quality report for maagCommunicationEukaryoticTranslation2003: % ? unused Journal abbr (“J.Mol Biol.”)

@article{macbethPhenotypeMutationsG26551999a, title = {The Phenotype of Mutations of {{G2655}} in the Sarcin/Ricin Domain of 23 {{S}} Ribosomal {{RNA}}}, author = {Macbeth, M.R. and Wool, I.G.}, year = 1999, month = jan, journal = {J.Mol.Biol.}, volume = {285}, number = {3}, pages = {965–975}, doi = {10.1006/jmbi.1998.2388}, url = {PM:9918717}, abstract = {The sarcin/ricin domain (SRD) in Escherichia coli 23 S rRNA forms a part of the site for the association of the elongation factors with the ribosome and hence is critical for the binding of aminoacyl-tRNA and for translocation. The domain is also the site of action of the eponymous toxins which catalyze covalent modification of single nucleotides that inactivate the ribosome. The conformation of the conserved guanosine at position 2655 is an especially prominent feature of the structure of the SRD: the nucleotide is bulged out of a helix and forms a base-triple with A2665 and U2656. G2655 in 23 S rRNA is protected from chemical modification when the elongation factors, EF-Tu and EF-G, are bound to ribosomes and the analog of G2655 in oligoribonucleotides is critical for recognition by the toxin sarcin and by EF-G. The contribution of G2655 to the function of the ribosome has been evaluated by constructing mutations in the nucleotide and determining the phenotype. Constitutive expression of a plasmid-encoded rrnB operon with a deletion of, or transversions in, G2655 is lethal to E. coli cells, whereas a defect in the growth of cells with a G2655A transition is observed only in competition with wild-type cells. The sedimentation profiles of ribosomes with mutations in G2655 are altered; most markedly by deletion or transversion of the nucleotide, less severely by transition to adenosine. Mutations of G2655 confer resistance to sarcin on ribosomes. Ribosomes with G2655Delta, G2655C, or G2655U mutations in 23 S rRNA are not active in protein synthesis, whereas those with the G2655A transition mutation suffer decreased activity}, keywords = {0,Adenosine,Base Sequence,BINDING,Cell Division,EFTu,elongation,Escherichia coli,ESCHERICHIA-COLI,expression,genetics,Guanosine,La,modification,Molecular Sequence Data,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Nucleotides,Oligoribonucleotides,Operon,Peptide Elongation Factors,pharmacology,Phenotype,Plasmids,Polyribosomes,protein,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,RIBOSOMAL-RNA,ribosome,Ribosomes,Ricin,Rna,RNARibosomal23S,rRNA,rRNA Operon,structure,supportu.s.gov’tp.h.s.,toxin,translocation} } % == BibTeX quality report for macbethPhenotypeMutationsG26551999a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{macbethCharacterizationVitroVivo1999a, title = {Characterization of in Vitro and in Vivo Mutations in Non-Conserved Nucleotides in the Ribosomal {{RNA}} Recognition Domain for the Ribotoxins Ricin and Sarcin and the Translation Elongation Factors}, author = {Macbeth, M.R. and Wool, I.G.}, year = 1999, month = jan, journal = {J.Mol.Biol.}, volume = {285}, number = {2}, pages = {567–580}, doi = {10.1006/jmbi.1998.2337}, url = {PM:9878430}, abstract = {The sarcin/ricin domain in 23 S/28 S rRNA is crucial for ribosome function, since it constitutes at least part of the binding site for the elongation factors and hence is essential for binding aminoacyl- tRNA and for translocation. The domain is also the site of action of ricin and sarcin and analysis of the effect of mutations in the RNA on recognition by the cytotoxins has helped to define the structure and to understand the function of the region. We have constructed deletions, separately, of pairs of non-conserved, juxtaposed but non-hydrogen- bonded nucleotides that correspond to C4317 and C4331, and to U4316 and C4332, in an oligoribonucleotide that mimics the sarcin/ricin domain in rat 28 S rRNA. The deletions had no effect on the depurination of A4324 by ricin nor on the cleavage of the phosphodiester bond on the 3’ side of G4325 by sarcin. However, simultaneous deletion of the four nucleotides decreased cleavage by sarcin but did not affect depurination by ricin. Removal of the non-canonical A4318.A4330 pair abolished recognition by both toxins. Deletion from oligoribonucleotides, that reproduce the sarcin/ricin domain of Escherichia coli 23 S rRNA, of U2653 and C2667 (equivalent to U4316, C4317 and C4331, C4332 in 28 S rRNA), or substitution of guanosine for U2653 (designed to form a Watson-Crick G2653.C2667 pair), reduced cleavage by sarcin whereas depurination by ricin was slightly increased. An increase in the stability of the mutant oligoribonucleotides may be the basis of the impairment in sarcin action. The tm for the wild-type RNA is 60 degreesC; for the double- deletion mutant U2653Delta/C2667Delta it is 65 degreesC; and for the U2653G transversion it is 69 degreesC. Expression of a mutant 23 S rRNA gene lacking U2653 and C2667 is lethal and a U2653G transversion mutation impairs growth. The mutant ribosomes are less active in protein synthesis than the wild-type and ribosomes with the U2653G mutation are resistant to sarcin. The binding of EF-G to oligoribonucleotides with a U2653/C2667 double deletion is reduced and an effect on the affinity of the factor for the sarcin/ricin domain may account in part for the decrease in ribosome efficiency. The results stress the potential importance in rRNA structure and function of non- conserved nucleotides, and suggest that the sarcin/ricin domain in ribosomes requires a region of structural flexibility for optimal efficiency}, keywords = {0,analysis,animal,Bacterial,Base Sequence,BINDING,Binding Sites,Catalysis,CLEAVAGE,efficiency,elongation,Endoribonucleases,Escherichia coli,ESCHERICHIA-COLI,expression,gene,genetics,Guanosine,In Vitro,IN-VITRO,IN-VIVO,La,metabolism,Molecular Sequence Data,Mutagenesis,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Nucleotides,Oligoribonucleotides,Peptide Elongation Factor G,Peptide Elongation Factors,Phenotype,Plasmids,protein,protein synthesis,PROTEIN-SYNTHESIS,rat,Rats,RIBOSOMAL-RNA,ribosome,Ribosomes,Ricin,Rna,RNABacterial,RNARibosomal23S,RNARibosomal28S,rRNA,rRNA Operon,stability,Structural,structure,supportu.s.gov’tp.h.s.,toxin,translation,TranslationGenetic,translocation,tRNA} } % == BibTeX quality report for macbethCharacterizationVitroVivo1999a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{macuraElucidationCrossrelaxationLiquids2004a, title = {Elucidation of Cross-Relaxation in Liquids by Two-Dimensional {{N}}.{{M}}.{{R}}. Spectroscopy.}, author = {Macura, S. and Ernst, R.R.}, year = 2004, journal = {Mol.Phys.}, volume = {41}, pages = {95–117}, doi = {10.1080/00268978000102601}, keywords = {2-D NMR,NMR,nosource,SPECTROSCOPY} } % == BibTeX quality report for macuraElucidationCrossrelaxationLiquids2004a: % ? Possibly abbreviated journal title Mol.Phys.

@article{madenRibosomecatalyzedPeptidylTransfer1968a, title = {Ribosome-Catalyzed Peptidyl Transfer. {{Effects}} of Cations and {{pH}} Value}, author = {Maden, B.E. and Monro, R.E.}, year = 1968, month = nov, journal = {Eur.J.Biochem.}, volume = {6}, number = {2}, pages = {309–316}, doi = {10.1111/j.1432-1033.1968.tb00450.x}, keywords = {69059790,Ammonium Compounds,biosynthesis,Calcium,Carbon Isotopes,Cations,Cesium,Escherichia coli,Glycine,Hydrogen-Ion Concentration,Lithium,Magnesium,Manganese,metabolism,Metals,Methionine,nosource,Peptides,peptidyl-transfer,pharmacology,Phenylalanine,Potassium,Proteins,Puromycin,Ribosomes,Rubidium,Sodium,Sulfur Isotopes} } % == BibTeX quality report for madenRibosomecatalyzedPeptidylTransfer1968a: % ? Possibly abbreviated journal title Eur.J.Biochem.

@article{madenRibosomecatalysedPeptidylTransfer1968, title = {Ribosome-Catalysed Peptidyl Transfer: The Polyphenylalanine System}, author = {Maden, B.E. and Traut, R.R. and Monro, R.E.}, year = 1968, month = jul, journal = {J.Mol.Biol.}, volume = {35}, number = {2}, pages = {333–345}, doi = {10.1016/S0022-2836(68)80028-2}, keywords = {72026764,analysis,biosynthesis,Carbon Isotopes,Cresols,Formaldehyde,Guanosine Triphosphate,Heat,Kinetics,nosource,Peptides,peptidyl-transfer,Phenylalanine,Puromycin,Ribosomes,RNABacterial,RNATransfer,Sulfates,SYSTEM,Time Factors,Urea} } % == BibTeX quality report for madenRibosomecatalysedPeptidylTransfer1968: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{madenNumerousModifiedNucleotides1990, title = {The Numerous Modified Nucleotides in Eukaryotic Ribosomal {{RNA}}}, author = {Maden, B.E.}, year = 1990, journal = {Progress in nucleic acid research and molecular biology}, volume = {39}, pages = {241–303}, publisher = {Elsevier}, doi = {10.1016/S0079-6603(08)60629-7}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0079660308606297}, keywords = {0,analysis,Animals,Base Sequence,Biochemistry,chemistry,genetics,Humans,La,metabolism,Methylation,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleotides,Review,ribosomal RNA,RIBOSOMAL-RNA,Rna,RNARibosomal,Support} } % == BibTeX quality report for madenNumerousModifiedNucleotides1990: % ? unused Journal abbr (“Prog.Nucleic Acid Res.Mol.Biol.”)

@article{madenHistoricalReviewPeptidyl2003, title = {Historical Review: {{Peptidyl}} Transfer, the {{Monro}} Era}, author = {Maden, B.E.}, year = 2003, month = nov, journal = {Trends in biochemical sciences}, volume = {28}, number = {11}, pages = {619–624}, publisher = {Elsevier}, doi = {10.1016/j.tibs.2003.09.008}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000403002512}, abstract = {The peptide bond-forming reaction of protein synthesis, the peptidyl transfer reaction, takes place in a region of the 50S ribosomal subunit that consists entirely of RNA, the peptidyl transferase centre. Basic to the present knowledge of peptidyl transfer was the discovery by Robin Monro and his colleagues in the 1960s that the reaction is catalyzed by the 50S ribosome. The Monro experiments, and the historical context in which they were conceived, are described in this personal recollection. Monro’s ‘fragment reaction’, the ribosome catalyzed reaction of a fragment of formylmethionyl-tRNA with puromycin, remains in use in work on peptidyl transfer}, keywords = {DISCOVERY,fragment reaction,La,nosource,peptidyl transferase,peptidyl-transfer,PEPTIDYL-TRANSFERASE,protein,protein synthesis,PROTEIN-SYNTHESIS,Puromycin,REGION,Review,RIBOSOMAL-SUBUNIT,ribosome,Rna,SUBUNIT} } % == BibTeX quality report for madenHistoricalReviewPeptidyl2003: % ? unused Journal abbr (“Trends Biochem.Sci.”)

@article{magerControlRibosomalProtein1988a, title = {Control of Ribosomal Protein Gene Expression.}, author = {Mager, W.H.}, year = 1988, journal = {Biochimica et biophysica acta}, volume = {949}, pages = {1–15}, doi = {10.1016/0167-4781(88)90048-6}, url = {http://cat.inist.fr/?aModele=afficheN&cpsidt=7810785}, keywords = {expression,gene,Gene Expression,GENE-EXPRESSION,nosource,protein,ribosome} } % == BibTeX quality report for magerControlRibosomalProtein1988a: % ? unused Journal abbr (“Biochim.Biophys.Acta”)

@article{magerMultifunctionalDNAbindingProteins1990, title = {Multifunctional {{DNA-binding}} Proteins Mediate Concerted Transcription Activation of Yeast Ribosomal Protein Genes}, author = {Mager, W.H. and Planta, R.J.}, year = 1990, journal = {Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression}, volume = {1050}, number = {1-3}, pages = {351–355}, publisher = {Elsevier}, doi = {10.1016/0167-4781(90)90193-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/0167478190901936}, abstract = {Transcription activation of ribosomal protein genes (rp genes) in yeast is mediated through two different abundant transacting proteins, RAP1 and ABF1. These factors are multifunctional proteins playing a part in diverse cellular processes, all related to cellular growth}, keywords = {91002672,activation,Amino Acid Sequence,Base Sequence,DNA-Binding Proteins,gene,Gene Expression RegulationFungal,Genes,GenesStructuralFungal,genetics,growth & development,metabolism,Molecular Sequence Data,nosource,Promoter Regions (Genetics),protein,Proteins,Ribosomal Proteins,Saccharomyces cerevisiae,transcription,Transcription Factors,TranscriptionGenetic,yeast} } % == BibTeX quality report for magerMultifunctionalDNAbindingProteins1990: % ? unused Journal abbr (“Biochim.Biophys.Acta”)

@article{magerNewNomenclatureCytoplasmic1997, title = {A New Nomenclature for the Cytoplasmic Ribosomal Proteins of {{Saccharomyces}} Cerevisiae}, author = {Mager, W.H. and Planta, R.J. and Ballesta, J.G. and Lee, J.C. and Mizuta, K. and Suzuki, K. and Warner, J.R. and Woolford, J.}, year = 1997, journal = {Nucleic.Acids.Res.}, volume = {25}, number = {24}, pages = {4872–4875}, doi = {10.1093/nar/25.24.4872}, keywords = {analysis,chemistry,classification,Fungal Proteins,gene,Genes,Genome,nomenclature,nosource,protein,Proteins,Ribosomal Proteins,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,yeast} } % == BibTeX quality report for magerNewNomenclatureCytoplasmic1997: % ? Possibly abbreviated journal title Nucleic.Acids.Res.

@article{magorTranscriptionalEnhancersEvolution1999, title = {Transcriptional Enhancers and the Evolution of the {{IgH}} Locus}, author = {Magor, B.G. and Ross, D.A. and Pilstrom, L. and Warr, G.W.}, year = 1999, month = jan, journal = {Immunology today}, volume = {20}, number = {1}, pages = {13–17}, publisher = {Elsevier}, doi = {10.1016/S0167-5699(98)01380-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0167569998013802}, keywords = {3’ Untranslated Regions,99181065,animal,biosynthesis,DNA Nucleotidyltransferases,enhancer elements (genetics),Evolution,EvolutionMolecular,Fishes,Gene Expression Regulation,Gene RearrangementB-Lymphocyte,GenesImmunoglobulin,genetics,human,Immunoglobulin Class Switching,ImmunoglobulinsHeavy-Chain,ImmunoglobulinsJ-Chain,immunology,nosource,Phylogeny,physiology,Rats,RecombinationGenetic,Review,RNAMessenger,supportu.s.gov’tnon-p.h.s.,transcription,TranscriptionGenetic,Vertebrates} } % == BibTeX quality report for magorTranscriptionalEnhancersEvolution1999: % ? unused Journal abbr (“Immunol.Today”)

@article{maguireProteinComponentHeart2005, title = {A Protein Component at the Heart of an {{RNA}} Machine: The Importance of Protein L27 for the Function of the Bacterial Ribosome}, author = {Maguire, B.A. and Beniaminov, A.D. and Ramu, H. and Mankin, A.S. and Zimmermann, R.A.}, year = 2005, month = nov, journal = {Mol Cell}, volume = {20}, number = {3}, pages = {427–435}, doi = {10.1016/j.molcel.2005.09.009}, url = {PM:16285924}, abstract = {Deletion of the gene for protein L27 from the E. coli chromosome results in severe defects in cell growth. This deficiency is corrected by the expression of wild-type (wt) protein L27 from a plasmid. Examination of strains expressing L27 variants truncated at the N terminus reveals that the absence of as few as three amino acids leads to a decrease in growth rate, an impairment in peptidyl transferase activity, and a sharp decline in the labeling of L27 from the 3’ end of a photoreactive tRNA at the ribosomal P site. These findings suggest that the flexible N-terminal sequence of L27, which protrudes onto the interface of the bacterial 50S subunit, can reach the peptidyl transferase active site and contribute to its function, possibly by helping to correctly position tRNA substrates at the catalytic site}, keywords = {0,3,ACID,ACIDS,ACTIVE-SITE,Amino Acids,AMINO-ACID,AMINO-ACIDS,Bacterial,Binding Sites,Biochemistry,BIOLOGY,ChromosomesBacterial,COMPONENT,deficiency,E,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,expression,gene,Gene Deletion,genetics,GROWTH,heart,interface,La,metabolism,Molecular Biology,nosource,P SITE,P-SITE,peptidyl transferase,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,physiology,PLASMID,POSITION,protein,Protein Biosynthesis,Proteins,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Rna,RNABacterial,RNATransfer,sequence,SITE,SUBUNIT,Support,Transferases,tRNA,WILD-TYPE} }

@article{maguireNovelChromatographySystem2008, title = {A Novel Chromatography System to Isolate Active Ribosomes from Pathogenic Bacteria}, author = {Maguire, B.A. and Wondrack, L.M. and Contillo, L.G. and Xu, Z.}, year = 2008, month = jan, journal = {RNA.}, volume = {14}, number = {1}, pages = {188–195}, doi = {10.1261/rna.692408}, url = {PM:17998293}, abstract = {We have developed a novel chromatography for the rapid isolation of active ribosomes from bacteria without the use of harsh conditions or lengthy procedures that damage ribosomes. Ribosomes interact with an alkyl linker attached to the resin, apparently through their RNA component. Examples are given with ribosomes from Escherichia coli, Deinococcus radiodurans, and with clinical isolates of Streptococcus pneumoniae and methicillin-resistant Staphylococcus aureus (MRSA). The ribosomes obtained by this method are unusually intact, so that highly active ribosomes can now be isolated from the clinical isolates, enabling significantly improved in vitro functional assays that will greatly assist the discovery and development of new ribosomally targeted antibiotics}, keywords = {0,antibiotic,antibiotics,assays,Bacteria,Bacteria: pathogenicity,Bacteria: ultrastructure,Bacterial,Bacterial: chemistry,Bacterial: isolation & purification,chemistry,chromatography,Chromatography,ChromatographyLiquid,COMPONENT,Deinococcus,development,DISCOVERY,Escherichia coli,ESCHERICHIA-COLI,In Vitro,IN-VITRO,isolation & purification,La,Liquid,Liquid: methods,Mass Spectrometry,Methods,MRSA,nosource,pathogenicity,pathogens,purification,ribosome,ribosomes,Ribosomes,Rna,RNA,RNABacterial,Staphylococcus aureus,STAPHYLOCOCCUS-AUREUS,SYSTEM,ultrastructure} } % == BibTeX quality report for maguireNovelChromatographySystem2008: % ? Possibly abbreviated journal title RNA.

@article{maherDNATriplehelixFormation1992, title = {{{DNA}} Triple-Helix Formation: An Approach to Artificial Gene Repressors?}, author = {Maher, L.J.}, year = 1992, month = dec, journal = {Bioessays}, volume = {14}, number = {12}, pages = {807–815}, publisher = {Wiley Online Library}, doi = {10.1002/bies.950141204}, url = {http://onlinelibrary.wiley.com/doi/10.1002/bies.950141204/abstract PM:1365896}, abstract = {Certain sequences of double-helical DNA can be recognized and tightly bound by oligonucleotides. The effects of such triple-helical structures on DNA binding proteins have been studied. Stabilities of DNA triple-helices at or near physiological conditions are sufficient to inhibit DNA binding proteins directed to overlapping sites. Such proteins include restriction endonucleases, methylases, transcription factors, and RNA polymerases. These and other results suggest that oligonucleotide-directed triple-helix formation could provide the basis for designing artificial gene repressors. The general question of whether biological systems employ RNA molecules for recognition and regulation of double-helical DNA is discussed}, keywords = {0,Base Sequence,BINDING,BINDING-PROTEIN,cancer,chemical synthesis,chemistry,disease,Dna,DNA Restriction-Modification Enzymes,DNA-Binding Proteins,Drug Design,Endonucleases,enzyme,gene,La,metabolism,Methylation,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Oligonucleotides,polymerase,protein,Protein Binding,Proteins,regulation,Repressor Proteins,Review,Rna,sequence,stability,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,transcription,TRANSCRIPTION FACTOR,Transcription Factors,TranscriptionGenetic,ultrastructure} }

@article{maiaGeneExpressionViral1996, title = {Gene Expression from Viral {{RNA}} Genomes}, author = {Maia, I.G. and Seron, K. and Haenni, A.L. and Bernardi, F.}, year = 1996, month = oct, journal = {Plant molecular biology}, volume = {32}, number = {1-2}, pages = {367–391}, publisher = {Springer}, doi = {10.1007/BF00039391}, url = {http://www.springerlink.com/index/J0V0M931UT242344.pdf}, abstract = {This review is centered on the major strategies used by plant RNA viruses to produce the proteins required for virus multiplication. The strategies at the level of transcription presented here are synthesis of mRNA or subgenomic RNAs from viral RNA templates, and ‘cap-snatching’. At the level of translation, several strategies have been evolved by viruses at the steps of initiation, elongation and termination. At the initiation step, the classical scanning mode is the most frequent strategy employed by viruses; however in a vast number of cases, leaky scanning of the initiation complex allows expression of more than one protein from the same RNA sequence. During elongation, frameshift allows the formation of two proteins differing in their carboxy terminus. At the termination step, suppression of termination produces a protein with an elongated carboxy terminus. The last strategy that will be described is co- and/or post-translational cleavage of a polyprotein precursor by virally encoded proteinases. Most (+)-stranded RNA viruses utilize a combination of various strategies}, keywords = {0,CLEAVAGE,COMPLEX,COMPLEXES,elongation,expression,frameshift,gene,Gene Expression,Gene Expression RegulationViral,GENE-EXPRESSION,genetics,Genome,GenomeViral,initiation,La,mRNA,nosource,Peptide Chain ElongationTranslational,Plant Viruses,POLYPROTEIN,PRECURSOR,protein,Protein Biosynthesis,Protein ProcessingPost-Translational,Proteins,Research SupportNon-U.S.Gov’t,Review,Rna,RNA Viruses,RnaViral,scanning,sequence,SUBGENOMIC RNAS,suppression,TEMPLATE,Templates,termination,Terminator Regions (Genetics),transcription,translation,VIRAL-RNA,virus,Viruses} } % == BibTeX quality report for maiaGeneExpressionViral1996: % ? unused Journal abbr (“Plant Mol.Biol.”)

@article{maicasTranslationSaccharomycesCerevisiaeTcm11990, title = {Translation of the {{Saccharomyces-Cerevisiae Tcm1 Gene}} in the {{Absence}} of {{A}} 5’-{{Untranslated Leader}}}, author = {Maicas, E. and Shago, M. and Friesen, J.D.}, year = 1990, month = oct, journal = {Nucleic Acids Research}, volume = {18}, number = {19}, pages = {5823–5828}, doi = {10.1093/nar/18.19.5823}, url = {ISI:A1990ED64500032}, keywords = {E,gene,nosource,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,TCM1,translation} } % == BibTeX quality report for maicasTranslationSaccharomycesCerevisiaeTcm11990: % ? Title looks like it was stored in title-case in Zotero

@article{makelainenFactorsAffectingTranslation2005, title = {Factors Affecting Translation at the Programmed -1 Ribosomal Frameshifting Site of {{Cocksfoot}} Mottle Virus {{RNA}} in Vivo.}, author = {Makelainen, K. and Makinen, K.}, year = 2005, month = jan, journal = {Nucleic acids research}, volume = {33}, number = {7}, pages = {2239–2247}, issn = {1362-4962}, doi = {10.1093/nar/gki521}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1083427&tool=pmcentrez&rendertype=abstract PM:15843686}, abstract = {The ratio between proteins P27 and replicase of Cocksfoot mottle virus (CfMV) is regulated via a -1 programmed ribosomal frameshift (-1 PRF). A minimal frameshift signal with a slippery U UUA AAC heptamer and a downstream stem-loop structure was inserted into a dual reporter vector and directed -1 PRF with an efficiency of 14.4 +/- 1.9% in yeast and 2.4 +/- 0.7% in bacteria. P27-encoding CfMV sequence flanking the minimal frameshift signal caused approximately 2-fold increase in the -1 PRF efficiencies both in yeast and in bacteria. In addition to the expected fusion proteins, termination products ending putatively at the frameshift site were found in yeast cells. We propose that the amount of premature translation termination from control mRNAs played a role in determining the calculated -1PRF efficiency. Co-expression of CfMV P27 with the dual reporter vector containing the minimal frameshift signal reduced the production of the downstream reporter, whereas replicase co-expression had no pronounced effect. This finding allows us to propose that CfMV protein P27 may influence translation at the frameshift site but the mechanism needs to be elucidated.}, pmid = {15843686}, keywords = {Bacteria,BIOLOGY,CELLS,DOWNSTREAM,efficiency,Escherichia coli,Escherichia coli: genetics,frameshift,Frameshifting,FUSION PROTEIN,Gene Expression Regulation,Genes,IN-VIVO,La,MECHANISM,mRNA,nosource,Plant Viruses,Plant Viruses: genetics,PRODUCT,PRODUCTS,protein,Proteins,REPLICASE,Reporter,Ribosomal,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,Rna,RNA,RNA Replicase,RNA Replicase: biosynthesis,RNA Replicase: genetics,RNA Viruses,RNA Viruses: genetics,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,sequence,SIGNAL,SITE,STEM-LOOP,structure,termination,translation,TRANSLATION TERMINATION,vector,Viral,Viral Proteins,Viral Proteins: biosynthesis,Viral Proteins: genetics,Viral Proteins: metabolism,Viral: chemistry,virus,VIRUS-RNA,yeast,YEAST-CELLS} } % == BibTeX quality report for makelainenFactorsAffectingTranslation2005: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{malacGlucoseinducedMDRPump2005, title = {Glucose-Induced {{MDR}} Pump Resynthesis in Respiring Yeast Cells Depends on Nutrient Level}, author = {Malac, J. and Sigler, K. and Gaskova, D.}, year = 2005, month = nov, journal = {Biochemical and biophysical research communications}, volume = {337}, number = {1}, pages = {138–141}, publisher = {Elsevier}, doi = {10.1016/j.bbrc.2005.09.024}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006291X05020292 PM:16176804}, abstract = {Glucose addition to a stationary culture of wild-type Saccharomyces cerevisiae BY4742 cells with zero activity of MDR pumps resuspended in a fresh medium causes pump resynthesis (measured as pump-effected diS-C3(3) efflux). In a stationary culture in its original growth medium, this glucose-induced pump resynthesis fails to occur due to depletion of essential nutrients or to extracellular metabolites produced by cells during growth. Direct pump inactivation by metabolites is excluded since exponential cells with high MDR pump activity cultured in a medium with high concentration of extracellular metabolites retain this activity for at least 2 h. The metabolites also do not affect pump synthesis on the level of gene expression as addition of concentrated growth medium or an amino acid mixture to stationary cells in spent growth medium restores glucose-induced pump synthesis. The block of MDR pump synthesis is therefore due to the lack of essential nutrients in spent medium}, keywords = {0,ACID,AMINO-ACID,among other things,biosynthesis,CELLS,CEREVISIAE,chemical stressors,Culture Media,drug effects,expression,fluorimetric assay,gene,Gene Expression,GENE-EXPRESSION,Glucose,GROWTH,growth medium composition,in protecting cells against,in saccharomyces cerevisiae,La,mdr pumps,mdr transporters are important,media,membrane proteins in-,metabolism,nosource,P-Glycoproteins,pharmacology,protein,Proteins,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Support,the best-,volved,WILD-TYPE,yeast,YEAST-CELLS} } % == BibTeX quality report for malacGlucoseinducedMDRPump2005: % ? unused Journal abbr (“Biochem.Biophys.Res.Commun.”)

@article{malamyFrameshiftMutationJunction1985, title = {A Frameshift Mutation at the Junction of an {{IS1}} Insertion within {{lacZ}} Restores [Beta]-Galactosidase Activity via Formation of an Active {{lacZ-IS1}} Fusion Protein{\(\bullet\)} 1}, author = {Malamy, M. H. and Rahaim, P. T. and Hoffman, C. S. and Baghdoyan, D. and O’Connor, M. B. and Miller, J. F.}, year = 1985, month = feb, journal = {Journal of molecular biology}, volume = {181}, number = {4}, pages = {551–555}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0022283685904279}, abstract = {The insertion of IS1 elements into lacZ results in the loss of beta-galactosidase activity, and such insertions exert a severe polar effect on the expression of the distal genes of the operon. In addition to these properties, the mutation lacZ::IS1-MS319 has the unique property of reversion to Lac+ (ts) spontaneously or after treatment with the frameshift mutagen ICR-191; such revertants retain the IS1 element. We have determined that the site of integration of IS1 into lacZ is at position 4338, 18 nucleotides from the end of the sequence encoding the C-terminus of beta-galactosidase. Reversion to Lac+ promoted by ICR-191 results from the loss of a G residue from a GGG sequence located at the junction of lacZ and IS1. As a result an active, but temperature-sensitive, lacZ-IS1 fusion protein is formed containing six amino acids derived from IS1 which replace six amino acids encoded by lacZ. The IS1 element in MS319 is a new member of the iso-IS1 family, which we designate IS1T}, keywords = {85210885,Amino Acids,Base Sequence,beta-Galactosidase,DNA Transposable Elements,DNABacterial,ELEMENTS,enzymology,Escherichia coli,expression,frameshift,Frameshift Mutation,Galactosidases,gene,Genes,genetics,Lac Operon,metabolism,Mutation,nosource,Nucleotides,Operon,Plasmids,protein,sequence} }

@article{mamnunExpressionRegulationYeast2004, title = {Expression Regulation of the Yeast {{PDR5 ATP-binding}} Cassette ({{ABC}}) Transporter Suggests a Role in Cellular Detoxification during the Exponential Growth Phase}, author = {Mamnun, Y.M. and Schuller, C. and Kuchler, K.}, year = 2004, month = feb, journal = {FEBS letters}, volume = {559}, number = {1-3}, pages = {111–117}, publisher = {Elsevier}, doi = {10.1016/S0014-5793(04)00046-8}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0014579304000468}, abstract = {The yeast ATP-binding cassette transporter Pdr5p mediates pleiotropic drug resistance (PDR) by effluxing a variety of xenobiotics. Immunoblotting demonstrates that Pdr5p levels are high in the logarithmic growth phase, while its levels decrease sharply when cells exit exponential growth. Here, we show that PDR5 promoter activity is dramatically reduced when cells stop growing due to a limitation of glucose or nitrogen or when they approach stationary phase. Interestingly, Pdr3p, a major transcriptional regulator of PDR5, shows the same regulatory pattern. Feeding glucose to starved cells rapidly re-induces both PDR5 and PDR3 transcription. Importantly, diminished Pdr5p levels, as present after starvation, are rapidly restored in response to xenobiotic challenges that activate the transcription factors Pdr1p and Pdr3p. Our data indicate a role for yeast Pdr5p in cellular detoxification during exponential growth}, keywords = {0,ATP-Binding Cassette Transporters,Biochemistry,biosynthesis,CELLS,CEREVISIAE,cytology,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,drug effects,Drug Resistance,expression,Gene Expression RegulationFungal,Genetic,genetics,Glucose,GROWTH,Immunoblotting,La,Metabolic DetoxicationDrug,MOLECULAR-GENETICS,Nitrogen,nosource,PDR5,pharmacology,physiology,PROMOTER,Promoter RegionsGenetic,protein,Proteins,regulation,RESISTANCE,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,stationary phase,Support,transcription,TRANSCRIPTION FACTOR,Transcription Factors,TranscriptionGenetic,yeast} } % == BibTeX quality report for mamnunExpressionRegulationYeast2004: % ? unused Journal abbr (“FEBS Lett.”)

@article{manchcitronExpressionPrevotellaLoescheii1994, title = {Expression of the {{Prevotella}} Loescheii Adhesin Gene ({{plaA}}) Is Mediated by a Programmed Frameshifting Hop.}, author = {Manchcitron, J.N. and London, J.}, year = 1994, month = apr, journal = {Journal of Bacteriology}, volume = {176}, number = {7}, pages = {1944–1948}, publisher = {Am Soc Microbiol}, doi = {10.1128/jb.176.7.1944-1948.1994}, url = {http://jb.asm.org/cgi/content/abstract/176/7/1944 ISI:A1994ND18300018}, abstract = {The 2.4-kb plaA gene, which encodes a Prevotella loescheii galactoside-specific adhesin, contains a programmed frameshifting hop. The frameshift region consists of two UAA termination codons, two repeats of four identical bases between the terminators, and a stem-loop structure that has the potential to form a pseudoknot located downstream from the second UAA. The stem-loop and pseudoknot are features found in a number of retroviruses where frameshifting is a more common occurrence. The terminators, sequence repeats, and secondary structures were identified in both the P. loescheii plaA gene and the mRNA transcript. An in-frame fusion of the entire plaA frameshift region between codons 9 and 10 of the lacZ gene permitted relatively efficient expression (4 to 25% of that of the control) of beta-galactosidase in Escherichia coli}, keywords = {BASE,BASES,beta-Galactosidase,cloning,Codon,CODONS,DOWNSTREAM,ENCODES,ENDOGLUCANASE GENE,Escherichia coli,ESCHERICHIA-COLI,expression,FORM,frameshift,Frameshifting,gene,MESSENGER-RNA,mitochondria,mRNA,nosource,programmed frameshifting,pseudoknot,REGION,SECONDARY STRUCTURE,sequence,STEM-LOOP,structure,termination,TERMINATION CODON,TERMINATION-CODON,TRANSCRIPT,virus,yeast} }

@article{mandeckiPositionLacZX90Mutation1981, title = {Position of the {{lacZX90}} Mutation and Hybridization between Complete and Incomplete Beta-Galactosidase.}, author = {Mandecki, W. and Fowler, A.V. and Zabin, I.}, year = 1981, journal = {Journal of Bacteriology}, volume = {147}, number = {2}, pages = {694–697}, publisher = {Am Soc Microbiol}, doi = {10.1128/jb.147.2.694-697.1981}, url = {http://jb.asm.org/cgi/content/abstract/147/2/694}, abstract = {The position of the termination codon in lacZX90 was determined by isolation of a lac+ revertant. Lysine was found to replace tyrosine at position 1,012 of beta-galactosidase, indicating that X90 protein lacked the carboxyl-terminal 10 residues. A heat- and urea-sensitive hybrid enzyme was formed in vivo when supC, which supplies tyrosine to the position in the polypeptide corresponding to the nonsense codon, was used to suppress lacZX90. This result shows that suppression that adds back the original amino acid may not lead to the production of the wild-type enzyme if the latter is multimeric, because incomplete chains can be incorporated into the oligomer}, keywords = {81264110,Amino Acid Sequence,beta-Galactosidase,Codon,enzyme,enzymology,Escherichia coli,Galactosidases,genetics,Heat,IN-VIVO,Lysine,Mutation,nosource,pharmacology,protein,Protein Hybridization,supportu.s.gov’tp.h.s.,suppression,SuppressionGenetic,termination,Urea} } % == BibTeX quality report for mandeckiPositionLacZX90Mutation1981: % ? unused Journal abbr (“J.Bacteriol.”)

@article{manguesRasActivationExperimental1992a, title = {Ras Activation in Experimental Carcinogenesis.}, author = {Mangues, R. and Pellicer, A.}, year = 1992, journal = {Seminars in Cancer.Biol.}, volume = {3}, pages = {229–239}, keywords = {activation,No DOI found,nosource,ras,Review} } % == BibTeX quality report for manguesRasActivationExperimental1992a: % ? Possibly abbreviated journal title Seminars in Cancer.Biol.

@article{mannConstructionRetrovirusPackaging1983, title = {Construction of a Retrovirus Packaging Mutant and Its Use to Produce Helper-Free Defective Retrovirus.}, author = {Mann, R. and Mulligan, R.C. and Baltimore, D.}, year = 1983, journal = {Cell}, volume = {33}, number = {1}, pages = {153–159}, publisher = {Elsevier}, doi = {10.1016/0092-8674(83)90344-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867483903446}, keywords = {nosource,packaging,psi,retrovirus,virus} }

@article{manskyLowerVivoMutation1995, title = {Lower in Vivo Mutation Rate of Human Immunodeficiency Virus Type 1 than That Predicted from the Fidelity of Purified Reverse Transcriptase}, author = {Mansky, L.M. and Temin, H.M.}, year = 1995, month = aug, journal = {Journal of Virology}, volume = {69}, number = {8}, pages = {5087–5094}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.69.8.5087-5094.1995}, url = {http://jvi.asm.org/cgi/content/abstract/69/8/5087}, keywords = {Cell-Free System,Fidelity,gene,Genetic,HIV,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,IN-VIVO,Mutation,MUTATIONS,nosource,Retroviridae,sequence,SYSTEM,transcription,virus} }

@article{mansouriPokeweedAntiviralProtein2006, title = {Pokeweed Antiviral Protein Depurinates the Sarcin/Ricin Loop of the {{rRNA}} Prior to Binding of Aminoacyl-{{tRNA}} to the Ribosomal {{A-site}}}, author = {Mansouri, S. and Nourollahzadeh, E. and Hudak, K.A.}, year = 2006, journal = {RNA}, volume = {12}, number = {9}, pages = {In press}, publisher = {Cold Spring Harbor Lab}, doi = {10.1261/rna.70306}, url = {http://rnajournal.cshlp.org/content/12/9/1683.short}, keywords = {A SITE,a-site,A-SITE,aminoacyl-,antiviral,BINDING,LOOP,nosource,pokeweed antiviral protein,Pokeweed antiviral protein,protein,ribosome inactivating protein,rRNA,translation elongation,translocation} }

@article{manuilovNewPhotoreactiveTRNA2007, title = {New Photoreactive {{tRNA}} Derivatives for Probing the Peptidyl Transferase Center of the Ribosome}, author = {Manuilov, A.V. and Hixson, S.S. and Zimmermann, R.A.}, year = 2007, month = may, journal = {RNA.}, volume = {13}, number = {5}, pages = {793–800}, publisher = {Cold Spring Harbor Lab}, doi = {10.1261/rna.425907}, url = {http://rnajournal.cshlp.org/content/13/5/793.short}, abstract = {Three new photoreactive tRNA derivatives have been synthesized for use as probes of the peptidyl transferase center of the ribosome. In two of these derivatives, the 3’ adenosine of yeast tRNA(Phe) has been replaced by either 2-azidodeoxyadenosine or 2-azido-2’-O-methyl adenosine, while in a third the 3’-terminal 2-azidodeoxyadenosine of the tRNA is joined to puromycin via a phosphoramidate linkage to generate a photoreactive transition-state analog. All three derivatives bind to the P site of 70S ribosomes with affinities similar to that of unmodified tRNA(Phe) and can be cross-linked to components of the 50S ribosomal subunit by irradiation with near-UV light. Characteristic differences in the cross-linking patterns suggest that these tRNA derivatives can be used to follow subtle changes in the position of the tRNA relative to the components of the peptidyl transferase center}, keywords = {0,3,70S RIBOSOME,Adenosine,Biochemistry,BIOLOGY,chemistry,COMPONENT,COMPONENTS,CROSS-LINKING,Cross-Linking Reagents,CROSSLINKING,Deoxyadenosines,derivatives,Escherichia coli,genetics,La,metabolism,Methods,Molecular Biology,nosource,P SITE,P-SITE,PATTERNS,peptidyl transferase,peptidyl transferase center,PEPTIDYL TRANSFERASE CENTER,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,Photochemistry,photoreactive trna probes,POSITION,Puromycin,RIBOSOMAL-SUBUNIT,ribosome,ribosomes,Ribosomes,Rna,RNATransfer,SITE,SUBUNIT,Support,TRANSFERASE CENTER,Transferases,tRNA,ultraviolet rays,yeast} } % == BibTeX quality report for manuilovNewPhotoreactiveTRNA2007: % ? Possibly abbreviated journal title RNA.

@article{manuvakhovaAminoglycosideAntibioticsMediate2000, title = {Aminoglycoside Antibiotics Mediate Context-Dependent Suppression of Termination Codons in a Mammalian Translation System.}, author = {Manuvakhova, M. and Keeling, K. and Bedwell, D.M.}, year = 2000, month = jul, journal = {RNA}, volume = {6}, number = {7}, pages = {1044–1055}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838200000716}, url = {http://rnajournal.cshlp.org/content/6/7/1044.short}, abstract = {The translation machinery recognizes codons that enter the ribosomal A site with remarkable accuracy to ensure that polypeptide synthesis proceeds with a minimum of errors. When a termination codon enters the A site of a eukaryotic ribosome, it is recognized by the release factor eRF1. It has been suggested that the recognition of translation termination signals in these organisms is not limited to a simple trinucleotide codon, but is instead recognized by an extended tetranucleotide termination signal comprised of the stop codon and the first nucleotide that follows. Interestingly, pharmacological agents such as aminoglycoside antibiotics can reduce the efficiency of translation termination by a mechanism that alters this ribosomal proofreading process. This leads to the misincorporation of an amino acid through the pairing of a near-cognate aminoacyl tRNA with the stop codon. To determine whether the sequence context surrounding a stop codon can influence aminoglycoside-mediated suppression of translation termination signals, we developed a series of readthrough constructs that contained different tetranucleotide termination signals, as well as differences in the three bases upstream and downstream of the stop codon. Our results demonstrate that the sequences surrounding a stop codon can play an important role in determining its susceptibility to suppression by aminoglycosides. Furthermore, these distal sequences were found to influence the level of suppression in remarkably distinct ways. These results suggest that the mRNA context influences the suppression of stop codons in response to subtle differences in the conformation of the ribosomal decoding site that result from aminoglycoside binding}, keywords = {0,A SITE,A-SITE,accuracy,ACID,AMINO-ACID,AMINOGLYCOSIDE ANTIBIOTICS,analogs & derivatives,animal,antibiotic,antibiotics,AntibioticsAminoglycoside,BASE,BASES,BINDING,chemistry,Codon,CODONS,CodonTerminator,CONFORMATION,decoding,Dose-Response RelationshipDrug,DOWNSTREAM,drug effects,efficiency,ERRORS,Escherichia coli,EUKARYOTIC RIBOSOME,GenesReporter,genetics,Gentamicins,human,Hygromycin B,Kanamycin,La,MECHANISM,metabolism,microbiology,mRNA,Neomycin,nosource,Paromomycin,pharmacology,PLASMID,Plasmids,POLYPEPTIDE,proofreading,Rabbits,readthrough,RECOGNITION,RELEASE,release factor,Reticulocytes,ribosome,Ribosomes,Rna,RNAMessenger,sequence,SEQUENCES,SERIES,SIGNAL,Sisomicin,SITE,STOP CODON,Streptomycin,suppression,SYSTEM,termination,TERMINATION CODON,TERMINATION-CODON,Tobramycin,translation,TRANSLATION TERMINATION,TranslationGenetic,tRNA,UPSTREAM} }

@article{maquatNAStyEffectsFibrillin2002, title = {{{NASty}} Effects on Fibrillin Pre-{{mRNA}} Splicing: Another Case of {{ESE}} Does It, but Proposals for Translation-Dependent Splice Site Choice Live On}, author = {Maquat, L.E.}, year = 2002, month = jul, journal = {Genes & Development}, volume = {16}, number = {14}, pages = {1743–1753}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.1014502}, url = {http://genesdev.cshlp.org/content/16/14/1743.short}, keywords = {EXON,fibrillin,HUMAN GENES,MAMMALIAN-CELLS,MESSENGER-RNA,MUTATIONS,nonsense-mediated decay,nosource,OPEN READING FRAME,PREMATURE TERMINATION CODON,SELECTION,SITE,splicing,transcription} }

@article{maquatNonsensemediatedMRNADecay2004, title = {Nonsense-Mediated {{mRNA}} Decay: Splicing, Translation and {{mRNP}} Dynamics}, shorttitle = {Nonsense-{{Mediated mRNA Decay}}}, author = {Maquat, L.E.}, year = 2004, month = feb, journal = {Nature Reviews Molecular Cell Biology}, volume = {5}, number = {February}, pages = {89–99}, publisher = {Nature Publishing Group}, issn = {1471-0072}, doi = {10.1038/nrm1310}, url = {http://www.nature.com/nrm/journal/v5/n2/abs/nrm1310.html http://www.ncbi.nlm.nih.gov/pubmed/15040442}, abstract = {Studies of nonsense-mediated mRNA decay in mammalian cells have proffered unforeseen insights into changes in mRNA-protein interactions throughout the lifetime of an mRNA. Remarkably, mRNA acquires a complex of proteins at each exon-exon junction during pre-mRNA splicing that influences the subsequent steps of mRNA translation and nonsense-mediated mRNA decay. Complex-loaded mRNA is thought to undergo a pioneer round of translation when still bound by cap-binding proteins CBP80 and CBP20 and poly(A)-binding protein 2. The acquisition and loss of mRNA-associated proteins accompanies the transition from the pioneer round to subsequent rounds of translation, and from translational competence to substrate for nonsense-mediated mRNA decay}, pmid = {15040442}, keywords = {0,Animals,Cap,Cap binding,CELLS,Codon,Codon-Nonsense,CodonNonsense,COMPLEX,COMPLEXES,DECAY,DYNAMICS,Exons,Fungal Proteins,Fungal Proteins: metabolism,Genetic,La,MAMMALIAN-CELLS,Messenger,Messenger: metabolism,metabolism,Models,Models-Genetic,ModelsGenetic,mRNA,mRNA decay,Nonsense,NONSENSE,nonsense-mediated mRNA decay,nosource,POLY(A)-BINDING PROTEIN,PRECURSOR,protein,Protein Biosynthesis,Proteins,Review,RIBONUCLEOPROTEIN,Ribonucleoproteins,Ribonucleoproteins: metabolism,Rna,Rna Caps,RNA Precursors,RNA Precursors: metabolism,RNA Splicing,RNA-Messenger,RNAMessenger,splicing,support-u.s.gov’t-p.h.s.,supportu.s.gov’tp.h.s.,translation,Translation-Genetic,TranslationGenetic} } % == BibTeX quality report for maquatNonsensemediatedMRNADecay2004: % ? unused Journal abbr (“Nat.Rev.Mol.Cell Biol.”) % ? unused Library catalog (“CrossRef”)

@article{marckTRNomicsAnalysisTRNA2002, title = {{{tRNomics}}: Analysis of {{tRNA}} Genes from 50 Genomes of {{Eukarya}}, {{Archaea}}, and {{Bacteria}} Reveals Anticodon-Sparing Strategies and Domain-Specific Features.}, author = {Marck, C. and Grosjean, H.}, year = 2002, month = oct, journal = {RNA}, volume = {8}, number = {10}, pages = {1189–1232}, publisher = {Cold Spring Harbor Laboratory Press}, doi = {10.1017/S1355838202022021}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370332/}, abstract = {From 50 genomes of the three domains of life (7 eukarya, 13 archaea, and 30 bacteria), we extracted, analyzed, and compared over 4,000 sequences corresponding to cytoplasmic, nonorganellar tRNAs. For each genome, the complete set of tRNAs required to read the 61 sense codons was identified, which permitted revelation of three major anticodon-sparing strategies. Other features and sequence peculiarities analyzed are the following: (1) fit to the standard cloverleaf structure, (2) characteristic consensus sequences for elongator and initiator tDNAs, (3) frequencies of bases at each sequence position, (4) type and frequencies of conserved 2D and 3D base pairs, (5) anticodon/tDNA usages and anticodon-sparing strategies, (6) identification of the tRNA-Ile with anticodon CAU reading AUA, (7) size of variable arm, (8) occurrence and location of introns, (9) occurrence of 3’-CCA and 5’-extra G encoded at the tDNA level, and (10) distribution of the tRNA genes in genomes and their mode of transcription. Among all tRNA isoacceptors, we found that initiator tDNA-iMet is the most conserved across the three domains, yet domain-specific signatures exist. Also, according to which tRNA feature is considered (5’-extra G encoded in tDNAs-His, AUA codon read by tRNA-Ile with anticodon CAU, presence of intron, absence of “two-out-of-three” reading mode and short V-arm in tDNA-Tyr) Archaea sequester either with Bacteria or Eukarya. No common features between Eukarya and Bacteria not shared with Archaea could be unveiled. Thus, from the tRNomic point of view, Archaea appears as an “intermediate domain” between Eukarya and Bacteria}, keywords = {0,3,Amino Acid Sequence,analysis,Animals,Anticodon,Archaea,Bacteria,BASE,Base Composition,Base Pairing,Base Sequence,BASE-PAIR,BASES,chemistry,Codon,CODONS,Comparative Study,Consensus Sequence,Conserved Sequence,DOMAIN,DOMAINS,Eukaryotic Cells,gene,Genes,genetics,Genome,Humans,IDENTIFICATION,INTRON,Introns,La,LOCATION,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Phylogeny,physiology,POSITION,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tNon-P.H.S.,Rna,RNA ProcessingPost-Transcriptional,RNATransfer,RNATransferIle,sequence,SEQUENCES,structure,transcription,TranscriptionGenetic,tRNA} }

@article{marczinkeHumanAstrovirusRNAdependent1994, title = {The Human Astrovirus {{RNA-dependent RNA}} Polymerase Coding Region Is Expressed by Ribosomal Frameshifting.}, author = {Marczinke, B. and Bloys, A.J. and Brown, T.D. and Willcocks, M.M. and Carter, M.J. and Brierley, I.}, year = 1994, journal = {Journal of virology}, volume = {68}, number = {9}, pages = {5588–5595}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.68.9.5588-5595.1994}, url = {http://jvi.asm.org/cgi/content/abstract/68/9/5588}, abstract = {The genomic RNA of human astrovirus serotype 1 (HAst-1) contains three open reading frames (ORFs), 1a, 1b, and 2. ORF 1b is located downstream of, and overlaps, 1a, and it has been suggested on the basis of sequence analysis that expression of ORF 1b is mediated through -1 ribosomal frameshifting. To examine this possibility, a cDNA fragment containing the 1a-1b overlap region was cloned within a reporter gene and placed under the control of the bacteriophage SP6 promoter in a recombinant plasmid. Synthetic transcripts derived from this plasmid, when translated in the rabbit reticulocyte lysate cell-free system, specified the synthesis of polypeptides whose size and antibody reactivity were consistent with an efficient -1 ribosomal frameshift event at the overlap region. The HAst-1 frameshift signal has two essential components, a heptanucleotide slippery sequence, A6C, and a stem-loop structure in the RNA. The presence of this structure was confirmed by complementary and compensatory mutation analysis and by direct structure probing with single- and double-stranded RNA-specific reagents. The HAst-1 frameshift signal, like that present at the overlap of the gag and pro genes of the retrovirus human T-cell lymphotrophic virus type II, does not involve the formation of an RNA pseudoknot}, keywords = {0,analysis,Animals,Antibodies,antibody,Astrovirus,Base Sequence,Cell-Free System,chemistry,CODING REGION,COMPONENT,COMPONENTS,Dna,DNA Primers,DOWNSTREAM,expression,FRAME,frameshift,Frameshifting,Gag,gene,Gene Expression,Genes,GenesStructuralViral,genetics,genomic,GENOMIC RNA,human,Hydrogen Bonding,In Vitro,La,lysate,metabolism,Molecular Sequence Data,MutagenesisSite-Directed,Mutation,nosource,Nucleic Acid Conformation,OPEN READING FRAME,Open Reading Frames,pathology,PLASMID,polymerase,POLYPEPTIDE,POLYPEPTIDES,PROMOTER,Protein Biosynthesis,pseudoknot,Rabbits,READING FRAME,Reading Frames,REGION,REPLICASE,Research SupportNon-U.S.Gov’t,retrovirus,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,Ribosomes,Rna,RNA PSEUDOKNOT,RNA Replicase,RNA-DEPENDENT RNA POLYMERASE,RNA-POLYMERASE,RNAMessenger,RnaViral,sequence,Sequence Analysis,SEQUENCE-ANALYSIS,SIGNAL,STEM-LOOP,structure,Structure-Activity Relationship,SYSTEM,TRANSCRIPT,virus} } % == BibTeX quality report for marczinkeHumanAstrovirusRNAdependent1994: % ? unused Journal abbr (“J.Virol.”)

@article{marczinkeQbaseAsparaginyltRNADispensable2000a, title = {The {{Q-base}} of Asparaginyl-{{tRNA}} Is Dispensable for Efficient-1 Ribosomal Frameshifting in Eukaryotes}, author = {Marczinke, B. and Hagervall, T. and Brierley, I.}, year = 2000, month = jan, journal = {Journal of Molecular Biology}, volume = {295}, number = {2}, pages = {179–191}, doi = {10.1006/jmbi.1999.3361}, url = {ISI:000084778700005}, abstract = {The frameshift signal of the avian coronavirus infectious bronchitis virus (IBV) contains two cis-acting signals essential for efficient frameshifting, a heptameric slippery sequence (UUUAAAC) and an RNA pseudoknot structure located downstream. The frameshift takes place at the slippery sequence with the two ribosome-bound tRNAs slipping back simultaneously by one nucleotide from the zero phase (U UUA AAC) to the -1 phase (UUU AAA). Asparaginyl-tRNA, which decodes the A-site codon AAC, has the modified base Q at the wobble position of the anticodon (5’ QUU 3’) and it has been speculated that Q may be required for frameshifting. To test this, we measured frameshifting in cos cells that had been passaged in growth medium containing calf serum or horse serum. Growth in horse serum, which contains no free queuine, eliminates Q from the cellular tRNA population upon repeated passage. Over ten cell passages, however, we found no significant difference in frameshift efficiency between the cell types, arguing against a role for Q in frameshifting. We confirmed that the cells cultured in horse serum were devoid of Q by purifying tRNAs and assessing their Q-content by tRNA transglycosylase assays and coupled HPLC-mass spectroscopy. Supplementation of the growth medium of cells grown either on horse serum or calf serum with free queuine had no effect on frameshifting either. These findings were recapitulated in an in vitro system using rabbit reticulocyte lysates that had been largely depleted of endogenous tRNAs and resupplemented with Q-free or Q-containing tRNA populations. Thus Q-base is not required for frameshifting at the IBV signal and some other explanation is required to account for the slipperiness of eukaryotic asparaginyl-tRNA. (C) 2000 Academic Press}, keywords = {3,A SITE,A-SITE,Anticodon,asparaginyl-tRNA,assays,BASE,CELLS,Codon,COLI-DNAX GENE,Cos Cells,DOWNSTREAM,efficiency,ESCHERICHIA-COLI,frameshift,Frameshifting,GROWTH,HELA-CELLS,In Vitro,IN-VITRO,Infectious bronchitis virus,lysate,MAMMALIAN-CELLS,media,MUTATIONAL ANALYSIS,nosource,PERFORMANCE LIQUID-CHROMATOGRAPHY,POSITION,POSTTRANSCRIPTIONALLY MODIFIED NUCLEOSIDES,pseudoknot,PSEUDOKNOT COMPONENT,pseudoknot structure,Q-base,ribosomal frameshifting,Rna,RNA PSEUDOKNOT,sequence,SIGNAL,SPECTROSCOPY,structure,SYSTEM,TRANSFER-RNA,tRNA,tRNA anticodon modification,virus} }

@article{marenchinoRapidEfficientPurification2009a, title = {Rapid and Efficient Purification of {{RNA-binding}} Proteins: Application to {{HIV-1 Rev}}}, author = {Marenchino, M. and Armbruster, D.W. and Hennig, M.}, year = 2009, month = feb, journal = {Protein Expr.Purif.}, volume = {63}, number = {2}, pages = {112–119}, doi = {10.1016/j.pep.2008.09.010}, url = {PM:18852051}, abstract = {Non-specifically bound nucleic acid contaminants are an unwanted feature of recombinant RNA-binding proteins purified from Escherichia coli (E. coli). Removal of these contaminants represents an important step for the proteins’ application in several biological assays and structural studies. The method described in this paper is a one-step protocol which is effective at removing tightly bound nucleic acids from overexpressed tagged HIV-1 Rev in E. coli. We combined affinity chromatography under denaturing conditions with subsequent on-column refolding, to prevent self-association of Rev while removing the nucleic acid contaminants from the end product. We compare this purification method with an established, multi-step protocol involving precipitation with polyethyleneimine (PEI). As our tailored protocol requires only one-step to simultaneously purify tagged proteins and eliminate bound cellular RNA and DNA, it represents a substantial advantage in time, effort, and expense}, keywords = {ACID,ACIDS,assays,Biochemistry,Biological Assay,BIOLOGY,Chromatography,Comparative Study,Dna,E,Escherichia coli,ESCHERICHIA-COLI,Hiv-1,La,Molecular Biology,nosource,Nucleic Acids,Precipitation,PRODUCT,protein,Proteins,purification,REQUIRES,Rna,RNA-Binding Proteins,RNA-BINDING-PROTEIN,Structural,Support} } % == BibTeX quality report for marenchinoRapidEfficientPurification2009a: % ? Possibly abbreviated journal title Protein Expr.Purif.

@article{marmorsteinStructureHistoneAcetyltransferases2001, title = {Structure of Histone Acetyltransferases}, author = {Marmorstein, R.}, year = 2001, journal = {Journal of Molecular Biology}, volume = {311}, number = {3}, pages = {433–444}, doi = {10.1006/jmbi.2001.4859}, url = {ISI:000170509200001}, abstract = {Histone acetyltranferase (HAT) enzymes are the catalytic subunits of multisubunit protein complexes that acetylate specific lysine residues on the N-terminal regions of the histone components of chromatin to promote gene activation. These enzymes, which now include more than 20 members, fall into distinct families that generally have high sequence similarity and related substrate specificity within families, but have divergent sequence and substrate specificity between families. Significant insights into the mode of catalysis and histone substrate binding have been provided by the structure determination of the divergent HAT enzymes Hat1, Gcn5/PCAF and Esa1. A comparison of these structures reveals a structurally conserved central core domain that mediates extensive interactions with the acetyl-coenzyme A cofactor, and structurally divergent N and C-terminal domains. A correlation of these structures with other studies reveals that the core domain plays a particularly important role in histone substrate catalysis and that the N and C-terminal domains play important roles in histone substrate binding. These correlations imply a related mode of catalysis and histone substrate binding by a diverse group of HAT enzymes. (C) 2001 Academic Press}, keywords = {Acetylation,Acetyltransferases,activation,ACUTE MYELOID-LEUKEMIA,BINDING,Catalysis,Chromatin,chromatin regulation,COENZYME-A,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,CRYSTAL-STRUCTURE,DNASE-I SENSITIVITY,DOMAINS,enzyme,FAMILY,GCN5 TRANSCRIPTIONAL COACTIVATOR,GCN5-RELATED N-ACETYLTRANSFERASE,gene,gene regulation,GNAT superfamily,histone acetyl transperases (HATs),histone modification,HIV-1 TAT,Lysine,nosource,protein,PROTEIN COMPLEX,REGION,RESIDUES,Review,sequence,structure,Substrate Specificity,SUBSTRATE-SPECIFICITY,SUBUNIT,YEAST GCN5P} }

@article{marquezFunctionsInterplayTRNAbinding2002a, title = {Functions and Interplay of the {{tRNA-binding}} Sites of the Ribosome.}, author = {Marquez, V. and Wilson, D.N. and Nierhaus, K.H.}, year = 2002, month = apr, journal = {Biochemical Society Transactions}, volume = {30}, number = {2}, pages = {133–140}, doi = {10.1042/bst0300133}, url = {ISI:000175499900026 http://www.ncbi.nlm.nih.gov/pubmed/12023840}, abstract = {The ribosome translates the genetic information of an mRNA molecule into a sequence of amino acids. The ribosome utilizes tRNAs to connect elements of the RNA and protein worlds during protein synthesis, i.e. an anticodon as a unit of genetic information with the corresponding amino acid as a building unit of proteins. Three tRNA-binding sites are located on the ribosome, termed the A, P and E sites. In recent years the tRNA-binding sites have been localized on the ribosome by three different techniques, small-angle neutron scattering, cryo-electron microscopy and X-ray analyses of 70 S crystals. These high-resolution glimpses into various ribosomal states together with a large body of biochemical data reveal an intricate interplay between the tRNAs and the three ribosomal binding sites, providing an explanation for the remarkable features of the ribosome, such as the ability to select the correct ternary complex aminoacyl-tRNA(.)EF-Tu(.)GTP out of more than 40 extremely similar tRNA complexes, the precise movement of the tRNA(2)(.)mRNA complex during translocation and the maintenance of the reading frame}, keywords = {0,A SITE,A-SITE,ACID,ACIDS,Amino Acids,AMINO-ACIDS,AMINOACYL-TRANSFER RNA,ANGSTROM RESOLUTION,Anticodon,BINDING,Binding Sites,BINDING-SITE,BODIES,COMPLEX,COMPLEXES,Cryoelectron Microscopy,E,E site,ELEMENTS,ELONGATION CYCLE,ESCHERICHIA-COLI RIBOSOMES,FRAME,gene,Genetic,Movement,mRNA,nosource,P SITE,P-SITE,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,READING FRAME,ribosome,Rna,S,sequence,SITE,SITES,SUBUNIT,techniques,translocation,tRNA,tRNA binding,WORLD} }

@article{marquezMaintainingRibosomalReading2004, title = {Maintaining the {{Ribosomal Reading Frame}}:: {{The Influence}} of the {{E Site}} during {{Translational Regulation}} of {{Release Factor}} 2}, author = {Marquez, V. and Wilson, D.N. and Tate, W.P. and {Triana-Alonso}, F. and Nierhaus, K.H.}, year = 2004, month = jul, journal = {Cell}, volume = {118}, number = {1}, pages = {45–55}, publisher = {Elsevier}, doi = {10.1016/j.cell.2004.06.012}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867404005744 PM:15242643}, abstract = {Maintenance of the translation reading frame is one of the most remarkable achievements of the ribosome while decoding the information of an mRNA. Loss of the reading frame through spontaneous frameshifting occurs with a frequency of one in 30,000 amino acid incorporations. However, at many recoding sites, the mechanism that controls reading frame maintenance is switched off. One such example is the programmed +1 frameshift site of the prfB gene encoding the termination factor RF2, in which slippage into the forward frame by one nucleotide can attain an efficiency of approximately 100%, namely, four orders of magnitude higher than normally observed. Here, using the RF2 frameshift window, we demonstrate that premature release of the E site tRNA from the ribosome is coupled with high-level frameshifting. Consistently, in a minimal system, the presence of the E site tRNA prevents the +1 frameshift event, illustrating the importance of the E site for reading-frame maintenance}, keywords = {0,ACID,Amino Acid Sequence,AMINO-ACID,Anticodon,Base Sequence,chemistry,Codon,decoding,E,E site,efficiency,Escherichia coli,FRAME,FRAME MAINTENANCE,frameshift,Frameshift Mutation,Frameshifting,FrameshiftingRibosomal,gene,genetics,Kinetics,La,MECHANISM,metabolism,ModelsGenetic,Molecular Sequence Data,mRNA,nosource,Peptide Termination Factors,READING FRAME,Reading Frames,recoding,regulation,RELEASE,release factor,ribosome,Ribosomes,Rna,RNAMessenger,RNATransferTrp,SITE,SITES,SLIPPAGE,supportnon-u.s.gov’t,SYSTEM,termination,translation,TranslationGenetic,tRNA} } % == BibTeX quality report for marquezMaintainingRibosomalReading2004: % ? Title looks like it was stored in title-case in Zotero

@article{marraGenomeSequenceSARSAssociated2003, title = {The {{Genome Sequence}} of the {{SARS-Associated Coronavirus}}}, author = {Marra, M.A. and Jones, S.J. and Astell, C.R. and Holt, R.A. and {Brooks-Wilson}, A. and Butterfield, Y.S. and Khattra, J. and Asano, J.K. and Barber, S.A. and Chan, S.Y. and Cloutier, A. and Coughlin, S.M. and Freeman, D. and Girn, N. and Griffith, O.L. and Leach, S.R. and Mayo, M. and McDonald, H. and Montgomery, S.B. and Pandoh, P.K. and Petrescu, A.S. and Robertson, A.G. and Schein, J.E. and Siddiqui, A. and Smailus, D.E. and Stott, J.M. and Yang, G.S. and Plummer, F. and Andonov, A. and Artsob, H. and Bastien, N. and Bernard, K. and Booth, T.F. and Bowness, D. and Drebot, M. and Fernando, L. and Flick, R. and Garbutt, M. and Gray, M. and Grolla, A. and Jones, S. and Feldmann, H. and Meyers, A. and Kabani, A. and Li, Y. and Normand, S. and Stroher, U. and Tipples, G.A. and Tyler, S. and Vogrig, R. and Ward, D. and Watson, B. and Brunham, R.C. and Krajden, M. and Petric, M. and Skowronski, D.M. and Upton, C. and Roper, R.L.}, year = 2003, month = may, journal = {Science}, volume = {300}, number = {5624}, pages = {1399–1404}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1085953}, url = {http://www.sciencemag.org/content/300/5624/1399.short}, abstract = {We sequenced the 29,751-base genome of the severe acute respiratory syndrome (SARS)-associated coronavirus known as the Tor2 isolate. The genome sequence reveals that this coronavirus is only moderately related to other known coronaviruses, including two human coronaviruses, HCoV-OC43 and HCoV-229E. Phylogenetic analysis of the predicted viral proteins indicates that the virus does not closely resemble any of the three previously known groups of coronaviruses. The genome sequence will aid in the diagnosis of SARS virus infection in humans and potential animal hosts (using PCR and immunological tests), in the development of antivirals (including neutralizing antibodies), and in the identification of putative epitopes for vaccine development}, keywords = {analysis,animal,Antibodies,antibody,antiviral,cancer,development,epitope,FrameshiftingRibosomal,Genome,human,IDENTIFICATION,nosource,PCR,protein,Proteins,SARS,sequence,Viral Proteins,virus} } % == BibTeX quality report for marraGenomeSequenceSARSAssociated2003: % ? Title looks like it was stored in title-case in Zotero

@article{martinez-salgadoGlomerularNephrotoxicityAminoglycosides2007, title = {Glomerular Nephrotoxicity of Aminoglycosides}, author = {{Martinez-Salgado}, C. and {Lopez-Hernandez}, F.J. and {Lopez-Novoa}, J.M.}, year = 2007, journal = {Toxicol.Appl.Pharmacol.}, volume = {223}, number = {1}, pages = {86–98}, doi = {10.1016/j.taap.2007.05.004}, url = {PM:17602717}, abstract = {Aminoglycoside antibiotics are the most commonly used antibiotics worldwide in the treatment of Gram-negative bacterial infections. However, aminoglycosides induce nephrotoxicity in 10-20% of therapeutic courses. Aminoglycoside-induced nephrotoxicity is characterized by slow rises in serum creatinine, tubular necrosis and marked decreases in glomerular filtration rate and in the ultrafiltration coefficient. Regulation of the ultrafiltration coefficient depends on the activity of intraglomerular mesangial cells. The mechanisms responsible for tubular nephrotoxicity of aminoglycosides have been intensively reviewed previously, but glomerular toxicity has received less attention. The purpose of this review is to critically assess the published literature regarding the toxic mechanisms of action of aminoglycosides on renal glomeruli and mesangial cells. The main goal of this review is to provide an actualized and mechanistic vision of pathways involved in glomerular toxic effects of aminoglycosides}, keywords = {0,adverse effects,AMINOGLYCOSIDE ANTIBIOTICS,Aminoglycosides,Animals,Anti-Bacterial Agents,antibiotic,antibiotics,Apoptosis,Bacterial,CELLS,chemically induced,drug effects,Gentamicins,Glomerular Filtration Rate,Humans,INFECTION,Kidney Diseases,La,MECHANISM,MECHANISMS,Mesangial Cells,metabolism,nosource,pathology,PATHWAY,regulation,Review,toxicity} } % == BibTeX quality report for martinez-salgadoGlomerularNephrotoxicityAminoglycosides2007: % ? Possibly abbreviated journal title Toxicol.Appl.Pharmacol.

@article{masisonDecoyingCapMRNA1995, title = {Decoying the Cap⬚-⬚ {{mRNA}} Degradation System by a Double-Stranded {{RNA}} Virus and Poly({{A}})⬚-⬚ {{mRNA}} Surveillance by a Yeast Antiviral System.}, author = {Masison, d.C. and Blanc, A. and Ribas, J.C. and Carroll, K. and Sonenberg, N. and Wickner, R.B.}, year = 1995, journal = {Mol.Cell.Biol.}, volume = {15}, pages = {2763–2771}, doi = {10.1128/MCB.15.5.2763}, abstract = {The major coat protein of the L-A double-stranded RNA virus of Saccharomyces cerevisiae covalently binds m7 GMP from 5’ capped mRNAs in vitro. We show that this cap binding also occurs in vivo and that, while this activity is required for expression of viral information (killer toxin mRNA level and toxin production) in a wild-type strain, this requirement is suppressed by deletion of SKI1/XRN1/SEP1. We propose that the virus creates decapped cellular mRNAs to decoy the 5’–{\(>\)}3’ exoribonuclease specific for cap- RNA encoded by XRN1. The SKI2 antiviral gene represses the copy numbers of the L-A and L-BC viruses and the 20S RNA replicon, apparently by specifically blocking translation of viral RNA. We show that SKI2, SKI3, and SKI8 inhibit translation of electroporated luciferase and beta-glucuronidase mRNAs in vivo, but only if they lack the 3’ poly(A) structure. Thus, L-A decoys the SKI1/XRN1/SEP1 exonuclease directed at 5’ uncapped ends, but translation of the L-A poly(A)- mRNA is repressed by Ski2,3,8p. The SKI2-SKI3-SKI8 system is more effective against cap+ poly(A)- mRNA, suggesting a (nonessential) role in blocking translation of fragmented cellular mRNAs.}, keywords = {3,antiviral,BINDING,Cap,Cap binding,CEREVISIAE,COAT PROTEIN,degradation,DOUBLE-STRANDED-RNA,expression,gene,In Vitro,IN-VITRO,IN-VIVO,INFORMATION,killer,killer toxin,L-A,L-BC,La,luciferase,mRNA,nosource,poly(A),protein,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SKI,SKI2,structure,SYSTEM,toxin,translation,VIRAL-RNA,virus,Viruses,WILD-TYPE,XRN1,yeast} } % == BibTeX quality report for masisonDecoyingCapMRNA1995: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{mastersMolecularBiologyCoronaviruses2006, title = {The Molecular Biology of Coronaviruses}, author = {Masters, P.S.}, year = 2006, journal = {Adv.Virus Res.}, volume = {66}, pages = {193–292}, doi = {10.1016/S0065-3527(06)66005-3}, url = {PM:16877062}, abstract = {Coronaviruses are large, enveloped RNA viruses of both medical and veterinary importance. Interest in this viral family has intensified in the past few years as a result of the identification of a newly emerged coronavirus as the causative agent of severe acute respiratory syndrome (SARS). At the molecular level, coronaviruses employ a variety of unusual strategies to accomplish a complex program of gene expression. Coronavirus replication entails ribosome frameshifting during genome translation, the synthesis of both genomic and multiple subgenomic RNA species, and the assembly of progeny virions by a pathway that is unique among enveloped RNA viruses. Progress in the investigation of these processes has been enhanced by the development of reverse genetic systems, an advance that was heretofore obstructed by the enormous size of the coronavirus genome. This review summarizes both classical and contemporary discoveries in the study of the molecular biology of these infectious agents, with particular emphasis on the nature and recognition of viral receptors, viral RNA synthesis, and the molecular interactions governing virion assembly}, keywords = {0,Animals,assembly,BIOLOGY,Cats,Cattle,classification,COMPLEX,COMPLEXES,Coronavirus,Coronavirus Infections,development,DISCOVERY,Dogs,expression,FAMILY,Frameshifting,gene,Gene Expression,GENE-EXPRESSION,Genetic,genetics,Genome,genomic,Humans,IDENTIFICATION,La,metabolism,Molecular Biology,nosource,PATHWAY,physiology,protein,Proteins,Rats,RECOGNITION,REPLICATION,Research SupportN.I.H.Extramural,Review,ribosome,Rna,RNA Viruses,RnaViral,SARS,Severe Acute Respiratory Syndrome,Syndrome,SYSTEM,SYSTEMS,translation,Viral Proteins,VIRAL-RNA,Virion,VIRIONS,virology,Virus Replication,Viruses} } % == BibTeX quality report for mastersMolecularBiologyCoronaviruses2006: % ? Possibly abbreviated journal title Adv.Virus Res.

@article{masucciInfluenceRelAGene2002, title = {Influence of the {{relA}} Gene on Ribosome Frameshifting}, author = {Masucci, J.P. and Gallant, J. and Lindsley, D. and Atkinson, J.}, year = 2002, journal = {Molecular Genetics and Genomics}, volume = {268}, number = {1}, pages = {81–86}, publisher = {Springer}, doi = {10.1007/s00438-002-0725-y}, url = {http://www.springerlink.com/index/8D6CMCEA90T53235.pdf}, abstract = {We have examined the influence of genotype at the relA locus on the kinetics of leftward (or -1) frameshifting at a variety of codons calling for a limiting aminoacyl-tRNA species. We used lacZ left-frameshift reporter constructs carrying the sequence U UUC xyz, where xyz was each of three triplets coding for three different amino acids; we slowed the ribosomes at each of these by limiting for the amino acid or for the aminoacyl-tRNA. In all cases, limitation stimulated leftward frameshifting. In all cases, the stimulation was greater in relA mutant cells than in their wild-type relA(+) counterparts. In the latter genotype, the increased frameshifting was constant from the start of the limitation regime. This was also true of the relA mutant strain during limitation for lysine-tRNA or for leucine; however, during limitation for isoleucine-tRNA (or for isoleucine) the mutant showed a gradual, progressive increase in frameshifting, suggesting an indirect effect. We suggest that gradual accumulation of undermodified tRNAs, which is characteristic of the relA response, is involved. However, the specific modification involved is unknown. It is not queosine: analysis of a tgt mutant that is completely defective in queosine modification showed no increase in leftward frameshifting on the reporter which showed the larger, gradual increase during the relA response to isoleucine-tRNA limitation}, keywords = {0,amino acid limitation,Amino Acids,analysis,Codon,DIRECTIONAL SPECIFICITY,ESCHERICHIA-COLI,Frameshifting,gene,Genome,Genotype,HUNGRY CODONS,Kinetics,Leucine,MECHANISM,modification,nosource,relA,ribosomal frameshifting,ribosome,Ribosomes,RULES,sequence,stringent response,tRNA} }

@article{matadeenEscherichiaColiLarge1999a, title = {The {{Escherichia}} Coli Large Ribosomal Subunit at 7.5 {{A}} Resolution}, author = {Matadeen, R. and Patwardhan, A. and Gowen, B. and Orlova, E.V. and Pape, T. and Cuff, M. and Mueller, F. and Brimacombe, R. and {}{van Heel}, M.}, year = 1999, month = dec, journal = {Structure.Fold.Des}, volume = {7}, number = {12}, pages = {1575–1583}, doi = {10.1016/S0969-2126(00)88348-3}, url = {PM:10647188}, abstract = {BACKGROUND: In recent years, the three-dimensional structure of the ribosome has been visualised in different functional states by single- particle cryo-electron microscopy (cryo-EM) at 13-25 A resolution. Even more recently, X-ray crystallography has achieved resolution levels better than 10 A for the ribosomal structures of thermophilic and halophilic organisms. We present here the 7.5 A solution structure of the 50S large subunit of the Escherichia coli ribosome, as determined by cryo-EM and angular reconstitution. RESULTS: The reconstruction reveals a host of new details including the long alpha helix connecting t}, keywords = {0,Bacterial,Bacterial Proteins,chemistry,Cryoelectron Microscopy,Crystallography,elongation,Escherichia coli,ESCHERICHIA-COLI,Image ProcessingComputer-Assisted,La,Methods,ModelsMolecular,nosource,Peptide Elongation Factor Tu,protein,Protein Conformation,Protein StructureSecondary,Proteins,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,structure,SUBUNIT,supportnon-u.s.gov’t,ultrastructure} } % == BibTeX quality report for matadeenEscherichiaColiLarge1999a: % ? Possibly abbreviated journal title Structure.Fold.Des

@article{mathewsExpandedSequenceDependence1999a, title = {Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of {{RNA}} Secondary Structure}, author = {Mathews, D.H. and Sabina, J. and Zuker, M. and Turner, D.H.}, year = 1999, month = may, journal = {J.Mol.Biol.}, volume = {288}, number = {5}, pages = {911–940}, doi = {10.1006/jmbi.1999.2700}, url = {PM:10329189}, abstract = {An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization. Thermodynamic parameters for the stabilities of secondary structure motifs are revised to include expanded sequence dependence as revealed by recent experiments. Additional algorithmic improvements include reduced search time and storage for multibranch loop free energies and improved imposition of folding constraints. An extended database of 151,503 nt in 955 structures? determined by comparative sequence analysis was assembled to allow optimization of parameters not based on experiments and to test the accuracy of the algorithm. On average, the predicted lowest free energy structure contains 73 % of known base-pairs when domains of fewer than 700 nt are folded; this compares with 64 % accuracy for previous versions of the algorithm and parameters. For a given sequence, a set of 750 generated structures contains one structure that, on average, has 86 % of known base-pairs. Experimental constraints, derived from enzymatic and flavin mononucleotide cleavage, improve the accuracy of structure predictions}, keywords = {0,accuracy,Algorithms,Amino Acid Sequence,analysis,Bacteriophage T4,BASE-PAIR,chemistry,CLEAVAGE,DATABASE,DatabasesFactual,DOMAIN,DOMAINS,dynamic programming,Escherichia coli,Flavin Mononucleotide,Kinetics,La,LOOP,MFOLD,ModelsGenetic,ModelsStatistical,Molecular Sequence Data,MOTIFS,nosource,Nucleic Acid Conformation,pharmacology,PREDICTION,Protein StructureSecondary,Rna,RNA SECONDARY STRUCTURE,RNARibosomal5S,search,SECONDARY STRUCTURE,secondary structure prediction,sequence,Sequence Analysis,SEQUENCE-ANALYSIS,stability,structure,supportu.s.gov’tp.h.s.,Thermodynamics,Time Factors} } % == BibTeX quality report for mathewsExpandedSequenceDependence1999a: % ? Possibly abbreviated journal title J.Mol.Biol.

@incollection{mathewsOriginsPrinciplesTranslational2007, title = {Origins and Principles of Translational Control.}, booktitle = {Translational {{Control}} in {{Biology}} and {{Medicine}}.}, author = {Mathews, M.B and Sonenberg, N. and Hershey, J.W.B.}, year = 2007, series = {Cold {{Spring Harbor Monograph Series}}}, pages = {1–40}, publisher = {Cold Spring Harbor Press}, address = {Cold Spring Harbor, NY}, collaborator = {Mathews, M.B and Sonenberg, N. and Hershey, J.W.B.}, keywords = {BIOLOGY,nosource,Review,ribosome,translation} }

@book{mathewsTranslationalControlBiology2007, title = {Translational Control in Biology and Medicine.}, author = {Mathews, M.B and Sonenberg, N. and Hershey, J.W.B.}, year = 2007, series = {Cold {{Spring Harbor Monograph Series}}}, publisher = {Cold Spring Harbor Press}, address = {Cold Spring Harbor, NY}, collaborator = {Mathews, M.B and Sonenberg, N. and Hershey, J.W.B.}, keywords = {BIOLOGY,nosource} }

@article{matsufujiAutoregulatoryFrameshiftingDecoding1995, title = {Autoregulatory Frameshifting in Decoding Mammalian Ornithine Decarboxylase Antizyme}, author = {Matsufuji, S. and Matsufuji, T. and Miyazaki, Y. and Murakami, Y. and Atkins, J.F. and Gesteland, R.F. and Hayashi, S.}, year = 1995, month = jan, journal = {Cell}, volume = {80}, number = {1}, pages = {51–60}, publisher = {Elsevier}, doi = {10.1016/0092-8674(95)90450-6}, keywords = {antizyme,Codon,decoding,degradation,efficiency,enzyme,expression,frameshift,Frameshifting,gene,Gene Expression,GENE-EXPRESSION,In Vitro,IN-VITRO,lysate,MECHANISM,mRNA,nosource,Ornithine Decarboxylase,ORNITHINE DECARBOXYLASE ANTIZYME,polyamine,Polyamines,pseudoknot,rat,ribosomal frameshifting,sequence,Spermidine,termination} }

@article{matsufujiReadingTwoBases1996, title = {Reading Two Bases Twice: Mammalian Antizyme Frameshifting in Yeast.}, author = {Matsufuji, S. and Matsufuji, T. and Wills, N.M. and Gesteland, R.F. and Atkins, J.F.}, year = 1996, journal = {The EMBO Journal}, volume = {15}, number = {6}, pages = {1360–1370}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1996.tb00478.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC450040/}, keywords = {+1 frameshifting,antizyme,Frameshifting,nosource,yeast} } % == BibTeX quality report for matsufujiReadingTwoBases1996: % ? unused Journal abbr (“EMBO J.”)

@article{matsumotoCircularSingleStrandedRna1990, title = {Circular {{Single-Stranded Rna Replicon}} in {{Saccharomyces-Cerevisiae}}}, author = {Matsumoto, Y. and Fishel, R. and Wickner, R.B.}, year = 1990, month = oct, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {87}, number = {19}, pages = {7628–7632}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.87.19.7628}, url = {http://www.pnas.org/content/87/19/7628.short}, keywords = {nosource,Rna,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE} } % == BibTeX quality report for matsumotoCircularSingleStrandedRna1990: % ? Title looks like it was stored in title-case in Zotero

@article{matsumotoYeast20SRNA1991, title = {Yeast 20-{{S RNA Replicon}} - {{Replication Intermediates}} and {{Encoded Putative Rna-Polymerase}}}, author = {Matsumoto, Y. and Wickner, R.B.}, year = 1991, month = jul, journal = {Journal of Biological Chemistry}, volume = {266}, number = {19}, pages = {12779–12783}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(18)98967-2}, url = {http://www.jbc.org/content/266/19/12779.short}, abstract = {The 20 S RNA genome is a circular single-stranded replicon, present in most laboratory yeast strains, whose copy number is induced 10,000-fold by transfer of cells to acetate medium without a carbon source. We have sequenced most of the 20 S RNA genome, and the (+) strand has a long open reading frame with the potential to encode a protein with homology to viral RNA-dependent RNA polymerases. The presence of a typical cAMP-dependent phosphorylation site in the putative RNA polymerase suggests that the acetate amplification of the 20 S RNA genome might be mediated by cAMP, a signal known to transmit the same nutritional status information to the sporulation-control system. Our inability to clone across the gap in the sequence suggests either autocatalytic cleavage of the RNA in the reverse transcriptase reaction, an unusual linkage of 5’ and 3’ ends of a fundamentally linear molecule, or a structure unusually resistant to reverse transcription. The identity of our sequence with that of the accompanying paper (Rodriguez-Cousino, N., Esteban, L. M., and Esteban, R. (1991) J. Biol. Chem. 266, 12772-12778) for W double-stranded RNA (dsRNA) suggests that W is the replicative form of 20 S RNA. The presence of single-stranded (+) and (-) strands and greater than unit length molecules suggests a rolling circle mode of replication as has been suggested for viroids}, keywords = {3,Carbon,carbon source,CELLS,CLEAVAGE,DEPENDENT PROTEIN-KINASE,DOUBLE-STRANDED-RNA,expression,FRAME,Genome,HAIRPINS,HSP26,INTERMEDIATE,M,media,nosource,OPEN READING FRAME,Phosphorylation,polymerase,protein,READING FRAME,REPLICATION,RESISTANT,Rna,RNA-POLYMERASE,S,SACCHAROMYCES-CEREVISIAE,SELF-CLEAVAGE,sequence,SIGNAL,SITE,SPORULATION,structure,SYSTEM,transcription,virus,yeast} } % == BibTeX quality report for matsumotoYeast20SRNA1991: % ? Title looks like it was stored in title-case in Zotero

@article{matsumotoYeastAntiviralProtein1993, title = {A Yeast Antiviral Protein, {{SKI8}}, Shares a Repeated Amino Acid Sequence Pattern with 'a-Subunits of {{G-proteins}} and Several Other Proteins.}, author = {Matsumoto, Y. and Sarkar, G. and Sommer, S. and Wickner, R.B.}, year = 1993, journal = {Yeast}, volume = {9}, pages = {43–51}, doi = {10.1002/yea.320090106}, keywords = {Amino Acid Sequence,antiviral,nosource,protein,Proteins,sequence,SKI,yeast} }

@article{matunisPUB1MajorYeast1993, title = {{{PUB1}}: A Major Yeast Poly ({{A}})+ {{RNA-binding}} Protein.}, author = {Matunis, M.J. and Matunis, E.L. and Dreyfuss, G.}, year = 1993, month = oct, journal = {Molecular and cellular biology}, volume = {13}, number = {10}, pages = {6114–6123}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/13/10/6114}, abstract = {The expression of RNA polymerase II transcripts can be regulated at the posttranscriptional level by RNA-binding proteins. Although extensively characterized in metazoans, relatively few RNA-binding proteins have been characterized in the yeast Saccharomyces cerevisiae. Three major proteins are cross-linked by UV light to poly(A)+ RNA in living S. cerevisiae cells. These are the 72-kDa poly(A)-binding protein and proteins of 60 and 50 kDa (S.A. Adam, T.Y. Nakagawa, M.S. Swanson, T. Woodruff, and G. Dreyfuss, Mol. Cell. Biol. 6:2932-2943, 1986). Here, we describe the 60-kDa protein, one of the major poly(A)+ RNA-binding proteins in S. cerevisiae. This protein, PUB1 [for poly(U)-binding protein 1], was purified by affinity chromatography on immobilized poly(rU), and specific monoclonal antibodies to it were produced. UV cross-linking demonstrated that PUB1 is bound to poly(A)+ RNA (mRNA or pre-mRNA) in living cells, and it was detected primarily in the cytoplasm by indirect immunofluorescence. The gene for PUB1 was cloned and sequenced, and the sequence was found to predict a 51-kDa protein with three ribonucleoprotein consensus RNA-binding domains and three glutamine- and asparagine-rich auxiliary domains. This overall structure is remarkably similar to the structures of the Drosophila melanogaster elav gene product, the human neuronal antigen HuD, and the cytolytic lymphocyte protein TIA-1. Each of these proteins has an important role in development and differentiation, potentially by affecting RNA processing. PUB1 was found to be nonessential in S. cerevisiae by gene replacement; however, further genetic analysis should reveal important features of this class of RNA-binding proteins}, keywords = {0,Amino Acid Sequence,analysis,animal,Antibodies,antibody,ANTIGEN,Base Sequence,CELLS,CEREVISIAE,Chromatography,CloningMolecular,CROSS-LINKING,CROSSLINKING,Cytoplasm,development,Dna,DNAFungal,DOMAIN,DOMAINS,Drosophila,Drosophila melanogaster,DROSOPHILA-MELANOGASTER,expression,Fluorescent Antibody Technique,Fungal Proteins,gene,GENE-PRODUCT,Genetic,genetics,Glutamine,growth & development,human,Immunoblotting,isolation & purification,La,metabolism,Molecular Sequence Data,mRNA,Multiple DOI,nonfile,nosource,POLY(A)-BINDING PROTEIN,polymerase,Precipitin Tests,PRODUCT,protein,Proteins,RIBONUCLEOPROTEIN,Rna,RNA Polymerase II,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNA-POLYMERASE,RNA-POLYMERASE-II,RNAFungal,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,T,TRANSCRIPT,yeast} } % == BibTeX quality report for matunisPUB1MajorYeast1993: % ? unused Journal abbr (“Mol Cell Biol.”)

@article{mazumderTranslationalControl32003, title = {Translational Control by the 3 ‘-{{UTR}}: The Ends Specify the Means}, author = {Mazumder, B. and Seshadri, V. and Fox, P.L.}, year = 2003, month = feb, journal = {Trends in Biochemical Sciences}, volume = {28}, number = {2}, pages = {91–98}, publisher = {Elsevier}, doi = {10.1016/S0968-0004(03)00002-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000403000021}, abstract = {In most cases, translational control mechanisms result from the interaction of RNA-binding proteins with 5’- or 3’-untranslated regions (UTRs) of mRNA. In organisms ranging from viruses to humans, protein-mediated interactions between transcript termini result in the formation of an RNA loop. Such RNA ‘circularization’ is thought to increase translational efficiency and, in addition, permits regulation by novel mechanisms, particularly 3’-UTR-mediated translational control. Two general mechanisms of translational inhibition by 3’-UTR-binding proteins have been proposed, one in which mRNA closure is disrupted and another in which mRNA closure is required. Experimental evidence for the latter is provided by studies of interferon-gamma-mediated translational silencing of ceruloplasmin expression in monocytic cells. A multi-species analysis has shown that, in most vertebrates, 3’-UTRs are substantially longer than their 5’ counterparts, indicating a significant potential for regulation. In addition, the average length of 3’-UTR sequences has increased during evolution, suggesting that their utilization might contribute to organism complexity}, keywords = {0,3,3’ UNTRANSLATED REGION,3’ Untranslated Regions,3’ UTR,3’-UNTRANSLATED REGION,analysis,BINDING-PROTEIN,CAENORHABDITIS-ELEGANS,CELLS,efficiency,EFFICIENT TRANSLATION,ERYTHROID-DIFFERENTIATION,Evolution,expression,human,INHIBITION,INITIATION-FACTOR 4G,INTERNAL RIBOSOME ENTRY,LOOP,MECHANISM,MECHANISMS,MESSENGER-RNA DEGRADATION,mRNA,nosource,POLY(A) TAIL,protein,Proteins,REGION,regulation,Review,Rna,RNA-Binding Proteins,sequence,SEQUENCES,Vertebrates} }

@article{mazumderRegulatedReleaseL13a2003, title = {Regulated Release of {{L13a}} from the {{60S}} Ribosomal Subunit as a Mechanism of Transcript-Specific Translational Control}, author = {Mazumder, B. and Sampath, P. and Seshadri, V. and Maitra, R.K. and DiCorleto, P.E. and Fox, P.L.}, year = 2003, month = oct, journal = {Cell}, volume = {115}, number = {2}, pages = {187–198}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(03)00773-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867403007736}, abstract = {Transcript-specific translational control is generally directed by binding of trans-acting proteins to structural elements in the untranslated region (UTR) of the target mRNA. Here, we elucidate a translational silencing mechanism involving regulated release of an integral ribosomal protein and subsequent binding to its target mRNA. Human ribosomal protein L13a was identified as a candidate interferon-Gamma-Activated Inhibitor of Translation (GAIT) of ceruloplasmin (Cp) mRNA by a genetic screen for Cp 3’-UTR binding proteins. In vitro activity of L13a was shown by inhibition of target mRNA translation by recombinant protein. In response to interferon-gamma in vivo, the entire cellular pool of L13a was phosphorylated and released from the 60S ribosomal subunit. Released L13a specifically bound the 3’-UTR GAIT element of Cp mRNA and silenced translation. We propose a model in which the ribosome functions not only as a protein synthesis machine, but also as a depot for regulatory proteins that modulate translation}, keywords = {0,3,3’ Untranslated Regions,3’ UTR,3’-UTR,Amino Acid Sequence,BINDING,BINDING PROTEIN,BINDING-PROTEIN,BIOLOGY,Ceruloplasmin,chemistry,drug effects,ELEMENTS,Gene Expression Regulation,Gene Silencing,Genetic,genetics,human,In Vitro,IN-VITRO,IN-VIVO,INHIBITION,INHIBITOR,Interferon Type II,La,MECHANISM,metabolism,MODEL,ModelsBiological,ModelsMolecular,Molecular Sequence Data,Molecular Structure,mRNA,nosource,pharmacology,Phosphorylation,protein,Protein StructureTertiary,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Recombinant Proteins,REGION,RELEASE,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNA ProcessingPost-Transcriptional,RNAMessenger,Structural,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,TARGET,Time Factors,translation,TranslationGenetic,U937 Cells,Untranslated Regions} }

@article{mccarthyPosttranscriptionalControlGene1998, title = {Posttranscriptional Control of Gene Expression in Yeast}, author = {McCarthy, J.E.}, year = 1998, month = dec, journal = {Microbiology and molecular biology reviews}, volume = {62}, number = {4}, pages = {1492–1553}, publisher = {Am Soc Microbiol}, doi = {10.1128/MMBR.62.4.1492-1553.1998}, url = {http://mmbr.asm.org/cgi/content/abstract/62/4/1492}, abstract = {Studies of the budding yeast Saccharomyces cerevisiae have greatly advanced our understanding of the posttranscriptional steps of eukaryotic gene expression. Given the wide range of experimental tools applicable to S. cerevisiae and the recent determination of its complete genomic sequence, many of the key challenges of the posttranscriptional control field can be tackled particularly effectively by using this organism. This article reviews the current knowledge of the cellular components and mechanisms related to translation and mRNA decay, with the emphasis on the molecular basis for rate control and gene regulation. Recent progress in characterizing translation factors and their protein-protein and RNA-protein interactions has been rapid. Against the background of a growing body of structural information, the review discusses the thermodynamic and kinetic principles that govern the translation process. As in prokaryotic systems, translational initiation is a key point of control. Modulation of the activities of translational initiation factors imposes global regulation in the cell, while structural features of particular 5’ untranslated regions, such as upstream open reading frames and effector binding sites, allow for gene-specific regulation. Recent data have revealed many new details of the molecular mechanisms involved while providing insight into the functional overlaps and molecular networking that are apparently a key feature of evolving cellular systems. An overall picture of the mechanisms governing mRNA decay has only very recently begun to develop. The latest work has revealed new information about the mRNA decay pathways, the components of the mRNA degradation machinery, and the way in which these might relate to the translation apparatus. Overall, major challenges still to be addressed include the task of relating principles of posttranscriptional control to cellular compartmentalization and polysome structure and the role of molecular channelling in these highly complex expression systems}, keywords = {0,Amino Acid Sequence,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,BODIES,CEREVISIAE,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,DECAY,DECAY PATHWAY,decay pathways,degradation,expression,FRAME,gene,Gene Expression,Gene Expression RegulationFungal,gene regulation,GENE-EXPRESSION,genetics,genomic,initiation,INITIATION-FACTOR,La,MECHANISM,MECHANISMS,metabolism,MOLECULAR MECHANISMS,Molecular Sequence Data,mRNA,mRNA decay,nosource,OPEN READING FRAME,Open Reading Frames,PATHWAY,READING FRAME,Reading Frames,REGION,regulation,Review,Rna,RNA ProcessingPost-Transcriptional,RNAFungal,RNAMessenger,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SITE,SITES,Structural,STRUCTURAL FEATURES,structure,supportnon-u.s.gov’t,SYSTEM,SYSTEMS,translation,TRANSLATIONAL INITIATION,TranslationGenetic,Untranslated Regions,UPSTREAM,yeast} } % == BibTeX quality report for mccarthyPosttranscriptionalControlGene1998: % ? unused Journal abbr (“Microbiol.Mol.Biol.Rev.”)

@article{mcgowanRibosomalMutationsCause2008, title = {Ribosomal Mutations Cause P53-Mediated Dark Skin and Pleiotropic Effects}, author = {McGowan, K.A. and Li, J.Z. and Park, C.Y. and Beaudry, V. and Tabor, H.K. and Sabnis, A.J. and Zhang, W. and Fuchs, H. and {}{de Angelis}, M.H. and Myers, R.M. and Attardi, L.D. and Barsh, G.S.}, year = 2008, journal = {Nature genetics}, volume = {40}, number = {8}, pages = {963–970}, publisher = {Nature Publishing Group}, doi = {10.1038/ng.188}, url = {http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.188.html}, abstract = {Mutations in genes encoding ribosomal proteins cause the Minute phenotype in Drosophila and mice, and Diamond-Blackfan syndrome in humans. Here we report two mouse dark skin (Dsk) loci caused by mutations in Rps19 (ribosomal protein S19) and Rps20 (ribosomal protein S20). We identify a common pathophysiologic program in which p53 stabilization stimulates Kit ligand expression, and, consequently, epidermal melanocytosis via a paracrine mechanism. Accumulation of p53 also causes reduced body size and erythrocyte count. These results provide a mechanistic explanation for the diverse collection of phenotypes that accompany reduced dosage of genes encoding ribosomal proteins, and have implications for understanding normal human variation and human disease}, keywords = {0,Animals,BODIES,cytology,disease,Drosophila,Epidermis,Erythrocytes,expression,gene,Genes,Genetic,genetics,human,Humans,IDENTIFY,Keratinocytes,La,MECHANISM,Melanocytes,metabolism,Mice,Mutation,MUTATIONS,nosource,p53,Phenotype,protein,Protein p53,Proteins,Ribosomal Protein S6,Ribosomal Proteins,RIBOSOMAL-PROTEIN,Skin Pigmentation,Stem Cell Factor,Support,Syndrome,Tumor Suppressor Protein p53} } % == BibTeX quality report for mcgowanRibosomalMutationsCause2008: % ? unused Journal abbr (“Nat.Genet.”)

@article{mcmahonTandemlyArrangedVariant1984a, title = {Tandemly Arranged Variant {{5S}} Ribosomal {{RNA}} Genes in the Yeast ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {McMahon, M.E. and Stamenkovich, D. and Petes, T.D.}, year = 1984, journal = {Nucleic Acids Res.}, volume = {12}, pages = {8001–8016}, doi = {10.1093/nar/12.21.8001}, keywords = {5S rRNA,gene,Genes,nosource,RDN1,RIBOSOMAL-RNA,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,yeast} } % == BibTeX quality report for mcmahonTandemlyArrangedVariant1984a: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{mearsModelingMinimalRibosome2002, title = {Modeling a Minimal Ribosome Based on Comparative Sequence Analysis}, author = {Mears, J.A. and Cannone, J.J. and Stagg, S.M. and Gutell, R.R. and Agrawal, R.K. and Harvey, S.C.}, year = 2002, journal = {Journal of molecular biology}, volume = {321}, number = {2}, pages = {215–234}, publisher = {Elsevier}, doi = {10.1016/S0022-2836(02)00568-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283602005685}, abstract = {We have determined the three-dimensional organization of ribosomal RNAs and proteins essential for minimal ribosome function. Comparative sequence analysis identifies regions of the ribosome that have been evolutionarily conserved, and the spatial organization of conserved domains is determined by mapping these onto structures of the 30S and 50S subunits determined by X-ray crystallography. Several functional domains of the ribosome are conserved in their three-dimensional organization in the Archaea, Bacteria, Eucaryotic nuclear, mitochondria and chloroplast ribosomes. In contrast, other regions from both subunits have shifted their position in three-dimensional space during evolution, including the L11 binding domain and the alpha-sarcin-ricin loop (SRL). We examined conserved bridge interactions between the two ribosomal subunits, giving an indication of which contacts are more significant. The tRNA contacts that are conserved were also determined, highlighting functional interactions as the tRNA moves through the ribosome during protein synthesis. To augment these studies of a large collection of comparative structural models sampled from all major branches on the phylogenetic tree, Caenorhabditis elegans mitochondrial rRNA is considered individually because it is among the smallest rRNA sequences known. The C.elegans model supports the large collection of comparative structure models while providing insight into the evolution of mitochondrial ribosomes}, keywords = {0,analysis,animal,Archaea,Bacteria,Base Sequence,BINDING,Binding Sites,Caenorhabditis,Caenorhabditis elegans,chemistry,Chloroplasts,Comparative Study,Computer Simulation,Conserved Sequence,Crystallography,cytology,Eukaryotic Cells,Evolution,EvolutionMolecular,Genetic,genetics,La,mapping,metabolism,mitochondria,models,ModelsMolecular,MOF,Molecular Conformation,Molecular Sequence Data,Movement,nosource,Phylogeny,protein,Protein StructureTertiary,Protein Subunits,protein synthesis,PROTEIN-SYNTHESIS,Proteins,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNARibosomal,RNATransfer,rRNA,sequence,Sequence Alignment,Sequence Analysis,Sequence Deletion,Structural,structure,SUBUNIT,Support,supportu.s.gov’tp.h.s.,tRNA} } % == BibTeX quality report for mearsModelingMinimalRibosome2002: % ? unused Journal abbr (“J.Mol.Biol”)

@article{medghalchiRent1TranseffectorNonsensemediated2001, title = {Rent1, a Trans-Effector of Nonsense-Mediated {{mRNA}} Decay, Is Essential for Mammalian Embryonic Viability}, author = {Medghalchi, S.M. and Frischmeyer, P.A. and Mendell, J.T. and Kelly, A.G. and Lawler, A.M. and Dietz, H.C.}, year = 2001, month = jan, journal = {Hum. Mol. Genet.}, volume = {10}, number = {2}, pages = {99–105}, publisher = {Oxford Univ Press}, issn = {14602083}, doi = {10.1093/hmg/10.2.99}, url = {http://hmg.oxfordjournals.org/content/10/2/99.short}, abstract = {The ability to detect and degrade transcripts that lack full coding potential is ubiquitous but non-essential in lower eukaryotes, leaving in question the evolutionary basis for complete maintenance of this function. One hypothesis holds that nonsense-mediated RNA decay (NMD) protects the organism by preventing the translation of truncated peptides with dominant negative or deleterious gain-of-function potential. All organisms studied to date that are competent for NMD express a structural homolog of Saccharomyces cerevisiae Upf1p. We have now explored the consequences of loss of NMD function in vertebrates through targeted disruption of the Rent1 gene in murine embryonic stem cells which encodes a mammalian ortholog of Upf1p. Mice heterozygous for the targeted allele showed no apparent phenotypic abnormalities but homozygosity was never observed, demonstrating that Rent1 is essential for embryonic viability. Homozygous targeted embryos show complete loss of NMD and are viable in the pre-implantation period, but resorb shortly after implantation. Furthermore, Rent1(-/-) blastocysts isolated at 3.5 days post-coitum undergo apoptosis in culture following a brief phase of cellular expansion. These data suggest that NMD is essential for mammalian cellular viability and support a critical role for the pathway in the regulated expression of selected physiologic transcripts}, keywords = {0,Animals,Blastocyst,Cell Line,Cell Nucleus,Cell Survival,CELLS,CellsCultured,CEREVISIAE,Codon,CodonNonsense,DECAY,DISRUPTION,DNA Fragmentation,ENCODES,expression,Fetal Viability,gene,genetics,Germ-Line Mutation,Heterozygote,homolog,human,La,Mice,MiceMutant Strains,mRNA,mRNA decay,NMD,NONSENSE,nonsense-mediated mRNA decay,nosource,PATHWAY,Peptides,Phenotype,physiology,protein,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Stem Cells,Structural,Support,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Trans-Activators,TRANSCRIPT,translation,ultrastructure,Vertebrates} } % == BibTeX quality report for medghalchiRent1TranseffectorNonsensemediated2001: % ? Possibly abbreviated journal title Hum. Mol. Genet.

@article{meilerModelfreeApproachDynamic2001, title = {Model-Free Approach to the Dynamic Interpretation of Residual Dipolar Couplings in Globular Proteins}, author = {Meiler, J. and Prompers, J.J. and Peti, W. and Griesinger, C. and Bruschweiler, R.}, year = 2001, month = jun, journal = {Journal of the American Chemical Society}, volume = {123}, number = {25}, pages = {6098–6107}, publisher = {ACS Publications}, doi = {10.1021/ja010002z}, url = {http://pubs.acs.org/doi/abs/10.1021/ja010002z}, abstract = {The effects of internal motions on residual dipolar NMR couplings of proteins partially aligned in a liquid-crystalline environment are analyzed using a 10 ns molecular dynamics (MD) computer simulation of ubiquitin. For a set of alignment tensors with different orientations and rhombicities, MD-averaged dipolar couplings are determined and subsequently interpreted for different scenarios in terms of effective alignment tensors, average orientations of dipolar vectors, and intramolecular reorientational vector distributions. Analytical relationships are derived that reflect similarities and differences between motional scaling of dipolar couplings and scaling of dipolar relaxation data (NMR order parameters). Application of the self-consistent procedure presented here to dipolar coupling measurements of biomolecules aligned in different liquid-crystalline media should allow one to extract in a “model-free” way average orientations of dipolar vectors and specific aspects of their motions}, keywords = {0,alignment,chemistry,computer,Computer Simulation,COMPUTER-SIMULATION,DYNAMICS,Electrochemistry,Kinetics,La,media,NMR,nosource,Nuclear Magnetic ResonanceBiomolecular,protein,Protein Conformation,Proteins,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,Ubiquitins,vector,vectors} } % == BibTeX quality report for meilerModelfreeApproachDynamic2001: % ? unused Journal abbr (“J.Am.Chem.Soc.”)

@article{melanconSinglebaseMutationsPosition1992, title = {Single-Base Mutations at Position 2661 of {{Escherichia}} Coli {{23S rRNA}} Increase Efficiency of Translational Proofreading.}, author = {Melancon, P. and Tapprich, W.E. and {Brakier-Gingras}, L.}, year = 1992, month = dec, journal = {Journal of bacteriology}, volume = {174}, number = {24}, pages = {7896–7901}, publisher = {Am Soc Microbiol}, doi = {10.1128/jb.174.24.7896-7901.1992}, url = {http://jb.asm.org/cgi/content/abstract/174/24/7896}, abstract = {Two single-base substitutions were constructed in the 2660 loop of Escherichia coli 23S rRNA (G2661–{\(>\)}C or U) and were introduced into the rrnB operon cloned in plasmid pKK3535. Ribosomes were isolated from bacteria transformed with the mutated plasmids and assayed in vitro in a poly(U)-directed system for their response to the misreading effect of streptomycin, neomycin, and gentamicin, three aminoglycoside antibiotics known to impair the proofreading control of translational accuracy. Both mutations decreased the stimulation of misreading by these drugs, but neither interfered with their binding to the ribosome. The response of the mutant ribosomes to these drugs suggests that the 2660 loop, which belongs to the elongation factor Tu binding site, is involved in the proofreading step of the accuracy control. In vivo, both mutations reduced read-through of nonsense codons and frameshifting, which can also be related to the increased efficiency in proofreading control which they confer to ribosomes}, keywords = {93094116,accuracy,antibiotic,antibiotics,Bacteria,Base Sequence,BINDING,Codon,drug effects,drugs,efficiency,elongation,Escherichia coli,ESCHERICHIA-COLI,Frameshift Mutation,Frameshifting,genetics,Gentamicins,In Vitro,IN-VITRO,IN-VIVO,metabolism,Molecular Sequence Data,Mutation,MUTATIONS,Neomycin,nosource,Operon,pharmacology,Plasmids,proofreading,readthrough,ribosome,Ribosomes,RNABacterial,RNARibosomal23S,rRNA,Streptomycin,supportnon-u.s.gov’t,SuppressionGenetic,SYSTEM,TranslationGenetic} } % == BibTeX quality report for melanconSinglebaseMutationsPosition1992: % ? unused Journal abbr (“J.Bacteriol.”)

@article{melnickDrosophilaStubaristaPhenotype1993, title = {The {{Drosophila}} Stubarista Phenotype Is Associated with a Dosage Effect of the Putative Ribosome-Associated Protein {{D-p40}} on Spineless}, author = {Melnick, M.B. and Noll, E. and Perrimon, N.}, year = 1993, month = oct, journal = {Genetics}, volume = {135}, number = {2}, pages = {553–564}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/135.2.553}, url = {http://www.genetics.org/content/135/2/553.short}, abstract = {We describe the molecular characterization of the Drosophila melanogaster gene stubarista (sta) that encodes the highly conserved putative ribosome-associated protein D-p40. sta maps to cytological position 2A3-B2 on the X chromosome and encodes a protein (D-p40) of 270 amino acids. D-p40 shares 63% identity with the human p40 ribosomal protein. P element-mediated transformation of a 4.4-kb genomic fragment encompassing the 1-kb transcript corresponding to D-p40 was used to rescue both a lethal (sta2) and a viable (sta1) mutation at the stubarista (sta) locus. Developmental analysis of the sta2 mutation implicates a requirement for D-p40 during oogenesis and imaginal development, which is consistent with the expression of sta throughout development. In addition, we have analyzed the basis of the sta1 visible phenotype which consists of shortened antennae and bristles. sta1 is a translocation of the 1E1-2 to 2B3-4 region of the X chromosome onto the third chromosome at 89B21-C4. We provide genetic evidence that Dp(1;3)sta1 is mutant at the spineless (ss) locus and that it is associated with partial D-p40 activity. We demonstrate that sta1 acts as a recessive enhancer of ss; reduction in the amount of D-p40 provided by the transposed X chromosomal region of sta1 reveals a haplo-insufficient phenotype of the otherwise recessive ss mutations. This phenomenon is reminiscent of the enhancing effect observed with Minute mutations, one of which, rp49, has previously been shown to encode a ribosomal protein}, keywords = {0,ACID,ACIDS,Amino Acid Sequence,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,anatomy & histology,Animals,Base Sequence,Comparative Study,Conserved Sequence,CrossesGenetic,development,Dna,DNAComplementary,Drosophila,Drosophila melanogaster,Drosophila Proteins,DROSOPHILA-MELANOGASTER,embryology,EmbryoNonmammalian,ENCODES,expression,Female,gene,Gene Expression,GenesLethal,Genetic,genetics,genomic,Genomic Library,human,Humans,Hydra,in situ hybridization,Insect Proteins,La,Male,Molecular Sequence Data,MutagenesisInsertional,Mutation,MUTATIONS,nosource,Oogenesis,Phenotype,physiology,POSITION,protein,Proteins,REGION,Restriction Mapping,RIBOSOMAL-PROTEIN,Sequence HomologyAmino Acid,Support,TRANSCRIPT,TranscriptionGenetic,TRANSFORMATION,translocation,X Chromosome} }

@article{mendenhallFrameshiftSuppressorMutations1987a, title = {Frameshift Suppressor Mutations Affecting the Major Glycine Transfer {{RNAs}} of {{Saccharomyces}} Cerevisiae.}, author = {Mendenhall, M.D. and Leeds, P. and Fen, H. and Mathison, L. and Zwick, M. and Sleiziz, C. and Culbertson, M.R.}, year = 1987, month = mar, journal = {Journal of Molecular Biology}, volume = {194}, number = {1}, eprint = {3039147}, eprinttype = {pubmed}, pages = {41–58}, doi = {10.1016/0022-2836(87)90714-5}, url = {http://www.ncbi.nlm.nih.gov/pubmed/3039147}, keywords = {frameshift,Glycine,Mutation,MUTATIONS,nosource,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,TRANSFER-RNA} }

@article{menendezIS1473PutativeInsertion1997a, title = {{{IS1473}}, a Putative Insertion Sequence Identified in the Plasmid {{pAO1}} from Arthrobacter Nicotinovorans - Isolation, Characterization, and Distribution among Arthrobacter Species.}, author = {Menendez, C. and Igloi, G.L. and Brandsch, R.}, year = 1997, journal = {Plasmid}, volume = {37}, number = {1}, pages = {35–41}, doi = {10.1006/plas.1996.1272}, keywords = {Dna,Frameshifting,gene,Genes,Genome,nosource,Open Reading Frames,Operon,Plasmids,protein,sequence} }

@article{menningerPeptidylTransferRNA1975, title = {Peptidyl Transfer {{RNA}} Dissociates during Protein Synthesis from Ribosomes of ⬚{{Escherichia}} Coli⬚.}, author = {Menninger, J.R.}, year = 1975, journal = {J.Biol.Chem.}, volume = {251}, pages = {3392–3398}, doi = {10.1016/S0021-9258(17)33450-6}, keywords = {BINDING,Escherichia coli,ESCHERICHIA-COLI,nosource,P-SITE,peptidyl-transfer,protein,protein synthesis,PROTEIN-SYNTHESIS,ribosome,Ribosomes,Rna,TRANSFER-RNA,tRNA} } % == BibTeX quality report for menningerPeptidylTransferRNA1975: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{mereauVivoVitroStructurefunction1997a, title = {An in Vivo and in Vitro Structure-Function Analysis of the {{Saccharomyces}} Cerevisiae {{U3A snoRNP}}: Protein-{{RNA}} Contacts and Base-Pair Interaction with the Pre-Ribosomal {{RNA}}}, author = {Mereau, A. and Fournier, R. and Gregoire, A. and Mougin, A. and Fabrizio, P. and Luhrmann, R. and Branlant, C.}, year = 1997, month = oct, journal = {J.Mol.Biol.}, volume = {273}, number = {3}, pages = {552–571}, doi = {10.1006/jmbi.1997.1320}, url = {PM:9356246}, abstract = {The structure and accessibility of the S. cerevisiae U3A snoRNA was studied in semi-purified U3A snoRNPs using both chemical and enzymatic probes and in vivo using DMS as the probe. The results obtained show that S. cerevisiae U3A snoRNA is composed of a short 5’ domain with two stem-loop structures containing the phylogenetically conserved boxes A’ and A and a large cruciform 3’ domain containing boxes B, C, C’ and D. A precise identification of RNA-protein contacts is provided. Protection by proteins in the snoRNP and in vivo are nearly identical and were exclusively found in the 3’ domain. There are two distinct protein anchoring sites: (i), box C’ and its surrounding region, this site probably includes box D, (ii) the boxes B and C pair and the bases of stem-loop 2 and 4. Box C’ is wrapped by the proteins. RNA-protein interactions are more loose at the level of boxes C and D and a box C and D interaction is preserved in the snoRNP. In accord with this location of the protein binding sites, an in vivo mutational analysis showed that box C’ is important for U3A snoRNA accumulation, whereas mutations in the 5’ domain have little effect on RNA stability. Our in vivo probing experiments strongly suggest that, in exponentially growing cells, most of the U3A snoRNA molecules are involved in the 10- bp interaction with the 5’-ETS region and in two of the interactions recently proposed with 18S rRNA sequences. Our experimental study leads to a slightly revised version of the model of interaction proposed by J. Hughes. Single-stranded segments linking the heterologous helices are highly sensitive to DMS in vivo and their functional importance was tested by a mutational analysis}, keywords = {0,analysis,animal,Base Composition,Base Sequence,BINDING,Binding Sites,chemistry,DMS,genetics,human,IDENTIFICATION,In Vitro,IN-VITRO,IN-VIVO,La,Molecular Sequence Data,Mutagenesis,Mutation,MUTATIONAL ANALYSIS,MUTATIONS,nosource,Nucleic Acid Conformation,physiology,PRE-RIBOSOMAL-RNA,protein,Protein Binding,Proteins,Ribonucleoproteins,RibonucleoproteinsSmall Nuclear,Rna,RNA Precursors,RNA Stability,RNAFungal,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence HomologyNucleic Acid,stability,structure,Structure-Activity Relationship,Sulfuric Acid Esters,supportnon-u.s.gov’t} } % == BibTeX quality report for mereauVivoVitroStructurefunction1997a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{merrickMechanismRegulationEukaryotic1992, title = {Mechanism and Regulation of Eukaryotic Protein Synthesis.}, author = {Merrick, W.}, year = 1992, journal = {Microbiology and Molecular Biology Reviews}, volume = {56}, number = {2}, pages = {291–315}, publisher = {Am Soc Microbiol}, doi = {10.1128/mr.56.2.291-315.1992}, url = {http://mmbr.asm.org/cgi/content/abstract/56/2/291}, keywords = {eIF3,MECHANISM,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,regulation,Review} } % == BibTeX quality report for merrickMechanismRegulationEukaryotic1992: % ? unused Journal abbr (“Microbiol.Reviews”)

@article{merrickAssaysEukaryoticProtein1979, title = {Assays for Eukaryotic Protein Synthesis.}, author = {Merrick, W.C.}, year = 1979, journal = {Met.Enzymol.}, volume = {60}, pages = {108–123}, doi = {10.1016/S0076-6879(79)60011-3}, keywords = {assays,ATP,GTP,Hydrolysis,Methods,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,translation} } % == BibTeX quality report for merrickAssaysEukaryoticProtein1979: % ? Possibly abbreviated journal title Met.Enzymol.

@article{merrickCharacterizationProteinSynthesis1990, title = {Characterization of Protein Synthesis Factors from Rabbit Reticulocytes}, author = {Merrick, W.C. and Dever, T.E. and Kinzy, T.G. and Conroy, S.C. and Cavallius, J. and Owens, C.L.}, year = 1990, month = aug, journal = {Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression}, volume = {1050}, number = {1-3}, pages = {235–240}, publisher = {Elsevier}, doi = {10.1016/0167-4781(90)90173-Y}, url = {http://linkinghub.elsevier.com/retrieve/pii/016747819090173Y}, keywords = {Amino Acid Sequence,Amino Acids,analysis,EF-1,EF-1 alpha,EFTu,human,modification,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Reticulocytes,sequence,structure,translation} }

@article{merrymanNucleotides23RRNA1999, title = {Nucleotides in 23 {{S rRNA}} Protected by the Association of 30 {{S}} and 50 {{S}} Ribosomal Subunits}, author = {Merryman, C. and Moazed, D. and Daubresse, G. and Noller, H.F.}, year = 1999, month = jan, journal = {Journal of Molecular Biology}, volume = {285}, number = {1}, pages = {107–113}, doi = {10.1006/jmbi.1998.2243}, url = {ISI:000077968200010}, abstract = {We have studied the effect of subunit association on the accessibility of nucleotides in 23 S and 5 S rRNA. Escherichia coli 50 S subunits and 70 S ribosomes were subjected to a combination of chemical probes and the sites of attack identified by primer extension. Since the ribose groups and all of the bases were probed, the present study provides a comprehensive map of the nucleotides that are likely to be involved in subunit-subunit interactions. Upon subunit association, the bases of 22 nucleotides and the ribose groups of more than 60 nucleotides are protected in 23 S rRNA; no changes are seen in 5S rRNA. interestingly, the bases of nucleotides A1866, A1891 and A1896, and G2505 become more reactive to chemical probes, indicating localized rearrangement of the structure of the 50 S subunit upon association with the 30 S subunit. Most of the protected nucleotides are located in four stem-loop structures around positions 715, 890, 1700, and 1920. In free 50 S subunits, virtually all of the ribose groups in these four regions are strongly cleaved by hydroxyl radicals, suggesting that these stems protrude from the 50 S subunit. When the 30 S subunit is bound, most of the ribose groups in the 715, 890, 1700 and 1920 stemloops are protected, as are many bases in and around the corresponding apical loops. Intriguingly, three of the protected regions of 23 S rRNA are known to be linked via tertiary interactions to features of the peptidyl transferase center. Together with the juxtaposition of the subunit-protected regions of 16 S rRNA with the small subunit tRNA binding sites, our findings suggest the existence of a communication pathway between the codon-anticodon binding sites of the 30 S subunit with the peptidyl transferase center of the 50 S subunit via rRNA-rRNA interactions. (C) 1999 Academic Press}, keywords = {23S-LIKE,30 S,5 S rRNA,5S rRNA,BINDING,Binding Sites,Escherichia coli,ESCHERICHIA-COLI,ESCHERICHIA-COLI RIBOSOME,interface,LOCALIZATION,LOOP,nosource,Nucleotides,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,primer extension,REGION,Ribose,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNA CROSS-LINKS,rRNA,SERIES,SITE,SITES,structure,SUBUNIT,subunit association,tRNA} }

@article{meskauskasDecreasedPeptidyltransferaseActivity2003, title = {Decreased Peptidyltransferase Activity Correlates with Increased Programmed -1 Ribosomal Frameshifting and Viral Maintenance Defects in the Yeast ⬚{{Saccharomyces}} Cerevisiae⬚}, author = {Meskauskas, A. and Harger, J.W. and Jacobs, K.L.M. and Dinman, J.D.}, year = 2003, month = aug, journal = {RNA}, volume = {9}, number = {8}, pages = {982–992}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, doi = {10.1261/rna.2165803}, url = {http://www.rnajournal.org/cgi/doi/10.1261/rna.2165803 http://rnajournal.cshlp.org/content/9/8/982.short}, abstract = {Increased efficiencies of programmed -1 ribosomal frameshifting⬚ in yeast cells expressing mutant forms of ribosomal protein L3 are unable to maintain the dsRNA “Killer” virus. Here we demonstrate that changes in frameshifting and virus maintenance in these mutants correlates with decreased peptidyltransferase activities. The mutants did not affect Ty⬚1⬚-directed programmed +1 ribosomal frameshifting or nonsense-mediated mRNA decay. Independent experiments demonstrate similar programmed -1 ribosomal frameshifting specific defects in cells lacking ribosomal protein L41, which has previously been shown to result in peptidyltransferase defects in yeast. These findings are consistent with the hypothesis that decreased peptidyltransferase activity should result in longer ribosome pause times after the accommodation step of the elongation cycle, allowing more time for ribosomal slippage at programmed -1 ribosomal frameshift signals. ⬚}, keywords = {1,antibiotics,DECAY,direction,drugs,efficiency,elongation,events most com-,frameshift,frameshifting,Frameshifting,in either the 5,L3,L41,monly induce translating ribosomes,mRNA,mRNA decay,nosource,or 3,Peptidyltransferase,prf,programmed ribosomal frameshift,protein,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,ribosome,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SIGNAL,single base,SLIPPAGE,though examples,to slip by a,virus,yeast} }

@article{meskauskasRibosomalProteinL32007, title = {Ribosomal Protein {{L3}}: {{Gatekeeper}} to the {{A-site}}.}, author = {Meskauskas, A. and Dinman, J.D.}, year = 2007, month = mar, journal = {Mol. Cell}, volume = {25}, number = {6}, pages = {877–888}, issn = {1097-2765}, doi = {10.1016/j.molcel.2007.02.015}, url = {⬚http://download.molecule.org/pdfs/1097-2765/PIIS1097276507001153.pdf ⬚}, abstract = {Ribosomal protein L3 (L3) is an essential and indispensable component for formation of the peptidyltransferase center (PTC), and many studies have demonstrated roles for L3 in virus propagation and resistance to specific antibiotics. Atomic resolution ribosome structures reveal the presence of N-terminal and central extensions of L3 that extend deep into the core of the large subunit. In the current study, site-specific mutagenesis was used to generate a library of mutants of the central extension of ⬚RPL3⬚ in ⬚Saccharomyces. cerevisiae⬚. Genetic analyses show that a predicted interaction between the tip of the central extension and A2940 of 25S rRNA (equivalent to ⬚E. coli⬚ 23S rRNA A2572) are critical for viability, and that this extension is able to flex toward its N-terminal side. Structural analyses of mutant ribosomes revealed large conformational changes in the A-loop, along the A-site periphery of the peptidyltransferase center, and along the path taken by aa-tRNA during the process of accommodation. Biochemical studies demonstrate that resistance to the A-site specific translational inhibitor anisomycin strongly correlates with increased affinity for aa-tRNA and decreased affinity for eEF-2, suggesting a model in which the L3 central extension functions as an allosteric switch to coordinate the functions of the ribosomal elongation factor binding site. These changes were also found to affect peptidyltransferase activity, which stimulated rates of programmed -1 ribosomal frameshifting, which in turn promoted virus propagation defects. Thus, these studies provide a basis for deeper insight for rational design of small molecule antiviral therapeutics.}, pmid = {17386264}, keywords = {A SITE,A-SITE,anisomycin,antibiotic,antibiotics,antiviral,Base Sequence,BINDING,Binding Sites,BINDING-SITE,CEREVISIAE,COMPONENT,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,E,elongation,Escherichia coli,Escherichia coli: genetics,Frameshifting,Gene Amplification,Genetic,INHIBITOR,Kinetics,L3,library,MODEL,Models,Molecular,Molecular Sequence Data,Mutagenesis,MUTANTS,nosource,Nucleic Acid Conformation,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,PROPAGATION,protein,Protein Conformation,Recombinant Proteins,Recombinant Proteins: chemistry,Recombinant Proteins: metabolism,RESISTANCE,RESOLUTION,Ribosomal,ribosomal frameshifting,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: metabolism,RIBOSOMAL-PROTEIN,Ribosomal: chemistry,Ribosomal: metabolism,ribosome,Ribosomes,RNA,rRNA,Saccharomyces,SITE,site specific,SITE-SPECIFIC MUTAGENESIS,Structural,structure,SUBUNIT,Tryptophan,Tryptophan: metabolism,virus} } % == BibTeX quality report for meskauskasRibosomalProteinL32007: % ? Possibly abbreviated journal title Mol. Cell

@article{meskauskasStructureFunctionAnalysis2008, title = {Structure/Function Analysis of Yeast Ribosomal Protein {{L2}}}, author = {Meskauskas, A. and Russ, J.R. and Dinman, J.D.}, year = 2008, month = apr, journal = {Nucleic Acids Res.}, volume = {36}, number = {6}, pages = {1826–1835}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkn034}, url = {http://nar.oxfordjournals.org/content/36/6/1826.short}, abstract = {Ribosomal protein L2 is a core element of the large subunit that is highly conserved among all three kingdoms. L2 contacts almost every domain of the large subunit rRNA and participates in an intersubunit bridge with the small subunit rRNA. It contains a solvent-accessible globular domain that interfaces with the solvent accessible side of the large subunit that is linked through a bridge to an extension domain that approaches the peptidyltransferase center. Here, screening of randomly generated library of yeast RPL2A alleles identified three translationally defective mutants, which could be grouped into two classes. The V48D and L125Q mutants map to the globular domain. They strongly affect ribosomal A-site associated functions, peptidyltransferase activity and subunit joining. H215Y, located at the tip of the extended domain interacts with Helix 93. This mutant specifically affects peptidyl-tRNA binding and peptidyltransferase activity. Both classes affect rRNA structure far away from the protein in the A-site of the peptidyltransferase center. These findings suggest that defective interactions with Helix 55 and with the Helix 65-66 structure may indicate a certain degree of flexibility in L2 in the neck region between the two other domains, and that this might help to coordinate tRNA-ribosome interactions}, keywords = {A SITE,A-SITE,Alleles,analysis,BINDING,BIOLOGY,DOMAIN,DOMAINS,Genetic,genetics,interface,L2,La,library,microbiology,MOLECULAR-GENETICS,MUTANTS,nosource,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,protein,REGION,RIBOSOMAL-PROTEIN,rRNA,structure,structure/function,SUBUNIT,Support,yeast} } % == BibTeX quality report for meskauskasStructureFunctionAnalysis2008: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{meskauskasRibosomalProteinL32008a, title = {Ribosomal Protein {{L3}} Functions as a ‘rocker Switch’ to Aid in Coordinating of Large Subunit-Associated Functions in Eukaryotes and {{Archaea}}}, author = {Meskauskas, A. and Dinman, J.D.}, year = 2008, month = oct, journal = {Nucleic Acids Res.}, volume = {36⬚ ⬚}, number = {19}, pages = {6175–6186}, doi = {10.1093/nar/gkn642}, url = {PM:18832371}, abstract = {Although ribosomal RNAs (rRNAs) comprise the bulk of the ribosome and carry out its main functions, ribosomal proteins also appear to play important structural and functional roles. Many ribosomal proteins contain long, nonglobular domains that extend deep into the rRNA cores. In eukaryotes and Archaea, ribosomal protein L3 contains two such extended domains tethered to a common globular hub, thus providing an excellent model to address basic questions relating to ribosomal protein structure/function relationships. Previous work in our laboratory identified the central ‘W-finger’ extension of yeast L3 in helping to coordinate ribosomal functions. New studies on the ‘N-terminal’ extension in yeast suggest that it works with the W-finger to coordinate opening and closing of the corridor through which the 3’ end of aa-tRNA moves during the process of accommodation. Additionally, the effect of one of the L3 N-terminal extension mutants on the interaction between C75 of the aa-tRNA and G2921 (Escherichia coli G2553) of 25S rRNA provides the first evidence of the effect of a ribosomal protein on aa-tRNA positioning and peptidyltransfer, possibly through the induced fit model. A model is presented describing how all three domains of L3 may function together as a ‘rocker switch’ to coordinate the stepwise processes of translation elongation}, keywords = {3,Archaea,BIOLOGY,DOMAIN,DOMAINS,elongation,Escherichia coli,ESCHERICHIA-COLI,Genetic,genetics,L3,La,microbiology,MODEL,MOF,MOLECULAR-GENETICS,MUTANTS,nosource,protein,Proteins,Ribosomal Proteins,ribosomal RNA,RIBOSOMAL-PROTEIN,RIBOSOMAL-RNA,ribosome,Rna,rRNA,Structural,structure/function,translation,yeast} } % == BibTeX quality report for meskauskasRibosomalProteinL32008a: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{meulenbergSubgenomicRnasLelystad1993, title = {Subgenomic {{Rnas}} of {{Lelystad Virus Contain A Conserved Leader Body Junction Sequence}}}, author = {Meulenberg, J.J.M. and Demeijer, E.J. and Moormann, R.J.M.}, year = 1993, journal = {Journal of General Virology}, volume = {74}, number = {8}, pages = {1697–1701}, publisher = {Soc General Microbiol}, doi = {10.1099/0022-1317-74-8-1697}, url = {http://vir.sgmjournals.org/cgi/content/abstract/74/8/1697}, abstract = {During the replication of Lelystad virus in alveolar lung macrophages, a 3’-coterminal nested set of six subgenomic RNAs (RNA2 to RNA7) is formed. These contain a common leader sequence derived from the 5’ non-coding region of the genomic RNA. In this study, the sequence of the junction sites. i.e. the sites where the leader sequence joins to the body of the subgenomic RNA, was determined for all six subgenomic RNAs. For each subgenomic RNA, six to nine cDNA clones were isolated by means of reverse transcription and PCR. The nucleotide sequence at the junction site was identical for all eight cDNA clones derived from subgenomic RNA4. However, heterogeneity was observed in the nucleotide sequence surrounding the junction sites of the cDNA clones derived from subgenomic RNAs 2, 3, 5, 6 and 7. This heterogeneity suggests that the fusion of the leader to the body of the subgenomic RNA may be imprecise. The junction sites of the six subgenomic RNAs had a conserved sequence motif of six nucleotides (UCAACC or a highly similar sequence). The distance between the junction site and the translation initiation codon of the downstream open reading frame varied from nine to 83 nucleotides}, keywords = {3,BODIES,Codon,Conserved Sequence,CORONAVIRUS MESSENGER-RNAS,DOWNSTREAM,FRAME,genomic,GENOMIC RNA,initiation,M,MOUSE HEPATITIS-VIRUS,nosource,NUCLEOTIDE-SEQUENCE,Nucleotides,OPEN READING FRAME,PCR,READING FRAME,REGION,REPLICATION,Rna,sequence,SITE,SITES,SUBGENOMIC RNAS,SYSTEM,transcription,translation,TRANSLATION INITIATION,virus} } % == BibTeX quality report for meulenbergSubgenomicRnasLelystad1993: % ? Title looks like it was stored in title-case in Zotero

@article{mialeNeuroblastomaStageIVS1994, title = {Neuroblastoma Stage {{IV-S}}.}, author = {Miale, T.D. and Kirpekar, K.}, year = 1994, journal = {Medical Oncology}, volume = {11}, number = {3}, pages = {89–100}, publisher = {Springer}, doi = {10.1007/BF02999856}, url = {http://www.springerlink.com/index/B8304365113116N5.pdf}, keywords = {nosource,ras,Review} }

@article{michaelDistinctDomainsRibosomal1996, title = {Distinct Domains in Ribosomal Protein {{L5}} Mediate 5 {{S rRNA}} Binding and Nucleolar Localization}, author = {Michael, W.M. and Dreyfuss, G.}, year = 1996, month = may, journal = {Journal of Biological Chemistry}, volume = {271}, number = {19}, pages = {11571–11574}, publisher = {ASBMB}, doi = {10.1074/jbc.271.19.11571}, url = {http://www.jbc.org/content/271/19/11571.short}, abstract = {Ribosomal protein L5, a 34-kDa large ribosomal subunit protein, binds to 5 S rRNA and has been implicated in the intracellular transport of 5 S rRNA. By immunofluorescence microscopy, L5 is detected mostly in the nucleolus with a fainter signal in the nucleoplasm, and it is known to also be a component of large ribosomal subunits in the cytoplasm. 5 S rRNA is transcribed in the nucleoplasm, and L5 is thought to play an important role in delivering 5 S rRNA to the nucleolus. Using RNA-binding assays and transfection experiments, we have delineated the domains within L5 that confer its 5 S rRNA binding activity and that localize it to the nucleolus. We found that the amino-terminal 93 amino acids are necessary and sufficient to bind 5 S rRNA in vitro, while the carboxyl-terminal half of the protein, comprising amino acids 151-296, serves to localize the protein to the nucleolus. L5, therefore, has a modular domain structure reminiscent of other RNA transport proteins where one region of the molecule serves to bind RNA while another determines subcellular localization}, keywords = {0,5 S rRNA,ACID,ACIDS,Amino Acid Sequence,Amino Acids,AMINO-ACID,AMINO-ACIDS,animal,Archaea,assays,BINDING,Cell Nucleolus,chemistry,Comparative Study,COMPONENT,Conserved Sequence,Cytoplasm,Dna,DNAComplementary,DOMAIN,DOMAINS,Gene Library,Hela Cells,human,In Vitro,IN-VITRO,L5,La,LOCALIZATION,metabolism,Molecular Sequence Data,nosource,nucleolus,Oryza sativa,Polymerase Chain Reaction,protein,Proteins,Rats,Recombinant Proteins,REGION,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,Rna,RNARibosomal5S,rRNA,S,Schizosaccharomyces,Sequence Deletion,Sequence HomologyAmino Acid,Sequence Tagged Sites,SIGNAL,structure,SUBCELLULAR-LOCALIZATION,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Transfection,TRANSPORT} } % == BibTeX quality report for michaelDistinctDomainsRibosomal1996: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{michelModellingThreedimensionalArchitecture1990, title = {Modelling of the {{Three-dimensional Architecture}} of {{Group I Catalytic Introns Based}} on {{Comparative Sequence Analysis}}.}, author = {Michel, F. and Westhof, E.}, year = 1990, month = dec, journal = {Journal of molecular biology}, volume = {216}, number = {3}, pages = {585–610}, publisher = {Elsevier}, doi = {10.1016/0022-2836(90)90386-Z}, url = {http://linkinghub.elsevier.com/retrieve/pii/002228369090386Z}, abstract = {Alignment of the 87 available sequences of group I self-splicing introns reveals numerous instances of covariation between distant sites. Some of these covariations cannot be ascribed to historical coincidences or the known secondary structure of group I introns, and are, therefore, best explained as reflecting tertiary contacts. With the help of stereochemical modelling, we have taken advantage of these novel interactions to derive a three-dimensional model of the conserved core of group I introns. Two noteworthy features of that model are its extreme compactness and the fact that all of the most evolutionarily conserved residues happen to converge around the two helices that constitute the substrate of the core ribozyme and the site that binds the guanosine cofactor necessary for self-splicing. Specific functional implications are discussed, both with regard to the way the substrate helices are recognized by the core and possible rearrangements of the introns during the self-splicing process. Concerning potential long- range interactions, emphasis is put on the possible recognition of two consecutive purines in the minor groove of a helix by a GAAA or related terminal loop}, keywords = {0,alignment,analysis,animal,Base Sequence,Computer Simulation,enzymology,Guanosine,Introns,La,ModelsGenetic,ModelsMolecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,physiology,Purines,ribozyme,Rna,RNACatalytic,Saccharomyces cerevisiae,sequence,Sequence Analysis,Sequence HomologyNucleic Acid,structure,Tetrahymena} } % == BibTeX quality report for michelModellingThreedimensionalArchitecture1990: % ? unused Journal abbr (“J.Mol.Biol.”)

@article{michielsSolutionStructurePseudoknot2001, title = {Solution Structure of the Pseudoknot of {{SRV}} -1 {{RNA}}, Involved in Ribosomal Frameshifting}, author = {Michiels, P.J. and Versleijen, A.A. and Verlaan, P.W. and Pleij, C.W. and Hilbers, C.W. and Heus, H.A.}, year = 2001, month = jul, journal = {Journal of Molecular Biology}, volume = {310}, number = {5}, pages = {1109–1123}, publisher = {Elsevier}, doi = {10.1006/jmbi.2001.4823}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283601948235 http://www.sciencedirect.com/science/article/pii/s0022-2836(01)94823-5}, abstract = {RNA pseudoknots play important roles in many biological processes. In the simian retrovirus type-1 (SRV-1) a pseudoknot together with a heptanucleotide slippery sequence are responsible for programmed ribosomal frameshifting, a translational recoding mechanism used to control expression of the Gag-Pol polyprotein from overlapping gag and pol open reading frames. Here we present the three-dimensional structure of the SRV-1 pseudoknot determined by NMR. The structure has a classical H-type fold and forms a triple helix by interactions between loop 2 and the minor groove of stem 1 involving base-base and base-sugar interactions and a ribose zipper motif, not identified in pseudoknots so far. Further stabilization is provided by a stack of five adenine bases and a uracil in loop 2, enforcing a cytidine to bulge. The two stems of the pseudoknot stack upon each other, demonstrating that a pseudoknot without an intercalated base at the junction can induce efficient frameshifting. Results of mutagenesis data are explained in context with the present three-dimensional structure. The two base-pairs at the junction of stem 1 and 2 have a helical twist of approximately 49 degrees, allowing proper alignment and close approach of the three different strands at the junction. In addition to the overwound junction the structure is somewhat kinked between stem 1 and 2, assisting the single adenosine in spanning the major groove of stem 2. Geometrical models are presented that reveal the importance of the magnitude of the helical twist at the junction in determining the overall architecture of classical pseudoknots, in particular related to the opening of the minor groove of stem 1 and the orientation of stem 2, which determines the number of loop 1 nucleotides that span its major groove}, keywords = {Adenine,Adenosine,alignment,Base Pairing,Base Sequence,chemistry,expression,Frameshifting,Frameshifting-Ribosomal,FrameshiftingRibosomal,Gag,Gag-pol,Gene Expression Regulation-Viral,Gene Expression RegulationViral,Genes-Viral,GenesViral,genetics,MECHANISM,metabolism,models,Models-Genetic,Models-Molecular,ModelsGenetic,ModelsMolecular,Molecular Sequence Data,Molecular Structure,Mutagenesis,Mutation,nosource,Nuclear Magnetic Resonance-Biomolecular,Nuclear Magnetic ResonanceBiomolecular,Nucleic Acid Conformation,Nucleotides,Open Reading Frames,pol,pseudoknot,recoding,retrovirus,Retroviruses-Simian,RetrovirusesSimian,Ribose,ribosomal frameshifting,Rna,RNA PSEUDOKNOT,RNA Stability,Rna-Viral,RnaViral,sequence,structure,support-non-u.s.gov’t,supportnon-u.s.gov’t,Thermodynamics} } % == BibTeX quality report for michielsSolutionStructurePseudoknot2001: % ? unused Journal abbr (“J.Mol.Biol.”)

@article{michimotoYeastPdr13pZuo1p2000, title = {Yeast {{Pdr13p}} and {{Zuo1p}} Molecular Chaperones Are New Functional {{Hsp70}} and {{Hsp40}} Partners}, author = {Michimoto, T. and Aoki, T. and {Toh-e}, A. and Kikuchi, Y.}, year = 2000, month = oct, journal = {Gene}, volume = {257}, number = {1}, pages = {131–137}, publisher = {Elsevier}, doi = {10.1016/S0378-1119(00)00381-4}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0378111900003814}, abstract = {The deletion of the TOM1 gene encoding a putative ubiquitin ligase causes a temperature sensitive cellular growth in Saccharomyces cerevisiae. The arrested cells exhibit pleiotropic defects in nuclear division, maintenance of nuclear structure and heat stress responses. We previously identified a zuo1 mutation as an extragenic suppressor of the tom1 mutant. ZUO1 encodes a DnaJ-related Hsp40. Here we show that a recessive cold sensitive mutation in PDR13 coding for an Hsp70 suppressed the tom1 mutation. The pdr13 deletion mutant was sensitive to high osmolarity, just like the zuo1 deletion mutant. A zuo1 pdr13 double deletion mutant did not show additive phenotypes. Furthermore, a tagged-Zuo1p was co-immunoprecipitated with a tagged Pdr13p. Taken together, we propose that Pdr13p and Zuo1p are a new pair of Hsp70:Hsp40 molecular chaperones. In addition, Pdr13p co-sedimented with translating ribosomes and this association was independent of the presence of Zuo1p. (C) 2000 Elsevier Science B.V. All rights reserved}, keywords = {ASSOCIATION,CELLS,CEREVISIAE,chaperone,Cold,DNAJ,DnaK-DnaJ pair,ENCODES,gene,GROWTH,Heat,heat shock proteins,Molecular Chaperones,Mutation,nosource,Phenotype,protein,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Stress,stress response,structure,Temperature,TOM1,translation,Ubiquitin,yeast} }

@article{mikulikChangesRibosomeFunction2001, title = {Changes in Ribosome Function Induced by Protein Kinase Associated with Ribosomes of {{Streptomyces}} Collinus Producing Kirromycin}, author = {Mikulik, K. and Suchan, P. and Bobek, J.}, year = 2001, month = nov, journal = {Biochemical and biophysical research communications}, volume = {289}, number = {2}, pages = {434–443}, publisher = {Elsevier}, doi = {10.1006/bbrc.2001.6017}, url = {PM:11716492 http://linkinghub.elsevier.com/retrieve/pii/S0006291X01960176}, abstract = {Protein kinase associated with ribosomes of streptomycetes phosphorylates 11 ribosomal proteins. Phosphorylation activity of protein kinase reaches its maximum at the end of exponential phase of growth. When (32)P-labeled cells from the end of exponential phase of growth were transferred to a fresh medium, after 2 h of cultivation ribosomal proteins lost more than 90% of (32)P and rate of polypeptide synthesis increases twice. Protein kinase cross-reacting with antibody raised against protein kinase C was partially purified from 1 M NH(4)Cl wash of ribosomes and used to phosphorylation of ribosomes. Phosphorylation of 50S subunits (L2, L3, L7, L16, L21, L23, and L27) had no effect on the integrity of subunits but affects association with 30 to 70S monosomes. In vitro system derived from ribosomal subunits was used to examine the activity of phosphorylated 50S at poly(U) translation. Replacement unphosphorylated 50S with 50S possessed of phosphorylated r-proteins leads to the reduction of polypeptide synthesis of about 52%. The binding of N-Ac[(14)C]Phe-tRNA to A-site of phosphorylated ribosomes is not affected but the rate of peptidyl transferase is more than twice lower than that in unphosphorylated ribosomes. These results provide evidence that phosphorylation of ribosomal proteins is involved in mechanisms regulating the translational system of Streptomyces collinus}, keywords = {0,A SITE,A-SITE,Anti-Bacterial Agents,Antibodies,antibody,ASSOCIATION,BINDING,Binding Sites,Cell-Free System,CELLS,chemistry,ElectrophoresisGelTwo-Dimensional,GROWTH,Guanosine,Guanosine Triphosphate,In Vitro,IN-VITRO,kinase,KINASE-C,L2,L3,La,M,MECHANISM,MECHANISMS,media,metabolism,microbiology,nosource,peptidyl transferase,PEPTIDYL-TRANSFERASE,Peptidyltransferase,Phosphorylation,physiology,POLYPEPTIDE,protein,Protein Binding,Protein Kinase C,Protein Kinases,PROTEIN-KINASE,Proteins,Pyridones,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNATransferAmino Acyl,Signal Transduction,Streptomyces,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,SYSTEM,Time Factors,translation,TranslationGenetic,tRNA} } % == BibTeX quality report for mikulikChangesRibosomeFunction2001: % ? unused Journal abbr (“Biochem.Biophys.Res.Commun.”)

@article{millerUseRetroviralVectors1993, title = {Use of Retroviral Vectors for Gene Transfer and Expression}, author = {Miller, A.D. and Miller, D.G. and Garcia, J.V. and Lynch, C.M.}, year = 1993, journal = {Methods in Enzymology}, volume = {217}, pages = {581–599}, publisher = {Elsevier}, doi = {10.1016/0076-6879(93)17090-R}, url = {http://cat.inist.fr/?aModele=afficheN&cpsidt=4744082}, keywords = {expression,gene,nosource,vector,vectors} }

@article{millerSequencesThatSurround1989a, title = {Sequences That Surround the Stop Codons of Upstream Open Reading Frames in ⬚{{GCN4}}⬚ {{mRNA}} Determine Their Distinct Functions in Translational Control.}, author = {Miller, P.F. and Hinnebusch, A.G.}, year = 1989, journal = {Genes & Dev.}, volume = {3}, pages = {1217–1225}, doi = {10.1101/gad.3.8.1217}, keywords = {Codon,GCN4,mRNA,nosource,Open Reading Frames,sequence,STOP CODON} } % == BibTeX quality report for millerSequencesThatSurround1989a: % ? Possibly abbreviated journal title Genes & Dev.

@article{millerPurificationCharacterizationGiardiaLamblia1988, title = {Purification and {{Characterization}} of the {{Giardia-Lamblia Double-Stranded-Rna Virus}}}, author = {Miller, R.L. and Wang, A.L. and Wang, C.C.}, year = 1988, month = apr, journal = {Molecular and Biochemical Parasitology}, volume = {28}, number = {3}, pages = {189–195}, publisher = {Elsevier}, doi = {10.1016/0166-6851(88)90003-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/0166685188900035}, keywords = {DOUBLE-STRANDED-RNA,nosource,purification,virus} } % == BibTeX quality report for millerPurificationCharacterizationGiardiaLamblia1988: % ? Title looks like it was stored in title-case in Zotero

@article{milliganOligoribonucleotideSynthesisUsing1987, title = {Oligoribonucleotide Synthesis Using {{T7 RNA}} Polymerase and Synthetic {{DNA}} Templates}, author = {Milligan, J.F. and Groebe, D.R. and Witherell, G.W. and Uhlenbeck, O.C.}, year = 1987, month = nov, journal = {Nucleic acids research}, volume = {15}, number = {21}, pages = {8783–8798}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/15.21.8783}, url = {http://nar.oxfordjournals.org/content/15/21/8783.short}, abstract = {A method is described to synthesize small RNAs of defined length and sequence using T7 RNA polymerase and templates of synthetic DNA which contain the T7 promoter. Partially single stranded templates which are base paired only in the -17 to +1 promoter region are just as active in transcription as linear plasmid DNA. Runoff transcripts initiate at a unique, predictable position, but may have one nucleotide more or less on the 3’ terminus. In addition to the full length products, the reactions also yield a large amount of smaller oligoribonucleotides in the range from 2 to 6 nucleotides which appear to be the result of abortive initiation events. Variants in the +1 to +6 region of the promoter are transcribed with reduced efficiency but increase the variety of RNAs which can be made. Transcription reaction conditions have been optimized to allow the synthesis of milligram amounts of virtually any RNA from 12 to 35 nucleotides in length}, keywords = {BASE,chemical synthesis,chemistry,Dna,DNA-Directed RNA Polymerase,DNA-Directed RNA Polymerases,efficiency,enzymology,genetics,initiation,La,metabolism,nosource,Nucleotides,Oligoribonucleotides,PLASMID,polymerase,POSITION,PRODUCT,PRODUCTS,PROMOTER,Promoter Regions (Genetics),protein,Proteins,REGION,Rna,RNA-POLYMERASE,sequence,supportu.s.gov’tp.h.s.,T-Phages,T7 RNA pol,TEMPLATE,Templates,TemplatesGenetic,TRANSCRIPT,transcription,TranscriptionGenetic,Viral Proteins} } % == BibTeX quality report for milliganOligoribonucleotideSynthesisUsing1987: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{mindellMultipleIndependentOrigins1998, title = {Multiple Independent Origins of Mitochondrial Gene Order in Birds}, author = {Mindell, D.P. and Sorenson, M.D. and Dimcheff, D.E.}, year = 1998, journal = {Proceedings of the National Academy of Sciences}, volume = {95}, number = {18}, pages = {10693–10697}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.95.18.10693}, url = {http://www.pnas.org/content/95/18/10693.short}, abstract = {Mitochondrial genomes of all vertebrate animals analyzed to date have the same 37 genes, whose arrangement in the circular DNA molecule varies only in the relative position of a few genes. This relative conservation suggests that mitochondrial gene order characters have potential utility as phylogenetic markers for higher-level vertebrate taxa. We report discovery of a mitochondrial gene order that has had multiple independent originations within birds, based on sampling of 137 species representing 13 traditionally recognized orders. This provides evidence of parallel evolution in mitochondrial gene order for animals. Our results indicate operation of physical constraints on mitochondrial gene order changes and support models for gene order change based on replication error. Bird mitochondria have a displaced OL (origin of light-strand replication site) as do various other Reptilia taxa prone to gene order changes. Our findings point to the need for broad taxonomic sampling in using mitochondrial gene order for phylogenetic analyses. We found, however, that the alternative mitochondrial gene orders distinguish the two primary groups of songbirds (order Passeriformes), oscines and suboscines, in agreement with other molecular as well as morphological data sets. Thus, although mitochondrial gene order characters appear susceptible to some parallel evolution because of mechanistic constraints, they do hold promise for phylogenetic studies}, keywords = {animal,Animals,ARRANGEMENT,BIOLOGY,CHARACTER,DISCOVERY,Dna,Evolution,gene,Genes,Genome,La,MARKER,mitochondria,MODEL,models,nosource,POSITION,REPLICATION,replication site,SITE,Support} } % == BibTeX quality report for mindellMultipleIndependentOrigins1998: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{mitchellMusingStructuralOrganization2000, title = {Musing on the Structural Organization of the Exosome Complex}, author = {Mitchell, P. and Tollervey, D.}, year = 2000, month = oct, journal = {Nature Structural & Molecular Biology}, volume = {7}, number = {10}, pages = {843–846}, publisher = {Nature Publishing Group}, doi = {10.1038/82817}, url = {http://www.nature.com/nsmb/journal/v7/n10/abs/nsb1000_843.html}, abstract = {The exosome complex of 3’–{\(>\)}5’ exoribonucleases functions in both the precise processing of 3’ extended precursor molecules to mature stable RNAs and the complete degradation of other RNAs. Both processing and degradative activities of the exosome depend on additional cofactors, notably the putative RNA helicases Mtr4p and Ski2p. It is not known how these factors regulate exosome function or how the exosome distinguishes RNAs destined for processing events from substrates that are to be completely degraded. Here we review the available data concerning the modes of action of the exosome and relate these to possible structural arrangements for the complex. As no detailed structural data are yet available for the exosome complex, or any of its constituent enzymes, this discussion will rely heavily on rather speculative models}, keywords = {20473220,Allosteric Regulation,chemistry,COMPLEX,COMPLEXES,degradation,enzyme,Exoribonucleases,exosome,Helicase,metabolism,models,ModelsMolecular,nosource,Protein Conformation,Review,Rna,RNA Helicases,Structural,Substrate Specificity,supportnon-u.s.gov’t} } % == BibTeX quality report for mitchellMusingStructuralOrganization2000: % ? unused Journal abbr (“Nat.Struct.Biol.”)

@article{mitchellMRNAStabilityEukaryotes2000, title = {{{mRNA}} Stability in Eukaryotes}, author = {Mitchell, P. and Tollervey, D.}, year = 2000, month = apr, journal = {Current opinion in genetics & development}, volume = {10}, number = {2}, pages = {193–198}, publisher = {Elsevier}, doi = {10.1016/S0959-437X(00)00063-0}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0959437X00000630}, abstract = {During the past two years, the role of the proteins HuR and hnRNP D in regulated mRNA degradation in humans has become clearer, and a putative mRNA deadenylase, DAN or PARN, has been identified. In yeast, the relationship between translation and mRNA turnover is clearer, but the mRNA decapping process has turned out to be unexpectedly complex}, keywords = {0,animal,BIOLOGY,COMPLEX,COMPLEXES,D,degradation,Eukaryotic Cells,human,La,metabolism,mRNA,mRNA stability,mRNA turnover,nosource,protein,Proteins,Review,Rna,RNA Stability,RNAMessenger,stability,supportnon-u.s.gov’t,translation,turnover,yeast} } % == BibTeX quality report for mitchellMRNAStabilityEukaryotes2000: % ? unused Journal abbr (“Curr.Opin.Genet.Dev.”)

@article{mitchellNMDPathwayYeast2003a, title = {An {{NMD}} Pathway in Yeast Involving Accelerated Deadenylation and Exosome-Mediated 3 ‘-{\(>\)} 5’ Degradation}, author = {Mitchell, P. and Tollervey, D.}, year = 2003, month = may, journal = {Molecular Cell}, volume = {11}, number = {5}, pages = {1405–1413}, doi = {10.1016/S1097-2765(03)00190-4}, url = {ISI:000183139400029}, abstract = {Eukaryotic mRNAs containing premature termination codons are subjected to accelerated turnover, known as nonsense-mediated decay (NMD). Recognition of translation termination events as premature requires a surveillance complex, which includes the RNA helicase Upf1p. In Saccharomyces cerevisiae, NMD provokes rapid decapping followed by 5’–{\(>\)}3’exonucleolytic decay. Here we report an alternative, decapping-independent NMD pathway involving deadenylation and subsequent 3’–{\(>\)}5’ exonucleolytic decay. Accelerated turnover via this pathway required Upf1p and was blocked by the translation inhibitor cycloheximide. Degradation of the deadenylated mRNA required the Rrp4p and Ski7p components of the cytoplasmic exosome complex, as well as the putative RNA helicase Ski2p. We conclude that recognition of NMD substrates by the Upf surveillance complex can target mRNAs to rapid deadenylation and exosome-mediated degradation}, keywords = {3,5.8S RIBOSOMAL-RNA,Codon,CODONS,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,Cycloheximide,CYTOPLASMIC TRANSLATION,DEADENYLATION,DECAPPING ENZYME,DECAY,degradation,EXON-EXON JUNCTIONS,exosome,Helicase,IDENTIFICATION,INHIBITOR,MESSENGER-RNA DECAY,mRNA,NMD,NONSENSE,nonsense-mediated decay,nosource,PREMATURE TERMINATION CODON,RECOGNITION,REQUIRES,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SURVEILLANCE,SURVEILLANCE COMPLEX,TARGET,termination,TERMINATION CODON,translation,TRANSLATION TERMINATION,turnover,UPF,yeast} }

@article{mitraYeastRibosomalProtein1984a, title = {A Yeast Ribosomal Protein Gene Whose Intron Is in the 5’ Leader}, author = {Mitra, G. and Warner, J.R.}, year = 1984, month = jul, journal = {J.Biol.Chem.}, volume = {259}, number = {14}, pages = {9218–9224}, doi = {10.1016/S0021-9258(17)47288-7}, abstract = {The complete gene encoding yeast ribosomal protein 29, a component of the 60 S ribosomal subunit of Saccharomyces cerevisiae has been isolated and its nucleotide sequence determined. The coordinates of transcription initiation and termination of the rp29 gene have been mapped. Transcription appears to start at several sites, spanning nearly 30 nucleotides. The gene is transcribed into a precursor RNA molecule of 1110 to 1085 nucleotides from which an intron of 458 nucleotides is spliced out. The splice junction has been determined by comparing the nucleotide sequences of the rp29 gene with those of a homologous cDNA clone. Interestingly, the intron of the rp29 gene resides in the 5’ untranslated region of the rp29 mRNA, the first instance where this has been observed in yeast. The single open reading frame in the rp29 gene encodes a very basic protein of 155 amino acid residues}, keywords = {84264556,Amino Acid Sequence,analysis,Base Sequence,COMPONENT,DNA Restriction Enzymes,gene,GenesFungal,GenesStructural,Genetic Vectors,genetics,initiation,mRNA,nosource,Nucleotides,Plasmids,protein,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,Rna,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,termination,transcription,TranscriptionGenetic,yeast} } % == BibTeX quality report for mitraYeastRibosomalProtein1984a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{mitraElongationArrestSecM2006, title = {Elongation Arrest by {{SecM}} via a Cascade of Ribosomal {{RNA}} Rearrangements}, author = {Mitra, K. and Schaffitzel, C. and Fabiola, F. and Chapman, M.S. and Ban, N. and Frank, J.}, year = 2006, month = may, journal = {Molecular cell}, volume = {22}, number = {4}, pages = {533–543}, publisher = {Elsevier}, doi = {10.1016/j.molcel.2006.05.003}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276506002942}, abstract = {In E. coli, the SecM nascent polypeptide causes elongation arrest, while interacting with 23S RNA bases A2058 and A749-753 in the exit tunnel of the large ribosomal subunit. We compared atomic models fitted by real-space refinement into cryo-electron microscopy reconstructions of a pretranslocational and SecM-stalled E. coli ribosome complex. A cascade of RNA rearrangements propagates from the exit tunnel throughout the large subunit, affecting intersubunit bridges and tRNA positions, which in turn reorient small subunit RNA elements. Elongation arrest could result from the inhibition of mRNA.(tRNAs) translocation, E site tRNA egress, and perhaps translation factor activation at the GTPase-associated center. Our study suggests that the specific secondary and tertiary arrangement of ribosomal RNA provides the basis for internal signal transduction within the ribosome. Thus, the ribosome may itself have the ability to regulate its progression through translation by modulating its structure and consequently its receptivity to activation by cofactors}, keywords = {23S RNA,activation,ARRANGEMENT,BASE,BASES,COMPLEX,COMPLEXES,Cryoelectron Microscopy,E,E site,ELEMENTS,elongation,INHIBITION,La,MODEL,models,nosource,POLYPEPTIDE,POSITION,POSITIONS,ribosomal RNA,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Rna,SIGNAL,Signal Transduction,SIGNAL-TRANSDUCTION,SITE,structure,SUBUNIT,translation,translocation,tRNA} } % == BibTeX quality report for mitraElongationArrestSecM2006: % ? unused Journal abbr (“Mol.Cell”)

@article{mitraRibosomeDynamicsInsights2006, title = {Ribosome Dynamics: Insights from Atomic Structure Modeling into Cryo-Electron Microscopy Maps}, author = {Mitra, K. and Frank, J.}, year = 2006, journal = {Annual Review Biophysical Biomolecular Structure}, volume = {35}, pages = {299–317}, publisher = {Annual Reviews}, doi = {10.1146/annurev.biophys.35.040405.101950}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.biophys.35.040405.101950}, abstract = {Single-particle cryo-electron microscopy (cryo-EM) is the method of choice for studying the dynamics of macromolecular machines both at a phenomenological and, increasingly, at the molecular level, with the advent of high-resolution component X-ray structures and of progressively improving fitting algorithms. Cryo-EM has shed light on the structure of the ribosome during the four steps of translation: initiation, elongation, termination, and recycling. Interpretation of cryo-EM reconstructions of the ribosome in quasi-atomic detail reveals a picture in which the ribosome uses RNA not only to catalyze chemical reactions, but also as a means for signal transduction over large distances}, keywords = {0,Algorithms,chemistry,COMPONENT,Computer Simulation,Cryoelectron Microscopy,DYNAMICS,elongation,initiation,La,Methods,ModelsChemical,ModelsMolecular,Motion,nosource,protein,Protein Conformation,Proteins,Review,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Rna,SIGNAL,Signal Transduction,SIGNAL-TRANSDUCTION,structure,Structure-Activity Relationship,Support,termination,translation,ultrastructure} } % == BibTeX quality report for mitraRibosomeDynamicsInsights2006: % ? unused Journal abbr (“Annu.Rev.Biophys.Biomol.Struct.”)

@article{mitrovichUnproductivelySplicedRibosomal2000, title = {Unproductively Spliced Ribosomal Protein {{mRNAs}} Are Natural Targets of {{mRNA}} Surveillance in {{C}}. Elegans}, author = {Mitrovich, Q.M. and Anderson, P.}, year = 2000, journal = {Genes & Development}, volume = {14}, number = {17}, pages = {2173–2184}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.819900}, url = {http://genesdev.cshlp.org/content/14/17/2173.short}, abstract = {Messenger RNA surveillance, the selective and rapid degradation of mRNAs containing premature stop codons, occurs in all eukaryotes tested. The biological role of this decay pathway, however, is not well understood. To identify natural substrates of mRNA surveillance, we used a cDNA-based representational difference analysis to identify mRNAs whose abundance increases in Caenorhabditis elegans smg(-) mutants, which are deficient for mRNA surveillance. Alternatively spliced mRNAs of genes encoding ribosomal proteins L3, L7a, L10a, and L12 are abundant natural targets of mRNA surveillance. Each of these genes expresses two distinct mRNAs. A productively spliced mRNA, whose abundance does not change in smg(-) mutants, encodes a normal, full-length, ribosomal protein. An unproductively spliced mRNA, whose abundance increases dramatically in smg(-) mutants, contains premature stop codons because of incomplete removal of an alternatively spliced intron. In transgenic animals expressing elevated quantities of RPL-12, a greater proportion of endogenous rpl-12 transcript is spliced unproductively. Thus, RPL-12 appears to autoregulate its own splicing, with unproductively spliced mRNAs being degraded by mRNA surveillance. We demonstrate further that alternative splicing of rpl introns is conserved among widely diverged nematodes. Our results suggest that one important role of mRNA surveillance is to eliminate unproductive by-products of gene regulation}, keywords = {20428552,Alternative Splicing,analysis,animal,AnimalsTransgenic,Base Sequence,BlottingNorthern,Caenorhabditis,Caenorhabditis elegans,CloningMolecular,Codon,DECAY,degradation,DNAComplementary,Exons,gene,Genes,Genetic,genetics,Introns,L3,MESSENGER-RNA,metabolism,ModelsGenetic,Molecular Sequence Data,mRNA,MutagenesisSite-Directed,nosource,protein,Proteins,regulation,Ribosomal Proteins,Ribosomes,Rna,RNA Splicing,RNAMessenger,Sequence HomologyNucleic Acid,splicing,STOP CODON,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,TransformationGenetic} } % == BibTeX quality report for mitrovichUnproductivelySplicedRibosomal2000: % ? unused Journal abbr (“Genes Dev.”)

@article{miyazakiCloningCharacterizationRat1992, title = {Cloning and Characterization of a Rat Gene Encoding Ornithine Decarboxylase Antizyme}, author = {Miyazaki, Y. and Matsufuji, S. and Hayashi, S.}, year = 1992, month = apr, journal = {Gene}, volume = {113}, number = {2}, pages = {191–197}, publisher = {Elsevier}, doi = {10.1016/0378-1119(92)90395-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/0378111992903956}, abstract = {We cloned an ornithine decarboxylase antizyme-encoding gene (Oaz) from a rat liver genomic library. The entire gene was located on a 4367-bp EcoRI fragment, which corresponded to one of two fragments hybridizable with the antizyme-encoding cDNA, Z1, on Southern blot analysis. Sequence analysis of the cloned gene showed that it consisted of five exons which were identical with the cDNA. The transcription start points of the Oaz mRNA were located 75 and 76 nucleotides upstream from the first ATG codon, as determined by S1 nuclease protection and primer extension analyses. The 5’-flanking region of the gene contained typical promoter motifs, such as a TATA box and Sp1-binding sites. Introduction of a chimeric gene consisting of the 5’-flanking region and the bacterial cat gene into Chinese hamster ovary cells revealed a promoter activity in the region, which was comparable in strength to that of the simian virus 40 promoter. In addition, we isolated a 12-kb EcoRI fragment, the other sequence hybridizable to the cDNA. Sequence analysis showed that it represented a processed Oaz pseudogene and was not able to encode any active protein}, keywords = {0,analysis,Animals,antagonists & inhibitors,antizyme,Bacterial,Base Sequence,BlottingSouthern,CELLS,Cho Cells,cloning,CloningMolecular,Codon,Dna,ElectrophoresisPolyacrylamide Gel,EXON,Exons,gene,genetics,genomic,Genomic Library,Hamsters,La,library,Liver,metabolism,Molecular Sequence Data,MOTIFS,mRNA,nosource,Nucleotides,Ornithine Decarboxylase,ORNITHINE DECARBOXYLASE ANTIZYME,Ovary,primer extension,PROMOTER,Promoter Regions (Genetics),PROTECTION,protein,Proteins,Pseudogenes,rat,Rats,REGION,Research SupportNon-U.S.Gov’t,Restriction Mapping,Rna,RNAMessenger,sequence,Sequence Analysis,Sequence HomologyNucleic Acid,SEQUENCE-ANALYSIS,Simian virus 40,SITE,SITES,Tata Box,transcription,TranscriptionGenetic,UPSTREAM,virus} }

@article{mizutaContinuedFunctioningSecretory1994, title = {Continued Functioning of the Secretory Pathway Is Essential for Ribosome Synthesis.}, author = {Mizuta, K. and Warner, J.R.}, year = 1994, month = apr, journal = {Molecular and cellular biology}, volume = {14}, number = {4}, pages = {2493–2502}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/14/4/2493}, abstract = {To explore the regulatory elements that maintain the balanced synthesis of the components of the ribosome, we isolated a temperature-sensitive (ts) mutant of Saccharomyces cerevisiae in which transcription both of rRNA and of ribosomal protein genes is defective at the nonpermissive temperature. Temperature sensitivity for growth is recessive and segregates 2:2. A gene that complements the ts phenotype was cloned from a genomic DNA library. Sequence analysis revealed that this gene is SLY1, encoding a protein essential for protein and vesicle transport between the endoplasmic reticulum and the Golgi apparatus. In the strain carrying our ts allele of SLY1, accumulation of the carboxypeptidase Y precursor was detected at the nonpermissive temperature, indicating that the secretory pathway is defective. To ask whether the effect of the ts allele on ribosome synthesis was specific for sly1 or was a general result of the inactivation of the secretion pathway, we assayed the levels of mRNA for several ribosomal proteins in cells carrying ts alleles of sec1, sec7, sec11, sec14, sec18, sec53, or sec63, representing all stages of secretion. In each case, the mRNA levels were severely depressed, suggesting that this is a common feature in mutants of protein secretion. For the mutants tested, transcription of rRNA was also substantially reduced. Furthermore, treatment of a sensitive strain with brefeldin A at a concentration sufficient to block the secretion pathway also led to a decrease of the level of ribosomal protein mRNA, with kinetics suggesting that the effect of a secretion defect is manifest within 15 to 30 min. We conclude that the continued function of the entire secretion pathway is essential for the maintenance of ribosome synthesis. The apparent coupling of membrane synthesis and ribosome synthesis suggest the existence of a regulatory network that connects the production of the various structural elements of the cell}, keywords = {94187721,Alleles,analysis,biosynthesis,BlottingNorthern,Carboxypeptidases,COMPONENT,Dna,ELEMENTS,Enzyme Precursors,gene,Gene Expression,Genes,GenesFungal,genetics,genomic,Genomic Library,Genotype,Kinetics,library,metabolism,ModelsBiological,mRNA,Multiple DOI,nonfile,nosource,Phenotype,Plasmids,protein,Protein ProcessingPost-Translational,Proteins,Ribosomal Proteins,ribosome,Ribosomes,RNAMessenger,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence Analysis,Structural,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Temperature,transcription,TranscriptionGenetic} } % == BibTeX quality report for mizutaContinuedFunctioningSecretory1994: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{moazedInteractionElongationFactors1988a, title = {Interaction of Elongation Factors {{EF-G}} and {{EF-Tu}} with a Conserved Loop in {{23S RNA}}}, author = {Moazed, D. and Robertson, J.M. and Noller, H.F.}, year = 1988, month = jul, journal = {Nature}, volume = {334}, number = {6180}, pages = {362–364}, doi = {10.1038/334362a0}, url = {http://www.nature.com/nature/journal/v334/n6180/abs/334362a0.html}, abstract = {The elongation factors EF-Tu and EF-G interact with ribosomes during protein synthesis: EF-Tu presents incoming aminoacyl transfer RNA to the programmed ribosome as an EF-Tu-GTP-tRNA ternary complex and EF-G promotes translocation of peptidyl-tRNA and its associated messenger RNA from the A to the P site after peptidyl transfer. Both events are accompanied by ribosome-dependent GTP hydrolysis. Here we use chemical probes to investigate the possible interaction of these factors with ribosomal RNA in E. coli ribosomes. We observe EF-G-dependent footprints in vitro and in vivo around position 1,067 in domain II of 23S rRNA, and in the loop around position 2,660 in domain VI.EF-Tu gives an overlapping footprint in vitro at positions 2,655 and 2,661, but shows no effect at position 1,067. The 1,067 region is the site of interaction of the antibiotic thiostrepton, which prevents formation of the EF-G-GTP-ribosome complex and is a site for interaction with the GTPase-related protein L11 (ref. 3). The universally conserved loop in the 2,660 region is the site of attack by the RNA-directed cytotoxins alpha-sarcin and ricin, whose effects abolish translation and include the loss of elongation factor-dependent functions in eukaryotic ribosomes}, keywords = {0,A-SITE,antibiotic,Bacterial,COMPLEX,COMPLEXES,EF-2,EFTu,elongation,Escherichia coli,genetics,GTP,Hydrolysis,In Vitro,IN-VITRO,IN-VIVO,La,MESSENGER-RNA,metabolism,nosource,Nucleic Acid Conformation,P-SITE,Peptide Elongation Factor G,Peptide Elongation Factor Tu,Peptide Elongation Factors,peptidyl-transfer,protein,protein synthesis,PROTEIN-SYNTHESIS,RIBOSOMAL-RNA,ribosome,Ribosomes,Ricin,Rna,RNABacterial,RNARibosomal,RNARibosomal23S,rRNA,supportu.s.gov’tp.h.s.,Thiostrepton,TRANSFER-RNA,translation,translocation} }

@article{moazedIntermediateStatesMovement1989a, title = {Intermediate States in the Movement of Transfer {{RNA}} in the Ribosome}, author = {Moazed, D. and Noller, H.F.}, year = 1989, month = nov, journal = {Nature}, volume = {342}, number = {6246}, pages = {142–148}, doi = {10.1038/342142a0}, abstract = {Direct chemical ‘footprinting’ shows that translocation of transfer RNA occurs in two discrete steps. During the first step, which occurs spontaneously after the formation of the peptide bond, the acceptor end of tRNA moves relative to the large ribosomal subunit resulting in ‘hybrid states’ of binding. During the second step, which is promoted by elongation factor EF-G, the anticodon end of tRNA, along with the messenger RNA, moves relative to the small ribosomal subunit}, keywords = {90044067,Anticodon,BINDING,Binding Sites,elongation,Escherichia coli,MESSENGER-RNA,metabolism,MOF,Movement,nosource,Peptide Chain Elongation,Peptide Elongation Factors,Puromycin,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNAMessenger,RNATransfer,RNATransferAmino Acyl,SUBUNIT,supportu.s.gov’tp.h.s.,TRANSFER-RNA,translocation,tRNA} }

@article{moazedInteractionTRNA23S1989, title = {Interaction of {{tRNA}} with {{23S rRNA}} in the Ribosomal {{A}}, {{P}}, and {{E}} Sites}, author = {Moazed, D. and Noller, H.F.}, year = 1989, month = may, journal = {Cell}, volume = {57}, number = {4}, pages = {585–597}, publisher = {Elsevier}, doi = {10.1016/0092-8674(89)90128-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867489901281}, abstract = {Three sets of conserved nucleotides in 23 rRNA are protected from chemical probes by binding of tRNA to the ribosomal A, P, and E sites, respectively. They are located almost exclusively in domain V, primarily in or adjacent to the loop identified with the peptidyl transferase function. Some of these sites are also protected by antibiotics such as chloramphenicol, which could explain how these drugs interfere with protein synthesis. Certain tRNA-dependent protections are abolished when the 3’-terminal A or CA or 2’,3’-linked acyl group is removed, providing direct evidence for the interaction of the conserved CCA terminus of tRNA with 23S rRNA. When the EF-Tu.GTP.aminoacyl-tRNA ternary complex is bound to the ribosome, no tRNA-dependent A site protections are detected in 23S rRNA until EF-Tu is released. Thus, EF-Tu prevents interaction of the 3’ terminus of the incoming aminoacyl-tRNA with the peptidyl transferase region of the ribosome during anticodon selection, thereby permitting translational proofreading}, keywords = {89249323,A-SITE,analysis,antibiotic,antibiotics,Anticodon,Base Sequence,BINDING,Chloramphenicol,COMPLEX,COMPLEXES,drugs,EFTu,Escherichia coli,metabolism,nosource,Nucleotides,peptidyl transferase,physiology,proofreading,protein,protein synthesis,PROTEIN-SYNTHESIS,ribosome,Ribosomes,RNABacterial,RNARibosomal,RNARibosomal23S,RNATransfer,RNATransferAmino Acyl,rRNA,supportu.s.gov’tp.h.s.,Transferases,tRNA,ultrastructure} }

@article{moazedSitesInteractionCCA1991a, title = {Sites of Interaction of the {{CCA}} End of Peptidyl-{{tRNA}} with {{23S rRNA}}}, author = {Moazed, D. and Noller, H.F.}, year = 1991, month = may, journal = {Proceedings of the National Academy of Sciences}, volume = {88}, number = {9}, pages = {3725–3728}, doi = {10.1073/pnas.88.9.3725}, url = {http://www.pnas.org/content/88/9/3725.short}, abstract = {Oligonucleotide fragments derived from the 3’ CCA terminus of acylated tRNA, such as CACCA-(AcPhe), UACCA-(AcLeu), and CAACCA-(fMet), bind specifically to ribosomes in the presence of sparsomycin and methanol [Monro, R. E., Celma, M. L. & Vazquez, D. (1969) Nature (London) 222, 356-358]. All three oligonucleotides protect a characteristic set of bases in 23S rRNA from chemical probes: G2252, G2253, A2439, A2451, U2506, and U2585. A2602 shows enhanced reactivity. These account for most of the same bases that are protected when peptidyl-tRNA analogues such as AcPhe-tRNA are bound to the ribosomal P site, and correspond precisely to those bases whose protection is abolished by removal of the 3’-CA end of tRNA. We conclude that most of the observed interactions between tRNA and 23S rRNA in the 50S ribosomal P site involve the conserved CCA terminus of tRNA. Sparsomycin may inhibit protein synthesis by stabilizing interaction between the peptidyl-CCA and the 23S P site, preventing formation of the intermediate A/P hybrid state}, keywords = {0,Base Sequence,Binding Sites,chemistry,Escherichia coli,In Vitro,La,metabolism,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Oligonucleotides,P-SITE,pharmacology,protein,protein synthesis,PROTEIN-SYNTHESIS,ribosome,Ribosomes,Rna,RNARibosomal23S,RNATransfer,rRNA,sparsomycin,Structure-Activity Relationship,supportu.s.gov’tp.h.s.,TranslationGenetic,tRNA} } % == BibTeX quality report for moazedSitesInteractionCCA1991a: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{moehleAssociationRAP1Binding1991, title = {Association of {{RAP1}} Binding Sites with Stringent Control of Ribosomal Protein Gene Transcription in {{Saccharomyces}} Cerevisiae.}, author = {Moehle, C.M. and Hinnebusch, A.G.}, year = 1991, month = may, journal = {Molecular and Cellular Biology}, volume = {11}, number = {5}, pages = {2723–2735}, url = {http://mcb.asm.org/cgi/content/abstract/11/5/2723}, abstract = {An amino acid limitation in bacteria elicits a global response, called stringent control, that leads to reduced synthesis of rRNA and ribosomal proteins and increased expression of amino acid biosynthetic operons. We have used the antimetabolite 3-amino-1,2,4-triazole to cause histidine limitation as a means to elicit the stringent response in the yeast Saccharomyces cerevisiae. Fusions of the yeast ribosomal protein genes RPL16A, CRY1, RPS16A, and RPL25 with the Escherichia coli lacZ gene were used to show that the expression of these genes is reduced by a factor of 2 to 5 during histidine-limited exponential growth and that this regulation occurs at the level of transcription. Stringent regulation of the four yeast ribosomal protein genes was shown to be associated with a nucleotide sequence, known as the UASrpg (upstream activating sequence for ribosomal protein genes), that binds the transcriptional regulatory protein RAP1. The RAP1 binding sites also appeared to mediate the greater ribosomal protein gene expression observed in cells growing exponentially than in cells in stationary phase. Although expression of the ribosomal protein genes was reduced in response to histidine limitation, the level of RAP1 DNA-binding activity in cell extracts was unaffected. Yeast strains bearing a mutation in any one of the genes GCN1 to GCN4 are defective in derepression of amino acid biosynthetic genes in 10 different pathways under conditions of histidine limitation. These Gcn- mutants showed wild-type regulation of ribosomal protein gene expression, which suggests that separate regulatory pathways exist in S. cerevisiae for the derepression of amino acid biosynthetic genes and the repression of ribosomal protein genes in response to amino acid starvation}, keywords = {91203893,amino acid limitation,Amitrole,Bacteria,Base Sequence,BINDING,Binding Sites,biosynthesis,CloningMolecular,development,DNA-Binding Proteins,DNAFungal,drug effects,Escherichia coli,ESCHERICHIA-COLI,expression,Fungal Proteins,GCN,GCN4,gene,Gene Expression,Gene Expression RegulationFungal,GENE-EXPRESSION,GENE-TRANSCRIPTION,Genes,GenesStructuralFungal,Genetic,genetics,Genotype,Histidine,human,Kinetics,metabolism,Molecular Sequence Data,Multiple DOI,Mutation,nonfile,nosource,Operon,pharmacology,protein,Proteins,Recombinant Fusion Proteins,regulation,Ribosomal Proteins,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,stringent response,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,transcription,TranscriptionGenetic,yeast} } % == BibTeX quality report for moehleAssociationRAP1Binding1991: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{mohrArginines29592000a, title = {Arginines 29 and 59 of Elongation Factor {{G}} Are Important for {{GTP}} Hydrolysis or Translocation on the Ribosome}, author = {Mohr, D. and Wintermeyer, W. and Rodnina, M.V.}, year = 2000, month = jul, journal = {The EMBO Journal}, volume = {19}, number = {13}, pages = {3458–3464}, doi = {10.1093/emboj/19.13.3458}, url = {http://www.nature.com/emboj/journal/v19/n13/abs/7593165a.html}, abstract = {GTP hydrolysis by elongation factor G (EF-G) is essential for the translocation step in protein elongation. The low intrinsic GTPase activity of EF-G is strongly stimulated by the ribosome. Here we show that a conserved arginine, R29, of Escherichia coli EF-G is crucial for GTP hydrolysis on the ribosome, but not for GTP binding or ribosome interaction, suggesting that it may be directly involved in catalysis. Another conserved arginine, R59, which is homologous to the catalytic arginine of G(alpha) proteins, is not essential for GTP hydrolysis, but influences ribosome binding and translocation. These results indicate that EF-G is similar to other GTPases in that an arginine residue is required for GTP hydrolysis, although the structural changes leading to GTPase activation are different}, keywords = {0,activation,Arginine,BINDING,Biological Transport,BIOLOGY,Catalysis,chemistry,EF-G,elongation,ELONGATION-FACTOR-G,Escherichia coli,ESCHERICHIA-COLI,genetics,GTP,GTP Phosphohydrolase,GTP Phosphohydrolases,GTPase,GTPASE ACTIVITY,Guanosine,Guanosine Triphosphate,Hydrolysis,La,metabolism,nosource,Peptide Elongation Factor G,protein,Proteins,ribosome,RIBOSOME BINDING,Ribosomes,Structural,supportnon-u.s.gov’t,translocation} } % == BibTeX quality report for mohrArginines29592000a: % ? unused Journal abbr (“EMBO J.”)

@article{molenaarStructureOrganizationTwo1984a, title = {Structure and Organization of Two Linked Ribosomal Protein Genes in Yeast}, author = {Molenaar, C.M. and Woudt, L.P. and Jansen, A.E. and Mager, W.H. and Planta, R.J. and Donovan, D.M. and Pearson, N.J.}, year = 1984, month = oct, journal = {Nucleic Acids Res.}, volume = {12}, number = {19}, pages = {7345–7358}, doi = {10.1093/nar/12.19.7345}, url = {http://nar.oxfordjournals.org/content/12/19/7345.short}, abstract = {The genes encoding yeast ribosomal proteins rp28 and S16A are linked and occur duplicated in the yeast genome. In both gene pairs the genes are approximately 600 bp apart and are both transcribed in the same direction. Both ribosomal protein genes resemble other ribosomal protein genes studied so far in many structural aspects. The genes are interrupted by an intron near the 5’-end of their coding sequence. In addition the flanking regions contain several conserved sequence elements, which may function in transcription initiation and termination. In agreement with findings concerning other cloned yeast ribosomal protein genes, upstream homology blocks occur that may be involved in coordinate control of ribosomal protein gene transcription. The complete pattern of conserved and diverged sequences between the two duplicate gene pairs is presented}, keywords = {85037916,Amino Acid Sequence,Base Sequence,Conserved Sequence,ELEMENTS,gene,GENE-TRANSCRIPTION,Genes,GenesFungal,GenesStructural,genetics,Genome,initiation,Linkage (Genetics),nosource,protein,Proteins,Ribosomal Proteins,RNAMessenger,Saccharomyces cerevisiae,sequence,Structural,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,termination,transcription,yeast} } % == BibTeX quality report for molenaarStructureOrganizationTwo1984a: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{mollenbeckEvolutionProgrammedRibosomal2004a, title = {Evolution of Programmed Ribosomal Frameshifting in the {{TERT}} Genes of {{Euplotes}}}, author = {Mollenbeck, M. and Gavin, M.C. and Klobutcher, L.A.}, year = 2004, month = jun, journal = {J.Mol.Evol.}, volume = {58}, number = {6}, pages = {701–711}, doi = {10.1007/s00239-004-2592-0}, url = {PM:15461427}, abstract = {A number of recent studies indicate that programmed + 1 ribosomal frameshifting is frequently required for the expression of genes in species of the genus Euplotes. In E. crassus, three genes encoding the telomerase reverse transcriptase (TERT) subunit have been previously found to possess one or two + 1 frameshift sites. To examine the origin of frameshift sites within the Euplotes group, we have isolated segments of the TERT gene from five Euplotes species. Coupled with phylogenetic analysis, the results indicate that one frameshift site in the TERT gene arose late in the evolution of the group. In addition, a novel frameshift site was identified in the TERT gene of E. minuta, a species where frameshifting has not been previously reported. Coupled with other studies, the results indicate that frameshift sites have arisen during the diversification of the euplotids. The results also are discussed in regard to the mutations necessary to generate frameshift sites, and the specialization of TERT protein function that has apparently occurred in E. crassus}, keywords = {0,Amino Acid Sequence,analysis,Animals,Base Sequence,BIOLOGY,Cluster Analysis,Comparative Study,E,Euplotes,Evolution,EvolutionMolecular,expression,frameshift,Frameshifting,FrameshiftingRibosomal,gene,Gene Components,Genes,genetics,La,Molecular Sequence Data,Mutation,MUTATIONS,nosource,Oligonucleotides,Phylogeny,protein,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tNon-P.H.S.,REVERSE-TRANSCRIPTASE,ribosomal frameshifting,Sequence Alignment,Sequence AnalysisDNA,Sequence Homology,SITE,SITES,SUBUNIT,Telomerase} } % == BibTeX quality report for mollenbeckEvolutionProgrammedRibosomal2004a: % ? Possibly abbreviated journal title J.Mol.Evol.

@article{monroActionSparsomycinRibosomecatalysed1969a, title = {Action of Sparsomycin on Ribosome-Catalysed Peptidyl Transfer}, author = {Monro, R.E. and Celma, M.L. and Vazquez, D.}, year = 1969, month = apr, journal = {Nature}, volume = {222}, number = {191}, pages = {356–358}, keywords = {69177764,antibiotics,Bacterial Proteins,Binding Sites,biosynthesis,drug effects,No DOI found,nosource,Peptides,peptidyl-transfer,pharmacology,Ribosomes,sparsomycin} }

@article{montanaroInhibitionRicinProtein1975a, title = {Inhibition by Ricin of Protein Synthesis in Vitro. {{Inhibition}} of the Binding of Elongation Factor 2 and of Adenosine Diphosphate-Ribosylated Elongation Factor 2 to Ribosomes}, author = {Montanaro, L. and Sperti, S. and Mattioli, A. and Testoni, G. and Stirpe, F.}, year = 1975, month = jan, journal = {Biochemical Journal}, volume = {146}, number = {1}, pages = {127–131}, doi = {10.1042/bj1460127}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1165282/}, abstract = {The binding of EF2 (elongation factor 2) and of ADP-ribosyl-EF 2 to rat liver ribosomes is inhibited by ricin. This result suggests that the native enzyme and its ADP-ribose derivative have the same or closely related binding sites on the ribosome. The inhibition by ricin of the binding of EF 2 to ribosomes is consistent with the previous observation that ricin affects EF 2-catalysed translocation during polypeptide chain elongation}, keywords = {Adenosine,BINDING,Binding Sites,EF-2,elongation,enzyme,In Vitro,IN-VITRO,INHIBITION,Liver,nosource,PAP,protein,protein synthesis,PROTEIN-SYNTHESIS,rat,ribosome,Ribosomes,Ricin,translocation} }

@incollection{moonComputationalIdentificationFrameshift2004, title = {Computational Identification of -1 Frameshift Signals.}, booktitle = {Lecture {{Notes}} in {{Computer Science}}}, author = {Moon, S. and Byun, Y. and Han, K.}, year = 2004, volume = {3036}, pages = {334–341}, publisher = {Springer-Verlag}, address = {Heidelberg}, url = {⬚http://springerlink.metapress.com/app/home/contribution.asp?wasp=g275mun1wg6ktmc10qau&referrer=parent&backto=searcharticlesresults,8,10;⬚⬚⬚ ⬚⬚}, abstract = {Ribosomal frameshifts in the -1 direction are used frequently by RNA viruses to synthesize a single fusion protein from two or more overlapping open reading frames. The slippery heptamer sequence XXX YYY Z is the best recognized of the signals that promote -1 frameshifting. We have developed an algorithm that predicts plausible -1 frameshift signals in long DNA sequences. Our algorithm is implemented in a working program called FSFinder (Frameshift Signal Finder). We tested FSFinder on 72 genomic sequences from a number of organisms and found that FSFinder predicts -1 frameshift signals efficiently and with greater sensitivity and selectivity than existing approaches. Sensitivity is improved by considering all potentially relevant components of frameshift signals, and selectivity is increased by focusing on overlapping regions of open reading frames and by prioritizing candidate frameshift signals. FSFinder is useful for analyzing -1 frameshift signals as well as discovering unknown genes.⬚ ⬚}, collaborator = {Bubak, M. and {}{van Albada}, G.D. and Sloot, P.M.}, isbn = {3-540-22114-X}, keywords = {COMPONENT,COMPONENTS,computer,Dna,DNA sequence,FRAME,frameshift,Frameshifting,FUSION PROTEIN,gene,Genes,genomic,IDENTIFICATION,nosource,OPEN READING FRAME,Open Reading Frames,protein,READING FRAME,Reading Frames,REGION,RIBOSOMAL FRAMESHIFT,Rna,RNA Viruses,sequence,SEQUENCES,SIGNAL} }

@article{moonPredictingGenesExpressed2004a, title = {Predicting Genes Expressed via -1 and +1 Frameshifts}, author = {Moon, S. and Byun, Y. and Kim, H.J. and Jeong, S. and Han, K.}, year = 2004, journal = {Nucleic Acids Res.}, volume = {32}, number = {16}, pages = {4884–4892}, doi = {10.1093/nar/gkh829}, url = {PM:15371551}, abstract = {Computational identification of ribosomal frameshift sites in genomic sequences is difficult due to their diverse nature, yet it provides useful information for understanding the underlying mechanisms and discovering new genes. We have developed an algorithm that searches entire genomic or mRNA sequences for frameshifting sites, and implements the algorithm as a web-based program called FSFinder (Frameshift Signal Finder). The current version of FSFinder is capable of finding -1 frameshift sites on heptamer sequences X XXY YYZ, and +1 frameshift sites for two genes: protein chain release factor B (prfB) and ornithine decarboxylase antizyme (oaz). We tested FSFinder on approximately 190 genomic and partial DNA sequences from a number of organisms and found that it predicted frameshift sites efficiently and with greater sensitivity and specificity than existing approaches. It has improved sensitivity because it considers many known components of a frameshifting cassette and searches these components on both + and - strands, and its specificity is increased because it focuses on overlapping regions of open reading frames and prioritizes candidate frameshift sites. FSFinder is useful for discovering unknown genes that utilize alternative decoding, as well as for analyzing frameshift sites. It is freely accessible at http://wilab.inha.ac.kr/FSFinder/}, keywords = {0,Algorithms,antizyme,CHAIN TERMINATION,chemistry,COMPONENT,COMPONENTS,Computational Biology,computer,decoding,Dna,DNA sequence,FRAME,frameshift,Frameshifting,FrameshiftingRibosomal,gene,Genes,genetics,GenomeBacterial,genomic,IDENTIFICATION,INFORMATION,Internet,La,MECHANISM,MECHANISMS,Methods,mRNA,nosource,OPEN READING FRAME,Open Reading Frames,Ornithine Decarboxylase,ORNITHINE DECARBOXYLASE ANTIZYME,Peptide Chain Termination,Peptide Termination Factors,protein,Proteins,READING FRAME,Reading Frames,REGION,RELEASE,release factor,Research SupportNon-U.S.Gov’t,RIBOSOMAL FRAMESHIFT,Rna,RNAMessenger,search,Sensitivity and Specificity,sequence,SEQUENCES,SIGNAL,SITE,SITES,Software,SPECIFICITY,termination} } % == BibTeX quality report for moonPredictingGenesExpressed2004a: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{moonFSDBFrameshiftSignal2007, title = {{{FSDB}}: A Frameshift Signal Database}, author = {Moon, S. and Byun, Y. and Han, K.}, year = 2007, journal = {Computational Biology and Chemistry}, volume = {31}, number = {4}, pages = {298–302}, publisher = {Elsevier}, doi = {10.1016/j.compbiolchem.2007.05.004}, url = {http://linkinghub.elsevier.com/retrieve/pii/s1476-9271(07)00079-5}, abstract = {Programmed frameshifting is a recoding event in which a ribosome shifts reading frame by one or more nucleotides at a specific mRNA signal between overlapping genes. Programmed frameshifting is involved in the expression of many genes in a wide range of organisms, especially in viruses and bacteria. The mechanism of programmed frameshifting is not fully understood despite many studies, and there are few databases available for detailed information on programmed frameshifting. We have developed a database called FSDB (Frameshift Signal Database), which is a comprehensive compilation of experimentally known or computationally predicted data about programmed ribosomal frameshifting. FSDB provides a graphical view of frameshift signals and the genes using programmed frameshifting for their expression. It also allows the user himself/herself to find programmed frameshift sites in genomic sequences using a program called FSFinder (http://wilab.inha.ac.kr/fsfinder2). We believe FSDB will be a valuable resource for scientists studying programmed ribosomal frameshifting. FSDB is freely accessible at http://wilab.inha.ac.kr/fsdb/}, keywords = {Bacteria,Base Sequence,computer,DATABASE,Database Management Systems,Databases,expression,FRAME,frameshift,Frameshift Mutation,Frameshifting,gene,Genes,genomic,INFORMATION,La,MECHANISM,mRNA,nosource,Nucleotides,programmed frameshifting,READING FRAME,recoding,ribosomal frameshifting,ribosome,sequence,SEQUENCES,SIGNAL,SITE,SITES,Support,User-Computer Interface,Viruses} } % == BibTeX quality report for moonFSDBFrameshiftSignal2007: % ? unused Journal abbr (“Comput.Biol Chem.”)

@article{mooreBirthDeathComplex2005a, title = {From Birth to Death: The Complex Lives of Eukaryotic {{mRNAs}}}, author = {Moore, M.J.}, year = 2005, journal = {Science}, volume = {309}, number = {5740}, pages = {1514–1518}, doi = {10.1126/science.1111443}, url = {http://www.sciencemag.org/content/309/5740/1514.short}, abstract = {Recent work indicates that the posttranscriptional control of eukaryotic gene expression is much more elaborate and extensive than previously thought, with essentially every step of messenger RNA (mRNA) metabolism being subject to regulation in an mRNA-specific manner. Thus, a comprehensive understanding of eukaryotic gene expression requires an appreciation for how the lives of mRNAs are influenced by a wide array of diverse regulatory mechanisms}, keywords = {0,Active TransportCell Nucleus,analysis,Animals,Biochemistry,biosynthesis,Cell Nucleus,chemistry,COMPLEX,COMPLEXES,Cytoplasm,Cytoplasmic Granules,Eukaryotic Cells,expression,gene,Gene Expression,Gene Expression Regulation,GENE-EXPRESSION,La,MECHANISM,MECHANISMS,MESSENGER-RNA,metabolism,mRNA,nosource,Protein Biosynthesis,regulation,REQUIRES,Review,RIBONUCLEOPROTEIN,Ribonucleoproteins,Rna,RNA ProcessingPost-Transcriptional,RNAMessenger} }

@article{mooreInvolvementRNARibosome2002a, title = {The Involvement of {{RNA}} in Ribosome Function}, author = {Moore, P.B. and Steitz, T.A.}, year = 2002, month = jul, journal = {Nature}, volume = {418}, number = {6894}, pages = {229–235}, doi = {10.1038/418229a}, url = {http://www.nature.com/nature/journal/v418/n6894/full/418229a.html?lang=en}, abstract = {The ribosome is a particle made of RNA and protein that is found in abundance in all cells that are actively making protein. It catalyses the messenger RNA-directed synthesis of proteins. Recent structural work has demonstrated a profound involvement of the ribosome’s RNA component in all aspects of its function, supporting the hypothesis that proteins were added to the ribosome late in its evolution}, keywords = {Binding Sites,chemistry,COMPONENT,Evolution,EvolutionMolecular,genetics,metabolism,ModelsChemical,ModelsMolecular,nosource,protein,Proteins,Review,ribosome,Ribosomes,Rna,RNARibosomal,RNATransfer,Structural,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.} }

@article{mooreStructuralBasisLarge2003a, title = {The Structural Basis of Large Ribosomal Subunit Function}, author = {Moore, P.B. and Steitz, T.A.}, year = 2003, journal = {Annual review of biochemistry}, volume = {72}, pages = {813–850}, doi = {10.1146/annurev.biochem.72.110601.135450}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.biochem.72.110601.135450}, abstract = {The ribosome crystal structures published in the past two years have revolutionized our understanding of ribonucleoprotein structure, and more specifically, the structural basis of the peptide bonding forming activity of the ribosome. This review concentrates on the crystallographic developments that made it possible to solve these structures. It also discusses the information obtained from these structures about the three-dimensional architecture of the large ribosomal subunit, the mechanism by which it facilitates peptide bond formation, and the way antibiotics inhibit large subunit function. The work reviewed, taken as a whole, proves beyond doubt that the ribosome is an RNA enzyme, as had long been surmised on the basis of less conclusive evidence}, keywords = {0,antagonists & inhibitors,antibiotic,antibiotics,Archaeal Proteins,Bacterial,Bacterial Proteins,Biochemistry,Biophysics,BOND FORMATION,chemistry,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,CrystallographyX-Ray,development,enzyme,INFORMATION,La,MECHANISM,metabolism,ModelsMolecular,nosource,Nucleic Acid Conformation,peptide bond formation,protein,Protein Conformation,Proteins,Review,RIBONUCLEOPROTEIN,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNAArchaeal,RNABacterial,RNARibosomal,Structural,STRUCTURAL BASIS,structure,SUBUNIT,Support} } % == BibTeX quality report for mooreStructuralBasisLarge2003a: % ? unused Journal abbr (“Annu.Rev.Biochem.”)

@article{mooreCompleteNucleotideSequenceMilkTransmitted1987, title = {Complete {{Nucleotide-Sequence}} of {{A Milk-Transmitted Mouse Mammary-Tumor Virus}} - 2 {{Frameshift Suppression Events Are Required}} for {{Translation}} of {{Gag}} and {{Pol}}}, author = {Moore, R. and Dixon, M. and Smith, R. and Peters, G. and Dickson, C.}, year = 1987, month = feb, journal = {Journal of Virology}, volume = {61}, number = {2}, pages = {480–490}, doi = {10.1128/jvi.61.2.480-490.1987}, url = {ISI:A1987F667300031}, keywords = {COMPLETE NUCLEOTIDE-SEQUENCE,frameshift,Gag,MAMMARY-TUMOR VIRUS,nosource,NUCLEOTIDE-SEQUENCE,pol,suppression,translation,virus} } % == BibTeX quality report for mooreCompleteNucleotideSequenceMilkTransmitted1987: % ? Title looks like it was stored in title-case in Zotero

@article{moosmayerExpressionFrameshiftingExtremely1991a, title = {Expression and Frameshifting but Extremely Inefficient Proteolytic Processing of the {{HIV-1}} Gag and Pol Gene Products in Stably Transfected Rodent Cell Lines}, author = {Moosmayer, D. and Reil, H. and Ausmeier, M. and Scharf, J.G. and Hauser, H. and Jentsch, K.D. and Hunsmann, G.}, year = 1991, month = jul, journal = {Virology}, volume = {183}, number = {1}, pages = {215–224}, doi = {10.1016/0042-6822(91)90134-W}, url = {http://linkinghub.elsevier.com/retrieve/pii/004268229190134W}, abstract = {Expression, ribosomal frameshifting, and proteolytic processing of HIV-1 GAG and POL proteins were investigated in heterologous mammalian cells in order to elucidate the influence of the cellular background on these events. DNA fragments encoded by the gag and pol region were expressed in two rodent cell lines, LTK- and BHK. Both stably transfected cell lines continuously produce recombinant proteins which react with HIV-specific antisera. The GAG precursor and a 39-kDa proteolytic fragment thereof were the major recombinant proteins detected. Expression of the gag-pol region leads to the production of the GAG-POL precursor. Ribosomal frameshifting at the HIV-1 shifty sequence to a typical extent could be positively demonstrated by an enzyme assay. Despite the presence of the viral protease within the GAG-POL precursors, proteolytic processing of the HIV-derived polyproteins was extremely inefficient. The efficiency could not be enhanced by overexpression of the HIV-1 protease encoding region}, keywords = {0,Animals,Base Sequence,Cell Line,cell lines,CELLS,Cercopithecus aethiops,Dna,efficiency,enzyme,expression,Frameshift Mutation,Frameshifting,Gag,Gag-pol,GAG-POL REGION,gene,Gene Expression,Gene Productsgag,Gene Productspol,GENE-PRODUCT,genetics,Hamsters,HIV,HIV Protease,Hiv-1,HIV-1 PROTEASE,Humans,Hydrolysis,La,LINE,MAMMALIAN-CELLS,metabolism,Mice,Molecular Sequence Data,nosource,OVEREXPRESSION,pol,POL GENE,POLYPROTEIN,Polyproteins,PRECURSOR,PRODUCT,PRODUCTS,protein,Protein ProcessingPost-Translational,Proteins,Recombinant Proteins,REGION,ribosomal frameshifting,sequence,Substrate Specificity,Transfection} }

@article{morasRNAproteinInteractionsDiverse1995a, title = {{{RNA-protein}} Interactions. {{Diverse}} Modes of Recognition. [{{Review}}] [18 Refs]}, author = {Moras, D. and Poterszman, A.}, year = 1995, month = mar, journal = {Current Biology}, volume = {5}, number = {3}, pages = {249–251}, doi = {10.1016/S0960-9822(95)00051-0}, keywords = {COMPLEX,COMPLEXES,nosource,poly(A),Review,Rna,Solutions,splicing,structure} }

@article{morelandIdentificationNuclearLocalization1985a, title = {Identification of a Nuclear Localization Signal of a Yeast Ribosomal Protein.}, author = {Moreland, R.B. and Nam, H.G. and Hereford, L.M. and Fried, H.M.}, year = 1985, journal = {Proc.Natl.Acad.Sci.USA}, volume = {82}, pages = {6561–6565}, doi = {10.1073/pnas.82.19.6561}, url = {http://www.pnas.org/content/82/19/6561.short}, keywords = {IDENTIFICATION,L3,nosource,protein,ribosome,SIGNAL,yeast} } % == BibTeX quality report for morelandIdentificationNuclearLocalization1985a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{morganComparisonYeastRabbit2000, title = {A Comparison of the Yeast and Rabbit 80 {{S}} Ribosome Reveals the Topology of the Nascent Chain Exit Tunnel, Inter-Subunit Bridges and Mammalian {{rRNA}} Expansion Segments}, author = {Morgan, D.G. and Menetret, J.F. and Radermacher, M. and Neuhof, A. and Akey, I.V. and Rapoport, T.A. and Akey, C.W.}, year = 2000, journal = {J.Mol.Biol.}, volume = {301}, number = {2}, pages = {301–321}, doi = {10.1006/jmbi.2000.3947}, url = {PM:10926511}, abstract = {Protein synthesis in eukaryotes is mediated by both cytoplasmic and membrane-bound ribosomes. During the co-translational translocation of secretory and membrane proteins, eukaryotic ribosomes dock with the protein conducting channel of the endoplasmic reticulum. An understanding of these processes will require the detailed structure of a eukaryotic ribosome. To this end, we have compared the three- dimensional structures of yeast and rabbit ribosomes at 24 A resolution. In general, we find that the active sites for protein synthesis and translocation have been highly conserved. It is interesting that a channel was visualized in the neck of the small subunit whose entrance is formed by a deep groove. By analogy with the prokaryotic small subunit, this channel may provide a conserved portal through which mRNA is threaded into the decoding center. In addition, both the small and large subunits are built around a dense tubular network. Our analysis further suggests that the nascent chain exit tunnel and the docking surface for the endoplasmic reticulum channel are formed by this network. We surmise that many of these features correspond to rRNA, based on biochemical and structural data.Ribosomal function is critically dependent on the specific association of small and large subunits. Our analysis of eukaryotic ribosomes reveals four conserved inter-subunit bridges with a geometry similar to that found in prokaryotes. In particular, a double-bridge connects the small subunit platform with the interface canyon on the large subunit. Moreover, a novel bridge is formed between the platform and the base of the L1 domain. Finally, size differences between mammalian and yeast large subunit rRNAs have been correlated with five expansion segments that form two large spines and three extended fingers. Overall, we find that expansion segments within the large subunit rRNA have been incorporated at positions distinct from the active sites for protein synthesis and translocation}, keywords = {0,80 s ribosome,analysis,animal,Animals,Catalytic Domain,chemistry,Comparative Study,Cryoelectron Microscopy,decoding,electron cryo-microscopy,exit tunnel,expansion,In Vitro,inter-subunit bridges,L1,La,Membrane Proteins,Membrane Proteins: chemistry,Membrane Proteins: metabolism,Membrane Transport Proteins,metabolism,Models,ModelsMolecular,Molecular,mRNA,nosource,physiology,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Rabbits,Reticulocytes,Reticulocytes: ultrastructure,Ribosomal,Ribosomal: chemistry,Ribosomal: metabolism,Ribosomal: ultrastructure,ribosome,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,Ribosomes: ultrastructure,Rna,RNA,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae Proteins,Saccharomyces: ultrastructure,segments,Structural,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,TranslationGenetic,translocation,ultrastructure,yeast} } % == BibTeX quality report for morganComparisonYeastRabbit2000: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{moriTranslationalRegulationAngiotensin1996a, title = {Translational Regulation of Angiotensin {{II}} Type {{1A}} Receptor. {{Role}} of Upstream {{AUG}} Triplets}, author = {Mori, Y. and Matsubara, H. and Murasawa, S. and Kijima, K. and Maruyama, K. and Tsukaguchi, H. and Okubo, N. and Hamakubo, T. and Inagami, T. and Iwasaka, T. and Inada, M.}, year = 1996, month = nov, journal = {Hypertension}, volume = {28}, number = {5}, pages = {810–817}, doi = {10.1161/01.HYP.28.5.810}, url = {http://hyper.ahajournals.org/cgi/content/abstract/hypertensionaha;28/5/810}, keywords = {analysis,Chloramphenicol,Codon,gene,Genes,genomic,In Vitro,in vitro translation,IN-VITRO,initiation,mRNA,Mutagenesis,nosource,polysomes,protein,rat,regulation,sequence,SYSTEM,translation,TRANSLATION INITIATION} }

@article{moriartySeleniumDeficiencyReduces1998, title = {Selenium Deficiency Reduces the Abundance of {{mRNA}} for {{Se-dependent}} Glutathione Peroxidase 1 by a {{UGA-dependent}} Mechanism Likely to Be Nonsense Codon-Mediated Decay of Cytoplasmic {{mRNA}}}, author = {Moriarty, P.M. and Reddy, C.C. and Maquat, L.E.}, year = 1998, month = may, journal = {Mol.Cell Biol.}, volume = {18}, number = {5}, pages = {2932–2939}, doi = {10.1128/MCB.18.5.2932}, url = {PM:9566912}, abstract = {The mammalian mRNA for selenium-dependent glutathione peroxidase 1 (Se- GPx1) contains a UGA codon that is recognized as a codon for the nonstandard amino acid selenocysteine (Sec). Inadequate concentrations of selenium (Se) result in a decrease in Se-GPx1 mRNA abundance by an uncharacterized mechanism that may be dependent on translation, independent of translation, or both. In this study, we have begun to elucidate this mechanism. We demonstrate using hepatocytes from rats fed either a Se-supplemented or Se-deficient diet for 9 to 13 weeks that Se deprivation results in an approximately 50-fold reduction in Se- GPx1 activity and an approximately 20-fold reduction in Se-GPx1 mRNA abundance. Reverse transcription-PCR analyses of nuclear and cytoplasmic fractions revealed that Se deprivation has no effect on the levels of either nuclear pre-mRNA or nuclear mRNA but reduces the level of cytoplasmic mRNA. The regulation of Se-GPx1 gene expression by Se was recapitulated in transient transfections of NIH 3T3 cells, and experiments were extended to examine the consequences of converting the Sec codon (TGA) to either a termination codon (TAA) or a cysteine codon (TGC). Regardless of the type of codon, an alteration in the Se concentration was of no consequence to the ratio of nuclear Se-GPx1 mRNA to nuclear Se-GPx1 pre-mRNA. The ratio of cytoplasmic Se-GPx1 mRNA to nuclear Se-GPx1 mRNA from the wild-type (TGA-containing) allele was reduced twofold when cells were deprived of Se for 48 h after transfection, which has been shown to be the extent of the reduction for the endogenous Se-GPx1 mRNA of cultured cells incubated as long as 20 days in Se-deficient medium. In contrast to the TGA allele, Se had no effect on expression of either the TAA allele or the TGC allele. Under Se-deficient conditions, the TAA and TGC alleles generated, respectively, 1.7-fold-less and 3-fold-more cytoplasmic Se-GPx1 mRNA relative to the amount of nuclear Se-GPx1 mRNA than the TGA allele. These results indicate that (i) under conditions of Se deprivation, the Sec codon reduces the abundance of cytoplasmic Se-GPx1 mRNA by a translation-dependent mechanism and (ii) there is no additional mechanism by which Se regulates Se-GPx1 mRNA production. These data suggest that the inefficient incorporation of Sec at the UGA codon during mRNA translation augments the nonsense-codon-mediated decay of cytoplasmic Se-GPx1 mRNA}, keywords = {0,3T3 Cells,Alleles,animal,biosynthesis,cancer,Cell Compartmentation,Cell Nucleus,Codon,CodonNonsense,Cytoplasm,DECAY,deficiency,Diet,enzymology,expression,gene,Gene Expression,Gene Expression RegulationEnzymologic,GENE-EXPRESSION,Genetic,genetics,Glutathione,Glutathione Peroxidase,human,La,Liver,Male,MECHANISM,media,metabolism,Mice,ModelsGenetic,mRNA,nosource,rat,Rats,regulation,Rna,RNA Precursors,RNA ProcessingPost-Transcriptional,RNAMessenger,Selenium,Selenocysteine,supportu.s.gov’tp.h.s.,termination,Transfection,translation} } % == BibTeX quality report for moriartySeleniumDeficiencyReduces1998: % ? Possibly abbreviated journal title Mol.Cell Biol.

@article{morikawaIdentificationAnalysisGagpol1992a, title = {Identification and Analysis of the Gag-Pol Ribosomal Frameshift Site of Feline Immunodeficiency Virus.}, author = {Morikawa, S. and Bishop, D.H.L.}, year = 1992, journal = {Virology}, volume = {186}, pages = {389–397}, doi = {10.1016/0042-6822(92)90004-9}, url = {http://linkinghub.elsevier.com/retrieve/pii/0042682292900049}, keywords = {analysis,frameshift,Gag-pol,IDENTIFICATION,IMMUNODEFICIENCY-VIRUS,nosource,pseudoknot,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,virus} }

@article{morimotoFunctionsRPS19Their2006, title = {The Functions of {{RPS19}} and Their Relationship to {{Diamond-Blackfan}} Anemia: {{A}} Review}, author = {Morimoto, K. and Lin, S. and Sakamoto, K.}, year = 2006, month = dec, journal = {Molecular Genetics and Metabolism}, url = {PM:17178250 http://linkinghub.elsevier.com/retrieve/pii/S1096719206003623}, abstract = {The relatively new study of ribosomal proteins has allowed for greater understanding of protein synthesis; however the connection between ribosomal proteins’ roles and that of disease pathophysiology has not yet been established. RPS19 is a ribosomal protein linked to Diamond-Blackfan anemia whose functions have begun to be elucidated. We review here the known roles of RPS19 in both ribosome construction and other extra-ribosomal functions and discuss their relationship to Diamond-Blackfan anemia}, keywords = {Anemia,cancer,disease,La,No DOI found,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Review,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome} } % == BibTeX quality report for morimotoFunctionsRPS19Their2006: % ? unused Journal abbr (“Mol.Genet.Metab”)

@article{moritzAssembly60SRibosomal1991, title = {Assembly of {{60S}} Ribosomal Subunits Is Perturbed in Temperature-Sensitive Yeast Mutants Defective in Ribosomal Protein {{L16}}.}, author = {Moritz, M. and Pulaski, B.A. and Woolford, J.L.}, year = 1991, month = nov, journal = {Molecular and cellular}, volume = {11}, number = {11}, pages = {5681–5692}, url = {http://mcb.asm.org/cgi/content/abstract/11/11/5681}, abstract = {Temperature-sensitive mutants defective in 60S ribosomal subunit protein L16 of Saccharomyces cerevisiae were isolated through hydroxylamine mutagenesis of the RPL16B gene and plasmid shuffling. Two heat-sensitive and two cold-sensitive isolates were characterized. The growth of the four mutants is inhibited at their restrictive temperatures. However, many of the cells remain viable if returned to their permissive temperatures. All of the mutants are deficient in 60S ribosomal subunits and therefore accumulate translational preinitiation complexes. Three of the mutants exhibit a shortage of mature 25S rRNA, and one accumulates rRNA precursors. The accumulation of rRNA precursors suggests that ribosome assembly may be slowed in this mutant. These phenotypes lead us to propose that mutants containing the rpl16b alleles are defective for 60S subunit assembly rather than function. In the mutant carrying the rpl16b-1 allele, ribosomes initiate translation at the noncanonical codon AUA, at least on the rpl16b-1 mRNA, bringing to light a possible connection between the rate and the fidelity of translation initiation}, keywords = {0,60S subunit,Alleles,Amino Acid Sequence,analysis,Animals,assembly,CELLS,CEREVISIAE,Codon,Comparative Study,COMPLEX,COMPLEXES,drug effects,Fidelity,Fungal Proteins,gene,GenesFungal,genetics,Genotype,GROWTH,Hydroxylamine,Hydroxylamines,initiation,La,metabolism,Molecular Sequence Data,mRNA,Multiple DOI,Mutagenesis,MUTANTS,nonfile,nosource,pharmacology,Phenotype,PLASMID,Polyribosomes,PRECURSOR,protein,Proteins,Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNA Precursors,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Sequence HomologyNucleic Acid,SUBUNIT,SUBUNITS,Temperature,translation,TRANSLATION INITIATION,yeast} } % == BibTeX quality report for moritzAssembly60SRibosomal1991: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{morrisUpstreamOpenReading2000a, title = {Upstream Open Reading Frames as Regulators of {{mRNA}} Translation}, author = {Morris, D.R. and Geballe, A.P.}, year = 2000, month = dec, journal = {Molecular and cellular biology}, volume = {20}, number = {23}, pages = {8635–8642}, doi = {10.1128/MCB.20.23.8635-8642.2000}, url = {http://mcb.asm.org/cgi/content/abstract/20/23/8635}, keywords = {0,Amino Acid Sequence,FRAME,Gene Expression Regulation,La,metabolism,ModelsGenetic,Molecular Sequence Data,mRNA,nosource,OPEN READING FRAME,Open Reading Frames,READING FRAME,Reading Frames,Regulatory SequencesNucleic Acid,Review,Ribosomes,Rna,RNAMessenger,supportu.s.gov’tp.h.s.,translation,TranslationGenetic,UPSTREAM} } % == BibTeX quality report for morrisUpstreamOpenReading2000a: % ? unused Journal abbr (“Mol Cell Biol.”)

@article{moserSequencespecificCleavageDouble1987a, title = {Sequence-Specific Cleavage of Double Helical {{DNA}} by Triple Helix Formation}, author = {Moser, H.E. and Dervan, P.B.}, year = 1987, month = oct, journal = {Science}, volume = {238}, number = {4827}, pages = {645–650}, doi = {10.1126/science.3118463}, url = {http://www.sciencemag.org/content/238/4827/645.short}, abstract = {Homopyrimidine oligodeoxyribonucleotides with EDTA-Fe attached at a single position bind the corresponding homopyrimidine-homopurine tracts within large double-stranded DNA by triple helix formation and cleave at that site. Oligonucleotides with EDTA.Fe at the 5’ end cause a sequence specific double strand break. The location and asymmetry of the cleavage pattern reveal that the homopyrimidine-EDTA probes bind in the major groove parallel to the homopurine strand of Watson-Crick double helical DNA. The sequence-specific recognition of double helical DNA by homopyrimidine probes is sensitive to single base mismatches. Homopyrimidine probes equipped with DNA cleaving moieties could be useful tools for mapping chromosomes}, keywords = {0,Base Sequence,chemistry,Chromosomes,CLEAVAGE,Dna,Edetic Acid,Ferrous Compounds,human,Hydrolysis,La,mapping,Middle Age,nosource,Nucleic Acid Conformation,Oligodeoxyribonucleotides,Oligonucleotides,Plasmids,sequence,Solvents,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.} }

@article{moutouhRecombinationLeadsRapid1996, title = {Recombination Leads to the Rapid Emergence of {{HIV-1}} Dually Resistant Mutants under Selective Drug Pressure}, author = {Moutouh, L. and Corbeil, J. and Richman, D.D.}, year = 1996, month = jun, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {93}, number = {12}, pages = {6106–6111}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.93.12.6106}, url = {http://www.pnas.org/content/93/12/6106.short}, keywords = {development,drugs,Genetic,Genotype,HIV,Hiv-1,Mutation,MUTATIONS,nosource,sequence,Virion,virus} }

@article{moxhamJunNterminalKinase1996a, title = {Jun {{N-terminal}} Kinase Mediates Activation of Skeletal Muscle Glycogen Synthase by Insulin ⬚in Vivo⬚.}, author = {Moxham, C.M. and Tabrizchi, A. and Davis, R.J. and Malbon, C.C.}, year = 1996, journal = {J.Biol.Chem.}, volume = {271}, pages = {30765–30773}, doi = {10.1074/jbc.271.48.30765}, keywords = {activation,anisomycin,IN-VIVO,kinase,nosource,p38,stress response} } % == BibTeX quality report for moxhamJunNterminalKinase1996a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{mozdyLowAbundanceTelomerase2006, title = {Low Abundance of Telomerase in Yeast: Implications for Telomerase Haploinsufficiency.}, author = {Mozdy, A.D. and Cech, T.R.}, year = 2006, month = sep, journal = {RNA.}, volume = {12}, number = {9}, pages = {1721–1737}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, doi = {10.1261/rna.134706}, url = {http://rnajournal.cshlp.org/content/12/9/1721.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1557690&tool=pmcentrez&rendertype=abstract}, abstract = {Telomerase is an RNA-dependent reverse transcriptase that maintains telomeric DNA at a species-specific equilibrium length. To determine an upper limit for the number of telomerase molecules in a Saccharomyces cerevisiae cell, we have established real-time RT-PCR assays to quantify the noncoding telomerase RNA, TLC1. We find that the number of TLC1 molecules in a haploid yeast cell is approximately 29, less than the number of chromosome ends (64) in late S-phase. Wild-type diploid cells contain approximately 37 telomerase RNAs, while diploids heterozygous for a null tlc1 allele have half the wild-type amount, approximately 19 TLC1 molecules. For comparison, there are approximately 480 molecules of the U2 snRNA per haploid cell. We show that a biological consequence of this low level of telomerase is haploinsufficiency: A TLC1/tlc1Delta heterozygote maintains shorter telomeres. A dominant-negative telomerase RNA, with a deletion of the template for telomeric DNA synthesis, further demonstrates that yeast telomere length is sensitive to telomerase dosage. Sixfold overexpression of tlc1Deltatemplate establishes a new telomere length set point, approximately 160 bp shorter than wild type. Removing telomerase protein-interaction sites from the tlc1Deltatemplate RNA mitigates the dominant-negative effect, suggesting that the tlc1Deltatemplate RNA competes with wild-type TLC1 for a limited supply of telomerase proteins or for telomeres. Because yeast telomerase is tethered at chromosome ends, the finding that it may be outnumbered by its telomeric DNA substrates provides a new perspective for interpreting the results of telomere maintenance studies.}, pmid = {16894218}, keywords = {0,analysis,assays,Base Sequence,Biochemistry,CELLS,CEREVISIAE,chemistry,Comparative Study,Diploidy,Dna,enzymology,Fungal,Fungal: genetics,Gene Deletion,Gene Dosage,genetics,Haploidy,haploinsufficiency,Haplotypes,Heterozygote,La,metabolism,Molecular Sequence Data,nosource,Nucleic Acid Amplification Techniques,OVEREXPRESSION,protein,Proteins,real-time pcr,REVERSE-TRANSCRIPTASE,Rna,RNA,RNA: analysis,RNA: chemistry,RNA: genetics,RNA: metabolism,RNAFungal,S Phase,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae: enzymology,Saccharomyces cerevisiae: genetics,SACCHAROMYCES-CEREVISIAE,SITE,SITES,Support,telomerase,Telomerase,Telomerase: analysis,Telomerase: chemistry,Telomerase: genetics,Telomerase: metabolism,Telomere,telomere length regulation,TEMPLATE,tlc1,U2 SNRNA,WILD-TYPE,yeast} } % == BibTeX quality report for mozdyLowAbundanceTelomerase2006: % ? Possibly abbreviated journal title RNA.

@article{mueller3DArrangement232000, title = {The {{3D}} Arrangement of the 23 {{S}} and 5 {{S rRNA}} in the {{Escherichia}} Coli 50 {{S}} Ribosomal Subunit Based on a Cryo-Electron Microscopic Reconstruction at 7.5 {{A}} Resolution}, author = {Mueller, F. and Sommer, I. and Baranov, P. and Matadeen, R. and Stoldt, M. and Wohnert, J. and Gorlach, M. and {}{van Heel}, M. and Brimacombe, R.}, year = 2000, month = apr, journal = {J.Mol.Biol.}, volume = {298}, number = {1}, pages = {35–59}, doi = {10.1006/jmbi.2000.3635}, url = {PM:10756104}, abstract = {The Escherichia coli 23 S and 5 S rRNA molecules have been fitted helix by helix to a cryo-electron microscopic (EM) reconstruction of the 50 S ribosomal subunit, using an unfiltered version of the recently published 50 S reconstruction at 7.5 A resolution. At this resolution, the EM density shows a well-defined network of fine structural elements, in which the major and minor grooves of the rRNA helices can be discerned at many locations. The 3D folding of the rRNA molecules within this EM density is constrained by their well-established secondary structures, and further constraints are provided by intra and inter-rRNA crosslinking data, as well as by tertiary interactions and pseudoknots. RNA-protein cross-link and foot-print sites on the 23 S and 5 S rRNA were used to position the rRNA elements concerned in relation to the known arrangement of the ribosomal proteins as determined by immuno-electron microscopy. The published X-ray or NMR structures of seven 50 S ribosomal proteins or RNA-protein complexes were incorporated into the EM density. The 3D locations of cross-link and foot-print sites to the 23 S rRNA from tRNA bound to the ribosomal A, P or E sites were correlated with the positions of the tRNA molecules directly observed in earlier reconstructions of the 70 S ribosome at 13 A or 20 A. Similarly, the positions of cross-link sites within the peptidyl transferase ring of the 23 S rRNA from the aminoacyl residue of tRNA were correlated with the locations of the CCA ends of the A and P site tRNA. Sites on the 23 S rRNA that are cross- linked to the N termini of peptides of different lengths were all found to lie within or close to the internal tunnel connecting the peptidyl transferase region with the presumed peptide exit site on the solvent side of the 50 S subunit. The post-transcriptionally modified bases in the 23 S rRNA form a cluster close to the peptidyl transferase area. The minimum conserved core elements of the secondary structure of the 23 S rRNA form a compact block within the 3D structure and, conversely, the points corresponding to the locations of expansion segments in 28 S rRNA all lie on the outside of the structure}, keywords = {0,Bacterial,Base Sequence,Binding Sites,chemistry,COMPLEX,COMPLEXES,Computer Simulation,Conserved Sequence,CROSS-LINKING,Cross-Linking Reagents,Cryoelectron Microscopy,CrystallographyX-Ray,ELEMENTS,elongation,Escherichia coli,ESCHERICHIA-COLI,Fungal Proteins,genetics,La,metabolism,MicroscopyImmunoelectron,ModelsMolecular,Molecular Sequence Data,nosource,Nuclear Magnetic ResonanceBiomolecular,Nucleic Acid Conformation,P-SITE,Peptide Elongation Factor Tu,Peptides,peptidyl transferase,protein,Proteins,pseudoknot,Ribonucleases,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Ricin,Rna,RNABacterial,RNARibosomal23S,RNARibosomal5S,RNATransfer,rRNA,Structural,structure,SUBUNIT,Thermodynamics,tRNA,ultrastructure} } % == BibTeX quality report for mueller3DArrangement232000: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{muhlradMutationsAffectingStability1992, title = {Mutations Affecting Stability and Deadenylation of the Yeast {{MFA2}} Transcript.}, author = {Muhlrad, D. and Parker, R.}, year = 1992, journal = {Genes & development}, volume = {6}, number = {11}, pages = {2100–2111}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.6.11.2100}, url = {http://genesdev.cshlp.org/content/6/11/2100.short}, keywords = {DEADENYLATION,Mutation,MUTATIONS,NMD,nosource,SKI,stability,XRN1,yeast} } % == BibTeX quality report for muhlradMutationsAffectingStability1992: % ? unused Journal abbr (“Genes & Dev.”)

@article{muhlradRapidMethodLocalized1992, title = {A Rapid Method for Localized Mutagenesis of Yeast Genes}, author = {Muhlrad, D. and Hunter, R. and Parker, R.}, year = 1992, month = feb, journal = {Yeast}, volume = {8}, number = {2}, pages = {79–82}, doi = {10.1002/yea.320080202}, url = {PM:1561838}, abstract = {We have developed a simple procedure for the localized mutagenesis of yeast genes. In this technique the region of interest is first amplified under mutagenic polymerase chain reaction (PCR) conditions. Cotransformation of the PCR product with a gapped plasmid containing homology to both ends of the PCR product allows in vivo recombination to repair the gap with the mutagenized DNA. This procedure is efficient, allows targeting of specific regions for mutagenesis, and requires no subcloning steps in Escherichia coli}, keywords = {0,BIOLOGY,Dna,DNAFungal,Escherichia coli,ESCHERICHIA-COLI,gene,Genes,GenesFungal,genetics,IN-VIVO,La,Mutagenesis,MutagenesisSite-Directed,nosource,PCR,Peptides,PLASMID,polymerase,Polymerase Chain Reaction,PRODUCT,RECOMBINATION,REGION,REQUIRES,Saccharomyces cerevisiae,TransformationGenetic,yeast} }

@article{mumbergYeastVectorsControlled1995, title = {Yeast {{Vectors}} for the {{Controlled Expression}} of {{Heterologous Proteins}} in {{Different Genetic Backgrounds}}}, author = {Mumberg, D. and Muller, R. and Funk, M.}, year = 1995, month = apr, journal = {Gene}, volume = {156}, number = {1}, pages = {119–122}, publisher = {Elsevier}, doi = {10.1016/0378-1119(95)00037-7}, url = {http://linkinghub.elsevier.com/retrieve/pii/0378111995000377}, abstract = {An expression system for Saccharomyces cerevisiae (Sc) has been developed which, depending on the chosen vector, allows the constitutive expression of proteins at different levels over a range of three orders of magnitude and in different genetic backgrounds. The expression system is comprised of cassettes composed of a weak CYC1 promoter, the ADH promoter or the stronger TEF and GPD promoters, flanked by a cloning array and the CYC1 terminator. The multiple cloning array based on pBIISK (Stratagene) provides six to nine unique restriction sites, which facilitates the cloning of genes and allows for the directed cloning of cDNAs by the widely used ZAP system (Stratagene). Expression cassettes were placed into both the centromeric and 2 mu plasmids of the pRS series [Sikorski and Hieter, Genetics 122 (1989) 19-27; Christianson et al., Gene 110 (1992) 119-122] containing HIS3, TRP1, LEU2 or URA3 markers. The 32 expression vectors created by this strategy provide a powerful tool for the convenient cloning and the controlled expression of genes or cDNAs in nearly every genetic background of the currently used Sc strains}, keywords = {CDNA CLONING,cloning,DEHYDROGENASE,Dna,EF-1-ALPHA,expression,gene,Genes,Genetic,genetics,HETEROLOGOUS EXPRESSION,MULTICOPY VECTOR,nosource,PLASMID,Plasmids,POLYLINKER,PROMOTER,protein,Proteins,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SHUTTLE VECTORS,SYSTEM,UPSTREAM,vector,vectors,yeast} } % == BibTeX quality report for mumbergYeastVectorsControlled1995: % ? Title looks like it was stored in title-case in Zotero

@article{munishkinRibosomeinpiecesBindingElongation1997, title = {The Ribosome-in-Pieces: {{Binding}} of Elongation Factor {{EF-G}} to Oligoribonucleotides That Mimic the Sarcin/Ricin and Thiostrepton Domains of {{23S}} Ribosomal {{RNA}}}, author = {Munishkin, A. and Wool, I.G.}, year = 1997, month = nov, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {94}, number = {23}, pages = {12280–12284}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.94.23.12280}, url = {http://www.pnas.org/content/94/23/12280.short}, abstract = {An oligoribonucleotide (a 27-mer) that mimics the sarcin/ricin (S/R) domain of Escherichia coli 23S rRNA binds elongation factor EF-G; the K-d is 6.9 mu M, whereas for binding to ribosomes it is 0.7 mu M. Binding saturates when EF-G and the S/R RNA are equimolar; at saturation 70% of the input RNA is in complexes with EF-G. Binding of EF-G to S/R RNA does not require GTP but is inhibited by GDP; the inhibition by GDP is overcome by GTP, The effects of mutations of the S/R domain nucleotides G2655, A2660, and G2661 suggest that EF-G recognizes the conformation of the RNA rather than the identity of the nucleotides. EF-G also binds to an oligoribonucleotide (an 84-mer) that has the thiostrepton region of 23S rRNA; however, EF-G binds independently to S/R and thiostrepton oligoribonucleotides}, keywords = {ALPHA-SARCIN,BINDING,COMPLEX,COMPLEXES,CONFORMATION,EF-G,elongation,Escherichia coli,ESCHERICHIA-COLI,GTP,INHIBITION,LOOP,Mutation,MUTATIONS,nosource,Nucleotides,Oligoribonucleotides,protein,REGION,RIBONUCLEIC-ACID,RIBOSOMAL-RNA,ribosome,Ribosomes,RICIN A-CHAIN,Rna,rRNA,SITE,Thiostrepton,translocation} }

@article{munroNewViewProtein2008a, title = {A New View of Protein Synthesis: Mapping the Free Energy Landscape of the Ribosome Using Single-Molecule {{FRET}}}, author = {Munro, J.B. and Vaiana, A. and Sanbonmatsu, K.Y. and Blanchard, S.C.}, year = 2008, month = jul, journal = {Biopolymers}, volume = {89}, number = {7}, pages = {565–577}, doi = {10.1002/bip.20961}, url = {PM:18286627}, abstract = {This article reviews the application of single-molecule fluorescence resonance energy transfer (smFRET) methods to the study of protein synthesis catalyzed by the ribosome. smFRET is a powerful new technique that can be used to investigate dynamic processes within enzymes spanning many orders of magnitude. The application of wide-field smFRET imaging methods to the study of dynamic processes in the ribosome offers a new perspective on the mechanism of protein synthesis. Using this technique, the structural and kinetic parameters of tRNA motions within wild-type and specifically mutated ribosome complexes have been obtained that provide valuable new insights into the mechanism and regulation of translation elongation. The results of these studies are discussed in the context of current knowledge of the ribosome mechanism from both structural and biophysical perspectives}, keywords = {Binding Sites,Biophysics,chemistry,COMPLEX,COMPLEXES,Computer Simulation,elongation,Energy Transfer,enzyme,Enzymes,Fluorescence,Fluorescence Resonance Energy Transfer,fret,genetics,La,mapping,MECHANISM,metabolism,Methods,Motion,MutagenesisSite-Directed,nosource,physiology,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,regulation,Review,ribosome,Ribosomes,Rna,RNATransfer,single-molecule,Structural,Thermodynamics,translation,tRNA,WILD-TYPE} }

@article{munshiOverexpressionTranslationElongation2001, title = {Overexpression of Translation Elongation Factor {{1A}} Affects the Organization and Function of the Actin Cytoskeleton in Yeast}, author = {Munshi, R. and Kandl, K.A. and {Carr-Schmid}, A. and Whitacre, J.L. and Adams, A.E.M. and Kinzy, T.G.}, year = 2001, month = apr, journal = {Genetics}, volume = {157}, number = {4}, pages = {1425–1436}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/157.4.1425}, url = {http://www.genetics.org/content/157/4/1425.short}, abstract = {The translation elongation factor 1 complex (eEF1) plays a central role in protein synthesis, delivering aminoacyl-tRNAs to the elongating ribosome. The eEF1A subunit, a classic G-protein, also performs roles aside from protein synthesis. The overexpression of either eEF1A or eEF1B alpha, the catalytic subunit of the guanine nucleotide exchange factor, in Saccharomyces cerevisiae results in effects on cell growth. Here we demonstrate that overexpression of either factor does not affect the levels of the other subunit or the rate or accuracy of protein synthesis. Instead, the major effects in vivo appear to be at the level of cell morphology and budding. eEF1A overexpression results in dosage-dependent reduced budding and altered actin distribution and cellular morphology. In addition, the effects of excess eEF1A in actin mutant strains show synthetic growth defects, establishing a genetic connection between the two proteins. As the ability of eEF1A to bind and bundle actin is conserved in yeast, these results link the established ability of eEF1A to bind and bundle actin in vitro with nontranslational roles for the protein in vivo}, keywords = {0,accuracy,Actins,BINDING PROTEIN,biosynthesis,cell cycle,Cell Division,CEREVISIAE,COMPLEX,COMPLEXES,CYTOSKELETON,elongation,F-ACTIN,FACTOR 1-ALPHA,Fungal Proteins,Gene Expression,GenesFungal,Genetic,GENETIC-CHARACTERIZATION,genetics,GROWTH,growth & development,Guanine,GUANINE-NUCLEOTIDE,GUANINE-NUCLEOTIDE-EXCHANGE,In Vitro,IN-VITRO,IN-VIVO,La,metabolism,microbiology,MOLECULAR-GENETICS,MUTATIONS,nosource,NUCLEOTIDE EXCHANGE,ORGANIZATION,OVEREXPRESSION,Peptide Elongation Factor 1,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,ribosome,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SHUTTLE VECTORS,SUBUNIT,supportu.s.gov’tp.h.s.,T,TRANSFER-RNA,translation,yeast} }

@article{murataIL13InducesPhosphorylation1996a, title = {{{IL-13}} Induces Phosphorylation and Activation of {{JAK2 Janus Kinase}} in Human Colon Carcinoma Cell Lines: Similarites between {{IL-4}} and {{IL-13}} Signaling.}, author = {Murata, T. and Noguchi, P.D. and Puri, R.K.}, year = 1996, journal = {J.Immunol.}, volume = {156}, pages = {2972–2978}, doi = {10.4049/jimmunol.156.8.2972}, keywords = {activation,cancer,Cell Line,cell lines,human,Jak,kinase,nosource,Phosphorylation} } % == BibTeX quality report for murataIL13InducesPhosphorylation1996a: % ? Possibly abbreviated journal title J.Immunol.

@article{muthSingleAdenosineNeutral2000, title = {A Single Adenosine with a Neutral {{pK}}(a) in the Ribosomal Peptidyl Transferase Center}, author = {Muth, G.W. and {Ortoleva-Donnelly}, L. and Strobel, S.A.}, year = 2000, journal = {Science}, volume = {289}, number = {5481}, pages = {947–950}, doi = {10.1126/science.289.5481.947}, url = {ISI:000088701200031}, abstract = {Biochemical and crystallographic evidence suggests that 23S ribosomal RNA (rRNA) is the catalyst of peptide bond formation. To explore the mechanism of this reaction, we screened for nucleotides in Escherichia coli 23S rRNA that may have a perturbed pK(a) (where K-a is the acid constant) based on the pH dependence of dimethylsulfate modification. A single universally conserved A (number 2451) within the central loop of domain V has a near neutral pK(a) of 7.6 +/- 0.2, which is about the same as that reported for the peptidyl transferase reaction. In vivo mutational analysis of this nucleotide indicates that it has an essential role in ribosomal function. These results are consistent with a mechanism wherein the nucleotide base of A2451 serves as a general acid base during peptide bond formation}, keywords = {A-SITES,ACID,Adenosine,analysis,Catalysis,Chloramphenicol,DOMAIN-V,Erythromycin,Escherichia coli,ESCHERICHIA-COLI,IN-VIVO,LOOP,MECHANISM,modification,MUTATIONAL ANALYSIS,nosource,Nucleotides,P-SITES,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,RESISTANCE,RIBOSOMAL-RNA,ribozyme,Rna,rRNA,SERINE PROTEASES,TRANSFER-RNA,TRANSFERASE CENTER} }

@article{nagaiRNPDomainSequencespecific1995a, title = {The {{RNP}} Domain: A Sequence-Specific {{RNA-binding}} Domain Involved in Processing and Transport of {{RNA}}. [{{Review}}] [32 Refs]}, author = {Nagai, K. and Oubridge, C. and Ito, N. and Avis, J. and Evans, P.}, year = 1995, month = jun, journal = {Trends in Biochemical Sciences}, volume = {20}, number = {6}, pages = {235–240}, doi = {10.1016/S0968-0004(00)89024-6}, keywords = {COMPLEX,COMPLEXES,CRYSTAL-STRUCTURE,mRNA,nosource,poly(A),protein,Proteins,Rna,splicing,structure} }

@article{nagaiRNAproteinComplexesReview1996a, title = {{{RNA-protein}} Complexes. [{{Review}}] [60 Refs]}, author = {Nagai, K.}, year = 1996, month = feb, journal = {Current Opinion in Structural Biology}, volume = {6}, number = {1}, pages = {53–61}, doi = {10.1016/S0959-440X(96)80095-9}, keywords = {BINDING,Capsid,COMPLEX,COMPLEXES,CRYSTAL-STRUCTURE,DOUBLE-STRANDED-RNA,mRNA,nosource,Operon,poly(A),protein,Proteins,Ribosomal Proteins,Rna,sequence,structure} }

@article{nagyRegulationTranspositionBacteria2004, title = {Regulation of Transposition in Bacteria}, author = {Nagy, Z. and Chandler, M.}, year = 2004, month = jun, journal = {Research in microbiology}, volume = {155}, number = {5}, pages = {387–398}, publisher = {Elsevier}, doi = {10.1016/j.resmic.2004.01.008}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0923250804000592}, abstract = {Mobile genetic elements (MGEs) play a central role in the evolution of bacterial genomes. Transposable elements (TE: transposons and insertion sequences) represent an important group of these elements. Comprehension of the dynamics of genome evolution requires an understanding of how the activity of TEs is regulated and how their activity responds to the physiology of the host cell. This article presents an overview of the large range of, often astute, regulatory mechanisms, which have been adopted by TEs. These include mechanisms intrinsic to the element at the level of gene expression, the presence of key checkpoints in the recombination pathway and the intervention of host proteins which provide a TE/host interface. The multiplicity and interaction of these mechanisms clearly illustrates the importance of limiting transposition activity and underlines the compromise that has been reached between TE activity and the host genome. Finally, we consider how TE activity can shape the host genome}, keywords = {0,antisense,Bacteria,Bacterial,Dna,DNA Methylation,DNA Repair,DNA Transposable Elements,DNASuperhelical,DYNAMICS,ELEMENTS,Evolution,EvolutionMolecular,expression,FrameshiftingRibosomal,gene,Gene Expression,Gene Expression RegulationBacterial,GENE-EXPRESSION,GenesBacterial,Genetic,genetics,Genome,GenomeBacterial,INSERTION SEQUENCES,Integration Host Factors,interface,La,MECHANISM,MECHANISMS,ModelsGenetic,nosource,PATHWAY,physiology,Promoter Regions (Genetics),protein,Protein Biosynthesis,Proteins,RECOMBINATION,regulation,REQUIRES,Research SupportNon-U.S.Gov’t,Review,Rna,RNA Stability,RNAAntisense,sequence,SEQUENCES,SOS Response (Genetics)} } % == BibTeX quality report for nagyRegulationTranspositionBacteria2004: % ? unused Journal abbr (“Res.Microbiol.”)

@article{nahasTyrosinePhosphorylationActivation1996a, title = {Tyrosine Phosphorylation and Activation of a New Mitogen-Activated Protein ({{MAP}})-Kinase Cascade in Human Neutrophils Steimulate with Various Agonists.}, author = {Nahas, N. and Molski, T.F. and Fernandez, G.A. and Sha’ari, R.I.}, year = 1996, journal = {Biochem.J.}, volume = {318}, pages = {247–253}, doi = {10.1042/bj3180247}, keywords = {activation,anisomycin,HOG1,human,nosource,p38,Phosphorylation,protein,stress activation,yeast} } % == BibTeX quality report for nahasTyrosinePhosphorylationActivation1996a: % ? Possibly abbreviated journal title Biochem.J.

@article{nairnCalciumCalmodulindependentProtein1994a, title = {Calcium/Calmodulin-Dependent Protein Kinases.}, author = {Nairn, A.C. and Picciotto, M.R.}, year = 1994, journal = {Sem.Cancer.Biol.}, volume = {5}, pages = {295–303}, keywords = {EF-2,EF-2 kinase,kinase,No DOI found,nosource,protein,Protein Kinases,Review} } % == BibTeX quality report for nairnCalciumCalmodulindependentProtein1994a: % ? Possibly abbreviated journal title Sem.Cancer.Biol.

@article{naitowVirus34Resolution2002, title = {L-{{A}} Virus at 3.4 {{A}} Resolution Reveals Particle Architecture and {{mRNA}} Decapping Mechanism}, author = {Naitow, H. and Tang, J. and Canady, M. and Wickner, R.B. and Johnson, J.E.}, year = 2002, month = oct, journal = {Nature Structural & }, volume = {9}, number = {10}, eprint = {12244300}, eprinttype = {pubmed}, pages = {725–728}, issn = {1072-8368}, doi = {10.1038/nsb844}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12244300 http://www.nature.com/nsmb/journal/v9/n10/abs/nsb844.html}, abstract = {The structure of the yeast L-A virus was determined by X-ray crystallography at 3.4 A resolution. The L-A dsRNA virus is 400 A in diameter and contains a single protein shell of 60 asymmetric dimers of the coat protein, a feature common among the inner protein shells of dsRNA viruses and probably related to their unique mode of transcription and replication. The two identical subunits in each dimer are in non-equivalent environments and show substantially different conformations in specific surface regions. The L-A virus decaps cellular mRNA to efficiently translate its own uncapped mRNA. Our structure reveals a trench at the active site of the decapping reaction and suggests a role for nearby residues in the reaction.}, pmid = {12244300}, keywords = {0,Binding Sites,BIOLOGY,chemistry,COAT PROTEIN,CONFORMATION,Crystallography,CrystallographyX-Ray,DIMER,Dimerization,DSRNA,dsRNA virus,Evolution,EvolutionMolecular,gag,Gag,gag: metabolism,gene,Gene Products,Gene Productsgag,GENE-PRODUCT,genetics,L-A,L-A-VIRUS,La,MECHANISM,Messenger,Messenger: chemistry,Messenger: metabolism,metabolism,Molecular,mRNA,nosource,PRODUCT,PRODUCTS,protein,Protein,REGION,REPLICATION,RESIDUES,RESOLUTION,Rna,RNA,RNA Viruses,RNA Viruses: chemistry,RNA Viruses: genetics,RNA Viruses: metabolism,RNAMessenger,Sequence Analysis,Sequence AnalysisProtein,SITE,structure,SUBUNIT,SUBUNITS,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,transcription,virus,X-Ray,yeast} } % == BibTeX quality report for naitowVirus34Resolution2002: % ? unused Journal abbr (“Nat.Struct.Biol.”)

@article{najafabadiErrorMinimizationExplains2007, title = {Error Minimization Explains the Codon Usage of Highly Expressed Genes in {{Escherichia}} Coli}, author = {Najafabadi, H.S. and Lehmann, J. and Omidi, M.}, year = 2007, month = jan, journal = {Gene}, volume = {387}, number = {1-2}, pages = {150–155}, publisher = {Elsevier}, doi = {10.1016/j.gene.2006.09.004}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0378-1119(06)00587-7}, abstract = {Different organisms use synonymous codons with different preferences. Several measures have been introduced to compute the extent of codon usage bias within a gene or genome, among which the codon adaptation index (CAI) has been shown to be well correlated with mRNA levels of Escherichia coli. In this work an error adaptation index (eAI) is introduced, which estimates the level at which a gene can tolerate the effects of mistranslations. It is shown that the eAI has a strong correlation with CAI, as well as with mRNA levels, which suggests that the codons of highly expressed genes are selected so that mistranslation would have the minimum possible effect on the structure and function of the related proteins}, keywords = {Codon,codon usage,CODONS,error adaptation index,error minimization,Escherichia coli,ESCHERICHIA-COLI,gene,gene expression,Genes,Genome,La,mRNA,nosource,protein,Proteins,structure,trna content} }

@article{nakagawaThreedimensionalStructureRNAbinding1999, title = {The Three-Dimensional Structure of the {{RNA-binding}} Domain of Ribosomal Protein {{L2}}; a Protein at the Peptidyl Transferase Center of the Ribosome}, author = {Nakagawa, A. and Nakashima, T. and Taniguchi, M. and Hosaka, H. and Kimura, M. and Tanaka, I.}, year = 1999, month = mar, journal = {The EMBO Journal}, volume = {18}, number = {6}, pages = {1459–1467}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/18.6.1459}, url = {http://www.nature.com/emboj/journal/v18/n6/abs/7591577a.html}, abstract = {Ribosomal protein L2 is the largest protein component in the ribosome. It is located at or near the peptidyl transferase center and has been a prime candidate for the peptidyl transferase activity. It binds directly to 23S rRNA and plays a crucial role in its assembly. The three-dimensional structure of the RNA-binding domain of L2 from Bacillus stearothermophilus has been determined at 2.3 A resolution by X-ray crystallography using the selenomethionyl MAD method. The RNA- binding domain of L2 consists of two recurring motifs of approximately 70 residues each. The N-terminal domain (positions 60-130) is homologous to the OB-fold, and the C-terminal domain (positions 131- 201) is homologous to the SH3-like barrel. Residues Arg86 and Arg155, which have been identified by mutation experiments to be involved in the 23S rRNA binding, are located at the gate of the interface region between the two domains. The molecular architecture suggests how this important protein has evolved from the ancient nucleic acid-binding proteins to create a 23S rRNA-binding domain in the very remote past}, keywords = {99177161,Amino Acid Sequence,Amino Acid Substitution,assembly,Bacillus stearothermophilus,BACILLUS-STEAROTHERMOPHILUS,BINDING,Binding Sites,chemistry,Comparative Study,COMPONENT,Computer Graphics,Crystallography,CrystallographyX-Ray,L2,metabolism,Methods,ModelsMolecular,Molecular Sequence Data,MutagenesisSite-Directed,Mutation,nosource,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,protein,Protein Folding,Protein StructureSecondary,Proteins,Recombinant Proteins,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNARibosomal23S,rRNA,Selenomethionine,Sequence Alignment,Sequence HomologyAmino Acid,structure,supportnon-u.s.gov’t,ultrastructure} } % == BibTeX quality report for nakagawaThreedimensionalStructureRNAbinding1999: % ? unused Journal abbr (“EMBO J.”)

@article{nakajimaSynthesisActivityPyrimidinylpropenamide2003, title = {Synthesis and Activity of Pyrimidinylpropenamide Antibiotics: The Alkyl Analogues of Sparsomycin}, author = {Nakajima, N. and Enomoto, T. and Watanabe, T. and Matsuura, N. and Ubukata, M.}, year = 2003, month = dec, journal = {Bioscience, biotechnology, and biochemistry}, volume = {67}, number = {12}, pages = {2556–2566}, publisher = {J-STAGE}, doi = {10.1271/bbb.67.2556}, url = {http://joi.jlc.jst.go.jp/JST.JSTAGE/bbb/67.2556?from=Google}, abstract = {Facile syntheses of sparsomycin (3) and its four analogues (4-7) based on diastereoselective oxidation of sulfide, sulfenylation, and coupling of 6-methyluracylacryllic acid with monooxodithioacetal amine, are described. Studies on the biological activity of morphological reversion on src(ts)-NRK cells were also carried out}, keywords = {0,3,ACID,Animals,antibiotic,antibiotics,AntibioticsAntineoplastic,Cell TransformationNeoplastic,CELLS,chemical synthesis,drug effects,La,metabolism,Mice,nosource,Oxidation-Reduction,pharmacology,Research SupportNon-U.S.Gov’t,Sarcoma VirusesAvian,sparsomycin,Tumor CellsCultured} } % == BibTeX quality report for nakajimaSynthesisActivityPyrimidinylpropenamide2003: % ? unused Journal abbr (“Biosci.Biotechnol.Biochem.”)

@article{nakamuraEmergingUnderstandingTranslation1996a, title = {Emerging Understanding of Translation Termination. [{{Review}}] [20 Refs]}, author = {Nakamura, Y. and Ito, K. and Isaksson, L.A.}, year = 1996, journal = {Cell}, volume = {87}, number = {2}, pages = {147–150}, doi = {10.1016/S0092-8674(00)81331-8}, keywords = {nosource,sup35,sup45,termination,translation,TRANSLATION TERMINATION} }

@article{nakamuraMakingSenseMimic2003a, title = {Making Sense of Mimic in Translation Termination}, author = {Nakamura, Y. and Ito, K.}, year = 2003, month = feb, journal = {Trends Biochem.Sci.}, volume = {28}, number = {2}, pages = {99–105}, doi = {10.1016/S0968-0004(03)00006-9}, url = {PM:12575998}, abstract = {The mechanism of translation termination has long been a puzzle. Recent crystallographic evidence suggests that the eukaryotic release factor (eRF1), the bacterial release factor (RF2) and the ribosome recycling factor (RRF) all mimic a tRNA structure, whereas biochemical and genetic evidence supports the idea of a tripeptide ‘anticodon’ in bacterial release factors RF1 and RF2. However, the suggested structural mimicry of RF2 is not in agreement with the tripeptide ‘anticodon’ hypothesis and, furthermore, recently determined structures using cryo-electron microscopy show that, when bound to the ribosome, RF2 has a conformation that is distinct from the RF2 crystal structure. In addition, hydroxyl-radical probings of RRF on the ribosome are not in agreement with the simple idea that RRF mimics tRNA in the ribosome A-site. All of this evidence seriously questions the simple concept of structural mimicry between proteins and RNA and, thus, leaves only functional mimicry of protein factors of translation to be investigated}, keywords = {0,A SITE,A-SITE,Anticodon,Bacterial,Binding Sites,chemistry,CONFORMATION,Cryoelectron Microscopy,crystal structure,CRYSTAL-STRUCTURE,Genetic,genetics,Hydroxyl Radical,La,MECHANISM,metabolism,ModelsBiological,ModelsMolecular,Molecular Mimicry,nosource,Peptide Termination Factors,physiology,protein,Protein Biosynthesis,Protein Conformation,Proteins,RELEASE,release factor,RELEASE FACTORS,Review,ribosome,RIBOSOME RECYCLING FACTOR,Rna,RNATransfer,Structural,structure,Support,termination,translation,TRANSLATION TERMINATION,tRNA} } % == BibTeX quality report for nakamuraMakingSenseMimic2003a: % ? Possibly abbreviated journal title Trends Biochem.Sci.

@article{naldiniVivoGeneDelivery1996a, title = {In Vivo Gene Delivery and Stable Transduction of Nondividing Cells by a Lentiviral Vector [See Comments]}, author = {Naldini, L. and Blomer, U. and Gallay, P. and Ory, D. and Mulligan, R. and Gage, F.H. and Verma, I.M. and Trono, D.}, year = 1996, month = apr, journal = {Science}, volume = {272}, number = {5259}, pages = {263–267}, doi = {10.1126/science.272.5259.263}, keywords = {cell cycle,gene,Genes,Hela Cells,HIV,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,IN-VIVO,nosource,rat,sequence,SYSTEM,vector,vectors,virus} }

@article{namEffectsProgressiveDepletion1986a, title = {Effects of Progressive Depletion of ⬚{{TCM1}}⬚ and ⬚{{CYH2}}⬚ {{mRNA}} on ⬚{{Saccharomyces}} Cerevisiae⬚ Ribosomal Protein Accumulation.}, author = {Nam, H.G. and Fried, H.M.}, year = 1986, journal = {Mol.Cell.Biol.}, volume = {6}, pages = {1535–1544}, keywords = {CYH2,mRNA,Multiple DOI,nonfile,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,regulation,ribosome,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,TCM1} } % == BibTeX quality report for namEffectsProgressiveDepletion1986a: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{namCharacterizationRibosomalFrameshifting1993, title = {Characterization of Ribosomal Frameshifting for Expression of Pol Gene Products of Human {{T-cell}} Leukemia Virus Type {{I}}.}, author = {Nam, S.H. and Copeland, T.D. and Hatanaka, M. and Oroszlan, S.}, year = 1993, month = jan, journal = {Journal of virology}, volume = {67}, number = {1}, pages = {196–203}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.67.1.196-203.1993}, url = {http://jvi.asm.org/cgi/content/abstract/67/1/196}, abstract = {For study of the pol gene expression of human T-cell leukemia virus type I (HTLV-I), RNA was transcribed in vitro from proviral DNA and translated in rabbit reticulocyte lysates. This cell-free translation resulted in two major translation products representing the Gag and Gag-Pro polyproteins. By contrast, the Gag-Pro-Pol polyprotein could be readily observed only when translation was performed with mutant mRNA in which the protease (pro) reading frame was aligned to gag to eliminate the frameshifting event in the gag-pro overlap. The results indicated that two independent ribosomal frameshifting events are required for expression of the HTLV-I pol gene product. Studies with mutant DNAs facilitated the characterization of the primary structure of the HTLV-I mRNA responsible for the ribosomal frameshift in the pro-pol overlap and demonstrated that the frameshift occurs at the signal sequence UUUAAAC. Direct amino acid sequencing of the transframe protein localized the site of the frameshift to the asparagine codon AAC}, keywords = {0,ACID,Amino Acid Sequence,AMINO-ACID,Base Sequence,biosynthesis,cancer,Cell-Free System,CELL-FREE TRANSLATION,Codon,development,Dna,expression,FRAME,frameshift,Frameshift Mutation,Frameshifting,Gag,gene,Gene Expression,Gene Productspol,GENE-EXPRESSION,GENE-PRODUCT,Genesgag,Genespol,genetics,HIV,HIV Protease,human,Human T-lymphotropic virus 1,In Vitro,IN-VITRO,La,LEUKEMIA,lysate,metabolism,Molecular Sequence Data,mRNA,MutagenesisSite-Directed,nosource,Open Reading Frames,pol,POL GENE,POLYPROTEIN,Polyproteins,PRODUCT,PRODUCTS,protein,Protein Biosynthesis,Proteins,READING FRAME,Recombinant Proteins,Research SupportU.S.Gov’tP.H.S.,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,Ribosomes,Rna,RNAMessenger,sequence,SIGNAL,SITE,structure,TranscriptionGenetic,translation,virology,virus} } % == BibTeX quality report for namCharacterizationRibosomalFrameshifting1993: % ? unused Journal abbr (“J.Virol.”)

@article{nambaVisualizationProteinnucleicAcid1989a, title = {Visualization of Protein-Nucleic Acid Interactions in a Virus. {{Refined}} Structure of Intact Tobacco Mosaic Virus at 2.9 {{A}} Resolution by {{X-ray}} Fiber Diffraction}, author = {Namba, K. and Pattanayek, R. and Stubbs, G.}, year = 1989, month = jul, journal = {J.Mol.Biol.}, volume = {208}, number = {2}, pages = {307–325}, doi = {10.1016/0022-2836(89)90391-4}, url = {PM:2769760}, abstract = {The structure of tobacco mosaic virus (TMV) has been determined by fiber diffraction methods at 2.9 A resolution, and refined by restrained least-squares to an R-factor of 0.096. Protein-nucleic acid interactions are clearly visible. The final model contains all of the non-hydrogen atoms of the RNA and the protein, 71 water molecules, and two calcium-binding sites. Viral disassembly is driven by electrostatic repulsions between the charges in two carboxyl-carboxylate pairs and a phosphate-carboxylate pair. The phosphate-carboxylate pair and at least one of the carboxyl-carboxylate pairs appear to be calcium-binding sites. Nucleotide specificity, enabling TMV to recognize its own RNA by a repeating pattern of guanine residues, is provided by two guanine-specific hydrogen bonds in one of the three base-binding sites}, keywords = {0,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,Binding Sites,BIOLOGY,Calcium,genetics,Guanine,Hydrogen Bonding,La,metabolism,Methods,MODEL,ModelsMolecular,ModelsStructural,Molecular Conformation,MOSAIC-VIRUS,nosource,protein,Proteins,RESIDUES,RESOLUTION,Rna,RnaViral,SITE,SITES,SPECIFICITY,structure,supportu.s.gov’tp.h.s.,Tobacco,Tobacco Mosaic Virus,Viral Proteins,virus,Water,X-Ray Diffraction} } % == BibTeX quality report for nambaVisualizationProteinnucleicAcid1989a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{namyGeneOverexpressionTool2002, title = {Gene Overexpression as a Tool for Identifying New Trans-Acting Factors Involved in Translation Termination in {{Saccharomyces}} Cerevisiae}, author = {Namy, O. and Hatin, I. and Stahl, G. and Liu, H.M. and Barnay, S. and Bidou, L. and Rousset, J.P.}, year = 2002, month = jun, journal = {Genetics}, volume = {161}, number = {2}, pages = {585–594}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/161.2.585}, url = {http://www.genetics.org/content/161/2/585.short}, abstract = {In eukaryotes, translation termination is dependent on the availability of both release factors, eRF1 and eRF3; however, the precise mechanisms involved remain poorly understood. In particular, the fact that the phenotype of release factor mutants is pleiotropic could imply that other factors and interactions are involved in translation termination. To identify unknown elements involved in this process, we performed a genetic screen using a reporter strain in which a leaky, stop codon is inserted in the lacZ reporter gene, attempting to isolate factors modifying termination efficiency, when overexpressed. Twelve suppressors and 11 antisuppressors, increasing or decreasing termination readthrough, respectively, were identified and analyzed for three secondary phenotypes often associated with translation Imitations: thermosensitivity, G418 sensitivity, and sensitivity to osmotic pressure. Interestingly among these candidates, we identified two genes, SSO1 and STU2, involved in protein transport and spindle pole body formation. respectively, suggesting puzzling connections with the translation termination process}, keywords = {0,BINDING PROTEIN,Codon,CYTOSKELETON,efficiency,ELEMENTS,ELONGATION-FACTOR 1-ALPHA,ESCHERICHIA-COLI,gene,Genes,Genetic,MAMMALIAN PROTEIN-SYNTHESIS,MECHANISM,MECHANISMS,MESSENGER-RNA,nosource,OMNIPOTENT SUPPRESSORS,Phenotype,protein,Protein Transport,readthrough,RELEASE FACTORS,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,STOP CODON,sup35,termination,translation,TRANSLATION TERMINATION,yeast} }

@article{namyTranslationalReadthroughPDE22002, title = {Translational Readthrough of the {{PDE2}} Stop Codon Modulates {{cAMP}} Levels in {{Saccharomyces}} Cerevisiae}, author = {Namy, O. and {Duchateau-Nguyen}, G. and Rousset, J.P.}, year = 2002, month = feb, journal = {Molecular Microbiology}, volume = {43}, number = {3}, pages = {641–652}, publisher = {Wiley Online Library}, doi = {10.1046/j.1365-2958.2002.02770.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2002.02770.x/full}, abstract = {The efficiency of translation termination in yeast can vary several 100-fold, depending on the context around the stop codon. We performed a computer analysis designed to identify yeast open reading frames (ORFs) containing a readthrough motif surrounding the termination codon. Eight ORFs were found to display inefficient stop codon recognition, one of which, PDE2, encodes the high-affinity cAMP phosphodiesterase. We demonstrate that Pde2p stability is very impaired by the readthrough-dependent extension of the protein. A 20-fold increase in readthrough of PDE2 was observed in a [PSI+] as compared with a [psi(-)] strain. Consistent with this observation, an important increase in cAMP concentration was observed in suppressor backgrounds. These results provide a molecular explanation for at least some of the secondary phenotypes associated with suppressor backgrounds}, keywords = {3,analysis,Codon,computer,computer analysis,efficiency,ELONGATION FACTOR-II,ESCHERICHIA-COLI,FRAME,GAMMA-SUBUNIT,Genome,HEAT-SHOCK,IDENTIFY,INVIVO FUNCTION,nosource,OPEN READING FRAME,Open Reading Frames,ORNITHINE DECARBOXYLASE ANTIZYME,Phenotype,POLYMERASE-III HOLOENZYME,protein,PROTEIN-KINASE,readthrough,RECOGNITION,RELEASE FACTOR-II,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,stability,STOP CODON,termination,TERMINATION CODON,TERMINATION EFFICIENCY,translation,TRANSLATION TERMINATION,yeast} }

@article{namyIdentificationStopCodon2003, title = {Identification of Stop Codon Readthrough Genes in {{Saccharomyces}} Cerevisiae}, author = {Namy, O. and {Duchateau-Nguyen}, G. and Hatin, I. and {Hermann-Le Denmat}, S. and Termier, M. and Rousset, J.P.}, year = 2003, month = may, journal = {Nucleic Acids Research}, volume = {31}, number = {9}, pages = {2289–2296}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkg330}, url = {http://nar.oxfordjournals.org/content/31/9/2289.short}, abstract = {We specifically sought genes within the yeast genome controlled by a non-conventional translation mechanism involving the stop codon. For this reason, we designed a computer program using the yeast database genomic regions, and seeking two adjacent open reading frames separated only by a unique stop codon (called SORFs). Among the 58 SORFs identified, eight displayed a stop codon bypass level ranging from 3 to 25%. For each of the eight sequences, we demonstrated the presence of a poly(A) mRNA. Using isogenic [PSI(+)] and [psi(-)] yeast strains, we showed that for two of the sequences the mechanism used is a bona fide readthrough. However, the six remaining sequences were not sensitive to the PSI state, indicating either a translation termination process independent of eRF3 or a new stop codon bypass mechanism. Our results demonstrate that the presence of a stop codon in a large ORF may not always correspond to a sequencing error, or a pseudogene, but can be a recoding signal in a functional gene. This emphasizes that genome annotation should take into account the fact that recoding signals could be more frequently used than previously expected}, keywords = {0,3,Base Sequence,beta-Galactosidase,CEREVISIAE,Codon,CodonTerminator,computer,DATABASE,FRAME,FUSION PROTEIN,gene,Genes,GenesFungal,genetics,Genome,genomic,IDENTIFICATION,La,Lac Operon,luciferase,Luciferases,MECHANISM,metabolism,mRNA,nosource,OPEN READING FRAME,Open Reading Frames,Plasmids,poly(A),protein,Protein Biosynthesis,Proteins,psi,READING FRAME,Reading Frames,readthrough,recoding,Recombinant Fusion Proteins,REGION,Research SupportNon-U.S.Gov’t,Rna,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence HomologyNucleic Acid,SEQUENCES,SIGNAL,Software,STOP CODON,termination,translation,TRANSLATION TERMINATION,yeast} } % == BibTeX quality report for namyIdentificationStopCodon2003: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{napthineProkaryoticstyleFrameshiftingPlant2003, title = {Prokaryotic-Style Frameshifting in a Plant Translation System: Conservation of an Unusual Single-{{tRNA}} Slippage Event}, author = {Napthine, S. and Vidakovic, M. and Girnary, R. and Namy, O. and Brierley, I.}, year = 2003, journal = {The EMBO Journal}, volume = {22}, number = {15}, pages = {3941–3950}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/cdg365}, url = {http://www.nature.com/emboj/journal/v22/n15/abs/7595275a.html}, abstract = {Ribosomal frameshifting signals are found in mobile genetic elements, viruses and cellular genes of prokaryotes and eukaryotes. Typically they comprise a slippery sequence, X XXY YYZ, where the frameshift occurs, and a stimulatory mRNA element. Here we studied the influence of host translational environment and the identity of slippery sequence-decoding tRNAs on the frameshift mechanism. By expressing candidate signals in Escherichia coli, and in wheatgerm extracts depleted of endogenous tRNAs and supplemented with prokaryotic or eukaryotic tRNA populations, we show that when decoding AAG in the ribosomal A-site, E.coli tRNA(Lys) promotes a highly unusual single-tRNA slippage event in both prokaryotic and eukaryotic ribosomes. This event does not appear to require slippage of the adjacent P-site tRNA, although its identity is influential. Conversely, asparaginyl-tRNA promoted a dual slippage event in either system. Thus, the tRNAs themselves are the main determinants in the selection of single- or dual-tRNA slippage mechanisms. We also show for the first time that prokaryotic tRNA(Asn) is not inherently ‘unslippery’ and induces efficient frameshifting when in the context of a eukaryotic translation system}, keywords = {A SITE,A-SITE,asparaginyl-tRNA,decoding,E.coli,ELEMENTS,Escherichia coli,ESCHERICHIA-COLI,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,EUKARYOTIC TRANSLATION,EXTRACTS,frameshift,Frameshifting,gene,Genes,Genetic,La,MECHANISM,MECHANISMS,mRNA,nosource,P SITE,P-SITE,pathology,PROKARYOTES,ribosomal frameshifting,RIBOSOMAL FRAMESHIFTING SIGNAL,ribosome,Ribosomes,SELECTION,sequence,SIGNAL,SLIPPAGE,SYSTEM,translation,tRNA,virology} } % == BibTeX quality report for napthineProkaryoticstyleFrameshiftingPlant2003: % ? unused Journal abbr (“EMBO J.”)

@article{narandaSUI1P16Required1996a, title = {{{SUI1}}/P16 Is Required for the Activity of Eukaryotic Translation Initiation Factor 3 in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Naranda, T. and Macmillan, S.E. and Donahue, T.F and Hershey, J.W.B.}, year = 1996, journal = {Mol.Cell.Biol.}, volume = {16}, pages = {2307–2313}, doi = {10.1128/MCB.16.5.2307}, keywords = {eIF3,initiation,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sui1,translation,TRANSLATION INITIATION} } % == BibTeX quality report for narandaSUI1P16Required1996a: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{nathansonNuclearProteinSynthesis2003a, title = {Nuclear Protein Synthesis: A Re-Evaluation}, author = {Nathanson, L. and Xia, T. and Deutscher, M.P.}, year = 2003, month = jan, journal = {RNA}, volume = {9}, number = {1}, pages = {9–13}, doi = {10.1261/rna.2990203}, url = {http://rnajournal.cshlp.org/content/9/1/9.short}, abstract = {It has been reported that nuclei from HeLa cells are responsible for approximately 10%-15% of total cellular protein synthesis. We show here that isolated Chinese hamster ovary (CHO) and HeLa cell nuclei are essentially inactive for translation, and that the earlier results were most likely due to cytoplasmic contamination. Moreover, we suggest that the nascent polypeptides observed in nuclei of permeabilized cells may have been due to “overpermeabilization” and consequent damage to the cells. Based on this information, we conclude that nuclear protein synthesis, if it exists, is limited to less than 1% of that in cells}, keywords = {0,animal,biosynthesis,CELLS,Cho Cells,Hamsters,Hela Cells,HELA-CELLS,human,La,nosource,Nuclear Proteins,POLYPEPTIDE,POLYPEPTIDES,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,supportu.s.gov’tp.h.s.,translation,TranslationGenetic} }

@article{nazar5SRNABinding1979a, title = {The 5-{{S RNA}} Binding Protein from Yeast ({{Saccharomyces}} Cerevisiae) Ribosomes. {{Evolution}} of the Eukaryotic 5-{{S RNA}} Binding Protein}, author = {Nazar, R.N. and Yaguchi, M. and Willick, G.E. and Rollin, C.F. and Roy, C.}, year = 1979, month = dec, journal = {Eur.J.Biochem.}, volume = {102}, number = {2}, pages = {573–582}, doi = {10.1111/j.1432-1033.1979.tb04274.x}, abstract = {The ribonucleoprotein complex between 5-S RNA and its binding protein (5-S RNA . protein complex) of yeast ribosomes was released from 60-S subunits with 25 mM EDTA and the protein component was purified by chromatography on DEAE-cellulose. This protein, designated YL3 (Mr = 36000 on dodecylsulfate gels), was relatively insoluble in neutral solutions (pH 4–9) and migrated as one of four acidic 60-S subunit proteins when analyzed by the Kaltschmidt and Wittman two-dimensional gel system. Amino acid analyses indicated lower amounts of lysine and arginine than most ribosomal proteins. Sequence homology was observed in the N terminus of YL3, and two prokaryotic 5-S RNA binding proteins, EL18 from Escherichia coli and HL13 from Halobacterium cutirubrum: Ala1-Phe2-Gln3-Lys4-Asp5-Ala6-Lys7-Ser8-Ser9-Ala10-Tyr11-Ser12-Ser13-Arg14 -Phe15-Gln16-Tyr17-Pro18-Phe19-Arg20-Arg21-Arg22-Arg23-Glu24-Gly25-Lys26-T hr27-Asp28-Tyr29-Tyr35; of particular interest was homology in the cluster of basic residues (18–23). Since the protein contained one methionine residue it could be split into two fragments, CN1 (Mr = 24700) and CN2 (Mr = 11300) by CNBr treatment; the larger fragment originated from the N terminus. The N-terminal amino acid sequence of CN2 shared a limited sequence homology with an internal portion of a second 5-S RNA binding protein from E. coli, EL5, and, based also on the molecular weights of the proteins and studies on the protein binding sites in 5-S RNAs, a model for the evolution of the eukaryotic 5-S RNA binding protein is suggested in which a fusion of the prokaryotic sequences may have occurred. Unlike the native 5-S RNA . protein complex, a variety of RNAs interacted with the smaller CN2 fragment to form homogeneous ribonucleoprotein complexes; the results suggest that the CN1 fragment may confer specificity on the natural 5-S RNA-protein interaction}, keywords = {60S subunit,80112896,Amino Acid Sequence,analysis,Arginine,BINDING,BINDING PROTEIN,Binding Sites,BINDING-PROTEIN,Carrier Proteins,Chromatography,Comparative Study,COMPLEX,COMPLEXES,COMPONENT,Escherichia coli,ESCHERICHIA-COLI,Evolution,Gels,Halobacterium,homolog,L5,Lysine,metabolism,Methionine,Molecular Weight,nosource,Nucleoproteins,protein,Protein Binding,PROTEIN COMPLEX,Proteins,Ribonucleoproteins,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNARibosomal,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Solutions,Species Specificity,SUBUNIT,SYSTEM,yeast} } % == BibTeX quality report for nazar5SRNABinding1979a: % ? Possibly abbreviated journal title Eur.J.Biochem.

@article{nazar5SRNAProtien1989a, title = {The {{5S RNA}} Protien Complex from an Extreme Halophile ⬚{{Halobacterium}} Cutirubrum⬚. {{Studies}} on the {{RNA-protein}} Interaction.}, author = {Nazar, R.N. and Willick, G.E. and Matheson, A.T.}, year = 1989, journal = {J.Biol.Chem.}, volume = {254}, pages = {1506–1512}, doi = {10.1016/S0021-9258(17)37798-0}, keywords = {5S rRNA,COMPLEX,COMPLEXES,Halobacterium,nosource,Rna} } % == BibTeX quality report for nazar5SRNAProtien1989a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{nazarHigherOrderStructure1991a, title = {Higher Order Structure of the Ribosomal {{5S rRNA}}.}, author = {Nazar, R.N.}, year = 1991, journal = {J.Biol Chem.}, volume = {226}, pages = {4562–4567}, doi = {10.1016/S0021-9258(20)64359-9}, keywords = {5S rRNA,nosource,rRNA,structure} } % == BibTeX quality report for nazarHigherOrderStructure1991a: % ? Possibly abbreviated journal title J.Biol Chem.

@article{nazarRibosomalRNAProcessing2004, title = {Ribosomal {{RNA}} Processing and Ribosome Biogenesis in Eukaryotes}, author = {Nazar, R.N.}, year = 2004, journal = {IUBMB.Life}, volume = {56}, number = {8}, pages = {457–465}, publisher = {Informa Healthcare}, doi = {10.1080/15216540400010867}, url = {http://www.informaworld.com/index/714028439.pdf}, abstract = {In eukaryotes nearly 500 rRNAs, ribosomal proteins, snoRNAs and trans-acting factors contribute to ribosome biogenesis. After more than 30 years of intense research, the incredible complexities of nucleolar function are revealed but details often remain unclear. Here we review this progress and the many intriguing questions which remain}, keywords = {0,Active TransportCell Nucleus,BIOGENESIS,BIOLOGY,Cell Nucleolus,chemistry,DNA Mutational Analysis,Eukaryotic Cells,Genetic,genetics,La,metabolism,ModelsBiological,ModelsGenetic,Molecular Biology,nosource,protein,Proteins,Review,Ribosomal Proteins,ribosomal RNA,RIBOSOMAL-PROTEIN,RIBOSOMAL-RNA,ribosome,ribosome biogenesis,Ribosomes,Rna,RNA ProcessingPost-Transcriptional,RNAFungal,RNARibosomal,RNASmall Nucleolar,rRNA,Saccharomyces cerevisiae,Schizosaccharomyces,TRANS-ACTING FACTORS} } % == BibTeX quality report for nazarRibosomalRNAProcessing2004: % ? Possibly abbreviated journal title IUBMB.Life

@article{neerAncientRegulatoryproteinFamily1994, title = {The Ancient Regulatory-Protein Family of {{WD-repeat}} Proteins.}, author = {Neer, E. and Schmidt, C.J. and Nambudripad, R. and Smith, T.F.}, year = 1994, journal = {Nature}, volume = {371}, number = {6495}, eprint = {8090199}, eprinttype = {pubmed}, pages = {297–300}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8090199}, keywords = {cdc40,Multiple DOI,nonfile,nosource,protein,Proteins,prp17,WD-40 repeats} }

@article{nelsonTranslationMachinery701992, title = {The Translation Machinery and 70 Kd Heat Shock Protein Cooperate in Protein Synthesis}, author = {Nelson, R.J. and Ziegelhoffer, T. and Nicolet, C. and {Werner-Washburne}, M. and Craig, E.A.}, year = 1992, month = oct, journal = {Cell}, volume = {71}, number = {1}, pages = {97–105}, publisher = {Elsevier}, doi = {10.1016/0092-8674(92)90269-I}, url = {http://linkinghub.elsevier.com/retrieve/pii/009286749290269I}, abstract = {The function of the yeast SSB 70 kd heatshock proteins (hsp70s) was investigated by a variety of approaches. The SSB hsp70s (Ssb1/2p) are associated with translating ribosomes. This association is disrupted by puromycin, suggesting that Ssb1/2p may bind directly to the nascent polypeptide. Mutant ssb1 ssb2 strains grow slowly, contain a low number of translating ribosomes, and are hypersensitive to several inhibitors of protein synthesis. The slow growth phenotype of ssb1 ssb2 mutants is suppressed by increased copy number of a gene encoding a novel translation elongation factor 1 alpha (EF-1 alpha)-like protein. We suggest that cytosolic hsp70 aids in the passage of the nascent polypeptide chain through the ribosome in a manner analogous to the role played by organelle-localized hsp70 in the transport of proteins across membranes}, keywords = {0,AIDS,Amino Acid Sequence,ASSOCIATION,Base Sequence,biosynthesis,CEREVISIAE,chemistry,drug effects,EF-1,elongation,elongation factors,ELONGATION-FACTORS,Fungal Proteins,gene,genetics,GROWTH,GTP-Binding Proteins,Heat,HEAT-SHOCK,HEAT-SHOCK PROTEINS,Heat-Shock Proteins 70,INHIBITOR,inhibitors,La,metabolism,Molecular Sequence Data,MUTANTS,nosource,Peptide Elongation Factor 1,Peptide Elongation Factors,pharmacology,Phenotype,physiology,POLYPEPTIDE,POLYPEPTIDE-CHAIN,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Puromycin,RIBONUCLEOPROTEIN,Ribonucleoproteins,ribosome,Ribosomes,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,translation,TRANSPORT,yeast} }

@article{niSnoRNAsToolsRNA1997a, title = {{{SnoRNAs}} as Tools for {{RNA}} Cleavage and Modification}, author = {Ni, J. and Samarsky, D.A. and Liu, B. and Ferbeyre, G. and Cedergren, R. and Fournier, M.J.}, year = 1997, journal = {Nucleic Acids Symp.Ser.}, number = {36}, pages = {61–63}, url = {PM:9478207}, abstract = {Eukaryotic small nucleolar RNAs (snoRNAs) influence rRNA synthesis at two stages: nucleolytic processing and selection of nucleotides to be ribose methylated (Nm) or converted to pseudouridine (psi). The two modification functions and some processing activities involve direct base pairing of snoRNA with rRNA. In addition to rRNA-targeting sequences, snoRNA function depends on the presence of conserved box elements involved in snoRNA synthesis and localization. The present investigation is directed at using snoRNAs as tools for two purposes: 1) introducing nucleotide modifications into novel sites in rRNA and other snoRNAs, and: 2) targeting nucleolar RNAs for destruction using snoRNA:ribozyme chimers (‘snorbozymes’). Early results demonstrate that snoRNAs can be used for both applications}, keywords = {0,Base Pairing,biosynthesis,Cell Nucleolus,CLEAVAGE,ELEMENTS,La,metabolism,modification,No DOI found,nosource,Nucleic Acid Conformation,Nucleotides,Pseudouridine,psi,Review,Ribose,Rna,RNA ProcessingPost-Transcriptional,RNARibosomal,RNASmall Nuclear,rRNA,sequence} } % == BibTeX quality report for niSnoRNAsToolsRNA1997a: % ? Possibly abbreviated journal title Nucleic Acids Symp.Ser.

@article{niSmallNucleolarRNAs1997, title = {Small Nucleolar {{RNAs}} Direct Site-Specific Synthesis of Pseudouridine in Ribosomal {{RNA}}}, author = {Ni, J. and Tien, A.L. and Fournier, M.J.}, year = 1997, month = may, journal = {Cell}, volume = {89}, number = {4}, pages = {565–573}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(00)80238-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0092-8674(00)80238-x}, abstract = {Ten ACA yeast small nucleolar RNAs (snoRNAs) were shown to be required for site-specific synthesis of pseudouridine psi in ribosomal RNA. A common secondary folding motif for the snoRNAs and rRNA target segments predicts that site selection involves: (1) base pairing of the snoRNA with complementary rRNA elements flanking the site of modification, and (2) identification of a uridine located at a near-constant distance from the snoRNA ACA box. The model is supported by mutations showing that: (1) reducing the complementarity between the snoRNA and rRNA disrupts psi formation, and (2) altering the distance between the ACA box and target uridine causes an adjacent uridine to be modified. This discovery implies that most snoRNAs function in targeting nucleotide modification in rRNA: ribose methylation for the box C/D snoRNAs and psi formation for the ACA snoRNAs}, keywords = {0,animal,Base Pairing,Base Sequence,biosynthesis,Cell Nucleolus,chemistry,Chick Embryo,ELEMENTS,genetics,IDENTIFICATION,La,metabolism,Methylation,ModelsBiological,modification,Molecular Sequence Data,Molecular Structure,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Pseudouridine,psi,Ribose,RIBOSOMAL-RNA,Rna,RNAFungal,RNARibosomal,RNASmall Nuclear,rRNA,Saccharomyces cerevisiae,site specific,supportu.s.gov’tp.h.s.,Uridine,yeast} }

@article{nielsenGrowthdependentTranslationIGFII1995, title = {Growth-Dependent Translation of {{IGF-II mRNA}} by a Rapamycin-Sensitive Pathway.}, author = {Nielsen, F.C. and Ostergarrd, L. and Nielsen, J. and Christiansen, J.}, year = 1995, journal = {Nature}, volume = {377}, pages = {358–362}, publisher = {Nature Publishing Group}, doi = {10.1038/377358a0}, url = {http://www.nature.com/nature/journal/v377/n6547/abs/377358a0.html}, keywords = {activation,mRNA,nosource,post-transcriptional regulation,translation} }

@article{nierhausAllostericThreesiteModel1990, title = {The Allosteric Three-Site Model for the Ribosomal Elongation Cycle: Features and Future}, author = {Nierhaus, K.H.}, year = 1990, month = may, journal = {Biochemistry}, volume = {29}, number = {21}, pages = {4997–5008}, publisher = {ACS Publications}, doi = {10.1021/bi00473a001}, url = {PM:2198935}, abstract = {The ribosome contains three binding sites for tRNA, viz., the A site for aminoacyl-tRNA (decoding site), the P site for peptidyl-tRNA, and the E site for deacylated tRNA (E for exit). The surprising finding of an allosteric linkage between the E and A sites in the sense of a negative cooperativity has three consequences: (a) it improves the proper selection of aminoacyl-tRNAs while preventing interference from noncognate aminoacyl-tRNAs in the decoding process, (b) it provides an explanation for the ribosomal accuracy without having to resort to the proofreading hypothesis, and (c) it has deepened our understanding of the mode of action of some antibiotics}, keywords = {0,A SITE,A-SITE,A-SITES,accuracy,Animals,Anti-Bacterial Agents,antibiotic,antibiotics,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,decoding,E,E site,elongation,ELONGATION CYCLE,La,metabolism,MODEL,ModelsChemical,nosource,P SITE,P-SITE,Peptide Chain ElongationTranslational,pharmacology,proofreading,Protein Biosynthesis,Review,ribosome,Ribosomes,Rna,RNATransferAmino Acyl,SELECTION,SITE,SITES,tRNA} }

@article{nierrasProteinKinaseEnables1999, title = {Protein Kinase {{C}} Enables the Regulatory Circuit That Connects Membrane Synthesis to Ribosome Synthesis in {{Saccharomyces}} Cerevisiae}, author = {Nierras, C.R. and Warner, J.R.}, year = 1999, month = may, journal = {Journal of Biological Chemistry}, volume = {274}, number = {19}, pages = {13235–13241}, publisher = {ASBMB}, doi = {10.1074/jbc.274.19.13235}, url = {http://www.jbc.org/content/274/19/13235.short}, abstract = {The balanced growth of a cell requires the integration of major systems such as DNA replication, membrane biosynthesis, and ribosome formation. An example of such integration is evident from our recent finding that, in Saccharomyces cerevisiae, any failure in the secretory pathway leads to severe repression of transcription of both rRNA and ribosomal protein genes. We have attempted to determine the regulatory circuit(s) that connects the secretory pathway with the transcription of ribosomal genes. Experiments show that repression does not occur through the circuit that responds to misfolded proteins in the endoplasmic reticulum, nor does it occur through circuits known to regulate ribosome synthesis, e.g. the stringent response, or the cAMP pathway. Rather, it appears to depend on a stress response at the plasma membrane that is transduced through protein kinase C (PKC). Deletion of PKC1 relieves the repression of both ribosomal protein and rRNA genes that occurs in response to a defect in the secretory pathway. We propose that failure of the secretory pathway prevents the synthesis of new plasma membrane. As protein synthesis continues, stress develops in the plasma membrane. This stress is monitored by Pkc1p, which initiates a signal transduction pathway that leads to repression of transcription of the rRNA and ribosomal protein genes. The importance of the transcription of the 137 ribosomal protein genes to the economy of the cell is apparent from the existence of at least three distinct pathways that can effect the repression of this set of genes}, keywords = {99240709,biosynthesis,Cell Membrane,Dna,DNA Replication,Enzyme Activation,enzymology,gene,Genes,kinase,metabolism,nosource,protein,Protein Kinase C,protein synthesis,PROTEIN-SYNTHESIS,Proteins,ribosome,Ribosomes,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SIGNAL,Signal Transduction,stress response,stringent response,supportu.s.gov’tp.h.s.,SYSTEM,transcription,TranscriptionGenetic,ultrastructure} } % == BibTeX quality report for nierrasProteinKinaseEnables1999: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{nilssonComparisonFungal802007, title = {Comparison of Fungal 80 {{S}} Ribosomes by Cryo-{{EM}} Reveals Diversity in Structure and Conformation of {{rRNA}} Expansion Segments}, author = {Nilsson, J. and Sengupta, J. and Gursky, R. and Nissen, P. and Frank, J.}, year = 2007, month = jun, journal = {Journal of molecular biology}, volume = {369}, number = {2}, pages = {429–438}, publisher = {Elsevier}, doi = {10.1016/j.jmb.2007.03.035}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283607003774}, abstract = {Compared to the prokaryotic 70 S ribosome, the eukaryotic 80 S ribosome contains additional ribosomal proteins and extra segments of rRNA, referred to as rRNA expansion segments (ES). These eukaryotic-specific rRNA ES are mainly on the periphery of the 80 S ribosome, as revealed by cryo-electron microscopy (cryo-EM) studies, but their precise function is not known. To address the question of whether the rRNA ES are structurally conserved among 80 S ribosomes of different fungi we performed cryo-electron microscopy on 80 S ribosomes from the thermophilic fungus Thermomyces lanuginosus and compared it to the Saccharomyces cerevisiae 80 S ribosome. Our analysis reveals general structural conservation of the rRNA expansion segments but also changes in ES27 and ES7/39, as well as the absence of a tertiary interaction between ES3 and ES6 in T. lanuginosus. The differences provide a hint on the role of rRNA ES in regulating translation. Furthermore, we show that the stalk region and interactions with elongation factor 2 (eEF2) are different in T. lanuginosus, exhibiting a more extensive contact with domain I of eEF2}, keywords = {analysis,BIOLOGY,CEREVISIAE,CONFORMATION,Cryoelectron Microscopy,DIVERSITY,DOMAIN,elongation,Fungi,La,Molecular Biology,nosource,protein,Proteins,REGION,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,rRNA,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Structural,structure,Support,T,translation} } % == BibTeX quality report for nilssonComparisonFungal802007: % ? unused Journal abbr (“J.Mol.Biol”)

@article{ninioKineticAmplificationEnzyme1975, title = {Kinetic {{Amplification}} of {{Enzyme Discrimination}}}, author = {Ninio, J.}, year = 1975, journal = {Biochimie}, volume = {57}, number = {5}, pages = {587–595}, publisher = {Elsevier}, doi = {10.1016/S0300-9084(75)80139-8}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0300908475801398}, keywords = {enzyme,nosource} } % == BibTeX quality report for ninioKineticAmplificationEnzyme1975: % ? Title looks like it was stored in title-case in Zotero

@article{nirenbergRNACodeProtein1966a, title = {The {{RNA}} Code and Protein Synthesis}, author = {Nirenberg, M. and Caskey, T. and Marshall, R. and Brimacombe, R. and Kellogg, D. and Doctor, B. and Hatfield, D. and Levin, J. and Rottman, F. and Pestka, S. and Wilcox, M. and Anderson, F.}, year = 1966, journal = {Cold Spring Harb.Symp.Quant.Biol.}, volume = {31:11-24.}, pages = {11–24}, doi = {10.1101/SQB.1966.031.01.008}, keywords = {Alanine,Amino Acids,biosynthesis,Coliphages,Dna,Genetic Code,Leucine,metabolism,nosource,Polynucleotides,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Ribosomes,Rna,RNAMessenger,RNATransfer,Templates} } % == BibTeX quality report for nirenbergRNACodeProtein1966a: % ? Possibly abbreviated journal title Cold Spring Harb.Symp.Quant.Biol.

@article{nishimuraMinorContributionInternal2007, title = {Minor Contribution of an Internal Ribosome Entry Site in the 5’-{{UTR}} of Ornithine Decarboxylase {{mRNA}} on Its Translation}, author = {Nishimura, K. and Sakuma, A. and Yamashita, T. and Hirokawa, G. and Imataka, H. and Kashiwagi, K. and Igarashi, K.}, year = 2007, month = dec, journal = {Biochemical and biophysical research communications}, volume = {364}, number = {1}, pages = {124–130}, publisher = {Elsevier}, doi = {10.1016/j.bbrc.2007.09.112}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006291X07021067}, abstract = {The mechanism of synthesis of ornithine decarboxylase (ODC) at the level of translation was studied using cell culture and cell-free systems. Synthesis of firefly luciferase (Fluc) from the second open reading frame (ORF) in a bicistronic construct transfected into FM3A and HeLa cells was enhanced by the presence of the 5’-untranslated region (5’-UTR) of ODC mRNA between the two ORFs. However, cotransfection of the gene encoding 2A protease inhibited the synthesis of Fluc. Synthesis of Fluc from the second cistron in the bicistronic mRNA in a cell-free system was not affected significantly by the 5’-UTR of ODC mRNA. Synthesis of ODC from ODC mRNA in a cell-free system was inhibited by 2A protease and cap analogue (m7GpppG). Rapamycin inhibited ODC synthesis by 40-50% at both the G1/S boundary and the G2/M phase. These results indicate that an IRES in the 5’-UTR of ODC mRNA does not function effectively}, keywords = {0,5’ Untranslated Regions,5’-UTR,Animals,bicistronic,biosynthesis,Cap,Cell Division,Cell LineTumor,Cell-Free System,CELLS,Cysteine,Cysteine Endopeptidases,drug effects,Endopeptidases,FIREFLY LUCIFERASE,FRAME,G1 Phase,G2 Phase,gene,Hela Cells,HELA-CELLS,Humans,INTERNAL RIBOSOME ENTRY,La,luciferase,MECHANISM,metabolism,Mice,mRNA,nosource,OPEN READING FRAME,Ornithine Decarboxylase,pharmacology,physiology,picornavirus,protein,Protein Biosynthesis,Proteins,Rabbits,READING FRAME,REGION,Reticulocytes,ribosome,RIBOSOME ENTRY SITE,Ribosomes,Rna,RNA Cap Analogs,RNAMessenger,S Phase,Sirolimus,SITE,Support,SYSTEM,SYSTEMS,translation,Untranslated Regions,Viral Proteins} } % == BibTeX quality report for nishimuraMinorContributionInternal2007: % ? unused Journal abbr (“Biochem.Biophys.Res.Commun.”)

@article{nissenCrystalStructureTernary1995a, title = {Crystal Structure of the Ternary Complex of {{Phe-tRNAPhe}}, {{EF-Tu}}, and a {{GTP}} Analog [See Comments]}, author = {Nissen, P. and Kjeldgaard, M. and Thirup, S. and Polekhina, G. and Reshetnikova, L. and Clark, B.F. and Nyborg, J.}, year = 1995, journal = {Science}, volume = {270}, number = {5241}, pages = {1464–1472}, doi = {10.1126/science.270.5241.1464}, keywords = {COMPLEX,COMPLEXES,CRYSTAL-STRUCTURE,EFTu,GTP,nosource,structure} }

@article{nissenStructuralBasisRibosome2000, title = {The Structural Basis of Ribosome Activity in Peptide Bond Synthesis}, author = {Nissen, P. and Hansen, J. and Ban, N. and Moore, P.B. and Steitz, T.A.}, year = 2000, journal = {Science}, volume = {289}, number = {5481}, pages = {920–930}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.289.5481.920}, url = {http://www.sciencemag.org/content/289/5481/920.short}, abstract = {Using the atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with two substrate analogs, we establish that the ribosome is a ribozyme and address the catalytic properties of its all-RNA active site. Both substrate analogs are contacted exclusively by conserved ribosomal RNA (rRNA) residues from domain V of 23S rRNA; there are no protein side-chain atoms closer than about 18 angstroms to the peptide bond being synthesized. The mechanism of peptide bond synthesis appears to resemble the reverse of the acylation step in serine proteases, with the base of A2486 (A2451 in Escherichia coli) playing the same general base role as histidine-57 in chymotrypsin. The unusual pK(a) (where K(a) is the acid dissociation constant) required for A2486 to perform this function may derive in part from its hydrogen bonding to G2482 (G2447 in E. coli), which also interacts with a buried phosphate that could stabilize unusual tautomers of these two bases. The polypeptide exit tunnel is largely formed by RNA but has significant contributions from proteins L4, L22, and L39e, and its exit is encircled by proteins L19, L22, L23, L24, L29, and L31e}, keywords = {0,antagonists & inhibitors,Archaeal Proteins,Base Pairing,Base Sequence,Binding Sites,Catalysis,chemistry,COMPLEX,COMPLEXES,Crystallization,Escherichia coli,ESCHERICHIA-COLI,EvolutionMolecular,Haloarcula,Haloarcula marismortui,Hydrogen Bonding,Hydrogen-Ion Concentration,L29,La,MECHANISM,metabolism,ModelsMolecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Oligonucleotides,Peptide Synthesis,Peptides,Peptidyltransferase,Phosphates,protein,Protein Conformation,Proteins,Puromycin,Ribosomal Proteins,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,ribozyme,Rna,RNAArchaeal,RNACatalytic,RNARibosomal23S,RNATransfer,RNATransferAmino Acyl,rRNA,Serine,Structural,STRUCTURAL BASIS,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,tRNA,ultrastructure} }

@article{nissenMacromolecularMimicry2000, title = {Macromolecular Mimicry}, author = {Nissen, P. and Kjeldgaard, M. and Nyborg, J.}, year = 2000, month = feb, journal = {The EMBO journal}, volume = {19}, number = {4}, pages = {489–495}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/19.4.489}, url = {http://www.nature.com/emboj/journal/v19/n4/abs/7592159a.html}, abstract = {Some proteins have been shown to mimic the overall shape and structure of nucleic acids. For some of the proteins involved in translating the genetic information into proteins on the ribosome particle, there are indications that such observations of macromolecular mimicry even extend to similarity in interaction with and function on the ribosome. A small number of structural results obtained outside the protein biosynthesis machinery could indicate that the concept of macromolecular mimicry between proteins and nucleic acids is more general. The implications for the function and evolution of protein biosynthesis are discussed}, keywords = {0,ACID,ACIDS,Animals,BIOLOGY,biosynthesis,chemistry,elongation,elongation factors,ELONGATION-FACTORS,Evolution,Genetic,genetics,GTP,GTP Phosphohydrolase-Linked Elongation Factors,Humans,INFORMATION,La,Macromolecular Substances,metabolism,ModelsMolecular,Molecular Mimicry,nosource,Nucleic Acid Conformation,Nucleic Acids,Nucleotides,protein,Protein Biosynthesis,Protein Conformation,Protein StructureTertiary,PROTEIN-BIOSYNTHESIS,Proteins,Review,ribosome,Rna,RNATransfer,Structural,structure,Support} } % == BibTeX quality report for nissenMacromolecularMimicry2000: % ? unused Journal abbr (“EMBO J.”)

@article{nissenRNATertiaryInteractions2001, title = {{{RNA}} Tertiary Interactions in the Large Ribosomal Subunit: The {{A-minor}} Motif}, author = {Nissen, P. and Ippolito, J.A. and Ban, N. and Moore, P.B. and Steitz, T.A.}, year = 2001, month = apr, journal = {Proceedings of the National Academy of Sciences}, volume = {98}, number = {9}, pages = {4899–4903}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.081082398}, url = {http://redirect.subscribe.ru/_/-/www.pnas.org/content/98/9/4899.full}, abstract = {Analysis of the 2.4-A resolution crystal structure of the large ribosomal subunit from Haloarcula marismortui reveals the existence of an abundant and ubiquitous structural motif that stabilizes RNA tertiary and quaternary structures. This motif is termed the A-minor motif, because it involves the insertion of the smooth, minor groove edges of adenines into the minor groove of neighboring helices, preferentially at C-G base pairs, where they form hydrogen bonds with one or both of the 2’ OHs of those pairs. A-minor motifs stabilize contacts between RNA helices, interactions between loops and helices, and the conformations of junctions and tight turns. The interactions between the 3’ terminal adenine of tRNAs bound in either the A site or the P site with 23S rRNA are examples of functionally significant A- minor interactions. The A-minor motif is by far the most abundant tertiary structure interaction in the large ribosomal subunit; 186 adenines in 23S and 5S rRNA participate, 68 of which are conserved. It may prove to be the universally most important long-range interaction in large RNA structures}, keywords = {5S rRNA,A-SITE,Adenine,analysis,CRYSTAL-STRUCTURE,Haloarcula,Haloarcula marismortui,La,nosource,P-SITE,RIBOSOMAL-SUBUNIT,Rna,rRNA,Structural,structure,SUBUNIT,tRNA} } % == BibTeX quality report for nissenRNATertiaryInteractions2001: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{nixonEnergeticsStronglyPH2000a, title = {Energetics of a Strongly {{pH}} Dependent {{RNA}} Tertiary Structure in a Frameshifting Pseudoknot}, author = {Nixon, P.L. and Giedroc, D.P.}, year = 2000, month = feb, journal = {Journal of Molecular Biology}, volume = {296}, number = {2}, pages = {659–671}, doi = {10.1006/jmbi.1999.3464}, url = {ISI:000085698900026}, abstract = {Retroviruses employ -1 translational frameshifting to regulate the relative concentrations of structural and non-structural proteins critical to the viral life cycle. The 1.6 Angstrom crystal structure of the -1 frameshifting pseudoknot from beet western yellows virus reveals, in addition to Watson-Crick base-pairing, many loop-stem RNA tertiary structural interactions and a bound Na+. Investigation of the thermodynamics of unfolding of the beet western yellows virus pseudoknot reveals strongly pH-dependent loop-stem tertiary structural interactions which stabilize the molecule, contributing a net of Delta H approximate to - 30 kcal mol(-1) and Delta G(37)degrees, of -3.3 kcal mol(-1) to a total Delta H and aG(37)degrees, of -121 and -16 kcal mol(-1), respectively, at pH 6.0, 0.5 M K+ by DSC. Characterization of mutant RNAs supports the presence of a C8(+).G12-C26 loop 1-stem 2 base-triple (pK(a) = 6.8), protonation of which contributes nearly -3.5 kcal mol(-1.) in net stability in the presence of a wild-type loop 2. Substitution of the nucleotides in loop 2 with uridine bases, which would eliminate the minor groove triplex, destroys pseudoknot formation. An examination of the dependence of the monovalent ion and type on melting profiles suggests that tertiary structure unfolding occurs in a manner quantitatively consistent with previous studies on the stabilizing effects of K+, NH4+ and Na+ on other simple duplex and pseudoknotted RNAs. (C) 2000 Academic Press}, keywords = {BASE,Base Pairing,BASES,crystal structure,CRYSTAL-STRUCTURE,D,DOMAIN,energetics,Frameshifting,IMMUNODEFICIENCY-VIRUS TYPE-1,Ions,LOOP,M,MESSENGER-RNA,MODEL,nosource,Nucleotides,protein,Proteins,pseudoknot,Rna,stability,Structural,structure,Support,SYSTEMS,Thermodynamics,translation,TRANSLATIONAL FRAMESHIFTING,Uridine,virus} }

@article{nixonThermodynamicAnalysisConserved2002, title = {Thermodynamic Analysis of Conserved Loop-Stem Interactions in {{P1-P2}} Frameshifting {{RNA}} Pseudoknots from Plant {{Luteoviridae}}}, author = {Nixon, P.L. and Cornish, P.V. and Suram, S.V. and Giedroc, D.P.}, year = 2002, journal = {Biochemistry}, volume = {41}, number = {34}, pages = {10665–10674}, publisher = {ACS Publications}, doi = {10.1021/bi025843c}, url = {http://pubs.acs.org/doi/abs/10.1021/bi025843c}, abstract = {The RNA genomes of plant luteovirids beet western yellows virus (BWYV), potato leaf roll virus (PLRV), and pea enation mosaic virus (PEMV RNA1; PEMV-1) contain a short mRNA pseudoknotted motif overlapping the P1 and P2 open reading frames required for programmed -1 mRNA ribosomal frameshifting. The relationship between structure, stability, and function is poorly understood in these RNA systems. A m(5)-C(8)-substituted BWYV RNA is employed to establish that the BWYV P1-P2 pseudoknot is protonated at cytidine 8 in loop L1 (delta(N(3)H)+ = 12.98 ppm), which stabilizes a C(+.)(G-C) major groove base triple by Delta(DeltaG(37))(protonation) = 3.1 (+/-0.4) kcal mol(-1). The stabilities of both the PLRV and PEMV-1 P1-P2 pseudoknots are also strongly pH-dependent, with Delta(DeltaG(37))(protonation) = 2.1 (+/-0.2) kcal mol(-1) for the PEMV-1 pseudoknot despite a distinct structural context. As previously found for the BWYV pseudoknot [Nixon and Giedroc (2000) J. Mol. Biol. 296, 659], both the PLRV and PEMV-1 RNAs are stabilized by DeltaH {\(>\)} or = 30 kcal mol(-)(1) in excess of secondary structure predictions, attributed to loop L2-stem S1 minor groove triplex interactions. BWYV RNAs containing single 2’-deoxy or A –{\(>\)} G substitutions that disrupt L2-S1 hydrogen bonding are strongly destabilized with Delta(DeltaG(37))(folding) (pH = 7.0) ranging from approximately 1.8 (+/-0.3) to {\(>\)} or =4.0 kcal mol(-1), relative to the wild-type BWYV RNA. These findings suggest that each member of this family of pseudoknots adopts a tightly folded structure that maximizes the cooperativity and complementarity of L1-S2 and L2-S1 loop-stem interactions required in part to offset the low intrinsic stability of the short three base pair pseudoknot stem S2}, keywords = {0,analysis,BASE,Base Pairing,Base Sequence,BASE-PAIR,Calorimetry,chemistry,FAMILY,FRAME,Frameshifting,FrameshiftingRibosomal,genetics,Genome,Hydrogen,Hydrogen Bonding,Hydrogen-Ion Concentration,L1,La,LOOP,Luteovirus,Magnetic Resonance Spectroscopy,metabolism,MOSAIC-VIRUS,mRNA,nosource,Nucleic Acid Conformation,OPEN READING FRAME,Open Reading Frames,PREDICTION,pseudoknot,pseudoknots,READING FRAME,Reading Frames,ribosomal frameshifting,Rna,RNA PSEUDOKNOT,RnaPlant,SECONDARY STRUCTURE,secondary structure prediction,stability,Structural,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,SYSTEMS,Temperature,Thermodynamics,virus,WILD-TYPE} }

@article{nixonSolutionStructureLuteoviral2002, title = {Solution Structure of a Luteoviral {{P1-P2}} Frameshifting {{mRNA}} Pseudoknot}, author = {Nixon, P.L. and Rangan, A. and Kim, Y.G. and Rich, A. and Hoffman, D.W. and Hennig, M. and Giedroc, D.P.}, year = 2002, journal = {Journal of Molecular Biology}, volume = {322}, number = {3}, pages = {621–633}, publisher = {Elsevier}, doi = {10.1016/S0022-2836(02)00779-9}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283602007799}, abstract = {A hairpin-type messenger RNA pseudoknot from pea enation mosaic virus RNA1 (PEMV-1) regulates the efficiency of programmed -1 ribosomal frameshifting. The solution structure and 15N relaxation rates reveal that the PEMV-1 pseudoknot is a compact-folded structure composed almost entirely of RNA triple helix. A three nucleotide reverse turn in loop 1 positions a protonated cytidine, C(10), in the correct orientation to form an A((n-1)).C(+).G-C(n) major groove base quadruple, like that found in the beet western yellows virus pseudoknot and the hepatitis delta virus ribozyme, despite distinct structural contexts. A novel loop 2-loop 1 A.U Hoogsteen base-pair stacks on the C(10)(+).G(28) base-pair of the A(12).C(10)(+).G(28)-C(13) quadruple and forms a wedge between the pseudoknot stems stabilizing a bent and over-rotated global conformation. Substitution of key nucleotides that stabilize the unique conformation of the PEMV-1 pseudoknot greatly reduces ribosomal frameshifting efficacy}, keywords = {0,BASE,Base Pairing,BASE-PAIR,chemistry,CONFORMATION,efficiency,FORM,Frameshifting,FrameshiftingRibosomal,Gene Expression Regulation,genetics,Hepatitis Delta Virus,La,LOOP,Luteovirus,Magnetic Resonance Spectroscopy,MESSENGER-RNA,metabolism,ModelsMolecular,MOSAIC-VIRUS,mRNA,nosource,Nucleic Acid Conformation,Nucleotides,Peas,POSITION,POSITIONS,pseudoknot,RELAXATION,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,ribosomal frameshifting,ribozyme,Rna,RNA PSEUDOKNOT,RNAMessenger,RnaViral,Solutions,Structural,structure,Thermodynamics,virology,virus} } % == BibTeX quality report for nixonSolutionStructureLuteoviral2002: % ? unused Journal abbr (“J.Mol.Biol.”)

@article{nogiApproachIsolationMutants1991, title = {An Approach for Isolation of Mutants Defective in {{35S}} Ribosomal {{RNA}} Synthesis in {{Saccharomyces}} Cerevisiae}, author = {Nogi, Y. and Vu, L. and Nomura, M.}, year = 1991, journal = {Proceedings of the National Academy of Sciences}, volume = {88}, number = {16}, pages = {7026–7030}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.88.16.7026}, url = {http://www.pnas.org/content/88/16/7026.short}, abstract = {We have developed a method to isolate mutants of Saccharomyces cerevisiae that are primarily defective in the transcription of 35S ribosomal RNA (rRNA) genes by RNA polymerase I. The method uses a system in which the 35S rRNA gene is fused to the GAL7 promoter and is transcribed by RNA polymerase II under control of the GAL regulatory system. Chromosomal mutations affecting components specifically involved in synthesis of 35S rRNA by RNA polymerase I can be suppressed by this hybrid gene in the presence of inducer (galactose) but not in its absence. We looked for mutants the growth of which depended on the presence of plasmid expressing the hybrid gene. For this purpose, we used a red/white-colony color assay as the initial screen followed by a test for galactose-dependent growth. We have thus isolated many mutants and identified at least nine genes (RRN1-RRN9) involved in 35S rRNA synthesis, two of which correspond to known RNA polymerase I subunit genes RPA190 and RPA135}, keywords = {0,CEREVISIAE,chemistry,COMPONENT,COMPONENTS,Dna,DNARibosomal,gene,Genes,GenesDominant,GenesFungal,GenesRecessive,Genetic Complementation Test,genetics,GROWTH,La,metabolism,Mutagenesis,MUTANTS,Mutation,MUTATIONS,nosource,PLASMID,Plasmids,polymerase,PROMOTER,Research SupportU.S.Gov’tP.H.S.,Restriction Mapping,ribosomal RNA,RIBOSOMAL-RNA,Rna,RNA Polymerase I,RNA Polymerase II,RNA-POLYMERASE,RNA-POLYMERASE-I,RNA-POLYMERASE-II,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUBUNIT,SYSTEM,transcription,TranscriptionGenetic} } % == BibTeX quality report for nogiApproachIsolationMutants1991: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{nogiSynthesisLargeRRNAs1991, title = {Synthesis of Large {{rRNAs}} by {{RNA}} Polymerase {{II}} in Mutants of {{Saccharomyces}} Cerevisiae Defective in {{RNA}} Polymerase {{I}}}, author = {Nogi, Y. and Yano, R. and Nomura, M.}, year = 1991, month = may, journal = {Proceedings of the National Academy of Sciences}, volume = {88}, number = {9}, pages = {3962–3966}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.88.9.3962}, url = {http://www.pnas.org/content/88/9/3962.short}, abstract = {The 35S rRNA gene of the yeast Saccharomyces cerevisiae was fused to the GAL7 promoter. This hybrid gene, when present on a multicopy plasmid and induced by galactose, suppressed the growth defects of a temperature-sensitive RNA polymerase I (pol I) mutant and those of a mutant in which the gene for the second largest subunit of pol I was deleted. Analysis of pulse-labeled RNA directly demonstrated that rRNA synthesis in this deletion mutant is from the GAL7 promoter. These experiments show that the sole essential function of pol I is the transcription of the rRNA genes, that pol I is not absolutely required for the synthesis of rRNA and ribosomes or cell growth if 35S rRNA synthesis is achieved by some other means, and that the tandemly repeated structure of the chromosomal rRNA genes is also not absolutely required for the synthesis of rRNA and ribosomes}, keywords = {0,analysis,Base Sequence,biosynthesis,BlottingSouthern,CEREVISIAE,chemistry,Dna,DNAFungal,gene,Genes,genetics,GROWTH,growth & development,La,metabolism,Molecular Sequence Data,MUTANTS,Mutation,nosource,physiology,PLASMID,pol,polymerase,PROMOTER,Promoter Regions (Genetics),Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,ribosome,Ribosomes,Rna,RNA Polymerase I,RNA Polymerase II,RNA-POLYMERASE,RNA-POLYMERASE-I,RNA-POLYMERASE-II,RNAFungal,RNARibosomal,rRNA,rRNA genes,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,structure,SUBUNIT,transcription,TranscriptionGenetic,yeast} } % == BibTeX quality report for nogiSynthesisLargeRRNAs1991: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{nollerRibosomalRNATranslation1991, title = {Ribosomal {{RNA}} and Translation.}, author = {Noller, H.F.}, year = 1991, journal = {Annual review of biochemistry}, volume = {60}, number = {1}, pages = {191–227}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, doi = {10.1146/annurev.bi.60.070191.001203}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.bi.60.070191.001203 http://www.annualreviews.org/doi/abs/10.1146/annurev.bi.53.070184.001003}, keywords = {nosource,Review,RIBOSOMAL-RNA,Rna,rRNA,translation} } % == BibTeX quality report for nollerRibosomalRNATranslation1991: % ? unused Journal abbr (“Annu.Rev.Biochem.”)

@article{nollerPeptidylTransferaseProtein1993, title = {Peptidyl Transferase: Protein, Ribonucleoprotein, or {{RNA}}?}, author = {Noller, H.F.}, year = 1993, journal = {Journal of bacteriology}, volume = {175}, number = {17}, pages = {5297–5300}, publisher = {Am Soc Microbiol}, doi = {10.1128/jb.175.17.5297-5300.1993}, url = {http://jb.asm.org/cgi/reprint/175/17/5297.pdf}, keywords = {nosource,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,protein,Review,review article,Rna,rRNA} } % == BibTeX quality report for nollerPeptidylTransferaseProtein1993: % ? unused Journal abbr (“J.Bacteriol.”)

@article{nollerTRNArRNAInteractionsPeptidyl1993a, title = {{{tRNA-rRNA}} Interactions and Peptidyl Transferase.}, author = {Noller, H.F.}, year = 1993, month = jan, journal = {The FASEB journal: official publication of the Federation of American Societies for Experimental Biology}, volume = {7}, number = {1}, eprint = {8422979}, eprinttype = {pubmed}, pages = {87–89}, doi = {10.1096/fasebj.7.1.8422979}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8422979}, abstract = {The extent to which ribosomal RNA is directly involved in the function of ribosomes has important implications for both the mechanism of translation and the molecular origins of life. Detailed evidence has accumulated that places the anticodon and acceptor ends of tRNA in close proximity to conserved features of rRNA in the ribosome. Recent studies are providing evidence that these features are important for ribosomal function}, keywords = {93138325,Anticodon,Base Sequence,MECHANISM,metabolism,Molecular Sequence Data,nosource,peptidyl transferase,Peptidyltransferase,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNARibosomal,RNATransfer,rRNA,translation,TranslationGenetic,tRNA} } % == BibTeX quality report for nollerTRNArRNAInteractionsPeptidyl1993a: % ? unused Journal abbr (“FASEB J.”)

@article{nollerStructureFunctionRibosomal1995, title = {Structure and Function of Ribosomal {{RNA}}}, author = {Noller, H.F. and Green, R. and Heilek, G. and Hoffarth, V. and Huttenhofer, A. and Joseph, S. and Lee, I. and Lieberman, K. and Mankin, A. and Merryman, C. and .}, year = 1995, month = nov, journal = {Biochem.Cell Biol.}, volume = {73}, number = {11-12}, pages = {997–1009}, doi = {10.1139/o95-107}, abstract = {A refined model has been developed for the folding of 16S rRNA in the 30S subunit, based on additional constraints obtained from new experimental approaches. One set of constraints comes from hydroxyl radical footprinting of each of the individual 30S ribosomal proteins, using free Fe(2+)-EDTA complex. A second approach uses localized hydroxyl radical cleavage from a single Fe2+ tethered to unique positions on the surface of single proteins in the 30S subunit. This has been carried out for one position on the surface of protein S4, two on S17, and three on S5. Nucleotides in 16S rRNA that are essential for P-site tRNA binding were identified by a modification interference strategy. Ribosomal subunits were partially inactivated by chemical modification at a low level. Active, partially modified subunits were separated from inactive ones by binding 3’-biotinderivatized tRNA to the 30S subunits and captured with streptavidin beads. Essential bases are those that are unmodified in the active population but modified in the total population. The four essential bases, G926, 2mG966, G1338, and G1401 are a subset of those that are protected from modification by P-site tRNA. They are all located in the cleft of our 30S subunit model. The rRNA neighborhood of the acceptor end of tRNA was probed by hydroxyl radical probing from Fe2+ tethered to the 5’ end of tRNA via an EDTA linker. Cleavage was detected in domains IV, V, and VI of 23S rRNA, but not in 5S or 16S rRNA. The sites were all found to be near bases that were protected from modification by the CCA end of tRNA in earlier experiments, except for a set of E-site cleavages in domain IV and a set of A-site cleavages in the alpha-sarcin loop of domain VI. In vitro genetics was used to demonstrate a base-pairing interaction between tRNA and 23S rRNA. Mutations were introduced at positions C74 and C75 of tRNA and positions 2252 and 2253 of 23S rRNA. Interaction of the CCA end of tRNA with mutant ribosomes was tested using chemical probing in conjunction with allele-specific primer extension. The interaction occurred only when there was a Watson-Crick pairing relationship between positions 74 of tRNA and 2252 of 23S rRNA. Using a novel chimeric in vitro reconstitution method, it was shown that the peptidyl transferase reaction depends on this same Watson-Crick base pair}, keywords = {96282703,A-SITE,Base Pairing,BINDING,chemistry,CLEAVAGE,COMPLEX,COMPLEXES,Genetic,genetics,In Vitro,IN-VITRO,ModelsBiological,ModelsMolecular,modification,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Nucleotides,P-SITE,peptidyl transferase,primer extension,protein,Proteins,Review,Ribosomal Proteins,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNA-Binding Proteins,RNARibosomal,RNARibosomal23S,RNATransfer,rRNA,structure,Structure-Activity Relationship,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,tRNA,tRNA footprinting} } % == BibTeX quality report for nollerStructureFunctionRibosomal1995: % ? Possibly abbreviated journal title Biochem.Cell Biol.

@article{nollerStructureRibosomeResolution2001, title = {Structure of the Ribosome at 5.5 {{A}} Resolution and Its Interactions with Functional Ligands}, author = {Noller, H.F. and Yusupov, M.M. and Yusupova, G.Z. and Baucom, A. and Lieberman, K. and Lancaster, L. and Dallas, A. and Fredrick, K. and Earnest, T.N. and Cate, J.H.}, year = 2001, journal = {Cold Spring Harb.Symp.Quant.Biol.}, volume = {66:57-66.}, pages = {57–66}, doi = {10.1101/sqb.2001.66.57}, keywords = {Binding Sites,BIOLOGY,chemistry,Ligands,metabolism,nosource,Nucleic Acid Conformation,Protein Conformation,RESOLUTION,Review,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNAMessenger,RNARibosomal,RNATransfer,Sensitivity and Specificity,structure,supportu.s.gov’tp.h.s.,Thermus thermophilus,ultrastructure} } % == BibTeX quality report for nollerStructureRibosomeResolution2001: % ? Possibly abbreviated journal title Cold Spring Harb.Symp.Quant.Biol.

@article{nollerTranslocationTRNAProtein2002, title = {Translocation of {{tRNA}} during Protein Synthesis}, author = {Noller, H.F. and Yusupov, M.M. and Yusupova, G.Z. and Baucom, A. and Cate, J.H.}, year = 2002, month = mar, journal = {FEBS Letters}, volume = {514}, number = {1}, pages = {11–16}, publisher = {Elsevier}, doi = {10.1016/S0014-5793(02)02327-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/S001457930202327X}, abstract = {Coupled translocation of tRNA and mRNA in the ribosome during protein synthesis is one of the most challenging and intriguing problems in the field of translation. We highlight several key questions regarding the mechanism of translocation, and discuss possible mechanistic models in light of the recent crystal structures of the ribosome and its subunits}, keywords = {animal,Binding Sites,Biological Transport,chemistry,CRYSTAL-STRUCTURE,human,MECHANISM,models,ModelsMolecular,mRNA,nosource,Nucleic Acid Conformation,physiology,protein,Protein Conformation,protein synthesis,PROTEIN-SYNTHESIS,Review,ribosome,Ribosomes,Rna,RNATransfer,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,translation,TranslationGenetic,translocation,tRNA} } % == BibTeX quality report for nollerTranslocationTRNAProtein2002: % ? unused Journal abbr (“FEBS Lett.”)

@incollection{nollerStructureBacterialRibosome2007, title = {Structure of the Bacterial Ribosome and Some Implications for Translational Regulation.}, booktitle = {Translational Control in Biology and Medicine.}, author = {Noller, H.F.}, year = 2007, pages = {41–58}, publisher = {Cold Spring Harbor Press}, address = {Cold Spring Harbor, NY}, collaborator = {Mathews, M.B and Sonenberg, N. and Hershey, J.W.B.}, keywords = {BIOLOGY,nosource,regulation,Review,ribosome,structure} }

@article{nomuraRegulationRibosomeBiosynthesis1999, title = {Regulation of Ribosome Biosynthesis in {{Escherichia}} Coli and {{Saccharomyces}} Cerevisiae: Diversity and Common Principles}, author = {Nomura, M.}, year = 1999, month = nov, journal = {Journal of bacteriology}, volume = {181}, number = {22}, pages = {6857–6864}, publisher = {Am Soc Microbiol}, doi = {10.1128/JB.181.22.6857-6864.1999}, url = {http://jb.asm.org/cgi/content/abstract/181/22/6857}, keywords = {20026796,Bacterial Proteins,biosynthesis,chemistry,Escherichia coli,ESCHERICHIA-COLI,Fungal Proteins,Gene Expression RegulationBacterial,Gene Expression RegulationFungal,GenesrRNA,genetics,metabolism,nosource,regulation,Ribosomal Proteins,ribosome,Ribosomes,RNABacterial,RNAFungal,RNARibosomal,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for nomuraRegulationRibosomeBiosynthesis1999: % ? unused Journal abbr (“J.Bacteriol.”)

@article{nowotnyInitiatorProteinsAssembly1982, title = {Initiator Proteins for the Assembly of the {{50S}} Subunit from {{Escherichia}} Coli Ribosomes}, author = {Nowotny, V. and Nierhaus, K.H.}, year = 1982, month = dec, journal = {Proceedings of the National Academy of Sciences}, volume = {79}, number = {23}, pages = {7238–7242}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.79.23.7238}, url = {http://www.pnas.org/content/79/23/7238.short}, abstract = {An rRNA-binding protein that binds to the rRNA independently of other proteins during the course of ribosomal assembly is termed “assembly initiator protein.” In spite of the large number of rRNA-binding proteins (more than 17 out of 32 proteins have been identified in the case of the large ribosomal subunit), only a very small number of proteins should actually initiate ribosomal assembly for theoretical reasons. Here we demonstrate that only two of the L proteins derived from the large subunit (50S) function as assembly initiator proteins. Two different techniques are used to identify these initiator proteins: reconstitution experiments with purified proteins and pulse-chase experiments during in vitro assembly. Both methods independently identify L24 and L3 as initiator proteins for the 50S assembly. The existence of two initiator proteins (not just one) resolves an apparent contradiction–namely, that on the one hand, rRNA is synthesized in excess under unfavorable growth conditions, whereas on the other hand, rRNA-binding proteins should be available for translational control}, keywords = {0,Animals,assembly,Escherichia coli,Escherichia coli ribosomes,ESCHERICHIA-COLI,GROWTH,IDENTIFY,In Vitro,IN-VITRO,L3,La,metabolism,Methods,morphogenesis,nosource,physiology,protein,Protein Binding,Proteins,RECONSTITUTION,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNARibosomal,rRNA,SUBUNIT,techniques,ultrastructure} } % == BibTeX quality report for nowotnyInitiatorProteinsAssembly1982: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{oconnorGeneticProbesRibosomal1995a, title = {Genetic Probes of Ribosomal {{RNA}} Function.}, author = {O’Connor, M. and Brunelli, C.A. and Firpo, M.A. and Gregory, S.T. and Lieberman, K.R. and Lodmell, J.S. and Moine, H. and Van Ryk, D.I. and Dahlberg, A.E.}, year = 1995, month = nov, journal = {Biochemistry and cell biology= Biochimie et biologie cellulaire}, volume = {73}, number = {11-12}, eprint = {8722001}, eprinttype = {pubmed}, pages = {859–868}, doi = {10.1139/o95-093}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8722001/}, abstract = {We have used a genetic approach to uncover the functional roles of rRNA in protein synthesis. Mutations were constructed in a cloned rrn operon by site-directed mutagenesis or isolated by genetic selections following random mutagenesis. We have identified mutations that affect each step in the process of translation. The data are consistent with the results of biochemical and phylogenetic analyses but, in addition, have provided novel information on regions of rRNA not previously investigated}, keywords = {96282689,Base Sequence,Genetic,genetics,Molecular Sequence Data,Mutagenesis,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Operon,protein,protein synthesis,PROTEIN-SYNTHESIS,Review,RIBOSOMAL-RNA,Rna,RNA Probes,RNAMessenger,RNARibosomal,RNARibosomal16S,RNATransfer,rRNA,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,translation} } % == BibTeX quality report for oconnorGeneticProbesRibosomal1995a: % ? unused Journal abbr (“Biochem.Cell Biol.”)

@article{oconnorInvolvementTwoDistinct1995, title = {The Involvement of Two Distinct Regions of 23 {{S}} Ribosomal {{RNA}} in {{tRNA}} Selection}, author = {O’Connor, M. and Dahlberg, A.E.}, year = 1995, month = dec, journal = {Journal of molecular biology}, volume = {254}, number = {5}, pages = {838–847}, publisher = {Elsevier}, doi = {10.1006/jmbi.1995.0659}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283685706596}, abstract = {The role of ribosomal RNA in maintaining the accuracy of translation has been investigated genetically by selecting for rRNA mutations that promoted frameshifting at a specific site in a reporter gene in Escherichia coli. Mutations were recovered in two different regions of 23 S rRNA and each promoted readthrough of stop codons as well as increasing the levels of frameshifting. The first group of mutations was in a small stem loop (the 1916 loop) in domain IV of 23 S rRNA. This stem-loop has been mapped to the subunit interface of the ribosome, close to the decoding center on the 30 S subunit. The second group of mutations was in helix 89, one of the helices emerging from the central loop of domain V. Helix 89 has been implicated in subunit- subunit interactions and peptidyltransferase activity, and it is proposed that mutations in helix 89 influence the accuracy of decoding by affecting the interaction of the CCA end of the tRNA with the peptidyltransferase center}, keywords = {0,30 S,accuracy,Base Sequence,Codon,decoding,Escherichia coli,ESCHERICHIA-COLI,Frameshift Mutation,Frameshifting,gene,Gene Expression RegulationBacterial,genetics,La,metabolism,Molecular Sequence Data,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Peptidyltransferase,Point Mutation,readthrough,RIBOSOMAL-RNA,ribosome,Rna,RNARibosomal23S,RNATransfer,rRNA,STOP CODON,SUBUNIT,supportu.s.gov’tp.h.s.,SuppressionGenetic,translation,tRNA} } % == BibTeX quality report for oconnorInvolvementTwoDistinct1995: % ? unused Journal abbr (“J.Mol.Biol.”)

@article{oconnorInfluenceBaseIdentity1996a, title = {The Influence of Base Identity and Base Pairing on the Function of the Alpha-Sarcin Loop of {{23S rRNA}}}, author = {O’Connor, M. and Dahlberg, A.E.}, year = 1996, month = jul, journal = {Nucleic Acids Research}, volume = {24}, number = {14}, pages = {2701–2705}, doi = {10.1093/nar/24.14.2701}, keywords = {a-sarcin,Base Pairing,Codon,COMPONENT,elongation,Escherichia coli,ESCHERICHIA-COLI,Frameshifting,gene,Genetic,Mutagenesis,Mutation,MUTATIONS,nosource,Operon,PLASMID,Plasmids,readthrough,ribosome,Ricin,rRNA,STOP CODON,structure,SUBUNIT} }

@article{oakesMutationalAnalysisStructure1998, title = {Mutational Analysis of the Structure and Localization of the Nucleolus in the Yeast {{Saccharomyces}} Cerevisiae}, author = {Oakes, M. and Aris, J.P. and Brockenbrough, J.S. and Wai, H. and Vu, L. and Nomura, M.}, year = 1998, month = oct, journal = {The Journal of cell biology}, volume = {143}, number = {1}, pages = {23–34}, publisher = {Rockefeller Univ Press}, doi = {10.1083/jcb.143.1.23}, url = {http://jcb.rupress.org/content/143/1/23.abstract}, abstract = {The nucleolus in Saccharomyces cerevisiae is a crescent-shaped structure that makes extensive contact with the nuclear envelope. In different chromosomal rDNA deletion mutants that we have analyzed, the nucleolus is not organized into a crescent structure, as determined by immunofluorescence microscopy, fluorescence in situ hybridization, and electron microscopy. A strain carrying a plasmid with a single rDNA repeat transcribed by RNA polymerase I (Pol I) contained a fragmented nucleolus distributed throughout the nucleus, primarily localized at the nuclear periphery. A strain carrying a plasmid with the 35S rRNA coding region fused to the GAL7 promoter and transcribed by Pol II contained a rounded nucleolus that often lacked extensive contact with the nuclear envelope. Ultrastructurally distinct domains were observed within the round nucleolus. A similar rounded nucleolar morphology was also observed in strains carrying the Pol I plasmid in combination with mutations that affect Pol I function. In a Pol I-defective mutant strain that carried copies of the GAL7-35S rDNA fusion gene integrated into the chromosomal rDNA locus, the nucleolus exhibited a round morphology, but was more closely associated with the nuclear envelope in the form of a bulge. Thus, both the organization of the rDNA genes and the type of polymerase involved in rDNA expression strongly influence the organization and localization of the nucleolus}, keywords = {5S rRNA,98437345,analysis,Cell Nucleolus,chemistry,ChromosomesFungal,DNARibosomal,expression,Fluorescence,gene,Genes,genetics,metabolism,MicroscopyElectron,Mutagenesis,Mutation,MUTATIONAL ANALYSIS,MUTATIONS,nosource,nucleolus,PLASMID,Plasmids,pol,polymerase,PROMOTER,RDN1,rDNA,Repetitive SequencesNucleic Acid,Rna,RNA Polymerase I,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Sequence Deletion,structure,supportu.s.gov’tp.h.s.,TranscriptionGenetic,ultrastructure,yeast} } % == BibTeX quality report for oakesMutationalAnalysisStructure1998: % ? unused Journal abbr (“J.Cell Biol.”)

@article{oconnorDecodingFidelityRibosomal1997, title = {Decoding Fidelity at the Ribosomal {{A}} and {{P}} Sites: Influence of Mutations in Three Different Regions of the Decoding Domain in 16s {{RNA}}.}, author = {Oconnor, M. and Thomas, C.L. and Zimmermann, R.A. and Dahlberg, A.E.}, year = 1997, month = mar, journal = {Nucleic Acids Research}, volume = {25}, number = {6}, pages = {1185–1193}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/25.6.1185}, url = {http://nar.oxfordjournals.org/content/25/6/1185.short ISI:A1997WP58300015}, abstract = {The involvement of defined regions of Escherichia coli 16S rRNA in the fidelity of decoding has been examined by analyzing the effects of rRNA mutations on misreading errors at the ribosomal A and P sites. Mutations in the 1400-1500 region, the 530 loop and in the 1050/1200 region (helix 34) all caused readthrough of stop codons and frameshifting during elongation and stimulated initiation from non-AUG codons at the initiation of protein synthesis. These results indicate the involvement of all three regions of 16S rRNA in decoding functions at both the A and P sites. The functional similarity of all three mutant classes are consistent with close physical proximity of the 1400-1500 region, the 530 loop and helix 34 and suggest that all three regions of rRNA comprise a decoding domain in the ribosome}, keywords = {AFFECT TRANSLATIONAL FIDELITY,BASE CHANGES,Codon,CODONS,decoding,DIRECTED CROSS-LINKING,elongation,Escherichia coli,ESCHERICHIA-COLI,Fidelity,Frameshifting,initiation,LOOP,MESSENGER-RNA ANALOGS,Mutation,MUTATIONS,nosource,P SITE,P-SITE,P-SITES,protein,protein synthesis,PROTEIN-SYNTHESIS,readthrough,REGION,RESISTANCE,ribosome,Rna,rRNA,SITE,SITES,STOP CODON,Streptomycin} }

@article{odomMovementTransferRnaNot1990a, title = {Movement of {{Transfer-Rna But Not}} the {{Nascent Peptide During Peptide-Bond Formation}} on {{Ribosomes}}}, author = {Odom, O.W. and Picking, W.D. and Hardesty, B.}, year = 1990, month = dec, journal = {Biochemistry}, volume = {29}, number = {48}, pages = {10734–10744}, doi = {10.1021/bi00500a004}, url = {ISI:A1990EL36400004}, keywords = {Movement,nosource,PEPTIDE-BOND FORMATION,ribosome,Ribosomes,TRANSFER-RNA} } % == BibTeX quality report for odomMovementTransferRnaNot1990a: % ? Title looks like it was stored in title-case in Zotero

@article{oenPeptidyltransferaseInhibitorsAlter1974, title = {Peptidyl-Transferase Inhibitors Alter the Covalent Reaction of {{BrAcPhe-tRNA}} with the ⬚{{E}}. Coli⬚ Ribosome.}, author = {Oen, H. and Pellegrini, M. and Cantor, C.R.}, year = 1974, journal = {FEBS Letts.}, volume = {45}, pages = {218–222}, doi = {10.1016/0014-5793(74)80848-3}, keywords = {COMPLEX,COMPLEXES,L2,nosource,peptidyl transferase,Peptidyltransferase,ribosome,sparsomycin} } % == BibTeX quality report for oenPeptidyltransferaseInhibitorsAlter1974: % ? Possibly abbreviated journal title FEBS Letts.

@article{ofengandMappingNucleotideResolution1997a, title = {Mapping to Nucleotide Resolution of Pseudouridine Residues in Large Subunit Ribosomal {{RNAs}} from Representative Eukaryotes, Prokaryotes, Archaebacteria, Mitochondria and Chloroplasts}, author = {Ofengand, J. and Bakin, A.}, year = 1997, month = feb, journal = {J.Mol.Biol.}, volume = {266}, number = {2}, pages = {246–268}, doi = {10.1006/jmbi.1996.0737}, url = {PM:9047361}, abstract = {The pseudouridine (psi) residues present in the high molecular mass RNA from the large ribosomal subunit (LSU) have been sequenced from representative species of the eukaryotes, prokaryotes and archaebacteria, and from mitochondrial and chloroplast organelles. Ribosomes from Bacillus subtilis, Halobacter halobium, Drosphilia melanogaster, Mus musculus, Homo sapiens, mitochondria of M. musculus, H. sapiens and Trypanosoma brucei, and Zea mays chloroplasts were examined, resulting in the exact localization of 190 psi residues. The number of psi residues per RNA varied from one in the mitochondrial RNAs to 57 in the cytoplasmic LSU RNA of D. melanogaster and M. musculus. Despite this, all of the psi residues were found in three domains, II, IV and V. All three are at or have been linked to the peptidyl transferase center according to the literature. Comparison of the sites for psi among the species examined revealed four conserved or semi-conserved segments. One is the region 1911 to 1917, which contains three psi or modified psi in almost all species examined. This site is also juxtaposed to the decoding site of the 30 S subunit in the 70 S ribosome and has been implicated in the fidelity of codon recognition. Three additional sites were at the peptidyl transferase center itself. The juxtaposition of the conserved sites for psi with the two important functions of the ribosome, codon recognition and peptide bond formation, implies an important role for psi in ribosome function. We report some new putative modified nucleosides in LSU RNAs as detected by reverse transcription, correct a segment of the sequence of Z. mays chloroplasts and D. melanogaster LSU RNA, correlate the secondary structural context for all known psi residues in ribosomal RNA, and compare the sites for psi with those known for methylated nucleosides in H. sapiens}, keywords = {0,30 S,30-S,analysis,Animals,Bacillus subtilis,Base Sequence,Binding Sites,Biochemistry,BIOLOGY,BOND FORMATION,chemistry,Chloroplasts,Codon,CODON RECOGNITION,D,decoding,Dna,DOMAIN,DOMAINS,Drosophila melanogaster,Fidelity,genetics,Halobacterium salinarum,Humans,La,LOCALIZATION,M,mapping,metabolism,Mice,mitochondria,Molecular Biology,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleosides,NUCLEOTIDE RESOLUTION,Organelles,peptide bond formation,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,polymerase,PROKARYOTES,Pseudouridine,psi,RECOGNITION,REGION,RESIDUES,RESOLUTION,ribosomal RNA,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNA-Directed DNA Polymerase,RNARibosomal,S,sequence,SITE,SITES,Structural,SUBUNIT,Support,transcription,TRANSFERASE CENTER,Transferases,Trypanosoma brucei brucei,Zea mays} } % == BibTeX quality report for ofengandMappingNucleotideResolution1997a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{ofengandRibosomalRNAPseudouridines2002, title = {Ribosomal {{RNA}} Pseudouridines and Pseudouridine Synthases}, author = {Ofengand, J.}, year = 2002, month = mar, journal = {FEBS letters}, volume = {514}, number = {1}, pages = {17–25}, publisher = {Elsevier}, doi = {10.1016/S0014-5793(02)02305-0}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0014579302023050}, abstract = {Pseudouridines are found in virtually all ribosomal RNAs but their function is unknown. There are four to eight times more pseudouridines in eukaryotes than in eubacteria. Mapping 19 Haloarcula marismortui pseudouridines on the three-dimensional 50S subunit does not show clustering. In bacteria, specific enzymes choose the site of pseudouridine formation. In eukaryotes, and probably also in archaea, selection and modification is done by a guide RNA-protein complex. No unique specific role for ribosomal pseudouridines has been identified. We propose that pseudouridine’s function is as a molecular glue to stabilize required RNA conformations that would otherwise be too flexible}, keywords = {0,analysis,animal,Animals,Archaea,Bacteria,Biochemistry,BIOLOGY,biosynthesis,chemistry,COMPLEX,COMPLEXES,CONFORMATION,enzyme,Enzymes,Eubacterium,Eukaryotic Cells,Haloarcula,Haloarcula marismortui,human,Humans,La,mapping,metabolism,ModelsMolecular,modification,Molecular Biology,nosource,Nucleic Acid Conformation,Pseudouridine,PSEUDOURIDINE SYNTHASE,Review,ribosomal RNA,RIBOSOMAL-RNA,Rna,RNA conformation,RNA CONFORMATIONS,RnaGuide,RNARibosomal,SELECTION,SITE,SUBUNIT,Support,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for ofengandRibosomalRNAPseudouridines2002: % ? unused Journal abbr (“FEBS Lett.”)

@article{ogasawaraNewClassEnzyme1999a, title = {A New Class of Enzyme Acting on Damaged Ribosomes: Ribosomal {{RNA}} Apurinic Site Specific Lyase Found in Wheat Germ}, author = {Ogasawara, T. and Sawasaki, T. and Morishita, R. and Ozawa, A. and Madin, K. and Endo, Y.}, year = 1999, month = nov, journal = {EMBO Journal}, volume = {18}, number = {22}, pages = {6522–6531}, doi = {10.1093/emboj/18.22.6522}, url = {ISI:000083870100032}, abstract = {A new enzyme, which we named ribosomal RNA apurinic site specific lyase (RALyase), is described. The protein was found in wheat embryos and has a molecular weight of 50 625 Da, The enzyme specifically cleaves the phosphodiester bond at the 3’ side of the apurinic site introduced by ribosome-inactivating proteins into the sarcin/ricin domain of 28S rRNA, The 3’ and 5’ ends of wheat 28S rRNA at the cleavage site are 5’-GUACG-alpha-hyroxy-alpha,beta-unsaturated aldehyde and pGAGGA-3’, demonstrating that the enzyme catalyzes a p-elimination reaction. The substrate specificity of the enzyme is extremely high: it acts only at the apurinic site in the sarcin/ricin domain of intact ribosomes, not on deproteinized rRNA or DNA containing apurinic sites, The amino acid sequences of five endopeptidase LysC-liberated peptides from the purified enzyme were determined and used to obtain a cDNA sequence. The open reading frame encodes a protein of 456 amino acids, and a homology search revealed a related rice protein. Similar enzyme activities were also found in other plants that express ribosome-inactivating proteins. We believe that RALyase is part of a complex self-defense mechanism}, keywords = {3,ACID,ACIDS,ALPHA-SARCIN,Amino Acid Sequence,Amino Acids,AMINO-ACIDS,apurinic site,CELL-FREE TRANSLATION,CLEAVAGE,CLEAVAGE SITE,COMPLEX,COMPLEXES,Dna,DOMAIN,ELONGATION-FACTORS,ENCODES,enzyme,EUKARYOTIC RIBOSOMES,FRAME,INACTIVATING PROTEINS,lyase,MECHANISM,Molecular Weight,N-GLYCOSIDASE ACTIVITY,nosource,OPEN READING FRAME,Peptides,Plants,Pokeweed antiviral protein,protein,Proteins,READING FRAME,ribosomal RNA,RIBOSOMAL-RNA,ribosome,RIBOSOME-INACTIVATING PROTEINS,Ribosomes,RICIN A-CHAIN,Rna,rRNA,sarcin-ricin domain,sarcin/ricin domain,search,sequence,SEQUENCES,SITE,site specific,SITES,SPECIFICITY,SUBCELLULAR-LOCALIZATION,Substrate Specificity,SUBSTRATE-SPECIFICITY,TOXIC LECTINS,Wheat} }

@article{ogleRecognitionCognateTransfer2001, title = {Recognition of Cognate Transfer {{RNA}} by the {{30S}} Ribosomal Subunit}, author = {Ogle, J.M. and Brodersen, D.E. and Clemons, W.M. and Tarry, M.J. and Carter, A.P. and Ramakrishnan, V.}, year = 2001, month = may, journal = {Science}, volume = {292}, number = {5518}, eprint = {11340196}, eprinttype = {pubmed}, pages = {897–902}, publisher = {American Association for the Advancement of Science}, issn = {0036-8075}, doi = {10.1126/science.1060612}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11340196 http://www.sciencemag.org/content/292/5518/897.short}, abstract = {Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or “wobble,” position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs}, pmid = {11340196}, keywords = {0,16S,16S: chemistry,16S: metabolism,A-SITE,Amino Acid-Specific,Amino Acid-Specific: chemistry,Amino Acid-Specific: metabolism,Anti-Bacterial Agents,Anti-Bacterial Agents: metabolism,Anti-Bacterial Agents: pharmacology,antibiotic,antibiotics,AntibioticsAminoglycoside,Anticodon,Anticodon: chemistry,Anticodon: metabolism,Bacterial,Bacterial: chemistry,Bacterial: metabolism,Base Pairing,BINDING,Binding Sites,chemistry,Codon,Codon: chemistry,Codon: metabolism,COMPLEX,COMPLEXES,CRYSTAL-STRUCTURE,Crystallography,CrystallographyX-Ray,elongation,Guanosine,Guanosine Triphosphate,Guanosine Triphosphate: metabolism,Hydrogen Bonding,La,Messenger,MESSENGER-RNA,Messenger: chemistry,Messenger: metabolism,metabolism,Models,ModelsMolecular,Molecular,Movement,nosource,Nucleic Acid Conformation,Paromomycin,Paromomycin: metabolism,Paromomycin: pharmacology,Peptide Chain Elongation,Peptide Elongation Factor Tu,Peptide Elongation Factor Tu: metabolism,pharmacology,Phe,Phe: chemistry,Phe: metabolism,Protein Biosynthesis,Ribosomal,RIBOSOMAL-SUBUNIT,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,Ribosomes: ultrastructure,Rna,RNA,RNABacterial,RNAMessenger,RNARibosomal16S,RNATransfer,RNATransferAmino Acid-Specific,RNATransferPhe,Structural,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Thermodynamics,Thermus thermophilus,Thermus thermophilus: chemistry,Thermus thermophilus: metabolism,Thermus thermophilus: ultrastructure,Transfer,TRANSFER-RNA,Transfer: chemistry,Transfer: metabolism,Translational,TranslationGenetic,tRNA,ultrastructure,X-Ray} }

@article{ogleSelectionTRNARibosome2002, title = {Selection of {{tRNA}} by the {{Ribosome Requires}} a {{Transition}} from an {{Open}} to a {{Closed Form}}}, author = {Ogle, J.M. and Murphy, F.V. and Tarry, M.J. and Ramakrishnan, V.}, year = 2002, month = nov, journal = {Cell}, volume = {111}, number = {5}, pages = {721–732}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(02)01086-3}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867402010863}, abstract = {A structural and mechanistic explanation for the selection of tRNAs by the ribosome has been elusive. Here, we report crystal structures of the 30S ribosomal subunit with codon and near-cognate tRNA anticodon stem loops bound at the decoding center and compare affinities of equivalent complexes in solution. In ribosomal interactions with near-cognate tRNA, deviation from Watson-Crick geometry results in uncompensated desolvation of hydrogen-bonding partners at the codon-anticodon minor groove. As a result, the transition to a closed form of the 30S induced by cognate tRNA is unfavorable for near-cognate tRNA unless paromomycin induces part of the rearrangement. We conclude that stabilization of a closed 30S conformation is required for tRNA selection, and thereby structurally rationalize much previous data on translational fidelity}, keywords = {Anticodon,Codon,COMPLEX,COMPLEXES,CRYSTAL-STRUCTURE,decoding,Fidelity,Hydrogen Bonding,nosource,Paromomycin,RIBOSOMAL-SUBUNIT,ribosome,Structural,structure,SUBUNIT,tRNA} } % == BibTeX quality report for ogleSelectionTRNARibosome2002: % ? Title looks like it was stored in title-case in Zotero

@article{ogleInsightsDecodingMechanism2003, title = {Insights into the Decoding Mechanism from Recent Ribosome Structures}, author = {Ogle, J.M. and Carter, A.P. and Ramakrishnan, V.}, year = 2003, month = may, journal = {Trends in biochemical sciences}, volume = {28}, number = {5}, pages = {259–266}, publisher = {Elsevier}, doi = {10.1016/S0968-0004(03)00066-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000403000665}, abstract = {During the decoding process, tRNA selection by the ribosome is far more accurate than expected from codon-anticodon pairing. Antibiotics such as streptomycin and paromomycin have long been known to increase the error rate of translation, and many mutations that increase or lower accuracy have been characterized. Recent crystal structures show that the specific recognition of base-pairing geometry leads to a closure of the domains of the small subunit around cognate tRNA. This domain closure is likely to trigger subsequent steps in tRNA selection. Many antibiotics and mutations act by making the domain closure more or less favourable. In conjunction with recent cryoelectron microscopy structures of the ribosome, a comprehensive structural understanding of the decoding process is beginning to emerge}, keywords = {0,accuracy,antibiotic,antibiotics,Anticodon,Base Pairing,Base Sequence,BIOLOGY,chemistry,Cryoelectron Microscopy,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,decoding,DOMAIN,DOMAINS,elongation,ELONGATION-FACTOR-TU,FACTOR TU,genetics,Guanosine,Guanosine Triphosphate,La,MECHANISM,metabolism,Mutation,MUTATIONS,nosource,Paromomycin,Peptide Elongation Factor Tu,Protein Biosynthesis,Protein StructureTertiary,RECOGNITION,Review,ribosome,Ribosomes,Rna,RNATransferAmino Acid-Specific,SELECTION,Streptomycin,Structural,structure,SUBUNIT,translation,tRNA,TU} } % == BibTeX quality report for ogleInsightsDecodingMechanism2003: % ? unused Journal abbr (“Trends Biochem.Sci.”)

@article{ogleStructuralInsightsTranslational2005, title = {Structural {{Insights}} into {{Translational Fidelity}}}, author = {Ogle, J.M. and Ramakrishnan, V.}, year = 2005, month = feb, journal = {Annual Review of Biochemistry}, volume = {74}, number = {1}, pages = {129–177}, publisher = {Annual Reviews}, issn = {0066-4154}, doi = {10.1146/annurev.biochem.74.061903.155440}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.biochem.74.061903.155440 http://www.ncbi.nlm.nih.gov/pubmed/15952884}, abstract = {The underlying basis for the accuracy of protein synthesis has been the subject of over four decades of investigations. Recent biochemical and structural data make it possible to understand at least in outline the structural basis for tRNA selection, in which codon recognition by cognate tRNA results in the hydrolysis of GTP by EF-Tu over 75 A away. The ribosome recognizes the geometry of codon-anticodon base pairing at the first two positions but monitors the third, or wobble position, less stringently. Part of the additional binding energy of cognate tRNA is used to induce conformational changes in the ribosome that stabilize a transition state for GTP hydrolysis by EF-Tu and subsequently result in accelerated accommodation of tRNA into the peptidyl transferase center. The transition state for GTP hydrolysis is characterized, among other things, by a distorted tRNA. This picture explains a large body of data on the effect of antibiotics and mutations on translational fidelity. However, many fundamental questions remain, such as the mechanism of activation of GTP hydrolysis by EF-Tu, and the relationship between decoding and frameshifting. Expected online publication date for the Annual Review of Biochemistry Volume 74 is June 2, 2005. Please see http://www.annualreviews.org/catalog/pub\_dates.asp for revised estimates}, pmid = {15952884}, keywords = {abstract the underlying basis,accuracy,activation,Anti-Bacterial Agents,Anti-Bacterial Agents: pharmacology,antibiotic,antibiotics,Bacterial,Bacterial: chemistry,Bacterial: genetics,BASE,Base Pairing,BINDING,BIOLOGY,BODIES,Codon,CODON RECOGNITION,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,Cryoelectron Microscopy,crystallography,Crystallography,decoding,EFTu,Escherichia coli,Escherichia coli: drug effects,Escherichia coli: genetics,Escherichia coli: metabolism,Fidelity,for the accuracy of,four decades of investigation,Frameshifting,Gene Expression,Genetic,GTP,Hydrolysis,Kinetics,La,MECHANISM,Models,Molecular,Mutation,MUTATIONS,nosource,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,POSITION,POSITIONS,protein,Protein Biosynthesis,Protein Biosynthesis: drug effects,protein synthesis,protein synthesis has been,PROTEIN-SYNTHESIS,recent biochemical and structural,RECOGNITION,Review,ribosome,Ribosomes,Ribosomes: genetics,Ribosomes: metabolism,Ribosomes: ultrastructure,RNA,SELECTION,Structural,STRUCTURAL BASIS,the subject of over,Transfer,Transfer: chemistry,Transfer: genetics,TRANSFERASE CENTER,translational fidelity,tRNA,X-Ray} } % == BibTeX quality report for ogleStructuralInsightsTranslational2005: % ? Title looks like it was stored in title-case in Zotero % ? unused Journal abbr (“Annu. Rev. Biochem.”) % ? unused Library catalog (“CrossRef”)

@article{ohtakeYeastVirusPropagation1995, title = {Yeast Virus Propagation Depends Critically on Free {{60S}} Ribosomal Subunit Concentration.}, author = {Ohtake, Y. and Wickner, R.B.}, year = 1995, journal = {Molecular and cellular biology}, volume = {15}, number = {5}, pages = {2772–2781}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.15.5.2772}, url = {http://mcb.asm.org/cgi/content/abstract/15/5/2772}, keywords = {nosource,RIBOSOMAL-SUBUNIT,Ribosomes,SUBUNIT,viral propagation,virus,yeast} } % == BibTeX quality report for ohtakeYeastVirusPropagation1995: % ? unused Journal abbr (“Mol.Cell.Biol.”)

@article{ohtakeKRB1SuppressorMak711995, title = {{{KRB1}}, a Suppressor of Mak7-1 (a Mutant {{RPL4A}}), Is {{RPL4B}}, a Second Ribosomal Protein {{L4}} Gene, on a Fragment of {{Saccharomyces}} Chromosome {{XII}}}, author = {Ohtake, Y. and Wickner, R.B.}, year = 1995, month = may, journal = {Genetics}, volume = {140}, number = {1}, pages = {129–137}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/140.1.129}, url = {http://www.genetics.org/content/140/1/129.short}, abstract = {The mak7-1 mutant loses the killer toxin-encoding M1 dsRNA. MAK7 is RPL4A, one of two genes encoding ribosomal protein L4. KRB1 is a dominant suppressor of mak7-1 that is tightly centromerelinked, but not linked to centromere markers of chromosomes I-XVI. Our orthogonal field agarose gel electrophoresis analysis of chromosomal DNA from strains with KRB1 shows a novel band of approximately 250 kb. This band hybridizes with an RPL4B-specific probe, but not an RPL4A (MAK7)-specific probe. The RPL4B-specific probe also hybridizes to chromosome XII where the original RPL4B is located. KRB1 is meiotically linked to this extra chromosome. Disruption of either the RPL4B gene on chromosome XII or that on the extra chromosome results in loss of the killer phenotype and a decreased concentration of free 60S subunits. Thus, the RPL4B on the extra chromosome is KRB1 and is active. The extra chromosome contains chromosome XII sequence between Lambda 5345 clone (ATCC70558) and Lambda 6639 clone (ATCC71085) of Olson’s Lambda library, indicating that KRB1 represents a chromosomal rearrangement involving chromosome XII and explaining the earlier genetic data}, keywords = {0,60S subunit,analysis,Base Sequence,Chromosome Mapping,Chromosomes,ChromosomesFungal,disease,DISRUPTION,Dna,DSRNA,Electrophoresis,ElectrophoresisGelPulsed-Field,GEL-ELECTROPHORESIS,gene,Genes,GenesStructuralFungal,GenesSuppressor,Genetic,genetics,killer,La,library,M1,MARKER,Molecular Sequence Data,nosource,Phenotype,protein,Proteins,Ribosomal Proteins,Saccharomyces,Saccharomyces cerevisiae,sequence,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t} }

@article{olarewajuTranslationElongationFactor2004a, title = {The Translation Elongation Factor,{{eEF1B}},Plays a Role in the Oxidative Stress Response Pathway.}, author = {Olarewaju, O. and Ortiz, P.A. and Chowdhury, W. and Chatterjee, I. and Kinzy, T.G.}, year = 2004, journal = {RNA Biology}, volume = {1}, number = {2}, eprint = {17179749}, eprinttype = {pubmed}, pages = {12–17}, doi = {10.4161/rna.1.2.1033}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17179749}, keywords = {elongation,nosource,PATHWAY,Stress,stress response,translation} }

@article{olivasPuf3ProteinTranscriptspecific2000, title = {The {{Puf3}} Protein Is a Transcript-Specific Regulator of {{mRNA}} Degradation in Yeast}, author = {Olivas, W. and Parker, R.}, year = 2000, month = dec, journal = {The EMBO journal}, volume = {19}, number = {23}, pages = {6602–6611}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/19.23.6602}, url = {http://www.nature.com/emboj/journal/v19/n23/abs/7593472a.html}, abstract = {Eukaryotic post-transcriptional regulation is often specified by control elements within mRNA 3’- untranslated regions (3’-UTRs). In order to identify proteins that regulate specific mRNA decay rates in Saccharomyces cerevisae, we analyzed the role of five members of the Puf family present in the yeast genome (referred to as JSN1/PUF1, PUF2, PUF3, PUF4 and MPT5/PUF5). Yeast strains lacking all five Puf proteins showed differential expression of numerous yeast mRNAs. Examination of COX17 mRNA indicates that Puf3p specifically promotes decay of this mRNA by enhancing the rate of deadenylation and subsequent turnover. Puf3p also binds to the COX17 mRNA 3’-UTR in vitro. This indicates that the function of Puf proteins as specific regulators of mRNA deadenylation has been conserved throughout eukaryotes. In contrast to the case in Caenorhabditis elegans and DROSOPHILA:, yeast Puf3p does not affect translation of COX17 mRNA. These observations indicate that Puf proteins are likely to play a role in the control of transcript-specific rates of degradation in yeast by interacting directly with the mRNA turnover machinery}, keywords = {0,3’ Untranslated Regions,3’ UTR,Caenorhabditis,Caenorhabditis elegans,DEADENYLATION,DECAY,degradation,Drosophila,ELEMENTS,expression,Genome,In Vitro,IN-VITRO,mRNA,mRNA decay,nosource,post-transcriptional regulation,protein,Proteins,regulation,Saccharomyces,translation,turnover,Untranslated Regions,yeast} } % == BibTeX quality report for olivasPuf3ProteinTranscriptspecific2000: % ? unused Journal abbr (“EMBO J.”)

@article{olsonRibosomalInhibitoryProteins1991a, title = {Ribosomal Inhibitory Proteins from Plants Inhibit {{HIV-1}} Replication in Acutely Infected Peripheral Blood Mononuclear Cells}, author = {Olson, M.C. and Ramakrishnan, S. and Anand, R.}, year = 1991, month = dec, journal = {AIDS research and human retroviruses}, volume = {7}, number = {12}, pages = {1025–1030}, doi = {10.1089/aid.1991.7.1025}, url = {http://www.liebertonline.com/doi/abs/10.1089/aid.1991.7.1025}, abstract = {Peripheral blood mononuclear cells from seronegative donors were stimulated with phytohemagglutinin and then infected with human immunodeficiency virus (HIV-1). Using this experimental system, the antiviral activity of two translation inhibitory proteins (pokeweed antiviral protein, PAP-S, and Luffa ribosomal inhibitory protein, LRIP- I) isolated from plants and a recombinant form of ricin A chain were studied. Previously, it had been shown that toxin polypeptides linked to monoclonal antibodies could inhibit HIV-infected cells. In the present study, the free, unconjugated, proteins were found to inhibit HIV replication at doses in which they were nontoxic to uninfected peripheral blood mononuclear cells. Among the inhibitory proteins, PAP- S and recombinant ricin A chain markedly reduced the reverse transcriptase activity and the expression of p24 core protein in infected cultures. Dose response studies indicate that the anti-HIV activity of PAP-S was comparable to AZT. The other ribosome inhibitory proteins (RIPs) showed moderate but significant antiviral activity}, keywords = {92256043,antagonists & inhibitors,Antibodies,antibody,antiviral,Cell Survival,Comparative Study,cytology,Dose-Response RelationshipDrug,drug effects,enzymology,expression,HIV,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,LeukocytesMononuclear,microbiology,nosource,PAP,pharmacology,physiology,Plant Proteins,Plants,Pokeweed antiviral protein,protein,Protein Synthesis Inhibitors,Proteins,Recombinant Proteins,ribosome,Ricin,RNA-Directed DNA Polymerase,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,toxin,translation,virus,Virus Replication,Zidovudine} } % == BibTeX quality report for olsonRibosomalInhibitoryProteins1991a: % ? unused Journal abbr (“AIDS Res.Hum.Retroviruses”)

@article{onoRetrotransposonderivedGenePEG102001, title = {A Retrotransposon-Derived Gene, {{PEG10}}, Is a Novel Imprinted Gene Located on Human Chromosome 7q21}, author = {Ono, R. and Kobayashi, S. and Wagatsuma, H. and Aisaka, K. and Kohda, T. and {Kaneko-Ishino}, T. and Ishino, F.}, year = 2001, month = apr, journal = {Genomics}, volume = {73}, number = {2}, pages = {232–237}, doi = {10.1006/geno.2001.6494}, url = {PM:11318613}, abstract = {A novel paternally expressed imprinted gene, PEG10 (Paternally Expressed 10), was identified on human chromosome 7q21. PEG10 is located near the SGCE (Sarcoglycan epsilon) gene, whose mouse homologue was recently shown to be imprinted. Therefore, it is highly possible that a new imprinted gene cluster exists on human chromosome 7q21. Analysis of two predicted open reading frames (ORF1 and ORF2) revealed that ORF1 and ORF2 have homology to the gag and pol proteins of some vertebrate retrotransposons, respectively. These data suggest that PEG10 is derived from a retrotransposon that was previously integrated into the mammalian genome. PEG10 is likely to be essential for understanding how exogenous genes become imprinted}, keywords = {0,Amino Acid Sequence,analysis,Animals,Choriocarcinoma,ChromosomesHumanPair 7,Female,FRAME,Gag,gene,Genes,Genesgag,Genespol,genetics,Genome,Genomic Imprinting,human,Humans,La,Male,Methods,Mice,Molecular Sequence Data,nosource,Nuclear Proteins,OPEN READING FRAME,Open Reading Frames,Physical Chromosome Mapping,pol,PolymorphismGenetic,protein,Proteins,Radiation Hybrid Mapping,READING FRAME,Reading Frames,Research SupportNon-U.S.Gov’t,Retroelements,retrotransposon,Sequence HomologyAmino Acid,Syndrome,transcription,TRANSCRIPTION FACTOR,Transcription Factors} }

@article{onoaRNAFoldingUnfolding2004, title = {{{RNA}} Folding and Unfolding}, author = {Onoa, B. and Tinoco, I.}, year = 2004, month = jun, journal = {Current Opinion in Structural Biology}, volume = {14}, number = {3}, pages = {374–379}, publisher = {Elsevier}, doi = {10.1016/j.sbi.2004.04.001}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0959440X04000685}, abstract = {Single-molecule studies of RNA folding and unfolding are providing impressive details of the intermediates that occur and their rates of interconversion. The folding and unfolding of RNA are controlled by varying the concentration of magnesium ions and measuring fluorescence energy transfer, or by applying force to the RNA and measuring the end-to-end distance. The hierarchical nature of RNA folding - first secondary structure, then tertiary structure - makes the process susceptible to analysis and prediction}, keywords = {analysis,Base Sequence,chemistry,development,Energy Transfer,Fluorescence,INTERMEDIATE,Ions,Kinetics,La,Magnesium,metabolism,Molecular Sequence Data,nosource,Nucleic Acid Conformation,PREDICTION,Review,Rna,RNA folding,SECONDARY STRUCTURE,structure,Thermodynamics} } % == BibTeX quality report for onoaRNAFoldingUnfolding2004: % ? unused Journal abbr (“Curr.Opin.Struct.Biol.”)

@article{oritaRapidSensitiveDetection1989, title = {Rapid and Sensitive Detection of Point Mutations and {{DNA}} Polymorphisms Using the Polymerase Chain Reaction}, author = {Orita, M. and Suzuki, Y. and Sekiya, T. and Hayashi, K.}, year = 1989, month = nov, journal = {Genomics}, volume = {5}, number = {4}, pages = {874–879}, publisher = {Elsevier}, doi = {10.1016/0888-7543(89)90129-8}, url = {http://linkinghub.elsevier.com/retrieve/pii/0888754389901298}, keywords = {activation,Dna,enzyme,Gels,genomic,human,Methods,Mutation,MUTATIONS,nosource,oncogenes,Point Mutation,polymerase,Polymerase Chain Reaction,ras,sequence,techniques} }

@article{orlovaReverseTranscriptaseMoloney2003, title = {Reverse Transcriptase of {{Moloney}} Murine Leukemia Virus Binds to Eukaryotic Release Factor 1 to Modulate Suppression of Translational Termination}, author = {Orlova, M. and Yueh, A. and Leung, J. and Goff, S.P.}, year = 2003, month = oct, journal = {Cell}, volume = {115}, number = {3}, pages = {319–331}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(03)00805-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867403008055}, abstract = {The pol (for polymerase) gene of the murine leukemia viruses (MuLVs) is expressed in the form of a large Gag-Pol precursor protein by the suppression of translational termination, or enhanced readthrough, of a UAG stop codon at the end of gag. A search for cellular proteins that interact with the reverse transcriptase of Moloney MuLV resulted in the identification of eRF1, the eukaryotic translation release factor 1. The proteins bound strongly in vitro, and the overexpression of eRF1 resulted in the RT-dependent incorporation of the protein into assembling virion particles. The overexpression of RT in trans enhanced the translational readthrough of a reporter construct containing the Gag-Pol boundary region. Noninteracting mutants of RT failed to synthesize adequate levels of Gag-Pol and could not replicate. These results suggest that RT enhances suppression of termination and that the interaction of RT with eRF1 is required for an appropriate level of translational readthrough}, keywords = {0,Animals,BindingCompetitive,BIOLOGY,biosynthesis,Cell Line,Cercopithecus aethiops,CHAIN TERMINATION,chemistry,Codon,Cos Cells,Dna,DNA-Directed DNA Polymerase,enzymology,EUKARYOTIC TRANSLATION,FORM,FUSION PROTEIN,Fusion Proteinsgag-pol,Gag,Gag-pol,gene,genetics,IDENTIFICATION,In Vitro,IN-VITRO,La,LEUKEMIA,metabolism,Mice,Moloney murine leukemia virus,MuLV,MUTANTS,Mutation,nosource,OVEREXPRESSION,PARTICLES,Peptide Chain Termination,Peptide Termination Factors,pharmacology,physiology,pol,polymerase,PRECURSOR,PRECURSOR PROTEIN,protein,Protein Binding,Protein StructureTertiary,Proteins,readthrough,REGION,RELEASE,release factor,REVERSE-TRANSCRIPTASE,Ribonuclease HCalf Thymus,Rna,RNA-Directed DNA Polymerase,RNATransfer,search,STOP CODON,Substrate Specificity,supportu.s.gov’tp.h.s.,suppression,termination,toxicity,translation,TRANSLATIONAL READTHROUGH,TRANSLATIONAL TERMINATION,Two-Hybrid System Techniques,Virion,virus,Virus Replication} }

@article{ortizTranslationElongationFactor2006, title = {Translation Elongation Factor 2 Anticodon Mimicry Domain Mutants Affect Fidelity and Diphtheria Toxin Resistance}, author = {Ortiz, P.A. and Ulloque, R. and Kihara, G.K. and Zheng, H. and Kinzy, T.G.}, year = 2006, month = oct, journal = {J. Biol. Chem.}, volume = {281}, number = {43}, pages = {32639–32648}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.M607076200}, url = {http://www.jbc.org/content/281/43/32639.short}, abstract = {Eukaryotic elongation factor 2 (eEF2) mediates translocation in protein synthesis. The molecular mimicry model proposes that the tip of domain IV mimics the anticodon loop of tRNA. His-699 in this region is post-translationally modified to diphthamide, the target for Corynebacterium diphtheriae and Pseudomonas aeruginosa toxins. ADP-ribosylation by these toxins inhibits eEF2 function causing cell death. Mutagenesis of the tip of domain IV was used to assess both functions. A H694A mutant strain was non-functional, whereas D696A, I698A, and H699N strains conferred conditional growth defects, sensitivity to translation inhibitors, and decreased total translation in vivo. These mutant strains and those lacking diphthamide modification enzymes showed increased -1 frameshifting. The effects are not due to reduced protein levels, ribosome binding, or GTP hydrolysis. Functional eEF2 forms substituted in domain IV confer dominant diphtheria toxin resistance, which correlates with an in vivo effect on translation-linked phenotypes. These results provide a new mechanism in which the translational machinery maintains the accurate production of proteins, establishes a role for the diphthamide modification, and provides evidence of the ability to suppress the lethal effect of a toxin targeted to eEF2}, pmid = {16950777}, keywords = {Anticodon,ANTICODON LOOP,Bacterial,Bacterial: genetics,BINDING,Corynebacterium diphtheriae,Diphtheria Toxin,Diphtheria Toxin: pharmacology,DOMAIN,Drug Resistance,elongation,enzyme,Enzymes,eukaryotic elongation factor,Fidelity,FORM,Frameshifting,Genetic,genetics,GROWTH,GTP,Hydrolysis,immunology,IN-VIVO,INHIBITOR,inhibitors,La,LOOP,MECHANISM,microbiology,MODEL,Models,modification,Molecular,Molecular Mimicry,MOLECULAR-GENETICS,Mutagenesis,MUTANTS,Mutation,nosource,Peptide Chain Elongation,Peptide Elongation Factor 2,Peptide Elongation Factor 2: chemistry,Peptide Elongation Factor 2: genetics,Peptide Elongation Factor 2: isolation & purificat,Peptide Elongation Factor 2: metabolism,pharmacology,Phenotype,protein,Protein,Protein Biosynthesis,Protein Structure,protein synthesis,PROTEIN-SYNTHESIS,Proteins,REGION,RESISTANCE,ribosome,RIBOSOME BINDING,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: growth & development,Saccharomyces cerevisiae: metabolism,Sequence Analysis,TARGET,Tertiary,toxin,Transfer,Transfer: metabolism,translation,Translational,translocation,tRNA} } % == BibTeX quality report for ortizTranslationElongationFactor2006: % ? Possibly abbreviated journal title J. Biol. Chem.

@article{osbornDualEffectsRicin1990a, title = {Dual Effects of the Ricin {{A}} Chain on Protein Synthesis in Rabbit Reticulocyte Lysate. {{Inhibition}} of Initiation and Translocation}, author = {Osborn, R.W. and Hartley, M.R.}, year = 1990, month = oct, journal = {European Journal of Biochemistry}, volume = {193}, number = {2}, pages = {401–407}, doi = {10.1111/j.1432-1033.1990.tb19353.x}, abstract = {Ricin A chain caused inhibition of protein synthesis by reticulocyte lysate with concomitant depurination of 28S rRNA. The partial reaction(s) of protein synthesis inhibited was investigated by following the appearance of [35S]methionine from initiator [35S]Met-tRNA into 40S ribosomal subunits, 80S monosomes and polysomes. Ricin A chain caused an accumulation of [35S]Met in monosomes which did not enter polysomes. In these respects the effects of the ricin A chain resembled those of diphtheria toxin, an inhibitor of elongation-factor-2-catalyzed translocation. This is consistent with the previously proposed site of action of ricin as an inhibitor of elongation. However, the inhibitory effects of the ricin A chain and diphtheria toxin are not equivalent because we observed that the rate of formation of the 80S initiation complex was reduced approximately sixfold with the ricin A chain relative to diphtheria toxin. Analysis of methionine-containing peptides bound to 80S monosomes in ricin-A-chain-inhibited and diphtheria-toxin-inhibited lysates, programmed with globin mRNA, revealed a predominance of Met-Val, suggesting that the elongation cycle is inhibited at the translocation step. Translocation was also implicated as the step blocked in both the ricin-A-chain-inhibited and diphtheria-toxin-inhibited lysates, by the finding that nascent peptide chains were unreactive towards puromycin. It is concluded that ricin-A-chain-modified ribosomes are deficient in two protein synthesis partial reactions: the formation of the 80S initiation complex during initiation and the translocation step of the elongation cycle}, keywords = {analysis,COMPLEX,COMPLEXES,Diphtheria Toxin,elongation,Globin,INHIBITION,initiation,lysate,mRNA,nosource,PAP,Peptides,polysomes,protein,protein synthesis,PROTEIN-SYNTHESIS,Puromycin,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Ricin,rRNA,SUBUNIT,toxin,translocation} }

@article{osswaldRibosomalNeighbourhoodCentral1995a, title = {The Ribosomal Neighbourhood of the Central Fold of {{tRNA}}: Cross-Links from Position 47 of {{tRNA}} Located at the {{A}}, {{P}} or {{E}} Site}, author = {Osswald, M. and Doring, T. and Brimacombe, R.}, year = 1995, month = nov, journal = {Nucleic Acids Res.}, volume = {23}, number = {22}, pages = {4635–4641}, doi = {10.1093/nar/23.22.4635}, url = {PM:8524654}, abstract = {The naturally occurring nucleotide 3-(3-amino-3-carboxy-propyl)uridine (acp3U) at position 47 of tRNA(Phe) from Escherichia coli was modified with a diazirine derivative and bound to ribosomes in the presence of suitable mRNA analogues under conditions specific for the ribosomal A, P or E sites. After photo-activation at 350 nm the cross-links to ribosomal proteins and RNA were identified by our standard procedures. In the 30S subunit protein S19 (and weakly S9 and S13) was the target of cross-linking from tRNA at the A site, S7, S9 and S13 from the P site and S7 from the E site. Similarly, in the 50S subunit L16 and L27 were cross-linked from the A site, L1, L5, L16, L27 and L33 from the P site and L1 and L33 from the E site. Corresponding cross-links to rRNA were localized by RNase H digestion to the following areas: in 16S rRNA between positions 687 and 727 from the P and E sites, positions 1318 and 1350 (P site) and 1350 and 1387 (E site); in the 23S rRNA between positions 865 and 910 from the A site, 1845 and 1892 (P site), 1892 and 1945 (A site), 2282 and 2358 (P site), 2242 and 2461 (P and E sites), 2461 and 2488 (A site), 2488 and 2539 (all three sites) and 2572 and 2603 (A and P sites). In most (but not all) cases, more precise localizations of the cross-link sites could be made by primer extension analysis}, keywords = {0,16S,A SITE,A-SITE,analysis,Bacterial,Base Sequence,Binding Sites,chemistry,CROSS-LINKING,Cross-Linking Reagents,CROSSLINKING,E,E site,ElectrophoresisPolyacrylamide Gel,Escherichia coli,ESCHERICHIA-COLI,genetics,isolation & purification,L1,L5,La,LOCALIZATION,metabolism,ModelsStructural,Molecular Sequence Data,mRNA,nosource,Nucleic Acid Conformation,P SITE,P-SITE,P-SITES,POSITION,POSITIONS,primer extension,protein,Proteins,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNABacterial,RNAMessenger,RNARibosomal16S,RNAse,RNATransfer,RNATransferMet,RNATransferPhe,rRNA,SITE,SITES,SUBUNIT,TARGET,tRNA,ultrastructure} } % == BibTeX quality report for osswaldRibosomalNeighbourhoodCentral1995a: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{osswaldEnvironment5SRRNA1999, title = {The Environment of {{5S rRNA}} in the Ribosome: Cross-Links to {{23S rRNA}} from Sites within Helices {{II}} and {{III}} of the {{5S}} Molecule}, author = {Osswald, M. and Brimacombe, R.}, year = 1999, month = jun, journal = {Nucleic acids research}, volume = {27}, number = {11}, pages = {2283–2290}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/27.11.2283}, url = {http://nar.oxfordjournals.org/content/27/11/2283.short}, abstract = {Three contiguous fragments of Escherichia coli 5S rRNA were prepared by T7 transcription from synthetic DNA templates. The central fragment, comprising residues 33-71 of the molecule, was transcribed in the presence of 4-thiouridine triphosphate together with [32P]UTP. The three transcripts were ligated together, yielding a 5S rRNA analogue carrying 4-thiouridine residues at positions 40, 48, 55 and 65 in helices II and III. After ligation, the 4-thiouridine residues were derivatised with p -azidophenacyl bromide. The modified 5S rRNA was reconstituted into 50S subunits and these subunits were used to prepare 70S ribosomes in the presence or absence of tRNA and mRNA. The azidophenyl groups were then photoactivated by mild irradiation at 300 nm and the products of cross-linking analysed by our standard procedures. Multiple cross-links from 5S rRNA to two distinct regions of the 23S rRNA were observed. The first region was located in helix 38 in Domain II of the 23S molecule, with cross-links at sites between nucleotides 885 and 922. The second region covered helices 81-85 in Domain V, with sites between nucleotides 2272 and 2345. Taken together with previous data, these results serve to define the arrangement of the 5S rRNA molecule relative to the 23S rRNA within the 50S subunit}, keywords = {5S rRNA,99263030,Bacteriophage T7,Base Sequence,Binding Sites,chemistry,CROSS-LINKING,Cross-Linking Reagents,Dna,DNA Ligases,DNA-Directed RNA Polymerase,enzymology,Escherichia coli,ESCHERICHIA-COLI,genetics,metabolism,Molecular Sequence Data,mRNA,nosource,Nucleic Acid Conformation,Nucleotides,Ribonuclease HCalf Thymus,ribosome,Ribosomes,RNABacterial,RNARibosomal23S,RNARibosomal5S,rRNA,SUBUNIT,Templates,transcription,tRNA} } % == BibTeX quality report for osswaldEnvironment5SRRNA1999: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{osterhageChromosomeEndMaintenance2009, title = {Chromosome End Maintenance by Telomerase.}, author = {Osterhage, J.L. and Friedman, K.L.}, year = 2009, month = jun, journal = {The Journal of Biological Chemistry}, volume = {284}, number = {24}, pages = {16061–16065}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.R900011200}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2713563&tool=pmcentrez&rendertype=abstract http://www.jbc.org/content/284/24/16061.short}, abstract = {Telomeres, protein-DNA complexes at the ends of eukaryotic linear chromosomes, are essential for genome stability. The accumulation of chromosomal abnormalities in the absence of proper telomere function is implicated in human aging and cancer. Repetitive telomeric sequences are maintained by telomerase, a ribonucleoprotein complex containing a reverse transcriptase subunit, a template RNA, and accessory components. Telomere elongation is regulated at multiple levels, including assembly of the telomerase holoenzyme, recruitment of telomerase to the chromosome terminus, and telomere accessibility. This minireview provides an overview of telomerase structure, function, and regulation and the role of telomerase in human disease.}, pmid = {19286666}, keywords = {Aging,Aging: physiology,Animals,assembly,BIOLOGY,cancer,Chromosomes,Chromosomes: physiology,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,disease,elongation,Genome,human,Humans,La,nosource,RECRUITMENT,regulation,REVERSE-TRANSCRIPTASE,RIBONUCLEOPROTEIN,Rna,sequence,SEQUENCES,stability,structure,SUBUNIT,Telomerase,Telomerase: genetics,Telomerase: metabolism,Telomere,TEMPLATE} } % == BibTeX quality report for osterhageChromosomeEndMaintenance2009: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{otakaYeastRibosomalProteins1983, title = {Yeast Ribosomal Proteins: {{VII}}. {{Cytoplasmic}} Ribosomal Proteins from {{Schizosaccharomyces}} Pombe}, author = {Otaka, E. and Higo, K. and Itoh, T.}, year = 1983, journal = {Molecular and General Genetics MGG}, volume = {191}, number = {3}, pages = {519–524}, publisher = {Springer}, doi = {10.1007/BF00425772}, url = {http://www.springerlink.com/index/KL84M034631R643N.pdf}, abstract = {The cytoplasmic ribosomal proteins from a fission yeast Schizosaccharomyces pombe were analysed by two-dimensional polyacrylamide gel electrophoresis. Seventy-three protein species were identified in the 80S ribosome, and named SP-S1 to SP-S33 and SP-L1 to SP-L40 in the small and large subunits, respectively. Many of these proteins could be correlated to those of Saccharomyces cerevisiae on the basis of their electrophoretic mobilities. Eleven proteins were isolated from the 80S ribosome, and their amino acid compositions were determined. Of these, SP-S6, SP-L1, SP-L12, SP-L15, SP-L17, SP-L27, SP-L36 and SP-L40c and d were sequenced from their amino-termini. SP-S28 and SP-L2 appear to have their amino-termini blocked. These results were compared with the data available for the S. cerevisiae and rat liver ribosomal proteins. The S. cerevisiae counterparts of the eight proteins mentioned above were found to be YS4, YL1, YL10, YL14, YL35, YL40 and YL44c and d, respectively. The rat liver counterparts of SP-S6, SP-L1, SP-L27 and SP-L40c and d were the rat S6, L4, L37 and P2, respectively. Comparison of the partial sequences of these ribosomal proteins suggests that these two yeasts are relatively far apart, phylogenetically}, keywords = {0,ACID,Amino Acid Sequence,AMINO-ACID,analysis,Animals,Ascomycota,CEREVISIAE,Comparative Study,Cytoplasm,D,Electrophoresis,ElectrophoresisPolyacrylamide Gel,Evolution,GEL-ELECTROPHORESIS,isolation & purification,La,Liver,Methods,nosource,POLYACRYLAMIDE-GEL-ELECTROPHORESIS,protein,Proteins,rat,Rats,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Schizosaccharomyces,sequence,SEQUENCES,SUBUNIT,SUBUNITS,Support,yeast,Yeasts} } % == BibTeX quality report for otakaYeastRibosomalProteins1983: % ? unused Journal abbr (“Mol Gen.Genet.”)

@article{ottoChaperonesMPP11Hsp70L12005, title = {The Chaperones {{MPP11}} and {{Hsp70L1}} Form the Mammalian Ribosome-Associated Complex}, author = {Otto, H. and Conz, C. and Maier, P. and Wolfle, T. and Suzuki, C.K. and Jeno, P. and Rucknagel, P. and Stahl, J. and Rospert, S.}, year = 2005, month = jul, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {29}, pages = {10064–10069}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.0504400102}, url = {http://www.pnas.org/content/102/29/10064.short}, abstract = {Soluble Hsp70 homologs cotranslationally interact with nascent polypeptides in all kingdoms of life. In addition, fungi possess a specialized Hsp70 system attached to ribosomes, which in Saccharomyces cerevisiae consists of the Hsp70 homologs Ssb1/2p, Ssz1p, and the Hsp40 homolog zuotin. Ssz1p and zuotin are assembled into a unique heterodimeric complex termed ribosome-associated complex. So far, no such specialized chaperones have been identified on ribosomes of higher eukaryotes. However, a family of proteins characterized by an N-terminal zuotin-homology domain fused to a C-terminal two-repeat Myb domain is present in animals and plants. Members of this family, like human MPP11 and mouse MIDA1, have been implicated in the regulation of cell growth. Specific targets of MPP11/MIDA1, however, have remained elusive. Here, we report that MPP11 is localized to the cytosol and associates with ribosomes. Purification of MPP11 revealed that it forms a stable complex with Hsp70L1, a distantly related homolog of Ssz1p. Complementation experiments indicate that mammalian ribosome-associated complex is functional in yeast. We conclude that despite a low degree of homology on the amino acid level cooperation of ribosome-associated chaperones with the translational apparatus is well conserved in eukaryotic cells}, keywords = {ACID,AMINO-ACID,animal,Animals,BLUE NATIVE ELECTROPHORESIS,CELLS,CEREVISIAE,chaperone,COMPLEX,COMPLEXES,Cytosol,DNA-BINDING-PROTEIN,DOMAIN,Eukaryotic Cells,FAMILY,FORM,Fungi,GROWTH,homolog,human,IN-VIVO,LEUKEMIA-ASSOCIATED ANTIGENS,MEMBRANE-PROTEIN COMPLEXES,Molecular Chaperones,myb domain,MYELOID-LEUKEMIA,NASCENT CHAIN,NatA,nosource,Plants,POLYACRYLAMIDE-GEL-ELECTROPHORESIS,POLYPEPTIDE,POLYPEPTIDES,protein,Protein Folding,Proteins,purification,regulation,ribosome,Ribosomes,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SYSTEM,TARGET,translation,yeast} }

@article{ouCloningCharacterizationHuman1987, title = {Cloning and Characterization of a Human Ribosomal Protein Gene with Enhanced Expression in Fetal and Neoplastic Cells.}, author = {Ou, J.H. and Yen, T.S. and Kam, W.K. and Rutter, W.J.}, year = 1987, journal = {Nucleic Acids Res.}, volume = {15}, pages = {8919–8934}, doi = {10.1093/nar/15.21.8919}, abstract = {Hepatocellular carcinoma is strongly associated with hepatitis B virus carrier patients who usually have HBV sequences integrated in the chromosomal DNA of liver cells. To assess the possible effects of HBV regulatory sequences (e.g., the enhancer) on expression of neighboring host genes we have screened for cellular genes that are both overexpressed and adjacent to integrated HBV sequences in hepatocellular carcinoma cells. The cloned cDNA for one such gene encodes a protein similar to the E. coli L-3 ribosomal protein which is thought to play a role in mRNA binding to the ribosome. The protein encoded by the cDNA localizes to the nucleolus and is also found in ribosomes; possibly it is the mammalian homologue of L-3 (MRL3). The expression of MRL3 is higher in colon carcinoma and lymphoma cell lines than in normal liver, placenta and diploid fibroblasts, and is also higher in fetal than in adult liver. Therefore, MRL3 overexpression seems to be a property of rapidly dividing cells and is not directly linked to oncogenesis}, keywords = {Adult,BINDING,cancer,Cell Line,cell lines,CELLS,cloning,Dna,E,ENCODES,expression,gene,Genes,homolog,human,L3,LINE,Liver,mof1,mRNA,mrpl9,nosource,nucleolus,OVEREXPRESSION,protein,ribosome,Ribosomes,sequence,SEQUENCES,virus} } % == BibTeX quality report for ouCloningCharacterizationHuman1987: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{ozakiIsolationThreeTestisspecific1996, title = {Isolation of Three Testis-Specific Genes ({{TSA303}}, {{TSA806}}, {{TSA903}}) by a Differential {{mRNA}} Display Method}, author = {Ozaki, K. and Kuroki, T. and Hayashi, S. and Nakamura, Y.}, year = 1996, month = sep, journal = {Genomics}, volume = {36}, number = {2}, pages = {316–319}, doi = {10.1006/geno.1996.0467}, keywords = {Amino Acids,analysis,assembly,Caenorhabditis,Caenorhabditis elegans,cell cycle,COMPLEX,COMPLEXES,differential display,Drosophila,gene,Genes,human,kinase,Methods,mRNA,nosource,Nucleotides,Open Reading Frames,protein,Proteins,SUBUNIT,Uridine,yeast} }

@article{pageMutationalAnalysisExoribonuclease1998, title = {Mutational Analysis of Exoribonuclease {{I}} from {{Saccharomyces}} Cerevisiae}, author = {Page, A.M. and Davis, K. and Molineux, C. and Kolodner, R.D. and Johnson, A.W.}, year = 1998, journal = {Nucleic acids research}, volume = {26}, number = {16}, pages = {3707–3716}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/26.16.3707}, url = {http://nar.oxfordjournals.org/content/26/16/3707.short}, abstract = {Exoribonuclease I from yeast is a 175 kDa protein that is responsible for the majority of cytoplasmic mRNA degradation. Alignment of the Xrn1p sequence with homologs from yeast as well as from higher eukaryotes suggests that the protein is composed of several domains: two acidic N-terminal domains which likely contain the exonuclease, a basic middle domainand a basic C-terminal domain. Deletion analysisdemonstrated that the C-terminus is dispensable for most in vivo and in vitro functions but confers a dominant negative growth inhibition when expressed at high levels. This growth inhibition is not due to the exonuclease function of the protein. To identify specific residues responsible for in vivo function, a screen was carried out for non-complementing missense mutations. Fourteen single point mutations were identified that altered highly conserved amino acids within the first N-terminal domain of Xrn1p. All of the mutations reduced exonuclease activity measured in vivo and in vitro using affinity-purified proteins. The mutants fell into two phenotypic classes, those that reduced or abolished exonuclease activity without qualitatively changing the products of RNA degradation and those that gave rise to novel degradation intermediates on certain RNAs}, keywords = {ACID,ACIDS,alignment,Amino Acid Sequence,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,animal,Base Sequence,Binding Sites,BIOLOGY,C-TERMINUS,CEREVISIAE,chemistry,Conserved Sequence,degradation,DNA Mutational Analysis,DNAFungal,DOMAIN,DOMAINS,enzymology,Exoribonucleases,GenesFungal,Genetic Complementation Test,genetics,GROWTH,homolog,IDENTIFY,In Vitro,IN-VITRO,IN-VIVO,INHIBITION,INTERMEDIATE,M,metabolism,Mice,microbiology,Molecular Sequence Data,mRNA,MUTANTS,Mutation,MUTATIONAL ANALYSIS,MUTATIONS,nosource,Oligonucleotide Probes,Phenotype,Plasmids,Point Mutation,PRODUCT,PRODUCTS,protein,Proteins,RESIDUES,Rna,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence HomologyAmino Acid,supportu.s.gov’tp.h.s.,yeast} } % == BibTeX quality report for pageMutationalAnalysisExoribonuclease1998: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{pageSMG2PhosphorylatedProtein1999, title = {{{SMG-2}} Is a Phosphorylated Protein Required for {{mRNA}} Surveillance in {{Caenorhabditis}} Elegans and Related to {{Upf1p}} of Yeast}, author = {Page, M.F. and Carr, B. and Anders, K.R. and Grimson, A. and Anderson, P.}, year = 1999, journal = {Molecular and cellular biology}, volume = {19}, number = {9}, pages = {5943–5951}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.19.9.5943}, url = {http://mcb.asm.org/cgi/content/abstract/19/9/5943}, abstract = {mRNAs that contain premature stop codons are selectively degraded in all eukaryotes tested, a phenomenon termed “nonsense-mediated mRNA decay” (NMD) or “mRNA surveillance.” NMD may function to eliminate aberrant mRNAs so that they are not translated, because such mRNAs might encode deleterious polypeptide fragments. In both yeasts and nematodes, NMD is a nonessential system. Mutations affecting three yeast UPF genes or seven nematode smg genes eliminate NMD. We report here the molecular analysis of smg-2 of Caenorhabditis elegans. smg-2 is homologous to UPF1 of yeast and to RENT1 (also called HUPF1), a human gene likely involved in NMD. The striking conservation of SMG-2, Upf1p, and RENT1/HUPF1 in both sequence and function suggests that NMD is an ancient system, predating the divergence of most eukaryotes. Despite similarities in the sequences of SMG-2 and Upf1p, expression of Upf1p in C. elegans does not rescue smg-2 mutants. We have prepared anti-SMG-2 polyclonal antibodies and identified SMG-2 on Western blots. SMG-2 is phosphorylated, and mutations of the six other smg genes influence the state of SMG-2 phosphorylation. In smg-1, smg-3, and smg-4 mutants, phosphorylation of SMG-2 was not detected. In smg-5, smg-6, and smg-7 mutants, a phosphorylated isoform of SMG-2 accumulated to abnormally high levels. In smg-2(r866) and smg-2(r895) mutants, which harbor single amino acid substitutions of the SMG-2 nucleotide binding site, phosphorylated SMG-2 accumulated to abnormally high levels, similar to those observed in smg-5, smg-6, and smg-7 mutants. We discuss these results with regard to the in vivo functions of SMG-2 and NMD}, keywords = {99384262,Alleles,Amino Acid Sequence,Amino Acid Substitution,analysis,animal,Antibodies,antibody,BINDING,Binding Sites,Caenorhabditis,Caenorhabditis elegans,Codon,CodonTerminator,enzymology,expression,gene,Gene Expression,Genes,GenesHelminth,Genetic,genetics,Helminth Proteins,human,IN-VIVO,metabolism,Molecular Sequence Data,mRNA,Mutation,MUTATIONS,NMD,nosource,Phosphoproteins,Phosphorylation,protein,RNA Helicases,RNAHelminth,RNAMessenger,Saccharomyces cerevisiae,sequence,Sequence HomologyAmino Acid,STOP CODON,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,TransformationGenetic,UPF,Upf1,yeast,Yeasts} } % == BibTeX quality report for pageSMG2PhosphorylatedProtein1999: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{pageTreeViewApplicationDisplay1996, title = {{{TreeView}}: An Application to Display Phylogenetic Trees on Personal Computers}, author = {Page, R.D.}, year = 1996, journal = {Comput.Appl.Biosci.}, volume = {12}, number = {4}, pages = {357–358}, publisher = {Citeseer}, url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.41.5743}, keywords = {BIOLOGY,computer,Computer Graphics,La,Microcomputers,No DOI found,nosource,Phylogeny,Software} } % == BibTeX quality report for pageTreeViewApplicationDisplay1996: % ? Possibly abbreviated journal title Comput.Appl.Biosci.

@article{paladeLiverMicrosomesIntegrated1956a, title = {Liver Microsomes; an Integrated Morphological and Biochemical Study}, author = {PALADE, G.E. and SIEKEVITZ, P.}, year = 1956, month = mar, journal = {J. Biophys. Biochem. Cyt.}, volume = {2}, number = {2}, pages = {171–200}, doi = {10.1083/jcb.2.2.171}, url = {PM:13319380}, keywords = {anatomy & histology,La,Liver,nosource} } % == BibTeX quality report for paladeLiverMicrosomesIntegrated1956a: % ? Possibly abbreviated journal title J. Biophys. Biochem. Cyt. % ? unused Journal abbr (“J.Biophys.Biochem.Cytol.”)

@article{palanimuruganPolyaminesRegulateTheir2004, title = {Polyamines Regulate Their Synthesis by Inducing Expression and Blocking Degradation of {{ODC}} Antizyme}, author = {Palanimurugan, R. and Scheel, H. and Hofmann, K. and Dohmen, R.J.}, year = 2004, month = dec, journal = {The EMBO Journal}, volume = {23}, number = {24}, pages = {4857–4867}, publisher = {Nature Publishing Group}, doi = {10.1038/sj.emboj.7600473}, url = {http://www.nature.com/emboj/journal/v23/n24/abs/7600473a.html}, abstract = {Polyamines are essential organic cations with multiple cellular functions. Their synthesis is controlled by a feedback regulation whose main target is ornithine decarboxylase (ODC), the rate-limiting enzyme in polyamine biosynthesis. In mammals, ODC has been shown to be inhibited and targeted for ubiquitin-independent degradation by ODC antizyme (AZ). The synthesis of mammalian AZ was reported to involve a polyamine-induced ribosomal frameshifting mechanism. High levels of polyamine therefore inhibit new synthesis of polyamines by inducing ODC degradation. We identified a previously unrecognized sequence in the genome of Saccharomyces cerevisiae encoding an orthologue of mammalian AZ. We show that synthesis of yeast AZ (Oaz1) involves polyamine-regulated frameshifting as well. Degradation of yeast ODC by the proteasome depends on Oaz1. Using this novel model system for polyamine regulation, we discovered another level of its control. Oaz1 itself is subject to ubiquitin-mediated proteolysis by the proteasome. Degradation of Oaz1, however, is inhibited by polyamines. We propose a model, in which polyamines inhibit their ODC-mediated biosynthesis by two mechanisms, the control of Oaz1 synthesis and inhibition of its degradation}, keywords = {0,Amino Acid Sequence,Animals,antizyme,Base Sequence,biosynthesis,Cations,CEREVISIAE,COMPLEX,COMPLEXES,degradation,enzyme,expression,Feedback,Frameshifting,FrameshiftingRibosomal,Genetic,genetics,Genome,Humans,INHIBITION,La,Mammals,MECHANISM,MECHANISMS,metabolism,MODEL,Molecular Sequence Data,nosource,Ornithine Decarboxylase,ORNITHINE DECARBOXYLASE ANTIZYME,polyamine,Polyamines,Proteasome Endopeptidase Complex,protein,Proteins,PROTEOLYSIS,regulation,Research SupportNon-U.S.Gov’t,ribosomal frameshifting,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,Sequence Alignment,Sequence HomologyNucleic Acid,Spermidine,SYSTEM,TARGET,Ubiquitin,yeast} } % == BibTeX quality report for palanimuruganPolyaminesRegulateTheir2004: % ? unused Journal abbr (“EMBO J.”)

@article{palmerPhenotypicSuppressionNonsense1979, title = {Phenotypic Suppression of Nonsense Mutants in Yeast by Aminoglycoside Antibiotics.}, author = {Palmer, E. and Wilhelm, J. and Sherman, F.}, year = 1979, journal = {Nature}, volume = {277}, pages = {148–150}, publisher = {Nature Publishing Group}, doi = {10.1038/277148a0}, url = {http://www.nature.com/nature/journal/v277/n5692/abs/277148a0.html}, keywords = {antibiotic,antibiotics,nosource,Paromomycin,suppression,translation,yeast} }

@article{panQuantitativeMicroarrayProfiling2006, title = {Quantitative Microarray Profiling Provides Evidence against Widespread Coupling of Alternative Splicing with Nonsense-Mediated {{mRNA}} Decay to Control Gene Expression.}, author = {Pan, Q. and Saltzman, A.L. and Kim, Y.K. and Misquitta, C. and Shai, O. and Maquat, L.E. and Frey, B.J. and Blencowe, B.J.}, year = 2006, month = jan, journal = {Genes & development}, volume = {20}, number = {2}, pages = {153–158}, publisher = {Cold Spring Harbor Lab}, issn = {0890-9369}, doi = {10.1101/gad.1382806}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1356107&tool=pmcentrez&rendertype=abstract http://genesdev.cshlp.org/content/20/2/153.short}, abstract = {Sequence-based analyses have predicted that approximately 35% of mammalian alternative splicing (AS) events produce premature termination codon (PTC)-containing splice variants that are targeted by the process of nonsense-mediated mRNA decay (NMD). This led to speculation that AS may often regulate gene expression by activating NMD. Using AS microarrays, we show that PTC-containing splice variants are generally produced at uniformly low levels across diverse mammalian cells and tissues, independently of the action of NMD. Our results suggest that most PTC-introducing AS events are not under positive selection pressure and therefore may not contribute important functional roles.}, pmid = {16418482}, keywords = {0,Alternative Splicing,Animals,CELLS,CEREVISIAE,Codon,CodonNonsense,Computational Biology,DECAY,expression,gene,Gene Expression,Gene Expression Regulation,GENE-EXPRESSION,genetics,Hela Cells,Helicase,Humans,La,MAMMALIAN-CELLS,Messenger,Messenger: genetics,Messenger: metabolism,metabolism,Mice,mRNA,mRNA decay,NMD,Nonsense,NONSENSE,nonsense-mediated mRNA decay,Nonsense: genetics,Nonsense: metabolism,nosource,Oligonucleotide Array Sequence Analysis,Open Reading Frames,PREMATURE TERMINATION CODON,protein,Proteins,Research SupportN.I.H.Extramural,Research SupportNon-U.S.Gov’t,Rna,RNA,RNA HELICASE,RNA Helicases,RNA Helicases: metabolism,RNA Stability,RNAMessenger,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SELECTION,splicing,termination,TERMINATION CODON,TERMINATION-CODON,Trans-Activators,Transfection} } % == BibTeX quality report for panQuantitativeMicroarrayProfiling2006: % ? unused Journal abbr (“Genes Dev.”)

@article{pandePullingRibosomeOut1995a, title = {Pulling the {{Ribosome Out}} of {{Frame}} by +1 at {{A Programmed Frameshift Site}} by {{Cognate Binding}} of {{Aminoacyl-Transfer-Rna}}}, author = {Pande, S. and Vimaladithan, A. and Zhao, H. and Farabaugh, P.J.}, year = 1995, month = jan, journal = {Molecular and Cellular Biology}, volume = {15}, number = {1}, pages = {298–304}, doi = {10.1128/MCB.15.1.298}, url = {ISI:A1995PX95300034}, abstract = {Programmed translational frameshifts efficiently alter a translational reading frame by shifting the reading frame during translation. A +1 frameshift has two simultaneous requirements: a translational pause which occurs when either an inefficiently recognized sense or termination codon occupies the A site, and the presence of a special peptidyl-tRNA occupying the P site during the pause. The special nature of the peptidyl-tRNA reflects its ability either to slip +1 on the mRNA or to facilitate binding of an incoming aminoacyl-tRNA out of frame in the A site. This second mechanism suggested that in some cases the first +1. frame tRNA could have an active role in frameshifting. We found that overproducing this tRNA can drive frameshifting, surprisingly regardless of whether frameshifting occurs by peptidyl-tRNA slippage or out-of-frame binding of aminoacyl-tRNA. This finding suggests that in both cases, the shift in reading frame occurs coincident with formation of a cognate codon-anticodon interaction in the shifted frame}, keywords = {A SITE,A-SITE,AMINOACYL-TRANSFER-RNA,BINDING,Codon,CODON-ANTICODON INTERACTION,CODONS,ESCHERICHIA-COLI,FRAME,frameshift,Frameshifting,gene,MECHANISM,mRNA,nosource,P SITE,P-SITE,PROTEIN-SYNTHESIS,ribosome,SELECTION,SIGNAL,SITE,SLIPPAGE,termination,TERMINATION CODON,TRANSFER-RNA,TRANSFORMATION,translation,TRANSLATIONAL TERMINATION,tRNA,yeast} } % == BibTeX quality report for pandePullingRibosomeOut1995a: % ? Title looks like it was stored in title-case in Zotero

@article{papeCompleteKineticMechanism1998, title = {Complete Kinetic Mechanism of Elongation Factor {{Tu-dependent}} Binding of Aminoacyl-{{tRNA}} to the {{A}} Site of the {{E}}. Coli Ribosome}, author = {Pape, T. and Wintermeyer, W. and Rodnina, M.V.}, year = 1998, month = dec, journal = {EMBO J.}, volume = {17}, number = {24}, pages = {7490–7497}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/17.24.7490}, url = {http://www.nature.com/emboj/journal/v17/n24/abs/7591434a.html}, abstract = {The kinetic mechanism of elongation factor Tu (EF-Tu)-dependent binding of Phe-tRNAPhe to the A site of poly(U)-programmed Escherichia coli ribosomes has been established by pre-steady-state kinetic experiments. Six steps were distinguished kinetically, and their elemental rate constants were determined either by global fitting, or directly by dissociation experiments. Initial binding to the ribosome of the ternary complex EF-Tu.GTP.Phe-tRNAPhe is rapid (k1 = 110 and 60/micromM/s at 10 and 5 mM Mg2+, 20 degreesC) and readily reversible (k-1 = 25 and 30/s). Subsequent codon recognition (k2 = 100 and 80/s) stabilizes the complex in an Mg2+-dependent manner (k-2 = 0.2 and 2/s). It induces the GTPase conformation of EF-Tu (k3 = 500 and 55/s), instantaneously followed by GTP hydrolysis. Subsequent steps are independent of Mg2+. The EF-Tu conformation switches from the GTP- to the GDP-bound form (k4 = 60/s), and Phe-tRNAPhe is released from EF-Tu.GDP. The accommodation of Phe-tRNAPhe in the A site (k5 = 8/s) takes place independently of EF-Tu and is followed instantaneously by peptide bond formation. The slowest step is dissociation of EF-Tu.GDP from the ribosome (k6 = 4/s). A characteristic feature of the mechanism is the existence of two conformational rearrangements which limit the rates of the subsequent chemical steps of A-site binding}, keywords = {0,A SITE,A-SITE,BINDING,BIOLOGY,BOND FORMATION,chemistry,Codon,CODON RECOGNITION,COMPLEX,COMPLEXES,Computer Simulation,CONFORMATION,E,EFTu,elongation,ELONGATION-FACTOR-TU,Escherichia coli,Escherichia coli ribosomes,ESCHERICHIA-COLI,FACTOR TU,FORM,GTP,GTPase,Guanosine,Guanosine Triphosphate,Hydrolysis,Kinetics,La,MECHANISM,metabolism,ModelsChemical,nosource,Nucleic Acid Conformation,peptide bond formation,Peptide Chain Elongation,Peptide Elongation Factor Tu,Phenylalanine,Poly U,Protein Conformation,RECOGNITION,ribosome,Ribosomes,Rna,RNATransferAmino Acyl,SITE,supportnon-u.s.gov’t,tRNA} } % == BibTeX quality report for papeCompleteKineticMechanism1998: % ? Possibly abbreviated journal title EMBO J.

@article{papeInducedFitInitial1999, title = {Induced Fit in Initial Selection and Proofreading of Aminoacyl-{{tRNA}} on the Ribosome}, author = {Pape, T. and Wintermeyer, W. and Rodnina, M.}, year = 1999, month = jul, journal = {EMBO J.}, volume = {18}, number = {13}, pages = {3800–3807}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/18.13.3800}, url = {http://www.nature.com/emboj/journal/v18/n13/abs/7591796a.html}, abstract = {The fidelity of aminoacyl-tRNA (aa-tRNA) selection by the bacterial ribosome is determined by initial selection before and proofreading after GTP hydrolysis by elongation factor Tu. Here we report the rate constants of A-site binding of a near-cognate aa-tRNA. The comparison with the data for cognate aa-tRNA reveals an additional, important contribution to aa-tRNA discrimination of conformational coupling by induced fit. It is found that two rearrangement steps that limit the chemical reactions of A-site binding, i.e. GTPase activation (preceding GTP hydrolysis) and A-site accommodation (preceding peptide bond formation), are substantially faster for cognate than for near-cognate aa-tRNA. This suggests an induced-fit mechanism of aa-tRNA discrimination on the ribosome that operates in both initial selection and proofreading. It is proposed that the cognate codon-anticodon interaction, more efficiently than the near-cognate one, induces a particular conformation of the decoding center of 16S rRNA, which in turn promotes GTPase activation and A-site accommodation of aa-tRNA, thereby accelerating the chemical steps. As kinetically favored incorporation of the correct substrate has also been suggested for DNA and RNA polymerases, the present findings indicate that induced fit may contribute to the fidelity of template-programed systems in general}, keywords = {99321767,A-SITE,activation,Anticodon,Bacterial,BINDING,Binding Sites,chemistry,Codon,Comparative Study,decoding,Dna,drug effects,elongation,Enzyme Activation,enzymology,Escherichia coli,Fidelity,Fluorescence,genetics,GTP,GTP Phosphohydrolase,GTPase,Guanosine Triphosphate,Hydrolysis,Kinetics,Magnesium,MECHANISM,metabolism,ModelsGenetic,nosource,Peptide Elongation Factor Tu,pharmacology,polymerase,proofreading,Protein Conformation,ribosome,Ribosomes,Rna,RNATransferLeu,RNATransferPhe,rRNA,supportnon-u.s.gov’t,SYSTEM,Templates,TranslationGenetic} } % == BibTeX quality report for papeInducedFitInitial1999: % ? Possibly abbreviated journal title EMBO J.

@article{pappenheimerDiphtheriaToxin1977a, title = {Diphtheria Toxin}, author = {Pappenheimer, A.M.}, year = 1977, journal = {Annual Review of Biochemistry}, volume = {46:69-94}, pages = {69–94}, doi = {10.1146/annurev.bi.46.070177.000441}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.bi.46.070177.000441}, keywords = {77265411,Adenosine Diphosphate Sugars,Amino Acid Sequence,Bacteriophages,Binding Sites,ChromosomesBacterial,Corynebacterium diphtheriae,Diphtheria Toxin,Endocytosis,Genes,Hela Cells,Hydrogen-Ion Concentration,Kinetics,Lysogeny,metabolism,Molecular Weight,Mutation,NAD+ Nucleosidase,nosource,Operon,Peptide Chain Elongation,Peptide Elongation Factors,physiology,ReceptorsDrug,Review,Ribose,Species Specificity,toxin} } % == BibTeX quality report for pappenheimerDiphtheriaToxin1977a: % ? unused Journal abbr (“Annu.Rev.Biochem.”)

@article{parentVectorSystemsExpression1985a, title = {Vector Systems for the Expression, Analysis and Cloning of {{DNA}} Sequences in {{S}}. Cerevisiae}, author = {Parent, S.A. and Fenimore, C.M. and Bostian, K.A.}, year = 1985, month = dec, journal = {Yeast}, volume = {1}, number = {2}, pages = {83–138}, doi = {10.1002/yea.320010202}, url = {PM:3916863}, keywords = {0,analysis,CEREVISIAE,cloning,CloningMolecular,Dna,DNA sequence,DNAFungal,expression,Gene Expression Regulation,Genetic,Genetic Vectors,genetics,La,nosource,Review,S,Saccharomyces cerevisiae,sequence,SEQUENCES,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,SYSTEMS,vector,vectors} }

@article{parikhPokeweedAntiviralProtein2002a, title = {Pokeweed Antiviral Protein Regulates the Stability of Its Own {{mRNA}} by a Mechanism That Requires Depurination but Can Be Separated from Depurination of the Alpha-Sarcin/Ricin Loop of {{rRNA}}}, author = {Parikh, B.A. and Coetzer, C. and Tumer, N.E.}, year = 2002, month = nov, journal = {Journal of Biological Chemistry}, volume = {277}, number = {44}, pages = {41428–41437}, doi = {10.1074/jbc.M205463200}, url = {ISI:000178985300019}, abstract = {Pokeweed antiviral protein (PAP), a single chain ribosome-inactivating protein (RIP) isolated from pokeweed plants (Phytolacca americana), removes specific adenine and guanine residues from the highly conserved, alpha-sarcin/ ricin loop in the large rRNA, resulting in inhibition of protein synthesis. We recently demonstrated that PAP could also inhibit translation of mRNAs and viral RNAs that are capped by binding to the cap structure and depurinating the RNAs downstream of the cap. Cell growth is inhibited when PAP cDNA is expressed in the yeast Saccharomyces cerevisiae under the control of the galactose-inducible GAL1 promoter. Here, we show that overexpression of wild type PAP in yeast leads to a decrease in PAP mRNA abundance. The decrease in mRNA levels is not observed with an active site mutant, indicating that it is due to the N-glycosidase activity of the protein. PAP expression had no effect on steady state levels of mRNA from four different endogenous yeast genes examined, indicating specificity. We demonstrate that PAP can depurinate the rRNA in trans in a translation-independent manner. When rRNA is depurinated and translation is inhibited, the steady state levels of PAP mRNA increase dramatically relative to the U3 snoRNA. Using a PAP variant which depurinates rRNA, inhibits translation but does not destabilize its mRNA, we demonstrate that PAP mRNA is destabilized after its levels are up-regulated by a mechanism that occurs independently of rRNA depurination and translation. We quantify the extent of rRNA depurination in vivo using a novel primer extension assay and show that the temporal pattern of rRNA depurination is similar to the pattern of PAP mRNA destabilization, suggesting that they may occur by a common mechanism. These results provide the first in vivo evidence that a single chain RIP targets not only the large rRNA but also its own mRNA. These findings have implications for understanding the biological function of RIPs}, keywords = {Adenine,antiviral,BINDING,Cap,CAP STRUCTURE,CEREVISIAE,E,expression,gene,Genes,GLYCOSIDASE ACTIVITY,GROWTH,Guanine,IN-VIVO,INFECTION,INHIBITION,LOOP,MECHANISM,mRNA,N-GLYCOSIDASE ACTIVITY,nosource,PAP,PHYTOLACCA-AMERICANA,Plants,Pokeweed antiviral protein,primer extension,PROMOTER,protein,protein synthesis,PROTEIN-SYNTHESIS,REQUIRES,RESIDUES,RETROTRANSPOSITION,RIBOSOME-INACTIVATING PROTEINS,Ricin,RICIN-A-CHAIN,Rna,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SITE,stability,structure,TARGET,TERMINAL DELETION MUTANT,translation,yeast} }

@article{parkSecondDoublestrandedRNA1996, title = {A Second Double-Stranded {{RNA}} Virus from Yeast.}, author = {Park, C.-M. and Lopinski, J.D. and Masuda, J. and Tzeng, T.-H. and Bruenn, J.A.}, year = 1996, journal = {Virology}, volume = {216}, pages = {451–454}, doi = {10.1006/viro.1996.0083}, keywords = {DOUBLE-STRANDED-RNA,L-BC,nosource,Rna,sequence,virus,yeast} }

@article{parkOverexpressionGagpolPrecursor1991a, title = {Overexpression of the ⬚gag-Pol⬚ Precursor from Human Immunodeficiency Virus Type-{{I}} Proviral Genomes Results in Efficient Proteolytic Processing in the Absence of Virion Production.}, author = {Park, J. and Morrow, C.D.}, year = 1991, journal = {J.Virol.}, volume = {65}, pages = {5111–5117}, doi = {10.1128/jvi.65.9.5111-5117.1991}, keywords = {Frameshifting,Gag,Gag-pol,Gag/Gag-pol ratio,Genome,HIV,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,nosource,Virion,virus} } % == BibTeX quality report for parkOverexpressionGagpolPrecursor1991a: % ? Possibly abbreviated journal title J.Virol.

@article{parkPhosphorylationRibosomalProtein1999a, title = {Phosphorylation of Ribosomal Protein {{L5}} by Protein Kinase {{CKII}} Decreases Its {{5S rRNA}} Binding Activity}, author = {Park, J.W. and Bae, Y.S.}, year = 1999, journal = {Biochem.Biophys.Res.Commun.}, volume = {263}, number = {2}, pages = {475–481}, doi = {10.1006/bbrc.1999.1345}, abstract = {We have recently reported that ribosomal protein L5 associates with the beta subunit of protein kinase CKII (CKII) (Kim, J.-M., Cha, J. -Y., Marshak, D. R., and Bae, Y.-S. (1996) Biochem. Biophys. Res. Commun. 226, 180-186). In this study, we demonstrate that CKII is able to catalyze the phosphorylation of the human L5 protein in vitro, which results in a decrease in 5S rRNA binding activity. Phosphoamino acid analysis indicated that the phosphorylation occurs on serine residues. Sequence analysis of cyanogen bromide-digested phosphopeptides and analysis of L5 deletion mutants indicates that the main phosphorylated residues are located within two fragments corresponding of residues 142- 200 and residues 272-297 of the human L5. Based on our present results, we suggest that the phosphorylation of L5 by CKII is one of the mechanisms that regulates nucleolar targeting of 5S rRNA and/or ribosome assembly in the cell. Copyright 1999 Academic Press}, keywords = {5S rRNA,99423489,Amino Acid Sequence,analysis,assembly,BINDING,Cell Nucleolus,CloningMolecular,Escherichia coli,genetics,human,In Vitro,IN-VITRO,isolation & purification,kinase,L5,L5/L1,MECHANISM,MECHANISMS,metabolism,Molecular Sequence Data,nosource,Peptide Mapping,Phosphoproteins,Phosphorylation,Phosphoserine,protein,Protein Binding,Protein-Serine-Threonine Kinases,Recombinant Proteins,Ribosomal Proteins,ribosome,Ribosomes,RNARibosomal5S,rRNA,sequence,Sequence Analysis,Serine,SUBUNIT,supportnon-u.s.gov’t} } % == BibTeX quality report for parkPhosphorylationRibosomalProtein1999a: % ? Possibly abbreviated journal title Biochem.Biophys.Res.Commun.

@article{parkerEnzymesControlEukaryotic2004, title = {The Enzymes and Control of Eukaryotic {{mRNA}} Turnover}, author = {Parker, R. and Song, H.}, year = 2004, month = feb, journal = {Nature Structural & Molecular Biology}, volume = {11}, number = {2}, pages = {121–127}, publisher = {Nature Publishing Group}, doi = {doi:10.1038/nsmb724}, url = {http://web.biosci.utexas.edu/395j/395J 2010/Readings/Lecture 24/Parker turnover review.pdf http://www.nature.com/nsmb/journal/v11/n2/abs/nsmb724.html http://web.biosci.utexas.edu/395j/395J 2010/Readings/Lecture 24/Parker turnover review.pdf}, abstract = {The degradation of eukaryotic mRNAs plays important roles in the modulation of gene expression, quality control of mRNA biogenesis and antiviral defenses. In the past five years, many of the enzymes involved in this process have been identified and mechanisms that modulate their activities have begun to be identified. In this review, we describe the enzymes of mRNA degradation and their properties. We highlight that there are a variety of enzymes with different specificities, suggesting that individual nucleases act on distinct subpopulations of transcripts within the cell. In several cases, translation factors that bind mRNA inhibit these nucleases. In addition, recent work has begun to identify distinct mRNP complexes that recruit the nucleases to transcripts through different mRNA-interacting proteins. These properties and complexes suggest multiple mechanisms by which mRNA degradation could be regulated}, keywords = {0,Adenosine,Adenosine Monophosphate,antiviral,BIOLOGY,COMPLEX,COMPLEXES,degradation,E,enzyme,Enzymes,Exonucleases,expression,gene,Gene Expression,GENE-EXPRESSION,IDENTIFY,La,MECHANISM,MECHANISMS,metabolism,mRNA,mRNA turnover,nosource,Polyribonucleotide Nucleotidyltransferase,protein,Proteins,Quality Control,QUALITY-CONTROL,Review,Rna,RNA-Messenger,RNAMessenger,SPECIFICITY,TRANSCRIPT,translation,turnover} } % == BibTeX quality report for parkerEnzymesControlEukaryotic2004: % ? unused Journal abbr (“Nat.Struct.Mol.Biol.”)

@article{parkinHumanImmunodeficiencyVirus1992, title = {Human Immunodeficiency Virus Type 1 Gag-Pol Frameshifting Is Dependent on Downstream {{mRNA}} Secondary Structure: Demonstration by Expression in Vivo.}, author = {Parkin, N.T. and Chamorro, M. and Varmus, H.E.}, year = 1992, month = aug, journal = {Journal of Virology}, volume = {66}, number = {8}, pages = {5147–5151}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.66.8.5147-5151.1992}, url = {http://jvi.asm.org/cgi/content/abstract/66/8/5147}, keywords = {expression,Frameshifting,Gag-pol,HIV,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,immunology,In Vitro,IN-VITRO,IN-VIVO,microbiology,mRNA,nosource,ribosomal frameshifting,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,structure,SYSTEM,virus} }

@article{parthasarathiGeneticRearrangementsOccurring1995a, title = {Genetic Rearrangements Occurring during a Single Cycle of {{Murine Leukemia Virus}} Vector Replication; {{Characterization}} and Implication.}, author = {Parthasarathi, S. and {Varela-Echavarria}, A. and Ron, Y. and Preston, B.D. and Dougherty, J.P.}, year = 1995, journal = {J.Virol.}, volume = {69}, pages = {7991–8000}, doi = {10.1128/jvi.69.12.7991-8000.1995}, keywords = {Genetic,MuLV,nosource,vector,vectors,virus} } % == BibTeX quality report for parthasarathiGeneticRearrangementsOccurring1995a: % ? Possibly abbreviated journal title J.Virol.

@article{pasquinelliControlDevelopmentalTiming2002, title = {Control of Developmental Timing by {{microRNAs}} and Their Targets}, author = {Pasquinelli, A.E. and Ruvkun, G.}, year = 2002, journal = { Review of Cell and Developmental }, volume = {18}, pages = {495–513}, doi = {10.1146/annurev.cellbio.18.012502.105832}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.cellbio.18.012502.105832}, abstract = {In Caenorhabditis elegans the timing of many developmental events is regulated by heterochronic genes. Such genes orchestrate the timing of cell divisions and fates appropriate for the developmental stage of an organism. Analyses of heterochronic mutations in the nematode C. elegans have revealed a genetic pathway that controls the timing of post-embryonic cell divisions and fates. Two of the genes in this pathway encode small regulatory RNAs. The 22 nucleotide (nt) RNAs downregulate the expression of protein-coding mRNAs of target heterochronic genes. Analogous variations in the timing of appearance of particular features have been noted among closely related species, suggesting that such explicit control of developmental timing may not be exclusive to C. elegans. In fact, some of the genes that globally pattern the temporal progression of C. elegans development, including one of the tiny RNA genes, are conserved and temporally regulated across much of animal phylogeny, suggesting that the molecular mechanisms of temporal control are ancient and universal. A very large family of tiny RNA genes called microRNAs, which are similar in structure to the heterochronic regulatory RNAs, have been detected in diverse animal species and are likely to be present in most metazoans. Functions of the newly discovered microRNAs are not yet known. Other examples of temporal programs during growth include the exquisitely choreographed temporal sequences of developmental fates in neurogenesis in Drosophila and the sequential programs of epidermal coloration in insect wing patterning. An interesting possibility is that microRNAs mediate transitions on a variety of time scales to pattern the activities of particular target protein-coding genes and in turn generate sets of cells over a period of time. Plasticity in these microRNA genes or their targets may lead to changes in relative developmental timing between related species, or heterochronic change. Instead of inventing new gene functions, even subtle changes in temporal expression of pre-existing control genes can result in speciation by altering the time at which they function}, keywords = {0,an organism,analyses of hetero-,and fates appropriate for,animal,Animals,c,Caenorhabditis,Caenorhabditis elegans,CAENORHABDITIS-ELEGANS,Cell Differentiation,Cell Division,Cell Lineage,CELLS,cytology,development,Drosophila,elegans,ELEGANS,elegans the timing of,EvolutionMolecular,expression,FAMILY,gene,Gene Expression RegulationDevelopmental,Genes,Genetic,genetics,GROWTH,growth & development,La,let-7,lin-4,many developmental events is,MECHANISM,MECHANISMS,MicroRNAs,mirnas,ModelsAnimal,MOLECULAR MECHANISMS,mRNA,Mutation,MUTATIONS,nosource,PATHWAY,Phylogeny,regulated by heterochronic genes,Review,Rna,s abstract in caenorhabditis,sequence,SEQUENCES,Species Specificity,strnas,structure,such genes orchestrate the,TARGET,the developmental stage of,timing of cell divisions} } % == BibTeX quality report for pasquinelliControlDevelopmentalTiming2002: % ? unused Journal abbr (“Annu.Rev.Cell Dev.Biol.”)

@article{passmoreEukaryoticTranslationInitiation2007, title = {The Eukaryotic Translation Initiation Factors {{eIF1}} and {{eIF1A}} Induce an Open Conformation of the {{40S}} Ribosome}, author = {Passmore, L.A. and Schmeing, T.M. and Maag, D. and Applefield, D.J. and Acker, M.G. and Algire, M.A. and Lorsch, J.R. and Ramakrishnan, V.}, year = 2007, month = apr, journal = {Molecular cell}, volume = {26}, number = {1}, pages = {41–50}, publisher = {Elsevier}, doi = {10.1016/j.molcel.2007.03.018}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276507001888 http://www.sciencedirect.com/science/article/pii/S1097276507001888}, abstract = {Initiation of translation is the process by which initiator tRNA and the start codon of mRNA are positioned in the ribosomal P site. In eukaryotes, one of the first steps involves the binding of two small factors, eIF1 and eIF1A, to the small (40S) ribosomal subunit. This facilitates tRNA binding, allows scanning of mRNA, and maintains fidelity of start codon recognition. Using cryo-EM, we have obtained 3D reconstructions of 40S bound to both eIF1 and eIF1A, and with each factor alone. These structures reveal that together, eIF1 and eIF1A stabilize a conformational change that opens the mRNA binding channel. Biochemical data reveal that both factors accelerate the rate of ternary complex (eIF2GTPMet-tRNA(i)(Met)) binding to 40S but only eIF1A stabilizes this interaction. Our results suggest that eIF1 and eIF1A promote an open, scanning-competent preinitiation complex that closes upon start codon recognition and eIF1 release to stabilize ternary complex binding and clamp down on mRNA}, keywords = {0,BINDING,Binding Sites,BIOLOGY,CEREVISIAE,chemistry,Codon,CODON RECOGNITION,COMPLEX,COMPLEXES,CONFORMATION,CONFORMATIONAL CHANGE,CONFORMATIONAL-CHANGE,Cryoelectron Microscopy,eIF1,eIF1A,Eukaryotic Initiation Factor-1,EUKARYOTIC TRANSLATION,Fidelity,genetics,initiation,INITIATION-FACTOR,La,metabolism,Models-Genetic,ModelsGenetic,Molecular Biology,Molecular Conformation,mRNA,nosource,P SITE,P-SITE,protein,Protein Binding,Protein Biosynthesis,Proteins,RECOGNITION,RELEASE,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNA-Messenger,RNA-Ribosomal,RNAMessenger,RNARibosomal,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,scanning,SITE,START CODON,structure,Structure-Activity Relationship,SUBUNIT,Support,translation,TRANSLATION INITIATION,tRNA,tRNA binding} } % == BibTeX quality report for passmoreEukaryoticTranslationInitiation2007: % ? unused Journal abbr (“Mol.Cell”)

@article{paulSequenceRequiredRibosomal01, title = {A {{Sequence Required}} for -1 {{Ribosomal Frameshifting Located Four Kilobases Downstream}} of the {{Frameshift Site}}.}, author = {Paul, C.P. and Barry, J.K. and {Dinesh-Kumar}, S.P. and Brault, V. and Miller, W.A.}, year = 1, month = jul, journal = {J.Mol.Biol.}, volume = {310}, number = {5}, pages = {987–999}, doi = {10.1006/jmbi.2001.4801}, abstract = {Programmed ribosomal frameshifting allows one mRNA to encode regulate expression of, multiple open reading frames (ORFs). The polymerase encoded by ORF 2 of Barley yellow dwarf virus (BYDV) is expressed via minus one (-1) frameshifting from the overlapping ORF 1. Previously, this appeared to be mediated by a 116 nt RNA sequence that contains canonical -1 frameshift signals including a shifty heptanucleotide followed by a highly structured region. However, unlike known -1 frameshift signals, the reporter system required the zero frame stop codon and did not require a consensus shifty site for expression of the -1 ORF. In contrast, full-length viral RNA required a functional shifty site for frameshifting in wheat germ extract, while the stop codon was not required. Increasing translation initiation efficiency by addition of a 5’ cap on the naturally uncapped viral RNA, decreased the frameshift rate. Unlike any other known RNA, a region four kilobases downstream of the frameshift site was required for frameshifting. This included an essential 55 base tract followed by a 179 base tract that contributed to full frameshifting. The effects of most mutations on frameshifting correlated with the ability of viral RNA to replicate in oat protoplasts, indicating that the wheat germ extract accurately reflected control of BYDV RNA translation in the infected cell. However, the overall frameshift rate appeared to be higher in infected cells, based on immunodetection of viral proteins. These findings show that use of short recoding sequences out of context in reporter constructs may overlook distant signals. Most importantly, the remarkably long-distance interaction reported here suggests the presence of a novel structure that can facilitate ribosomal frameshifting.}, keywords = {Cap,Codon,efficiency,expression,frameshift,Frameshifting,initiation,Luteovirus; recoding; reporter genes; 3’ untranslated region; plant virus translation,mRNA,Mutation,MUTATIONS,nosource,Open Reading Frames,polymerase,protein,Proteins,recoding,ribosomal frameshifting,Rna,sequence,SIGNAL,STOP CODON,structure,SYSTEM,translation,TRANSLATION INITIATION,Viral Proteins,virus,Wheat} } % == BibTeX quality report for paulSequenceRequiredRibosomal01: % ? Possibly abbreviated journal title J.Mol.Biol. % ? Title looks like it was stored in title-case in Zotero

@article{paulusCompetitiveInhibitionHuman1999, title = {Competitive Inhibition of Human Immunodeficiency Virus Type-1 Protease by the {{Gag-Pol}} Transframe Protein}, author = {Paulus, C. and Hellebrand, S. and Tessmer, U. and Wolf, H. and Krausslich, H.G. and Wagner, R.}, year = 1999, month = jul, journal = {Journal of Biological Chemistry}, volume = {274}, number = {31}, pages = {21539–21543}, publisher = {ASBMB}, doi = {10.1074/jbc.274.31.21539}, url = {http://www.jbc.org/content/274/31/21539.short}, abstract = {The human immunodeficiency virus type-1 (HIV-1) transframe protein p6* is located between the structural and enzymatic domains of the Gag-Pol polyprotein, Banked by the nucleocapsid (NC) and the protease (PR) domain at its amino and carboxyl termini, respectively. Here, we report that recombinant highly purified HIV-1 p6* specifically inhibits mature HIV-1 PR activity. Kinetic analyses and cross-linking experiments revealed a competitive mechanism for PR inhibition by p6. We further demonstrate that the four carboxyl-terminal residues of p6 are essential but not sufficient for p6-mediated inhibition of PR activity. Based on these results, we suggest a role of the transframe protein p6 in regulating HIV-1 PR activity during viral replication}, keywords = {ASPARTIC PROTEASE,CROSS-LINKING,CROSSLINKING,DIMER,DOMAIN,DOMAINS,expression,Gag-pol,Hiv-1,HIV-1 PROTEASE,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,INHIBITION,MECHANISM,nosource,PARTICLE FORMATION,POLYPROTEIN,PRECURSOR,protein,REPLICATION,RESIDUES,RETROVIRAL PROTEASES,sequence,Structural,VIRAL INFECTIVITY,virus} }

@article{pawsonCellfreeTranslationVirion1976, title = {Cell-Free Translation of Virion {{RNA}} from Nondefective and Transformation-Defective {{Rous}} Sarcoma Viruses.}, author = {Pawson, T. and Martin, G.S. and Smith, A.E.}, year = 1976, journal = {Journal of Virology}, volume = {19}, number = {3}, pages = {950–967}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.19.3.950-967.1976}, url = {http://jvi.asm.org/cgi/content/abstract/19/3/950}, abstract = {Nondefective and transformation-defective virion subunit RNAs from two strains of Rous sarcoma virus (RSV) were translated in cell-free systems derived from Krebs IIA ascites cells, wheat germ, and L-cells. In each case the predominant viral-specific product was a polypeptide of molecular weight 76,000 that is related to the internal viral group-specific antigens, as judged by immunoprecipitation with monospecific antisera and tryptic peptide fingerprinting. No difference could be detected between the translation products of 35S RNA from nondefective and transformation-defective RSV virions, nor of 35S RNA from different strains of RSV. The 76,000-molecular-weight polypeptide synthesized in response to 35S RNA in vitro was labeled with formyl-methionine from initiator tRNA. Models for viral protein synthesis are discussed in the light of these results, and arguments positioning the group-specific antigen gene at the 5’ end of the 35S RNA are presented}, keywords = {0,ANTIGEN,AntigensViral,biosynthesis,Cell TransformationNeoplastic,Cell-Free System,CELL-FREE TRANSLATION,CELLS,Comparative Study,Defective Viruses,gene,immunology,In Vitro,IN-VITRO,La,metabolism,MODEL,models,Molecular Weight,nosource,Peptide Biosynthesis,Peptides,POLYPEPTIDE,PRODUCT,PRODUCTS,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Rna,RnaViral,Sarcoma VirusesAvian,SUBUNIT,SYSTEM,SYSTEMS,translation,tRNA,Viral Proteins,Virion,VIRIONS,virus,Viruses,Wheat} } % == BibTeX quality report for pawsonCellfreeTranslationVirion1976: % ? unused Journal abbr (“J.Virol.”)

@article{pazinWhatHistoneDeacetylation1997, title = {What’s up and down with Histone Deacetylation and Transcription?}, author = {Pazin, M.J. and Kadonaga, J.T.}, year = 1997, month = may, journal = {Cell}, volume = {89}, number = {3}, pages = {325–328}, doi = {10.1016/S0092-8674(00)80211-1}, keywords = {97294375,Acetylation,animal,Genetic,genetics,Histones,La,metabolism,nosource,physiology,Review,transcription,TranscriptionGenetic} }

@article{pearProductionHightiterHelperfree1993, title = {Production of High-Titer Helper-Free Retroviruses by Transient Transfection}, author = {Pear, W.S. and Nolan, G.P. and Scott, M.L. and Baltimore, D.}, year = 1993, month = sep, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {90}, number = {18}, pages = {8392–8396}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.90.18.8392}, url = {http://www.pnas.org/content/90/18/8392.short}, keywords = {Cell Line,cell lines,gene,Genes,Methods,nosource,packaging,retrovirus,SYSTEM,Transfection,vector,vectors,virus} }

@article{pearsonYeastUseTranslational1982, title = {Yeast Use Translational Control to Compensate for Extra Copies of a Ribosomal Protein Gene.}, author = {Pearson, N.J. and Fried, J.M. and Warner, J.R.}, year = 1982, journal = {Cell}, volume = {29}, number = {2}, pages = {347–355}, publisher = {Elsevier}, doi = {10.1016/0092-8674(82)90151-9}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867482901519}, keywords = {gene,L3,nosource,protein,ribosome,translation,yeast} }

@article{pearsonFlexibleSequenceSimilarity2000, title = {Flexible Sequence Similarity Searching with the {{FASTA3}} Program Package}, author = {Pearson, W.R.}, year = 2000, journal = {Methods Mol.Biol.}, volume = {132}, pages = {185–219}, publisher = {Springer}, url = {http://www.springerlink.com/index/LV50377825580701.pdf}, abstract = {The FASTA3 and FASTA2 packages provide a flexible set of sequence-comparison programs that are particularly valuable because of their accurate statistical estimates and high-quality alignments. Traditionally, sequence similarity searches have sought to ask one question: “Is my query sequence homologous to anything in the database?” Both FASTA and BLAST can provide reliable answers to this question with their statistical estimates; if the expectation value E is {\(<\)} 0.001-0.01 and you are not doing hundreds of searches a day, the answer is probably yes. In general, the most effective search strategies follow these rules: 1. Whenever possible, compare at the amino acid level, rather than the nucleotide level. Search first with protein sequences (blastp, fasta3, and ssearch3), then with translated DNA sequences (fastx, blastx), and only at the DNA level as a last resort (Table 5). 2. Search the smallest database that is likely to contain the sequence of interest (but it must contain many unrelated sequences for accurate statistical estimates). 3. Use sequence statistics, rather than percent identity or percent similarity, as your primary criterion for sequence homology. 4. Check that the statistics are likely to be accurate by looking for the highest-scoring unrelated sequence, using prss3 to confirm the expectation, and searching with shuffled copies of the query sequence [randseq, searches with shuffled sequences should have E approx 1.0]. 5. Consider searches with different gap penalties and other scoring matrices. Searches with long query sequences against full-length sequence libraries will not change dramatically when BLOSUM62 is used instead of BLOSUM50 (20), or a gap penalty of -14/-2 is used in place of -12/-2. However, shallower or more stringent scoring matrices are more effective at uncovering relationships in partial sequences (3,18), and they can be used to sharpen dramatically the scope of the similarity search. However, as illustrated in the last section, the E value is only the first step in characterizing a sequence relationship. Once one has confidence that the sequences are homologous, one should look at the sequence alignments and percent identities, particularly when searching with lower quality sequences. When sequence alignments are very short, the alignment should become more significant when a shallower scoring matrix is used, e.g., BLOSUM62 rather than BLOSUM50 (remember to change the gap penalties). Homology can be reliably inferred from statistically significant similarity. Whereas homology implies common three-dimensional structure, homology need not imply common function. Orthologous sequences usually have similar functions, but paralogous sequences often acquire very different functional roles. Motif databases, such as PROSITE (21), can provide evidence for the conservation of critical functional residues. However, motif identity in the absence of overall sequence similarity is not a reliable indicator of homology}, keywords = {3,ACID,alignment,Amino Acid Sequence,AMINO-ACID,BLAST,DATABASE,Database Management Systems,Databases,Dna,DNA sequence,E,EvolutionMolecular,Information Storage and Retrieval,La,library,Methods,Molecular Sequence Data,No DOI found,nosource,protein,RESIDUES,RULES,search,sequence,Sequence Alignment,Sequence HomologyAmino Acid,SEQUENCES,Statistics,structure,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for pearsonFlexibleSequenceSimilarity2000: % ? Possibly abbreviated journal title Methods Mol.Biol.

@article{pedenChangesGrowthProperties1991, title = {Changes in Growth Properties on Passage in Tissue Culture of Viruses Derived from Infectious Molecular Clones of {{HIV-1LAI}}, {{HIV- 1MAL}}, and {{HIV-1ELI}}}, author = {Peden, K. and Emerman, M. and Montagnier, L.}, year = 1991, month = dec, journal = {Virology}, volume = {185}, number = {2}, pages = {661–672}, publisher = {Elsevier}, doi = {10.1016/0042-6822(91)90537-L}, url = {http://linkinghub.elsevier.com/retrieve/pii/004268229190537L}, keywords = {Cell Line,cell lines,Genotype,HIV,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,In Vitro,IN-VITRO,Kinetics,nosource,sequence,virus} }

@article{pedersenCrystallizationYeastElongation2001a, title = {Crystallization of the Yeast Elongation Factor Complex {{eEF1A-eEF1Balpha}}}, author = {Pedersen, L. and Andersen, G.R. and Knudsen, C.R. and Kinzy, T.G. and Nyborg, J.}, year = 2001, month = jan, journal = {Acta Crystallogr.D.Biol.Crystallogr.}, volume = {57}, number = {Pt 1}, pages = {159–161}, url = {PM:11134944}, abstract = {Crystals of the Saccharomyces cerevisiae elongation factor eEF1A (formerly EF-1alpha) in complex with a catalytic C-terminal fragment of the nucleotide-exchange factor eEF1Balpha (formerly EF-1beta) were grown by the sitting-drop vapour-diffusion technique, using polyethylene glycol 2000 monomethyl ether as precipitant. Crystals diffract to better than 1.7 A and belong to the space group P2(1)2(1)2(1). The unit-cell parameters of the crystals are sensitive to the choice of cryoprotectant. The structure of the 61 kDa complex was determined with the multiple anomalous dispersion technique using three selenomethionine residues in a 11 kDa eEF1Balpha fragment generated by limited proteolysis of full-length eEF1Balpha expressed in Escherichia coli}, keywords = {0,COMPLEX,COMPLEXES,Crystallization,elongation,Escherichia coli,ESCHERICHIA-COLI,La,No DOI found,nosource,PROTEOLYSIS,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Selenomethionine,Structural,structure,yeast} } % == BibTeX quality report for pedersenCrystallizationYeastElongation2001a: % ? Possibly abbreviated journal title Acta Crystallogr.D.Biol.Crystallogr.

@article{pedersonNucleolusFourRibonucleoproteins2000, title = {The Nucleolus and the Four Ribonucleoproteins of Translation}, author = {Pederson, T. and Politz, J.C.}, year = 2000, month = mar, journal = {The Journal of Cell Biology}, volume = {148}, number = {6}, pages = {1091–1095}, publisher = {Rockefeller Univ Press}, doi = {10.1083/jcb.148.6.1091}, url = {http://jcb.rupress.org/content/148/6/1091.full}, abstract = {The classical view of the nucleolus as solely committed to ribosome biosynthesis has been modified by recent studies pointing to additional roles for this nuclear domain. These newly recognized features include the nucleolar presence of several nonribosomal RNAs transcribed by RNA polymerase III, as well as nucleolar roles in gene silencing, cell cycle progression, and cellular senescence. The signal recognition particle (SRP)(1) RNA, and several protein components of the SRP also recently have been detected in the nucleolus. Thus, the large and small ribosomal subunits, the 5S rRNA-ribonucleoprotein complex, and now the SRP, are known to be assembled in or pass through the nucleolus. These findings, together with the recent observations that some transfer RNA precursor molecules and the pretransfer RNA processing enzyme, RNase P, are also found in the nucleolus, raise the possibility that these translational components are congressed in the nucleolus in order to probatively interact with one another, perhaps as a test of proper conformational fit. We hypothesize that such interactions may be an important checkpoint during nucleolar assembly of the translational machinery at steps ranging from the regulation of nascent transcript processing to a possible transient preassembly of the entire translational apparatus}, keywords = {assembly,biosynthesis,cell cycle,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,DOMAIN,DOMAINS,enzyme,gene,Gene Silencing,Genes,LOCALIZATION,MAMMALIAN-CELLS,nosource,nucleolus,PARTICLES,polymerase,POLYMERASE-III,PRECURSOR,protein,RECOGNITION,regulation,Review,RIBONUCLEOPROTEIN,Ribonucleoproteins,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Rna,RNA Polymerase III,RNA-POLYMERASE,RNAse,SIGNAL,SMALL NUCLEAR RNAS,SUBUNIT,T,TRANSCRIPT,TRANSFER-RNA,translation} }

@article{pelsyEffectsOchreNonsense1984a, title = {Effects of Ochre Nonsense Mutations on Yeast ⬚{{URA1}}⬚ Stability.}, author = {Pelsy, F. and LaCroute, F.}, year = 1984, journal = {Curr.Genet.}, volume = {8}, pages = {277–282}, doi = {10.1007/BF00419725}, keywords = {Mutation,MUTATIONS,NMD,nosource,Review,stability,yeast} } % == BibTeX quality report for pelsyEffectsOchreNonsense1984a: % ? Possibly abbreviated journal title Curr.Genet.

@article{peltzRegulationMRNATurnover1991a, title = {Regulation of {{mRNA}} Turnover in Eukaryotic Cells.}, author = {Peltz, S.W. and Brewer, G. and Bernstein, P. and Kratzke, R. and Ross, J.}, year = 1991, journal = {Critical Reviews in Eukaryotic Gene Expression}, volume = {1}, number = {2}, eprint = {1802106}, eprinttype = {pubmed}, pages = {99–126}, url = {http://www.ncbi.nlm.nih.gov/pubmed/1802106}, keywords = {Eukaryotic Cells,mRNA,NMD,No DOI found,nosource,regulation,Review,turnover,UPF} } % == BibTeX quality report for peltzRegulationMRNATurnover1991a: % ? unused Journal abbr (“CRC Crit.Rev.in Euk.Gene Expr.”)

@incollection{peltzMRNATurnoverSaccharomyces1993a, title = {{{mRNA}} Turnover in ⬚{{Saccharomyces}} Cerevisiae⬚.}, booktitle = {Control of {{mRNA}} Stability.}, author = {Peltz, S.W. and Jacobson, A.J.}, year = 1993, pages = {291–328}, publisher = {Academic Press}, address = {New York}, collaborator = {Brawerman, G. and Belasco, J.}, keywords = {mRNA,nosource,Review,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,stability,turnover,UPF} }

@incollection{peltzIdentificationCisActing1993, title = {Identification of the ⬚cis⬚-Acting Sequences and ⬚trans⬚-Acting Factors Involved in Nonsense-Mediated {{mRNA}} Decay.}, booktitle = {Protein Synthesis and Targetting in Yeast.}, author = {Peltz, S.W. and Trotta, C. and He, F. and Brown, A. and Donahue, J. and Welch, E. and Jacobson, A.}, year = 1993, pages = {1–10}, publisher = {Springer-Verlag}, collaborator = {Tuite, M. and McCarthy, J. and Brown, A. and Sherman, F.}, keywords = {DECAY,IDENTIFICATION,mRNA,mRNA decay,nonsense-mediated decay,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Review,review article,sequence,yeast} }

@article{peltzNonsensemediatedMRNADecay1994a, title = {Nonsense-Mediated {{mRNA}} Decay in Yeast.}, author = {Peltz, S.W. and He, F. and Welch, E. and Jacobson, A.J.}, year = 1994, journal = {Progress in Nucleic Acid Research}, volume = {47}, pages = {271–298}, doi = {10.1016/S0079-6603(08)60254-8}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0079660308602548}, keywords = {DECAY,mRNA,mRNA decay,NMD,nonsense-mediated decay,nosource,Review,review article,yeast} } % == BibTeX quality report for peltzNonsensemediatedMRNADecay1994a: % ? unused Journal abbr (“Prog.in Nucleid Acids.Res.”)

@incollection{peltzIdentificationCisActing1996, title = {Identification of the ⬚cis⬚-Acting Sequences and ⬚trans⬚-Acting Factors Involved in Nonsense-Mediated {{mRNA}} Decay.}, booktitle = {Protein Systnesis and Targeting in Yeast.}, author = {Peltz, S.W. and Trotta, C. and Feng, H. and Grown, A. and Donahue, J. and Welch, E. and Jacobson, A.}, year = 1996, pages = {1–10}, publisher = {NATO ASI Series}, keywords = {DECAY,IDENTIFICATION,mRNA,mRNA decay,nonsense-mediated decay,nosource,protein,sequence,UPF,yeast}, annotation = {II} }

@article{peltzRibosomalProteinL31999, title = {Ribosomal {{Protein L3 Mutants Alter Translational Fidelity}} and {{Promote Rapid Loss}} of the {{Yeast Killer Virus}}}, author = {Peltz, S.W. and Hammell, A.B. and Cui, Y. and Yasenchak, J. and Puljanowski, L. and Dinman, J.D.}, year = 1999, month = jan, journal = {Molecular and Cellular Biology}, volume = {19}, number = {1}, pages = {384–391}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.19.1.384}, url = {http://mcb.asm.org/cgi/content/abstract/19/1/384}, abstract = {Programmed -1 ribosomal frameshifting is utilized by a number of RNA viruses as a means of ensuring the correct ratio of viral structural to enzymatic proteins available for viral particle assembly. Altering frameshifting efficiencies upsets this ratio, interfering with virus propagation. We have previously demonstrated that compounds that alter the kinetics of the peptidyl-transfer reaction affect programmed -1 ribosomal frameshift efficiencies and interfere with viral propagation in yeast. Here, the use of a genetic approach lends further support to the hypothesis that alterations affecting the ribosome’s peptidyltransferase activity lead to changes in frameshifting efficiency and virus loss. Mutations in the RPL3 gene, which encodes a ribosomal protein located at the peptidyltransferase center, promote approximately three- to fourfold increases in programmed -1 ribosomal frameshift efficiencies and loss of the M1 killer virus of yeast. The mak8-1 allele of RPL3 contains two adjacent missense mutations which are predicted to structurally alter the Mak8-1p. Furthermore, a second allele that encodes the N-terminal 100 amino acids of L3 (called L3Delta) exerts a trans-dominant effect on programmed -1 ribosomal frameshifting and killer virus maintenance. Taken together, these results support the hypothesis that alterations in the peptidyltransferase center affect programmed -1 ribosomal frameshifting}, keywords = {Amino Acids,assembly,cancer,drugs,efficiency,Fidelity,frameshift,Frameshifting,Gag/Gag-pol ratio,gene,Genetic,killer,Kinetics,L3,M1,Mutation,MUTATIONS,nosource,peptidyl-transfer,Peptidyltransferase,protein,Proteins,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,ribosome,Rna,RNA Viruses,Structural,Support,viral particle,viral particle assembly,viral propagation,virus,yeast} } % == BibTeX quality report for peltzRibosomalProteinL31999: % ? Title looks like it was stored in title-case in Zotero % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{penalvaFungalPerspectiveHuman2001, title = {A Fungal Perspective on Human Inborn Errors of Metabolism: {{Alkaptonuria}} and Beyond}, author = {Penalva, M.A.}, year = 2001, month = oct, journal = {Fungal Genetics and Biology}, volume = {34}, number = {1}, pages = {1–10}, doi = {10.1006/fgbi.2001.1284}, url = {ISI:000171511500001}, abstract = {Penalva, M. A. 2001. A fungal perspective on human inborn errors of metabolism: Alkaptonuria and beyond. Fungal Genetics and Biology 34, 1-10. Crucial for the establishment and development of biochemical genetics as a self-standing discipline was Beadle and Tatum’s choice of Neurospora crassa as experimental organism some 60 years ago. Altough Garrod’s insights on biochemical genetics and his as tonishingly modern concepts of biochemical individuality and susceptibility to disease had been ignored by their contemporaries, Beadle acknowledged on several occasions how close Garrod had come to the “one-gene-one-enzyme” hypothesis. In an unexpected turn of events, several genes involved in human inborn errors of metabolism, including the gene for Garrod’s favorite disease, alkaptonuria, have been characterized by exploitation of the experimental advantages of another mold, Aspergillus nidulans, which shares with N. crassa the experimental advantages that prompted pioneers of biochemical genetics to use them: rapid growth, facile genetic manipulation, and an environment (the composition of the growth medium) that can be manipulated a la carte. (C) 2001 Academic Press}, keywords = {0,3-methylcrotonylglycinuria,alkaptonuria,amino acid metabolism,Aspergillus,ASPERGILLUS-NIDULANS,BIOLOGY,development,disease,enzyme deficiency,ERRORS,functional genomics,Fungi,gene,Genes,Genetic,genetics,GROWTH,HEREDITARY TYROSINEMIA,HOMOGENTISATE DIOXYGENASE,human,HUMAN MOLYBDOPTERIN SYNTHASE,La,M,MALEYLACETOACETATE ISOMERASE,media,Mendelian inheritance,metabolism,MURINE MODEL,MUTATIONS,Neurospora,NEUROSPORA-CRASSA,nosource,NUCLEAR MIGRATION,tyrosinemia,TYROSINEMIA TYPE-I} }

@article{percudaniTransferRNAGene1997a, title = {Transfer {{RNA}} Gene Redundancy and Translational Selection in {{Saccharomyces}} Cerevisiae}, author = {Percudani, R. and Pavesi, A. and Ottonello, S.}, year = 1997, month = may, journal = {J.Mol.Biol}, volume = {268}, number = {2}, pages = {322–330}, doi = {10.1006/jmbi.1997.0942}, url = {PM:9159473}, abstract = {A total of 274 transfer RNA genes, representing the entire tRNA gene set of the yeast Saccharomyces cerevisiae, has been extracted from the whole genome sequence of this organism using a dedicated search algorithm (Pol3scan). All tRNA genes were assigned to 42 classes of distinct codon specificity. Accordingly, four deviations from previously proposed rules for third position wobble pairing in yeast, three G:U and one A:I codon-anticodon pairings, were found to be required to account for the reading of 61 coding triplets. The gene copy number for individual tRNA species, which ranges from one to 16, correlates well with both the frequency of codon occurrence in a sample of 1756 distinct protein coding sequences (r = 0.82) and the previously measured intracellular content of 21 tRNA species. A close link between tRNA gene redundancy and the overall amino acid composition of yeast proteins was also observed. Regression analysis values for individual protein coding sequences proved to be effective descriptions of the translational selective pressure operating on a particular gene. A significantly stronger co-adaptation between codon choice and tRNA gene copy number was observed in highly expressed genes. These observations strongly support the notion that intracellular tRNA levels in normally growing yeast cells are mainly determined by gene copy number, which, along with codon choice, is the key parameter acted upon by translational selection}, keywords = {0,ACID,AMINO-ACID,analysis,Anticodon,CELLS,CEREVISIAE,coding sequence,Codon,gene,Gene Expression RegulationFungal,Genes,GenesFungal,genetics,Genome,La,nosource,POSITION,protein,Protein Biosynthesis,Proteins,Rna,RNAFungal,RNATransfer,RULES,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,search,SELECTION,sequence,Sequence Analysis,SEQUENCES,Software,SPECIFICITY,Support,TRANSFER-RNA,tRNA,yeast,YEAST-CELLS} } % == BibTeX quality report for percudaniTransferRNAGene1997a: % ? Possibly abbreviated journal title J.Mol.Biol

@article{perez-canadillasHighlyRefinedSolution2000a, title = {The Highly Refined Solution Structure of the Cytotoxic Ribonuclease Alpha-Sarcin Reveals the Structural Requirements for Substrate Recognition and Ribonucleolytic Activity}, author = {{Perez-Canadillas}, J.M. and Santoro, J. and {Campos-Olivas}, R. and Lacadena, J. and {}{del Pozo}, A.M. and Gavilanes, J.G. and Rico, M. and Bruix, M.}, year = 2000, month = jun, journal = {Journal of Molecular Biology}, volume = {299}, number = {4}, pages = {1061–1073}, doi = {10.1006/jmbi.2000.3813}, url = {ISI:000087680400019}, abstract = {alpha-Sarcin selectively cleaves a single phosphodiester bond in a universally conserved sequence of the major rRNA, that inactivates the ribosome. The elucidation of the three-dimensional solution structure of this 150 residue enzyme is a crucial step towards understanding alpha-sarcin’s conformational stability, ribonucleolytic activity, and its exceptionally high level of specificity. Here, the solution structure has been determined on the basis of 2658 conformationally relevant distances restraints (including stereoespecific assignments) and 119 torsional angular restraints, by nuclear magnetic resonance spectroscopy methods. A total of 60 converged structures have been computed using the program DYANA. The 47 best DYANA structures, following restrained energy minimization by GROMOS, represent the solution structure of alpha-sarcin. The resulting average pairwise root-mean-square-deviation is 0.86 Angstrom for backbone atoms and 1.47 A for all heavy atoms. When the more variable regions are excluded from the analysis, the pairwise root-mean-square deviation drops to 0.50 Angstrom and 1.00 Angstrom, for backbone and heavy atoms, respectively. The alpha-sarcin structure is similar to that reported for restrictocin, although some differences are clearly evident, especially in the loop regions. The average rmsd between the structurally aligned backbones of the 47 final alpha-sarcin structures and the crystal structure of restrictocin is 1.46 Angstrom. On the basis of a docking model constructed with alpha-sarcin solution structure and the crystal structure of a 29-nt RNA containing the sarcin/ricin domain, the regions in the protein that could interact specifically with the substrate have been identified. The structural elements that account for the specificity of RNA recognition are located in two separate regions of the protein. One is composed by residues 51 to 55 and loop 5, and the other region, located more than 11 A away in the structure, is the positively charged segment formed by residues 110 to 114. (C) 2000 Academic Press}, keywords = {3-DIMENSIONAL STRUCTURE,ALPHA-SARCIN,AMINO-ACID SEQUENCE,analysis,ASPERGILLUS-GIGANTEUS,ASSIGNMENT,Conserved Sequence,COUPLING-CONSTANTS,crystal structure,CRYSTAL-STRUCTURE,DOMAIN,ELEMENTS,enzyme,LOOP,M,Magnetic Resonance Spectroscopy,MECHANISM,Methods,MODEL,NMR,NMR solution structure,nosource,nuclear magnetic resonance,NUCLEAR-MAGNETIC-RESONANCE,protein,protein-RNA interaction,RECOGNITION,REGION,RESIDUES,RESOLUTION,restrictocin,ribonucleolytic activity,ribosome,ribosome-inactivating protein,Rna,RNA recognition,rRNA,sarcin/ricin domain,sequence,SPECIFICITY,SPECTROSCOPY,stability,Structural,structure} }

@article{perez-gosalbezAffinityLabellingYeast1978, title = {Affinity Labelling of Yeast Ribosomal Peptidyl Transferase}, author = {{Perez-Gosalbez}, M. and Vazquez, D. and Ballesta, J.P.}, year = 1978, month = jul, journal = {Molecular and General Genetics MGG}, volume = {163}, number = {1}, pages = {29–34}, publisher = {Springer}, doi = {10.1007/BF00268961}, url = {PM:355841 http://www.springerlink.com/index/G20471660U095744.pdf}, abstract = {Using p-nitrophenylcarbamyl-phenylalanyl-tRNA (PNPC-Phe-tRNA) and N-Iodoacetylphenylalanyl-tRNA as affinity labels we have attempted to identify the components of the aminoacyl-tRNA binding sites located in the vicinity of the peptidyl transferase centre of the yeast ribosome. Both Phe-tRNA derivatives bind to the ribosomal A-site in the presence of 20 mM Mg++ ion concentration and can be translocated to the ribosomal P-site in the presence of elongation factor. After the labels have been allowed to react covalently with ribosomes they were found associated with the large ribosomal subunit. Proteins L36, L43, L42, L29, L2, L17/18, L19/20 and proteins L26, L38, L22/23, L7/9, L4/6, L36, L11, L43, L39 were labelled in samples treated with PNPC-Phe-tRNA and N-iodoacetyl-Phe-tRNA respectively. In contrast, when only the components of the ribosomal P-site were analysed by reacting the treated particles with puromycin fewer spots were labelled, corresponding to proteins L36 and L19/20 using PNPC-Phe-tRNA and proteins L4/6, L36, and L43 using N-Iodoacetyl-Phe-tRNA}, keywords = {0,A SITE,A-SITE,Acyltransferases,Affinity Labels,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,COMPONENT,COMPONENTS,derivatives,elongation,enzymology,IDENTIFY,L2,L29,La,Magnesium,metabolism,nosource,P SITE,P-SITE,PARTICLES,peptidyl transferase,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,pharmacology,Phenylalanine,protein,Proteins,Puromycin,RIBOSOMAL PEPTIDYL TRANSFERASE,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNATransfer,Saccharomyces cerevisiae,SITE,SITES,SUBUNIT,Transferases,yeast} } % == BibTeX quality report for perez-gosalbezAffinityLabellingYeast1978: % ? unused Journal abbr (“Mol Gen.Genet.”)

@article{perlickMammalianOrthologuesYeast1996, title = {Mammalian Orthologues of a Yeast Regulator of Nonsense-Transcript Stability.}, author = {Perlick, H.A. and Medghalchi, S.M. and Spencer, F.A. and Kendzior, {R.J.Jr}. and Dietz, H.C.}, year = 1996, journal = {Proceedings of the National Academy of Sciences}, volume = {93}, number = {20}, pages = {10928–10932}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/93/20/10928.short}, keywords = {cloning,human homologue,Mammals,No DOI found,nonsense-mediated decay,nosource,stability,Upf1,yeast} }

@article{pervushinNMRScalarCouplings1998a, title = {{{NMR}} Scalar Couplings across {{Watson-Crick}} Base Pair Hydrogen Bonds in {{DNA}} Observed by Transverse Relaxation-Optimized Spectroscopy}, author = {Pervushin, K. and Ono, A. and Fernandez, C. and Szyperski, T. and Kainosho, M. and Wuthrich, K.}, year = 1998, month = nov, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {24}, pages = {14147–14151}, doi = {10.1073/pnas.95.24.14147}, url = {ISI:000077191200030}, abstract = {This paper describes the NMR observation of N-15-N-15 and H-1-N-15 scalar couplings across the hydrogen bonds in Watson-Crick base pairs in a DNA duplex, (h)J(NN) and (h)J(HN). These couplings represent new parameters of interest for both structural studies of DNA and theoretical investigations into the nature of the hydrogen bonds. Two dimensional [N-15,H-1]-transverse relaxation-optimized spectroscopy (TROSY) with a N-15-labeled 14-mer DNA duplex was used to measure (h)J(NN), which is in the range 6-7 Hz, and the two-dimensional (h)J(NN)-correlation-[N-15,H-1]-TROSY experiment was used to correlate the chemical shifts of pairs of hydrogen bond-related N-15 spins and to observe, for the first time, (h)J(HN) scalar couplings, with values in the range 2-3.6 Hz, TROSY-based studies of scalar couplings across hydrogen bonds should be applicable for large molecular sizes, including protein-bound nucleic acids}, keywords = {0,ACID,ACIDS,ANGLES,BASE,Base Pairing,Base Sequence,BASE-PAIR,CHEMICAL-SHIFT ANISOTROPY,chemistry,CONSTANTS,Dna,HOMONUCLEAR,Hydrogen,Hydrogen Bonding,INFORMATION,La,Methods,ModelsChemical,NMR,nosource,Nuclear Magnetic ResonanceBiomolecular,Nucleic Acid Conformation,Nucleic Acids,Oligodeoxyribonucleotides,Proteins,PYROCOCCUS-FURIOSUS,QUANTITATIVE MEASUREMENT,RELAXATION,RUBREDOXIN,SPECTROSCOPY,Structural,supportnon-u.s.gov’t,TENSORS} } % == BibTeX quality report for pervushinNMRScalarCouplings1998a: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{pestkaStudiesFormationTransfer1969, title = {Studies on the Formation of Transfer Ribonucleic Acid-Ribosome Complexes. {{XI}}. {{Antibiotic}} Effects on Phenylalanyl-Oligonucleotide Binding to Ribosomes.}, author = {Pestka, S.}, year = 1969, journal = {Proceedings of the National Academy of Sciences}, volume = {64}, number = {2}, pages = {709–714}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.64.2.709}, url = {http://www.pnas.org/content/64/2/709.short}, keywords = {antibiotic,antibiotics,BINDING,COMPLEX,COMPLEXES,doner stem,nosource,ribosome,Ribosomes,sparsomycin} } % == BibTeX quality report for pestkaStudiesFormationTransfer1969: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.USA”)

@article{pestkaStudiesFormationTransfer1970a, title = {Studies on the Formation of Transfer Ribonucleic Acid-Ribosome Complexes. 8. {{Aminoacyl}} Oligonucleotide Binding to Ribosomes: Characteristics and Requirements.}, author = {Pestka, S. and Hishizawa, T. and Lessard, J.L.}, year = 1970, month = nov, journal = {The Journal of biological chemistry}, volume = {245}, number = {22}, pages = {6208–6219}, doi = {10.1016/S0021-9258(18)62680-8}, url = {http://ukpmc.ac.uk/abstract/MED/5484475}, keywords = {0,Amino Acid Sequence,Ammonium Compounds,BINDING,Binding Sites,chemistry,COMPLEX,COMPLEXES,Ethanol,HIV,La,Magnesium,metabolism,nosource,Nucleotides,pharmacology,Potassium,Protein Binding,ribosome,Ribosomes,Rna,RNATransfer,Tritium} } % == BibTeX quality report for pestkaStudiesFormationTransfer1970a: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{pestkaInhibitorsRibosomeFunctions1971a, title = {Inhibitors of Ribosome Functions}, author = {Pestka, S.}, year = 1971, journal = {Annual Reviews in Microbiology}, volume = {25}, pages = {487–562}, doi = {10.1146/annurev.mi.25.100171.002415}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.mi.25.100171.002415}, keywords = {Alkaloids,antibiotics,Bacterial Proteins,biosynthesis,chemistry,Chloramphenicol,Cyclohexanecarboxylic Acids,Cycloheximide,drug effects,Emetine,Erythromycin,Escherichia coli,Genetic Code,GeneticsMicrobial,Lincomycin,metabolism,ModelsChemical,nosource,pharmacology,physiology,Puromycin,Review,ribosome,Ribosomes,RNAMessenger,RNATransfer,Streptomycin,Tetracycline} } % == BibTeX quality report for pestkaInhibitorsRibosomeFunctions1971a: % ? unused Journal abbr (“Annu.Rev.Microbiol.”)

@article{pestkaStudiesFormationRibonucleic1971, title = {Studies on {{Formation}} of {{Ribonucleic Acid-Ribosome Complexes}} .16. {{Effect}} of {{Ribosomal Translocation Inhibitors}} on {{Polyribosomes}}}, author = {Pestka, S. and Hintikka, H.}, year = 1971, journal = {Journal of Biological Chemistry}, volume = {246}, number = {24}, pages = {7723-&}, url = {ISI:A1971L353000041}, keywords = {COMPLEX,COMPLEXES,INHIBITOR,Multiple DOI,nonfile,nosource,Polyribosomes,translocation} } % == BibTeX quality report for pestkaStudiesFormationRibonucleic1971: % ? Title looks like it was stored in title-case in Zotero

@article{pestkaFormationTransferRibonucleic1972a, title = {The Formation of Transfer Ribonucleic Acid-Ribosome Complexes. {{XXI}}. {{Effect}} of Antibiotics on Peptidyl-Puromycin Synthesis by Mammalian Polyribosomes.}, author = {Pestka, S. and Rosenfeld, H. and Harris, R. and Hintikka, H.}, year = 1972, journal = {J.Biol.Chem.}, volume = {247}, pages = {6895–600}, doi = {10.1016/S0021-9258(19)44669-3}, keywords = {antibiotic,antibiotics,COMPLEX,COMPLEXES,nosource,peptidyl-transfer,Polyribosomes,sparsomycin} } % == BibTeX quality report for pestkaFormationTransferRibonucleic1972a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{pestkaUseInhibitorsStudies1974a, title = {The Use of Inhibitors in Studies on Protein Synthesis.}, author = {Pestka, S.}, year = 1974, journal = {Methods in enzymology}, volume = {30}, eprint = {4605358}, eprinttype = {pubmed}, pages = {261–282}, doi = {10.1016/0076-6879(74)30030-4}, url = {http://www.ncbi.nlm.nih.gov/pubmed/4605358}, keywords = {74309417,antibiotics,Antimetabolites,biosynthesis,Chloramphenicol,Comparative Study,drug effects,fragment reaction,Fusidic Acid,Kanamycin,Kinetics,metabolism,Methods,ModelsBiological,Neomycin,nosource,Peptide Chain Elongation,Peptide Chain Initiation,Peptide Chain Termination,Peptide Elongation Factors,Peptide Initiation Factors,Peptide Termination Factors,pharmacology,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Puromycin,Review,Ribosomes,RNAMessenger,Streptomycin,Tetracycline,TranslationGenetic,Tricarboxylic Acids} } % == BibTeX quality report for pestkaUseInhibitorsStudies1974a: % ? unused Journal abbr (“Methods Enzymol.”)

@incollection{pestkaThiostriptonGroupAntibiotics1974, title = {The Thiostripton Group of Antibiotics.}, booktitle = {Antibiotics {{Vol}}. {{III}}. {{Mechanism}} of Action of Antimicrobial and Antitumor Agents.}, author = {Pestka, S. and Bodley, J.W.}, year = 1974, pages = {551–573}, publisher = {Springer-VErlag}, address = {New York NY}, collaborator = {Corcoran, J.W. and Hahn, F.E.}, keywords = {antibiotic,antibiotics,antitumor,drugs,MECHANISM,nosource,review article} }

@incollection{pestkaInhibitorsProteinSynthesis1977, title = {Inhibitors of Protein Synthesis.}, booktitle = {Molecular Mechanismns of Protein Biosynthesis.}, author = {Pestka, S.}, year = 1977, pages = {467–553}, publisher = {Academic Press}, address = {New York}, collaborator = {Weissbach, H. and Pestka, S.}, keywords = {antibiotic,antibiotics,biosynthesis,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Review,review article} }

@article{pestovaEukaryoticRibosomesRequire1998, title = {Eukaryotic Ribosomes Require Initiation Factors 1 and {{1A}} to Locate Initiation Codons.}, author = {Pestova, T.V and Borukhov, S.I and Hellen, C.U.T.}, year = 1998, journal = {Nature}, volume = {394}, number = {6696}, pages = {854–859}, publisher = {[London: Macmillan Journals], 1869-}, doi = {10.1038/29703}, url = {http://www.bmb.uga.edu/wschmidt/bcmb8020files/pestova.pdf}, abstract = {The scanning model of translation initiation is a coherent description of how eukaryotic ribosomes reach the initiation codon after being recruited to the capped 5’ end of messenger RNA. Five eukaryotic initiation factors (eIF 2, 3, 4A, 4B and 4F) with established functions have been assumed to be sufficient to mediate this process. Here we report that eIF1 and eIF1A are also both essential for translation initiation. In their absence, 43S ribosomal preinitiation complexes incubated with ATP, eIF4A, eIF4B and eIF4F bind exclusively to the cap-proximal region but are unable to reach the initiation codon. Individually, eIF1A enhances formation of this cap-proximal complex, and eIF1 weakly promotes formation of a 48S ribosomal complex at the initiation codon. These proteins act synergistically to mediate assembly of ribosomal initiation complexes at the initiation codon and dissociate aberrant complexes from the mRNA.}, pmid = {9732867}, keywords = {assembly,Codon,COMPLEX,COMPLEXES,eIF1,eIF1A,elongation,initiation,nosource,ribosome,Ribosomes,Rna,sui1,techniques,toeprinting,translation} }

@article{pestovaMolecularMechanismsTranslation2001, title = {Molecular Mechanisms of Translation Initiation in Eukaryotes}, author = {Pestova, T.V. and Kolupaeva, V.G. and Lomakin, I.B. and Pilipenko, E.V. and Shatsky, I.N. and Agol, V.I. and Hellen, C.U.}, year = 2001, month = jun, journal = {Proc.Natl.Acad.Sci.U.S.A}, volume = {98}, number = {13}, pages = {7029–7036}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.111145798}, url = {http://www.pnas.org/content/98/13/7029.short}, abstract = {Translation initiation is a complex process in which initiator tRNA, 40S, and 60S ribosomal subunits are assembled by eukaryotic initiation factors (eIFs) into an 80S ribosome at the initiation codon of mRNA. The cap-binding complex eIF4F and the factors eIF4A and eIF4B are required for binding of 43S complexes (comprising a 40S subunit, eIF2/GTP/Met-tRNAi and eIF3) to the 5’ end of capped mRNA but are not sufficient to promote ribosomal scanning to the initiation codon. eIF1A enhances the ability of eIF1 to dissociate aberrantly assembled complexes from mRNA, and these factors synergistically mediate 48S complex assembly at the initiation codon. Joining of 48S complexes to 60S subunits to form 80S ribosomes requires eIF5B, which has an essential ribosome-dependent GTPase activity and hydrolysis of eIF2-bound GTP induced by eIF5. Initiation on a few mRNAs is cap-independent and occurs instead by internal ribosomal entry. Encephalomyocarditis virus (EMCV) and hepatitis C virus epitomize distinct mechanisms of internal ribosomal entry site (IRES)-mediated initiation. The eIF4A and eIF4G subunits of eIF4F bind immediately upstream of the EMCV initiation codon and promote binding of 43S complexes. EMCV initiation does not involve scanning and does not require eIF1, eIF1A, and the eIF4E subunit of eIF4F. Initiation on some EMCV-like IRESs requires additional noncanonical initiation factors, which alter IRES conformation and promote binding of eIF4A/4G. Initiation on the hepatitis C virus IRES is even simpler: 43S complexes containing only eIF2 and eIF3 bind directly to the initiation codon as a result of specific interaction of the IRES and the 40S subunit}, keywords = {0,60S subunit,Amino Acid Sequence,animal,assembly,BINDING,Cap binding,CAP-BINDING COMPLEX,chemistry,Codon,COMPLEX,COMPLEXES,CONFORMATION,Consensus Sequence,DISTINCT MECHANISMS,eIF1,eIF1A,eIF3,EIF5,ENCEPHALOMYOCARDITIS VIRUS,Eukaryotic Cells,FORM,genetics,Globin,Globins,GTP,GTP-Binding Proteins,GTPase,GTPASE ACTIVITY,HEPATITIS-C,human,Hydrolysis,immunology,initiation,INITIATION-FACTOR,INTERNAL RIBOSOMAL ENTRY,internal ribosomal entry site,La,MECHANISM,MECHANISMS,metabolism,microbiology,MOLECULAR MECHANISMS,Molecular Sequence Data,mRNA,nosource,Peptide Chain Initiation,Peptide Initiation Factors,physiology,protein,Proteins,REQUIRES,Review,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNAMessenger,RNATransferMet,scanning,SITE,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,translation,TRANSLATION INITIATION,tRNA,UPSTREAM,virus} } % == BibTeX quality report for pestovaMolecularMechanismsTranslation2001: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.U.S.A

@article{pestovaRolesIndividualEukaryotic2002, title = {The Roles of Individual Eukaryotic Translation Initiation Factors in Ribosomal Scanning and Initiation Codon Selection}, author = {Pestova, T.V. and Kolupaeva, V.G.}, year = 2002, month = nov, journal = {Genes & Development}, volume = {16}, number = {22}, pages = {2906–2922}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.1020902}, url = {http://genesdev.cshlp.org/content/16/22/2906.short}, abstract = {To elucidate an outline of the mechanism of eukaryotic translation initiation, 48S complex formation was analyzed on defined mRNAs in reactions reconstituted in vitro from fully purified translation components. We found that a ribosomal 40S subunit, eukaryotic initiation factor (eIF) 3, and the eIF2 tertiary complex form a 43S complex that can bind to the 5’-end of an unstructured 5’-untranslated region (5’-UTR) and in the presence of cIF1 scan along it and locate the initiation codon without a requirement for adenosine triphosphate (ATP) or factors (eIF4A, eIF4B, eIF4F) associated with ATP hydrolysis. Scanning oil unstructured 5’-UTRs was enhanced by ATP, eIFs 4A and 4B, and the central domain of the eIF4G subunit of cIF4F. Their omission increased the dependence of scanning on eIFs I and 1A. Ribosomal movement oil 5’-UTRs containing even weak secondary structures required ATP and RNA helicases. eIF4F was essential for scanning, and eIFs 4A and 4B were insufficient to promote this process in the absence of eIF4F. We report that in addition to its function in scanning, eIF1 also plays a principal role in initiation codon selection. In the absence of eIF1, 43S complexes could no longer discriminate between cognate and noncognate initiation codons or sense the nucleotide context of initiation codons and were able to assemble 48S complexes on 5’-proximal AUG triplets located only 1, 2, and 4 nt from the 5’-end of mRNA}, keywords = {3,Adenosine,Adenosine Triphosphate,ATP,AUG,BINDING PROTEIN,CAP STRUCTURE,Codon,CODONS,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,DOMAIN,eIF1,EUKARYOTIC TRANSLATION,FACTOR 4G EIF4G,Helicase,HELICASE ACTIVITY,Hydrolysis,In Vitro,IN-VITRO,initiation,MAMMALIAN-CELLS,MECHANISM,MESSENGER-RNA,Movement,mRNA,nosource,REGION,ribosome,Rna,RNA Helicases,RNA SECONDARY STRUCTURE,scanning,SECONDARY STRUCTURE,SELECTION,sequence,START CODON,structure,SUBUNIT,T,translation,TRANSLATION INITIATION} }

@article{pestovaTranslationElongationAssembly2003a, title = {Translation Elongation after Assembly Ribosomes on the {{Cricket}} Paralysis Virus Internal Ribosomal Entry Site without Initiation Factors or Initiator {{tRNA}}}, author = {Pestova, T.V. and Hellen, C.U.T.}, year = 2003, month = jan, journal = {Genes & Development}, volume = {17}, number = {2}, pages = {181–186}, doi = {10.1101/gad.1040803}, url = {ISI:000180496600003}, abstract = {Reconstitution of translation elongation from purified components confirmed that ribosomes that assembled on the Cricket paralysis virus intercistronic internal ribosomal entry site (IRES) without the involvement of initiation factors or initiator tRNA were active in elongation and are, therefore, true initiation complexes. The first elongation cycle occurred without peptide bond formation on 80S ribosomes that did not contain tRNA in the P site. It required elongation factors 1A and 2 and A site-cognate aminoacylated tRNA. Cycloheximide arrested ribosomes on the IRES only after two cycles of elongation, when the first deacylated tRNA reached the E-site after translocation from the A-site}, keywords = {A SITE,A-SITE,AMINO-ACID,ANGSTROM RESOLUTION,assembly,BOND FORMATION,Codon,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,Cricket paralysis virus,Cycloheximide,CYCLOHEXIMIDE RESISTANCE,E site,elongation,ELONGATION CYCLE,elongation factors,ELONGATION-FACTORS,eukaryotic elongation factor,HEPATITIS-C,IN-VITRO,initiation,INTERNAL RIBOSOMAL ENTRY,internal ribosomal entry site,L41,MESSENGER-RNA,nosource,P SITE,P-SITE,protein,RECONSTITUTION,ribosome,Ribosomes,SITE,SUBUNIT,T,translation,translocation,tRNA,virus} }

@article{petersonNewApplications2D2004, title = {New Applications of {{2D}} Filtered/Edited {{NOESY}} for Assignment and Structure Elucidation of {{RNA}} and {{RNA-protein}} Complexes}, author = {Peterson, R.D. and Theimer, C.A. and Wu, H. and Feigon, J.}, year = 2004, month = jan, journal = {Journal of Biomolecular NMR}, volume = {28}, number = {1}, pages = {59–67}, publisher = {Springer}, doi = {10.1023/B:JNMR.0000012861.95939.05}, url = {http://www.springerlink.com/index/k479373r430w32w3.pdf}, abstract = {NMR spectra of large RNAs are difficult to assign because of extensive spectral overlap and unfavorable relaxation properties. Here we present a new approach to facilitate assignment of RNA spectra using a suite of four 2D-filtered/edited NOESY experiments in combination with base-type-specific isotopically labeled RNA. The filtering method was developed for use in 3D filtered NOESY experiments (Zwahlen et al., 1997), but the 2D versions are both more sensitive and easier to interpret for larger RNAs than their 3D counterparts. These experiments are also useful for identifying intermolecular NOEs in RNA-protein complexes. Applications to NOE assignment of larger RNAs and an RNA-protein complex are presented}, keywords = {ASSIGNMENT,BIOLOGY,chemistry,COMPLEX,COMPLEXES,La,NMR,nosource,Rna,structure} } % == BibTeX quality report for petersonNewApplications2D2004: % ? unused Journal abbr (“J.Biomol.NMR”)

@article{petesSimpleMendelianInheritance1977, title = {Simple {{Mendelian}} Inheritance of the Reiterated Ribosomal {{DNA}} of Yeast}, author = {Petes, T.D. and Botstein, D.}, year = 1977, month = nov, journal = {Proceedings of the National Academy of Sciences}, volume = {74}, number = {11}, pages = {5091–5095}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.74.11.5091}, url = {http://www.pnas.org/content/74/11/5091.short}, abstract = {A diploid strain of yeast (Saccharomyces cerevisiae) was found to be heterozygous for two forms of the highly repetitious ribosomal DNA. These forms could be distinguished by the pattern of fragments produced after digestion with the site-specific restriction endonuclease EcoRI. The mode of inheritance of ribosomal DNA was determined by tetrad analysis. Of 14 tetrads analyzed, 12 clearly showed the ribosomal DNA forms segregating as a single Mendelian unit. The simplest interpretation of this result is that all of the approximately 100 copies of the ribosomal DNA genes of the yeast cell are located on one chromosome and that meiotic recombination within these genes is suppressed. Two of the 14 tetrads showed the segregation patterns expected as the result of mitotic recombination within the ribosomal DNA}, keywords = {78053057,analysis,Base Sequence,Chromosomes,Dna,gene,Genes,genetics,Mitosis,nosource,Nucleic Acid Hybridization,physiology,RecombinationGenetic,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,site specific,SporesFungal,supportu.s.gov’tp.h.s.,yeast} } % == BibTeX quality report for petesSimpleMendelianInheritance1977: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{petesCharacterizationTypesYeast1978, title = {Characterization of 2 {{Types}} of {{Yeast Ribosomal Dna Genes}}}, author = {Petes, T.D. and Hereford, L.M. and Skryabin, K.G.}, year = 1978, journal = {Journal of Bacteriology}, volume = {134}, number = {1}, pages = {295–305}, doi = {10.1128/jb.134.1.295-305.1978}, url = {ISI:A1978EV26000037}, keywords = {Dna,gene,Genes,nosource,yeast} } % == BibTeX quality report for petesCharacterizationTypesYeast1978: % ? Title looks like it was stored in title-case in Zotero

@article{petesMeioticMappingYeast1979, title = {Meiotic Mapping of Yeast Ribosomal Deoxyribonucleic Acid on Chromosome {{XII}}.}, author = {Petes, T.D.}, year = 1979, month = apr, journal = {Journal of Bacteriology}, volume = {138}, number = {1}, pages = {185–192}, publisher = {Am Soc Microbiol}, doi = {10.1128/jb.138.1.185-192.1979}, url = {http://jb.asm.org/cgi/content/abstract/138/1/185}, abstract = {We have used meiotic mapping techniques to locate the position of the repeating ribosomal DNA (rDNA) genes of the yeast Saccharomyces cerevisiae. We found that the rDNA genes are located on the right arm of chromosome XII, approximately 45 map units centromere distal to the gene gal2. Together with mapping data from previous studies, this result suggests that the tandem array of rDNA genes contains at least two junctions with the non-rDNA of the yeast chromosome. In addition, we observed segregation patterns of the rDNA genes consistent with meiotic recombination within the rDNA gene tandem array in 3 of the 59 tetrads examined}, keywords = {0,3,ACID,CEREVISIAE,Chromosome Mapping,cytology,Dna,gene,Genes,genetics,La,mapping,nosource,PATTERNS,POSITION,rDNA,RECOMBINATION,RecombinationGenetic,Research SupportU.S.Gov’tP.H.S.,Rna,RNARibosomal,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,techniques,UNITS,yeast} } % == BibTeX quality report for petesMeioticMappingYeast1979: % ? unused Journal abbr (“J.Bacteriol.”)

@article{petesYeastRibosomalDNA1979, title = {Yeast Ribosomal {{DNA}} Genes Are Located on Chromosome {{XII}}}, author = {Petes, T.D.}, year = 1979, month = jan, journal = {Proceedings of the National Academy of Sciences}, volume = {76}, number = {1}, pages = {410–414}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.76.1.410}, url = {http://www.pnas.org/content/76/1/410.short}, abstract = {Two lines of experimental evidence indicate that the repeating ribosomal DNA (rDNA) genes of the yeast Saccharomyces cerevisiae are located on chromosome XII. First, the rDNA genes are linked mitotically to genes that have been previously mapped to chromosome XII. Second, yeast strains that have two copies of the chromosome containing the rDNA genes in every strain examined also have two copies of chromosome XII; this is not true for the other yeast chromosomes. These data also establish that in mitosis most of the rDNA genes in yeast are not extrachromosomal}, keywords = {0,Aneuploidy,CEREVISIAE,Chromosome Mapping,Chromosomes,Dna,gene,Genes,GenesStructural,genetics,La,LINE,Linkage (Genetics),Mitosis,nosource,rDNA,RecombinationGenetic,Research SupportU.S.Gov’tP.H.S.,Rna,RNARibosomal,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,yeast} } % == BibTeX quality report for petesYeastRibosomalDNA1979: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{petrovRibosomalProteinL32004, title = {Ribosomal Protein {{L3}}: Influence on Ribosome Structure and Function}, author = {Petrov, A. and Meskauskas, A. and Dinman, J.D.}, year = 2004, month = may, journal = {RNA.Biol}, volume = {1}, number = {1}, pages = {59–65}, url = {PM:17194937}, abstract = {Early studies demonstrated roles for ribosomal protein L3 in peptidyltransferase center formation and the ability of cells to propagate viruses. More recent studies have linked these two processes via the effects of mutants and drugs on programmed -1 ribosomal frameshifting. Here, we show that mutant forms of L3 result in ribosomes having increased affinities for both aminoacyl- and peptidyl-tRNAs. These defects potentiate the effects of sparsomycin, which promotes increased aminoalcyl-tRNA binding at the P-site, while antagonizing the effects anisomycin, a drug that promotes decreased peptidyl-tRNA binding at the A-site. The changes in ribosome affinities for tRNAs also correlate with decreased peptidyltransferase activities of mutant ribosomes, and with decreased rates of cell growth and protein synthesis. In vivo dimethylsulfate (DMS) protection studies reveal that small changes in L3 primary sequence also have significant effects on rRNA structure as far away as 100 A, supporting an allosteric model of ribosome function}, keywords = {0,A SITE,A-SITE,ACID,Allosteric Site,anisomycin,Base Sequence,BINDING,BIOLOGY,CELLS,chemistry,DMS,drugs,FORM,Frameshifting,Gene Expression Regulation,Genetic,genetics,GROWTH,Haloarcula marismortui,IN-VIVO,Kinetics,L3,La,metabolism,MODEL,Molecular Sequence Data,MOLECULAR-GENETICS,MUTANTS,Mutation,No DOI found,nosource,Nucleic Acid Conformation,P SITE,P-SITE,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,pharmacology,physiology,PROTECTION,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,ribosomal frameshifting,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Rna,RNA Stability,RNARibosomal,rRNA,sequence,sparsomycin,structure,Sulfuric Acid Esters,Support,tRNA,Viruses} } % == BibTeX quality report for petrovRibosomalProteinL32004: % ? Possibly abbreviated journal title RNA.Biol

@article{petrovYeastRibosomalProtein2008, title = {Yeast Ribosomal Protein {{L10}} Helps Coordinate {{tRNA}} Movement through the Large Subunit.}, author = {Petrov, A.N. and Meskauskas, A. and Roshwalb, S.C. and Dinman, J.D.}, year = 2008, month = nov, journal = {Nucleic Acids Res.}, volume = {36⬚ ⬚}, number = {19}, pages = {6187–6198}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gkn643}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2577338&tool=pmcentrez&rendertype=abstract http://nar.oxfordjournals.org/content/36/19/6187.short}, abstract = {Yeast ribosomal protein L10 (E. coli L16) is located at the center of a topological nexus that connects many functional regions of the large subunit. This essential protein has previously been implicated in processes as diverse as ribosome biogenesis, translational fidelity and mRNA stability. Here, the inability to maintain the yeast Killer virus was used as a proxy for large subunit defects to identify a series of L10 mutants. These mapped to roughly four discrete regions of the protein. A detailed analysis of mutants located in the N-terminal ‘hook’ of L10, which inserts into the bulge of 25S rRNA helix 89, revealed strong effects on rRNA structure corresponding to the entire path taken by the tRNA 3’ end as it moves through the large subunit during the elongation cycle. The mutant-induced structural changes are wide-ranging, affecting ribosome biogenesis, elongation factor binding, drug resistance/hypersensitivity, translational fidelity and virus maintenance. The importance of L10 as a potential transducer of information through the ribosome, and of a possible role of its N-terminal domain in switching between the pre- and post-translocational states are discussed.}, pmid = {18824477}, keywords = {3,Alleles,analysis,Base Sequence,BINDING,BIOGENESIS,BIOLOGY,DOMAIN,E,elongation,ELONGATION CYCLE,Eukaryotic,Eukaryotic: chemistry,Eukaryotic: metabolism,Fidelity,Genetic,genetics,IDENTIFY,INFORMATION,killer,killer virus,L10,La,Large,microbiology,Models,MOF,Molecular,Molecular Sequence Data,MOLECULAR-GENETICS,Movement,mRNA,mRNA stability,MUTANTS,Mutation,nosource,Peptide Chain Elongation,protein,Protein Biosynthesis,REGION,Ribosomal,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: genetics,RIBOSOMAL-PROTEIN,Ribosomal: chemistry,ribosome,ribosome biogenesis,Ribosome Subunits,Ribosomes,Ribosomes: chemistry,RNA,rRNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: chemistry,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: growth & development,SERIES,stability,Structural,structure,SUBUNIT,Transfer,Transfer: chemistry,Transfer: metabolism,Translational,translational fidelity,tRNA,virus,yeast} } % == BibTeX quality report for petrovYeastRibosomalProtein2008: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{petrovTelomeraseSaccharomycesCerevisiae1998, title = {Telomerase from {{Saccharomyces}} Cerevisiae Contains Several Protein Subunits and May Have Different Activities Depending on the Protein Content}, author = {Petrov, A.V. and Dokudovskaya, S.S. and Sokolov, K.A. and Lavrik, O.I. and Favre, A. and Dontsova, O.A. and Bogdanov, A.A.}, year = 1998, journal = {FEBS letters}, volume = {436}, number = {1}, pages = {35–40}, publisher = {Elsevier}, doi = {10.1016/S0014-5793(98)01091-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579398010916}, abstract = {Telomerase is a ribonucleoprotein responsible for maintaining telomeres during the cell cycle [1,2]. Here we describe a two-step purification procedure for the Saccharomyces cerevisiae telomerase complex. We have found that the properties (processivity, nuclease activity) of telomerase depend on the isolation procedure. Using a cross-linking approach, we have revealed several proteins that could be components of the telomerase complex. Furthermore, spectra of cross-linked proteins differ in processive and non-processive telomerase complexes}, keywords = {0,antisense,Antisense Elements (Genetics),cell cycle,chemistry,ChromatographyLiquid,COMPLEX,COMPLEXES,COMPONENT,CROSS-LINKING,Cross-Linking Reagents,Dna,DNA Primers,ELEMENTS,enzymology,Fungal Proteins,Genetic,genetics,isolation & purification,La,metabolism,Methods,ModelsChemical,nosource,protein,Protein Subunits,Proteins,purification,Repetitive SequencesNucleic Acid,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUBUNIT,supportnon-u.s.gov’t,Telomerase,Telomere,Ultracentrifugation} } % == BibTeX quality report for petrovTelomeraseSaccharomycesCerevisiae1998: % ? unused Journal abbr (“FEBS Lett.”)

@article{pfundMolecularChaperoneSsb1998a, title = {The Molecular Chaperone {{Ssb}} from {{Saccharomyces}} Cerevisiae Is a Component of the Ribosome Nascent Chain Complex}, author = {Pfund, C. and {Lopez-Hoyo}, N. and Ziegelhoffer, T. and Schilke, B.A. and {Lopez-Buesa}, P. and Walter, W.A. and Wiedmann, M. and Craig, E.A.}, year = 1998, month = jul, journal = {EMBO Journal}, volume = {17}, number = {14}, pages = {3981–3989}, doi = {10.1093/emboj/17.14.3981}, url = {ISI:000074980000018}, abstract = {The 70 kDa heat shock proteins (Hsp70s) are a ubiquitous class of molecular chaperones. The Ssbs of Saccharomyces cerevisiae are an abundant type of Hsp70 found associated with translating ribosomes, To understand better the function of Ssb in association with ribosomes, the Ssb-ribosome interaction was characterized. Incorporation of the aminoacyl-tRNA analog puromycin by translating ribosomes caused the release of Ssb concomitant with the release of nascent chains. In addition, Ssb could be cross-linked to nascent chains containing a modified lysine residue with a photoactivatable cross-linker. Together, these results suggest an interaction of Ssb with the nascent chain. The interaction of Ssb with the ribosome-nascent chain complex was stable, as demonstrated by resistance to treatment with high salt; however, Ssb interaction with the ribosome in the absence of nascent chain was salt sensitive. We propose that Ssb is a core component of the translating ribosome which interacts with both the nascent polypeptide chain and the ribosome, These interactions allow Ssb to function as a chaperone on the ribosome, preventing the misfolding of newly synthesized proteins}, keywords = {ASSOCIATION,ATP HYDROLYSIS,CEREVISIAE,chaperone,COGNATE PROTEIN,COMPLEX,COMPLEXES,COMPONENT,E,ENDOPLASMIC-RETICULUM,ESCHERICHIA-COLI,Heat,HEAT-SHOCK,HEAT-SHOCK PROTEIN,Lysine,Molecular Chaperones,Multigene Family,nosource,PEPTIDE BINDING,POLYPEPTIDE,POLYPEPTIDE-CHAIN,POLYPEPTIDE-CHAINS,protein,Protein Folding,Proteins,Puromycin,RELEASE,RESISTANCE,ribosome,ribosome-nascent chain complex,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SIGNAL RECOGNITION PARTICLE,Ssb,TRIGGER FACTOR} }

@article{phelpsUniversallyConservedInteractions2002, title = {Universally Conserved Interactions between the Ribosome and the Anticodon Stem-Loop of {{A}} Site {{tRNA}} Important for Translocation}, author = {Phelps, S.S. and Jerinic, O. and Joseph, S.}, year = 2002, month = oct, journal = {Molecular cell}, volume = {10}, number = {4}, pages = {799–807}, publisher = {Elsevier}, doi = {10.1016/S1097-2765(02)00686-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/s109727650200686x}, abstract = {The iterative movement of the tRNA-mRNA complex through the ribosome is a hallmark of the elongation phase of protein synthesis. We used synthetic anticodon stem-loop analogs (ASL) of tRNA(Phe) to systematically identify ribose 2’-hydroxyl groups that are essential for binding and translocation from the ribosomal A site. Our results show that 2’-hydroxyl groups at positions 33, 35, and 36 in the A site ASL are important for translocation. Consistent with the view that the molecular basis of translocation may be similar in all organisms, the 2’-hydroxyl groups at positions 35 and 36 in the ASL interact with universally conserved bases G530 and A1493, respectively, in 16S rRNA. Furthermore, these interactions are also essential for the decoding process, indicating a functional relationship between decoding and translocation}, keywords = {A-SITE,Anticodon,Base Sequence,BINDING,Binding Sites,chemistry,COMPLEX,COMPLEXES,decoding,elongation,Escherichia coli,Gene Expression RegulationBacterial,genetics,Hydroxylation,La,metabolism,Methylation,ModelsMolecular,Movement,nosource,Nucleic Acid Conformation,Peptide Elongation Factor G,protein,Protein Subunits,protein synthesis,PROTEIN-SYNTHESIS,Ribose,ribosome,Ribosomes,RNATransferPhe,rRNA,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Time Factors,TranslationGenetic,translocation,tRNA} } % == BibTeX quality report for phelpsUniversallyConservedInteractions2002: % ? unused Journal abbr (“Mol.Cell”)

@article{philippeRibosomalProteinS15EscherichiaColi1993, title = {Ribosomal-{{Protein S15}} from {{Escherichia-Coli Modulates Its Own Translation}} by {{Trapping}} the {{Ribosome}} on the {{Messenger-Rna Initiation Loading Site}}}, author = {Philippe, C. and Eyermann, F. and Benard, L. and Portier, C. and Ehresmann, B. and Ehresmann, C.}, year = 1993, month = may, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {90}, number = {10}, pages = {4394–4398}, doi = {10.1073/pnas.90.10.4394}, url = {ISI:A1993LC72000016}, abstract = {From genetic and biochemical evidence, we previously proposed that S15 inhibits its own translation by binding to its mRNA in a region overlapping the ribosome loading site. This binding was postulated to stabilize a pseudoknot structure that exists in equilibrium with two stem-loops. Here, we use ‘’toeprint’’ experiments with Moloney murine leukemia virus reverse transcriptase to analyze the effect of S15 on the formation of the ternary mRNA-30S-tRNA(f)Met complex. We show that the binding of the 30S subunit on the mRNA stops reverse transcriptase near position +10, corresponding to the 3’ terminus of the pseudoknot, most likely by stabilizing the pseudoknot conformation. Furthermore, S15 is found to stabilize the binary 30S-mRNA complex. When the ternary 30S-mRNA-tRNA(f)Met complex is formed, a toeprint is observed at position +17. This toeprint progressively disappears when the ternary complex is formed in the presence of increasing concentrations of S15, while a shift from position +17 to position +10 is observed. Beside, RNase T1 footprinting experiments reveal the simultaneous binding of S15 and 30S subunit on the mRNA. Otherwise, we show by filter binding assays that initiator tRNA remains bound to the 30S subunit even in the presence of S15. Our results indicate that S15 prevents the formation of a functional ternary 30S-mRNA-tRNA(f)Met complex, the ribosome being trapped in a preternary 30S-mRNA-tRNA(f)Met complex}, keywords = {assays,BINDING,COMPLEX,COMPLEXES,CONFORMATION,Escherichia coli,ESCHERICHIA-COLI,Genetic,initiation,MESSENGER-RNA,mRNA,nosource,pseudoknot,REPRESSOR,ribosome,RNAse,structure,SUBUNIT,translation,tRNA,virus} } % == BibTeX quality report for philippeRibosomalProteinS15EscherichiaColi1993: % ? Title looks like it was stored in title-case in Zotero

@article{phillipsMurineIgMSecretory1997, title = {The Murine {{IgM}} Secretory Poly ({{A}}) Site Contains Dual Upstream and Downstream Elements Which Affect Polyadenylation}, author = {Phillips, C. and Virtanen, A.}, year = 1997, month = jun, journal = {Nucleic Acids Research}, volume = {25}, number = {12}, pages = {2344–2351}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/25.12.2344}, url = {http://nar.oxfordjournals.org/content/25/12/2344.short}, keywords = {COMPLEX,COMPLEXES,COMPONENT,downstream element,efficiency,ELEMENTS,expression,gene,Gene Expression,GENE-EXPRESSION,Genes,Genetic,genetics,In Vitro,IN-VITRO,IN-VIVO,nosource,poly(A),regulation,sequence,structure,UPSTREAM} }

@article{pichovaMutantsSaccharomycesCerevisiae1997, title = {Mutants in the {{Saccharomyces}} Cerevisiae {{RAS2}} Gene Influence Life Span, Cytoskeleton, and Regulation of Mitosis}, author = {Pichova, A. and Vondrakova, D. and Breitenbach, M.}, year = 1997, journal = {Canadian journal of microbiology}, volume = {43}, number = {8}, pages = {774–781}, publisher = {National Research Council of Canada}, doi = {10.1139/m97-111}, url = {http://cat.inist.fr/?aModele=afficheN&cpsidt=2835209}, abstract = {We investigated the phenotypic consequences in Saccharomyces cerevisiae of a disruption allele (ras2::LEU2) and of a dominant mutant form (RAS2ala18,val19) of RAS2. In addition to the phenotypes described earlier for these mutants, we observed a small increase in the life span for the disruption allele and a drastic decrease of life span for the dominant mutant form, as compared with the isogenic wild type. This was found by analyzing these alleles in two different genetic backgrounds with nearly the same results. Life spans were determined by micromanipulating mother cells and counting generations until no further cell division occurred. A morphological analysis of the terminal phenotypes of very old mother cells was performed showing enlarged or rounded cells and in some cases elongated buds, some of which were difficult to separate from the mother cell. This was observed in wild-type cells, as well as mutant cells. However, the dominant RAS2 mutant (but not the wild-type or ras2::LEU2 mutant cells) after 2 days on complex media displayed phenotypes similar to the terminal phenotype of old mothers. A substantial fraction of the cells were enlarged and generated elongated buds, they lost Calcofluor staining of the bud scars, the cell surface appeared folded, the actin cytoskeleton was aberrant, and the mitotic spindle and the cytoplasmic microtubles were defective in their proper orientation, resulting in aberrant mitoses and empty buds. These phenotypic characteristics of the RAS2ala18,val19 mutation could be causative for the previously observed rapid loss of viability of these cells in stationary phase}, keywords = {0,Actins,Alleles,analysis,Cell Division,CELLS,CEREVISIAE,COMPLEX,COMPLEXES,cytology,CYTOSKELETON,DISRUPTION,FORM,Fungal Proteins,gene,Genetic,Genetic Variation,genetics,La,media,metabolism,microbiology,MicroscopyFluorescence,Microtubules,Mitosis,Mitotic Spindle Apparatus,Mutagenesis,MUTANTS,Mutation,nosource,Phenotype,physiology,protein,Proteins,ras,ras Proteins,regulation,S,S Phase,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Staining,stationary phase,Support,WILD-TYPE} } % == BibTeX quality report for pichovaMutantsSaccharomycesCerevisiae1997: % ? unused Journal abbr (“Can.J.Microbiol.”)

@article{piekna-przybylskaNewBioinformaticTools2007, title = {New Bioinformatic Tools for Analysis of Nucleotide Modifications in Eukaryotic {{rRNA}}}, author = {{Piekna-Przybylska}, D. and Decatur, W.A. and Fournier, M.J.}, year = 2007, month = mar, journal = {RNA.}, volume = {13}, number = {3}, pages = {305–312}, publisher = {Cold Spring Harbor Lab}, doi = {10.1261/rna.373107}, url = {http://rnajournal.cshlp.org/content/13/3/305.short}, abstract = {This report presents a valuable new bioinformatics package for research on rRNA nucleotide modifications in the ribosome, especially those created by small nucleolar RNA:protein complexes (snoRNPs). The interactive service, which is not available elsewhere, enables a user to visualize the positions of pseudouridines, 2’-O-methylations, and base methylations in three-dimensional space in the ribosome and also in linear and secondary structure formats of ribosomal RNA. Our tools provide additional perspective on where the modifications occur relative to functional regions within the rRNA and relative to other nearby modifications. This package of new tools is presented as a major enhancement of an existing but significantly upgraded yeast snoRNA database available publicly at http://people.biochem.umass.edu/sfournier/fournierlab/snornadb/. The other key features of the enhanced database include details of the base pairing of snoRNAs with target RNAs, genomic organization of the yeast snoRNA genes, and information on corresponding snoRNAs and modifications in other model organisms}, keywords = {0,analysis,BASE,Base Pairing,Base Sequence,Biochemistry,BIOLOGY,CEREVISIAE,chemistry,COMPLEX,COMPLEXES,Computational Biology,DATABASE,DatabasesGenetic,gene,Genes,genetics,GenomeFungal,genomic,INFORMATION,La,metabolism,Methods,Methylation,MODEL,modification,Molecular Biology,nosource,Nucleic Acid Conformation,ORGANIZATION,POSITION,POSITIONS,protein,Proteins,Pseudouridine,REGION,RIBONUCLEOPROTEIN,Ribonucleoproteins,RibonucleoproteinsSmall Nucleolar,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Rna,RNAFungal,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SECONDARY STRUCTURE,Sequence AnalysisRNA,Software,structure,Support,TARGET,yeast} } % == BibTeX quality report for piekna-przybylskaNewBioinformaticTools2007: % ? Possibly abbreviated journal title RNA.

@article{piekna-przybylskaRibosomePerformanceEnhanced2008, title = {Ribosome Performance Is Enhanced by a Rich Cluster of Pseudouridines in the {{A-site}} Finger Region of the Large Subunit}, author = {{Piekna-Przybylska}, D. and Przybylski, P. and {Baudin-Baillieu}, A. and Rousset, J.P. and Fournier, M.J.}, year = 2008, journal = {Journal of Biological Chemistry}, volume = {283}, number = {38}, pages = {26026–26036}, publisher = {ASBMB}, doi = {10.1074/jbc.M803049200}, url = {http://www.jbc.org/content/283/38/26026.short}, abstract = {The large subunit rRNA in eukaryotes contains an unusually dense cluster of 8-10 pseudouridine (Psi) modifications located in a three-helix structure (H37-H39) implicated in several functions. This region is dominated by a long flexible helix (H38) known as the “A-site finger” (ASF). The ASF protrudes from the large subunit just above the A-site of tRNA binding, interacts with 5 S rRNA and tRNA, and through the terminal loop, forms a bridge (B1a) with the small subunit. In yeast, the three-helix domain contains 10 Psis and 6 are concentrated in the ASF helix (3 of the ASF Psis are conserved among eukaryotes). Here, we show by genetic depletion analysis that the Psis in the ASF helix and adjoining helices are not crucial for cell viability; however, their presence notably enhances ribosome fitness. Depleting different combinations of Psis suggest that the modification pattern is important and revealed that loss of multiple Psis negatively influences ribosome performance. The effects observed include slower cell growth (reduced rates up to 23% at 30 degrees C and 40-50% at 37 degrees C and 11 degrees C), reduced level of the large subunit (up to 17%), impaired polysome formation (appearance of half-mers), reduced translation activity (up to 20% at 30 degrees C and 25% at 11 degrees C), and increased sensitivity to ribosome-based drugs. The results indicate that the Psis in the three-helix region improve fitness of a eukaryotic ribosome}, keywords = {0,3,5 S rRNA,A SITE,A-SITE,analysis,Base Sequence,BINDING,Biochemistry,BIOLOGY,chemistry,DOMAIN,drugs,EUKARYOTIC RIBOSOME,FORM,Genetic,GROWTH,La,LOOP,metabolism,ModelsGenetic,ModelsMolecular,modification,Molecular Biology,Molecular Conformation,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Plasmids,Polyribosomes,Protein StructureTertiary,Pseudouridine,psi,REGION,ribosome,Ribosomes,Rna,RNAFungal,RNASmall Nucleolar,rRNA,S,Saccharomyces cerevisiae,structure,SUBUNIT,Support,Temperature,translation,tRNA,tRNA binding,yeast} } % == BibTeX quality report for piekna-przybylskaRibosomePerformanceEnhanced2008: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{pielerStructuralRequirementsInteraction1984, title = {Structural Requirements for the Interaction of {{5S rRNA}} with the Eukaryotic Transcription Factor {{IIIA}}}, author = {Pieler, T. and Erdmann, V.A. and Appel, B.}, year = 1984, month = nov, journal = {Nucleic acids research}, volume = {12}, number = {22}, pages = {8393–8406}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/12.22.8393}, url = {http://nar.oxfordjournals.org/content/12/22/8393.short}, abstract = {In order to study the binding of the eukaryotic transcription factor IIIA to heterologous 5S rRNAs with a low degree of overall sequence conservation (less than 20%) we have utilized a transcription competition assay involving eubacterial, archaebacterial and eukaryotic 5S rRNAs. All the molecules inhibit Xenopus 5S rRNA transcription specifically, which suggests that only a small amount of specific conserved RNA sequences, if indeed any, are essential for the interaction of the transcription factor with the 5S rRNA molecule, whereas universal 5S rRNA secondary structure elements seem to be required. A fragment of Xenopus laevis oocyte 5S rRNA (nucleotides 41- 120), which partially maintains the original 5S rRNA structure, also competes for TF III A. In vitro transcription of a naturally occurring mutant of the Xenopus laevis oocyte 5S rRNA gene, the pseudogene, which carries several point mutations within the TF III A binding domain is equally inhibited by exogenous Xenopus 5S rRNA}, keywords = {5S rRNA,85062822,animal,Base Sequence,BINDING,Comparative Study,DNARibosomal,ELEMENTS,Escherichia coli,gene,Genes,genetics,In Vitro,in vitro transcription,IN-VITRO,Kinetics,metabolism,Mutation,MUTATIONS,nosource,Nucleotides,Plants,Point Mutation,Rats,Rna,RNARibosomal,rRNA,Saccharomyces,sequence,Species Specificity,Structural,structure,supportnon-u.s.gov’t,Thermoplasma,transcription,TRANSCRIPTION FACTOR,Transcription Factors,TranscriptionGenetic,Xenopus,Xenopus laevis} } % == BibTeX quality report for pielerStructuralRequirementsInteraction1984: % ? unused Journal abbr (“Nucleic.Acids.Res.”)

@article{pietzschIncreasedClearanceLow1996, title = {Increased Clearance of Low Density Lipoprotein Precursors in Patients with Heterozygous Familial Defective Apolipoprotein {{B-}} 100: A Stable Isotope Approach}, author = {Pietzsch, J. and Wiedemann, B. and Julius, U. and Nitzsche, S. and Gehrisch, S. and Bergmann and S and Leonhardt, W. and Jaross, W. and Hanefeld, M.}, year = 1996, month = oct, journal = {Journal of Lipid Research}, volume = {37}, number = {10}, pages = {2074–2087}, publisher = {ASBMB}, doi = {10.1016/S0022-2275(20)37290-4}, url = {http://www.jlr.org/content/37/10/2074.short}, keywords = {analysis,IN-VIVO,Kinetics,MECHANISM,MECHANISMS,nosource} }

@article{pinardPosition13Position914EscherichiaColi1994a, title = {Position-13 and {{Position-914}} in {{Escherichia-Coli 16S Ribosomal-Rna Are Involved}} in the {{Control}} of {{Translational Accuracy}}}, author = {Pinard, R. and Cote, M. and Payant, C. and Brakiergingras, L.}, year = 1994, month = feb, journal = {Nucleic Acids Research}, volume = {22}, number = {4}, pages = {619–624}, doi = {10.1093/nar/22.4.619}, url = {ISI:A1994MY81700010}, abstract = {Using a conditional expression system with the temperature-inducible lambda P-L promoter, we previously showed that the single mutations 13U–{\(>\)}A and 914A–{\(>\)}U, and the double mutation 13U–{\(>\)}A and 914A–{\(>\)}U in Escherichia coil 16S ribosomal RNA impair the binding of streptomycin (Pinard at al., The EASED Journal, 1993, 7, 173 - 176). In this study, we found that the two single mutations and the double mutation increase translational fidelity, reducing in vivo readthrough of nonsense codons and frameshifting, and decreasing in vitro misincorporation in a poly(U)-directed system. Using oligodeoxyribonucleotide probes which hybridize to the 530 loop and to the 1400 region of 16S rRNA, two regions involved in the control of tRNA binding to the A site, we observed that the mutations in rRNA increase the binding of the probe to the 530 loop but not to the 1400 region. We suggest that the mutations at positions 13 and 914 of 16S rRNA induce a conformational rearrangement in the 530 loop, which contributes to the increased accuracy of the ribosome}, keywords = {A-SITE,accuracy,BINDING,Codon,CODONS,CONFORMATION,Escherichia coli,ESCHERICHIA-COLI,expression,Fidelity,Frameshifting,Genes,In Vitro,IN-VITRO,IN-VIVO,LOOP,Mutation,MUTATIONS,nosource,PROMOTER,PROTEIN-S12,readthrough,REGION,RESISTANCE,RIBOSOMAL-RNA,ribosome,Rna,rRNA,SITE,SITES,Streptomycin,SUBUNIT,SYSTEM,tRNA} } % == BibTeX quality report for pinardPosition13Position914EscherichiaColi1994a: % ? Title looks like it was stored in title-case in Zotero

@article{piolettiCrystalStructuresComplexes2001, title = {Crystal Structures of Complexes of the Small Ribosomal Subunit with Tetracycline, Edeine and {{IF3}}}, author = {Pioletti, M. and Schlunzen, F. and Harms, J. and Zarivach, R. and Gluhmann, M. and Avila, H. and Bashan, A. and Bartels, H. and Auerbach, T. and Jacobi, C. and Hartsch, T. and Yonath, A. and Franceschi, F.}, year = 2001, month = apr, journal = {The EMBO journal}, volume = {20}, number = {8}, pages = {1829–1839}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/20.8.1829}, url = {http://www.nature.com/emboj/journal/v20/n8/abs/7593684a.html}, abstract = {The small ribosomal subunit is responsible for the decoding of genetic information and plays a key role in the initiation of protein synthesis. We analyzed by X-ray crystallography the structures of three different complexes of the small ribosomal subunit of Thermus thermophilus with the A-site inhibitor tetracycline, the universal initiation inhibitor edeine and the C-terminal domain of the translation initiation factor IF3. The crystal structure analysis of the complex with tetracycline revealed the functionally important site responsible for the blockage of the A-site. Five additional tetracycline sites resolve most of the controversial biochemical data on the location of tetracycline. The interaction of edeine with the small subunit indicates its role in inhibiting initiation and shows its involvement with P-site tRNA. The location of the C-terminal domain of IF3, at the solvent side of the platform, sheds light on the formation of the initiation complex, and implies that the anti-association activity of IF3 is due to its influence on the conformational dynamics of the small ribosomal subunit}, keywords = {0,A-SITE,analysis,Binding Sites,chemistry,COMPLEX,COMPLEXES,CRYSTAL-STRUCTURE,Crystallography,CrystallographyX-Ray,decoding,Edeine,eIF3,Genetic,initiation,La,ModelsMolecular,nosource,P-SITE,Peptide Chain Initiation,Peptide Initiation Factors,protein,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,RIBOSOMAL-SUBUNIT,Ribosomes,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Tetracycline,Thermus,Thermus thermophilus,translation,TRANSLATION INITIATION,tRNA} } % == BibTeX quality report for piolettiCrystalStructuresComplexes2001: % ? unused Journal abbr (“EMBO J.”)

@article{pittmanFeedbackLoopCoupling1999, title = {A Feedback Loop Coupling 5 {{S rRNA}} Synthesis to Accumulation of a Ribosomal Protein}, author = {Pittman, R.H. and Andrews, M.T. and Setzer, D.R.}, year = 1999, month = nov, journal = {J.Biol.Chem.}, volume = {274}, number = {47}, pages = {33198–33201}, doi = {10.1074/jbc.274.47.33198}, abstract = {We have shown that elevated expression of ribosomal protein L5 in Xenopus embryos results in the ectopic activation of 5 S rRNA genes that are normally inactive. This transcriptional stimulation mimics the effect of overexpressing transcription factor IIIA (TFIIIA), the 5 S rRNA gene-specific transcription factor. The results support a model in which a network of nucleic acid-protein interactions involving 5 S rRNA, the 5 S rRNA gene, TFIIIA, and L5 mediates both feedback inhibition of 5 S rRNA synthesis and coupling of 5 S rRNA synthesis to accumulation of a ribosomal protein, L5. We propose that these mechanisms contribute to the homeostatic control of ribosome assembly}, keywords = {20026837,activation,animal,assembly,biosynthesis,expression,Feedback,gene,Genes,INHIBITION,L5,MECHANISM,MECHANISMS,metabolism,nosource,protein,Ribosomal Proteins,ribosome,RNARibosomal5S,rRNA,Support,supportu.s.gov’tp.h.s.,TFIIIA,transcription,TRANSCRIPTION FACTOR,Xenopus} } % == BibTeX quality report for pittmanFeedbackLoopCoupling1999: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{plantDifferentiatingNoncognateCodons2007, title = {Differentiating between Near- and Non-Cognate Codons in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Plant, E.P. and Nguyen, P. and Russ, J.R. and Pittman, Y.R. and Nguyen, T. and Quesinberry, J.T. and Kinzy, T.G. and Dinman, J.D.}, year = 2007, journal = {PLoS ONE}, volume = {2}, pages = {e517}, doi = {10.1371/journal.pone.0000517}, url = {PM:17565370}, abstract = {BACKGROUND: Decoding of mRNAs is performed by aminoacyl tRNAs (aa-tRNAs). This process is highly accurate, however, at low frequencies (10(-3) - 10(-4)) the wrong aa-tRNA can be selected, leading to incorporation of aberrant amino acids. Although our understanding of what constitutes the correct or cognate aa-tRNA:mRNA interaction is well defined, a functional distinction between near-cognate or single mismatched, and unpaired or non-cognate interactions is lacking. METHODOLOGY/PRINCIPAL FINDINGS: Misreading of several synonymous codon substitutions at the catalytic site of firefly luciferase was assayed in Saccharomyces cerevisiae. Analysis of the results in the context of current kinetic and biophysical models of aa-tRNA selection suggests that the defining feature of near-cognate aa-tRNAs is their potential to form mini-helical structures with A-site codons, enabling stimulation of GTPase activity of eukaryotic Elongation Factor 1A (eEF1A). Paromomycin specifically stimulated misreading of near-cognate but not of non-cognate aa-tRNAs, providing a functional probe to distinguish between these two classes. Deletion of the accessory elongation factor eEF1Bgamma promoted increased misreading of near-cognate, but hyperaccurate reading of non-cognate codons, suggesting that this factor also has a role in tRNA discrimination. A mutant of eEF1Balpha, the nucleotide exchange factor for eEF1A, promoted a general increase in fidelity, suggesting that the decreased rates of elongation may provide more time for discrimination between aa-tRNAs. A mutant form of ribosomal protein L5 promoted hyperaccurate decoding of both types of codons, even though it is topologically distant from the decoding center. CONCLUSIONS/SIGNFICANCE: It is important to distinguish between near-cognate and non-cognate mRNA:tRNA interactions, because such a definition may be important for informing therapeutic strategies for suppressing these two different categories of mutations underlying many human diseases. This study suggests that the defining feature of near-cognate aa-tRNAs is their potential to form mini-helical structures with A-site codons in the ribosomal decoding center. An aminoglycoside and a ribosomal factor can be used to distinguish between near-cognate and non-cognate interactions}, keywords = {A SITE,A-SITE,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,BIOLOGY,CEREVISIAE,Codon,CODONS,decoding,disease,elongation,eukaryotic elongation factor,Fidelity,FIREFLY LUCIFERASE,FORM,Genetic,genetics,GTPase,GTPASE ACTIVITY,human,L5,La,luciferase,MODEL,models,MOLECULAR-GENETICS,mRNA,Mutation,MUTATIONS,nosource,NUCLEOTIDE EXCHANGE,Paromomycin,protein,RIBOSOMAL-PROTEIN,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SELECTION,SITE,structure,tRNA,United States} }

@article{plantRoleProgrammed1Ribosomal2008, title = {The Role of Programmed-1 Ribosomal Frameshifting in Coronavirus Propagation}, author = {Plant, E.P. and Dinman, J.D.}, year = 2008, journal = {Front Biosci.}, volume = {13}, pages = {4873–4881}, doi = {10.2741/3046}, url = {PM:18508552}, abstract = {Coronaviruses have the potential to cause significant economic, agricultural and health problems. The severe acute respiratory syndrome (SARS) associated coronavirus outbreak in late 2002, early 2003 called attention to the potential damage that coronaviruses could cause in the human population. The ensuing research has enlightened many to the molecular biology of coronaviruses. A programmed -1 ribosomal frameshift is required by coronaviruses for the production of the RNA dependent RNA polymerase which in turn is essential for viral replication. The frameshifting signal encoded in the viral genome has additional features that are not essential for frameshifting. Elucidation of the differences between coronavirus frameshift signals and signals from other viruses may help our understanding of these features. Here we summarize current knowledge and add additional insight regarding the function of the programmed -1 ribosomal frameshift signal in the coronavirus lifecycle}, keywords = {BIOLOGY,Coronavirus,disease,frameshift,Frameshifting,FrameshiftingRibosomal,genetics,Genome,growth & development,human,Humans,La,Molecular Biology,nosource,Open Reading Frames,physiology,polymerase,PROPAGATION,REPLICATION,Review,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,Rna,RNA-POLYMERASE,SARS,Sars Virus,Severe Acute Respiratory Syndrome,SIGNAL,Support,Syndrome,virology,Viruses} } % == BibTeX quality report for plantRoleProgrammed1Ribosomal2008: % ? Possibly abbreviated journal title Front Biosci.

@article{plantaGlobalRegulatorsRibosome1995, title = {Global Regulators of Ribosome Biosynthesis in Yeast}, author = {Planta, R.J. and Goncalves, P.M. and Mager, W.H.}, year = 1995, month = nov, journal = {Biochemistry and cell biology}, volume = {73}, number = {11-12}, pages = {825–834}, publisher = {NATIONAL RESEARCH COUNCIL CANADA}, doi = {10.1139/o95-090}, url = {http://www.nrcresearchpress.com/doi/abs/10.1139/o95-090}, abstract = {Three abundant ubiquitous DNA-binding protein factors appear to play a major role in the control of ribosome biosynthesis in yeast. Two of these factors mediate the regulation of transcription of ribosomal protein genes (rp-genes) in yeasts. Most yeast rp-genes are under transcriptional control of Rap1p (repressor-activator protein), while a small subset of rp-genes is activated through Abf1p (ARS binding factor). The third protein, designated Reb1p (rRNA enhancer binding protein), which binds strongly to two sites located upstream of the enhancer and the promoter of the rRNA operon, respectively, appears to play a crucial role in the efficient transcription of the chromosomal rDNA. All three proteins, however, have many target sites on the yeast genome, in particular, in the upstream regions of several Pol II transcribed genes, suggesting that they play a much more general role than solely in the regulation of ribosome biosynthesis. Furthermore, some evidence has been obtained suggesting that these factors influence the chromatin structure and creat a nucleosome-free region surrounding their binding sites. Recent studies indicate that the proteins can functionally replace each other in various cases and that they act synergistically with adjacent additional DNA sequences. These data suggest that Abf1p, Rap1p, and Reb1p are primary DNA-binding proteins that serve to render adjacent cis-acting elements accessible to specific trans-acting factors}, keywords = {96282686,Base Sequence,BINDING,BINDING PROTEIN,Binding Sites,BINDING-PROTEIN,biosynthesis,Chromatin,Dna,DNA-Binding Proteins,ELEMENTS,Fungal Proteins,gene,Genes,Genome,GTP-Binding Proteins,metabolism,Molecular Sequence Data,nosource,Operon,physiology,pol,PROMOTER,protein,Proteins,rDNA,regulation,ribosome,Ribosomes,rRNA,rRNA Operon,Saccharomyces cerevisiae,sequence,structure,supportnon-u.s.gov’t,transcription,Transcription Factors,UPSTREAM,yeast,Yeasts} } % == BibTeX quality report for plantaGlobalRegulatorsRibosome1995: % ? unused Journal abbr (“Biochem.Cell Biol.”)

@article{plantaListCytoplasmicRibosomal1998, title = {The List of Cytoplasmic Ribosomal Proteins of {{Saccharomyces}} Cerevisiae}, author = {Planta, R.J. and Mager, W.H.}, year = 1998, month = mar, journal = {Yeast}, volume = {14}, number = {5}, pages = {471–477}, publisher = {Wiley Online Library}, doi = {10.1002/(SICI)1097-0061(19980330)14:5<471::AID-YEA241>3.0.CO;2-U}, url = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0061(19980330)14:5<471::AID-YEA241>3.0.CO;2-U/pdf}, abstract = {Screening of the complete genome sequence from the yeast Saccharomyces cerevisiae has enabled us to compile a complete list of the genes encoding cytoplasmic ribosomal proteins in this organism. Putative ribosomal protein genes were selected primarily on the basis of the sequence similarity of their products with ribosomal proteins from other eukaryotic organisms, in particular the rat. These genes were subsequently screened for typical yeast rp-gene characteristics, viz. (1) a high codon adaptation index; (2) their promoter structure and (3) their responses to changes in growth conditions. The yeast genome appears to carry 78 different genes, of which 59 are duplicated, encoding 32 different small-subunit and 46 large-subunit proteins. A new nomenclature for these ribosomal proteins is proposed}, keywords = {chemistry,classification,Codon,Cytoplasm,Fungal Proteins,gene,Genes,Genes-Fungal,GenesFungal,genetics,Genome,Genome-Fungal,GenomeFungal,nomenclature,nosource,PROMOTER,protein,Proteins,rat,Ribosomal Proteins,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,structure,support-non-u.s.gov’t,supportnon-u.s.gov’t,Terminology,yeast} }

@misc{plewniakGCGDocumentation2007, title = {{{GCG Documentation}}}, author = {Plewniak, F.}, year = 2007, url = {⬚http://www.vet.gla.ac.uk/GCGdoc/Data_Files/codon_freq_tables.html⬚⬚⬚ ⬚⬚}, keywords = {Codon,nosource} } % == BibTeX quality report for plewniakGCGDocumentation2007: % ? Title looks like it was stored in title-case in Zotero

@article{pohjanpeltoPolyamineDeprivationCauses1982a, title = {Polyamine Deprivation Causes Major Chromosome Aberrations in a Polyamine-Dependent {{Chinese}} Hamster Ovary Cell Line}, author = {Pohjanpelto, P. and Knuutila, S.}, year = 1982, month = oct, journal = {Exp.Cell Res.}, volume = {141}, number = {2}, pages = {333–339}, doi = {10.1016/0014-4827(82)90221-X}, url = {PM:6183133}, keywords = {0,Animals,Bucladesine,Cell Line,Chromosome Aberrations,Chromosomes,Cricetinae,Crossing OverGenetic,Culture Media,DEPRIVATION,drug effects,Female,La,LINE,media,Mitosis,nosource,Ovary,pharmacology,polyamine,Putrescine,Sister Chromatid Exchange,Staining and Labeling,Support,ultrastructure} } % == BibTeX quality report for pohjanpeltoPolyamineDeprivationCauses1982a: % ? Possibly abbreviated journal title Exp.Cell Res.

@article{polacekRibosomalPeptidylTransferase2001, title = {Ribosomal Peptidyl Transferase Can Withstand Mutations at the Putative Catalytic Nucleotide}, author = {Polacek, N. and Gaynor, M. and Yassin, A. and Mankin, A.S.}, year = 2001, month = may, journal = {Nature}, volume = {411}, number = {6836}, pages = {498–501}, publisher = {Nature Publishing Group}, doi = {10.1038/35078113}, url = {http://www.nature.com/nature/journal/v411/n6836/abs/411498a0.html}, abstract = {Peptide bond formation is the principal reaction of protein synthesis. It takes place in the peptidyl transferase centre of the large (50S) ribosomal subunit. In the course of the reaction, the polypeptide is transferred from peptidyl transfer RNA to the alpha-amino group of amino acyl-tRNA. The crystallographic structure of the 50S subunit showed no proteins within 18 A from the active site, revealing peptidyl transferase as an RNA enzyme. Reported unique structural and biochemical features of the universally conserved adenine residue A2451 in 23S ribosomal RNA (Escherichia coli numbering) led to the proposal of a mechanism of rRNA catalysis that implicates this nucleotide as the principal catalytic residue. In vitro genetics allowed us to test the importance of A2451 for the overall rate of peptide bond formation. Here we report that large ribosomal subunits with mutated A2451 showed significant peptidyl transferase activity in several independent assays. Mutations at another nucleotide, G2447, which is essential to render catalytic properties to A2451 (refs 2, 3), also did not dramatically change the transpeptidation activity. As alterations of the putative catalytic residues do not severely affect the rate of peptidyl transfer the ribosome apparently promotes transpeptidation not through chemical catalysis, but by properly positioning the substrates of protein synthesis}, keywords = {Adenine,assays,Catalysis,enzyme,Escherichia coli,ESCHERICHIA-COLI,Genetic,genetics,In Vitro,IN-VITRO,La,MECHANISM,Mutation,MUTATIONS,nosource,peptidyl transferase,peptidyl-transfer,PEPTIDYL-TRANSFERASE,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Rna,rRNA,Structural,structure,SUBUNIT,TRANSFER-RNA} }

@article{polacekSPARKNovelMethod2002, title = {{{SPARK}} - {{A}} Novel Method to Monitor Ribosomal Peptidyl Transferase Activity}, author = {Polacek, N. and Swaney, S. and Shinabarger, D. and Mankin, A.S.}, year = 2002, month = oct, journal = {Biochemistry}, volume = {41}, number = {39}, pages = {11602–11610}, publisher = {ACS Publications}, doi = {10.1021/bi026040s}, url = {http://pubs.acs.org/doi/abs/10.1021/bi026040s}, abstract = {The key enzymatic activity of the ribosome is catalysis of peptide bond formation. This reaction is a target for many clinically important antibiotics. However, the molecular mechanisms of the peptidyl transfer reaction, the catalytic contribution of the ribosome, and the mechanisms of antibiotic action are still poorly understood. Here we describe a novel, simple, convenient, and sensitive method for monitoring peptidyl transferase activity (SPARK). In this method, the ribosomal peptidyl transferase forms a peptide bond between two ligands, one of which is tritiated whereas the other is biotin-tagged. Transpeptidation results in covalent attachment of the biotin moiety to a tritiated compound. The amount of the reaction product is then directly quantified using the scintillation proximity assay technology: binding of the tritiated radioligand to the commercially available streptavidin-coated beads causes excitation of the bead-embedded scintillant, resulting in detection of radioactivity. The reaction is readily inhibited by known antibiotics, inhibitors of peptide bond formation. The method we developed is amenable to simple automation which makes it useful for screening for new antibiotics. The method is useful for different types of ribosomal research. Using this method, we investigated the effect of mutations at a universally conserved nucleotide of the active site of 23S rRNA, A2602 (Escherichia coli numbering), on the peptidyl transferase activity of the ribosome. The activities of the in vitro reconstituted mutant subunits, though somewhat reduced, were comparable with those of the subunits assembled with the wild-type 23S rRNA, indicating that A2602 mutations do not abolish the ability of the ribosome to catalyze peptide bond formation. Similar results were obtained with double mutants carrying mutations at A2602 and another universally conserved nucleotide in the peptidyl transferase center, A2451. The obtained results agree with our previous conclusion that the ribosome accelerates peptide bond formation primarily through entropic rather than chemical catalysis}, keywords = {A-SITE,ANGSTROM RESOLUTION,antibiotic,antibiotics,BINDING,Biotin,BOND FORMATION,Catalysis,conserved nucleotide,D,Escherichia coli,ESCHERICHIA-COLI,In Vitro,IN-VITRO,INHIBITOR,Ligands,MECHANISM,MECHANISMS,MOLECULAR MECHANISMS,MUTANTS,Mutation,MUTATIONS,nosource,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,peptidyl-transfer,PEPTIDYL-TRANSFERASE,RECONSTITUTION,RIBOSOMAL PEPTIDYL TRANSFERASE,ribosome,rRNA,S,SITE,STRUCTURAL BASIS,SUBUNIT,TARGET,Tetracycline,THERMUS-AQUATICUS,TRANSFER-RNA BINDING,TRANSFERASE CENTER} }

@article{polacekCriticalRoleUniversally2003a, title = {The Critical Role of the Universally Conserved {{A2602}} of {{23S}} Ribosomal {{RNA}} in the Release of the Nascent Peptide during Translation Termination}, author = {Polacek, N. and Gomez, M.J. and Ito, K. and Xiong, L.Q. and Nakamura, Y. and Mankin, A.}, year = 2003, month = jan, journal = {Molecular Cell}, volume = {11}, number = {1}, pages = {103–112}, doi = {10.1016/S1097-2765(02)00825-0}, url = {ISI:000180848900014}, abstract = {The ribosomal peptidyl transferase center is responsible for two fundamental reactions, peptide bond formation and nascent peptide release, during the elongation and termination phases of protein synthesis, respectively. We used in vitro genetics to investigate the functional importance of conserved 23S rRNA nucleotides located in the peptidyl transferase active site for transpeptidation and peptidyl-tRNA hydrolysis. While mutations at A2451, U2585, and C2063 (E. coli numbering) did not significantly affect either of the reactions, substitution of A2602 with C or its deletion abolished the ribosome ability to promote peptide release but had little effect on transpeptidation. This indicates that the mechanism of peptide release is distinct from that of peptide bond formation, with A2602 playing a critical role in peptide release during translation termination}, keywords = {ANGSTROM RESOLUTION,BINDING,BOND FORMATION,CRYSTAL-STRUCTURE,E,elongation,ESCHERICHIA-COLI RIBOSOMES,FUNCTIONAL SITES,Genetic,genetics,Hydrolysis,In Vitro,IN-VITRO,MECHANISM,Mutation,MUTATIONS,NASCENT-PEPTIDE,nosource,Nucleotides,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,protein,protein synthesis,PROTEIN-SYNTHESIS,RELEASE,RIBOSOMAL PEPTIDYL TRANSFERASE,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Rna,rRNA,S,SITE,STOP CODON RECOGNITION,SUBUNIT,termination,TRANSFERASE CENTER,translation,TRANSLATION TERMINATION} }

@article{polevodaNterminalAcetyltransferasesSequence2003, title = {N-Terminal Acetyltransferases and Sequence Requirements for {{N-terminal}} Acetylation of Eukaryotic Proteins}, author = {Polevoda, B. and Sherman, F.}, year = 2003, month = jan, journal = {Journal of molecular biology}, volume = {325}, number = {4}, pages = {595–622}, publisher = {Elsevier}, doi = {10.1016/S0022-2836(02)01269-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/S002228360201269X}, abstract = {N(alpha)-terminal acetylation occurs in the yeast Saccharomyces cerevisiae by any of three N-terminal acetyltransferases (NAT), NatA, NatB, and NatC, which contain Ard1p, Nat3p and Mak3p catalytic subunits, respectively. The N-terminal sequences required for N-terminal acetylation, i.e. the NatA, NatB, and NatC substrates, were evaluated by considering over 450 yeast proteins previously examined in numerous studies, and were compared to the N-terminal sequences of more than 300 acetylated mammalian proteins. In addition, acetylated sequences of eukaryotic proteins were compared to the N termini of 810 eubacterial and 175 archaeal proteins, which are rarely acetylated. Protein orthologs of Ard1p, Nat3p and Mak3p were identified with the eukaryotic genomes of the sequences of model organisms, including Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, Mus musculus and Homo sapiens. Those and other putative acetyltransferases were assigned by phylogenetic analysis to the following six protein families: Ard1p; Nat3p; Mak3p; CAM; BAA; and Nat5p. The first three families correspond to the catalytic subunits of three major yeast NATs; these orthologous proteins were identified in eukaryotes, but not in prokaryotes; the CAM family include mammalian orthologs of the recently described Camello1 and Camello2 proteins whose substrates are unknown; the BAA family comprise bacterial and archaeal putative acetyltransferases whose biochemical activity have not been characterized; and the new Nat5p family assignment was on the basis of putative yeast NAT, Nat5p (YOR253W). Overall patterns of N-terminal acetylated proteins and the orthologous genes possibly encoding NATs suggest that yeast and higher eukaryotes have the same systems for N-terminal acetylation}, keywords = {0,Acetylation,Acetyltransferases,Amino Acid Sequence,analysis,Animals,Arabidopsis,Archaeal Proteins,ASSIGNMENT,Bacterial,Base Sequence,Binding Sites,Caenorhabditis,Caenorhabditis elegans,CAENORHABDITIS-ELEGANS,CEREVISIAE,chemistry,Drosophila,Drosophila melanogaster,DROSOPHILA-MELANOGASTER,ELEGANS,FAMILY,gene,Genes,genetics,Genome,Humans,La,metabolism,Methionine,MODEL,Molecular Sequence Data,NatA,nosource,PATTERNS,Phylogeny,PROKARYOTES,protein,Proteins,Research SupportU.S.Gov’tP.H.S.,Review,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,SUBUNIT,SUBUNITS,SYSTEM,SYSTEMS,yeast} } % == BibTeX quality report for polevodaNterminalAcetyltransferasesSequence2003: % ? unused Journal abbr (“J.Mol.Biol.”)

@article{pooleMolecularMimicryDecoding2003, title = {Molecular Mimicry in the Decoding of Translational Stop Signals}, author = {Poole, E.S. and {Askarian-Amiri}, M.E. and Major, L.L. and McCaughan, K.K. and Scarlett, D.J. and Wilson, D.N. and Tate, W.P.}, year = 2003, journal = {Progress in nucleic acid research and molecular biology}, volume = {74}, pages = {83–121}, publisher = {Elsevier}, doi = {10.1016/S0079-6603(03)01011-0}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0079660303010110}, abstract = {Molecular mimicry was a concept that was revived as we understood more about the ligands that bound to the active center of the ribosome, and the characteristics of the active center itself. It has been particularly useful for the termination phase of protein synthesis, because for many years this major process seemed not only to be out of step) with the initiation and elongation phases but also there were no common features of the process between eubacteria and eukaryotes. As the facts that supported molecular mimicry emerged, it was seen that the protein factors that facilitated polypeptide chain release when the decoding of an mRNA was complete had common features with the ligands involved in the other phases. Moreover, now common features and mechanisms began to emerge between the eubacterial and eukaryotic RFs and suddenly there seemed to be remarkable synergy between the external ligands and commonality in at least some features of the mechanistic prnciples. Almost 10 years after molecular mimicry took hold as a framework concept, we can now see that this idea is probably too simple. For example, structural mimicry can be apparent if there are extensive conformational changes either in the ribosome active center or in the ligand itself or, most likely, both. Early indications are that the bacterial RF may indeed undergo extensive conformational changes from its solution structure to achieve this accommodation. Thus, as important if not more important than structural and functional mimicry among the ligands, might be their accomodation of a common single active center made up of at least three parts to carry out a complex series of reactions. One part of the ribosomal active center is committed to decoding, a second is committed to the chemistry of putting the protein together and releasing it, and a third part, perhaps residing in the subdomains, is committed to binding ligands so that they can perform their respective single or multiple functions. It might be more accurate to regard the decoding RF as the cuckoo taking over the nest that was crafted and honed through evolution by another, the tRNA. A somewhat ungainly RF, perhaps bigger in dimensions than the tRNA, is able, nevertheless, like the cuckoo, to maneuvre into the nest. Perhaps it pushes the nest a little out of shape, but is still able to use the site for its own functions of stop signal decoding and for facilitating the release of the polypeptide. The term molecular mimicry has been dominant in the literature for a period of important advances in the understanding of protein synthesis. When the first structures of the ribosome appeared, the concept survived and was seen to be valid still. Now, we are at the stage of understanding the more detailed molecular interactions between ligands and the rRNA in particular, and how subtle changes in localized spatial orientations of atoms occur within these interactions. The simplicity of the original concept of mimicry will inevitably be blurred by this more detailed analysis. Nevertheless, it has provided a significant set of principles that allowed development of experimental programs to enhance our understanding of the dynamic events at this remarkable active site at the interface between the two subunits of this fascinating cell organelle, the ribosome}, keywords = {0,Amino Acid Sequence,analysis,Anticodon,Bacterial,Bacterial Physiology,BINDING,Binding Sites,chemistry,Codon,CodonTerminator,COMPLEX,COMPLEXES,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,decoding,development,elongation,Eubacterium,Evolution,initiation,interface,La,Ligands,MECHANISM,MECHANISMS,ModelsMolecular,Molecular Mimicry,Molecular Sequence Data,mRNA,nosource,physiology,POLYPEPTIDE,POLYPEPTIDE-CHAIN,protein,Protein StructureSecondary,protein synthesis,PROTEIN-SYNTHESIS,RELEASE,Review,ribosome,Ribosomes,Rna,RNATransfer,rRNA,SERIES,SIGNAL,SITE,Structural,structure,SUBUNIT,SUBUNITS,termination,TranslationGenetic,tRNA} } % == BibTeX quality report for pooleMolecularMimicryDecoding2003: % ? unused Journal abbr (“Prog.Nucleic Acid Res.Mol.Biol.”)

@article{popescuSilencingRibosomalProtein2004, title = {Silencing of Ribosomal Protein {{L3}} Genes in {{N}}. Tabacum Reveals Coordinate Expression and Significant Alterations in Plant Growth, Development and Ribosome Biogenesis}, author = {Popescu, S.C. and Tumer, N.E.}, year = 2004, month = jul, journal = {The Plant Journal}, volume = {39}, number = {1}, pages = {29–44}, publisher = {Wiley Online Library}, doi = {10.1111/j.1365-313X.2004.02109.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2004.02109.x/full}, abstract = {The expression of ribosomal protein genes is coordinately regulated in bacteria, yeast, and vertebrates, so that equimolar amounts of ribosomal proteins accumulate for assembly into ribosomes. To understand how expression of ribosomal protein genes is regulated in plants, we altered expression of the large subunit ribosomal protein L3 (RPL3) genes in Nicotiana tabacum using post-transcriptional gene silencing (PTGS). L3 is encoded by two genes, RPL3A and RPL3B, with 80.2% amino acid sequence identity in tobacco. Two types of ‘hairpin’ RNA (hpRNA) vectors carrying the RPL3A or RPL3B sequences in both sense and antisense orientation were generated in order to alter the expression level of both RPL3 genes. Tobacco plants transformed with a vector containing a 5’-terminal fragment of RPL3A gene displayed decreased RPL3A mRNA levels and a marked increase in the abundance of RPL3B mRNA. These results indicated that expression of the RPL3 genes is coordinately regulated in tobacco. The transgenic plants that contained higher levels of RPL3B mRNA exhibited leaf overgrowth and mottling. Epidermal cells of these plants were increased in number and decreased in size. The precursor rRNA (pre-rRNA) and the mature rRNAs accumulated in these plants, suggesting that ribosome biogenesis is upregulated. Tobacco plants transformed with an hpRNA vector harboring the full-length RPL3B cDNA exhibited efficient silencing of both RPL3A and RPL3B genes, reduced L3 levels, and an abnormal phenotype characterized by a delay in development, stunting, and inhibition of lateral root growth. L3 deficiency led to a reduction in cell number and an increase in cell size, suggesting that L3 positively regulates cell division. Decreasing RPL3 gene expression resulted in a decrease in accumulation of the pre-rRNA, establishing a prominent role for L3 in ribosome biogenesis in plants}, keywords = {0,ACID,Amino Acid Sequence,AMINO-ACID,antisense,assembly,Bacteria,BIOLOGY,Cell Division,cell size,CELLS,deficiency,development,expression,gene,Gene Expression,Gene Expression RegulationPlant,Gene Silencing,GENE-EXPRESSION,Genes,Genetic,Genetic Vectors,genetics,GROWTH,growth & development,INHIBITION,L3,La,metabolism,mRNA,nosource,pathology,Phenotype,Plant Leaves,Plants,PlantsGenetically Modified,PRECURSOR,protein,Proteins,Ribosomal Proteins,ribosome,ribosome biogenesis,Ribosomes,Rna,RNA Interference,RNAMessenger,RnaPlant,RNARibosomal,RNASmall Interfering,rRNA,sequence,SEQUENCES,SUBUNIT,supportu.s.gov’tnon-p.h.s.,Tobacco,TransformationGenetic,ultrastructure,vector,vectors,Vertebrates,yeast} } % == BibTeX quality report for popescuSilencingRibosomalProtein2004: % ? unused Journal abbr (“Plant J.”)

@article{popovicDetectionIsolationContinuous1984, title = {Detection, Isolation, and Continuous Production of Cytopathic Retroviruses ({{HTLV-III}}) from Patients with {{AIDS}} and Pre-{{AIDS}}}, author = {Popovic, M. and Sarngadharan, M.G. and Read, E. and Gallo, R.C.}, year = 1984, month = may, journal = {Science}, volume = {224}, number = {4648}, pages = {497–500}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.6200935}, url = {http://www.sciencemag.org/content/224/4648/497.short}, abstract = {A cell system was developed for the reproducible detection of human T-lymphotropic retroviruses (HTLV family) from patients with the acquired immunodeficiency syndrome (AIDS) or with signs or symptoms that frequently precede AIDS (pre-AIDS). The cells are specific clones from a permissive human neoplastic T-cell line. Some of the clones permanently grow and continuously produce large amounts of virus after infection with cytopathic (HTLV-III) variants of these viruses. One cytopathic effect of HTLV-III in this system is the arrangement of multiple nuclei in a characteristic ring formation in giant cells of the infected T-cell population. These structures can be used as an indicator to detect HTLV-III in clinical specimens. This system opens the way to the routine detection of HTLV-III and related cytopathic variants of HTLV in patients with AIDS or pre-AIDS and in healthy carriers, and it provides large amounts of virus for detailed molecular and immunological analyses}, keywords = {Acquired Immunodeficiency Syndrome,AIDS,ARRANGEMENT,Cell Division,Cell Line,Cell Nucleus,Cell Survival,CELLS,Clone Cells,Cytopathogenic EffectViral,Deltaretrovirus,DISCOVERY,Dna,FAMILY,growth & development,HIV,Hiv-1,human,Humans,INFECTION,isolation & purification,La,LINE,metabolism,microbiology,nosource,polymerase,RETROVIRUSES,RNA-Directed DNA Polymerase,structure,Syndrome,SYSTEM,T-Lymphocytes,ultrastructure,Variation (Genetics),virus,Virus Cultivation,Viruses} }

@article{porseDirectCrosslinkingAntitumor1999, title = {Direct Crosslinking of the Antitumor Antibiotic Sparsomycin, and Its Derivatives, to {{A2602}} in the Peptidyl Transferase Center of {{23S-like rRNA}} within Ribosome-{{tRNA}} Complexes}, author = {Porse, B.T. and Kirillov, S.V. and Awayez, M.J. and Ottenheijm, H.C. and Garrett, R.A.}, year = 1999, journal = {Proceedings of the National Academy of Sciences}, volume = {96}, number = {16}, pages = {9003–9008}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.96.16.9003}, url = {http://www.pnas.org/content/96/16/9003.short}, abstract = {The antitumor antibiotic sparsomycin is a universal and potent inhibitor of peptide bond formation and selectively acts on several human tumors. It binds to the ribosome strongly, at an unknown site, in the presence of an N-blocked donor tRNA substrate, which it stabilizes on the ribosome. Its site of action was investigated by inducing a crosslink between sparsomycin and bacterial, archaeal, and eukaryotic ribosomes complexed with P-site-bound tRNA, on irradiating with low energy ultraviolet light (at 365 nm). The crosslink was localized exclusively to the universally conserved nucleotide A2602 within the peptidyl transferase loop region of 23S-like rRNA by using a combination of a primer extension approach, RNase H fragment analysis, and crosslinking with radioactive [(125)I]phenol-alanine-sparsomycin. Crosslinking of several sparsomycin derivatives, modified near the sulfoxy group, implicated the modified uracil residue in the rRNA crosslink. The yield of the antibiotic crosslink was weak in the presence of deacylated tRNA and strong in the presence of an N-blocked P-site-bound tRNA, which, as was shown earlier, increases the accessibility of A2602 on the ribosome. We infer that both A2602 and its induced conformational switch are critically important both for the peptidyl transfer reaction and for antibiotic inhibition. This supposition is reinforced by the observation that other antibiotics that can prevent peptide bond formation in vitro inhibit, to different degrees, formation of the crosslink}, keywords = {analogs &,analysis,antibiotic,antibiotics,AntibioticsAntineoplastic,antitumor,Bacillus megaterium,Bacterial,Base Sequence,chemistry,COMPLEX,COMPLEXES,Cross-Linking Reagents,derivatives,drug effects,Escherichia coli,Halobacterium halobium,human,In Vitro,IN-VITRO,INHIBITION,metabolism,Molecular Sequence Data,nosource,Nucleic Acid Conformation,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,peptidyl-transfer,PEPTIDYL-TRANSFERASE,Peptidyltransferase,pharmacology,primer extension,regulation,ribosome,Ribosomes,Rna,RNABacterial,RNAFungal,RNARibosomal23S,RNAse,RNATransfer,rRNA,Saccharomyces cerevisiae,sparsomycin,supportnon-u.s.gov’t,tRNA,ultrastructure} } % == BibTeX quality report for porseDirectCrosslinkingAntitumor1999: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{powersRegulationRibosomeBiogenesis1999, title = {Regulation of Ribosome Biogenesis by the Rapamycin-Sensitive {{TOR-signaling}} Pathway in {{Saccharomyces}} Cerevisiae}, author = {Powers, T. and Walter, P.}, year = 1999, month = apr, journal = {Molecular biology of the cell}, volume = {10}, number = {4}, pages = {987–1000}, publisher = {Am Soc Cell Biol}, doi = {10.1091/mbc.10.4.987}, url = {http://www.molbiolcell.org/cgi/content/abstract/10/4/987}, abstract = {The TOR (target of rapamycin) signal transduction pathway is an important mechanism by which cell growth is controlled in all eucaryotic cells. Specifically, TOR signaling adjusts the protein biosynthetic capacity of cells according to nutrient availability. In mammalian cells, one branch of this pathway controls general translational initiation, whereas a separate branch specifically regulates the translation of ribosomal protein (r-protein) mRNAs. In Saccharomyces cerevisiae, the TOR pathway similarly regulates general translational initiation, but its specific role in the synthesis of ribosomal components is not well understood. Here we demonstrate that in yeast control of ribosome biosynthesis by the TOR pathway is surprisingly complex. In addition to general effects on translational initiation, TOR exerts drastic control over r-protein gene transcription as well as the synthesis and subsequent processing of 35S precursor rRNA. We also find that TOR signaling is a prerequisite for the induction of r-protein gene transcription that occurs in response to improved nutrient conditions. This induction has been shown previously to involve both the Ras-adenylate cyclase as well as the fermentable growth medium-induced pathways, and our results therefore suggest that these three pathways may be intimately linked}, keywords = {99213991,Adenylate Cyclase,biosynthesis,COMPLEX,COMPLEXES,COMPONENT,drug effects,Fungal Proteins,gene,GENE-TRANSCRIPTION,genetics,initiation,MECHANISM,metabolism,mRNA,nosource,Peptide Chain Initiation,pharmacology,Phosphotransferases (Alcohol Group Acceptor),physiology,Polyribosomes,protein,ras Proteins,regulation,Ribosomal Proteins,ribosome,ribosome biogenesis,Ribosomes,RNAMessenger,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SIGNAL,Signal Transduction,Sirolimus,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,transcription,TranscriptionGenetic,translation,TranslationGenetic,ultrastructure,yeast} } % == BibTeX quality report for powersRegulationRibosomeBiogenesis1999: % ? unused Journal abbr (“Mol.Biol.Cell”)

@article{poznanskyGeneTransferHuman1991, title = {Gene Transfer into Human Lymphocytes by a Defective Human Immunodeficiency Virus Type 1 Vector.}, author = {Poznansky, M. and Lever, A. and Bergeron, L. and Haseltine, W. and Sodroski, J.}, year = 1991, month = jan, journal = {Journal of Virology}, volume = {65}, number = {1}, pages = {532–536}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.65.1.532-536.1991}, url = {http://jvi.asm.org/cgi/content/abstract/65/1/532}, keywords = {ELEMENTS,expression,gene,Genes,Genetic,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,nosource,Nucleotides,packaging,PLASMID,Plasmids,protein,Proteins,Proviruses,Rna,sequence,SYSTEM,transcription,vector,Viral Proteins,Virion,virus} }

@article{prasherPrimaryStructureAequorea1992, title = {Primary Structure of the {{Aequorea}} Victoria Green-Fluorescent Protein}, author = {Prasher, D.C. and Eckenrode, V.K. and Ward, W.W. and Prendergast, F.G. and Cormier, M.J.}, year = 1992, month = feb, journal = {Gene}, volume = {111}, number = {2}, pages = {229–233}, publisher = {Elsevier}, doi = {10.1016/0378-1119(92)90691-H}, url = {http://linkinghub.elsevier.com/retrieve/pii/037811199290691H}, keywords = {cloning,COMPLEX,COMPLEXES,enzyme,Exons,gene,Genes,genomic,gfp,IN-VIVO,nosource,protein,Proteins,sequence,structure} }

@article{presuttiRibosomalProteinL21991, title = {The Ribosomal Protein {{L2}} in {{S}}. Cerevisiae Controls the Level of Accumulation of Its Own {{mRNA}}.}, author = {Presutti, C. and Ciafre, S.A. and Bozzoni, I.}, year = 1991, journal = {The EMBO Journal}, volume = {10}, number = {8}, pages = {2215–2221}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1991.tb07757.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC452910/}, abstract = {The expression of the yeast L2 r-protein gene is controlled at the level of mRNA accumulation. The product of the gene appears to participate in this regulation by an autogenous feedback mechanism. This control does not operate at the level of transcription but instead affects L2 mRNA accumulation. This autogenous regulation of mRNA accumulation provides an interesting analogy to the autogenous translational regulation of r-proteins in Escherichia coli}, keywords = {91293097,BlottingNorthern,BlottingSouthern,DNAFungal,Escherichia coli,ESCHERICHIA-COLI,expression,Feedback,gene,Gene Expression RegulationFungal,Genetic,genetics,L2,La,MECHANISM,metabolism,mRNA,nosource,Plasmids,protein,regulation,Ribosomal Proteins,RNA ProcessingPost-Transcriptional,RNAFungal,RNAMessenger,Saccharomyces cerevisiae,supportnon-u.s.gov’t,transcription,TranscriptionGenetic,yeast} } % == BibTeX quality report for presuttiRibosomalProteinL21991: % ? unused Journal abbr (“EMBO J.”)

@article{presuttiIdentificationCiselementsMediating1995, title = {Identification of the Cis-Elements Mediating the Autogenous Control of Ribosomal Protein {{L2 mRNA}} Stability in Yeast.}, author = {Presutti, C. and Villa, T. and Hall, D. and Pertica, C. and Bozzoni, I.}, year = 1995, journal = {The EMBO Journal}, volume = {14}, number = {16}, pages = {4022–4030}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1995.tb00073.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC394480/}, abstract = {The ribosomal protein L2 (rpL2) of Saccharomyces cerevisiae regulates the accumulation of its own mRNA by a feedback mechanism. An RNA sequence is responsible for this control, initially characterized as a 360 nucleotide-long region, localized at the 5’ end of the transcript. This region, fused to an unrelated coding sequence, is able to down-regulate the accumulation of the chimeric transcript when increased levels of rpL2 are induced in the cell. The target regulatory region also responds to regulation when inserted inside an intron, demonstrating that the control process can take place inside the nucleus. Deletion analysis from the 5’ and 3’ borders have restricted the responsive region to approximately 200 nt. The insertion of a poly-G cassette downstream of the regulatory region allowed the identification of truncated 3’ cut-off poly(A)+ RNA molecules. The parallel identification of cut-off molecules containing the 5’ portion of the transcript allowed us to deduce that the truncated products originate by endonucleolytic cleavage. Altogether, these results are consistent with a mechanism by which the presence of excess amounts of rpL2 in the cell triggers its own mRNA to a degradative pathway; this involves an initial endonucleolytic cleavage that is followed by exonucleolytic trimming. Such a regulatory mechanism shows interesting analogies with the translational regulation of r-proteins in Escherichia coli}, keywords = {95393978,analysis,Base Sequence,beta-Galactosidase,biosynthesis,Chimeric Proteins,CLEAVAGE,Endoribonucleases,Escherichia coli,ESCHERICHIA-COLI,Exoribonucleases,Feedback,Gene Expression RegulationFungal,genetics,IDENTIFICATION,Introns,L2,La,MECHANISM,metabolism,Molecular Sequence Data,mRNA,nosource,Poly G,protein,regulation,Regulatory SequencesNucleic Acid,Ribosomal Proteins,Rna,RNA Precursors,RNA ProcessingPost-Transcriptional,RNA Splicing,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence Deletion,stability,supportnon-u.s.gov’t,yeast} } % == BibTeX quality report for presuttiIdentificationCiselementsMediating1995: % ? unused Journal abbr (“EMBO J.”)

@article{preveligeStructuralStudiesAcetylated1987, title = {Structural Studies of Acetylated and Control Inner Core Histones}, author = {Prevelige, P.E. and Fasman, G.D.}, year = 1987, month = may, journal = {Biochemistry}, volume = {26}, number = {10}, pages = {2944–2955}, publisher = {ACS Publications}, doi = {10.1021/bi00384a041}, url = {PM:3607000 http://pubs.acs.org/doi/abs/10.1021/bi00384a041}, abstract = {The role of acetylation on the conformation and association state of the inner core histone octamer isolated from HeLa cells was examined. Preparation of suitable quantities of pure acetylated and control inner core histones from HeLa cells required the development of a new preparative procedure. The results from size-exclusion high-performance liquid chromatography and sedimentation equilibrium studies indicated that acetylated inner core histones associate to species larger than the octamer and form a more stable complex. Circular dichroism studies demonstrated that the amount of alpha-helix increases with increasing association of the histones. Furthermore, acetylation results in an increase in the amount of alpha-helix, perhaps coupled through its effect on the association state. At high protein concentration and elevated temperature, the acetylated sample displays a greater increase in beta-sheet content, relative to the control sample. This increase in beta-sheet content may be induced during the association of the acetylated sample to species larger than the octamer. There is a marked effect on the conformation of both acetylated and control inner core histones as a function of protein concentration, ionic strength, and temperature. The difference in conformational flexibility and association state of the acetylated vs. the control inner histone core may play a significant role in the control of transcription in the nucleus}, keywords = {0,Acetylation,analysis,ASSOCIATION,Cell Nucleus,CELLS,Chromatin,Chromatography,ChromatographyHigh Pressure Liquid,Chromosomal ProteinsNon-Histone,Circular Dichroism,COMPLEX,COMPLEXES,CONFORMATION,development,FORM,Hela Cells,HELA-CELLS,Histones,Humans,isolation & purification,La,Methods,Micrococcal Nuclease,nosource,protein,Proteins,Structural,Support,Temperature,transcription,Urea} }

@article{pringleFluorescenceMicroscopyMethods1989, title = {Fluorescence Microscopy Methods for Yeast.}, author = {Pringle, J.R. and Preston, R.A. and Adams, A.E. and Stearns, T. and Drubin, D.G. and Haarer, B.K. and Jones, E.W.}, year = 1989, journal = {Methods in cell biology}, volume = {31}, pages = {357–435}, publisher = {Elsevier}, doi = {10.1016/S0091-679X(08)61620-9}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0091679X08616209}, keywords = {Fluorescence,Methods,nosource,yeast} } % == BibTeX quality report for pringleFluorescenceMicroscopyMethods1989: % ? unused Journal abbr (“Met.Cell.Biol.”)

@article{prowellerEfficientTranslationPoly1994a, title = {Efficient {{Translation}} of {{Poly}}({{A}})-{{Deficient Messenger-Rnas}} in {{Saccharomyces-Cerevisiae}}}, author = {Proweller, A. and Butler, S.}, year = 1994, month = nov, journal = {Genes & Development}, volume = {8}, number = {21}, pages = {2629–2640}, doi = {10.1101/gad.8.21.2629}, url = {ISI:A1994PR22000010}, abstract = {The polyadenylate tail of eukaryotic mRNAs is thought to influence various metabolic phenomena including mRNA stability, translation initiation, and nucleo-cytoplasmic transport. We have analyzed the fate of mRNAs following inactivation of poly(A) polymerase in Saccharomyces cerevisiae containing a temperature-sensitive, lethal mutation (pap1-1) in the gene for poly(A) polymerase (PAP1). Inactivation of poly(A) polymerase (Pap1) by shifting cells to the nonpermissive temperature resulted in the loss of at least 80% of measurable poly(A) within 60 min. Northern blot analysis revealed the disappearance of some mRNAs (CYH2 and HIS4) consistent with a role for poly(A) tails in mRNA stability. However, other mRNAs (TCM1, PAB1, ACT1, and HTB2) accumulate as poly(A)-deficient (A}, keywords = {3’ UNTRANSLATED REGION,analysis,CELLS,CEREVISIAE,CYH2,efficiency,EFFICIENT TRANSLATION,gene,initiation,mapping,MESSENGER-RNA,MESSENGER-RNA STABILITY,MESSENGER-RNA TRANSLATION,MESSENGER-RNAS,mRNA,mRNA stability,Mutation,nosource,poly(A),POLY(A) TAIL,POLY(A)-BINDING PROTEIN,Polyadenylation,polymerase,Polyribosomes,POSSIBLE INVOLVEMENT,protein synthesis,PROTEIN-SYNTHESIS,ribosome,Ribosomes,RNAse,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,stability,TCM1,Temperature,TRANSCRIPT,translation,TRANSLATION INITIATION,TRANSPORT,XENOPUS-LAEVIS,YEAST-CELLS} } % == BibTeX quality report for prowellerEfficientTranslationPoly1994a: % ? Title looks like it was stored in title-case in Zotero

@article{puglisiStructureConservedRNA1997a, title = {Structure of a Conserved {{RNA}} Component of the Peptidyl Transferase Centre.}, author = {Puglisi, E.V. and Green, R. and Noller, H.F. and Puglisi, J.D.}, year = 1997, month = oct, journal = {Nature Structural Biology}, volume = {4}, number = {10}, eprint = {9334738}, eprinttype = {pubmed}, pages = {775–778}, doi = {10.1038/nsb1097-775}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9334738/}, abstract = {The structure of a conserved hairpin loop involved in peptidyl-tRNA recognition by 50S ribosomal subunits has been solved by NMR. The loop is closed by a novel G-C base pair and presents guanine residues for RNA recognition}, keywords = {0,Base Composition,Base Sequence,chemistry,COMPONENT,Conserved Sequence,Guanine,La,metabolism,ModelsMolecular,nosource,Nuclear Magnetic ResonanceBiomolecular,Nucleic Acid Conformation,Oligoribonucleotides,peptidyl transferase,PEPTIDYL-TRANSFERASE,Peptidyltransferase,RIBOSOMAL-SUBUNIT,Ribosomes,Rna,RNARibosomal23S,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Thermodynamics,ultrastructure} } % == BibTeX quality report for puglisiStructureConservedRNA1997a: % ? unused Journal abbr (“Nat.Struct.Biol.”)

@article{puglisiPseudoknottedRNAOligonucleotide1988, title = {A Pseudoknotted {{RNA}} Oligonucleotide}, author = {Puglisi, J.D. and Wyatt, J.R. and Tinoco, I.}, year = 1988, month = jan, journal = {Nature}, volume = {331}, number = {6153}, pages = {283–286}, doi = {10.1038/331283a0}, url = {PM:3336440}, abstract = {The diverse functions of RNA, which include enzymatic activities, regulatory roles in transcription and translation, are made possible by tertiary structure. Computer algorithms can predict the secondary structure of an RNA molecule using free-energy parameters for base pairing and stacking, loops and bulges. However, with the exception of transfer RNA, little is known about the structures and thermodynamics of interactions involved in the tertiary structure of RNA. Recently, it has been proposed that a novel form of RNA folding called pseudoknotting occurs at the 3’ end of certain viral RNAs from plants. A pseudoknot involves intramolecular pairing of bases in a hairpin loop with a few bases outside the stem of the loop to form an additional stem and loop region (Fig. 1). If each stem contained a full helical turn, a true knot would be formed. We present evidence from single-strand specific (S1) and double-strand specific (V1) nuclease digestion, that a short RNA oligonucleotide (19 nucleotides long) adopts a stable pseudoknotted structure. The nuclease digestion and thermodynamic properties of this oligonucleotide were compared with those of oligonucleotides which form hairpin structures containing the two possible stem regions in the pseudoknot. These results show that appropriate sequences can form pseudoknots and indicate that pseudoknots are a significant type of local tertiary structure which must be considered in the folding of complex RNA molecules}, keywords = {0,3,Algorithms,BASE,Base Composition,Base Pairing,Base Sequence,BASES,chemical synthesis,chemistry,ChemistryPhysical,COMPLEX,COMPLEXES,computer,FORM,La,LOOP,nosource,Nucleic Acid Conformation,Nucleic Acid Denaturation,Nucleotides,Oligonucleotides,Oligoribonucleotides,Plants,pseudoknot,pseudoknots,REGION,Rna,RNA folding,SECONDARY STRUCTURE,sequence,SEQUENCES,structure,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Thermodynamics,transcription,TRANSFER-RNA,translation,VIRAL-RNA} }

@article{puglisiConformationTARRNAarginine1992, title = {Conformation of the {{TAR RNA-arginine}} Complex by {{NMR}} Spectroscopy}, author = {Puglisi, J.D. and Tan, R. and Calnan, B.J. and Frankel, A.D. and Williamson, J.R.}, year = 1992, month = jul, journal = {Science}, volume = {257}, number = {5066}, pages = {76–80}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1621097}, url = {http://www.sciencemag.org/content/257/5066/76.short}, abstract = {The messenger RNAs of human immunodeficiency virus-1 (HIV-1) have an RNA hairpin structure, TAR, at their 5’ ends that contains a six- nucleotide loop and a three-nucleotide bulge. The conformations of TAR RNA and of TAR with an arginine analog specifically bound at the binding site for the viral protein, Tat, were characterized by nuclear magnetic resonance (NMR) spectroscopy. Upon arginine binding, the bulge changes conformation, and essential nucleotides for binding, U23 and A27.U38, form a base-triple interaction that stabilizes arginine hydrogen bonding to G26 and phosphates. Specificity in the arginine-TAR interaction appears to be derived largely from the structure of the RNA}, keywords = {0,Arginine,Base Sequence,BINDING,Binding Sites,chemistry,COMPLEX,COMPLEXES,gene,Gene Productstat,genetics,Hiv-1,human,Hydrogen Bonding,La,Magnetic Resonance Spectroscopy,MESSENGER-RNA,metabolism,Methods,ModelsMolecular,Molecular Sequence Data,nosource,nuclear magnetic resonance,Nucleic Acid Conformation,Nucleotides,Phosphates,protein,Proteins,Rna,RNA-Binding Proteins,RNAMessenger,RnaViral,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,TAR RNA} }

@article{puglisiApproachingTranslationAtomic2000, title = {Approaching Translation at Atomic Resolution}, author = {Puglisi, J.D. and Blanchard, S.C. and Green, R.}, year = 2000, month = oct, journal = {Nature Structural & Molecular Biology}, volume = {7}, number = {10}, pages = {855–861}, publisher = {Nature Publishing Group}, doi = {10.1038/79603}, url = {http://www.nature.com/nsmb/journal/v7/n10/abs/nsb1000_855.html}, abstract = {Atomic resolution structures of 50S and 30S ribosomal particles have recently been solved by X-ray diffraction. These ribosomal structures show often unusual folds of ribosomal RNAs and proteins, and provide molecular explanations for fundamental aspects of translation. In the 50S structure, the active site for peptide bond formation was localized and found to consist of RNA. The ribosome is thus a ribozyme. In the 30S structures, tRNA binding sites were located, and molecular mechanisms for ribosomal fidelity were proposed. The 30S subunit particle has three globular domains, and relative movements of these domains may be required for translocation of the ribosome during protein synthesis. The structures are consistent with and rationalize decades of biochemical analysis of translation and usher in a molecular age in understanding the ribosome}, keywords = {analysis,BINDING,Binding Sites,chemistry,Fidelity,La,MECHANISM,MECHANISMS,ModelsMolecular,Movement,nosource,protein,Protein Conformation,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Review,RIBOSOMAL-RNA,ribosome,Ribosomes,ribozyme,Rna,Structural,structure,SUBUNIT,translation,TranslationGenetic,translocation,tRNA,X-Ray Diffraction} } % == BibTeX quality report for puglisiApproachingTranslationAtomic2000: % ? unused Journal abbr (“Nat.Struct.Biol”)

@article{pulakMRNASurveillanceCaenorhaditis1993a, title = {{{mRNA}} Surveillance by the ⬚{{Caenorhaditis}} Elegans Smg⬚ Genes.}, author = {Pulak, R. and Anderson, P.}, year = 1993, journal = {Genes & Dev.}, volume = {7}, pages = {1885–1897}, doi = {10.1101/gad.7.10.1885}, keywords = {gene,Genes,mRNA,NMD,nosource} } % == BibTeX quality report for pulakMRNASurveillanceCaenorhaditis1993a: % ? Possibly abbreviated journal title Genes & Dev.

@article{purvisEffectsAlterations31987, title = {The Effects of Alterations within the 3’ Untranslated Region of the Pyruvate Kinase Messenger {{RNA}} upon Its Stability and Translation in {{Saccharomyces}} Cerevisiae}, author = {Purvis, I.J. and Bettany, A.J. and Loughlin, L. and Brown, A.J.}, year = 1987, month = oct, journal = {Nucleic Acids Research}, volume = {15}, number = {19}, pages = {7951–7962}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/15.19.7951}, url = {http://nar.oxfordjournals.org/content/15/19/7951.short}, abstract = {A 53 basepair deletion was constructed within the 3’ untranslated region (3’ UTR) of the yeast pyruvate kinase (PYK) gene borne upon a centromeric plasmid. Various modular assemblies of the pUC13 polylinker DNA (single unit = 44 bp) were used to replace the deleted region, and the effects of these modifications upon both transcript stability and translation ascertained in yeast. The use of a differential probing stratagem, based on the hybridisation of specific oligonucleotides to either pUC13 polylinker or unaltered PYK 3’ UTR sequences, allowed for discrimination between mutant (plasmid borne) and wild-type (chromosomal) PYK transcripts. In no construct was there any significant alteration in mRNA stability, but translation of the PYK mRNA was severely curtailed by truncation of the 3’ UTR or the presence of a strong hairpin-loop structure in the 3’ UTR. A specific mutation in the N-terminal coding sequences, which created a premature termination codon in both a 3’ ‘tagged’ PYK plasmid and a PYK/LacZ fusion gene, aborted the translation of a majority of their transcripts but left their chemical half-lives unaltered. This observation is at variance with some previously published data (Losson & Lacroute (1979) Proc Natl Acad Sci USA 76, 5134; Pelsey & Lacroute (1984) Curr Genet 8, 277), but is consistent with our own earlier observation that there is no obvious link between ribosome loading and mRNA stability in yeast (Santiago et al. (1986) Nucleic Acids Res 14, 8347). Possible reasons for this disparity are discussed}, keywords = {88040420,assembly,biosynthesis,Codon,Dna,Fungal Proteins,gene,Genetic,genetics,Half-Life,kinase,MESSENGER-RNA,metabolism,modification,mRNA,Mutation,nosource,Nucleic Acids,Oligonucleotides,PLASMID,POLYLINKER,Polyribosomes,Pyruvate Kinase,Recombinant Proteins,ribosome,Rna,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,stability,structure,supportnon-u.s.gov’t,termination,translation,TranslationGenetic,yeast} } % == BibTeX quality report for purvisEffectsAlterations31987: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{pyronnetCellCycledependentInternal2000, title = {A Cell Cycle-Dependent Internal Ribosome Entry Site}, author = {Pyronnet, S. and Pradayrol, L. and Sonenberg, N.}, year = 2000, month = apr, journal = {Molecular cell}, volume = {5}, number = {4}, pages = {607–616}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276500802403}, abstract = {The eukaryotic mRNA 5’ cap structure facilitates translation. However, cap-dependent translation is impaired at mitosis, suggesting a cap-independent mechanism for mRNAs translated during mitosis. Translation of ornithine decarboxylase (ODC), the rate-limiting enzyme in the biosynthesis of polyamines, peaks twice during the cell cycle, at the G1/S transition and at G2/M. Here, we describe a cap-independent internal ribosome entry site (IRES) in the ODC mRNA that functions exclusively at G2/M. This ensures elevated levels of polyamines, which are implicated in mitotic spindle formation and chromatin condensation. c-myc mRNA also contains an IRES that functions during mitosis. Thus, IRES-dependent translation is likely to be a general mechanism to synthesize short-lived proteins even at mitosis, when cap-dependent translation is interdicted}, keywords = {0,5’ Untranslated Regions,biosynthesis,cancer,Cap,CAP STRUCTURE,cell cycle,Chromatin,Codon,CodonInitiator,drug effects,enzyme,Enzyme Induction,G1 Phase,G2 Phase,genetics,Hela Cells,human,INTERNAL RIBOSOME ENTRY,Interphase,La,MECHANISM,Mitosis,mRNA,nosource,Ornithine Decarboxylase,Peptide Chain Initiation,pharmacology,physiology,Picornaviridae,polyamine,Polyamines,protein,Proteins,Proto-Oncogene Proteins,Proto-Oncogene Proteins c-myc,REGION,ribosome,RIBOSOME ENTRY SITE,Rna,Rna Caps,Sirolimus,SITE,structure,supportnon-u.s.gov’t,translation,Untranslated Regions} }

@article{pyronnetCellcycledependentTranslationalControl2001, title = {Cell-Cycle-Dependent Translational Control}, author = {Pyronnet, S. and Sonenberg, N.}, year = 2001, month = feb, journal = {Current Opinion in Genetics & Development}, volume = {11}, number = {1}, pages = {13–18}, publisher = {Elsevier}, doi = {10.1016/S0959-437X(00)00150-7}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0959437X00001507}, abstract = {Control of translation in eukaryotes occurs mainly at the initiation step. Translation rates in mammals are robust in the G1 phase of the cell cycle but are low during mitosis. These changes correlate with the activity of several canonical translation initiation factors, which is modulated during the cell cycle to regulate translation}, keywords = {0,Animals,Biochemistry,cancer,Cap,cell cycle,G1 Phase,Gene Expression Regulation,genetics,initiation,INITIATION-FACTOR,Interphase,La,Mammals,metabolism,Mitosis,nosource,Picornaviridae,Protein Biosynthesis,Review,Rna,Rna Caps,Signal Transduction,Support,translation,TRANSLATION INITIATION,Yeasts} } % == BibTeX quality report for pyronnetCellcycledependentTranslationalControl2001: % ? unused Journal abbr (“Curr.Opin.Genet.Dev.”)

@article{qinSitespecificLabelingRNA1999, title = {Site-Specific Labeling of {{RNA}} with Fluorophores and Other Structural Probes}, author = {Qin, P.Z. and Pyle, A.M.}, year = 1999, month = may, journal = {Methods}, volume = {18}, number = {1}, pages = {60–70}, doi = {10.1006/meth.1999.0757}, url = {PM:10208817}, abstract = {Site-specific probes provide a powerful tool for structure and function studies of nucleic acids, especially in elucidating tertiary structures of large ribozymes and other folded RNA molecules. Among many types of extrinsic labels, fluorophores are most attractive because they can provide structural information at millisecond time resolution, thus allowing real-time observation of structural transition during biological function. Methods for introducing fluorophores in RNA molecules are summarized here. These methods are robust and readily applicable to the labeling of other types of probes. However, as each case of RNA modification is unique, fine tuning of the general methodology is beneficial}, keywords = {0,ACID,ACIDS,Amines,Biochemistry,Biophysics,chemistry,Fluorescein,Fluoresceins,Fluorescent Dyes,INFORMATION,La,metabolism,Methods,ModelsChemical,ModelsGenetic,modification,Molecular Biology,nosource,Nucleic Acids,Oligonucleotides,RESOLUTION,ribozyme,Rna,site specific,Structural,structure,Sulfhydryl Compounds,Support} }

@article{qinInhibitingHIV1Infection2003, title = {Inhibiting {{HIV-1}} Infection in Human {{T}} Cells by Lentiviral-Mediated Delivery of Small Interfering {{RNA}} against {{CCR5}}}, author = {Qin, X.F. and An, D.S. and Chen, I.S. and Baltimore, D.}, year = 2003, month = jan, journal = {Proceedings of the National Academy of Sciences}, volume = {100}, number = {1}, pages = {183–188}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.232688199}, url = {http://www.pnas.org/content/100/1/183.short}, abstract = {Double-stranded RNAs approximately 21 nucleotides long [small interfering RNA (siRNA)] are recognized as powerful reagents to reduce the expression of specific genes. To use them as reagents to protect cells against viral infection, effective methods for introducing siRNAs into primary cells are required. Here, we describe success in constructing a lentivirus-based vector to introduce siRNAs against the HIV-1 coreceptor, CCR5, into human peripheral blood T lymphocytes. With high-titer vector stocks, {\(>\)}40% of the peripheral blood T lymphocytes could be transduced, and the expression of a potent CCR5-siRNA resulted in up to 10-fold inhibition of CCR5 expression on the cell surface over a period of 2 weeks in the absence of selection. In contrast, the expression of another major HIV-1 coreceptor, CXCR4, was not affected. Importantly, blocking CCR5 expression by siRNAs provided a substantial protection for the lymphocyte populations from CCR5-tropic HIV-1 virus infection, dropping infected cells by 3- to 7-fold; only a minimal effect on infection by a CXCR4-tropic virus was observed. Thus, our studies demonstrate the feasibility and potential of lentiviral vector-mediated delivery of siRNAs as a general means of intracellular immunization for the treatment of HIV-1 and other viral diseases}, keywords = {0,3,Acquired Immunodeficiency Syndrome,administration & dosage,antagonists & inhibitors,BIOLOGY,blood,CELLS,CellsCultured,disease,DOUBLE-STRANDED-RNA,expression,gene,Genes,Genetic Vectors,genetics,Hiv-1,human,Humans,Immunization,immunology,INFECTED CELLS,INFECTED-CELLS,INFECTION,INHIBITION,La,Lentivirus,Lymphocytes,Methods,nosource,Nucleotides,physiology,prevention & control,PROTECTION,ReceptorsCCR5,Rna,RNASmall Interfering,SELECTION,Support,T,T-Lymphocytes,vector,Vesicular stomatitis-Indiana virus,virology,virus} } % == BibTeX quality report for qinInhibitingHIV1Infection2003: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{quCapindependentTranslationalEnhancement2000, title = {Cap-Independent Translational Enhancement of Turnip Crinkle Virus Genomic and Subgenomic {{RNAs}}}, author = {Qu, F. and Morris, T.J.}, year = 2000, month = feb, journal = {Journal of virology}, volume = {74}, number = {3}, pages = {1085–1093}, publisher = {Am Soc Microbiol}, doi = {10.1128/JVI.74.3.1085-1093.2000}, url = {http://jvi.asm.org/cgi/content/abstract/74/3/1085}, abstract = {The presence of translational control elements and cap structures has not been carefully investigated for members of the Carmovirus genus, a group of small icosahedral plant viruses with positive-sense RNA genomes. In this study, we examined both the 5’ and 3’ untranslated regions (UTRs) of the turnip crinkle carmovirus (TCV) genomic RNA (4 kb) as well as the 5’ UTR of the coat protein subgenomic RNA (1.45 kb) for their roles in translational regulation. All three UTRs enhanced translation of the firefly luciferase reporter gene to different extents. Optimal translational efficiency was achieved when mRNAs contained both 5’ and 3’ UTRs. The synergistic effect due to the 5’-3’ cooperation was at least fourfold greater than the sum of the contributions of the individual UTRs. The observed translational enhancement of TCV mRNAs occurred in a cap-independent manner, a result consistent with the demonstration, using a cap-specific antibody, that the 5’ end of the TCV genomic RNA was uncapped. Finally, the translational enhancement activity within the 5’ UTR of 1.45-kb subgenomic RNA was shown to be important for the translation of coat protein in protoplasts and for virulent infection in Arabidopsis plants}, keywords = {0,3,3’ Untranslated Regions,5’ Untranslated Regions,Antibodies,antibody,Arabidopsis,Base Sequence,Brassica,Cap,CAP STRUCTURE,Capsid,Carmovirus,COAT PROTEIN,efficiency,ELEMENTS,FIREFLY LUCIFERASE,gene,Gene Expression RegulationViral,genetics,Genome,GenomeViral,genomic,GENOMIC RNA,INFECTION,La,luciferase,Luciferases,metabolism,Molecular Sequence Data,mRNA,nosource,Plant Viruses,Plants,protein,Protein Biosynthesis,PROTOPLASTS,REGION,regulation,Rna,Rna Caps,RNA Stability,RNAMessenger,RnaViral,structure,SUBGENOMIC RNAS,Support,translation,Untranslated Regions,virology,virus,Viruses} } % == BibTeX quality report for quCapindependentTranslationalEnhancement2000: % ? unused Journal abbr (“J.Virol.”)

@article{quackenbushComputationalAnalysisMicroarray2001, title = {Computational Analysis of Microarray Data}, author = {Quackenbush, J.}, year = 2001, month = jun, journal = {Nature Reviews Genetics}, volume = {2}, number = {6}, pages = {418–427}, publisher = {Nature Publishing Group}, doi = {10.1038/35076576}, url = {http://www.nature.com/nrg/journal/v2/n6/abs/nrg0601_418a.html}, abstract = {Microarray experiments are providing unprecedented quantities of genome-wide data on gene-expression patterns. Although this technique has been enthusiastically developed and applied in many biological contexts, the management and analysis of the millions of data points that result from these experiments has received less attention. Sophisticated computational tools are available, but the methods that are used to analyse the data can have a profound influence on the interpretation of the results. A basic understanding of these computational tools is therefore required for optimal experimental design and meaningful data analysis}, keywords = {analysis,ARRAYS,cancer,DISCOVERY,Gene Expression,GENE-EXPRESSION,genomic,Methods,nosource,PATTERNS,Review} }

@article{rachofskyKineticModelsData2000, title = {Kinetic Models and Data Analysis Methods for Fluorescence Anisotropy Decay}, author = {Rachofsky, E.L. and Laws, W.R.}, year = 2000, journal = {Methods in Enzymology}, volume = {321:216-38.}, pages = {216–238}, publisher = {Elsevier}, doi = {10.1016/S0076-6879(00)21196-8}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0076687900211968}, keywords = {analysis,anisotropy,DECAY,Fluorescence,Fluorescence Polarization,Kinetics,Least-Squares Analysis,Methods,models,ModelsStatistical,nosource,Review,Statistics,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Time Factors} } % == BibTeX quality report for rachofskyKineticModelsData2000: % ? unused Journal abbr (“Methods Enzymol.”)

@article{raineriRolesAUF1Isoforms2004, title = {Roles of {{AUF1}} Isoforms, {{HuR}} and {{BRF1}} in {{ARE-dependent mRNA}} Turnover Studied by {{RNA}} Interference}, author = {Raineri, I. and Wegmueller, D. and Gross, B. and Certa, U. and Moroni, C.}, year = 2004, journal = {Nucleic acids research}, volume = {32}, number = {4}, pages = {1279–1288}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkh282}, url = {http://nar.oxfordjournals.org/content/32/4/1279.short}, abstract = {HT1080 cells stably expressing green fluorescent protein (GFP) linked to a 3’ terminal AU-rich element (ARE) proved to be a convenient system to study the dynamics of mRNA stability, as changes in mRNA levels are reflected in increased or decreased fluorescence intensity. This study examined whether mRNA stability can be regulated by small interfering RNAs (siRNAs) targeted to AU-binding proteins (AUBPs), which in turn should reveal their intrinsic role as stabilizers or destabilizers of ARE-mRNAs. Indeed, siRNAs targeting HuR or BRF1 decreased or increased fluorescence, respectively. This effect was abolished if cells were treated with both siRNAs, thus indicating antagonistic control of ARE-mRNA stability. Unexpectedly, downregulation of all four AUF1 isoforms by targeting common exons did not affect fluorescence whereas selective downregulation of p40AUF1/p45AUF1 strongly increased fluorescence by stabilizing the GFP-ARE reporter mRNA. This observation was fully confirmed by the finding that only selective reduction of p40AUF1/p45AUF1 induced the production of GM-CSF, an endogenous target of AUF1. These data suggest that the relative levels of individual isoforms, rather than the absolute amount of AUF1, determine the net mRNA stability of ARE-containing transcripts, consistent with the differing ARE-binding capacities of the isoforms}, keywords = {0,3,ACID,antagonists & inhibitors,ANTIGEN,Antigens,AntigensSurface,Butyrate Response Factor 1,Cell Line,CELLS,D,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,DYNAMICS,EXON,Exons,Fluorescence,genetics,gfp,Granulocyte-Macrophage Colony-Stimulating Factor,GREEN FLUORESCENT PROTEIN,Heterogeneous-Nuclear Ribonucleoprotein D,human,Humans,Immediate-Early Proteins,La,metabolism,microbiology,mRNA,mRNA stability,mRNA turnover,nosource,pharmacology,physiology,protein,Protein Isoforms,Proteins,Regulatory SequencesRibonucleic Acid,RIBONUCLEIC-ACID,RIBONUCLEOPROTEIN,Rna,RNA Interference,RNA Stability,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAMessenger,RNASmall Interfering,sequence,SEQUENCES,stability,Support,SYSTEM,TARGET,TRANSCRIPT,turnover} } % == BibTeX quality report for raineriRolesAUF1Isoforms2004: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{rajamohanHighlevelExpressionPurification1999, title = {High-Level Expression and Purification of Biologically Active Recombinant Pokeweed Antiviral Protein}, author = {Rajamohan, F. and Engstrom, C.R. and Denton, T.J. and Engen, L.A. and Kourinov, I. and Uckun, F.M.}, year = 1999, month = jul, journal = {Protein Expression and Purification}, volume = {16}, number = {2}, pages = {359–368}, publisher = {Elsevier}, doi = {10.1006/prep.1999.1084}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1046592899910847}, abstract = {Pokeweed antiviral protein (PAP) from the leaves of the pokeweed plant, Phytolacca americana, is a naturally occurring single-chain ribosome-inactivating protein, which catalytically inactivates both prokaryotic and eukaryotic ribosomes. The therapeutic potential of PAP has gained considerable interest in recent years due to the clinical use of native PAP as the active moiety of immunoconjugates against cancer and AIDS. The clinical use of native PAP is limited due to inherent difficulties in obtaining sufficient quantities of a homogenously pure and active PAP preparation with minimal batch to batch variability from its natural source, Previous methods for expression of recombinant PAP in yeast, transgenic plants and Escherichia coil have resulted in either unacceptably low yields or were too toxic to the host system. Here, we report a successful strategy which allows high level expression of PAP as inclusion bodies in E. coil. Purification of refolded recombinant protein from solubilized inclusion bodies by size-exclusion chromatography yielded biologically active recombinant PAP (final yield: 10 to 12 mg/L). The ribosome depurinating in vitro N-glycosidase activity and cellular anti-HIV activity of recombinant PAP were comparable to those of the native PAP. This expression and purification system makes it possible to obtain sufficient quantities of biologically active and homogenous recombinant PAP sufficient to carry out advanced clinical trials. To our knowledge, this is the first large-scale expression and purification of biologically active recombinant PAP from E. coil. (C) 1999 Academic Press}, keywords = {AIDS,antiviral,cancer,Chromatography,ESCHERICHIA-COLI,EUKARYOTIC RIBOSOMES,expression,GLYCOSIDASE ACTIVITY,In Vitro,IN-VITRO,INHIBITION,LEUKEMIA,Methods,nosource,PAP,PHYTOLACCA-AMERICANA,Plants,Pokeweed antiviral protein,protein,purification,REPLICATION,ribosome,RIBOSOME-INACTIVATING PROTEINS,Ribosomes,Rna,SACCHAROMYCES-CEREVISIAE,SYSTEM,yeast} }

@article{rajamohanExpressionBiologicallyActive2000, title = {Expression of Biologically Active Recombinant Pokeweed Antiviral Protein in Methylotrophic Yeast {{Pichia}} Pastoris}, author = {Rajamohan, F. and Doumbia, S.O. and Engstrom, C.R. and Pendergras, S.L. and Maher, D.L. and Uckun, F.M.}, year = 2000, month = mar, journal = {Protein Expression and Purification}, volume = {18}, number = {2}, pages = {193–201}, publisher = {Elsevier}, doi = {10.1006/prep.1999.1181}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1046592899911816}, abstract = {Pokeweed antiviral protein (PAP)-I from the spring leaves of Phytolacca americana is a naturally occurring RNA-depurinating enzyme with broad-spectrum antiviral activity. Interest in PAP is growing due to its use as a potential anti-HIV agent. However, the clinical use of native PAP is limited due to inherent difficulties in obtaining sufficient quantities of homogeneously pure active PAP without batch-to-batch variation from its natural resource. Here, we report the expression of mature PAP (residues 23 to 284) with a C-terminal hexahistidine tag in the methylotrophic yeast Pichia pastoris, as a secreted soluble protein. The final yield of the secreted PAP is greater than 10 mg/L culture in shaker flasks. The secreted recombinant protein is not toxic to the yeast cells and has an apparent molecular mass of 33-kDa on SDS-PAGE gels. The in vitro enzymatic activity and cellular anti-HIV activity of recombinant PAP were of the same magnitude as those of the native PAP purified from P. americana. To our knowledge, this is the first large-scale expression and purification of soluble and biologically active recombinant mature PAP from yeast. (C) 2000 Academic Press}, keywords = {anti-HIV,antiviral,Dna,enzyme,expression,Gels,Immunotoxins,In Vitro,IN-VITRO,INHIBITION,LEUKEMIA,nosource,PAP,PHYTOLACCA-AMERICANA,Pokeweed antiviral protein,protein,protein synthesis inhibition,purification,REPLICATION,ribosome depurination,SDS-PAGE,virus,yeast} }

@article{rakauskaiteArcUnpairedHinge2006, title = {An Arc of Unpaired “Hinge Bases” Facilitates Information Exchange among Functional Centers of the Ribosome}, author = {Rakauskaite, R. and Dinman, J.D.}, year = 2006, journal = {Molecular and Cellular Biology}, volume = {26}, number = {23}, pages = {8992–9002}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.01311-06}, url = {http://mcb.asm.org/cgi/content/abstract/26/23/8992}, abstract = {Information must be shared and functions coordinated among the spatially distinct functional centers of the ribosome. To address these issues, a yeast-based genetic system enabling generation of stable strains expressing only mutant forms of rRNA was devised. The B1a bridge (helix 38) has been implicated in the subtle modulation of numerous ribosomal functions. Base-specific mutations were introduced into helix 38 at sites affecting the B1a bridge, and where it contacts the aa-tRNA D-loop. Both sets of mutants promoted increased affinities for aa-tRNA, but had different effects in their responses to two A-site specific drugs and on suppression nonsense codons. Structural analyses revealed an arc of nucleotides in 25S rRNA that link the B1a bridge, the peptidyltransferase center, the GTAase-associated center, and the sarcin/ricin loop. We propose that a series of regularly spaced “hinge bases” provide fulcrums around which rigid helices can reorient themselves depending on the occupancy status of the A-site}, keywords = {A SITE,A-SITE,BIOLOGY,Codon,CODONS,drugs,FORM,Genetic,genetics,INFORMATION,La,LOOP,microbiology,MOLECULAR-GENETICS,MUTANTS,Mutation,MUTATIONS,NONSENSE,nosource,Nucleotides,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,ribosome,rRNA,SERIES,SITE,SITES,Structural,suppression,SYSTEM} } % == BibTeX quality report for rakauskaiteArcUnpairedHinge2006: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{rakauskaiteRRNAMutantsYeast2008, title = {{{rRNA}} Mutants in the Yeast Peptidyltransferase Center Reveal Allosteric Information Networks and Mechanisms of Drug Resistance}, author = {Rakauskaite, R. and Dinman, J.D.}, year = 2008, month = mar, journal = {Nucleic Acids Res.}, volume = {36}, number = {5}, pages = {1497–1507}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkm1179}, url = {PM:18203742}, abstract = {To ensure accurate and rapid protein synthesis, nearby and distantly located functional regions of the ribosome must dynamically communicate and coordinate with one another through a series of information exchange networks. The ribosome is approximately 2/3 rRNA and information should pass mostly through this medium. Here, two viable mutants located in the peptidyltransferase center (PTC) of yeast ribosomes were created using a yeast genetic system that enables stable production of ribosomes containing only mutant rRNAs. The specific mutants were C2820U (Escherichia coli C2452) and Psi2922C (E. coli U2554). Biochemical and genetic analyses of these mutants suggest that they may trap the PTC in the ‘open’ or aa-tRNA bound conformation, decreasing peptidyl-tRNA binding. We suggest that these structural changes are manifested at the biological level by affecting large ribosomal subunit biogenesis, ribosomal subunit joining during initiation, susceptibility/resistance to peptidyltransferase inhibitors, and the ability of ribosomes to properly decode termination codons. These studies also add to our understanding of how information is transmitted both locally and over long distances through allosteric networks of rRNA-rRNA and rRNA-protein interactions}, keywords = {0,Allosteric Regulation,anisomycin,antagonists & inhibitors,Base Sequence,BINDING,BIOGENESIS,BIOLOGY,chemistry,Codon,Codon-Terminator,CODONS,CodonTerminator,CONFORMATION,drug effects,Drug Resistance,E,enzymology,Escherichia coli,ESCHERICHIA-COLI,Genetic,genetics,INFORMATION,INHIBITOR,inhibitors,initiation,La,MECHANISM,MECHANISMS,media,metabolism,microbiology,Molecular Sequence Data,MOLECULAR-GENETICS,MUTANTS,Mutation,nosource,Paromomycin,peptidyl transferase,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,pharmacology,prion,Prions,protein,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,REGION,RESISTANCE,RIBOSOMAL-SUBUNIT,ribosome,Ribosome Subunits-Large-Eukaryotic,Ribosome SubunitsLargeEukaryotic,Ribosomes,Rna,RNA-Ribosomal,RNA-Transfer,RNARibosomal,RNATransfer,rRNA,rRNA mutants,SERIES,sparsomycin,Structural,SUBUNIT,SUBUNIT BIOGENESIS,Support,SYNTHESIS INHIBITORS,SYSTEM,termination,TERMINATION CODON,TERMINATION-CODON,Transferases,yeast,Yeasts} } % == BibTeX quality report for rakauskaiteRRNAMutantsYeast2008: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{ramirezMutationsActivatingYeast1992a, title = {Mutations Activating the Yeast {{eIF-2`a}} Kinase ⬚{{GCN2}}⬚: Isolation of Alleles Altering the Domain Related to Histidyl-{{tRNA}} Synthetases.}, author = {Ramirez, M. and Wek, R.C. and {Vazquez de Aldana}, C.R. and Jackson, B.M. and Freeman, B. and Hinnebusch, A.G.}, year = 1992, journal = {Mol.Cell.Biol.}, volume = {12}, pages = {5801–5815}, keywords = {Alleles,GCN,kinase,Multiple DOI,Mutation,MUTATIONS,nonfile,nosource,translation,yeast} } % == BibTeX quality report for ramirezMutationsActivatingYeast1992a: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{ramirezMutationsActivatingYeast1992, title = {Mutations Activating the Yeast {{eIF-2}} Alpha Kinase {{GCN2}}: Isolation of Alleles Altering the Domain Related to Histidyl-{{tRNA}} Synthetases.}, author = {Ramirez, M. and Wek, R.C. and {Vazquez de Aldana}, C.R. and Jackson, B.M. and Freeman, B. and Hinnebusch, A.G.}, year = 1992, month = dec, journal = {Molecular and Cellular Biology}, volume = {12}, number = {12}, pages = {5801–5815}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/12/12/5801}, abstract = {The protein kinase GCN2 stimulates expression of the yeast transcriptional activator GCN4 at the translational level by phosphorylating the alpha subunit of translation initiation factor 2 (eIF-2 alpha) in amino acid-starved cells. Phosphorylation of eIF-2 alpha reduces its activity, allowing ribosomes to bypass short open reading frames present in the GCN4 mRNA leader and initiate translation at the GCN4 start codon. We describe here 17 dominant GCN2 mutations that lead to derepression of GCN4 expression in the absence of amino acid starvation. Seven of these GCN2c alleles map in the protein kinase moiety, and two in this group alter the presumed ATP-binding domain, suggesting that ATP binding is a regulated aspect of GCN2 function. Six GCN2c alleles map in a region related to histidyl-tRNA synthetases, and two in this group alter a sequence motif conserved among class II aminoacyl-tRNA synthetases that directly interacts with the acceptor stem of tRNA. These results support the idea that GCN2 kinase function is activated under starvation conditions by binding uncharged tRNA to the domain related to histidyl-tRNA synthetase. The remaining GCN2c alleles map at the extreme C terminus, a domain required for ribosome association of the protein. Representative mutations in each domain were shown to depend on the phosphorylation site in eIF-2 alpha for their effects on GCN4 expression and to increase the level of eIF-2 alpha phosphorylation in the absence of amino acid starvation. Synthetic GCN2c double mutations show greater derepression of GCN4 expression than the parental single mutations, and they have a slow-growth phenotype that we attribute to inhibition of general translation initiation. The phenotypes of the GCN2c alleles are dependent on GCN1 and GCN3, indicating that these two positive regulators of GCN4 expression mediate the inhibitory effects on translation initiation associated with activation of the yeast eIF-2 alpha kinase GCN2}, keywords = {0,ACID,activation,Alleles,Amino Acid Sequence,AMINO-ACID,ASSOCIATION,ATP,BINDING,C-TERMINUS,CELLS,CEREVISIAE,chemistry,Child,CloningMolecular,Codon,development,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,DOMAIN,Eif-2,elongation,elongation factors,ELONGATION-FACTORS,enzymology,Eukaryotic Initiation Factor-2B,expression,FRAME,Fungal Proteins,GCN4,GenesFungal,Genetic,genetics,Histidine-tRNA Ligase,human,INHIBITION,initiation,INITIATION-FACTOR,kinase,KINASE GCN2,La,metabolism,Molecular Sequence Data,MOLECULAR-GENETICS,mRNA,Multiple DOI,Mutation,MUTATIONS,nonfile,nosource,OPEN READING FRAME,Open Reading Frames,Peptide Elongation Factors,Phenotype,Phosphorylation,protein,Protein Kinases,Protein StructureSecondary,PROTEIN-KINASE,Protein-Serine-Threonine Kinases,Proteins,READING FRAME,Reading Frames,REGION,ribosome,Ribosomes,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,Sequence HomologyAmino Acid,SITE,START CODON,SUBUNIT,Support,transcription,TRANSCRIPTION FACTOR,Transcription Factors,translation,TRANSLATION INITIATION,tRNA,yeast} } % == BibTeX quality report for ramirezMutationsActivatingYeast1992: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{rashidCrystalStructureCbf5Nop10Gar12006, title = {Crystal Structure of a {{Cbf5-Nop10-Gar1}} Complex and Implications in {{RNA-guided}} Pseudouridylation and Dyskeratosis Congenita}, author = {Rashid, R. and Liang, B. and Baker, D.L. and Youssef, O.A. and He, Y. and Phipps, K. and Terns, R.M. and Terns, M.P. and Li, H.}, year = 2006, month = jan, journal = {Molecular cell}, volume = {21}, number = {2}, pages = {249–260}, publisher = {Elsevier}, doi = {10.1016/j.molcel.2005.11.017}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276505018046}, abstract = {H/ACA RNA-protein complexes, comprised of four proteins and an H/ACA guide RNA, modify ribosomal and small nuclear RNAs. The H/ACA proteins are also essential components of telomerase in mammals. Cbf5 is the H/ACA protein that catalyzes isomerization of uridine to pseudouridine in target RNAs. Mutations in human Cbf5 (dyskerin) lead to dyskeratosis congenita. Here, we describe the 2.1 A crystal structure of a specific complex of three archaeal H/ACA proteins, Cbf5, Nop10, and Gar1. Cbf5 displays structural properties that are unique among known pseudouridine synthases and are consistent with its distinct function in RNA-guided pseudouridylation. We also describe the previously unknown structures of both Nop10 and Gar1 and the structural basis for their essential roles in pseudouridylation. By using information from related structures, we have modeled the entire ribonucleoprotein complex including both guide and substrate RNAs. We have also identified a dyskeratosis congenita mutation cluster site within a modeled dyskerin structure}, keywords = {0,Amino Acid Sequence,Archaeal Proteins,Binding Sites,Biochemistry,Biophysics,CBF5,cell cycle,Cell Cycle Proteins,chemistry,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,crystal structure,CRYSTAL-STRUCTURE,CrystallographyX-Ray,Dyskeratosis Congenita,genetics,human,Humans,Hydro-Lyases,In Vitro,IN-VITRO,INFORMATION,La,Mammals,metabolism,ModelsMolecular,Molecular Sequence Data,Multiprotein Complexes,Mutation,MUTATIONS,nosource,Nuclear Proteins,protein,Proteins,Pseudouridine,PSEUDOURIDINE SYNTHASE,pseudouridylation,Pyrococcus furiosus,Recombinant Proteins,RIBONUCLEOPROTEIN,Ribonucleoproteins,RibonucleoproteinsSmall Nucleolar,Rna,Sequence HomologyAmino Acid,SITE,SMALL NUCLEAR RNAS,Structural,STRUCTURAL BASIS,structure,Support,TARGET,Telomerase,Uridine} } % == BibTeX quality report for rashidCrystalStructureCbf5Nop10Gar12006: % ? unused Journal abbr (“Mol.Cell”)

@article{rashkovaGagProteinsTwo2002, title = {Gag Proteins of the Two {{Drosophila}} Telomeric Retrotransposons Are Targeted to Chromosome Ends}, author = {Rashkova, S. and Karam, S.E. and Kellum, R. and Pardue, M.L.}, year = 2002, month = nov, journal = {The Journal of cell biology}, volume = {159}, number = {3}, pages = {397–402}, publisher = {Rockefeller Univ Press}, doi = {10.1083/jcb.200205039}, url = {http://jcb.rupress.org/content/159/3/397.abstract}, abstract = {Drosophila telomeres are formed by two non-LTR retrotransposons, HeT-A and TART, which transpose only to chromosome ends. Successive transpositions of these telomeric elements yield arrays that are functionally equivalent to the arrays generated by telomerase in other organisms. In contrast, other Drosophila non-LTR retrotransposons transpose widely through gene-rich regions, but not to ends. The two telomeric elements encode very similar Gag proteins, suggesting that Gag may be involved in their unique targeting to chromosome ends. To test the intrinsic potential of these Gag proteins for targeting, we tagged the coding sequences with sequence of GFP and expressed the constructs in transiently transfected Drosophila-cultured cells. Gag proteins from both elements are efficiently transported into the nucleus where the protein from one element, HeT-A, forms structures associated with chromosome ends in interphase nuclei. Gag from the second element, TART moves into telomere-associated structures only when co-expressed with HeT-A Gag. The results suggest that these Gag proteins are capable of delivering the retrotransposons to telomeres, although TART requires assistance from HeT-A. They also imply a symbiotic relationship between the two elements, with HeT-A Gag directing the telomere-specific targeting of the elements, whereas TART provides reverse transcriptase for transposition}, keywords = {ARRAYS,CELLS,coding sequence,Drosophila,ELEMENTS,Gag,gfp,HeT-A,intracellular targeting,LINE,M,MOF,nosource,protein,Proteins,REGION,REQUIRES,retrotransposon,retrovirus,sequence,SEQUENCES,structure,TART,Telomerase,Telomere,transcription} }

@article{ratcliffSimilarityViralDefense1997, title = {A Similarity between Viral Defense and Gene Silencing in Plants.}, author = {Ratcliff, F. and Harrison, B.D. and Baulcombe, D.C.}, year = 1997, journal = {Science}, volume = {276⬚ ⬚}, number = {5318}, pages = {1558–1560}, doi = {10.1126/science.276.5318.1558}, url = {⬚http://www.sciencemag.org/cgi/content/full/276/5318/1558⬚⬚⬚ ⬚⬚}, abstract = {Gene silencing in plants, in which an endogenous gene is suppressed by introduction of a related transgene, has been used⬚ for crop improvement. Observations that viruses are potentially both initiators and targets of gene silencing suggested that this phenomenon may be related to natural defense against viruses. Supporting this idea, it was found that nepovirus infection of nontransgenic plants induces a resistance mechanism that is similar to transgene-induced gene silencing. ⬚}, keywords = {gene,Gene Silencing,INFECTION,MECHANISM,nosource,Plants,RESISTANCE,TARGET,Viruses} }

@article{raughtTargetRapamycinTOR2001, title = {The Target of Rapamycin ({{TOR}}) Proteins}, author = {Raught, B. and Gingras, A.C. and Sonenberg, N.}, year = 2001, month = jun, journal = {Proceedings of the National Academy of Sciences}, volume = {98}, number = {13}, pages = {7037–7044}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.121145898}, url = {http://www.pnas.org/content/98/13/7037.short}, abstract = {Rapamycin potently inhibits downstream signaling from the target of rapamycin (TOR) proteins. These evolutionarily conserved protein kinases coordinate the balance between protein synthesis and protein degradation in response to nutrient quality and quantity. The TOR proteins regulate (i) the initiation and elongation phases of translation, (ii) ribosome biosynthesis, (iii) amino acid import, (iv) the transcription of numerous enzymes involved in multiple metabolic pathways, and (v) autophagy. Intriguingly, recent studies have also suggested that TOR signaling plays a critical role in brain development, learning, and memory formation}, keywords = {0,ACID,AMINO-ACID,animal,antibiotic,antibiotics,AntibioticsMacrolide,biosynthesis,cancer,CEREVISIAE,degradation,development,DOWNSTREAM,drug effects,elongation,enzyme,Fungal Proteins,genetics,human,initiation,kinase,La,Learning,Long-Term Potentiation,Memory,metabolism,ModelsBiological,nosource,PATHWAY,Peptide Chain Elongation,pharmacology,Phosphotransferases (Alcohol Group Acceptor),physiology,protein,Protein Kinases,protein synthesis,PROTEIN-KINASE,PROTEIN-SYNTHESIS,Proteins,Review,ribosome,Ribosomes,S,S-CEREVISIAE,Saccharomyces cerevisiae,Signal Transduction,Sirolimus,supportnon-u.s.gov’t,Synapses,TARGET,transcription,translation} } % == BibTeX quality report for raughtTargetRapamycinTOR2001: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{rawatCryoelectronMicroscopicStudy2003, title = {A Cryo-Electron Microscopic Study of Ribosome-Bound Termination Factor {{RF2}}}, author = {Rawat, U.B.S. and Zavialov, A.V. and Sengupta, J. and Valle, M. and Grassucci, R.A. and Linde, J. and Vestergaard, B. and Ehrenberg, M. and Frank, J.}, year = 2003, month = jan, journal = {Nature}, volume = {421}, number = {6918}, pages = {87–90}, doi = {10.1038/nature01224}, url = {ISI:000180165500043}, abstract = {Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into the ribosomal decoding centre (DC) and is recognized by a class-1 release factor (RF). RFs have a conserved GGQ amino-acid motif, which is crucial for peptide release and is believed to interact directly with the peptidyl-transferase centre (PTC) of the 50S ribosomal subunit(1),(2). Another conserved motif of RFs (SPF in RF2) has been proposed to interact directly with stop codons in the DC of the 30S subunit(3). The distance between the DC and PTC is, 73 Angstrom. However, in the X-ray structure of RF2, SPF and GGQ are only 23 Angstrom apart(4), indicating that they cannot be at DC and PTC simultaneously. Here we show that RF2 is in an open conformation when bound to the ribosome, allowing GGQ to reach the PTC while still allowing SPF-stop-codon interaction. The results indicate new interpretations of accuracy in termination, and have implications for how the presence of a stop codon in the DC is signalled to PTC}, keywords = {accuracy,ACID,ACIDS,Amino Acids,AMINO-ACIDS,BINDING,CHAIN TERMINATION,Codon,CODON RECOGNITION,CODONS,CONFORMATION,decoding,FACTOR-II,Genetic,LOCATION,MESSENGER-RNA,MOF,nosource,peptidyl transferase,PEPTIDYL-TRANSFERASE,Peptidyltransferase,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,RELEASE,release factor,RESOLUTION,ribosome,Rna,sequence,STOP CODON,structure,termination,TRANSLATION TERMINATION} }

@article{rayCharacteristicsEukaryoticInitiation1993, title = {Characteristics of the Eukaryotic Initiation Factor 2 Associated 67-{{kDa}} Polypeptide}, author = {Ray, M.K. and Chakraborty, A. and Datta, B. and Chattopadhyay, A. and Saha, D. and Bose, A. and Kinzy, T.G. and Wu, S. and Hileman, R.E. and Merrick, W.C. and {}{et al.}}, year = 1993, month = may, journal = {Biochemistry}, volume = {32}, number = {19}, pages = {5151–5159}, publisher = {ACS Publications}, doi = {10.1021/bi00070a026}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00070a026}, keywords = {Antibodies,antibody,BINDING,Eif-2,GAMMA-SUBUNIT,Histones,INHIBITION,initiation,kinase,lysate,MECHANISM,nosource,Phosphorylation,protein,protein synthesis,PROTEIN-SYNTHESIS,SUBUNIT} }

@article{rayMacromolecularComplexesDepots2007, title = {Macromolecular Complexes as Depots for Releasable Regulatory Proteins}, author = {Ray, P.S. and Arif, A. and Fox, P.L.}, year = 2007, month = apr, journal = {Trends in biochemical sciences}, volume = {32}, number = {4}, pages = {158–164}, publisher = {Elsevier}, doi = {10.1016/j.tibs.2007.02.003}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000407000357}, abstract = {Multi-component, macromolecular complexes perform essential cellular functions that require spatial or temporal coordination of activities. Complexes also facilitate co-regulation of protein amounts and cellular localization of individual components. We propose a novel function of multi-component complexes as depots for regulatory proteins that, upon release, acquire new auxiliary functions. We further propose that component release is inducible and context-dependent. We describe two cases in which multi-component assemblies - the ribosome and tRNA multi-synthetase complex - function as depots. Both complexes have crucial roles in supporting protein synthesis but they also release regulatory proteins for inflammation-responsive, transcript-specific translational control. Recent evidence indicates that other macromolecular assemblies might be sources for proteins with auxiliary functions, and the depot mechanism might be widespread in nature}, keywords = {assembly,BIOLOGY,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,La,LOCALIZATION,MECHANISM,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,RELEASE,ribosome,tRNA} } % == BibTeX quality report for rayMacromolecularComplexesDepots2007: % ? unused Journal abbr (“Trends Biochem.Sci.”)

@article{raymondRemovalMRNADestabilizing1989a, title = {Removal of an {{mRNA}} Destabilizing Element Correlates with the Increased Oncogenicity of Proto-Oncogene c-⬚fos⬚.}, author = {Raymond, V. and Atwater, J.A. and Verma, I.M.}, year = 1989, journal = {Oncogene Res.}, volume = {5}, pages = {1–12}, keywords = {cancer,fos,mRNA,No DOI found,nosource,stability} } % == BibTeX quality report for raymondRemovalMRNADestabilizing1989a: % ? Possibly abbreviated journal title Oncogene Res.

@article{razgaRibosomalRNAKinkturn2004a, title = {Ribosomal {{RNA}} Kink-Turn Motif–a Flexible Molecular Hinge}, author = {Razga, F. and Spackova, N. and Reblova, K. and Koca, J. and Leontis, N.B. and Sponer, J.}, year = 2004, month = oct, journal = {J.Biomol.Struct.Dyn.}, volume = {22}, number = {2}, pages = {183–194}, doi = {10.1080/07391102.2004.10506994}, url = {PM:15317479}, abstract = {Ribosomal RNA K-turn motifs are asymmetric internal loops characterized by a sharp bend in the phosphodiester backbone resulting in “V” shaped structures, recurrently observed in ribosomes and showing a high degree of sequence conservation. We have carried out extended explicit solvent molecular dynamics simulations of selected K-turns, in order to investigate their intrinsic structural and dynamical properties. The simulations reveal an unprecedented dynamical flexibility of the K-turns around their X-ray geometries. The K-turns sample, on the nanosecond timescale, different conformational substates. The overall behavior of the simulations suggests that the sampled geometries are essentially isoenergetic and separated by minimal energy barriers. The nanosecond dynamics of isolated K-turns can be qualitatively considered as motion of two rigid helix stems controlled by a very flexible internal loop which then leads to substantial hinge-like motions between the two stems. This internal dynamics of K-turns is strikingly different for example from the bacterial 5S rRNA Loop E motif or BWYV frameshifting pseudoknot which appear to be rigid in the same type of simulations. Bistability and flexibility of K-turns was also suggested by several recent biochemical studies. Although the results of MD simulations should be considered as a qualitative picture of the K-turn dynamics due to force field and sampling limitations, the main advantage of the MD technique is its ability to investigate the region close to K-turn ribosomal-like geometries. This part of the conformational space is not well characterized by the solution experiments due to large-scale conformational changes seen in the experiments. We suggest that K-turns are well suited to act as flexible structural elements of ribosomal RNA. They can for example be involved in mediation of large-scale motions or they can allow a smooth assembling of the other parts of the ribosome}, keywords = {0,5S rRNA,Bacterial,Base Sequence,Binding Sites,chemistry,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,CrystallographyX-Ray,DYNAMICS,E,Electrostatics,ELEMENTS,Frameshifting,genetics,Haloarcula marismortui,Hydrogen Bonding,La,LOOP,LOOP-E,ModelsMolecular,MOTIFS,nosource,Nucleic Acid Conformation,pseudoknot,REGION,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNAArchaeal,RNARibosomal,rRNA,sequence,Structural,structure,Thermodynamics,Water} } % == BibTeX quality report for razgaRibosomalRNAKinkturn2004a: % ? Possibly abbreviated journal title J.Biomol.Struct.Dyn.

@article{razgaRNAKinkturnsMolecular2006, title = {{{RNA}} Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics}, author = {Razga, F. and Zacharias, M. and Reblova, K. and Koca, J. and Sponer, J.}, year = 2006, month = may, journal = {Structure.}, volume = {14}, number = {5}, pages = {825–835}, doi = {10.1016/j.str.2006.02.012}, url = {PM:16698544}, abstract = {The presence of Kink-turns (Kt) at key functional sites in the ribosome (e.g., A-site finger and L7/L12 stalk) suggests that some Kink-turns can confer flexibility on RNA protuberances that regulate the traversal of tRNAs during translocation. Explicit solvent molecular dynamics demonstrates that Kink-turns can act as flexible molecular elbows. Kink-turns are associated with a unique network of long-residency static and dynamical hydration sites that is intimately involved in modulating their conformational dynamics. An implicit solvent conformational search confirms the flexibility of Kink-turns around their X-ray geometries and identifies a second low-energy region with open structures that could correspond to Kink-turn geometries seen in solution experiments. An extended simulation of Kt-42 with the factor binding site (helices 43 and 44) shows that the local Kt-42 elbow-like motion fully propagates beyond the Kink-turn, and that there is no other comparably flexible site in this rRNA region. Kink-turns could mediate large-scale adjustments of distant RNA segments}, keywords = {A SITE,A-SITE,BINDING,BINDING-SITE,DYNAMICS,FUNCTIONAL SITES,IDENTIFY,La,nosource,REGION,ribosome,Rna,rRNA,search,SITE,SITES,structure,translocation,tRNA} } % == BibTeX quality report for razgaRNAKinkturnsMolecular2006: % ? Possibly abbreviated journal title Structure.

@article{rechtBasisProkaryoticSpecificity1999, title = {Basis for Prokaryotic Specificity of Action of Aminoglycoside Antibiotics}, author = {Recht, M.I. and Douthwaite, S. and Puglisi, J.D.}, year = 1999, month = jun, journal = {The EMBO Journal}, volume = {18}, number = {11}, pages = {3133–3138}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/18.11.3133}, url = {http://www.nature.com/emboj/journal/v18/n11/abs/7591733a.html}, abstract = {The aminoglycosides, a group of structurally related antibiotics, bind to rRNA in the small subunit of the prokaryotic ribosome. Most aminoglycosides are inactive or weakly active against eukaryotic ribosomes. A major difference in the binding site for these antibiotics between prokaryotic and eukaryotic ribosomes is the identity of the nucleotide at position 1408 (Escherichia coli numbering), which is an adenosine in prokaryotic ribosomes and a guanosine in eukaryotic ribosomes. Expression in E.coli of plasmid-encoded 16S rRNA containing an A1408 to G substitution confers resistance to a subclass of the aminoglycoside antibiotics that contain a 6’ amino group on ring I. Chemical footprinting experiments indicate that resistance arises from the lower affinity of the drug for the eukaryotic rRNA sequence. The 1408G ribosomes are resistant to the same subclass of aminoglycosides as previously observed both for eukaryotic ribosomes and bacterial ribosomes containing a methylation at the N1 position of A1408. The results indicate that the identity of the nucleotide at position 1408 is a major determinant of specificity of aminoglycoside action, and agree with prior structural studies of aminoglycoside-rRNA complexes}, keywords = {0,16S,ACID,Adenosine,Amino Acid Substitution,AMINOGLYCOSIDE ANTIBIOTICS,Aminoglycosides,Ampicillin,Anti-Bacterial Agents,antibiotic,antibiotics,Bacterial,Base Sequence,BINDING,Binding Sites,BINDING-SITE,BIOLOGY,chemistry,Comparative Study,COMPLEX,COMPLEXES,drug effects,Drug ResistanceMicrobial,E.coli,Escherichia coli,ESCHERICHIA-COLI,Eukaryotic Cells,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,expression,genetics,growth & development,Guanosine,La,MAJOR DETERMINANT,metabolism,Methylation,Microbial Sensitivity Tests,nosource,pharmacology,POSITION,RESISTANCE,RESISTANT,ribosome,Ribosomes,Rna,RNARibosomal16S,rRNA,sequence,SITE,Species Specificity,SPECIFICITY,Spectinomycin,Structural,Substrate Specificity,SUBUNIT,Sulfuric Acid Esters,Support} } % == BibTeX quality report for rechtBasisProkaryoticSpecificity1999: % ? unused Journal abbr (“EMBO J.”)

@article{reijoDeletionSingleCopyTransferRna1993, title = {Deletion of {{A Single-Copy Transfer-Rna Affects Microtubule Function}} in {{Saccharomyces-Cerevisiae}}}, author = {Reijo, R.A. and Cho, D.S. and Huffaker, T.C.}, year = 1993, month = dec, journal = {Genetics}, volume = {135}, number = {4}, pages = {955–962}, doi = {10.1093/genetics/135.4.955}, url = {ISI:A1993MH93800003}, abstract = {rts1-1 was identified as an extragenic suppressor of tub2-104, a cold-sensitive allele of the sole gene encoding P-tubulin in the yeast, Saccharomyces cerevisiae. In addition, rts1-1 cells are heat sensitive and resistant to the microtubule-destabilizing drug, benomyl. The rts1-1 mutation is a deletion of approximately 5 kb of genomic DNA on chromosome X that includes one open reading frame and three tRNA genes. Dissection of this region shows that heat sensitivity is due to deletion of the open reading frame (HIT1). Suppression and benomyl resistance are caused by deletion of the gene encoding a tRNA(AGG)(Arg) (HSX1). Northern analysis of rts1-1 cells indicates that HSX1 is the only gene encoding this tRNA. Deletion of HSX1 does not suppress the tub2-104 mutation by misreading at the AGG codons in TUB2. It also does not suppress by interfering with the protein arginylation that targets certain proteins for degradation. These results leave open the prospect that this tRNA(AGG)(Arg) plays a novel role in the cell}, keywords = {3,analysis,ASTRAL MICROTUBULES,BODIES,CELLS,CEREVISIAE,Codon,CODONS,degradation,DELTA-SEQUENCES,Dna,FRAME,gene,Genes,genomic,Heat,Mutation,MUTATIONS,nosource,OPEN READING FRAME,PATHWAY,protein,Proteins,READING FRAME,REGION,RESISTANCE,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,suppression,TARGET,TRANSFER-RNA,tRNA,yeast} } % == BibTeX quality report for reijoDeletionSingleCopyTransferRna1993: % ? Title looks like it was stored in title-case in Zotero

@article{reilHeptanucleotideSequenceMediates1993a, title = {A Heptanucleotide Sequence Mediates Ribosomal Frameshifting in Mammalian Cells.}, author = {Reil, H. and Kollmus, H. and Wiedle, U.H. and Hauser, H.}, year = 1993, journal = {J.Virol.}, volume = {67}, pages = {5579–5584}, doi = {10.1128/jvi.67.9.5579-5584.1993}, keywords = {Chromosomes,frameshift,Frameshifting,HIV,nosource,ribosomal frameshifting,sequence,SIGNAL} } % == BibTeX quality report for reilHeptanucleotideSequenceMediates1993a: % ? Possibly abbreviated journal title J.Virol.

@article{remachaProteinsP1P21995a, title = {Proteins {{P1}}, {{P2}}, and {{P0}}, Components of the Eukaryotic Ribosome Stalk. {{New}} Structural and Functional Aspects}, author = {Remacha, M. and {Jimenez-Diaz}, A. and Santos, C. and Briones, E. and Zambrano, R. and Rodriguez Gabriel, M.A. and Guarinos, E. and Ballesta, J.P.}, year = 1995, month = nov, journal = {Biochem. Cell Biol.}, volume = {73}, number = {11-12}, pages = {959–968}, publisher = {Ottawa: National Research Council of Canada= Conseil national de recherches du Canada, 1986-}, doi = {10.1139/o95-103}, abstract = {The eukaryoic ribosomal stalk is thought to consist of the phosphoproteins P1 and P2, which form a complex with protein PO. This complex interacts at the GTPase domain in the large subunit rRNA, overlapping the binding site of the protein L11-like eukaryotic counterpart (Saccharomyces cerevisiae protein L15 and mammalian protein L12). An unusual pool of the dephosphorylated forms of proteins P1 and P2 is detected in eukaryotic cytoplasm, and an exchange between the proteins in the pool and on the ribosome takes place during translation. Quadruply disrupted yeast strains, carrying four inactive acidic protein genes and, therefore, containing ribosomes totally depleted of acidic proteins, are viable but grow with a doubling time threefold higher than wild-type cells. The in vitro translation systems derived from these stains are active but the two-dimensional gel electrophoresis pattern of proteins expressed in vivo and in vitro is partially different. These results indicate that the P1 and P2 proteins are not essential for ribosome activity but are able to affect the translation of some specific mRNAs. Protein PO is analogous to bacterial ribosomal protein L10 but carries an additional carboxyl domain showing a high sequence homology to the acidic proteins P1 and P2, including the terminal peptide DDDMGFGLFD. Successive deletions of the PO carboxyl domain show that removal of the last 21 amino acids from the PO carboxyl domain only slightly affects the ribosome activity in a wild-type genetic background; however, the same deletion is lethal in a quadruple disruptant deprived of acidic P1/P2 proteins. Additional deletions affect the interaction of PO with the P1 and P2 proteins and with the rRNA. The experimental data available support the implication of the eukaryotic stalk components in some regulatory process that modulates the ribosomal activity}, keywords = {96282699,Amino Acid Sequence,Amino Acids,Bacterial,BINDING,chemistry,COMPLEX,COMPLEXES,COMPONENT,Cytoplasm,Electrophoresis,Fungal Proteins,gene,Genes,Genetic,GTPase,In Vitro,in vitro translation,IN-VITRO,IN-VIVO,Molecular Sequence Data,mRNA,nosource,Phosphoproteins,Phosphorylation,physiology,protein,Proteins,Ribosomal Proteins,ribosome,Ribosomes,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Structural,Structure-Activity Relationship,SUBUNIT,Support,supportnon-u.s.gov’t,SYSTEM,translation,yeast} } % == BibTeX quality report for remachaProteinsP1P21995a: % ? Possibly abbreviated journal title Biochem. Cell Biol.

@article{rettbergThreewayJunctionConstituent1999a, title = {A Three-Way Junction and Constituent Stem-Loops as the Stimulator for Programmed -1 Frameshifting in Bacterial Insertion Sequence {{IS911}}}, author = {Rettberg, C.C. and Prere, M.F. and Gesteland, R.F. and Atkins, J.F. and Fayet, O.}, year = 1999, month = mar, journal = {J.Mol.Biol.}, volume = {286}, number = {5}, pages = {1365–1378}, doi = {10.1006/jmbi.1999.2546}, url = {PM:10064703}, abstract = {Several signals are required for the programmed frameshifting in translation of IS911 mRNA. These include a Shine Dalgarno (SD)-like sequence, a slippery sequence of six adenine residues and a guanine residue (A6G) and a 3’ secondary structure. The structure of the mRNA containing these elements was investigated using chemical and enzymatic probing. The probing data show that the 3’ structure is a three-way junction of stems. The function of the three-way junction was investigated by mutagenesis. Disrupting the stability of the structure greatly affects frameshifting and transposition levels as tested by separate in vivo assays. Structural probing and thermal melting profiles indicate that the disrupted three-way junctions have altered structures}, keywords = {0,Adenine,Aldehydes,analogs & derivatives,assays,Bacterial,Base Pairing,Base Sequence,biosynthesis,chemistry,CME-Carbodiimide,Dna,DNA Transposable Elements,ELEMENTS,Escherichia coli,Frameshifting,FrameshiftingRibosomal,Genetic,genetics,Guanine,human,Imidazoles,IN-VIVO,La,metabolism,Molecular Sequence Data,mRNA,Mutagenesis,Mutation,nosource,Nucleic Acid Conformation,pharmacology,programmed frameshifting,RecombinationGenetic,Regulatory SequencesNucleic Acid,Ribonucleases,Rna,RNABacterial,RNADouble-Stranded,RNAMessenger,sequence,SIGNAL,stability,Structural,structure,Structure-Activity Relationship,Sulfuric Acid Esters,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Temperature,translation} } % == BibTeX quality report for rettbergThreewayJunctionConstituent1999a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{reyesStructureYeastRibosomes1978, title = {Structure of the Yeast Ribosomes:: {{Proteins}} Associated with the {{rRNA}}}, author = {Reyes, R. and Vazquez, D. and Ballesta, J.P.}, year = 1978, month = nov, journal = {Biochimica et Biophysica Acta (BBA)-Nucleic Acids and Protein Synthesis}, volume = {521}, number = {1}, pages = {229–234}, publisher = {Elsevier}, doi = {10.1016/0005-2787(78)90265-4}, url = {http://linkinghub.elsevier.com/retrieve/pii/0005278778902654}, abstract = {Polyamines have been shown to bind to doubled stranded regions of rRNA [3]. Therefore, ribosomal proteins that can be cross linked to these molecules in the ribosomes structure must be bound to or located in the vicinity of the RNA. This technique is the first to yield results on the proteins associated with the rRNA in the eukaryotic ribosome where the lack of purified ribosomal proteins does not allow the use of direct binding studies as in bacterial systems. Proteins S7, S10, S13, S21, S22 and S27 in the small subunit and L2/3, L5, L10/12, L19/20, L22, L23, L36/37, L42 and L43’ in the large subunit are labelled when cross linked to [14C]spermidine using 1,5-difluoro 2,4-dinitrobenzene and are good candidates to be RNA-binding proteins in ribosomes from Saccharomyces cerevisiae}, keywords = {0,Bacterial,BINDING,CEREVISIAE,EUKARYOTIC RIBOSOME,L5,La,metabolism,Molecular Weight,nosource,polyamine,Polyamines,protein,Proteins,REGION,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Rna,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Spermidine,structure,SUBUNIT,SYSTEM,SYSTEMS,ultrastructure,yeast} } % == BibTeX quality report for reyesStructureYeastRibosomes1978: % ? unused Journal abbr (“Biochim.Biophys.Acta”)

@article{rheinbergerThreeTRNABinding1981, title = {Three {{tRNA}} Binding Sites on {{Escherichia}} Coli Ribosomes.}, author = {Rheinberger, H.J. and Sternbach, H. and Nierhaus, K.H.}, year = 1981, month = sep, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {78}, number = {9}, pages = {5310–5314}, issn = {0027-8424}, doi = {10.1073/pnas.78.9.5310}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=348734&tool=pmcentrez&rendertype=abstract}, abstract = {The binding of N-acetyl-Phe-tRNAPhe (an analogue of peptidyl-tRNA), Phe-tRNAPhe, and deacylated tRNAPhe to poly(U)-programmed tightly coupled 70S ribosomes was studied. The N-acetyl-Phe-tRNAPhe binding is governed by an exclusion principle: not more than one N-acetyl-Phe-tRNAPhe can be bound per ribosome, although this peptidyl-tRNA analogue can be present either at the aminoacyl-tRNA (A) site or the peptidyl-tRNA (P) site. Two Phe-tRNAPhe molecules are accepted by one ribosome in the presence of poly(U). This aminoacyl-tRNA binds enzymatically (in the presence of elongation factor Tu and GTP) and nonenzymatically to the A site and is then transferred to the P site, if that site is free. If this elongation factor G-independent movement is hampered, either by using an incubation temperature of 0 degrees C or by the addition of the translocation inhibitor viomycin, only one Phe-tRNAPhe per ribosome can be bound. The effect of the peptidyltransferase inhibitor chloramphenicol on the binding is similar to that of viomycin. In the absence of poly(U), Phe-tRNAPhe cannot bind to the ribosome. Deacylated [14C]tRNAPhe can bind in three copies to one ribosome. The new third tRNA binding site is called the “E” site. The sequence of filling the sites is P, E, and A. The apparent binding constants for the P and the E sites are both approximately 9 X 10(6) M-1 and that for the A site is 1.3 X 10(6) M-1. In the absence of poly(U), only one deacylated tRNAPhe can be bound per ribosome. This tRNAPhe most likely occupies the P site.}, pmid = {7029532}, keywords = {0,70S RIBOSOME,A SITE,A-SITE,Amino Acyl,Amino Acyl: metabolism,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,Chloramphenicol,CONSTANTS,E,E site,elongation,elongation factors,ELONGATION-FACTOR-TU,ELONGATION-FACTORS,Escherichia coli,Escherichia coli ribosomes,ESCHERICHIA-COLI,FACTOR TU,GTP,INHIBITOR,La,M1,Messenger,Messenger: metabolism,metabolism,Movement,nosource,P SITE,P-SITE,Peptide Elongation Factors,Peptide Elongation Factors: metabolism,Peptidyltransferase,ribosome,Ribosomes,Ribosomes: metabolism,Ribosomes: ultrastructure,Rna,RNA,RNAMessenger,RNATransfer,RNATransferAmino Acyl,sequence,SITE,SITES,Temperature,Transfer,Transfer: metabolism,translocation,tRNA,tRNA binding,TU,ultrastructure,Viomycin} } % == BibTeX quality report for rheinbergerThreeTRNABinding1981: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{rheinbergerParametersPreparationEscherichia1988a, title = {Parameters for the Preparation of {{Escherichia}} Coli Ribosomes and Ribosomal Subunits Active in {{tRNA}} Binding.}, author = {Rheinberger, H.J. and Geigenmuller, U. and Wedde, M. and Nierhaus, K.H.}, year = 1988, journal = {Methods in enzymology}, volume = {164}, eprint = {3071687}, eprinttype = {pubmed}, pages = {658–670}, doi = {10.1016/S0076-6879(88)64076-6}, url = {http://www.ncbi.nlm.nih.gov/pubmed/3071687}, keywords = {0,BINDING,Carbon,Carbon Radioisotopes,Cell Fractionation,CentrifugationDensity Gradient,ChromatographyDEAE-Cellulose,Escherichia coli,Escherichia coli ribosomes,ESCHERICHIA-COLI,Indicators and Reagents,La,metabolism,Methods,nosource,Puromycin,Radioisotope Dilution Technique,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNATransfer,RNATransferPhe,SUBUNIT,SUBUNITS,tRNA,tRNA binding,ultrastructure} } % == BibTeX quality report for rheinbergerParametersPreparationEscherichia1988a: % ? unused Journal abbr (“Methods Enzymol.”)

@article{ribasRNAdependentRNAPolymerase1992a, title = {{{RNA-dependent RNA}} Polymerase Consensus Sequence of the {{L-A}} Double-Stranded {{RNA}} Virus: Definition of Essential Domains.}, author = {Ribas, J.C. and Wickner, R.B.}, year = 1992, journal = {Proc.Natl.Acad.Sci.USA}, volume = {89}, pages = {2185–2189}, doi = {10.1073/pnas.89.6.2185}, keywords = {Consensus Sequence,DOUBLE-STRANDED-RNA,L-A,La,nosource,polymerase,Rna,sequence,virus} } % == BibTeX quality report for ribasRNAdependentRNAPolymerase1992a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{ribasSaccharomycesCerevisiaeLBC1996a, title = {Saccharomyces Cerevisiae {{L-BC}} Double-Stranded {{RNA}} Virus Replicase Recognizes the {{L-A}} Positive-Strand {{RNA}} 3’ End}, author = {Ribas, J.C. and Wickner, R.B.}, year = 1996, month = jan, journal = {Journal of Virology}, volume = {70}, number = {1}, pages = {292–297}, doi = {10.1128/jvi.70.1.292-297.1996}, url = {ISI:A1996TJ65000037}, abstract = {L-A and L-BC are two double-stranded RNA viruses present in almost all strains of Saccharomyces cervisiae. L-A, the major species, has been extensively characterized with in vitro systems established, but little is known about L-BC, Here we report in vitro template-dependent transcription, replication, and RNA recognition activities of L-BC. The L-BC replicase activity converts positive, single stranded RNA to double-stranded RNA by synthesis of the complementary RNA strand, Although L-A and L-BC do not interact in vivo, in vitro L-BC virions can replicate the positive, single-stranded RNA of L-A and its satellite, M(1), with the same 3’ end sequence and stem-loop requirements shown by L-A virions for its own template, However, the L-BC virions do not recognize the internal replication enhancer of the L-A positive strand. In a direct comparison of L-A and L-BC virions, each preferentially recognizes its own RNA for binding, replication, and transcription, These results suggest a close evolutionary relation of these two viruses, consistent with their RNA-dependent RNA polymerase sequence similarities}, keywords = {3,BINDING,CEREVISIAE,COAT PROTEIN,DOUBLE-STRANDED-RNA,ENCAPSIDATION,expression,Gag-pol,In Vitro,IN-VITRO,IN-VIVO,INVITRO,L-A,L-BC,La,MESSENGER-RNA,nosource,PARTICLES,POL FUSION PROTEIN,polymerase,Q-BETA REPLICASE,RECOGNITION,REPLICATION,Rna,RNA recognition,RNA Viruses,RNA-POLYMERASE,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SYSTEM,SYSTEMS,TEMPLATE,transcription,Virion,virus,yeast} }

@article{ribasGagDomainGagPol1998a, title = {The {{Gag}} Domain of the {{Gag-Pol}} Fusion Protein Directs Incorporation into the {{L-A}} Double-Stranded {{RNA}} Viral Particles in {{Saccharomyces}} Cerevisiae}, author = {Ribas, J.C. and Wickner, R.B.}, year = 1998, month = apr, journal = {Journal of Biological Chemistry}, volume = {273}, number = {15}, pages = {9306–9311}, doi = {10.1074/jbc.273.15.9306}, url = {ISI:000072990800102}, abstract = {The L-A double-stranded RNA virus of yeast encodes its major coat protein, Gag, and a Gag-Pol fusion protein made by a -1 ribosomal frameshift, a coding strategy used by many retroviruses. We find that cells expressing only Gag from one plasmid and only Gag-Pol (in frame) from a separate plasmid can support the propagation of M-1 double-stranded RNA, encoding the killer toxin. We use this system to separately investigate the functions of Gag and the Gag part of Gag-Pol. L-A contains two fusion protein molecules per particle, and although N-terminal acetylation of Gag is essential for viral assembly, it is completely dispensable for function of Gag-Pol. In general, the requirements on Gag for viral assembly and propagation are more stringent than on the Gag part of Gag-Pol. Finally, we directly show that it is Gag that instructs the incorporation of Gag-Pol into the viral particles}, keywords = {Acetylation,assembly,CELLS,CEREVISIAE,COAT PROTEIN,DOMAIN,DOUBLE-STRANDED-RNA,ENCAPSIDATION,ENCODES,expression,FRAME,frameshift,FUSION PROTEIN,Gag,Gag-pol,IMMUNODEFICIENCY-VIRUS TYPE-1,killer,killer toxin,L-A,La,M1,MAK3,Mutagenesis,N-ACETYLTRANSFERASE,nosource,PARTICLES,PLASMID,polymerase,PR160GAG-POL,PROPAGATION,protein,REPLICATION,RETROVIRUSES,RIBOSOMAL FRAMESHIFT,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Support,SYSTEM,toxin,viral particle,VIRAL PARTICLES,virus,yeast} }

@article{riceGagPolGenes1985a, title = {The {{Gag}} and {{Pol Genes}} of {{Bovine Leukemia-Virus}} - {{Nucleotide-Sequence}} and {{Analysis}}}, author = {Rice, N.R. and Stephens, R.M. and Burny, A. and Gilden, R.V.}, year = 1985, journal = {Virology}, volume = {142}, number = {2}, pages = {357–377}, doi = {10.1016/0042-6822(85)90344-7}, url = {ISI:A1985AEL3000014}, keywords = {analysis,Gag,gene,Genes,nosource,NUCLEOTIDE-SEQUENCE,pol} } % == BibTeX quality report for riceGagPolGenes1985a: % ? Title looks like it was stored in title-case in Zotero

@article{richTriplexRNA1991, title = {Triplex {{RNA}}}, author = {Rich, A. and Davies, D.R. and Felsenfeld, G.}, year = 1991, month = jul, journal = {Science}, volume = {253}, number = {5015}, pages = {17}, doi = {10.1126/science.1712122}, url = {PM:1712122}, keywords = {chemistry,La,Molecular Structure,nosource,Rna} } % == BibTeX quality report for richTriplexRNA1991: % ? Title looks like it was stored in title-case in Zotero

@article{richterdahlforsNovelMutantsElongation1990, title = {Novel Mutants of Elongation Factor {{G}}}, author = {Richter Dahlfors, A.A. and Kurland, C.G.}, year = 1990, month = oct, journal = {J.Mol.Biol.}, volume = {215}, number = {4}, pages = {549–557}, doi = {10.1016/S0022-2836(05)80167-6}, abstract = {A novel mutant form of elongation factor G (EF-G) in Escherichia coli is described. This variant EF-G restricts reading frame errors by a factor of 2 to 3 in vivo at two different positions in a lacIZ fusion. In addition, a conventional fusidic acid resistant (fusR) mutant of EF-G was compared with the restrictive mutant. Both mutants were characterized in vitro in a steady-state poly(U) translating system. The data indicate that the restrictive EF-G variant has an altered interaction with the ribosome both in vivo and in vitro. In contrast, the conventional fusR variant is altered in its interaction with GTP, which is evident in vitro}, keywords = {+1 frameshifting,91039317,biosynthesis,Comparative Study,drug effects,Drug ResistanceMicrobial,EF-2,elongation,Escherichia coli,ESCHERICHIA-COLI,Fusidic Acid,genetics,GTP,Guanosine Triphosphate,In Vitro,IN-VITRO,IN-VIVO,Kinetics,Lac Operon,metabolism,Mutation,nosource,Peptide Elongation Factor G,Peptide Elongation Factors,pharmacology,ribosome,Ribosomes,RNAMessenger,supportnon-u.s.gov’t,SYSTEM,TranslationGenetic} } % == BibTeX quality report for richterdahlforsNovelMutantsElongation1990: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{richterThinkGloballyTranslate2001, title = {Think Globally, Translate Locally: What Mitotic Spindles and Neuronal Synapses Have in Common}, author = {Richter, J.D.}, year = 2001, month = jun, journal = {Proceedings of the National Academy of Sciences}, volume = {98}, number = {13}, pages = {7069–7071}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.111146498}, url = {http://www.pnas.org/content/98/13/7069.short}, abstract = {Early metazoan development is programmed by maternal mRNAs inherited by the egg at the time of fertilization. These mRNAs are not translated en masse at any one time or at any one place, but instead their expression is regulated both temporally and spatially. Recent evidence has shown that one maternal mRNA, cyclin B1, is concentrated on mitotic spindles in the early Xenopus embryo, where its translation is controlled by CPEB (cytoplasmic polyadenylation element binding protein), a sequence-specific RNA binding protein. Disruption of the spindle-associated translation of this mRNA results in a morphologically abnormal mitotic apparatus and inhibited cell division. Mammalian neurons, particularly in the synapto-dendritic compartment, also contain localized mRNAs such as that encoding alpha-CaMKII. Here, synaptic activation drives local translation, an event that is involved in synaptic plasticity and possibly long-term memory storage. Synaptic translation of alpha-CaMKII mRNA also appears to be controlled by CPEB, which is enriched in the postsynaptic density. Therefore, CPEB-controlled local translation may influence such seemingly disparate processes as the cell cycle and synaptic plasticity}, keywords = {0,activation,Animals,BINDING,BINDING PROTEIN,BINDING-PROTEIN,Calcium-Calmodulin-Dependent Protein Kinase Type 2,Calcium-Calmodulin-Dependent Protein Kinases,cell cycle,Cell Division,Dendrites,development,DISRUPTION,Embryo,embryology,EmbryoNonmammalian,expression,Female,Genetic,genetics,Genomic Imprinting,kinase,La,Mammals,Memory,microbiology,Mitotic Spindle Apparatus,MOLECULAR-GENETICS,mRNA,Neuronal Plasticity,Neurons,nosource,physiology,Polyadenylation,protein,Protein Kinases,PROTEIN-KINASE,Review,Rna,RNA-BINDING-PROTEIN,RNAMessenger,Synapses,translation,Xenopus,Xenopus laevis} } % == BibTeX quality report for richterThinkGloballyTranslate2001: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{ridleySuperkillerMutationsSaccharomyces1984a, title = {Superkiller Mutations in {{Saccharomyces}} Cerevisiae Suppress Exclusion of {{M2}} Double-Stranded {{RNA}} by {{L-A-HN}} and Confer Cold Sensitivity in the Presence of {{M}} and {{L-A-HN}}}, author = {Ridley, S.P. and Sommer, S.S. and Wickner, R.B.}, year = 1984, month = apr, journal = {Molecular & Cellular Biology}, volume = {4}, number = {4}, pages = {761–770}, keywords = {Cold,DOUBLE-STRANDED-RNA,gene,Genes,L-A,La,M1,Multiple DOI,Mutation,MUTATIONS,nonfile,nosource,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SKI,Temperature} }

@article{rieberCyclindependentKinaseCyclin1994a, title = {Cyclin-Dependent Kinase 2 and Cyclin {{A}} Interaction with {{E2F}} Are Targets for Tyrosine Induction of {{B16}} Melanoma Terminal Differentiation.}, author = {Rieber, M.S.}, year = 1994, journal = {Cell growth & differentiation}, volume = {5}, number = {12}, eprint = {7696182}, eprinttype = {pubmed}, pages = {1339–1346}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7696182}, keywords = {cancer,cdk2,cell lines,cyclins,kinase,No DOI found,nosource} } % == BibTeX quality report for rieberCyclindependentKinaseCyclin1994a: % ? unused Journal abbr (“Cell Growth & Diff.”)

@article{rifferMutationalAnalysisK282002, title = {Mutational Analysis of {{K28}} Preprotoxin Processing in the Yeast {{Saccharomyces}} Cerevisiae}, author = {Riffer, F. and Eisfeld, K. and Breinig, F. and Schmitt, M.J.}, year = 2002, month = may, journal = {Microbiology}, volume = {148}, number = {Pt 5}, pages = {1317–1328}, publisher = {Soc General Microbiol}, url = {http://mic.sgmjournals.org/cgi/content/abstract/148/5/1317}, abstract = {K28 killer strains of Saccharomyces cerevisiae are permanently infected with a cytoplasmic persisting dsRNA virus encoding a secreted alpha/beta heterodimeric protein toxin that kills sensitive cells by cell-cycle arrest and inhibition of DNA synthesis. In vivo processing of the 345 aa toxin precursor (preprotoxin; pptox) involves multiple internal and carboxy-terminal cleavage events by the prohormone convertases Kex2p and Kex1p. By site-directed mutagenesis of the preprotoxin gene and phenotypic analysis of its in vivo effects it is now demonstrated that secretion of a biological active virus toxin requires signal peptidase cleavage after Gly(36) and Kex2p-mediated processing at the alpha subunit N terminus (after Glu-Arg(49)), the alpha subunit C terminus (after Ser-Arg(149)) and at the beta subunit N terminus (after Lys-Arg(245)). The mature C terminus of the beta subunit is trimmed by Kex1p, which removes the terminal Arg(345) residue, thus uncovering the toxin’s endoplasmic reticulum targeting signal (HDEL) which–in a sensitive target cell–is essential for retrograde toxin transport. Interestingly, both toxin subunits are covalently linked by a single disulfide bond between alpha-Cys(56) and beta-Cys(340), and expression of a mutant toxin in which beta-Cys(340) had been replaced by Ser(340) resulted in the secretion of a non-toxic alpha/beta heterodimer that is blocked in retrograde transport and incapable of entering the yeast cell cytosol, indicating that one important in vivo function of beta-Cys(340) might be to ensure accessibility of the toxin’s beta subunit C terminus to the HDEL receptor of the target cell}, keywords = {0,analysis,C-TERMINUS,cell cycle,CELLS,CEREVISIAE,chemistry,CLEAVAGE,Cytosol,Disulfides,Dna,DSRNA,dsRNA virus,Endopeptidases,Endoplasmic Reticulum,ENDOPLASMIC-RETICULUM,expression,gene,Gene Deletion,genetics,IN-VIVO,INHIBITION,killer,La,metabolism,ModelsBiological,Mutagenesis,MutagenesisSite-Directed,MUTATIONAL ANALYSIS,Mycotoxins,No DOI found,nosource,Oligopeptides,Phenotype,PRECURSOR,Proprotein Convertases,protein,Protein ProcessingPost-Translational,Protein Sorting Signals,Protein Transport,Proteins,REQUIRES,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Serine,Serine Endopeptidases,SIGNAL,Subtilisins,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,TARGET,toxicity,toxin,TRANSPORT,virus,yeast} }

@article{rilesPhysicalMapsSix1993a, title = {Physical Maps of the Six Smallest Chromosomes of ⬚{{Saccharomyces}} Cerevieiae ⬚at the Resolution of 2.6 Kilobase Pairs.}, author = {Riles, L. and Dutchik, J.E. and Baktha, A. and McCauley, B.K. and Thayer, E.C. and Leckie, M.P. and Braden, V.V. and Depke, J.E. and Olsen, M.V.}, year = 1993, journal = {Genetics}, volume = {134}, pages = {81–154}, doi = {10.1093/genetics/134.1.81}, keywords = {Chromosomes,lambda grids,mapping,nosource,Saccharomyces,yeast} }

@article{ringnerFoldingFreeEnergies2005, title = {Folding Free Energies of 5’-{{UTRs}} Impact Post-Transcriptional Regulation on a Genomic Scale in Yeast}, author = {Ringner, M. and Krogh, M.}, year = 2005, month = dec, journal = {PLoS.Comput.Biol.}, volume = {1}, number = {7}, pages = {e72}, doi = {10.1371/journal.pcbi.0010072}, url = {PM:16355254 http://dx.plos.org/10.1371/journal.pcbi.0010072}, abstract = {Using high-throughput technologies, abundances and other features of genes and proteins have been measured on a genome-wide scale in Saccharomyces cerevisiae. In contrast, secondary structure in 5’-untranslated regions (UTRs) of mRNA has only been investigated for a limited number of genes. Here, the aim is to study genome-wide regulatory effects of mRNA 5’-UTR folding free energies. We performed computations of secondary structures in 5’-UTRs and their folding free energies for all verified genes in S. cerevisiae. We found significant correlations between folding free energies of 5’-UTRs and various transcript features measured in genome-wide studies of yeast. In particular, mRNAs with weakly folded 5’-UTRs have higher translation rates, higher abundances of the corresponding proteins, longer half-lives, and higher numbers of transcripts, and are upregulated after heat shock. Furthermore, 5’-UTRs have significantly higher folding free energies than other genomic regions and randomized sequences. We also found a positive correlation between transcript half-life and ribosome occupancy that is more pronounced for short-lived transcripts, which supports a picture of competition between translation and degradation. Among the genes with strongly folded 5’-UTRs, there is a huge overrepresentation of uncharacterized open reading frames. Based on our analysis, we conclude that (i) there is a widespread bias for 5’-UTRs to be weakly folded, (ii) folding free energies of 5’-UTRs are correlated with mRNA translation and turnover on a genomic scale, and (iii) transcripts with strongly folded 5’-UTRs are often rare and hard to find experimentally}, keywords = {0,5’ Untranslated Regions,5’-UTR,analysis,Base Sequence,CEREVISIAE,chemistry,COMPLEX,COMPLEXES,degradation,FRAME,gene,Gene Expression RegulationFungal,Genes,genetics,GenomeFungal,genomic,Half-Life,Heat,HEAT-SHOCK,La,metabolism,Molecular Sequence Data,mRNA,nosource,Nucleic Acid Conformation,OPEN READING FRAME,Open Reading Frames,post-transcriptional regulation,POSTTRANSCRIPTIONAL REGULATION,protein,Protein Biosynthesis,Proteins,READING FRAME,Reading Frames,REGION,regulation,Research SupportNon-U.S.Gov’t,ribosome,Ribosomes,RNA-Binding Proteins,RNA-BINDING-PROTEIN,S,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SECONDARY STRUCTURE,sequence,SEQUENCES,structure,Support,SYSTEM,SYSTEMS,Thermodynamics,TRANSCRIPT,TranscriptionGenetic,translation,turnover,Untranslated Regions,yeast} } % == BibTeX quality report for ringnerFoldingFreeEnergies2005: % ? Possibly abbreviated journal title PLoS.Comput.Biol.

@article{rinke-appelRibosomalEnvironmentTRNA1995, title = {The Ribosomal Environment of {{tRNA}}: Crosslinks to {{rRNA}} from Positions 8 and 20: 1 in the Central Fold of {{tRNA}} Located at the {{A}}, {{P}}, or {{E}} Site.}, author = {{Rinke-Appel}, J. and Junke, N. and Osswald, M. and Brimacombe, R.}, year = 1995, month = dec, journal = {RNA.}, volume = {1}, number = {10}, pages = {1018–1028}, publisher = {Cold Spring Harbor Lab}, url = {http://rnajournal.cshlp.org/content/1/10/1018.short}, abstract = {The naturally occurring nucleotide 3-(3-amino-3-carboxy-propyl) uridine (“acp3U”) at position 20:1 of lupin tRNAMet was coupled to a photoreactive diazirine derivative. Similarly, the 4-thiouridine at position 8 of Escherichia coli tRNAPhe was modified with an aromatic azide. Each of the derivatized tRNAs was bound to E. coli ribosomes in the presence of suitable mRNA analogues, under conditions specific for the A, P, or E sites. After photoactivation of the diazirine or azide groups, the sites of crosslinking from the tRNAs to 16S or 23S rRNA were analyzed by our standard procedures, involving a combination of ribonuclease H digestion and primer extension analysis. The crosslinked ribosomal proteins were also identified. The results for the rRNA showed a well-defined series of crosslinks to both the 16S and 23S molecules, the most pronounced being (1) an entirely A-site-specific crosslink from tRNA position 20:1 to the loop-end region (nt 877-913) of helix 38 of the 23S RNA (a region that has not so far been associated at all with tRNA binding), and (2) a largely P-site-specific crosslink from tRNA position 8 to nt 2111-2112 of the 23S RNA (nt 2112 being a position that has previously been identified in footprinting studies as belonging to the ribosomal E site). The data are compared with results from a parallel study of crosslinks from position 47 (also in the central fold of the tRNA), as well as with previously published crosslinks from the anticodon loop (positions 32, 34, and 37) and the CCA-end region (position 76, and the aminoacyl residue)}, keywords = {0,16S,23S RNA,analysis,Anticodon,ANTICODON LOOP,Bacterial,Base Sequence,BINDING,Binding Sites,chemistry,CROSS-LINKING,Cross-Linking Reagents,CROSSLINKING,E,E site,Escherichia coli,ESCHERICHIA-COLI,Fabaceae,genetics,La,LOOP,metabolism,ModelsMolecular,Molecular Sequence Data,mRNA,No DOI found,nosource,Nucleic Acid Conformation,PlantsMedicinal,POSITION,POSITIONS,primer extension,protein,Proteins,REGION,Research SupportNon-U.S.Gov’t,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNABacterial,RnaPlant,RNARibosomal16S,RNARibosomal23S,RNATransfer,RNATransferMet,RNATransferPhe,rRNA,SERIES,SITE,SITES,tRNA,tRNA binding,Uridine} } % == BibTeX quality report for rinke-appelRibosomalEnvironmentTRNA1995: % ? Possibly abbreviated journal title RNA.

@article{rivlinContributionZincFinger1999a, title = {The Contribution of a Zinc Finger Motif to the Function of Yeast Ribosomal Protein {{YL37a}}}, author = {Rivlin, A.A. and Chan, Y.L. and Wool, I.G.}, year = 1999, month = dec, journal = {Journal of Molecular Biology}, volume = {294}, number = {4}, pages = {909–919}, doi = {10.1006/jmbi.1999.3309}, url = {ISI:000084188400007}, abstract = {Eukaryotic ribosomes have a large number of proteins but the exact nature of their contribution to the structure and to the function of the particle is not known. Of the 78 proteins in yeast ribosomes, six have zinc finger motifs of the C-2-C-2 variety. Both genes encoding the essential yeast ribosomal protein YL37a, which has such a zinc finger motif, were disrupteXXPd. The double deletion, which is lethal, can be rescued with a plasmid-encoded copy of a YL37a gene. Mutations were constructed in a plasmid-encoded copy of YL37a; the mutations caused the cysteine residues in the motif (at positions 39, 42, 57 and 60) to be replaced, one at a time, with serine. The cysteine residue at position 39, the first of the four in the motif, is essential for the function of YL37a, since a C39S mutation did not complement the null phenotype. However, plasmids encoding variants with C42S, C57S, or C60S mutations in the zinc finger motif were able to rescue the null mutant. YL37a binds zinc, but none of the mutant proteins, C39S, C42S, C57S, or C60S, was able to bind the metal. Thus, all four cysteine residues are essential for the binding of zinc; only one, C39, is essential for the function of the ribosomal protein. (C) 1999 Academic Press}, keywords = {BINDING,COMPLEX,DNA-BINDING,ESCHERICHIA-COLI,EUKARYOTIC GENES,EUKARYOTIC RIBOSOMES,gene,Genes,HIGH-LEVEL EXPRESSION,L25,Mutation,MUTATIONS,nosource,Phenotype,PLASMID,Plasmids,protein,Proteins,RECOGNITION,RESIDUES,Ribosomal Proteins,ribosome,Ribosomes,RNA-POLYMERASE,SACCHAROMYCES-CEREVISIAE,Serine,structure,TRANSCRIPTION FACTOR-IIIA,yeast,yeast YL37a,zinc finger motif} }

@article{robertsHeritableActivityPrion2003, title = {Heritable Activity: A Prion That Propagates by Covalent Autoactivation}, author = {Roberts, B.T. and Wickner, R.B.}, year = 2003, journal = {Genes & development}, volume = {17}, number = {17}, pages = {2083–2087}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.1115803}, url = {http://genesdev.cshlp.org/content/17/17/2083.short}, abstract = {Known prions (infectious proteins) are self-propagating amyloids or conformationally altered proteins, but in theory an enzyme necessary for its own activation could also be a prion (or a gene composed of protein).We show that yeast protease B is such a prion, called [beta].[beta] is infectious, reversibly curable, and its de novo generation is induced by overexpression of the pro-protease. Present in normal cells but masked by the functionally redundant protease A, [beta] is advantageous during starvation and necessary for sporulation.We propose that other enzymes whose active, modified, form is necessary for their maturation might also be prions}, keywords = {0,activation,biosynthesis,CELLS,disease,Endopeptidases,enzyme,Enzymes,FORM,gene,Genetic,genetics,Kidney,La,MATURATION,metabolism,nosource,OVEREXPRESSION,Phenotype,prion,Prions,protein,Proteins,yeast,Yeasts} } % == BibTeX quality report for robertsHeritableActivityPrion2003: % ? unused Journal abbr (“Genes Dev.”)

@article{robertsonRegulationProteinKinase1996, title = {The Regulation of the Protein Kinase {{PKR}} by {{RNA}}}, author = {Robertson, H.D. and Mathews, M.B.}, year = 1996, journal = {Biochimie}, volume = {78}, number = {11-12}, pages = {909–914}, publisher = {Elsevier}, doi = {10.1016/S0300-9084(97)86712-0}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0300-9084(97)86712-0}, abstract = {A model is presented for the regulation of the double-stranded RNA (dsRNA)-activated mammalian protein kinase PKR, which is involved in protein synthesis inhibition and the antiviral response in cells. A series of previous findings abut PKROs behavior are reviewed, including its effects on translation; the activation of its protein kinase activity; binding sites for PKR on RNA; PKROs protein domains, which include two double-stranded RNA binding motifs (dsRBMs); and the likelihood of PKR dimer formation. The model which emerges to account for many of these observations includes the suggestion that PKR dimers form which are stabilized and rearranged upon binding to dsRNA regions 60 bp or longer. The hypothesis includes protein conformational changes within each member of a PKR dimer bound to dsRNA which re-position an inhibitory polypeptide domain and thus allow kinase activation. Also considered are ways in which PKR interacts with imperfectly duplexed, highly structured RNA molecules}, keywords = {0,activation,Animals,antiviral,BINDING,BINDING MOTIF,Binding Sites,BINDING-SITE,BINDING-SITES,Biochemistry,biosynthesis,CELLS,chemistry,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,DIMER,Dimerization,DOMAIN,DOMAINS,DOUBLE-STRANDED-RNA,DSRNA,Eif-2,eIF-2 Kinase,Enzyme Activation,FORM,Gene Expression RegulationEnzymologic,Humans,INHIBITION,kinase,La,metabolism,MODEL,ModelsStructural,MOTIFS,nosource,POLYPEPTIDE,protein,Protein Biosynthesis,Protein Conformation,protein synthesis,protein synthesis inhibition,PROTEIN-KINASE,Protein-Serine-Threonine Kinases,PROTEIN-SYNTHESIS,REGION,regulation,Review,Rna,RNADouble-Stranded,SERIES,SITE,SITES,Support,translation} }

@article{rodninaElongationFactorTu1995, title = {Elongation Factor {{Tu}}, a {{GTPase}} Triggered by Codon Recognition on the Ribosome: Mechanism and {{GTP}} Consumption.}, author = {Rodnina, M.V. and Pape, T. and Fricke, R. and Wintermeyer, W.}, year = 1995, month = nov, journal = {Biochemistry and Cell Biology}, volume = {73}, number = {11-12}, pages = {1221–1227}, publisher = {NATIONAL RESEARCH COUNCIL CANADA}, doi = {10.1139/o95-132}, url = {http://www.nrcresearchpress.com/doi/abs/10.1139/o95-132}, abstract = {The mechanism of elongation factor Tu (EF-Tu) catalyzed aminoacyl-tRNA (aa-tRNA) binding to the A site of the ribosome was studied. Two types of complexes of EF-Tu with GTP and aa-tRNA, EF-Tu.GTP-aa-tRNA (ternary) and (EF-Tu.GTP)2.aa-tRNA (quinternary), can be formed in vitro depending on the conditions. On interaction with the ribosomal A site, generally only one molecule of GTP is hydrolysed per aa-tRNA bound and peptide bond formed. The second GTP molecule from the quinternary complex is hydrolyzed only during translation of an oligo(U) tract in the presence of EF-G. The first step in the interaction between the ribosome and the ternary complex is the codon-independent formation of an initial complex. In the absence of codon recognition, the aa-tRNA-EF- Tu complex does not enter further steps of A site binding and remains in the initial binding state. Despite the rapid formation of the initial complex, the rate constant of GTP hydrolysis in the noncognate complex is four orders of magnitude lower compared with the cognate complex. This, together with the results of time-resolved fluorescence measurements, suggests that codon recognition by the ternary complex on the ribosome initiates a series of structural rearrangements that result in a conformational change of EF-Tu, presumably involving the effector region, which, in turn, triggers GTP hydrolysis and the subsequent steps of A site binding}, keywords = {96282728,A-SITE,Base Sequence,BINDING,Catalysis,Codon,COMPLEX,COMPLEXES,EFTu,elongation,Fluorescence,genetics,GTP,GTP Phosphohydrolase,GTPase,Guanosine Triphosphate,Hydrolysis,In Vitro,IN-VITRO,MECHANISM,metabolism,Molecular Sequence Data,nosource,Peptide Elongation Factor Tu,proofreading,ribosome,Ribosomes,RNATransferAmino Acid-Specific,Structural,supportnon-u.s.gov’t,translation} } % == BibTeX quality report for rodninaElongationFactorTu1995: % ? unused Journal abbr (“Biochem.Cell Biol.”)

@article{rodninaCodondependentConformationalChange1995, title = {Codon-Dependent Conformational Change of Elongation Factor {{Tu}} Preceding {{GTP}} Hydrolysis on the Ribosome.}, author = {Rodnina, M.V. and Fricke, R. and Kuhn, L. and Wintermeyer, W.}, year = 1995, month = jun, journal = {The EMBO Journal}, volume = {14}, number = {11}, pages = {2613–2619}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1995.tb07259.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC398375/}, abstract = {The mechanisms by which elongation factor Tu (EF-Tu) promotes the binding of aminoacyl-tRNA to the A site of the ribosome and, in particular, how GTP hydrolysis by EF-Tu is triggered on the ribosome, are not understood. We report steady-state and time-resolved fluorescence measurements, performed in the Escherichia coli system, in which the interaction of the complex EF-Tu.GTP.Phe-tRNAPhe with the ribosomal A site is monitored by the fluorescence changes of either mant-dGTP [3’-O-(N-methylanthraniloyl)-2-deoxyguanosine triphosphate], replacing GTP in the complex, or of wybutine in the anticodon loop of the tRNA. Additionally, GTP hydrolysis is measured by the quench-flow technique. We find that codon-anticodon interaction induces a rapid rearrangement within the G domain of EF-Tu around the bound nucleotide, which is followed by GTP hydrolysis at an approximately 1.5-fold lower rate. In the presence of kirromycin, the activated conformation of EF- Tu appears to be frozen. The steps following GTP hydrolysis–the switch of EF-Tu to the GDP-bound conformation, the release of aminoacyl-tRNA from EF-Tu to the A site, and the dissociation of EF-Tu-GDP from the ribosome–which are altogether suppressed by kirromycin, are not distinguished kinetically. The results suggest that codon recognition by the ternary complex on the ribosome initiates a series of structural rearrangements resulting in a conformational change of EF-Tu, possibly involving the effector region, which, in turn, triggers GTP hydrolysis}, keywords = {95300794,A-SITE,analogs & derivatives,Anthranilic Acids,Anticodon,BINDING,Binding Sites,chemistry,Codon,COMPLEX,COMPLEXES,drug effects,EFTu,elongation,Escherichia coli,ESCHERICHIA-COLI,Fluorescence,genetics,GTP,Guanosine Diphosphate,Guanosine Triphosphate,Hydrolysis,MECHANISM,MECHANISMS,metabolism,nosource,Nucleic Acid Conformation,Peptide Elongation Factor Tu,pharmacology,proofreading,Protein Conformation,Pyridones,ribosome,Ribosomes,RNATransferAmino Acyl,Structural,supportnon-u.s.gov’t,SYSTEM,techniques,tRNA} } % == BibTeX quality report for rodninaCodondependentConformationalChange1995: % ? unused Journal abbr (“EMBO J.”)

@article{rodninaGTPConsumptionElongation1995, title = {{{GTP}} Consumption of Elongation Factor {{Tu}} during Translation of Heteropolymeric {{mRNAs}}}, author = {Rodnina, M.V. and Wintermeyer, W.}, year = 1995, month = mar, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {92}, number = {6}, pages = {1945–1949}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.92.6.1945}, url = {http://www.pnas.org/content/92/6/1945.short}, keywords = {BINDING,Chromatography,Codon,COMPLEX,COMPLEXES,EFTu,elongation,Escherichia coli,ESCHERICHIA-COLI,Frameshifting,GTP,Hydrolysis,mRNA,nosource,ribosome,Ribosomes,sequence,SYSTEM,translation,translocation} }

@article{rodninaInitialBindingElongation1996a, title = {Initial Binding of the Elongation Factor {{Tu}}.{{GTP}}.Aminoacyl-{{tRNA}} Complex Preceding Codon Recognition on the Ribosome}, author = {Rodnina, M.V. and Pape, T. and Fricke, R. and Kuhn, L. and Wintermeyer, W.}, year = 1996, month = jan, journal = {Journal of Biological Chemistry}, volume = {271}, number = {2}, pages = {646–652}, doi = {10.1074/jbc.271.2.646}, abstract = {The first step in the sequence of interactions between the ribosome and the complex of elongation factor Tu (EF-Tu), GTP, and aminoacyl-tRNA, which eventually leads to A site-bound aminoacyl-tRNA, is the codon- independent formation of an initial complex. We have characterized the initial binding and the resulting complex by time-resolved (stopped- flow) and steady-state fluorescence measurements using several fluorescent tRNA derivatives. The complex is labile, with rate constants of 6 x 10(7) M-1 s-1 and 24 s-1 (20 degrees C, 10 mM Mg2+) for binding and dissociation, respectively. Both thermodynamic and activation parameters of initial binding were determined, and five Mg2+ ions were estimated to participate in the interaction. While a cognate ternary complex proceeds form initial binding through codon recognition to rapid GTP hydrolysis, the rate constant of GTP hydrolysis in the non- cognate complex is 4 orders of magnitude lower, despite the rapid formation of the initial complex in both cases. Hence, the ribosome- induced GTP hydrolysis by EF-Tu is strongly affected by the presence of the tRNA. This suggests that codon-anticodon recognition, which takes place after the formation of the initial binding complex, provides a specific signal that triggers fast GTP hydrolysis by EF-Tu on the ribosome}, keywords = {96132790,activation,BINDING,Codon,COMPLEX,COMPLEXES,derivatives,EFTu,elongation,Escherichia coli,Fluorescence,Fluorescent Dyes,GTP,Guanosine Triphosphate,Hydrolysis,Ions,M1,metabolism,ModelsBiological,nosource,Peptide Elongation Factor Tu,proofreading,ribosome,Ribosomes,RNATransferAmino Acyl,sequence,SIGNAL,supportnon-u.s.gov’t,tRNA} } % == BibTeX quality report for rodninaInitialBindingElongation1996a: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{rodninaHydrolysisGTPElongation1997a, title = {Hydrolysis of {{GTP}} by Elongation Factor {{G}} Drives {{tRNA}} Movement on the Ribosome.}, author = {Rodnina, M.V. and Savelsbergh, A. and Katunin, V.I. and Wintermeyer, W.}, year = 1997, month = jan, journal = {Nature}, volume = {385}, number = {6611}, pages = {37–41}, doi = {10.1038/385037a0}, url = {http://www.researchgate.net/publication/14223372_Hydrolysis_of_GTP_by_elongation_factor_G_drives_tRNA_movement_on_the_ribosome/file/79e4150bc63028b2a0.pdf http://tetrad.ucsf.edu/bioreg_2008/downloads/TlnLec1-Rodnina-Recom.pdf}, keywords = {Bacterial,biosynthesis,elongation,GTP,GTPase,Hydrolysis,MESSENGER-RNA,models,Movement,nosource,protein,ribosome,Ribosomes,Rna,structure,translocation,tRNA} }

@article{rodninaFidelityAminoacyltRNASelection2001, title = {Fidelity of Aminoacyl-{{tRNA}} Selection on the Ribosome: Kinetic and Structural Mechanisms}, author = {Rodnina, M.V. and Wintermeyer, W.}, year = 2001, journal = {Ann. Rev. Biochem.}, volume = {70}, number = {1}, pages = {415–435}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, doi = {10.1146/annurev.biochem.70.1.415}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.biochem.70.1.415}, abstract = {The ribosome discriminates between correct and incorrect aminoacyl-tRNAs (aa-tRNAs), or their complexes with elongation factor Tu (EF-Tu) and GTP, according to the match between anticodon and mRNA codon in the A site. Selection takes place at two stages, prior to GTP hydrolysis (initial selection) and after GTP hydrolysis but before peptide bond formation (proofreading). In part, discrimination results from different rejection rates that are due to different stabilities of the respective codon-anticodon complexes. An important additional contribution is provided by induced fit, in that only correct codon recognition leads to acceleration of rate-limiting rearrangements that precede chemical steps. Recent elucidation of ribosome structures and mutational analyses suggest which residues of the decoding center may be involved in signaling formation of the correct codon-anticodon duplex to the functional centers of the ribosome. In utilizing induced fit for substrate discrimination, the ribosome resembles other nucleic acid-programmed polymerases}, pmid = {11395413}, keywords = {0,A SITE,A-SITE,Anticodon,Binding Sites,Biochemistry,BOND FORMATION,chemistry,Codon,CODON RECOGNITION,COMPLEX,COMPLEXES,decoding,EFTu,elongation,ELONGATION-FACTOR-TU,FACTOR TU,Fidelity,Germany,GTP,Hydrolysis,Kinetics,La,MECHANISM,MECHANISMS,metabolism,mRNA,nosource,peptide bond formation,Peptide Elongation Factor Tu,polymerase,proofreading,RECOGNITION,RESIDUES,Review,ribosome,Ribosomes,Rna,RNATransferAmino Acyl,SELECTION,SITE,stability,Structural,structure,Support,TU} } % == BibTeX quality report for rodninaFidelityAminoacyltRNASelection2001: % ? Possibly abbreviated journal title Ann. Rev. Biochem. % ? unused Journal abbr (“Annu.Rev.Biochem.”)

@article{rodninaRecognitionSelectionTRNA2005, title = {Recognition and Selection of {{tRNA}} in Translation}, author = {Rodnina, M.V. and Gromadski, K.B. and Kothe, U. and Wieden, H.J.}, year = 2005, month = feb, journal = {FEBS Letters}, volume = {579}, number = {4}, pages = {938–942}, publisher = {Elsevier}, doi = {10.1016/j.febslet.2004.11.048}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579304014310}, abstract = {Aminoacyl-tRNA (aa-tRNA) is delivered to the ribosome in a ternary complex with elongation factor Tu (EF-Tu) and GTP. The stepwise movement of aa-tRNA from EF-Tu into the ribosomal A site entails a number of intermediates. The ribosome recognizes aa-tRNA through shape discrimination of the codon-anticodon duplex and regulates the rates of GTP hydrolysis by EF-Tu and aa-tRNA accommodation in the A site by an induced fit mechanism. Recent results of kinetic measurements, ribosome crystallography, single molecule FRET measurements, and cryo-electron microscopy suggest the mechanism of tRNA recognition and selection}, keywords = {0,A SITE,A-SITE,chemistry,COMPLEX,COMPLEXES,Cryoelectron Microscopy,Crystallography,EFTu,elongation,ELONGATION-FACTOR-TU,FACTOR TU,genetics,GTP,Hydrolysis,INTERMEDIATE,La,MECHANISM,metabolism,Movement,nosource,physiology,Protein Biosynthesis,RECOGNITION,Research SupportNon-U.S.Gov’t,Review,ribosome,Ribosomes,Rna,RNAMessenger,RNATransferAmino Acyl,SELECTION,SITE,translation,tRNA,TU} } % == BibTeX quality report for rodninaRecognitionSelectionTRNA2005: % ? unused Journal abbr (“FEBS Lett.”)

@article{rodninaHowRibosomesMake2007, title = {How Ribosomes Make Peptide Bonds}, author = {Rodnina, M.V. and Beringer, M. and Wintermeyer, W.}, year = 2007, month = jan, journal = {Trends Biochem.Sci.}, volume = {32}, number = {1}, pages = {20–26}, publisher = {Elsevier}, doi = {10.1016/j.tibs.2006.11.007}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000406003240 http://www.sciencedirect.com/science/article/pii/S0968000406003240}, abstract = {Ribosomes are molecular machines that synthesize proteins in the cell. Recent biochemical analyses and high-resolution crystal structures of the bacterial ribosome have shown that the active site for the formation of peptide bonds - the peptidyl-transferase center - is composed solely of rRNA. Thus, the ribosome is the largest known RNA catalyst and the only natural ribozyme that has a synthetic activity. The ribosome employs entropic catalysis to accelerate peptide-bond formation by positioning substrates, reorganizing water in the active site and providing an electrostatic network that stabilizes reaction intermediates. Proton transfer during the reaction seems to be promoted by a concerted shuttle mechanism that involves ribose hydroxyl groups on the tRNA substrate}, keywords = {ACTIVE-SITE,Bacterial,Biochemistry,Catalysis,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,Germany,INTERMEDIATE,La,MECHANISM,nosource,peptide bond formation,PEPTIDE-BOND FORMATION,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,protein,Proteins,PROTON,Ribose,ribosome,Ribosomes,ribozyme,Rna,rRNA,SITE,structure,tRNA,Water} } % == BibTeX quality report for rodninaHowRibosomesMake2007: % ? Possibly abbreviated journal title Trends Biochem.Sci.

@article{rodriguez-cousinoYeastPositivestrandedViruslike1998a, title = {Yeast Positive-Stranded Virus-like {{RNA}} Replicons - 20 {{S}} and 23 {{S RNA}} Terminal Nucleotide Sequences and 3 ’ End Secondary Structures Resemble Those of {{RNA}} Coliphages}, author = {{Rodriguez-Cousino}, N. and Solorzano, A. and Fujimura, T. and Esteban, R.}, year = 1998, journal = {The Journal of biological chemistry}, volume = {273}, number = {32}, eprint = {9685388}, eprinttype = {pubmed}, pages = {20363–20371}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9685388}, abstract = {Saccharomyces cerevisiae strains carry single-stranded RNAs called 20 S RNA and 23 S RNA. These RNAs and their double-stranded counterparts, W and T dsRNAs, have been cloned and sequenced, A few nucleotides at both ends, however, remained unknown, These RNAs do not encode coat proteins but their own RNA-dependent RNA polymerases that share a high degree of conservation to each other. The polymerases are also similar to the replicases of RNA coliphages, such as Q beta, Here we have determined the nucleotide sequences of W and T dsRNAs at both ends using reverse transcriptase polymerase chain reaction-generated cDNA clones, We confirmed the terminal sequences by primer-extension and RNase protection experiments. Furthermore, these analyses demonstrated that W and T dsRNAs and their single-stranded RNA counterparts (i) are linear molecules, (ii) have identical nucleotide sequences at their ends, and (iii) have no poly(A) tails at their 3’ ends. Both 20 S and 23 S RNAs have GGGGC at the 5’ ends and the complementary 5-nucleotides sequence, GCCCC-OH, at their 3’ ends. S1 and V1 secondary structure-mapping of the 3’ ends of 20 S and 23 S RNAs shows the presence of a stem-loop structure that partially overlaps with the conserved 3’ end sequence. Nucleotide sequences and stem-loop structures similar to those described here have been found at the 3’ ends of RNA coliphages, These data, together with the similarity of the RNA-dependent RNA polymerases encoded among these RNAs and RNA coliphages, suggest that 20 S and 23 S RNAs are plus-strand single-stranded virus-like RNA replicons in yeast}, keywords = {3,CEREVISIAE,COAT PROTEIN,Coliphages,FAMILY,FORM,IDENTIFICATION,No DOI found,nosource,NUCLEOTIDE-SEQUENCE,Nucleotides,poly(A),POLY(A) TAIL,polymerase,primer extension,PROTECTION,protein,Proteins,REPLICATION,Rna,RNA-POLYMERASE,RNAse,RNAse protection,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SECONDARY STRUCTURE,sequence,SEQUENCES,STEM-LOOP,structure,T,yeast} }

@article{rodriguez-fonsecaFineStructurePeptidyl1995a, title = {Fine Structure of the Peptidyl Transferase Centre on 23 {{S-like rRNAs}} Deduced from Chemical Probing of Antibiotic-Ribosome Complexes}, author = {{Rodriguez-Fonseca}, C. and Amils, R. and Garrett, R.A.}, year = 1995, month = mar, journal = {J.Mol.Biol}, volume = {247}, number = {2}, pages = {224–235}, doi = {10.1006/jmbi.1994.0135}, url = {PM:7707371}, abstract = {Ribosomal binding sites were investigated for the diverse group of antibiotics: anisomycin, anthelmycin, blasticidin S, bruceantin, carbomycin, chloramphenicol, griseoviridin, narciclasine, T2 toxin, tylosin and virginiamycin M1 all of which are considered to inhibit the peptidyl transferase reaction by different mechanisms. The drugs also exhibit differing degrees of specificity for bacterial, archaeal and eukaryotic ribosomes despite a high level of conservation of sequence and secondary structure at the peptidyl transferase centre of the 23 S-like rRNAs. The drug binding sites were characterized by incubating each antibiotic with ribosomes from a bacterium, an archaeon and a eukaryote and chemically probing the 23 S-like rRNA. The complexity of the changes in reactivity ranged from one or two nucleotides (anthelmycin, narciclasine) to eight or nine (virginiamycin M1) and it was inferred, at least for those drugs producing complex changes, that they induce, and stabilize, a particular functional conformer in the peptidyl transferase centre. The results were correlated with literature data on both ribosomal ligand binding and the putative inhibitory mechanisms of the drugs, and the following inferences are made concerning the fine structure of the peptidyl transferase centre. (1) An irregular secondary structural motif, which includes unpaired A2439 (Escherichia coli numbering), lies close to the catalytic centre; (2) nucleotides A2451 and C2452 contribute to a site for the binding of the side chains of aromatic amino acids; (3) the P-substrate site encompasses U2585, U2506 and, possibly, a site in domain IV (A1787), and (4) the sequence A2058 to A2062 and nucleotide U2609 contribute to, or modulate, the start of the peptide channel. No drug effects were found that could be directly attributed to an A-site and the possibility is raised that, if it exists, it consists mainly of ribosomal proteins. However, two drugs T2 toxin and virginiamycin M1 protected the only nucleotide in the peptidyl transferase loop region (C2394) associated with the E-site. Finally, it is proposed that the putative sub-sites are physically separated, that some drugs bind to more than one of them, and that they are conformationally interdependent}, keywords = {0,3,A SITE,A-SITE,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,anisomycin,Anti-Bacterial Agents,antibiotic,antibiotics,Bacteria,Bacterial,Base Sequence,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,BIOLOGY,Catalysis,Chloramphenicol,Comparative Study,COMPLEX,COMPLEXES,DOMAIN,drug effects,drugs,E site,Escherichia coli,ESCHERICHIA-COLI,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,Evolution,genetics,La,LOOP,M1,MECHANISM,MECHANISMS,metabolism,Molecular Biology,Molecular Probes,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleotides,peptidyl transferase,PEPTIDYL-TRANSFERASE,protein,Protein Biosynthesis,Proteins,REGION,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Rna,RNARibosomal23S,rRNA,S,SECONDARY STRUCTURE,sequence,SITE,SITES,Species Specificity,SPECIFICITY,Structural,structure,Structure-Activity Relationship,Support,toxin,Virginiamycin} } % == BibTeX quality report for rodriguez-fonsecaFineStructurePeptidyl1995a: % ? Possibly abbreviated journal title J.Mol.Biol

@article{rodriguezcousinoBothYeastWDoubleStranded1992, title = {Both {{Yeast W-Double-Stranded Rna}} and {{Its Single-Stranded Form 20S Rna Are Linear}}}, author = {Rodriguezcousino, N. and Esteban, R.}, year = 1992, month = jun, journal = {Nucleic Acids Research}, volume = {20}, number = {11}, pages = {2761–2766}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/20.11.2761}, url = {ISI:A1992HZ67300019 http://nar.oxfordjournals.org/content/20/11/2761.short}, abstract = {Most yeast strains carry a cytoplasmic double-stranded RNA (dsRNA) molecule called W, of 2.5 kb in size. We have cloned and sequenced most of W genome (1), and we proposed that W (+) strands were identical to 20S RNA, a single-stranded RNA (ssRNA) species, whose copy number is highly induced under stress conditions. Recently it was proposed that 20S RNA was circular (2). In this paper, however, we demonstrate that both W dsRNA and 20S RNA are linear. Linearity of W dsRNA is shown by the stoichiometric labelling of both strands of W with P-32-pCp and T4 RNA ligase. The last 3’ end nucleotide of both strands is about 70 to 80% C and 20 to 30% A. Linearity of 20S RNA is directly demonstrated by a site-specific cleavage of 20S RNA with RNase H, using an oligodeoxynucleotide complementary to an internal site of 20S RNA. The cleavage produced not one but two RNA fragments expected from the linearity of 20S RNA}, keywords = {3,CLEAVAGE,COMPLETE NUCLEOTIDE-SEQUENCE,DOUBLE-STRANDED-RNA,ENCAPSIDATION,FORM,Genome,nosource,REPLICASE,Rna,RNAse,SACCHAROMYCES-CEREVISIAE,SELF-CLEAVAGE,SITE,site specific,virus,yeast} } % == BibTeX quality report for rodriguezcousinoBothYeastWDoubleStranded1992: % ? Title looks like it was stored in title-case in Zotero

@article{rohdeCellSurfaceExpression1996, title = {Cell Surface Expression of {{HIP}}, a Novel Heparin/Heparan Sulfate Binding Protein, of Human Uterine Epithelial Cells and Cell Lines}, author = {Rohde, L.H. and Julian, J. and Babaknia, A. and Carson, D.D.}, year = 1996, month = may, journal = {Journal of Biological Chemistry}, volume = {271}, number = {20}, pages = {11824–11830}, publisher = {ASBMB}, doi = {10.1074/jbc.271.20.11824}, url = {http://www.jbc.org/content/271/20/11824.short}, abstract = {Previous studies established that uterine epithelial cells and cell lines express cell surface heparin/heparan sulfate (HP/HS)-binding proteins (Wilson, O., Jacobs, A. L., Stewart, S., and Carson, D. D. (1990) J. Cell. Physiol. 143, 60-67; Raboudi, N., Julian, J., Rohde, L. H., and Carson, D. D. (1992) J. Biol. Chem. 267, 11930-11939). The accompanying paper (Liu, S., Smith, S. E., Julian, J., Rohde, L. H., Karin, N. J., and Carson, D. D. (1996) J. Biol. Chem. 271, 11817-11823) describes the cloning of a full-length cDNA corresponding to a candidate cell surface HP/HS interacting protein, HIP, expressed by a variety of human epithelia. A synthetic peptide was synthesized corresponding to an amino acid sequence predicted from the cDNA sequence and used to prepare a rabbit polyclonal antibody. This antibody reacted with a protein with an apparent Mr of 24,000 by SDS-polyacrylamide gel electrophoresis that was highly enriched in the 100,000 x g particulate fraction of RL95 cells. This molecular weight is similar to that of the protein expressed by 3T3 cells transfected with HIP cDNA. HIP was solubilized from this particulate fraction with NaCl concentrations {\(>\)} or = 0.8 M demonstrating a peripheral association consistent with the lack of a membrane spanning domain in the predicted cDNA sequence. HIP was not released by heparinase digestion suggesting that the association is not via membrane-bound HS proteoglycans. NaCl-solubilized HIP bound to heparin-agarose in physiological saline and eluted with NaCl concentrations of 0.75 M and above. Furthermore, incubation of 125I-HP with transblots of the NaCl-solubilized HIP preparations separated by two-dimensional gel electrophoresis demonstrated direct binding of HP to HIP. Indirect immunofluorescence studies demonstrated that HIP is expressed on the surfaces of intact RL95 cells. Binding of HIP antibodies to RL95 cell surfaces at 4 degrees C was saturable and blocked by preincubation with the peptide antigen. Single cell suspensions of RL95 cells formed large aggregates when incubated with antibodies directed against HIP but not irrelevant antibodies. Finally, indirect immunofluorescence studies demonstrate that HIP is expressed in both lumenal and glandular epithelium of normal human endometrium throughout the menstrual cycle. In addition, HIP expression increases in the predecidual cells of post-ovulatory day 13-15 stroma. Collectively, these data indicate that HIP is a membrane-associated HP-binding protein expressed on the surface of normal human uterine epithelia and uterine epithelial cell lines}, keywords = {0,3T3 Cells,ACID,Amino Acid Sequence,AMINO-ACID,analysis,Animals,Antibodies,antibody,ANTIGEN,ASSOCIATION,BINDING,BINDING PROTEIN,BINDING-PROTEIN,Biochemistry,BIOLOGY,blood,Blood Coagulation Factors,cancer,Carrier Proteins,Cell Line,cell lines,CELLS,chemistry,cloning,D,DOMAIN,E,Electrophoresis,Endometrium,expression,Female,GEL-ELECTROPHORESIS,Heparin,Heparitin Sulfate,human,Humans,La,LINE,M,metabolism,Molecular Biology,Molecular Sequence Data,Molecular Weight,nosource,protein,Proteins,Rabbits,S,sequence,Support,Uterus} } % == BibTeX quality report for rohdeCellSurfaceExpression1996: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{romPolyaminesRegulateExpression1994a, title = {Polyamines Regulate the Expression of Orinithine Decarboxylase Antizyme ⬚in Vitro⬚ by Inducing Ribosomal Frameshifting.}, author = {Rom, E. and Kahana, C.}, year = 1994, journal = {Proc.Natl.Acad.Sci.USA}, volume = {91}, pages = {3959–3963}, doi = {10.1073/pnas.91.9.3959}, keywords = {+1 frameshifting,antizyme,expression,Frameshifting,In Vitro,IN-VITRO,nosource,polyamine,Polyamines,rat,ribosomal frameshifting} } % == BibTeX quality report for romPolyaminesRegulateExpression1994a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{roseStructureFunctionYeast1984, title = {Structure and {{Function}} of the {{Yeast Ura3 Gene}} - {{Expression}} in {{Escherichia-Coli}}}, author = {Rose, M. and Grisafi, P. and Botstein, D.}, year = 1984, journal = {Gene}, volume = {29}, number = {1-2}, pages = {113–124}, publisher = {Elsevier}, doi = {10.1016/0378-1119(84)90172-0}, url = {http://linkinghub.elsevier.com/retrieve/pii/0378111984901720}, keywords = {Escherichia coli,ESCHERICHIA-COLI,expression,gene,Gene Expression,M,nosource,structure,yeast} } % == BibTeX quality report for roseStructureFunctionYeast1984: % ? Title looks like it was stored in title-case in Zotero

@article{roseSaccharomycesCerevisiaeGenomic1987, title = {A {{Saccharomyces}} Cerevisiae Genomic Plasmid Bank Based on a Centromere-Containing Shuttle Vector}, author = {Rose, M.D. and Novick, P. and Thomas, J.H. and Botstein, D. and Fink, G.R.}, year = 1987, journal = {Gene}, volume = {60}, number = {2-3}, pages = {237–243}, doi = {10.1016/0378-1119(87)90232-0}, abstract = {A set of genomic plasmid banks was constructed using the centromere-containing yeast shuttle vector YCp50. The centromere-containing vector is useful for the isolation of genes that are toxic to yeast when present in high copy number. Fourteen independent banks were prepared each with an average representation of two to three times the yeast genome. Any individual plasmid from a given bank is guaranteed to be of independent origin from plasmids obtained from each of the other banks. The banks were constructed from three different size classes of DNA fragments that resulted from varying conditions of partial digestion with Sau3A. This avoided the bias caused by differential sensitivity of sites to cleavage with Sau3A. Insert DNA is sufficiently large that most genes will be present in the set of plasmid banks at a frequency of about 0.1%}, keywords = {CLEAVAGE,Dna,gene,Genes,Genome,genomic,library,nosource,PLASMID,Plasmids,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,vector,YCp50,yeast} }

@book{roseMethodsYeastGenetics1990a, title = {Methods in {{Yeast Genetics}}.}, author = {Rose, M.D. and Winston, F. and Hieter, P.}, year = 1990, publisher = {Cold Spring Harbor Press}, address = {Cold Spring Harbor, NY}, keywords = {Genetic,genetics,Methods,nosource,plasmid shuffle,Plasmids,yeast} } % == BibTeX quality report for roseMethodsYeastGenetics1990a: % ? Title looks like it was stored in title-case in Zotero

@article{rosenwaldTransientInhibitionProrein1995, title = {Transient Inhibition of Prorein Synthesis Induces Expression of Proto-Oncogenes and Stimulates Resting Cells to Enter the Cell Cycle.}, author = {Rosenwald, I.B. and Setkov, N.A. and Kazakov, V.N. and Chen, J.J. and Ryazanov, A.G. and London, I.M. and Epifanova, O.I.}, year = 1995, journal = {Cell Prolif.}, volume = {28}, pages = {631–644}, doi = {10.1111/j.1365-2184.1995.tb00050.x}, keywords = {cancer,cell cycle,EF-2,EF-2 kinase,expression,INHIBITION,kinase,nosource} } % == BibTeX quality report for rosenwaldTransientInhibitionProrein1995: % ? Possibly abbreviated journal title Cell Prolif.

@article{rosoriusHumanRibosomalProtein2000a, title = {Human Ribosomal Protein {{L5}} Contains Defined Nuclear Localization and Export Signals.⬚⬚ ⬚⬚}, author = {Rosorius, O. and Fries, B. and Stauber, R.H. and Hirschmann, N. and Bevec, D. and Hauber, J.}, year = 2000, month = apr, journal = {J.Biol.Chem.}, volume = {275}, number = {16}, pages = {12061–12068}, doi = {10.1074/jbc.275.16.12061}, abstract = {Ribosomal protein L5 is part of the 60 S ribosomal subunit and localizes in both the cytoplasm and the nucleus of eukaryotic cells, accumulating particularly in the nucleoli. L5 is known to bind specifically to 5 S rRNA and is involved in nucleocytoplasmic transport of this rRNA. Here, we report a detailed analysis of the domain organization of the human ribosomal protein L5. We show that a signal that mediates nuclear import and nucleolar localization maps to amino acids 21-37 within the 297-amino acid L5 protein. Furthermore, carboxyl-terminal residues at positions 255-297 serve as an additional nuclear/nucleolar targeting signal. Domains involved in 5 S rRNA binding are located at both the amino terminus and the carboxyl terminus of L5. Microinjection studies in somatic cells demonstrate that a nuclear export signal (NES) that maps to amino acids 101-111 resides in the central region of L5. This NES is characterized by a pronounced clustering of critical leucine residues, which creates a peptide motif not previously observed in other leucine-rich NESs. Finally, we present a refined model of the multidomain structure of human ribosomal protein L5}, keywords = {20229811,Amino Acids,analysis,BINDING,Cytoplasm,Eukaryotic Cells,human,L5,Leucine,nosource,protein,RIBOSOMAL-SUBUNIT,rRNA,SIGNAL,structure,SUBUNIT,virology} } % == BibTeX quality report for rosoriusHumanRibosomalProtein2000a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{rospertRibosomeFunctionGoverning2004, title = {Ribosome Function: Governing the Fate of a Nascent Polypeptide}, author = {Rospert, S.}, year = 2004, month = may, journal = {Current biology}, volume = {14}, number = {10}, pages = {R386-R388}, publisher = {Elsevier}, doi = {10.1016/j.cub.2004.05.013}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982204003355}, abstract = {Recent data highlight how eukaryotic ribosomes connect polypeptide synthesis to translational regulation and targeting. Information contained in nascent polypeptides can be transmitted by surprisingly diverse routes}, keywords = {0,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,genetics,INFORMATION,La,ModelsMolecular,Molecular Mimicry,nosource,Peptides,peptidyl transferase,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,physiology,POLYPEPTIDE,POLYPEPTIDES,Protein Biosynthesis,Protein StructureTertiary,RECOGNITION,regulation,Review,ribosome,Ribosomes,SIGNAL,SIGNAL RECOGNITION PARTICLE,Signal Transduction,Transferases} } % == BibTeX quality report for rospertRibosomeFunctionGoverning2004: % ? unused Journal abbr (“Curr.Biol.”)

@article{rossMRNAStabilityMammalian1995, title = {{{mRNA}} Stability in Mammalian Cells.}, author = {Ross, J.}, year = 1995, journal = {Microbiology and Molecular Biology Reviews}, volume = {59}, number = {3}, pages = {423–450}, publisher = {Am Soc Microbiol}, doi = {10.1128/mr.59.3.423-450.1995}, url = {http://mmbr.asm.org/cgi/content/abstract/59/3/423}, abstract = {This review concerns how cytoplasmic mRNA half-lives are regulated and how mRNA decay rates influence gene expression. mRNA stability influences gene expression in virtually all organisms, from bacteria to mammals, and the abundance of a particular mRNA can fluctuate manyfold following a change in the mRNA half-life, without any change in transcription. The processes that regulate mRNA half-lives can, in turn, affect how cells grow, differentiate, and respond to their environment. Three major questions are addressed. Which sequences in mRNAs determine their half-lives? Which enzymes degrade mRNAs? Which (trans-acting) factors regulate mRNA stability, and how do they function? The following specific topics are discussed: techniques for measuring eukaryotic mRNA stability and for calculating decay constants, mRNA decay pathways, mRNases, proteins that bind to sequences shared among many mRNAs [like poly(A)- and AU-rich-binding proteins] and proteins that bind to specific mRNAs (like the c-myc coding-region determinant-binding protein), how environmental factors like hormones and growth factors affect mRNA stability, and how translation and mRNA stability are linked. Some perspectives and predictions for future research directions are summarized at the end}, keywords = {96035698,animal,Bacteria,Base Sequence,cancer,DECAY,drug effects,enzyme,expression,gene,Gene Expression,GENE-EXPRESSION,genetics,Growth Substances,Half-Life,Hormones,Ions,Mammals,metabolism,Molecular Sequence Data,mRNA,mRNA decay,nosource,physiology,poly(A),protein,Proteins,Review,Ribonucleases,RNAMessenger,sequence,SEQUENCES,stability,supportu.s.gov’tp.h.s.,techniques,Trans-Activators,transcription,translation,TranslationGenetic,UPF} } % == BibTeX quality report for rossMRNAStabilityMammalian1995: % ? unused Journal abbr (“Microbiol.Rev.”)

@article{rossiIdentificationCharacterisationRPD31998a, title = {Identification and Characterisation of an {{RPD3}} Homologue from Maize ({{Zea}} Mays {{L}}.) That Is Able to Complement an Rpd3 Null Mutant of {{Saccharomyces}} Cerevisiae}, author = {Rossi, V. and Hartings, H. and Motto, M.}, year = 1998, month = may, journal = {Mol.Gen.Genet.}, volume = {258}, number = {3}, pages = {288–296}, doi = {10.1007/s004380050733}, abstract = {In mammals, yeast and Drosophila, the histone deacetylase RPD3 proteins can alter the expression of genes involved in fundamental biological processes by affecting the degree of acetylation of histones and changing chromatin structure. Here we report the isolation of a cDNA sequence encoding an RPD3 homologue from maize, which is able to complement the phenotype of an rpd3 null mutant of the yeast Saccharomyces cerevisiae. The expression of the corresponding gene(s) was assessed in different maize tissues. The number of homologous loci was estimated by Southern hybridisation to be in the range of two to three, and the chromosomal location of one of these loci was determined. Phylogenetic analysis and tests for relative divergence rates, using related RPD3 sequences from different species, were performed, and suggest that different polymorphic forms of RPD3-like proteins that evolve at distinct rates are present in the species considered}, keywords = {98307342,Acetylation,analysis,chemistry,Chromatin,CloningMolecular,Corn,Drosophila,enzymology,expression,Fungal Proteins,gene,Genes,GenesReporter,Genetic Complementation Test,genetics,Histone Deacetylase,Histones,IDENTIFICATION,La,Mammals,Mutation,nosource,Phenotype,Phylogeny,Plant Proteins,protein,Proteins,RNAMessenger,RPD3,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence Alignment,Sequence AnalysisDNA,SEQUENCES,structure,supportnon-u.s.gov’t,Transcription Factors,yeast} } % == BibTeX quality report for rossiIdentificationCharacterisationRPD31998a: % ? Possibly abbreviated journal title Mol.Gen.Genet.

@article{rotaCharacterizationNovelCoronavirus2003, title = {Characterization of a {{Novel Coronavirus Associated}} with {{Severe Acute Respiratory Syndrome}}}, author = {Rota, P.A. and Oberste, M.S. and Monroe, S.S. and Nix, W.A. and Campagnoli, R. and Icenogle, J.P. and Penaranda, S. and Bankamp, B. and Maher, K. and Chen, M.H. and Tong, S. and Tamin, A. and Lowe, L. and Frace, M. and DeRisi, J.L. and Chen, Q. and Wang, D. and Erdman, D.D. and Peret, T.C. and Burns, C. and Ksiazek, T.G. and Rollin, P.E. and Sanchez, A. and Liffick, S. and Holloway, B. and Limor, J. and McCaustland, K. and {Olsen-Rassmussen}, M. and Fouchier, R. and Gunther, S. and Osterhaus, A.D. and Drosten, C. and Pallansch, M.A. and Anderson, L.J. and Bellini, W.J.}, year = 2003, month = may, journal = {Science}, volume = {300}, number = {5624}, pages = {1394–1399}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1085952}, url = {http://www.sciencemag.org/content/300/5624/1394.short}, abstract = {In March 2003, a novel coronavirus (SARS-CoV) was discovered in association with cases of severe acute respiratory syndrome (SARS). The sequence of the complete genome of SARS-CoV was determined, and the initial characterization of the viral genome is presented in this report. The genome of SARS-CoV is 29,727 nucleotides in length, has 11 open reading frames, and the genome organization is similar to that of other coronaviruses. Phylogenetic analyses and sequence comparisons showed that SARS-CoV is not closely related to any of the previously characterized coronaviruses}, keywords = {disease,FrameshiftingRibosomal,Genome,nosource,Nucleotides,Open Reading Frames,SARS,sequence,virus} } % == BibTeX quality report for rotaCharacterizationNovelCoronavirus2003: % ? Title looks like it was stored in title-case in Zotero

@article{rotenbergDepletionSaccharomycesCerevisiae1988, title = {Depletion of {{Saccharomyces}} Cerevisiae Ribosomal Protein {{L16}} Causes a Decrease in {{60S}} Ribosomal Subunits and Formation of Half-Mer Polyribosomes.}, author = {Rotenberg, M.O. and Moritz, M. and Woolford, J.L.}, year = 1988, month = feb, journal = {Genes & development}, volume = {2}, number = {2}, pages = {160–172}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.2.2.160}, url = {http://genesdev.cshlp.org/content/2/2/160.short}, abstract = {We constructed yeast strains containing deletion-insertion null alleles of the RPL16A or RPL16B genes encoding the 60S ribosomal subunit protein L16 to determine the role of L16 in the synthesis and function of ribosomes. Strains lacking a functional RPL16A gene grow as rapidly as wild type, whereas those containing a null allele of RPL16B grow more slowly than wild type. RNA analysis using RPL16 probes revealed that both RPL16 genes are transcribed and that RPL16B transcripts accumulate to twice the level of RPL16A transcripts. No evidence was obtained for the occurrence of dosage compensation at the level of RPL16 mRNA accumulation in either mutant. Strains lacking both RPL16 genes are apparently inviable, demonstrating that L16 is an essential yeast ribosomal protein. Introduction of an extra copy of either RPL16 gene into rpl16b mutants restored wild-type growth rates, indicating that the two forms of the L16 protein are interchangeable. rpl16 mutants are deficient in 60S ribosomal subunits relative to 40S subunits. 43S preinitiation complexes accumulate in half-mer polyribosomes in the absence of sufficient 60S subunits. We postulate that the slow-growth phenotype of rpl16 mutants results from the perturbation of initiation of protein synthesis}, keywords = {60S subunit,88196881,Alleles,analysis,COMPLEX,COMPLEXES,Fungal Proteins,gene,Genes,GenesFungal,genetics,initiation,metabolism,mRNA,Mutation,nomenclature,nosource,Phenotype,Polyribosomes,protein,protein synthesis,PROTEIN-SYNTHESIS,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNAFungal,RNAMessenger,RNARibosomal,RPL11,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUBUNIT,supportu.s.gov’tp.h.s.,yeast} } % == BibTeX quality report for rotenbergDepletionSaccharomycesCerevisiae1988: % ? unused Journal abbr (“Genes Dev.”)

@article{rothAssemblyMap50S1980, title = {Assembly Map of the 50-{{S}} Subunit from {{Escherichia}} Coli Ribosomes, Covering the Proteins Present in the First Reconstitution Intermediate Particle}, author = {Roth, H.E. and Nierhaus, K.H.}, year = 1980, month = jan, journal = {European Journal of Biochemistry}, volume = {103}, number = {1}, pages = {95–98}, publisher = {Wiley Online Library}, doi = {10.1111/j.1432-1033.1980.tb04292.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1980.tb04292.x/abstract}, abstract = {Highly purified proteins and 23-S RNA from the 50-S subunit of Escherichia coli ribosomes were used to study the assembly dependences of the early assembly proteins. The proteins under observation and the RNA were incubated at 4 mM Mg2+ and 44 degrees C, the unbound proteins were separated by sucrose gradient centrifugation, the RNA . protein complex was precipitated with trichloroacetic acid, and the complex- bound proteins was identified by means of sodium dodecylsulfate gel electrophoresis. A systematic analysis led to the establishment of an assembly map including 17 proteins which represent the protein moiety of the first reconstitution intermediate particle}, keywords = {0,analysis,assembly,Bacterial,Bacterial Proteins,biosynthesis,CentrifugationDensity Gradient,COMPLEX,COMPLEXES,Electrophoresis,Escherichia coli,ESCHERICHIA-COLI,La,metabolism,nosource,protein,PROTEIN COMPLEX,Proteins,Ribosomal Proteins,ribosome,Ribosomes,Rna,RNABacterial,Sodium,SUBUNIT} } % == BibTeX quality report for rothAssemblyMap50S1980: % ? unused Journal abbr (“Eur.J.Biochem.”)

@article{rothFrameshiftSuppression1981a, title = {Frameshift Suppression}, author = {Roth, J.R.}, year = 1981, month = jun, journal = {Cell}, volume = {24}, number = {3}, pages = {601–602}, doi = {10.1016/0092-8674(81)90086-6}, url = {PM:6166384}, keywords = {0,Anticodon,Bacterial,Base Sequence,Codon,COMPLEX,COMPLEXES,Electron Transport Complex IV,frameshift,Genetic Code,genetics,La,metabolism,mitochondria,Mutation,nosource,Protein Biosynthesis,Review,Rna,RNABacterial,RNATransfer,Salmonella,suppression,SuppressionGenetic,TRANSPORT,Yeasts} }

@article{ruanComparativeFulllengthGenome2003, title = {Comparative Full-Length Genome Sequence Analysis of 14 {{SARS}} Coronavirus Isolates and Common Mutations Associated with Putative Origins of Infection}, author = {Ruan, Y.J. and Wei, C.L. and Ee, A.L. and Vega, V.B. and Thoreau, H. and Su, S.T. and Chia, J.M. and Ng, P. and Chiu, K.P. and Lim, L. and Zhang, T. and Peng, C.K. and Lin, E.O. and Lee, N.M. and Yee, S.L. and Ng, L.F. and Chee, R.E. and Stanton, L.W. and Long, P.M. and Liu, E.T.}, year = 2003, month = may, journal = {The Lancet}, volume = {361}, number = {9371}, pages = {1779–1785}, publisher = {Elsevier}, doi = {10.1016/S0140-6736(03)13414-9}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0140673603134149}, abstract = {BACKGROUND: The cause of severe acute respiratory syndrome (SARS) has been identified as a new coronavirus. Whole genome sequence analysis of various isolates might provide an indication of potential strain differences of this new virus. Moreover, mutation analysis will help to develop effective vaccines. METHODS: We sequenced the entire SARS viral genome of cultured isolates from the index case (SIN2500) presenting in Singapore, from three primary contacts (SIN2774, SIN2748, and SIN2677), and one secondary contact (SIN2679). These sequences were compared with the isolates from Canada (TOR2), Hong Kong (CUHK-W1 and HKU39849), Hanoi (URBANI), Guangzhou (GZ01), and Beijing (BJ01, BJ02, BJ03, BJ04). FINDINGS: We identified 129 sequence variations among the 14 isolates, with 16 recurrent variant sequences. Common variant sequences at four loci define two distinct genotypes of the SARS virus. One genotype was linked with infections originating in Hotel M in Hong Kong, the second contained isolates from Hong Kong, Guangzhou, and Beijing with no association with Hotel M (p{\(<\)}0.0001). Moreover, other common sequence variants further distinguished the geographical origins of the isolates, especially between Singapore and Beijing. INTERPRETATION: Despite the recent onset of the SARS epidemic, genetic signatures are emerging that partition the worldwide SARS viral isolates into groups on the basis of contact source history and geography. These signatures can be used to trace sources of infection. In addition, a common variant associated with a non-conservative aminoacid change in the S1 region of the spike protein, suggests that immunological pressures might be starting to influence the evolution of the SARS virus in human populations}, keywords = {Amino Acid Sequence,analysis,ASSOCIATION,Base Sequence,classification,Comparative Study,Coronavirus,Evolution,Genetic,genetics,Genome,GenomeViral,Genotype,history,human,INFECTION,isolation & purification,La,M,Methods,Molecular Sequence Data,Mutation,MUTATIONS,nosource,Open Reading Frames,Phylogeny,Polymorphism (Genetics),protein,REGION,SARS,Sars Virus,sequence,Sequence Analysis,SEQUENCE-ANALYSIS,SEQUENCES,Severe Acute Respiratory Syndrome,Singapore,supportnon-u.s.gov’t,virus} }

@article{rubinNucleotideSequenceSaccharomyces1973, title = {The Nucleotide Sequence of {{Saccharomyces}} Cerevisiae 5.8 {{S}} Ribosomal Ribonucleic Acid}, author = {Rubin, G.M.}, year = 1973, month = jun, journal = {Journal of Biological Chemistry}, volume = {248}, number = {11}, pages = {3860–3875}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(19)43814-3}, url = {http://www.jbc.org/content/248/11/3860.short}, keywords = {0,ACID,analysis,Autoradiography,Base Sequence,CEREVISIAE,chemistry,Coliphages,Drug Stability,Electrophoresis,ElectrophoresisPolyacrylamide Gel,enzymology,isolation & purification,La,ModelsStructural,nosource,NUCLEOTIDE-SEQUENCE,Oligonucleotides,Pancreas,Phosphorus Isotopes,Ribonucleases,RIBONUCLEIC-ACID,Ribonucleotides,Rna,RNARibosomal,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Species Specificity} } % == BibTeX quality report for rubinNucleotideSequenceSaccharomyces1973: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{rudraWhatBetterMeasure2004, title = {What Better Measure than Ribosome Synthesis?}, author = {Rudra, D. and Warner, J.R.}, year = 2004, month = oct, journal = {Genes & development}, volume = {18}, number = {20}, pages = {2431–2436}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.1256704}, url = {http://genesdev.cshlp.org/content/18/20/2431.short}, keywords = {0,Apoptosis,BIOLOGY,Cell Enlargement,Cell Proliferation,genetics,La,nosource,physiology,protein,Proteins,Review,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,RIBOSOME SYNTHESIS,Ribosomes,Support} } % == BibTeX quality report for rudraWhatBetterMeasure2004: % ? unused Journal abbr (“Genes Dev.”)

@article{ruggeroDyskeratosisCongenitaCancer2003, title = {Dyskeratosis Congenita and Cancer in Mice Deficient in Ribosomal {{RNA}} Modification}, author = {Ruggero, D. and Grisendi, S. and Piazza, F. and Rego, E. and Mari, F. and Rao, P.H. and {Cordon-Cardo}, C. and Pandolfi, P.P.}, year = 2003, month = jan, journal = {Science}, volume = {299}, number = {5604}, pages = {259–262}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1079447}, url = {http://www.sciencemag.org/content/299/5604/259.short}, abstract = {Mutations in DKC1 cause dyskeratosis congenita (DC), a disease characterized by premature aging and increased tumor susceptibility. The DKC1 protein binds to the box H + ACA small nucleolar RNAs and the RNA component of telomerase. Here we show that hypomorphic Dkc1 mutant (Dkc1m) mice recapitulate in the first and second generations (G1 and G2) the clinical features of DC. Dkc1m cells from G1 and G2 mice were impaired in ribosomal RNA pseudouridylation before the onset of disease. Reductions of telomere length in Dkc1m mice became evident only in later generations. These results suggest that deregulated ribosome function is important in the initiation of DC, whereas telomere shortening may modify and/or exacerbate DC}, keywords = {0,Anemia,Animals,Apoptosis,BIOLOGY,Bone Marrow Cells,cancer,cell cycle,Cell Cycle Proteins,CELLS,Colony-Forming Units Assay,complications,COMPONENT,disease,Disease ModelsAnimal,Dyskeratosis Congenita,etiology,Female,Genetic Predisposition to Disease,genetics,Hematopoietic Stem Cells,human,In Situ HybridizationFluorescence,initiation,La,Male,metabolism,Mice,modification,Molecular Biology,Mutation,MUTATIONS,Neoplasms,nosource,Nuclear Proteins,pathology,physiology,protein,Proteins,Pseudouridine,pseudouridylation,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNARibosomal,SMALL NUCLEOLAR RNAS,Support,Telomerase,Telomere,ultrastructure} }

@article{ruiz-echevarriaUtilizingGCN4Leader1996, title = {Utilizing the {{GCN4}} Leader Region to Investigate the Role of the Sequence Determinants in Nonsense-Mediated {{mRNA}} Decay.}, author = {{Ruiz-Echevarria}, M.J. and Peltz, S.W.}, year = 1996, journal = {The EMBO Journal}, volume = {15}, number = {11}, pages = {2810–2819}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1996.tb00641.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC450218/}, keywords = {DECAY,GCN4,mRNA,mRNA decay,nosource,sequence} } % == BibTeX quality report for ruiz-echevarriaUtilizingGCN4Leader1996: % ? unused Journal abbr (“EMBO J.”)

@article{ruiz-echevarriaMakingSenseNonsense1996, title = {Making Sense of Nonsense in Yeast.}, author = {{Ruiz-Echevarria}, M.J. and Czaplinski, K. and Peltz, S.W.}, year = 1996, journal = {Trends in Biochemical Sciences}, volume = {21}, number = {11}, pages = {433–438}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000496100554}, abstract = {NMD review article}, keywords = {NMD,No DOI found,nosource,Review,review article,yeast} }

@article{ruiz-echevarriaUpf3pComponentSurveillance1998, title = {The {{Upf3p}} Is a Component of the Surveillance Complex That Monitors Both Translation and {{mRNA}} Turnover and Affects Viral Maintenance.}, author = {{Ruiz-Echevarria}, M.J. and Yasenchak, J.M. and Han, X. and Dinman, J.D. and Peltz, S.W.}, year = 1998, journal = {Proc.Natl.Acad.Sci.USA}, volume = {95}, pages = {8721–8726}, doi = {10.1073/pnas.95.15.8721}, keywords = {COMPLEX,COMPLEXES,COMPONENT,elongation,Frameshifting,Gag/Gag-pol ratio,L-A,mRNA,nosource,surveillence complex,translation,turnover,UPF3,viral propagation} } % == BibTeX quality report for ruiz-echevarriaUpf3pComponentSurveillance1998: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{ruiz-echevarriaIdentifyingRightStop1998, title = {Identifying the Right Stop: Determining How the Surveillance Complex Recognizes and Degrades an Aberrant {{mRNA}}.}, author = {{Ruiz-Echevarria}, M.J. and Gonzalez, C.I. and Peltz, S.W.}, year = 1998, journal = {The EMBO Journal}, volume = {17}, number = {2}, pages = {575–589}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/17.2.575}, url = {http://www.nature.com/emboj/journal/v17/n2/abs/7590774a.html}, keywords = {COMPLEX,COMPLEXES,GCN4,mRNA,nonsense suppression,nonsense-mediated decay,nosource,surveillence complex,UPF} } % == BibTeX quality report for ruiz-echevarriaIdentifyingRightStop1998: % ? unused Journal abbr (“EMBO J.”)

@article{ruiz-echevarriaRNABindingProtein2000a, title = {The {{RNA}} Binding Protein {{Pub1}} Modulates the Stability of Transcripts Containing Upstream Open Reading Frames [{{In Process Citation}}]}, author = {{Ruiz-Echevarria}, M.J. and Peltz, S.W.}, year = 2000, month = jun, journal = {Cell}, volume = {101}, number = {7}, pages = {741–751}, doi = {10.1016/S0092-8674(00)80886-7}, abstract = {The nonsense-mediated mRNA decay (NMD) pathway functions to degrade transcripts containing nonsense codons. Transcripts containing mutations that insert an upstream open reading frame (uORF) in the 5’-UTR are degraded through NMD. However, several naturally occurring uORF-containing transcripts are resistant to NMD. Here we demonstrate that the GCN4 and YAP1 mRNAs, which contain uORFs, harbor a stabilizer element (STE) that prevents rapid NMD by interacting with the RNA binding protein Pub1. Conversely, a uORF-containing mRNA that lacks an STE, such as CPA1, is degraded by the NMD pathway. These results indicate that uORFs can play a pivotal role regulating both translation and turnover and that the Pub1p is a critical factor that modulates the stability of uORF-containing transcripts}, keywords = {20348834,BINDING,BINDING PROTEIN,BINDING-PROTEIN,Codon,DECAY,GCN4,Genetic,genetics,microbiology,mRNA,mRNA decay,Mutation,MUTATIONS,NMD,nosource,Open Reading Frames,protein,Rna,stability,translation,turnover,UPSTREAM} }

@article{ruiz-echevarriaCharacterizationGeneralStabilizer2001, title = {Characterization of a General Stabilizer Element That Blocks Deadenylation-Dependent {{mRNA}} Decay}, author = {{Ruiz-Echevarria}, M.J. and Munshi, R. and Tomback, J. and Kinzy, T.G. and Peltz, S.W.}, year = 2001, journal = {Journal of Biological Chemistry}, volume = {276}, number = {33}, pages = {30995–31003}, publisher = {ASBMB}, doi = {10.1074/jbc.M010833200}, url = {http://www.jbc.org/content/276/33/30995.short}, abstract = {mRNA degradation is a regulated process that can play an important role in determining the level of expression of specific genes. The rate at which a specific mRNA is degraded depends largely on specific cis-acting sequences located throughout the transcript. cis-Acting destabilizer sequences that promote increased rates of decay have been identified in several short-lived mRNAs. However, little is known about elements that promote stability, known as stabilizer elements (STEs), and how they function. The work presented here describes the characterization of a STE in the PGK1 transcript. The PGK1 stabilizer element (P-STE) has been delineated to a 64-nucleotide sequence from the coding region that can stabilize a chimeric transcript containing the instability elements from the 3’-untranslated region of the MFA2 transcript. The P-STE is located within the PGK1 coding region and functions when located in the translated portion of the transcript and at a minimum distance from the 3’-untranslated region. These results further support the link between translation and mRNA degradation. A conserved sequence in the TEF1/2 transcript has been identified that also functions as a STE, suggesting that this sequence element maybe a general stability determinant found in other yeast mRNAs}, keywords = {3’ Untranslated Regions,cancer,chemistry,Codon,Conserved Sequence,DECAY,degradation,ELEMENTS,expression,gene,Genes,Genetic,genetics,metabolism,microbiology,mRNA,mRNA decay,nosource,RNA-Messenger,RNAMessenger,sequence,SEQUENCES,stability,Support,support-non-u.s.gov’t,support-u.s.gov’t-non-p.h.s.,support-u.s.gov’t-p.h.s.,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,translation,Translation-Genetic,TranslationGenetic,yeast} } % == BibTeX quality report for ruiz-echevarriaCharacterizationGeneralStabilizer2001: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{rundlettHDA1RPD3Are1996, title = {{{HDA1}} and {{RPD3}} Are Members of Distinct Yeast Histone Deacetylase Complexes That Regulate Silencing and Transcription}, author = {Rundlett, S.E. and Carmen, A.A. and Kobayashi, R. and Bavykin, S. and Turner, B.M. and Grunstein, M.}, year = 1996, month = dec, journal = {Proceedings of the National Academy of Sciences}, volume = {93}, number = {25}, pages = {14503–14508}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.93.25.14503}, url = {http://www.pnas.org/content/93/25/14503.short}, abstract = {Increased histone acetylation has been correlated with increased transcription, and regions of heterochromatin are generally hypoacetylated. In investigating the cause-and-effect relationship between histone acetylation and gene activity, we have characterized two yeast histone deacetylase complexes. Histone deacetylase-A (HDA) is an approximately 350-kDa complex that is highly sensitive to the deacetylase inhibitor trichostatin A. Histone deacetylase-B (HDB) is an approximately 600-kDa complex that is much less sensitive to trichostatin A. The HDA1 protein (a subunit of the HDA activity) shares sequence similarity to RPD3, a factor required for optimal transcription of certain yeast genes. RPD3 is associated with the HDB activity. HDA1 also shares similarity to three new open reading frames in yeast, designated HOS1, HOS2, and HOS3. We find that both hda1 and rpd3 deletions increase acetylation levels in vivo at all sites examined in both core histones H3 and H4, with rpd3 deletions having a greater impact on histone H4 lysine positions 5 and 12. Surprisingly, both hda1 and rpd3 deletions increase repression at telomeric loci, which resemble heterochromatin with rpd3 having a greater effect. In addition, rpd3 deletions retard full induction of the PHO5 promoter fused to the reporter lacZ. These data demonstrate that histone acetylation state has a role in regulating both heterochromatic silencing and regulated gene expression}, keywords = {97121415,Acetylation,Amino Acid Sequence,chemistry,COMPLEX,COMPLEXES,expression,Fungal Proteins,gene,Gene Expression,Gene Expression RegulationFungal,GENE-EXPRESSION,Genes,GenesFungal,genetics,Histone Deacetylase,Histones,IN-VIVO,Lysine,Molecular Sequence Data,nosource,Open Reading Frames,PROMOTER,protein,RPD3,Saccharomyces cerevisiae,sequence,Sequence Alignment,SUBUNIT,supportu.s.gov’tp.h.s.,transcription,Transcription Factors,TranscriptionGenetic,yeast} } % == BibTeX quality report for rundlettHDA1RPD3Are1996: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{rundlettTranscriptionalRepressionUME61998, title = {Transcriptional Repression by {{UME6}} Involves Deacetylation of Lysine 5 of Histone {{H4}} by {{RPD3}}}, author = {Rundlett, S.E. and Carmen, A.A. and Suka, N. and Turner, B.M. and Grunstein, M.}, year = 1998, month = apr, journal = {Nature}, volume = {392}, number = {6678}, pages = {831–835}, publisher = {Nature Publishing Group}, doi = {10.1038/33952}, url = {http://www.nature.com/nature/journal/v392/n6678/abs/392831a0.html}, abstract = {The histone deacetylase RPD3 can be targeted to certain genes through its interaction with DNA-binding regulatory proteins. RPD3 can then repress gene transcription. In the yeast Saccharomyces cerevisiae, association of RPD3 with the transcriptional repressors SIN3 and UME6 results in repression of reporter genes containing the UME6-binding site. RPD3 can deacetylate all histone H4 acetylation sites in cell extracts. However, it is unknown how H4 proteins located at genes near UME6-binding sites are affected, nor whether the effect of RPD3 is localized to the promoter regions. Here we study the mechanism by which RPD3 represses gene activity by examining the acetylation state of histone proteins at UME6-regulated genes. We used antibodies specific for individual acetylation sites in H4 to immunoprecipitate chromatin fragments. A deletion of RPD3 or SIN3, but not of the related histone- deacetylase gene HDA1, results in increased acetylation of the lysine 5 residue of H4 in the promoters of the UME6-regulated INO1, IME2 and SPO13 genes. As increased acetylation of this residue is not merely a consequence of gene transcription, acetylation of this site may be essential for regulating gene activity}, keywords = {98231854,Acetylation,Antibodies,antibody,chemistry,Chromatin,DNA-Binding Proteins,Fungal Proteins,gene,Gene Expression RegulationFungal,GENE-TRANSCRIPTION,Genes,GenesReporter,genetics,Histone Deacetylase,Histones,Lysine,MECHANISM,metabolism,myo-Inositol-1-Phosphate Synthase,nosource,physiology,PROMOTER,protein,Protein Kinases,Proteins,Repressor Proteins,RPD3,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportu.s.gov’tp.h.s.,transcription,Transcription Factors,TranscriptionGenetic,yeast} }

@article{russellCloningSequencingExpression1997, title = {Cloning, Sequencing and Expression of a Full-Length {{cDNA}} Copy of the {{M1}} Double-Stranded {{RNA}} Virus from the Yeast, {{Saccharomyces}} Cerevisiae}, author = {Russell, P.J. and Bennett, A.M. and Love, Z. and Baggott, D.M.}, year = 1997, month = jul, journal = {Yeast}, volume = {13}, number = {9}, pages = {829–836}, publisher = {Wiley Online Library}, doi = {10.1002/(SICI)1097-0061(199707)13:9<829::AID-YEA144>3.0.CO;2-R}, url = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0061(199707)13:9<829::AID-YEA144>3.0.CO;2-R/abstract}, abstract = {Strains of the budding yeast, Saccharomyces cerevisiae, may contain one or more cytoplasmic viruses with double-stranded RNA (dsRNA) genomes. The killer phenomenon in yeast, in which one cell secretes a killer toxin that is lethal to another cell, is dependent upon the presence of the L-A and M1 dsRNA viruses. The L-A viral genome encodes proteins for the viral capsid, and for synthesis and encapsidation of single-stranded RNA replication cycle intermediates. The M1 virus depends upon the L-A-encoded proteins for its capsid and for the replication of its killer-toxin-encoding genome. A full-length cDNA clone of an M1 genome has been made from a single dsRNA molecule and shown to encode functional killer and killer-immunity functions. The sequence of the clone indicates minor differences from previously published sequences of parts of the M1 genome and of the complete genome of S14 (an internal deletion derivative of M1) but no unreported amino acid variants and no changes in putative secondary structures of the single-stranded RNA. A 118-nucleotide contiguous segment of the M1 genome has not previously been reported; 92 of those nucleotides comprise a segment of A nucleotides in the AU-rich bubble that follows the toxin-encoding reading frame. The GenBank Accession Number for the sequence is U78817; the locus is SCU78817. (C) 1997 by John Wiley & Sons, Ltd}, keywords = {0,ACID,Amino Acid Sequence,AMINO-ACID,Base Sequence,BIOLOGY,Capsid,CEREVISIAE,CHARACTER,cloning,CloningMolecular,CODING REGION,Dna,DNA Primers,DNA sequence,DNAComplementary,DnaViral,DOMAINS,DOUBLE-STRANDED-RNA,DSRNA,ENCAPSIDATION,ENCODES,expression,FRAME,Genes,genetics,Genome,GENOME ENCODES,INTERMEDIATE,isolation & purification,killer,killer gene expression,killer toxin,killer virus,killer yeast,L-A,La,M,M1,M1 cDNA clone,M1 dsRNA virus,Molecular Sequence Data,MUTANTS,nosource,Nucleotides,POL FUSION PROTEIN,polymerase,protein,Proteins,READING FRAME,REPLICATION,Rna,RNA Viruses,RNADouble-Stranded,RnaViral,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SECONDARY STRUCTURE,sequence,SEQUENCES,structure,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,toxin,virology,virus,yeast} }

@article{ruvinskyRibosomalProteinS62006, title = {Ribosomal Protein {{S6}} Phosphorylation: From Protein Synthesis to Cell Size}, author = {Ruvinsky, I. and Meyuhas, O.}, year = 2006, month = jun, journal = {Trends in biochemical sciences}, volume = {31}, number = {6}, pages = {342–348}, publisher = {Elsevier}, doi = {10.1016/j.tibs.2006.04.003}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000406001137}, abstract = {Recent studies are beginning to disclose a signaling network involved in regulating cell size. Although many links and effectors are still unknown, central components of this network include the mammalian target of rapamycin (mTOR) and its downstream effectors - the ribosomal protein S6 kinase (S6K) and the translational repressor eukaryotic initiation factor 4E-binding protein. Until recently, the role of S6K and its many substrates in cell-size control remained obscure; however, a knockin mouse carrying mutations at all phosphorylation sites in the primary S6K substrate, ribosomal protein S6 (rpS6), has provided insight into the physiological role of this protein phosphorylation event. In addition to its role in glucose homeostasis in the whole mouse, phosphorylation of rpS6 is essential for regulating the size of at least some cell types, but is dispensable for translational control of mRNAs with a 5’ terminal oligopyrimidine tract (TOP mRNAs) - its previously assigned targets. It therefore seems that establishing the function of the phosphorylation of other effectors of mTOR or S6K will inevitably require genetic manipulation of the respective sites within these targets}, keywords = {0,5’ Untranslated Regions,Animals,Biochemistry,cell size,COMPONENT,COMPONENTS,DOWNSTREAM,Eukaryotic Initiation Factor-4E,Genetic,Glucose,Humans,initiation,INITIATION-FACTOR,kinase,La,metabolism,Mice,mRNA,Mutation,MUTATIONS,nosource,Phosphorylation,physiology,protein,Protein Biosynthesis,Protein Kinases,Protein ProcessingPost-Translational,protein synthesis,PROTEIN-KINASE,PROTEIN-SYNTHESIS,REGION,REPRESSOR,Review,Ribosomal Protein S6,Ribosomal Protein S6 Kinases,RIBOSOMAL-PROTEIN,SITE,SITES,Support,TARGET,Untranslated Regions} } % == BibTeX quality report for ruvinskyRibosomalProteinS62006: % ? unused Journal abbr (“Trends Biochem.Sci.”)

@article{sachsPolyBindingProtein1989, title = {The Poly ({{A}}) Binding Protein Is Required for Poly ({{A}}) Shortening and {{60S}} Ribosomal Subunit-Dependent Translation Initiation}, author = {Sachs, A.B. and Davis, R.W.}, year = 1989, journal = {Cell}, volume = {58}, number = {5}, pages = {857–867}, publisher = {Elsevier}, doi = {10.1016/0092-8674(89)90938-0}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867489909380}, keywords = {BINDING,BINDING PROTEIN,BINDING-PROTEIN,initiation,nosource,poly(A),polysomes,protein,translation,TRANSLATION INITIATION} }

@article{sachsToeprintAnalysisPositioning2002, title = {Toeprint Analysis of the Positioning of Translation Apparatus Components at Initiation and Termination Codons of Fungal {{mRNAs}}}, author = {Sachs, M.S. and Wang, Z. and Gaba, A. and Fang, P. and Belk, J. and Ganesan, R. and Amrani, N. and Jacobson, A.}, year = 2002, month = feb, journal = {Methods}, volume = {26}, number = {2}, pages = {105–114}, publisher = {Elsevier}, doi = {10.1016/S1046-2023(02)00013-0}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1046202302000130}, abstract = {The ability to map the position of ribosomes and their associated factors on mRNAs is critical for an understanding of translation mechanisms. Earlier approaches to monitoring these important cellular events characterized nucleotide sequences rendered nuclease-resistant by ribosome binding. While these approaches furthered our understanding of translation initiation and ribosome pausing, the pertinent techniques were technically challenging and not widely applied. Here we describe an alternative assay for determining the mRNA sites at which ribosomes or other factors are bound. This approach uses primer extension inhibition, or “toeprinting,” to map the 3’ boundaries of mRNA-associated complexes. This methodology, previously used to characterize initiation mechanisms in prokaryotic and eukaryotic systems, is used here to gain an understanding of two interesting translational regulatory phenomena in the fungi Neurospora crassa and Saccharomyces cerevisiae: (a) regulation of translation in response to arginine concentration by an evolutionarily conserved upstream open reading frame, and (b) atypical termination events that occur as a consequence of the presence of premature stop codons}, keywords = {0,analysis,Arginine,Base Sequence,BINDING,BIOLOGY,CEREVISIAE,Chromatography,Codon,CODONS,CodonTerminator,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,FRAME,Fungi,GenesFungal,genetics,INHIBITION,initiation,La,MECHANISM,MECHANISMS,metabolism,Methods,Molecular Sequence Data,mRNA,Neurospora,Neurospora crassa,NEUROSPORA-CRASSA,Nitrogen,nosource,NUCLEOTIDE-SEQUENCE,OPEN READING FRAME,Open Reading Frames,pausing,POSITION,primer extension,Protein Biosynthesis,READING FRAME,regulation,Research SupportU.S.Gov’tP.H.S.,Review,ribosome,RIBOSOME BINDING,Ribosomes,Rna,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,SITE,SITES,STOP CODON,SYSTEM,SYSTEMS,techniques,Temperature,termination,TERMINATION CODON,TOEPRINT ASSAY,translation,TRANSLATION INITIATION,UPSTREAM} }

@article{sakaguchiDNADamageActivates1998a, title = {{{DNA}} Damage Activates P53 through a Phosphorylation-Acetylation Cascade}, author = {Sakaguchi, K. and Herrera, J.E. and Saito, S. and Miki, T. and Bustin, M. and Vassilev, A. and Anderson, C.W. and Appella, E.}, year = 1998, journal = {Genes Dev.}, volume = {12}, number = {18}, pages = {2831–2841}, doi = {10.1101/gad.12.18.2831}, abstract = {Activation of p53-mediated transcription is a critical cellular response to DNA damage. p53 stability and site-specific DNA-binding activity and, therefore, transcriptional activity, are modulated by post-translational modifications including phosphorylation and acetylation. Here we show that p53 is acetylated in vitro at separate sites by two different histone acetyltransferases (HATs), the coactivators p300 and PCAF. p300 acetylates Lys-382 in the carboxy- terminal region of p53, whereas PCAF acetylates Lys-320 in the nuclear localization signal. Acetylations at either site enhance sequence- specific DNA binding. Using a polyclonal antisera specific for p53 that is phosphorylated or acetylated at specific residues, we show that Lys- 382 of human p53 becomes acetylated and Ser-33 and Ser-37 become phosphorylated in vivo after exposing cells to UV light or ionizing radiation. In vitro, amino-terminal p53 peptides phosphorylated at Ser- 33 and/or at Ser-37 differentially inhibited p53 acetylation by each HAT. These results suggest that DNA damage enhances p53 activity as a transcription factor in part through carboxy-terminal acetylation that, in turn, is directed by amino-terminal phosphorylation}, keywords = {98417608,Acetylation,Acetyltransferases,activation,Amino Acid Sequence,Base Sequence,BINDING,Binding Sites,cancer,Cell Cycle Proteins,chemistry,Dna,DNA Damage,DNA Probes,genetics,human,In Vitro,IN-VITRO,IN-VIVO,metabolism,ModelsBiological,modification,nosource,Nuclear Localization Signal,p53,Peptides,Phosphorylation,physiology,Protein p53,sequence,SIGNAL,Signal Transduction,site specific,stability,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,transcription,TRANSCRIPTION FACTOR,Transcription Factors,TranscriptionGenetic,Tumor CellsCultured} } % == BibTeX quality report for sakaguchiDNADamageActivates1998a: % ? Possibly abbreviated journal title Genes Dev.

@article{salas-marcoDistinctPathsStop2006a, title = {Distinct Paths to Stop Codon Reassignment by the Variant-Code Organisms {{Tetrahymena}} and {{Euplotes}}}, author = {{Salas-Marco}, J. and {Fan-Minogue}, H. and Kallmeyer, A.K. and Klobutcher, L.A. and Farabaugh, P.J. and Bedwell, D.M.}, year = 2006, month = jan, journal = {Mol.Cell Biol.}, volume = {26}, number = {2}, pages = {438–447}, doi = {10.1128/MCB.26.2.438-447.2006}, url = {PM:16382136}, abstract = {The reassignment of stop codons is common among many ciliate species. For example, Tetrahymena species recognize only UGA as a stop codon, while Euplotes species recognize only UAA and UAG as stop codons. Recent studies have shown that domain 1 of the translation termination factor eRF1 mediates stop codon recognition. While it is commonly assumed that changes in domain 1 of ciliate eRF1s are responsible for altered stop codon recognition, this has never been demonstrated in vivo. To carry out such an analysis, we made hybrid proteins that contained eRF1 domain 1 from either Tetrahymena thermophila or Euplotes octocarinatus fused to eRF1 domains 2 and 3 from Saccharomyces cerevisiae. We found that the Tetrahymena hybrid eRF1 efficiently terminated at all three stop codons when expressed in yeast cells, indicating that domain 1 is not the sole determinant of stop codon recognition in Tetrahymena species. In contrast, the Euplotes hybrid facilitated efficient translation termination at UAA and UAG codons but not at the UGA codon. Together, these results indicate that while domain 1 facilitates stop codon recognition, other factors can influence this process. Our findings also indicate that these two ciliate species used distinct approaches to diverge from the universal genetic code}, keywords = {0,3,analysis,Animals,CELLS,CEREVISIAE,Codon,CODON RECOGNITION,CODONS,CodonTerminator,DOMAIN,DOMAINS,EFFICIENT TRANSLATION,Euplotes,FUSION PROTEIN,Genetic,Genetic Code,GENETIC-CODE,genetics,IN-VIVO,La,metabolism,microbiology,nosource,Peptide Termination Factors,protein,Protein Biosynthesis,Protein StructureTertiary,Proteins,RECOGNITION,Recombinant Fusion Proteins,Research SupportN.I.H.Extramural,Research SupportU.S.Gov’tNon-P.H.S.,Rna,RNATransfer,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,STOP CODON,STOP CODON RECOGNITION,termination,Tetrahymena,Tetrahymena thermophila,translation,TRANSLATION TERMINATION,UAA,yeast,YEAST-CELLS} } % == BibTeX quality report for salas-marcoDistinctPathsStop2006a: % ? Possibly abbreviated journal title Mol.Cell Biol.

@article{samahaBasePairTRNA1995, title = {A Base Pair between {{tRNA}} and {{23S rRNA}} in the Peptidyl Transferase Centre of the Ribosome}, author = {Samaha, R. R. and Green, R. and Noller, H. F.}, year = 1995, journal = {Nature}, volume = {377}, number = {6547}, pages = {309–314}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/nature/journal/v377/n6547/abs/377309a0.html}, abstract = {Interaction of the conserved CCA terminus of tRNA with rRNA in the peptidyl transferase P site has been studied by in vitro genetics. A watson-Crick G-C pair between G2252 in a conserved hairpin loop of 23S rRNA and C74 at the acceptor end of tRNA is required for proper functional interaction of the CCA end of tRNA with the ribosomal P site. These findings establish a direct role for 23S rRNA in protein synthesis}, keywords = {0,Bacterial,Base Composition,Base Sequence,Conserved Sequence,Escherichia coli,Genetic,genetics,In Vitro,IN-VITRO,La,metabolism,Molecular Sequence Data,Mutagenesis,nosource,Nucleic Acid Conformation,P-SITE,peptidyl transferase,PEPTIDYL-TRANSFERASE,Peptidyltransferase,protein,protein synthesis,PROTEIN-SYNTHESIS,ribosome,Ribosomes,Rna,RNABacterial,RNARibosomal23S,RNATransfer,rRNA,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,tRNA} }

@article{samantaGlobalIdentificationNoncoding2006, title = {Global Identification of Noncoding {{RNAs}} in {{Saccharomyces}} Cerevisiae by Modulating an Essential {{RNA}} Processing Pathway}, author = {Samanta, M.P. and Tongprasit, W. and Sethi, H. and Chin, C.S. and Stolc, V.}, year = 2006, month = mar, journal = {Proceedings of the National Academy of Sciences}, volume = {103}, number = {11}, pages = {4192–4197}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.0507669103}, url = {http://www.pnas.org/content/103/11/4192.short}, abstract = {Noncoding RNAs (ncRNAs) perform essential cellular tasks and play key regulatory roles in all organisms. Although several new ncRNAs in yeast were recently discovered by individual studies, to our knowledge no comprehensive empirical search has been conducted. We demonstrate a powerful and versatile method for global identification of previously undescribed ncRNAs by modulating an essential RNA processing pathway through the depletion of a key ribonucleoprotein enzyme component, and monitoring differential transcriptional activities with genome tiling arrays during the time course of the ribonucleoprotein depletion. The entire Saccharomyces cerevisiae genome was scanned during cell growth decay regulated by promoter-mediated depletion of Rpp1, an essential and functionally conserved protein component of the RNase P enzyme. In addition to most verified genes and ncRNAs, expression was detected in 98 antisense and intergenic regions, 74 that were further confirmed to contain previously undescribed RNAs. A class of ncRNAs, located antisense to coding regions of verified protein-coding genes, is discussed in this article. One member, HRA1, is likely involved in 18S rRNA maturation}, keywords = {0,antisense,ARRAYS,Base Sequence,CEREVISIAE,CODING REGION,COMPONENT,DECAY,Dna,DNA-Fungal,DNAFungal,Endoribonucleases,enzyme,expression,gene,Gene Expression,Genes,Genes-Fungal,GenesFungal,genetics,Genome,GROWTH,IDENTIFICATION,La,MATURATION,metabolism,Molecular Sequence Data,nosource,PATHWAY,protein,Proteins,REGION,RIBONUCLEOPROTEIN,Rna,RNA Processing-Post-Transcriptional,RNA ProcessingPost-Transcriptional,RNA-Antisense,RNA-Fungal,RNA-Untranslated,RNAAntisense,RNAFungal,RNAse,RNAUntranslated,rRNA,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,search,Support,yeast} } % == BibTeX quality report for samantaGlobalIdentificationNoncoding2006: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@book{sambrookMolecularCloningLaboratory1989a, title = {Molecular Cloning, a Laboratory Manual.}, author = {Sambrook, J. and Fritsch, E.F. and Maniatis, T.}, year = 1989, series = {Molecular {{Cloning}} a Laboratory Manual.}, volume = {2}, publisher = {Cold Spring Harbor Press}, address = {Cold Spring Harbor, NY}, collaborator = {Nolan, C. and Ford, N. and Ferguson, M.}, keywords = {cloning,Methods,nosource} }

@article{samsonResistanceHIV1Infection1996a, title = {Resistance to {{HIV-1}} Infection in Caucasian Individuals Bearing Mutant Alleles of the {{CCR-5}} Chemokine Receptor Gene}, author = {Samson, M. and Libert, F. and Doranz, B.J. and Rucker, J. and Liesnard, C. and Farber, C.M. and Saragosti, S. and Lapoumeroulie, C. and Cognaux, J. and Forceille, C. and Muyldermans, G. and Verhofstede, C. and Burtonboy, G. and Georges, M. and Imai, T. and Rana, S. and Yi, Y. and Smyth, R.J. and Collman, R.G. and Doms, R.W. and Vassart, G. and Parmentier, M.}, year = 1996, journal = {Nature}, volume = {382}, number = {6593}, pages = {722–725}, doi = {10.1038/382722a0}, url = {http://www.cbs.umn.edu/BMBB/html/Education/BioC8213/F10/SMcI/samson.ccr5.nature'96.pdf http://www.andrew.cmu.edu/user/rule/03_390/write_ass/w4_hiv_paper.pdf}, abstract = {HIV-1 and related viruses require co-receptors, in addition to CD4, to infect target cells. The chemokine receptor CCR-5 (ref.1) was recently demonstrated to be a co-receptor for macrophage-tropic (M-tropic) HIV-1 strains, and the orphan receptor LESTR (also called fusin) allows infection by strains adapted for growth in transformed T-cell lines (T-tropic strains). Here we show that a mutant allele of CCR-5 is present at a high frequency in caucasian populations (allele frequency, 0.092), but is absent in black populations from Western and Central Africa and Japanese populations. A 32-base-pair deletion within the coding region results in a frame shift, and generates a non-functional receptor that does not support membrane fusion or infection by macrophage- and dual-tropic HIV-1 strains. In a cohort of HIV-1 infected caucasian subjects, no individual homozygous for the mutation was found, and the frequency of heterozygotes was 35% lower than in the general population. White blood cells from an individual homozygous for the null allele were found to be highly resistant to infection by M-tropic HIV-1 viruses, confirming that CCR-5 is the major co-receptor for primary HIV-1 strains. The lower frequency of heterozygotes in seropositive patients may indicate partial resistance}, keywords = {0,Alleles,Amino Acid Sequence,Base Sequence,blood,CELLS,chemistry,CloningMolecular,CODING REGION,Cohort Studies,Dna,DNA Primers,European Continental Ancestry Group,FRAME,Frameshift Mutation,gene,Gene Frequency,genetics,Genotype,GROWTH,Heterozygote,HIV,HIV Infections,HIV Seropositivity,Hiv-1,Humans,ImmunityNatural,immunology,INFECTION,La,LINE,Membrane Fusion,Molecular Sequence Data,Mutation,nosource,Polymerase Chain Reaction,Protein Conformation,ReceptorsCCR5,ReceptorsCytokine,ReceptorsHIV,REGION,RESISTANCE,RESISTANT,Support,TARGET,Viruses} }

@article{samsonMolecularCloningFunctional1996, title = {Molecular Cloning and Functional Expression of a New Human {{CC-chemokine}} Receptor Gene}, author = {Samson, M. and Labbe, O. and Mollereau, C. and Vassart, G. and Parmentier, M.}, year = 1996, month = mar, journal = {Biochemistry}, volume = {35}, number = {11}, pages = {3362–3367}, publisher = {ACS Publications}, doi = {10.1021/bi952950g}, url = {http://pubs.acs.org/doi/abs/10.1021/bi952950g}, abstract = {The cloning of several receptors activated by either CC or CXC chemokines and belonging to the G protein-coupled family of receptors has been reported recently. In the present work, we describe the cloning of a human gene, named ChemR13, encoding a new CC-chemokine receptor. The gene encodes a protein of 352 amino acids with a calculated molecular mass of 40 600 Da and displaying a single potential site for N-linked glycosylation. Using a set of overlapping lambda clones, the genomic organisation of the locus was investigated, demonstrating that the ChemR13 gene is physically linked, and in the same orientation, as the CC-CKR2 gene that encodes a receptor for the monocyte chemoattractant protein-1 (MCP-1). A distance of 17.5 kb separates the two coding regions, which share 75% identity in nucleic acid and amino acid sequences. Human ChemR13 was functionally expressed in a stably transfected CHO-K1 cell line. Physiological responses to chemokines were monitored using a microphysiometer. Macrophage inflammatory protein 1 alpha (MIP-1 alpha) was the most potent agonist. MIP-1 beta and RANTES were also active at physiological concentrations. The other CC-chemokines, MCP-1, MCP-2 and MCP-3, as well as CXC-chemokines (IL-8, GRO alpha) had no effect. ChemR13 receptor transcripts were detected by Northern blotting in the promyeloblastic cell line KG-1A, suggesting a potential role in the control of granulocytic lineage proliferation or differentiation. ChemR13 is thus a new member of the growing family of chemokine receptors that mediate the recruitment of cells involved in immune and inflammatory processes. Being the fifth functionally identified receptor in his class, this new CC-chemokine receptor (CC-CKR) is tentatively designated CC-CKR5}, keywords = {0,ACID,ACIDS,Amino Acid Sequence,Amino Acids,AMINO-ACID,AMINO-ACIDS,Animals,Cell Line,CELLS,chemistry,Chemokines,Cho Cells,cloning,CloningMolecular,CODING REGION,Cricetinae,Dna,DNA Primers,ENCODES,expression,FAMILY,gene,Gene Expression,Genes,genetics,genomic,Glycosylation,human,Humans,La,LINE,Linkage (Genetics),Molecular Sequence Data,Multigene Family,nosource,PROLIFERATION,protein,ReceptorsCCR5,ReceptorsCytokine,RECRUITMENT,REGION,Restriction Mapping,Rna,RNAMessenger,sequence,Sequence Alignment,Sequence HomologyAmino Acid,SEQUENCES,SITE,Support,TRANSCRIPT} }

@article{sanbonmatsuUnderstandingDiscriminationRibosome2003, title = {Understanding Discrimination by the Ribosome: Stability Testing and Groove Measurement of Codon-Anticodon Pairs}, author = {Sanbonmatsu, K.Y. and Joseph, S.}, year = 2003, month = apr, journal = {Journal of molecular biology}, volume = {328}, number = {1}, pages = {33–47}, publisher = {Elsevier}, doi = {10.1016/S0022-2836(03)00236-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283603002365}, abstract = {The ribosome must discriminate between correct and incorrect tRNAs with sufficient speed and accuracy to sustain an adequate rate of cell growth. Here, we report the results of explicit solvent molecular dynamics simulations, which address the mechanism of discrimination by the ribosome. The universally conserved 16S rRNA base A1493 and the kink in mRNA between A and P sites amplify differences in stability between cognate and near-cognate codon-anticodon pairs. Destabilization by the mRNA kink also provides a geometric explanation for the higher error rates observed for mismatches in the first codon position relative to mismatches in the second codon position. For more stable near-cognates, the repositioning of the universally conserved bases A1492 and G530 results in increased solvent exposure and an uncompensated loss of hydrogen bonds, preventing correct codon-anticodon-ribosome interactions from forming}, keywords = {0,16S,accuracy,Anticodon,BASE,Base Pairing,BASES,BIOLOGY,Biophysics,chemistry,Codon,Computer Simulation,DYNAMICS,genetics,GROWTH,Hydrogen,Hydrogen Bonding,La,MECHANISM,metabolism,ModelsGenetic,ModelsMolecular,mRNA,nosource,Nucleic Acid Conformation,P SITE,P-SITE,P-SITES,POSITION,Protein Biosynthesis,ribosome,Ribosomes,Rna,RNA Stability,RNAMessenger,RNARibosomal16S,rRNA,SITE,SITES,stability,Support,tRNA} } % == BibTeX quality report for sanbonmatsuUnderstandingDiscriminationRibosome2003: % ? unused Journal abbr (“J.Mol.Biol”)

@article{sanbonmatsuAlignmentMisalignmentHypothesis2006, title = {Alignment/Misalignment Hypothesis for {{tRNA}} Selection by the Ribosome}, author = {Sanbonmatsu, K.Y.}, year = 2006, journal = {Biochimie}, volume = {88}, number = {8}, pages = {1075–1089}, publisher = {Elsevier}, doi = {10.1016/j.biochi.2006.07.002}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0300-9084(06)00141-6}, abstract = {Transfer RNAs (tRNAs) are the adaptor molecules that allow the ribosome to decode genetic information during protein synthesis. During decoding, the ribosome must chose the tRNA whose anticodon corresponds to the codon inscribed in the messenger RNA to incorporate the correct amino acid into the growing polypeptide chain. Fidelity is improved dramatically by a GTP hydrolysis event. Information about the correctness of the anticodon must be sent from the decoding center to the elongation factor, EF-Tu, where the GTP hydrolysis takes place. A second discrimination event entails the accommodation of the aminoacyl-tRNA into its fully bound A/A state inside the ribosome. Here, we present a hypothesis for a specific mechanism of signal transduction through the tRNA, which operates during GTPase activation and accommodation. We propose that the rigidity of the tRNA plays an important role in the transmission of the decoding signal. While the tRNA must flex during binding and accommodation, its anisotropic stiffness enables precise positioning of the acceptor arm in the A/T state, the A/A state and the accommodation corridor. Correct alignment will result in optimal GTPase activation and accommodation rates. Incorrect tRNAs, however, whose anticodons are misaligned, will also have acceptor arms that are misaligned, resulting in sub-optimal GTPase activation and accommodation rates. In the case of GTPase activation, it is possible that the misalignment of the acceptor arm affects the rate directly, by altering the conformational change of the switch region of EF-Tu, or indirectly, by changing the alignment of EF-Tu with respect to the sarcin-ricin loop (SRL) of the large ribosomal subunit}, keywords = {0,ACID,activation,adaptor,alignment,AMINO-ACID,Anticodon,BINDING,Binding Sites,BIOLOGY,Biophysics,chemistry,Codon,CONFORMATIONAL CHANGE,CONFORMATIONAL-CHANGE,decoding,EFTu,elongation,Fidelity,Genetic,genetics,GTP,GTP Phosphohydrolase,GTP Phosphohydrolases,GTPase,Hydrolysis,INFORMATION,La,LOOP,MECHANISM,MESSENGER-RNA,metabolism,ModelsMolecular,nosource,Nucleic Acid Conformation,POLYPEPTIDE,POLYPEPTIDE-CHAIN,protein,protein synthesis,PROTEIN-SYNTHESIS,REGION,Review,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNATransfer,SARCIN RICIN LOOP,SELECTION,SIGNAL,Signal Transduction,SIGNAL-TRANSDUCTION,SUBUNIT,Support,TRANSFER-RNA,transmission,tRNA} }

@article{sanbonmatsuEnergyLandscapeRibosomal2006, title = {Energy Landscape of the Ribosomal Decoding Center}, author = {Sanbonmatsu, K.Y.}, year = 2006, journal = {Biochimie}, volume = {88}, number = {8}, pages = {1053–1059}, doi = {10.1016/j.biochi.2006.06.012}, url = {PM:16905237}, abstract = {The ribosome decodes the genetic information that resides in nucleic acids. A key component of the decoding mechanism is a conformational switch in the decoding center of the small ribosomal subunit discovered in high-resolution X-ray crystallography studies. It is known that small subunit nucleotides A1492 and A1493 flip out of helix 44 upon transfer RNA (tRNA) binding; however, the operation principles of this switch remain unknown. Replica molecular dynamics simulations reveal a low free energy barrier between flipped-out and flipped-in states, consistent with a switch that can be controlled by shifting the equilibrium between states. The barrier determined by the simulations is sufficiently small for the binding of ligands, such as tRNAs or aminoglycoside antibiotics, to shift the equilibrium}, keywords = {0,16S,ACID,ACIDS,Algorithms,AMINOGLYCOSIDE ANTIBIOTICS,antibiotic,antibiotics,BINDING,Binding Sites,BIOLOGY,Biophysics,chemistry,COMPONENT,Crystallography,CrystallographyX-Ray,decoding,DYNAMICS,Genetic,genetics,INFORMATION,La,Ligands,MECHANISM,metabolism,Methods,ModelsMolecular,nosource,Nucleic Acid Conformation,Nucleic Acids,Nucleotides,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNARibosomal,RNARibosomal16S,SUBUNIT,Support,Thermodynamics,TRANSFER-RNA,tRNA} }

@article{sandbakenMutationsElongationFactor1988a, title = {Mutations in Elongation Factor {{EF-1`a}} Affect the Frequency of Frameshifting and Amino Acid Misincorporation in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Sandbaken, M.G. and Culbertson, M.R.}, year = 1988, journal = {Genetics}, volume = {120}, pages = {923–934}, doi = {10.1093/genetics/120.4.923}, keywords = {EF-1,elongation,Frameshifting,Mutation,MUTATIONS,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,translation} }

@article{sandmeierRPD3RequiredInactivation2002, title = {{{RPD3}} Is Required for the Inactivation of Yeast Ribosomal {{DNA}} Genes in Stationary Phase}, author = {Sandmeier, J.J. and French, S. and Osheim, Y. and Cheung, W.L. and Gallo, C.M. and Beyer, A.L. and Smith, J.S.}, year = 2002, journal = {The EMBO Journal}, volume = {21}, number = {18}, pages = {4959–4968}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/cdf498}, url = {http://www.nature.com/emboj/journal/v21/n18/abs/7594712a.html}, abstract = {rRNA transcription in Saccharomyces cerevisiae is performed by RNA polymerase I and regulated by changes in growth conditions. During log phase, similar to50% of the ribosomal DNA (rDNA) genes in each cell are transcribed and maintained in an open, psoralen-accessible conformation. During stationary phase, the percentage of open rDNA genes is greatly reduced. In this study we found that the Rpd3 histone deacetylase was required to inactivate (close) individual rDNA genes as cells entered stationary phase. Even though similar to50% of the rDNA genes remained open during stationary phase in rpd3Delta mutants, overall rRNA synthesis was still reduced. Using electron microscopy of Miller chromatin spreads, we found that the number of RNA polymerases transcribing each open gene in the rpd3Delta mutant was significantly reduced when cells grew past log phase. Bulk levels of histone H3 and H4 acetylation were reduced during stationary phase in an RPD3-dependent manner. However, histone H3 and H4 acetylation was not significantly altered at the rDNA locus in an rpd3Delta mutant. Rpd3 therefore regulates the number of open rDNA repeats}, keywords = {Acetylation,CELLS,CEREVISIAE,Chromatin,CONFORMATION,deacetylation,Dna,ELECTRON-MICROSCOPY,ENCODES,gene,Genes,GROWTH,Histone Deacetylase,HISTONE DEACETYLASE COMPLEX,initiation,MUTANTS,nosource,polymerase,rDNA,RDNA TRANSCRIPTION,RECRUITMENT,repression,Rna,RNA Polymerase I,RNA-POLYMERASE,RNA-POLYMERASE-I,RPD3,rRNA,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,stationary phase,TATA-BINDING PROTEIN,transcription,TRANSCRIPTION FACTOR UAF,yeast} }

@article{sandovalNonnephrotoxicGentamicinCongener2006, title = {A Non-Nephrotoxic Gentamicin Congener That Retains Antimicrobial Efficacy}, author = {Sandoval, R.M. and Reilly, J.P. and Running, W. and Campos, S.B. and Santos, J.R. and Phillips, C.L. and Molitoris, B.A.}, year = 2006, month = oct, journal = {J.Am.Soc.Nephrol.}, volume = {17}, number = {10}, pages = {2697–2705}, doi = {10.1681/ASN.2005101124}, url = {PM:16971659}, abstract = {Aminoglycoside antibiotics, although of major clinical importance in the treatment of serious Gram- negative infections and a potential therapeutic agent in the amelioration of diseases that are characterized by premature stop mutations, are associated with a high incidence of acute renal failure. With the use of HPLC techniques, the four components (congeners) of gentamicin, the most commonly used aminoglycoside, were isolated and characterized. Described here is a congener with minimal cytotoxicity in cell culture and animal studies that retained normal bactericidal properties in both Bacillus subtilis and a multidrug-resistant form of Klebsiella pneumoniae. Furthermore, in animal studies, this congener failed to induce the functional and pathologic changes that are characteristic of gentamicin nephrotoxicity that is seen with the native compound. Finally, internalization of this non-nephrotoxic component was unaltered, but the subcellular distribution was different from native gentamicin or the other three cytotoxic congeners. These studies have identified a component of the native gentamicin congener mixture that retains its bactericidal properties with minimal or no apparent nephrotoxicity}, keywords = {0,AMINOGLYCOSIDE ANTIBIOTICS,animal,Animals,Anti-Bacterial Agents,antibiotic,antibiotics,Bacillus subtilis,chemistry,ChromatographyHigh Pressure Liquid,COMPONENT,COMPONENTS,disease,drug effects,Fluorescent Antibody TechniqueIndirect,FORM,Gentamicins,Incidence,INFECTION,isolation & purification,Kidney,Klebsiella pneumoniae,La,Llc-Pk1 Cells,Male,Mutation,MUTATIONS,nosource,pathology,pharmacology,Rats,RatsSprague-Dawley,Subcellular Fractions,Support,techniques} } % == BibTeX quality report for sandovalNonnephrotoxicGentamicinCongener2006: % ? Possibly abbreviated journal title J.Am.Soc.Nephrol.

@article{sangerDNASequencingChainterminating1977, title = {{{DNA}} Sequencing with Chain-Terminating Inhibitors}, author = {Sanger, F. and Nicklen, S. and Coulson, A.R.}, year = 1977, month = dec, journal = {Proceedings of the National Academy of Sciences}, volume = {74}, number = {12}, pages = {5463–5467}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.74.12.5463}, url = {http://www.pnas.org/content/74/12/5463.short}, keywords = {0,analysis,antagonists & inhibitors,Base Sequence,Coliphages,Deoxyribonucleotides,Dna,DNA Polymerase I,DNA Restriction Enzymes,DnaViral,enzyme,Enzymes,INHIBITOR,inhibitors,La,metabolism,Methods,nosource,pharmacology,polymerase} } % == BibTeX quality report for sangerDNASequencingChainterminating1977: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{sarkhelWaternucleobaseStackingHpi2003, title = {Water-Nucleobase “Stacking”: {{H-pi}} and Lone Pair-Pi Interactions in the Atomic Resolution Crystal Structure of an {{RNA}} Pseudoknot}, author = {Sarkhel, S. and Rich, A. and Egli, M.}, year = 2003, month = jul, journal = {J.Am.Chem.Soc.}, volume = {125}, number = {30}, pages = {8998–8999}, doi = {10.1021/ja0357801}, url = {PM:15369340}, keywords = {0,chemistry,crystal structure,CRYSTAL-STRUCTURE,CrystallographyX-Ray,FrameshiftingRibosomal,Hydrogen,La,ModelsMolecular,nosource,Nucleic Acid Conformation,pseudoknot,RESOLUTION,Rna,RNA PSEUDOKNOT,RnaViral,structure,supportu.s.gov’tp.h.s.,Water} } % == BibTeX quality report for sarkhelWaternucleobaseStackingHpi2003: % ? Possibly abbreviated journal title J.Am.Chem.Soc.

@article{satoComprehensiveGeneticSelection2006, title = {Comprehensive Genetic Selection Revealed Essential Bases in the Peptidyl-Transferase Center}, author = {Sato, N.S. and Hirabayashi, N. and Agmon, I. and Yonath, A. and Suzuki, T.}, year = 2006, month = oct, journal = {Proceedings of the National Academy of Sciences}, volume = {103}, number = {42}, pages = {15386–15391}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.0605970103}, url = {http://www.pnas.org/content/103/42/15386.short}, abstract = {During protein synthesis, the ribosome catalyzes peptide-bond formation. Biochemical and structural studies revealed that conserved nucleotides in the peptidyl-transferase center (PTC) and its proximity may play a key role in peptide-bond formation; the exact mechanism involved remains unclear. To more precisely define the functional importance of the highly conserved residues, we used a systematic genetic method, which we named SSER (systematic selection of functional sequences by enforced replacement), that allowed us to identify essential nucleotides for ribosomal function from randomized rRNA libraries in Escherichia coli cells. These libraries were constructed by complete randomization of the critical regions in and around the PTC. The selected variants contained natural rRNA sequences from other organisms and organelles as well as unnatural functional sequences; hence providing insights into the functional roles played by these essential bases and suggesting how the universal catalytic mechanism of peptide-bond formation could evolve in all living organisms. Our results highlight essential bases and interactions, which are shaping the PTC architecture and guiding the motions of the tRNA terminus from the A to the P site, found to be crucial not only for the formation of the peptide bond but also for nascent chain elongation}, keywords = {BASE,BASES,CELLS,chemistry,conserved nucleotide,elongation,Escherichia coli,ESCHERICHIA-COLI,Genetic,IDENTIFY,La,library,MECHANISM,NASCENT CHAIN,nosource,Nucleotides,Organelles,P SITE,P-SITE,peptide bond formation,PEPTIDE-BOND FORMATION,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,protein,protein synthesis,PROTEIN-SYNTHESIS,REGION,RESIDUES,ribosome,rRNA,SELECTION,sequence,SEQUENCES,SITE,Structural,tRNA} } % == BibTeX quality report for satoComprehensiveGeneticSelection2006: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{satrianoAgmatineSuppressesProliferation1998, title = {Agmatine Suppresses Proliferation by Frameshift Induction of Antizyme and Attenuation of Cellular Polyamine Levels}, author = {Satriano, J. and Matsufuji, S. and Murakami, Y. and Lortie, M.J. and Schwartz, D. and Kelly, C.J. and Hayashi, S. and Blantz, R.C.}, year = 1998, month = jun, journal = {Journal of Biological Chemistry}, volume = {273}, number = {25}, pages = {15313–15316}, publisher = {ASBMB}, doi = {10.1074/jbc.273.25.15313}, url = {http://www.jbc.org/content/273/25/15313.short}, abstract = {Polyamines are required for entry and progression of the cell cycle. As such, augmentation of polyamine levels is essential for cellular transformation. Polyamines are autoregulated through induction of antizyme, which represses both the rate-limiting polyamine biosynthetic enzyme ornithine decarboxylase and cellular polyamine transport. In the present study we demonstrate that agmatine, a metabolite of arginine via arginine decarboxylase (an arginine pathway distinct from that of the classical polyamines), also serves the dual regulatory functions of suppressing polyamine biosynthesis and cellular polyamine uptake through induction of antizyme, The capacity of agmatine to induce antizyme is demonstrated by: (a) an agmatine-dependent translational frameshift of antizyme mRNA to produce a full-length protein and (b) suppression of agmatine-dependent inhibitory activity by either anti-antizyme IgG or antizyme inhibitor. Furthermore, agmatine administration depletes intracellular polyamine levels to suppress cellular proliferation in a transformed cell lime. This suppression is reversible with polyamine supplementation. We propose a novel regulatory pathway in which agmatine acts as an antiproliferative molecule and potential tumor suppressor by restricting the cellular polyamine supply required to support growth}, keywords = {antizyme,Arginine,biosynthesis,cell cycle,CELLS,CHEMOTHERAPY,DEPRIVATION,enzyme,expression,frameshift,GROWTH,INHIBITOR,La,metabolism,mRNA,nosource,Ornithine Decarboxylase,ORNITHINE DECARBOXYLASE-ANTIZYME,polyamine,Polyamines,protein,Support,suppression,TRANSPORT} }

@article{saulquinFrameshiftingNovelMechanism2002, title = {+1 Frameshifting as a Novel Mechanism to Generate a Cryptic Cytotoxic {{T}} Lymphocyte Epitope Derived from Human Interleukin 10}, author = {Saulquin, X. and Scotet, E. and Trautmann, L. and Peyrat, M.A. and Halary, F. and Bonneville, M. and Houssaint, E.}, year = 2002, month = feb, journal = {Journal of Experimental Medicine}, volume = {195}, number = {3}, pages = {353–358}, doi = {10.1084/jem.20011399}, url = {ISI:000176110000009}, abstract = {Recent data indicate that some cytotoxic T cells (CTLs) recognize so-called cryptic epitopes, encoded by nonprimary open reading frame (ORF) sequences or other nonclassical expression pathways. We describe here a novel mechanism leading to generation of a cryptic CTL epitope. We isolated from the synovial fluid of a patient suffering from a Reiter’s syndrome an autoreactive T cell clone that recognized cellular IL-10 in the HLA-B()2705 context. The minimal IL-10 sequence corresponding to nucleotides 379-408 was shown to activate this clone, upon cotransfection into COS cells with the DNA encoding HLA-B()2705, but the synthetic peptide deduced from this sequence did not stimulate the clone. Using a site-directed multagenesis approach, we found that this clone recognized a transframe epitope generated by an internal +1 frameshifting in the IL-10 sequence and so derived partly from ORF1, partly from ORF2. We defined that +1 frameshifting was induced by a specific heptamer sequence. These observations illustrate the variety of mechanisms leading to generation of cryptic epitopes and suggest that frameshifting in normal cellular genes may be more common than expected}, keywords = {+1 frameshifting,0,ANTIGEN,autoimmunity,CELLS,Cos Cells,CTL,CTL EPITOPES,Dna,E,epitope,EPSTEIN-BARR-VIRUS,expression,FRAME,frameshift,Frameshifting,gene,Genes,human,IL-10,MECHANISM,MECHANISMS,nosource,Nucleotides,OPEN READING FRAME,READING FRAME,RECOGNITION,sequence,SEQUENCES,T} }

@article{schaperYeastHomologChromatin2001a, title = {A Yeast Homolog of Chromatin Assembly Factor 1 Is Involved in Early Ribosome Assembly}, author = {Schaper, S. and {Fromont-Racine}, M. and Linder, P. and {}{de la Cruz}, J. and Namane, A. and Yaniv, M.}, year = 2001, month = nov, journal = {Current Biology}, volume = {11}, number = {23}, pages = {1885–1890}, doi = {10.1016/S0960-9822(01)00584-X}, url = {ISI:000172475700025}, abstract = {Cells have a recurrent need for the correct assembly of protein-nucleic acid complexes. We have studied a yeast homolog of the smallest subunit of chromatin assembly factor 1 (CAM), encoded by YMR131c and termed “RRB1” [1]. Unlike other yeast homologs, Msi1p, and Hat2p, Rrb1p is essential for cell viability. Impairment of Rrb1p function results in decreased levels of free 60S ribosomal subunits and the appearance of half-mer polysomes, suggesting its involvement in ribosome biogenesis. Using tandem affinity purification (TAP [2]) combined with mass spectrometry, we show that Rrb1p is associated with ribosomal protein L3. A fraction of Rrb1p is also found in a protein-precursor rRNA complex containing at least ten other early-assembling ribosomal proteins. We propose that Rrb1p is required for proper assembly of preribosomal particles during early ribosome biogenesis, presumably by targeting L3 onto the 35S precursor rRNA. This action may resemble the mechanism by which CAM assembles histones H3/H4 onto newly replicated DNA}, keywords = {ACID,assembly,CELLS,Chromatin,COMPLEX,COMPLEXES,Dna,Histones,homolog,L25,L3,MECHANISM,nosource,oncogenes,PARTICLES,Polyribosomes,polysomes,PRECURSOR,protein,Proteins,purification,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,ribosome biogenesis,Rna,rRNA,S,SACCHAROMYCES-CEREVISIAE,SUBUNIT,SUBUNITS,TRANS-ACTING FACTORS,virus,yeast} }

@article{schenaMammalianGlucocorticoidReceptor1988a, title = {Mammalian Glucocorticoid Receptor Derivitives Enhance Transcription Transcription in Yeast.}, author = {Schena, M. and Yamamoto, K.}, year = 1988, journal = {Science}, volume = {241}, pages = {965–967}, doi = {10.1126/science.3043665}, keywords = {nosource,pG-1,transcription,vector,yeast} }

@article{scheperTranslationMattersProtein2007, title = {Translation Matters: Protein Synthesis Defects in Inherited Disease}, author = {Scheper, G.C. and {}{van der Knaap}, M.S. and Proud, C.G.}, year = 2007, journal = {Nature Reviews Genetics}, volume = {8}, number = {9}, pages = {711–723}, publisher = {Nature Publishing Group}, doi = {10.1038/nrg2142}, url = {http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg2142.html}, abstract = {The list of genetic diseases caused by mutations that affect mRNA translation is rapidly growing. Although protein synthesis is a fundamental process in all cells, the disease phenotypes show a surprising degree of heterogeneity. Studies of some of these diseases have provided intriguing new insights into the functions of proteins involved in the process of translation; for example, evidence suggests that several have other functions in addition to their roles in translation. Given the numerous proteins involved in mRNA translation, it is likely that further inherited diseases will turn out to be caused by mutations in genes that are involved in this complex process}, keywords = {0,5’ Untranslated Regions,Animals,CELLS,Child,COMPLEX,COMPLEXES,disease,elongation,elongation factors,ELONGATION-FACTORS,gene,Gene Expression Regulation,Genes,Genetic,Genetic DiseasesInborn,genetics,Humans,initiation,INITIATION-FACTOR,La,metabolism,mitochondria,ModelsBiological,mRNA,Mutation,MUTATIONS,nosource,Peptide Elongation Factors,Peptide Initiation Factors,Peptide Termination Factors,Phenotype,physiology,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,Proteins,REGION,Review,Ribosomes,Rna,RNATransfer,Support,termination,translation,Untranslated Regions} } % == BibTeX quality report for scheperTranslationMattersProtein2007: % ? unused Journal abbr (“Nat.Rev.Genet.”)

@article{scherlFunctionalProteomicAnalysis2002, title = {Functional Proteomic Analysis of Human Nucleolus}, author = {Scherl, A. and Coute, Y. and Deon, C. and Calle, A. and Kindbeiter, K. and Sanchez, J.C. and Greco, A. and Hochstrasser, D. and Diaz, J.J.}, year = 2002, month = nov, journal = {Molecular biology of the cell}, volume = {13}, number = {11}, pages = {4100–4109}, publisher = {Am Soc Cell Biol}, doi = {10.1091/mbc.e02-05-0271}, url = {http://www.molbiolcell.org/cgi/content/abstract/13/11/4100}, abstract = {The notion of a “plurifunctional” nucleolus is now well established. However, molecular mechanisms underlying the biological processes occurring within this nuclear domain remain only partially understood. As a first step in elucidating these mechanisms we have carried out a proteomic analysis to draw up a list of proteins present within nucleoli of HeLa cells. This analysis allowed the identification of 213 different nucleolar proteins. This catalog complements that of the 271 proteins obtained recently by others, giving a total of 350 different nucleolar proteins. Functional classification of these proteins allowed outlining several biological processes taking place within nucleoli. Bioinformatic analyses permitted the assignment of hypothetical functions for 43 proteins for which no functional information is available. Notably, a role in ribosome biogenesis was proposed for 31 proteins. More generally, this functional classification reinforces the plurifunctional nature of nucleoli and provides convincing evidence that nucleoli may play a central role in the control of gene expression. Finally, this analysis supports the recent demonstration of a coupling of transcription and translation in higher eukaryotes}, keywords = {analysis,chemistry,classification,expression,gene,Gene Expression,GENE-EXPRESSION,Hela Cells,human,IDENTIFICATION,MECHANISM,MECHANISMS,nosource,nucleolus,protein,Proteins,ribosome,ribosome biogenesis,Support,transcription,translation} } % == BibTeX quality report for scherlFunctionalProteomicAnalysis2002: % ? unused Journal abbr (“Mol.Biol.Cell”)

@article{schilling-bartetzkoApparentAssociationConstants1992a, title = {Apparent Association Constants of Transfer-{{RNAs}} for the Ribosomal {{A-Site}}, {{P-Site}}, and {{E-Site}}}, author = {{Schilling-Bartetzko}, S. and Franceschi, F. and Sternbach, H. and Nierhaus, K.H.}, year = 1992, month = mar, journal = {J.Biol Chem.}, volume = {267}, number = {7}, pages = {4693–4702}, doi = {10.1016/S0021-9258(18)42889-X}, url = {ISI:A1992HF64200064}, abstract = {Association constants for tRNA binding to poly(U) programmed ribosomes were assessed under standardized conditions with a single preparation of ribosomes, tRNAs, and elongation factors, respectively, at 15 and 10 mM Mg2+. Association constants were determined by Scatchard plot analysis (the constants are given in units of [10(7)/M] measured at 15 mM Mg2+): the ternary complex Phe-tRNA.elongation factor EF-Tu.GTP (12 +/- 3), Phe-tRNA (1 +/- 0.4), AcPhe-tRNA (0.7 +/- 0.3), and deacylated tRNA(Phe) (0.4 +/- 0.15) bind with decreasing affinity to the A site of poly(U)-programmed ribosomes. tRNA(Phe) (7.2 +/- 0.8) binds to the P site with higher affinity than AcPhe-tRNA (3.7 +/- 1.3). The affinity of the E site for deacylated tRNA(Phe) (1 +/- 0.2) is about the same as that of the A site for AcPhe-tRNA (0.7 +/- 0.3). At lower Mg2+ concentrations the affinity of the E site ligand becomes stronger relative to the affinities of the A site ligands. Phe-tRNA and ternary complexes can occupy the A site at 0-degrees-C in the presence of poly(U) even if the P site is free, whereas, as already known, deacylated tRNA or AcPhe-tRNA bind first to the P site of programmed ribosomes. Hill plot analyses of the binding data confirm an allosteric linkage between A and E sites in the sense of a negative cooperativity}, keywords = {3,A SITE,A-SITE,ALLOSTERIC 3-SITE MODEL,analysis,ASSOCIATION,BINDING,BINDING-SITES,CODON-ANTICODON INTERACTION,COMPLEX,COMPLEXES,CONSTANTS,E,E site,elongation,ELONGATION CYCLE,elongation factors,ELONGATION-FACTORS,ESCHERICHIA-COLI RIBOSOMES,Ligands,MESSENGER-RNA,nosource,P SITE,P-SITE,PROTEIN-BIOSYNTHESIS,ribosome,Ribosomes,SCATCHARD PLOTS,SITE,SITES,SUBUNITS,TRANSFER-RNA,translocation,tRNA,tRNA binding,UNITS} } % == BibTeX quality report for schilling-bartetzkoApparentAssociationConstants1992a: % ? Possibly abbreviated journal title J.Biol Chem.

@article{schimmelRnaPseudoknotsThat1989, title = {Rna {{Pseudoknots That Interact}} with {{Components}} of the {{Translation Apparatus}}}, author = {Schimmel, P.}, year = 1989, month = jul, journal = {Cell}, volume = {58}, number = {1}, pages = {9–12}, publisher = {Cell Press}, doi = {10.1016/0092-8674(89)90395-4}, url = {http://cat.inist.fr/?aModele=afficheN&cpsidt=6633310}, keywords = {COMPONENT,nosource,pseudoknot,pseudoknots,Review,Rna,RNA PSEUDOKNOT,translation} } % == BibTeX quality report for schimmelRnaPseudoknotsThat1989: % ? Title looks like it was stored in title-case in Zotero

@article{schindlerTrichoderminResistanceMutation1974a, title = {Trichodermin Resistance–Mutation Affecting Eukaryotic Ribosomes.}, author = {Schindler, D. and Grant, P. and Davies, J.}, year = 1974, journal = {Nature}, volume = {248}, pages = {535–536}, doi = {10.1038/248535a0}, keywords = {antibiotics,L3,nosource,ribosome,Ribosomes,translation,trichodermin,yeast} }

@article{schindlerTwoClassesInhibitors1974a, title = {Two Classes of Inhibitors of Peptidyl Transferase Activity in Eukaryotes.}, author = {Schindler, D.}, year = 1974, journal = {Nature}, volume = {249}, pages = {38–41}, doi = {10.1038/249038a0}, keywords = {anisomycin,drugs,nosource,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Peptidyltransferase,ribosome} }

@article{schluenzenStructureFunctionallyActivated2000b, title = {Structure of Functionally Activated Small Ribosomal Subunit at 3.3 Angstroms Resolution}, author = {Schluenzen, F. and Tocilj, A. and Zarivach, R. and Harms, J. and Gluehmann, M. and Janell, D. and Bashan, A. and Bartels, H. and Agmon, I. and Franceschi, F. and Yonath, A.}, year = 2000, journal = {Cell}, volume = {102}, number = {5}, pages = {615–623}, doi = {10.1016/S0092-8674(00)00084-2}, url = {PM:11007480}, abstract = {The small ribosomal subunit performs the decoding of genetic information during translation. The structure of that from Thermus thermophilus shows that the decoding center, which positions mRNA and three tRNAs, is constructed entirely of RNA. The entrance to the mRNA channel will encircle the message when a latch-like contact closes and contributes to processivity and fidelity. Extended RNA helical elements that run longitudinally through the body transmit structural changes, correlating events at the particle’s far end with the cycle of mRNA translocation at the decoding region. 96% of the nucleotides were traced and the main fold of all proteins was determined. The latter are either peripheral or appear to serve as linkers. Some may assist the directionality of translocation}, keywords = {0,Bacterial,Base Pairing,Binding Sites,chemistry,CrystallographyX-Ray,cytology,decoding,ELEMENTS,Fidelity,Genetic,genetics,La,metabolism,ModelsMolecular,mRNA,nosource,Nucleic Acid Conformation,Nucleotides,protein,Protein Conformation,Proteins,RIBOSOMAL-SUBUNIT,Ribosomes,Rna,RNABacterial,RNAMessenger,RNARibosomal16S,RNATransfer,Structural,structure,Structure-Activity Relationship,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Thermus,Thermus thermophilus,translation,translocation,tRNA} }

@article{schlunsCytokineControlMemory2003, title = {Cytokine Control of Memory {{T-cell}} Development and Survival}, author = {Schluns, K.S. and Lefrancois, L.}, year = 2003, month = apr, journal = {Nature Reviews Immunology}, volume = {3}, number = {4}, pages = {269–279}, publisher = {Nature Publishing Group}, doi = {10.1038/nri1052}, url = {http://www.nature.com/nri/journal/v3/n4/abs/nri1052.html}, abstract = {Evidence has accumulated that cytokines have a fundamental role in the differentiation of memory T cells. Here, we follow the CD8+ T cell from initial activation to memory-cell generation, indicating the checkpoints at which cytokines determine the fate of the T cell. Members of the common cytokine-receptor gamma-chain (gammac)-cytokine family–in particular, interleukin-7 (IL-7) and IL-15–act at each stage of the immune response to promote proliferation and survival. In this manner, a stable and protective, long-lived memory CD8+ T-cell pool can be propagated and maintained}, keywords = {0,activation,Animals,ANTIGEN,Antigens,CD4-Positive T-Lymphocytes,CD8-Positive T-Lymphocytes,Cell Differentiation,Cell Survival,CELLS,Cytokines,cytology,development,Gene Expression,genetics,human,Humans,Immunologic Memory,immunology,Interleukin-15,Interleukin-2,Interleukin-7,La,Lymphocyte Activation,Memory,Models-Immunological,ModelsImmunological,nosource,physiology,PROLIFERATION,protein,Receptors-Cytokine,Receptors-Interleukin-15,Receptors-Interleukin-2,Receptors-Interleukin-7,ReceptorsCytokine,ReceptorsInterleukin-15,ReceptorsInterleukin-2,ReceptorsInterleukin-7,Review,Support,T,T-Lymphocyte Subsets} } % == BibTeX quality report for schlunsCytokineControlMemory2003: % ? unused Journal abbr (“Nat.Rev.Immunol.”)

@article{schlunzenStructuralBasisInteraction2001, title = {Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Centre in Eubacteria}, author = {Schlunzen, F. and Zarivach, R. and Harms, R. and Bashan, A. and Tocilj, A. and Albrecht, R. and Yonath, A. and Franceschi, F.}, year = 2001, month = oct, journal = {Nature}, volume = {413}, number = {6858}, pages = {814–821}, publisher = {Nature Publishing Group}, doi = {10.1038/35101544}, url = {ISI:000171750200038 http://www.nature.com/nature/journal/v413/n6858/abs/413814a0.html}, abstract = {Ribosomes, the site of protein synthesis, are a major target for natural and synthetic antibiotics. Detailed knowledge of antibiotic binding sites is central to understanding the mechanisms of drug action. Conversely, drugs are excellent tools for studying the ribosome function. To elucidate the structural basis of ribosome-antibiotic interactions, we determined the high-resolution X-ray structures of the 50S ribosomal subunit of the eubacterium Deinococcus radiodurans, complexed with the clinically relevant antibiotics chloramphenicol, clindamycin and the three macrolides erythromycin, clarithromycin and roxithromycin. We found that antibiotic binding sites are composed exclusively of segments of 23S ribosomal RNA at the peptidyl transferase cavity and do not involve any interaction of the drugs with ribosomal proteins. Here we report the details fo antibiotic interactions with the components of their binding sites. Our results also show the importance of putative Mg+2 ions for the binding of some drugs. This structural analysis should facilitate rational drug design}, keywords = {23S RIBOSOMAL-RNA,analysis,ANGSTROM RESOLUTION,antibiotic,antibiotics,BINDING,Binding Sites,BINDING-SITE,Chloramphenicol,COMPONENT,COMPONENTS,CONFORMATION,DOMAIN-II,Drug Design,drugs,Erythromycin,ERYTHROMYCIN RESISTANCE,ESCHERICHIA-COLI,Eubacterium,Ions,Macrolides,MECHANISM,MECHANISMS,MUTATIONS,nosource,peptidyl transferase,PEPTIDYL-TRANSFERASE,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Ribosomal Proteins,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,SITE,SITES,Structural,STRUCTURAL BASIS,structure,SUBUNIT} }

@article{schlunzenInhibitionPeptideBond2004, title = {Inhibition of Peptide Bond Formation by Pleuromutilins: The Structure of the {{50S}} Ribosomal Subunit from {{Deinococcus}} Radiodurans in Complex with Tiamulin}, author = {Schlunzen, F. and Pyetan, E. and Fucini, P. and Yonath, A. and Harms, J.M.}, year = 2004, month = dec, journal = {Mol.Microbiol.}, volume = {54}, number = {5}, pages = {1287–1294}, publisher = {Wiley Online Library}, doi = {10.1111/j.1365-2958.2004.04346.x}, url = {PM:15554968 http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2004.04346.x/full}, abstract = {Tiamulin, a prominent member of the pleuromutilin class of antibiotics, is a potent inhibitor of protein synthesis in bacteria. Up to now the effect of pleuromutilins on the ribosome has not been determined on a molecular level. The 3.5 A structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin provides for the first time a detailed picture of its interactions with the 23S rRNA, thus explaining the molecular mechanism of the antimicrobial activity of the pleuromutilin class of antibiotics. Our results show that tiamulin is located within the peptidyl transferase center (PTC) of the 50S ribosomal subunit with its tricyclic mutilin core positioned in a tight pocket at the A-tRNA binding site. Also, the extension, which protrudes from its mutilin core, partially overlaps with the P-tRNA binding site. Thereby, tiamulin directly inhibits peptide bond formation. Comparison of the tiamulin binding site with other PTC targeting drugs, like chloramphenicol, clindamycin and streptogramins, may facilitate the design of modified or hybridized drugs that extend the applicability of this class of antibiotics}, keywords = {antibiotic,antibiotics,Bacteria,BINDING,BINDING-SITE,BOND FORMATION,Chloramphenicol,Clindamycin,COMPLEX,COMPLEXES,Deinococcus,drugs,Genetic,genetics,INHIBITION,INHIBITOR,La,MECHANISM,MOLECULAR-GENETICS,nosource,peptide bond formation,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,protein,protein synthesis,PROTEIN-SYNTHESIS,RIBOSOMAL-SUBUNIT,ribosome,rRNA,SITE,structure,SUBUNIT,TRANSFERASE CENTER} } % == BibTeX quality report for schlunzenInhibitionPeptideBond2004: % ? Possibly abbreviated journal title Mol.Microbiol.

@article{schmeingPretranslocationalIntermediateProtein2002, title = {A Pre-Translocational Intermediate in Protein Synthesis Observed in Crystals of Enzymatically Active {{50S}} Subunits}, author = {Schmeing, T.M. and Seila, A.C. and Hansen, J.L. and Freeborn, B. and Soukup, J.K. and Scaringe, S.A. and Strobel, S.A. and Moore, P.B. and Steitz, T.A.}, year = 2002, month = mar, journal = {Nat.Struct.Biol.}, volume = {9}, number = {3}, pages = {225–230}, url = {PM:11828326}, abstract = {The large ribosomal subunit catalyzes peptide bond formation during protein synthesis. Its peptidyl transferase activity has often been studied using a ‘fragment assay’ that depends on high concentrations of methanol or ethanol. Here we describe a version of this assay that does not require alcohol and use it to show, both crystallographically and biochemically, that crystals of the large ribosomal subunits from Haloarcula marismortui are enzymatically active. Addition of these crystals to solutions containing substrates results in formation of products, which ceases when crystals are removed. When substrates are diffused into large subunit crystals, the subsequent structure shows that products have formed. The CC-puromycin-peptide product is found bound to the A-site and the deacylated CCA is bound to the P-site, with its 3prime prime or minute OH near N3 A2486 (Escherichia coli A2451). Thus, this structure represents a state that occurs after peptide bond formation but before the hybrid state of protein synthesis}, keywords = {0,A-SITE,Alcohols,Bacterial,Bacterial Proteins,Binding Sites,biosynthesis,Catalysis,chemistry,Crystallization,Escherichia coli,ESCHERICHIA-COLI,Ethanol,Haloarcula,Haloarcula marismortui,La,metabolism,ModelsMolecular,N-Formylmethionine,No DOI found,nosource,P-SITE,peptidyl transferase,PEPTIDYL-TRANSFERASE,protein,Protein Conformation,Protein Subunits,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Puromycin,RIBOSOMAL-SUBUNIT,Ribosomes,Solutions,Solvents,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,TranslationGenetic,X-Ray Diffraction} } % == BibTeX quality report for schmeingPretranslocationalIntermediateProtein2002: % ? Possibly abbreviated journal title Nat.Struct.Biol.

@article{schmeingInducedfitMechanismPromote2005, title = {An Induced-Fit Mechanism to Promote Peptide Bond Formation and Exclude Hydrolysis of Peptidyl-{{tRNA}}}, author = {Schmeing, T.M. and Huang, K.S. and Strobel, S.A. and Steitz, T.A.}, year = 2005, month = nov, journal = {Nature}, volume = {438}, number = {7067}, pages = {520–524}, publisher = {Nature Publishing Group}, doi = {10.1038/nature04152}, url = {http://www.nature.com/nature/journal/v438/n7067/abs/nature04152.html}, abstract = {The large ribosomal subunit catalyses the reaction between the alpha-amino group of the aminoacyl-tRNA bound to the A site and the ester carbon of the peptidyl-tRNA bound to the P site, while preventing the nucleophilic attack of water on the ester, which would lead to unprogrammed deacylation of the peptidyl-tRNA. Here we describe three new structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with peptidyl transferase substrate analogues that reveal an induced-fit mechanism in which substrates and active-site residues reposition to allow the peptidyl transferase reaction. Proper binding of an aminoacyl-tRNA analogue to the A site induces specific movements of 23S rRNA nucleotides 2618-2620 (Escherichia coli numbering 2583-2585) and 2541(2506), thereby reorienting the ester group of the peptidyl-tRNA and making it accessible for attack. In the absence of the appropriate A-site substrate, the peptidyl transferase centre positions the ester link of the peptidyl-tRNA in a conformation that precludes the catalysed nucleophilic attack by water. Protein release factors may also function, in part, by inducing an active-site rearrangement similar to that produced by the A-site aminoacyl-tRNA, allowing the carbonyl group and water to be positioned for hydrolysis}, keywords = {0,A SITE,A-SITE,ACTIVE-SITE,Acylation,Archaeal Proteins,BINDING,Binding Sites,biosynthesis,BOND FORMATION,Carbon,chemistry,CONFORMATION,Escherichia coli,ESCHERICHIA-COLI,genetics,Haloarcula,Haloarcula marismortui,Hydrolysis,La,MECHANISM,metabolism,ModelsMolecular,Movement,nosource,Nucleotides,P SITE,P-SITE,peptide bond formation,Peptides,peptidyl transferase,PEPTIDYL-TRANSFERASE,POSITION,POSITIONS,protein,Protein Biosynthesis,Protein Subunits,Proteins,RELEASE,release factor,RELEASE FACTORS,Research SupportN.I.H.Extramural,Research SupportU.S.Gov’tNon-P.H.S.,RESIDUES,RIBOSOMAL-SUBUNIT,Ribosomes,Rna,RNARibosomal23S,RNATransfer,rRNA,SITE,sparsomycin,structure,SUBUNIT,SUBUNITS,Water} }

@article{schmittCloningExpressionCDNA1995a, title = {Cloning and Expression of a {{cDNA}} Copy of the Viral {{K28}} Killer Toxin Gene in Yeast}, author = {Schmitt, M.J.}, year = 1995, month = jan, journal = {Mol.Gen.Genet.}, volume = {246}, number = {2}, pages = {236–246}, doi = {10.1007/BF00294687}, abstract = {The killer toxin K28, secreted by certain killer strains of the yeast Saccharomyces cerevisiae is genetically encoded by a 1.9 kb double- stranded RNA, M-dsRNA (M28), that is present within the cell as a cytoplasmically inherited virus-like particle (VLP). For stable maintenance and replication, M28-VLPs depend on a second dsRNA virus (LA), which has been shown to encode the major capsid protein (cap) and a capsid-polymerase fusion protein (cap-pol) that provides the toxin- coding M-satellites with their transcription and replicase functions. K28 toxin-coding M28-VLPs were isolated, purified and used in vitro for the synthesis of the single-stranded M28 transcript, which was shown to be of plus strand polarity and to bind to oligo(dT)-cellulose, indicating that M28(+)ssRNA contains an internal A-rich tract. Strand separation of the 1.9 kb M28-dsRNA and direct RNA sequencing of its 3’ ends was performed in order to obtain specific DNA oligonucleotides that could be used as primers for cDNA synthesis. The nucleotide sequence of the toxin-coding M28-cDNA identified a single open reading frame (ORF) coding for a polypeptide of 345 amino acids, which contained two potential Kex2p/Kex1p processing sites and three potential sites for protein N-glycosylation. The toxin-coding cDNA was cloned and expressed in sensitive non-killer strains under the control of the yeast PGK promoter. Upon transformation, this construct conferred the complete K28 phenotype, demonstrating that both toxin and immunity determinants are contained within the cloned cDNA. In vitro translational analysis of the M28(+)ssRNA in vitro transcript identified the primary gene product of M28 as a K28 preprotoxin of 38 kDa (M-p38)}, keywords = {95166181,Amino Acid Sequence,Amino Acids,analysis,Base Sequence,biosynthesis,Cap,Capsid,cloning,CloningMolecular,Dna,DNA-Directed RNA Polymerase,DNAComplementary,expression,gene,genetics,In Vitro,IN-VITRO,isolation & purification,killer,killer toxin,La,metabolism,Molecular Sequence Data,Mycotoxins,nosource,Nucleic Acid Conformation,Oligonucleotides,Open Reading Frames,Phenotype,Polarity of Translation,PROMOTER,protein,Protein Precursors,Rna,RNADouble-Stranded,RNAFungal,RnaViral,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence AnalysisDNA,Sequence AnalysisRNA,supportnon-u.s.gov’t,toxin,transcription,TranscriptionGenetic,TranslationGenetic,virology,virus,yeast} } % == BibTeX quality report for schmittCloningExpressionCDNA1995a: % ? Possibly abbreviated journal title Mol.Gen.Genet.

@article{schmittSequenceM28DsRNA1995, title = {Sequence of the {{M28 dsRNA}}: Preprotoxin Is Processed to an [Alpha]/[Beta] Heterodimeric Protein Toxin}, author = {Schmitt, M.J. and Tipper, D.J.}, year = 1995, month = nov, journal = {Virology}, volume = {213}, number = {2}, pages = {341–351}, publisher = {Elsevier}, doi = {10.1006/viro.1995.0007}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0042682285700074}, abstract = {The killer and immunity phenotypes of K28 killer strains of Saccharomyces cerevisiae are determined by the 1.75-kb M28 dsRNA virus. In the plus strand, M28p, the K28 preprotoxin gene, comprises bases 13-1047 and is followed, after an additional 85 bases, by a 63-bp poly(A) sequence and a 553-base 3’-sequence. This 3’-sequence contains two potential stem-loop structures predicted to bind the L-A encoded cap-pol protein, initiating encapsidation; high-level expression results in curing of M1 dsRNA. Expression of M28p confers the complete K28 killer and immunity phenotype on a cell lacking M28 dsRNA. K28 toxin is a disulfide-bonded heterodimer of alpha (10.5 kDa) and beta (11 kDa) components whose N-termini correspond to M28p residues 50-61 and 246-257, respectively. alpha is preceded by a potentially redundant pair of secretion signal peptides; deletion of the first reduces toxin secretion by 75%. While M28p bears no sequence similarity to M1p, the K1 preprotoxin, the predicted patterns of processing by glycosylation and cleavage are remarkably similar. The beta N- and C-termini are probably processed by Kex2p and Kex1p, respectively; the mechanism of cleavage at the less typical sites bounding the alpha component is under investigation. While a kex2 Delta mutation prevents toxin secretion, secreted toxin retains 20% activity in a kex1 Delta mutant. Neither mutation affects immunity. (C) 1995 academic Press, Inc}, keywords = {ASPARTYL PROTEASE,BASE,BASES,CEREVISIAE,CLEAVAGE,CLEAVAGE SITES,COMPONENT,COMPONENTS,curing,DOUBLE-STRANDED-RNA,dsRNA virus,ENCAPSIDATION,expression,gene,HIGH-LEVEL EXPRESSION,killer,killer toxin,L-A,La,M,M1,MECHANISM,Mutation,nosource,PATTERNS,Peptides,Phenotype,poly(A),protein,REPLICATION,RESIDUES,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SIGNAL,Signal Peptides,SITE,SITES,STEM-LOOP,structure,toxin,virus,yeast} }

@article{schmittYeastViralKiller2006, title = {Yeast Viral Killer Toxins: Lethality and Self-Protection}, author = {Schmitt, M.J. and Breinig, F.}, year = 2006, month = mar, journal = {Nature Reviews Microbiology}, volume = {4}, number = {3}, pages = {212–221}, publisher = {Nature Publishing Group}, doi = {10.1038/nrmicro1347}, url = {http://www.nature.com/nrmicro/journal/v4/n3/abs/nrmicro1347.html}, abstract = {Since the discovery of toxin-secreting killer yeasts more than 40 years ago, research into this phenomenon has provided insights into eukaryotic cell biology and virus-host-cell interactions. This review focuses on the most recent advances in our understanding of the basic biology of virus-carrying killer yeasts, in particular the toxin-encoding killer viruses, and the intracellular processing, maturation and toxicity of the viral protein toxins. The strategy of using eukaryotic viral toxins to effectively penetrate and eventually kill a eukaryotic target cell will be discussed, and the cellular mechanisms of self-defence and protective immunity will also be addressed}, keywords = {0,Apoptosis,Biological Transport,BIOLOGY,Cytosol,DISCOVERY,Fungal Proteins,Germany,immunology,Ion Channels,killer,killer toxin,killer yeast,La,MATURATION,MECHANISM,MECHANISMS,metabolism,Molecular Biology,Mycotoxins,nosource,physiology,protein,Proteins,Review,Rna,RNA Viruses,RNADouble-Stranded,RnaViral,Saccharomyces cerevisiae,Support,TARGET,toxicity,toxin,virology,Virus Replication,Viruses,yeast,Yeasts} } % == BibTeX quality report for schmittYeastViralKiller2006: % ? unused Journal abbr (“Nat.Rev.Microbiol.”)

@article{schneiderTranscriptionElongationRNA2007, title = {Transcription Elongation by {{RNA}} Polymerase {{I}} Is Linked to Efficient {{rRNA}} Processing and Ribosome Assembly}, author = {Schneider, D.A. and Michel, A. and Sikes, M.L. and Vu, L. and Dodd, J.A. and Salgia, S. and Osheim, Y.N. and Beyer, A.L. and Nomura, M.}, year = 2007, month = apr, journal = {Molecular cell}, volume = {26}, number = {2}, pages = {217–229}, publisher = {Elsevier}, doi = {10.1016/j.molcel.2007.04.007}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276507002237}, abstract = {The synthesis of ribosomes in eukaryotic cells is a complex process involving many nonribosomal protein factors and snoRNAs. In general, the processes of rRNA transcription and ribosome assembly are treated as temporally or spatially distinct. Here, we describe the identification of a point mutation in the second largest subunit of RNA polymerase I near the active center of the enzyme that results in an elongation-defective enzyme in the yeast Saccharomyces cerevisiae. In vivo, this mutant shows significant defects in rRNA processing and ribosome assembly. Taken together, these data suggest that transcription of rRNA by RNA polymerase I is linked to rRNA processing and maturation. Thus, RNA polymerase I, elongation factors, and rRNA sequence elements appear to function together to optimize transcription elongation, coordinating cotranscriptional interactions of many factors/snoRNAs with pre-rRNA for correct rRNA processing and ribosome assembly}, keywords = {0,assembly,CELLS,CEREVISIAE,chemistry,COMPLEX,COMPLEXES,ELEMENTS,elongation,elongation factors,ELONGATION-FACTORS,enzyme,Eukaryotic Cells,GenesFungal,genetics,IDENTIFICATION,IN-VIVO,La,MATURATION,metabolism,Mutation,nosource,Point Mutation,polymerase,protein,Protein Subunits,ribosome,Ribosomes,Rna,RNA Polymerase I,RNA ProcessingPost-Transcriptional,RNA-POLYMERASE,RNA-POLYMERASE-I,RNAFungal,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SUBUNIT,SUBUNITS,Support,transcription,TranscriptionGenetic,yeast} } % == BibTeX quality report for schneiderTranscriptionElongationRNA2007: % ? unused Journal abbr (“Mol.Cell”)

@article{schneiderTranslationInitiationViral2003a, title = {Translation Initiation and Viral Tricks}, author = {Schneider, R.J. and Mohr, I.}, year = 2003, month = mar, journal = {Trends in Biochemical Sciences}, volume = {28}, number = {3}, pages = {130–136}, doi = {10.1016/S0968-0004(03)00029-X}, url = {ISI:000181747900007}, abstract = {A variety of viral strategies are utilized for dominance of the host-cell protein synthetic machinery, optimization of viral mRNA translation and evasion of host-cell antiviral responses that act at the translational level. Many viruses exploit regulated steps in the initiation of cellular protein synthesis to their own advantage. They have developed some rather unconventional means for mRNA translation, which were probably adapted from specialized cellular mRNA translation systems. Regardless of the type of translational tricks exploited, viruses typically ensure efficient viral translation, often at the expense of host-cell protein synthesis}, keywords = {0,antiviral,ENCEPHALOMYOCARDITIS VIRUS,EPSTEIN-BARR-VIRUS,HEPATITIS-C,HERPES-SIMPLEX VIRUS,IN-VITRO,initiation,MESSENGER-RNA,MOLECULAR MECHANISMS,mRNA,NONSTRUCTURAL 5A PROTEIN,nosource,POLY(A)-BINDING PROTEIN,protein,protein synthesis,PROTEIN-SYNTHESIS,Review,RNA-BINDING-PROTEIN,SYSTEM,SYSTEMS,translation,TRANSLATION INITIATION} }

@incollection{schneiderTranslationalControlCancer2006, title = {Translational Control in Cancer Development and Progression.}, booktitle = {Translational Control in Biology and Medicine.}, author = {Schneider, R.J.}, year = 2006, pages = {1⬚ ⬚-47}, publisher = {Cold Spring Harbor Press}, address = {Cold Spring Harbor, NY}, collaborator = {Mathews, M.B. and Hershey, J.W.B. and Sonenberg, N.}, keywords = {BIOLOGY,cancer,development,nosource} }

@article{schroederStructuresAntibioticsBound2007, title = {The Structures of Antibiotics Bound to the {{E}} Site Region of the 50 {{S}} Ribosomal Subunit of {{Haloarcula}} Marismortui: 13-Deoxytedanolide and Girodazole}, author = {Schroeder, S.J. and Blaha, G. and {Tirado-Rives}, J. and Steitz, T.A. and Moore, P.B.}, year = 2007, month = apr, journal = {Journal of molecular biology}, volume = {367}, number = {5}, pages = {1471–1479}, publisher = {Elsevier}, doi = {10.1016/j.jmb.2007.01.081}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283607001593}, abstract = {Crystal structures of the 50 S ribosomal subunit from Haloarcula marismortui complexed with two antibiotics have identified new sites at which antibiotics interact with the ribosome and inhibit protein synthesis. 13-Deoxytedanolide binds to the E site of the 50 S subunit at the same location as the CCA of tRNA, and thus appears to inhibit protein synthesis by competing with deacylated tRNAs for E site binding. Girodazole binds near the E site region, but is somewhat buried and may inhibit tRNA binding by interfering with conformational changes that occur at the E site. The specificity of 13-deoxytedanolide for eukaryotic ribosomes is explained by its extensive interactions with protein L44e, which is an E site component of archaeal and eukaryotic ribosomes, but not of eubacterial ribosomes. In addition, protein L28, which is unique to the eubacterial E site, overlaps the site occupied by 13-deoxytedanolide, precluding its binding to eubacterial ribosomes. Girodazole is specific for eukarytes and archaea because it makes interactions with L15 that are not possible in eubacteria}, keywords = {0,Anti-Bacterial Agents,antibiotic,antibiotics,Archaea,BINDING,BindingCompetitive,chemistry,COMPONENT,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,E,E site,Eubacterium,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,Haloarcula,Haloarcula marismortui,Hydrophobicity,Imidazoles,L15,La,LOCATION,Macrolides,metabolism,ModelsMolecular,nosource,Propanolamines,protein,Protein Binding,Protein StructureTertiary,Protein Subunits,protein synthesis,PROTEIN-SYNTHESIS,Proteins,REGION,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,S,SITE,SITES,SPECIFICITY,structure,SUBUNIT,SUBUNITS,Support,tRNA,tRNA binding} } % == BibTeX quality report for schroederStructuresAntibioticsBound2007: % ? unused Journal abbr (“J.Mol.Biol”)

@article{schulerGMCSFOncogeneMRNA1988a, title = {{{GM-CSF}} and Oncogene {{mRNA}} Stabilities Are Independently Regulated ⬚in Trans⬚ in a Mouse Monocytic Tumor.}, author = {Schuler, G.D. and Cole, M.D.}, year = 1988, journal = {Cell}, volume = {55}, pages = {1115–1122}, doi = {10.1016/0092-8674(88)90256-5}, keywords = {mRNA,nosource,oncogenes,stability} }

@article{schulerStructureRibosomeboundCricket2006, title = {Structure of the Ribosome-Bound Cricket Paralysis Virus {{IRES RNA}}}, author = {Schuler, M. and Connell, S.R. and Lescoute, A. and Giesebrecht, J. and Dabrowski, M. and Schroeer, B. and Mielke, T. and Penczek, P.A. and Westhof, E. and Spahn, C.M.}, year = 2006, month = dec, journal = {Nature Structural & Molecular Biology}, volume = {13}, number = {12}, pages = {1092–1096}, publisher = {Nature Publishing Group}, doi = {10.1038/nsmb1177}, url = {PM:17115051 http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb1177.html}, abstract = {Internal ribosome entry sites (IRESs) facilitate an alternative, end-independent pathway of translation initiation. A particular family of dicistroviral IRESs can assemble elongation-competent 80S ribosomal complexes in the absence of canonical initiation factors and initiator transfer RNA. We present here a cryo-EM reconstruction of a dicistroviral IRES bound to the 80S ribosome. The resolution of the cryo-EM reconstruction, in the subnanometer range, allowed the molecular structure of the complete IRES in its active, ribosome-bound state to be solved. The structure, harboring three pseudoknot-containing domains, each with a specific functional role, shows how defined elements of the IRES emerge from a compactly folded core and interact with the key ribosomal components that form the A, P and E sites, where tRNAs normally bind. Our results exemplify the molecular strategy for recruitment of an IRES and reveal the dynamic features necessary for internal initiation}, keywords = {COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,Cricket paralysis virus,DOMAIN,DOMAINS,E,E site,ELEMENTS,FAMILY,FORM,Germany,initiation,INITIATION-FACTOR,INTERNAL RIBOSOME ENTRY,La,Molecular Structure,nosource,PATHWAY,RECRUITMENT,RESOLUTION,ribosome,RIBOSOME ENTRY SITE,RIBOSOME ENTRY SITES,Rna,SITE,SITES,structure,TRANSFER-RNA,translation,TRANSLATION INITIATION,tRNA,virus} } % == BibTeX quality report for schulerStructureRibosomeboundCricket2006: % ? unused Journal abbr (“Nat.Struct.Mol.Biol.”)

@article{schultesEstimatingContributionsSelection1999, title = {Estimating the Contributions of Selection and Self-Organization in {{RNA}} Secondary Structure}, author = {Schultes, E.A. and Hraber, P.T. and LaBean, T.H.}, year = 1999, month = jul, journal = {Journal of molecular evolution}, volume = {49}, number = {1}, pages = {76–83}, publisher = {Springer}, doi = {10.1007/PL00006536}, url = {http://www.springerlink.com/index/w244drd0r097fgfg.pdf}, abstract = {In addition to characteristic structural properties imposed by evolutionary modification, evolved, single-stranded RNAs also display characteristic structural properties imposed by intrinsic physical constraints on RNA polymer folding. The balance of intrinsic and functionally selected characters in the folded conformation of evolved secondary structures was determined by comparing the predicted secondary structures of evolved and unevolved (random) RNA sequences. Though evolved conformations are significantly more ordered than conformations of random-sequence RNA, this analysis demonstrates that the majority of conformational order within evolved structures results not from evolutionary optimization but from constraints imposed by rules intrinsic to RNA polymer folding}, keywords = {Algorithms,analysis,CHARACTER,chemistry,Comparative Study,CONFORMATION,EvolutionMolecular,La,modification,nosource,Nucleic Acid Conformation,Random Allocation,Research SupportU.S.Gov’tNon-P.H.S.,Rna,RNA SECONDARY STRUCTURE,RULES,SECONDARY STRUCTURE,SELECTION,Selection (Genetics),sequence,SEQUENCES,Structural,structure} } % == BibTeX quality report for schultesEstimatingContributionsSelection1999: % ? unused Journal abbr (“J.Mol.Evol.”)

@article{schultzNucleotideSequenceTcm11983, title = {Nucleotide Sequence of the ⬚tcm1⬚ Gene (Ribosomal Protein {{L3}}) of ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Schultz, L.D. and Friesen, J.D.}, year = 1983, journal = {J.Bacteriol.}, volume = {155}, pages = {8–14}, doi = {10.1128/jb.155.1.8-14.1983}, abstract = {The yeast tcml gene, which codes for ribosomal protein L3, has been isolated by using recombinant DNA and genetic complementation. The DNA fragment carrying this gene has been subcloned and we have determined its DNA sequence. The 20 amino acid residues at the amino terminus as inferred from the nucleotide sequence agreed exactly with the amino acid sequence data. The amino acid composition of the encoded protein agreed with that determined for purified ribosomal protein L3. Codon usage in the tcml gene was strongly biased in the direction found for several other abundant Saccharomyces cerevisiae proteins. The tcml gene has no introns, which appears to be atypical of ribosomal protein structural genes.}, keywords = {Amino Acid Sequence,Codon,Dna,drugs,gene,Genes,Genetic,Introns,L3,nosource,protein,Proteins,ribosome,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,Structural,TCM1,yeast} } % == BibTeX quality report for schultzNucleotideSequenceTcm11983: % ? Possibly abbreviated journal title J.Bacteriol.

@article{schultzeMinimalSetRibosomal1982, title = {Minimal Set of Ribosomal Components for Reconstitution of the Peptidyltransferase Activity.}, author = {Schultze, H. and Nierhaus, K.H.}, year = 1982, journal = {the The European Molecular Biology Organization Journal}, volume = {5}, number = {5}, pages = {609–613}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1982.tb01216.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC553095/}, abstract = {A new approach is described to gain further information concerning the ribosomal components involved in the peptidyltransferase (PTF) activity exerted by Escherichia coli 50S subunits. A particle is reconstituted from highly purified proteins and RNA under modified incubation conditions. This particle contains only 16 out of the 34 distinct components constituting the native subunit, and yet still exhibits significant PTF activity. Single omission tests at the level of this “minimal ribosomal particle” indicate the limits set on a further reduction of the components, and in particular reveal that protein L18 can be excluded from the set of proteins which are essential for PTF activity, thus leaving L2, L3, L4, L15, and L16 as primary candidates for this function. 5S RNA is not needed for PTF activity of the “minimal ribosomal particle”. Furthermore, a buffer condition is described which drastically improves the stability of total protein preparations and facilitates the isolation of individual proteins.}, pmid = {6765232}, keywords = {0,84236022,Acyltransferases,COMPONENT,enzymology,Escherichia coli,ESCHERICHIA-COLI,isolation & purification,L2,L3,La,metabolism,nosource,peptidyl transferase,Peptidyltransferase,protein,Proteins,Ribosomal Proteins,ribosome,Ribosomes,Rna,stability,SUBUNIT,ultrastructure} } % == BibTeX quality report for schultzeMinimalSetRibosomal1982: % ? unused Journal abbr (“EMBO J.”)

@article{schwartzL657398Novel1988a, title = {L-657,398, a Novel Antifungal Agent: Fermentation, Isolation, Structural Elucidation and Biological Properties.}, author = {Schwartz, R.E. and Liesch, J. and Hensens, O. and Zitano, L. and Honeycutt, S. and Garrity, G. and Fromtling, R.A. and Onishi, J. and Monaghan, R.}, year = 1988, month = dec, journal = {The Journal of antibiotics}, volume = {41}, number = {12}, eprint = {3209471}, eprinttype = {pubmed}, pages = {1774–1779}, doi = {10.7164/antibiotics.41.1774}, url = {http://www.ncbi.nlm.nih.gov/pubmed/3209471}, abstract = {L-657,398 is a broad spectrum antifungal agent isolated from solid fermentation or from the mycelium of the liquid fermentation of Aspergillus ochraceus. Structurally, the compound is a novel pyrollidine related to anisomycin}, keywords = {0,analogs & derivatives,anisomycin,antibiotic,antibiotics,AntibioticsAntifungal,Aspergillus,chemistry,Fermentation,isolation & purification,La,metabolism,nosource,pharmacology,Pyrrolidines,Structural} } % == BibTeX quality report for schwartzL657398Novel1988a: % ? unused Journal abbr (“J.Antibiot.(Tokyo)”)

@article{scolnickReleaseFactorsDiffering1968, title = {Release Factors Differing in Specificity for Terminator Codons.}, author = {Scolnick, E. and Tompkins, R. and Caskey, T. and Nirenberg, M.}, year = 1968, journal = {Proceedings of the National Academy of Sciences}, volume = {61}, number = {2}, pages = {768–774}, publisher = {National Academy of Sciences}, doi = {10.1073/pnas.61.2.768}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC225226/}, keywords = {anisomycin,Codon,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,RELEASE FACTORS,ribosome,sparsomycin,termination} } % == BibTeX quality report for scolnickReleaseFactorsDiffering1968: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.USA”)

@article{scottMajorSpermProtein1989b, title = {Major Sperm Protein Genes from ⬚{{Onchocerca}} Volvulus⬚.}, author = {Scott, A.L. and Dinman, J.D. and Sussman, D.J. and Yenbutr, P. and Ward, S.}, year = 1989, journal = {Mol.Biochem.Parasitol.}, volume = {36}, pages = {119–126}, doi = {10.1016/0166-6851(89)90184-9}, keywords = {CV,gene,Genes,nosource,protein,worms} } % == BibTeX quality report for scottMajorSpermProtein1989b: % ? Possibly abbreviated journal title Mol.Biochem.Parasitol.

@article{scottMajorSpermProtein1989, title = {Major Sperm Protein and Actin Genes in Free-Living and Parasitic Nematodes.}, author = {Scott, A.L. and Dinman, J.D. and Sussman, D.J. and Ward, S.}, year = 1989, journal = {Parasitology}, volume = {98}, number = {03}, pages = {471–478}, publisher = {Cambridge Univ Press}, doi = {10.1017/S0031182000061564}, url = {http://journals.cambridge.org/abstract_S0031182000061564}, keywords = {CV,gene,Genes,nosource,protein,worms} }

@article{scottPreparationSpecifically2H2000a, title = {Preparation of Specifically {{2H-}} and {{13C-labeled}} Ribonucleotides}, author = {Scott, L.G. and Tolbert, T.J. and Williamson, J.R.}, year = 2000, journal = {Methods Enzymol.}, volume = {317}, pages = {18–38}, doi = {10.1016/S0076-6879(00)17004-1}, url = {PM:10829270}, keywords = {0,Carbon,Carbon Isotopes,chemical synthesis,chemistry,ChromatographyHigh Pressure Liquid,Deuterium,enzyme,Enzymes,Hiv-2,La,Magnetic Resonance Spectroscopy,nosource,Ribonucleotides,Rna,RnaViral,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for scottPreparationSpecifically2H2000a: % ? Possibly abbreviated journal title Methods Enzymol.

@article{scriptureAnalysisBindingXenopus1995a, title = {Analysis of the Binding of {{Xenopus}} Ribosomal Protein {{L5}} to Oocyte 5 {{S rRNA}}. {{The}} Major Determinants of Recognition Are Located in Helix {{III-}} Loop {{C}}}, author = {Scripture, J.B. and Huber, P.W.}, year = 1995, month = nov, journal = {J.Biol.Chem.}, volume = {270}, number = {45}, pages = {27358–27365}, doi = {10.1074/jbc.270.45.27358}, url = {PM:7592999}, abstract = {Xenopus ribosomal protein L5 was expressed in Escherichia coli and exhibits high affinity (Kd = 2 nM) and specificity for oocyte 5 S rRNA. The pH dependence of the association constant for the complex reveals an ionization with a pK alpha value of 10.1, indicating that tyrosine and/or lysine residues are important for specific binding of L5 to the RNA. Formation of the L5.5 S rRNA complex is remarkably insensitive to ionic strength, providing evidence that nonelectrostatic interactions make significant contributions to binding. Together, these results suggest that one or more tyrosine residues may form critical contacts through stacking interactions with bases in the RNA. In order to locate recognition elements within 5 S rRNA, we measured binding of L5 to a collection of site-specific mutants. Mutations in the RNA that affected the interaction are confined to the hairpin structure comprised of helix III and loop C. Earlier experiments with a rhodium structural probe had shown that the two-nucleotide bulge in helix III and the intrinsic structure of loop C create sites in the major groove that are opened and accessible to stacking interactions with the metal complex. In the present studies, we detect a correlation between the intercalative binding of the rhodium complex to mutants in the hairpin and binding of L5, supporting the proposal that binding of the protein is mediated, in some part, by stacking interactions. Furthermore, the results from mutagenesis establish that, despite overlapping binding sites on 5 S rRNA, L5 and transcription factor IIIA utilize distinct structural elements for recognition}, keywords = {0,analysis,animal,Base Sequence,BINDING,Binding Sites,chemistry,COMPLEX,COMPLEXES,Dna,DNA Primers,ELEMENTS,Escherichia coli,ESCHERICHIA-COLI,Female,genetics,Helix-Loop-Helix Motifs,HIV,Kinetics,L5,La,Lysine,metabolism,Molecular Sequence Data,Mutagenesis,MutagenesisSite-Directed,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Oocytes,protein,Protein Binding,Proteins,Recombinant Fusion Proteins,Ribosomal Proteins,Rna,RNARibosomal5S,rRNA,site specific,Structural,structure,supportu.s.gov’tp.h.s.,transcription,TRANSCRIPTION FACTOR,Xenopus,Xenopus laevis} } % == BibTeX quality report for scriptureAnalysisBindingXenopus1995a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{searfossLinking3PolyA2001, title = {Linking the 3 ’ Poly({{A}}) Tail to the Subunit Joining Step of Translation Initiation: {{Relations}} of {{Pab1p}}, Eukaryotic Translation Initiation Factor {{5B}} ({{Fun12p}}), and {{Ski2p-Slh1p}}}, author = {Searfoss, A. and Dever, T.E. and Wickner, R.}, year = 2001, journal = {Molecular and Cellular Biology}, volume = {21}, number = {15}, pages = {4900–4908}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.21.15.4900-4908.2001}, url = {http://mcb.asm.org/cgi/content/abstract/21/15/4900}, abstract = {The 3 ’ poly(A) structure improves translation of a eukaryotic mRNA by 50-fold in vivo. This enhancement has been suggested to be due to an interaction of the poly(A) binding protein, Pab1p, with eukaryotic translation initiation factor 4G (eIF4G), However, we find that mutation of eIF4G eliminating its interaction with Pab1p does not diminish the preference for poly(A)(+) mRNA in vivo, indicating another role for poly(A). We show that either the absence of Fun12p (eIF5B), or a defect in eIF5, proteins involved in 60S ribosomal subunit joining, specifically reduces the translation of poly(A)(+) mRNA, suggesting that poly(A) may have a role in promoting the joining step. Deletion of two nonessential putative RNA helicases (genes SKI2 and SLH1) makes poly(A) dispensable for translation. However, in the absence of Fun12p, eliminating Ski2p and Slh1p shows little enhancement of expression of non-poly(A) mRNA. This suggests that Ski2p and Slh1p block translation of non-poly(A) mRNA by an effect on Fun12p, possibly by affecting 60S subunit joining}, keywords = {3,60S subunit,ANTIVIRAL SYSTEM,BINDING,BINDING PROTEIN,BINDING-PROTEIN,DEPENDENT TRANSLATION,EIF5,EUKARYOTIC TRANSLATION,expression,FACTOR 4G,gene,Genes,Helicase,homolog,IDENTIFICATION,IN-VIVO,initiation,INITIATION-FACTOR,MESSENGER-RNA,mRNA,Mutation,nosource,poly(A),POLY(A) TAIL,protein,Proteins,RIBOSOMAL-SUBUNIT,Rna,RNA HELICASE,RNA Helicases,SACCHAROMYCES-CEREVISIAE,SKI2,structure,SUBUNIT,translation,TRANSLATION INITIATION,yeast} }

@article{searfoss3PolyDispensable2000, title = {3{\(\prime\)} Poly ({{A}}) Is Dispensable for Translation}, author = {Searfoss, A. M. and Wickner, R. B.}, year = 2000, journal = {Proceedings of the National Academy of Sciences}, volume = {97}, number = {16}, pages = {9133}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/97/16/9133.short}, abstract = {In wild-type cells, the 3’ poly(A) structure is necessary for translation of mRNA and for mRNA stability. The superkiller 2 (ski2), ski3, ski6, ski7, and ski8 mutations enhance the expression of the poly(A)(-) mRNAs of yeast RNA viruses. Ski2p is a DEVH-box RNA helicase and Slh1p resembles Ski2p. Both repress L-A double-stranded RNA (dsRNA) virus copy number, further suggesting that their functions may overlap. We find that slh1Delta ski2Delta double mutants are healthy (in the absence of viruses) and show normal rates of turnover of several cellular mRNAs. The slh1Delta ski2Delta strains translate electroporated nonpoly(A) mRNA with the same kinetics as polyA(+) mRNA. Thus, the translation apparatus is inherently capable of efficiently using nonpoly(A) mRNA even in the presence of normal amounts of competing poly(A)(+) mRNA, but is normally prevented from doing so by the combined action of the nonessential proteins Ski2p and Slh1p}, keywords = {0,3,Carrier Proteins,CELLS,CEREVISIAE,disease,DOUBLE-STRANDED-RNA,DSRNA,Exoribonucleases,expression,Fungal Proteins,Genetic,genetics,Helicase,human,Kidney,kinase,Kinetics,L-A,La,metabolism,mRNA,mRNA stability,MUTANTS,Mutation,MUTATIONS,nosource,Phosphoglycerate Kinase,Poly A,poly(A),protein,Proteins,Rna,RNA HELICASE,RNA Viruses,RNAMessenger,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SKI2,stability,structure,Trans-Activators,translation,TranslationGenetic,turnover,virus,WILD-TYPE,yeast} }

@article{searfossProteinSynthesisAssayed2002, title = {Protein Synthesis Assayed by Electroporation of {{mRNA}} in {{Saccharomyces}} Cerevisiae}, author = {Searfoss, A.M. and Masison, D.C.. and Wickner, R.B.}, year = 2002, journal = {Methods in enzymology}, volume = {351}, pages = {631–639}, publisher = {Elsevier}, doi = {10.1016/S0076-6879(02)51873-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0076687902518735}, keywords = {0,biosynthesis,CEREVISIAE,Electroporation,Fungal Proteins,genetics,La,library,metabolism,mRNA,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Review,Rna,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE} } % == BibTeX quality report for searfossProteinSynthesisAssayed2002: % ? unused Journal abbr (“Methods Enzymol.”)

@article{sedlackDNAMicroarrayAnalysis2003, title = {{{DNA}} Microarray Analysis of the Expression of the Genes Encoding the Major Enzymes in Ethanol Production during Glucose and Xylose Co-Fermentation by Metabolically Engineered ⬚{{Saccharomyces}}⬚ Yeast.}, author = {Sedlack, M. and Edenberg, H.J.}, year = 2003, journal = {Enzyme Microbial Technology}, volume = {33}, pages = {19–28}, doi = {10.1016/S0141-0229(03)00067-X}, keywords = {analysis,Dna,enzyme,Enzymes,Ethanol,expression,gene,Genes,Glucose,nosource,Saccharomyces,Xylose,yeast} }

@article{seipeltAlternativeProcessingIgA1995, title = {Alternative Processing of {{IgA}} Pre-{{mRNA}} Responds like {{IgM}} to Alterations in the Efficiency of the Competing Splice and Cleavage-Polyadenylation Reactions}, author = {Seipelt, R.L. and Peterson, M.L.}, year = 1995, month = mar, journal = {Molecular Immunology}, volume = {32}, number = {4}, pages = {277–285}, publisher = {Elsevier}, doi = {10.1016/0161-5890(94)00141-M}, url = {http://linkinghub.elsevier.com/retrieve/pii/016158909400141M}, keywords = {efficiency,expression,gene,Genes,immunology,MECHANISM,microbiology,modification,nosource,poly(A),protein,Proteins,regulation,Rna,splicing,structure} }

@article{sekineFrameshiftingRequiredProduction1989, title = {Frameshifting Is Required for Production of the Transposase Encoded by Insertion Sequence 1}, author = {Sekine, Y. and Ohtsubo, E.}, year = 1989, month = jun, journal = {Proceedings of the National Academy of Sciences}, volume = {86}, number = {12}, pages = {4609–4613}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.86.12.4609}, url = {http://www.pnas.org/content/86/12/4609.short}, abstract = {Insertion sequence IS1 has two coding frames, insA and insB, which are essential for its transposition. Here, we show that a frameshifting event in the -1 direction from the 3’ end region of the insA frame to an open reading frame (B’ frame), extending from the 5’ end of the insB frame, is involved in production of the InsA-B’-InsB fusion protein that has IS1 transposase activity. The frameshifting event is likely to have occurred at the sequence AAAAAC where the insA frame overlaps the B’ frame. Interestingly, this sequence is also present in one of the two sequences identified in retroviruses as frameshift signals for production of transframe polyproteins from the overlapping genes gag-pro or gag-pro-pol}, keywords = {0,3,Amino Acid Sequence,Base Sequence,Dna,DNA Transposable Elements,ELEMENTS,enzymology,Escherichia coli,FRAME,frameshift,Frameshifting,FUSION PROTEIN,gene,Genes,GenesBacterial,genetics,INSA,La,microbiology,Molecular Sequence Data,Mutation,nosource,Nucleotidyltransferases,OPEN READING FRAME,POLYPROTEIN,Polyproteins,protein,READING FRAME,REGION,Research SupportNon-U.S.Gov’t,Restriction Mapping,RETROVIRUSES,sequence,SEQUENCES,Shigella sonnei,SIGNAL,Transposases} } % == BibTeX quality report for sekineFrameshiftingRequiredProduction1989: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{selimogluAminoglycosideinducedOtotoxicity2007, title = {Aminoglycoside-Induced Ototoxicity}, author = {Selimoglu, E.}, year = 2007, journal = {Curr.Pharm.Des}, volume = {13}, number = {1}, pages = {119–126}, doi = {10.2174/138161207779313731}, url = {PM:17266591}, abstract = {It has long been known that the major irreversible toxicity of aminoglycosides is ototoxicity. Among them, streptomycin and gentamicin are primarily vestibulotoxic, whereas amikacin, neomycin, dihydrosterptomycin, and kanamicin are primarily cochleotoxic. Cochlear damage can produce permanent hearing loss, and damage to the vestibular apparatus results in dizziness, ataxia, and/or nystagmus. Aminoglycosides appear to generate free radicals within the inner ear, with subsequent permanent damage to sensory cells and neurons, resulting in permanent hearing loss. Two mutations in the mitochondrial 12S ribosomal RNA gene have been previously reported to predispose carriers to aminoglycoside-induced ototoxicity. As aminoglycosides are indispensable agents both in the treatment of infections and Meniere’s disease, a great effort has been made to develop strategies to prevent aminoglycoside ototoxicity. Anti-free radical agents, such as salicylate, have been shown to attenuate the ototoxic effects of aminoglycosides. In this paper, incidence, predisposition, mechanism, and prevention of aminoglycoside-induced ototoxicity is discussed in the light of literature data}, keywords = {0,administration & dosage,adverse effects,Aminoglycosides,Animals,Anti-Bacterial Agents,CELLS,chemically induced,cochlea,disease,Dose-Response RelationshipDrug,Drug Administration Schedule,drug effects,drug therapy,Free Radicals,gene,Genetic Predisposition to Disease,Genetic Screening,genetics,Hair Cells,Hearing Disorders,Humans,Incidence,INFECTION,La,MECHANISM,Meniere’s Disease,Mutation,MUTATIONS,Neomycin,Neurons,nosource,prevention & control,Review,ribosomal RNA,RIBOSOMAL-RNA,Risk Assessment,Risk Factors,Rna,RNARibosomal,Streptomycin,toxicity,Vestibule} } % == BibTeX quality report for selimogluAminoglycosideinducedOtotoxicity2007: % ? Possibly abbreviated journal title Curr.Pharm.Des

@article{selmerStructure70SRibosome2006, title = {Structure of the {{70S}} Ribosome Complexed with {{mRNA}} and {{tRNA}}}, author = {Selmer, M. and Dunham, C.M. and Murphy, F.V. and Weixlbaumer, A. and Petry, S. and Kelley, A.C. and Weir, J.R. and Ramakrishnan, V.}, year = 2006, month = sep, journal = {Science}, volume = {313}, number = {5795}, pages = {1935–1942}, publisher = {American Association for the Advancement of Science}, issn = {1095-9203}, doi = {10.1126/science.1131127}, url = {http://www.sciencemag.org/content/313/5795/1935.short}, abstract = {The crystal structure of the bacterial 70S ribosome refined to 2.8 angstrom resolution reveals atomic details of its interactions with messenger RNA (mRNA) and transfer RNA (tRNA). A metal ion stabilizes a kink in the mRNA that demarcates the boundary between A and P sites, which is potentially important to prevent slippage of mRNA. Metal ions also stabilize the intersubunit interface. The interactions of E-site tRNA with the 50S subunit have both similarities and differences compared to those in the archaeal ribosome. The structure also rationalizes much biochemical and genetic data on translation}, pmid = {16959973}, keywords = {0,70S RIBOSOME,ANGSTROM RESOLUTION,ANGSTROM-RESOLUTION,Anticodon,Bacterial,Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: metabolism,Bacterial: chemistry,Bacterial: metabolism,BIOLOGY,chemistry,Codon,crystal structure,CRYSTAL-STRUCTURE,Crystallization,Crystallography,CrystallographyX-Ray,E site,Genetic,interface,Ions,La,Magnesium,Magnesium: metabolism,Messenger,MESSENGER-RNA,Messenger: chemistry,Messenger: metabolism,Met,Met: chemistry,Met: metabolism,metabolism,Models,ModelsMolecular,Molecular,Molecular Biology,mRNA,nosource,Nucleic Acid Conformation,P SITE,P-SITE,P-SITES,peptidyl transferase,Peptidyl Transferases,Peptidyl Transferases: chemistry,Peptidyl Transferases: metabolism,PEPTIDYL-TRANSFERASE,Phe,Phe: chemistry,Phe: metabolism,protein,Protein Biosynthesis,Protein Conformation,Proteins,Research SupportN.I.H.Extramural,Research SupportNon-U.S.Gov’t,RESOLUTION,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: metabolism,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,Ribosomes: ultrastructure,Rna,RNA,RNABacterial,RNAMessenger,RNATransfer,RNATransferMet,RNATransferPhe,SITE,SITES,SLIPPAGE,structure,SUBUNIT,Thermus thermophilus,Thermus thermophilus: chemistry,Thermus thermophilus: ultrastructure,Transfer,TRANSFER-RNA,Transfer: chemistry,Transfer: metabolism,Transferases,translation,tRNA,ultrastructure,X-Ray} }

@article{semenkovAllostericThreesiteModel1996, title = {The “Allosteric Three-Site Model” of Elongation Cannot Be Confirmed in a Well-Defined Ribosome System from {{Escherichia}} Coli}, author = {Semenkov, Y.P. and Rodnina, M.V. and Wintermeyer, W.}, year = 1996, month = oct, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {93}, number = {22}, pages = {12183–12188}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.93.22.12183}, url = {http://www.pnas.org/content/93/22/12183.short}, keywords = {A-SITE,BINDING,Codon,COMPLEX,COMPLEXES,elongation,Escherichia coli,ESCHERICHIA-COLI,models,mRNA,nosource,P-SITE,polyamine,Polyamines,ribosome,Ribosomes,SYSTEM,translocation,tRNA} }

@article{senSodiumpotassiumSwitchFormation1990a, title = {A Sodium-Potassium Switch in the Formation of Four-Stranded {{G4-DNA}}}, author = {Sen, D. and Gilbert, W.}, year = 1990, month = mar, journal = {Nature}, volume = {344}, number = {6265}, pages = {410–414}, doi = {10.1038/344410a0}, url = {PM:2320109}, abstract = {Single-stranded complex guanine-rich DNA sequences from chromosomal telomeres and elsewhere can associate to form stable parallel four- stranded structures termed G4-DNA by a process that is anomalously dependent on the particular alkali metal cation that is present. The anomaly, which is not found in the formation of G4-DNA by oligonucleotides containing short, single runs of three or more guanines, is caused by potassium cations excessively stabilizing fold- back intermediate structures, or pathway by-products}, keywords = {0,animal,Base Sequence,Cations,CationsMonovalent,Chromosomes,COMPLEX,COMPLEXES,development,Dna,Electrophoresis,genetics,Guanine,La,Macromolecular Systems,Methylation,Molecular Sequence Data,nosource,Oligonucleotides,pharmacology,Potassium,Repetitive SequencesNucleic Acid,sequence,SEQUENCES,Sodium,structure,supportu.s.gov’tp.h.s.,SYSTEM,Telomere,Tetrahymena} }

@article{senguptaThreehybridSystemDetect1996a, title = {A Three-Hybrid System to Detect {{RNA-protein}} Interactions in Vivo}, author = {SenGupta, D.J. and Zhang, B. and Kraemer, B. and Pochart, P. and Fields, S. and Wickens, M.}, year = 1996, month = aug, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {93}, number = {16}, pages = {8496–8501}, doi = {10.1073/pnas.93.16.8496}, keywords = {3-hybrid,analysis,BINDING,development,gene,Genes,Genetic,genetics,HIV,IDENTIFICATION,IN-VIVO,Methods,microbiology,mRNA,nosource,protein,Proteins,Rna,RNA Viruses,RNA-Binding Proteins,sequence,SYSTEM,transcription,translation,yeast} }

@article{senguptaIdentificationVersatileScaffold2004, title = {Identification of the Versatile Scaffold Protein {{RACK1}} on the Eukaryotic Ribosome by Cryo-{{EM}}}, author = {Sengupta, J. and Nilsson, J. and Gursky, R. and Spahn, C.M. and Nissen, P. and Frank, J.}, year = 2004, month = oct, journal = {Nature structural & molecular biology}, volume = {11}, number = {10}, pages = {957–962}, publisher = {Nature Publishing Group}, doi = {10.1038/nsmb822}, url = {http://www.nature.com/nsmb/journal/v11/n10/abs/nsmb822.html}, abstract = {RACK1 serves as a scaffold protein for a wide range of kinases and membrane-bound receptors. It is a WD-repeat family protein and is predicted to have a beta-propeller architecture with seven blades like a Gbeta protein. Mass spectrometry studies have identified its association with the small subunit of eukaryotic ribosomes and, most recently, it has been shown to regulate initiation by recruiting protein kinase C to the 40S subunit. Here we present the results of a cryo-EM study of the 80S ribosome that positively locate RACK1 on the head region of the 40S subunit, in the immediate vicinity of the mRNA exit channel. One face of RACK1 exposes the WD-repeats as a platform for interactions with kinases and receptors. Using this platform, RACK1 can recruit other proteins to the ribosome}, keywords = {0,ASSOCIATION,Cryoelectron Microscopy,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,FAMILY,GTP-Binding Proteins,human,IDENTIFICATION,initiation,kinase,KINASE-C,La,Mass Spectrometry,metabolism,ModelsMolecular,mRNA,Neoplasm Proteins,nosource,protein,Protein Binding,Protein Kinase C,PROTEIN-KINASE,Proteins,ReceptorsCell Surface,REGION,ribosome,Ribosomes,SUBUNIT,Support} } % == BibTeX quality report for senguptaIdentificationVersatileScaffold2004: % ? unused Journal abbr (“Nat.Struct.Mol.Biol.”)

@article{sergievEnvironment5SRRNA1998, title = {The Environment of {{5S rRNA}} in the Ribosome: Cross-Links to the {{GTPase-}} Associated Area of {{23S rRNA}}}, author = {Sergiev, P. and Dokudovskaya, S. and Romanova, E. and Topin, A. and Bogdanov, A. and Brimacombe, R. and Dontsova, O.}, year = 1998, month = jun, journal = {Nucleic acids research}, volume = {26}, number = {11}, pages = {2519–2525}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/26.11.2519}, url = {http://nar.oxfordjournals.org/content/26/11/2519.short}, abstract = {Two photoreactive diazirine derivatives of uridine were used to study contacts between 5S rRNA and 23 rRNA in situ in Escherichia coli ribosomes. 2’-Amino-2’-deoxy-uridine or 5-methyleneaminouridine were introduced into 5S rRNA by T7 transcription. After incorporation of these uridine analogues into the transcript their amino groups were modified with 4-[3-(trifluoromethyl)-3 H -diazirin-3-yl]benzyl isothiocyanate or the N -hydroxysuccinimide ester of 4-[3- (trifluoromethyl)-3 H -diazirin-3-yl]benzoic acid respectively. 5S rRNA carrying the photoreactive diazirine groups (referred to as the 2’- aminoribose derivative and the 5-methyleneamino derivative respectively) was reconstituted into 50S subunits or 70S ribosomes. After mild UV irradiation cross-links formed to 23S rRNA were analysed by standard procedures. All of the observed cross-links involved residue U89 of the 5S rRNA. Three nucleotides of 23S rRNA were cross- linked to this residue with the 5-methyleneamino derivative, namely U958, G1022 and G1138. With the 2’-aminoribose derivative a single cross-link was found, to U958. The significance of these cross-links for our understanding of the structure and function of 5S rRNA and its environment in the ribosome are discussed}, keywords = {5S rRNA,98256417,analogs & derivatives,Base Sequence,Binding Sites,chemistry,Cross-Linking Reagents,Deoxyuridine,derivatives,Escherichia coli,ESCHERICHIA-COLI,GTP Phosphohydrolase,GTPase,metabolism,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleotides,ribosome,Ribosomes,RNABacterial,RNARibosomal23S,RNARibosomal5S,rRNA,structure,SUBUNIT,supportnon-u.s.gov’t,transcription,Uridine,Uridine Triphosphate} } % == BibTeX quality report for sergievEnvironment5SRRNA1998: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{sergievCorrelatingXrayStructures2001a, title = {Correlating the {{X-ray}} Structures for Halo- and Thermophilic Ribosomal Subunits with Biochemical Data for the {{Escherichia}} Coli Ribosome}, author = {Sergiev, P. and Leonov, A. and Dokudovskaya, S. and Shpanchenko, O. and Dontsova, O. and Bogdanov, A. and {Rinke-Appel}, J. and Mueller, F. and Osswald, M. and {}{von Knoblauch}, K. and Brimacombe, R.}, year = 2001, journal = {Cold Spring Harb.Symp.Quant.Biol.}, volume = {66:87-100.}, pages = {87–100}, doi = {10.1101/sqb.2001.66.87}, keywords = {chemistry,CrystallographyX-Ray,Escherichia coli,ESCHERICHIA-COLI,ModelsMolecular,nosource,Nucleic Acid Conformation,Protein Conformation,Review,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,RNARibosomal,structure,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,ultrastructure} } % == BibTeX quality report for sergievCorrelatingXrayStructures2001a: % ? Possibly abbreviated journal title Cold Spring Harb.Symp.Quant.Biol.

@article{sergievPathMRNABacterial1997, title = {The Path of {{mRNA}} through the Bacterial Ribosome: A Site-Directed Crosslinking Study Using New Photoreactive Derivatives of Guanosine and Uridine.}, author = {Sergiev, P.V. and Lavrik, I.N. and Wlasoff, V.A. and Dokudovskaya, S.S. and Dontsova, O.A. and Bogdanov, A.A. and Brimacombe, R.}, year = 1997, month = may, journal = {RNA}, volume = {3}, number = {5}, pages = {464–475}, publisher = {Cold Spring Harbor Laboratory Press}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1369497/}, abstract = {Two new photoreactive nucleotide derivatives have been applied in site- directed crosslinking studies with mRNA analogues. 6-Thioguanosine triphosphate or 5-methyleneaminouridine triphosphate was incorporated into mRNA analogues by T7 transcription; after transcription, the 5- methyleneaminouridine residues were converted to a diazirine derivative. mRNA analogues carrying either 6-thioguanosine or the diazirine derivative were bound to Escherichia coli ribosomes in the presence of tRNA(f)(Met), and photo-crosslinking was induced by irradiation at 350 nm. With 6-thioguanosine, specific crosslinks were observed from downstream positions +8 or +9 of the mRNA to nt 1196 in helix 34 of the 16S rRNA, and from position +12 to nt 530 in helix 18. With the diazirine derivative, a crosslink from position +2 (within the AUG codon) to nt 926 in helix 28 was found. Taken together with previous data obtained from downstream sites in mRNA analogues carrying 4-thiouridine residues, specific crosslinks have now been identified from downstream mRNA positions +2, +4, +6, +7, +8, +9, +11, and +12. The data confirm that the three 16S rRNA regions involved-helices 18, 28, and 34-are in the direct neighborhood of the decoding area of the 30S subunit}, keywords = {0,analogs & derivatives,Bacterial,Bacteriophage T7,Base Sequence,biosynthesis,chemical synthesis,chemistry,Codon,CROSS-LINKING,Cross-Linking Reagents,decoding,derivatives,Escherichia coli,ESCHERICHIA-COLI,Guanosine,Guanosine Triphosphate,La,metabolism,Molecular Sequence Data,mRNA,No DOI found,nosource,Nucleic Acid Conformation,ribosome,Ribosomes,Rna,RNABacterial,RNAMessenger,RNARibosomal16S,RNATransferMet,rRNA,SUBUNIT,supportnon-u.s.gov’t,Thionucleotides,transcription,TranscriptionGenetic,Uridine,Uridine Triphosphate} }

@article{sergievStructureDecodingCenter1998a, title = {Structure of the Decoding Center of the Ribosome.}, author = {Sergiev, P.V. and Lavrik, I.N. and Dokudovskaya, S.S. and Dontsova, O.A. and Bogdanov, A.A.}, year = 1998, journal = {Biochemistry. Biokhimii͡a}, volume = {63}, number = {8}, eprint = {9767188}, eprinttype = {pubmed}, pages = {963–976}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9767188}, abstract = {The decoding center of the ribosome provides mRNA translation and the fidelity of the codon–anticodon interactions along with mRNA translocation in the course of protein biosynthesis. The three- dimensional structure of the ribosome decoding center is still unknown. However, up to now a number of direct and indirect experimental data on the structural and functional organization of the decoding center have been obtained. In this paper the main components of the decoding center are described on the basis of our own experimental results combined with data from the literature. A model of their spatial arrangement at the small ribosomal subunit is suggested}, keywords = {0,Base Sequence,biosynthesis,chemistry,COMPONENT,decoding,elongation,Fidelity,genetics,La,metabolism,ModelsMolecular,ModelsStructural,Molecular Sequence Data,mRNA,No DOI found,nosource,Nucleic Acid Conformation,Peptide Elongation Factors,protein,Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNAMessenger,RNARibosomal,RNARibosomal16S,Structural,structure,SUBUNIT,supportnon-u.s.gov’t,translation,TranslationGenetic,translocation,ultrastructure} } % == BibTeX quality report for sergievStructureDecodingCenter1998a: % ? Possibly abbreviated journal title Biochemistry. Biokhimii͡a % ? unused Journal abbr (“Biochemistry (Mosc.)”)

@article{sergievMutationsPositionA9602000a, title = {Mutations at Position {{A960}} of {{E}}. Coli 23 {{S}} Ribosomal {{RNA}} Influence the Structure of 5 {{S}} Ribosomal {{RNA}} and the Peptidyltransferase Region of 23 {{S}} Ribosomal {{RNA}}}, author = {Sergiev, P.V. and Bogdanov, A.A. and Dahlberg, A.E. and Dontsova, O.}, year = 2000, month = jun, journal = {J.Mol.Biol.}, volume = {299}, number = {2}, pages = {379–389}, doi = {10.1006/jmbi.2000.3739}, abstract = {The proximity of loop D of 5 S rRNA to two regions of 23 S rRNA, domain II involved in translocation and domain V involved in peptide bond formation, is known from previous cross-linking experiments. Here, we have used site-directed mutagenesis and chemical probing to further define these contacts and possible sites of communication between 5 S and 23 S rRNA. Three different mutants were constructed at position A960, a highly conserved nucleotide in domain II previously crosslinked to 5 S rRNA, and the mutant rRNAs were expressed from plasmids as homogeneous populations of ribosomes in Escherichia coli deficient in all seven chromosomal copies of the rRNA operon. Mutations A960U, A960G and, particularly, A960C caused structural rearrangements in the loop D of 5 S rRNA and in the peptidyltransferase region of domain V, as well as in the 960 loop itself. These observations support the proposal that loop D of 5 S rRNA participates in signal transmission between the ribosome centers responsible for peptide bond formation and translocation}, keywords = {20318772,Aldehydes,analogs &,Base Sequence,Binding Sites,chemistry,CME-Carbodiimide,CROSS-LINKING,derivatives,development,Escherichia coli,ESCHERICHIA-COLI,GenesBacterial,genetics,growth &,GTP Phosphohydrolases,metabolism,Molecular Sequence Data,Mutagenesis,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Operon,Peptidyltransferase,Phenotype,PLASMID,Plasmids,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNA-Binding Proteins,RNABacterial,RNARibosomal23S,RNARibosomal5S,RNATransfer,rRNA,rRNA Operon,SIGNAL,Structural,structure,Structure-Activity Relationship,Sulfuric Acid Esters,Support,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,TranslationGenetic,translocation} } % == BibTeX quality report for sergievMutationsPositionA9602000a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{sergievAlterationLocationConserved2005, title = {Alteration in Location of a Conserved {{GTPase-associated}} Center of the Ribosome Induced by Mutagenesis Influences the Structure of Peptidyltransferase Center and Activity of Elongation Factor {{G}}}, author = {Sergiev, P.V. and Lesnyak, D.V. and Burakovsky, D.E. and Kiparisov, S.V. and Leonov, A.A. and Bogdanov, A.A. and Brimacombe, R. and Dontsova, O.A.}, year = 2005, journal = {Journal of Biological Chemistry}, volume = {280}, number = {36}, pages = {31882–31889}, publisher = {ASBMB}, doi = {10.1074/jbc.M505670200}, url = {http://www.jbc.org/content/280/36/31882.short}, abstract = {Translocation catalyzed by elongation factor G occurs after the peptidyltransferase reaction on the large ribosomal subunit. Deacylated tRNA in the P-site stimulates multiple turnover GTPase activity of EF-G. We suggest that the allosteric signal from the peptidyltransferase center that activates EF-G may involve the alteration in the conformation of elongation factor binding center of the ribosome. The latter consists of the moveable GTPase-associated center and the sarcin-ricin loop that keeps its position on the ribosome during translation elongation. The position of the GTPase-associated center was altered by mutagenesis. An insertion of additional base pair at positions C1030/G1124 was lethal and affected function of EF-G, but not that of EF-Tu. Structure probing revealed a putative allosteric signal pathway connecting the P-site with the binding site of the elongation factors. The results are consistent with the different structural requirements for EF-G and EF-Tu function, where the integrity of the path between the peptidyltransferase center and both GTPase-associated center and sarcin-ricin loop is important for EF-G binding}, keywords = {0,BASE,BASE-PAIR,BINDING,Binding Sites,BINDING-SITE,BIOLOGY,chemistry,CONFORMATION,Conserved Sequence,Deinococcus,EF-G,EFTu,elongation,elongation factors,ELONGATION-FACTOR-G,ELONGATION-FACTORS,genetics,GTP,GTP Phosphohydrolase,GTP Phosphohydrolases,GTPase,GTPASE ACTIVITY,Haloarcula marismortui,La,LOCATION,LOOP,metabolism,Mutagenesis,Mutation,nosource,Nucleic Acid Conformation,P SITE,P-SITE,PATHWAY,Peptide Elongation Factor G,peptidyl transferase,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,physiology,POSITION,POSITIONS,Protein StructureTertiary,Research SupportNon-U.S.Gov’t,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNARibosomal23S,RNATransfer,SARCIN RICIN LOOP,SIGNAL,SITE,Structural,structure,SUBUNIT,Transferases,translation,translocation,tRNA,turnover} } % == BibTeX quality report for sergievAlterationLocationConserved2005: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{sergievHowCanElongation2005, title = {How Can Elongation Factors {{EF-G}} and {{EF-Tu}} Discriminate the Functional State of the Ribosome Using the Same Binding Site?}, author = {Sergiev, P.V. and Bogdanov, A.A. and Dontsova, O.A.}, year = 2005, month = oct, journal = {FEBS letters}, volume = {579}, number = {25}, pages = {5439–5442}, publisher = {Elsevier}, doi = {10.1016/j.febslet.2005.09.010}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579305011038}, abstract = {Elongation factors EF-G and EF-Tu are structural homologues and share near-identical binding sites on the ribosome, which encompass the GTPase-associated centre (GAC) and the sarcin-ricin loop (SRL). The SRL is fixed structure in the ribosome and contacts elongation factors in the vicinity of their GTP-binding site. In contrast, the GAC is mobile and we hypothesize that it interacts with the alpha helix D of the EF-Tu G-domain in the same way as with the alpha helix A of the G’-domain of EF-G. The mutual locations of these helices and GTP-binding sites in the structures of EF-Tu and EF-G are different. Thus, the orientation of the GAC relative to the SRL determines whether EF-G or EF-Tu will bind to the ribosome}, keywords = {0,ALPHA-SARCIN,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,chemistry,D,EF-G,EFTu,elongation,elongation factors,ELONGATION-FACTOR-G,ELONGATION-FACTOR-TU,ELONGATION-FACTORS,Endoribonucleases,FACTOR TU,Fungal Proteins,GTP,GTP Phosphohydrolase,GTP Phosphohydrolases,La,LOCATION,LOOP,metabolism,nosource,Peptide Elongation Factor G,Peptide Elongation Factor Tu,protein,Protein Conformation,Proteins,Research SupportNon-U.S.Gov’t,Review,ribosome,Ribosomes,SARCIN RICIN LOOP,SITE,SITES,Structural,structure,TU} } % == BibTeX quality report for sergievHowCanElongation2005: % ? unused Journal abbr (“FEBS Lett.”)

@article{serinIdentificationCharacterizationHuman2001, title = {Identification and Characterization of Human Orthologues to Saccharomyces Cerevisiae Upf2 Protein and Upf3 Protein ({{Caenorhabditis}} Elegans {{SMG-4}}).}, author = {Serin, G. and Gersappe, A. and Black, J.D. and Aronoff, R. and Maquat, L.E.}, year = 2001, month = jan, journal = {Molecular and Cellular Biology}, volume = {21}, number = {1}, pages = {209–223}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.21.1.209-223.2001}, url = {http://mcb.asm.org/cgi/content/abstract/21/1/209}, abstract = {Nonsense-mediated mRNA decay (NMD), also called mRNA surveillance, is an important pathway used by all organisms that have been tested to degrade mRNAs that prematurely terminate translation and, as a consequence, eliminate the production of aberrant proteins that could be potentially harmful. In mammalian cells, NMD appears to involve splicing-dependent alterations to mRNA as well as ribosome-associated components of the translational apparatus. To date, human (h) Upf1 protein (p) (hUpf1p), a group 1 RNA helicase named after its Saccharomyces cerevisiae orthologue that functions in both translation termination and NMD, has been the only factor shown to be required for NMD in mammalian cells. Here, we describe human orthologues to S. cerevisiae Upf2p and S. cerevisiae Upf3p (Caenorhabditis elegans SMG-4) based on limited amino acid similarities. The existence of these orthologues provides evidence for a higher degree of evolutionary conservation of NMD than previously appreciated. Interestingly, human orthologues to S. cerevisiae Upf3p (C. elegans SMG-4) derive from two genes, one of which is X-linked and both of which generate multiple isoforms due to alternative pre-mRNA splicing. We demonstrate using immunoprecipitations of epitope-tagged proteins transiently produced in HeLa cells that hUpf2p interacts with hUpf1p, hUpf3p-X, and hUpf3p, and we define the domains required for the interactions. Furthermore, we find by using indirect immunofluorescence that hUpf1p is detected only in the cytoplasm, hUpf2p is detected primarily in the cytoplasm, and hUpf3p-X localizes primarily to nuclei. The finding that hUpf3p-X is a shuttling protein provides additional indication that NMD has both nuclear and cytoplasmic components}, keywords = {20565755,Caenorhabditis,Caenorhabditis elegans,cancer,COMPONENT,Cytoplasm,DECAY,gene,Genes,Genetic,genetics,Hela Cells,Helicase,human,IDENTIFICATION,mRNA,mRNA decay,NMD,nosource,protein,Proteins,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,splicing,termination,translation,TRANSLATION TERMINATION,Upf1,UPF3} } % == BibTeX quality report for serinIdentificationCharacterizationHuman2001: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{seshadriGeneticStudiesPRP171996, title = {Genetic Studies of the {{PRP17}} Gene of {{Saccharomyces}} Cerevisiae: A Domain Essential for Function Maps to a Nonconserved Region of the Protein}, author = {Seshadri, V. and Vaidya, V.C. and Vijayraghavan, U.}, year = 1996, month = may, journal = {Genetics}, volume = {143}, number = {1}, pages = {45–55}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/143.1.45}, url = {http://www.genetics.org/cgi/content/abstract/143/1/45}, keywords = {Alleles,Amino Acids,analysis,gene,Genetic,In Vitro,IN-VITRO,IN-VIVO,mRNA,Mutation,MUTATIONS,nosource,Phenotype,protein,prp17,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,splicing} }

@article{sharmaEFGindependentReactivityPretranslocationstate2004, title = {{{EF-G-independent}} Reactivity of a Pre-Translocation-State Ribosome Complex with the Aminoacyl {{tRNA}} Substrate Puromycin Supports an Intermediate (Hybrid) State of {{tRNA}} Binding}, author = {Sharma, D. and Southworth, D.R. and Green, R.}, year = 2004, month = jan, journal = {RNA}, volume = {10}, number = {1}, pages = {102–113}, publisher = {Cold Spring Harbor Lab}, doi = {10.1261/rna.5148704}, url = {http://rnajournal.cshlp.org/content/10/1/102.short}, abstract = {Following peptide-bond formation, the mRNA:tRNA complex must be translocated within the ribosomal cavity before the next aminoacyl tRNA can be accommodated in the A site. Previous studies suggested that following peptide-bond formation and prior to EF-G recognition, the tRNAs occupy an intermediate (hybrid) state of binding where the acceptor ends of the tRNAs are shifted to their next sites of occupancy (the E and P sites) on the large ribosomal subunit, but where their anticodon ends (and associated mRNA) remain fixed in their prepeptidyl transferase binding states (the P and A sites) on the small subunit. Here we show that pre-translocation-state ribosomes carrying a dipeptidyl-tRNA substrate efficiently react with the minimal A-site substrate puromycin and that following this reaction, the pre-translocation-state bound deacylated tRNA:mRNA complex remains untranslocated. These data establish that pre-translocation-state ribosomes must sample or reside in an intermediate state of tRNA binding independent of the action of EF-G}, keywords = {0,A SITE,A-SITE,A-SITES,Anticodon,BINDING,BIOLOGY,Chimera,Comparative Study,COMPLEX,COMPLEXES,E,EF-G,elongation,ELONGATION-FACTOR-G,Escherichia coli,Genetic,genetics,INTERMEDIATE,Kinetics,La,metabolism,mRNA,MutagenesisSite-Directed,Mutation,nosource,P and A sites,P SITE,P-SITE,P-SITES,peptide bond formation,Peptide Chain Elongation,Peptide Elongation Factor G,PEPTIDE-BOND FORMATION,Peptidyltransferase,Puromycin,RECOGNITION,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNAMessenger,RNATransferAmino Acyl,RNATransferMet,SITE,SITES,SUBUNIT,Support,supportnon-u.s.gov’t,TranslationGenetic,Translocation (Genetics),tRNA,tRNA binding,Trypanocidal Agents} }

@article{sharmaMutationalAnalysisS122007, title = {Mutational Analysis of {{S12}} Protein and Implications for the Accuracy of Decoding by the Ribosome}, author = {Sharma, D. and Cukras, A.R. and Rogers, E.J. and Southworth, D.R. and Green, R.}, year = 2007, month = dec, journal = {Journal of molecular biology}, volume = {374}, number = {4}, pages = {1065–1076}, publisher = {Elsevier}, doi = {10.1016/j.jmb.2007.10.003}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283607013071}, abstract = {The fidelity of aminoacyl-tRNA selection by the ribosome depends on a conformational switch in the decoding center of the small ribosomal subunit induced by cognate but not by near-cognate aminoacyl-tRNA. The aminoglycosides paromomycin and streptomycin bind to the decoding center and induce related structural rearrangements that explain their observed effects on miscoding. Structural and biochemical studies have identified ribosomal protein S12 (as well as specific nucleotides in 16S ribosomal RNA) as a critical molecular contributor in distinguishing between cognate and near-cognate tRNA species as well as in promoting more global rearrangements in the small subunit, referred to as “closure.” Here we use a mutational approach to define contributions made by two highly conserved loops in S12 to the process of tRNA selection. Most S12 variant ribosomes tested display increased levels of fidelity (a “restrictive” phenotype). Interestingly, several variants, K42A and R53A, were substantially resistant to the miscoding effects of paromomycin. Further characterization of the compromised paromomycin response identified a probable second, fidelity-modulating binding site for paromomycin in the 16S ribosomal RNA that facilitates closure of the small subunit and compensates for defects associated with the S12 mutations}, keywords = {16S,accuracy,Aminoglycosides,analysis,BINDING,BINDING-SITE,BIOLOGY,CONSERVED LOOP,decoding,Fidelity,Genetic,genetics,La,LOOP,Molecular Biology,Mutation,MUTATIONAL ANALYSIS,MUTATIONS,nosource,Nucleotides,Paromomycin,Phenotype,protein,PROTEIN-S12,RESISTANT,ribosomal RNA,RIBOSOMAL-PROTEIN,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,SELECTION,SITE,Streptomycin,Structural,SUBUNIT,tRNA} } % == BibTeX quality report for sharmaMutationalAnalysisS122007: % ? unused Journal abbr (“J.Mol Biol”)

@article{sharpRegulationAdenovirusMRNA1980, title = {Regulation of Adenovirus {{mRNA}} Synthesis}, author = {Sharp, P.A. and Manley, J. and Fire, A. and Gefter, M.}, year = 1980, journal = {Ann.N.Y.Acad.Sci.}, volume = {354}, pages = {1–15}, doi = {10.1111/j.1749-6632.1980.tb27954.x}, abstract = {The lytic cycle of adenovirus is a tightly regulated sequence of stages. When this regulation is studied at the level of mRNA production, the most significant step in controlling gene expression is initiation of transcription. Thus in preceding from one stage of expression to another, viral factors seem to turn on transcription of new sets of genes. At the moment, it is thought that viral mRNA synthesis involves initiation of transcription at ten different promoter sites. It is likely that in some manner the frequency of an initiation of transcription at nine of these sites is affected by one or more viral gene products. With the recent development of soluble in vitro transcription systems that respond to exogenously added DNA, it should be possible to begin to study regulation of gene expression at this stage of transcription. At present, these systems yield the paradoxical observation that extracts prepared from uninfected human cells more efficiently recognize the late promoter as compared to the early promoter of adenovirus. As more is learned about regulation of synthesis of viral mRNAs, examples will surely be found where RNA processing and RNA turnover play a critical role in determining the level of mRNAs. Such cases are more likely to appear in the balancing of synthesis of different mRNAs derived from one transcriptional unit. Few experiments have been directed to this possibility and the study of adenovirus molecular biology is only now entering the age of maturity where these experiments are feasible}, keywords = {81182525,AdenovirusesHuman,biosynthesis,Cell Line,development,Dna,DNA Replication,expression,gene,Gene Expression,Gene Expression Regulation,GENE-EXPRESSION,Genes,GenesViral,genetics,growth &,human,In Vitro,in vitro transcription,IN-VITRO,initiation,metabolism,mRNA,nosource,PROMOTER,regulation,Rna,RNAMessenger,RnaViral,sequence,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,SYSTEM,transcription,TranscriptionGenetic,TranslationGenetic,turnover,Virus Replication} } % == BibTeX quality report for sharpRegulationAdenovirusMRNA1980: % ? Possibly abbreviated journal title Ann.N.Y.Acad.Sci.

@article{sheju-shilagaMaintenanceGagGagPol2001, title = {Maintenance of the {{Gag}}/{{Gag-Pol}} Ratio Is Important for Human Immunodeficiency Virus Type 1 {{RNA}} Dimerization and Viral Infectivity.}, author = {{Sheju-Shilaga}, M. and Crowe, S.M. and Mak, J.}, year = 2001, month = feb, journal = {Journal of virology}, volume = {75}, number = {4}, pages = {1834–1841}, publisher = {Am Soc Microbiol}, doi = {10.1128/JVI.75.4.1834-1841.2001}, url = {http://jvi.asm.org/cgi/content/abstract/75/4/1834}, keywords = {Gag,Gag/Gag-pol ratio,HIV,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,nosource,pol,retrovirus,Rna,virus} } % == BibTeX quality report for sheju-shilagaMaintenanceGagGagPol2001: % ? unused Journal abbr (“J.Virol.”)

@article{shenviAccessibility18SRRNA2005a, title = {Accessibility of {{18S rRNA}} in Human {{40S}} Subunits and {{80S}} Ribosomes at Physiological Magnesium Ion Concentrations–Implications for the Study of Ribosome Dynamics}, author = {Shenvi, C.L. and Dong, K.C. and Friedman, E.M. and Hanson, J.A. and Cate, J.H.}, year = 2005, month = dec, journal = {RNA.}, volume = {11}, number = {12}, pages = {1898–1908}, doi = {10.1261/rna.2192805}, url = {PM:16314459}, abstract = {Protein biosynthesis requires numerous conformational rearrangements within the ribosome. The structural core of the ribosome is composed of RNA and is therefore dependent on counterions such as magnesium ions for function. Many steps of translation can be compromised or inhibited if the concentration of Mg(2+) is too low or too high. Conditions previously used to probe the conformation of the mammalian ribosome in vitro used high Mg(2+) concentrations that we find completely inhibit translation in vitro. We have therefore probed the conformation of the small ribosomal subunit in low concentrations of Mg(2+) that support translation in vitro and compared it with the conformation of the 40S subunit at high Mg(2+) concentrations. In low Mg(2+) concentrations, we find significantly more changes in chemical probe accessibility in the 40S subunit due to subunit association or binding of the hepatitis C internal ribosomal entry site (HCV IRES) than had been observed before. These results suggest that the ribosome is more dynamic in its functional state than previously appreciated}, keywords = {0,ASSOCIATION,BINDING,biosynthesis,chemical probing,chemistry,Comparative Study,CONFORMATION,drug effects,DYNAMICS,genetics,HEPATITIS-C,human,Humans,In Vitro,IN-VITRO,INTERNAL RIBOSOMAL ENTRY,internal ribosomal entry site,Ions,La,Magnesium,metabolism,ModelsGenetic,ModelsMolecular,nosource,Nucleic Acid Conformation,pharmacology,protein,Protein Biosynthesis,protein synthesis,PROTEIN-BIOSYNTHESIS,REQUIRES,RIBOSOMAL-SUBUNIT,ribosome,ribosome dynamics,Ribosomes,Rna,RNAMessenger,RNARibosomal,RNARibosomal18S,rRNA,SITE,Structural,SUBUNIT,subunit association,SUBUNITS,Support,translation,translation initiation} } % == BibTeX quality report for shenviAccessibility18SRRNA2005a: % ? Possibly abbreviated journal title RNA.

@article{shinUncouplingInitiationFactor2002, title = {Uncoupling of Initiation Factor {{eIF5B}}/{{IF2 GTPase}} and Translational Activities by Mutations That Lower Ribosome Affinity}, author = {Shin, B.S. and Maag, D. and {Roll-Mecak}, A. and Arefin, M.S. and Burley, S.K. and Lorsch, J.R. and Dever, T.E.}, year = 2002, month = dec, journal = {Cell}, volume = {111}, number = {7}, pages = {1015–1025}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(02)01171-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867402011716}, abstract = {Translation initiation factor eIF5B/IF2 is a GTPase that promotes ribosomal subunit joining. We show that eIF5B mutations in Switch I, an element conserved in all GTP binding domains, impair GTP hydrolysis and general translation but not eIF5B subunit joining function. Intragenic suppressors of the Switch I mutation restore general translation, but not eIF5B GTPase activity. These suppressor mutations reduce the ribosome affinity of eIF5B and increase AUG skipping/leaky scanning. The uncoupling of translation and eIF5B GTPase activity suggests a regulatory rather than mechanical function for eIF5B GTP hydrolysis in translation initiation. The translational defect suggests eIF5B stabilizes Met-tRNA(i)(Met) binding and that GTP hydrolysis by eIF5B is a checkpoint monitoring 80S ribosome assembly in the final step of translation initiation}, keywords = {0,Alleles,Amino Acid Sequence,assembly,AUG,BINDING,BINDING DOMAINS,Cell Division,development,DOMAIN,DOMAINS,enzymology,Eukaryotic Cells,gene,Gene Expression RegulationEnzymologic,Gene Expression RegulationFungal,gene regulation,genetics,GTP,GTP Phosphohydrolase,GTP Phosphohydrolases,GTPase,GTPASE ACTIVITY,Guanosine,Guanosine Triphosphate,human,Hydrolysis,initiation,INITIATION-FACTOR,La,metabolism,Mutation,MUTATIONS,nosource,Prokaryotic Initiation Factor-2,regulation,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNATransfer,scanning,SUBUNIT,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,SuppressionGenetic,Threonine,translation,TRANSLATION INITIATION,TranslationGenetic,Yeasts} }

@article{shirleyNuclearImportUpf3p2002b, title = {Nuclear {{Import}} of {{Upf3p Is Mediated}} by {{Importin-alpha}}/-Beta and {{Export}} to the {{Cytoplasm Is Required}} for a {{Functional Nonsense-Mediated mRNA Decay Pathway}} in {{Yeast}}}, author = {Shirley, R.L. and Ford, A.S. and Richards, M.R. and Albertini, M. and Culbertson, M.R.}, year = 2002, journal = {Genetics}, volume = {161}, number = {4}, pages = {1465–1482}, doi = {10.1093/genetics/161.4.1465}, url = {PM:12196393}, abstract = {Upf3p, which is required for nonsense-mediated mRNA decay (NMD) in yeast, is primarily cytoplasmic but accumulates inside the nucleus when UPF3 is overexpressed or when upf3 mutations prevent nuclear export. Upf3p physically interacts with Srp1p (importin-alpha). Upf3p fails to be imported into the nucleus in a temperature-sensitive srp1-31 strain, indicating that nuclear import is mediated by the importin-alpha/beta heterodimer. Nuclear export of Upf3p is mediated by a leucine-rich nuclear export sequence (NES-A), but export is not dependent on the Crm1p exportin. Mutations identified in NES-A prevent nuclear export and confer an Nmd(-) phenotype. The addition of a functional NES element to an export-defective upf(-) allele restores export and partially restores an Nmd(+) phenotype. Our findings support a model in which the movement of Upf3p between the nucleus and the cytoplasm is required for a fully functional NMD pathway. We also found that overexpression of Upf2p suppresses the Nmd(-) phenotype in mutant strains carrying nes-A alleles but has no effect on the localization of Upf3p. To explain these results, we suggest that the mutations in NES-A that impair nuclear export cause additional defects in the function of Upf3p that are not rectified by restoration of export alone}, keywords = {Alleles,Cytoplasm,DECAY,Genetic,genetics,La,Movement,mRNA,mRNA decay,Mutation,MUTATIONS,NMD,nosource,Phenotype,sequence,Support,UPF3,yeast} }

@article{shpanchenko5SRRNASugarphosphate1996, title = {{{5S rRNA}} Sugar-Phosphate Backbone Protection in Complexes with Specific Ribosomal Proteins}, author = {Shpanchenko, O. V. and Zvereva, M. I. and Dontsova, O. A. and Nierhaus, K. H. and Bogdanov, A. A.}, year = 1996, journal = {FEBS letters}, volume = {394}, number = {1}, pages = {71–75}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0014579396008721}, abstract = {5S ribosomal RNA forms stable specific complexes with ribosomal proteins L18, L25 and L5. In this work, interaction of phosphate residues of E. coli 5S rRNA within 5S rRNA-protein complexes has been studied. For this purpose 5S rRNA with statistically distributed phosphorothioate residues has been used for complex formation and the accessibility of phosphorothioates to iodine cleavage in the complex and in the free state has been studied. In free 5S rRNA, the phosphate residue at A73 was partially protected, probably due to being involved in the organization of the spatial structure of 5S rRNA. This protection is stronger in the complex with three proteins when the 5S rRNA structure is stabilized. In the 5S rRNA-L18 complex only two phosphate groups, G7 and A34, were protected. L25 in a complex with 5S rRNA protects large numbers of phosphorothioate groups concentrating in two clusters, indicating the possibility of two binding sites for this protein on 5S rRNA. The protection pattern differs from that for individual proteins because of the possible rearrangement of the structure}, keywords = {0,5S rRNA,Bacterial,Bacteriophage T7,Base Sequence,BINDING,Binding Sites,chemistry,CLEAVAGE,COMPLEX,COMPLEXES,DNA-Directed RNA Polymerase,ElectrophoresisAgar Gel,Escherichia coli,genetics,Iodine,L5,La,metabolism,Molecular Sequence Data,nosource,Nucleic Acid Conformation,pharmacology,polymerase,protein,Proteins,Ribosomal Proteins,RIBOSOMAL-RNA,Rna,RNABacterial,RNARibosomal5S,rRNA,structure,supportnon-u.s.gov’t,Thionucleotides,TranscriptionGenetic} }

@article{shpanchenkoStructure5SRRNA1998, title = {Structure of {{5S rRNA}} within the {{Escherichia}} Coli Ribosome: Iodine- Induced Cleavage Patterns of Phosphorothioate Derivatives}, author = {Shpanchenko, O.V. and Dontsova, O.A. and Bogdanov, A.A. and Nierhaus, K.H.}, year = 1998, journal = {RNA}, volume = {4}, number = {9}, pages = {1154–1164}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838298980359}, url = {http://rnajournal.cshlp.org/content/4/9/1154.short}, abstract = {The protection patterns of 5S rRNA in solution, within the ribosomal 50S subunit, 70S ribosomes, and functional complexes, were assessed with the phosphorothioate method. About 20% of the analyzed positions (G9-G107) showed strong assembly defects: A phosphorothioate at one of these positions significantly impaired the incorporation of 5S rRNA into 50S particles. The reverse has also been observed: A phosphorothioate is preferred over a phosphate residue in the assembly process at a few positions. The results further demonstrate that 5S rRNA undergoes conformational changes during the assembly in the central protuberance of the 50S subunit and upon association with the small ribosomal subunit forming a 70S ribosome. In striking contrast, when the 70S ribosomes are once formed, the contact pattern of the 5S rRNA is the same in various functional states such as initiation-like complexes and pre- and posttranslocational states}, keywords = {5S rRNA,98410848,assembly,Base Sequence,Binding Sites,chemistry,CLEAVAGE,COMPLEX,COMPLEXES,derivatives,Escherichia coli,ESCHERICHIA-COLI,genetics,Iodine,metabolism,Molecular Sequence Data,nosource,Nucleic Acid Conformation,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,RNABacterial,RNARibosomal5S,rRNA,structure,SUBUNIT,supportnon-u.s.gov’t,Thionucleotides} }

@article{shuActivationJNKSAPK1996a, title = {Activation of {{JNK}}/{{SAPK}} Pathway Is Not Directly Inhibitory for Cell Cycle Progression in {{NIH3T3}} Cells.}, author = {Shu, J. and Hitomi, M. and Stacey, D.}, year = 1996, journal = {Oncogene}, volume = {13}, pages = {2421–2430}, keywords = {activation,anisomycin,cell cycle,No DOI found,nosource,oncogenes} }

@article{siddiqiTranscriptionChromosomalRRNA2001, title = {Transcription of Chromosomal {{rRNA}} Genes by Both {{RNA}} Polymerase {{I}} and {{II}} in Yeast Uaf30 Mutants Lacking the 30 {{kDa}} Subunit of Transcription Factor {{UAF}}}, author = {Siddiqi, I.N. and Dodd, J.A. and Vu, L. and Eliason, K. and Oakes, M.L. and Keener, J. and Moore, R. and Young, M.K. and Nomura, M.}, year = 2001, journal = {The EMBO journal}, volume = {20}, number = {16}, pages = {4512–4521}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/20.16.4512}, url = {http://www.nature.com/emboj/journal/v20/n16/abs/7593948a.html}, abstract = {UAF, a yeast RNA polymerase I transcription factor, contains Rrn5p, Rrn9p, Rrn10p, histones H3 and H4, and uncharacterized protein p30. Mutants defective in RRN5, RRN9 or RRN10 are unable to transcribe rDNA by polymerase I and grow extremely slowly, but give rise to variants able to grow by transcribing chromosomal rDNA by polymerase II. Thus, UAF functions as both an activator of polymerase I and a silencer of polymerase II for rDNA transcription. We have now identified the gene for subunit p30. This gene, UAF30, is not essential for growth, but its deletion decreases the cellular growth rate. Remarkably, the deletion mutants use both polymerase I and II for rDNA transcription, indicating that the silencer function of UAF is impaired, even though rDNA transcription by polymerase I is still occurring. A UAF complex isolated from the uaf30 deletion mutant was found to retain the in vitro polymerase I activator function to a large extent. Thus, Uaf30p plays only a minor role in its activator function. Possible reasons for slow growth caused by uaf30 mutations are discussed}, keywords = {0,activation,Amino Acid Sequence,CEREVISIAE,chemistry,Chromosomes,COMPLEX,COMPLEXES,Dna,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,DNARibosomal,gene,Genes,genetics,GROWTH,Histones,Humans,In Vitro,IN-VITRO,La,metabolism,Molecular Sequence Data,MUTANTS,Mutation,MUTATIONS,nosource,polymerase,protein,Proteins,rDNA,RDNA TRANSCRIPTION,Rna,RNA Polymerase I,RNA Polymerase II,RNA-POLYMERASE,RNA-POLYMERASE-I,RNA-POLYMERASE-II,RNARibosomal,rRNA,rRNA genes,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SUBUNIT,Support,transcription,TRANSCRIPTION FACTOR,TRANSCRIPTION FACTOR UAF,Transcription Factors,TranscriptionGenetic,UPSTREAM,UPSTREAM ACTIVATION FACTOR,yeast} } % == BibTeX quality report for siddiqiTranscriptionChromosomalRRNA2001: % ? unused Journal abbr (“EMBO J.”)

@article{sieronDKC1OverexpressionAssociated2009, title = {{{DKC1}} Overexpression Associated with Prostate Cancer Progression}, author = {Sieron, P. and Hader, C. and Hatina, J. and Engers, R. and Wlazlinski, A. and Muller, M. and Schulz, W.A.}, year = 2009, month = oct, journal = {British journal of cancer}, volume = {101}, number = {8}, pages = {1410–1416}, publisher = {Nature Publishing Group}, doi = {10.1038/sj.bjc.6605299}, url = {http://www.nature.com/bjc/journal/vaop/ncurrent/full/6605299a.html}, abstract = {BACKGROUND: Dyskerin encoded by the DKC1 gene is a predominantly nucleolar protein essential for the formation of pseudouridine in RNA and the telomerase RNA subunit hTR. Inherited mutations inactivating dyskerin cause dyskeratosis congenita, a syndrome with progeroid features characterised by skin defects and haematopoiesis failure, as well as cancer susceptibility. In this study, we report DKC1 overexpression in prostate cancers. METHODS: Expression of DKC1 was measured by quantitative RT-PCR in prostate cancer tissues in relation to hTR and the proliferation marker MKI67. Effects of dyskerin downregulation on proliferation, apoptosis and senescence of prostate cancer cell lines were determined. RESULTS: DKC1 was significantly overexpressed in prostate cancers, particularly in high-stage and recurring cases, correlating moderately with hTR and MKI67. Dyskerin downregulation in prostate carcinoma cell lines by siRNA diminished cell proliferation, but elicited neither apoptosis nor senescence. Apoptosis induction by TNF-alpha or tunicamycin was not enhanced. Long-term downregulation led predominantly to cell shrinking and loss of adhesion. INTERPRETATION: DKC1 upregulation in prostate cancers is common and likely to be necessary for extensive tumour growth. The phenotype of prostate carcinoma cell lines after dyskerin downregulation suggests that its most critical function is sustaining protein biosynthesis. Intriguingly, compromised function and overexpression of dyskerin can both contribute to cancer development}, keywords = {Apoptosis,biosynthesis,cancer,Cell Line,cell lines,Cell Proliferation,development,Dyskeratosis Congenita,expression,gene,Germany,GROWTH,La,LINE,MARKER,Methods,Mutation,MUTATIONS,nosource,OVEREXPRESSION,Phenotype,PROLIFERATION,protein,Protein Biosynthesis,PROTEIN-BIOSYNTHESIS,Pseudouridine,Rna,SUBUNIT,Support,Syndrome,Telomerase,Tunicamycin} } % == BibTeX quality report for sieronDKC1OverexpressionAssociated2009: % ? unused Journal abbr (“Br.J.Cancer”)

@article{sigmundAntibioticResistanceMutations1988a, title = {Antibiotic Resistance Mutations in Ribosomal {{RNA}} Genes of {{Escherichia}} Coli.}, author = {Sigmund, C.D. and Ettayebi, M. and Borden, A. and Morgan, E.A.}, year = 1988, journal = {Methods in enzymology}, volume = {164}, eprint = {3071688}, eprinttype = {pubmed}, pages = {673–690}, doi = {10.1016/S0076-6879(88)64077-8}, url = {http://www.ncbi.nlm.nih.gov/pubmed/3071688}, keywords = {0,16S,Anti-Bacterial Agents,antibiotic,Base Sequence,Colicins,CrossesGenetic,Dna,DNARibosomal,Drug ResistanceMicrobial,Escherichia coli,ESCHERICHIA-COLI,gene,Genes,GenesBacterial,Genetic Engineering,genetics,La,Methods,Molecular Sequence Data,Mutation,MUTATIONS,nosource,PLASMID,Plasmids,RESISTANCE,RESISTANCE MUTATIONS,ribosomal RNA,RIBOSOMAL-RNA,Rna,RNARibosomal,RNARibosomal16S,RNARibosomal23S} } % == BibTeX quality report for sigmundAntibioticResistanceMutations1988a: % ? unused Journal abbr (“Methods Enzymol.”)

@article{sikorskiSystemShuttleVectors1989, title = {A System of Shuttle Vectors and Yeast Host Strains Designed for Efficient Manipulation of {{DNA}} in {{Saccharomyces}} Cerevisiae.}, author = {Sikorski, R.S. and Hieter, P.}, year = 1989, journal = {Genetics}, volume = {122}, pages = {19–27}, doi = {10.1093/genetics/122.1.19}, keywords = {Dna,nosource,Plasmids,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SHUTTLE VECTORS,SYSTEM,vector,vectors,yeast} }

@article{simonsonTransorientationHypothesisCodon2002a, title = {The Transorientation Hypothesis for Codon Recognition during Protein Synthesis}, author = {Simonson, A.B. and Lake, J.A.}, year = 2002, month = mar, journal = {Nature}, volume = {416}, number = {6878}, pages = {281–285}, publisher = {[London: Macmillan Journals], 1869-}, doi = {10.1038/416281a}, url = {http://users.isr.ist.utl.pt/~jmrs/research/TopicsLinks/Genomics/papers/Simonson2002.pdf}, abstract = {During decoding, a codon of messenger RNA is matched with its cognate aminoacyl-transfer RNA and the amino acid carried by the tRNA is added to the growing protein chain. Here we propose a molecular mechanism for the decoding phase of translation: the transorientation hypothesis. The model incorporates a newly identified tRNA binding site and utilizes a flip between two tRNA anticodon loop structures, the 5’-stacked and the 3’-stacked conformations. The anticodon loop acts as a three- dimensional hinge permitting rotation of the tRNA about a relatively fixed codon-anticodon pair. This rotation, driven by a conformational change in elongation factor Tu involving GTP hydrolysis, transorients the incoming tRNA into the A site from the D site of initial binding and decoding, where it can be proofread and accommodated. The proposed mechanisms are compatible with the known structures, conformations and functions of the ribosome and its component parts including tRNAs and EF-Tu, in both the GTP and GDP states}, keywords = {0,A-SITE,Anticodon,BINDING,biosynthesis,Codon,COMPONENT,decoding,EFTu,elongation,genetics,GTP,Hydrolysis,La,MECHANISM,MECHANISMS,MESSENGER-RNA,metabolism,ModelsGenetic,ModelsMolecular,nosource,Peptide Elongation Factor Tu,physiology,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,ribosome,Ribosomes,Rna,RNATransfer,structure,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,translation,TranslationGenetic,tRNA} }

@article{singhPhenotypicSuppressionMisreading1979a, title = {Phenotypic Suppression and Misreading in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Singh, A. and Ursic, D. and Davies, J.}, year = 1979, journal = {Nature}, volume = {277}, pages = {146–148}, doi = {10.1038/277146a0}, keywords = {drugs,elongation,nosource,Paromomycin,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,suppression,yeast} }

@article{singhAnalysisTelomeraseCandida2002, title = {Analysis of Telomerase in {{Candida}} Albicans: Potential Role in Telomere End Protection}, author = {Singh, S.M. and {Steinberg-Neifach}, O. and Mian, I.S. and Lue, N.F.}, year = 2002, month = dec, journal = {Eukaryotic cell}, volume = {1}, number = {6}, pages = {967–977}, publisher = {Am Soc Microbiol}, doi = {10.1128/EC.1.6.967-977.2002}, url = {http://ec.asm.org/cgi/content/abstract/1/6/967}, abstract = {Telomerase is a ribonucleoprotein reverse transcriptase responsible for the maintenance of one strand of telomere terminal repeats. Analysis of the telomerase complex in the budding yeast Saccharomyces cerevisiae has revealed the presence of one catalytic protein subunit (Est2p/TERT) and at least two noncatalytic components (Est1p and Est3p). The genome of the pathogenic yeast Candida albicans contains putative orthologues of all three telomerase components. Disruption of each homologue resulted in significant but distinct telomere dysfunction in Candida: Similar to S. cerevisiae, the Candida EST3 disruption strain exhibits progressive telomere loss over many generations, at a rate that is consistent with incomplete replication. In contrast, telomeres in both the Candida TERT and EST1 disruption strains can contract rapidly, followed by partial or nearly complete recovery, suggesting a defect in telomere “capping.” We propose that these two telomerase subunits may participate in the protection of chromosomal ends in Candida: Analysis of telomerase-mediated primer extension in vitro indicates that only the TERT protein is absolutely essential for enzyme activity. Our results support the conservation of telomerase protein components beyond the catalytic subunit but reveal species-specific phenotypic alterations in response to loss of individual telomerase component. We also identify potential homologues of Est1p in phylogenetically diverse organisms. The Est1p sequence family possesses a conserved N-terminal domain predicted to be structurally related to tetratricopeptide repeat-containing proteins}, keywords = {0,Amino Acid Sequence,analysis,Base Sequence,Candida albicans,CEREVISIAE,chemistry,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,Conserved Sequence,DISRUPTION,DOMAIN,enzyme,enzymology,EvolutionMolecular,Expressed Sequence Tags,FAMILY,Fungal Proteins,genetics,Genome,IDENTIFY,immunology,In Vitro,IN-VITRO,La,metabolism,microbiology,ModelsGenetic,Molecular Sequence Data,nosource,Phylogeny,primer extension,PROTECTION,protein,Protein StructureTertiary,Proteins,RecombinationGenetic,REPLICATION,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tNon-P.H.S.,REVERSE-TRANSCRIPTASE,RIBONUCLEOPROTEIN,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,Sequence HomologyAmino Acid,SUBUNIT,SUBUNITS,Support,Telomerase,Telomere,ultrastructure,yeast} } % == BibTeX quality report for singhAnalysisTelomeraseCandida2002: % ? unused Journal abbr (“Eukaryot.Cell”)

@article{sklenarSpinEchoWaterSuppression1987, title = {Spin-{{Echo Water Suppression}} for the {{Generation}} of {{Pure-Phase Two-Dimensional Nmr-Spectra}}}, author = {Sklenar, V. and Bax, A.}, year = 1987, month = oct, journal = {Journal of Magnetic Resonance (1969)}, volume = {74}, number = {3}, pages = {469–479}, publisher = {Elsevier}, url = {ISI:A1987K421500007 http://linkinghub.elsevier.com/retrieve/pii/0022236487902691}, keywords = {No DOI found,nosource,suppression,Water,WATER SUPPRESSION} } % == BibTeX quality report for sklenarSpinEchoWaterSuppression1987: % ? Title looks like it was stored in title-case in Zotero

@article{sklenarOptimizationTripleresonanceHCN1998, title = {Optimization of Triple-Resonance {{HCN}} Experiments for Application to Larger {{RNA}} Oligonucleotides}, author = {Sklenar, V. and Dieckmann, T. and Butcher, S.E. and Feigon, J.}, year = 1998, month = jan, journal = {Journal of Magnetic Resonance}, volume = {130}, number = {1}, pages = {119–124}, doi = {10.1006/jmre.1997.1291}, url = {PM:9469906 http://adsabs.harvard.edu/abs/1998JMagR.130..119S}, keywords = {0,chemistry,Comparative Study,Image ProcessingComputer-Assisted,La,Magnetic Resonance Spectroscopy,Molecular Structure,nosource,Oligonucleotides,Rna,Sensitivity and Specificity,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for sklenarOptimizationTripleresonanceHCN1998: % ? unused Journal abbr (“J.Magn Reson.”)

@article{skogersonSeparationCharacterizationYeast1979a, title = {Separation and Characterization of Yeast Elongation Factors.}, author = {Skogerson, L.}, year = 1979, journal = {Methods in enzymology}, volume = {60:676-85.}, pages = {676–685}, doi = {10.1016/S0076-6879(79)60063-0}, url = {http://ukpmc.ac.uk/abstract/MED/379539}, keywords = {Diphtheria Toxin,drug effects,elongation,elongation factors,ELONGATION-FACTORS,Guanosine Triphosphate,isolation &,Kinetics,metabolism,Methods,nosource,Peptide Chain Elongation,Peptide Elongation Factors,pharmacology,Phenylalanine,purification,RNATransferAmino Acyl,Saccharomyces cerevisiae,yeast} } % == BibTeX quality report for skogersonSeparationCharacterizationYeast1979a: % ? unused Journal abbr (“Methods Enzymol.”)

@article{skryabinLocation8SRibosomalRna1978a, title = {Location of 5.{{8S Ribosomal-Rna Gene}} of {{Saccharomyces-Cerevisiae}}}, author = {Skryabin, K.G. and Maxam, A.M. and Petes, T.D. and Hereford, L.}, year = 1978, journal = {Journal of Bacteriology}, volume = {134}, number = {1}, pages = {306–309}, doi = {10.1128/jb.134.1.306-309.1978}, url = {ISI:A1978EV26000038}, keywords = {5.8S RIBOSOMAL-RNA,gene,nosource,ribosomal RNA,RIBOSOMAL-RNA,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE} } % == BibTeX quality report for skryabinLocation8SRibosomalRna1978a: % ? Title looks like it was stored in title-case in Zotero

@article{slobinPurificationPropertiesElongation1978, title = {Purification and Properties of an Elongation Factor Functionally Analogous to Bacterial Elongation Factor {{Ts}} from Embryos of {{Artemia}} Salina}, author = {Slobin, L.I. and Moller, W.}, year = 1978, month = mar, journal = {European Journal of Biochemistry}, volume = {84}, number = {1}, pages = {69–77}, publisher = {Wiley Online Library}, doi = {10.1111/j.1432-1033.1978.tb12142.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1978.tb12142.x/full}, keywords = {0,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,Artemia,Bacterial,Decapoda (Crustacea),elongation,elongation factors,ELONGATION-FACTORS,Embryo,embryology,Guanine,Guanine Nucleotides,GUANINE-NUCLEOTIDE,isolation & purification,La,metabolism,Molecular Weight,nosource,Nucleotides,Peptide Biosynthesis,Peptide Elongation Factors,Phenylalanine,purification,Ribosomes,Rna,RNATransfer} } % == BibTeX quality report for slobinPurificationPropertiesElongation1978: % ? unused Journal abbr (“Eur.J.Biochem.”)

@article{slomovicPolyadenylationRibosomalRNA2006, title = {Polyadenylation of Ribosomal {{RNA}} in Human Cells}, author = {Slomovic, S. and Laufer, D. and Geiger, D. and Schuster, G.}, year = 2006, journal = {Nucleic acids research}, volume = {34}, number = {10}, pages = {2966–2975}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkl357}, url = {http://nar.oxfordjournals.org/content/34/10/2966.short}, abstract = {The addition of poly(A)-tails to RNA is a process common to almost all organisms. In eukaryotes, stable poly(A)-tails, important for mRNA stability and translation initiation, are added to the 3’ ends of most nuclear-encoded mRNAs, but not to rRNAs. Contrarily, in prokaryotes and organelles, polyadenylation stimulates RNA degradation. Recently, polyadenylation of nuclear-encoded transcripts in yeast was reported to promote RNA degradation, demonstrating that polyadenylation can play a double-edged role for RNA of nuclear origin. Here we asked whether in human cells ribosomal RNA can undergo polyadenylation. Using both molecular and bioinformatic approaches, we detected non-abundant polyadenylated transcripts of the 18S and 28S rRNAs. Interestingly, many of the post-transcriptionally added tails were composed of heteropolymeric poly(A)-rich sequences containing the other nucleotides in addition to adenosine. These polyadenylated RNA fragments are most likely degradation intermediates, as primer extension (PE) analysis revealed the presence of distal fragmented molecules, some of which matched the polyadenylation sites of the proximal cleavage products revealed by oligo(dT) and circled RT-PCR. These results suggest the presence of a mechanism to degrade ribosomal RNAs in human cells, that possibly initiates with endonucleolytic cleavages and involves the addition of poly(A) or poly(A)-rich tails to truncated transcripts, similar to that which operates in prokaryotes and organelles}, keywords = {0,3,Adenosine,analysis,BIOLOGY,Cell LineTumor,CELLS,chemistry,CLEAVAGE,degradation,Expressed Sequence Tags,human,Humans,initiation,INTERMEDIATE,La,MECHANISM,metabolism,mRNA,mRNA stability,nosource,Nucleotides,Oligonucleotide Probes,Organelles,Poly A,poly(A),POLY(A) TAIL,Polyadenylation,primer extension,PRODUCT,PRODUCTS,PROKARYOTES,Reverse Transcriptase Polymerase Chain Reaction,ribosomal RNA,RIBOSOMAL-RNA,Rna,RNA Stability,RNARibosomal,RNARibosomal18S,RNARibosomal28S,rRNA,sequence,SEQUENCES,SITE,SITES,stability,Support,TRANSCRIPT,translation,TRANSLATION INITIATION,yeast} } % == BibTeX quality report for slomovicPolyadenylationRibosomalRNA2006: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{smailovStudyPhosphorylationTranslation1993, title = {Study of Phosphorylation of Translation Elongation Factor 2 ({{EF-2}}) from Wheat Germ.}, author = {Smailov, S.K. and Lee, A.V. and Iskakov, B.K.}, year = 1993, journal = {FEBS letters}, volume = {321}, number = {2-3}, pages = {219–223}, publisher = {Elsevier}, doi = {10.1016/0014-5793(93)80112-8}, url = {http://linkinghub.elsevier.com/retrieve/pii/0014579393801128}, keywords = {EF-2,EF-2 kinase,elongation,kinase,nosource,Phosphorylation,translation,Wheat} } % == BibTeX quality report for smailovStudyPhosphorylationTranslation1993: % ? unused Journal abbr (“FEBS Lett.”)

@article{smithTranscriptomeProfilingIdentify2002, title = {Transcriptome Profiling to Identify Genes Involved in Peroxisome Assembly and Function}, author = {Smith, J.J. and Marelli, M. and Christmas, R.H. and Vizeacoumar, F.J. and Dilworth, D.J. and Ideker, T. and Galitski, T. and Dimitrov, K. and Rachubinski, R.A. and Aitchison, J.D.}, year = 2002, month = jul, journal = {The Journal of cell biology}, volume = {158}, number = {2}, pages = {259–271}, publisher = {Rockefeller Univ Press}, doi = {10.1083/jcb.200204059}, url = {http://jcb.rupress.org/content/158/2/259.abstract}, abstract = {Yeast cells were induced to proliferate peroxisomes, and microarray transcriptional profiling was used to identify PEX genes encoding peroxins involved in peroxisome assembly and genes involved in peroxisome function. Clustering algorithms identified 224 genes with expression profiles similar to those of genes encoding peroxisomal proteins and genes involved in peroxisome biogenesis. Several previously uncharacterized genes were identified, two of which, YPL112c and YOR084w, encode proteins of the peroxisomal membrane and matrix, respectively. Ypl112p, renamed Pex25p, is a novel peroxin required for the regulation of peroxisome size and maintenance. These studies demonstrate the utility of comparative gene profiling as an alternative to functional assays to identify genes with roles in peroxisome biogenesis}, keywords = {Algorithms,assays,assembly,BIOGENESIS,BIOLOGY,CELLS,expression,gene,Gene Expression Profiling,Gene Expression RegulationFungal,Genes,GenesFungal,genetics,IDENTIFY,La,metabolism,nosource,Peroxisomes,protein,Proteins,regulation,Research SupportNon-U.S.Gov’t,Saccharomyces cerevisiae,SYSTEM,SYSTEMS,Trans-Activation (Genetics),yeast,YEAST-CELLS} } % == BibTeX quality report for smithTranscriptomeProfilingIdentify2002: % ? unused Journal abbr (“J.Cell Biol.”)

@article{smithSaturationMutagenesis5S2001, title = {Saturation Mutagenesis of {{5S rRNA}} in {{Saccharomyces}} Cerevisiae.}, author = {Smith, M.W. and Meskauskas, A. and Wang, P. and Sergiev, P.V. and Dinman, J.D.}, year = 2001, journal = {Molecular and Cellular Biology}, volume = {21}, number = {24}, pages = {8264–8275}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.21.24.8264-8275.2001}, url = {http://mcb.asm.org/cgi/content/abstract/21/24/8264}, abstract = {Ribosomal RNAs (rRNAs) are the central players in the reactions catalyzed by ribosomes, and the individual rRNAs are actively involved in different ribosome functions. Our previous demonstration that mutants of the yeast 5S rRNA (called ⬚mof9⬚) can impact on translational reading frame maintenance showed an unexpected function for this ubiquitous biomolecule. A the time, however, the highly repetitive nature of the genes encoding rRNAs precluded more detailed genetic and molecular analyses. A new genetic system allows all 5S rRNAs in the cell to be transcribed from a small, easily manipulated plasmid. The system is also amenable for the study of the other rRNAs, and provides an ideal genetic platform for detailed structural and functional studies. Saturation mutagenesis reveals regions of 5S rRNA that are required for cell viability, translational accuracy, and virus propagation. Unexpectedly, very few lethal alleles were identified demonstrating the resilience of this molecule. Superimposition of genetic phenotypes on a physical map of 5S rRNA reveals the existence of phenotypic clusters of mutants, suggesting that specific regions of 5S rRNA are important for specific functions. Mapping of these mutants onto the ⬚Haloarcula marismortui⬚ large subunit reveals that these clusters occur at important points of physical interaction between 5S rRNA and the different functional centers of the ribosome. Our analyses lead us to propose that one of the major functions of 5S rRNA may be to enhance translational fidelity by acting as a physical transducer of information between all of the different functional centers of the ribosome.}, keywords = {5S rRNA,accuracy,Alleles,Fidelity,FRAME MAINTENANCE,Frameshifting,gene,Genes,Genetic,Haloarcula,Haloarcula marismortui,mapping,Mutagenesis,nosource,Phenotype,PLASMID,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Structural,structure,SUBUNIT,SYSTEM,virus,yeast} } % == BibTeX quality report for smithSaturationMutagenesis5S2001: % ? unused Journal abbr (“Mol.Cell.Biol.”)

@article{smogorzewskaRegulationTelomeraseTelomeric2004, title = {Regulation of Telomerase by Telomeric Proteins}, author = {Smogorzewska, A. and {}{de Lange}, T.}, year = 2004, month = jan, journal = {Annual review of biochemistry}, volume = {73}, number = {1}, pages = {177–208}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, issn = {0066-4154}, doi = {10.1146/annurev.biochem.73.071403.160049}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.biochem.73.071403.160049 http://www.ncbi.nlm.nih.gov/pubmed/15189140}, abstract = {Telomeres are essential for genome stability in all eukaryotes. Changes in telomere functions and the associated chromosomal abnormalities have been implicated in human aging and cancer. Telomeres are composed of repetitive sequences that can be maintained by telomerase, a complex containing a reverse transcriptase (hTERT in humans and Est2 in budding yeast), a template RNA (hTERC in humans and Tlc1 in yeast), and accessory factors (the Est1 proteins and dyskerin in humans and Est1, Est3, and Sm proteins in budding yeast). Telomerase is regulated in cis by proteins that bind to telomeric DNA. This regulation can take place at the telomere terminus, involving single-stranded DNA-binding proteins (POT1 in humans and Cdc13 in budding yeast), which have been proposed to contribute to the recruitment of telomerase and may also regulate the extent or frequency of elongation. In addition, proteins that bind along the length of the telomere (TRF1/TIN2/tankyrase in humans and Rap1/Rif1/Rif2 in budding yeast) are part of a negative feedback loop that regulates telomere length. Here we discuss the details of telomerase and its regulation by the telomere.}, pmid = {15189140}, keywords = {0,abnormalities have,aging,aging and cancer,and the associated chromosomal,Animals,Base Sequence,been implicated in human,BINDING,BINDING PROTEIN,BINDING-PROTEIN,Biological,cancer,cell cycle,Cell Cycle Proteins,Cell Cycle Proteins: metabolism,CEREVISIAE,changes in telomere functions,COMPLEX,COMPLEXES,Dna,DNA,DNA Damage,DNA Replication,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,DNA: genetics,DNA: metabolism,elongation,essential for genome stability,f abstract telomeres are,Feedback,genetics,Genome,human,Humans,in all eukaryotes,La,LOOP,metabolism,Models,ModelsBiological,nosource,Nuclear Proteins,Nuclear Proteins: metabolism,protein,Proteins,RECRUITMENT,regulation,repetitive,REVERSE-TRANSCRIPTASE,Review,Rna,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: metabolism,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,stability,Support,Telomerase,Telomerase: metabolism,telomere,Telomere,Telomere-Binding Proteins,Telomere-Binding Proteins: metabolism,Telomere: metabolism,telomeres are composed of,Telomeric Repeat Binding Protein 1,Telomeric Repeat Binding Protein 1: metabolism,TEMPLATE,yeast} } % == BibTeX quality report for smogorzewskaRegulationTelomeraseTelomeric2004: % ? unused Journal abbr (“Annu.Rev.Biochem.”)

@article{snijderCarboxylTerminalPartPutative1990, title = {The {{Carboxyl-Terminal Part}} of the {{Putative Berne Virus Polymerase Is Expressed}} by {{Ribosomal Frameshifting}} and {{Contains Sequence Motifs Which Indicate That Toro-Viruses}} and {{Coronaviruses Are Evolutionarily Related}}}, author = {Snijder, E.J. and Denboon, J.A. and Bredenbeek, P.J. and Horzinek, M.C. and Rijnbrand, R. and Spaan, W.J.M.}, year = 1990, journal = {Nucleic Acids Research}, volume = {18}, number = {15}, pages = {4535–4542}, doi = {10.1093/nar/18.15.4535}, url = {ISI:A1990DV48300028}, keywords = {Frameshifting,MOTIFS,nosource,polymerase,ribosomal frameshifting,sequence,virus} } % == BibTeX quality report for snijderCarboxylTerminalPartPutative1990: % ? Title looks like it was stored in title-case in Zotero

@article{snijderUniqueConservedFeatures2003, title = {Unique and Conserved Features of Genome and Proteome of {{SARS-coronavirus}}, an Early Split-off from the Coronavirus Group 2 Lineage}, author = {Snijder, E.J. and Bredenbeek, P.J. and Dobbe, J.C. and Thiel, V. and Ziebuhr, J. and Poon, L.L. and Guan, Y. and Rozanov, M. and Spaan, W.J. and Gorbalenya, A.E.}, year = 2003, journal = {Journal of molecular biology}, volume = {331}, number = {5}, pages = {991–1004}, publisher = {Elsevier}, doi = {10.1016/S0022-2836(03)00865-9}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283603008659}, abstract = {The genome organization and expression strategy of the newly identified severe acute respiratory syndrome coronavirus (SARS-CoV) were predicted using recently published genome sequences. Fourteen putative open reading frames were identified, 12 of which were predicted to be expressed from a nested set of eight subgenomic mRNAs. The synthesis of these mRNAs in SARS-CoV-infected cells was confirmed experimentally. The}, keywords = {0,Amino Acid Sequence,Animals,CELLS,Cercopithecus aethiops,chemistry,classification,Comparative Study,Conserved Sequence,Coronavirus,EvolutionMolecular,expression,FRAME,genetics,Genome,GENOME ORGANIZATION,GenomeViral,human,La,metabolism,microbiology,Molecular Sequence Data,mRNA,nosource,OPEN READING FRAME,Open Reading Frames,ORGANIZATION,Phylogeny,protein,Protein StructureTertiary,Protein Subunits,Proteins,Proteome,READING FRAME,Reading Frames,REPLICASE,Rna,RNA ProcessingPost-Transcriptional,RNA Replicase,RNAMessenger,RnaViral,Sars Virus,sequence,Sequence HomologyAmino Acid,SEQUENCES,Severe Acute Respiratory Syndrome,SUBUNIT,SUBUNITS,Vero Cells,Viral Proteins} } % == BibTeX quality report for snijderUniqueConservedFeatures2003: % ? unused Journal abbr (“J.Mol.Biol.”)

@article{snyderPolyamineDepletionAssociated1989, title = {Polyamine Depletion Is Associated with Altered Chromatin Structure in {{HeLa}} Cells.}, author = {Snyder, R.D.}, year = 1989, month = jun, journal = {Biochemical Journal}, volume = {260}, number = {3}, pages = {697–704}, publisher = {Portland Press Ltd}, doi = {10.1042/bj2600697}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1138733/}, abstract = {HeLa cells depleted of polyamines by treatment with alpha-difluoromethylornithine (DFMO), methylglyoxal bis(guanylhydrazone) (MGBG) or a combination of the two, were examined for sensitivity to micrococcal nuclease, DNAase I and DNAase II. The degrees of chromatin accessibility to DNAase I and II appeared enhanced somewhat in all three treatment groups, and the released digestion products differed from those in non-depleted cells. DNA released from}, keywords = {0,antagonists & inhibitors,CELLS,Chromatin,Deoxyribonuclease I,DeoxyribonucleasesType II Site-Specific,Dna,Eflornithine,Hela Cells,HELA-CELLS,Humans,La,Micrococcal Nuclease,Mitoguazone,nosource,polyamine,Polyamines,PRODUCT,PRODUCTS,site specific,structure,ultrastructure} } % == BibTeX quality report for snyderPolyamineDepletionAssociated1989: % ? unused Journal abbr (“Biochem.J.”)

@article{sommerCocuringPlasmidsAffecting1982a, title = {Co-Curing of Plasmids Affecting Killer Double-Stranded {{RNAs}} of ⬚{{Saccharomyces}} Cerevisiae⬚: [{{HOK}}], [{{NEX}}], and the Abundance of {{L}} Are Related and Further Evidence That {{M}}⬚1⬚ Requires {{L}}.}, author = {Sommer, S.S. and Wickner, R.B.}, year = 1982, journal = {J.Bacteriol.}, volume = {150}, pages = {545–551}, doi = {10.1128/jb.150.2.545-551.1982}, keywords = {curing,DOUBLE-STRANDED-RNA,Heat,killer,L-A,La,M1,nosource,PLASMID,Plasmids,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE} } % == BibTeX quality report for sommerCocuringPlasmidsAffecting1982a: % ? Possibly abbreviated journal title J.Bacteriol.

@article{sommerDoubleStrandedRnasThat1984, title = {Double-{{Stranded Rnas That Encode Killer Toxins}} in {{Saccharomyces-Cerevisiae}} - {{Unstable Size}} of {{M-Double-Stranded Rna}} and {{Inhibition}} of {{M2 Replication}} by {{M1}}}, author = {Sommer, S.S. and Wickner, R.B.}, year = 1984, journal = {Molecular and Cellular Biology}, volume = {4}, number = {9}, pages = {1747–1753}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/4/9/1747}, keywords = {DOUBLE-STRANDED-RNA,INHIBITION,killer,killer toxin,M1,Multiple DOI,nonfile,nosource,REPLICATION,Rna,S,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,toxin} } % == BibTeX quality report for sommerDoubleStrandedRnasThat1984: % ? Title looks like it was stored in title-case in Zotero

@article{sommerGeneDisruptionIndicates1987, title = {Gene {{Disruption Indicates That}} the {{Only Essential Function}} of the {{Ski8 Chromosomal Gene Is}} to {{Protect Saccharomyces-Cerevisiae}} from {{Viral Cytopathology}}}, author = {Sommer, S.S. and Wickner, R.B.}, year = 1987, month = mar, journal = {Virology}, volume = {157}, number = {1}, pages = {252–256}, publisher = {Elsevier}, doi = {10.1016/0042-6822(87)90338-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/0042682287903382}, keywords = {DISRUPTION,gene,nosource,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE} } % == BibTeX quality report for sommerGeneDisruptionIndicates1987: % ? Title looks like it was stored in title-case in Zotero

@article{sonenbergMappingEscherichiaColi1973, title = {Mapping of {{Escherichia}} Coli Ribosomal Components Involved in Peptidyl Transferase Activity}, author = {Sonenberg, N. and Wilchek, M. and Zamir, A.}, year = 1973, month = may, journal = {Proceedings of the National Academy of Sciences}, volume = {70}, number = {5}, pages = {1423–1426}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.70.5.1423}, url = {http://www.pnas.org/content/70/5/1423.short}, abstract = {The method of affinity labeling has been used to identify protein components of 50S ribosomal subunits involved in peptidyl transferase activity. E. coli 50S ribosomal subunits were mapped by reaction with the N-bromoacetyl analog of chloramphenicol, an antibiotic known to interact specifically with the active center of the enzyme. The synthetic analog competes with chloramphenicol in binding to 50S ribosomal subunits and inhibits peptidyl transferase activity. It attaches covalently to the ribosome under appropriate conditions and causes an irreversible loss in peptidyl transferase activity. The reagent specifically alkylates cysteine residues of proteins L2 and L27}, keywords = {0,Acetamides,Acyltransferases,Alkylation,analysis,antagonists & inhibitors,Anti-Bacterial Agents,antibiotic,Bacterial,Bacterial Proteins,BINDING,BindingCompetitive,biosynthesis,Bromine,Carbon,Carbon Isotopes,Chloramphenicol,COMPONENT,COMPONENTS,Cysteine,E,elongation,elongation factors,ELONGATION-FACTORS,enzyme,enzymology,Escherichia coli,ESCHERICHIA-COLI,Ethylmaleimide,IDENTIFY,L2,La,mapping,metabolism,Methionine,Methods,nosource,Peptide Elongation Factors,Peptides,peptidyl transferase,PEPTIDYL-TRANSFERASE,Phenethylamines,Phenylalanine,protein,Proteins,RESIDUES,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,SUBUNIT,SUBUNITS,Succinimides} } % == BibTeX quality report for sonenbergMappingEscherichiaColi1973: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{songEfficientExpression15kDa2006, title = {Efficient Expression of the 15-{{kDa}} Form of Infectious Pancreatic Necrosis Virus {{VP5}} by Suppression of a {{UGA}} Codon}, author = {Song, H. and {Baxter-Roshek}, J.L. and Dinman, J.D. and Vakharia, V.N.}, year = 2006, month = dec, journal = {Virus Research}, volume = {122}, number = {1-2}, pages = {61–68}, publisher = {Elsevier}, doi = {10.1016/j.virusres.2006.06.012}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0168170206002310}, abstract = {Infectious pancreatic necrosis virus (IPNV), a member of the Birnaviridae family, encodes a nonstructural VP5 protein from a small open reading frame (ORF), which overlaps with a major ORF encoding pVP2, VP4 and VP3 proteins. In majority of the Sp strains of IPNV sequenced to date, VP5 gene codes for a 15-kDa protein. However, we have shown that in highly virulent strains, there is a premature in-frame stop codon (UGA) at nucleotide (nt) position 427, (preceding the 15-kDa stop codon at nt position 511) which could encode a 12-kDa protein. Using reverse genetics, we recovered recombinant rNVI15, rNVI15-15K and rNVI15-DeltaVP5 viruses (which could encode 12 or 15-kDa VP5 or lack the expression of VP5, respectively) and demonstrated that VP5 is dispensable for viral replication in vivo but is not involved in virulence (Santi, N., Song, H., Vakharia, V. N., Evensen, O., 2005a. Infectious pancreatic necrosis virus VP5 is dispensable for virulence and persistence. J. Virol. 79, 9206-9216). Here, we utilized these viruses to investigate the gene expression of VP5 in vitro. Our results indicate that a 15-kDa VP5 is produced in rNVI15-infected cells, albeit at lower levels than in rNVI15-15K-infected cells, suggesting that the opal stop codon at nt 427 is suppressed. Furthermore, to examine translational suppression of the opal stop codon in VP5 gene, we constructed plasmids containing VP5-specific sequence and employed a yeast-based bicistronic dual-luciferase reporter system (Harger, J.W., Dinman, J.D., 2003. An in vivo dual-luciferase assay system for studying translational recoding in the yeast Saccharomyces cerevisiae. RNA 9, 1019-1024). Our results demonstrate that the VP5 sequence (with or without a stop codon) yielded approximately 13% termination suppression and the efficiency is directly related to the base immediately 3’ of the termination codon, C{\(>\)}A{\(>\)}U{\(>\)}G}, keywords = {3,BASE,bicistronic,CELLS,CEREVISIAE,Codon,efficiency,ENCODES,expression,FAMILY,FORM,FRAME,gene,Gene Expression,GENE-EXPRESSION,Genetic,genetics,In Vitro,IN-VITRO,IN-VIVO,La,nosource,OPEN READING FRAME,PLASMID,Plasmids,POSITION,protein,Proteins,READING FRAME,recoding,REPLICATION,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,STOP CODON,suppression,SYSTEM,termination,TERMINATION CODON,TERMINATION-CODON,TRANSLATIONAL SUPPRESSION,virus,Viruses,yeast} } % == BibTeX quality report for songEfficientExpression15kDa2006: % ? unused Journal abbr (“Virus Res.”)

@article{songElongationFactorEF1a1989, title = {Elongation Factor {{EF-1`a}} Gene Dosage Alters Translational Fidelity in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Song, J.M. and Picologlou, S. and Grant, C.M. and Firoozan, M. and Tuite, M.F. and Liebman, S.}, year = 1989, journal = {Mol.Cell.Biol.}, volume = {9}, pages = {4571–4575}, keywords = {EF-1,elongation,Fidelity,gene,Gene Dosage,Multiple DOI,nonfile,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,translation} } % == BibTeX quality report for songElongationFactorEF1a1989: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{songMutagenesisGlu89Residue1992, title = {Mutagenesis of the {{Glu-89}} Residue in Human Immunodeficiency Virus Type 1 ({{HIV-1}}) and {{HIV-2}} Reverse Transcriptases: Effects on Nucleoside Analog Resistance.}, author = {Song, Q. and Yang, G. and Goff, S.P. and Prasad, V.R.}, year = 1992, month = dec, journal = {Journal of Virology}, volume = {66}, number = {12}, pages = {7568–7571}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.66.12.7568-7571.1992}, url = {http://jvi.asm.org/cgi/content/abstract/66/12/7568}, keywords = {Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,INHIBITION,Mutagenesis,nosource,virus} }

@article{songModificationRRNAQuality2002, title = {Modification of {{rRNA}} as a [] Quality Control Mechanism’in Ribosome Biogenesis}, author = {Song, X. and Nazar, R.N.}, year = 2002, month = jul, journal = {FEBS letters}, volume = {523}, number = {1-3}, pages = {182–186}, publisher = {Elsevier}, doi = {10.1016/S0014-5793(02)02986-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579302029861}, abstract = {An efficiently expressed rDNA plasmid was used to quantitatively analyze the effect of base changes in modified positions associated with the peptidyl transferase center of the 25S rRNA from the yeast Schizosaccharomyces pombe. The results show that, unlike normal RNA and relative to a less conserved modified position outside the center, these mutant RNAs are highly unstable and rapidly degraded with little or no effect on cell growth. These results provide direct evidence that the positions of modification can be critical sites for nuclease attack. Taken together with previous genetic analyses of rRNA modification, they raise the possibility that rRNA modification may act, at least in part, as a quality control mechanism to help ensure that only functional RNA is incorporated into active ribosomes}, keywords = {0,chemistry,Genetic,genetics,La,MECHANISM,metabolism,modification,Mutation,nosource,Nucleic Acid Conformation,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Peptidyltransferase,PLASMID,Quality Control,rDNA,Ribonucleases,ribosome,ribosome biogenesis,Ribosomes,Rna,RNARibosomal,rRNA,Schizosaccharomyces,supportnon-u.s.gov’t,ultrastructure,yeast} } % == BibTeX quality report for songModificationRRNAQuality2002: % ? unused Journal abbr (“FEBS Lett.”)

@article{soukupRelationshipInternucleotideLinkage1999, title = {Relationship between Internucleotide Linkage Geometry and the Stability of {{RNA}}}, author = {Soukup, G.A. and Breaker, R.R.}, year = 1999, month = oct, journal = {RNA}, volume = {5}, number = {10}, pages = {1308–1325}, publisher = {Cambridge Univ Press}, doi = {10.1017/S1355838299990891}, url = {http://journals.cambridge.org/abstract_S1355838299990891}, abstract = {The inherent chemical instability of RNA under physiological conditions is primarily due to the spontaneous cleavage of phosphodiester linkages via intramolecular transesterification reactions. Although the protonation state of the nucleophilic 2’-hydroxyl group is a critical determinant of the rate of RNA cleavage, the precise geometry of the chemical groups that comprise each internucleotide linkage also has a significant impact on cleavage activity. Specifically, transesterification is expected to be proportional to the relative in-line character of the linkage. We have examined the rates of spontaneous cleavage of various RNAs for which the secondary and tertiary structures have previously been modeled using either NMR or X-ray crystallographic data. Rate constants determined for the spontaneous cleavage of different RNA linkages vary by almost 10,000-fold, most likely reflecting the contribution that secondary and tertiary structures make towards the overall chemical stability of RNA. Moreover, a correlation is observed between RNA cleavage rate and the relative in-line fitness of each internucleotide linkage. One linkage located within an ATP-binding RNA aptamer is predicted to adopt most closely the ideal conformation for in-line attack. This linkage has a rate constant for transesterification that is approximately 12-fold greater than is observed for an unconstrained linkage and was found to be the most labile among a total of 136 different sites examined. The implications of this relationship for the chemical stability of RNA and for the mechanisms of nucleases and ribozymes are discussed}, keywords = {0,Adenosine,Adenosine Triphosphate,Base Sequence,BIOLOGY,CHARACTER,chemistry,CLEAVAGE,CONFORMATION,CONSTANTS,Flavin Mononucleotide,genetics,Hepatitis Delta Virus,La,MECHANISM,MECHANISMS,metabolism,ModelsMolecular,Molecular Sequence Data,NMR,nosource,Nucleic Acid Conformation,Nucleotides,Research SupportNon-U.S.Gov’t,ribozyme,Rna,RNA Stability,RNACatalytic,RNAProtozoan,RnaViral,SITE,SITES,stability,structure} }

@article{southworthEFGindependentTranslocationMRNA2002, title = {{{EFG-independent}} Translocation of the {{mRNA}}: {{tRNA}} Complex Is Promoted by Modification of the Ribosome with Thiol-Specific Reagents}, author = {Southworth, D.R. and Brunelle, J.L. and Green, R.}, year = 2002, month = dec, journal = {Journal of molecular biology}, volume = {324}, number = {4}, pages = {611–623}, publisher = {Elsevier}, doi = {10.1016/S0022-2836(02)01196-8}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283602011968}, abstract = {Translation of polyphenylalanine from a polyuridine template by the ribosome in the absence of the elongation factors EFG and EFTu (and the energy derived from GTP hydrolysis) is promoted by modification of the ribosome with thiol-specific reagents such as para-chloromercuribenzoate (pCMB). Here, we examine the translational cycle of modified ribosomes and show that peptide bond formation and tRNA binding are largely unaffected, whereas translocation of the mRNA:tRNA complex is substantially promoted by pCMB modification. The translocation movements that we observe are authentic by multiple criteria including the processivity of translation, accuracy of movement (three-nucleotide) along a defined mRNA template and sensitivity to antibiotics. Characterization of the modified ribosomes reveals that the protein content of the ribosomes is not depleted but that their subunit association properties are severely compromised. These data suggest that molecular targets (ribosomal proteins) in the interface region of the ribosome are critical barriers that influence the translocation of the mRNA:tRNA complex}, keywords = {accuracy,antibiotic,antibiotics,BINDING,COMPLEX,COMPLEXES,EFTu,elongation,Genetic,genetics,GTP,Hydrolysis,modification,Movement,mRNA,nosource,protein,Proteins,Ribosomal Proteins,ribosome,Ribosomes,SUBUNIT,translation,translocation,tRNA} } % == BibTeX quality report for southworthEFGindependentTranslocationMRNA2002: % ? unused Journal abbr (“J.Mol.Biol.”)

@article{spahnDomainMovementsElongation2004, title = {Domain Movements of Elongation Factor {{eEF2}} and the Eukaryotic {{80S}} Ribosome Facilitate {{tRNA}} Translocation}, author = {Spahn, C.M. and {Gomez-Lorenzo}, M.G. and Grassucci, R.A. and Jorgensen, R. and Andersen, G.R. and Beckmann, R. and Penczek, P.A. and Ballesta, J.P. and Frank, J.}, year = 2004, month = mar, journal = {EMBO J.}, volume = {23}, number = {5}, pages = {1008–1019}, publisher = {Nature Publishing Group}, doi = {10.1038/sj.emboj.7600102}, url = {http://www.nature.com/emboj/journal/v23/n5/abs/7600102a.html}, abstract = {An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the functionally important ribosomal intersubunit bridges. Sordarin positions domain III of eEF2 so that it can interact with the sarcin-ricin loop of 25S rRNA and protein rpS23 (S12p). This particular conformation explains the inhibitory action of sordarin and suggests that eEF2 is stalled on the 80S ribosome in a conformation that has similarities with the GTPase activation state. A ratchet-like subunit rearrangement (RSR) occurs in the 80S.eEF2.sordarin complex that, in contrast to Escherichia coli 70S ribosomes, is also present in vacant 80S ribosomes. A model is suggested, according to which the RSR is part of a mechanism for moving the tRNAs during the translocation reaction}, keywords = {70S RIBOSOME,activation,antibiotic,COMPLEX,COMPLEXES,CONFORMATION,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,DOMAIN,elongation,Escherichia coli,ESCHERICHIA-COLI,GTPase,La,LOOP,MECHANISM,MODEL,Movement,nosource,POSITION,POSITIONS,protein,ribosome,Ribosomes,rRNA,SARCIN RICIN LOOP,sordarin,SUBUNIT,translocation,tRNA,yeast} } % == BibTeX quality report for spahnDomainMovementsElongation2004: % ? Possibly abbreviated journal title EMBO J.

@article{speddingAllostericMechanismTranslational1993, title = {Allosteric {{Mechanism}} for {{Translational Repression}} in the {{Escherichia-Coli Alpha-Operon}}}, author = {Spedding, G. and Draper, D.E.}, year = 1993, month = may, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {90}, number = {10}, pages = {4399–4403}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.90.10.4399}, url = {http://www.pnas.org/content/90/10/4399.short}, abstract = {The ribosomal protein S4 is a translational repressor that binds to a complex mRNA pseudoknot structure containing the ribosome binding site for the first gene of the a operon. Either 30S subunits or S4 protein bound to the mRNA causes Moloney murine leukemia virus reverse transcriptase to pause near the 3’ terminus of the pseudoknot. There is no competition between subunits and S4 for mRNA binding. The kinetics of forming S4-30S-mRNA complexes are biphasic, and the fraction of mRNA molecules reacting more rapidly decreases as the temperature is increased from 30-degrees-C to 40-degrees-C. The complex cannot be detected with mRNA mutants that cannot be repressed. We have previously shown similar kinetic behavior for the formation of tRNA(f)Met initiation complexes with tRNA(f)Met, 30S subunits, and mRNA, except that the fraction reacting rapidly increases when the temperature is increased over the same 30-40-degrees-C range. Thus the two sets of experiments show that there are two forms of 30S-mRNA complexes that differ in their abilities to bind S4 and tRNA(f)Met. The results support an allosteric model for translational repression in which S4 traps the mRNA in a conformation able to bind 30S subunits but unable to form an initiation complex with tRNA(f)Met}, keywords = {BINDING,COMPLEX,COMPLEXES,CONFORMATION,Escherichia coli,ESCHERICHIA-COLI,gene,GENE-EXPRESSION,initiation,INITIATION SITE,Kinetics,MECHANISM,MESSENGER-RNA TRANSLATION,mRNA,nosource,Operon,protein,pseudoknot,REPRESSOR,RIBOSOMAL-PROTEIN S20,ribosome,Ribosomes,RNA PSEUDOKNOT,S4-PROTEIN,sequence,structure,SUBUNIT,Support,Temperature,TRANSLATIONAL INITIATION,virus} } % == BibTeX quality report for speddingAllostericMechanismTranslational1993: % ? Title looks like it was stored in title-case in Zotero

@article{speddingRibosomeInitiationComplexFormation1993a, title = {Ribosome {{Initiation Complex-Formation}} with the {{Pseudoknotted Alpha Operon Messenger-Rna}}}, author = {Spedding, G. and Gluick, T.C. and Draper, D.E.}, year = 1993, month = feb, journal = {Journal of Molecular Biology}, volume = {229}, number = {3}, pages = {609–622}, doi = {10.1006/jmbi.1993.1067}, url = {ISI:A1993KM69800006}, keywords = {BINDING,ESCHERICHIA-COLI RIBOSOME,expression,gene,initiation,MESSENGER-RNA,nosource,Operon,PROKARYOTES,protein,REGULATORY SITE,ribosome,Ribosomes,RNA CONFORMATIONS,RNA PSEUDOKNOT,SECONDARY STRUCTURE,SUBUNIT,TOEPRINT ASSAY,translation,TRANSLATION INITIATION} } % == BibTeX quality report for speddingRibosomeInitiationComplexFormation1993a: % ? Title looks like it was stored in title-case in Zotero

@article{spirinRibosomeRNAbasedMolecular2004a, title = {The Ribosome as an {{RNA-based}} Molecular Machine.}, author = {Spirin, A.S.}, year = 2004, month = may, journal = {RNA biology}, volume = {1}, number = {1}, eprint = {17194938}, eprinttype = {pubmed}, pages = {3–9}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17194938}, abstract = {The ribosome is a protein-synthesizing ribonucleoprotein particle where RNA forms its structural and functional core. Compact self-folding of ribosomal RNA resulting in its specific tertiary structure and its conformational mobility underlie the functional behavior of the ribosome. In addition to the functions of ligand recognition (binding of mRNA, tRNA and translation factors) and catalysis (peptidyltransferase activity), the ribosomal RNA with its movable blocks principally contributes to the construction of the ribosome as a molecular machine. The oscillations between open (unlocked) and closed (locked) conformations are proposed to be necessary events in the processes of aminoacyl-tRNA binding, transpeptidation and translocation. Elongation factors EF-Tu and EF-G with GTP are considered as catalysts of conformational transitions during aminoacyl-tRNA binding and translocation, and the theory of NTP-dependent conformational catalysis via conformational intermediates is discussed. Thermal fluctuations are assumed to serve as the main “motive force” to move RNA parts and ligands in the translating ribosome. The binding of functional ligands, such as aminoacyl-tRNA and an elongation factor with GTP, and the chemical reactions of transpeptidation and GTP hydrolysis play the role of a Maxwell’s Demon: they rectify the random fluctuations to produce the unidirectional conveyance process and translation (“thermal ratchet” model)}, keywords = {0,BINDING,Catalysis,chemistry,CONFORMATION,EF-G,EFTu,elongation,elongation factors,ELONGATION-FACTORS,FORM,GTP,Guanosine,Guanosine Triphosphate,Hydrogen-Ion Concentration,Hydrolysis,INTERMEDIATE,La,Ligands,MODEL,ModelsBiological,ModelsMolecular,Molecular Conformation,mRNA,No DOI found,nosource,Nucleic Acid Conformation,Peptide Elongation Factors,Peptides,Peptidyltransferase,physiology,protein,Protein Binding,RECOGNITION,REGION,Review,RIBONUCLEOPROTEIN,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNATransfer,Structural,structure,translation,translocation,tRNA} } % == BibTeX quality report for spirinRibosomeRNAbasedMolecular2004a: % ? unused Journal abbr (“RNA.Biol”)

@article{sprinzlCompilationTRNASequences1998, title = {Compilation of {{tRNA}} Sequences and Sequences of {{tRNA}} Genes}, author = {Sprinzl, M. and Horn, C. and Brown, M. and Ioudovitch, A. and Steinberg, S.}, year = 1998, month = jan, journal = {Nucleic acids research}, volume = {26}, number = {1}, pages = {148–153}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/26.1.148}, url = {http://nar.oxfordjournals.org/content/26/1/148.short}, abstract = {Sequences of 3279 sequences of tRNA genes and tRNAs published up to December 1996 are included in the compilation. Alignment of the sequences, which is most compatible with the tRNA phylogeny and known three-dimensional structures of tRNA, is used. Sequences and references are available under http://www.uni-bayreuth. de/departments/biochemie/trna/}, keywords = {0,alignment,Animals,Base Sequence,Computer Communication Networks,DatabasesFactual,gene,Genes,genetics,Humans,La,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Phylogeny,Research SupportNon-U.S.Gov’t,Rna,RNATransfer,sequence,Sequence Alignment,SEQUENCES,structure,tRNA} } % == BibTeX quality report for sprinzlCompilationTRNASequences1998: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{srisawatStreptavidinAptamersAffinity2001, title = {Streptavidin Aptamers: Affinity Tags for the Study of {{RNAs}} and Ribonucleoproteins}, author = {Srisawat, C. and Engelke, D.R.}, year = 2001, month = apr, journal = {RNA.}, volume = {7}, number = {4}, pages = {632–641}, publisher = {Cambridge Univ Press}, doi = {10.1017/S135583820100245X}, url = {http://journals.cambridge.org/abstract_S135583820100245X}, abstract = {RNA affinity tags would be very useful for the study of RNAs and ribonucleoproteins (RNPs) as a means for rapid detection, immobilization, and purification. To develop a new affinity tag, streptavidin-binding RNA ligands, termed “aptamers,” were identified from a random RNA library using in vitro selection. Individual aptamers were classified into two groups based on common sequences, and representative members of the groups had sufficiently low dissociation constants to suggest they would be useful affinity tools. Binding of the aptamers to streptavidin was blocked by presaturation of the streptavidin with biotin, and biotin could be used to dissociate RNA/streptavidin complexes. To investigate the practicality of using the aptamer as an affinity tag, one of the higher affinity aptamers was inserted into RPR1 RNA, the large RNA subunit of RNase P. The aptamer-tagged RNase P could be specifically isolated using commercially available streptavidin-agarose and recovered in a catalytically active form when biotin was used as an eluting agent under mild conditions. The aptamer tag was also used to demonstrate that RNase P exists in a monomeric form, and is not tightly associated with RNase MRP, a closely related ribonucleoprotein enzyme. These results show that the streptavidin aptamers are potentially powerful tools for the study of RNAs or RNPs}, keywords = {0,Affinity Labels,BINDING,Binding Sites,Biotin,chemistry,COMPLEX,COMPLEXES,CONSTANTS,Directed Molecular Evolution,Endoribonucleases,enzyme,FORM,In Vitro,IN-VITRO,isolation & purification,La,library,Ligands,metabolism,ModelsMolecular,nosource,Nucleic Acid Conformation,purification,Ribonuclease P,RIBONUCLEOPROTEIN,Ribonucleoproteins,Rna,RNACatalytic,RNAse,SELECTION,sequence,SEQUENCES,Streptavidin,SUBUNIT,Support} } % == BibTeX quality report for srisawatStreptavidinAptamersAffinity2001: % ? Possibly abbreviated journal title RNA.

@article{srivastavaYeastAssayHigh2003a, title = {A Yeast Assay for High Throughput Screening of Natural Anti-Viral Agents}, author = {Srivastava, R. and Lal, S.K.}, year = 2003, month = jan, journal = {Biochem.Biophys.Res.Commun.}, volume = {301}, number = {1}, pages = {218–221}, doi = {10.1016/S0006-291X(02)02995-9}, abstract = {Over the last decade the yeast Saccharomyces cerevisiae has become a popular organism for studying heterologous gene expression and in vivo protein-protein interactions. Many variations of these basic systems have originated over the years. Besides these vast and varied applications of the yeast expression system, S. cerevisiae has also been used extensively in fundamental research as a model simple eukaryote. We have used the S. cerevisiae system to design a high throughput screen for anti-viral agents from natural sources. The design of the assay rests on the ability of the L-A helper virus and the M(1) satellite virus to detect small variations in -1 ribosomal frameshifting. A minor change in frameshifting efficiencies can be detected and clearly shown phenotypically in terms of zones of clearing on an agar plate. Using such a process, we have initiated a high throughput screening process for natural anti-viral agents}, keywords = {anisomycin,antiviral,Antiviral Agents,drugs,efficiency,expression,Frameshifting,gene,Gene Expression,GENE-EXPRESSION,Genetic,IN-VIVO,L-A,La,nosource,ribosomal frameshifting,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sparsomycin,SYSTEM,virology,virus,yeast} } % == BibTeX quality report for srivastavaYeastAssayHigh2003a: % ? Possibly abbreviated journal title Biochem.Biophys.Res.Commun.

@article{srivastava3DimensionalReconstructionMammalian1995, title = {3-{{Dimensional Reconstruction}} of {{Mammalian}} 40 {{S Ribosomal-Subunit Embedded}} in {{Ice}}}, author = {Srivastava, S. and Verschoor, A. and Radermacher, M. and Grassucci, R. and Frank, J.}, year = 1995, month = feb, journal = {Journal of Molecular Biology}, volume = {245}, number = {5}, pages = {461–466}, url = {ISI:A1995QE94000001}, abstract = {A platform-like structure, which appears equivalent to the platform or lobe structure of the 30 S subunit of the eubacterial ribosome, is observed in the reconstruction of the small 40 S ribosomal subunit from images of ice-embedded particles. This cup-shaped structure, 15.0 nm in side length and 13.5 nm wide at its rim, extends obliquely upward on the back of the subunit. Other previously characterized features of the 40 S subunit can readily be identified: the head with its prominent beak structure, the body with its two back lobes expressed as relatively small-scale features, and the two widely separated feet that comprise the base of the subunit}, keywords = {3-DIMENSIONAL RECONSTRUCTION,30 S,40 S RIBOSOMAL SUBUNIT,BASE,Cryoelectron Microscopy,ELECTRON-MICROSCOPY,ESCHERICHIA-COLI,EUKARYOTIC RIBOSOME,MICROGRAPHS,nosource,PARTICLES,RIBOSOMAL-SUBUNIT,ribosome,Rna,structure,SUBUNIT} } % == BibTeX quality report for srivastava3DimensionalReconstructionMammalian1995: % ? Title looks like it was stored in title-case in Zotero

@article{stadlerSARSBeginningUnderstand2003a, title = {{{SARS–beginning}} to Understand a New Virus}, author = {Stadler, K. and Masignani, V. and Eickmann, M. and Becker, S. and Abrignani, S. and Klenk, H.D. and Rappuoli, R.}, year = 2003, month = dec, journal = {Nat.Rev.Microbiol.}, volume = {1}, number = {3}, pages = {209–218}, doi = {10.1038/nrmicro775}, url = {PM:15035025}, abstract = {The 114-day epidemic of the severe acute respiratory syndrome (SARS) swept 29 countries, affected a reported 8,098 people, left 774 patients dead and almost paralyzed the Asian economy. Aggressive quarantine measures, possibly aided by rising summer temperatures, successfully terminated the first eruption of SARS and provided at least a temporal break, which allows us to consolidate what we have learned so far and plan for the future. Here, we review the genomics of the SARS coronavirus (SARS-CoV), its phylogeny, antigenic structure, immune response and potential therapeutic interventions should the SARS epidemic flare up again}, keywords = {0,Animals,classification,genetics,GenomeViral,genomic,Genomics,human,immunology,La,metabolism,nosource,Phylogeny,physiology,protein,Proteins,Review,SARS,Sars Virus,Severe Acute Respiratory Syndrome,structure,supportnon-u.s.gov’t,Temperature,therapy,Viral Proteins,virology,virus} } % == BibTeX quality report for stadlerSARSBeginningUnderstand2003a: % ? Possibly abbreviated journal title Nat.Rev.Microbiol.

@article{stage-zimmermannFactorsAffectingNuclear2000, title = {Factors Affecting Nuclear Export of the {{60S}} Ribosomal Subunit in Vivo}, author = {{Stage-Zimmermann}, T. and Schmidt, U. and Silver, P.A.}, year = 2000, month = nov, journal = {Molecular biology of the cell}, volume = {11}, number = {11}, pages = {3777–3789}, publisher = {Am Soc Cell Biol}, doi = {10.1091/mbc.11.11.3777}, url = {http://www.molbiolcell.org/cgi/content/abstract/11/11/3777}, abstract = {In Saccharomyces cerevisiae, the 60S ribosomal subunit assembles in the nucleolus and then is exported to the cytoplasm, where it joins the 40S subunit for translation. Export of the 60S subunit from the nucleus is known to be an energy-dependent and factor-mediated process, but very little is known about the specifics of its transport. To begin to address this problem, an assay was developed to follow the localization of the 60S ribosomal subunit in S. cerevisiae. Ribosomal protein L11b (Rpl11b), one of the approximately 45 ribosomal proteins of the 60S subunit, was tagged at its carboxyl terminus with the green fluorescent protein (GFP) to enable visualization of the 60S subunit in living cells. A panel of mutant yeast strains was screened for their accumulation of Rpl11b-GFP in the nucleus as an indicator of their involvement in ribosome synthesis and/or transport. This panel included conditional alleles of several rRNA-processing factors, nucleoporins, general transport factors, and karyopherins. As predicted, conditional alleles of rRNA-processing factors that affect 60S ribosomal subunit assembly accumulated Rpl11b-GFP in the nucleus. In addition, several of the nucleoporin mutants as well as a few of the karyopherin and transport factor mutants also mislocalized Rpl11b-GFP. In particular, deletion of the previously uncharacterized karyopherin KAP120 caused accumulation of Rpl11b-GFP in the nucleus, whereas ribosomal protein import was not impaired. Together, these data further define the requirements for ribosomal subunit export and suggest a biological function for KAP120}, keywords = {0,60S subunit,Active TransportCell Nucleus,Alleles,assembly,cancer,Carrier Proteins,Cell Division,Cell Nucleus,CELLS,CEREVISIAE,chemistry,COMPLEX,COMPLEXES,Cytoplasm,Fungal Proteins,FUSION PROTEIN,Gene Deletion,genetics,gfp,GREEN FLUORESCENT PROTEIN,Green Fluorescent Proteins,growth & development,IN-VIVO,Karyopherins,La,LOCALIZATION,Luminescent Proteins,metabolism,Methods,Molecular Biology,MUTANTS,Mutation,nosource,Nuclear Pore Complex Proteins,Nuclear Proteins,Nucleocytoplasmic Transport Proteins,nucleolus,pharmacology,PRECURSOR,protein,Proteins,ReceptorsCytoplasmic and Nuclear,Recombinant Fusion Proteins,Research SupportU.S.Gov’tP.H.S.,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,RIBOSOME SYNTHESIS,Ribosomes,Rna,RNA Precursors,RNA ProcessingPost-Transcriptional,RNA-Binding Proteins,RNA-BINDING-PROTEIN,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SUBUNIT,translation,TRANSPORT,VISUALIZATION,yeast} } % == BibTeX quality report for stage-zimmermannFactorsAffectingNuclear2000: % ? unused Journal abbr (“Mol.Biol.Cell”)

@article{staggProblemsTransorientationHypothesis2002, title = {Problems with the Transorientation Hypothesis}, author = {Stagg, S.M. and Valle, M. and Agrawal, R.K. and Frank, J. and Harvey, S.C.}, year = 2002, journal = {RNA.}, volume = {8}, number = {9}, pages = {1093–1094}, publisher = {Cambridge Univ Press}, doi = {10.1017/S1355838202027061}, url = {http://journals.cambridge.org/abstract_S1355838202027061}, keywords = {La,nosource} } % == BibTeX quality report for staggProblemsTransorientationHypothesis2002: % ? Possibly abbreviated journal title RNA.

@article{stahlVersatileVectorsStudy1995, title = {Versatile Vectors to Study Recoding: Conservation of Rules between Yeast and Mammalian Cells.}, author = {Stahl, G. and Bidou, L. and Rousset, J.-P. and Cassan, M.}, year = 1995, journal = {Nucleic acids research}, volume = {23}, number = {9}, pages = {1557–1560}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/23.9.1557}, url = {http://nar.oxfordjournals.org/content/23/9/1557.short}, keywords = {bicistronic,Frameshifting,human,nosource,recoding,RULES,vector,vectors,yeast} } % == BibTeX quality report for stahlVersatileVectorsStudy1995: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{stahlCaseInvolvementNMD2000, title = {The Case against the Involvement of the {{NMD}} Proteins in Programmed Frameshifting.}, author = {Stahl, G. and Bidou, L. and Hatin, I. and Namy, O. and Rousset, J.P. and Farabaugh, P.}, year = 2000, month = dec, journal = {RNA}, volume = {6}, number = {12}, pages = {1687–1688}, publisher = {Cambridge Univ Press}, doi = {10.1017/S1355838200001874}, url = {http://journals.cambridge.org/abstract_S1355838200001874}, abstract = {Sequences in certain mRNAs program the ribosome to undergo a noncanonical translation event, translational frameshifting, translational hopping, or termination readthrough. These sequences are termed recoding sites, because they cause the ribosome to change temporarily its coding rules. Cis and trans-acting factors sensitively modulate the efficiency of recoding events. In an attempt to quantitate the effect of these factors we have developed a dual-reporter vector using the lacZ and luc genes to directly measure recoding efficiency. We were able to confirm the effect of several factors that modulate frameshift or readthrough efficiency at a variety of sites. Surprisingly, we were not able to confirm that the complex of factors termed the surveillance complex regulates translational frameshifting. This complex regulates degradation of nonsense codon-containing mRNAs and we confirm that it also affects the efficiency of nonsense suppression. Our data suggest that the surveillance complex is not a general regulator of translational accuracy, but that its role is closely tied to the translational termination and initiation processes}, keywords = {accuracy,Amino Acid Sequence,Base Sequence,Codon,COMPLEX,COMPLEXES,DECAY,degradation,efficiency,Escherichia coli,frameshift,Frameshift Mutation,Frameshifting,gene,Genes,Genes-Reporter,genetics,hopping,initiation,metabolism,Molecular Sequence Data,mRNA,Mutation,NMD,nonsense suppression,nonsense-mediated decay,nosource,Plasmids,programmed frameshifting,protein,Proteins,readthrough,recoding,ribosomal frameshifting,ribosome,RULES,Saccharomyces cerevisiae,sequence,support-non-u.s.gov’t,support-u.s.gov’t-p.h.s.,suppression,termination,Trans-Activation (Genetics),translation,Translation-Genetic,vector} }

@article{stahlProgrammedTranslationalFrameshifting2001a, title = {Programmed +1 Translational Frameshifting in the Yeast {{Saccharomyces}} Cerevisiae Results from Disruption of Translational Error Correction}, author = {Stahl, G. and Ben Salem, S. and Li, Z. and McCarty, G. and Raman, A. and Shah, M. and Farabaugh, P.J.}, year = 2001, journal = {Cold Spring Harbor Symposia on Quantitative Biology}, volume = {66:249-58.}, pages = {249–258}, doi = {10.1101/sqb.2001.66.249}, keywords = {Base Sequence,BIOLOGY,CEREVISIAE,chemistry,DISRUPTION,Frameshift Mutation,Frameshifting,genetics,ModelsMolecular,Mutagenesis,nosource,Nucleic Acid Conformation,Retroelements,Review,Ribosomes,RNAFungal,RNARibosomal,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,TRANSLATIONAL FRAMESHIFTING,TranslationGenetic,yeast} } % == BibTeX quality report for stahlProgrammedTranslationalFrameshifting2001a: % ? unused Journal abbr (“Cold Spring Harb.Symp.Quant.Biol.”)

@article{stahlRibosomeStructureRevisiting2002, title = {Ribosome Structure: Revisiting the Connection between Translational Accuracy and Unconventional Decoding}, author = {Stahl, G. and McCarty, G.P. and Farabaugh, P.J.}, year = 2002, month = apr, journal = {Trends in Biochemical Sciences}, volume = {27}, number = {4}, pages = {178–183}, publisher = {Elsevier}, doi = {10.1016/S0968-0004(02)02064-9}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000402020649}, abstract = {The ribosome is a molecular machine that converts genetic information in the form of RNA, into protein. Recent structural studies reveal a complex set of interactions between the ribosome and its ligands, mRNA and tRNA, that indicate ways in which the ribosome could avoid costly translational errors. Ribosomes must decode each successive codon accurately, and structural data provide a clear indication of how ribosomes limit recruitment of the wrong tRNA (sense errors). In a triplet-based genetic code there are three potential forward reading frames, only one of which encodes the correct protein. Errors in which the ribosome reads a codon out of the normal reading frame (frameshift errors) occur less frequently than sense errors, although it is not clear from structural data how these errors are avoided. Some mRNA sequences, termed programmed-frameshift sites, cause the ribosome to change reading frame. Based on recent work on these sites, this article proposes that the ribosome uses the structure of the codon-anticodon complex formed by the peptidyl-tRNA, especially its wobble interaction, to constrain the incoming aminoacyl-tRNA to the correct reading frame}, keywords = {accuracy,chemistry,Codon,COMPLEX,COMPLEXES,decoding,frameshift,Frameshifting,Genetic,Genetic Code,genetics,Ligands,mRNA,nosource,protein,Protein Conformation,Review,ribosome,Ribosomes,Rna,RNARibosomal,sequence,SEQUENCES,Structural,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,TranslationGenetic,tRNA} } % == BibTeX quality report for stahlRibosomeStructureRevisiting2002: % ? unused Journal abbr (“Trends Biochem.Sci.”)

@article{stansfieldProductsSUP45ERF11995a, title = {The Products of the ⬚{{SUP45}}⬚ ({{eRF1}}) and ⬚{{SUP35}}⬚ Genes Interact to Mediate Translational Termination in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Stansfield, I. and Jones, K.M. and Kushnirov, V.V. and Dagkesamanskaya, A.R. and Poznyakovski, A.I. and Paushkin, S.V. and Nierras, C.R. and Cox, B.S. and {Ter-Avanesyan}, M.D. and Tuite, M.F.}, year = 1995, journal = {EMBO J.}, volume = {14}, pages = {4365–4673}, doi = {10.1002/j.1460-2075.1995.tb00111.x}, keywords = {gene,Genes,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sup35,sup45,termination,translation,yeast} } % == BibTeX quality report for stansfieldProductsSUP45ERF11995a: % ? Possibly abbreviated journal title EMBO J.

@article{stansfieldMissenseTranslationErrors1998a, title = {Missense Translation Errors in {{Saccharomyces}} Cerevisiae}, author = {Stansfield, I. and Jones, K.M. and Herbert, P. and Lewendon, A. and Shaw, W.V. and Tuite, M.F.}, year = 1998, journal = {Journal of Molecular Biology}, volume = {282}, number = {1}, pages = {13–24}, doi = {10.1006/jmbi.1998.1976}, url = {ISI:000075854900002}, abstract = {We describe the development of a novel plasmid-based assay for measuring the in vivo frequency of misincorporation of amino acids into polypeptide chains in the yeast Saccharomyces cerevisiae. The assay is based upon the measurement of the catalytic activity of an active site mutant of type III chloramphenicol acetyl transferase (CAT(III)) expressed in S. cerevisiae. A His195(CAC) –{\(>\)} Tyr195(UAC) mutant of CAT(III) is completely inactive, but catalytic activity can be restored by misincorporation of histidine at the mutant UAC codon. The average error frequency of misincorporation of histidine at this tyrosine UAC codon in wild-type yeast strains was measured as 0.5 x 10(-5) and this frequency was increased some 50-fold by growth in the presence of paromomycin, a known translational-error-inducing antibiotic. A detectable frequency of misincorporation of histidine at a mutant Ala195 GCU codon was also measured as 2 x 10(-5), but in contrast to the Tyr195 –{\(>\)} His195 misincorporation event, the frequency of histidine misincorporation at Ala195 GCU was not increased by paromomycin, inferring that this error did not result from miscognate codon-anticodon interaction. The His195 to Tyr195 missense error assay was used to demonstrate increased frequencies of missense error at codon 195 in SUP44 and SUP46 mutants. These two mutants have previously been shown to exhibit a translation termination error phenotype and the sup44(+) and sup46(+) genes encode the yeast ribosomal proteins S4 and S9, respectively. These data represent the first accurate in vivo measurement of a specific mistranslation event in a eukaryotic cell and directly confirm that the eukaryotic ribosome plays an important role in controlling missense errors arising from non-cognate codon-anticodon interactions. (C) 1998 Academic Press}, keywords = {ACID,ACIDS,ACTIVE-SITE,Amino Acids,AMINO-ACID,AMINO-ACIDS,antibiotic,CEREVISIAE,Chloramphenicol,chloramphenicol acetyl transferase (CAT),CHLORAMPHENICOL ACETYLTRANSFERASE,Codon,CODON-ANTICODON INTERACTION,development,ERRORS,ESCHERICHIA-COLI,EUKARYOTIC RIBOSOME,gene,Genes,GROWTH,Histidine,IN-VIVO,M,MAJOR DETERMINANT,misincorporation,missense translation,MUTANTS,MUTATIONS,nosource,Paromomycin,Phenotype,PHENOTYPIC SUPPRESSION,POLYPEPTIDE,POLYPEPTIDE-CHAIN,POLYPEPTIDE-CHAINS,protein,Proteins,RAM PROTEIN,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SITE,termination,TRANSFER-RNA,translation,TRANSLATION TERMINATION,WILD-TYPE,yeast,yeast (Saccharomyces cerevisiae)} }

@article{stapleGuanidinoneomycinRecognitionHIV12008, title = {Guanidinoneomycin {{B Recognition}} of an {{HIV-1 RNA Helix}}}, author = {Staple, D.W. and Venditti, V. and Niccolai, N. and {Elson-Schwab}, L. and Tor, Y. and Butcher, S.E.}, year = 2008, journal = {Chembiochem.}, volume = {9}, number = {1}, pages = {93–102}, publisher = {Wiley Online Library}, doi = {10.1002/cbic.200700251}, url = {http://onlinelibrary.wiley.com/doi/10.1002/cbic.200700251/full}, abstract = {Aminoglycoside antibiotics are small-molecule drugs that bind RNA. The affinity and specificity of aminoglycoside binding to RNA can be increased through chemical modification, such as guanidinylation. Here, we report the binding of guanidinoneomycin B (GNB) to an RNA helix from the HIV-1 frameshift site. The binding of GNB increases the melting temperature (T(m)) of the frameshift-site RNA by at least 10 degrees C, to a point at which a melting transition is not even observed in 2 M urea. A structure of the complex was obtained by using multidimensional heteronuclear NMR spectroscopic methods. We also used a novel paramagnetic-probe assay to identify the site of GNB binding to the surface of the RNA. GNB makes major-groove contacts to two sets of Watson-Crick bases and is in van der Waals contact with a highly structured ACAA tetraloop. Rings I and II of GNB fit into the major groove and form the binding interface with the RNA, whereas rings III and IV are exposed to the solvent and disordered. The binding of GNB causes a broadening of the major groove across the binding site}, keywords = {AMINOGLYCOSIDE ANTIBIOTICS,antibiotic,antibiotics,BASE,BASES,BINDING,BINDING-SITE,Biochemistry,CHEMICAL MODIFICATION,COMPLEX,COMPLEXES,drugs,FORM,frameshift,Hiv-1,IDENTIFY,interface,La,M,Methods,modification,NMR,nosource,RECOGNITION,Rna,SITE,SPECIFICITY,structure,Temperature,Urea} } % == BibTeX quality report for stapleGuanidinoneomycinRecognitionHIV12008: % ? Possibly abbreviated journal title Chembiochem. % ? Title looks like it was stored in title-case in Zotero

@article{starckPuromycinOligonucleotidesReveal2002, title = {Puromycin Oligonucleotides Reveal Steric Restrictions for Ribosome Entry and Multiple Modes of Translation Inhibition.}, author = {Starck, S.R. and Roberts, R.W.}, year = 2002, month = jul, journal = {RNA}, volume = {8}, number = {7}, pages = {890–903}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838202022069}, url = {http://rnajournal.cshlp.org/content/8/7/890.short}, abstract = {Peptidyl transferase inhibitors have generally been studied using simple systems and remain largely unexamined In in vitro translation extracts. Here, we investigate the potency, product distribution, and mechanism of various puromycin-oligonucleotide conjugates (1 to 44 nt with 3’-puromycin) In a reticulocyte lysate cell-free translation system. Surprisingly, the potency decreases as the chain length of the oligonucleotide is increased in this series, and only very short puromycin conjugates function efficiently (IC50 {\(<\)} 50 microM). This observation stands in contrast with work on isolated large ribosomal subunits, which Indicates that many of the puromycin-oligonucleotide conjugates we studied should have higher affinity for the peptidyl transferase center than puromycin itself. Two tRNA(Al)-derived minihelices containing puromycin provide an exception to the size trend, and are the only constructs longer than 4 nt with any appreciable potency (IC50 = 40-56 microM). However, the puromycin minihelices inhibit translation by sequestering one or more soluble translation factors, and do not appear to participate in detectable peptide bond formation with the nascent chain. In contrast, puromycin and other short derivatives act in a factor-independent fashion at the peptidyl transferase center and readily become conjugated to the nascent protein chain. However, even for the short derivatives, much of the translation inhibition occurs without peptide bond formation between puromycin and the nascent chain, a revision of the classical model for puromycin function. This peptide bond-independent mode is likely a combination of multiple effects including inhibition of initiation and failure to properly recycle translation complexes that have reacted with puromycin}, keywords = {animal,Base Sequence,Binding Sites,Carboxypeptidases,Cell-Free System,chemistry,COMPLEX,COMPLEXES,derivatives,drug effects,genetics,Globins,In Vitro,in vitro translation,IN-VITRO,INHIBITION,initiation,lysate,MECHANISM,metabolism,ModelsBiological,nosource,Nucleic Acid Conformation,Oligonucleotides,Oligoribonucleotides,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,pharmacology,protein,Puromycin,Rabbits,Reticulocytes,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,RNAMessenger,SUBUNIT,supportu.s.gov’tp.h.s.,SYSTEM,translation,TranslationGenetic} }

@article{starkArrangementTRNAsPre1997, title = {Arrangement of {{tRNAs}} in Pre- and Posttranslocational Ribosomes Revealed by Electron Cryomicroscopy}, author = {Stark, H. and Orlova, E.V. and RinkeAppel, J. and Junke, N. and Mueller, F. and Rodnina, M. and Wintermeyer, W. and Brimacombe, R. and {vanHeel}, M.}, year = 1997, month = jan, journal = {Cell}, volume = {88}, number = {1}, pages = {19–28}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(00)81854-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867400818541}, abstract = {The three-dimensional structure of the translating 70S E. coli ribosome is presented in its two main conformations: the pretranslocational and the posttranslocational states. Using electron cryomicroscopy and angular reconstitution, structures at 20 Angstrom resolution were obtained, which, when compared with our earlier reconstruction of ‘’empty’’ ribosomes, showed densities corresponding to tRNA molecules-at the P and E sites for posttranslocational ribosomes and at the A and P sites for pretranslocational ribosomes. The P-site tRNA lies directly above the bridge connecting the two ribosomal subunits, with the A-site tRNA fitted snugly against it at an angle of similar to 50 degrees, toward the L7/L12 side of the ribosome. The E-site tRNA appears to lie between the side robe of the 30S subunit and the L1 protuberance}, keywords = {16S RNA,A SITE,A-SITE,ANGSTROM RESOLUTION,ANGSTROM-RESOLUTION,ANGULAR RECONSTITUTION,ARRANGEMENT,CONFORMATION,CROSS-LINKING,DECODING REGION,E,E site,ESCHERICHIA-COLI RIBOSOMES,EXIT SITE,FLUORESCENCE ENERGY-TRANSFER,L1,MESSENGER-RNA,nosource,P SITE,P-SITE,P-SITES,PHENYLALANINE TRANSFER-RNA,RECONSTITUTION,RESOLUTION,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,SITE,SITES,structure,SUBUNIT,SUBUNITS,tRNA} }

@article{starkRibosomeInteractionsAminoacyltRNA2002, title = {Ribosome Interactions of Aminoacyl-{{tRNA}} and Elongation Factor {{Tu}} in the Codon-Recognition Complex}, author = {Stark, H. and Rodnina, M.V. and Wieden, H.J. and Zemlin, F. and Wintermeyer, W. and {}{van Heel}, M.}, year = 2002, month = nov, journal = {Nature Structural & Molecular Biology}, volume = {9}, number = {11}, pages = {849–854}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/nsmb/journal/v9/n11/abs/nsb859.html}, abstract = {The mRNA codon in the ribosomal A-site is recognized by aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 A resolution three-dimensional reconstruction determined by cryo-electron microscopy of the kirromycin-stalled codon-recognition complex. The structure of the ternary complex is distorted by binding of the tRNA anticodon arm in the decoding center. The aa-tRNA interacts with 16S rRNA, helix 69 of 23S rRNA and proteins S12 and L11, while the sarcin-ricin loop of 23S rRNA contacts domain 1 of EF-Tu near the nucleotide-binding pocket. These results provide a detailed snapshot view of an important functional state of the ribosome and suggest mechanisms of decoding and GTPase activation}, keywords = {A-SITE,activation,Anticodon,BINDING,chemistry,Codon,COMPLEX,COMPLEXES,Cryoelectron Microscopy,decoding,EFTu,elongation,GTP,GTPase,MECHANISM,MECHANISMS,mRNA,No DOI found,nosource,protein,Proteins,ribosome,rRNA,structure,tRNA} } % == BibTeX quality report for starkRibosomeInteractionsAminoacyltRNA2002: % ? unused Journal abbr (“Nat.Struct.Biol.”)

@article{starkThreedimensionalElectronCryomicroscopy2002, title = {Three-Dimensional Electron Cryomicroscopy of Ribosomes}, author = {Stark, H.}, year = 2002, month = feb, journal = {Current Protein and Peptide Science}, volume = {3}, number = {1}, pages = {79–91}, publisher = {Bentham Science Publishers}, doi = {10.2174/1389203023380873}, url = {http://www.ingentaconnect.com/content/ben/cpps/2002/00000003/00000001/art00006}, abstract = {Single particle electron cryomicroscopy is nowadays routinely used to generate three-dimensional structural information of ribosomal complexes without the need of crystallization. A large number of structures of functional important ribosomal complexes have thus been determined using this technique. In E. coli 70S ribosomes all three tRNA binding sites could be localized. The ternary complex of EF-TutRNAGTP that delivers the tRNA to the ribosome was directly visualized in a ribosomal complex blocked by the antibiotic kirromycin. Three different functional states of translocation have been studied and the respective EF-G binding sites have been mapped. The level of resolution achievable with electron cryomicroscopy allows conformational changes in the domain structures of elongation factors to be modelled in terms of rigid body movements. Structural information on eukaryotic ribosomes is also available for yeast and mammalian 80S ribosomes. The structural differences between rabbit 80S and E. coli 70S ribosomes could be interpreted in terms of ribosomal RNA expansion segments in the 18S and 23S RNA. The EF-G homologue EF2 was mapped analysing the structure of an 80SEF2sodarin complex and most recently the binding of a hepatitis C virus IRES element to a yeast 40S subunit has been studied. The first electron cryomicroscopical 3D reconstructions have further been used to overcome the initial phasing problems in X-ray crystallographic studies of the ribosome facilitating structure determination of the recent atomic resolution structures of the 30S and 50S ribosomal subunits. In turn, the knowledge of the atomic structure of the ribosome makes detailed interpretations of cryo-EM maps possible at approximately 20 A resolution}, keywords = {0,23S RNA,70S RIBOSOME,antibiotic,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,BODIES,chemistry,COMPLEX,COMPLEXES,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,Cryoelectron Microscopy,Crystallization,CrystallographyX-Ray,DOMAIN,E,EF-G,elongation,elongation factors,ELONGATION-FACTOR-G,ELONGATION-FACTOR-TU,ELONGATION-FACTORS,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,FACTOR TU,Germany,HEPATITIS-C,INFORMATION,La,metabolism,Methods,Movement,nosource,Nucleic Acid Conformation,Peptide Elongation Factor G,Peptide Elongation Factor Tu,protein,Protein Conformation,Proteins,RESOLUTION,Review,Ribosomal Proteins,ribosomal RNA,RIBOSOMAL-PROTEIN,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNARibosomal,RNATransfer,SITE,SITES,Structural,structure,SUBUNIT,SUBUNITS,translocation,tRNA,tRNA binding,TU,ultrastructure,virus,yeast} } % == BibTeX quality report for starkThreedimensionalElectronCryomicroscopy2002: % ? unused Journal abbr (“Curr.Protein Pept.Sci.”)

@article{steelSequenceDevelopmentalRegulation1995, title = {Sequence and Developmental Regulation of the Gene That Encodes the {{Dictyostelium}} Discoideum {{L3}} Ribosomal Protein}, author = {Steel, L.F. and Farnum, P.D. and Kunapoli, P.}, year = 1995, journal = {Gene}, volume = {162}, number = {1}, pages = {123–128}, publisher = {Elsevier}, doi = {10.1016/0378-1119(95)00361-9}, url = {http://linkinghub.elsevier.com/retrieve/pii/0378111995003619}, abstract = {We have isolated and characterized genomic and cDNA recombinant plasmids that encode the Dictyostelium discoideum (Dd) ribosomal protein L3 (rpL3). Genomic plasmids were identified using a probe derived from the Saccharomyces cerevisiae TCM1 gene, that encodes the yeast rpL3. The DdL3 gene contains two introns and encodes a protein 398 amino acids in length that shows a high degree of homology to the conserved rpL3 protein of both lower and higher eukaryotes. During development, both the pattern of accumulation of DdL3 mRNA and changes in its translational activity are identical to those observed for other r-protein mRNAs}, keywords = {0,ACID,ACIDS,Amino Acid Sequence,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,Animals,Base Sequence,cancer,CEREVISIAE,CloningMolecular,development,Dictyostelium,ENCODES,gene,Gene Expression RegulationDevelopmental,GenesProtozoan,genetics,genomic,growth & development,INTRON,Introns,L3,La,Molecular Sequence Data,mRNA,nosource,PLASMID,Plasmids,protein,Proteins,regulation,Ribosomal Proteins,Rna,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence AnalysisDNA,supportu.s.gov’tp.h.s.,TCM1,TranscriptionGenetic,TranslationGenetic,yeast} }

@article{steinCloningCharacterizationMEK61996, title = {Cloning and Characterization of {{MEK6}}, a Novel Member of the Mitogen-Activated Protein Kinase Kinase Cascade.}, author = {Stein, B. and Brady, H. and Yang, M.X. and Young, D.B. and Barbosa, M.S.}, year = 1996, journal = {Journal of Biological Chemistry}, volume = {271}, number = {19}, pages = {11427–11433}, publisher = {ASBMB}, doi = {10.1074/jbc.271.19.11427}, url = {http://www.jbc.org/content/271/19/11427.short}, keywords = {anisomycin,cloning,kinase,nosource,p38,protein} } % == BibTeX quality report for steinCloningCharacterizationMEK61996: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{steinTorsionangleMolecularDynamics1997b, title = {Torsion-Angle Molecular Dynamics as a New Efficient Tool for {{NMR}} Structure Calculation}, author = {Stein, E.G. and Rice, L.M. and Brunger, A.T.}, year = 1997, month = jan, journal = {Journal of Magnetic Resonance}, volume = {124}, number = {1}, pages = {154–164}, publisher = {San Diego: Academic Press, 1993-1996.}, doi = {10.1006/jmre.1996.1027}, url = {http://saturn.med.nyu.edu/~stein/pdfs/Stein1997.pdf}, abstract = {Molecular dynamics in torsion-angle space was applied to nuclear magnetic resonance structure calculation using nuclear Overhauser effect-derived distances and J-coupling-constant-derived dihedral angle restraints. Compared to two other commonly used algorithms, molecular dynamics in Cartesian space and metric-matrix geometry combined with Cartesian molecular dynamics, the method shows increased computational efficiency and success rate for large proteins, and it shows a dramatically increased radius of convergence for DNA. The torsion-angle molecular dynamics algorithm starts from an extended strand conformation and proceeds in four stages: high-temperature torsion-angle molecular dynamics, slow-cooling torsion-angle molecular dynamics, Cartesian molecular dynamics, and minimization. Tests were carried out using experimental NMR data for protein G, interleukin-8, villin 14T, and a 12 base-pair duplex of DNA, and simulated NMR data for bovine pancreatic trypsin inhibitor. For villin 14T , a monomer consisting of 126 residues, structure determination by torsion-angle molecular dynamics has a success rate of 85%, a more than twofold improvement over other methods. In the case of the 12 base-pair DNA duplex, torsion-angle molecular dynamics had a success rate of 52% while Cartesian molecular dynamics and metric-matrix distance geometry always failed}, keywords = {0,Algorithms,Animals,BASE-PAIR,Carrier Proteins,Cattle,chemistry,Comparative Study,CONFORMATION,Dna,DYNAMICS,efficiency,Energy Transfer,INHIBITOR,inhibitors,Interleukin-8,La,Methods,Microfilament Proteins,Nerve Tissue Proteins,NMR,nosource,nuclear magnetic resonance,Nuclear Magnetic ResonanceBiomolecular,NUCLEAR-MAGNETIC-RESONANCE,Nucleic Acid Conformation,protein,Protein Conformation,Proteins,Reproducibility of Results,RESIDUES,structure,supportu.s.gov’tnon-p.h.s.,Trypsin,Trypsin Inhibitors} } % == BibTeX quality report for steinTorsionangleMolecularDynamics1997b: % ? unused Journal abbr (“J.Magn Reson.”)

@article{steinbergerFunctionalDeletionCCR52000, title = {Functional Deletion of the {{CCR5}} Receptor by Intracellular Immunization Produces Cells That Are Refractory to {{CCR5-dependent HIV-1}} Infection and Cell Fusion}, author = {Steinberger, P. and {Andris-Widhopf}, J. and Buhler, B. and Torbett, B.E. and Barbas, C.F.}, year = 2000, month = jan, journal = {Proceedings of the National Academy of Sciences}, volume = {97}, number = {2}, pages = {805–810}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.97.2.805}, url = {http://www.pnas.org/content/97/2/805.short}, abstract = {Studies of naturally occurring polymorphisms of the CCR5 gene have shown that deletion of the functional receptor or reduced expression of the gene can have beneficial effects in preventing HIV-1 infection or delaying disease. Because these polymorphisms are found in otherwise healthy people, strategies that aim to prevent or limit expression of CCR5 should be beneficial in the treatment of HIV-1 disease. To test this approach we have developed a CCR5-specific single-chain antibody that was expressed intracellularly and retained in the endoplasmic reticulum. This CCR5-intrabody efficiently blocked surface expression of human and rhesus CCR5 and thus prevented cellular interactions with CCR5-dependent HIV-1 and simian immunodeficiency virus envelope glycoprotein. Intrabody-expressing cells were shown to be highly refractory to challenge with R5 HIV-1 viruses or infected cells. These results suggest that gene therapy approaches that deliver this intracellular antibody could be of benefit to infected individuals. Because the antibody reacts with a conserved primate epitope on CCR5 this strategy can be tested in nonhuman lentivirus models of HIV-1 disease}, keywords = {0,Animals,Antibodies,AntibodiesMonoclonal,antibody,BIOLOGY,Cell Fusion,Cell Line,CELLS,Cos Cells,disease,Endoplasmic Reticulum,ENDOPLASMIC-RETICULUM,epitope,expression,gene,Gene Expression Regulation,Gene Productsenv,GENE-PRODUCT,genetics,growth & development,HIV Infections,Hiv-1,human,Humans,Immunization,IMMUNODEFICIENCY-VIRUS,immunology,INFECTED CELLS,INFECTED-CELLS,INFECTION,La,Macaca mulatta,MODEL,models,Molecular Biology,nosource,physiology,Plasmids,prevention & control,PRODUCT,PRODUCTS,ReceptorsCCR5,ReceptorsCell Surface,Support,therapy,Transfection,virology,virus,Viruses} } % == BibTeX quality report for steinbergerFunctionalDeletionCCR52000: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{steitzRNAFirstMacromolecular2003, title = {{{RNA}}, the First Macromolecular Catalyst: The Ribosome Is a Ribozyme}, author = {Steitz, T.A. and Moore, P.B.}, year = 2003, journal = {Trends in biochemical sciences}, volume = {28}, number = {8}, pages = {411–418}, publisher = {Elsevier}, doi = {10.1016/S0968-0004(03)00169-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0968000403001695}, abstract = {Recently, the atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with substrates have been determined. These have provided exciting new insights into the principles of RNA structure, the mechanism of the peptidyl-transferase reaction and early events in the evolution of this RNA-protein complex assembly that is essential in all cells. The structures of the large subunit bound to a variety of antibiotics explain the effects of antibiotic resistance mutations and provide promise for the development of new antibiotics}, keywords = {antibiotic,antibiotics,assembly,CELLS,COMPLEX,COMPLEXES,development,Evolution,Haloarcula,Haloarcula marismortui,La,MECHANISM,Mutation,MUTATIONS,nosource,peptidyl transferase,PEPTIDYL-TRANSFERASE,Peptidyltransferase,RESISTANCE,RESISTANCE MUTATIONS,Review,review article,RIBOSOMAL-SUBUNIT,ribosome,ribozyme,Rna,structure,SUBUNIT} } % == BibTeX quality report for steitzRNAFirstMacromolecular2003: % ? unused Journal abbr (“Trends Biochem.Sci.”)

@article{steitzStructuralBasisPeptidebond2005, title = {On the Structural Basis of Peptide-Bond Formation and Antibiotic Resistance from Atomic Structures of the Large Ribosomal Subunit}, author = {Steitz, T.A.}, year = 2005, month = feb, journal = {FEBS letters}, volume = {579}, number = {4}, pages = {955–958}, publisher = {Elsevier}, doi = {10.1016/j.febslet.2004.11.053}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579304014358}, abstract = {The atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with substrates and antibiotics have provided insights into the way the 3000 nucleotide 23S rRNA folds into a compact, specific structure and interacts with 27 ribosomal proteins as well as the structural basis of the peptidyl transferase reaction and its inhibition by antibiotics. The structure shows that the ribosome is indeed a ribozyme}, keywords = {0,Anti-Bacterial Agents,antibiotic,antibiotics,Biochemistry,Biophysics,chemistry,COMPLEX,COMPLEXES,drug effects,Drug ResistanceMicrobial,Haloarcula,Haloarcula marismortui,INHIBITION,La,metabolism,Molecular Structure,nosource,Nucleic Acid Conformation,peptide bond formation,Peptide Chain ElongationTranslational,PEPTIDE-BOND FORMATION,peptidyl transferase,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,pharmacology,physiology,protein,Protein Biosynthesis,Proteins,RESISTANCE,Review,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,ribozyme,Rna,RNARibosomal23S,RNATransfer,rRNA,Structural,STRUCTURAL BASIS,structure,SUBUNIT,Transferases} } % == BibTeX quality report for steitzStructuralBasisPeptidebond2005: % ? unused Journal abbr (“FEBS Lett.”)

@article{steitzStructuralUnderstandingDynamic2008a, title = {A Structural Understanding of the Dynamic Ribosome Machine}, author = {Steitz, T.A.}, year = 2008, month = mar, journal = {Nat.Rev.Mol Cell Biol}, volume = {9}, number = {3}, pages = {242–253}, doi = {10.1038/nrm2352}, url = {PM:18292779}, abstract = {Ribosomes, which are central to protein synthesis and convert transcribed mRNAs into polypeptide chains, have been the focus of structural and biochemical studies for more than 50 years. The structure of its larger subunit revealed that the ribosome is a ribozyme with RNA at the heart of its enzymatic activity that catalyses peptide bond formation. Numerous initiation, elongation and release factors ensure that protein synthesis occurs progressively and with high specificity. In the past few years, high-resolution structures have provided molecular snapshots of different intermediates in ribosome-mediated translation in atomic detail. Together, these studies have revolutionized our understanding of the mechanism of protein synthesis}, keywords = {0,Aminoacylation,Animals,Biochemistry,Biophysics,BOND FORMATION,Catalysis,chemistry,elongation,heart,Humans,initiation,INTERMEDIATE,La,MECHANISM,metabolism,mRNA,nosource,peptide bond formation,POLYPEPTIDE,POLYPEPTIDE-CHAIN,POLYPEPTIDE-CHAINS,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,RELEASE,release factor,RELEASE FACTORS,Review,ribosome,Ribosomes,ribozyme,Rna,RNAMessenger,RNATransferAla,SPECIFICITY,Structural,structure,SUBUNIT,Support,translation} } % == BibTeX quality report for steitzStructuralUnderstandingDynamic2008a: % ? Possibly abbreviated journal title Nat.Rev.Mol Cell Biol

@article{stelzlRNAstructuralMimicryEscherichia2003, title = {{{RNA-structural}} Mimicry in {{Escherichia}} Coli Ribosomal Protein {{L4-dependent}} Regulation of the {{S10}} Operon}, author = {Stelzl, U. and Zengel, J.M. and Tovbina, M. and Walker, M. and Nierhaus, K.H. and Lindahl, L. and Patel, D.J.}, year = 2003, month = jul, journal = {Journal of Biological Chemistry}, volume = {278}, number = {30}, pages = {28237–28245}, publisher = {ASBMB}, doi = {10.1074/jbc.M302651200}, url = {http://www.jbc.org/content/278/30/28237.short}, abstract = {Ribosomal protein L4 regulates the 11-gene S10 operon in Escherichia coli by acting, in concert with transcription factor NusA, to cause premature transcription termination at a Rho-independent termination site in the leader sequence. This process presumably involves L4 interaction with the leader mRNA. Here, we report direct, specific, and independent binding of ribosomal protein L4 to the S10 mRNA leader in vitro. Most of the binding energy is contributed by a small hairpin structure within the leader region, but a 64-nucleotide sequence is required for the bona fide interaction. Binding to the S10 leader mRNA is competed by the 23 S rRNA L4 binding site. Although the secondary structures of the mRNA and rRNA binding sites appear different, phosphorothioate footprinting of the L4-RNA complexes reveals close structural similarity in three dimensions. Mutational analysis of the mRNA binding site is compatible with the structural model. In vitro binding of L4 induces structural changes of the S10 leader RNA, providing a first clue for how protein L4 may provoke transcription termination}, keywords = {0,5’ Untranslated Regions,Amino Acid Sequence,analysis,Base Sequence,BINDING,Binding Sites,BINDING-SITE,BINDING-SITES,BindingCompetitive,Biochemistry,Biophysics,cancer,chemistry,Collodion,COMPLEX,COMPLEXES,DNA Mutational Analysis,Dose-Response RelationshipDrug,Escherichia coli,ESCHERICHIA-COLI,Gene Expression RegulationEnzymologic,In Vitro,IN-VITRO,Iodine,La,metabolism,MODEL,ModelsMolecular,Molecular Sequence Data,mRNA,MUTATIONAL ANALYSIS,nosource,Nucleic Acid Conformation,Operon,pharmacology,Phylogeny,protein,Protein Binding,Protein StructureSecondary,Proteins,REGION,regulation,Ribosomal Proteins,RIBOSOMAL-PROTEIN,Rna,RNAMessenger,RNARibosomal23S,rRNA,S,SECONDARY STRUCTURE,sequence,Sequence HomologyAmino Acid,SITE,SITES,Structural,structure,Support,termination,transcription,TRANSCRIPTION FACTOR,TRANSCRIPTION TERMINATION,TranscriptionGenetic,Untranslated Regions} } % == BibTeX quality report for stelzlRNAstructuralMimicryEscherichia2003: % ? unused Journal abbr (“J.Biol Chem.”)

@article{stenbergTranslationalReadthroughHdc1998, title = {Translational Readthrough in the ⬚hdc⬚ {{mRNA}} Generates a Novel Branching Inhibitor in the ⬚{{Drosophila}}⬚ Trachea.}, author = {Stenberg, P. and Englund, C. and Kronhamn, J. and Weaver, T.A. and Samakovlis, C.}, year = 1998, journal = {Genes & Development}, volume = {12}, pages = {956–967}, doi = {10.1101/gad.12.7.956}, keywords = {development,Drosophila,elongation,Fidelity,mRNA,nosource,readthrough,regulation,suppression} }

@article{sternStructuralAnalysisRNA1988a, title = {Structural Analysis of {{RNA}} Using Chemical and Enzymatic Probing Monitored by Primer Extension.}, author = {Stern, S. and Moazed, D. and Noller, H.F.}, year = 1988, journal = {Methods Enzymol.}, volume = {164}, pages = {481–489}, doi = {10.1016/S0076-6879(88)64064-X}, url = {PM:2468070}, keywords = {0,16S,analysis,ElectrophoresisPolyacrylamide Gel,genetics,Indicators and Reagents,isolation & purification,La,metabolism,Methods,nosource,Nucleic Acid Hybridization,primer extension,Rna,RNARibosomal16S,Structural} } % == BibTeX quality report for sternStructuralAnalysisRNA1988a: % ? Possibly abbreviated journal title Methods Enzymol.

@article{sternerAcetylationHistonesTranscriptionrelated2000a, title = {Acetylation of Histones and Transcription-Related Factors}, author = {Sterner, D.E. and Berger, S.L.}, year = 2000, month = jun, journal = {Microbiology and Molecular Biology Reviews}, volume = {64}, number = {2}, pages = {435-+}, doi = {10.1128/MMBR.64.2.435-459.2000}, url = {ISI:000087486200006}, abstract = {The state of chromatin (the packaging of DNA in eukaryotes) has long been recognized to have major effects on levels of gene expression, and numerous chromatin-altering strategies-including ATP-dependent remodeling and histone modification-are employed in the cell to bring about transcriptional regulation. Of these, histone acetylation is one of the best characterized, as recent years have seen the identification and further study of many histone acetyltransferase (HAT) proteins and their associated complexes. Interestingly, most of these proteins were previously shown to have coactivator or other transcription-related functions. Confirmed and putative HAT proteins have been identified from various organisms from yeast to humans, and they include Gcn5-related N-acetyltransferase (GNAT) superfamily members Gcn5, PCAF, Elp3, Hpa2 and Hat1: MYSTproteins Sas2, Sas3, Esa1, MOF, Tip60, MOZ, MORF, and HBO1; global coactivators p300 and CREB-binding protein; nuclear receptor coactivators SRC-1, ACTR, and TIF2; TATA-binding protein-associated factor TAF(II)250 and its homologs; and subunits of RNA polymerase III general factor TFIIIC. The acetylation and transcriptional functions of these HATs and the native complexes containing them (such as yeast SAGA, NuA4, and possibly analogous human complexes) are discussed. In addition some of these HA Ts are also known to modify certain nonhistone transcription-related proteins, including high-mobility-group chromatin proteins activators such as p53, coactivators, and general factors. Thus, we also detail these known factor acetyltransferase (FAT) substrates and the demonstrated or potential roles of their acetylation in transcriptional processes}, keywords = {Acetylation,ACIDIC ACTIVATION DOMAINS,ADENOVIRAL ONCOPROTEIN E1A,Chromatin,COMPLEX,COMPLEXES,CREB-BINDING-PROTEIN,Dna,expression,GCN5-RELATED N-ACETYLTRANSFERASE,gene,Gene Expression,GENE-EXPRESSION,HIGH-MOBILITY-GROUP,Histones,homolog,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IDENTIFICATION,KRUPPEL-LIKE FACTOR,MOF,nosource,NUCLEAR RECEPTOR-COACTIVATOR,ORIGIN RECOGNITION COMPLEX,p53,packaging,polymerase,POLYMERASE-III,protein,Proteins,regulation,Review,Rna,RNA Polymerase III,RNA-POLYMERASE,RNA-POLYMERASE-II,S,SUBUNIT,yeast} }

@article{stevensPurificationCharacterizationSaccharomyces1980, title = {Purification and Characterization of a {{Saccharomyces}} Cerevisiae Exoribonuclease Which Yields 5’-Mononucleotides by a 5’ Leads to 3’ Mode of Hydrolysis}, author = {Stevens, A.}, year = 1980, month = apr, journal = {Journal of Biological Chemistry}, volume = {255}, number = {7}, pages = {3080–3085}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(19)85855-6}, url = {http://www.jbc.org/content/255/7/3080.short}, keywords = {enzyme,Hydrolysis,nosource,Oligonucleotides,Phosphorylation,poly(A),purification,ribosome,Ribosomes,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SKI,XRN1} }

@article{stevens53exoribonucleaseSaccharomyces1987, title = {A 5’–{\(>\)} 3’exoribonuclease of {{Saccharomyces}} Cerevisiae: {{Size}} and Novel Substrate Specificity{\(\bullet\)} 1}, author = {Stevens, A. and Maupin, M. K.}, year = 1987, month = feb, journal = {Archives of biochemistry and biophysics}, volume = {252}, number = {2}, pages = {339–347}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0003986187900403}, keywords = {Chromatography,Dna,Electrophoresis,enzyme,Hydrolysis,Molecular Weight,nosource,Phosphorylation,poly(A),purification,Rna,RNAse,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SKI,Sodium,Substrate Specificity,SUBSTRATE-SPECIFICITY} }

@article{stirpeModificationRibosomalRNA1988, title = {Modification of Ribosomal {{RNA}} by Ribosome-Inactivating Proteins from Plants}, author = {Stirpe, F. and Bailey, S. and Miller, S.P. and Bodley, J.W.}, year = 1988, journal = {Nucleic.Acids.Research.}, volume = {16}, number = {4}, pages = {1349–1357}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/16/4/1359.short}, keywords = {modification,Multiple DOI,nonfile,nosource,Plants,protein,Proteins,RIBOSOMAL-RNA,Rna} } % == BibTeX quality report for stirpeModificationRibosomalRNA1988: % ? Possibly abbreviated journal title Nucleic.Acids.Research.

@article{stockleinAlteredRibosomalProtein1980a, title = {Altered Ribosomal Protein {{L29}} in a Cycloheximide-Resistant Strain of ⬚{{S}}. {{Cerevisiae}}⬚.}, author = {Stocklein, W. and Piepersberg, W.}, year = 1980, journal = {Curr.Genet.}, volume = {1}, pages = {177–183}, doi = {10.1007/BF00390941}, keywords = {Cycloheximide,CYH2,L29,nosource,protein} } % == BibTeX quality report for stockleinAlteredRibosomalProtein1980a: % ? Possibly abbreviated journal title Curr.Genet.

@article{stofflerRibosomalProteinsXIX1971a, title = {Ribosomal Proteins. {{XIX}}. {{Altered S5}} Ribosomal Protein in an {{Escherichia}} Coli Revertant from Strptomycin Dependence to Independence}, author = {Stoffler, G. and Deusser, E. and Wittmann, H.G. and Apirion, D.}, year = 1971, journal = {Mol.Gen.Genet.}, volume = {111}, number = {4}, pages = {334–341}, doi = {10.1007/BF00569785}, url = {PM:4936310}, keywords = {0,analysis,Bacterial,Bacterial Proteins,cytology,ElectrophoresisDisc,Escherichia coli,ESCHERICHIA-COLI,GeneticsMicrobial,Immunochemistry,La,Mutation,nosource,protein,Proteins,Ribosomal Proteins,Ribosomes,Streptomycin} } % == BibTeX quality report for stofflerRibosomalProteinsXIX1971a: % ? Possibly abbreviated journal title Mol.Gen.Genet.

@article{stoletzkiSynonymousCodonUsage2007, title = {Synonymous {{Codon Usage}} in {{Escherichia}} Coli: {{Selection}} for {{Translational Accuracy}}}, author = {Stoletzki, N. and {Eyre-Walker}, A.}, year = 2007, month = feb, journal = {Molecular biology and evolution}, volume = {24}, number = {2}, pages = {374–381}, publisher = {SMBE}, doi = {10.1093/molbev/msl166}, url = {http://mbe.oxfordjournals.org/content/24/2/374.short}, abstract = {In many organisms, selection acts on synonymous codons to improve translation. However, the precise basis of this selection remains unclear in the majority of species. Selection could be acting to maximize the speed of elongation, to minimize the costs of proofreading, or to maximize the accuracy of translation. Using several data sets, we find evidence that codon use in Escherichia coli is biased to reduce the costs of both missense and nonsense translational errors. Highly conserved sites and genes have higher codon bias than less conserved ones, and codon bias is positively correlated to gene length and production costs, both indicating selection against missense errors. Additionally, codon bias increases along the length of genes, indicating selection against nonsense errors. Doublet mutations or replacement substitutions do not explain our observations. The correlations remain when we control for expression level and for conflicting selection pressures at the start and end of genes. Considering each amino acid by itself confirms our results. We conclude that selection on synonymous codon use in E. coli is largely due to selection for translational accuracy, to reduce the costs of both missense and nonsense errors}, keywords = {accuracy,ACID,AMINO-ACID,Codon,CODONS,E,elongation,ERRORS,Escherichia coli,ESCHERICHIA-COLI,expression,gene,Genes,Germany,La,Mutation,MUTATIONS,NONSENSE,nosource,proofreading,SELECTION,SITE,SITES,synonymous codon use,transla-,translation,translational accuracy} } % == BibTeX quality report for stoletzkiSynonymousCodonUsage2007: % ? unused Journal abbr (“Mol.Biol Evol.”)

@article{storzExpandingUniverseNoncoding2002, title = {An Expanding Universe of Noncoding {{RNAs}}}, author = {Storz, G.}, year = 2002, month = may, journal = {Science}, volume = {296}, number = {5571}, pages = {1260–1263}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1072249}, url = {http://www.sciencemag.org/content/296/5571/1260.short}, abstract = {Noncoding RNAs (ncRNAs) have been found to have roles in a great variety of processes, including transcriptional regulation, chromosome replication, RNA processing and modification, messenger RNA stability and translation, and even protein degradation and translocation. Recent studies indicate that ncRNAs are far more abundant and important than initially imagined. These findings raise several fundamental questions: How many ncRNAs are encoded by a genome? Given the absence of a diagnostic open reading frame, how can these genes be identified? How can all the functions of ncRNAs be elucidated?}, keywords = {CAENORHABDITIS-ELEGANS,COMPARATIVE GENOMICS,DATABASE,degradation,ESCHERICHIA-COLI,FRAME,gene,Genes,Genome,IDENTIFICATION,MESSENGER-RNA,modification,nosource,OPEN READING FRAME,protein,READING FRAME,regulation,REPLICATION,Rna,RNA Stability,SIGNAL RECOGNITION PARTICLE,SMALL NUCLEOLAR RNAS,stability,transcription,translation,translocation,WORLD} }

@incollection{stfflerImmunoElectronMicroscopy1986, title = {Immuno Electron Microscopy on ⬚{{Escherchia}} Coli⬚ Ribosomes.}, booktitle = {Structure, Function and Genetics of Ribosomes.}, author = {St’‘ffler, G and {St’’ffler-Meilicke}, M}, year = 1986, pages = {28–46}, publisher = {Springer Verlag}, address = {New York}, collaborator = {Hardesty, B. and Kramer, B.}, keywords = {5S rRNA,Genetic,genetics,nosource,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,rRNA,structure,SUBUNIT} }

@article{strizkiSCHCSCH3511252001, title = {{{SCH-C}} ({{SCH}} 351125), an Orally Bioavailable, Small Molecule Antagonist of the Chemokine Receptor {{CCR5}}, Is a Potent Inhibitor of {{HIV-1}} Infection in Vitro and in Vivo}, author = {Strizki, J.M. and Xu, S. and Wagner, N.E. and Wojcik, L. and Liu, J. and Hou, Y. and Endres, M. and Palani, A. and Shapiro, S. and Clader, J.W. and Greenlee, W.J. and Tagat, J.R. and McCombie, S. and Cox, K. and Fawzi, A.B. and Chou, C.C. and {Pugliese-Sivo}, C. and Davies, L. and Moreno, M.E. and Ho, D.D. and Trkola, A. and Stoddart, C.A. and Moore, J.P. and Reyes, G.R. and Baroudy, B.M.}, year = 2001, month = oct, journal = {Proceedings of the National Academy of Sciences}, volume = {98}, number = {22}, pages = {12718–12723}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.221375398}, url = {http://www.pnas.org/content/98/22/12718.short}, abstract = {We describe here the identification and properties of SCH-C (SCH 351125), a small molecule inhibitor of HIV-1 entry via the CCR5 coreceptor. SCH-C, an oxime-piperidine compound, is a specific CCR5 antagonist as determined in multiple receptor binding and signal transduction assays. This compound specifically inhibits HIV-1 infection mediated by CCR5 in U-87 astroglioma cells but has no effect on infection of CXCR4-expressing cells. SCH-C has broad and potent antiviral activity in vitro against primary HIV-1 isolates that use CCR5 as their entry coreceptor, with mean 50% inhibitory concentrations ranging between 0.4 and 9 nM. Moreover, SCH-C strongly inhibits the replication of an R5-using HIV-1 isolate in SCID-hu Thy/Liv mice. SCH-C has a favorable pharmacokinetic profile in rodents and primates with an oral bioavailability of 50-60% and a serum half-life of 5-6 h. On the basis of its novel mechanism of action, potent antiviral activity, and in vivo pharmacokinetic profile, SCH-C is a promising new candidate for therapeutic intervention of HIV infection}, keywords = {0,Acquired Immunodeficiency Syndrome,Animals,antagonists & inhibitors,anti-HIV,Anti-HIV Agents,antiviral,assays,BINDING,CELLS,Cyclic N-Oxides,drug effects,drug therapy,Half-Life,HIV,Hiv-1,Humans,IDENTIFICATION,In Vitro,IN-VITRO,IN-VIVO,INFECTION,INHIBITOR,La,Macaca fascicularis,Male,MECHANISM,Mice,MiceScid,nosource,pharmacokinetics,pharmacology,Piperidines,Pyridines,Rantes,Rats,RatsSprague-Dawley,ReceptorsCCR5,REPLICATION,SIGNAL,Signal Transduction,SIGNAL-TRANSDUCTION,Support,therapeutic use} } % == BibTeX quality report for strizkiSCHCSCH3511252001: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{struhlHistoneAcetylationTranscriptional1998, title = {Histone Acetylation and Transcriptional Regulatory Mechanisms}, author = {Struhl, K.}, year = 1998, month = mar, journal = {Genes & development}, volume = {12}, number = {5}, pages = {599–606}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.12.5.599}, url = {http://genesdev.cshlp.org/content/12/5/599.short}, keywords = {0,Acetylation,Acetylesterase,Acetyltransferases,animal,chemistry,Gene Expression Regulation,genetics,Histone Deacetylase,Histones,La,MECHANISM,MECHANISMS,metabolism,ModelsBiological,nosource,pharmacology,protein,Proteins,Review,RPD3,supportu.s.gov’tp.h.s.,transcription,TRANSCRIPTION FACTOR,Transcription Factors,TranscriptionGenetic} } % == BibTeX quality report for struhlHistoneAcetylationTranscriptional1998: % ? unused Journal abbr (“Genes Dev.”)

@article{stupinaProximalTranslationalEnhancer2008a, title = {The 3’ Proximal Translational Enhancer of {{Turnip}} Crinkle Virus Binds to {{60S}} Ribosomal Subunits}, author = {Stupina, V.A. and Meskauskas, A. and McCormack, J.C. and Yingling, Y.G. and Shapiro, B.A. and Dinman, J.D. and Simon, A.E.}, year = 2008, journal = {RNA.}, volume = {14⬚ ⬚}, pages = {2379–2393}, doi = {10.1261/rna.1227808}, url = {PM:18824512}, abstract = {During cap-dependent translation of eukaryotic mRNAs, initiation factors interact with the 5’ cap to attract ribosomes. When animal viruses translate in a cap-independent fashion, ribosomes assemble upstream of initiation codons at internal ribosome entry sites (IRES). In contrast, many plant viral genomes do not contain 5’ ends with substantial IRES activity but instead have 3’ translational enhancers that function by an unknown mechanism. A 393-nucleotide (nt) region that includes the entire 3’ UTR of the Turnip crinkle virus (TCV) synergistically enhances translation of a reporter gene when associated with the TCV 5’ UTR. The major enhancer activity was mapped to an internal region of approximately 140 nt that partially overlaps with a 100-nt structural domain previously predicted to adopt a form with some resemblance to a tRNA, according to a recent study by J.C. McCormack and colleagues. The T-shaped structure binds to 80S ribosomes and 60S ribosomal subunits, and binding is more efficient in the absence of surrounding sequences and in the presence of a pseudoknot that mimics the tRNA-acceptor stem. Untranslated TCV satellite RNA satC, which contains the TCV 3’ end and 6-nt differences in the region corresponding to the T-shaped element, does not detectably bind to 80S ribosomes and is not predicted to form a comparable structure. Binding of the TCV T-shaped element by 80S ribosomes was unaffected by salt-washing, reduced in the presence of AcPhe-tRNA, which binds to the P-site, and enhanced binding of Phe-tRNA to the ribosome A site. Mutations that reduced translation in vivo had similar effects on ribosome binding in vitro. This strong correlation suggests that ribosome entry in the 3’ UTR is a key function of the 3’ translational enhancer of TCV and that the T-shaped element contains some tRNA-like properties}, keywords = {3,A SITE,A-SITE,animal,BINDING,BIOLOGY,Cap,Codon,CODONS,DOMAIN,FORM,gene,Genetic,genetics,Genome,In Vitro,IN-VITRO,IN-VIVO,initiation,INITIATION-FACTOR,INTERNAL RIBOSOME ENTRY,La,MECHANISM,MOLECULAR-GENETICS,mRNA,Mutation,MUTATIONS,nosource,P SITE,P-SITE,pseudoknot,REGION,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,RIBOSOME BINDING,RIBOSOME ENTRY SITE,RIBOSOME ENTRY SITES,Ribosomes,Rna,sequence,SEQUENCES,SITE,SITES,Structural,structure,SUBUNIT,SUBUNITS,translation,tRNA,UPSTREAM,virus,Viruses} } % == BibTeX quality report for stupinaProximalTranslationalEnhancer2008a: % ? Possibly abbreviated journal title RNA.

@article{suGenomicOrganizationSequence1996a, title = {Genomic Organization and Sequence Conservation in Type {{I Trichomonas}} Vaginalis Viruses}, author = {Su, H.M. and Tai, J.H.}, year = 1996, month = aug, journal = {Virology}, volume = {222}, number = {2}, pages = {470–473}, doi = {10.1006/viro.1996.0446}, keywords = {biosynthesis,Capsid,Frameshifting,gene,Genetic,genomic,initiation,nosource,polymerase,protein,ribosomal frameshifting,Rna,sequence,SLIPPAGE,UPSTREAM} }

@article{subbaraoPriorInfectionPassive2004, title = {Prior Infection and Passive Transfer of Neutralizing Antibody Prevent Replication of Severe Acute Respiratory Syndrome Coronavirus in the Respiratory Tract of Mice}, author = {Subbarao, K. and McAuliffe, J. and Vogel, L. and Fahle, G. and Fischer, S. and Tatti, K. and Packard, M. and Shieh, W.J. and Zaki, S. and Murphy, B.}, year = 2004, month = apr, journal = {Journal of virology}, volume = {78}, number = {7}, pages = {3572–3577}, publisher = {Am Soc Microbiol}, doi = {10.1128/JVI.78.7.3572-3577.2004}, url = {http://jvi.asm.org/cgi/content/abstract/78/7/3572}, abstract = {Following intranasal administration, the severe acute respiratory syndrome (SARS) coronavirus replicated to high titers in the respiratory tracts of BALB/c mice. Peak replication was seen in the absence of disease on day 1 or 2, depending on the dose administered, and the virus was cleared within a week. Viral antigen and nucleic acid were detected in bronchiolar epithelial cells during peak viral replication. Mice developed a neutralizing antibody response and were protected from reinfection 28 days following primary infection. Passive transfer of immune serum to naive mice prevented virus replication in the lower respiratory tract following intranasal challenge. Thus, antibodies, acting alone, can prevent replication of the SARS coronavirus in the lung, a promising observation for the development of vaccines, immunotherapy, and immunoprophylaxis regimens}, keywords = {0,ACID,analysis,Animals,Antibodies,AntibodiesViral,antibody,ANTIGEN,CELLS,Coronavirus,development,disease,Female,genetics,ImmunizationPassive,immunology,INFECTION,La,Lung,Mice,MiceInbred BALB C,Neutralization Tests,nosource,pathology,physiology,prevention & control,REPLICATION,Rna,RnaViral,SARS,Sars Virus,Severe Acute Respiratory Syndrome,virology,virus,Virus Replication} } % == BibTeX quality report for subbaraoPriorInfectionPassive2004: % ? unused Journal abbr (“J.Virol.”)

@article{suessConditionalGeneExpression2003, title = {Conditional Gene Expression by Controlling Translation with Tetracycline-Binding Aptamers}, author = {Suess, B. and Hanson, S. and Berens, C. and Fink, B. and Schroeder, R. and Hillen, W.}, year = 2003, month = apr, journal = {Nucleic acids research}, volume = {31}, number = {7}, pages = {1853–1858}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/gkg285}, url = {http://nar.oxfordjournals.org/content/31/7/1853.short}, abstract = {We present a conditional gene expression system in Saccharomyces cerevisiae which exploits direct RNA-metabolite interactions as a mechanism of genetic control. We inserted preselected tetracycline (tc) binding aptamers into the 5’-UTR of a GFP encoding mRNA. While aptamer insertion generally reduces GFP expression, one group of aptamers displayed an additional, up to 6-fold, decrease in fluorescence upon tc addition. Regulation is observed for aptamers inserted cap-proximal or near the start codon, but is more pronounced from the latter position. Increasing the thermodynamic stability of the aptamer augments regulation but reduces expression of GFP. Decreasing the stability leads to the opposite effect. We defined nucleotides which influence the regulatory properties of the aptamer. Exchanging a nucleotide probably involved in tc binding only influences regulation, while mutations at another position alter expression in the absence of tc, without affecting regulation. Thus, we have developed and characterized a regulatory system which is easy to establish and controlled by a non-toxic, small ligand with good cell permeability}, keywords = {0,5’ Untranslated Regions,5’-UTR,Base Sequence,BINDING,CEREVISIAE,Codon,drug effects,expression,Fluorescence,gene,Gene Expression,Gene Expression Regulation,GENE-EXPRESSION,Genetic,genetics,gfp,GREEN FLUORESCENT PROTEIN,La,Luminescent Proteins,MECHANISM,metabolism,mRNA,MutagenesisInsertional,Mutation,MUTATIONS,nosource,Nucleotides,Oligoribonucleotides,pharmacology,PLASMID,Plasmids,POSITION,protein,Proteins,REGION,regulation,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,stability,START CODON,supportnon-u.s.gov’t,SYSTEM,Tetracycline,thermodynamic stability,TransformationGenetic,translation,TranslationGenetic,Untranslated Regions} } % == BibTeX quality report for suessConditionalGeneExpression2003: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{sukaRegulationGeneActivity1998a, title = {The Regulation of Gene Activity by Histones and the Histone Deacetylase {{RPD3}}}, author = {Suka, N. and Carmen, A.A. and Rundlett, S.E. and Grunstein, M.}, year = 1998, journal = {Cold Spring Harb.Symp.Quant.Biol.}, volume = {63}, pages = {391–399}, doi = {10.1101/sqb.1998.63.391}, url = {PM:10384304}, keywords = {0,animal,chemistry,Chromatin,Fungal Proteins,gene,Gene Expression Regulation,genetics,Histone Deacetylase,Histones,human,La,metabolism,ModelsGenetic,nosource,Nucleosomes,protein,Proteins,regulation,Review,RPD3,Saccharomyces cerevisiae,supportu.s.gov’tp.h.s.,transcription,TRANSCRIPTION FACTOR,Transcription Factors,TranscriptionGenetic} } % == BibTeX quality report for sukaRegulationGeneActivity1998a: % ? Possibly abbreviated journal title Cold Spring Harb.Symp.Quant.Biol.

@article{sunNonsensemediatedDecayMRNA2001, title = {Nonsense-Mediated Decay of {{mRNA}} for the Selenoprotein Phospholipid Hydroperoxide Glutathione Peroxidase Is Detectable in Cultured Cells but Masked or Inhibited in Rat Tissues}, author = {Sun, X. and Li, X. and Moriarty, P.M. and Henics, T. and LaDuca, J.P. and Maquat, L.E.}, year = 2001, month = apr, journal = {Molecular Biology of the Cell}, volume = {12}, number = {4}, pages = {1009–1017}, publisher = {Am Soc Cell Biol}, doi = {10.1091/mbc.12.4.1009}, url = {http://www.molbiolcell.org/cgi/content/abstract/12/4/1009}, abstract = {Previous studies of mRNA for classical glutathione peroxidase 1 (GPx1) demonstrated that hepatocytes of rats fed a selenium-deficient diet have less cytoplasmic GPx1 mRNA than hepatocytes of rats fed a selenium- adequate diet. This is because GPx1 mRNA is degraded by the surveillance pathway called nonsense-mediated mRNA decay (NMD) when the selenocysteine codon is recognized as nonsense. Here, we examine the mechanism by which the abundance of phospholipid hydroperoxide glutathione peroxidase (PHGPx) mRNA, another selenocysteine-encoding mRNA, fails to decrease in the hepatocytes and testicular cells of rats fed a selenium-deficient diet. We demonstrate with cultured NIH3T3 fibroblasts or H35 hepatocytes transiently transfected with PHGPx gene variants under selenium-supplemented or selenium-deficient conditions that PHGPx mRNA is, in fact, a substrate for NMD when the selenocysteine codon is recognized as nonsense. We also demonstrate that the endogenous PHGPx mRNA of untransfected H35 cells is subject to NMD. The failure of previous reports to detect the NMD of PHGPx mRNA in cultured cells is likely attributable to the expression of PHGPx cDNA rather than the PHGPx gene. We conclude that 1) the sequence of the PHGPx gene is adequate to support the NMD of product mRNA, and 2) there is a mechanism in liver and testis but not cultured fibroblasts and hepatocytes that precludes or masks the NMD of PHGPx mRNA}, keywords = {0,3T3 Cells,animal,cancer,CellsCultured,Codon,CodonNonsense,DECAY,Diet,expression,gene,Genetic,genetics,Glutathione,Glutathione Peroxidase,La,Liver,Male,MECHANISM,metabolism,Mice,mRNA,mRNA decay,NMD,nonsense-mediated decay,nosource,Peptides,physiology,protein,Proteins,rat,Rats,RatsLong-Evans,Rna,RNAMessenger,Selenium,Selenocysteine,sequence,Support,supportu.s.gov’tp.h.s.,Testis} } % == BibTeX quality report for sunNonsensemediatedDecayMRNA2001: % ? unused Journal abbr (“Mol.Biol.Cell”)

@article{sunGeneralRequirementSin3Rpd31999, title = {A General Requirement for the {{Sin3-Rpd3}} Histone Deacetylase Complex in Regulating Silencing in {{Saccharomyces}} Cerevisiae}, author = {Sun, Z.W. and Hampsey, M.}, year = 1999, month = jul, journal = {Genetics}, volume = {152}, number = {3}, pages = {921–932}, doi = {10.1093/genetics/152.3.921}, abstract = {The Sin3-Rpd3 histone deacetylase complex, conserved between human and yeast, represses transcription when targeted by promoter-specific transcription factors. SIN3 and RPD3 also affect transcriptional silencing at the HM mating loci and at telomeres in yeast. Interestingly, however, deletion of the SIN3 and RPD3 genes enhances silencing, implying that the Sin3-Rpd3 complex functions to counteract, rather than to establish or maintain, silencing. Here we demonstrate that Sin3, Rpd3, and Sap30, a novel component of the Sin3-Rpd3 complex, affect silencing not only at the HMR and telomeric loci, but also at the rDNA locus. The effects on silencing at all three loci are dependent upon the histone deacetylase activity of Rpd3. Enhanced silencing associated with sin3Delta, rpd3Delta, and sap30Delta is differentially dependent upon Sir2 and Sir4 at the telomeric and rDNA loci and is also dependent upon the ubiquitin-conjugating enzyme Rad6 (Ubc2). We also show that the Cac3 subunit of the CAF-I chromatin assembly factor and Sin3-Rpd3 exert antagonistic effects on silencing. Strikingly, deletion of GCN5, which encodes a histone acetyltransferase, enhances silencing in a manner similar to deletion of RPD3. A model that integrates the effects of rpd3Delta, gcn5Delta, and cac3Delta on silencing is proposed}, keywords = {99318828,Acetylation,assembly,Chromatin,COMPLEX,COMPLEXES,COMPONENT,enzyme,enzymology,Fungal Proteins,gene,Genes,genetics,Genotype,Histone Deacetylase,Histones,human,Ligases,metabolism,ModelsBiological,Mutagenesis,nosource,Nucleic Acids,physiology,Protein Kinases,rDNA,RPD3,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUBUNIT,supportu.s.gov’tp.h.s.,Telomere,transcription,TRANSCRIPTION FACTOR,Transcription Factors,yeast} }

@article{sunkaraRolePolyaminesChromosome1983, title = {Role of Polyamines during Chromosome Condensation of Mammalian Cells}, author = {Sunkara, P.S. and Chang, C.C. and Prakash, N.J.}, year = 1983, month = jun, journal = {Cell biology international reports}, volume = {7}, number = {6}, pages = {455–465}, publisher = {Elsevier}, doi = {10.1016/0309-1651(83)90135-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/0309165183901352}, abstract = {The objective of the present study was to investigate the role of polyamines in the process of chromosome condensation. The phenomenon of premature chromosome condensation (PCC) involving fusion between mitotic and interphase cells was used as the assay system. The factors present in the mitotic cells would bring about the breakdown of the nuclear membrane and condensation of the interphase chromatin into chromosomes, similar to that which occurs during the initiation of mitosis. Alpha-difluoromethyl ornithine (DFMO), a specific irreversible inhibitor of ornithine decarboxylase was used to deplete both mitotic and interphase cells of polyamines. The results indicate that the polyamine depleted mitotic cells have a diminished ability to induce PCC. This inhibition could easily be reversed by exogenous addition of polyamines at the time of fusion. Furthermore, exogenously added polyamines hastened the entry of exponentially growing cells into mitosis. These observations suggest an essential role for polyamines during the process of chromosome condensation of mammalian cells}, keywords = {0,analogs & derivatives,antagonists & inhibitors,CELLS,Chromatin,Chromosomes,ChromosomesHuman,Comparative Study,drug effects,Eflornithine,Hela Cells,Humans,INHIBITION,INHIBITOR,initiation,Interphase,La,MAMMALIAN-CELLS,metabolism,Mitosis,nosource,Ornithine,Ornithine Decarboxylase,pharmacology,polyamine,Polyamines,SYSTEM,ultrastructure} } % == BibTeX quality report for sunkaraRolePolyaminesChromosome1983: % ? unused Journal abbr (“Cell Biol Int.Rep.”)

@article{sunoharaNascentpeptidemediatedRibosomeStalling2004, title = {Nascent-Peptide-Mediated Ribosome Stalling at a Stop Codon Induces {{mRNA}} Cleavage Resulting in Nonstop {{mRNA}} That Is Recognized by {{tmRNA}}}, author = {Sunohara, T. and Jojima, K. and Yamamoto, Y. and Inada, T. and Aiba, H.}, year = 2004, month = mar, journal = {RNA}, volume = {10}, number = {3}, pages = {378–386}, publisher = {Cold Spring Harbor Lab}, doi = {10.1261/rna.5169404}, url = {http://rnajournal.cshlp.org/content/10/3/378.short}, abstract = {Recent studies have established that tmRNA-mediated protein tagging occurs at stop codons depending on the C-terminal amino acid sequence of the nascent polypeptide immediately adjacent to those codons. We investigate here how the trans-translation at a stop codon occurs by using model crp genes encoding variants of cAMP receptor protein (CRP). We demonstrate that a truncated crp mRNA is efficiently produced along with a normal transcript from the model gene where tmRNA-mediated protein tagging occurs. The truncated crp mRNA was not detected in the presence of tmRNA, indicating that its degradation was facilitated by tmRNA. The major 3’-ends of the truncated crp mRNA in cells unable to express tmRNA were mapped at and near the stop codon. When RNA derived from the model crp-crr fusion gene was analyzed, crr mRNA was detected as a downstream cleavage product along with the upstream crp mRNA. These results are compatible with the hypothesis that ribosome stalling caused by the tagging-provoking sequences leads to endonucleolytic cleavage of mRNA around the stop codon, resulting in nonstop mRNA. In addition, the data are consistent with the view that mRNA cleavage is the cause of trans-translation at stop codons. Neither the bacterial toxin RelE nor the known major endoribonucleases are required for this cleavage, indicating that either other endoribonuclease(s) or the ribosome itself would be responsible for the mRNA cleavage in response to ribosome stalling caused by the particular nascent peptides}, keywords = {0,3’-END,ACID,Amino Acid Sequence,AMINO-ACID,Bacterial,Bacterial Toxins,CELLS,CLEAVAGE,Codon,CODONS,CodonTerminator,degradation,DOWNSTREAM,E,Endoribonucleases,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,gene,Genes,genetics,La,metabolism,MODEL,mRNA,NASCENT-PEPTIDE,nosource,Peptides,POLYPEPTIDE,PRODUCT,protein,Proteins,ReceptorsCell Surface,Research SupportNon-U.S.Gov’t,ribosome,Ribosomes,Rna,RNABacterial,RNAMessenger,sequence,SEQUENCES,STOP CODON,toxin,TRANSCRIPT,transcription,TRANSCRIPTION FACTOR,Transcription Factors,UPSTREAM} }

@article{suzukiATPdependentProteasesThat1997, title = {{{ATP-dependent}} Proteases That Also Chaperone Protein Biogenesis.}, author = {Suzuki, C.K. and Rep, M. and {}{van Dijl}, J.M. and Suda, K. and Frivell, L.A. and Schatz, G.}, year = 1997, journal = {Trends in biochemical sciences}, volume = {22}, number = {4}, pages = {118–123}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000497010207}, keywords = {No DOI found,nosource,protein,protein synthesis,review article} }

@article{swatkoskiIntegrationResiduespecificAcid2007, title = {Integration of Residue-Specific Acid Cleavage into Proteomic Workflows}, author = {Swatkoski, S. and Gutierrez, P. and Ginter, J. and Petrov, A. and Dinman, J.D. and Edwards, N. and Fenselau, C.}, year = 2007, month = nov, journal = {Journal of Proteome Research}, volume = {6}, number = {11}, pages = {4525–4527}, publisher = {ACS Publications}, doi = {10.1021/pr0704682}, url = {http://pubs.acs.org/doi/abs/10.1021/pr0704682}, abstract = {Microwave-accelerated proteolysis using acetic acid has been shown to occur specifically on either or both sides of aspartate residues. This chemical cleavage is applied to the yeast ribosome proteome to evaluate its suitability for incorporation into high-throughput automated workflows. Peptide product mixtures were analyzed using either an HPLC-ESI-LTQ-Orbitrap or an HPLC-MALDI-TOF2. The peptides were readily identified, using MASCOT with a modified enzyme rule, and provided information about 73% of the proteome. Implications are considered of the extended length and the presence of multiple basic residues in these peptides}, keywords = {0,ACID,Amino Acid Sequence,Biochemistry,chemistry,ChromatographyHigh Pressure Liquid,CLEAVAGE,enzyme,Fungal Proteins,INFORMATION,La,Mass Spectrometry,metabolism,Methods,Microwaves,Molecular Sequence Data,nosource,Peptide Mapping,Peptides,PRODUCT,protein,Proteins,PROTEOLYSIS,Proteome,Proteomics,RESIDUES,ribosome,Ribosomes,SpectrometryMassElectrospray Ionization,Trypsin,yeast} } % == BibTeX quality report for swatkoskiIntegrationResiduespecificAcid2007: % ? unused Journal abbr (“J.Proteome.Res.”)

@article{swatkoskiEvaluationMicrowaveacceleratedResiduespecific2008, title = {Evaluation of Microwave-Accelerated Residue-Specific Acid Cleavage for Proteomic Applications}, author = {Swatkoski, S. and Gutierrez, P. and Wynne, C. and Petrov, A. and Dinman, J.D. and Edwards, N. and Fenselau, C.}, year = 2008, month = feb, journal = {J.Proteome.Res.}, volume = {7}, number = {2}, pages = {579–586}, doi = {10.1021/pr070502c}, url = {PM:18189344}, abstract = {Microwave-accelerated proteolysis using acetic acid has been shown to occur specifically on either or both sides of aspartic acid residues. This chemical cleavage has been applied to ovalbumin and several model peptides to test the effect on some of the more common post-translational modifications. No oxidation of methionine or cysteine was observed; however, hydrolysis of phosphate groups proceeds at a detectable rate. Acid cleavage was also extended to the yeast ribosome model proteome, where it provided information on 74% of that proteome. Aspartic acid occurs across the proteome with approximately half the frequency of the combined occurrence of the trypsin residues lysine and arginine, and implications of this are considered}, keywords = {ACID,Arginine,Aspartic Acid,Biochemistry,chemistry,CLEAVAGE,Cysteine,Hydrolysis,INFORMATION,La,Lysine,Methionine,MODEL,modification,nosource,Peptides,PROTEOLYSIS,Proteome,RESIDUES,ribosome,Support,Trypsin,yeast} } % == BibTeX quality report for swatkoskiEvaluationMicrowaveacceleratedResiduespecific2008: % ? Possibly abbreviated journal title J.Proteome.Res.

@article{swederPurificationCharacterizationProteins1988, title = {Purification and Characterization of Proteins That Bind to Yeast {{ARSs}}.}, author = {Sweder, K.S. and Rhode, P.R. and Campbell, J.L.}, year = 1988, month = nov, journal = {Journal of Biological Chemistry}, volume = {263}, number = {33}, pages = {17270–17277}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(19)77831-4}, url = {http://www.jbc.org/content/263/33/17270.short}, abstract = {Two proteins that bind to yeast ARS DNA have been purified using conventional and oligonucleotide affinity chromatography. One protein has been purified to homogeneity and has a mass of 135 kDa. Competitive binding studies and DNase I footprinting show that the protein binds to a sequence about 80 base pairs away from the core consensus in the region known as domain B. This region has previously been shown to be required for efficient replication of plasmids carrying ARS1 elements. To investigate further whether the protein might have a function related to the ability of ARSs to act as replicators, binding to another ARS was tested. The protein binds to the functional ARS adjacent to the silent mating type locus HMR, called the HMR-E ARS, about 60 base pairs from the core consensus sequence. Surprisingly, there is little homology between the binding site at the HMR-E ARS and the binding site at ARS1. The 135-kDa protein is probably the same as ABF-I (SBF I) (Shore, D., Stillman, D. J. Brand, A. H., and Nasmyth, K. A. (1987) EMBO J. 6, 461-467; Buchman, A. R., Kimmerly, W. J., Rine, J., and Kornberg, R. D. (1988) Mol. Cell. Biol. 8, 210-225). A second DNA-binding protein was separated from ABF-I during later stages of the purification. This protein, which we designate ABF-III, also binds specifically to the ARS1 sequence, as shown by DNase I footprinting, at a site adjacent to the ABF-I recognition site. Purification of these two ARS binding proteins should aid in our understanding of the complex mechanisms that regulate eukaryotic DNA replication}, keywords = {89034244,A-SITE,Base Sequence,BINDING,BINDING PROTEIN,BINDING-PROTEIN,Carrier Proteins,Chromatography,ChromatographyAffinity,ChromatographyIon Exchange,COMPLEX,COMPLEXES,Consensus Sequence,Deoxyribonuclease I,Dna,DNA Replication,ELEMENTS,genetics,isolation & purification,MECHANISM,MECHANISMS,metabolism,Molecular Sequence Data,nosource,PLASMID,Plasmids,protein,Proteins,purification,Restriction Mapping,Saccharomyces cerevisiae,sequence,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,yeast} } % == BibTeX quality report for swederPurificationCharacterizationProteins1988: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{sweeneyMutationLargeSubunit1991a, title = {A Mutation in the Large Subunit Ribosomal {{RNA}} Gene of {{Tetrahymena}} Confers Anisomycin Resistance and Cold Sensitivity}, author = {Sweeney, R. and Yao, C.H. and Yao, M.C.}, year = 1991, month = feb, journal = {Genetics}, volume = {127}, number = {2}, pages = {327–334}, doi = {10.1093/genetics/127.2.327}, url = {PM:2004706}, abstract = {Anisomycin, an antibiotic that specifically inhibits the peptidyl transfer function of eukaryotic ribosomes, has been used to select resistant mutants in Tetrahymena thermophila. A mutation conferring anisomycin resistance (an-r) has been localized to a 1.2-kb fragment of the large subunit ribosomal RNA (rRNA) gene by transformation via microinjection. A single base pair change was detected within this region. Nine independently isolated an-r mutants had the same base pair change. T. thermophila strains that are homozygous for this mutation are cold sensitive, unable to mate and grossly abnormal in cell morphology}, keywords = {0,animal,anisomycin,antibiotic,Base Sequence,cancer,CloningMolecular,Cold,CrossesGenetic,Cycloheximide,Dna,DNARibosomal,drug effects,Drug Resistance,gene,genetics,growth & development,Kinetics,La,Molecular Sequence Data,Mutation,nosource,Oligonucleotide Probes,Paromomycin,peptidyl-transfer,pharmacology,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNARibosomal,rRNA,SUBUNIT,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Tetrahymena,Tetrahymena thermophila} }

@article{sweeneyIntragenicSuppressorCold1998, title = {An Intragenic Suppressor of Cold Sensitivity Identifies Potentially Interacting Bases in the Peptidyl Transferase Center of {{Tetrahymena rRNA}}}, author = {Sweeney, R. and Yao, M.C.}, year = 1998, month = jun, journal = {Genetics}, volume = {149}, number = {2}, pages = {937–946}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/149.2.937}, url = {http://www.genetics.org/content/149/2/937.short}, abstract = {Peptidyl transfer of a growing peptide on a ribosome-bound transfer RNA (tRNA) to an incoming amino acyl tRNA is the central step in translation, and it may be catalyzed primarily by the large subunit (LSU) ribosomal RNA (rRNA). Genetic and biochemical evidence suggests that the central loop of domain V of the LSU rRNA plays a direct role in peptidyl transfer. It was previously found that a single base change at a universally conserved site in this region of the Tetrahymena thermophila LSU rRNA confers anisomycin resistance (an-r) as well as extremely slow growth, cold sensitivity, and aberrant cell morphology. Because anisomycin specifically inhibits peptidyl transfer, possibly by interfering with tRNA binding, it is likely that this mutant rRNA is defective in efficiently completing one of these steps. In the present study, we have isolated an intragenic suppressor mutation located only three bases away from the original mutation that partially reverses the slow growth and cold-sensitive phenotypes. These data imply that the functional interaction of these two bases is necessary for normal rRNA function, perhaps for peptidyl transfer or tRNA binding. These data provide the first demonstration of a functional interaction between bases within this rRNA region}, keywords = {0,animal,anisomycin,Base Composition,Base Sequence,BINDING,cancer,Chromosome Mapping,Cold,GenesSuppressor,Genetic,genetics,La,Molecular Sequence Data,Mutation,nosource,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,peptidyl-transfer,PEPTIDYL-TRANSFERASE,Peptidyltransferase,Phenotype,RIBOSOMAL-RNA,Rna,RNAProtozoan,RNARibosomal,rRNA,Sequence AnalysisDNA,SUBUNIT,supportu.s.gov’tnon-p.h.s.,Tetrahymena,Tetrahymena thermophila,TRANSFER-RNA,TransformationGenetic,translation,tRNA} }

@article{swillensInterpretationBindingCurves1995, title = {Interpretation of Binding Curves Obtained with High Receptor Concentrations: Practical Aid for Computer Analysis.}, author = {Swillens, S.}, year = 1995, month = jun, journal = {Molecular pharmacology}, volume = {47}, number = {6}, pages = {1197–1203}, publisher = {ASPET}, url = {http://molpharm.aspetjournals.org/content/47/6/1197.short}, abstract = {Typical equilibrium binding experiments cannot be quantitatively analyzed on the basis of classical mathematical equations when the receptor concentration is so high that a significant fraction of the added radioligand concentration is in the bound form. In this paper, the appropriate equations are derived and used in a commercial graphics package to estimate the binding parameters, by applying nonlinear regression to pseudo-experimental data. The analysis of saturation and homologous displacement curves obtained with high receptor concentrations reveals that the empirical determination of nonspecific binding by addition of an excess of unlabeled ligand is incorrect}, keywords = {0,analysis,BINDING,computer,computer analysis,FORM,La,Ligands,ModelsChemical,No DOI found,nosource,Protein Binding,Radioligand Assay,ReceptorsCell Surface,Research SupportNon-U.S.Gov’t,Software} } % == BibTeX quality report for swillensInterpretationBindingCurves1995: % ? unused Journal abbr (“Mol.Pharmacol.”)

@article{sylvesterMitochondrialRibosomalProteins2004a, title = {Mitochondrial Ribosomal Proteins: Candidate Genes for Mitochondrial Disease}, author = {Sylvester, J.E. and {Fischel-Ghodsian}, N. and Mougey, E.B. and O’Brien, T.W.}, year = 2004, month = mar, journal = {Genetics in Medicine}, volume = {6}, number = {2}, pages = {73–80}, doi = {10.1097/01.GIM.0000117333.21213.17}, url = {http://journals.lww.com/geneticsinmedicine/Abstract/2004/03000/Mitochondrial_ribosomal_proteins__Candidate_genes.1.aspx}, abstract = {Most of the energy requirement for cell growth, differentiation, and development is met by the mitochondria in the form of ATP produced by the process of oxidative phosphorylation. Human mitochondrial DNA encodes a total of 13 proteins, all of which are essential for oxidative phosphorylation. The mRNAs for these proteins are translated on mitochondrial ribosomes. Recently, the genes for human mitochondrial ribosomal proteins (MRPs) have been identified. In this review, we summarize their refined chromosomal location. It is well known that mutations in the mitochondrial translation system, i.e., ribosomal RNA and transfer RNA cause various pathologies. In this review, we suggest possible associations between clinical conditions and MRPs based on coincidence of genetic map data and chromosomal location. These MRPs may be candidate genes for the clinical condition or may act as modifiers of existing known gene mutations (mt-tRNA, mt-rRNA, etc.)}, keywords = {0,ASSOCIATION,ATP,Chromosome Mapping,development,disease,Dna,DNAMitochondrial,ENCODES,FORM,gene,Gene Order,Genes,Genetic,Genetic DiseasesInborn,genetics,GROWTH,human,Humans,La,LOCATION,mitochondria,Mitochondrial Diseases,mRNA,Mutation,MUTATIONS,nosource,pathology,Phosphorylation,protein,Proteins,Review,Ribosomal Proteins,ribosomal RNA,RIBOSOMAL-PROTEIN,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,Support,SYSTEM,therapy,TRANSFER-RNA,translation} } % == BibTeX quality report for sylvesterMitochondrialRibosomalProteins2004a: % ? unused Journal abbr (“Genet.Med.”)

@article{synetosStudiesCatalyticRate1987, title = {Studies on the Catalytic Rate Constant of Ribosomal Peptidyltransferase}, author = {Synetos, D. and Coutsogeorgopoulos, C.}, year = 1987, month = feb, journal = {Biochimica et Biophysica Acta (BBA)-General Subjects}, volume = {923}, number = {2}, pages = {275–285}, publisher = {Elsevier}, doi = {10.1016/0304-4165(87)90014-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/0304416587900146}, abstract = {A detailed kinetic analysis of a model reaction for the ribosomal peptidyltransferase is described, using fMet-tRNA or Ac-Phe-tRNA as the peptidyl donor and puromycin as the acceptor. The initiation complex (fMet-tRNA X AUG X 70 S ribosome) or (Ac-Phe-tRNA X poly(U) X 70 S ribosome) (complex C) is isolated and then reacted with excess puromycin (S) to give fMet-puromycin or Ac-Phe-puromycin. This reaction (puromycin reaction) is first order at all concentrations of S tested. An important asset of this kinetic analysis is the fact that the relationship between the first order rate constant kobs and [S] shows hyperbolic saturation and that the value of kobs at saturating [S] is a measure of the catalytic rate constant (k cat) of peptidyltransferase in the puromycin reaction. With fMet-tRNA as the donor, this kcat of peptidyltransferase is 8.3 min-1 when the 0.5 M NH4Cl ribosomal wash is present, compared to 3.8 min-1 in its absence. The kcat of peptidyltransferase is 2.0 min-1 when Ac-Phe-tRNA replaces fMet-tRNA in the presence of the ribosomal wash and decreases to 0.8 min-1 in its absence. This kinetic procedure is the best method available for evaluating changes in the activity of peptidyltransferase in vitro. The results suggest that peptidyltransferase is subjected to activation by the binding of fMet-tRNA to the 70 S initiation complex}, keywords = {0,activation,Acyltransferases,analysis,AUG,BINDING,Binding Sites,Catalysis,COMPLEX,COMPLEXES,enzymology,Escherichia coli,In Vitro,IN-VITRO,initiation,Kinetics,La,M,metabolism,MODEL,ModelsBiological,nosource,Peptides,peptidyl transferase,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,Peptidyltransferase,Puromycin,Research SupportNon-U.S.Gov’t,ribosome,Ribosomes,Rna,RNATransferAmino Acyl,RNATransferMet,S,Transferases,tRNA} } % == BibTeX quality report for synetosStudiesCatalyticRate1987: % ? unused Journal abbr (“Biochim.Biophys.Acta”)

@article{synetosMutationsYeastRibosomal1996, title = {Mutations in Yeast Ribosomal Proteins {{S28}} and {{S4}} Affect the Accuracy of Translation and Alter the Sensitivity of the Ribosomes to Paromomycin}, author = {Synetos, D. and Frantziou, C.P. and Alksne, L.E.}, year = 1996, month = nov, journal = {Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression}, volume = {1309}, number = {1-2}, pages = {156–166}, publisher = {Elsevier}, doi = {10.1016/S0167-4781(96)00128-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0167478196001285}, abstract = {Ribosomal proteins S12, S5 and S4 of Escherichia coli are essential for the control of translational accuracy. Their yeast equivalents, i.e., S28, S4 and S13, have also been implicated in this process. Using a poly(U)-dependent cell-free translation system, we determined the accuracy of translation and the sensitivity to antibiotic paromomycin of yeast ribosomes carrying mutant ribosomal proteins S28 and/or S4. Our results confirm by quantitative biochemical methods previous genetic data showing that proteins S28 and S4 are involved in the decoding activity of the ribosome and interact to control translational accuracy. We find that the suppressor mutation SUP44 in yeast S4, decreased the accuracy of translation. To examine the effect of mutant S28, we disrupted RPS28B and introduced in RPS28A the same substitutions that cause hyperaccurate translation or antibiotic resistance in bacteria. Three of these substitutions (Lys-62–{\(>\)}Asn, Thr or Gln) similarly increased translational accuracy in vitro or antibiotic resistance. In the presence of the SUP44 mutation, these substitutions partially reversed the decrease of translational accuracy caused by SUP44. However, the Lys-62–{\(>\)}Arg substitution decreased translational accuracy and caused antibiotic sensitivity both in nonsuppressor and in SUP44 haploids. These results establish the role of Lys-62 of S28 in optimizing translational accuracy and provide a more precise view of the functional role of two important ribosomal proteins}, keywords = {0,accuracy,Anti-Bacterial Agents,antibiotic,Bacteria,CELL-FREE TRANSLATION,CEREVISIAE,decoding,drug effects,Escherichia coli,ESCHERICHIA-COLI,Genetic,genetics,In Vitro,IN-VITRO,La,Methods,MutagenesisSite-Directed,Mutation,MUTATIONS,nosource,Paromomycin,pharmacology,protein,Protein Biosynthesis,Proteins,Research SupportNon-U.S.Gov’t,RESISTANCE,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SuppressionGenetic,SYSTEM,translation,yeast} } % == BibTeX quality report for synetosMutationsYeastRibosomal1996: % ? unused Journal abbr (“Biochim.Biophys.Acta”)

@article{szewczakConformationSarcinRicin1993, title = {The Conformation of the Sarcin/Ricin Loop from {{28S}} Ribosomal {{RNA}}}, author = {Szewczak, A.A. and Moore, P.B. and Chang, Y.L. and Wool, I.G.}, year = 1993, month = oct, journal = {Proceedings of the National Academy of Sciences}, volume = {90}, number = {20}, pages = {9581–9585}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.90.20.9581}, url = {http://www.pnas.org/content/90/20/9581.short}, abstract = {The sarcin/ricin loop is a highly conserved sequence found in the RNA of all large ribosomal subunits. The cytotoxins alpha-sarcin and ricin both inactivate ribosomes by cleaving a single bond in that loop. Once it has been attacked, ribosomes no longer interact with elongation factors properly, and translation stops. We have determined the conformation of the sarcin/ricin loop by multinuclear NMR spectroscopy using E73, a 29-nucleotide RNA that has the sarcin/ricin loop sequence and that is sensitive to both toxins in vitro. The sarcin/ricin loop has a compact structure that contains several purine.purine base pairs, a GAGA tetraloop, and a bulged guanosine adjacent to a reverse Hoogsteen A.U pair. It is stabilized by an unusual set of cross-strand base-stacking interactions and imino proton to phosphate oxygen hydrogen bonds. In addition to having interesting structural features, this model explains many of the biochemical observations made about the loop’s structure and its reactivity with cytotoxins, and it sheds light on the loop’s interactions with elongation factors}, keywords = {94022419,animal,Base Sequence,chemistry,Conserved Sequence,elongation,Fungal Proteins,Guanosine,Hydrogen Bonding,In Vitro,IN-VITRO,ModelsMolecular,Molecular Sequence Data,nosource,nuclear magnetic resonance,Nucleic Acid Conformation,Oligonucleotides,PAP,Rats,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Ricin,Rna,RNARibosomal28S,S/R loop,sequence,Structural,structure,SUBUNIT,supportu.s.gov’tp.h.s.,Thermodynamics,toxicity,toxin,translation,ultrastructure} } % == BibTeX quality report for szewczakConformationSarcinRicin1993: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{szymanski5SRibosomalRNA2002, title = {{{5S}} Ribosomal {{RNA}} Database}, author = {Szymanski, M. and Barciszewska, M. Z. and Erdmann, V. A. and Barciszewski, J.}, year = 2002, month = jan, journal = {Nucleic Acids Research}, volume = {30}, number = {1}, pages = {176}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/30/1/176.short}, abstract = {Ribosomal 5S RNA (5S rRNA) is an integral component of the large ribosomal subunit in all known organisms with the exception only of mitochondrial ribosomes of fungi and animals. It is thought to enhance protein synthesis by stabilization of a ribosome structure. This paper presents the updated database of 5S rRNA and their genes (5S rDNA). Its short characteristics are presented in the Introduction. The database contains 2280 primary structures of 5S rRNA and 5S rRNA genes. These include 536 eubacterial, 61 archaebacterial, 1611 eukaryotic and 72 organelle sequences. The database is available on line through the World Wide Web at http://biobases.ibch.poznan.pl/5SData/}, keywords = {0,5S RNA,5S rRNA,animal,Animals,Base Sequence,chemistry,COMPONENT,DATABASE,DatabasesNucleic Acid,Fungi,gene,Genes,GenesrRNA,genetics,Information Storage and Retrieval,Internet,La,LINE,Molecular Sequence Data,nosource,Nucleic Acid Conformation,protein,protein synthesis,PROTEIN-SYNTHESIS,rDNA,Research SupportNon-U.S.Gov’t,ribosomal RNA,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNARibosomal5S,rRNA,rRNA genes,sequence,SEQUENCES,structure,SUBUNIT,WORLD,World Wide Web} }

@article{taborPolyamines1984a, title = {Polyamines}, author = {Tabor, C.W. and Tabor, H.}, year = 1984, journal = {Annual review of biochemistry}, volume = {53}, pages = {749–790}, doi = {10.1146/annurev.bi.53.070184.003533}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.bi.53.070184.003533}, keywords = {0,Adenosylmethionine Decarboxylase,analogs & derivatives,Animals,antagonists & inhibitors,Arginase,Arginine,Aspergillus nidulans,biosynthesis,Carboxy-Lyases,CloningMolecular,Dna,Escherichia coli,genetics,kinase,La,Lysine,metabolism,Mutation,Neoplasms,Neurospora crassa,nosource,Ornithine Decarboxylase,Physarum,Plants,polyamine,Polyamines,protein,Protein Biosynthesis,Protein Kinases,Protein ProcessingPost-Translational,PROTEIN-KINASE,Putrescine,Review,Rna,Saccharomyces cerevisiae,Spermidine,Spermidine Synthase,Spermine,Spermine Synthase} } % == BibTeX quality report for taborPolyamines1984a: % ? unused Journal abbr (“Annu.Rev.Biochem.”)

@article{taborDNASequenceAnalysis1987, title = {{{DNA}} Sequence Analysis with a Modified Bacteriophage {{T7 DNA}} Polymerase}, author = {Tabor, S. and Richardson, C.C.}, year = 1987, month = jul, journal = {Proceedings of the National Academy of Sciences}, volume = {84}, number = {14}, pages = {4767–4771}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.84.14.4767}, url = {http://www.pnas.org/content/84/14/4767.short}, abstract = {A chemically modified phage T7 DNA polymerase has three properties that make it ideal for DNA sequencing by the chain-termination method. The enzyme is highly processive, catalyzing the polymerization of thousands of nucleotides without dissociating. By virtue of the modification the 3’ to 5’ exonuclease activity is eliminated. The modified polymerase efficiently uses nucleotide analogs that increase the electrophoretic resolution of bands in gels. Consequently, dideoxynucleotide-terminated fragments have highly uniform radioactive intensity throughout the range of a few to thousands of nucleotides in length. There is virtually no background due to terminations at pause sites or secondary- structure impediments. Processive synthesis with dITP in place of dGTP eliminates band compressions, making possible the unambiguous determination of sequences from a single orientation}, keywords = {0,analysis,Bacteriophage T7,Base Sequence,Deoxyribonucleotides,diagnostic use,Dna,DNA-Directed DNA Polymerase,DNARecombinant,DnaViral,enzyme,enzymology,Exodeoxyribonucleases,Free Radicals,Gels,La,metabolism,Methods,modification,nosource,Nucleotide Mapping,Nucleotides,Oxidation-Reduction,polymerase,protein,Protein Hybridization,Proteins,SECONDARY STRUCTURE,sequence,Sequence Analysis,SEQUENCES,structure,supportu.s.gov’tp.h.s.,T-Phages,termination,Thioredoxin,Viral Proteins} } % == BibTeX quality report for taborDNASequenceAnalysis1987: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{tachedjianZidovudineResistanceSuppressed1996, title = {Zidovudine Resistance Is Suppressed by Mutations Conferring Resistance of Human Immunodeficiency Virus Type 1 to Foscarnet}, author = {Tachedjian, G. and Mellors, J. and Bazmi, H. and Birch, C. and Mills, J.}, year = 1996, month = oct, journal = {Journal of Virology}, volume = {70}, number = {10}, pages = {7171–7181}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.70.10.7171-7181.1996}, url = {http://jvi.asm.org/cgi/content/abstract/70/10/7171}, keywords = {Codon,drugs,Genetic,HIV,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,In Vitro,IN-VITRO,Mutation,MUTATIONS,nosource,suppression,virus,Zidovudine} }

@article{taggartTelomeraseWhatAre2003, title = {Telomerase: What Are the {{Est}} Proteins Doing?}, author = {Taggart, A.K. and Zakian, V.A.}, year = 2003, month = jun, journal = {Current Opinion in Cell Biology}, volume = {15}, number = {3}, pages = {275–280}, publisher = {Elsevier}, doi = {10.1016/S0955-0674(03)00040-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0955067403000401 http://www.sciencedirect.com/science/article/pii/S0955067403000401}, abstract = {Saccharomyces cerevisiae has proven to be a useful model organism for the study of telomerase, a specialized cellular reverse transcriptase that helps maintain genomic stability by adding telomeric DNA repeats to the ends of chromosomes. Yeast telomerase is thought to be a holoenzyme containing Est2p and TLC1 RNA, the catalytic subunit and its intrinsic template, respectively, as well as the TLC1-RNA-associated factors Est1p and Est3p. Cdc13p, a sequence-specific telomere-DNA-binding protein, is also required for action in vivo. A current model for telomerase regulation is that telomere-associated Cdc13p binds Est1p, thereby recruiting telomerase. However, recent chromatin immunoprecipitation experiments suggest an alternate role for Est1p in activating Est2p-TLC1-RNA that is already bound to the telomere. Three models for Est1p activation are presented}, keywords = {0,activation,BIOLOGY,CEREVISIAE,Chromatin,Chromosomes,Cyclin B,Dna,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,enzymology,EST,Fungal Proteins,genetics,genomic,Immunoprecipitation,IN-VIVO,La,metabolism,MODEL,models,Molecular Biology,nosource,protein,Proteins,regulation,REVERSE-TRANSCRIPTASE,Review,Rna,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,stability,SUBUNIT,Support,Telomerase,Telomere,TEMPLATE,yeast} } % == BibTeX quality report for taggartTelomeraseWhatAre2003: % ? unused Journal abbr (“Curr.Opin.Cell Biol.”)

@article{taiCourseGiardiavirusInfection1991, title = {The {{Course}} of {{Giardiavirus Infection}} in the {{Giardia-Lamblia Trophozoites}}}, author = {Tai, J.H. and Wang, A.L. and Ong, S.J. and Lai, K.S. and Lo, C. and Wang, C.C.}, year = 1991, month = nov, journal = {Experimental Parasitology}, volume = {73}, number = {4}, pages = {413–423}, publisher = {Elsevier}, doi = {10.1016/0014-4894(91)90065-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/0014489491900655}, keywords = {DOUBLE-STRANDED-RNA,Genome,IDENTIFICATION,INFECTION,INSITU HYBRIDIZATION,LEISHMANIA,LOCALIZATION,nosource,protein,SEQUENCES,Transfection,virus} } % == BibTeX quality report for taiCourseGiardiavirusInfection1991: % ? Title looks like it was stored in title-case in Zotero

@article{takahashiAttachmentTerminalPortion1985a, title = {Attachment of the 5’-Terminal Portion of Globin {{mRNAs}} to {{5S-RNA}}⬚.⬚{{L5}} Protein in the {{80S}} Initiation Complex.}, author = {Takahashi, Y. and Ogata, K.}, year = 1985, journal = {Eur.J.Biochem.}, volume = {152}, pages = {279–286}, doi = {10.1111/j.1432-1033.1985.tb09195.x}, keywords = {5S rRNA,COMPLEX,COMPLEXES,Globin,initiation,L1,mRNA,nosource,P-SITE,protein,yeast} } % == BibTeX quality report for takahashiAttachmentTerminalPortion1985a: % ? Possibly abbreviated journal title Eur.J.Biochem.

@article{takakuraNH2terminalAcetylationRibosomal1992, title = {{{NH2-terminal}} Acetylation of Ribosomal Proteins of {{Saccharomyces}} Cerevisiae.}, author = {Takakura, H. and Tsunasawa, S. and Miyagi, M. and Warner, J.R.}, year = 1992, month = mar, journal = {Journal of Biological Chemistry}, volume = {267}, number = {8}, pages = {5442–5445}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(18)42785-8}, url = {http://www.jbc.org/content/267/8/5442.short}, abstract = {Using a mutant of Saccharomyces cerevisiae defective in the NAT1 gene, that encodes one of the NH2-terminal acetyltransferases, we have identified 14 ribosomal proteins whose electrophoretic mobility at pH 5.0 suggests they carry an additional charge, presumably due to the lack of NH2-terminal acetylation. At least 30 other ribosomal proteins from the mutant are electrophoretically normal. Attempted NH2-terminal analysis of most of the presumed acetylated proteins from wild type cells indicated that all were blocked. NH2-terminal analysis of the same proteins from the nat1 mutant strain yielded unique sequences. Each one carries an NH2-terminal serine. We conclude that these are normally acetylated due to the presence of the NAT1 gene product. It seems surprising that cells whose ribosomes have been altered to this degree grow rather well and synthesize the same spectrum of proteins as do wild type cells (Mullen, J. R., Kayne, P. S., Moerschell, R. P., Tsunasawa, S. Gribskov, M., Sherman, F., and Sternglanz, R. (1989) EMBO J. 8, 2067-2075). Finally, this analysis has provided the first sequence information available for several of the acetylated ribosomal proteins and for one non-acetylated ribosomal protein, which is clearly the product of the MFT1 gene (Garrett, J. M., Singh, K. K., Vonder Haar, R. A., and Emr. S. D. (1991) Mol. Gen. Gen. 225, 483-491)}, keywords = {0,Acetylation,Acetyltransferases,Amino Acid Sequence,analysis,CELLS,CEREVISIAE,D,ElectrophoresisGelTwo-Dimensional,ENCODES,gene,GENE-PRODUCT,GenesBacterial,genetics,INFORMATION,isolation & purification,La,M,metabolism,Molecular Sequence Data,nosource,PRODUCT,protein,Proteins,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,Serine,SPECTRA,Substrate Specificity,WILD-TYPE} } % == BibTeX quality report for takakuraNH2terminalAcetylationRibosomal1992: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{takyarMRNAHelicaseActivity2005, title = {{{mRNA}} Helicase Activity of the Ribosome}, author = {Takyar, S. and Hickerson, R.P. and Noller, H.F.}, year = 2005, month = jan, journal = {Cell}, volume = {120}, number = {1}, pages = {49–58}, doi = {10.1016/j.cell.2004.11.042}, url = {PM:15652481}, abstract = {Most mRNAs contain secondary structure, yet their codons must be in single-stranded form to be translated. Until now, no helicase activity has been identified which could account for the ability of ribosomes to translate through downstream mRNA secondary structure. Using an oligonucleotide displacement assay, together with a stepwise in vitro translation system made up of purified components, we show that ribosomes are able to disrupt downstream helices, including a perfect 27 base pair helix of predicted T(m) = 70 degrees . Using helices of different lengths and registers, the helicase active site can be localized to the middle of the downstream tunnel, between the head and shoulder of the 30S subunit. Mutation of residues in proteins S3 and S4 that line the entry to the tunnel impairs helicase activity. We conclude that the ribosome itself is an mRNA helicase and that proteins S3 and S4 may play a role in its processivity}, keywords = {0,ACID,ACTIVE-SITE,BASE,Base Sequence,BASE-PAIR,Binding Sites,BIOLOGY,Codon,CODONS,COMPONENT,COMPONENTS,Dna,DOWNSTREAM,enzymology,Escherichia coli,FORM,genetics,Helicase,HELICASE ACTIVITY,In Vitro,in vitro translation,IN-VITRO,La,LINE,metabolism,Models-Molecular,ModelsMolecular,Molecular Biology,Molecular Sequence Data,mRNA,Mutagenesis-Site-Directed,MutagenesisSite-Directed,Mutation,nosource,Nucleic Acid Heteroduplexes,physiology,Plasmids,protein,Protein Conformation,Proteins,RESIDUES,ribosome,Ribosomes,Rna,RNA HELICASE,RNA Helicases,RNA-Messenger,RNAMessenger,SECONDARY STRUCTURE,SITE,structure,SUBUNIT,Support,SYSTEM,Thermus thermophilus,translation} }

@article{taliaferroTestingConstraintsRRNA2007, title = {Testing Constraints on {{rRNA}} Bases That Make Nonsequence-Specific Contacts with the Codon*anticodon Complex in the Ribosomal {{A}} Site}, author = {Taliaferro, D.L. and Farabaugh, P.J.}, year = 2007, journal = {RNA.}, volume = {13}, number = {8}, pages = {1279–1286}, publisher = {Cold Spring Harbor Laboratory Press}, doi = {10.1261/rna.552007}, url = {http://ukpmc.ac.uk/articles/PMC1924888 http://rnajournal.cshlp.org/content/13/8/1279.short}, abstract = {During protein synthesis, interactions between the decoding center of the ribosome and the codon.anticodon complexes maintain translation accuracy. Correct aminoacyl-tRNAs induce the ribosome to shift into a “closed” conformation that both blocks tRNA dissociation and accelerates the process of tRNA acceptance. As part of the ribosomal recognition of cognate tRNAs, the rRNA nucleotides G530 and A1492 form a hydrogen-bonded pair that interacts with the middle position of the codon.anticodon complex and recognizes correct Watson-Crick base pairs. Exchanging these two nucleotides (A530 and G1492) would not disrupt these interactions, suggesting that such a double mutant ribosome might properly recognize tRNAs and support viability. We find, however, that exchange mutants retain little ribosomal activity. We suggest that even though the exchanged nucleotides might function properly during tRNA recruitment, they might disrupt one or more other functions of the nucleotides during other stages of protein synthesis}, keywords = {A SITE,A-SITE,accuracy,BASE,BASE-PAIR,BASES,COMPLEX,COMPLEXES,CONFORMATION,decoding,FORM,La,MUTANTS,nosource,Nucleotides,POSITION,protein,protein synthesis,PROTEIN-SYNTHESIS,RECOGNITION,RECRUITMENT,ribosome,rRNA,SITE,Support,translation,tRNA} } % == BibTeX quality report for taliaferroTestingConstraintsRRNA2007: % ? Possibly abbreviated journal title RNA.

@article{talloczyKILdCytoplasmicGenetic1998, title = {The [{{KIL-d}}] Cytoplasmic Genetic Element of Yeast Results in Epigenetic Regulation of Viral {{M}} Double-Stranded {{RNA}} Gene Expression}, author = {Talloczy, Z. and Menon, S. and Neigeborn, L. and Leibowitz, M.J.}, year = 1998, journal = {Genetics}, volume = {150}, number = {1}, pages = {21–30}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/150.1.21}, url = {http://www.genetics.org/content/150/1/21.short}, abstract = {[KIL-d] is a cytoplasmically inherited genetic trait that causes killer virus-infected cells of Saccharomyces cerevisiae to express the normal killer phenotypes in a/alpha cells, but to show variegated defective killer phenotypes in a or alpha type cells. Mating of [KIL-d] haploids results in “healing” of their phenotypic defects, while meiosis of the resulting diploids results in “resetting” of the variegated, but mitotically stable, defects. We show that [KIL-d] does not reside on the double-stranded RNA genome of killer virus. Thus, the [KIL-d] effect on viral gene expression is epigenetic in nature. Resetting requires nuclear events of meiosis, since [KIL-d] can be cytoplasmically transmitted during cytoduction without causing defects in killer virus expression. Subsequently, mating of these cytoductants followed by meiosis generates spore clones expressing variegated defective phenotypes. Cytoduction of wild-type cytoplasm into a phenotypically defective [KIL-d] haploid fails to heal, nor does simultaneous or sequential expression of both MAT alleles cause healing. Thus, healing is not triggered by the appearance of heterozygosity at the MAT locus, but rather requires the nuclear fusion events which occur during mating. Therefore, [KIL-d] appears to interact with the nucleus in order to exert its effects on gene expression by the killer virus RNA genome}, keywords = {98393567,Alleles,Base Sequence,Cytoplasm,DNA Primers,DOUBLE-STRANDED-RNA,expression,gene,Gene Expression,Gene Expression RegulationFungal,GENE-EXPRESSION,Genetic,genetics,Genome,Haploidy,Heterozygote,killer,L-A,Meiosis,microbiology,Mutation,nosource,Peptides,Phenotype,regulation,Rna,RNA Viruses,RNADouble-Stranded,RNAFungal,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,virology,virus,yeast} }

@article{tamaDynamicReorganizationFunctionally2003, title = {Dynamic Reorganization of the Functionally Active Ribosome Explored by Normal Mode Analysis and Cryo-Electron Microscopy}, author = {Tama, F. and Valle, M. and Frank, J. and Brooks, C.L.}, year = 2003, month = jul, journal = {Proceedings of the National Academy of Sciences}, volume = {100}, number = {16}, pages = {9319–9323}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.1632476100}, url = {http://www.pnas.org/content/100/16/9319.short}, abstract = {Combining structural data for the ribosome from x-ray crystallography and cryo-electron microscopy with dynamic models based on elastic network normal mode analysis, an atomically detailed picture of functionally important structural rearrangements that occur during translocation is elucidated. The dynamic model provides a near-atomic description of the ratchet-like rearrangement of the 70S ribosome seen in cryo-electron microscopy, and permits the identification of bridging interactions that either facilitate the conformational switching or maintain structural integrity of the 50S/30S interface. Motions of the tRNAs residing in the A and P sites also suggest the early stages of tRNA translocation as a result of this ratchet-like movement. Displacement of the L1 stalk, alternately closing and opening the intersubunit space near the E site, is observed in the dynamic model, in line with growing experimental evidence for the role of this structural component in facilitating the exiting of tRNA. Finally, a hinge-like transition in the 30S ribosomal subunit, similar to that observed in crystal structures of this complex, is also manifest as a dynamic mode of the ribosome. The coincidence of these dynamic transitions with the individual normal modes of the ribosome and the good correspondence between these motions and those observed in experiment suggest an underlying principle of nature to exploit the shape of molecular assemblies such as the ribosome to provide robustness to functionally important motions}, keywords = {analysis,assembly,COMPLEX,COMPLEXES,COMPONENT,Cryoelectron Microscopy,CRYSTAL-STRUCTURE,Crystallography,IDENTIFICATION,L1,La,models,Movement,nosource,P-SITE,RIBOSOMAL-SUBUNIT,ribosome,Structural,structure,SUBUNIT,translocation,tRNA} } % == BibTeX quality report for tamaDynamicReorganizationFunctionally2003: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{tanProgrammedTranslationalFrameshifting2001, title = {Programmed Translational Frameshifting Is Likely Required for Expressions of Genes Encoding Putative Nuclear Protein Kinases of the Ciliate {{Euplotes}} Octocarinatus}, author = {Tan, M. and Liang, A. and {Brunen-Nieweler}, C. and Heckmann, K.}, year = 2001, journal = {Journal of Eukaryotic Microbiology}, volume = {48}, number = {5}, pages = {575–582}, publisher = {Wiley Online Library}, doi = {10.1111/j.1550-7408.2001.tb00193.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1550-7408.2001.tb00193.x/full}, abstract = {Three macronuclear genes encoding putative nuclear protein kinases of the ciliate Euplotes octocarinatus syngen 1 were isolated and sequenced. All three deduced gene products share significant properties with a group of recently identified nuclear serine/threonine protein kinases named Ndr. The three predicted proteins contain the twelve conserved catalytic subdomains of protein kinases and 22 near universally-conserved amino acids residues that are characteristic of serine/threonine protein kinases. In addition, there is an approximately 30 amino acid-peptide insertion between subdomains VII and VIII that contains a potential nuclear localization signal. Sequence analysis suggests that expression of the Eondr2 gene requires a + 1 programmed translational frameshift for its translation. Comparison of the deduced EoNdr2 with other known Ndr protein kinases implies that a + 1 ribosomal frameshift occurs at the motif AAATAA}, keywords = {0,ACID,ACIDS,Amino Acid Sequence,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,animal,Base Sequence,Cell Nucleus,chemistry,Chromosomes,Dna,DNAComplementary,DNAProtozoan,enzymology,Euplotes,expression,frameshift,Frameshifting,FrameshiftingRibosomal,gene,Gene Dosage,GENE-PRODUCT,Genes,genetics,kinase,La,LOCALIZATION,metabolism,Molecular Sequence Data,nosource,Nuclear Localization Signal,PRODUCT,PRODUCTS,protein,Protein Kinases,PROTEIN-KINASE,Protein-Serine-Threonine Kinases,Proteins,REQUIRES,RESIDUES,RIBOSOMAL FRAMESHIFT,sequence,Sequence Alignment,Sequence Analysis,Sequence AnalysisDNA,SEQUENCE-ANALYSIS,SIGNAL,supportnon-u.s.gov’t,translation,TRANSLATIONAL FRAMESHIFTING} } % == BibTeX quality report for tanProgrammedTranslationalFrameshifting2001: % ? unused Journal abbr (“J.Eukaryot.Microbiol.”)

@article{tangStructureYeastRibosomal1991a, title = {Structure of the Yeast Ribosomal {{5S RNA-binding}} Protein {{YL3}}.}, author = {Tang, B. and Nazar, R.N.}, year = 1991, journal = {J.Biol.Chem.}, volume = {226}, pages = {6120–6123}, doi = {10.1016/S0021-9258(18)38092-X}, keywords = {5S rRNA,L1,nosource,protein,structure,yeast} } % == BibTeX quality report for tangStructureYeastRibosomal1991a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{tangUnbalancedRegulationRibosomal1992, title = {Unbalanced Regulation of the Ribosomal 5 {{S RNA-binding}} Protein in {{Saccharomyces}} Cerevisiae Expressing Mutant 5 {{S rRNAs}}.}, author = {Tang, B. and Nazar, R.N.}, year = 1992, journal = {Journal of Biological Chemistry}, volume = {267}, number = {25}, pages = {17738–17742}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(19)37105-4}, url = {http://www.jbc.org/content/267/25/17738.short}, abstract = {A gene encoding the 5 S rRNA-binding protein (YL3) in yeast (Saccharomyces cerevisiae) was further characterized with respect to its chromosomal localization, the controlling sequence regions, and the influence of 5 S rRNA gene expression. Sequence and chromosome blot analyses localized the gene on chromosome XVI immediately downstream of a cytochrome oxidase assembly gene, COXII. S1 nuclease protection studies identified two major initiation sites, 20 and 65 nucleotides upstream of the coding sequence, and a single polyadenylation site, 98 nucleotides downstream of the stop codon. Northern blot analyses and S1 nuclease protection indicated a normal pattern of gene regulation in media supporting alternate rates of growth, but significantly unbalanced regulation was observed in the presence of mutant 5 S rRNA genes which under-produce RNA and result in reduced growth rates. The results suggest a co-ordinating regulatory mechanism which maintains appropriate levels of 5 S rRNA-protein complex; an internal control region-like sequence in the upstream region of the YL3 gene is consistent with this feedback mechanism}, keywords = {0,5 S rRNA,animal,assembly,Base Sequence,BIOLOGY,CEREVISIAE,Chromosome Mapping,ChromosomesFungal,coding sequence,Codon,Comparative Study,COMPLEX,COMPLEXES,CYTOCHROME-C OXIDASE,Dna,DNAFungal,DNARibosomal,DOWNSTREAM,expression,Feedback,gene,Gene Expression,gene regulation,GENE-EXPRESSION,Genes,GenesFungal,GenesRegulator,Genetic,genetics,GROWTH,IMMEDIATELY DOWNSTREAM,initiation,INITIATION SITE,La,LOCALIZATION,MECHANISM,media,metabolism,Molecular Sequence Data,nosource,Nucleotides,Polyadenylation,PROTECTION,protein,Proteins,REGION,regulation,Rna,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAMessenger,RNARibosomal5S,rRNA,rRNA genes,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence HomologyNucleic Acid,SITE,SITES,STOP CODON,TranscriptionGenetic,UPSTREAM,Xenopus,yeast} } % == BibTeX quality report for tangUnbalancedRegulationRibosomal1992: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{tangUnusualMessengerRnaPseudoknot1989, title = {Unusual {{Messenger-Rna Pseudoknot Structure Is Recognized}} by {{A Protein Translational Repressor}}}, author = {Tang, C.K. and Draper, D.E.}, year = 1989, month = may, journal = {Cell}, volume = {57}, number = {4}, pages = {531–536}, doi = {10.1016/0092-8674(89)90123-2}, url = {ISI:A1989U743600006}, keywords = {MESSENGER-RNA,nosource,protein,pseudoknot,REPRESSOR,structure} } % == BibTeX quality report for tangUnusualMessengerRnaPseudoknot1989: % ? Title looks like it was stored in title-case in Zotero

@article{tarrLr1CandidateRna1988, title = {Lr1 - {{A Candidate Rna Virus}} of {{Leishmania}}}, author = {Tarr, P.I. and Aline, R.F. and Smiley, B.L. and Scholler, J. and Keithly, J. and Stuart, K.}, year = 1988, month = dec, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {85}, number = {24}, pages = {9572–9575}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.85.24.9572}, url = {http://www.pnas.org/content/85/24/9572.short}, keywords = {nosource,Rna,virus} } % == BibTeX quality report for tarrLr1CandidateRna1988: % ? Title looks like it was stored in title-case in Zotero

@article{tarunCommonFunctionMRNA1995, title = {A Common Function for {{mRNA}} 5’ and 3’ Ends in Translation Initiation in Yeast.}, author = {Tarun, S. and Sachs, A.B.}, year = 1995, journal = {Genes & Dev.}, volume = {9}, pages = {2997–3007}, doi = {10.1101/gad.9.23.2997}, keywords = {In Vitro,in vitro translation,IN-VITRO,initiation,mRNA,nosource,translation,TRANSLATION INITIATION,yeast} } % == BibTeX quality report for tarunCommonFunctionMRNA1995: % ? Possibly abbreviated journal title Genes & Dev.

@article{tateTranslationalTerminationStop1992a, title = {Translational Termination: “{{Stop}}” for Protein Synthesis of “{{Pause}}” for Regulation of Gene Expression.}, author = {Tate, W.P. and Brown, C.M.}, year = 1992, journal = {Biochemistry}, volume = {31}, pages = {2443–2450}, doi = {10.1021/bi00124a001}, keywords = {expression,gene,Gene Expression,GENE-EXPRESSION,nosource,pausing,protein,protein synthesis,PROTEIN-SYNTHESIS,regulation,ribosome,termination,translation} }

@article{tauntonMammalianHistoneDeacetylase1996a, title = {A Mammalian Histone Deacetylase Related to the Yeast Transcriptional Regulator {{Rpd3p}} [See Comments]}, author = {Taunton, J. and Hassig, C.A. and Schreiber, S.L.}, year = 1996, month = apr, journal = {Science}, volume = {272}, number = {5260}, pages = {408–411}, doi = {10.1126/science.272.5260.408}, abstract = {Trapoxin is a microbially derived cyclotetrapeptide that inhibits histone deacetylation in vivo and causes mammalian cells to arrest in the cell cycle. A trapoxin affinity matrix was used to isolate two nuclear proteins that copurified with histone deacetylase activity. Both proteins were identified by peptide microsequencing, and a complementary DNA encoding the histone deacetylase catalytic subunit (HD1) was cloned from a human Jurkat T cell library. As the predicted protein is very similar to the yeast transcriptional regulator Rpd3p, these results support a role for histone deacetylase as a key regulator of eukaryotic transcription}, keywords = {96185499,Amino Acid Sequence,animal,antagonists & inhibitors,AntibioticsPeptide,Cattle,cell cycle,chemistry,CloningMolecular,Dna,drug effects,Enzyme Inhibitors,enzymology,Fungal Proteins,Gene Expression Regulation,genetics,Histone Deacetylase,human,Hydroxamic Acids,IN-VIVO,isolation & purification,library,metabolism,Molecular Sequence Data,Molecular Weight,nosource,Nuclear Proteins,pharmacology,protein,Proteins,Saccharomyces cerevisiae,SUBUNIT,Support,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,T-Lymphocytes,transcription,Transcription Factors,TranscriptionGenetic,Tumor CellsCultured,yeast} }

@incollection{taylorEukaryoticRibosomesElongation2006, title = {Eukaryotic Ribosomes and the Elongation Pathway.}, booktitle = {Translational Control of Gene Expression.}, author = {Taylor, D.J. and Frank, J. and Kinzy, T.G.}, year = 2006, pages = {59–85}, publisher = {Cold Spring Harbor Laboratory Press}, address = {Cold Spring Harbor, NY}, collaborator = {Sonenberg, N. and Hershey, J.W.B. and Mathews, M.B.}, keywords = {elongation,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,expression,gene,Gene Expression,GENE-EXPRESSION,nosource,PATHWAY,ribosome,Ribosomes} }

@article{taylorStructuresModifiedEEF22007, title = {Structures of Modified {{eEF2 80S}} Ribosome Complexes Reveal the Role of {{GTP}} Hydrolysis in Translocation}, author = {Taylor, D.J. and Nilsson, J. and Merrill, A.R. and Andersen, G.R. and Nissen, P. and Frank, J.}, year = 2007, month = may, journal = {The EMBO Journal}, volume = {26}, number = {9}, pages = {2421–2431}, doi = {10.1038/sj.emboj.7601677}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Structures+of+modified+eEF2+80S+ribosome+complexes+reveal+the+role+of+GTP+hydrolysis+in+translocation#1 http://www.nature.com/emboj/journal/vaop/ncurrent/full/7601677a.html http://onlinelibrary.wiley.com/doi/10.1038/sj.emboj.7601677/full}, abstract = {On the basis of kinetic data on ribosome protein synthesis, the mechanical energy for translocation of the mRNA-tRNA complex is thought to be provided by GTP hydrolysis of an elongation factor (eEF2 in eukaryotes, EF-G in bacteria). We have obtained cryo-EM reconstructions of eukaryotic ribosomes complexed with ADP-ribosylated eEF2 (ADPR-eEF2), before and after GTP hydrolysis, providing a structural basis for analyzing the GTPase-coupled mechanism of translocation. Using the ADP-ribosyl group as a distinct marker, we observe conformational changes of ADPR-eEF2 that are due strictly to GTP hydrolysis. These movements are likely representative of native eEF2 motions in a physiological context and are sufficient to uncouple the mRNA-tRNA complex from two universally conserved bases in the ribosomal decoding center (A1492 and A1493 in Escherichia coli) during translocation. Interpretation of these data provides a detailed two-step model of translocation that begins with the eEF2/EF-G binding-induced ratcheting motion of the small ribosomal subunit. GTP hydrolysis then uncouples the mRNA-tRNA complex from the decoding center so translocation of the mRNA-tRNA moiety may be completed by a head rotation of the small subunit}, keywords = {0,Adenosine,Adenosine Diphosphate,Ascomycota,Bacteria,BASE,BASES,chemistry,COMPLEX,COMPLEXES,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,cryo-em,Cryoelectron Microscopy,decoding,ef-g,EF-G,elongation,ELONGATION-FACTOR-G,Escherichia coli,ESCHERICHIA-COLI,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,GTP,gtpase,Guanosine,Guanosine Triphosphate,Hydrolysis,La,MARKER,MECHANISM,metabolism,Methods,MODEL,ModelsMolecular,Molecular Sequence Data,Motion,Movement,nosource,Peptide Elongation Factor 2,Peptide Elongation Factor G,protein,Protein StructureTertiary,protein synthesis,PROTEIN-SYNTHESIS,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNA Transport,RNAMessenger,RNATransfer,Rotation,Structural,STRUCTURAL BASIS,structure,SUBUNIT,Support,switch 1,translocation} } % == BibTeX quality report for taylorStructuresModifiedEEF22007: % ? unused Journal abbr (“EMBO J.”)

@article{taylorComprehensiveMolecularStructure2009, title = {Comprehensive Molecular Structure of the Eukaryotic Ribosome.}, author = {Taylor, D.J. and Devkota, B. and Huang, A.D. and Topf, M. and Narayanan, E. and Sali, A. and Harvey, S.C. and Frank, J.}, year = 2009, month = dec, journal = {Structure}, volume = {17}, number = {12}, pages = {1591–1604}, publisher = {Elsevier}, issn = {1878-4186}, doi = {10.1016/j.str.2009.09.015}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2814252&tool=pmcentrez&rendertype=abstract http://linkinghub.elsevier.com/retrieve/pii/s0969-2126(09)00416-x}, abstract = {Despite the emergence of a large number of X-ray crystallographic models of the bacterial 70S ribosome over the past decade, an accurate atomic model of the eukaryotic 80S ribosome is still not available. Eukaryotic ribosomes possess more ribosomal proteins and ribosomal RNA than do bacterial ribosomes, which are implicated in extraribosomal functions in the eukaryotic cells. By combining cryo-EM with RNA and protein homology modeling, we obtained an atomic model of the yeast 80S ribosome complete with all ribosomal RNA expansion segments and all ribosomal proteins for which a structural homolog can be identified. Mutation or deletion of 80S ribosomal proteins can abrogate maturation of the ribosome, leading to several human diseases. We have localized one such protein unique to eukaryotes, rpS19e, whose mutations are associated with Diamond-Blackfan anemia in humans. Additionally, we characterize crucial interactions between the dynamic stalk base of the ribosome with eukaryotic elongation factor 2.}, pmid = {20004163}, keywords = {70S RIBOSOME,Anemia,Bacterial,BASE,CELLS,cryoelectron microscopy,crystallography,disease,elongation,Eukaryotic Cells,eukaryotic elongation factor,EUKARYOTIC RIBOSOME,EUKARYOTIC RIBOSOMES,homolog,human,Humans,MATURATION,MODEL,models,molecular,molecular structure,Molecular Structure,Mutation,MUTATIONS,nosource,nucleic acid conformation,protein,Proteins,ribosomal,ribosomal chemistry,Ribosomal Proteins,ribosomal RNA,RIBOSOMAL-PROTEIN,RIBOSOMAL-RNA,Ribosomal: chemistry,ribosome,ribosomes,Ribosomes,ribosomes chemistry,Ribosomes: chemistry,rna,Rna,Structural,structure,x ray,X-Ray,yeast} }

@article{taylorBasisNewApproaches1994, title = {A Basis for New Approaches to the Chemotherapy of {{AIDS}}: Novel Genes in {{HIV-1}} Potentially Encode Selenoproteins Expressed by Ribosomal Frameshifting and Termination Suppression}, author = {Taylor, E. W. and Ramanathan, C. S. and Jalluri, R. K. and Nadimpalli, R. G.}, year = 1994, journal = {Journal of medicinal chemistry}, volume = {37}, number = {17}, pages = {2637–2654}, publisher = {ACS Publications}, url = {http://pubs.acs.org/doi/abs/10.1021/jm00043a004}, keywords = {Frameshifting,gene,Genes,HIV,Hiv-1,nosource,pseudoknot,pseudoknots,ribosomal frameshifting,sequence,suppression,termination} }

@article{taylorCorrelationActivitiesFive1994, title = {Correlation between the Activities of Five Ribosome-Inactivating Proteins in Depurination of Tobacco Ribosomes and Inhibition of Tobacco Mosaic Virus Infection}, author = {Taylor, S. and Massiah, A. and Lomonossoff, G. and Roberts, L.M. and Lord, J.M. and Hartley, M.}, year = 1994, month = jun, journal = {The Plant Journal}, volume = {5}, number = {6}, pages = {827–835}, publisher = {Wiley Online Library}, doi = {10.1046/j.1365-313X.1994.5060827.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-313X.1994.5060827.x/abstract}, abstract = {The rRNA depurination activities of five ribosome-inactivating proteins (RIPs) were compared in vitro using yeast and tobacco leaf ribosomes as substrates. All of the RIPs (pokeweed antiviral protein (PAP), dianthin 32, tritin, barley RIP and ricin A-chain) were active on yeast ribosomes. PAP and dianthin 32 were highly active and ricin A-chain weakly active on tobacco ribosomes, whereas tritin and barley RIP were inactive. PAP and dianthin 32 were highly effective in inhibiting the formation of local lesions caused by tobacco mosaic virus (TMV) on tobacco leaves, whereas tritin, barley RIP and ricin A-chain were ineffective. The apparent anomaly between the in vitro rRNA depurination activity, but lack of antiviral activity of ricin A-chain was further investigated by assaying for rRNA depurination in situ following the topical application of the RIP to leaves. No activity was detected, a finding consistent with the apparent lack of antiviral activity of this RIP. Thus, it is concluded that there is a positive correlation between RIP-catalysed depurination of tobacco ribosomes and antiviral activity which gives strong support to the hypothesis that the antiviral activity of RIPs works through ribosome inactivation}, keywords = {94332158,Aniline Compounds,antiviral,Antiviral Agents,Base Sequence,chemistry,Comparative Study,drug effects,In Vitro,IN-VITRO,INHIBITION,metabolism,Molecular Sequence Data,nosource,PAP,pharmacology,physiology,Plant Proteins,Pokeweed antiviral protein,protein,Protein Synthesis Inhibitors,Proteins,Purines,ribosome,Ribosomes,Ricin,RNARibosomal,rRNA,Support,Tobacco,Tobacco Mosaic Virus,virus,yeast,Yeasts} } % == BibTeX quality report for taylorCorrelationActivitiesFive1994: % ? unused Journal abbr (“Plant J.”)

@article{teixeiraTelomereLengthHomeostasis2004, title = {Telomere Length Homeostasis Is Achieved via a Switch between Telomerase- Extendible and -Nonextendible States}, author = {Teixeira, M.T. and Arneric, M. and Sperisen, P. and Lingner, J.}, year = 2004, month = apr, journal = {Cell}, volume = {117}, number = {3}, pages = {323–335}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(04)00334-4}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867404003344}, abstract = {Telomerase counteracts telomere erosion that stems from incomplete chromosome end replication and nucleolytic processing. A precise understanding of telomere length homeostasis has been hampered by the lack of assays that delineate the nonuniform telomere extension events of single chromosome molecules. Here, we measure telomere elongation at nucleotide resolution in Saccharomyces cerevisiae. The number of nucleotides added to a telomere in a single cell cycle varies between a few to more than 100 nucleotides and is independent of telomere length. Telomerase does not act on every telomere in each cell cycle, however. Instead, it exhibits an increasing preference for telomeres as their lengths decline. Deletion of the telomeric proteins Rif1 or Rif2 gives rise to longer telomeres by increasing the frequency of elongation events. Thus, by taking a molecular snapshot of a single round of telomere replication, we demonstrate that telomere length homeostasis is achieved via a switch between telomerase-extendible and -nonextendible states}, keywords = {0,analysis,assays,Base Sequence,cancer,cell cycle,CEREVISIAE,Chromosomes-Fungal,ChromosomesFungal,Comparative Study,Crosses-Genetic,CrossesGenetic,deficiency,Dna,elongation,enzymology,Gene Expression Regulation-Enzymologic,Gene Expression Regulation-Fungal,Gene Expression RegulationEnzymologic,Gene Expression RegulationFungal,Genetic,Genetic Variation,genetics,Homeostasis,Kinetics,La,metabolism,Models-Biological,ModelsBiological,nosource,NUCLEOTIDE RESOLUTION,Nucleotides,Polymerase Chain Reaction,protein,Proteins,Recombination-Genetic,RecombinationGenetic,REPLICATION,RESOLUTION,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Support,Telomerase,Telomere} }

@article{telentiAnalysisNaturalVariants2002, title = {Analysis of {{Natural Variants}} of the {{Human Immunodeficiency Virus Type}} 1 Gag-Pol {{Frameshift Stem-Loop Structure}}}, author = {Telenti, A. and Martinez, R. and Munoz, M. and Bleiber, G. and Greub, G. and Sanglard, D. and Peters, S.}, year = 2002, journal = {Journal of Virology}, volume = {76}, number = {15}, pages = {7868–7873}, publisher = {Am Soc Microbiol}, doi = {10.1128/JVI.76.15.7868-7873.2002}, url = {http://jvi.asm.org/cgi/content/abstract/76/15/7868}, abstract = {Human immunodeficiency virus type 1 uses ribosomal frameshifting for translation of the Gag-Pol polyprotein. Frameshift activities are thought to be tightly regulated. Analysis of gag p1 sequences from 270 plasma virions identified in 64% of the samples the occurrence of polymorphism that could lead to changes in thermodynamic stability of the stem-loop. Expression in Saccharomyces cerevisiae of p1-beta- galactosidase fusion proteins from 10 representative natural stem-loop variants and three laboratory mutant constructs (predicted the thermodynamic stability [DeltaG degrees ] ranging from -23.0 to -4.3 kcal/mol) identified a reduction in frameshift activity of 13 to 67% compared with constructs with the wild-type stem-loop (DeltaG degrees, - 23.5 kcal/mol). Viruses carrying stem-loops associated with greater than 60% reductions in frameshift activity presented profound defects in viral replication. In contrast, viruses with stem-loop structures associated with 16 to 42% reductions in frameshift efficiency displayed no significant viral replication deficit}, keywords = {analysis,disease,efficiency,expression,frameshift,Frameshifting,Gag,Gag-pol,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,La,microbiology,nosource,protein,Proteins,ribosomal frameshifting,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,stability,structure,thermodynamic stability,translation,Virion,virus} } % == BibTeX quality report for telentiAnalysisNaturalVariants2002: % ? unused Journal abbr (“J.Virol.”)

@article{tendamIdentificationAnalysisPseudoknotcontaining1994, title = {Identification and Analysis of the Pseudoknot-Containing Gag-pro Ribosomal Frameshift Signal of Simian Retrovirus-1}, author = {{}{ten Dam}, E. and Brierley, I. and Inglis, S. and Pleij, C.}, year = 1994, month = jun, journal = {Nucleic Acids Research}, volume = {22}, number = {12}, pages = {2304–2310}, publisher = {Oxford Univ Press}, url = {PM:8036158 http://nar.oxfordjournals.org/content/22/12/2304.short}, abstract = {The pro and pol genes of simian retrovirus-1 (SRV-1) are expressed as parts of a fusion protein generated by -1 ribosomal frameshifting. To investigate the requirements for frameshifting at the gag-pro overlap, we have inserted a stretch of 58 nucleotides containing the proposed frameshift signal into a plasmid that allows monitoring of translation in all three reading frames. In vitro translation of mRNAs derived from this plasmid indicated that the 58 nucleotides from the SRV-1 gag-pro overlap were sufficient to induce an efficient -1 shift in a heterologous context. Mutational analysis demonstrated that the slip site is formed at the heptanucleotide G GGA AAC. The frameshift efficiency of the wild type sequence in rabbit reticulocyte lysate was 23%. A second component of the frameshift signal is formed by a pseudoknot seven bases downstream of the slip site. The presence of this pseudoknot was confirmed by mutational analysis, employing complementary and compensatory base changes, and by probing the structure of short RNA transcripts containing the frameshift signal. Adding increasing amounts of an SRV-1 pseudoknot containing RNA transcript to a translation reaction programmed with an SRV-1 frameshift reporter mRNA had no effect on the frameshift efficiency, arguing against the role of a specific pseudoknot-recognising factor in the frameshifting process}, keywords = {0,analysis,BASE,BASE CHANGES,Base Sequence,BASES,chemistry,CloningMolecular,COMPONENT,DOWNSTREAM,efficiency,FRAME,frameshift,Frameshift Mutation,Frameshifting,FUSION PROTEIN,gene,Gene Expression RegulationViral,Genes,Genesgag,Genespol,genetics,IDENTIFICATION,In Vitro,in vitro translation,IN-VITRO,La,lysate,Molecular Sequence Data,mRNA,MUTATIONAL ANALYSIS,No DOI found,nosource,Nucleic Acid Conformation,Nucleotides,PLASMID,pol,POL GENE,protein,Protein Biosynthesis,Proteins,pseudoknot,READING FRAME,Reading Frames,Regulatory SequencesNucleic Acid,Research SupportNon-U.S.Gov’t,RetrovirusesSimian,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,Rna,RnaViral,sequence,SIGNAL,SIMIAN RETROVIRUS-1,SITE,structure,TRANSCRIPT,translation,Viral Proteins,WILD-TYPE} } % == BibTeX quality report for tendamIdentificationAnalysisPseudoknotcontaining1994: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{tendamRNAPseudoknotsTranslational1990, title = {{{RNA}} Pseudoknots: Translational Frameshifting and Readthrough on Viral {{RNAs}}.}, author = {TenDam, E. and Pleij, K. and Bosch, L.}, year = 1990, journal = {Virus Genes}, volume = {4}, number = {2}, pages = {121–136}, publisher = {Springer}, doi = {10.1007/BF00678404}, url = {http://www.springerlink.com/index/W58704264X618188.pdf}, keywords = {Frameshifting,nosource,pseudoknot,pseudoknots,readthrough,Review,Rna,RNA PSEUDOKNOT} }

@article{tendamStructuralFunctionalAspects1992, title = {Structural and Functional Aspects of {{RNA}} Pseudoknots.}, author = {TenDam, E. and Pleij, K. and Draper, D.}, year = 1992, journal = {Biochemistry}, volume = {31}, number = {47}, pages = {11665–11676}, publisher = {ACS Publications}, doi = {10.1021/bi00162a001}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00162a001}, keywords = {Frameshifting,nosource,pseudoknot,pseudoknots,Rna,RNA PSEUDOKNOT,Structural,virus} }

@article{teoTelomeraseSubunitOverexpression2001, title = {Telomerase Subunit Overexpression Suppresses Telomere-Specific Checkpoint Activation in the Yeast Yku80 Mutant}, author = {Teo, S.H. and Jackson, S.P.}, year = 2001, month = mar, journal = {EMBO reports}, volume = {2}, number = {3}, pages = {197–202}, publisher = {Nature Publishing Group}, doi = {10.1093/embo-reports/kve038}, url = {http://www.nature.com/embor/journal/v2/n3/abs/embor470.html}, abstract = {Ku is a conserved heterodimeric DNA-binding protein that plays critical roles in DNA repair and telomere homeostasis. In Saccharomyces cerevisiae, deletion of YKU70 or YKU80 results in an inability to grow at 37 degrees C. This is suppressed by overexpression of several components of telomerase (EST1, EST2 and TLC1). We show that overexpression of EST2 or TLC1 in yku80 mutants does not restore efficient DNA repair, or restore normal telomere function, as measured by telomere length, single-stranded G-rich strand or transcriptional silencing. Instead, yku80 mutants activate a Rad53p-dependent DNA-damage checkpoint at 37 degrees C and this is suppressed by overexpression of EST2 or TLC1. Indeed, deletion of genes required for Rad53p activation also suppresses the yku80 temperature sensitivity. These results suggest that activation of the DNA-damage checkpoint in yku mutants at 37 degrees C does not result from reduced telomere length per se, but reflects an alteration of the telomere structure that is recognized as damaged DNA}, keywords = {0,activation,ANTIGEN,Antigens,AntigensNuclear,BIOLOGY,cancer,cell cycle,Cell Cycle Proteins,CEREVISIAE,chemistry,COMPONENT,COMPONENTS,Dna,DNA Damage,DNA Helicases,DNA Repair,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,Fungal Proteins,gene,Gene Expression,Genes,GenesFungal,genetics,growth & development,Helicase,human,kinase,La,metabolism,MUTANTS,Mutation,nosource,Nuclear Proteins,OVEREXPRESSION,Phosphorylation,protein,Protein Kinases,Protein Subunits,PROTEIN-KINASE,Protein-Serine-Threonine Kinases,Proteins,Rna,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,structure,SUBUNIT,SUBUNITS,Support,Telomerase,Telomere,Temperature,yeast} } % == BibTeX quality report for teoTelomeraseSubunitOverexpression2001: % ? unused Journal abbr (“EMBO Rep.”)

@article{teraoCrosslinkingL5Protein1980, title = {Cross-Linking of {{L5}} Protein to 5 {{S RNA}} in Rat Liver 60-{{S}} Subunits by Ultraviolet Irradiation}, author = {Terao, K. and Uchiumi, T. and Ogata, K.}, year = 1980, journal = {Biochimica et Biophysica Acta (BBA)-Nucleic Acids and Protein Synthesis}, volume = {609}, number = {2}, pages = {306–312}, publisher = {Elsevier}, doi = {10.1016/0005-2787(80)90242-7}, url = {http://linkinghub.elsevier.com/retrieve/pii/0005278780902427}, abstract = {After rat liver 60-S ribosomal subunits were irradiated with ultraviolet light at 254 nm, they were treated with EDTA and then subjected to sucrose density-gradient centrifugation to isolate 5 S RNA-protein complex. When 5 S RNA-protein was analyzed by SDS-acrylamide gel electrophoresis which dissociated noncovalent 5 S RNA-protein, two protein bands were observed. The one showed a slower mobility than the protein band (L5) of 5 S RNA-protein from non-irradiated 60 S subunit and the other showed the same mobility as L5 protein. Since the former band was shown to be specific to ultraviolet-irradiation, it was considered as cross-linked 5 S RNA-protein. After the two protein bands were iodinated with 125 I, labeled protein was extracted and treated with RNAase. Thereafter, it was analyzed by two-dimensional acrylamide gel electrophoresis, followed by autoradiography. The results indicate that the protein component of cross-linked 5 S RNA-protein is L5 protein (ribosomal protein; these proteins are designated according to the proposed uniform nomenclature. The correlation between that and our nomenclature was reported by McConkey et al. (1979) Mol. Gen. Genet. 169, 1-6. They also confirm the results previously reported (Terao, K., Takahashi, Y. and O(gata, K. (1975) Biochim. Biophys. Acta 402, 230-237)}, keywords = {0,60S subunit,Animals,Autoradiography,COMPLEX,COMPLEXES,COMPONENT,CROSS-LINKING,CROSSLINKING,Electrophoresis,ElectrophoresisPolyacrylamide Gel,GEL-ELECTROPHORESIS,L5,La,Liver,nomenclature,nosource,protein,Proteins,radiation effects,rat,Rats,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,Rna,RNARibosomal,S,SUBUNIT,SUBUNITS,ultrastructure,ultraviolet rays} } % == BibTeX quality report for teraoCrosslinkingL5Protein1980: % ? unused Journal abbr (“Biochim.Biophys.Acta”)

@article{terceroLocalizedMutagenesisEvidence1992, title = {Localized Mutagenesis and Evidence for Post-Transcriptional Regulation of {{MAK3}}. {{A}} Putative {{N-acetyltransferase}} Required for Double-Stranded {{RNA}} Virus Propagation in {{Saccharomyces}} Cerevisiae.}, author = {Tercero, J.C. and Riles, L.E. and Wickner, R.B.}, year = 1992, month = oct, journal = {Journal of Biological Chemistry}, volume = {267}, number = {28}, pages = {20270–20276}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(19)88696-9}, url = {http://www.jbc.org/content/267/28/20270.short}, abstract = {The MAK3 gene of Saccharomyces cerevisiae is necessary for the propagation of the L-A double-stranded RNA virus and its satellites, such as M1 that encodes a killer toxin. We cloned the MAK3 gene based on its genetic map position using physically mapped lambda-clones covering nearly all of the yeast genome. The minimal sequence necessary to complement the mak3-1 mutation contained 3 open reading frames (ORFs). Only one (ORF3) was necessary to complement mak3-1. A deletion insertion mutant of ORF3 grew slowly on nonfermentable carbon sources, an effect not due simply to its loss of L-A. Although ORF3 alone is sufficient for MAK3 activity when expressed from an expression vector, in its native context an additional 669 base pairs 3’ to the ORF and complementary to the gene for a non-histone protein are necessary for expression, but not for normal steady state transcript levels. This suggests a post-transcriptional control of MAK3 expression by the 3’ region. The MAK3 protein has substantial homology with several N-acetyltransferases with consensus patterns h..h.h. . . Y..[HK]GI[AG][KR].Lh. . .h and h.h[DE]. . . .N..A. . .Y . . .GF. . . .. . . .Y . . [DE]G, (h = hydrophobic). Mutation of any of the underlined conserved residues (94GI—-AA, 123N—-A, 130Y—-A, 134GF—-SL, 144Y—-A, and 149G—-A) inactivated the gene, supporting the hypothesis that MAK3 encodes an N-acetyltransferase}, keywords = {93015901,Amino Acid Sequence,Arylamine N-Acetyltransferase,Base Sequence,Carbon,carbon source,Chromosome Mapping,Chromosome Walking,CloningMolecular,disease,DNAFungal,DOUBLE-STRANDED-RNA,enzymology,expression,Fungal Proteins,gene,Gene Expression RegulationFungal,Genetic,genetics,Genome,killer,killer toxin,L-A,La,M1,metabolism,Molecular Sequence Data,Mutagenesis,Mutation,nosource,Open Reading Frames,physiology,Plasmids,post-transcriptional regulation,protein,regulation,Restriction Mapping,Rna,RNA Viruses,RNADouble-Stranded,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence HomologyAmino Acid,supportnon-u.s.gov’t,toxin,vector,virus,Virus Replication,yeast} } % == BibTeX quality report for terceroLocalizedMutagenesisEvidence1992: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{terceroYeastMAK3Acetyltransferase1993, title = {Yeast ⬚{{MAK3}}⬚ ⬚{{N-}}⬚{{Acetyltransferase}} Recognizes the {{N-terminal}} Four Amino Acids of the Major Coat Protein (⬚gag⬚) of the {{L-A}} Double-Stranded {{RNA}} Virus.}, author = {Tercero, J.C. and Dinman, J.D. and Wickner, R.B.}, year = 1993, journal = {J.Bacteriol.}, volume = {175}, number = {10}, pages = {3192–3194}, doi = {10.1128/jb.175.10.3192-3194.1993}, keywords = {Amino Acids,CV,DOUBLE-STRANDED-RNA,Gag,L-A,La,nosource,protein,Rna,virus,yeast} } % == BibTeX quality report for terceroYeastMAK3Acetyltransferase1993: % ? Possibly abbreviated journal title J.Bacteriol.

@article{theimerEquilibriumUnfoldingPathway1999a, title = {Equilibrium Unfolding Pathway of an {{H-type RNA}} Pseudoknot Which Promotes Programmed-1 Ribosomal Frameshifting}, author = {Theimer, C.A. and Giedroc, D.P.}, year = 1999, month = jun, journal = {Journal of Molecular Biology}, volume = {289}, number = {5}, pages = {1283–1299}, doi = {10.1006/jmbi.1999.2850}, url = {ISI:000081223100011}, abstract = {The equilibrium unfolding pathway of a 41-nucleotide frameshifting RNA pseudoknot from the gag-pro junction of mouse intracisternal A-type particles (mIAP), an endogenous retrovirus, has been determined through analysis of dual optical wavelength, equilibrium thermal melting profiles and differential scanning calorimetry. The mIAP pseudoknot is an H-type pseudoknot proposed to have structural features in common with the gag-pro frameshifting pseudoknots from simian retrovirus-l (SRV-1) and mouse mammary tumor virus (MMTV). Ln particular, the mIAP pseudoknot is proposed to contain an unpaired adenosine base at the junction of the two helical stems (A15), as well as one in the middle of stem 2 (A35). A mutational analysis of stem 1 hairpins and compensatory base-pair substitutions incorporated into helical stem 2 was used to assign optical melting transitions to molecular unfolding events. The optical melting profile of the wild-type RNA is most simply described by four sequential two-state unfolding transitions. Stem 2 melts first in two closely coupled low-enthalpy transitions at low t(m) in which the stem 3’ to A35, unfolds first, followed by unfolding of the remainder of the helical stem. The third unfolding transition is associated with some type of stacking interactions in the stem 1 hairpin loop not present in the pseudoknot. The fourth transition is assigned to unfolding of stem 1. in all RNAs investigated, Delta H-vH approximate to Delta H-cal, suggesting that Delta C-p for unfolding is small. A35 has the thermodynamic properties expected for an extrahelical, unpaired nucleotide. Deletion of A15 destabilizes the stem 2 unfolding transition in the context of both the wild-type and Delta A35 mutant RNAs only slightly, by Delta Delta G degrees approximate to 1 kcal mol(-1) (at 37 degrees C). The Delta A15 RNA is considerably more susceptible to thermal denaturation in the presence of moderate urea concentrations than is the wild-type RNA, further evidence of a detectable global destabilization of the molecule. interestingly, substitution of the nine loop 2 nucleotides with uridine residues induces a more pronounced destabilization of the molecule (Delta Delta G degrees approximate to 2.0 kcal mol(-1)), a long-range, non-nearest neighbor effect. These findings provide the thermodynamic basis with which to further refine the relationship between efficient ribosomal frameshifting and pseudoknot structure and stability. (C) 1998 Academic Press}, keywords = {3,Adenosine,analysis,BASE,BASE-PAIR,CONFORMATION,D,Frameshifting,HAIRPINS,Ions,LOOP,MAMMARY-TUMOR VIRUS,MESSENGER-RNA,MMTV,MUTATIONAL ANALYSIS,nosource,nucleic acid stability,Nucleotides,PARTICLES,PATHWAY,pseudoknot,pseudoknot structure,pseudoknots,READ-THROUGH,RESIDUES,retrovirus,ribosomal frameshifting,Rna,RNA folding,RNA PSEUDOKNOT,scanning,SIMIAN RETROVIRUS-1,stability,STOP CODON,Structural,STRUCTURAL FEATURES,structure,Thermodynamics,translation,Urea,Uridine,virus,WILD-TYPE} }

@article{theimerContributionIntercalatedAdenosine2000, title = {Contribution of the Intercalated Adenosine at the Helical Junction to the Stability of the Gag-pro Frameshifting Pseudoknot from Mouse Mammary Tumor Virus.}, author = {Theimer, C.A. and Giedroc, D.P.}, year = 2000, month = mar, journal = {RNA}, volume = {6}, number = {3}, pages = {409–421}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838200992057}, url = {http://rnajournal.cshlp.org/content/6/3/409.short}, abstract = {The mouse mammary tumor virus (MMTV) gag-pro frameshifting pseudoknot is an H-type RNA pseudoknot that contains an unpaired adenosine (A14) at the junction of the two helical stems required for efficient frameshifting activity. The thermodynamics of folding of the MMTV vpk pseudoknot have been compared with a structurally homologous mutant RNA containing a G x U to G-C substitution at the helical junction (U13C RNA), and an A14 deletion mutation in that context (U13CdeltaA14 RNA). Dual wavelength optical melting and differential scanning calorimetry reveal that the unpaired adenosine contributes 0.7 (+/-0.2) kcal mol(-1) at low salt and 1.4 (+/-0.2) kcal mol(-1) to the stability (deltaG(0)37) at 1 M NaCl. This stability increment derives from a favorable enthalpy contribution to the stability deltadeltaH = 6.6 (+/-2.1) kcal mol(-1) with deltadeltaG(0)37 comparable to that predicted for the stacking of a dangling 3’ unpaired adenosine on a G-C or G x U base pair. Group 1A monovalent ions, NH4+, Mg2+, and Co(NH3)6(3+) ions stabilize the A14 and deltaA14 pseudoknots to largely identical extents, revealing that the observed differences in stability in these molecules do not derive from a differential or specific accumulation of ions in the A14 versus deltaA14 pseudoknots. Knowledge of this free energy contribution may facilitate the prediction of RNA pseudoknot formation from primary nucleotide sequence (Gultyaev et al., 1999, RNA 5:609-617)}, keywords = {0,3,Adenosine,Animals,BASE,Base Sequence,BASE-PAIR,Calorimetry,CalorimetryDifferential Scanning,Cations,CationsDivalent,chemistry,Comparative Study,Frameshifting,FrameshiftingRibosomal,Genesgag,Genespol,genetics,Heat,Intercalating Agents,Ions,La,M,Mammary Tumor VirusMouse,metabolism,Metals,Mice,MMTV,Molecular Sequence Data,Mutation,nosource,Nucleic Acid Conformation,Nucleic Acid Denaturation,NUCLEOTIDE-SEQUENCE,pharmacology,physiology,PREDICTION,pseudoknot,pseudoknots,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,Retroviridae Infections,Rna,RNA PSEUDOKNOT,RNA Stability,RnaViral,scanning,sequence,stability,Thermodynamics,Tumor Virus Infections,virus} }

@article{theocharisRecoveryActiveRibosomal1989, title = {Recovery of Active Ribosomal Complexes from Cellulose Nitrate Membranes}, author = {Theocharis, D.A. and Coutsogeorgopoulos, C.}, year = 1989, month = feb, journal = {Analytical biochemistry}, volume = {176}, number = {2}, pages = {278–283}, publisher = {Elsevier}, doi = {10.1016/0003-2697(89)90309-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/0003269789903096}, abstract = {The ternary Ac-[3H]Phe-tRNA-poly(U)-ribosome complex (complex C) [D. L. Kalpaxis, D.A. Theocharis, and C. Coutsogeorgopoulos (1986) Eur. J. Biochem. 154, 267-271] was used in model experiments aiming at the purification of this complex via adsorption on cellulose nitrate membranes and then desorbing the complex back into solution. The desorption was carried out at pH 7.2 in the presence of the nonionic detergent Zwittergent (ZW). The activity status of complex C was assessed with the aid of the puromycin reaction which characterizes ribosomal peptidyltransferase as part of complex C. The optimal conditions for desorbing complex C were 5 degrees C and a buffered solution containing 0.1% ZW. The kinetic constants of peptidyltransferase in the adsorbed state were kcat = 2.0 min-1, Ks = 0.4 mM. In the desorbed state, in solution, kcat = 3.4 min-1 and Ks = 0.3 mM. The method promises to be suitable for the rapid purification of ribosomal complexes containing mRNA and aminoacyl-tRNA}, keywords = {analysis,Collodion,COMPLEX,COMPLEXES,CONSTANTS,diagnostic use,Escherichia coli,Heat,Kinetics,La,MembranesArtificial,metabolism,MODEL,mRNA,nosource,peptidyl transferase,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,Peptidyltransferase,Polyribosomes,purification,Puromycin,Research SupportNon-U.S.Gov’t,Transferases} } % == BibTeX quality report for theocharisRecoveryActiveRibosomal1989: % ? unused Journal abbr (“Anal.Biochem.”)

@article{thielMechanismsEnzymesInvolved2003, title = {Mechanisms and Enzymes Involved in {{SARS}} Coronavirus Genome Expression}, author = {Thiel, V. and Ivanov, K.A. and Putics, A. and Hertzig, T. and Schelle, B. and Bayer, S. and Weissbrich, B. and Snijder, E.J. and Rabenau, H. and Doerr, H.W. and Gorbalenya, A.E. and Ziebuhr, J.}, year = 2003, journal = {Journal of general virology}, volume = {84}, number = {Pt 9}, pages = {2305–2315}, publisher = {Soc General Microbiol}, doi = {10.1099/vir.0.19424-0}, url = {http://vir.sgmjournals.org/cgi/content/abstract/84/9/2305}, abstract = {A novel coronavirus is the causative agent of the current epidemic of severe acute respiratory syndrome (SARS). Coronaviruses are exceptionally large RNA viruses and employ complex regulatory mechanisms to express their genomes. Here, we determined the sequence of SARS coronavirus (SARS-CoV), isolate Frankfurt 1, and characterized key RNA elements and protein functions involved in viral genome expression. Important regulatory mechanisms, such as the (discontinuous) synthesis of eight subgenomic mRNAs, ribosomal frameshifting and post-translational proteolytic processing, were addressed. Activities of three SARS coronavirus enzymes, the helicase and two cysteine proteinases, which are known to be critically involved in replication, transcription and/or post-translational polyprotein processing, were characterized. The availability of recombinant forms of key replicative enzymes of SARS coronavirus should pave the way for high-throughput screening approaches to identify candidate inhibitors in compound libraries}, keywords = {0,COMPLEX,COMPLEXES,Cysteine,ELEMENTS,enzyme,expression,FORM,Frameshifting,Genome,Helicase,IDENTIFY,immunology,INHIBITOR,La,library,MECHANISM,MECHANISMS,microbiology,mRNA,nosource,POLYPROTEIN,protein,REPLICATION,ribosomal frameshifting,Rna,RNA Viruses,SARS,sequence,transcription,virology} } % == BibTeX quality report for thielMechanismsEnzymesInvolved2003: % ? unused Journal abbr (“J.Gen.Virol.”)

@article{thieleElongationFactor11985, title = {Elongation Factor 1 Alpha from {{Saccharomyces}} Cerevisiae. {{Rapid}} Large-Scale Purification and Molecular Characterization.}, author = {Thiele, D. and Cottrelle, P. and Iborra, F. and Buhler, J.M. and Sentenac, A. and Fromageot, P.}, year = 1985, month = mar, journal = {Journal of Biological Chemistry}, volume = {260}, number = {5}, pages = {3084–3089}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(18)89476-5}, url = {http://www.jbc.org/content/260/5/3084.short}, abstract = {Cytoplasmic elongation factor 1 alpha (EF-1 alpha) was purified to homogeneity from the yeast Saccharomyces cerevisiae using a large-scale procedure. The three steps of purification used were batch adsorption on phosphocellulose, phosphocellulose chromatography and, as the last step, GDP-Sepharose or Biorex column chromatography. The protein is very basic (pI = 9.2) and has an apparent molecular mass of 49 kDa, as determined by polyacrylamide gel electrophoresis using denaturing conditions. It is one of the most abundant proteins in yeast (about 5% of total soluble protein), as shown by two-dimensional gel electrophoresis and by immunological titration. A strong immunological and structural homology was found between yeast EF-1 alpha and elongation factors from other sources. Common immunological features were found between yeast and wheat germ EF-1 alpha. Tryptic hydrolysis of yeast EF-1 alpha in the presence of 25% glycerol generated a large trypsin-resistant polypeptide (Mr = 43,000) which had the same NH2-terminal sequence as the proteolyzed product from rabbit reticulocyte, Artemia salina EF-1 alpha and Escherichia coli EF-Tu. Completed DNA sequence determination of one structural gene for yeast EF-1 alpha confirmed a remarkable conservation of several protein sequence domains in yeast and animal EF-1 alpha (Cottrelle, P., Thiele, D., Price, V., Memet, S., Micouin, J.Y., Marck, C., Buhler, J.M. Sentenac, A., and Fromageot, P. (1985) J. Biol. Chem. 260, 3090-3096)}, keywords = {0,analysis,animal,Artemia,CEREVISIAE,Chromatography,D,Dna,DNA sequence,DOMAIN,DOMAINS,EF-1,EF-1 alpha,EF-1-ALPHA,EFTu,Electrophoresis,ElectrophoresisPolyacrylamide Gel,elongation,elongation factors,ELONGATION-FACTORS,Escherichia coli,ESCHERICHIA-COLI,GEL-ELECTROPHORESIS,gene,Hydrolysis,Immunosorbent Techniques,isolation & purification,Kinetics,La,metabolism,Molecular Weight,nosource,Peptide Elongation Factor 1,Peptide Elongation Factors,POLYACRYLAMIDE-GEL-ELECTROPHORESIS,POLYPEPTIDE,PRODUCT,protein,Proteins,purification,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Structural,Trypsin,Wheat,yeast} } % == BibTeX quality report for thieleElongationFactor11985: % ? unused Journal abbr (“J.Biol Chem.”)

@article{thieleGenomeStructureExpression1984, title = {Genome Structure and Expression of a Defective Interfering Mutant of the Killer Virus of Yeast}, author = {Thiele, D.J. and Hannig, E.M. and Leibowitz, M.J.}, year = 1984, month = aug, journal = {Virology}, volume = {137}, number = {1}, pages = {20–31}, publisher = {Elsevier}, doi = {10.1016/0042-6822(84)90004-7}, url = {http://linkinghub.elsevier.com/retrieve/pii/0042682284900047}, keywords = {analysis,Cap,Conserved Sequence,expression,Genome,In Vitro,IN-VITRO,IN-VIVO,killer,M1,MESSENGER-RNA,models,nosource,poly(A),Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence Analysis,SEQUENCES,structure,Support,toxin,transcription,translation,Virion,virus,yeast} }

@article{thieleMultipleDoublestrandedRNA1984, title = {Multiple {{L}} Double-Stranded {{RNA}} Species of {{Saccharomyces}} Cerevisiae: Evidence for Separate Encapsidation.}, author = {Thiele, D.J. and Hannig, E.M. and Leibowitz, M.J.}, year = 1984, month = jan, journal = {Molecular and cellular biology}, volume = {4}, number = {1}, pages = {92–100}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/4/1/92}, abstract = {The L double-stranded (ds) RNA component of Saccharomyces cerevisiae may contain up to three dsRNA species, each with a distinct sequence but with identical molecular weights. These dsRNAs have been separated from each other by denaturation and polyacrylamide gel electrophoresis. The 3’ terminal sequences of the major species, LA dsRNA, were determined. Secondary structural analysis supported the presence of two stem and loop structures at the 3’ terminus of the LA positive strand. In strain T132B NK-3, both the LA and LC species are virion encapsidated. Two distinct classes of virions were purified from this strain, each with a different RNA polymerase activity and with distinct protein components. The heavy virions harbored LA dsRNA, whereas the LC dsRNA species co purified with the light virion peak. Thus, LA and LC dsRNAs, when present in the same cell, may be separately encapsidated}, keywords = {0,3,analysis,Base Sequence,CEREVISIAE,Comparative Study,COMPONENT,COMPONENTS,DOUBLE-STRANDED-RNA,DSRNA,Electrophoresis,ENCAPSIDATION,GEL-ELECTROPHORESIS,isolation & purification,La,LOOP,metabolism,Molecular Weight,Multiple DOI,nonfile,nosource,Nucleic Acid Conformation,polymerase,POLYMERASE ACTIVITY,protein,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,Rna,RNA Viruses,RNA-POLYMERASE,RNADouble-Stranded,RnaViral,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,Structural,structure,Virion,VIRIONS} } % == BibTeX quality report for thieleMultipleDoublestrandedRNA1984: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{thompsonAnalysisMutationsResidues2001, title = {Analysis of Mutations at Residues {{A2451}} and {{G2447}} of {{23S rRNA}} in the Peptidyltransferase Active Site of the {{50S}} Ribosomal Subunit}, author = {Thompson, J. and Kim, D.F. and O’Connor, M. and Lieberman, K.R. and Bayfield, M.A. and Gregory, S.T. and Green, R. and Noller, H.F. and Dahlberg, A.E.}, year = 2001, month = jul, journal = {Proceedings of the National Academy of Sciences}, volume = {98}, number = {16}, pages = {9002–9007}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.151257098}, url = {http://www.pnas.org/content/98/16/9002.short}, abstract = {On the basis of the recent atomic-resolution x-ray structure of the 50S ribosomal subunit, residues A2451 and G2447 of 23S rRNA were proposed to participate directly in ribosome-catalyzed peptide bond formation. We have examined the peptidyltransferase and protein synthesis activities of ribosomes carrying mutations at these nucleotides. In Escherichia coli, pure mutant ribosome populations carrying either the G2447A or G2447C mutations maintained cell viability. In vitro, the G2447A ribosomes supported protein synthesis at a rate comparable to that of wild-type ribosomes. In single-turnover peptidyltransferase assays, G2447A ribosomes were shown to have essentially unimpaired peptidyltransferase activity at saturating substrate concentrations. All three base changes at the universally conserved A2451 conferred a dominant lethal phenotype when expressed in E. coli. Nonetheless, significant amounts of 2451 mutant ribosomes accumulated in polysomes, and all three 2451 mutations stimulated frameshifting and readthrough of stop codons in vivo. Furthermore, ribosomes carrying the A2451U transversion synthesized full-length beta-lactamase chains in vitro. Pure mutant ribosome populations with changes at A2451 were generated by reconstituting Bacillus stearothermophilus 50S subunits from in vitro transcribed 23S rRNA. In single-turnover peptidyltransferase assays, the rate of peptide bond formation was diminish}, keywords = {0,analysis,assays,Bacillus stearothermophilus,BACILLUS-STEAROTHERMOPHILUS,Codon,Escherichia coli,ESCHERICHIA-COLI,Frameshifting,Genetic,genetics,In Vitro,IN-VITRO,IN-VIVO,La,Mutation,MUTATIONS,nosource,Nucleotides,Peptidyltransferase,Phenotype,polysomes,protein,protein synthesis,PROTEIN-SYNTHESIS,readthrough,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,rRNA,STOP CODON,structure,SUBUNIT} } % == BibTeX quality report for thompsonAnalysisMutationsResidues2001: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{thompsonCLUSTALImprovingSensitivity1994, title = {{{CLUSTAL W}}: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice.}, author = {Thompson, J.D. and Higgins, D.G. and Gibson, T.J.}, year = 1994, journal = {Nucleic acids research}, volume = {22}, number = {22}, pages = {4673–4680}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/22.22.4673}, url = {http://nar.oxfordjournals.org/content/22/22/4673.short}, keywords = {alignment,clustal w,computer analysis,nosource,sequence,Sequence Alignment} } % == BibTeX quality report for thompsonCLUSTALImprovingSensitivity1994: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{thompsonProofreadingCodonAnticodonInteraction1977, title = {Proofreading of {{Codon-Anticodon Interaction}} on {{Ribosomes}}}, author = {Thompson, R.C. and Stone, P.J.}, year = 1977, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {74}, number = {1}, pages = {198–202}, doi = {10.1073/pnas.74.1.198}, url = {ISI:A1977CT87000042}, keywords = {CODON-ANTICODON INTERACTION,nosource,proofreading,ribosome,Ribosomes} } % == BibTeX quality report for thompsonProofreadingCodonAnticodonInteraction1977: % ? Title looks like it was stored in title-case in Zotero

@article{thompsonAccuracyProteinBiosynthesis1982, title = {Accuracy of Protein Biosynthesis.}, author = {Thompson, R.C. and Dix, D.B.}, year = 1982, journal = {J.Biol.Chem.}, volume = {257}, pages = {6677–6682}, keywords = {accuracy,biosynthesis,EFTu,No DOI found,nosource,protein,ribosome,translation} } % == BibTeX quality report for thompsonAccuracyProteinBiosynthesis1982: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{thompsonEFTuProvidesInternal1988, title = {{{EFTu}} Provides an Internal Kinetic Standard for Translational Accuracy.}, author = {Thompson, R.C.}, year = 1988, journal = {Trends in biochemical sciences}, volume = {13}, number = {3}, pages = {91–93}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0968000488900473}, keywords = {accuracy,EF-1 alpha,EFTu,No DOI found,nosource,proofreading,Review} }

@article{thompsonInternalInitiationSaccharomyces2001, title = {Internal Initiation in {{Saccharomyces}} Cerevisiae Mediated by an Initiator {{tRNA}}/{{eIF2-independent}} Internal Ribosome Entry Site Element}, author = {Thompson, S.R. and Gulyas, K.D. and Sarnow, P.}, year = 2001, month = nov, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {23}, pages = {12972–12977}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.241286698}, url = {http://www.pnas.org/content/98/23/12972.short}, abstract = {Internal initiation of translation can be mediated by specific internal ribosome entry site (IRES) elements that are located in certain mammalian and viral mRNA molecules. Thus far, these mammalian cellular and viral IRES elements have not been shown to function in the yeast Saccharomyces cerevisiae. We report here that a recently discovered IRES located in the genome of cricket paralysis virus can direct the efficient translation of a second URA3 cistron in dicistronic mRNAs in S. cerevisiae, thereby conferring uracil-independent growth. Curiously, the IRES functions poorly in wild-type yeast but functions efficiently either in the presence of constitutive expression of the eIF2 kinase GCN2 or in cells that have two initiator tRNA(met) genes disrupted. Both of these conditions have been shown to lower the amounts of ternary eIF2-GTP/initiator tRNA(met) complexes. Furthermore, tRNA(met)-independent initiation was also observed in translation-competent extracts prepared from S. cerevisiae in the presence of edeine, a compound that has been shown to interfere with start codon recognition by ribosomal subunits carrying ternary complexes. Therefore, the cricket paralysis virus IRES is likely to recruit ribosomes by internal initiation in S. cerevisiae in the absence of eIF2 and initiator tRNA(met), by the same mechanism of factor-independent ribosome recruitment used in mammalian cells. These findings will allow the use of yeast genetics to determine the mechanism of internal ribosome entry}, keywords = {0,Base Sequence,BINDING,CELLS,CEREVISIAE,Codon,CODON RECOGNITION,COMPLEX,COMPLEXES,Cricket paralysis virus,Dna,DNA Primers,Edeine,EFFICIENT TRANSLATION,ELEMENTS,Eukaryotic Initiation Factor-2,expression,EXTRACTS,GCN4,gene,GENE-EXPRESSION,Genes,Genetic,genetics,Genome,GROWTH,immunology,initiation,INTERNAL RIBOSOME ENTRY,kinase,KINASE GCN2,La,MAMMALIAN-CELLS,MECHANISM,MESSENGER-RNAS,metabolism,microbiology,mRNA,Mutation,nosource,pharmacology,Phosphorylation,protein,Protein Kinases,PROTEIN-KINASE,Protein-Serine-Threonine Kinases,Proteins,RECOGNITION,RECRUITMENT,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,RIBOSOME ENTRY SITE,Ribosomes,Rna,RNA-Transfer-Met,RNATransferMet,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SITE,START CODON,SUBUNIT,SUBUNITS,Support,translation,virus,VIRUS-RNA,WILD-TYPE,yeast} } % == BibTeX quality report for thompsonInternalInitiationSaccharomyces2001: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{thrasIdentificationSaccharomycesCerevisiae1984, title = {Identification Of⬚ {{Saccharomyces}} Cerevisiae ⬚mutants Deficient in {{DNA}} Topoisomerase {{I}}}, author = {Thras, H.C. and Voelkel, K. and DiNardo, S. and Sternglanz, R.}, year = 1984, journal = {J.Biol.Chem.}, volume = {259}, pages = {1375–1379}, doi = {10.1016/S0021-9258(17)43412-0}, keywords = {Dna,IDENTIFICATION,MAK,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,yeast} } % == BibTeX quality report for thrasIdentificationSaccharomycesCerevisiae1984: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{timmersNuclearNucleolarLocalization1999, title = {Nuclear and Nucleolar Localization of {{Saccharomyces}} Cerevisiae Ribosomal Proteins {{S22}} and {{S25}}}, author = {Timmers, A.C. and Stuger, R. and Schaap, P.J. and {}{van ’t}, Riet J. and Raue, H.A.}, year = 1999, month = jun, journal = {FEBS letters}, volume = {452}, number = {3}, pages = {335–340}, publisher = {Elsevier}, doi = {10.1016/S0014-5793(99)00669-9}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579399006699}, abstract = {Nuclear import usually relies on the presence of nuclear localization sequences (NLSs). NLSs are recognized by NLS receptors (importins), which target their substrates to the nuclear pore. We identified the NLSs of the yeast ribosomal proteins S22 and S25 and studied the former by mutational analysis. Furthermore, in S25 the nucleolar targeting information was found to overlap with its NLS. Comparison with previously published data on yeast ribosomal protein NLSs and computer analysis indicates the existence of a novel type of ribosomal protein- specific NLS that differs from the classical Chelsky and bipartite NLSs. The existence of such a ribosomal protein-specific NLS is in accordance with the recent identification of ribosomal protein-specific importins}, keywords = {99313188,Amino Acid Sequence,analysis,beta-Galactosidase,Cell Nucleolus,Cell Nucleus,chemistry,Comparative Study,computer,computer analysis,cytology,genetics,IDENTIFICATION,Immunohistochemistry,Molecular Sequence Data,MUTATIONAL ANALYSIS,nosource,Peptide Fragments,protein,Proteins,Recombinant Fusion Proteins,Ribosomal Proteins,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,supportnon-u.s.gov’t,ultrastructure,yeast} } % == BibTeX quality report for timmersNuclearNucleolarLocalization1999: % ? unused Journal abbr (“FEBS Lett.”)

@article{tjandraRotationalDynamicsCalciumfree1995, title = {Rotational Dynamics of Calcium-Free Calmodulin Studied by {{15N-NMR}} Relaxation Measurements}, author = {Tjandra, N. and Kuboniwa, H. and Ren, H. and Bax, A.}, year = 1995, month = jun, journal = {European Journal of Biochemistry}, volume = {230}, number = {3}, pages = {1014–1024}, publisher = {Wiley Online Library}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1995.1014g.x/full}, abstract = {The backbone motions of calcium-free Xenopus calmodulin have been characterized by measurements of the 15N longitudinal relaxation times (T1) at 51 and 61 MHz, and by conducting transverse relaxation (T2), spin-locked transverse relaxation (T1 rho), and 15N-[1H] heteronuclear NOE measurements at 61 MHz 15N frequency. Although backbone amide hydrogen exchange experiments indicate that the N-terminal domain is more stable than calmodulin’s C-terminal half, slowly exchanging backbone amide protons are found in all eight alpha-helices and in three of the four short beta-strands. This confirms that the calcium-free form consists of stable secondary structure and does not adopt a ‘molten globule’ type of structure. However, the C-terminal domain of calmodulin is subject to conformational exchange on a time scale of about 350 microseconds, which affects many of the C-terminal domain residues. This results in significant shortening of the 15N T2 values relative to T1 rho, whereas the T1 rho and T2 values are of similar magnitude in the N-terminal half of the protein. A model in which the motion of the protein is assumed to be isotropic suggests a rotational correlation time for the protein of about 8 ns but quantitatively does not agree with the magnetic field dependence of the T1 values and does not explain the different T2 values found for different alpha-helices in the N-terminal domain. These latter parameters are compatible with a flexible dumb-bell model in which each of calmodulin’s two domains freely diffuse in a cone with a semi-angle of about 30 degrees and a time constant of about 3 ns, whereas the overall rotation of the protein occurs on a much slower time scale of about 12 ns. The difference in the transverse relaxation rates observed between the amides in helices C and D suggests that the change in interhelical angle upon calcium binding is less than predicted by Herzberg et al. Strynadka and James [Strynadka, N. C. J. & James, M. N. G. (1988) Proteins Struct. Funct. Genet. 3, 1-17]}, keywords = {0,3,Amides,analysis,Animals,anisotropy,BINDING,Calcium,Calmodulin,chemistry,D,disease,DOMAIN,DOMAINS,DYNAMICS,FORM,Kidney,La,M,Magnetic Resonance Spectroscopy,MODEL,Multiple DOI,nonfile,nosource,protein,Protein Conformation,Proteins,Protons,Recombinant Proteins,RESIDUES,Rotation,SECONDARY STRUCTURE,structure,supportu.s.gov’tp.h.s.,Xenopus} } % == BibTeX quality report for tjandraRotationalDynamicsCalciumfree1995: % ? unused Journal abbr (“Eur.J.Biochem.”)

@article{tjandraMeasurementDipolarContributions1997a, title = {Measurement of Dipolar Contributions to {{1JCH}} Splittings from Magnetic-Field Dependence of {{J}} Modulation in Two-Dimensional {{NMR}} Spectra}, author = {Tjandra, N. and Bax, A.}, year = 1997, month = feb, journal = {Journal of Magnetic Resonance}, volume = {124}, number = {2}, pages = {512–515}, doi = {10.1006/jmre.1996.1088}, url = {http://spin.niddk.nih.gov/bax/lit/pdf/247.pdf}, keywords = {0,anisotropy,chemistry,disease,Dna,Electron Spin Resonance Spectroscopy,human,Kidney,La,Magnetic Resonance Spectroscopy,Methods,NMR,nosource,protein,Proteins,Rna,Spin Labels,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for tjandraMeasurementDipolarContributions1997a: % ? unused Journal abbr (“J.Magn Reson.”)

@article{todaThreeDifferentGenes1987a, title = {Three Different Genes in ⬚{{S}}. Cerevisiae⬚ Encode the Catlytic Subunits of the {{cAMp-dependent}} Protein Kinase.}, author = {Toda, T. and Comeron, S. and Sass, P. and Zoller, M. and Wigler, M.}, year = 1987, journal = {Cell}, volume = {50}, pages = {277–287}, doi = {10.1016/0092-8674(87)90223-6}, keywords = {cloning,gene,Genes,kinase,nosource,protein,ras,SUBUNIT} }

@article{toh-eChromosomalSuperkillerMutants1978, title = {Chromosomal Superkiller Mutants of {{Saccharomyces}} Cerevisiae.}, author = {{Toh-e}, A. and Guerry, P. and Wickner, R.B.}, year = 1978, month = dec, journal = {Journal of Bacteriology}, volume = {136}, number = {3}, pages = {1002–1007}, publisher = {Am Soc Microbiol}, doi = {10.1128/jb.136.3.1002-1007.1978}, url = {http://jb.asm.org/cgi/content/abstract/136/3/1002}, abstract = {Yeast strains carrying a 1.5 X 10(6)-dalton double-stranded RNA in virus-like particles secrete a protein toxin which is lethal to strains not carrying this species of double-stranded RNA. We find that recessive mutations in any of four chromosomal genes result in the superkiller phenotype, i.e., increased secretion of killer toxin activity by strains carrying the killer genome. These genes are designated ski1 through ski4 (for superkiller), ski3 and ski4 are located on chromosome XIV, and ski1 is on chromosome VII. A ski1 mutation results in a decreased rate of cell growth. The kex1 and kex2 mutations are epistatic to each ski mutation}, keywords = {0,analysis,CEREVISIAE,CHROMOSOMAL GENES,Chromosome Mapping,DOUBLE-STRANDED-RNA,Fungal Proteins,gene,Genes,GenesRecessive,genetics,Genome,GROWTH,killer,killer toxin,La,Linkage (Genetics),metabolism,MUTANTS,Mutation,MUTATIONS,Mycotoxins,nosource,PARTICLES,Phenotype,PLASMID,Plasmids,protein,Proteins,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SKI,toxin,VIRUS-LIKE PARTICLES,yeast} } % == BibTeX quality report for toh-eChromosomalSuperkillerMutants1978: % ? unused Journal abbr (“J.Bacteriol.”)

@article{toh-eSuperkillerMutationsSuppress1980a, title = {“{{Superkiller}}” Mutations Suppress Chromosomal Mutations Affecting Double-Stranded {{RNA}} Killer Plasmid Replication in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {{Toh-e}, A. and Wickner, R.B.}, year = 1980, journal = {Proc.Natl.Acad.Sci.USA}, volume = {77}, pages = {527–530}, doi = {10.1073/pnas.77.1.527}, keywords = {DOUBLE-STRANDED-RNA,killer,L-A,MAK,Mutation,MUTATIONS,nosource,PLASMID,Plasmids,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SKI} } % == BibTeX quality report for toh-eSuperkillerMutationsSuppress1980a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{tokiwaInhibitionG1Cyclin1994, title = {Inhibition of {{G1}} Cyclin Activity by the {{Ras}}/{{cAMP}} Pathway in Yeast.}, author = {Tokiwa, G. and Tyers, M. and Volpe, T. and Futcher, B.}, year = 1994, journal = {Nature}, volume = {371}, pages = {342–345}, doi = {10.1038/371342a0}, keywords = {INHIBITION,nosource,ras,yeast} }

@article{tolmanStructuralDynamicAnalysis2001, title = {Structural and Dynamic Analysis of Residual Dipolar Coupling Data for Proteins}, author = {Tolman, J.R. and Al Hashimi, H.M. and Kay, L.E. and Prestegard, J.H.}, year = 2001, month = feb, journal = {Journal of the }, volume = {123}, number = {14}, pages = {1416–1424}, doi = {10.1021/ja002500y}, url = {http://pubs.acs.org/doi/abs/10.1021/ja002500y}, abstract = {The measurement of residual dipolar couplings in weakly aligned proteins can potentially provide unique information on their structure and dynamics in the solution state. The challenge is to extract the information of interest from the measurements, which normally reflect a convolution of the structural and dynamic properties. We discuss here a formalism which allows a first order separation of their effects, and thus, a simultaneous extraction of structural and motional parameters from residual dipolar coupling data. We introduce some terminology, namely a generalized degree of order, which is necessary for a meaningful discussion of the effects of motion on residual dipolar coupling measurements. We also illustrate this new methodology using an extensive set of residual dipolar coupling measurements made on (15)N,(13)C-labeled human ubiquitin solvated in a dilute bicelle solution. Our results support a solution structure of ubiquitin which on average agrees well with the X-ray structure (Vijay-Kumar, et al., J. Mol. Biol. 1987, 194, 531–544) for the protein core. However, the data are also consistent with a dynamic model of ubiquitin, exhibiting variable amplitudes, and anisotropy, of internal motions. This work suggests the possibility of primary use of residual dipolar couplings in characterizing both structure and anisotropic internal motions of proteins in the solution state}, keywords = {0,analysis,anisotropy,chemistry,DYNAMICS,human,La,MODEL,Models-Chemical,ModelsChemical,Molecular Conformation,nosource,protein,Protein Conformation,Proteins,Solutions,Structural,structure,Support,support-non-u.s.gov’t,support-u.s.gov’t-non-p.h.s.,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,Terminology,Ubiquitins,X-Ray Diffraction} } % == BibTeX quality report for tolmanStructuralDynamicAnalysis2001: % ? unused Journal abbr (“J.Am.Chem.Soc.”)

@article{tolmanDipolarCouplingsProbe2001, title = {Dipolar Couplings as a Probe of Molecular Dynamics and Structure in Solution}, author = {Tolman, J.R.}, year = 2001, month = oct, journal = {Current Opinion in Structural Biology}, volume = {11}, number = {5}, pages = {532–539}, publisher = {Elsevier}, doi = {10.1016/S0959-440X(00)00245-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0959440X00002451}, abstract = {The introduction of residual dipolar coupling methodology has increased the scope of structural biological problems that can be addressed by NMR spectroscopy. Conformational changes, the relative orientation of domains, and intermolecular complexes can now be characterized accurately and rapidly using NMR. The development of residual dipolar coupling methodology for the rapid recognition of homologous protein folds and for studies of submillisecond timescale dynamics has also seen considerable progress}, keywords = {0,chemistry,COMPLEX,COMPLEXES,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,development,DOMAIN,DOMAINS,DYNAMICS,La,Macromolecular Systems,Methods,ModelsMolecular,NMR,NMR-SPECTROSCOPY,nosource,Nuclear Magnetic ResonanceBiomolecular,protein,Protein Conformation,Proteins,RECOGNITION,Review,Solutions,SPECTROSCOPY,Structural,structure,SYSTEM,SYSTEMS,Thermodynamics} } % == BibTeX quality report for tolmanDipolarCouplingsProbe2001: % ? unused Journal abbr (“Curr.Opin.Struct.Biol.”)

@article{tomlinsonInhibitionInfectionCucumber1974, title = {The Inhibition of Infection by Cucumber Mosaic Virus and Influenza Virus by Extracts from {{Phytolacca}} Americana}, author = {Tomlinson, J.A. and Walker, V.M. and Flewett, T.H. and Barclay, G.R.}, year = 1974, journal = {Journal.of.General.Virology}, volume = {22}, number = {2}, pages = {225–232}, publisher = {Soc General Microbiol}, doi = {10.1099/0022-1317-22-2-225}, url = {http://jgv.sgmjournals.org/cgi/content/abstract/22/2/225}, keywords = {INHIBITION,nosource,virus} } % == BibTeX quality report for tomlinsonInhibitionInfectionCucumber1974: % ? Possibly abbreviated journal title Journal.of.General.Virology

@article{tothEvidenceUnique1St1988, title = {Evidence for {{A Unique 1St Position Codon Anticodon Mismatch Invivo}}}, author = {Toth, M.J. and Murgola, E.J. and Schimmel, P.}, year = 1988, month = may, journal = {Journal of Molecular Biology}, volume = {201}, number = {2}, pages = {451–454}, doi = {10.1016/0022-2836(88)90152-0}, url = {ISI:A1988N543900018}, keywords = {Anticodon,Codon,M,nosource,POSITION} } % == BibTeX quality report for tothEvidenceUnique1St1988: % ? Title looks like it was stored in title-case in Zotero

@article{triana-alonsoElongationFactor31995, title = {The Elongation Factor 3 Unique in Higher Fungi and Essential for Protein Biosynthesis Is an {{E}} Site Factor}, author = {{Triana-Alonso}, F.J. and Chakraburtty, K. and Nierhaus, K.H.}, year = 1995, journal = {Journal of Biological Chemistry}, volume = {270}, number = {35}, pages = {20473–20478}, publisher = {ASBMB}, doi = {10.1074/jbc.270.35.20473}, url = {http://www.jbc.org/content/270/35/20473.short}, abstract = {Two elongation factors drive the ribosomal elongation cycle; elongation factor 1 alpha (EF-1 alpha) mediates the binding of an aminoacyl-tRNA to the ribosomal A site, whereas elongation factor 2 (EF-2) catalyzes the translocation reaction. Ribosomes from yeast and other higher fungi require a third elongation factor (EF-3) which is essential for the elongation process, but the step affected by EF-3 has not yet been identified. Here we demonstrate that the first and the third tRNA binding site (A and E sites, respectively) of yeast ribosomes are reciprocally linked; if the A site is occupied the E site has lost its binding capability, and vice versa, if the E site is occupied the A site has a low affinity for tRNAs. EF-3 is essential for EF-1 alpha-dependent A site binding of amino-acyl-tRNA only when the E site is occupied with a deacylated tRNA. The ATP-dependent activity of EF-3 is required for the release of deacylated tRNA from the E site during A site occupation}, keywords = {0,3,A SITE,A-SITE,Adenosine,Adenosine Triphosphate,Base Sequence,BINDING,Binding Sites,BINDING-SITE,biosynthesis,Comparative Study,E,E site,EF-1,EF-1 alpha,EF-1-ALPHA,EF-2,elongation,ELONGATION CYCLE,elongation factors,ELONGATION-FACTORS,Fungal Proteins,Fungi,Germany,Kinetics,La,metabolism,Molecular Sequence Data,nosource,Peptide Elongation Factor 1,Peptide Elongation Factor 2,Peptide Elongation Factors,protein,Protein Biosynthesis,PROTEIN-BIOSYNTHESIS,Proteins,RELEASE,ribosome,Ribosomes,Rna,RNAFungal,RNAMessenger,RNATransfer,RNATransferPhe,Saccharomyces cerevisiae,SITE,SITES,Support,Time Factors,translocation,tRNA,tRNA binding,yeast} } % == BibTeX quality report for triana-alonsoElongationFactor31995: % ? unused Journal abbr (“J.Biol Chem.”)

@article{triana-alonsoExperimentalPrerequisitesDetermination2000a, title = {Experimental Prerequisites for Determination of {{tRNA}} Binding to Ribosomes from {{Escherichia}} Coli.}, author = {{Triana-Alonso}, F.J. and Spahn, C.M. and Burkhardt, N. and Rohrdanz, B. and Nierhaus, K.H.}, year = 2000, journal = {Methods in enzymology}, volume = {317}, eprint = {10829285}, eprinttype = {pubmed}, pages = {261–276}, doi = {10.1016/S0076-6879(00)17019-3}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10829285}, keywords = {0,BINDING,chemistry,Escherichia coli,ESCHERICHIA-COLI,La,metabolism,nosource,ribosome,Ribosomes,Rna,RNATransfer,RNATransferAmino Acyl,tRNA,tRNA binding} } % == BibTeX quality report for triana-alonsoExperimentalPrerequisitesDetermination2000a: % ? unused Journal abbr (“Methods Enzymol.”)

@article{trianaTransferRNABinding1994a, title = {Transfer {{RNA}} Binding to {{80S}} Ribosomes from Yeast: Evidence for Three Sites.}, author = {Triana, F. and Nierhaus, K.H. and Chakraburtty, K.}, year = 1994, journal = {Biochemistry and molecular biology international}, volume = {33}, number = {5}, eprint = {7987260}, eprinttype = {pubmed}, pages = {909–915}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7987260}, abstract = {The number of tRNA binding sites in 80S ribosomes from Saccharomyces cerevisiae was assessed by means of tRNA saturation and translocation experiments. In the absence of cognate mRNA yeast ribosomes could bind 0.6 [32P]tRNA(Phe) per 80S while poly(U) programmed ribosomes accepted up to 1.7 tRNA(Phe) molecules per 80S or 0.5 molecules of Ac[14C]Phe-tRNA(Phe) per 80S. Compared with the known features of E. coli ribosomes these binding values indicated both the presence of three tRNA binding sites and the validity of the exclusion principle for peptidyl-tRNA binding to yeast ribosomes. Upon EF-2 dependent translocation of a complex containing deacyl-tRNA in the P-site and AcPHe-tRNA in the A-site, the deacylated tRNA does not leave the ribosome quantitatively. This observation suggests the presence of an E site in 80S ribosomes which is functionally equivalent to the one previously characterized in prokaryotic systems}, keywords = {A-SITE,BINDING,Binding Sites,biosynthesis,COMPLEX,COMPLEXES,EF-2,Kinetics,metabolism,mRNA,No DOI found,nosource,P-SITE,Peptide Elongation Factor 2,Peptide Elongation Factors,Poly U,Puromycin,ribosome,Ribosomes,Rna,RNAMessenger,RNATransferAmino Acyl,RNATransferPhe,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SYSTEM,TRANSFER-RNA,translocation,tRNA,yeast} } % == BibTeX quality report for trianaTransferRNABinding1994a: % ? unused Journal abbr (“Biochem.Mol.Biol.Int.”)

@article{triteeraprapabMolecularCloningGene1995a, title = {Molecular Cloning of a Gene Expressed during Early Embryonic Development in ⬚{{Onchocerca}} Volvulus⬚.}, author = {Triteeraprapab, S. and Richie, T.L. and Tuan, R.S. and Shepley, K.J. and Dinman, J.D. and Neubert, T.A. and Scott, A.L.}, year = 1995, journal = {Mol.Biochem.Parasitol.}, volume = {69}, pages = {161–171}, doi = {10.1016/0166-6851(94)00187-R}, keywords = {cloning,CV,development,gene,nosource,worms} } % == BibTeX quality report for triteeraprapabMolecularCloningGene1995a: % ? Possibly abbreviated journal title Mol.Biochem.Parasitol.

@article{trottaCoordinatedNuclearExport2003, title = {Coordinated Nuclear Export of {{60S}} Ribosomal Subunits and {{NMD3}} in Vertebrates}, author = {Trotta, C.R. and Lund, E. and Kahan, L. and Johnson, A.W. and Dahlberg, J.E.}, year = 2003, month = jun, journal = {EMBO J.}, volume = {22}, number = {11}, pages = {2841–2851}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/cdg249}, url = {PM:12773398}, abstract = {60S and 40S ribosomal subunits are assembled in the nucleolus and exported from the nucleus to the cytoplasm independently of each other. We show that in vertebrate cells, transport of both subunits requires the export receptor CRM1 and Ran.GTP. Export of 60S subunits is coupled with that of the nucleo- cytoplasmic shuttling protein NMD3. Human NMD3 (hNMD3) contains a CRM-1-dependent leucine-rich nuclear export signal (NES) and a complex, dispersed nuclear localization signal (NLS), the basic region of which is also required for nucleolar accumulation. When present in Xenopus oocytes, both wild-type and export-defective mutant hNMD3 proteins bind to newly made nuclear 60S pre-export particles at a late step of subunit maturation. The export-defective hNMD3, but not the wild-type protein, inhibits export of 60S subunits from oocyte nuclei. These results indicate that the NES mutant protein competes with endogenous wild-type frog NMD3 for binding to nascent 60S subunits, thereby preventing their export. We propose that NMD3 acts as an adaptor for CRM1-Ran.GTP-mediated 60S subunit export, by a mechanism that is conserved from vertebrates to yeast}, keywords = {0,60S subunit,Active TransportCell Nucleus,adaptor,Amino Acid Sequence,Animals,BINDING,BindingCompetitive,CELLS,chemistry,COMPLEX,COMPLEXES,Conserved Sequence,Cytoplasm,Female,FUSION PROTEIN,genetics,Hela Cells,human,In Vitro,Karyopherins,La,LOCALIZATION,MATURATION,MECHANISM,metabolism,Molecular Sequence Data,Mutation,nosource,Nuclear Localization Signal,nucleolus,Oocytes,PARTICLES,protein,Proteins,ran GTP-Binding Protein,Recombinant Fusion Proteins,REGION,REQUIRES,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,Ribosomes,RNA-Binding Proteins,RNA-BINDING-PROTEIN,Sequence HomologyAmino Acid,SIGNAL,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Transfection,TRANSPORT,Vertebrates,WILD-TYPE,Xenopus,Xenopus laevis,Xenopus oocyte,yeast} } % == BibTeX quality report for trottaCoordinatedNuclearExport2003: % ? Possibly abbreviated journal title EMBO J.

@article{trueYeastPrionProvides2000a, title = {A Yeast Prion Provides a Mechanism for Genetic Variation and Phenotypic Diversity}, author = {True, H.L. and Lindquist, S.L.}, year = 2000, journal = {Nature}, volume = {407}, number = {6803}, pages = {477–483}, doi = {10.1038/35035005}, abstract = {A major enigma in evolutionary biology is that new forms or functions often require the concerted effects of several independent genetic changes. It is unclear how such changes might accumulate when they are likely to be deleterious individually and be lost by selective pressure. The Saccharomyces cerevisiae prion [PSI+] is an epigenetic modifier of the fidelity of translation termination, but its impact on yeast biology has been unclear. Here we show that [PSI+] provides the means to uncover hidden genetic variation and produce new heritable phenotypes. Moreover, in each of the seven genetic backgrounds tested, the constellation of phenotypes produced was unique. We propose that the epigenetic and metastable nature of [PSI+] inheritance allows yeast cells to exploit pre-existing genetic variation to thrive in fluctuating environments. Further, the capacity of [PSI+] to convert previously neutral genetic variation to a non-neutral state may facilitate the evolution of new traits}, keywords = {20479963,antibiotics,Binding Sites,development,drug effects,Ethanol,Evolution,Fidelity,Fungal Proteins,Genetic,genetics,growth &,MECHANISM,nosource,pharmacology,Phenotype,physiology,prion,Prions,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,termination,translation,TRANSLATION TERMINATION,TranslationGenetic,Variation (Genetics),yeast} }

@article{tsayRibosomalProteinSynthesis1988, title = {Ribosomal Protein Synthesis Is Not Regulated at the Translational Level in {{Saccharomyces}} Cerevisiae: Balanced Accumulation of Ribosomal Proteins {{L16}} and Rp59 Is Mediated by Turnover of Excess Protein.}, author = {Tsay, Y.F. and Thompson, J.R. and Rotenberg, M.O. and Larkin, J.C. and Woolford, J.L.}, year = 1988, month = jun, journal = {Genes & development}, volume = {2}, number = {6}, pages = {664–676}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.2.6.664}, url = {http://genesdev.cshlp.org/content/2/6/664.short}, abstract = {We have investigated the mechanisms whereby equimolar quantities of ribosomal proteins accumulate and assemble into ribosomes of the yeast Saccharomyces cerevisiae. Extra copies of the cry1 or RPL16 genes encoding ribosomal proteins rp59 or L16 were introduced into yeast by transformation. Excess cry1 or RPL16 mRNA accumulated in polyribosomes in these cells and was translated at wild-type rates into rp59 or L16 proteins. These excess proteins were degraded until their levels reached those of other ribosomal proteins. Identical results were obtained when the transcription of RPL16A was rapidly induced using GAL1-RPL16A promoter fusions, including a construct in which the entire RPL16A 5’-noncoding region was replaced with the GAL1 leader sequence. Our results indicate that posttranscriptional expression of the cry1 and RPL16 genes is regulated by turnover of excess proteins rather than autogenous regulation of mRNA splicing or translation. The turnover of excess rp59 or L16 is not affected directly by mutations that inactivate vacuolar hydrolases}, keywords = {88329708,biosynthesis,expression,gene,Gene Expression Regulation,Genes,GenesFungal,GenesStructural,genetics,Kinetics,MECHANISM,MECHANISMS,metabolism,mRNA,Mutation,MUTATIONS,nosource,Plasmids,Polyribosomes,PROMOTER,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,regulation,Ribosomal Proteins,ribosome,Ribosomes,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,splicing,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,transcription,translation,TranslationGenetic,turnover,yeast} } % == BibTeX quality report for tsayRibosomalProteinSynthesis1988: % ? unused Journal abbr (“Genes Dev.”)

@article{tsuchihashiTranslationalFrameshiftingGenerates1990, title = {Translational Frameshifting Generates the Gamma Subunit of {{DNA}} Polymerase {{III}} Holoenzyme}, author = {Tsuchihashi, Z. and Kornberg, A.}, year = 1990, month = apr, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {87}, number = {7}, pages = {2516–2520}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.87.7.2516}, url = {http://www.pnas.org/content/87/7/2516.short}, keywords = {0,Adenine,Bacterial,Bacterial/ge [Genetics],Base Sequence,Chromosome Deletion,Codon,Dna,DNA Polymerase III/ge [Genetics],DNA Polymerases/ge [Genetics],ELEMENTS,Escherichia coli,Escherichia coli/en [Enzymology],Escherichia coli/ge [Genetics],ESCHERICHIA-COLI,expression,frameshift,Frameshifting,GAMMA-SUBUNIT,gene,Gene Expression,Genes,Genetic,Lysine,Macromolecular Systems,Molecular Sequence Data,mRNA,Mutation,MUTATIONS,Non-P.H.S.,nosource,Nucleic Acid Conformation,Nucleotides,P.H.S.,PLASMID,Plasmids,pol,polymerase,protein,sequence,SIGNAL,STOP CODON,Structural,structure,SUBUNIT,Support,SYSTEM,translation,U.S.Gov’t} }

@article{tsuchihashiSequenceRequirementsEfficient1992a, title = {Sequence {{Requirements}} for {{Efficient Translational Frameshifting}} in the {{Escherichia-Coli-Dnax Gene}} and the {{Role}} of {{An Unstable Interaction Between Transfer Rna}}({{Lys}}) and {{An Aag Lysine Codon}}}, author = {Tsuchihashi, Z. and Brown, P.O.}, year = 1992, month = mar, journal = {Genes & Development}, volume = {6}, number = {3}, pages = {511–519}, doi = {10.1101/gad.6.3.511}, url = {ISI:A1992HM44400015}, abstract = {Synthesis of the gamma-subunit of DNA polymerase III holoenzyme depends on precise and efficient translational frameshifting to the -1 frame at a specific site in the dnaX gene of Escherichia coli. In vitro mutagenesis of this frameshift site demonstrated the importance of an A AAA AAG heptanucleotide sequence, which allows two adjacent tRNAs to retain a stable interaction with mRNA after they slip to the -1 position. The AAG lysine codon present in the 3’ half of this heptanucleotide was a key element for highly efficient frameshifting. A tRNA(Lys) with a CUU anticodon, which has a strong affinity for AAG lysine codons, is present in eukaryotic cells but absent in E. coli. Expression in E. coli of a mutant tRNA(Lys) with a CUU anticodon specifically inhibited the frameshifting at the AAG codon, suggesting that the absence of this tRNA in E. coli contributes to the efficiency of the dnaX frameshift}, keywords = {3,Anticodon,CELLS,Codon,CODONS,Dna,dnaX,DNAX GENE,E,efficiency,Escherichia coli,ESCHERICHIA-COLI,Eukaryotic Cells,expression,FRAME,frameshift,Frameshifting,Gag,GAMMA-SUBUNIT,gene,In Vitro,IN-VITRO,INVITRO MUTAGENESIS,Lysine,MAMMARY-TUMOR VIRUS,mRNA,Mutagenesis,nosource,pol,polymerase,POLYMERASE-III,POLYMERASE-III HOLOENZYME,Proteins,sequence,SITE,SLIPPAGE,TRANSFER RNA(LYS),TRANSFER-RNA,TRANSLATIONAL FRAMESHIFTING,tRNA} } % == BibTeX quality report for tsuchihashiSequenceRequirementsEfficient1992a: % ? Title looks like it was stored in title-case in Zotero

@article{tuRibosomalMovementImpeded1992a, title = {Ribosomal Movement Impeded at a Pseudoknot Required for Ribosomal Frameshifting.}, author = {Tu, C. and Tzeng, T.-H. and Bruenn, J.A.}, year = 1992, journal = {Proc.Natl.Acad.Sci.USA}, volume = {89}, pages = {8636–8640}, doi = {10.1073/pnas.89.18.8636}, keywords = {Frameshifting,L-A,Movement,nosource,pausing,pseudoknot,ribosomal frameshifting,virus} } % == BibTeX quality report for tuRibosomalMovementImpeded1992a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{tuerkRnaPseudoknotsThat1992, title = {Rna {{Pseudoknots That Inhibit Human-Immunodeficiency-Virus Type-1 Reverse-Transcriptase}}}, author = {Tuerk, C. and Macdougal, S. and Gold, L.}, year = 1992, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {89}, number = {15}, pages = {6988–6992}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.89.15.6988}, url = {http://www.pnas.org/content/89/15/6988.short}, abstract = {High-affinity ligands of the reverse transcriptase of human immunodeficiency virus type 1 (HIV-1) were isolated by the SELEX procedure (systematic evolution of ligands by exponential enrichment) from RNA populations randomized at 32 positions. Analysis of these ligands revealed a pseudoknot consensus with primary sequence bias at some positions. We demonstrated that at least one of the ligands inhibits cDNA synthesis by HIV reverse transcriptase but fails to inhibit other reverse transcriptases. These experiments highlight the power of SELEX to yield highly specific ligands that reduce the activity of target proteins. Such ligands may provide therapeutic reagents for viral and other diseases}, keywords = {3,AIDS,analysis,BACTERIOPHAGE-T4 DNA-POLYMERASE,CELLULAR DNA,D,DIRECTED LIGAND EVOLUTION,disease,E,Evolution,EXPONENTIAL ENRICHMENT,HIV,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,Ligands,M,nosource,PRIMER BINDING,protein,Proteins,pseudoknot,pseudoknots,REPLICATION,REVERSE TRANSCRIPTASE INHIBITORS,Rna,RNA PSEUDOKNOT,RNA SECONDARY STRUCTURE,S,sequence,SYSTEMATIC EVOLUTION,T,TEMPLATE,therapy,virus,ZIDOVUDINE AZT} } % == BibTeX quality report for tuerkRnaPseudoknotsThat1992: % ? Title looks like it was stored in title-case in Zotero

@article{tumerCterminalDeletionMutant1997, title = {C-Terminal Deletion Mutant of Pokeweed Antiviral Protein Inhibits Viral Infection but Does Not Depurinate Host Ribosomes.}, author = {Tumer, N.E. and Hwang, D.-J. and Bonness, M.}, year = 1997, journal = {Proceedings of the National Academy of Sciences}, volume = {94}, number = {8}, pages = {3866–3871}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.94.8.3866}, url = {http://www.pnas.org/content/94/8/3866.short}, keywords = {antiviral,nosource,PAP,Pokeweed antiviral protein,protein,ribosome,Ribosomes} } % == BibTeX quality report for tumerCterminalDeletionMutant1997: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.USA”)

@article{tumerPokeweedAntiviralProtein1998a, title = {Pokeweed Antiviral Protein Specifically Inhibits {{Ty}}⬚1⬚ Directed +1 Ribosomal Frameshifting and {{Ty}}⬚1⬚ Retrotransposition in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Tumer, N.E. and Parikh, B. and Li, P. and Dinman, J.D.}, year = 1998, journal = {J.Virol.}, volume = {72}, pages = {1036–1042}, doi = {10.1128/JVI.72.2.1036-1042.1998}, keywords = {antiviral,Frameshifting,Gag/Gag-pol ratio,L-A,M1,nosource,PAP,Pokeweed antiviral protein,protein,ribosomal frameshifting,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Ty1,TY1 RETROTRANSPOSITION} } % == BibTeX quality report for tumerPokeweedAntiviralProtein1998a: % ? Possibly abbreviated journal title J.Virol.

@article{tuplinThermodynamicPhylogeneticPrediction2002, title = {Thermodynamic and Phylogenetic Prediction of {{RNA}} Secondary Structures in the Coding Region of Hepatitis {{C}} Virus.}, author = {Tuplin, A. and Wood, J. and Evans, D.J. and Patel, A.H. and Simmonds, P.}, year = 2002, month = jun, journal = {RNA}, volume = {8}, number = {6}, pages = {824–841}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838202554066}, url = {http://rnajournal.cshlp.org/content/8/6/824.short}, abstract = {The existence and functional importance of RNA secondary structure in the replication of positive-stranded RNA viruses is increasingly recognized. We applied several computational methods to detect RNA secondary structure in the coding region of hepatitis C virus (HCV), including thermodynamic prediction, calculation of free energy on folding, and a newly developed method to scan sequences for covariant sites and associated secondary structures using a parsimony-based algorithm. Each of the prediction methods provided evidence for complex RNA folding in the core- and NS5B-encoding regions of the genome. The positioning of covariant sites and associated predicted stem-loop structures coincided with thermodynamic predictions of RNA base pairing, and localized precisely in parts of the genome with marked suppression of variability at synonymous sites. Combined, there was evidence for a total of six evolutionarily conserved stem-loop structures in the NS5B-encoding region and two in the core gene. The virus most closely related to HCV, GB virus-B (GBV-B) also showed evidence for similar internal base pairing in its coding region, although predictions of secondary structures were limited by the absence of comparative sequence data for this virus. While the role(s) of stem-loops in the coding region of HCV and GBV-B are currently unknown, the structure predictions in this study could provide the starting point for functional investigations using recently developed self-replicating clones of HCV}, keywords = {0,BASE,Base Pairing,Base Sequence,chemistry,CODING REGION,COMPLEX,COMPLEXES,gene,genetics,Genome,Hepacivirus,HEPATITIS-C,La,Methods,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Phylogeny,PREDICTION,REGION,REPLICATION,Rna,RNA folding,RNA SECONDARY STRUCTURE,RNA Viruses,RnaViral,SECONDARY STRUCTURE,sequence,SEQUENCES,SITE,SITES,STEM-LOOP,structure,suppression,Thermodynamics,virology,virus,Viruses} }

@article{tyersComparisonSaccharomycesCerevisiae1993a, title = {Comparison of the ⬚{{Saccharomyces}} Cerevisiae⬚ {{G1}} Cyclins: {{Cln3}} May Be an Upstream Activator of {{Cln1}}, {{Cln2}} and Other Cyclins.}, author = {Tyers, M. and Tokiwa, G. and Futcher, B.}, year = 1993, journal = {EMBO J.}, volume = {12}, pages = {1955–1968}, doi = {10.1002/j.1460-2075.1993.tb05845.x}, keywords = {cell cycle,cyclins,epitope,HA-tag,nosource,Plasmids,ras,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,UPSTREAM} } % == BibTeX quality report for tyersComparisonSaccharomycesCerevisiae1993a: % ? Possibly abbreviated journal title EMBO J.

@article{tzengRibosomalFrameshiftingRequires1992, title = {Ribosomal Frameshifting Requires a Pseudoknot in the {{Saccharomyces}} Cerevisiae Double-Stranded {{RNA}} Virus.}, author = {Tzeng, T.H. and Tu, C.L. and Bruenn, J.A.}, year = 1992, month = feb, journal = {Journal of virology}, volume = {66}, number = {2}, pages = {999–1006}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.66.2.999-1006.1992}, url = {http://jvi.asm.org/cgi/content/abstract/66/2/999}, abstract = {The large double-stranded RNA of the Saccharomyces cerevisiae (yeast) virus has two large overlapping open reading frames on the plus strand, one of which is translated via a -1 ribosomal frameshift. Sequences including the overlapping region, placed in novel contexts, can direct ribosomes to make a -1 frameshift in wheat germ extract, Escherichia coli and S. cerevisiae. This sequence includes a consensus slippery sequence, GGGUUUA, and has the potential to form a pseudoknot 3’ to the putative frameshift site. Based on deletion analysis, a region of 71 nucleotides including the potential pseudoknot and the putative slippery sequence is sufficient for frameshifting. Site-directed mutagenesis demonstrates that the pseudoknot is essential for frameshifting}, keywords = {92114205,analysis,Base Composition,Base Sequence,beta-Galactosidase,Chromosome Deletion,DOUBLE-STRANDED-RNA,Escherichia coli,ESCHERICHIA-COLI,frameshift,Frameshift Mutation,Frameshifting,genetics,metabolism,ModelsStructural,Molecular Sequence Data,Mutagenesis,MutagenesisSite-Directed,nosource,Nucleic Acid Conformation,Nucleotides,Oligodeoxyribonucleotides,Open Reading Frames,physiology,Plasmids,Promoter Regions (Genetics),pseudoknot,Restriction Mapping,RIBOSOMAL FRAMESHIFT,ribosomal frameshifting,ribosome,Ribosomes,Rna,RNA Viruses,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,virus,Wheat,yeast} } % == BibTeX quality report for tzengRibosomalFrameshiftingRequires1992: % ? unused Journal abbr (“J.Virol.”)

@article{uchiumiInteractionSarcinRicin1999, title = {Interaction of the Sarcin/Ricin Domain of 23 {{S}} Ribosomal {{RNA}} with Proteins {{L3}} and {{L6}}}, author = {Uchiumi, T. and Sato, N. and Wada, A. and Hachimori, A.}, year = 1999, month = jan, journal = {Journal of Biological Chemistry}, volume = {274}, number = {2}, pages = {681–686}, publisher = {ASBMB}, doi = {10.1074/jbc.274.2.681}, url = {http://www.jbc.org/content/274/2/681.short}, abstract = {We investigated interaction of an RNA domain covering the target site of alpha-sarcin and ricin (sarcin/ricin domain) of Escherichia coli 23 S rRNA with ribosomal proteins. RNA fragments comprising residues 2630- 2788 (Tox-1) and residues 2640-2774 (Tox-2) of 23 S rRNA were transcribed in vitro and used to analyze the binding proteins by gel shift and filter binding. Protein L6 bound to both Tox-1 (Kd: 0.31 microM) and Tox-2 (Kd: 0.18 microM), and L3 bound only to Tox-1 (Kd: 0.069 microM) in a solution containing 10 mM MgCl2 and 175 mM KCl at 0 degreesC. Footprinting studies were performed using the chemical probe dimethyl sulfate on full-length 23 S rRNA. Binding of L6 protected a single base, A-2757, and strongly enhanced reactivity of C-2752. A direct role of A-2757 in the L6 binding was verified by site-directed mutagenesis; replacements of A-2757 with G and C impaired the L6 binding. On the other hand, binding of L3 protected A-2632, A-2634, A- 2635, A-2675, A-2726, A-2733, A-2749, and A-2750. Interestingly, binding of L6 and L3 together protected additional bases A-2657, A- 2662, C-2666, and C-2667 in the sarcin/ricin loop, in addition to A- 2740, A-2741, A-2748, A-2753, A-2764, A-2765, and A-2766 in the other stem-loop. This appears to be due to cooperative interaction of L3 and L6 with the RNA. The results are discussed with respect to conformational modulation of the sarcin/ricin domain by the protein binding}, keywords = {0,Base Sequence,BINDING,BINDING PROTEIN,Binding Sites,BINDING-PROTEIN,chemistry,Endoribonucleases,Escherichia coli,ESCHERICHIA-COLI,In Vitro,IN-VITRO,L3,metabolism,Molecular Sequence Data,Mutagenesis,nosource,Nucleic Acid Conformation,PAP,protein,Protein Binding,Proteins,Ribosomal Proteins,RIBOSOMAL-RNA,Ricin,Rna,RNARibosomal23S,rRNA} } % == BibTeX quality report for uchiumiInteractionSarcinRicin1999: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{uechiRibosomalProteinGene2006a, title = {Ribosomal Protein Gene Knockdown Causes Developmental Defects in Zebrafish}, author = {Uechi, T. and Nakajima, Y. and Nakao, A. and Torihara, H. and Chakraborty, A. and Inoue, K. and Kenmochi, N.}, year = 2006, month = dec, journal = {PLoS ONE}, volume = {1}, number = {1}, pages = {e37}, url = {http://dx.plos.org/10.1371/journal.pone.0000037}, abstract = {The ribosomal proteins (RPs) form the majority of cellular proteins and are mandatory for cellular growth. RP genes have been linked, either directly or indirectly, to various diseases in humans. Mutations in RP genes are also associated with tissue-specific phenotypes, suggesting a possible role in organ development during early embryogenesis. However, it is not yet known how mutations in a particular RP gene result in specific cellular changes, or how RP genes might contribute to human diseases. The development of animal models with defects in RP genes will be essential for studying these questions. In this study, we knocked down 21 RP genes in zebrafish by using morpholino antisense oligos to inhibit their translation. Of these 21, knockdown of 19 RPs resulted in the development of morphants with obvious deformities. Although mutations in RP genes, like other housekeeping genes, would be expected to result in nonspecific developmental defects with widespread phenotypes, we found that knockdown of some RP genes resulted in phenotypes specific to each gene, with varying degrees of abnormality in the brain, body trunk, eyes, and ears at about 25 hours post fertilization. We focused further on the organogenesis of the brain. Each knocked-down gene that affected the morphogenesis of the brain produced a different pattern of abnormality. Among the 7 RP genes whose knockdown produced severe brain phenotypes, 3 human orthologs are located within chromosomal regions that have been linked to brain-associated diseases, suggesting a possible involvement of RP genes in brain or neurological diseases. The RP gene knockdown system developed in this study could be a powerful tool for studying the roles of ribosomes in human diseases}, keywords = {3,animal,antisense,BODIES,Brain,development,disease,FORM,gene,Genes,GROWTH,human,Humans,La,MODEL,models,morphogenesis,Mutation,MUTATIONS,No DOI found,nosource,Phenotype,POSSIBLE INVOLVEMENT,protein,Proteins,REGION,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,SYSTEM,translation,Zebrafish} }

@article{uedaPolyamineDepletionInduces2008, title = {Polyamine Depletion Induces {{G1}} and {{S}} Phase Arrest in Human Retinoblastoma {{Y79}} Cells}, author = {Ueda, A. and Araie, M. and Kubota, S.}, year = 2008, journal = {Cancer Cell International}, volume = {8}, number = {1}, pages = {1–8}, publisher = {BioMed Central Ltd}, doi = {10.1186/1475-2867-8-2}, url = {http://www.biomedcentral.com/1475-2867/8/2}, abstract = {ABSTRACT: BACKGROUND: Polyamines and ornithine decarboxylase (ODC) are essential for cell proliferation. DL-alpha-difluoromethylornithine (DFMO), a synthetic inhibitor of ODC, induces G1 arrest through dephosphorylation of retinoblastoma protein (pRb). The effect of DFMO on cell growth of pRb deficient cells is not known. We examined the effects of DFMO on pRb deficient human retinoblastoma Y79 cell proliferation and its molecular mechanism. METHODS: Using cultured Y79 cells, the effects of DFMO were studied by using polyamine analysis, western blot, gel shift, FACS and promoter analysis. RESULTS: DFMO suppressed the proliferation of Y79 cells, which accumulated in the G1 and S phase. DFMO induced p27/Kip1 protein expression, p107 dephosphorylation and accumulation of p107/E2F-4 complex in Y79 cells. CONCLUSION: These results indicate that p107 dephosphorylation and accumulation of p107/E2F-4 complex is involved in G1 and S phase arrest of DFMO treated Y79 cells}, keywords = {analysis,Cell Proliferation,CELLS,COMPLEX,COMPLEXES,expression,GROWTH,human,INHIBITOR,La,MECHANISM,Methods,nosource,Ornithine,Ornithine Decarboxylase,polyamine,Polyamines,PROLIFERATION,PROMOTER,protein,Retinoblastoma,S,S Phase} } % == BibTeX quality report for uedaPolyamineDepletionInduces2008: % ? unused Journal abbr (“Cancer Cell Int.”)

@article{uemuraSuppressionChromosomalMutations1988a, title = {Suppression of Chromosomal Mutations Affecting {{M}}⬚1⬚ Virus Replication in ⬚{{Saccharomyces}} Cerevisiae⬚ by a Variant of a Viral {{RNA}} Sebment ({{L-A}}) That Encodes Coat Protein.}, author = {Uemura, H. and Wickner, R.B.}, year = 1988, journal = {Mol.Cell.Biol.}, volume = {8}, pages = {938–944}, keywords = {L-A,La,M1,Multiple DOI,Mutation,MUTATIONS,nonfile,nosource,protein,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,suppression,virus,Virus Replication} } % == BibTeX quality report for uemuraSuppressionChromosomalMutations1988a: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{uhleinFunctionalImplicationsRibosomal1998, title = {Functional Implications of Ribosomal Protein {{L2}} in Protein Biosynthesis as Shown by in Vivo Replacement Studies.}, author = {Uhlein, M. and Weglohner, W. and Urlaub, H. and {Wittmann-Liebold}, B.}, year = 1998, month = apr, journal = {Biochemical Journal}, volume = {331 ( Pt 2)}, number = {Pt 2}, pages = {423–430}, publisher = {Portland Press Ltd}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1219371/}, abstract = {The translational apparatus is a highly complex structure containing three to four RNA molecules and more than 50 different proteins. In recent years considerable evidence has accumulated to indicate that the RNA participates intensively in the catalysis of peptide-bond formation, whereas a direct involvement of the ribosomal proteins has yet to be demonstrated. Here we report the functional and structural conservation of a peptidyltransferase centre protein in all three phylogenetic domains. In vivo replacement studies show that the Escherichia coli L2 protein can be replaced by its homologous proteins from human and archaebacterial ribosomes. These hybrid ribosomes are active in protein biosynthesis, as proven by polysome analysis and poly(U)-dependent polyphenylalanine synthesis. Furthermore, we demonstrate that a specific, highly conserved, histidine residue in the C-terminal region of L2 is essential for the function of the translational apparatus. Replacement of this histidine residue in the human and archaebacterial proteins by glycine, arginine or alanine had no effect on ribosome assembly, but strongly reduced the translational activity of ribosomes containing these mutants}, keywords = {0,Alanine,Amino Acid Sequence,analysis,Arginine,assembly,biosynthesis,Catalysis,chemistry,COMPLEX,COMPLEXES,DOMAIN,DOMAINS,Escherichia coli,ESCHERICHIA-COLI,Gene Expression,genetics,Germany,Glycine,Haloarcula marismortui,Histidine,human,Humans,IN-VIVO,L2,La,metabolism,Molecular Sequence Data,Mutagenesis,MUTANTS,No DOI found,nosource,peptide bond formation,PEPTIDE-BOND FORMATION,Peptides,Peptidyltransferase,pharmacology,physiology,Poly U,Polyribosomes,protein,Protein Biosynthesis,PROTEIN-BIOSYNTHESIS,Proteins,Recombinant Proteins,REGION,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Rna,Sequence Homology,Structural,structure,Structure-Activity Relationship} } % == BibTeX quality report for uhleinFunctionalImplicationsRibosomal1998: % ? unused Journal abbr (“Biochem.J.”)

@article{unbehaunPositionEukaryoticInitiation2007, title = {Position of Eukaryotic Initiation Factor {{eIF5B}} on the {{80S}} Ribosome Mapped by Directed Hydroxyl Radical Probing}, author = {Unbehaun, A. and Marintchev, A. and Lomakin, I.B. and Didenko, T. and Wagner, G. and Hellen, C.U. and Pestova, T.V.}, year = 2007, month = jul, journal = {EMBO J.}, volume = {26}, number = {13}, pages = {3109–3123}, publisher = {Nature Publishing Group}, doi = {10.1038/sj.emboj.7601751}, url = {http://www.nature.com/emboj/journal/v26/n13/abs/7601751a.html}, abstract = {Eukaryotic translation initiation factor eIF5B is a ribosome-dependent GTPase that mediates displacement of initiation factors from the 40S ribosomal subunit in 48S initiation complexes and joining of 40S and 60S subunits. Here, we determined eIF5B’s position on 80S ribosomes by directed hydroxyl radical cleavage. In the resulting model, eIF5B is located in the intersubunit cleft of the 80S ribosome: domain 1 is positioned near the GTPase activating center of the 60S subunit, domain 2 interacts with the 40S subunit (helices 3, 5 and the base of helix 15 of 18S rRNA and ribosomal protein (rp) rpS23), domain 3 is sandwiched between subunits and directly contacts several ribosomal elements including Helix 95 of 28S rRNA and helix 44 of 18S rRNA, domain 4 is near the peptidyl-transferase center and its helical subdomain contacts rpL10E. The cleavage data also indicate that binding of eIF5B might induce conformational changes in both subunits, with ribosomal segments wrapping around the factor. Some of these changes could also occur upon binding of other translational GTPases, and may contribute to factor recognition}, keywords = {3,60S subunit,BASE,BINDING,CLEAVAGE,COMPLEX,COMPLEXES,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,DOMAIN,ELEMENTS,EUKARYOTIC TRANSLATION,GTPase,Hydroxyl Radical,immunology,initiation,INITIATION-FACTOR,La,microbiology,MODEL,nosource,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,POSITION,protein,RECOGNITION,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,rRNA,SUBUNIT,SUBUNITS,translation,TRANSLATION INITIATION} } % == BibTeX quality report for unbehaunPositionEukaryoticInitiation2007: % ? Possibly abbreviated journal title EMBO J.

@article{urbonaviciusTransferRNAModifications2003, title = {Transfer {{RNA}} Modifications That Alter +1 Frameshifting in General Fail to Affect -1 Frameshifting}, author = {Urbonavicius, J. and Stahl, G. and Durand, J.M. and Ben Salem, S.N. and Qian, Q. and Farabaugh, P.J. and Bjork, G.R.}, year = 2003, month = jun, journal = {RNA}, volume = {9}, number = {6}, pages = {760–768}, publisher = {Cold Spring Harbor Lab}, doi = {10.1261/rna.5210803}, url = {http://rnajournal.cshlp.org/content/9/6/760.short PM:12756333}, abstract = {Using mutants (tgt, mnmA(asuE, trmU), mnmE(trmE), miaA, miaB, miaE, truA(hisT), truB) of either Escherichia coli or Salmonella enterica serovar Typhimurium and the trm5 mutant of Saccharomyces cerevisiae, we have analyzed the influence by the modified nucleosides Q34, mnm(5)s(2)U34, ms(2)io(6)A37, Psi39, Psi55, m(1)G37, and yW37 on -1 frameshifts errors at various heptameric sequences, at which at least one codon is decoded by tRNAs having these modified nucleosides. The frequency of -1 frameshifting was the same in congenic strains only differing in the allelic state of the various tRNA modification genes. In fact, in one case (deficiency of mnm(5)s(2)U34), we observed a reduced ability of the undermodified tRNA to make a -1 frameshift error. These results are in sharp contrast to earlier observations that tRNA modification prevents +1 frameshifting suggesting that the mechanisms by which -1 and +1 frameshift errors occur are different. Possible mechanisms explaining these results are discussed}, keywords = {+1 frameshifting,0,Anticodon,Base Sequence,BIOLOGY,CEREVISIAE,chemistry,Codon,deficiency,ERRORS,Escherichia coli,ESCHERICHIA-COLI,frameshift,Frameshifting,FrameshiftingRibosomal,gene,Genes,genetics,La,MECHANISM,MECHANISMS,metabolism,ModelsGenetic,modification,MUTANTS,Mutation,nosource,Nucleosides,Rna,RNATransfer,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Salmonella typhimurium,sequence,SEQUENCES,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,TRANSFER-RNA,tRNA} }

@article{usseryInhibitionPoliovirusReplication1977, title = {Inhibition of Poliovirus Replication by a Plant Antiviral Peptide}, author = {Ussery, M.A. and Irvin, J.D. and Hardesty, B.}, year = 1977, month = mar, journal = {Annals of the New York Academy of Sciences}, volume = {284}, pages = {431–440}, doi = {10.1111/j.1749-6632.1977.tb21979.x}, keywords = {antiviral,INHIBITION,nosource,PAP} }

@article{utansChronicCardiacRejection1994, title = {Chronic Cardiac Rejection: Identification of Five Upregulated Genes in Transplanted Hearts by Differential {{mRNA}} Display}, author = {Utans, U. and Liang, P. and Wyner, L.R. and Karnovsky, M.J. and Russell, M.E.}, year = 1994, month = jul, journal = {Proceedings of the National Academy of Sciences}, volume = {91}, number = {14}, pages = {6463–6467}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.91.14.6463}, url = {http://www.pnas.org/content/91/14/6463.short}, keywords = {analysis,differential display,disease,gene,Genes,heart,IDENTIFICATION,IN-VIVO,mRNA,nosource,PCR,protein,rat,Rna,sequence,Sequence Analysis,yeast} } % == BibTeX quality report for utansChronicCardiacRejection1994: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.USA”)

@article{vaishnavBiochemistryAIDS1991, title = {The Biochemistry of {{AIDS}}.}, author = {Vaishnav, Y.N. and {Wong-Staal}, F.}, year = 1991, journal = {Annual Review of Biochemistry}, volume = {60}, number = {1}, pages = {577–630}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, doi = {10.1146/annurev.bi.60.070191.003045}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.bi.60.070191.003045}, keywords = {nosource} }

@article{vaismanRoleSaccharomycesCerevisiae1995, title = {The Role of ⬚{{Saccharomyces}} Cerevisiae⬚ {{Cdc40p}} in {{DNA}} Replication and Mitotic Spindle Formation and/or Maintenance.}, author = {Vaisman, N. and Txouladze, A. and Robzyk, K. and {Ben-Yehuda}, S. and Kupiec, M. and Kassir, Y.}, year = 1995, journal = {Mol.Gen.Genet.}, volume = {247}, pages = {123–136}, doi = {10.1007/BF00705642}, keywords = {cdc40,Dna,DNA Replication,mof5,nosource,prp17,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,yeast} } % == BibTeX quality report for vaismanRoleSaccharomycesCerevisiae1995: % ? Possibly abbreviated journal title Mol.Gen.Genet.

@article{valenteYeastSensorFactors2003, title = {Yeast as a Sensor of Factors Affecting the Accuracy of Protein Synthesis}, author = {Valente, L. and Kinzy, T.G.}, year = 2003, month = oct, journal = {Cellular and molecular life sciences}, volume = {60}, number = {10}, pages = {2115–2130}, publisher = {Springer}, doi = {10.1007/s00018-003-2334-2}, url = {http://www.springerlink.com/index/cjq534alxpkvaxbm.pdf}, abstract = {The cell monitors and maintains the fidelity of translation during the three stages of protein synthesis: initiation, elongation and termination. Errors can arise by multiple mechanisms, such as altered start site selection, reading frame shifts, misincorporation or nonsense codon suppression. All of these events produce incorrect protein products. Translational accuracy is affected by both cis- and trans-acting elements that insure the proper peptide is synthesized by the protein synthetic machinery. Many cellular components are involved in the accuracy of translation, including RNAs (transfer RNAs, messenger RNAs and ribosomal RNAs) and proteins (ribosomal proteins and translation factors). The yeast Saccharomyces cerevisiae has proven an ideal system to study translational fidelity by integrating genetic approaches with biochemical analysis. This review focuses on the ways studies in yeast have contributed to our understanding of the roles translation factors and the ribosome play in assuring the accuracy of protein synthesis}, keywords = {accuracy,analysis,CEREVISIAE,Codon,COMPONENT,COMPONENTS,ELEMENTS,elongation,ERRORS,Fidelity,FRAME,Genetic,genetics,immunology,initiation,La,MECHANISM,MECHANISMS,MESSENGER-RNA,MESSENGER-RNAS,microbiology,MOLECULAR-GENETICS,NONSENSE,nosource,PRODUCT,PRODUCTS,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,READING FRAME,Review,Ribosomal Proteins,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SELECTION,SITE,SITE SELECTION,suppression,SYSTEM,termination,TRANSFER-RNA,translation,translational fidelity,yeast} } % == BibTeX quality report for valenteYeastSensorFactors2003: % ? unused Journal abbr (“Cell Mol.Life Sci.”)

@article{valleCryoEMRevealsActive2002, title = {Cryo-{{EM}} Reveals an Active Role for Aminoacyl-{{tRNA}} in the Accommodation Process}, author = {Valle, M. and Sengupta, J. and Swami, N.K. and Grassucci, R.A. and Burkhardt, N. and Nierhaus, K.H. and Agrawal, R.K. and Frank, J.}, year = 2002, month = jul, journal = {EMBO J.}, volume = {21}, number = {13}, pages = {3557–3567}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/cdf326}, url = {http://www.nature.com/emboj/journal/v21/n13/abs/7594545a.html}, abstract = {During the elongation cycle of protein biosynthesis, the specific amino acid coded for by the mRNA is delivered by a complex that is comprised of the cognate aminoacyl-tRNA, elongation factor Tu and GTP. As this ternary complex binds to the ribosome, the anticodon end of the tRNA reaches the decoding center in the 30S subunit. Here we present the cryo- electron microscopy (EM) study of an Escherichia coli 70S ribosome-bound ternary complex stalled with an antibiotic, kirromycin. In the cryo-EM map the anticodon arm of the tRNA presents a new conformation that appears to facilitate the initial codon-anticodon interaction. Furthermore, the elbow region of the tRNA is seen to contact the GTPase-associated center on the 50S subunit of the ribosome, suggesting an active role of the tRNA in the transmission of the signal prompting the GTP hydrolysis upon codon recognition}, keywords = {0,antibiotic,Anticodon,biosynthesis,chemistry,Codon,COMPLEX,COMPLEXES,Cryoelectron Microscopy,decoding,drug effects,elongation,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,genetics,GTP,Guanosine,Guanosine Diphosphate,Guanosine Triphosphate,Hydrolysis,Image ProcessingComputer-Assisted,La,Macromolecular Systems,metabolism,ModelsMolecular,mRNA,nosource,Nucleic Acid Conformation,Peptide Chain Elongation,Peptide Elongation Factor Tu,pharmacology,Phenylalanine,physiology,protein,Protein Conformation,Proteins,Pyridones,ribosome,Ribosomes,Rna,RNATransfer,RNATransferAmino Acyl,RNATransferPhe,SIGNAL,Structure-Activity Relationship,SUBUNIT,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,SYSTEM,tRNA,ultrastructure} } % == BibTeX quality report for valleCryoEMRevealsActive2002: % ? Possibly abbreviated journal title EMBO J.

@article{valleLockingUnlockingRibosomal2003, title = {Locking and Unlocking of Ribosomal Motions}, author = {Valle, M. and Zavialov, A. and Sengupta, J. and Rawat, U. and Ehrenberg, M. and Frank, J.}, year = 2003, month = jul, journal = {Cell}, volume = {114}, number = {1}, pages = {123–134}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(03)00476-8}, abstract = {During the ribosomal translocation, the binding of elongation factor G (EF-G) to the pretranslocational ribosome leads to a ratchet-like rotation of the 30S subunit relative to the 50S subunit in the direction of the mRNA movement. By means of cryo-electron microscopy we observe that this rotation is accompanied by a 20 A movement of the L1 stalk of the 50S subunit, implying that this region is involved in the translocation of deacylated tRNAs from the P to the E site. These ribosomal motions can occur only when the P-site tRNA is deacylated. Prior to peptidyl-transfer to the A-site tRNA or peptide removal, the presence of the charged P-site tRNA locks the ribosome and prohibits both of these motions}, keywords = {A-SITE,BINDING,Cryoelectron Microscopy,elongation,L1,Movement,mRNA,nosource,P-SITE,peptidyl-transfer,ribosome,SUBUNIT,translocation,tRNA} }

@article{valleVisualizingTmRNAEntry2003, title = {Visualizing {{tmRNA}} Entry into a Stalled Ribosome}, author = {Valle, M. and Gillet, R. and Kaur, S. and Henne, A. and Ramakrishnan, V. and Frank, J.}, year = 2003, month = apr, journal = {Science}, volume = {300}, number = {5616}, pages = {127–130}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1081798}, url = {http://www.sciencemag.org/content/300/5616/127.short}, abstract = {Bacterial ribosomes stalled on defective messenger RNAs (mRNAs) are rescued by tmRNA, an similar to300-nucleotide-long molecule that functions as both transfer RNA (tRNA) and mRNA. Translation then switches from the defective message to a short open reading frame on tmRNA that tags the defective nascent peptide chain for degradation. However, the mechanism by which tmRNA can enter and move through the ribosome is unknown. We present a cryo-electron microscopy study at similar to13 to 15 angstroms of the entry of tmRNA into the ribosome. The structure reveals how tmRNA could move through the ribosome despite its complicated topology and also suggests roles for proteins S1 and SmpB in the function of tmRNA}, keywords = {AMINOACYL-TRANSFER-RNA,Bacterial,CONFORMATIONAL CHANGE,Cryoelectron Microscopy,CRYSTAL-STRUCTURE,degradation,ELONGATION-FACTOR TU,ESCHERICHIA-COLI RIBOSOME,FRAME,MECHANISM,MESSAGE,MESSENGER-RNA,MESSENGER-RNAS,mRNA,NASCENT-PEPTIDE,nosource,OPEN READING FRAME,protein,PROTEIN S1,Proteins,READING FRAME,ribosome,Ribosomes,Rna,SECONDARY STRUCTURE,SMPB SYSTEM,structure,TAGGING SYSTEM,TRANSFER-RNA,translation,tRNA} }

@article{valleEliminationDoublestrandedRNA1993a, title = {Elimination of {{L-A}} Double-Stranded {{RNA}} Virus of ⬚{{Saccharomyces}} Cerevisiae⬚ by Expression of {{Gag}} and {{Gag-Pol}} from an {{L-A cDNA}} Clone.}, author = {Valle, R.P.C. and Wickner, R.B.}, year = 1993, journal = {J.Virol.}, volume = {67}, pages = {2764–2771}, doi = {10.1128/jvi.67.5.2764-2771.1993}, keywords = {curing,DOUBLE-STRANDED-RNA,expression,Gag,Gag-pol,L-A,La,nosource,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,virus} } % == BibTeX quality report for valleEliminationDoublestrandedRNA1993a: % ? Possibly abbreviated journal title J.Virol.

@article{vangelderComplexSecondaryStructure1993, title = {A Complex Secondary Structure in {{U1A}} Pre-{{mRNA}} That Binds Two Molecules of {{U1A}} Protein Is Required for Regulation of Polyadenylation}, author = {{}{van Gelder}, C.W. and Gunderson, S.I. and Jansen, E.J. and Boelens, W.C. and {Polycarpou-Schwarz}, M. and Mattaj, I.W. and {}{van Venrooij}, W.J.}, year = 1993, month = dec, journal = {EMBO J.}, volume = {12}, number = {13}, pages = {5191–5200}, doi = {10.1002/j.1460-2075.1993.tb06214.x}, abstract = {The human U1A protein-U1A pre-mRNA complex and the relationship between its structure and function in inhibition of polyadenylation in vitro were investigated. Two molecules of U1A protein were shown to bind to a conserved region in the 3’ untranslated region of U1A pre-mRNA. The secondary structure of this region was determined by a combination of theoretical prediction, phylogenetic sequence alignment, enzymatic structure probing and molecular genetics. The U1A binding sites form (part of) a complex secondary structure which is significantly different from the binding site of U1A protein on U1 snRNA. Studies with mutant pre-mRNAs showed that the integrity of much of this structure is required for both high affinity binding to U1A protein and specific inhibition of polyadenylation in vitro. In particular, binding of a single molecule of U1A protein to U1A pre-mRNA is not sufficient to produce efficient inhibition of polyadenylation}, keywords = {94085394,alignment,Base Sequence,BINDING,Binding Sites,Comparative Study,COMPLEX,COMPLEXES,Genetic,genetics,human,In Vitro,IN-VITRO,INHIBITION,metabolism,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleic Acid Precursors,Poly A,protein,regulation,RibonucleoproteinU1 Small Nuclear,RNA ProcessingPost-Transcriptional,RNAMessenger,RNASmall Nuclear,SECONDARY STRUCTURE,sequence,Sequence Alignment,Sequence HomologyNucleic Acid,structure,supportnon-u.s.gov’t} } % == BibTeX quality report for vangelderComplexSecondaryStructure1993: % ? Possibly abbreviated journal title EMBO J.

@article{vanhoofFunctionSki4pCsl4p2000, title = {Function of the Ski4p ({{Csl4p}}) and {{Ski7p}} Proteins in 3’-to-5’ Degradation of {{mRNA}}}, author = {{}{van Hoof}, A. and Staples, R.R. and Baker, R.E. and Parker, R.}, year = 2000, month = nov, journal = {Molecular and Cellular Biology}, volume = {20}, number = {21}, pages = {8230–8243}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.20.21.8230-8243.2000}, url = {http://mcb.asm.org/cgi/content/abstract/20/21/8230}, abstract = {One of two general pathways of mRNA decay in the yeast Saccharomyces cerevisiae occurs by deadenylation followed by 3’-to-5’ degradation of the mRNA body. Previous results have shown that this degradation requires components of the exosome and the Ski2p, Ski3p, and Ski8p proteins, which were originally identified due to their superkiller phenotype. In this work, we demonstrate that deletion of the SKI7 gene, which encodes a putative GTPase, also causes a defect in 3’-to-5’ degradation of mRNA. Deletion of SKI7, like deletion of SKI2, SKI3, or SKI8, does not affect various RNA-processing reactions of the exosome. In addition, we show that a mutation in the SKI4 gene also causes a defect in 3’-to-5’ mRNA degradation. We show that the SKI4 gene is identical to the CSL4 gene, which encodes a core component of the exosome. Interestingly, the ski4-1 allele contains a point mutation resulting in a mutation in the putative RNA binding domain of the Csl4p protein. This point mutation strongly affects mRNA degradation without affecting exosome function in rRNA or snRNA processing, 5’ externally transcribed spacer (ETS) degradation, or viability. In contrast, the csl4-1 allele of the same gene affects rRNA processing but not 3’-to-5’ mRNA degradation. We identify csl4-1 as resulting from a partial-loss-of-function mutation in the promoter of the CSL4 gene. These data indicate that the distinct functions of the exosome can be separated genetically and suggest that the RNA binding domain of Csl4p may have a specific function in mRNA degradation}, keywords = {0,Alleles,Amino Acid Sequence,BINDING,Binding Sites,BIOLOGY,biosynthesis,BODIES,Cell Nucleus,CEREVISIAE,COMPONENT,COMPONENTS,Cytoplasm,DEADENYLATION,DECAY,degradation,DOMAIN,ENCODES,exosome,Fungal Proteins,FUSION PROTEIN,Galactose,gene,genetics,Genotype,Glucose,GREEN FLUORESCENT PROTEIN,Green Fluorescent Proteins,GTP,GTP Phosphohydrolase,GTP Phosphohydrolases,GTP-Binding Proteins,GTPase,IDENTIFY,La,Lac Operon,Luminescent Proteins,metabolism,Models-Genetic,ModelsGenetic,Molecular Sequence Data,mRNA,mRNA decay,Mutation,nosource,Nuclear Proteins,PATHWAY,Phenotype,physiology,Plasmids,Point Mutation,PROMOTER,Promoter Regions (Genetics),protein,Protein Structure-Tertiary,Protein StructureTertiary,Proteins,Recombinant Fusion Proteins,REQUIRES,Rna,RNA-Messenger,RNA-Ribosomal,RNA-Ribosomal-5.8S,RNA-Small Nuclear,RNAMessenger,RNARibosomal,RNARibosomal5.8S,RNASmall Nuclear,rRNA,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Sequence Homology-Amino Acid,Sequence HomologyAmino Acid,SKI2,Sucrose,Support,Temperature,Time Factors,Transcription-Genetic,TranscriptionGenetic,yeast} } % == BibTeX quality report for vanhoofFunctionSki4pCsl4p2000: % ? unused Journal abbr (“Mol.Cell Biol”)

@article{vanhoofExosomemediatedRecognitionDegradation2002, title = {Exosome-Mediated Recognition and Degradation of {{mRNAs}} Lacking a Termination Codon}, author = {{}{van Hoof}, A. and Frischmeyer, P.A. and Dietz, H.C. and Parker, R.}, year = 2002, month = mar, journal = {Science}, volume = {295}, number = {5563}, pages = {2262–2264}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1067272}, url = {http://www.sciencemag.org/content/295/5563/2262.short}, abstract = {One role of messenger RNA (mRNA) degradation is to maintain the fidelity of gene expression by degrading aberrant transcripts. Recent results show that mRNAs without translation termination codons are unstable in eukaryotic cells. We used yeast mutants to demonstrate that these “nonstop” mRNAs are degraded by the exosome in a 3’-to-5’ direction. The degradation of nonstop transcripts requires the exosome-associated protein Ski7p. Ski7p is closely related to the translation elongation factor EF1A and the translation termination factor eRF3. This suggests that the recognition of nonstop mRNAs involves the binding of Ski7p to an empty aminoacyl-(RNA-binding) site (A site) on the ribosome, thereby bringing the exosome to a mRNA with a ribosome stalled near the 3’ end. This system efficiently degrades mRNAs that are prematurely polyadenylated within the coding region and prevents their expression}, keywords = {0,3,A SITE,A-SITE,Alleles,Amino Acid Sequence,Base Sequence,BINDING,Binding Sites,CELLS,CEREVISIAE,chemistry,CODING REGION,Codon,CODONS,CodonTerminator,degradation,elongation,Eukaryotic Cells,exosome,expression,Fidelity,Fungal Proteins,gene,Gene Expression,Gene Expression RegulationFungal,GENE-EXPRESSION,GenesFungal,genetics,GTP-Binding Proteins,Half-Life,La,MESSENGER-RNA,metabolism,Molecular Sequence Data,mRNA,MUTANTS,nosource,Polyadenylation,protein,Protein Binding,Protein Biosynthesis,Proteins,RECOGNITION,REGION,REQUIRES,Research SupportNon-U.S.Gov’t,ribosome,Ribosomes,Rna,RNA 3’ End Processing,RNA ProcessingPost-Transcriptional,RNA Stability,RNAFungal,RNAMessenger,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Sequence Alignment,Sequence Deletion,SITE,SYSTEM,termination,TERMINATION CODON,TERMINATION-CODON,TRANSCRIPT,translation,TRANSLATION TERMINATION,yeast} }

@article{vannessADPribosylationElongationFactor1980, title = {{{ADP-ribosylation}} of Elongation Factor 2 by Diptheria Toxin. {{Isolation}} and Properties of the Novel Ribosyl-Amino Acid and Its Hydrolysis Products.}, author = {Van Ness, B.G. and Howard, J.B. and Bodley, J.W.}, year = 1980, journal = {J.Biol Chem.}, volume = {255}, pages = {10717–10720}, keywords = {EF-2,elongation,Hydrolysis,Multiple DOI,nonfile,nosource,toxin,translation,yeast} } % == BibTeX quality report for vannessADPribosylationElongationFactor1980: % ? Possibly abbreviated journal title J.Biol Chem.

@article{vanrykEfficientExpressionUtilization1990, title = {Efficient Expression and Utilization of Mutant 5 {{S rRNA}} in {{Saccharomyces}} Cerevisiae.}, author = {Van Ryk, D.I. and Lee, Y. and Nazar, R.N.}, year = 1990, month = may, journal = {Journal of Biological Chemistry}, volume = {265}, number = {15}, pages = {8377–8381}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(19)38896-9}, url = {http://www.jbc.org/content/265/15/8377.short}, abstract = {The expression of mutant 5 S rRNA genes in vivo is examined as a basis for further studies on the control, structure, and function of the ribosomal 5 S RNA. Specific single base substitutions (e.g. positions 98 or 99) or short insertions can result in substantial structural changes that can easily be detected by gel electrophoresis and permit the assay of mutant RNA synthesis and utilization. In addition, the use of high and low copy shuttle vectors as well as alternate growth conditions permits the adjustment of mutant RNA levels in vivo. Despite the high genomic copy number for the 5 S rRNA gene, under optimized conditions as much as 80% of the cellular 5 S RNA can be mutant, and RNA structure analyses indicate that some of these RNAs can readily be assembled into the ribosome structure resulting in an in vivo ribosome population which is also approximately 80% mutant. The results indicate that plasmid integrated 5 S rRNA genes are preferentially expressed and suggest that additional features of the chromosome structure regulate 5 S rRNA gene expression in vivo}, keywords = {90256746,Base Sequence,DNARibosomal,Electrophoresis,expression,gene,Gene Expression,GENE-EXPRESSION,Genes,GenesStructuralFungal,Genetic,genetics,genomic,IN-VIVO,metabolism,Molecular Sequence Data,Mutation,nosource,Nucleic Acid Conformation,PLASMID,Plasmids,ribosome,Rna,RNARibosomal,RNARibosomal5S,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SHUTTLE VECTORS,Structural,structure,supportnon-u.s.gov’t,TransformationGenetic,vector,vectors} } % == BibTeX quality report for vanrykEfficientExpressionUtilization1990: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{vanrykEffectSequenceMutations1992, title = {Effect of Sequence Mutations on the Higher Order Structure of the Yeast {{5S rRNA}}.}, author = {Van Ryk, D.I. and Nazar, R.N.}, year = 1992, journal = {J.Mol.Biol.}, volume = {226}, pages = {1027–1035}, doi = {10.1016/0022-2836(92)91050-Y}, keywords = {5S rRNA,Mutation,MUTATIONS,nosource,rRNA,sequence,structure,yeast} } % == BibTeX quality report for vanrykEffectSequenceMutations1992: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{vanziProteinSynthesisSingle2003, title = {Protein Synthesis by Single Ribosomes}, author = {Vanzi, F. and Vladimirov, S. and Knudsen, C.R. and Goldman, Y.E. and Cooperman, B.S.}, year = 2003, month = oct, journal = {RNA.}, volume = {9}, number = {10}, pages = {1174–1179}, publisher = {Cold Spring Harbor Lab}, doi = {10.1261/rna.5800303}, url = {http://rnajournal.cshlp.org/content/9/10/1174.short}, abstract = {The ribosome is universally responsible for synthesizing proteins by translating the genetic code transcribed in mRNA into an amino acid sequence. Ribosomes use cellular accessory proteins, soluble transfer RNAs, and metabolic energy to accomplish the initiation, elongation, and termination of peptide synthesis. In translocating processively along the mRNA template during the elongation cycle, ribosomes act as supramolecular motors. Here we demonstrate that ribosomes adsorbed on a surface, as for mechanical or spectroscopic studies, are capable of polypeptide synthesis and that tethered particle analysis of fluorescent beads connected to ribosomes via polyuridylic acid can be used to estimate the rate of polyphenylalanine synthesis by individual ribosomes. This work opens the way for application of biophysical techniques, originally developed for the classical motor proteins, to the understanding of protein biosynthesis}, keywords = {0,ACID,Amino Acid Sequence,AMINO-ACID,analysis,biosynthesis,chemical synthesis,elongation,ELONGATION CYCLE,elongation factors,ELONGATION-FACTORS,Escherichia coli,Fluorescent Dyes,Genetic,Genetic Code,GENETIC-CODE,initiation,La,metabolism,MicroscopyAtomic Force,mRNA,nosource,Peptide Biosynthesis,Peptide Chain ElongationTranslational,Peptide Elongation Factors,Peptide Fragments,Peptide Synthesis,Peptides,Poly U,POLYPEPTIDE,protein,Protein Biosynthesis,protein synthesis,PROTEIN-BIOSYNTHESIS,PROTEIN-SYNTHESIS,Proteins,ribosome,Ribosomes,Rna,RNATransferAmino Acyl,sequence,Solubility,Support,techniques,TEMPLATE,termination,TRANSFER-RNA} } % == BibTeX quality report for vanziProteinSynthesisSingle2003: % ? Possibly abbreviated journal title RNA.

@article{vanziMechanicalStudiesSingle2005, title = {Mechanical Studies of Single Ribosome/{{mRNA}} Complexes}, author = {Vanzi, F. and Takagi, Y. and Shuman, H. and Cooperman, B.S. and Goldman, Y.E.}, year = 2005, journal = {Biophysical journal}, volume = {89}, number = {3}, pages = {1909–1919}, publisher = {Elsevier}, doi = {10.1529/biophysj.104.056283}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006349505728368}, abstract = {Methodology was developed for specifically anchoring Escherichia coli 70S ribosomes onto a chemically modified, cysteine-reactive glass surface. Immobilized ribosomes maintain the capability of binding a polyuridylic acid (poly(U)) template, enabling investigation of mechanical properties of individual ribosome-poly(U) complexes using laser tweezers. Streptavidin-coated polystyrene microspheres bound specifically to the biotinylated 3’ end of long (up to 10,000 bases) poly(U) strands. A novel optical method was built to control the position of the laser trap along the microscope optical axis at 2 nm resolution, facilitating measurement of the force-extension relationship for poly(U). Some immobilized ribosome-poly(U) complexes supported 100 pN of force applied at the 3’ end of the mRNA. Binding of N-acetylated Phe-tRNA(Phe), an analog of the initiator fMet-tRNA(Met), enhanced the population of complexes that could withstand high forces. The persistence length of poly(U) RNA homopolymer, modeled as a worm-like chain, was found to be 0.79 +/- 0.05 nm and the backbone elasticity was 900 +/- 140 pN, similar to values for single-stranded DNA}, keywords = {0,3,70S RIBOSOME,ACID,BASE,BASES,BINDING,Biochemistry,Biomechanics,Biophysics,Biotinylation,chemistry,COMPLEX,COMPLEXES,Cysteine,Dna,DNASingle-Stranded,elasticity,Escherichia coli,ESCHERICHIA-COLI,Fluorescence Resonance Energy Transfer,Glass,La,Lasers,metabolism,Methods,Microspheres,ModelsStatistical,mRNA,nosource,Peptide Chain ElongationTranslational,pharmacology,Poly U,Polymers,Polystyrenes,POSITION,Research SupportN.I.H.Extramural,Research SupportU.S.Gov’tP.H.S.,RESOLUTION,ribosome,Ribosomes,Rna,RNAMessenger,Streptavidin,Surface Properties,Temperature,TEMPLATE,Time Factors} } % == BibTeX quality report for vanziMechanicalStudiesSingle2005: % ? unused Journal abbr (“Biophys.J.”)

@article{varela-echavarriaComparisonMoloneyMurine1992a, title = {Comparison of {{Moloney}} Murine Leukemia Virus Rate with the Fidelity of Its Reverse Transcriptase.}, author = {{Varela-Echavarria}, A. and Garvey, N. and Preston, B.D. and Dougherty, J.P.}, year = 1992, journal = {J.Biol.Chem.}, volume = {34}, pages = {24681–24688}, doi = {10.1016/S0021-9258(18)35818-6}, keywords = {Fidelity,MuLV,nosource,virus} } % == BibTeX quality report for varela-echavarriaComparisonMoloneyMurine1992a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{varshavskyNendRule1992, title = {The {{N-end}} Rule}, author = {Varshavsky, A.}, year = 1992, month = may, journal = {Cell}, volume = {69}, number = {5}, pages = {725–735}, doi = {10.1016/0092-8674(92)90285-K}, url = {PM:1317266}, keywords = {0,Amino Acid Sequence,Animals,BIOLOGY,chemistry,Escherichia coli,La,metabolism,Molecular Sequence Data,nosource,protein,Protein ProcessingPost-Translational,Proteins,Research SupportU.S.Gov’tP.H.S.,Review,Saccharomyces cerevisiae,Ubiquitin,Ubiquitins} }

@article{varshavskyFelixHoppeSeylerLecture2000a, title = {Felix {{Hoppe-Seyler Lecture}} 2000. {{The}} Ubiquitin System and the {{N-end}} Rule Pathway.}, author = {Varshavsky, A. and Turner, G. and Du, F. and Xie, Y.}, year = 2000, journal = {Biological chemistry}, volume = {381}, number = {9-10}, eprint = {11076011}, eprinttype = {pubmed}, pages = {779–789}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11076011}, abstract = {Eukaryotes contain a highly conserved multienzyme system which covalently links a small protein, ubiquitin, to a variety of intracellular proteins that bear degradation signals recognized by this system. The resulting ubiquitin-protein conjugates are degraded by the 26S proteasome, an ATP-dependent protease. Pathways that involve ubiquitin play major roles in a huge variety of processes, including cell differentiation, cell cycle, and responses to stress. In this article we briefly review the design of the ubiquitin system, and describe two recent advances, the finding that ubiquitin ligases interact with specific components of the 26S proteasome, and the demonstration that peptides accelerate their uptake into cells by activating the N-end rule pathway, one of several proteolytic pathways of the ubiquitin system}, keywords = {0,Animals,Awards and Prizes,Biochemistry,BIOLOGY,cell cycle,Cell Differentiation,Cell Physiology,CELLS,COMPONENT,COMPONENTS,degradation,Eukaryotic Cells,Germany,Humans,La,Ligases,No DOI found,nosource,PATHWAY,Peptides,physiology,protein,Proteins,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,Review,SIGNAL,Signal Transduction,Stress,SYSTEM,Ubiquitin,Ubiquitins} } % == BibTeX quality report for varshavskyFelixHoppeSeylerLecture2000a: % ? unused Journal abbr (“Biol.Chem.”)

@incollection{vazquezTranslationInhibitors1973, title = {Translation Inhibitors.}, booktitle = {Proceedings of the {{Tenth FEBS Meeting}}}, author = {Vazquez, D. and Jimenez, A. and Sanchez, L. and Reyes, R and Bernabeu, C. and Ballesta, {JPG}}, year = 1973, pages = {243–259}, publisher = {Federation of European Biochemical Societies}, keywords = {drugs,INHIBITOR,nosource,review article,translation} }

@article{vazquezInhibitorsProteinSynthesis1974, title = {Inhibitors of {{Protein-Synthesis}}}, author = {Vazquez, D.}, year = 1974, journal = {FEBS Letters}, volume = {43}, pages = {S63-S84}, url = {ISI:A1974T050100007}, keywords = {0,No DOI found,nosource,protein synthesis,PROTEIN-SYNTHESIS} } % == BibTeX quality report for vazquezInhibitorsProteinSynthesis1974: % ? Title looks like it was stored in title-case in Zotero

@article{velculescuSerialAnalysisGene1995, title = {Serial Analysis of Gene Expression.}, author = {Velculescu, V.E. and Zhang, L. and Vogelstein, B. and Kinzler, K.W.}, year = 1995, month = oct, journal = {Science}, volume = {270}, number = {5235}, pages = {484–487}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.270.5235.484}, url = {http://www.sciencemag.org/content/270/5235/484.short}, keywords = {analysis,disease,expression,gene,Gene Expression,GENE-EXPRESSION,Genes,Methods,nosource,SAGE,sequence} }

@article{velichutinaMutationsHelix272000, title = {Mutations in Helix 27 of the Yeast {{Saccharomyces}} Cerevisiae {{18S rRNA}} Affect the Function of the Decoding Center of the Ribosome}, author = {Velichutina, I.V. and Dresios, J. and Hong, J.Y. and Li, C. and Mankin, A. and Synetos, D. and Liebman, S.W.}, year = 2000, journal = {RNA.}, volume = {6}, number = {8}, pages = {1174–1184}, publisher = {Cambridge Univ Press}, doi = {10.1017/S1355838200000637}, url = {http://journals.cambridge.org/abstract_S1355838200000637}, abstract = {A dynamic structural rearrangement in the phylogenetically conserved helix 27 of Escherichia coli 16S rRNA has been proposed to directly affect the accuracy of translational decoding by switching between “accurate” and “error-prone” conformations. To examine the function of helix 27 in eukaryotes, random and site-specific mutations in helix 27 of the yeast Saccharomyces cerevisiae 18S rRNA have been characterized. Mutations at positions of yeast 18S rRNA corresponding to E. coli 886 (rdn8), 888 (rdn6), and 912 (rdn4) increased translational accuracy in vivo and in vitro, and caused a reduction in tRNA binding to the A-site of mutant ribosomes. The double rdn4rdn6 mutation separated the killing and stop-codon readthrough effects of the aminoglycoside antibiotic, paromomycin, implicating a direct involvement of yeast helix 27 in accurate recognition of codons by tRNA or release factor eRF1. Although our data in yeast does not support a conformational switch model analogous to that proposed for helix 27 of E. coli 16S rRNA, it strongly suggests a functional conservation of this region in tRNA selection}, keywords = {0,16S,A SITE,A-SITE,accuracy,Aldehydes,Anti-Bacterial Agents,antibiotic,AntibioticsAminoglycoside,antiviral,Antiviral Agents,Base Sequence,BINDING,Cell-Free System,CEREVISIAE,Codon,CODONS,CONFORMATION,decoding,Drug ResistanceMicrobial,E,Escherichia coli,ESCHERICHIA-COLI,Fidelity,genetics,In Vitro,IN-VITRO,IN-VIVO,La,metabolism,MODEL,Molecular Sequence Data,Mutagenesis,MutagenesisSite-Directed,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Paromomycin,pharmacology,Phenotype,physiology,Plasmids,Poly U,POSITION,POSITIONS,Protein Biosynthesis,readthrough,RECOGNITION,REGION,RELEASE,release factor,ribosome,Ribosomes,Rna,RNAFungal,RNARibosomal18S,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SELECTION,site specific,STOP CODON,Structural,Support,Temperature,TranslationGenetic,tRNA,tRNA binding,yeast} } % == BibTeX quality report for velichutinaMutationsHelix272000: % ? Possibly abbreviated journal title RNA.

@article{vemulaMaintenanceRegulationMRNA2003, title = {Maintenance and Regulation of {{mRNA}} Stability of the {{Saccharomyces}} Cerevisiae {{OLE1}} Gene Requires Multiple Elements within the Transcript That Act through Translation-Independent Mechanisms}, author = {Vemula, M. and Kandasamy, P. and Oh, C.S. and Chellappa, R. and Gonzalez, C.I. and Martin, C.E.}, year = 2003, month = nov, journal = {Journal of Biological Chemistry}, volume = {278}, number = {46}, pages = {45269–45279}, publisher = {ASBMB}, doi = {10.1074/jbc.M308812200}, url = {http://www.jbc.org/content/278/46/45269.short}, abstract = {The Saccharomyces cerevisiae OLE1 gene encodes a membrane-bound Delta-9 fatty acid desaturase, whose expression is regulated by unsaturated fatty acids through both transcriptional and mRNA stability controls. In fatty acid-free medium, the mRNA has a half-life of 10 +/- 1.5 min (basal stability) that drops to 2 +/- 1.5 min when cells are exposed to unsaturated fatty acids (regulated stability). A deletion analysis of elements within the transcript revealed that the sequences within the protein-coding region that encode transmembrane sequences and a part of the cytochrome b5 domain are essential for the basal stability of the transcript. Deletion of any of the three essential elements produced unstable transcripts and loss of regulated instability. By contrast, substitution of the 3’-untranslated region with that of the stable PGK1 gene did not affect the basal stability of the transcript and did not block regulated decay. Given that Ole1p is a membrane-bound protein whose activities are a major determinant of membrane fluidity, we asked whether membrane-associated translation of the protein was essential for basal and regulated stability. Insertion of stop codons within the transcript that blocked either translation of the entire protein or parts of the protein required for co-translation insertion of Ole1p had no effect. We conclude that the basal and regulated stability of the OLE1 transcript is resistant to the nonsense-mediated decay pathway and that the essential protein-encoding elements for basal stability act cooperatively as stabilizing sequences through RNA-protein interactions via a translation-independent mechanism}, keywords = {0,3,3’ UNTRANSLATED REGION,3’ Untranslated Regions,3’-UNTRANSLATED REGION,ACID,ACIDS,analysis,BIOLOGY,CELLS,CEREVISIAE,chemistry,Codon,CODONS,CodonTerminator,Cytochromes b5,DECAY,DECAY PATHWAY,Dna,DOMAIN,ELEMENTS,ENCODES,expression,Fatty Acid Desaturases,gene,Gene Deletion,genetics,GREEN FLUORESCENT PROTEIN,Half-Life,Kinetics,La,Luminescent Proteins,MECHANISM,MECHANISMS,media,metabolism,ModelsGenetic,mRNA,mRNA stability,nonsense-mediated decay,nosource,PATHWAY,physiology,PLASMID,Plasmids,protein,Protein Binding,Protein StructureTertiary,PROTEIN-CODING REGION,Proteins,REGION,regulation,REQUIRES,RESISTANT,Rna,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,stability,STOP CODON,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Time Factors,TRANSCRIPT,TranscriptionGenetic,translation,TranslationGenetic,Untranslated Regions} } % == BibTeX quality report for vemulaMaintenanceRegulationMRNA2003: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{venemaDevelopmentApplicationVivo1995, title = {Development and Application of an in Vivo System to Study Yeast Ribosomal {{RNA}} Biogenesis and Function}, author = {Venema, J. and {Dirks-Mulder}, A. and Faber, A.W. and Raue, H.A.}, year = 1995, month = feb, journal = {Yeast.}, volume = {11}, number = {2}, pages = {145–156}, publisher = {Wiley Online Library}, doi = {10.1002/yea.320110206}, url = {http://onlinelibrary.wiley.com/doi/10.1002/yea.320110206/abstract}, abstract = {We have developed a system for mutational analysis of Saccharomyces cerevisiae ribosomal RNA in vivo in which yeast cells can be made completely dependent on mutant rRNA and ribosomes by a simple switch in carbon source. The system is based on a yeast strain defective in RNA polymerase I (Pol I) transcription [Nogi et al. (1991) Proc. Natl. Acad. Sci. USA 88, 3962-3966]. This normally inviable strain was rescued by integration of multiple copies of the complete 37S pre-rRNA operon under control of the inducible, Pol II-transcribed GAL7 promoter into the rDNA repeat on chromosome XII. The resulting YJV100 strain can only grow on medium containing galactose as the carbon source. A second, episomal vector was constructed in which the rDNA unit was placed under control of the constitutive PGK1 promoter. YJV100 cells transformed with this vector are now also able to grow on glucose-based medium making the cells completely dependent on plasmid-encoded rRNA. We show that the Pol II-transcribed pre-rRNA is processed and assembled similarly to authentic Pol I-synthesised pre-rRNA, making this ‘in vivo Pol II system’ suitable for the detailed analysis of rRNA mutations, even highly deleterious ones, affecting ribosome biogenesis or function. A clear demonstration of this is our finding that an insertion into variable region V8 in 17S rRNA, previously judged to be neutral with respect to processing of 17S rRNA, its assembly into 40S subunits and the polysomal distribution of these subunits [Musters et al. (1989), Mol. Cell. Biol. 9, 551-559], is in fact a lethal mutation}, keywords = {95250372,analysis,assembly,Base Sequence,biosynthesis,Carbon,carbon source,development,genetics,IN-VIVO,media,metabolism,Molecular Sequence Data,Mutation,MUTATIONAL ANALYSIS,MUTATIONS,nosource,Operon,pol,polymerase,PROMOTER,RDN1,rDNA,RIBOSOMAL-RNA,ribosome,ribosome biogenesis,Ribosomes,Rna,RNA Polymerase I,RNA Precursors,RNAFungal,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SUBUNIT,supportnon-u.s.gov’t,SYSTEM,transcription,TransformationGenetic,vector,yeast} } % == BibTeX quality report for venemaDevelopmentApplicationVivo1995: % ? Possibly abbreviated journal title Yeast.

@article{venemaRibosomeSynthesisSaccharomyces1999, title = {Ribosome Synthesis in {{Saccharomyces}} Cerevisiae}, author = {Venema, J. and Tollervey, D.}, year = 1999, journal = {Annual review of genetics}, volume = {33}, number = {1}, pages = {261–311}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, doi = {10.1146/annurev.genet.33.1.261}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.genet.33.1.261}, abstract = {The synthesis of ribosomes is one of the major metabolic pathways in all cells. In addition to around 75 individual ribosomal proteins and 4 ribosomal RNAs, synthesis of a functional eukaryotic ribosome requires a remarkable number of trans-acting factors. Here, we will discuss the recent, and often surprising, advances in our understanding of ribosome synthesis in the yeast Saccharomyces cerevisiae. These will underscore the unexpected complexity of eukaryotic ribosome synthesis}, keywords = {0,Fungal Proteins,genetics,La,metabolism,nosource,physiology,protein,Proteins,Review,Ribosomal Proteins,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNAFungal,RNARibosomal,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportnon-u.s.gov’t,yeast} } % == BibTeX quality report for venemaRibosomeSynthesisSaccharomyces1999: % ? unused Journal abbr (“Annu.Rev.Genet.”)

@article{vermutSequenceMKT1Needed1994, title = {Sequence of ⬚{{MKT1}},⬚ Needed for Propagation of {{M}}⬚2⬚ {{Satellite dsRNA}} of the {{L-A}} Virus of ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Vermut, M. and Widner, W. and Dinman, J.D. and Wickner, R.B.}, year = 1994, journal = {Yeast}, volume = {10}, pages = {1477–1479}, doi = {10.1002/yea.320101111}, keywords = {CV,L-A,La,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,virus} }

@article{verschoorThreedimensionalStructureYeast1998, title = {Three-Dimensional Structure of the Yeast Ribosome}, author = {Verschoor, A. and Warner, J.R. and Srivastava, S. and Grassucci, R.A. and Frank, J.}, year = 1998, month = jan, journal = {Nucleic acids research}, volume = {26}, number = {2}, pages = {655–661}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/26.2.655}, url = {http://nar.oxfordjournals.org/content/26/2/655.short}, abstract = {The 80S ribosome from Saccharomyces cerevisiae has been reconstructed from cryo electron micrographs to a resolution of 35 A. It is strikingly similar to the 70S ribosome from Escherichia coli, while displaying the characteristic eukaryotic features familiar from reconstructions of ribosomes from higher eukaryotes. Aside from the elaboration of a number of peripherally located features on the two subunits and greater overall size, the largest difference between the yeast and E.coli ribosomes is in a mass increase on one side of the large (60S) subunit. It thus appears more elliptical than the characteristically globular 50S subunit from E.coli. The interior of the 60S subunit reveals a variable diameter tunnel spanning the subunit between the interface canyon and a site on the lower back of the subunit, presumably the exit site through which the nascent polypeptide chain emerges from the ribosome}, keywords = {60S subunit,98083203,A-SITE,Comparative Study,E.coli,Escherichia coli,ESCHERICHIA-COLI,Image ProcessingComputer-Assisted,MicroscopyElectron,nosource,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,structure,SUBUNIT,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,ultrastructure,yeast} } % == BibTeX quality report for verschoorThreedimensionalStructureYeast1998: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{vershonMeioticInductionYeast1992, title = {Meiotic Induction of the Yeast {{HOP1}} Gene Is Controlled by Positive and Negative Regulatory Sites.}, author = {Vershon, A.K. and Hollingsworth, N.M. and Johnson, A.D.}, year = 1992, journal = {Molecular and cellular biology}, volume = {12}, number = {9}, pages = {3706–3714}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/12/9/3706}, abstract = {The process of meiosis and sporulation in the yeast Saccharomyces cerevisiae is a highly regulated developmental pathway dependent on genetic as well as nutritional signals. The HOP1 gene, which encodes a component of meiotic chromosomes, is not expressed in mitotically growing cells, but its transcription is induced shortly after yeast cells enter the meiotic pathway. Through a series of deletions and mutations in the HOP1 promoter, we located two regulatory sites that are essential for proper regulation of HOP1. One site, called URS1H, brings about repression of HOP1 in mitotic cells and functions as an activator sequence in cells undergoing meiosis. The second site, which we designated UASH, acts as an activator sequence in meiotic cells and has similarity to the binding site of the mammalian CCAAT/enhancer binding protein (C/EBP). Both sites are required for full meiotic induction of the HOP1 promoter. We conclude that in mitotic yeast cells, the URS1H site maintains the repressed state of the HOP1 promoter, masking the effect of the UASH site. Upon entry into meiosis, repression is lifted, allowing the URS1H and UASH sites to activate high-level transcription}, keywords = {Base Sequence,BINDING,BINDING PROTEIN,BINDING-PROTEIN,Chromosomes,COMPONENT,DNAFungal,gene,Gene Expression RegulationFungal,Genetic,Genetic Complementation Test,genetics,immunology,Meiosis,microbiology,Molecular Sequence Data,Multiple DOI,Mutation,MUTATIONS,nonfile,nosource,PROMOTER,Promoter Regions (Genetics),protein,regulation,Regulatory SequencesNucleic Acid,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SIGNAL,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,transcription,yeast} } % == BibTeX quality report for vershonMeioticInductionYeast1992: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{vialatGermistonVirusTranscriptase1992, title = {Germiston Virus Transcriptase Requires Active {{40S}} Ribosomal Subunits and Utilizes Capped Cellular {{RNAs}}.}, author = {Vialat, P. and Bouloy, M.}, year = 1992, month = feb, journal = {Journal of Virology}, volume = {66}, number = {2}, pages = {685–693}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.66.2.685-693.1992}, url = {http://jvi.asm.org/cgi/content/abstract/66/2/685}, abstract = {The transcriptase associated with Germiston virus was assayed in an in vitro reaction in which transcription was coupled to translation by adding reticulocyte lysate under the appropriate salt conditions. When analyzed in polyacrylamide gels, the major transcripts migrated like authentic S mRNAs and possessed 12- to 18-base-long nontemplated 5’ extensions similar to the 5’ end of viral mRNAs. These transcripts were functional for the synthesis of at least proteins N and NS(S). When translation was inhibited by adding protein synthesis inhibitors such as puromycin, cycloheximide, and anisomycin, a drastic inhibitory effect was observed on the synthesis of the complete S mRNA transcripts. However, initiation and part of the elongation process were still active, since short and incomplete RNA molecules with RNA primers at their 5’ ends were synthesized. On the other hand, we found that edeine, another inhibitor of protein synthesis, stimulated not only synthesis of S mRNAs but also that of the full-length S cRNAs. Taking into account the mode of action of this antibiotic, we discuss the results, which emphasize the crucial role of active ribosomes during bunyavirus transcription and confirm the observations reported on La Crosse virions. Moreover, we showed that the RNA transcripts synthesized in a transcription-translation reaction were capped and that most of them have acquired the 5’ terminal sequences of the alpha- or beta-globin mRNA}, keywords = {anisomycin,antibiotic,BUNYAMWERA VIRUS,COMPLEMENTARY RNA,Cycloheximide,Edeine,elongation,Gels,GENE-PRODUCT,GLOBIN MESSENGER-RNA,HARE BUNYAVIRUS S,In Vitro,IN-VITRO,INFECTED CELLS,INHIBITOR,initiation,La,lysate,M-SEGMENT,mRNA,nosource,NUCLEOTIDE-SEQUENCE,protein,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,Proteins,Puromycin,RABBIT ALPHA,REQUIRES,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,S,sequence,SEQUENCES,TRANSCRIPT,transcription,translation,TRANSLATIONAL REQUIREMENT,Virion,VIRIONS,virus} }

@article{vicensCrystalStructureParomomycin2001, title = {Crystal Structure of Paromomycin Docked into the Eubacterial Ribosomal Decoding {{A}} Site}, author = {Vicens, Q. and Westhof, E.}, year = 2001, journal = {Structure.(Camb.)}, volume = {9}, number = {8}, pages = {647–658}, publisher = {Elsevier}, doi = {10.1016/S0969-2126(01)00629-3}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0969212601006293}, abstract = {BACKGROUND: Aminoglycoside antibiotics interfere with translation in both gram-positive and gram-negative bacteria by binding to the tRNA decoding A site of the 16S ribosomal RNA. RESULTS: Crystals of complexes between oligoribonucleotides incorporating the sequence of the ribosomal A site of Escherichia coli and the aminoglycoside paromomycin have been solved at 2.5 A resolution. Each RNA fragment contains two A sites inserted between Watson-Crick pairs. The paromomycin molecules interact in an enlarged deep groove created by two bulging and one unpaired adenines. In both sites, hydroxyl and ammonium side chains of the antibiotic form 13 direct hydrogen bonds to bases and backbone atoms of the A site. In the best-defined site, 8 water molecules mediate 12 other hydrogen bonds between the RNA and the antibiotics. Ring I of paromomycin stacks over base G1491 and forms pseudo-Watson-Crick contacts with A1408. Both the hydroxyl group and one ammonium group of ring II form direct and water-mediated hydrogen bonds to the U1495oU1406 pair. The bulging conformation of the two adenines A1492 and A1493 is stabilized by hydrogen bonds between phosphate oxygens and atoms of rings I and II. The hydrophilic sites of the bulging A1492 and A1493 contact the shallow groove of G=C pairs in a symmetrical complex. CONCLUSIONS: Water molecules participate in the binding specificity by exploiting the antibiotic hydration shell and the typical RNA water hydration patterns. The observed contacts rationalize the protection, mutation, and resistance data. The crystal packing mimics the intermolecular contacts induced by aminoglycoside binding in the ribosome}, keywords = {0,A-SITE,Adenine,Amino Acid Motifs,antibiotic,antibiotics,AntibioticsAminoglycoside,Bacteria,Base Sequence,BINDING,Binding Sites,chemistry,COMPLEX,COMPLEXES,CRYSTAL-STRUCTURE,CrystallographyX-Ray,decoding,Escherichia coli,ESCHERICHIA-COLI,La,Magnetic Resonance Spectroscopy,metabolism,ModelsMolecular,Molecular Sequence Data,Mutation,nosource,Oligoribonucleotides,Paromomycin,Protein StructureSecondary,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNARibosomal16S,sequence,SpectrometryMassMatrix-Assisted Laser Desorption-Ionization,structure,supportnon-u.s.gov’t,Tobramycin,translation,tRNA,Water} } % == BibTeX quality report for vicensCrystalStructureParomomycin2001: % ? Possibly abbreviated journal title Structure.(Camb.)

@article{vickersEnhancementRibosomalFrameshifting1992a, title = {Enhancement of Ribosomal Frameshifting by Oligonucleotides Targeted to the {{HIV}} Gag-Pol Region}, author = {Vickers, T.A. and Ecker, D.J.}, year = 1992, month = aug, journal = {Nucleic Acids Research}, volume = {20}, number = {15}, pages = {3945–3953}, doi = {10.1093/nar/20.15.3945}, keywords = {antisense,efficiency,enzyme,frameshift,Frameshifting,Gag,Gag-pol,gene,Genes,HIV,Hiv-1,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,In Vitro,in vitro translation,IN-VITRO,luciferase,nosource,Nucleotides,Oligonucleotides,pol,protein,regulation,ribosomal frameshifting,Rna,SECONDARY STRUCTURE,sequence,SEQUENCES,structure,translation,UPSTREAM,virus} }

@article{vidalRPD3EncodesSecond1991, title = {{{RPD3}} Encodes a Second Factor Required to Achieve Maximum Positive and Negative Transcriptional States in {{Saccharomyces}} Cerevisiae.}, author = {Vidal, M. and Gaber, R.F.}, year = 1991, month = dec, journal = {Molecular and cellular biology}, volume = {11}, number = {12}, pages = {6317–6327}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/11/12/6317}, abstract = {In Saccharomyces cerevisiae, TRK1 and TRK2 encode the high- and low- affinity K+ transporters, respectively. In cells containing a deletion of TRK1, transcription levels of TRK2 are extremely low and are limiting for growth in media containing low levels of K+ (Trk- phenotype). Recessive mutations in RPD1 and RPD3 suppress the TRK2, conferring an approximately fourfold increase in transcription. rpd3 mutations confer pleiotropic phenotypes, including (i) mating defects, (ii) hypersensitivity to cycloheximide, (iii) inability to sporulate as homozygous diploids, and (iv) constitutive derepression of acid phosphatase. RPD3 was cloned and is predicted to encode a 48-kDa protein with no extensive similarity to proteins contained in current data bases. Deletion of RPD3 is not lethal but confers phenotypes identical to those caused by spontaneous mutations. RPD3 is required for both full repression and full activation of transcription of target genes including PHO5, STE6, and TY2. RPD3 is the second gene required for this function, since RPD1 is also required. The effects of mutations in RPD1 and RPD3 are not additive, suggesting that these genes are involved in the same transcriptional regulatory function or pathway}, keywords = {92049362,activation,Amino Acid Sequence,Base Sequence,BlottingSouthern,Carrier Proteins,CrossesGenetic,Cycloheximide,Diploidy,DNAFungal,Fungal Proteins,gene,Gene Expression RegulationFungal,Genes,genetics,media,metabolism,Molecular Sequence Data,Multiple DOI,Mutation,MUTATIONS,nonfile,nosource,Phenotype,Potassium,protein,Proteins,Repressor Proteins,Restriction Mapping,RPD3,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,transcription,Transcription Factors,TranscriptionGenetic} } % == BibTeX quality report for vidalRPD3EncodesSecond1991: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{vijayraghavanIsolationCharacterizationPremRNA1989a, title = {Isolation and Characterization of Pre-{{mRNA}} Splicing Mutants of ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Vijayraghavan, U. and Company, M. and Abelson, J.}, year = 1989, journal = {Genes & Dev.}, volume = {3}, pages = {1206–1216}, doi = {10.1101/gad.3.8.1206}, keywords = {mof5,mRNA,nosource,prp17,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,splicing} } % == BibTeX quality report for vijayraghavanIsolationCharacterizationPremRNA1989a: % ? Possibly abbreviated journal title Genes & Dev.

@article{vila-sanjurjoMutationalAnalysisConserved2001a, title = {Mutational Analysis of the Conserved Bases {{C1402}} and {{A1500}} in the Center of the Decoding Domain of {{Escherichia}} Coli 16 {{S rRNA}} Reveals an Important Tertiary Interaction}, author = {{Vila-Sanjurjo}, A. and Dahlberg, A.E.}, year = 2001, month = may, journal = {Journal of Molecular Biology}, volume = {308}, number = {3}, pages = {457–463}, doi = {10.1006/jmbi.2001.4576}, url = {ISI:000168655500002}, abstract = {Interactions within the decoding center of the 30 S ribosomal subunit have been investigated by constructing all 15 possible mutations at nucleotides C1402 and A1500 in helix 44 of 16 S rRNA. As expected, most of the mutations resulted in highly deleterious phenotypes, consistent with the high degree of conservation of this region and its functional importance. A total of seven mutants were viable under conditions where the mutant ribosomes comprised 100 % of the ribosomal pool. A suppressor mutation specific for the C1402U-A1500G mutant was isolated at position 1520 in helix 45 of 16 S rRNA. In addition, lack of dimethylation of A1518/A1519 caused by mutation of the ksgA methylase enhanced the deleterious effect of many of the 1402/1500 mutations. These data suggest that a higher-order interaction between helices 44 and 45 in 16 S rRNA is important for the proper functioning of the ribosome. This is consistent with the recent high-resolution crystal structures of the 30 S subunit, which show a tertiary interaction between the 1402/1500 region of helix 44 and the dimethyl A stem loop. (C) 2001 Academic Press}, keywords = {16S-RIBOSOMAL RNA,30 S,30S RIBOSOMAL-SUBUNIT,analysis,BASES,crystal structure,CRYSTAL-STRUCTURE,decoding,DIRECTED CROSS-LINKING,Escherichia coli,ESCHERICHIA-COLI,IDENTIFICATION,kasugamycin resistance,LOOP,MESSENGER-RNA,MUTANTS,Mutation,MUTATIONAL ANALYSIS,MUTATIONS,nosource,Nucleotides,P-SITE,Phenotype,posttranscriptional modification,REGION,ribosomal RNA mutations,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,RNA-RNA interactions,rRNA,structure,SUBUNIT,translation} }

@article{vila-sanjurjoXrayCrystalStructures2003, title = {X-Ray Crystal Structures of the {{WT}} and a Hyper-Accurate Ribosome from {{Escherichia}} Coli}, author = {{Vila-Sanjurjo}, A. and Ridgeway, W.K. and Seymaner, V. and Zhang, W. and Santoso, S. and Yu, K. and Cate, J.H.}, year = 2003, month = jul, journal = {Proceedings of the National Academy of Sciences}, volume = {100}, number = {15}, pages = {8682–8687}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.1133380100}, url = {http://www.pnas.org/content/100/15/8682.short}, abstract = {Protein biosynthesis on the ribosome requires accurate reading of the genetic code in mRNA. Two conformational rearrangements in the small ribosomal subunit, a closing of the head and body around the incoming tRNA and an RNA helical switch near the mRNA decoding site, have been proposed to select for complementary base-pairing between mRNA codons and tRNA anticodons. We determined x-ray crystal structures of the WT and a hyper-accurate variant of the Escherichia coli ribosome at resolutions of 10 and 9 A, respectively, revealing that formation of the intact 70S ribosome from its two subunits closes the conformation of the head of the small subunit independent of mRNA decoding. Moreover, no change in the conformation of the switch helix is observed in two steps of tRNA discrimination. These 70S ribosome structures indicate that mRNA decoding is coupled primarily to movement of the small subunit body, consistent with previous proposals, whereas closing of the head and the helical switch may function in other steps of protein synthesis}, keywords = {70S RIBOSOME,Anticodon,Base Pairing,BIOLOGY,biosynthesis,BODIES,Codon,CODONS,CONFORMATION,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,decoding,Escherichia coli,ESCHERICHIA-COLI,Genetic,Genetic Code,GENETIC-CODE,La,Movement,mRNA,nosource,protein,protein synthesis,PROTEIN-BIOSYNTHESIS,PROTEIN-SYNTHESIS,REQUIRES,RESOLUTION,RIBOSOMAL-SUBUNIT,ribosome,Rna,SITE,structure,SUBUNIT,SUBUNITS,tRNA} } % == BibTeX quality report for vila-sanjurjoXrayCrystalStructures2003: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{vilardellRegulationSplicingIntermediate1994, title = {Regulation of Splicing at an Intermediate Step in the Formation of the Spliceosome.}, author = {Vilardell, J. and Warner, J.R.}, year = 1994, month = jan, journal = {Genes & development}, volume = {8}, number = {2}, pages = {211–220}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.8.2.211}, url = {http://genesdev.cshlp.org/content/8/2/211.short}, abstract = {In vivo experiments have demonstrated that the ribosomal protein L32 of Saccharomyces cerevisiae brings about the inhibition of splicing of the transcript of its own gene through an RNA structure comprised largely of the first exon. We now show that L32, itself, binds specifically to this RNA. Splicing of the RPL32 transcript in vitro is blocked by the presence of L32. Furthermore, addition of the 75-nucleotide RNA representing the 5’ end of the RPL32 transcript stimulates specifically the splicing of the RPL32 substrate, presumably by competing for L32 present in the extract. Use of RNAs carrying mutations shown to abolish the regulation of splicing, either as substrates or as competitors, confirmed that the in vitro reaction is a faithful representation of the situation in vivo. We conclude that the regulation of splicing occurs through the specific binding of L32 to an RNA structure within the first 75 nucleotides of the RPL32 transcript. The RPL32 substrate, bound to L32, forms a complex with U1 snRNP, the first step in spliceosome assembly. The presence of L32 prevents the ATP-dependent association of the U2 snRNP necessary to form a complete spliceosome}, keywords = {94131274,assembly,Base Sequence,BINDING,Binding Sites,COMPLEX,COMPLEXES,gene,genetics,In Vitro,IN-VITRO,IN-VIVO,INHIBITION,metabolism,Molecular Sequence Data,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Nucleotides,protein,Recombinant Fusion Proteins,regulation,RibonucleoproteinU1 Small Nuclear,Ribosomal Proteins,Rna,RNA Splicing,RNAFungal,RNAMessenger,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Spliceosomes,splicing,structure,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for vilardellRegulationSplicingIntermediate1994: % ? unused Journal abbr (“Genes Dev.”)

@article{vimaladithanSpecialPeptidylTransferRNAMolecules1994, title = {Special {{Peptidyl-Transfer-RNA Molecules Can Promote Translational Frameshifting Without Slippage}}}, author = {Vimaladithan, A. and Farabaugh, P.J.}, year = 1994, month = dec, journal = {Molecular and Cellular Biology}, volume = {14}, number = {12}, pages = {8107–8116}, url = {ISI:A1994PV67400040}, abstract = {Recently we described an unusual programmed +1 frameshift event in yeast retrotransposon Ty3. Frameshifting depends on the presence of peptidyl-tRNA(CGC)(Ala) on the GCG codon in the ribosomal P site and on a translational pause stimulated by the slowly decoded AGU codon. Frameshifting occurs on the sequence GCG-AGU-U by out-of-frame binding of a valyl-tRNA to GUU without slippage of peptidyl-tRNA(CGC)(Ala). This mechanism challenges the conventional understanding that frameshift efficiency must correlate with the ability of mRNA-bound tRNA to slip between cognate or near-cognate codons. Though frameshifting does not require slippery tRNAs, it does require special peptidyl-tRNAs. We show that overproducing second isoacceptor whose anticodon had been changed to CGC eliminated frameshifting; peptidyl-tRNA(CGC)(Ala) must have a special capacity to induce +1 frameshifting in the adjacent ribosomal A site. In order to identify other special peptidyl-tRNAs, we tested the ability of each of the other 63 codons to replace GCG in the P site. We found no correlation between the ability to stimulate +1 frameshifting and the ability of the cognate tRNA to slip on the mRNA-several codons predicted to slip efficiently do not stimulate frameshifting, while several predicted not to slip do stimulate frameshifting. By inducing a severe translational pause, we identified eight tRNAs capable of inducing measurable +1 frameshifting, only four of which are predicted to slip on the mRNA. We conclude that in Saccharomyces cerevisiae, special peptidyl-tRNAs can induce frameshifting dependent on some characteristic(s) other than the ability to slip on the mRNA}, keywords = {+1 frameshifting,A SITE,A-SITE,Anticodon,BINDING,Codon,CODONS,efficiency,ELONGATION-FACTOR-TU,ESCHERICHIA-COLI,frameshift,Frameshifting,GENE-EXPRESSION,IDENTIFY,MECHANISM,mRNA,Multiple DOI,nonfile,nosource,P SITE,P-SITE,PEPTIDYL-TRANSFER-RNA,PROTEIN-SYNTHESIS,RELEASE FACTOR-II,retrotransposon,RIBOSOMAL FRAMESHIFT,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SITE,SLIPPAGE,TRANSFER-RNA BINDING,TRANSLATIONAL FRAMESHIFTING,tRNA,TY3,yeast} } % == BibTeX quality report for vimaladithanSpecialPeptidylTransferRNAMolecules1994: % ? Title looks like it was stored in title-case in Zotero

@article{vitreschakRiboswitchesOldestMechanism2004, title = {Riboswitches: The Oldest Mechanism for the Regulation of Gene Expression?}, author = {Vitreschak, A.G. and Rodionov, D.A. and Mironov, A.A. and Gelfand, M.S.}, year = 2004, month = jan, journal = {TRENDS in Genetics}, volume = {20}, number = {1}, pages = {44–50}, publisher = {Elsevier}, doi = {10.1016/j.tig.2003.11.008}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0168952503003238}, abstract = {Riboswitches are structures that form in mRNA and regulate gene expression in bacteria. Unlike other known RNA regulatory structures, they are directly bound by small ligands. The mechanism by which gene expression is regulated involves the formation of alternative structures that, in the repressing conformation, cause premature termination of transcription or inhibition of translation initiation. Riboswitches regulate several metabolic pathways including the biosynthesis of vitamins (e.g. riboflavin, thiamin and cobalamin) and the metabolism of methionine, lysine and purines. Candidate riboswitches have also been observed in archaea and eukaryotes. The taxonomic diversity of genomes containing riboswitches and the diversity of molecular mechanisms of regulation, in addition to the fact that direct interaction of riboswitches with their effectors does not require additional factors, suggest that riboswitches represent one of the oldest regulatory systems}, keywords = {0,Archaea,Bacillus subtilis,Bacteria,Bacterial,biosynthesis,chemistry,CONFORMATION,DIVERSITY,EvolutionMolecular,expression,FORM,gene,Gene Expression,Gene Expression RegulationBacterial,GENE-EXPRESSION,genetics,Genome,INHIBITION,initiation,La,Ligands,Lysine,MECHANISM,MECHANISMS,metabolism,Methionine,ModelsMolecular,MOLECULAR MECHANISMS,mRNA,nosource,Nucleic Acid Conformation,PATHWAY,Purines,ras,regulation,Review,Rna,RNABacterial,RNAMessenger,structure,SYSTEM,SYSTEMS,termination,transcription,translation,TRANSLATION INITIATION,transmission} } % == BibTeX quality report for vitreschakRiboswitchesOldestMechanism2004: % ? unused Journal abbr (“Trends Genet.”)

@article{vogelPossibleInvolvementPeptidyl1969a, title = {The Possible Involvement of Peptidyl Transferase in the Termination Step of Protein Biosynthesis.}, author = {Vogel, Z. and Zamir, A. and Elson, D.}, year = 1969, journal = {Biochemistry}, volume = {8}, number = {12}, pages = {5161–5168}, doi = {10.1021/bi00840a070}, keywords = {anisomycin,biosynthesis,nosource,peptidyl transferase,PEPTIDYL-TRANSFERASE,protein,sparsomycin,termination,translation} }

@article{vogeleHighLevelRibosomalFrameshifting1991, title = {High-{{Level Ribosomal Frameshifting Directs}} the {{Synthesis}} of {{Is150 Gene-Products}}}, author = {Vogele, K. and Schwartz, E. and Welz, C. and Schiltz, E. and Rak, B.}, year = 1991, journal = {Nucleic Acids Research}, volume = {19}, number = {16}, pages = {4377–4385}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/19.16.4377}, url = {ISI:A1991GD89300007 http://nar.oxfordjournals.org/content/19/16/4377.short}, abstract = {IS150 contains two tandem, out-of-phase, overlapping genes, ins150A and ins150B, which are controlled by the same promoter. These genes encode proteins of 19 and 31 kD, respectively. A third protein of 49kD is a transframe gene product consisting of domains encoded by both genes. Specific -1 ribosomal frameshifting is responsible for the synthesis of the large protein. Expression of ins150B also involves frameshifting. The IS150 frameshifting signals operate with a remarkably high efficiency, causing about one third of the ribosomes to switch frame. All of the signals required for this process are encoded in a 83-bp segment of the element. The heptanucleotide A AAA AAG and a potential stem-loop-forming sequence mark the frameshifting site. Similar sequence elements are found in -1 frameshifting regions of bacterial and retroviral genes. A mutation within the stem-loop sequence reduces the rate of frameshifting by about 80%. Artificial transposons carrying this mutation transpose at a normal frequency, but form cointegrates at a almost-equal-to 100-fold reduced rate}, keywords = {Bacterial,CLONING VEHICLES,DOMAIN,DOMAINS,efficiency,ELEMENTS,ESCHERICHIA-COLI,expression,FORM,FRAME,Frameshifting,GAMMA-SUBUNIT,gene,Genes,INSERTION ELEMENT,IS3 FAMILY,Mutation,nosource,POLYMERASE-III HOLOENZYME,PROMOTER,protein,Proteins,REGION,ribosomal frameshifting,ribosome,Ribosomes,RNA-POLYMERASE,sequence,SIGNAL,SITE,SITE-SPECIFIC MUTAGENESIS,STEM-LOOP,TURN-ON} } % == BibTeX quality report for vogeleHighLevelRibosomalFrameshifting1991: % ? Title looks like it was stored in title-case in Zotero

@article{vonahsenFootprintingSitesInteraction1993, title = {Footprinting the Sites of Interaction of Antibiotics with Catalytic Group {{I}} Intron {{RNA}}.}, author = {Von Ahsen, U. and Noller, H.F.}, year = 1993, journal = {Science}, volume = {260}, number = {5113}, pages = {1500–1503}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.8502993}, url = {http://www.sciencemag.org/content/260/5113/1500.short}, keywords = {antibiotic,antibiotics,nosource,Rna} }

@article{vonahsenIdentificationBases16S1995, title = {Identification of Bases in {{16S rRNA}} Essential for {{tRNA}} Binding at the {{30S}} Ribosomal {{P}} Site}, author = {Von Ahsen, U. and Noller, H.F.}, year = 1995, journal = {Science}, volume = {267}, number = {5195}, pages = {234–237}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.7528943}, url = {http://www.sciencemag.org/content/267/5195/234.short}, keywords = {BINDING,ELEMENTS,IDENTIFICATION,MESSENGER-RNA,nosource,Open Reading Frames,P-SITE,ribosome,Ribosomes,Rna,rRNA,SUBUNIT,translation,tRNA} }

@article{vonderhaarPurificationAminoacyltRNASynthetases1979, title = {Purification of Aminoacyl-{{tRNA}} Synthetases}, author = {{Von der Haar}, F}, year = 1979, journal = {Methods in Enzymology}, volume = {59⬚ ⬚}, pages = {257–267}, doi = {10.1016/0076-6879(79)59088-0}, keywords = {AMINOACYL-TRANSFER RNA,nosource,purification} }

@article{vonderAffinityElutionPrinciples1974, title = {Affinity Elution: Principles and Applications to Purification of Aminoacyl-{{tRNA}} Synthetases}, author = {{}{von der}, Haar F.}, year = 1974, journal = {Methods Enzymol.}, volume = {34}, pages = {163–171}, doi = {10.1016/S0076-6879(74)34014-1}, url = {PM:4449447}, keywords = {0,ACID,ACIDS,Amino Acids,Amino Acyl-tRNA Synthetases,AMINO-ACID,AMINO-ACIDS,Cellulose,ChromatographyAffinity,ChromatographyDEAE-Cellulose,isolation & purification,Kinetics,La,Ligands,nosource,Phenylalanine,purification} } % == BibTeX quality report for vonderAffinityElutionPrinciples1974: % ? Possibly abbreviated journal title Methods Enzymol.

@article{voorn-boruwerSequencePAS8Gene1993a, title = {Sequence of the ⬚{{PAS8}}⬚ Gene, the Product of Which Is Essential for Biogenesis of Peroxisomes in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {{Voorn-Boruwer}, T. and {}{van der Leij}, I. and Hemrika, W. and Distel, B. and Tabak, H.F.}, year = 1993, journal = {Biochim.Biophys.Acta.}, volume = {1216}, pages = {325–328}, doi = {10.1016/0167-4781(93)90166-B}, keywords = {gene,MOF6,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence} } % == BibTeX quality report for voorn-boruwerSequencePAS8Gene1993a: % ? Possibly abbreviated journal title Biochim.Biophys.Acta.

@article{vulliamyDyskeratosisCongenita2006, title = {Dyskeratosis Congenita}, author = {Vulliamy, T. and Dokal, I.}, year = 2006, month = jul, journal = {Semin.Hematol.}, volume = {43}, number = {3}, pages = {157–166}, doi = {10.1053/j.seminhematol.2006.04.001}, url = {PM:16822458}, abstract = {Dyskeratosis congenita (DC) is a rare inherited multi-system disorder. Although DC is classically characterized by mucocutaneous features, the vast majority of patients develop hematologic abnormalities, and in its occult form the disease can present as aplastic anemia. The gene responsible for the X-linked form of the disease encodes a protein involved in ribosome biogenesis and in stabilizing the telomerase complex, while the autosomal dominant form is caused by mutations in the core RNA component of telomerase. It has been suggested that DC is primarily a disease of defective telomere maintenance. Premature shortening of telomeres resulting in a limited proliferative potential of stem cells would explain the pathology observed in DC, as the affected tissues are those that require constant renewal}, keywords = {Amino Acid Sequence,Anemia,AnemiaAplastic,BIOGENESIS,CELLS,COMPLEX,COMPLEXES,COMPONENT,disease,Dyskeratosis Congenita,ENCODES,enzymology,FORM,gene,genetics,Humans,La,Molecular Sequence Data,Mutation,MUTATIONS,nosource,pathology,protein,Review,ribosome,ribosome biogenesis,Rna,Stem Cells,Support,Telomerase,Telomere} } % == BibTeX quality report for vulliamyDyskeratosisCongenita2006: % ? Possibly abbreviated journal title Semin.Hematol.

@article{waasRoleTRNABase2007, title = {Role of a {{tRNA}} Base Modification and Its Precursors in Frameshifting in Eukaryotes}, author = {Waas, W.F. and Druzina, Z. and Hanan, M. and Schimmel, P.}, year = 2007, month = jul, journal = {Journal of Biological Chemistry}, volume = {282}, number = {36}, pages = {26026}, publisher = {ASBMB}, url = {http://www.jbc.org/content/282/36/26026.short}, abstract = {Little is known about the role of specific base modifications of transfer RNAs. Wyosine bases (Ybs) are tRNAPhe-specific modifications that are distinguished by differentiated, lateral side chains and base methylations appended to the core ring structure of a universally conserved G37, adjacent to the anticodon of Phe tRNAs. Based on previous data, we hypothesized that this modification was needed for -1 frameshifting. Using a reporter system incorporating a SCV-LA yeast virus slippery site for detecting -1 frameshifts in vivo, yeast strains were created that enabled chemical-genetic dissection of the role of different functional groups of wyebutosine (yW) that are added in a 3-step post-transcriptional set of reactions. With this system, hypomodification increased Phe-specific frameshifting, with incremental changes in frameshift efficiency following specific intermediates in the progression of yW synthesis. These data, combined with investigations of wild-type and hypomodified tRNA binding to ribosomes, suggest that frameshift efficiency is kinetically and not thermodynamically controlled. The progressive nature of frameshift efficiency with stage of modification is consistent with a step-wise evolution and tuning of frameshift potential. The stepwise tuning of frameshift efficiency could explain why tRNAPhe in some eukaryotes is not fully modified, but rather hypomodified to capture a specific frameshift potential}, keywords = {Anticodon,BASE,BASES,BINDING,BIOLOGY,efficiency,Evolution,frameshift,Frameshifting,IN-VIVO,INTERMEDIATE,La,Methylation,modification,Molecular Biology,No DOI found,nosource,PRECURSOR,ribosome,Ribosomes,Rna,SITE,slippery site,structure,SYSTEM,TRANSFER-RNA,tRNA,tRNA binding,virus,WILD-TYPE,yeast} } % == BibTeX quality report for waasRoleTRNABase2007: % ? unused Journal abbr (“J.Biol Chem.”)

@article{wagnerRateElongationPolyphenylalanine1982, title = {Rate of Elongation of Polyphenylalanine in Vitro}, author = {Wagner, E.G. and Jelenc, P.C. and Ehrenberg, M. and Kurland, C.G.}, year = 1982, month = feb, journal = {European Journal of Biochemistry}, volume = {122}, number = {1}, pages = {193–197}, publisher = {Wiley Online Library}, doi = {10.1111/j.1432-1033.1982.tb05866.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1982.tb05866.x/full}, abstract = {Ribosomes purified from Escherichia coli were preincubated with AcPhe-tRNA and poly(U). Then purified components necessary for polypeptide synthesis were added. Incubation of the complete system led to a burst of elongation which lasted for nearly 10 s. During the initial burst approximately 10% of the ribosomes participated in the elongation of poly(Phe) at an average rate per ribosome close to eight peptide bonds/s. The missense error rate with leucine was 4 x 10(-4) during the burst. Accordingly, the preincubated elongation system functions at a rate, as well as an accuracy, close to those of protein synthesis in vivo}, keywords = {0,accuracy,Amino Acyl-tRNA Ligases,COMPONENT,COMPONENTS,elongation,elongation factors,ELONGATION-FACTOR-G,ELONGATION-FACTORS,Escherichia coli,ESCHERICHIA-COLI,In Vitro,IN-VITRO,IN-VIVO,Kinetics,La,Leucine,Ligases,metabolism,nosource,Peptide Chain Elongation,Peptide Elongation Factor G,Peptide Elongation Factors,Peptide Synthesis,pharmacology,Poly U,POLYPEPTIDE,protein,protein synthesis,PROTEIN-SYNTHESIS,ribosome,Ribosomes,Rna,RNATransfer,RNATransferAmino Acyl,S,SYSTEM,Time Factors,TranslationGenetic,tRNA} } % == BibTeX quality report for wagnerRateElongationPolyphenylalanine1982: % ? unused Journal abbr (“Eur.J.Biochem.”)

@article{wagnerLossHomotypicFusion2006, title = {Loss of the Homotypic Fusion and Vacuole Protein Sorting or Golgi-Associated Retrograde Protein Vesicle Tethering Complexes Results in Gentamicin Sensitivity in the Yeast {{Saccharomyces}} Cerevisiae}, author = {Wagner, M.C. and Molnar, E.E. and Molitoris, B.A. and Goebl, M.G.}, year = 2006, month = feb, journal = {Antimicrob.Agents Chemother.}, volume = {50}, number = {2}, pages = {587–595}, doi = {10.1128/AAC.50.2.587-595.2006}, url = {PM:16436714}, abstract = {Gentamicin continues to be a primary antibiotic against gram-negative infections. Unfortunately, associated nephro- and ototoxicity limit its use. Our previous mammalian studies showed that gentamicin is trafficked to the endoplasmic reticulum in a retrograde manner and subsequently released into the cytosol. To better dissect the mechanism through which gentamicin induces toxicity, we have chosen to study its toxicity using the simple eukaryote Saccharomyces cerevisiae. A recent screen of the yeast deletion library identified multiple gentamicin-sensitive strains, many of which participate in intracellular trafficking. Our approach was to evaluate gentamicin sensitivity under logarithmic growth conditions. By quantifying growth inhibition in the presence of gentamicin, we determined that several of the sensitive strains were part of the Golgi-associated retrograde protein (GARP) and homotypic fusion and vacuole protein sorting (HOPS) complexes. Further evaluation of their other components showed that the deletion of any GARP member resulted in gentamicin-hypersensitive strains, while the deletion of other HOPS members resulted in less gentamicin sensitivity. Other genes whose deletion resulted in gentamicin hypersensitivity included ZUO1, SAC1, and NHX1. Finally, we utilized a Texas Red gentamicin conjugate to characterize gentamicin uptake and localization in both gentamicin-sensitive and -insensitive strains. These studies were consistent with our mammalian studies, suggesting that gentamicin toxicity in yeast results from alterations to intracellular trafficking pathways. The identification of genes whose absence results in gentamicin toxicity will help target specific pathways and mechanisms that contribute to gentamicin toxicity}, keywords = {0,analysis,Anti-Bacterial Agents,antibiotic,Cation Transport Proteins,CEREVISIAE,chemistry,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,Cytosol,DNA-BINDING,DNA-Binding Proteins,DNA-BINDING-PROTEIN,drug effects,Endoplasmic Reticulum,ENDOPLASMIC-RETICULUM,gene,Genes,Gentamicins,Golgi Apparatus,GROWTH,growth & development,IDENTIFICATION,INFECTION,INHIBITION,La,library,LOCALIZATION,MECHANISM,MECHANISMS,Membrane Proteins,metabolism,nosource,PATHWAY,pharmacology,protein,Protein Transport,Proteins,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Sodium-Hydrogen Antiporter,Support,TARGET,toxicity,TRANSPORT,Vesicular Transport Proteins,yeast} } % == BibTeX quality report for wagnerLossHomotypicFusion2006: % ? Possibly abbreviated journal title Antimicrob.Agents Chemother.

@article{waiYeastRNAPolymerase2001, title = {Yeast {{RNA}} Polymerase {{I}} Enhancer Is Dispensable for Transcription of the Chromosomal {{rRNA}} Gene and Cell Growth, and Its Apparent Transcription Enhancement from Ectopic Promoters Requires {{Fob1}} Protein}, author = {Wai, H. and Johzuka, K. and Vu, L. and Eliason, K. and Kobayashi, T. and Horiuchi, T. and Nomura, M.}, year = 2001, journal = {Molecular and cellular biology}, volume = {21}, number = {16}, pages = {5541–5553}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.21.16.5541-5553.2001}, url = {http://mcb.asm.org/cgi/content/abstract/21/16/5541}, abstract = {At the end of the 35S rRNA gene within ribosomal DNA (rDNA) repeats in Saccharomyces cerevisiae lies an enhancer that has been shown to greatly stimulate rDNA transcription in ectopic reporter systems. We found, however, that the enhancer is not necessary for normal levels of rRNA synthesis from chromosomal rDNA or for cell growth. Yeast strains which have the entire enhancer from rDNA deleted did not show any defects in growth or rRNA synthesis. We found that the stimulatory activity of the enhancer for ectopic reporters is not observed in cells with disrupted nucleolar structures, suggesting that reporter genes are in general poorly accessible to RNA polymerase I (Pol I) machinery in the nucleolus and that the enhancer improves accessibility. We also found that a fob1 mutation abolishes transcription from the enhancer-dependent rDNA promoter integrated at the HIS4 locus without any effect on transcription from chromosomal rDNA. FOB1 is required for recombination hot spot (HOT1) activity, which also requires the enhancer region, and for recombination within rDNA repeats. We suggest that Fob1 protein stimulates interactions between rDNA repeats through the enhancer region, thus helping ectopic rDNA promoters to recruit the Pol I machinery normally present in the nucleolus}, keywords = {0,Cell Division,CELLS,CEREVISIAE,chemistry,Dna,DNA-BINDING,DNA-Binding Proteins,DNARibosomal,enhancer elements (genetics),Fungal Proteins,gene,Gene Expression RegulationFungal,Genes,genetics,GROWTH,La,Mutation,nosource,nucleolus,pol,polymerase,PROMOTER,Promoter Regions (Genetics),PROMOTERS,protein,Proteins,rDNA,RDNA TRANSCRIPTION,RECOMBINATION,REGION,REQUIRES,Rna,RNA Polymerase I,RNA-POLYMERASE,RNA-POLYMERASE-I,rRNA,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,SYSTEMS,transcription,TranscriptionGenetic,yeast} } % == BibTeX quality report for waiYeastRNAPolymerase2001: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{waiCompleteDeletionYeast2000, title = {Complete Deletion of Yeast Chromosomal {{rDNA}} Repeats and Integration of a New {{rDNA}} Repeat: Use of {{rDNA}} Deletion Strains for Functional Analysis of {{rDNA}} Promoter Elements in Vivo}, author = {Wai, H.H. and Vu, L. and Oakes, M. and Nomura, M.}, year = 2000, journal = {Nucleic acids research}, volume = {28}, number = {18}, pages = {3524–3534}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/28.18.3524}, url = {http://nar.oxfordjournals.org/content/28/18/3524.short}, abstract = {Strains of Saccharomyces cerevisiae were constructed}, keywords = {0,analysis,ChromosomesFungal,Dna,DNAFungal,DNARibosomal,ELEMENTS,Gene Dosage,Genetic Techniques,genetics,IN-VIVO,La,metabolism,nosource,physiology,PLASMID,Plasmids,polymerase,PROMOTER,Promoter Regions (Genetics),rDNA,Repetitive SequencesNucleic Acid,Rna,RNA Polymerase I,RNA Polymerase II,RNARibosomal,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Sequence Deletion,supportu.s.gov’tp.h.s.,Templates,TranscriptionGenetic,yeast} } % == BibTeX quality report for waiCompleteDeletionYeast2000: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{wainbergEnhancedFidelity3TCselected1996a, title = {Enhanced Fidelity of {{3TC-selected}} Mutant {{HIV-1}} Reverse Transcriptase [See Comments]}, author = {Wainberg, M.A. and Drosopoulos, W.C. and Salomon, H. and Hsu, M. and Borkow, G. and Parniak, M. and Gu, Z. and Song, Q. and Manne, J. and Islam, S. and Castriota, G. and Prasad, V.R.}, year = 1996, month = mar, journal = {Science}, volume = {271}, number = {5253}, pages = {1282–1285}, doi = {10.1126/science.271.5253.1282}, keywords = {Antibodies,antibody,Drug Resistance,drugs,enzyme,Fidelity,HIV,Hiv-1,human,nosource} }

@article{wakatsukiDistinctMRNAEncoding1995, title = {A Distinct {{mRNA}} Encoding a Soluble Form of {{ICAM-1}} Molecule Expressed in Human Tissues}, author = {Wakatsuki, T. and Kimura, K. and Kimura, F. and Shinomiya, N. and Ohtsubo, M. and Ishizawa, M. and Yamamoto, M.}, year = 1995, month = nov, journal = {Cell Adhesion & Communication}, volume = {3}, number = {4}, pages = {283–292}, doi = {10.3109/15419069509081014}, keywords = {Cell Line,cell lines,COMPLEX,COMPLEXES,Cytokines,expression,frameshift,genomic,human,MECHANISM,mRNA,nosource,polymerase,Polymerase Chain Reaction,regulation,transcription,UPSTREAM} }

@article{wakemChromosomalAssignmentMutations1990, title = {Chromosomal {{Assignment}} of {{Mutations}} by {{Specific Chromosome Loss}} in the {{Yeast Saccharomyces-Cerevisiae}}}, author = {Wakem, L.P. and Sherman, F.}, year = 1990, month = jun, journal = {Genetics}, volume = {125}, number = {2}, pages = {333–340}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/125.2.333}, url = {http://www.genetics.org/content/125/2/333.short}, keywords = {ASSIGNMENT,Mutation,MUTATIONS,nosource,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,yeast,YEAST SACCHAROMYCES-CEREVISIAE} } % == BibTeX quality report for wakemChromosomalAssignmentMutations1990: % ? Title looks like it was stored in title-case in Zotero

@article{walkerRNAAffinityTags2008, title = {{{RNA}} Affinity Tags for the Rapid Purification and Investigation of {{RNAs}} and {{RNA-protein}} Complexes}, author = {Walker, S.C. and Scott, F.H. and Srisawat, C. and Engelke, D.R.}, year = 2008, journal = {Methods Mol. Biol}, volume = {488}, pages = {23–40}, publisher = {Springer}, doi = {10.1007/978-1-60327-475-3_3}, url = {http://www.springerlink.com/index/m62r26481l027238.pdf}, abstract = {Isolation of ribonucleoprotein particles from living cells and cell lysates has allowed the identification of both simple bimolecular interactions and the members of large, extended complexes. A number of different strategies have been devised to isolate these complexes by using affinity purification methods that are specific for the RNA rather than the protein components of these complexes. We describe the use of two such RNA affinity tags: small RNAs that bind with high affinity and specificity to either Sephadex beads or streptavidin affinity resins and can be eluted under mild, native conditions that retain intact complexes. The tags can be inserted into appropriate locations in genes encoding the RNA components, and ribonucleoproteins can be assembled either in vivo or in vitro before affinity isolation. Strategies toward the design and production of these tagged RNA sequences are discussed, and the purification procedure is outlined}, keywords = {0,CELLS,chemistry,ChromatographyAffinity,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,Dextrans,gene,Genes,IDENTIFICATION,In Vitro,IN-VITRO,IN-VIVO,isolation & purification,La,LOCATION,lysate,metabolism,Methods,nosource,PARTICLES,protein,Protein Binding,purification,RIBONUCLEOPROTEIN,Ribonucleoproteins,Rna,sequence,SEQUENCES,SPECIFICITY,Streptavidin,Support} } % == BibTeX quality report for walkerRNAAffinityTags2008: % ? Possibly abbreviated journal title Methods Mol. Biol

@book{wallProgrammingPerl2000a, title = {Programming {{Perl}}.}, author = {Wall, L. and Christiansen, T. and Orwant, J.}, year = 2000, publisher = {O’Reilly Media}, address = {Beijing, Cambridge MA}, url = {http://books.google.com/books?hl=en&lr=&id=xx5JBSqcQzIC&oi=fnd&pg=PR5&dq=Programming+Perl.&ots=nW9hC0Auil&sig=aSj2ixVaIdaxJW2-0cEfDDCwIT0}, keywords = {nosource} } % == BibTeX quality report for wallProgrammingPerl2000a: % ? Title looks like it was stored in title-case in Zotero

@article{wangHDAC4HumanHistone1999, title = {{{HDAC4}}, a Human Histone Deacetylase Related to Yeast {{HDA1}}, Is a Transcriptional Corepressor}, author = {Wang, A.H. and Bertos, N.R. and Vezmar, M. and Pelletier, N. and Crosato, M. and Heng, H.H. and Th’ng, J. and Han, J. and Yang, X.J.}, year = 1999, month = nov, journal = {Molecular and cellular biology}, volume = {19}, number = {11}, pages = {7816–7827}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.19.11.7816}, url = {http://mcb.asm.org/cgi/content/full/19/11/7816?view=full&pmid=10523670}, abstract = {Histone acetylation plays an important role in regulating chromatin structure and thus gene expression. Here we describe the functional characterization of HDAC4, a human histone deacetylase whose C-terminal part displays significant sequence similarity to the deacetylase domain of yeast HDA1. HDAC4 is expressed in various adult human tissues, and its gene is located at chromosome band 2q37. HDAC4 possesses histone deacetylase activity intrinsic to its C-terminal domain. When tethered to a promoter, HDAC4 represses transcription through two independent repression domains, with repression domain 1 consisting of the N- terminal 208 residues and repression domain 2 containing the deacetylase domain. Through a small region located at its N-terminal domain, HDAC4 interacts with the MADS-box transcription factor MEF2C. Furthermore, HDAC4 and MEF2C individually upregulate but together downmodulate c-jun promoter activity. These results suggest that HDAC4 interacts with transcription factors such as MEF2C to negatively regulate gene expression}, keywords = {99455038,Acetylation,Amino Acid Sequence,Chromatin,Chromosome Mapping,ChromosomesHumanPair 2,CloningMolecular,DNA-Binding Proteins,expression,gene,Gene Expression,Gene Expression Regulation,GENE-EXPRESSION,genetics,Histone Deacetylase,human,In Situ HybridizationFluorescence,metabolism,Molecular Sequence Data,Multigene Family,nosource,PROMOTER,Promoter Regions (Genetics),Protein Binding,Proto-Oncogene Proteins c-jun,Repressor Proteins,RPD3,sequence,Sequence HomologyAmino Acid,structure,supportnon-u.s.gov’t,Tissue Distribution,transcription,TRANSCRIPTION FACTOR,Transcription Factors,TranscriptionGenetic,yeast} } % == BibTeX quality report for wangHDAC4HumanHistone1999: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{wangLinearDoubleStrandedRnaTrichomonasVaginalis1985, title = {A {{Linear Double-Stranded-Rna}} in {{Trichomonas-Vaginalis}}}, author = {Wang, A.L. and Wang, C.C.}, year = 1985, journal = {Journal of Biological Chemistry}, volume = {260}, number = {6}, pages = {3697–3702}, doi = {10.1016/S0021-9258(19)83679-7}, url = {ISI:A1985ADZ0700072}, keywords = {DOUBLE-STRANDED-RNA,nosource} } % == BibTeX quality report for wangLinearDoubleStrandedRnaTrichomonasVaginalis1985: % ? Title looks like it was stored in title-case in Zotero

@article{wangDoubleStrandedRnaTrichomonasVaginalisMay1986, title = {The {{Double-Stranded-Rna}} in {{Trichomonas-Vaginalis May Originate}} from {{Virus-Like Particles}}}, author = {Wang, A.L. and Wang, C.C.}, year = 1986, month = oct, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {83}, number = {20}, pages = {7956–7960}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.83.20.7956}, url = {http://www.pnas.org/content/83/20/7956.short}, keywords = {DOUBLE-STRANDED-RNA,nosource,PARTICLES} } % == BibTeX quality report for wangDoubleStrandedRnaTrichomonasVaginalisMay1986: % ? Title looks like it was stored in title-case in Zotero

@article{wangDiscoverySpecificDoubleStrandedRna1986, title = {Discovery of {{A Specific Double-Stranded-Rna Virus}} in {{Giardia-Lamblia}}}, author = {Wang, A.L. and Wang, C.C.}, year = 1986, month = dec, journal = {Molecular and Biochemical Parasitology}, volume = {21}, number = {3}, pages = {269–276}, publisher = {Elsevier}, doi = {10.1016/0166-6851(86)90132-5}, url = {http://linkinghub.elsevier.com/retrieve/pii/0166685186901325}, keywords = {DISCOVERY,DOUBLE-STRANDED-RNA,nosource,virus} } % == BibTeX quality report for wangDiscoverySpecificDoubleStrandedRna1986: % ? Title looks like it was stored in title-case in Zotero

@article{wangGiardiavirusDoubleStrandedRnaGenome1993, title = {Giardiavirus {{Double-Stranded-Rna Genome Encodes A Capsid Polypeptide}} and {{A Gag Pol-Like Fusion Protein}} by {{A Translation Frameshift}}}, author = {Wang, A.L. and Yang, H.M. and Shen, K.A. and Wang, C.C.}, year = 1993, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {90}, number = {18}, pages = {8595–8599}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.90.18.8595}, url = {http://www.pnas.org/content/90/18/8595.short}, abstract = {Giardiavirus is a small, nonenveloped virus comprising a monopartite double-stranded RNA genome, a major protein of 100 kDa, and a less abundant polypeptide of 190 kDa. It can be isolated from the culture supernatant of Giardia lamblia, a parasitic flagellate in human and other mammals, and efficiently infects other virus-free G. lamblia. A single-stranded copy of the viral RNA can be electroporated into uninfected G. lamblia cells to complete the viral replication cycle. Giardiavirus genomic cDNA of 6100 nt was constructed and its sequence revealed the presence of two large open reading frames that are separated by a -1 frameshift and share an overlap of 220 nt. The 3’ open reading frame contains all consensus RNA-dependent RNA polymerase sequence motifs. A heptamer-pseudoknot structure similar to those found at ribosomal slippage sites in retroviruses and yeast killer virus was identified within this overlap. Immunostudies using antisera against synthesized peptides from four regions in the two open reading frames indicated that the 100- and 190-kDa viral proteins share a common domain in the amino-terminal region. But the 190-kDa protein makes a -1 switch of its reading frame beyond the presumed slippage heptamer and is therefore a -1 frameshift fusion protein similar to the gag-pol fusion protein found in retroviruses}, keywords = {3,Capsid,CELLS,DOMAIN,DOUBLE-STRANDED-RNA,ENCODES,FRAME,frameshift,FUSION PROTEIN,Gag,Gag-pol,Genome,GENOME ENCODES,genomic,GIARDIA-LAMBLIA,human,IDENTIFICATION,initiation,killer,killer virus,LAMBLIA,LEISHMANIA,Mammals,MESSENGER-RNAS,MOTIFS,nosource,OPEN READING FRAME,Open Reading Frames,Peptides,polymerase,POLYPEPTIDE,protein,Proteins,pseudoknot,READING FRAME,Reading Frames,REGION,REPLICATION,Rna,RNA-DEPENDENT RNA POLYMERASE,RNA-POLYMERASE,sequence,SITE,SITES,SLIPPAGE,STRUCTURAL FEATURES,structure,translation,TRANSLATION FRAMESHIFT,Viral Proteins,VIRAL-RNA,virus,yeast} } % == BibTeX quality report for wangGiardiavirusDoubleStrandedRnaGenome1993: % ? Title looks like it was stored in title-case in Zotero

@article{wangPokeweedAntiviralProtein1999a, title = {Pokeweed Antiviral Protein Cleaves Double-Stranded Supercoiled {{DNA}} Using the Same Active Site Requiredto Depurinate {{rRNA}}}, author = {Wang, P. and Tumer, N.E.}, year = 1999, month = apr, journal = {Nucleic Acids Res.}, volume = {27}, number = {8}, pages = {1900–1905}, doi = {10.1093/nar/27.8.1900}, abstract = {Ribosome-inactivating proteins (RIPs) are N-glycosyl-ases that remove a specific adenine from the sarcin/ricin loop of the large rRNA in a manner analogous to N-glycosylases that are involved in DNA repair. Some RIPs have been reported to remove adenines from single-stranded DNA and cleave double-stranded supercoiled DNA. The molecular basis for the activity of RIPs on double-stranded DNA is not known. Pokeweed antiviral protein (PAP), a single-chain RIP from Phytolacca americana, cleaves supercoiled DNA into relaxed and linear forms. Double-stranded DNA treated with PAP contains apurinic/apyrimidinic (AP) sites due to the removal of adenine. Using an active-site mutant of PAP (PAPx) which does not depurinate rRNA, we present evidence that double-stranded DNA treated with PAPx does not contain AP sites and is not cleaved. These results demonstrate for the first time that PAP cleaves supercoiled double-stranded DNA using the same active site that is required for depurination of rRNA}, keywords = {0,Adenine,antiviral,Dna,DNA Repair,nosource,PAP,pathology,Pokeweed antiviral protein,protein,Proteins,rRNA} } % == BibTeX quality report for wangPokeweedAntiviralProtein1999a: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{wangHighaccuracyMassMeasurement1994, title = {High-Accuracy Mass Measurement as a Tool for Studying Proteins.}, author = {Wang, R. and Chait, B.T.}, year = 1994, journal = {Current opinion in biotechnology}, volume = {5}, number = {1}, pages = {77–84}, publisher = {Elsevier}, doi = {10.1016/S0958-1669(05)80074-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0958166905800746}, keywords = {analysis,mass spectroscopy,nosource,protein,Proteins,Review,review article,sequence} } % == BibTeX quality report for wangHighaccuracyMassMeasurement1994: % ? unused Journal abbr (“Curr.Opin.Biotech.”)

@article{wangIdentificationCharacterizationUnique2006, title = {Identification and Characterization of a Unique Ribosomal Frameshifting Signal in {{SARS-CoV ORF3a}}}, author = {Wang, X.X. and Liao, Y. and Wong, S.M. and Liu, D.X.}, year = 2006, journal = {Adv.Exp.Med.Biol}, volume = {581}, pages = {89–92}, publisher = {Springer}, doi = {10.1007/978-0-387-33012-9_14}, url = {http://www.springerlink.com/index/NT24554253676102.pdf}, keywords = {0,Animals,Cercopithecus aethiops,Coronavirus,Cos Cells,Frameshift Mutation,Frameshifting,Gene Deletion,genetics,IDENTIFICATION,La,metabolism,ModelsGenetic,Mutagenesis,Mutation,nosource,Plasmids,protein,Proteins,ribosomal frameshifting,RIBOSOMAL FRAMESHIFTING SIGNAL,Ribosomes,Rna,RnaViral,SARS,Sars Virus,SIGNAL,Singapore,Structural,Viral Proteins,Viral Structural Proteins} } % == BibTeX quality report for wangIdentificationCharacterizationUnique2006: % ? Possibly abbreviated journal title Adv.Exp.Med.Biol

@article{wangComparativeStudiesFrameshifting2002, title = {Comparative Studies of Frameshifting and Nonframeshifting {{RNA}} Pseudoknots: A Mutational and {{NMR}} Investigation of Pseudoknots Derived from the Bacteriophage {{T2}} Gene 32 {{mRNA}} and the Retroviral Gag-pro Frameshift Site.}, author = {Wang, Y. and Wills, N.M. and Du, Z. and Rangan, A. and Atkins, J.F. and Gesteland, R.F. and Hoffman, D.W.}, year = 2002, journal = {RNA.}, volume = {8}, number = {8}, pages = {981–996}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838202024044}, url = {http://rnajournal.cshlp.org/content/8/8/981.short}, abstract = {Mutational and NMR methods were used to investigate features of sequence, structure, and dynamics that are associated with the ability of a pseudoknot to stimulate a -1 frameshift. In vitro frameshift assays were performed on retroviral gag-pro frameshift-stimulating pseudoknots and their derivatives, a pseudoknot from the gene 32 mRNA of bacteriophage T2 that is not naturally associated with frameshifting, and hybrids of these pseudoknots. Results show that the gag-pro pseudoknot from human endogenous retrovirus-K10 (HERV) stimulates a -1 frameshift with an efficiency similar to that of the closely related retrovirus MMTV. The bacteriophage T2 mRNA pseudoknot was found to be a poor stimulator of frameshifting, supporting a hypothesis that the retroviral pseudoknots have distinctive properties that make them efficient frameshift stimulators. A hybrid, designed by combining features of the bacteriophage and retroviral pseudoknots, was found to stimulate frameshifting while retaining significant structural similarity to the nonframeshifting bacteriophage pseudoknot. Mutational analyses of the retroviral and hybrid pseudoknots were used to evaluate the effects of an unpaired (wedged) adenosine at the junction of the pseudoknot stems, changing the base pairs near the junction of the two stems, and changing the identity of the loop 2 nucleotide nearest the junction of the stems. Pseudoknots both with and without the wedged adenosine can stimulate frameshifting, though the identities of the nucleotides near the stem1/stem2 junction do influence efficiency. NMR data showed that the bacteriophage and hybrid pseudoknots are similar in their local structure at the junction of the stems, indicating that pseudoknots that are similar in this structural feature can differ radically in their ability to stimulate frameshifting. NMR methods were used to compare the internal motions of the bacteriophage T2 pseudoknot and representative frameshifting pseudoknots. The stems of the investigated pseudoknots are similarly well ordered on the time scales to which nitrogen-15 relaxation data are sensitive; however, solvent exchange rates for protons at the junction of the two stems of the nonframeshifting bacteriophage pseudoknot are significantly slower than the analogous protons in the representative frameshifting pseudoknots}, keywords = {0,Adenosine,assays,Bacteriophage T4,Base Pairing,Base Sequence,chemistry,Comparative Study,derivatives,efficiency,Endogenous Retroviruses,frameshift,Frameshifting,FrameshiftingRibosomal,gene,Genesgag,genetics,human,In Vitro,IN-VITRO,La,Methods,MMTV,ModelsMolecular,mRNA,Mutation,nosource,Nuclear Magnetic ResonanceBiomolecular,Nucleic Acid Conformation,Nucleotides,Protons,pseudoknot,pseudoknots,retrovirus,Rna,RNA PSEUDOKNOT,RNAMessenger,RnaViral,sequence,Structural,structure,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.} } % == BibTeX quality report for wangComparativeStudiesFrameshifting2002: % ? Possibly abbreviated journal title RNA.

@article{wangHighlyConservedMechanism1999a, title = {A Highly Conserved Mechanism of Regulated Ribosome Stalling Mediated by Fungal Arginine Attenuator Peptides That Appears Independent of the Charging Status of Arginyl-{{tRNAs}}}, author = {Wang, Z. and Gaba, A. and Sachs, M.S.}, year = 1999, month = dec, journal = {J.Biol.Chem.}, volume = {274}, number = {53}, pages = {37565–37574}, doi = {10.1074/jbc.274.53.37565}, abstract = {The Arg attenuator peptide (AAP) is an evolutionarily conserved peptide involved in Arg-specific negative translational control. It is encoded as an upstream open reading frame (uORF) in fungal mRNAs specifying the small subunit of Arg-specific carbamoyl phosphate synthetase. We examined the functions of the Saccharomyces cerevisiae CPA1 and Neurospora crassa arg-2 AAPs using translation extracts from S. cerevisiae, N. crassa, and wheat germ. Synthetic RNA containing AAP and firefly luciferase (LUC) sequences were used to program translation; analyses of LUC activity indicated that the AAPs conferred Arg-specific negative regulation in each system. The AAPs functioned either as uORFs or fused in-frame at the N terminus of LUC. Mutant AAPs lacking function in vivo did not function in vitro. Therefore, trans-acting factors conferring AAP-mediated regulation are in both fungal and plant systems. Analyses of ribosome stalling in the fungal extracts by primer extension inhibition (toeprint) assays showed that these AAPs acted similarly to stall ribosomes in the region immediately distal to the AAP coding region in response to Arg. The regulatory effect increased as the Arg concentration increased; all of the arginyl-tRNAs examined appeared maximally charged at low Arg concentrations. Therefore, AAP-mediated Arg-specific regulation appeared independent of the charging status of arginyl-tRNA}, keywords = {20076416,Amino Acid Sequence,Arginine,assays,Base Sequence,Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor,Cell-Free System,chemistry,Conserved Sequence,Fungal Proteins,genetics,In Vitro,IN-VITRO,IN-VIVO,INHIBITION,luciferase,MECHANISM,metabolism,Molecular Sequence Data,mRNA,nosource,Peptide Fragments,Peptides,physiology,primer extension,regulation,ribosome,Ribosomes,Rna,RNATransferArg,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence HomologyAmino Acid,SEQUENCES,SUBUNIT,supportu.s.gov’tp.h.s.,SYSTEM,toeprinting,translation,TranslationGenetic,UPSTREAM,Wheat} } % == BibTeX quality report for wangHighlyConservedMechanism1999a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{wantanabeEncapsidationSequencesSpleen1982, title = {Encapsidation Sequences for Spleen Necrosis Virus, an Avian Retrovirus, Are between the 5’ Long Terminal Repeat and the Start of the ⬚gag⬚ Gene.}, author = {Wantanabe, S. and Temin, H.}, year = 1982, journal = {Proc.Natl.Acad.Sci.USA}, volume = {79}, pages = {5986–5990}, doi = {10.1073/pnas.79.19.5986}, keywords = {Gag,gene,nosource,packaging,psi,retrovirus,sequence,SEQUENCES,virus} } % == BibTeX quality report for wantanabeEncapsidationSequencesSpleen1982: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{warnerSynthesisEucaryoticRibosomal1977a, title = {The Synthesis of Eucaryotic Ribosomal Proteins in Vitro}, author = {Warner, J.R. and Gorenstein, C.}, year = 1977, month = may, journal = {Cell}, volume = {11}, number = {1}, pages = {201–212}, doi = {10.1016/0092-8674(77)90331-2}, keywords = {77203347,biosynthesis,Cell-Free System,Fungal Proteins,In Vitro,IN-VITRO,metabolism,Mutation,nosource,Plant Extracts,protein,Proteins,Ribosomal Proteins,Ribosomes,RNAMessenger,Saccharomyces cerevisiae,supportu.s.gov’tnon-p.h.s.,Temperature,TranscriptionGenetic,TranslationGenetic,Wheat} }

@article{warnerEconomicsRibosomeBiosynthesis1999a, title = {The Economics of Ribosome Biosynthesis in Yeast}, author = {Warner, J.R.}, year = 1999, month = nov, journal = {Trends Biochem.Sci.}, volume = {24}, number = {11}, pages = {437–440}, doi = {10.1016/S0968-0004(99)01460-7}, abstract = {In a rapidly growing yeast cell, 60% of total transcription is devoted to ribosomal RNA, and 50% of RNA polymerase II transcription and 90% of mRNA splicing are devoted to ribosomal proteins (RPs). Coordinate regulation of the approximately 150 rRNA genes and 137 RP genes that make such prodigious use of resources is essential for the economy of the cell. This is entrusted to a number of signal transduction pathways that can abruptly induce or silence the ribosomal genes, leading to major implications for the expression of other genes as well}, keywords = {20021947,biosynthesis,cell cycle,chemistry,cytology,DNA-Binding Proteins,expression,Fungal Proteins,gene,Gene Expression RegulationFungal,Genes,GenesrRNA,genetics,metabolism,mRNA,nosource,physiology,polymerase,protein,Proteins,regulation,Review,Ribosomal Proteins,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNA Polymerase II,rRNA,Saccharomyces cerevisiae,SIGNAL,Signal Transduction,splicing,supportu.s.gov’tp.h.s.,transcription,TranscriptionGenetic,yeast} } % == BibTeX quality report for warnerEconomicsRibosomeBiosynthesis1999a: % ? Possibly abbreviated journal title Trends Biochem.Sci.

@article{warnerEconomicsRibosomeBiosynthesis2001a, title = {Economics of Ribosome Biosynthesis}, author = {Warner, J.R. and Vilardell, J. and Sohn, J.H.}, year = 2001, journal = {Cold Spring Harb.Symp.Quant.Biol}, volume = {66}, pages = {567–574}, doi = {10.1101/sqb.2001.66.567}, url = {PM:12762058}, keywords = {0,Base Sequence,BIOLOGY,biosynthesis,Cap,genetics,GenomeFungal,Kinetics,La,metabolism,nosource,protein,Proteins,Review,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Rna,Rna Caps,RNARibosomal,Saccharomyces cerevisiae,Support} } % == BibTeX quality report for warnerEconomicsRibosomeBiosynthesis2001a: % ? Possibly abbreviated journal title Cold Spring Harb.Symp.Quant.Biol

@article{warnerHowCommonAre2009a, title = {How Common Are Extraribosomal Functions of Ribosomal Proteins?}, author = {Warner, J.R. and McIntosh, K.B.}, year = 2009, month = apr, journal = {Mol.Cell}, volume = {34}, number = {1}, pages = {3–11}, doi = {10.1016/j.molcel.2009.03.006}, url = {PM:19362532}, abstract = {Ribosomal proteins are ubiquitous, abundant, and RNA binding: prime candidates for recruitment to extraribosomal functions. Indeed, they participate in balancing the synthesis of the RNA and protein components of the ribosome itself. An exciting new story is that ribosomal proteins are sentinels for the self-evaluation of cellular health. Perturbation of ribosome synthesis frees ribosomal proteins to interface with the p53 system, leading to cell-cycle arrest or to apoptosis. Yet in only a few cases can we clearly identify the recruitment of ribosomal proteins for other extraribosomal functions. Is this due to a lack of imaginative evolution by cells and viruses, or to a lack of imaginative experiments by molecular biologists?}, keywords = {0,Apoptosis,BINDING,BIOLOGY,cell cycle,CELLS,COMPONENT,COMPONENTS,Evolution,genetics,IDENTIFY,interface,La,metabolism,Neoplasms,nosource,p53,physiology,protein,Proteins,RECRUITMENT,Review,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,RIBOSOME SYNTHESIS,Ribosomes,Rna,Saccharomyces cerevisiae,Support,SYSTEM,Viruses} } % == BibTeX quality report for warnerHowCommonAre2009a: % ? Possibly abbreviated journal title Mol.Cell

@article{warringerAutomatedScreeningEnvironmental2003, title = {Automated Screening in Environmental Arrays Allows Analysis of Quantitative Phenotypic Profiles in {{Saccharomyces}} Cerevisiae}, author = {Warringer, J. and Blomberg, A.}, year = 2003, month = jan, journal = {Yeast}, volume = {20}, number = {1}, pages = {53–67}, publisher = {Wiley Online Library}, doi = {10.1002/yea.931}, url = {http://onlinelibrary.wiley.com/doi/10.1002/yea.931/pdf}, abstract = {A methodology for large-scale automated phenotypic profiling utilizing quantitative changes in yeast growth has been tested and applied to the analysis of some commonly used laboratory strains. This yeast-adjusted methodology is based on microcultivation in 350 microl liquid medium, where growth is frequently optically recorded, followed by automated extraction of relevant variables from obtained growth curves. We report that cultivation at this micro-scale displayed overall growth features and protein expression pattern highly similar to growth in well aerated medium-scale (10 ml) culture. However, differences were also encountered, mainly relating to the respiratory potential and the production of stress-induced proteins. Quantitative phenotypic profiles for the laboratory yeast strains W303, FY1679 and CEN-PK.2 were screened for in environmental arrays, including 98 different conditions composed of low, medium and high concentrations of 33 growth inhibitors. We introduce the concepts phenotypic index(rate) and phenotypic index(stationary), which relate to changes in rate of growth and the stationary phase optical density increment, respectively, in a particular environment relative a reference strain. The laboratory strains presented selective phenotypic profiles in both phenotypic indexes and the two features appeared in many cases to be independent characteristics. We propose the utilization of this methodology in large-scale screening of the complete collection of yeast deletion mutants}, keywords = {0,analysis,ARRAYS,BIOLOGY,CEREVISIAE,expression,Fungal Proteins,GROWTH,growth & development,INHIBITOR,inhibitors,La,media,MUTANTS,nosource,Phenotype,protein,Proteins,Research SupportNon-U.S.Gov’t,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,stationary phase,yeast} }

@article{warringerHighresolutionYeastPhenomics2003, title = {High-Resolution Yeast Phenomics Resolves Different Physiological Features in the Saline Response}, author = {Warringer, J. and Ericson, E. and Fernandez, L. and Nerman, O. and Blomberg, A.}, year = 2003, month = dec, journal = {Proceedings of the national academy of sciences}, volume = {100}, number = {26}, pages = {15724–15729}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.2435976100}, url = {http://www.pnas.org/content/100/26/15724.short}, abstract = {We present a methodology for gene functional prediction based on extraction of physiologically relevant growth variables from all viable haploid yeast knockout mutants. This quantitative phenomics approach, here applied to saline cultivation, identified marginal but functionally important phenotypes and allowed the precise determination of time to adapt to an environmental challenge, rate of growth, and efficiency of growth. We identified approximately 500 salt-sensitive gene deletions, the majority of which were previously uncharacterized and displayed salt sensitivity for only one of the three physiological features. We also report a high correlation to protein-protein interaction data; in particular, several salt-sensitive subcellular networks indicating functional modules were revealed. In contrast, no correlation was found between gene dispensability and gene expression. It is proposed that high-resolution phenomics will be instrumental in systemwide descriptions of intragenomic functional networks}, keywords = {BIOLOGY,CYTOSKELETON,drug effects,efficiency,Endosomes,expression,gene,Gene Deletion,Gene Expression,GENE-EXPRESSION,genetics,GenomeFungal,Genomics,Golgi Apparatus,GROWTH,growth & development,La,MUTANTS,nosource,pharmacology,Phenotype,PREDICTION,Research SupportNon-U.S.Gov’t,Saccharomyces cerevisiae,Sodium,Sodium Chloride,yeast} } % == BibTeX quality report for warringerHighresolutionYeastPhenomics2003: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{weijersArabidopsisMinutelikePhenotype2001, title = {An {{Arabidopsis Minute-like}} Phenotype Caused by a Semi-Dominant Mutation in a {{RIBOSOMAL PROTEIN S5}} Gene}, author = {Weijers, D. and {Franke-van Dijk}, M. and Vencken, R.J. and Quint, A. and Hooykaas, P. and Offringa, R.}, year = 2001, month = nov, journal = {Development}, volume = {128}, number = {21}, pages = {4289–4299}, publisher = {The Company of Biologists Limited}, doi = {10.1242/dev.128.21.4289}, url = {http://dev.biologists.org/content/128/21/4289.short}, abstract = {Mutations in ribosomal protein (RP) genes in Drosophila lead to strong developmental phenotypes, expressed in the semi-dominant Minute syndrome. In plants, however, mutations in RP genes have so far only been reported to result in recessive developmental phenotypes. We present the analysis of an Arabidopsis promoter-trap line, in which a T-DNA insertion in an RPS5 gene (AtRPS5A) causes semi-dominant developmental phenotypes. Most cell-division processes are delayed or disturbed in the heterozygous mutant, and development is completely arrested at an early embryonic stage in the homozygous mutant. By analogy with Drosophila rp mutants, we have named this mutant Arabidopsis Minute-like 1 (aml1). As with other Arabidopsis RPs, RPS5 is represented by a small gene family, but in contrast to other described plant RPs, this family comprises only two members. The AtRPS5A gene (mutated in aml1) is strongly expressed in dividing cells, whereas expression of the second RPS5 gene, AtRPS5B, is lower than that of AtRPS5A, and is correlated with cell differentiation rather than cell division. From expression analyses we conclude that AtRPS5A is the most abundantly expressed RPS5 gene in Arabidopsis. The Minute-like defects in the aml1 mutant provide the first evidence that ribosome insufficiency leads to similar consequences in both plants and insects, and emphasize the general importance of efficient protein translation for cell proliferation in higher eukaryotes}, keywords = {0,Amino Acid Sequence,analysis,Arabidopsis,Cell Differentiation,Cell Division,Cell Proliferation,CELLS,development,Dna,DNA Transposable Elements,Drosophila,ELEMENTS,expression,FAMILY,gene,Gene Expression RegulationPlant,Genes,GenesDominant,genetics,growth & development,Insects,La,LINE,metabolism,Molecular Sequence Data,Multigene Family,MUTANTS,Mutation,MUTATIONS,nosource,Phenotype,Plant Proteins,Plants,PROLIFERATION,Promoter Regions (Genetics),protein,Proteins,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Seeds,Sequence HomologyAmino Acid,Support,Syndrome,translation} }

@article{weijlandModelInteractionElongation1993a, title = {Toward a Model for the Interaction between Elongation Factor {{Tu}} and the Ribosome [See Comments]}, author = {Weijland, A. and Parmeggiani, A.}, year = 1993, journal = {Science}, volume = {259}, number = {5099}, pages = {1311–1314}, doi = {10.1126/science.8446899}, keywords = {BINDING,elongation,Guanine,Magnesium,MECHANISM,MESSENGER-RNA,modification,nosource,P-SITE,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,rRNA,SUBUNIT,TRANSFER-RNA,translation,tRNA} }

@article{weissSeleniumRegulationClassical1997a, title = {Selenium Regulation of Classical Glutathione Peroxidase Expression Requires the 3’ Untranslated Region in {{Chinese}} Hamster Ovary Cells}, author = {Weiss, S.L. and Sunde, R.A.}, year = 1997, month = jul, journal = {J.Nutr.}, volume = {127}, number = {7}, pages = {1304–1310}, doi = {10.1093/jn/127.7.1304}, url = {PM:9202084}, abstract = {Classical glutathione peroxidase (GPX) mRNA levels fall dramatically in selenium (Se)-deficient animals, but it is not known whether this mechanism is related to the mRNA 3’ untranslated region (3’UTR) sequences that have been shown to direct Se incorporation. In this study, we used recombinant GPX constructs to investigate the role of the GPX 3’UTR in Se regulation of GPX mRNA levels in Chinese hamster ovary (CHO) cells. The CHO cells were transfected with GPX (pRc/GPX), GPX lacking the 3’UTR (pRc/Delta3’UTR) or the pRc/CMV vector alone, and GPX activity and GPX mRNA levels were determined in stable transfectants grown in low Se basal medium with a range of added Se concentrations. We identified two pRc/GPX transfectants with significantly elevated GPX activity levels compared with pRc/CMV transfectants. The elevated GPX expression did not dramatically shift the amount of Se that was sufficient for GPX activity to reach the Se- adequate plateau level (100 nmol/L added Se). As expected, GPX activity was not significantly different when pRc/Delta3’UTR transfectants were compared with pRc/CMV control transfectants. Among the wild type and transfected CHO cells, Se-deficient GPX activity levels averaged 35 +/- 5% of Se-adequate levels. Selenium-deficient levels of endogenous GPX mRNA as well as recombinant pRc/GPX mRNA averaged 54-58% of Se-adequate levels; 3-4 nmol/L added Se was sufficient for maximal GPX mRNA levels. In contrast, pRc/Delta3’UTR mRNA levels in the unsupplemented cells remained at Se-adequate levels and showed no distinct Se regulation. These studies demonstrate that the GPX 3’UTR is necessary for Se regulation of GPX mRNA levels in addition to its role in Se incorporation}, keywords = {0,analysis,Analysis of Variance,animal,biosynthesis,BlottingNorthern,Cho Cells,cytology,deficiency,Dose-Response RelationshipDrug,drug effects,enzymology,expression,Gene Expression RegulationEnzymologic,genetics,Glutathione,Glutathione Peroxidase,Hamsters,La,MECHANISM,media,metabolism,mRNA,nosource,pharmacology,physiology,regulation,Rna,RNAMessenger,Selenium,sequence,SEQUENCES,supportu.s.gov’tnon-p.h.s.,Transfection,vector} } % == BibTeX quality report for weissSeleniumRegulationClassical1997a: % ? Possibly abbreviated journal title J.Nutr.

@article{weissCisactingElementsAre1998, title = {Cis-Acting Elements Are Required for Selenium Regulation of Glutathione Peroxidase-1 {{mRNA}} Levels.}, author = {Weiss, S.L. and Sunde, R.A.}, year = 1998, month = jul, journal = {RNA}, volume = {4}, number = {7}, pages = {816–827}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838298971990}, url = {http://rnajournal.cshlp.org/content/4/7/816.short}, abstract = {Classical glutathione peroxidase (GPX1) mRNA levels can decrease to less than 10% in selenium (Se)-deficient rat liver. The cis-acting nucleic acid sequence requirements for Se regulation of GPX1 mRNA levels were studied by transfecting Chinese hamster ovary (CHO) cells with GPX1 DNA constructs in which specific regions of the GPX1 gene were mutated, deleted, or replaced by comparable regions from unregulated genes such as phospholipid hydroperoxide glutathione peroxidase (GPX4). For each construct, stable transfectants were pooled two weeks after transfection, divided into Se-deficient (2 nM Se) or Se- adequate (200 nM Se) medium, and grown for an additional four days. On day of harvest, Se-deficient GPX1 and GPX4 activities averaged 13 +/- 2% and 15 +/- 2% of Se adequate levels, confirming that cellular Se status was dramatically altered by Se supplementation. RNA was isolated from replicate plates of cells and transfected mRNA levels were specifically determined by RNase protection assay. Analysis of chimeric GPX1/GPX4 constructs showed that the GPX4 3’-UTR can completely replace the GPX1 3’-UTR in Se regulation of GPX1 mRNA. We did not find any GPX1 coding regions that could be replaced by the corresponding GPX4 coding regions without diminishing or eliminating Se regulation of the transfected GPX1 mRNA. Further analysis of the GPX1 coding region demonstrated that the GPX1 Sec codon (UGA) and the GPX1 intron sequences are required for full Se regulation of transfected GPX1 mRNA levels. Mutations that moved the GPX1 Sec codon to three different positions within the GPX1 coding region suggest that the mechanism for Se regulation of GPX1 mRNA requires a Sec codon within exon 1. Lastly, we found that addition of the GPX1 3’-UTR to beta-globin mRNA can convey significant Se regulation to beta-globin mRNA levels when a UGA codon is placed within exon 1. We conclude that Se regulation of GPX1 mRNA requires a functional selenocysteine insertion sequence (SECIS) in the 3’-UTR and a Sec codon followed by an intron}, keywords = {0,3’ UTR,analysis,animal,biosynthesis,Chimeric Proteins,Cho Cells,Codon,Dna,Down-Regulation (Physiology),ELEMENTS,gene,Gene Expression RegulationEnzymologic,Genes,genetics,Globin,Globins,Glutathione,Glutathione Peroxidase,Hamsters,La,Liver,MECHANISM,media,Mice,mRNA,Mutation,MUTATIONS,nosource,pharmacology,protein,Proteins,rat,regulation,Regulatory SequencesNucleic Acid,Rna,RNAMessenger,RNAse,RNAse protection,Selenium,Selenocysteine,SELENOCYSTEINE INSERTION,sequence,SEQUENCES,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,Transfection} }

@article{weissbrummerParomomycinResistanceMutation1989a, title = {The {{Paromomycin Resistance Mutation}} ({{Parr-454}}) in the 15-{{S Ribosomal-Rna Gene}} of the {{Yeast Saccharomyces-Cerevisiae Is Involved}} in {{Ribosomal Frameshifting}}}, author = {Weissbrummer, B. and Huttenhofer, A.}, year = 1989, month = jun, journal = {Molecular & General Genetics}, volume = {217}, number = {2-3}, pages = {362–369}, doi = {10.1007/BF02464905}, url = {ISI:A1989AD22200026}, keywords = {Frameshifting,gene,Mutation,nosource,Paromomycin,ribosomal frameshifting,RIBOSOMAL-RNA,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,yeast,YEAST SACCHAROMYCES-CEREVISIAE} } % == BibTeX quality report for weissbrummerParomomycinResistanceMutation1989a: % ? Title looks like it was stored in title-case in Zotero

@article{weissbrummerMutationHighlyConserved1995a, title = {Mutation of {{A Highly Conserved Base}} in the {{Yeast Mitochondrial 21S Ribosomal-Rna Restricts Ribosomal Frameshifting}}}, author = {Weissbrummer, B. and Zollner, A. and Haid, A. and Thompson, S.}, year = 1995, month = jul, journal = {Molecular & General Genetics}, volume = {248}, number = {2}, pages = {207–216}, doi = {10.1007/BF02190802}, url = {ISI:A1995RP47700011}, abstract = {A mutation shown to cause resistance to chloramphenicol in Saccharomyces cerevisiae was mapped to the central loop in domain V of the yeast mitochondrial 21S rRNA. The mutant 21S rRNA has a basepair exchange from U-2677 (corresponding to U-2504 in Escherichia coli) to C-2677, which significantly reduces rightward frameshifting at a UU UUU UCC A site in a + 1 U mutant. There is evidence to suggest that this reduction also applies to leftward frameshifting at the same site in a - 1 U mutant. The mutation did not increase the rate of misreading of a number of mitochondrial missense, nonsense or frameshift (of both signs) mutations, and did not adversely affect the synthesis of wild-type mitochondrial gene products. It is suggested here that ribosomes bearing either the C-2677 mutation or its wild-type allele may behave identically during normal decoding and only differ at sites where a ribosomal stall, by permitting non-standard decoding, differentially affects the normal interaction of tRNAs with the chloramphenicol resistant domain V. Chloramphenicol-resistant mutations mapping at two other sites in domain V are described. These mutations had no effect on frameshifting}, keywords = {21S RIBOSOMAL-RNA,A-SITE,Chloramphenicol,CHLORAMPHENICOL RESISTANCE,CYTOCHROME-C OXIDASE,decoding,DOMAIN-V,Escherichia coli,ESCHERICHIA-COLI,frameshift,Frameshifting,gene,HUNGRY CODON,LOOP,mapping,MESSENGER-RNA,mitochondria,Mutation,MUTATIONS,nosource,PAROMOMYCIN-RESISTANCE,peptidyl transferase,RESISTANCE,ribosomal frameshifting,RIBOSOMAL-RNA,ribosome,Ribosomes,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SITE,SITES,SUBUNIT-II,TRANSFER-RNA,tRNA,yeast} } % == BibTeX quality report for weissbrummerMutationHighlyConserved1995a: % ? Title looks like it was stored in title-case in Zotero

@article{welchInternalOpenReading1999, title = {An Internal Open Reading Frame Triggers Nonsense-Mediated Decay of the Yeast {{SPT10 mRNA}}}, author = {Welch, E.M. and Jacobson, A.}, year = 1999, month = nov, journal = {The EMBO journal}, volume = {18}, number = {21}, pages = {6134–6145}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/18.21.6134}, url = {http://www.nature.com/emboj/journal/v18/n21/abs/7592015a.html}, abstract = {Yeast cells containing a temperature-sensitive mutation in the PRT1 gene were found to selectively stabilize mRNAs harboring early nonsense codons. The similarities between the mRNA decay phenotypes of prt1-1 cells and those lacking the nonsense-mediated mRNA decay (NMD) factor Upf1p led us to determine whether both types of mutations cause the accumulation of the same mRNAs. Differential display analysis and mRNA half-life measurements demonstrated that the HHF2 mRNA increased in abundance in prt1-1 and upf1Delta cells, but did not manifest a change in decay rate. In both mutant strains this increase was attributable to stabilization of the SPT10 transcript, an mRNA encoding a transcriptional regulator of HHF2. Analyses of chimeric mRNAs used to identify the cis-acting basis for NMD of the SPT10 mRNA indicated that ribosomes scan beyond its initiator AUG and initiate at the next downstream AUG, resulting in premature translation termination. By searching a yeast database for transcripts with sequence features similar to those of the SPT10 mRNA, other transcripts that decay by the NMD pathway were identified. Our results demonstrate that mRNAs undergoing leaky scanning are a new class of endogenous NMD substrate, and suggest the existence of a novel cellular regulatory circuit}, keywords = {0,5’ Untranslated Regions,Amino Acid Sequence,analysis,Base Sequence,Codon,CodonNonsense,DATABASE,Databases,DECAY,differential display,eIF3,Fungal Proteins,gene,Gene Expression RegulationFungal,GenesFungal,Genetic,genetics,Half-Life,Helicase,initiation,Kinetics,La,metabolism,microbiology,Molecular Sequence Data,mRNA,mRNA decay,Mutation,MUTATIONS,NMD,nonsense-mediated decay,nosource,Open Reading Frames,Peptide Initiation Factors,Phenotype,Polyribosomes,protein,Proteins,PRT1,ribosome,Ribosomes,Rna,RNA Helicases,RNAMessenger,Saccharomyces cerevisiae,sequence,supportu.s.gov’tp.h.s.,termination,translation,TRANSLATION TERMINATION,TranslationGenetic,Untranslated Regions,Upf1,yeast} } % == BibTeX quality report for welchInternalOpenReading1999: % ? unused Journal abbr (“EMBO J.”)

@incollection{welchTranslationTerminationIt2000a, title = {Translation Termination: {{It}}’s Not the End of the Story.}, booktitle = {Translational {{Control}}}, author = {Welch, E.M. and Wang, W and Peltz, S.W.}, year = {in press 2000}, publisher = {Cold Spring Harbor Laboratory Press}, address = {Cold Spring Harbor, NY}, collaborator = {Hershey, J.W. and Mathews, M.B. and Sonenberg, N.;}, keywords = {nosource,termination,translation,TRANSLATION TERMINATION} }

@article{welchPTC124TargetsGenetic2007, title = {{{PTC124}} Targets Genetic Disorders Caused by Nonsense Mutations}, author = {Welch, E.M. and Barton, E.R. and Zhuo, J. and Tomizawa, Y. and Friesen, W.J. and Trifillis, P. and Paushkin, S. and Patel, M. and Trotta, C.R. and Hwang, S. and Wilde, R.G. and Karp, G. and Takasugi, J. and Chen, G. and Jones, S. and Ren, H. and Moon, Y.C. and Corson, D. and Turpoff, A.A. and Campbell, J.A. and Conn, M.M. and Khan, A. and Almstead, N.G. and Hedrick, J. and Mollin, A. and Risher, N. and Weetall, M. and Yeh, S. and Branstrom, A.A. and Colacino, J.M. and Babiak, J. and Ju, W.D. and Hirawat, S. and Northcutt, V.J. and Miller, L.L. and Spatrick, P. and He, F. and Kawana, M. and Feng, H. and Jacobson, A. and Peltz, S.W. and Sweeney, H.L.}, year = 2007, month = may, journal = {Nature}, volume = {447}, number = {7140}, pages = {87–91}, publisher = {Nature Publishing Group}, doi = {10.1038/nature05756}, url = {http://www.nature.com/nature/journal/vaop/ncurrent/full/nature05756.html}, abstract = {Nonsense mutations promote premature translational termination and cause anywhere from 5-70% of the individual cases of most inherited diseases. Studies on nonsense-mediated cystic fibrosis have indicated that boosting specific protein synthesis from {\(<\)}1% to as little as 5% of normal levels may greatly reduce the severity or eliminate the principal manifestations of disease. To address the need for a drug capable of suppressing premature termination, we identified PTC124-a new chemical entity that selectively induces ribosomal readthrough of premature but not normal termination codons. PTC124 activity, optimized using nonsense-containing reporters, promoted dystrophin production in primary muscle cells from humans and mdx mice expressing dystrophin nonsense alleles, and rescued striated muscle function in mdx mice within 2-8 weeks of drug exposure. PTC124 was well tolerated in animals at plasma exposures substantially in excess of those required for nonsense suppression. The selectivity of PTC124 for premature termination codons, its well characterized activity profile, oral bioavailability and pharmacological properties indicate that this drug may have broad clinical potential for the treatment of a large group of genetic disorders with limited or no therapeutic options}, keywords = {0,administration & dosage,Alleles,animal,Animals,Biological Availability,biosynthesis,blood,CELLS,Codon,Codon-Nonsense,CodonNonsense,CODONS,disease,drug effects,drug therapy,Dystrophin,Genetic,Genetic Diseases-Inborn,Genetic DiseasesInborn,genetics,human,Humans,La,metabolism,Mice,Mice-Inbred mdx,MiceInbred mdx,Muscle Cells,Mutation,MUTATIONS,NONSENSE,NONSENSE MUTATIONS,nonsense suppression,nosource,Oxadiazoles,pharmacokinetics,pharmacology,Phenotype,PREMATURE TERMINATION CODON,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,readthrough,Rna,RNA-Messenger,RNAMessenger,Substrate Specificity,Support,suppression,TARGET,termination,TERMINATION CODON,TERMINATION-CODON,therapeutic use,TRANSLATIONAL TERMINATION} }

@article{wengLinkingMRNATurnover1996, title = {Linking {{mRNA}} Turnover and Translational Termination by the {{Upf1}} Protein.}, author = {Weng, Y. and Czaplinski, K. and Peltz, S.W.}, year = {in press 1996}, journal = {Genes & Dev.}, keywords = {2-hybrid,mRNA,No DOI found,nosource,NTPase assays,protein,termination,turnover,Upf1} } % == BibTeX quality report for wengLinkingMRNATurnover1996: % ? Possibly abbreviated journal title Genes & Dev.

@article{wengIdentificationCharacterizationMutations1996a, title = {Identification and Characterization of Mutations in the ⬚{{UPF1}}⬚ Gene That Affect Nonsense Suppression and the Formation of the {{Upf}} Protein Complex but Not {{mRNA}} Turnover.}, author = {Weng, Y. and Czaplinski, K. and Peltz, S.W.}, year = 1996, journal = {Mol.Cell.Biol.}, volume = {16}, pages = {5491–5506}, doi = {10.1128/MCB.16.10.5491}, keywords = {COMPLEX,COMPLEXES,gene,IDENTIFICATION,mRNA,mRNA decay,Mutation,MUTATIONS,nonsense suppression,nosource,protein,PROTEIN COMPLEX,suppression,turnover,UPF,Upf1} } % == BibTeX quality report for wengIdentificationCharacterizationMutations1996a: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{wengGeneticBiochemicalCharacterization1996, title = {Genetic and Biochemical Characterization of Mutations in the {{ATPase}} and {{Helicase}} Regions of the {{Upf1}} Protein.}, author = {Weng, Y. and Czaplinski, K. and Peltz, S.W.}, year = 1996, journal = {Mol.Cell.Biochem.}, volume = {16}, pages = {5477–5490}, doi = {10.1128/MCB.16.10.5477}, keywords = {ATPase,Genetic,Helicase,Mutation,MUTATIONS,nosource,protein,Upf1} } % == BibTeX quality report for wengGeneticBiochemicalCharacterization1996: % ? Possibly abbreviated journal title Mol.Cell.Biochem.

@article{wengATPCofactorUpf11998, title = {{{ATP}} Is a Cofactor of the {{Upf1}} Protein That Modulates Its Translation Termination and {{RNA}} Binding Activities.}, author = {Weng, Y. and Czaplinski, K. and Peltz, S.W.}, year = 1998, journal = {RNA}, volume = {4}, number = {2}, pages = {205–214}, publisher = {Cold Spring Harbor Lab}, url = {http://rnajournal.cshlp.org/content/4/2/205.short}, keywords = {ATP,BINDING,NMD,No DOI found,nonsense-mediated decay,nosource,protein,Rna,termination,translation,TRANSLATION TERMINATION,Upf1} }

@article{wenthzelGrowthPhaseDependent1998, title = {Growth Phase Dependent Stop Codon Readthrough and Shift of Translation Reading Frame in {{Escherichia}} Coli}, author = {Wenthzel, A.M. and Stancek, M. and Isaksson, L.A.}, year = 1998, month = jan, journal = {FEBS Letters}, volume = {421}, number = {3}, pages = {237–242}, publisher = {Elsevier}, doi = {10.1016/S0014-5793(97)01570-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579397015706}, keywords = {Codon,Escherichia coli,ESCHERICHIA-COLI,frameshift,Frameshifting,Gels,gene,Genes,microbiology,nosource,PLASMID,Plasmids,protein,Proteins,readthrough,regulation,sequence,STOP CODON,termination,translation,tRNA} }

@article{westhofComputerModelingSolution1989a, title = {Computer Modeling from Solution Data of Spinach Chloroplast and of {{Xenopus}} Laevis Somatic and Oocyte 5 {{S rRNAs}}}, author = {Westhof, E. and Romby, P. and Romaniuk, P.J. and Ebel, J.P. and Ehresmann, C. and Ehresmann, B.}, year = 1989, month = may, journal = {J.Mol.Biol.}, volume = {207}, number = {2}, pages = {417–431}, doi = {10.1016/0022-2836(89)90264-7}, url = {PM:2754730}, abstract = {Detailed atomic models of a eubacterial 5 S rRNA (spinach chloroplast 5 S rRNA) and of a eukaryotic 5 S rRNA (somatic and oocyte 5 S rRNA from Xenopus laevis) were built using computer graphic. Both models integrate stereochemical constraints and experimental data on the accessibility of bases and phosphates towards several structure- specific probes. The base sequence was first inserted on to three- dimensional structural fragments picked up in a specially devised databank. The fragments were modified and assembled interactively on an Evans & Sutherland PS330. Modeling was finalized by stereochemical and energy refinement. In spite of some uncertainty in the relative spatial orientation of the substructures, the broad features of the models can be generalized and several conclusions can be reached: (1) both models adopt a distorted Y-shape structure, with helices B and D not far from colinearity; (2) no tertiary interactions exist between loop c and region d or loop e; (3) the internal loops, in particular region d, contain several non-canonical base-pairs of A.A, U.U and A.G types; (4) invariant residues appear to be more important for protein or RNA binding than for maintaining the tertiary structure. The models are corroborated by footprinting experiments with ribosomal proteins and by the analysis of various mutants. Such models help to clarify the structure-function relationship of 5 S rRNA and are useful for designing site-directed mutagenesis experiments}, keywords = {0,analysis,animal,Base Sequence,BINDING,Chloroplasts,computer,Computer Simulation,genetics,La,LOOP-E,models,ModelsMolecular,Molecular Sequence Data,Mutagenesis,nosource,Nucleic Acid Conformation,Oocytes,Phosphates,protein,Proteins,Ribosomal Proteins,Rna,RNARibosomal,RNARibosomal5S,rRNA,sequence,Spinach,Structural,structure,supportnon-u.s.gov’t,Vegetables,Xenopus,Xenopus laevis} } % == BibTeX quality report for westhofComputerModelingSolution1989a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{wheelerDatabaseResourcesNational2000a, title = {Database Resources of the {{National Center}} for {{Biotechnology Information}}.}, author = {Wheeler, D.L. and Chappey, C. and Lash, A.E. and Leipe, D.D. and Madden, T.L. and Schuler, G.D. and Tatusova, T.A. and Rapp, B.A.}, year = 2000, month = jan, journal = {Nucleic Acids Research}, volume = {28}, number = {1}, pages = {10–14}, doi = {10.1093/nar/28.1.10}, url = {PM:10592169}, abstract = {In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval and resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing pages, GeneMap’99, Davis Human-Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP) pages, Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP) pages, SAGEmap, Online Mendelian Inheritance in Man (OMIM) and the Molecular Modeling Database (MMDB). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih. gov}, keywords = {ACID,analysis,Animals,BIOLOGY,BLAST,cancer,DATABASE,DatabasesFactual,Gene Expression,genetics,Genome,GenomeHuman,human,human genome,Information Storage and Retrieval,La,library,Mendelian inheritance,Mice,ModelsMolecular,National Library of Medicine (U.S.),Neoplasms,nosource,PCR,Phenotype,RefSeq,search,sequence,SITE,United States} } % == BibTeX quality report for wheelerDatabaseResourcesNational2000a: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{whiteRnaDependentRnaPolymerase1990, title = {Rna {{Dependent Rna-Polymerase Activity Associated}} with the {{Double-Stranded-Rna Virus}} of {{Giardia-Lamblia}}}, author = {White, T.C. and Wang, C.C.}, year = 1990, month = feb, journal = {Nucleic Acids Research}, volume = {18}, number = {3}, pages = {553–559}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/18.3.553}, url = {http://nar.oxfordjournals.org/content/18/3/553.short}, keywords = {DOUBLE-STRANDED-RNA,nosource,Rna,RNA-POLYMERASE,T,virus} } % == BibTeX quality report for whiteRnaDependentRnaPolymerase1990: % ? Title looks like it was stored in title-case in Zotero

@article{wicknerMutantsSaccharomycesCerevisiae1974a, title = {Mutants of ⬚{{Saccharomyces}} Cerevisiae⬚ That Incorporate Deoxythymidine-5’-Monophosphate into Deoxyribonucleic Acid ⬚in Vivo⬚.}, author = {Wickner, R.B.}, year = 1974, journal = {J.Bacteriol.}, volume = {117}, pages = {1356–1357}, keywords = {IN-VIVO,Multiple DOI,nonfile,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,yeast} } % == BibTeX quality report for wicknerMutantsSaccharomycesCerevisiae1974a: % ? Possibly abbreviated journal title J.Bacteriol.

@article{wicknerChromosomalNonchromosomalMutations1974a, title = {Chromosomal and Non-Chromosomal Mutations Affecting the “Killer Character” of ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Wickner, R.B. and Leibowitz, M.J.}, year = 1974, journal = {Genetics}, volume = {76}, pages = {423–432}, doi = {10.1093/genetics/76.3.423}, keywords = {Genetic,killer toxin,L3,MAK,Mutation,MUTATIONS,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,yeast} }

@article{wicknerTwoChromosomalGenes1976, title = {Two Chromosomal Genes Required for Killing Expression in Killer Strains of {{Saccharomyces}} Cerevisiae}, author = {Wickner, R.B. and Leibowitz, M.J.}, year = 1976, month = mar, journal = {Genetics}, volume = {82}, number = {3}, pages = {429–442}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/82.3.429}, url = {http://www.genetics.org/content/82/3/429.short}, abstract = {The killer character of yeast is determined by a 1.4 X 10(6) molecular weight double-stranded RNA plasmid and at least 12 chromosomal genes. Wild-type strains of yeast that carry this plasmid (killers) secret a toxin which is lethal only to strains not carrying this plasmid (sensitives).–We have isolated 28 independent recessive chromosomal mutants of a killer strain that have lost the ability to secrete an active toxin but remain resistant to the effects of the toxin and continue to carry the complete cytoplasmic killer genome. These mutants define two complementation groups, kex1 and kex2. Kex1 is located on chromosome VII between ade5 and lys5. Kex2 is located on chromosome XIV, but it does not show meiotic linkage to any gene previously located on this chromosome.–When the killer plasmid of kex1 or kex2 strains is eliminated by curing with heat or cycloheximide, the strains become sensitive to killing. The mutant phenotype reappears among the meiotic segregants in a cross with a normal killer. Thus, the kex phenotype does not require an alteration of the killer plasmid.–Kex1 and kex2 strains each contain near-normal levels of the 1.4 x 10(6) molecular weight double-stranded RNA, whose presence is correlated with the presence of the killer genome}, keywords = {76188499,biosynthesis,Chromosome Mapping,curing,Cycloheximide,DOUBLE-STRANDED-RNA,drug effects,expression,gene,Genes,Genome,Genotype,Heat,killer,media,metabolism,Methods,Molecular Weight,Mutation,Mycotoxins,nosource,pharmacology,Phenotype,PLASMID,Plasmids,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Species Specificity,toxin,yeast} }

@article{wicknerMutantsKillerPlasmid1976a, title = {Mutants of {{Killer Plasmid}} of {{Saccharomyces-Cerevisiae Dependent}} on {{Chromosomal Diploidy}} for {{Expression}} and {{Maintenance}}}, author = {Wickner, R.B.}, year = 1976, journal = {Genetics}, volume = {82}, number = {2}, pages = {273–285}, doi = {10.1093/genetics/82.2.273}, url = {ISI:A1976BH28700008}, keywords = {Diploidy,expression,killer,MUTANTS,nosource,PLASMID,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE} } % == BibTeX quality report for wicknerMutantsKillerPlasmid1976a: % ? Title looks like it was stored in title-case in Zotero

@article{wicknerKillerSaccharomycesCerevisiaeDoubleStranded1976, title = {Killer of {{Saccharomyces-Cerevisiae}} - {{Double-Stranded Ribonucleic-Acid Plasmid}}}, author = {Wickner, R.B.}, year = 1976, journal = {Bacteriological Reviews}, volume = {40}, number = {3}, pages = {757–773}, doi = {10.1128/br.40.3.757-773.1976}, url = {ISI:A1976CE90700009}, keywords = {killer,nosource,PLASMID,RIBONUCLEIC-ACID,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE} } % == BibTeX quality report for wicknerKillerSaccharomycesCerevisiaeDoubleStranded1976: % ? Title looks like it was stored in title-case in Zotero

@article{wicknerTwentysixChromosomalGenes1978, title = {Twenty-Six Chromosomal Genes Needed to Maintain the Killer Double-Stranded {{RNA}} Plasmid of {{Saccharomyces}} Cerevisiae}, author = {Wickner, R.B.}, year = 1978, month = mar, journal = {Genetics}, volume = {88}, number = {3}, pages = {419–425}, doi = {10.1093/genetics/88.3.419}, keywords = {DOUBLE-STRANDED-RNA,gene,Genes,killer,MAK,Mutation,MUTATIONS,nosource,PLASMID,Plasmids,protein,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,toxin,yeast} }

@article{wicknerMakMutantsYeast1979, title = {Mak Mutants of Yeast: Mapping and Characterization.}, author = {Wickner, R.B. and Leibowitz, M.J.}, year = 1979, month = oct, journal = {Journal of Bacteriology}, volume = {140}, number = {1}, pages = {154–160}, publisher = {Am Soc Microbiol}, doi = {10.1128/jb.140.1.154-160.1979}, url = {http://jb.asm.org/cgi/content/abstract/140/1/154}, keywords = {COMPLEX,COMPLEXES,gene,Genes,killer,MAK,mapping,Meiosis,Mutation,MUTATIONS,nosource,protein,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Temperature,toxin,yeast} }

@article{wicknerRibosomalProteinL31982a, title = {Ribosomal Protein {{L3}} Is Involved in Replication or Maintenance of the Killer Double-Stranded {{RNA}} Genome of ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Wickner, R.B. and {Porter-Ridley}, S. and Fried, H.M. and Ball, S.G.}, year = 1982, journal = {Proc.Natl.Acad.Sci.USA}, volume = {79}, pages = {4706–4708}, doi = {10.1073/pnas.79.15.4706}, keywords = {antibiotics,curing,DOUBLE-STRANDED-RNA,drugs,Genome,killer,L-A,L3,La,MAK,nosource,protein,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,TCM1} } % == BibTeX quality report for wicknerRibosomalProteinL31982a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{wicknerGeneticControlReplication1983a, title = {Genetic Control of Replication of the Double-Stranded {{RNA}} Segments of the Killer Systems in {{Saccharomyces}} Cerevisiae.}, author = {Wickner, R.B.}, year = 1983, journal = {Archives of Biochemistry and Biophysics}, volume = {222}, number = {1}, eprint = {6340610}, eprinttype = {pubmed}, pages = {1–11}, doi = {10.1016/0003-9861(83)90496-4}, url = {http://www.ncbi.nlm.nih.gov/pubmed/6340610}, keywords = {DOUBLE-STRANDED-RNA,killer,KILLER SYSTEMS,nosource,REPLICATION,Review,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SYSTEM,SYSTEMS} }

@article{wicknerDoublestrandedRNAReplication1986a, title = {Double-Stranded {{RNA}} Replication in the Yeast: The Killer System.}, author = {Wickner, R.B.}, year = 1986, journal = {Annu.Rev.Biochem.}, volume = {55}, pages = {373–395}, doi = {10.1146/annurev.bi.55.070186.002105}, keywords = {DOUBLE-STRANDED-RNA,killer,L-A,M1,nosource,Review,Rna,SYSTEM,yeast} } % == BibTeX quality report for wicknerDoublestrandedRNAReplication1986a: % ? Possibly abbreviated journal title Annu.Rev.Biochem.

@article{wicknerMKT1NonessentialSaccharomyces1987, title = {{{MKT1}}, a Nonessential {{Saccharomyces}} Cerevisiae Gene with a Temperature-Dependent Effect on Replication of {{M2}} Double-Stranded {{RNA}}.}, author = {Wickner, R.B.}, year = 1987, month = nov, journal = {Journal of Bacteriology}, volume = {169}, number = {11}, pages = {4941–4945}, publisher = {Am Soc Microbiol}, doi = {10.1128/jb.169.11.4941-4945.1987}, url = {http://jb.asm.org/cgi/content/abstract/169/11/4941}, keywords = {DOUBLE-STRANDED-RNA,gene,nosource,REPLICATION,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE} }

@article{wicknerMolecularCloningChromosome1987, title = {Molecular Cloning of Chromosome {{I DNA}} from {{Saccharomyces}} Cerevisiae: Isolation of the {{MAK16}} Gene and Analysis of an Adjacent Gene Essential for Growth at Low Temperatures}, author = {Wickner, R.B. and Koh, T.J. and Crowley, J.C. and O’Neil, J. and Kaback, D.B.}, year = 1987, month = mar, journal = {Yeast}, volume = {3}, number = {1}, pages = {51–57}, publisher = {Wiley Online Library}, doi = {10.1002/yea.320030108}, url = {http://onlinelibrary.wiley.com/doi/10.1002/yea.320030108/abstract}, abstract = {MAK16 is an essential gene on chromosome I defined by the thermosensitive lethal mak16-1 mutation. MAK16 is also necessary for M double-stranded RNA replication at the permissive temperature for cell growth. As part of an effort to clone all the DNA from chromosome I, plasmids that complemented both the temperature-sensitive growth defect, and the M1 replication defects of mak16-1 strains were isolated from a plasmid YCp50: Saccharomyces cerevisiae recombinant DNA library. The two plasmids analysed contained overlapping inserts that hybridized proportionally to strains carrying different dosages of chromosome I. Furthermore, integration of a fragment of one of these clones occurred at a site linked to ade 1, confirming that this clone was derived from the appropriate region of chromosome I. An open reading frame adjacent to MAK16 potentially coding for a 468 amino acid protein was defined by sequence analysis. 185 amino acids of this open reading frame were replaced with a 1.2 kb fragment carrying the S. cerevisiae URA3 gene by a one-step gene disruption. The resulting strains grew at a rate indistinguishable from the wild type at 20 degrees C, 30 degrees C, or 37 degrees C, but could not grow at 8 degrees C. The deleted region is thus essential only at 8 degrees C, and we name this gene LTE1 (low temperature essential)}, keywords = {0,A SITE,A-SITE,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,Base Sequence,BlottingSouthern,CBF5,cloning,CloningMolecular,disease,DISRUPTION,Dna,DNAFungal,DOUBLE-STRANDED-RNA,FRAME,Gag/Gag-pol ratio,gene,Genetic,genetics,GROWTH,growth & development,La,library,M,M1,Molecular Sequence Data,Mutation,nosource,OPEN READING FRAME,PLASMID,Plasmids,protein,READING FRAME,REGION,REPLICATION,Restriction Mapping,Review,ribosome,Rna,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence Analysis,SEQUENCE-ANALYSIS,SITE,supportu.s.gov’tnon-p.h.s.,TAP-tag,Temperature,TransformationGenetic,WILD-TYPE,YCp50,yeast} }

@article{wicknerHostFunctionMAK161988a, title = {Host Function of ⬚{{MAK16}}:⬚ {{G1}} Arrest by a ⬚mak16⬚ Mutant of ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Wickner, R.B.}, year = 1988, journal = {Proc.Natl.Acad.Sci.USA}, volume = {85}, pages = {6007–6011}, doi = {10.1073/pnas.85.16.6007}, keywords = {cell cycle,L-A,M1,MAK,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,yeast} } % == BibTeX quality report for wicknerHostFunctionMAK161988a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{wicknerYeastVirology1989, title = {Yeast {{Virology}}}, author = {Wickner, R.B.}, year = 1989, journal = {The FASEB Journal}, volume = {3}, number = {11}, pages = {2257–2265}, publisher = {FASEB}, doi = {10.1096/fasebj.3.11.2550303}, url = {http://www.fasebj.org/content/3/11/2257.short}, keywords = {nosource,Review,virology,yeast} } % == BibTeX quality report for wicknerYeastVirology1989: % ? Title looks like it was stored in title-case in Zotero

@article{wicknerExpressionYeastDoubleStrandedRNA1991, title = {Expression of {{Yeast L-A Double-Stranded-RNA Virus Proteins Produces Derepressed Replication}} - {{A Ski- Phenocopy}}}, author = {Wickner, R.B. and Icho, T. and Fujimura, T. and Widner, W.R.}, year = 1991, month = jan, journal = {Journal of Virology}, volume = {65}, number = {1}, pages = {155–161}, doi = {10.1128/jvi.65.1.155-161.1991}, url = {ISI:A1991EM92600019}, abstract = {The plus strand of the L-A double-stranded RNA virus of Saccharomyces cerevisiae has two large open reading frames, ORF1, which encodes the major coat protein, and ORF2, which encodes a single-stranded RNA-binding protein having a sequence diagnostic of viral RNA-dependent RNA polymerases. ORF2 is expressed only as a Gag-Pol-type fusion protein with ORF1. We have constructed a plasmid which expresses these proteins from the yeast PGK1 promoter. We show that this plasmid can support the replication of the killer toxin-encoding M1 satellite virus in the absence of an L-A double-stranded RNA helper virus itself. This requires ORF2 expression, providing a potential in vivo assay for the RNA polymerase and single-stranded RNA-binding activities of the fusion protein determined by ORF2. ORF1 expression, like a host ski- mutation, can suppress the usual requirement of M1 for the MAK11, MAK18, and MAK27 genes and allow a defective L-A (L-A-E) to support M1 replication. These results suggest that expression of ORF1 from the vector makes the cell a ski- phenocopy. Indeed, expression of ORF1 in a wild-type killer makes it a superkiller, suggesting that a target of the SKI antiviral system may be the major coat protein}, keywords = {0,antiviral,ANTIVIRAL SYSTEM,Capsid,CEREVISIAE,CHROMOSOMAL GENES,COAT PROTEIN,CYTO-PATHOLOGY,disease,DNA-Directed RNA Polymerase,DNA-Directed RNA Polymerases,DOUBLE-STRANDED-RNA,ENCODES,enzymology,Escherichia coli,expression,FRAME,FUSION PROTEIN,gene,Genes,GenesViral,Genetic,Genetic Vectors,genetics,Genotype,IN-VIVO,INVITRO,Kidney,killer,KILLER SYSTEMS,L-A,La,M1,Mutagenesis,Mutation,nosource,OPEN READING FRAME,Open Reading Frames,PARTICLES,PLASMID,Plasmids,polymerase,PROMOTER,protein,Proteins,READING FRAME,Reading Frames,REPLICATION,REQUIRES,Restriction Mapping,Rna,RNA Viruses,RNA-BINDING-PROTEIN,RNA-DEPENDENT RNA POLYMERASE,RNA-dependent RNA polymerases,RNA-POLYMERASE,RNADouble-Stranded,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SKI,SUPERKILLER MUTATIONS,Support,SuppressionGenetic,SYSTEM,TARGET,vector,vectors,virus,WILD-TYPE,yeast} } % == BibTeX quality report for wicknerExpressionYeastDoubleStrandedRNA1991: % ? Title looks like it was stored in title-case in Zotero % ? unused Journal abbr (“J.Virol.”)

@article{wicknerDoublestrandedSinglestrandedRNA1992a, title = {Double-Stranded and Single-Stranded {{RNA}} Viruses of ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Wickner, R.B.}, year = 1992, journal = {Annu.Rev.Microbiol.}, volume = {46}, pages = {347–375}, doi = {10.1146/annurev.mi.46.100192.002023}, keywords = {L-A,nosource,Review,Rna,RNA Viruses,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,virus,yeast} } % == BibTeX quality report for wicknerDoublestrandedSinglestrandedRNA1992a: % ? Possibly abbreviated journal title Annu.Rev.Microbiol.

@article{wicknerDoubleStrandedRNAVirusReplicationPackaging1993, title = {Double-{{Stranded-RNA Virus-Replication}} and {{Packaging}}}, author = {Wickner, R.B.}, year = 1993, month = feb, journal = {Journal of Biological Chemistry}, volume = {268}, number = {6}, pages = {3797–3800}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(18)53539-0}, url = {http://www.jbc.org/content/268/6}, keywords = {BACTERIOPHAGE-PHI-6,DOUBLE-STRANDED-RNA,ENCODES,L-A,nosource,packaging,PARTICLES,POLYPEPTIDES,protein,Reading Frames,Review,rotavirus,SACCHAROMYCES-CEREVISIAE,Virus Replication,yeast} } % == BibTeX quality report for wicknerDoubleStrandedRNAVirusReplicationPackaging1993: % ? Title looks like it was stored in title-case in Zotero

@article{wicknerURE3AlteredURE21994, title = {[{{URE3}}] as an Altered {{URE2}} Protein: Evidence for a Prion Analog in {{Saccharomyces}} Cerevisiae}, author = {Wickner, R.B.}, year = 1994, month = apr, journal = {Science}, volume = {264}, number = {5158}, pages = {566–569}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.7909170}, url = {http://www.sciencemag.org/content/264/5158/566.abstract}, abstract = {A cytoplasmically inherited element, [URE3], allows yeast to use ureidosuccinate in the presence of ammonium ion. Chromosomal mutations in the URE2 gene produce the same phenotype. [URE3] depends for its propagation on the URE2 product (Ure2p), a negative regulator of enzymes of nitrogen metabolism. Saccharomyces cerevisiae strains cured of [URE3] with guanidium chloride were shown to return to the [URE3]-carrying state without its introduction from other cells. Overproduction of Ure2p increased the frequency with which a strain became [URE3] by 100-fold. In analogy to mammalian prions, [URE3] may be an altered form of Ure2p that is inactive for its normal function but can convert normal Ure2p to the altered form. The genetic evidence presented here suggests that protein-based inheritance, involving a protein unrelated to the mammalian prion protein, can occur in a microorganism}, keywords = {0,ACID,analogs & derivatives,Aspartic Acid,Base Sequence,CELLS,CEREVISIAE,chemistry,CrossesGenetic,disease,enzyme,Enzymes,FORM,Fungal Proteins,gene,GenesDominant,GenesFungal,GenesRecessive,Genetic,genetics,Guanidine,Guanidines,Kidney,La,metabolism,Molecular Sequence Data,Mutation,MUTATIONS,Nitrogen,nosource,pharmacology,Phenotype,Plasmids,prion,Prions,PRODUCT,PROPAGATION,protein,Proteins,PrPSc Proteins,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,yeast} }

@article{wicknerDoublestrandedRNAViruses1996a, title = {Double-Stranded {{RNA}} Viruses of ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Wickner, R.B.}, year = 1996, journal = {Microbiol.Rev.}, volume = {60}, pages = {250–265}, doi = {10.1128/mr.60.1.250-265.1996}, keywords = {DOUBLE-STRANDED-RNA,nosource,Review,review article,Rna,RNA Viruses,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE} } % == BibTeX quality report for wicknerDoublestrandedRNAViruses1996a: % ? Possibly abbreviated journal title Microbiol.Rev.

@article{wicknerPrionsRNAViruses1996, title = {Prions and {{RNA}} Viruses of ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Wickner, R.B.}, year = 1996, journal = {Annu.Rev.Genet.}, volume = {30}, pages = {109–139}, doi = {10.1146/annurev.genet.30.1.109}, keywords = {nosource,prion,Prions,Review,Rna,RNA Viruses,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,virus,yeast} } % == BibTeX quality report for wicknerPrionsRNAViruses1996: % ? Possibly abbreviated journal title Annu.Rev.Genet.

@article{widmerCharacterizationRnaVirus1989, title = {Characterization of {{A Rna Virus}} from the {{Parasite Leishmania}}}, author = {Widmer, G. and Comeau, A.M. and Furlong, D.B. and Wirth, D.F. and Patterson, J.L.}, year = 1989, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {86}, number = {15}, pages = {5979–5982}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.86.15.5979}, url = {http://www.pnas.org/content/86/15/5979.short}, keywords = {nosource,Rna,virus} } % == BibTeX quality report for widmerCharacterizationRnaVirus1989: % ? Title looks like it was stored in title-case in Zotero

@article{widmerRNAPolymeraseActivity1990, title = {{{RNA}} Polymerase Activity Is Associated with Viral Particles Isolated from {{Leishmania}} Braziliensis Subsp. Guyanensis.}, author = {Widmer, G. and Keenan, M.C. and Patterson, J.L.}, year = 1990, journal = {Journal of Virology}, volume = {64}, number = {8}, pages = {3712–3715}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.64.8.3712-3715.1990}, url = {http://jvi.asm.org/cgi/content/abstract/64/8/3712}, keywords = {nosource,PARTICLES,RNA-POLYMERASE,viral particle} }

@article{widner20SRNANaked1991a, title = {Is {{20S RNA Naked}}}, author = {Widner, W.R. and Matsumoto, Y. and Wickner, R.B.}, year = 1991, month = may, journal = {Molecular and Cellular Biology}, volume = {11}, number = {5}, pages = {2905–2908}, doi = {10.1128/mcb.11.5.2905-2908.1991}, url = {ISI:A1991FJ15500064}, abstract = {The 20S RNA of Saccharomyces cerevisiae is a single-stranded, circular RNA virus. A previous study suggested that this RNA is part of a 32S ribonucleoprotein particle, being associated with multiple copies of a 23-kilodalton protein. We show here that this protein is, in fact, the chromosome-encoded heat shock protein Hsp26. Furthermore, it is apparently not associated with 20S RNA and plays no obvious role in the life cycle of the virus}, keywords = {CEREVISIAE,Heat,HEAT-SHOCK,HEAT-SHOCK PROTEINS,HSP26,nosource,protein,RIBONUCLEOPROTEIN,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SPORULATION,virus,yeast} } % == BibTeX quality report for widner20SRNANaked1991a: % ? Title looks like it was stored in title-case in Zotero

@article{widnerEvidenceThatSKI1993, title = {Evidence That the {{SKI}} Antiviral System of {{Saccharomyces}} Cerevisiae Acts by Blocking Expression of Viral {{mRNA}}.}, author = {Widner, W.R. and Wickner, R.B.}, year = 1993, month = jul, journal = {Molecular and cellular biology}, volume = {13}, number = {7}, pages = {4331–4341}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/13/7/4331}, abstract = {The SKI2 gene is part of a host system that represses the copy number of the L-A double-stranded RNA (dsRNA) virus and its satellites M and X dsRNA, of the L-BC dsRNA virus, and of the single-stranded replicon 20S RNA. We show that SKI2 encodes a 145-kDa protein with motifs characteristic of helicases and nucleolar proteins and is essential only in cells carrying M dsRNA. Unexpectedly, Ski2p does not repress M1 dsRNA copy number when M1 is supported by aN L-A cDNA clone; nonetheless, it did lower the levels of M1 dsRNA-encoded toxin produced. Since toxin secretion from cDNA clones of M1 is unaffected by Ski2p, these data suggest that Ski2p acts by specifically blocking translation of viral mRNAs, perhaps recognizing the absence of cap or poly(A). In support of this idea, we find that Ski2p represses production of beta-galactosidase from RNA polymerase I [no cap and no poly(A)] transcripts but not from RNA polymerase II (capped) transcripts}, keywords = {0,Amino Acid Sequence,antagonists & inhibitors,antiviral,Antiviral Agents,ANTIVIRAL SYSTEM,Base Sequence,beta-Galactosidase,Cap,CELLS,CEREVISIAE,CloningMolecular,COMPLEX,COMPLEXES,disease,Dna,DNAFungal,DOUBLE-STRANDED-RNA,DSRNA,dsRNA virus,ENCODES,expression,Fungal Proteins,gene,Gene Expression RegulationViral,GenesFungal,Genetic,genetics,growth & development,Helicase,Kidney,L-A,L-BC,La,M,M1,metabolism,Molecular Sequence Data,MOTIFS,mRNA,Multienzyme Complexes,Multiple DOI,MutagenesisSite-Directed,nonfile,nosource,Nuclear Proteins,poly(A),polymerase,Promoter Regions (Genetics),protein,Proteins,Restriction Mapping,Rna,RNA Polymerase I,RNA Polymerase II,RNA-POLYMERASE,RNA-POLYMERASE-I,RNA-POLYMERASE-II,RNADouble-Stranded,RNAMessenger,RnaViral,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SKI,SKI2,Support,SYSTEM,toxin,TRANSCRIPT,translation,virus} } % == BibTeX quality report for widnerEvidenceThatSKI1993: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{wildSRPMeetsRibosome2004, title = {{{SRP}} Meets the Ribosome}, author = {Wild, K. and Halic, M. and Sinning, I. and Beckmann, R.}, year = 2004, month = nov, journal = {Nature Structural & Molecular Biology}, volume = {11}, number = {11}, pages = {1049–1053}, publisher = {Nature Publishing Group}, doi = {10.1038/nsmb853}, url = {http://www.nature.com/nsmb/journal/v11/n11/abs/nsmb853.html}, abstract = {Cotranslational targeting directly couples synthesis of proteins to their translocation across or insertion into membranes. The signal recognition particle (SRP) and its membrane-bound receptor facilitate the targeting of the translation machinery, the ribosome, via recognition of a signal sequence in the nascent peptide chain. By combining structures of free and ribosome-bound SRP we derive a structural model describing the dynamic nature of SRP when it meets the ribosome}, keywords = {0,Animals,CEREVISIAE,chemistry,CrystallographyX-Ray,Germany,Guanosine,Guanosine Triphosphate,Humans,La,metabolism,MODEL,ModelsBiological,NASCENT-PEPTIDE,nosource,physiology,protein,Protein Biosynthesis,Protein Conformation,Protein StructureTertiary,Protein Transport,Proteins,RECOGNITION,Review,ribosome,Ribosomes,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,SIGNAL,SIGNAL RECOGNITION PARTICLE,Signal Transduction,Structural,structure,Sulfolobus,Support,translation,translocation} } % == BibTeX quality report for wildSRPMeetsRibosome2004: % ? unused Journal abbr (“Nat.Struct.Mol Biol”)

@article{williamsDevelopmentalRegulationRibosomal1995, title = {Developmental Regulation of Ribosomal Protein {{L16}} Genes in {{Arabidopsis}} Thaliana}, author = {Williams, M.E. and Sussex, I.M.}, year = 1995, month = jul, journal = {The Plant Journal}, volume = {8}, number = {1}, pages = {65–76}, publisher = {Wiley Online Library}, doi = {10.1046/j.1365-313X.1995.08010065.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-313X.1995.08010065.x/pdf}, abstract = {Lateral roots can be synchronously induced in Arabidopsis by a brief auxin treatment. An early event in the development of a lateral root primordium is the accumulation of mRNAs encoding ribosomal proteins. In situ hybridizations show that mRNA encoding one ribosomal protein, L16, accumulates in all rapidly proliferating tissues including the shoot and root apical meristems and lateral root primordia. To understand further the mechanisms by which ribosomal proteins are coordinately synthesized, two genes encoding the ribosomal protein L16 were isolated from Arabidopsis thaliana. Promoter sequences from each RPL16A and RPL16B were fused to the beta-glucuronidase reporter gene GUS. The promoter of RPL16B(from -848 to -19) conferred X-Gluc staining in proliferating tissues including the shoot and root apical meristems. When GUS was expressed from the RPL16A promoter (from -875 to -22), X-Gluc staining was observed in cells in the root stele and in anthers. When seedlings transformed with either promoter construct were treated with auxin to induce lateral roots, X-Gluc staining accumulated in the lateral root primordia by 16 h after induction. Transcription of the RPL16B promoter appears to be correlated with cell division, while transcription of the RPL16A promoter is very cell specific. Expression of two genes encoding L16 during the early phase of lateral root initiation and in developing pollen may serve to increase levels of ribosomal proteins during the rapid growth of these tissues}, keywords = {0,Amino Acid Sequence,Arabidopsis,Base Sequence,BIOLOGY,Cell Division,CELLS,development,Dna,DNAComplementary,expression,FUSION PROTEIN,gene,Gene Expression RegulationDevelopmental,Gene Expression RegulationPlant,Genes,genetics,Glucuronidase,GROWTH,in situ hybridization,initiation,La,MECHANISM,MECHANISMS,Molecular Sequence Data,mRNA,nosource,PROMOTER,Promoter Regions (Genetics),protein,Proteins,Recombinant Fusion Proteins,regulation,Research SupportU.S.Gov’tNon-P.H.S.,Ribosomal Proteins,RIBOSOMAL-PROTEIN,sequence,Sequence HomologyAmino Acid,Sequence HomologyNucleic Acid,SEQUENCES,Staining,transcription} } % == BibTeX quality report for williamsDevelopmentalRegulationRibosomal1995: % ? unused Journal abbr (“Plant J.”)

@article{williamsMutationsStructuralGenes1989a, title = {Mutations in the Structural Genes for Eukaryotic Initiation Factors 2`a and 2'a of ⬚{{Saccharomyces}} Cerevisiae⬚ Disrupt Translational Control of ⬚{{GCN4}}⬚ {{mRNA}}.}, author = {Williams, N.P. and Hinnebusch, A.G. and Donahue, T.F.}, year = 1989, journal = {Proc.Natl.Acad.Sci.USA}, volume = {86}, pages = {7515–7519}, doi = {10.1073/pnas.86.19.7515}, keywords = {GCN4,gene,Genes,initiation,mRNA,Mutation,MUTATIONS,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Structural,SUI2,SUI3} } % == BibTeX quality report for williamsMutationsStructuralGenes1989a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{williamsonPosttranslationalProcessingRat1997a, title = {Post-Translational Processing of Rat Ribosomal Proteins. {{Ubiquitous}} Methylation of {{Lys22}} within the Zinc-Finger Motif of {{RL40}} (Carboxy-Terminal Extension Protein 52) and Tissue-Specific Methylation of {{Lys4}} in {{RL29}}.}, author = {Williamson, N.A. and Raliegh, J. and Morrice, N.A. and Wettenhall, R.E.}, year = 1997, month = jun, journal = {European journal of biochemistry/FEBS}, volume = {246}, number = {3}, eprint = {9219540}, eprinttype = {pubmed}, pages = {786–793}, doi = {10.1111/j.1432-1033.1997.00786.x}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9219540/}, abstract = {The complete amino acid sequences of rat and yeast (Saccharomyces cerevisiae) ribosomal proteins derived from precursors containing an N-terminal ubiquitin or ubiquitin-like sequence (C-terminal extension proteins or CEPs) were determined and investigated for any post-translational modifications by reverse-phase HPLC purification, direct amino acid sequence and mass spectrometric analyses. Covalent modifications were detected in the rat liver proteins RS27a (CEP-80), RL29, RL37 and RL40 (CEP-52), while RS30 (CEP), RL36a, RL39 and RL41 were unmodified. Heterogeneity of RS27a was due to C-terminal truncations, with Lys80 missing from about 20% of the liver RS27a population; C-terminal processing was also detected with RL29 and RL37. No other covalent modifications of liver, brain or thymus RS27a were detected. The rat RL40 structure was identical to the cDNA-predicted sequence except for complete stoichiometric N epsilon-trimethylation of Lys22 within its zinc-finger motif; this modification occurred in the ribosomes of all three rat tissues investigated but not in yeast ribosomes. The methylation characteristics of RL40 were distinct from those of ribosomal protein RL29 in the rat, which was differentially monomethylated at Lys4 in the liver, brain and thymus (27%, {\(>\)} 99% and 95% methylation, respectively). In the case of liver, there was no appreciable difference in the RL29 methylation status of free and membrane-bound ribosomes. The possibilities of an essential role for RL40 methylation in the formation of rat ribosomes, and a distinct regulatory role for RL29 methylation in the rat, are discussed}, keywords = {0,ACID,Amino Acid Sequence,AMINO-ACID,Animals,Biochemistry,BIOLOGY,Brain,CEREVISIAE,chemistry,ChromatographyHigh Pressure Liquid,Comparative Study,Fungal Proteins,La,Liver,Lysine,metabolism,Methylation,modification,Molecular Biology,Molecular Sequence Data,nosource,PRECURSOR,protein,Protein Precursors,Protein ProcessingPost-Translational,Proteins,purification,rat,Rats,Research SupportNon-U.S.Gov’t,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,structure,Subcellular Fractions,Thymus Gland,Ubiquitin,Ubiquitins,yeast,zinc finger motif,Zinc Fingers} } % == BibTeX quality report for williamsonPosttranslationalProcessingRat1997a: % ? unused Journal abbr (“Eur.J.Biochem.”)

@article{willsEvidenceThatDownstream1991, title = {Evidence That a Downstream Pseudoknot Is Required for Translational Read-through of the {{Moloney}} Murine Leukemia Virus Gag Stop Codon.}, author = {Wills, N.M. and Gesteland, R.F. and Atkins, J.F.}, year = 1991, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {88}, number = {August}, pages = {6991–6995}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.88.16.6991}, url = {http://www.pnas.org/content/88/16/6991.short}, abstract = {Approximately 5% of the ribosomes translating the gag gene of murine leukemia viruses read through the UAG terminator and translate the in-frame pol gene to produce the gag-pol fusion polyprotein, the sole source of the pol gene products. We show that a pseudoknot located eight nucleotides 3’ of the UAG codon in the Moloney murine leukemia virus is required for read-through. This requirement is markedly different from that known to be involved in other cases of read-through but surprisingly similar to some stimulatory sequences known to promote ribosomal frameshifting}, keywords = {3,AMBER TERMINATION CODON,CELLS,Codon,DOWNSTREAM,Frameshifting,Gag,Gag-pol,gene,human,LEUKEMIA,M,MESSENGER-RNA,MURINE LEUKEMIA-VIRUS,nosource,NUCLEOTIDE-SEQUENCE,Nucleotides,pol,POL GENE,POLYPEPTIDE,POLYPROTEIN,Polyproteins,PRODUCT,PRODUCTS,protein,protein synthesis,pseudoknot,READ-THROUGH,readthrough,retrovirus,ribosomal frameshifting,ribosome,Ribosomes,sequence,SEQUENCES,STOP CODON,SUPPRESSOR TRANSFER-RNA,TRANSLATIONAL READTHROUGH,UAA,UAG TERMINATOR,virus} }

@article{willsPseudoknotDependentReadThroughRetroviral1994, title = {Pseudoknot-{{Dependent Read-Through}} of {{Retroviral Gag Termination Codons}} - {{Importance}} of {{Sequences}} in the {{Spacer}} and {{Loop-2}}}, author = {Wills, N.M. and Gesteland, R.F. and Atkins, J.F.}, year = 1994, journal = {The EMBO journal}, volume = {13}, number = {17}, pages = {4137–4144}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1994.tb06731.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC395336/pdf/emboj00065-0219.pdf http://www.ncbi.nlm.nih.gov/pmc/articles/PMC395336/}, abstract = {Retroviruses whose gag and pol genes are in the same reading frame depend upon similar to 5% read-through of the gag UAG termination codon to make the gag-pol polyprotein. For murine leukemia virus, this read-through is dependent on a pseudoknot located eight nucleotides 3’ of the UAG. Other retroviruses whose gag and pol genes are in the same frame can potentially form similar pseudoknots 3’ of their UAG codons. Beyond the similar secondary structures, there is strong sequence conservation in the spacer region and in loop 2 of the pseudoknots. The detrimental effects of substitutions of several of these conserved spacer and loop 2 nucleotides in the murine leukemia virus sequence show their importance for the read-through process. The importance of specific nucleotides in loop 2 of the pseudoknot contrasts with the flexibility of sequence in loop 2 of the most intensively studied frameshift-promoting pseudoknot which occurs in infectious bronchitis virus. Two nucleotides in loop 2 of the murine leukemia virus pseudoknot, which were shown to be important by mutagenic analysis, display hypersensitivity to the single-strand specific nuclease, S1. They are likely to be particularly accessible or are in an unusually reactive conformation}, keywords = {3,analysis,Codon,CODONS,COMPLETE NUCLEOTIDE-SEQUENCE,CONFORMATION,FORM,FRAME,Gag,Gag-pol,gene,GENE-EXPRESSION,Genes,human,IMMEDIATELY DOWNSTREAM,IMMEDIAY DOWNSTREAM,Infectious bronchitis virus,LEUKEMIA,LOOP,M,MESSENGER-RNA,MURINE LEUKEMIA-VIRUS,MUTATIONAL ANALYSIS,nosource,Nucleotides,pol,POL FUSION PROTEIN,POLYPROTEIN,pseudoknot,pseudoknots,read-through,READ-THROUGH,READING FRAME,readthrough,recoding,REGION,retrovirus,RETROVIRUSES,RIBOSOMAL FRAMESHIFTING SIGNAL,RNA PSEUDOKNOT,SECONDARY STRUCTURE,sequence,SEQUENCES,structure,termination,TERMINATION CODON,TERMINATION-CODON,TRANSLATIONAL READTHROUGH,virus} } % == BibTeX quality report for willsPseudoknotDependentReadThroughRetroviral1994: % ? Title looks like it was stored in title-case in Zotero

@article{willsReportedTranslationalBypass1997a, title = {Reported Translational Bypass in a {{trpR}}‘-{{lacZ}}’ Fusion Is Accounted for by Unusual Initiation and +1 Frameshifting}, author = {Wills, N.M. and Ingram, J.A. and Gesteland, R.F. and Atkins, J.F.}, year = 1997, month = aug, journal = {Journal of Molecular Biology}, volume = {271}, number = {4}, pages = {491–498}, doi = {10.1006/jmbi.1997.1187}, keywords = {+1 frameshifting,beta-Galactosidase,decoding,Escherichia coli,ESCHERICHIA-COLI,expression,Frameshifting,gene,Genes,initiation,nosource,PROMOTER,translational bypass} }

@article{wilsonMutationsExon31993, title = {Mutations in Exon 3 of the Lipoprotein Lipase Gene Segregating in a Family with Hypertriglyceridemia, Pancreatitis, and Non-Insulin-Dependent Diabetes.}, author = {Wilson, D.E. and Hata, A. and Kwona, L.K. and Lingam, A. and Shuhua, J. and Ridinger, D.N. and Yeager, C. and Kaltenborn, K.C. and Iverius, P.-H. and Lalouel, J.-M.}, year = 1993, journal = {Journal of Clinical Investigation}, volume = {92}, number = {1}, pages = {203–211}, publisher = {American Society for Clinical Investigation}, doi = {10.1172/JCI116551}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC293568/}, keywords = {frameshift,gene,heart,human,Mutation,MUTATIONS,nosource} } % == BibTeX quality report for wilsonMutationsExon31993: % ? unused Journal abbr (“J.Clin.Invest.”)

@article{wilsonRibosomeLookingGlass2003, title = {The {{Ribosome}} through the {{Looking Glass}}}, author = {Wilson, D.N. and Nierhaus, K.H.}, year = 2003, journal = {Angewandte Chemie International Edition}, volume = {42}, number = {30}, pages = {3464–3486}, publisher = {Wiley Online Library}, doi = {10.1002/anie.200200544}, url = {http://onlinelibrary.wiley.com/doi/10.1002/anie.200200544/full}, abstract = {For almost 20 years crystallographers have sought to solve the structure of the ribosome, the largest and most complicated RNA-protein complex in the cell. All ribosomes are composed of a large and small subunit which for the humble bacterial ribosome comprise more than 4000 ribonucleotides, 54 different proteins, and have a molecular mass totaling over 2.5 million Daltons. The past few years have seen the resolution of structures at the atomic level for both large and small subunits and of the complete 70S ribosome from Thermus thermophilus at a resolution of 5.5-A. Soaking of small ligands (such as antibiotics, substrate analogues, and small translational factors) into the crystals of the subunits has revolutionized our understanding of the central functions of the ribosome. Coupled with the power of cryo-electron microscopic studies of translation complexes, a collection of snap-shots is accumulating, which can be assembled to create a likely motion picture of the bacterial ribosome during translation. Recent analyses show yeast ribosomes have a remarkable structural similarity to bacterial ribosomes. This Review aims to follow the bacterial ribosome through each sequential “frame” of the translation cycle, emphasizing at each point the features that are found in all organisms}, keywords = {70S RIBOSOME,antibiotic,antibiotics,Bacterial,COMPLEX,COMPLEXES,Glass,La,Ligands,nosource,protein,Proteins,RESOLUTION,Review,Ribonucleotides,ribosome,Ribosomes,Structural,structure,SUBUNIT,SUBUNITS,Thermus,Thermus thermophilus,THERMUS-THERMOPHILUS,translation,yeast} } % == BibTeX quality report for wilsonRibosomeLookingGlass2003: % ? Title looks like it was stored in title-case in Zotero % ? unused Journal abbr (“Angew.Chem.Int.Ed Engl.”)

@article{wilsonAssemblyAUF1Oligomers1999, title = {Assembly of {{AUF1}} Oligomers on {{U-rich RNA}} Targets by Sequential Dimer Association}, author = {Wilson, G.M. and Sun, Y. and Lu, H. and Brewer, G.}, year = 1999, month = nov, journal = {Journal of Biological Chemistry}, volume = {274}, number = {47}, pages = {33374–33381}, publisher = {ASBMB}, doi = {10.1074/jbc.274.47.33374}, url = {http://www.jbc.org/content/274/47/33374.short}, abstract = {Many labile mammalian mRNAs are targeted for rapid cytoplasmic turnover by the presence of A + U-rich elements (AREs) within their 3’- untranslated regions. These elements are selectively recognized by AUF1, a component of a multisubunit complex that may participate in the initiation of mRNA decay. In this study, we have investigated the recognition of AREs by AUF1 in vitro using oligoribonucleotide substrates. Gel mobility shift assays demonstrated that U-rich RNA targets were specifically bound by AUF1, generating two distinct RNA- protein complexes in a concentration-dependent manner. Chemical cross- linking revealed the interaction of AUF1 dimers to form tetrameric structures involving protein-protein interactions in the presence of high affinity RNA targets. From these data, a model of AUF1 association with AREs involving sequential dimer binding was developed. Using fluorescent RNA substrates, binding parameters of AUF1 dimer-ARE and tetramer-ARE equilibria were evaluated in solution by fluorescence anisotropy measurements. Using two AUF1 deletion mutants, sequences C- terminal to the RNA recognition motifs are shown to contribute to the formation of the AUF1 tetramer.ARE complex but are not obligate for RNA binding activity. Kinetic studies demonstrated rapid turnover of AUF1.ARE complexes in solution, suggesting that these interactions are very dynamic in character. Taken together, these data support a model where ARE-dependent oligomerization of AUF1 may function to nucleate the formation of a trans-acting, RNA-destabilizing complex in vivo}, keywords = {0,3’ UNTRANSLATED REGION,3’ Untranslated Regions,3’-UNTRANSLATED REGION,anisotropy,assays,assembly,ASSOCIATION,Base Sequence,BINDING,Binding Sites,Biopolymers,CHARACTER,chemistry,COMPLEX,COMPLEXES,COMPONENT,CROSS-LINKING,CROSSLINKING,D,DECAY,DIMER,Dimerization,ELEMENTS,Fluorescence,Fluorescence Polarization,FORM,Heterogeneous-Nuclear Ribonucleoprotein D,HIV,human,Humans,In Vitro,IN-VITRO,IN-VIVO,initiation,La,metabolism,microbiology,MODEL,MOTIFS,mRNA,mRNA decay,MUTANTS,nosource,protein,PROTEIN COMPLEX,Proteins,RECOGNITION,Recombinant Proteins,REGION,RIBONUCLEOPROTEIN,Rna,RNA recognition,RNA-Binding Proteins,RNA-BINDING-PROTEIN,sequence,SEQUENCES,structure,Support,supportu.s.gov’tp.h.s.,TARGET,turnover,Untranslated Regions} } % == BibTeX quality report for wilsonAssemblyAUF1Oligomers1999: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{wilsonFluorescencebasedAssay32000, title = {A Fluorescence-Based Assay for 3’–{\(>\)} 5’exoribonucleases: Potential Applications to the Study of {{mRNA}} Decay.}, author = {Wilson, G. M. and Lu, H. and Sun, Y. and Kennedy, A. and Brewer, G.}, year = 2000, month = mar, journal = {RNA}, volume = {6}, number = {3}, pages = {458}, publisher = {Cold Spring Harbor Lab}, url = {http://rnajournal.cshlp.org/content/6/3/458.short}, abstract = {A cell-free mRNA decay assay has been adapted to permit the kinetics of 3’ –{\(>\)} 5’ exoribonuclease activities to be monitored in real time. RNA probes containing 5’ caps and 3’ poly(A) tails generated by transcription in vitro are 3’ labeled using fluorescein-N6-ATP and poly(A) polymerase. Release of fluorescein-conjugated adenosine residues from the 3’ end of the RNA substrate is monitored by a time- dependent decrease in fluorescence anisotropy in the presence of cytosolic proteins. To demonstrate the utility of the assay, an RNA probe was constructed containing a fragment of the c-myc 3’ untranslated region and an 85-base poly(A) tail. Following 3’ fluorescein labeling, the rate of 3’-terminal adenosine excision was monitored in the presence of an S100 cytosolic extract prepared from K562 erythroleukemia cells. Removal of the fluorescein-tagged A residues resolved to a first-order decay function, allowing the rate constant and enzyme-specific activity to be determined in this extract. Further applications and advantages of this technology are discussed}, keywords = {0,Adenosine,Adenosine Triphosphate,anisotropy,Cap,Cell Extracts,Cell-Free System,chemistry,Cytosol,DECAY,enzymology,Exodeoxyribonucleases,Exoribonucleases,Fluorescein,Fluorescence,Fluorescence Polarization,Genetic,genetics,human,In Vitro,IN-VITRO,K562 Cells,Kinetics,La,metabolism,microbiology,mRNA,mRNA decay,nosource,Poly A,poly(A),polymerase,protein,Proteins,Rna,RNA Probes,RNAMessenger,SpectrometryFluorescence,supportu.s.gov’tp.h.s.,transcription,TranscriptionGenetic} }

@article{wilsonFoldingUrichRNA2001a, title = {Folding of {{A}}+{{U-rich RNA Elements Modulates AUF1 Binding}}. {{POTENTIAL ROLES IN REGULATION OF mRNA TURNOVER}}}, author = {Wilson, G.M. and Sutphen, K. and Chuang, Ky and Brewer, G.}, year = 2001, month = mar, journal = {Journal of Biological Chemistry}, volume = {276}, number = {12}, pages = {8695–8704}, doi = {10.1074/jbc.M009848200}, url = {PM:11124962}, abstract = {In mammals, A+U-rich elements (AREs) are potent cis-acting determinants of rapid cytoplasmic mRNA turnover. Recognition of these sequences by AUF1 is associated with acceleration of mRNA decay, likely involving recruitment or assembly of multi-subunit trans-acting complexes. Previously, we demonstrated that AUF1 deletion mutants formed tetramers on U-rich RNA substrates by sequential addition of protein dimers (Wilson, G. M., Sun, Y., Lu, H., and Brewer, G. (1999) J. Biol. Chem. 274, 33374-33381). Here, we show that binding of the full-length p37 isoform of AUF1 to these RNAs proceeds via a similar mechanism, allowing delineation of equilibrium binding constants for both stages of tetramer assembly. However, association of AUF1 with the ARE from tumor necrosis factor (TNFalpha) mRNA was significantly inhibited by magnesium ions. Further fluorescence and hydrodynamic experiments indicated that Mg(2+) induced or stabilized a conformational change in the TNFalpha ARE. Based on the solution of parameters describing both the protein-RNA and Mg(2+)-RNA equilibria, we present a dynamic, global equilibrium binding model describing the relationship between Mg(2+) and AUF1 binding to the TNFalpha ARE. These studies provide the first evidence that some AREs may adopt higher order RNA structures that regulate their interaction with trans-acting factors and indicate that mRNA structural remodeling has the potential to modulate the turnover rates of some ARE-containing mRNAs}, keywords = {assembly,BINDING,COMPLEX,COMPLEXES,DECAY,ELEMENTS,Fluorescence,Genetic,genetics,HIV,Ions,La,Magnesium,Mammals,MECHANISM,microbiology,mRNA,mRNA decay,nosource,protein,regulation,Rna,sequence,SEQUENCES,Structural,structure,turnover} } % == BibTeX quality report for wilsonFoldingUrichRNA2001a: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{wilsonThermodynamicsKineticsHsp702001, title = {Thermodynamics and Kinetics of {{Hsp70}} Association with {{A}} + {{U-rich mRNA-destabilizing}} Sequences}, author = {Wilson, G.M. and Sutphen, K. and Bolikal, S. and Chuang, K.Y. and Brewer, G.}, year = 2001, month = nov, journal = {Journal of Biological Chemistry}, volume = {276}, number = {48}, pages = {44450–44456}, publisher = {ASBMB}, doi = {10.1074/jbc.M108521200}, url = {http://www.jbc.org/content/276/48/44450.short}, abstract = {Rapid mRNA degradation directed by A + U-rich elements (AREs) is mediated by the interaction of specific RNA-binding proteins to these sequences. The protein chaperone Hsp70 has been identified in a cellular complex containing the ARE-binding protein AUF1 and has also been detected in direct contact with A + U-rich RNA substrates, indicating that Hsp70 may be involved in the regulation of ARE-directed mRNA turnover. By using gel mobility shift and fluorescence anisotropy assays, we have determined that Hsp70 directly and specifically associates with U-rich RNA substrates in solution. With the ARE from tumor necrosis factor alpha (TNFalpha) mRNA, Hsp70 forms a dynamic complex consistent with a 1:1 association of protein:RNA but demonstrates cooperative binding behavior on polyuridylate substrates. Unlike AUF1, the RNA binding activity of Hsp70 is not regulated by ion-dependent folding of the TNFalpha ARE, suggesting that AUF1 and Hsp70 recognize distinct binding determinants on this RNA substrate. Binding of Hsp70 to the TNFalpha ARE is driven entirely by enthalpy at physiological temperatures, indicating that burial of hydrophobic surfaces is likely the principal mechanism stabilizing the Hsp70.RNA complex. Potential roles for the interaction of Hsp70 with ARE-containing mRNAs in the regulation of mRNA turnover and/or translational efficiency are discussed}, keywords = {0,Adenosine,Animals,anisotropy,assays,ASSOCIATION,BINDING,Binding Sites,chaperone,chemistry,COMPLEX,COMPLEXES,degradation,Dose-Response RelationshipDrug,efficiency,ELEMENTS,Fluorescence,Fluorescence Polarization,FORM,Genetic,genetics,heat shock proteins,HEAT-SHOCK,HEAT-SHOCK PROTEIN,HEAT-SHOCK PROTEINS,Histidine,HSP70 Heat-Shock Proteins,Ions,Kinetics,La,MECHANISM,metabolism,microbiology,MOLECULAR-GENETICS,mRNA,mRNA turnover,nosource,Poly U,protein,Protein Binding,Protein Biosynthesis,Proteins,Rabbits,Recombinant Proteins,regulation,Rna,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAMessenger,sequence,SEQUENCES,Support,Temperature,Thermodynamics,Time Factors,Tumor Necrosis Factor-alpha,turnover,Uracil} } % == BibTeX quality report for wilsonThermodynamicsKineticsHsp702001: % ? unused Journal abbr (“J.Biol Chem.”)

@incollection{wilsonRNAFoldingRNAprotein2005, title = {{{RNA}} Folding and {{RNA-protein}} Binding Analyzed by Fluorescence Anisotropy and Resonance Energy Transfer.}, booktitle = {Reviews in Fluorescence, {{Vol}}. 2.}, author = {Wilson, G.M.}, year = 2005, pages = {223–243}, publisher = {Springer Science+Business Media, Inc.}, address = {New York}, collaborator = {Geddes, C.D. and Lakowicz, J.R.}, keywords = {anisotropy,BINDING,Energy Transfer,Fluorescence,nosource,Review,Rna,RNA folding} }

@article{wilsonInitiationProteinSynthesis2000, title = {Initiation of Protein Synthesis from the {{A}} Site of the Ribosome}, author = {Wilson, J.E. and Pestova, T.V. and Hellen, C.U. and Sarnow, P.}, year = 2000, journal = {Cell}, volume = {102}, number = {4}, pages = {511–520}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(00)00055-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867400000556}, abstract = {Positioning of the translation initiation complex on mRNAs requires interaction between the anticodon of initiator Met-tRNA, associated with eIF2-GTP and 40S ribosomal subunit, and the cognate start codon of the mRNA. We show that an internal ribosome entry site located in the genome of cricket paralysis virus can form 80S ribosomes without initiator Met-tRNA, eIF2, or GTP hydrolysis, with a CCU triplet in the ribosomal P site and a GCU triplet in the A site. P-site mutagenesis revealed that the P site was not decoded, and protein sequence analysis showed that translation initiates at the triplet in the A site. Translational initiation from the A site of the ribosome suggests that the repertoire of translated open reading frames in eukaryotic mRNAs may be greater than anticipated}, keywords = {0,A SITE,A-SITE,analysis,Animals,Anticodon,Base Sequence,Codon,CodonTerminator,COMPLEX,COMPLEXES,Cricket paralysis virus,Eukaryotic Initiation Factor-2,FORM,FRAME,genetics,Genome,GTP,Guanosine,Guanosine Triphosphate,Hydrolysis,immunology,initiation,INTERNAL RIBOSOME ENTRY,La,metabolism,microbiology,Molecular Sequence Data,mRNA,Mutagenesis,MutagenesisSite-Directed,nosource,Nucleic Acid Conformation,OPEN READING FRAME,Open Reading Frames,P SITE,P-SITE,Peptide Chain InitiationTranslational,protein,Protein Biosynthesis,protein synthesis,PROTEIN-SYNTHESIS,Rabbits,READING FRAME,Reading Frames,REQUIRES,RIBOSOMAL-SUBUNIT,ribosome,RIBOSOME ENTRY SITE,Ribosomes,Rna,RNAMessenger,RNATransferMet,sequence,Sequence Analysis,SEQUENCE-ANALYSIS,SITE,START CODON,SUBUNIT,Support,translation,TRANSLATION INITIATION,TRANSLATIONAL INITIATION,virus} }

@article{wilsonMolecularMovementTranslational1998a, title = {Molecular Movement inside the Translational Engine}, author = {Wilson, K.S. and Noller, H.F.}, year = 1998, month = feb, journal = {Cell}, volume = {92}, number = {3}, pages = {337–349}, doi = {10.1016/S0092-8674(00)80927-7}, url = {PM:9476894}, keywords = {0,BIOLOGY,chemistry,elongation,elongation factors,ELONGATION-FACTORS,La,ModelsGenetic,ModelsMolecular,Movement,nosource,Peptide Chain Elongation,Peptide Elongation Factors,physiology,Review,Ribosomes,Rna,RNATransfer} }

@article{wilsonInteractionsTranslationalFactor2004a, title = {Interactions of Translational Factor {{EF-G}} with the Bacterial Ribosome before and after {{mRNA}} Translocation}, author = {Wilson, K.S. and Nechifor, R.}, year = 2004, month = mar, journal = {J.Mol.Biol.}, volume = {337}, number = {1}, pages = {15–30}, doi = {10.1016/j.jmb.2004.01.013}, url = {PM:15001349}, abstract = {A conserved translation factor, known as EF-G in bacteria, promotes the translocation of tRNA and mRNA in the ribosome during protein synthesis. Here, EF-G.ribosome complexes in two intermediate states, before and after mRNA translocation, have been probed with hydroxyl radicals generated from free Fe(II)-EDTA. Before mRNA translocation and GTP hydrolysis, EF-G protected a limited set of nucleotides in both subunits of the ribosome from cleavage by hydroxyl radicals. In this state, an extensive set of nucleotides, in the platform and head domains of the 30S subunit and in the L7/L12 stalk region of the 50S subunit, became more exposed to hydroxyl radical attack, suggestive of conformational changes in these domains. Following mRNA translocation, EF-G protected a larger set of nucleotides (23S rRNA helices H43, H44, H89, and H95; 16S rRNA helices h5 and h15). No nucleotide with enhanced reactivity to hydroxyl radicals was detected in this latter state. Both before and after mRNA translocation, EF-G protected identical nucleotides in h5 and h15 of the 30S subunit. These results suggest that h5 and h15 may remain associated with EF-G during the dynamic course of the translocation mechanism. Nucleotides in H43 and H44 of the 50S subunit were protected only after translocation and GTP hydrolysis, suggesting that these helices interact dynamically with EF-G. The effects in H95 suggest that EF-G interacts weakly with H95 before mRNA translocation and strongly and more extensively with this helix following mRNA translocation}, keywords = {0,16S,Active TransportCell Nucleus,Bacteria,Bacterial,Bacterial Proteins,Base Sequence,chemistry,CLEAVAGE,COMPLEX,COMPLEXES,CONFORMATIONAL CHANGE,CONFORMATIONAL CHANGES,CONFORMATIONAL-CHANGE,DOMAIN,DOMAINS,EF-G,elongation,ELONGATION-FACTOR-G,genetics,GTP,Guanosine,Guanosine Triphosphate,Hydrolysis,Hydroxyl Radical,INTERMEDIATE,La,Macromolecular Systems,MECHANISM,metabolism,ModelsMolecular,Molecular Sequence Data,mRNA,nosource,Nucleic Acid Conformation,Nucleotides,Peptide Chain Elongation,Peptide Elongation Factor G,physiology,protein,Protein Conformation,Protein Subunits,protein synthesis,PROTEIN-SYNTHESIS,Proteins,REGION,ribosome,Ribosomes,Rna,RNABacterial,RNAMessenger,RNARibosomal16S,RNARibosomal23S,rRNA,SUBUNIT,SUBUNITS,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,SYSTEMS,translation,TranslationGenetic,translocation,tRNA} } % == BibTeX quality report for wilsonInteractionsTranslationalFactor2004a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{wilsonExpressionStrategiesYeast1986, title = {Expression Strategies of the Yeast Retrotransposon {{Ty}}: A Short Sequence Directs Ribosomal Frameshifting}, author = {Wilson, W. and Malim, M.H. and Mellor, J. and Kingsman, A.J. and Kingsman, S.M.}, year = 1986, journal = {Nucleic acids research}, volume = {14}, number = {17}, pages = {7001–7016}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/14.17.7001}, url = {http://nar.oxfordjournals.org/content/14/17/7001.short}, abstract = {The Ty element of yeast is a member of a class of eukaryotic transposons which bear a striking resemblance to retroviral proviruses in their structure and expression strategies (1,2). A direct comparison can be drawn between the production of a fusion protein encoded by Ty, resulting from a frameshift event which fuses two out-of-phase open reading frames TYA and TYB, and the production of Pr180gag-pol in a retrovirus such as Rous Sarcoma Virus (RSV) (3,4). We present data which shows, definitively, that RNA splicing is not responsible for the frameshift in Ty. By in vitro mutation of a class I element, Ty1-15, we demonstrate that 31 nucleotides contained within the region where the TYA and TYB open reading frames overlap direct the frameshift. Within this short sequence there is a region of homology with a class II element which we show is also able to frameshift}, keywords = {0,Base Sequence,CloningMolecular,Dna,DNA Transposable Elements,DNAFungal,ELEMENTS,expression,FRAME,frameshift,Frameshifting,FUSION PROTEIN,Gene Expression Regulation,genetics,In Vitro,IN-VITRO,La,Mutation,nosource,Nucleotides,OPEN READING FRAME,Open Reading Frames,physiology,protein,Protein Biosynthesis,Proviruses,READING FRAME,Reading Frames,REGION,Research SupportNon-U.S.Gov’t,retrotransposon,retrovirus,ribosomal frameshifting,Ribosomes,Rna,RNA Splicing,Saccharomyces cerevisiae,sequence,splicing,structure,Ty,virus,yeast} } % == BibTeX quality report for wilsonExpressionStrategiesYeast1986: % ? unused Journal abbr (“Nucleic Acids Res.”)

@article{wilsonHIVExpressionStrategies1988a, title = {{{HIV}} Expression Strategies: Ribosomal Frameshifting Is Directed by a Short Sequence in Both Mammalian and Yeast Systems.}, author = {Wilson, W. and Braddock, M. and Adams, S.E. and Rathjen, P.D. and Kingsman, S.M. and Kingsman, A.J.}, year = 1988, journal = {Cell}, volume = {55}, pages = {1159–1169}, doi = {10.1016/0092-8674(88)90260-7}, keywords = {expression,frameshift,Frameshifting,HIV,human,nosource,ribosomal frameshifting,sequence,SIGNAL,SYSTEM,yeast} }

@article{wimberlyDetailedViewRibosomal1999, title = {A Detailed View of a Ribosomal Active Site: The Structure of the {{L11- RNA}} Complex.}, author = {Wimberly, B.T. and Guymon, R. and McCutcheon, J.P. and White, S.W. and Ramakrishnan, V.}, year = 1999, month = may, journal = {Cell}, volume = {97}, number = {4}, pages = {491–502}, doi = {10.1016/S0092-8674(00)80759-X}, abstract = {We report the crystal structure of a 58 nucleotide fragment of 23S ribosomal RNA bound to ribosomal protein L11. This highly conserved ribonucleoprotein domain is the target for the thiostrepton family of antibiotics that disrupt elongation factor function. The highly compact RNA has both familiar and novel structural motifs. While the C-terminal domain of L11 binds RNA tightly, the N-terminal domain makes only limited contacts with RNA and is proposed to function as a switch that reversibly associates with an adjacent region of RNA. The sites of mutations conferring resistance to thiostrepton and micrococcin line a narrow cleft between the RNA and the N-terminal domain. These antibiotics are proposed to bind in this cleft, locking the putative switch and interfering with the function of elongation factors}, keywords = {99268535,Amino Acid Sequence,antibiotic,antibiotics,AntibioticsPeptide,Bacterial Proteins,Binding Sites,chemistry,COMPLEX,COMPLEXES,CRYSTAL-STRUCTURE,CrystallographyX-Ray,elongation,genetics,GTP Phosphohydrolase,metabolism,Metals,Molecular Sequence Data,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,protein,Protein Conformation,Ribose,Ribosomal Proteins,RIBOSOMAL-RNA,Ribosomes,Rna,RNABacterial,RNARibosomal23S,Sequence HomologyAmino Acid,Structural,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Thermotoga maritima,Thiostrepton} }

@article{wimberlyStructure30SRibosomal2000, title = {Structure of the {{30S}} Ribosomal Subunit.}, author = {Wimberly, B.T. and Brodersen, D.E. and Clemons, W.M. and {Morgan-Warren}, R.J. and Carter, A.P. and Vonrhein, C. and Hartsch, T. and Ramakrishnan, V.}, year = 2000, journal = {Nature}, volume = {407}, number = {6802}, pages = {327–339}, doi = {10.1038/35030006}, abstract = {Genetic information encoded in messenger RNA is translated into protein by the ribosome, which is a large nucleoprotein complex comprising two subunits, denoted 30S and 50S in bacteria. Here we report the crystal structure of the 30S subunit from Thermus thermophilus, refined to 3 A resolution. The final atomic model rationalizes over four decades of biochemical data on the ribosome, and provides a wealth of information about RNA and protein structure, protein-RNA interactions and ribosome assembly. It is also a structural basis for analysis of the functions of the 30S subunit, such as decoding, and for understanding the action of antibiotics. The structure will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography}, keywords = {20466110,analysis,antibiotic,antibiotics,assembly,Bacteria,Bacterial Proteins,chemistry,COMPLEX,COMPLEXES,CRYSTAL-STRUCTURE,Crystallography,CrystallographyX-Ray,decoding,Genetic,Macromolecular Systems,MESSENGER-RNA,ModelsMolecular,nosource,Nucleic Acid Conformation,protein,Protein Conformation,protein-RNA interactions,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNABacterial,RNARibosomal,Structural,STRUCTURAL BASIS,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,Thermus,Thermus thermophilus} }

@article{winklerThiamineDerivativesBind2002, title = {Thiamine Derivatives Bind Messenger {{RNAs}} Directly to Regulate Bacterial Gene Expression}, author = {Winkler, W. and Nahvi, A. and Breaker, R.R.}, year = 2002, month = oct, journal = {Nature}, volume = {419}, number = {6910}, pages = {952–956}, publisher = {Nature Publishing Group}, doi = {10.1038/nature01145}, url = {http://www.nature.com/nature/journal/v419/n6910/abs/nature01145.html}, abstract = {Although proteins fulfil most of the requirements that biology has for structural and functional components such as enzymes and receptors, RNA can also serve in these capacities. For example, RNA has sufficient structural plasticity to form ribozyme and receptor elements that exhibit considerable enzymatic power and binding specificity. Moreover, these activities can be combined to create allosteric ribozymes that are modulated by effector molecules. It has also been proposed that certain messenger RNAs might use allosteric mechanisms to mediate regulatory responses depending on specific metabolites. We report here that mRNAs encoding enzymes involved in thiamine (vitamin B(1)) biosynthesis in Escherichia coli can bind thiamine or its pyrophosphate derivative without the need for protein cofactors. The mRNA-effector complex adopts a distinct structure that sequesters the ribosome-binding site and leads to a reduction in gene expression. This metabolite-sensing regulatory system provides an example of a ‘riboswitch’ whose evolutionary origin might pre-date the emergence of proteins}, keywords = {0,ACID,Allosteric Regulation,Allosteric Site,analogs & derivatives,Bacteria,Bacterial,Bacterial Proteins,Base Sequence,BINDING,BIOLOGY,biosynthesis,Caenorhabditis,Caenorhabditis elegans,Caenorhabditis elegans Proteins,CAENORHABDITIS-ELEGANS,chemistry,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,derivatives,drug effects,ELEGANS,ELEMENTS,enzyme,Enzymes,Escherichia coli,Escherichia coli Proteins,ESCHERICHIA-COLI,expression,FORM,gene,Gene Expression,Gene Expression RegulationBacterial,GENE-EXPRESSION,GenesBacterial,genetics,La,MECHANISM,MECHANISMS,MESSENGER-RNA,MESSENGER-RNAS,metabolism,Molecular Sequence Data,mRNA,Mutation,nosource,Nucleic Acid Conformation,pharmacology,protein,Proteins,ReceptorsNeuropeptide Y,Regulatory SequencesRibonucleic Acid,RIBONUCLEIC-ACID,RIBOSOME BINDING,Ribosomes,riboswitch,ribozyme,Rna,RNABacterial,RNAMessenger,sequence,SEQUENCES,SITE,SPECIFICITY,Structural,structure,Substrate Specificity,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,SYSTEM,Thiamine,Thiamine Pyrophosphate,TranslationGenetic} }

@article{winklerMRNAStructureThat2003a, title = {An {{mRNA}} Structure That Controls Gene Expression by Binding {{S-adenosylmethionine}}}, author = {Winkler, W.C. and Nahvi, A. and Sudarsan, N. and Barrick, J.E. and Breaker, R.R.}, year = 2003, journal = {Nature structural biology}, volume = {10}, number = {9}, pages = {701–707}, doi = {10.1038/nsb967}, url = {http://ws1.izbi.uni-leipzig.de/pdf/wink-03-10-701-riboswitch-GE.pdf}, abstract = {Riboswitches are metabolite-binding RNA structures that serve as genetic control elements for certain messenger RNAs. These RNA switches have been identified in all three kingdoms of life and are typically responsible for the control of genes whose protein products are involved in the biosynthesis, transport or utilization of the target metabolite. Herein, we report that a highly conserved RNA domain found in bacteria serves as a riboswitch that responds to the coenzyme S-adenosylmethionine (SAM) with remarkably high affinity and specificity. SAM riboswitches undergo structural reorganization upon introduction of SAM, and these allosteric changes regulate the expression of 26 genes in Bacillus subtilis. This and related findings indicate that direct interaction between small metabolites and allosteric mRNAs is an important and widespread form of genetic regulation in bacteria}, keywords = {0,Bacillus subtilis,Bacteria,Base Sequence,BINDING,BIOLOGY,biosynthesis,chemistry,Dna,DOMAIN,ELEMENTS,expression,FORM,gene,Gene Expression,GENE-EXPRESSION,Genes,Genetic,Kinetics,La,MESSENGER-RNA,MESSENGER-RNAS,metabolism,ModelsChemical,Molecular Sequence Data,mRNA,Mutation,nosource,Nucleic Acid Conformation,PRODUCT,PRODUCTS,protein,Protein Binding,Protein StructureSecondary,Protein StructureTertiary,regulation,riboswitch,Rna,RNAMessenger,S-Adenosylmethionine,SPECIFICITY,Structural,structure,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,TARGET,TranscriptionGenetic,TRANSPORT} } % == BibTeX quality report for winklerMRNAStructureThat2003a: % ? unused Journal abbr (“Nat.Struct.Biol.”)

@article{winklerControlGeneExpression2004a, title = {Control of Gene Expression by a Natural Metabolite-Responsive Ribozyme}, author = {Winkler, W.C. and Nahvi, A. and Roth, A. and Collins, J.A. and Breaker, R.R.}, year = 2004, month = mar, journal = {Nature}, volume = {428}, number = {6980}, pages = {281–286}, doi = {10.1038/nature02362}, url = {http://staff.washington.edu/lgoo/PABIO551TA/Readings/Lecture 8/Winkler et al.pdf}, abstract = {Most biological catalysts are made of protein; however, eight classes of natural ribozymes have been discovered that catalyse fundamental biochemical reactions. The central functions of ribozymes in modern organisms support the hypothesis that life passed through an ‘RNA world’ before the emergence of proteins and DNA. We have identified a new class of ribozymes that cleaves the messenger RNA of the glmS gene in Gram-positive bacteria. The ribozyme is activated by glucosamine-6-phosphate (GlcN6P), which is the metabolic product of the GlmS enzyme. Additional data indicate that the ribozyme serves as a metabolite-responsive genetic switch that represses the glmS gene in response to rising GlcN6P concentrations. These findings demonstrate that ribozyme switches may have functioned as metabolite sensors in primitive organisms, and further suggest that modern cells retain some of these ancient genetic control systems}, keywords = {0,analogs & derivatives,Bacillus subtilis,Bacteria,Bacterial,Bacterial Proteins,Base Sequence,BIOLOGY,CELLS,COMPONENT,Dna,enzyme,Enzyme Activation,enzymology,expression,FeedbackBiochemical,gene,Gene Expression,Gene Expression RegulationBacterial,GENE-EXPRESSION,Genetic,genetics,Glucosamine,Glucose-6-Phosphate,La,MESSENGER-RNA,metabolism,Molecular Sequence Data,Mutation,nosource,PRODUCT,protein,Proteins,ribozyme,Rna,RNA world,RNABacterial,RNACatalytic,S,Support,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,SYSTEM,SYSTEMS,WORLD} }

@article{wittmannCrystallizationEscherichiaColi1982a, title = {Crystallization of {{Escherichia}} Coli Ribosomes}, author = {Wittmann, H.G. and Mussig, J. and Piefke, J. and Gewitz, H.S. and Rheinberger, H.J. and Yonath, A.}, year = 1982, journal = {FEBS Lett.}, volume = {146}, number = {1}, pages = {217–220}, doi = {10.1016/0014-5793(82)80739-4}, url = {http://webout.weizmann.ac.il/Structural_Biology/faculty_pages/Yonath/Wittmann-1982FL.pdf}, keywords = {Cell Fractionation,CentrifugationDensity Gradient,Crystallization,Escherichia coli,Escherichia coli ribosomes,ESCHERICHIA-COLI,La,metabolism,MicroscopyElectron,nosource,Poly U,ribosome,Ribosomes,ultrastructure} } % == BibTeX quality report for wittmannCrystallizationEscherichiaColi1982a: % ? Possibly abbreviated journal title FEBS Lett.

@article{woeseTranslationRetrospectProspect2001, title = {Translation: In Retrospect and Prospect.}, author = {Woese, C.R.}, year = 2001, journal = {Rna-A Publication of the Rna Society}, volume = {7}, number = {8}, pages = {1055–1067}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838201010615}, url = {http://rnajournal.cshlp.org/content/7/8/1055.short}, abstract = {This review is occasioned by the fact that the problem of translation, which has simmered on the biological sidelines for the last 40 years, is about to erupt center stage-thanks to the recent spectacular advances in ribosome structure. This most complex, beautiful, and fascinating of cellular mechanisms, the translation apparatus, is also the most important. Translation not only defines gene expression, but it is the sine qua non without which modern (protein-based) cells would not have come into existence. Yet from the start, the problem of translation has been misunderstood-a reflection of the molecular perspective that dominated Biology of the last century. In that the our conception of translation will play a significant role in creating the structure that is 21st century Biology, it is critical that our current (and fundamentally flawed) view of translation be understood for what it is and be reformulated to become an all-embracing perspective about which 21st century Biology can develop. Therefore, the present review is both a retrospective and a plea to biologists to establish a new evolutionary, RNA-World-centered concept of translation. What is needed is an evolutionarily oriented perspective that, first and foremost, focuses on the nature (and origin) of a primitive translation apparatus, the apparatus that transformed an ancient evolutionary era of nucleic acid life, the RNA World, into the world of modern cells.}, pmid = {11497425}, keywords = {A-site-P-site,ACID,adaptor,ANGSTROM RESOLUTION,BIOLOGY,CELLS,COMPLEX,COMPLEXES,Evolution,expression,gene,Gene Expression,GENE-EXPRESSION,GENETIC-CODE,MECHANISM,MECHANISMS,nosource,paradigm shift,Review,RIBOSOMAL-SUBUNIT,ribosome,Rna,RNA world,S,structure,templating,TRANSFER-RNA,translation,WORLD} }

@article{wohlgemuthRapidPeptideBond2006, title = {Rapid Peptide Bond Formation on Isolated {{50S}} Ribosomal Subunits}, author = {Wohlgemuth, I. and Beringer, M. and Rodnina, M.V.}, year = 2006, month = jul, journal = {EMBO Reports}, volume = {7}, number = {7}, pages = {699–703}, publisher = {Nature Publishing Group}, doi = {10.1038/sj.embor.7400732}, url = {http://www.nature.com/embor/journal/v7/n7/abs/7400732.html}, abstract = {The catalytic site of the ribosome, the peptidyl transferase centre, is located on the large (50S in bacteria) ribosomal subunit. On the basis of results obtained with small substrate analogues, isolated 50S subunits seem to be less active in peptide bond formation than 70S ribosomes by several orders of magnitude, suggesting that the reaction mechanisms on 50S subunits and 70S ribosomes may be different. Here we show that with full-size fMet-tRNA(fMet) and puromycin or C-puromycin as peptide donor and acceptor substrates, respectively, the reaction proceeds as rapidly on 50S subunits as on 70S ribosomes, indicating that the intrinsic activity of 50S subunits is not different from that of 70S ribosomes. The faster reaction on 50S subunits with fMet-tRNA(fMet), compared with oligonucleotide substrate analogues, suggests that full-size transfer RNA in the P site is important for maintaining the active conformation of the peptidyl transferase centre}, keywords = {0,70S RIBOSOME,Bacteria,Binding Sites,Biochemistry,BOND FORMATION,chemistry,CONFORMATION,Germany,In Vitro,IN-VITRO,Kinetics,La,MECHANISM,MECHANISMS,metabolism,nosource,P SITE,P-SITE,peptide bond formation,Peptides,peptidyl transferase,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,protein,Protein Subunits,Proteins,Puromycin,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNATransferMet,SITE,SUBUNIT,SUBUNITS,Support,TRANSFER-RNA,Transferases} } % == BibTeX quality report for wohlgemuthRapidPeptideBond2006: % ? unused Journal abbr (“EMBO Rep.”)

@article{wolfeMolecularEvidenceAncient1997, title = {Molecular Evidence for an Ancient Duplication of the Entire Yeast Genome}, author = {Wolfe, K.H. and Shields, D.C.}, year = 1997, month = jun, journal = {Nature}, volume = {387}, number = {6634}, pages = {708–713}, publisher = {Nature Publishing Group}, doi = {10.1038/42711}, url = {http://www.nature.com/nature/journal/v387/n6634/abs/387708a0.html}, abstract = {Gene duplication is an important source of evolutionary novelty. Most duplications are of just a single gene, but Ohno proposed that whole-genome duplication (polyploidy) is an important evolutionary mechanism. Many duplicate genes have been found in Saccharomyces cerevisiae, and these often seem to be phenotypically redundant. Here we show that the arrangement of duplicated genes in the S. cerevisiae genome is consistent with Ohno’s hypothesis. We propose a model in which this species is a degenerate tetraploid resulting from a whole-genome duplication that occurred after the divergence of Saccharomyces from Kluyveromyces. Only a small fraction of the genes were subsequently retained in duplicate (most were deleted), and gene order was rearranged by many reciprocal translocations between chromosomes. Protein pairs derived from this duplication event make up 13% of all yeast proteins, and include pairs of transcription factors, protein kinases, myosins, cyclins and pheromones. Tetraploidy may have facilitated the evolution of anaerobic fermentation in Saccharomyces}, keywords = {97336101,Chromosomes,ChromosomesFungal,classification,cyclins,Evolution,EvolutionMolecular,Fermentation,gene,Genes,Genetic,genetics,Genome,GenomeFungal,kinase,Kluyveromyces,MECHANISM,ModelsGenetic,Multigene Family,nosource,Pheromones,Phylogeny,Ploidies,protein,Protein Kinases,Proteins,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,supportnon-u.s.gov’t,transcription,TRANSCRIPTION FACTOR,Transcription Factors,translocation,yeast} }

@article{wolffTwoIsoformsEIF5A1992, title = {Two Isoforms of {{eIF-5A}} in Chick Embryo. {{Isolation}}, Activity, and Comparison of Sequences of the Hypusine-Containing Proteins.}, author = {Wolff, E.C. and Kinzy, T.G. and Merrick, W.C. and Park, M.H.}, year = 1992, month = mar, journal = {Journal of Biological Chemistry}, volume = {267}, number = {9}, pages = {6107–6113}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(18)42668-3}, url = {http://www.jbc.org/content/267/9/6107.short}, keywords = {Amino Acid Sequence,analysis,Chick Embryo,initiation,Lysine,nosource,protein,Proteins,purification,sequence,Sequence Analysis,SEQUENCES,Spermidine,Structural,Terminology,translation,TRANSLATION INITIATION} }

@article{wolinRibosomePausingStacking1988, title = {Ribosome Pausing and Stacking during Translation of a Eukaryotic {{mRNA}}.}, author = {Wolin, S.L. and Walter, P.}, year = 1988, journal = {The EMBO Journal}, volume = {7}, number = {11}, pages = {3559–3569}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1988.tb03233.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC454858/}, keywords = {mRNA,nosource,pausing,ribosome,translation} } % == BibTeX quality report for wolinRibosomePausingStacking1988: % ? unused Journal abbr (“EMBO J.”)

@article{woolRibotoxinRecognitionRibosomal1992, title = {Ribotoxin Recognition of Ribosomal {{RNA}} and a Proposal for the Mechanism of Translocation}, author = {Wool, I.G. and Gluck, A. and Endo, Y.}, year = 1992, month = jul, journal = {Trends in biochemical sciences}, volume = {17}, number = {7}, pages = {266–269}, publisher = {Elsevier}, doi = {10.1016/0968-0004(92)90407-Z}, url = {http://linkinghub.elsevier.com/retrieve/pii/096800049290407Z}, abstract = {The ribotoxins alpha-sarcin and ricin catalyse covalent modifications in adjacent nucleotides in 28S rRNA, yet the elements of nucleic acid structure that they recognize are not only different but incompatible. This suggests that this ribosomal domain (which in two dimensions is a seven-base-pair helical stem and a 17-member single-stranded loop) has alternate conformers. Since the domain is involved in binding of aminoacyl-tRNA and GTP hydrolysis, we propose that the switch between the two configurations, perhaps initiated by the binding of elongation factors, plays a role in translocation}, keywords = {92367228,animal,Aspergillus,Base Sequence,BINDING,Binding Sites,chemistry,ELEMENTS,elongation,Fungal Proteins,GTP,Guanosine Triphosphate,Hydrolysis,MECHANISM,metabolism,modification,Molecular Sequence Data,nosource,Nucleotides,PAP,Protein Synthesis Inhibitors,RIBOSOMAL-RNA,Ricin,Rna,RNARibosomal28S,RNATransferAmino Acyl,rRNA,S/R loop,structure,translocation} } % == BibTeX quality report for woolRibotoxinRecognitionRibosomal1992: % ? unused Journal abbr (“Trends Biochem.Sci.”)

@article{wowerRibosomalProteinL271998, title = {Ribosomal Protein {{L27}} Participates in Both 50 {{S}} Subunit Assembly and the Peptidyl Transferase Reaction}, author = {Wower, I.K. and Wower, J. and Zimmermann, R.A.}, year = 1998, month = jul, journal = {Journal of Biological Chemistry}, volume = {273}, number = {31}, pages = {19847–19852}, publisher = {ASBMB}, doi = {10.1074/jbc.273.31.19847}, url = {http://www.jbc.org/content/273/31/19847.short}, abstract = {Protein L27 has been implicated as a constituent of the peptidyl transferase center of the Escherichia coli 50 S ribosomal subunit by a variety of experimental observations. To define better the functional role of this protein, we constructed a strain in which the rpmA gene, which encodes L27, was replaced by a kanamycin resistance marker. The deletion mutant grows five to six times slower than the wild-type parent and is both cold- and temperature-sensitive. This phenotype is reversed when L27 is expressed from a plasmid-borne copy of the rpmA gene. Analysis of ribosomes from the L27-lacking strain revealed deficiencies in both the assembly and activity of the 50 S ribosomal subunits. Although functional 50 S subunits are formed in the mutant, an assembly “bottleneck” was evidenced by the accumulation of a prominent 40 S precursor to the 50 S subunit which was deficient in proteins L16, L20, and L21, as well as L27. In addition, the peptidyl transferase activity of 70 S ribosomes containing mutant 50 S subunits was determined to be three to four times lower than for wild-type ribosomes. Ribosomes lacking L27 were found to be impaired in the enzymatic binding of Phe-tRNAPhe to the A site, although the interaction of N-acetyl-Phe-tRNAPhe with the P site was largely unperturbed. We therefore infer that L27 contributes to peptide bond formation by facilitating the proper placement of the acceptor end of the A-site tRNA at the peptidyl transferase center}, keywords = {0,A SITE,A-SITE,analysis,assembly,BINDING,Binding Sites,Biochemistry,BIOLOGY,BOND FORMATION,chemistry,Cold,CROSS-LINKING,Cross-Linking Reagents,CROSSLINKING,deficiency,ElectrophoresisGelTwo-Dimensional,elongation,ELONGATION-FACTOR-TU,ENCODES,Escherichia coli,ESCHERICHIA-COLI,FACTOR TU,gene,Genetic,Genetic Markers,genetics,Kanamycin,Kinetics,La,MARKER,metabolism,Molecular Biology,Mutation,nosource,P SITE,P-SITE,peptide bond formation,Peptide Elongation Factor Tu,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,Peptidyl Transferases,PEPTIDYL-TRANSFERASE,pharmacology,Phenotype,physiology,PRECURSOR,protein,Proteins,RESISTANCE,Ribosomal Proteins,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Ribosomes,Rna,RNATransferPhe,S,SITE,SUBUNIT,SUBUNITS,Support,TRANSFERASE CENTER,Transferases,tRNA,TU,WILD-TYPE} } % == BibTeX quality report for wowerRibosomalProteinL271998: % ? unused Journal abbr (“J.Biol Chem.”)

@article{wowerPhotochemicalCrosslinkingYeast1988a, title = {Photochemical Cross-Linking of Yeast {{tRNA}}({{Phe}}) Containing 8-Azidoadenosine at Positions 73 and 76 to the {{Escherichia}} Coli Ribosome}, author = {Wower, J. and Hixson, S.S. and Zimmermann, R.A.}, year = 1988, month = oct, journal = {Biochemistry}, volume = {27}, number = {21}, pages = {8114–8121}, doi = {10.1021/bi00421a021}, url = {PM:3069129}, abstract = {The 3’-terminal -A-C-C-A sequence of yeast tRNA(Phe) has been modified by replacing either adenosine-73 or adenosine-76 with the photoreactive analogue 8-azidoadenosine (8N3A). The incorporation of 8N3A into tRNA(Phe) was accomplished by ligation of 8-azidoadenosine 3’,5’-bisphosphate to the 3’ end of tRNA molecules which were shortened by either one or four nucleotides. Replacement of the 3’-terminal A76 with 8N3A completely blocked aminoacylation of the tRNA. In contrast, the replacement of A73 with 8N3A has virtually no effect on the aminoacylation of tRNA(Phe). Neither substitution hindered binding of the modified tRNAs to Escherichia coli ribosomes in the presence of poly(U). Photoreactive tRNA derivatives bound noncovalently to the ribosomal P site were cross-linked to the 50S subunit upon irradiation at 300 nm. Nonaminoacylated tRNA(Phe) containing 8N3A at either position 73 or position 76 cross-linked exclusively to protein L27. When N-acetylphenylalanyl-tRNA(Phe) containing 8N3A at position 73 was bound to the P site and irradiated, 23S rRNA was the main ribosomal component labeled, while smaller amounts of the tRNA were cross-linked to proteins L27 and L2. Differences in the labeling pattern of nonaminoacylated and aminoacylated tRNA(Phe) containing 8N3A in position 73 suggest that the aminoacyl moiety may play an important role in the proper positioning of the 3’ end of tRNA in the ribosomal P site. More generally, the results demonstrate the utility of 8N3A-substituted tRNA probes for the specific labeling of ribosomal components at the peptidyltransferase center}, keywords = {0,3,Adenosine,Affinity Labels,analogs & derivatives,Azides,BINDING,Biochemistry,COMPONENT,COMPONENTS,CROSS-LINKING,Cross-Linking Reagents,CROSSLINKING,derivatives,drug effects,Escherichia coli,Escherichia coli ribosomes,ESCHERICHIA-COLI,L2,La,metabolism,nosource,Nucleic Acid Conformation,Nucleotides,P SITE,P-SITE,Peptidyltransferase,PEPTIDYLTRANSFERASE CENTER,pharmacology,Phenylalanine,Photochemistry,POSITION,POSITIONS,protein,Proteins,Puromycin,ribosome,Ribosomes,Rna,RNATransferAmino Acyl,rRNA,sequence,SITE,SUBUNIT,Support,tRNA,yeast} }

@article{wowerTransitTRNAEscherichia2000a, title = {Transit of {{tRNA}} through the {{Escherichia}} Coli Ribosome. {{Cross-linking}} of the 3’ End of {{tRNA}} to Specific Nucleotides of the 23 {{S}} Ribosomal {{RNA}} at the {{A}}, {{P}}, and {{E}} Sites}, author = {Wower, J. and Kirillov, S.V. and Wower, I.K. and Guven, S. and Hixson, S.S. and Zimmermann, R.A.}, year = 2000, month = dec, journal = {The Journal of biological chemistry}, volume = {275}, number = {48}, eprint = {10961994}, eprinttype = {pubmed}, pages = {37887–37894}, doi = {10.1074/jbc.M005031200}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10961994}, abstract = {When bound to Escherichia coli ribosomes and irradiated with near-UV light, various derivatives of yeast tRNA(Phe) containing 2-azidoadenosine at the 3’ terminus form cross-links to 23 S rRNA and 50 S subunit proteins in a site-dependent manner. A and P site-bound tRNAs, whose 3’ termini reside in the peptidyl transferase center, label primarily nucleotides U2506 and U2585 and protein L27. In contrast, E site-bound tRNA labels nucleotide C2422 and protein L33. The cross-linking patterns confirm the topographical separation of the peptidyl transferase center from the E site domain. The relative amounts of label incorporated into the universally conserved residues U2506 and U2585 depend on the occupancy of the A and P sites by different tRNA ligands and indicates that these nucleotides play a pivotal role in peptide transfer. In particular, the 3’-adenosine of the peptidyl-tRNA analogue, AcPhe-tRNA(Phe), remains in close contact with U2506 regardless of whether its anticodon is located in the A site or P site. Our findings, therefore, modify and extend the hybrid state model of tRNA-ribosome interaction. We show that the 3’-end of the deacylated tRNA that is formed after transpeptidation does not immediately progress to the E site but remains temporarily in the peptidyl transferase center. In addition, we demonstrate that the E site, defined by the labeling of nucleotide C2422 and protein L33, represents an intermediate state of binding that precedes the entry of deacylated tRNA into the F (final) site from which it dissociates into the cytoplasm}, keywords = {A-SITE,animal,Anticodon,BINDING,chemistry,CROSS-LINKING,Cytoplasm,derivatives,Escherichia coli,ESCHERICHIA-COLI,genetics,Ligands,metabolism,nosource,Nucleic Acid Conformation,Nucleotides,P-SITE,peptidyl transferase,PEPTIDYL TRANSFERASE CENTER,PEPTIDYL-TRANSFERASE,protein,Proteins,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNABacterial,RNARibosomal23S,RNATransfer,rRNA,SUBUNIT,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,tRNA,yeast} } % == BibTeX quality report for wowerTransitTRNAEscherichia2000a: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{wuResonanceEnergyTransfer1994, title = {Resonance Energy Transfer: Methods and Applications}, author = {Wu, P. and Brand, L.}, year = 1994, month = apr, journal = {Analytical biochemistry}, volume = {218}, number = {1}, pages = {1–13}, publisher = {Elsevier}, doi = {10.1006/abio.1994.1134}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0003269784711341}, abstract = {Resonance energy transfer is widely used in studies of biomolecular structure and dynamics. It provides information about distances on the order of 10 to 100 A and is thus suitable for investigating spatial relationships of interest in biochemistry. The information available from energy transfer studies has been enhanced by the advances in instrumental methods and procedures of data analysis related to fluorescence decay studies. Some practical aspects of the method are reviewed. These include sample preparation, Forster type distance determination, methods of detecting energy transfer and calculating transfer efficiency, time-resolved measurements, and data analysis. Applications of resonance energy transfer, including qualitative measurements as well as microscopy, average distance estimation, and distance distribution analysis, are surveyed}, keywords = {0,ACID,ACIDS,analysis,Biochemistry,BIOLOGY,Carbohydrates,chemistry,Data InterpretationStatistical,DECAY,DYNAMICS,efficiency,Energy Transfer,Fluorescence,INFORMATION,La,Methods,nosource,Nucleic Acids,Review,structure,Support} } % == BibTeX quality report for wuResonanceEnergyTransfer1994: % ? unused Journal abbr (“Anal.Biochem.”)

@article{wuCloningCharacterizationComplementary1993, title = {Cloning and Characterization of Complementary {{DNA}} Encoding the Eukaryotic Initiation Factor 2-Associated 67-{{kDa}} Protein (P67).}, author = {Wu, S. and Gupta, S. and Chatterjee, N. and Hileman, R.E. and Kinzy, T.G. and Denslow, N.D. and Merrick, W.C. and Chakrabarti, D. and Osterman, J.C. and Gupta, N.K.}, year = 1993, month = may, journal = {Journal of Biological Chemistry}, volume = {268}, number = {15}, pages = {10796–10781}, publisher = {ASBMB}, doi = {10.1016/S0021-9258(18)82055-5}, url = {http://www.jbc.org/content/268/15/10796.short}, keywords = {Amino Acid Sequence,analysis,animal,Antibodies,antibody,CDNA CLONING,cloning,Dna,Eif-2,Electrophoresis,human,In Vitro,IN-VITRO,initiation,kinase,library,Liver,lysate,mRNA,nosource,Oligonucleotides,Phosphorylation,polymerase,Polymerase Chain Reaction,protein,protein synthesis,PROTEIN-SYNTHESIS,rat,Rna,sequence,SEQUENCES,structure,translation} }

@article{wurmbachIsolationProteinSynthesis1979a, title = {Isolation of the Protein Synthesis Elongation Factors {{EF-Tu}}, {{EF-Ts}}, and {{EF-G}} from {{Escherichia}} Coli.}, author = {Wurmbach, P. and Nierhaus, K.H.}, year = 1979, journal = {Methods in enzymology}, volume = {60}, eprint = {379535}, eprinttype = {pubmed}, pages = {593–606}, doi = {10.1016/S0076-6879(79)60056-3}, url = {http://www.ncbi.nlm.nih.gov/pubmed/379535}, keywords = {0,EFTu,elongation,Escherichia coli,ESCHERICHIA-COLI,GTP,GTP Phosphohydrolase-Linked Elongation Factors,Guanosine,Guanosine Diphosphate,isolation & purification,Kinetics,La,metabolism,Methods,Molecular Weight,nosource,Peptide Chain Elongation,Peptide Elongation Factors,Phenylalanine,protein,protein synthesis,PROTEIN-SYNTHESIS,Rna,RNATransferAmino Acyl} } % == BibTeX quality report for wurmbachIsolationProteinSynthesis1979a: % ? unused Journal abbr (“Methods Enzymol.”)

@article{xingNegativeSelectionPressure2004, title = {Negative Selection Pressure against Premature Protein Truncation Is Reduced by Alternative Splicing and Diploidy}, author = {Xing, Y. and Lee, C.J.}, year = 2004, month = oct, journal = {Trends in Genetics}, volume = {20}, number = {10}, pages = {472–475}, publisher = {Elsevier}, doi = {10.1016/j.tig.2004.07.009}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0168952504002094}, abstract = {The importance of alternative splicing in many genomes has raised interesting questions about its role in evolution. We analyzed 13 384 full-length transcript isoforms from human and 2227 isoforms from mouse to identify sequences containing premature termination codons (PTCs) that are likely targets of mRNA nonsense-mediated decay. We found that alternatively spliced isoforms have a much higher frequency of PTCs (11.1%) compared with the major transcript form of each gene (3.7%). On the X chromosome, which is generally expressed as a single copy, the overall PTC rate was much lower (3.5%, versus 8.9% on diploid autosomes), and the effect of alternative splicing was enhanced. Thus, diploidy and alternative splicing each increased tolerance for PTC by about threefold, as approximately additive effects. These data suggest that nonsense mediated decay might itself reduce negative selection pressure during evolution, via rapid degradation of aberrant transcripts that might yield dominant negative phenotypes}, keywords = {0,Alternative Splicing,Animals,BIOLOGY,chemistry,Codon,CodonNonsense,CODONS,Comparative Study,DatabasesGenetic,DECAY,degradation,Diploidy,Evolution,EvolutionMolecular,Expressed Sequence Tags,FORM,gene,genetics,Genome,genomic,Genomics,human,Humans,IDENTIFY,La,Mice,Molecular Biology,mRNA,NONSENSE,nonsense-mediated decay,nosource,Phenotype,PREMATURE TERMINATION CODON,protein,Protein Isoforms,Research SupportU.S.Gov’tNon-P.H.S.,Research SupportU.S.Gov’tP.H.S.,Rna,RNAMessenger,SELECTION,Selection (Genetics),sequence,SEQUENCES,splicing,TARGET,termination,TERMINATION CODON,TERMINATION-CODON,TRANSCRIPT,X Chromosome} } % == BibTeX quality report for xingNegativeSelectionPressure2004: % ? unused Journal abbr (“Trends Genet.”)

@article{xiongTwoCrystalForms2000, title = {Two Crystal Forms of Helix {{II}} of {{Xenopus}} Laevis {{5S rRNA}} with a Cytosine Bulge}, author = {Xiong, Y. and Sundaralingam, M.}, year = 2000, journal = {RNA.}, volume = {6}, number = {9}, pages = {1316–1324}, publisher = {Cambridge Univ Press}, doi = {10.1017/S135583820000090X}, url = {http://journals.cambridge.org/abstract_S135583820000090X}, abstract = {The crystal structure of r(GCCACCCUG).r(CAGGGUCGGC), helix II of the Xenopus laevis 5S rRNA with a cytosine bulge (underlined), has been determined in two forms at 2.2 A (Form I, space group P4(2)2(1)2, a = b = 57.15 A and c = 43.54 A) and 1.7 A (Form II, space group P4(3)2(1)2, a = b = 32.78 A and c = 102.5 A). The helical regions of the nonamers are found in the standard A-RNA conformations and the two forms have an RMS deviation of 0.75 A. However, the cytosine bulge adopts two significantly different conformations with an RMS deviation of 3.9 A. In Form I, the cytosine bulge forms an intermolecular C+G.C triple in the major groove of a symmetry-related duplex with intermolecular hydrogen bonds between N4C and O6G, and between protonated N3+C and N7G. In contrast, a minor groove CG.C triple is formed in Form II with intermolecular hydrogen bonds between O2C and N2G, and between N3C and N3G with a water bridge. A partial major groove opening was observed in Form I structure at the bulge site. Two Ca2+ ions were found in Form I helix whereas there were none in Form II. The structural comparison of these two forms indicates that bulged residues can adopt a variety of conformations with little perturbation to the global helix structure. This suggests that bulged residues could function as flexible latches in bridging double helical motifs and facilitate the folding of large RNA molecules}, keywords = {0,5S rRNA,Animals,Ca2+,Calcium,chemistry,CONFORMATION,crystal structure,CRYSTAL-STRUCTURE,Cytosine,FORM,genetics,Hydrogen,Ions,La,metabolism,ModelsMolecular,MOTIFS,nosource,Nucleic Acid Conformation,physiology,Pliability,Purines,REGION,Research SupportNon-U.S.Gov’t,Research SupportU.S.Gov’tP.H.S.,RESIDUES,Rna,RNARibosomal5S,rRNA,SITE,Structural,structure,Water,Xenopus,Xenopus laevis,XENOPUS-LAEVIS} } % == BibTeX quality report for xiongTwoCrystalForms2000: % ? Possibly abbreviated journal title RNA.

@article{xiongSynthesisPutativeRedClover1993, title = {Synthesis of the {{Putative Red-Clover Necrotic Mosaic-Virus Rna-Polymerase}} by {{Ribosomal Frameshifting Invitro}}}, author = {Xiong, Z. and Kim, K.H. and Kendall, T.L. and Lommel, S.A.}, year = 1993, month = mar, journal = {Virology}, volume = {193}, number = {1}, pages = {213–221}, doi = {10.1006/viro.1993.1117}, url = {ISI:A1993KN05700021}, keywords = {AMBER TERMINATION CODON,COMPLETE NUCLEOTIDE-SEQUENCE,Frameshifting,gene,GENOME ORGANIZATION,INVITRO,MOSAIC-VIRUS,nosource,protein,PROTOPLASTS,readthrough,REPLICATION,RETROVIRUSES,ribosomal frameshifting,RNA-POLYMERASE,translation} } % == BibTeX quality report for xiongSynthesisPutativeRedClover1993: % ? Title looks like it was stored in title-case in Zotero

@article{xuHighfrequencyDeletionHomologous1987a, title = {High-Frequency Deletion between Homologous Sequences during Retrotransposition of {{Ty}} Elements in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Xu, H. and Boeke, J.D.}, year = 1987, journal = {Proc.Natl.Acad.Sci.USA}, volume = {84}, pages = {8553–8557}, doi = {10.1073/pnas.84.23.8553}, keywords = {ELEMENTS,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,tRNA,Ty,yeast} } % == BibTeX quality report for xuHighfrequencyDeletionHomologous1987a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{xuHostGenesThat1990a, title = {Host Genes That Influence Transposition in Yeast: The Abundance of a Rare {{tRNA}} Regulates {{Ty}}⬚1⬚ Transposition Frequency.}, author = {Xu, J. and Boeke, J.D.}, year = 1990, journal = {Proc.Natl.Acad.Sci.USA}, volume = {87}, pages = {8360–8364}, doi = {10.1073/pnas.87.21.8360}, keywords = {Gag/Gag-pol ratio,gene,Genes,nosource,tRNA,Ty1,yeast} } % == BibTeX quality report for xuHostGenesThat1990a: % ? Possibly abbreviated journal title Proc.Natl.Acad.Sci.USA

@article{xuSynthesisNovelHepatitis2001, title = {Synthesis of a Novel Hepatitis {{C}} Virus Protein by Ribosomal Frameshift}, author = {Xu, Z. and Choi, J. and Yen, T.S. and Lu, W. and Strohecker, A. and Govindarajan, S. and Chien, D. and Selby, M.J. and Ou, J.}, year = 2001, month = jul, journal = {The EMBO journal}, volume = {20}, number = {14}, pages = {3840–3848}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/20.14.3840}, url = {http://www.nature.com/emboj/journal/v20/n14/abs/7593881a.html}, abstract = {Hepatitis C virus (HCV) is an important human pathogen that affects approximately 100 million people worldwide. Its RNA genome codes for a polyprotein, which is cleaved by viral and cellular proteases to produce at least 10 mature viral protein products. We report here the discovery of a novel HCV protein synthesized by ribosomal frameshift. This protein, which we named the F protein, is synthesized from the initiation codon of the polyprotein sequence followed by ribosomal frameshift into the -2/+1 reading frame. This ribosomal frameshift requires only codons 8-14 of the core protein-coding sequence, and the shift junction is located at or near codon 11. An F protein analog synthesized in vitro reacted with the sera of HCV patients but not with the sera of hepatitis B patients, indicating the expression of the F protein during natural HCV infection. This unexpected finding may open new avenues for the development of anti-HCV drugs}, keywords = {0,Amino Acid Sequence,Base Sequence,C-PROTEIN,chemistry,Codon,CODONS,development,DISCOVERY,Dna,DnaViral,drugs,expression,FRAME,frameshift,FrameshiftingRibosomal,genetics,Genome,GenomeViral,Hepacivirus,HEPATITIS-C,human,immunology,In Vitro,IN-VITRO,INFECTION,initiation,La,metabolism,microbiology,Molecular Sequence Data,nosource,Open Reading Frames,POLYPROTEIN,PRODUCT,PRODUCTS,protein,Proteins,READING FRAME,REQUIRES,RIBOSOMAL FRAMESHIFT,Rna,sequence,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Viral Core Proteins,virus} } % == BibTeX quality report for xuSynthesisNovelHepatitis2001: % ? unused Journal abbr (“EMBO J.”)

@article{xueSaccharomycesCerevisiaeRAI12000, title = {Saccharomyces Cerevisiae {{RAI1}} ({{YGL246c}}) Is Homologous to Human {{DOM3Z}} and Encodes a Protein That Binds the Nuclear Exoribonuclease {{Rat1p}}}, author = {Xue, Y. and Bai, X. and Lee, I. and Kallstrom, G. and Ho, J. and Brown, J. and Stevens, A. and Johnson, A.W.}, year = 2000, month = jun, journal = {Molecular and cellular biology}, volume = {20}, number = {11}, pages = {4006–4015}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.20.11.4006-4015.2000}, url = {http://mcb.asm.org/cgi/content/abstract/20/11/4006}, abstract = {The RAT1 gene of Saccharomyces cerevisiae encodes a 5’–{\(>\)}3’ exoribonuclease which plays an essential role in yeast RNA degradation and/or processing in the nucleus. We have cloned a previously uncharacterized gene (YGL246c) that we refer to as RAI1 (Rat1p interacting protein 1). RAI1 is homologous to Caenorhabditis elegans DOM-3 and human DOM3Z. Deletion of RAI1 confers a growth defect which can be complemented by an additional copy of RAT1 on a centromeric vector or by directing Xrn1p, the cytoplasmic homolog of Rat1p, to the nucleus through the addition of a nuclear targeting sequence. Deletion of RAI1 is synthetically lethal with the rat1-1(ts) mutation and shows genetic interaction with a deletion of SKI2 but not XRN1. Polysome analysis of an rai1 deletion mutant indicated a defect in 60S biogenesis which was nearly fully reversed by high-copy RAT1. Northern blot analysis of rRNAs revealed that rai1 is required for normal 5.8S processing. In the absence of RAI1, 5.8S(L) was the predominant form of 5.8S and there was an accumulation of 3’-extended forms but not 5’-extended species of 5. 8S. In addition, a 27S pre-rRNA species accumulated in the rai1 mutant. Thus, deletion of RAI1 affects both 5’ and 3’ processing reactions of 5.8S rRNA. Consistent with the in vivo data suggesting that RAI1 enhances RAT1 function, purified Rai1p stabilized the in vitro exoribonuclease activity of Rat1p}, keywords = {20266289,Amino Acid Sequence,analysis,Base Sequence,Caenorhabditis,Caenorhabditis elegans,CloningMolecular,degradation,DNAFungal,enzymology,Exoribonucleases,exosome,Fungal Proteins,gene,GenesFungal,Genetic,genetics,homolog,human,In Vitro,IN-VITRO,IN-VIVO,Major Histocompatibility Complex,metabolism,microbiology,Molecular Sequence Data,Mutation,nosource,Nuclear Proteins,protein,Protein-Serine-Threonine Kinases,RAI1,Rna,RNA ProcessingPost-Transcriptional,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence AnalysisDNA,vector,XRN1,yeast} } % == BibTeX quality report for xueSaccharomycesCerevisiaeRAI12000: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{yamamotoRolesRibosomalProtein2007, title = {Roles of the Ribosomal Protein {{S19}} Dimer and the {{C5a}} Receptor in Pathophysiological Functions of Phagocytic Leukocytes}, author = {Yamamoto, T.}, year = 2007, month = jan, journal = {Pathol.Int.}, volume = {57}, number = {1}, pages = {1–11}, url = {PM:17199736}, abstract = {Monocytes and neutrophils, the major phagocytic leukocytes, migrate to inflammatory sites by sensing chemoattractants such as anaphylatoxin C5a with membrane receptors such as C5a receptor. Upon stimulation, the leukocytes increase cytoplasmic Ca(2+) concentration and generate radical oxygen species. These leukocytes have different functions in inflammation. Neutrophils migrate more rapidly and induce vascular plasma leakage upon infiltration. Monocytes infiltrate tissue more slowly but have superior capacities of phagocytosis and antigen presentation. There must be mechanisms to separately recruit the leukocyte species at an inflammatory site. Ribosomal protein S19 (RP S19) is a component of ribosome. During apoptosis, RP S19 is dimerized and obtains a ligand capacity to C5a receptor. The RP S19 dimer attracts monocytes to phagocytically clear the apoptotic cells that released the dimer molecules. The phagocytic monocytes/macrophages then translocate to regional lymph nodes and present apoptotic cell-derived antigens. Oppositely, the RP S19 dimer inhibits C5a-induced neutrophil migration and promotes apoptosis of neutrophils via the C5a receptor. The RP S19 dimer seems to prevent excessive tissue destruction induced by neutrophils. Skp is a molecular chaperon of Gram-negative bacteria. Skp also attracts monocytes and neutrophils as a ligand of C5a receptor. However, it promotes neither cytoplasmic Ca(2+) enhancement nor radical oxygen generation}, keywords = {0,ANTIGEN,Apoptosis,Bacteria,CELLS,Chemotactic Factors,COMPONENT,DIMER,Humans,La,MECHANISM,MECHANISMS,Monocytes,Multiple DOI,Neutrophils,nonfile,nosource,pathology,Phagocytosis,physiology,protein,Proteins,ReceptorAnaphylatoxin C5a,Review,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,SITE,SITES} } % == BibTeX quality report for yamamotoRolesRibosomalProtein2007: % ? Possibly abbreviated journal title Pathol.Int.

@article{yanAssessmentPutativeProtein2003, title = {Assessment of Putative Protein Targets Derived from the {{SARS}} Genome}, author = {Yan, L. and Velikanov, M. and Flook, P. and Zheng, W. and Szalma, S. and Kahn, S.}, year = 2003, month = nov, journal = {FEBS letters}, volume = {554}, number = {3}, pages = {257–263}, publisher = {Elsevier}, doi = {10.1016/S0014-5793(03)01115-3}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579303011153}, abstract = {The ability to rapidly and reliably develop hypotheses on the function of newly discovered protein sequences requires systematic and comprehensive analysis. Such an analysis, embodied within the DS GeneAtlas pipeline, has been used to critically evaluate the severe acute respiratory syndrome (SARS) genome with the goal of identifying new potential targets for viral therapeutic intervention. This paper discusses several new functional hypotheses on the roles played by the constituent gene products of SARS, and will serve as an example of how such assignments can be developed or extended on other systems of interest}, keywords = {0,Amino Acid Sequence,analysis,Animals,ASSIGNMENT,Binding Sites,chemistry,Dna,DNA Helicases,DNA-Directed RNA Polymerase,DNA-Directed RNA Polymerases,enzymology,gene,GENE-PRODUCT,genetics,Genome,GenomeViral,Helicase,Humans,La,metabolism,ModelsMolecular,Molecular Sequence Data,nosource,polymerase,PRODUCT,PRODUCTS,protein,Protein StructureSecondary,Proteins,REQUIRES,Rna,RNA HELICASE,RNA Helicases,RNA-POLYMERASE,SARS,Sars Virus,sequence,Sequence Alignment,Sequence AnalysisProtein,Sequence HomologyAmino Acid,SEQUENCES,Severe Acute Respiratory Syndrome,Support,Swine,Syndrome,SYSTEM,SYSTEMS,TARGET,TranscriptionGenetic,Viral Proteins} } % == BibTeX quality report for yanAssessmentPutativeProtein2003: % ? unused Journal abbr (“FEBS Lett.”)

@article{yanZuotinRibosomeassociatedDnaJ1998, title = {Zuotin, a Ribosome-Associated {{DnaJ}} Molecular Chaperone}, author = {Yan, W. and Schilke, B. and Pfund, C. and Walter, W. and Kim, S. and Craig, E.A.}, year = 1998, journal = {The EMBO journal}, volume = {17}, number = {16}, pages = {4809–4817}, publisher = {Nature Publishing Group}, doi = {10.1093/emboj/17.16.4809}, url = {http://www.nature.com/emboj/journal/v17/n16/abs/7591177a.html}, abstract = {Correct folding of newly synthesized polypeptides is thought to be facilitated by Hsp70 molecular chaperones in conjunction with DnaJ cohort proteins. In Saccharomyces cerevisiae, SSB proteins are ribosome-associated Hsp70s which interact with the newly synthesized nascent polypeptide chain. Here we report that the phenotypes of an S.cerevisiae strain lacking the DnaJ-related protein Zuotin (Zuo1) are very similar to those of a strain lacking Ssb, including sensitivities to low temperatures, certain protein synthesis inhibitors and high osmolarity. Zuo1, which has been shown previously to be a nucleic acid-binding protein, is also a ribosome-associated protein localized predominantly in the cytosol. Analysis of zuo1 deletion and truncation mutants revealed a positive correlation between the ribosome association of Zuo1 and its ability to bind RNA. We propose that Zuo1 binds to ribosomes, in part, by interaction with ribosomal RNA and that Zuo1 functions with Ssb as a chaperone on the ribosome}, keywords = {0,analysis,ASSOCIATION,CEREVISIAE,chemistry,Cytosol,DNA-BINDING,DNA-Binding Proteins,Fungal Proteins,HEAT-SHOCK,HEAT-SHOCK PROTEINS,Heat-Shock Proteins 70,INHIBITOR,inhibitors,La,metabolism,Molecular Chaperones,MUTANTS,nosource,Phenotype,POLYPEPTIDE,POLYPEPTIDE-CHAIN,POLYPEPTIDES,protein,protein synthesis,Protein Synthesis Inhibitors,PROTEIN-SYNTHESIS,Proteins,Research SupportU.S.Gov’tP.H.S.,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,SYNTHESIS INHIBITORS,Temperature} } % == BibTeX quality report for yanZuotinRibosomeassociatedDnaJ1998: % ? unused Journal abbr (“EMBO J.”)

@article{yanagiharaAssociationElongationFactor1997a, title = {Association of Elongation Factor 1 Alpha and Ribosomal Protein 13 with the Proline-Rich Region of Yeast Adenylyl Cyclase-Associated Protein {{CAP}}}, author = {Yanagihara, C. and Shinkai, M. and Kariya, K. and YamawakiKataoka, Y. and Hu, C.D. and Masuda, T. and Kataoka, T.}, year = 1997, month = mar, journal = {Biochemical and Biophysical Research Communications}, volume = {232}, number = {2}, pages = {503–507}, doi = {10.1006/bbrc.1997.6326}, url = {ISI:A1997WP22300050}, abstract = {CAP is a multifunctional protein; the N-terminal region binds adenylyl cyclase and controls its response to Ras while the C-terminal region is involved in cytoskeletal regulation. In between the two regions, CAP possesses two proline-rich segments, P-1 and P-2, resembling a consensus sequence for binding SH3 domains, We have identified two yeast proteins with molecular sizes of 48 and 46 kDa associated specifically with P-2. Determination of partial protein sequences demonstrated that the 48-kDa and 46-kDa proteins correspond to EF1 alpha and rL3, respectively, neither of which contains any SH3-domain-like sequence. Deletion of P-2 from CAP resulted in loss of the activity to bind the two proteins either in vivo or in vitro. Yeast cells whose chromosomal CAP was replaced by the P-2-deletion mutant displayed an abnormal phenotype represented by dissociated localizations of CAP and F-actin, which were colocalized in wild-type cells. These results suggest that these associations may have functional significance. (C) 1997 Academic Press}, keywords = {ASSOCIATION,BINDING,Cap,CELLS,cloning,Consensus Sequence,DOMAIN,DOMAINS,elongation,F-ACTIN,Genes,homolog,IDENTIFICATION,In Vitro,IN-VITRO,IN-VIVO,LOCALIZATION,nosource,Phenotype,protein,Proteins,ras,REGION,regulation,SACCHAROMYCES-CEREVISIAE,sequence,SEQUENCES,yeast,YEAST-CELLS} }

@article{yangClassIIHistone2005a, title = {Class {{II}} Histone Deacetylases: From Sequence to Function, Regulation, and Clinical Implication}, author = {Yang, X.J. and Gregoire, S.}, year = 2005, month = apr, journal = {Mol.Cell Biol}, volume = {25}, number = {8}, pages = {2873–2884}, doi = {10.1128/MCB.25.8.2873-2884.2005}, url = {PM:15798178}, keywords = {0,Amino Acid Sequence,Animals,antagonists & inhibitors,chemistry,enzyme,Enzyme Activators,Enzyme Inhibitors,enzymology,HDAC,Histone Deacetylase,Histone Deacetylases,Humans,INHIBITOR,inhibitors,La,Molecular Sequence Data,nosource,physiology,Protein StructureTertiary,regulation,Review,sequence,Support,therapeutic use,Yeasts} } % == BibTeX quality report for yangClassIIHistone2005a: % ? Possibly abbreviated journal title Mol.Cell Biol

@article{yapEffectsStoichiometryRetroviral2000, title = {Effects of Stoichiometry of Retroviral Components on Virus Production.}, author = {Yap, M.W. and Kingsman, S.M. and Kingsman, A.J.}, year = 2000, journal = {Journal of General Virology}, volume = {81 Pt 9:2195-202}, number = {9}, pages = {2195–2202}, publisher = {Soc General Microbiol}, doi = {10.1099/0022-1317-81-9-2195}, url = {http://jgv.sgmjournals.org/cgi/content/abstract/81/9/2195}, abstract = {A study was conducted to investigate the effects of increasing the amount of each retroviral component on vector production. It was found that, while the components of both amphotropic and ecotropic vectors were expressed independently of each other in a transient transfection system, increasing the amount of the gag/gag-pol component resulted in a decrease in virus titres for the amphotropic particles but not ecotropic particles. Analyses of the virus stocks produced indicated that the negative effect on titres was closely linked to the availability of envelope proteins for virion incorporation. The negative effect was not observed for ecotropic particle production in 293T cells, where the ecotropic receptor was absent, but was manifested when production was conducted in 293/12 cells expressing the ecotropic receptor. This suggested that the premature interaction between envelope and receptor in producer cells could limit the amount of envelope available for virion incorporation. In designing optimal vector production systems it is essential, therefore, to balance the concentration of the vector components and to ensure that there is never an excess of Gag/Gag-Pol}, keywords = {COMPONENT,Frameshifting,Gag/Gag-pol ratio,nosource,protein,Proteins,SYSTEM,Transfection,vector,vectors,Virion,virus} } % == BibTeX quality report for yapEffectsStoichiometryRetroviral2000: % ? unused Journal abbr (“J.Gen.Virol.”)

@article{yarusProofreadingNTPasesTranslation1992, title = {Proofreading, {{NTPases}} and Translation: Successful Increase in Specificity}, author = {Yarus, M.}, year = 1992, month = may, journal = {Trends in Biochemical Sciences}, volume = {17}, number = {5}, pages = {171–174}, publisher = {Elsevier}, doi = {10.1016/0968-0004(92)90257-A}, url = {http://linkinghub.elsevier.com/retrieve/pii/096800049290257A}, abstract = {The discussion of proofreading started in the April issue of TIBS is completed by treating the two branched Michaelis-Menten enzymes that can proofread. The conditions required for proofreading can be seen to determine the expression of proofreading in its biological settings. There are surely instances of proofreading as yet unrecognized}, keywords = {92280017,enzyme,expression,Kinetics,nosource,Phosphoric Monoester Hydrolases,physiology,proofreading,Substrate Specificity,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,translation,TranslationGenetic} } % == BibTeX quality report for yarusProofreadingNTPasesTranslation1992: % ? unused Journal abbr (“Trends.Biochem.Sci.”)

@article{yarusPrimordialGeneticsPhenotype2002, title = {Primordial Genetics: {{Phenotype}} of the Ribocyte}, author = {Yarus, M.}, year = 2002, journal = {Annual Review of Genetics}, volume = {36}, number = {1}, pages = {125–151}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, doi = {10.1146/annurev.genet.36.031902.105056}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.genet.36.031902.105056}, abstract = {The idea that the ancestors of modem cells were RNA cells (ribocytes) can be investigated by asking whether all essential cellular functions might be performed by RNAs. This requires isolating suitable molecules by selection- amplification when the predicted molecules are presently extinct. In fact, RNAs with many properties required during a period in which RNA was the major macromolecular agent in cells (an RNA world) have been selected in modem experiments. There is, accordingly, reason to inquire how such a ribocyte might appear, based on the properties of the RNAs that composed it. Combining the intrinsic qualities of RNA with the fundamental characteristics of selection from randomized sequence pools, one predicts ribocytes with a cell cycle measured (roughly) in weeks. Such cells likely had a rapidly varying genome, composed of many small genetic and catalytic elements made of tens of ribonucleotides. There are substantial arguments that, at the mid-RNA era, a subset of these nucleotides are reproducibly available and resemble the modem four. Such cells are predicted to evolve rapidly. Instead of modifying preexisting genes, ribocytes frequently draw new functions from an internal pool containing zeptomoles ({\(<\)} 1 attomole) of predominantly inactive random sequences}, keywords = {0,AMINO-ACIDS,BINDING-SITE,CARBON BOND FORMATION,CATALYZED RNA POLYMERIZATION,cell cycle,CELLS,ELEMENTS,Evolution,gene,Genes,Genetic,genetics,Genome,M,MOLECULAR RECOGNITION,nosource,Nucleotides,Phenotype,REPLICATION,REQUIRES,Review,Ribonucleotides,RIBOSOMAL PEPTIDYL TRANSFERASE,Rna,RNA cell,RNA world,SELECTION,selection-amplification,SELEX,sequence,SEQUENCES,STRUCTURAL BASIS,TETRAHYMENA RIBOZYME,translation,WORLD} }

@article{yarusTwistedTRNAIntermediate2003a, title = {A Twisted {{tRNA}} Intermediate Sets the Threshold for Decoding}, author = {Yarus, M. and Valle, M. and Frank, J.}, year = 2003, month = apr, journal = {RNA}, volume = {9}, number = {4}, pages = {384–385}, doi = {10.1261/rna.2184703}, url = {PM:12649490}, abstract = {Putting together consistent cryo-EM structure, transient kinetic and mutant tRNA suppressor data, it appears that a deformed or waggling aminoacyl-tRNA is the critical transitional structure examined by the ribosome during decoding at the A site. The unusual conformation may be required for effective proofreading of the codon-anticodon complex}, keywords = {0,A SITE,A-SITE,Bacterial,BIOLOGY,COMPLEX,COMPLEXES,CONFORMATION,decoding,Escherichia coli,genetics,INTERMEDIATE,Kinetics,La,metabolism,MicroscopyElectron,Mutation,nosource,proofreading,ribosome,Ribosomes,Rna,RNABacterial,RNATransfer,SITE,structure,tRNA} }

@article{yassinDeleteriousMutationsSmall2005, title = {Deleterious Mutations in Small Subunit Ribosomal {{RNA}} Identify Functional Sites and Potential Targets for Antibiotics}, author = {Yassin, A. and Fredrick, K. and Mankin, A.S.}, year = 2005, month = nov, journal = {Proceedings of the National Academy of Sciences}, volume = {102}, number = {46}, pages = {16620–16625}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.0508444102}, url = {http://www.pnas.org/content/102/46/16620.short}, abstract = {Many clinically useful antibiotics interfere with protein synthesis in bacterial pathogens by inhibiting ribosome function. The sites of action of known drugs are limited in number, are composed primarily of ribosomal RNA (rRNA), and coincide with functionally critical centers of the ribosome. Nucleotide alterations within such sites are often deleterious. To identify functional sites and potential sites of antibiotic action in the ribosome, we prepared a random mutant library of rRNA genes and selected dominant mutations in 16S rRNA that interfere with cell growth. Fifty-three 16S rRNA positions were identified whose mutation inhibits protein synthesis. Mutations were ranked according to the severity of the phenotype, and the detrimental effect of several mutations on translation was verified in a specialized ribosome system. Analysis of the polysome profiles of mutants suggests that the majority of the mutations directly interfered with ribosome function, whereas a smaller fraction of mutations affected assembly of the small ribosomal subunit. Twelve of the identified mutations mapped to sites targeted by known antibiotics, confirming that deleterious mutations can be used to identify antibiotic targets. About half of the mutations coincided with known functional sites in the ribosome, whereas the rest of the mutations affected ribosomal sites with less clear functional significance. Four clusters of deleterious mutations in otherwise unremarkable ribosomal sites were identified, suggesting their functional importance and potential as antibiotic targets}, keywords = {0,16S,analysis,Anti-Bacterial Agents,antibiotic,antibiotics,assembly,Bacterial,Base Sequence,chemistry,Dna,DNA Primers,drugs,FUNCTIONAL SITES,gene,Genes,genetics,GROWTH,IDENTIFY,La,library,Molecular Sequence Data,MUTANTS,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,pharmacology,Phenotype,POSITION,POSITIONS,protein,protein synthesis,PROTEIN-SYNTHESIS,Research SupportN.I.H.Extramural,ribosomal RNA,RIBOSOMAL-RNA,RIBOSOMAL-SUBUNIT,ribosome,Rna,RNARibosomal,rRNA,rRNA genes,SITE,SITES,SUBUNIT,SYSTEM,TARGET,translation} } % == BibTeX quality report for yassinDeleteriousMutationsSmall2005: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{yehVitroSystemStudying1995, title = {An in Vitro System for Studying {{RNA-protein}} Interaction: Application to a Study of Yeast Ribosomal Protein {{L1}} Binding to {{5S rRNA}}}, author = {Yeh, L.C. and Lee, J.C.}, year = 1995, journal = {Biochimie}, volume = {77}, number = {3}, pages = {167–173}, publisher = {Elsevier}, doi = {10.1016/0300-9084(96)88121-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/0300908496881211}, abstract = {Previous attempts to study the binding of yeast ribosomal protein L1 with 5S rRNA in vitro have been impeded by the failure to form RNA- protein complexes with purified protein and RNA. To circumvent this difficulty, we have developed an in vitro system that allowed RNP formation. The system involved in vitro expression of the protein L1 from its cloned gene in the presence of exogenous yeast 5S rRNA. A protein of the expected size (34 kDa) was synthesized by in vitro transcription and translation. A specific 5S rRNA-protein L1 complex (RNP) was formed when the rRNA molecule was present during protein L1 synthesis. However, the full-length protein L1 failed to bind 5S rRNA. The extent of RNP formation was proportional to the concentration of the exogenous yeast 5S rRNA in the reaction. The RNP displayed properties identical to those isolated from mature 60S ribosome subunits. Addition of yeast 5.8S rRNA did not result in the formation of a specific RNP. Using this in vitro system, we examined the ability of several deletion mutant proteins to bind yeast 5S rRNA and concluded that protein L1 missing residues 261 to 295 from the C-terminus could not bind yeast 5S rRNA. This in vitro system should be useful for future studies on the molecular nature of 5S rRNA-protein L1 interaction}, keywords = {5S rRNA,95375032,BINDING,chemistry,COMPLEX,COMPLEXES,expression,gene,genetics,In Vitro,in vitro transcription,IN-VITRO,L1,metabolism,nosource,protein,Protein Binding,PROTEIN COMPLEX,Proteins,Ribosomal Proteins,ribosome,Rna,RNAFungal,RNARibosomal5S,rRNA,Sequence Deletion,SUBUNIT,supportu.s.gov’tp.h.s.,SYSTEM,transcription,TranscriptionGenetic,translation,TranslationGenetic,yeast} }

@article{yehInvolvementLysine2701996, title = {Involvement of Lysine 270 and Lysine 271 of Yeast {{5S rRNA}} Binding Protein in {{RNA}} Binding and Ribosome Assembly}, author = {Yeh, L.C. and Deshmukh, M. and Woolford, J.L. and Lee, J.C.}, year = 1996, journal = {Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression}, volume = {1308}, number = {2}, pages = {133–141}, publisher = {Elsevier}, doi = {10.1016/0167-4781(96)00085-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/0167478196000851}, abstract = {Contributions of the highly conserved K270 and its neighboring K271 in the C-terminal region of the yeast ribosomal protein L1 to 5S rRNA binding and ribosome assembly were examined by in vivo and in vitro studies on the consequences of 14 substitution mutations. All mutant proteins with a single amino-acid substitution at either position were able to bind 5S rRNA in vitro to an extent comparable to the wild-type. Yeast cells expressing these mutant proteins, except the K270G mutant, grew at nearly normal rates. Mutations of K270 appeared to produce more demonstrable effects than those of K271. The double mutant K270,271G bound RNA poorly and yeast cells expressing the mutant protein grew 30% slower. Double mutants K270,271E and K270,271R were lethal, although the mutant protein was assembled into the 60S ribosomal subunits. The resultant subunits were not stable leading eventually to cell death. The in vitro RNA binding ability of the respective protein was reduced by 60% and 20%. Taken together, the present data identified K270 and K271 as important amino-acid residues in the function of the yeast ribosomal protein L1}, keywords = {5S rRNA,96350466,Amino Acid Sequence,Amino Acid Substitution,assembly,BINDING,BINDING PROTEIN,BINDING-PROTEIN,Comparative Study,Fungal Proteins,GenesLethal,genetics,In Vitro,IN-VITRO,IN-VIVO,L1,Lysine,metabolism,Molecular Sequence Data,MutagenesisSite-Directed,Mutation,MUTATIONS,nosource,protein,Protein StructureSecondary,Proteins,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNA-Binding Proteins,RNARibosomal5S,rRNA,Sequence HomologyAmino Acid,Structure-Activity Relationship,SUBUNIT,supportu.s.gov’tp.h.s.,yeast,Yeasts} } % == BibTeX quality report for yehInvolvementLysine2701996: % ? unused Journal abbr (“Biochim.Biophys.Acta”)

@article{yelvertonFunctionRibosomalFrameshifting1994, title = {The {{Function}} of {{A Ribosomal Frameshifting Signal}} from {{Human Immunodeficiency Virus-1}} in {{Escherichia-Coli}}}, author = {Yelverton, E. and Lindsley, D. and Yamauchi, P. and Gallant, J.A.}, year = 1994, month = jan, journal = {Molecular Microbiology}, volume = {11}, number = {2}, pages = {303–313}, publisher = {Wiley Online Library}, doi = {10.1111/j.1365-2958.1994.tb00310.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.1994.tb00310.x/abstract}, abstract = {A 15-17 nucleotide sequence from the gag-pol ribosome frameshift site of HIV-1 directs analogous ribosomal frameshifting in Escherichia coil Limitation for leucine, which is encoded precisely at the frameshift site, dramatically increased the frequency of left-ward frameshifting. Limitation for phenylalanine or arginine, which are encoded just before and lust after the frameshift, did not Significantly affect frameshifting. Protein sequence analysis demonstrated the occurrence of two closely related frameshift mechanisms. In the first, ribosomes appear to bind leucyl-tRNA at the frameshift site and then slip leftward. This is the ‘simultaneous slippage’ mechanism. In the second, ribosomes appear to slip before binding aminoacyl-tRNA, and then bind phenylalanyl-tRNA, which is encoded in the left-shifted reading frame. This mechanism is identical to the ‘overlapping reading’ we have demonstrated at other bacterial frameshift sites. The HIV-1 sequence is prone to frameshifting by both mechanisms in E. coli}, keywords = {analysis,Arginine,Bacterial,BINDING,E,Escherichia coli,ESCHERICHIA-COLI,EXPRESSION INVITRO,FRAME,frameshift,Frameshifting,Gag-pol,GENETIC-CODE,Hiv-1,human,Lac Operon,Leucine,MECHANISM,MECHANISMS,nosource,NUCLEOTIDE-SEQUENCE,Phenylalanine,protein,READING FRAME,RELEASE FACTOR-II,ribosomal frameshifting,RIBOSOMAL FRAMESHIFTING SIGNAL,ribosome,Ribosomes,sequence,Sequence Analysis,SEQUENCE-ANALYSIS,SIGNAL,SITE,SITES,SLIPPAGE} } % == BibTeX quality report for yelvertonFunctionRibosomalFrameshifting1994: % ? Title looks like it was stored in title-case in Zotero

@article{yewdellDRiPHypothesisDecennial2006, title = {The {{DRiP}} Hypothesis Decennial: Support, Controversy, Refinement and Extension}, author = {Yewdell, J.W. and Nicchitta, C.V.}, year = 2006, journal = {Trends Immunol.}, volume = {27}, number = {8}, pages = {368–373}, doi = {10.1016/j.it.2006.06.008}, url = {PM:16815756}, abstract = {In 1996, to explain the rapid presentation of viral proteins to CD8+ T cells, it was proposed that peptides presented by MHC class I molecules derive from defective ribosomal products (DRiPs), presumed to be polypeptides arising from in-frame translation that fail to achieve native structure owing to inevitable imperfections in transcription, translation, post-translational modifications or protein folding. Here, we consider findings that address the DRiP hypothesis, and extend the hypothesis by proposing that cells possess specialized machinery, possibly in the form of “immunoribosomes”, to couple protein synthesis to antigen presentation}, keywords = {0,Animals,ANTIGEN,Antigen Presentation,CELLS,disease,FORM,genetics,Histocompatibility Antigens Class I,Humans,immunology,La,metabolism,ModelsBiological,modification,nosource,Peptides,POLYPEPTIDE,POLYPEPTIDES,PRODUCT,PRODUCTS,protein,Protein Folding,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Ribosomal Proteins,RIBOSOMAL-PROTEIN,Ribosomes,structure,Support,T,T-Lymphocytes,transcription,translation,Viral Proteins} } % == BibTeX quality report for yewdellDRiPHypothesisDecennial2006: % ? Possibly abbreviated journal title Trends Immunol.

@article{yonathCrystallographicStudiesRibosome1998, title = {Crystallographic Studies on the Ribosome, a Large Macromolecular Assembly Exhibiting Severe Nonisomorphism, Extreme Beam Sensitivity and No Internal Symmetry}, author = {Yonath, A. and Harms, J. and Hansen, H.A. and Bashan, A. and Schlunzen, F. and Levin, I. and Koelln, I. and Tocilj, A. and Agmon, I. and Peretz, M. and Bartels, H. and Bennett, W.S. and Krumbholz, S. and Janell, D. and Weinstein, S. and Auerbach, T. and Avila, H. and Piolleti, M. and Morlang, S. and Franceschi, F.}, year = 1998, month = nov, journal = {Acta Crystallographica Section A: Foundations of Crystallography}, volume = {54}, number = {Pt 6 Pt 1}, pages = {945–955}, publisher = {International Union of Crystallography}, url = {http://scripts.iucr.org/cgi-bin/paper?S010876739800991X}, abstract = {Crystals, diffracting best to around 3 A, have been grown from intact large and small ribosomal subunits. The bright synchrotron radiation necessary for the collection of the higher-resolution X-ray diffraction data introduces significant decay even at cryo temperatures. Nevertheless, owing to the reasonable isomorphism of the recently improved crystals of the small ribosomal subunits, reliable phases have been extracted at medium resolution (5-6 A) and an interpretable five- derivative MIR map has been constructed. For the crystals of the large subunits, however, the situation is more complicated because at higher resolution (2.7-7 A) they suffer from substantial radiation sensitivity, a low level of isomorphism, instability of the longest unit-cell axis and nonisotropic mosaicity. The 8 A MIR map, constructed to gain insight into this unusual system, may provide feasible reasoning for the odd combination of the properties of these crystals as well as hints for future improvement. Parallel efforts, in which electron-microscopy-reconstructed images are being exploited for molecular-replacement studies, are also discussed}, keywords = {animal,assembly,chemistry,CrystallographyX-Ray,DECAY,human,La,media,No DOI found,nosource,Review,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,structure,SUBUNIT,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,SYSTEM,Temperature,ultrastructure,X-Ray Diffraction} } % == BibTeX quality report for yonathCrystallographicStudiesRibosome1998: % ? unused Journal abbr (“Acta Crystallogr.A”)

@article{yoonImpairedControlIRESmediated2006, title = {Impaired Control of {{IRES-mediated}} Translation in {{X-linked}} Dyskeratosis Congenita}, author = {Yoon, A. and Peng, G. and Brandenburger, Y. and Zollo, O. and Xu, W. and Rego, E. and Ruggero, D.}, year = 2006, month = may, journal = {Science}, volume = {312}, number = {5775}, pages = {902–906}, publisher = {American Association for the Advancement of Science}, issn = {1095-9203}, doi = {10.1126/science.1123835}, url = {http://www.sciencemag.org/content/312/5775/902.short http://www.ncbi.nlm.nih.gov/pubmed/16690864}, abstract = {The DKC1 gene encodes a pseudouridine synthase that modifies ribosomal RNA (rRNA). DKC1 is mutated in people with X-linked dyskeratosis congenita (X-DC), a disease characterized by bone marrow failure, skin abnormalities, and increased susceptibility to cancer. How alterations in ribosome modification might lead to cancer and other features of the disease remains unknown. Using an unbiased proteomics strategy, we discovered a specific defect in IRES (internal ribosome entry site)-dependent translation in Dkc1(m) mice and in cells from X-DC patients. This defect results in impaired translation of messenger RNAs containing IRES elements, including those encoding the tumor suppressor p27(Kip1) and the antiapoptotic factors Bcl-xL and XIAP (X-linked Inhibitor of Apoptosis Protein). Moreover, Dkc1(m) ribosomes were unable to direct translation from IRES elements present in viral messenger RNAs. These findings reveal a potential mechanism by which defective ribosome activity leads to disease and cancer}, pmid = {16690864}, keywords = {0,5’ Untranslated Regions,Animals,bcl-X Protein,bcl-X Protein: biosynthesis,bcl-X Protein: genetics,biosynthesis,cancer,cell cycle,Cell Cycle Proteins,Cell Cycle Proteins: chemistry,Cell Cycle Proteins: genetics,Cell Cycle Proteins: physiology,Cell Line,Cells,CELLS,CellsCultured,chemistry,Cultured,Cyclin-Dependent Kinase Inhibitor p27,Cyclin-Dependent Kinase Inhibitor p27: biosynthesi,Cyclin-Dependent Kinase Inhibitor p27: genetics,disease,Dyskeratosis Congenita,Dyskeratosis Congenita: genetics,ELEMENTS,ENCODES,gene,Genetic,genetics,human,Humans,INHIBITOR,Insect Viruses,Insect Viruses: genetics,INTERNAL RIBOSOME ENTRY,kinase,La,Lymphocytes,Lymphocytes: metabolism,Male,MECHANISM,Messenger,MESSENGER-RNA,MESSENGER-RNAS,Messenger: genetics,Messenger: metabolism,metabolism,Mice,modification,nosource,Nuclear Proteins,Nuclear Proteins: chemistry,Nuclear Proteins: genetics,Nuclear Proteins: physiology,Oligonucleotide Array Sequence Analysis,physiology,Point Mutation,Polyribosomes,Polyribosomes: metabolism,protein,Protein Biosynthesis,Proteins,Proteomics,Pseudouridine,PSEUDOURIDINE SYNTHASE,Pseudouridine: metabolism,REGION,Ribosomal,ribosomal RNA,RIBOSOMAL-RNA,Ribosomal: metabolism,ribosome,Ribosomes,Rna,RNA,RNA Viruses,RNA Viruses: genetics,RNAMessenger,RNARibosomal,rRNA,Transfection,translation,Untranslated Regions,X-Linked Inhibitor of Apoptosis Protein,X-Linked Inhibitor of Apoptosis Protein: biosynthe,X-Linked Inhibitor of Apoptosis Protein: genetics} }

@article{yoonSui1SuppressorLocus1992, title = {The ⬚sui1⬚ Suppressor Locus in ⬚{{Saccharomyces}} Cerevisiae⬚ Encodes a Translation Factor That Functions during {{tRNA}}⬚i⬚⬚{{Met}}⬚ Recognition of the Start Codon.}, author = {Yoon, H. and Donahue, T.F.}, year = 1992, journal = {Mol.Cell.Biol.}, volume = {12}, pages = {248–260}, keywords = {Codon,Multiple DOI,nonfile,nosource,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sui,sui1,translation,yeast} } % == BibTeX quality report for yoonSui1SuppressorLocus1992: % ? Possibly abbreviated journal title Mol.Cell.Biol.

@article{yoonControlTranslationInitiation1992a, title = {Control of Translation Initiation in ⬚{{Saccharomyces}} Cerevisiae⬚.}, author = {Yoon, H. and Donahue, T.F.}, year = 1992, journal = {Molecular Microbiol.}, volume = {6}, pages = {1413–1419}, doi = {10.1111/j.1365-2958.1992.tb00861.x}, keywords = {initiation,nosource,Review,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sui,translation,TRANSLATION INITIATION} } % == BibTeX quality report for yoonControlTranslationInitiation1992a: % ? Possibly abbreviated journal title Molecular Microbiol.

@article{yoshidaTrichostatinTrapoxinNovel1995, title = {Trichostatin {{A}} and Trapoxin: Novel Chemical Probes for the Role of Histone Acetylation in Chromatin Structure and Function}, author = {Yoshida, M. and Horinouchi, S. and Beppu, T.}, year = 1995, month = may, journal = {Bioessays}, volume = {17}, number = {5}, pages = {423–430}, publisher = {Wiley Online Library}, doi = {10.1002/bies.950170510}, url = {http://onlinelibrary.wiley.com/doi/10.1002/bies.950170510/pdf}, abstract = {Reversible acetylation at the epsilon-amino group of lysines located at the conserved domain of core histones is supposed to play an important role in the regulation of chromatin structure and its transcriptional activity. One promising strategy for analyzing the precise function of histone acetylation is to block the activities of acetylating or deacetylating enzymes by specific inhibitors. Recently, two microbial metabolites, trichostatin A and trapoxin, were found to be potent inhibitors of histone deacetylases. Trichostatin A reversibly inhibits the mammalian histone deacetylase, whereas trapoxin causes inhibition through irreversible binding to the enzyme. The histone deacetylase from a trichostatin A-resistant cell line is resistant to trichostatin A, indicating that the enzyme is the primary target. Both of the agents induce a variety of biological responses of cells such as induction of differentiation and cell cycle arrest. Trichostatin A and trapoxin are useful in analyzing the role of histone acetylation in chromatin structure and function as well as in determining the genes whose activities are regulated by histone acetylation}, keywords = {95305851,Acetylation,animal,AntibioticsPeptide,BINDING,cell cycle,Cell Line,chemistry,Chromatin,enzyme,gene,Gene Expression Regulation,Genes,Histone Deacetylase,Histones,Hydroxamic Acids,INHIBITION,Lysine,metabolism,Microbial,nosource,pharmacology,regulation,RPD3,structure,TranscriptionGenetic} }

@article{yoshiokaEfficientAmplificationDrosophila1992, title = {Efficient Amplification of {{Drosophila}} Simulans Copia Directed by High-Level Reverse Transcriptase Activity Associated with Copia Virus-like Particles}, author = {Yoshioka, K. and Kanda, H. and Takamatsu, N. and Togashi, S. and Kondo, S. and Miyake, T. and Sakaki, Y. and Shiba, T.}, year = 1992, month = oct, journal = {Gene}, volume = {120}, number = {2}, pages = {191–196}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0378111992900935}, abstract = {The number of retrotransposon copia per genome in Drosophila melanogaster cultured cells is two to three times higher than that in D. melanogaster embryo cells. Here, we have found that the genome of the related species, Drosophila simulans, contains in cultured cells more efficiently amplified copia DNA (approximately ten fold). Furthermore, we analyzed copia virus-like particles (VLPs) prepared from D. melanogaster and D. simulans cultured cells, which contain copia RNA and reverse transcriptase (RT) activity, and thus, play a major role in copia replication. The RT activity associated with the D. simulans VLPs was 25 times higher than that associated with the D. melanogaster VLPs. Taken together with the fact that copia is believed to transpose through an RNA intermediate, these results suggest that the amplification of copia DNA should relate to copia RNA-mediated transposition, and the higher RT activity associated with the D. simulans VLPs would lead to the efficient amplification of copia DNA. In a comparison between D. melanogaster and D. simulans copia nucleotide (nt) sequences, five nt substitutions, which cause the respective amino acid changes, were found in the copia RT-coding region. Polymerase chain reaction direct sequencing showed that these five substitutions are the vast majority in each Drosophila species. The substitutions, therefore, may be responsible for the high level of the RT activity associated with the D. simulans VLPs}, keywords = {93013034,Amino Acid Sequence,animal,Base Sequence,BlottingSouthern,CellsCultured,Comparative Study,Dna,DNA Transposable Elements,DnaViral,Drosophila,Drosophila melanogaster,EmbryoNonmammalian,enzymology,genetics,Genome,isolation &,metabolism,Methods,microbiology,Molecular Sequence Data,No DOI found,nosource,Oligodeoxyribonucleotides,polymerase,Polymerase Chain Reaction,purification,Restriction Mapping,retrotransposon,Retroviridae,Rna,RNA-Directed DNA Polymerase,sequence,SEQUENCES} }

@article{youngPartialCorredtionSevere1997, title = {Partial Corredtion of a Severe Molecular Defect in Hemphilia {{A}}, Because of Errors during Expression of the Factor {{VIII}} Gene.}, author = {Young, M. and Inaba, H. and Hoyer, L.W. and Higuchi, M. and Kazazian, H.H. and Antonarakis, S.E.}, year = 1997, month = mar, journal = {American Journal of Human Genetics}, volume = {60}, number = {3}, pages = {565–573}, keywords = {Adenine,analysis,COMPLEX,COMPLEXES,Dna,expression,frameshift,Frameshift Mutation,Frameshifting,gene,Gene Expression,GENE-EXPRESSION,In Vitro,IN-VITRO,MECHANISM,MECHANISMS,Mutation,No DOI found,nosource,Phenotype,protein,ribosomal frameshifting,Rna,sequence,transcription} }

@article{youngmanActiveSiteRibosome2004, title = {The Active Site of the Ribosome Is Composed of Two Layers of Conserved Nucleotides with Distinct Roles in Peptide Bond Formation and Peptide Release}, author = {Youngman, E.M. and Brunelle, J.L. and Kochaniak, A.B. and Green, R.}, year = 2004, month = may, journal = {Cell}, volume = {117}, number = {5}, pages = {589–599}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(04)00411-8}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867404004118}, abstract = {Peptide bond formation and peptide release are catalyzed in the active site of the large subunit of the ribosome where universally conserved nucleotides surround the CCA ends of the peptidyl- and aminoacyl-tRNA substrates. Here, we describe the use of an affinity-tagging system for the purification of mutant ribosomes and analysis of four universally conserved nucleotides in the innermost layer of the active site: A2451, U2506, U2585, and A2602. While pre-steady-state kinetic analysis of the peptidyl transferase activity of the mutant ribosomes reveals substantially reduced rates of peptide bond formation using the minimal substrate puromycin, their rates of peptide bond formation are unaffected when the substrates are intact aminoacyl-tRNAs. These mutant ribosomes do, however, display substantial defects in peptide release. These results reveal a view of the catalytic center in which an inner shell of conserved nucleotides is pivotal for peptide release, while an outer shell is responsible for promoting peptide bond formation}, keywords = {analysis,BIOLOGY,BOND FORMATION,conserved nucleotide,Genetic,genetics,La,nosource,Nucleotides,peptide bond formation,peptidyl transferase,PEPTIDYL-TRANSFERASE,purification,Puromycin,RELEASE,ribosome,Ribosomes,SITE,SUBUNIT,SYSTEM} }

@article{youngmanAffinityPurificationVivoassembled2005, title = {Affinity Purification of in Vivo-Assembled Ribosomes for in Vitro Biochemical Analysis}, author = {Youngman, E.M. and Green, R.}, year = 2005, month = jul, journal = {Methods}, volume = {36}, number = {3}, pages = {305–312}, publisher = {Elsevier}, doi = {10.1016/j.ymeth.2005.04.007}, url = {http://www.sciencedirect.com/science/article/pii/S1046202305000903 http://linkinghub.elsevier.com/retrieve/pii/S1046202305000903}, abstract = {As it has become increasingly clear that the RNA components of the ribosome are central to its function, the in vitro analysis of mutations in the ribosomal RNAs has become an important tool for understanding the molecular details of ribosome function. However, the frequent dominant lethal phenotypes of mutations at interesting rRNA residues has long presented a hurdle to this analysis, as their lethality has rendered it impossible to generate pure populations of in vivo-derived ribosomes for study. We present here the details of a method for affinity purification of ribosomes bearing any mutation in the 16S or 23S rRNA and demonstrate that ribosomes purified using this technology are highly active in the several steps of translation we have examined}, keywords = {0,16S,analysis,aynity puriwcation,Base Sequence,BIOLOGY,chemistry,ChromatographyAffinity,COMPONENT,COMPONENTS,Genetic,genetics,In Vitro,IN-VITRO,La,Methods,Molecular Biology,Molecular Sequence Data,mutagenesis,Mutation,MUTATIONS,nosource,Phenotype,purification,RESIDUES,ribosomal RNA,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNARibosomal16S,RNARibosomal23S,rRNA,Support,translation} }

@article{yountReverseGeneticsFulllength2003, title = {Reverse Genetics with a Full-Length Infectious {{cDNA}} of Severe Acute Respiratory Syndrome Coronavirus}, author = {Yount, B. and Curtis, K.M. and Fritz, E.A. and Hensley, L.E. and Jahrling, P.B. and Prentice, E. and Denison, M.R. and Geisbert, T.W. and Baric, R.S.}, year = 2003, month = oct, journal = {Proceedings of the National Academy of Sciences}, volume = {100}, number = {22}, pages = {12995–13000}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.1735582100}, url = {http://www.pnas.org/content/100/22/12995.short}, abstract = {A previously undescribed coronavirus (CoV) is the etiologic agent responsible for severe acute respiratory syndrome (SARS). Using a panel of contiguous cDNAs that span the entire genome, we have assembled a full-length cDNA of the SARS-CoV Urbani strain, and have rescued molecularly cloned SARS viruses (infectious clone SARS-CoV) that contained the expected marker mutations inserted into the component clones. Recombinant viruses replicated as efficiently as WT virus and both were inhibited by treatment with the cysteine proteinase inhibitor (2S,3S)-transepoxysuccinyl-L-leucylamido-3-methylbutane ethyl ester. In addition, subgenomic transcripts were initiated from the consensus sequence ACGAAC in both the WT and infectious clone SARS-CoV. Availability of a SARS-CoV full-length cDNA provides a template for manipulation of the viral genome, allowing for the rapid and rational development and testing of candidate vaccines and therapeutics against this important human pathogen}, keywords = {0,Animals,Base Sequence,Cercopithecus aethiops,CloningMolecular,COMPONENT,Consensus Sequence,Cysteine,development,Dna,DNAComplementary,epidemiology,Genetic,Genetic Markers,Genetic Techniques,genetics,Genome,human,INHIBITOR,La,MARKER,microbiology,Mutation,MUTATIONS,nosource,Open Reading Frames,pathogenicity,SARS,Sars Virus,sequence,Severe Acute Respiratory Syndrome,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,TEMPLATE,TRANSCRIPT,TranscriptionGenetic,Vero Cells,virology,virus} } % == BibTeX quality report for yountReverseGeneticsFulllength2003: % ? unused Journal abbr (“Proc.Natl.Acad.Sci.U.S.A”)

@article{yuIdentificationCisactingSignals1996, title = {Identification of Cis-Acting Signals in the Giardiavirus ({{GLV}}) Genome Required for Expression of Firefly Luciferase in {{Giardia}} Lamblia.}, author = {Yu, D.C. and Wang, C.C.}, year = 1996, journal = {Rna-A Publication of the Rna Society}, volume = {2}, number = {8}, pages = {824–834}, publisher = {Cold Spring Harbor Lab}, url = {http://rnajournal.cshlp.org/content/2/8/824.short}, abstract = {Giardiavirus (GLV) is a 6,277-bp double-stranded RNA virus of Giardia lamblia, one of the earliest eukaryotic divergents from the prokaryotes, Our previous success in GLV-mediated transfection of G. lamblia has provided an effective way of monitoring the mechanisms underlining GLV gene replication and mRNA translation in this organism. Here we have investigated the cis-acting signals in the GLV genome that regulate replication, transcription, and translation of an inserted firefly luciferase gene in GLV-infected G. lamblia. By modifying the two terminal regions of a full-length GLV cDNA clone used to flank a luciferase gene, various in vitro chimeric transcripts were generated and introduced into GLV-infected G. lamblia via electroporation, Expression of luciferase (+) strand and (-) strand RNAs in the transfected cells was monitored and the luciferase activity assayed. The results indicated that the 5’-untranslated region (UTR) of 366 nt and the 3’-terminal 2,022 nt of the viral transcript are both needed for optimal expression of the two RNA strands. Although the entire 5’-UTR is needed for the chimeric mRNA synthesis, both the primary sequence and the secondary structure at the 3’ end of GLV transcript are essential for the synthesis of (-) strand RNA. When the 5’ end of GLV transcript was extended 265 nt into the capsid protein open reading frame and fused with that of luciferase, there was no change in the level of luciferase chimeric RNA, but a 5,000-fold increase of luciferase activity was observed that may be attributed to an enhanced translational efficiency of the chimeric mRNA in G. lamblia}, keywords = {3,3’-UTR,5’-UTR,Capsid,CELLS,D,DOUBLE-STRANDED-RNA,dsRNA virus,efficiency,expression,FRAME,gene,Genome,IDENTIFICATION,In Vitro,IN-VITRO,L-A-VIRUS,LACKING PROTOZOAN,luciferase,MECHANISM,MECHANISMS,MESSENGER-RNA,mRNA,No DOI found,nosource,OPEN READING FRAME,PHYLOGENETIC PLACE,POL FUSION PROTEIN,PROKARYOTES,protein,READING FRAME,REGION,REPLICATION,replication site,Rna,SACCHAROMYCES-CEREVISIAE,SECONDARY STRUCTURE,sequence,SIGNAL,structure,TRANSCRIPT,transcription,transcription site,Transfection,translation,VIRAL-RNA,virus,yeast} }

@article{yuAmplificationExpressionPackaging1996, title = {Amplification, Expression, and Packaging of a Foreign Gene by Giardiavirus in {{Giardia}} Lamblia}, author = {Yu, D.C. and Wang, A.L. and Wang, C.C.}, year = 1996, month = dec, journal = {Journal of Virology}, volume = {70}, number = {12}, pages = {8752–8757}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.70.12.8752-8757.1996}, url = {http://jvi.asm.org/cgi/content/abstract/70/12/8752}, abstract = {Giardia lamblia is an intestinal protozoan parasite and one of the earliest enkaryotic divergents. The trophozoite multiplies via asexual binary fission and lacks all natural means of lateral gene transfer. A system is developed here for long-term expression of a foreign gene in this organism by exploiting recombinant virions derived from the giardiavirus (GLV), a double-stranded RNA virus that infects many Giardia isolates. An in vitro transcript of the cloned GLV cDNA, comprising the firefly luciferase-encoding region Banked by 5’ and 3’ fragments of GLV positive-strand RNA, was electroporated into GLV-infected trophozoites. Luciferase activity in electroporated cells peaked on day 2 at levels 6 orders of magnitude above background, Expression of this foreign gene remained at 80% of its peak level after 30 days in the absence of selective pressure. The chimeric RNA was replicated as double-stranded RNA and packaged into virus-like particles. The recombinant virions mere partially purified from the wild-type helper virus by CsCl equilibrium density-gradient centrifugation and used to superinfect Giardia trophozoites. At multiplicities of infection of 100 or higher, these chimeric virions were able to initiate new rounds of expression of luciferase activity in the superinfected cells, Thus, the engineered virion can be successfully used to introduce and efficiently express a heterologous gene in this enkaryotic microorganism}, keywords = {3,CELLS,DOUBLE-STRANDED-RNA,expression,FIREFLY LUCIFERASE,gene,Genome,In Vitro,IN-VITRO,INFECTION,LACKING PROTOZOAN,luciferase,nosource,packaging,PARTICLES,PHYLOGENETIC PLACE,protein,REGION,RESISTANT,Rna,SEQUENCES,SIMPLEX VIRUS VECTORS,SYSTEM,TRANSCRIPT,Transfection,Virion,virus} }

@article{yuUntyingFIVFrameshifting2005, title = {Untying the {{FIV}} Frameshifting Pseudoknot Structure by {{MS3D}}}, author = {Yu, E.T. and Zhang, Q. and Fabris, D.}, year = 2005, month = jan, journal = {Journal of molecular biology}, volume = {345}, number = {1}, pages = {69–80}, publisher = {Elsevier}, doi = {10.1016/j.jmb.2004.10.014}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283604013063}, abstract = {The structure of the putative feline immunodeficiency virus (FIV) ribosomal frameshifting pseudoknot (PK) has been investigated by a mass spectrometric three-dimensional (MS3D) approach, which involves the application of established solvent-accessibility probes and chemical crosslinkers with detection by electrospray ionization (ESI) Fourier transform mass spectrometry (FTMS). Regardless of their size, probed substrates can be treated with ribonucleases and analyzed by ESI-FTMS to obtain the correct position of chemically modified nucleotides. Protection maps and distance information can be utilized to generate 3D models using the constraint satisfaction algorithm provided by MC-SYM and the energy minimization modules included in CNS. Control experiments were performed on a mutant of mouse mammary tumor virus pseudoknot (VPK), for which an NMR structure is available. Comparison between the MS3D model and the high-resolution structure provided a approximately 3A root-mean-square deviation calculated from all the atoms present in double-stranded regions. Applied to FIV-PK, the MS3D approach confirmed that the selected sequence could fold into an actual pseudoknot, supporting the sequence alignment predictions. Characteristic features of H-type pseudoknots were recognized immediately, but a putative A13-U30 pair was not observed at the stem junction, making FIV-PK resemble VPK more closely than the initially suggested simian retrovirus type-1 pseudoknot. In our model, the unpaired U30 protrudes into the medium, while the hinging A13 assumes a stacked conformation that enables the stems to form a approximately 60 degrees bend and relieve the strain caused by a short loop 1. The model provided the basis to explain the different alkylation patterns observed in the absence and presence of Mg(2+), suggesting the possible formation of a specific metal-binding site between loop 1 and stem 2. This instance illustrates how the MS3D model of FIV-PK can be utilized effectively to generate hypotheses and support functional observations in the absence of a high-resolution structure}, keywords = {0,Algorithms,alignment,Animals,Base Sequence,Cats,chemistry,CONFORMATION,FORM,Frameshifting,FrameshiftingRibosomal,genetics,Immunodeficiency VirusFeline,IMMUNODEFICIENCY-VIRUS,INFORMATION,La,LOOP,Mammary Tumor VirusMouse,media,Methods,Mice,MODEL,models,ModelsMolecular,NMR,nosource,Nucleic Acid Conformation,Nucleotides,PATTERNS,POSITION,PREDICTION,PROTECTION,pseudoknot,pseudoknot structure,pseudoknots,REGION,Research SupportU.S.Gov’tP.H.S.,retrovirus,Ribonucleases,ribosomal frameshifting,Rna,RnaViral,sequence,Sequence Alignment,SITE,Spectrum AnalysisMass,structure,Support,TYPE-1,virus} } % == BibTeX quality report for yuUntyingFIVFrameshifting2005: % ? unused Journal abbr (“J.Mol.Biol.”)

@article{yuInducibleHumanImmunodeficiency1996, title = {Inducible Human Immunodeficiency Virus Type 1 Packaging Cell Lines.}, author = {Yu, H. and Rabson, A.B. and Kaul, M. and Ron, Y. and Dougherty, J.P.}, year = 1996, journal = {Journal of virology}, volume = {70}, number = {7}, pages = {4530–4537}, publisher = {Am Soc Microbiol}, doi = {10.1128/jvi.70.7.4530-4537.1996}, url = {http://jvi.asm.org/cgi/content/abstract/70/7/4530}, keywords = {Cell Line,cell lines,HIV,human,HUMAN-IMMUNODEFICIENCY-VIRUS,IMMUNODEFICIENCY-VIRUS,nosource,packaging,virus} } % == BibTeX quality report for yuInducibleHumanImmunodeficiency1996: % ? unused Journal abbr (“J.Virol.”)

@article{yuActivationNovelCalciumdependent1996a, title = {Activation of a Novel Calcium-Dependent Protein-Tyrosine Kinase. {{Correlation}} with c-{{Jun N-terminal}} Kinase but Not Mitogen-Activated Protein Kinase Activation.}, author = {Yu, H. and Li, X. and Marchetto, G.S. and Dy, R. and Hunter, D. and Calvo, B. and Dawson, T.L. and Wilm, M. and Anderegg, R.J. and Graves, L.M. and Earp, H.S.}, year = 1996, journal = {J.Biol.Chem.}, volume = {271}, pages = {29993–29998}, doi = {10.1074/jbc.271.47.29993}, keywords = {activation,anisomycin,Ca2+,kinase,nosource,protein,stress activated} } % == BibTeX quality report for yuActivationNovelCalciumdependent1996a: % ? Possibly abbreviated journal title J.Biol.Chem.

@article{yuExpressionMicroprotein2001, title = {Expression of a Micro-Protein}, author = {Yu, X. and Warner, J.R.}, year = 2001, journal = {Journal of Biological Chemistry}, volume = {276}, number = {36}, pages = {33821–33825}, publisher = {ASBMB}, doi = {10.1074/jbc.M103772200}, url = {http://www.jbc.org/content/276/36/33821.short}, abstract = {The smallest known open reading frame encodes the ribosomal protein L41, which in yeast is composed of only 24 amino acids, 17 of which are arginine or lysine. Because of the unique problems that might attend the translation of such a short open reading frame, we have investigated the properties and the translation of the mRNAs encoding L41. In Saccharomyces cerevisiae L41 is encoded by two linked genes, RPL41A and RPL41B. These genes give rise to mRNAs that have short 5’ leaders of 18 and 22 nucleotides and rather long 3’ leaders of 203 and 210 nucleotides not including their poly(A) tails. The mRNAs are translated exclusively on monosomes, suggesting that ribosomes do not remain attached to the mRNA after termination of translation. Calculations based on the abundance of ribosomes and of L41 mRNA indicate that the entire translation event, from initiation through termination, must occur in similar to2 s. Termination of translation after only 25 codons does not subject the mRNAs encoding L41 to nonsense-mediated decay. Surprisingly, despite the L41 ribosomal protein being conserved from the archaea through the mammalia, S. cerevisiae can grow relatively normally after deletion of both RPL41A and RPL41B}, keywords = {Amino Acids,Archaea,Arginine,Codon,COMPLEX,DECAY,expression,gene,Genes,Genome,IN-SILICO,initiation,L41,Lysine,MESSENGER-RNA TURNOVER,mRNA,nonsense-mediated decay,nosource,Nucleotides,poly(A),protein,ribosome,Ribosomes,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SUBUNIT,termination,translation,yeast,YEAST RIBOSOMAL-PROTEINS} }

@article{yurievaThermusThermophilisDnaX1997a, title = {Thermus Thermophilis {{dnaX}} Homolog Encoding Gamma- and Tau-like Proteins of the Chromosomal Replicase}, author = {Yurieva, O. and Skangalis, M. and Kuriyan, J. and O’Donnell, M.}, year = 1997, month = oct, journal = {Journal of Biological Chemistry}, volume = {272}, number = {43}, pages = {27131–27139}, doi = {10.1074/jbc.272.43.27131}, keywords = {ATPase,Bacteria,Dna,dnaX,Escherichia coli,ESCHERICHIA-COLI,frameshift,gene,Genes,homolog,human,nosource,polymerase,protein,Proteins,SUBUNIT,Thermus} }

@article{yusupovCrystalStructureRibosome2001, title = {Crystal {{Structure}} of the {{Ribosome}} at 5.5 {{A Resolution}}}, author = {Yusupov, M.M. and Yusupova, G.Z. and Baucom, A. and Lieberman, K. and Earnest, T.N. and Cate, J.H. and Noller, H.F.}, year = 2001, month = mar, journal = {Science}, volume = {292}, number = {5518}, eprint = {11283358}, eprinttype = {pubmed}, pages = {57883–869}, publisher = {Cold Spring Harbor Laboratory Press}, issn = {0036-8075}, doi = {10.1126/science.1060089}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11283358 http://symposium.cshlp.org/content/66/57.extract http://www.sciencemag.org/content/292/5518/883.short}, abstract = {We describe the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound messenger RNA and transfer RNAs (tRNAs) at 5.5 angstrom resolution. All of the 16S, 23S, and 5S ribosomal RNA (rRNA) chains, the A-, P-, and E-site tRNAs, and most of the ribosomal proteins can be fitted to the electron density map. The core of the interface between the 30S small subunit and the 50S large subunit, where the tRNA substrates are bound, is dominated by RNA, with proteins located mainly at the periphery, consistent with ribosomal function being based on rRNA. In each of the three tRNA binding sites, the ribosome contacts all of the major elements of tRNA, providing an explanation for the conservation of tRNA structure. The tRNAs are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 angstrom movements associated with tRNA translocation with intersubunit movement.}, pmid = {11283358}, keywords = {0,5S rRNA,Amino Acid-Specific,Amino Acid-Specific: chemistry,Amino Acid-Specific: metabolism,Anticodon,Bacterial,Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: metabolism,Bacterial: chemistry,Bacterial: metabolism,Base Sequence,BINDING,Binding Sites,BIOLOGY,chemistry,CRYSTAL-STRUCTURE,Crystallography,ELEMENTS,La,Ligands,Messenger,Messenger: chemistry,Messenger: metabolism,metabolism,Models,Molecular,Molecular Sequence Data,Movement,mRNA,nosource,Nucleic Acid Conformation,protein,Protein Biosynthesis,Protein Conformation,Proteins,RESOLUTION,Review,Ribosomal,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: metabolism,Ribosomal: chemistry,Ribosomal: metabolism,ribosome,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,Ribosomes: ultrastructure,Rna,RNA-Messenger,RNA-Ribosomal,RNA-Transfer,rRNA,Sensitivity and Specificity,structure,SUBUNIT,support-u.s.gov’t-p.h.s.,Thermus,Thermus thermophilus,Thermus thermophilus: chemistry,Thermus thermophilus: ultrastructure,Transfer,Transfer: chemistry,Transfer: metabolism,translocation,tRNA,ultrastructure,X-Ray} } % == BibTeX quality report for yusupovCrystalStructureRibosome2001: % ? Title looks like it was stored in title-case in Zotero

@article{yusupovaStructuralBasisMessenger2006, title = {Structural Basis for Messenger {{RNA}} Movement on the Ribosome}, author = {Yusupova, G. and Jenner, L. and Rees, B. and Moras, D. and Yusupov, M.}, year = 2006, month = oct, journal = {Nature}, volume = {444}, number = {7171}, pages = {391–394}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/nature/journal/v444/n7117/abs/nature05281.html}, abstract = {Translation initiation is a major determinant of the overall expression level of a gene. The translation of functionally active protein requires the messenger RNA to be positioned on the ribosome such that the start/initiation codon will be read first and in the correct frame. Little is known about the molecular basis for the interaction of mRNA with the ribosome at different states of translation. Recent crystal structures of the ribosomal subunits, the empty 70S ribosome and the 70S ribosome containing functional ligands have provided information about the general organization of the ribosome and its functional centres. Here we compare the X-ray structures of eight ribosome complexes modelling the translation initiation, post-initiation and elongation states. In the initiation and post-initiation complexes, the presence of the Shine-Dalgarno (SD) duplex causes strong anchoring of the 5’-end of mRNA onto the platform of the 30S subunit, with numerous interactions between mRNA and the ribosome. Conversely, the 5’ end of the ‘elongator’ mRNA lacking SD interactions is flexible, suggesting a different exit path for mRNA during elongation. After the initiation of translation, but while an SD interaction is still present, mRNA moves in the 3’–{\(>\)}5’ direction with simultaneous clockwise rotation and lengthening of the SD duplex, bringing it into contact with ribosomal protein S2}, keywords = {70S RIBOSOME,Codon,COMPLEX,COMPLEXES,crystal structure,CRYSTAL-STRUCTURE,CRYSTAL-STRUCTURES,elongation,expression,FRAME,gene,INFORMATION,initiation,La,Ligands,MAJOR DETERMINANT,MESSENGER-RNA,MOF,Movement,mRNA,No DOI found,nosource,ORGANIZATION,protein,REQUIRES,RIBOSOMAL-PROTEIN,RIBOSOMAL-SUBUNIT,RIBOSOMAL-SUBUNITS,ribosome,Rna,Rotation,Structural,STRUCTURAL BASIS,structure,SUBUNIT,SUBUNITS,translation,TRANSLATION INITIATION} }

@article{zaragozaRapamycinInducesG01998, title = {Rapamycin Induces the {{G0}} Program of Transcriptional Repression in Yeast by Interfering with the {{TOR}} Signaling Pathway}, author = {Zaragoza, D. and Ghavidel, A. and Heitman, J. and Schultz, M.C.}, year = 1998, journal = {Molecular and cellular biology}, volume = {18}, number = {8}, pages = {4463–4470}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.18.8.4463}, url = {http://mcb.asm.org/cgi/content/abstract/18/8/4463}, abstract = {The macrolide antibiotic rapamycin inhibits cellular proliferation by interfering with the highly conserved TOR (for target of rapamycin) signaling pathway. Growth arrest of budding yeast cells treated with rapamycin is followed by the program of molecular events that characterizes entry into G0 (stationary phase), including the induction of polymerase (Pol) II genes typically expressed only in G0. Normally, progression into G0 is characterized by transcriptional repression of the Pol I and III genes. Here, we show that rapamycin treatment also causes the transcriptional repression of Pol I and III genes. The down-regulation of Pol III transcription is TOR dependent. While it coincides with translational repression by rapamycin, transcriptional repression is due in part to a translation-independent effect that is evident in extracts from a conditional tor2 mutant. Biochemical experiments reveal that RNA Pol III and probably transcription initiation factor TFIIIB are targets of repression by rapamycin. In view of previous evidence that TFIIIB and Pol III are inhibited when protein phosphatase 2A (PP2A) function is impaired, and that PP2A is a component of the TOR pathway, our results suggest that TOR signaling regulates Pol I and Pol III transcription in response to nutrient growth signals}, keywords = {98336252,antagonists & inhibitors,antibiotic,AntibioticsAntifungal,COMPONENT,drug effects,G0 Phase,G1 Phase,gene,Gene Expression RegulationFungal,Genes,genetics,initiation,metabolism,nosource,pharmacology,Phosphotransferases (Alcohol Group Acceptor),pol,Polyenes,polymerase,protein,Rna,RNA Polymerase III,Saccharomyces cerevisiae,SIGNAL,Signal Transduction,supportnon-u.s.gov’t,Temperature,transcription,TranscriptionGenetic,TranslationGenetic,yeast} } % == BibTeX quality report for zaragozaRapamycinInducesG01998: % ? unused Journal abbr (“Mol.Cell Biol.”)

@article{zarlingInhibitionHIVReplication1990, title = {Inhibition of {{HIV}} Replication by Pokeweed Antiviral Protein Targeted to {{CD4}}+ Cells by Monoclonal Antibodies.}, author = {Zarling, J.M. and Moran, P.A. and Haffar, O. and Sias, J. and Richman, D.D. and Spina, C.A. and Myers, D.E. and Kuelbeck, V. and Ledbetter, J.A. and Uckun, F.M.}, year = 1990, journal = {Nature}, volume = {347}, pages = {92–95}, publisher = {Nature Publishing Group}, doi = {10.1038/347092a0}, url = {http://www.nature.com/nature/journal/v347/n6288/abs/347092a0.html}, keywords = {Antibodies,antibody,antiviral,HIV,INHIBITION,nosource,PAP,Pokeweed antiviral protein,protein} }

@article{zarlingInhibitionHIV1Replication1991, title = {Inhibition of {{HIV-1}} Replication in Seropositive Patients’ {{CD4}}+ {{T-cells}} by Pokeweed Antiviral Protein-Monoclonal Antibody Conjugates}, author = {Zarling, J.M. and Moran, P.A. and Haffar, O. and Diegel, M. and Myers, D.E. and Kuelbeck, V. and Ledbetter, J.A. and Uckun, F.M.}, year = 1991, journal = {International journal of immunopharmacology}, volume = {13 Suppl 1:63-8}, pages = {63–68}, publisher = {Elsevier}, doi = {10.1016/0192-0561(91)90126-R}, url = {http://linkinghub.elsevier.com/retrieve/pii/019205619190126R}, abstract = {Pokeweed antiviral protein (PAP) inhibits HIV-1 replication in HIV-1 infected CD4+ cells and PAP targeted to CD4+T-cells by conjugation with monoclonal antibodies (mAb) against CD4 is approximately 1000 times more potent than non-conjugated PAP. Furthermore, PAP-antiCD4 inhibits HIV-1 production in seropositive patients’ CD4+ T-cells activated with mAb to CD3 which was found to be the most potent means to activate HIV- 1 production. These findings, together with previous observations that PAP-mAb conjugates have an in vivo plasma half-life of about 30 times that of non-conjugated PAP, suggest that PAP-antiCD4 may be a useful therapy in HIV-infected humans. Additionally, because PAP is known to have antiviral activity against several other human viruses, PAP-mAb conjugates may also have clinical potential for treating other viral diseases}, keywords = {92387832,administration & dosage,Antibodies,AntibodiesMonoclonal,antibody,antiviral,Antiviral Agents,CD4-Positive T-Lymphocytes,disease,drug effects,Half-Life,HIV,HIV Seropositivity,Hiv-1,human,Immunotoxins,IN-VIVO,INHIBITION,microbiology,nosource,PAP,pharmacology,physiology,Plant Proteins,Pokeweed antiviral protein,protein,supportnon-u.s.gov’t,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,therapeutic use,therapy,Virus Replication} } % == BibTeX quality report for zarlingInhibitionHIV1Replication1991: % ? unused Journal abbr (“Int.J.Immunopharmacol.”)

@article{zavialovPeptidyltRNARegulatesGTPase2003, title = {Peptidyl-{{tRNA}} Regulates the {{GTPase}} Activity of Translation Factors}, author = {Zavialov, A.V. and Ehrenberg, M.}, year = 2003, month = jul, journal = {Cell}, volume = {114}, number = {1}, pages = {113–122}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(03)00478-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867403004781}, abstract = {Rapid protein synthesis in bacteria requires the G proteins IF2, EF-Tu, EF-G, and RF3. These factors catalyze all major steps of mRNA translation in a GTP-dependent manner. Here, it is shown how the position of peptidyl-tRNA in the ribosome and presence of its peptide control the binding and GTPase activity of these translation factors. The results explain how idling GTPase activity and negative interference between different translation factors are avoided and suggest that hybrid sites for tRNA on the ribosome play essential roles in translocation of tRNAs, recycling of class 1 release factors by RF3, and recycling of ribosomes back to a new round of initiation. We also propose a model for translocation of tRNAs in two separate steps, which clarifies the roles of EF-G.GTP and GTP hydrolysis in this process}, keywords = {Bacteria,BINDING,EFTu,GTP,GTPase,Hydrolysis,initiation,mRNA,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,RELEASE FACTORS,ribosome,Ribosomes,translation,translocation,tRNA} }

@article{zebarjadianPointMutationsYeast1999, title = {Point Mutations in Yeast {{CBF5}} Can Abolish in Vivo Pseudouridylation of {{rRNA}}}, author = {Zebarjadian, Y. and King, T. and Fournier, M.J. and Clarke, L. and Carbon, J.}, year = 1999, month = nov, journal = {Molecular and Cellular Biology}, volume = {19}, number = {11}, pages = {7461–7472}, doi = {10.1128/MCB.19.11.7461}, url = {PM:10523634}, abstract = {In budding yeast (Saccharomyces cerevisiae), the majority of box H/ACA small nucleolar RNPs (snoRNPs) have been shown to direct site-specific pseudouridylation of rRNA. Among the known protein components of H/ACA snoRNPs, the essential nucleolar protein Cbf5p is the most likely pseudouridine (Psi) synthase. Cbf5p has considerable sequence similarity to Escherichia coli TruBp, a known Psi synthase, and shares the “KP” and “XLD” conserved sequence motifs found in the catalytic domains of three distinct families of known and putative Psi synthases. To gain additional evidence on the role of Cbf5p in rRNA biosynthesis, we have used in vitro mutagenesis techniques to introduce various alanine substitutions into the putative Psi synthase domain of Cbf5p. Yeast strains expressing these mutated cbf5 genes in a cbf5Delta null background are viable at 25 degrees C but display pronounced cold- and heat-sensitive growth phenotypes. Most of the mutants contain reduced levels of Psi in rRNA at extreme temperatures. Substitution of alanine for an aspartic acid residue in the conserved XLD motif of Cbf5p (mutant cbf5D95A) abolishes in vivo pseudouridylation of rRNA. Some of the mutants are temperature sensitive both for growth and for formation of Psi in the rRNA. In most cases, the impaired growth phenotypes are not relieved by transcription of the rRNA from a polymerase II-driven promoter, indicating the absence of polymerase I-related transcriptional defects. There is little or no abnormal accumulation of pre-rRNAs in these mutants, although preferential inhibition of 18S rRNA synthesis is seen in mutant cbf5D95A, which lacks Psi in rRNA. A subset of mutations in the Psi synthase domain impairs association of the altered Cbf5p proteins with selected box H/ACA snoRNAs, suggesting that the functional catalytic domain is essential for that interaction. Our results provide additional evidence that Cbf5p is the Psi synthase component of box H/ACA snoRNPs and suggest that the pseudouridylation of rRNA, although not absolutely required for cell survival, is essential for the formation of fully functional ribosomes}, keywords = {0,ACID,Alanine,Amino Acid Sequence,Aspartic Acid,ASSOCIATION,BIOLOGY,biosynthesis,Catalytic Domain,CBF5,Cell Survival,CEREVISIAE,Cold,COMPONENT,COMPONENTS,Conserved Sequence,DOMAIN,DOMAINS,Escherichia coli,ESCHERICHIA-COLI,ESSENTIAL NUCLEOLAR PROTEIN,FAMILY,gene,Genes,genetics,GROWTH,Hydro-Lyases,In Vitro,IN-VITRO,IN-VIVO,INHIBITION,La,metabolism,Microtubule-Associated Proteins,Molecular Biology,Molecular Sequence Data,MOTIFS,Mutagenesis,MUTANTS,Mutation,MUTATIONS,nosource,Phenotype,Point Mutation,polymerase,PRECURSOR,PROMOTER,protein,Proteins,Pseudouridine,pseudouridylation,psi,RIBONUCLEOPROTEIN,Ribonucleoproteins,Ribonucleoproteins-Small Nuclear,Ribonucleoproteins-Small Nucleolar,RibonucleoproteinsSmall Nuclear,RibonucleoproteinsSmall Nucleolar,ribosome,Ribosomes,Rna,RNA Polymerase II,RNA Precursors,RNA Processing-Post-Transcriptional,RNA ProcessingPost-Transcriptional,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNA-POLYMERASE,RNA-POLYMERASE-II,RNA-Ribosomal,RNARibosomal,rRNA,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,sequence,site specific,Support,techniques,Temperature,transcription,Transcription-Genetic,TranscriptionGenetic,Uridine,Uridine Monophosphate,yeast} } % == BibTeX quality report for zebarjadianPointMutationsYeast1999: % ? unused Journal abbr (“Mol Cell Biol”)

@article{zengContributionCterminalTail1997, title = {Contribution of the {{C-terminal}} Tail of {{U1A RBD1}} to {{RNA}} Recognition and Protein Stability.}, author = {Zeng, Q. and Hall, K.B.}, year = 1997, month = mar, journal = {RNA}, volume = {3}, number = {3}, pages = {303–314}, publisher = {Cold Spring Harbor Lab}, url = {http://rnajournal.cshlp.org/content/3/3/303.short}, keywords = {Amino Acid Substitution,BINDING,human,No DOI found,nosource,Nucleotides,poly(A),protein,Proteins,Rna,SECONDARY STRUCTURE,sequence,stability,structure,thermodynamic stability} }

@article{zhangPeptideBondFormation1997a, title = {Peptide Bond Formation by ⬚in Vitro⬚ Selected Ribozymes.}, author = {Zhang, B. and Cech, T.R.}, year = 1997, journal = {Nature}, volume = {390}, pages = {96–100}, doi = {10.1038/36375}, keywords = {In Vitro,in vitro translation,IN-VITRO,nosource,peptidyl transferase,PEPTIDYL-TRANSFERASE,ribozyme,Rna} }

@article{zhangMultifunctionalTurnipCrinkle2003a, title = {A Multifunctional Turnip Crinkle Virus Replication Enhancer Revealed by in Vivo Functional {{SELEX}}}, author = {Zhang, G. and Simon, A.E.}, year = 2003, month = feb, journal = {J.Mol.Biol.}, volume = {326}, number = {1}, pages = {35–48}, doi = {10.1016/S0022-2836(02)01366-9}, url = {PM:12547189}, abstract = {The motif1-hairpin (M1H), located on (-)-strands of Turnip Crinkle Virus (TCV)-associated satellite RNA C (satC), is a replication enhancer and recombination hotspot. Results of in vivo genetic selection (SELEX: systematic evolution of ligands by exponential enrichment), where 28 bases of the M1H were randomized and then subjected to selection in plants, revealed that most winners contained one to three short motifs, many of which in their (-)-sense orientation are found in TCV and satC (-)-strand promoter elements. Ability to replicate in protoplasts correlated with fitness to accumulate in plants with one significant exception. Winner UC, containing only a seven-base replacement sequence, was the second most fit winner, yet replicated no better than a 28-base random replacement sequence. Fitness of satC containing different M1H replacement sequences could be due to enhanced satC replication or enhanced ability to affect TCV movement, since satC interferes with TCV virion accumulation, which is correlated with enhanced movement to younger tissue. Cells inoculated with TCV and UC accumulated fewer virions when compared to other winners that replicated better in protoplasts but were less fit in plants. UC, and other first and second round winners, contained structures that were on average 33% more stable in their (+)-strand orientation, and most formed hairpins with a A-rich sequence at the base. These results suggest that M1H replacement sequences contribute to the fitness of satC by either containing (-)-strand elements that enhance satRNA replication and/or a (+)-strand hairpin flanked with single-stranded sequence that enhances TCV movement}, keywords = {0,BASE,Base Sequence,BASES,BIOLOGY,Brassica napus,CELLS,ELEMENTS,Evolution,EXPONENTIAL ENRICHMENT,Genetic,genetics,HAIRPINS,IN-VIVO,La,Ligands,Molecular Sequence Data,MOLECULAR-GENETICS,MOTIFS,Movement,nosource,physiology,Plant Viruses,Plants,PROMOTER,Promoter Regions (Genetics),PROTOPLASTS,RECOMBINATION,RecombinationGenetic,Regulatory SequencesNucleic Acid,REPLICATION,Rna,RNASatellite,SELECTION,SELEX,sequence,SEQUENCES,structure,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,SYSTEMATIC EVOLUTION,Virion,VIRIONS,virology,virus,Virus Replication} } % == BibTeX quality report for zhangMultifunctionalTurnipCrinkle2003a: % ? Possibly abbreviated journal title J.Mol.Biol.

@article{zhangStructureExpressionFibrillin21994, title = {Structure and Expression of Fibrillin-2, a Novel Microfibrillar Component Preferentially Located in Elastic Matrices.}, author = {Zhang, H. and Apfelroth, S.D. and Hu, W. and Cavis, E.C. and Sanguineti, C. and Bonadio, J. and Mecham, R.P. and Ramirez, F.}, year = 1994, journal = {The Journal of cell biology}, volume = {124}, number = {5}, eprint = {1616180}, eprinttype = {jstor}, pages = {855–863}, publisher = {JSTOR}, doi = {10.1083/jcb.124.5.855}, url = {http://www.jstor.org/stable/1616180}, keywords = {COMPONENT,expression,fibrillin,human,nosource,structure} } % == BibTeX quality report for zhangStructureExpressionFibrillin21994: % ? unused Journal abbr (“J.Cell Biol.”)

@article{zhangAssemblyFactorsRpf22007, title = {Assembly Factors {{Rpf2}} and {{Rrs1}} Recruit {{5S rRNA}} and Ribosomal Proteins {{rpL5}} and {{rpL11}} into Nascent Ribosomes}, author = {Zhang, J. and Harnpicharnchai, P. and Jakovljevic, J. and Tang, L. and Guo, Y. and Oeffinger, M. and Rout, M.P. and Hiley, S.L. and Hughes, T. and Woolford, J.L.}, year = 2007, month = oct, journal = {Genes & development}, volume = {21}, number = {20}, pages = {2580–2592}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gad.1569307}, url = {http://genesdev.cshlp.org/content/21/20/2580.short}, abstract = {More than 170 proteins are necessary for assembly of ribosomes in eukaryotes. However, cofactors that function with each of these proteins, substrates on which they act, and the precise functions of assembly factors–e.g., recruiting other molecules into preribosomes or triggering structural rearrangements of pre-rRNPs–remain mostly unknown. Here we investigated the recruitment of two ribosomal proteins and 5S ribosomal RNA (rRNA) into nascent ribosomes. We identified a ribonucleoprotein neighborhood in preribosomes that contains two yeast ribosome assembly factors, Rpf2 and Rrs1, two ribosomal proteins, rpL5 and rpL11, and 5S rRNA. Interactions between each of these four proteins have been confirmed by binding assays in vitro. These molecules assemble into 90S preribosomal particles containing 35S rRNA precursor (pre-rRNA). Rpf2 and Rrs1 are required for recruiting rpL5, rpL11, and 5S rRNA into preribosomes. In the absence of association of these molecules with pre-rRNPs, processing of 27SB pre-rRNA is blocked. Consequently, the abortive 66S pre-rRNPs are prematurely released from the nucleolus to the nucleoplasm, and cannot be exported to the cytoplasm}, keywords = {0,5S rRNA,Active TransportCell Nucleus,assays,assembly,ASSOCIATION,BINDING,CEREVISIAE,chemistry,Cytoplasm,GenesFungal,genetics,In Vitro,IN-VITRO,L10,L5,La,Macromolecular Substances,metabolism,ModelsBiological,ModelsMolecular,NEIGHBORHOOD,nosource,Nuclear Proteins,nucleolus,PARTICLES,PRECURSOR,protein,Proteins,RECRUITMENT,RIBONUCLEOPROTEIN,Ribosomal Proteins,ribosomal RNA,RIBOSOMAL-PROTEIN,RIBOSOMAL-RNA,ribosome,Ribosomes,Rna,RNA ProcessingPost-Transcriptional,RNA-Binding Proteins,RNA-BINDING-PROTEIN,RNAFungal,RNARibosomal5S,RPL11,rRNA,S,S-CEREVISIAE,Saccharomyces,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,SACCHAROMYCES-CEREVISIAE,Structural,Support,yeast} } % == BibTeX quality report for zhangAssemblyFactorsRpf22007: % ? unused Journal abbr (“Genes Dev.”)

@article{zhangMonitoringMRNADecapping1999, title = {Monitoring {{mRNA}} Decapping Activity}, author = {Zhang, S. and Williams, C.J. and Wormington, M. and Stevens, A. and Peltz, S.W.}, year = 1999, month = jan, journal = {Methods-A Companion to Methods in Enzymology}, volume = {17}, number = {1}, pages = {46–51}, publisher = {Elsevier}, doi = {10.1006/meth.1998.0706}, url = {http://linkinghub.elsevier.com/retrieve/pii/S104620239890706X}, abstract = {mRNA decapping is a common step shared between two important mRNA decay pathways in yeast, Saccharomyces cerevisiae. To investigate how mRNAs are decapped, we have developed an assay that can be easily used to measure the decapping activity. This assay has been used to isolate yeast strains with altered decapping activities. The results demonstrated that decreased decapping activity in vitro corresponds well with the decapping-deficient phenotype in vivo. This assay has been applied to the purified yeast decapping enzyme Dcp1 protein as well as crude yeast extracts and Xenopus oocyte extracts. (C) 1999 Academic Press}, keywords = {CAP STRUCTURE,CEREVISIAE,DEADENYLATION,decapping activity,DECAPPING ENZYME,DECAY,DECAY PATHWAY,decay pathways,degradation,enzyme,EXTRACTS,In Vitro,IN-VITRO,IN-VIVO,MESSENGER-RNA TURNOVER,mRNA,mRNA decay,mRNA turnover,nosource,PATHWAY,Phenotype,protein,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,stability,TRANSCRIPT,Xenopus,Xenopus oocyte,yeast} }

@article{zhangCommon5SRRNA2003, title = {Common {{5S rRNA}} Variants Are Likely to Be Accepted in Many Sequence Contexts}, author = {Zhang, Z. and D’Souza, L.M. and Lee, Y.H. and Fox, G.E.}, year = 2003, month = jan, journal = {Journal of molecular evolution}, volume = {56}, number = {1}, pages = {69–76}, publisher = {Springer}, doi = {10.1007/s00239-002-2381-6}, url = {PM:12569424 http://www.springerlink.com/index/g8ahbfqvuhfmjvhv.pdf}, abstract = {Over evolutionary time RNA sequences which are successfully fixed in a population are selected from among those that satisfy the structural and chemical requirements imposed by the function of the RNA. These sequences together comprise the structure space of the RNA. In principle, a comprehensive understanding of RNA structure and function would make it possible to enumerate which specific RNA sequences belong to a particular structure space and which do not. We are using bacterial 5S rRNA as a model system to attempt to identify principles that can be used to predict which sequences do or do not belong to the 5S rRNA structure space. One promising idea is the very intuitive notion that frequently seen sequence changes in an aligned data set of naturally occurring 5S rRNAs would be widely accepted in many other 5S rRNA sequence contexts. To test this hypothesis, we first developed well-defined operational definitions for a Vibrio region of the 5S rRNA structure space and what is meant by a highly variable position. Fourteen sequence variants (10 point changes and 4 base-pair changes) were identified in this way, which, by the hypothesis, would be expected to incorporate successfully in any of the known sequences in the Vibrio region. All 14 of these changes were constructed and separately introduced into the Vibrio proteolyticus 5S rRNA sequence where they are not normally found. Each variant was evaluated for its ability to function as a valid 5S rRNA in an E. coli cellular context. It was found that 93% (13/14) of the variants tested are likely valid 5S rRNAs in this context. In addition, seven variants were constructed that, although present in the Vibrio region, did not meet the stringent criteria for a highly variable position. In this case, 86% (6/7) are likely valid. As a control we also examined seven variants that are seldom or never seen in the Vibrio region of 5S rRNA sequence space. In this case only two of seven were found to be potentially valid. The results demonstrate that changes that occur multiple times in a local region of RNA sequence space in fact usually will be accepted in any sequence context in that same local region}, keywords = {0,5S rRNA,Bacterial,BASE-PAIR,BIOLOGY,E,genetics,IDENTIFY,La,MODEL,nosource,Point Mutation,POSITION,REGION,Research SupportU.S.Gov’tNon-P.H.S.,Rna,RNARibosomal5S,rRNA,S,sequence,SEQUENCES,Structural,structure,SYSTEM,Variation (Genetics),Vibrio} } % == BibTeX quality report for zhangCommon5SRRNA2003: % ? unused Journal abbr (“J.Mol.Evol.”)

@article{zhaoAutoregulationBiosynthesisRibosomes2003, title = {Autoregulation in the Biosynthesis of Ribosomes}, author = {Zhao, Y. and Sohn, J.H. and Warner, J.R.}, year = 2003, month = jan, journal = {Molecular and cellular biology}, volume = {23}, number = {2}, pages = {699–707}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.23.2.699-707.2003}, url = {http://mcb.asm.org/cgi/content/abstract/23/2/699}, abstract = {The synthesis of ribosomes in Saccharomyces cerevisiae consumes a prodigious amount of the cell’s resources and, consequently, is tightly regulated. The rate of ribosome synthesis responds not only to nutritional cues but also to signals dependent on other macromolecular pathways of the cell, e.g., a defect in the secretory pathway leads to severe repression of transcription of both rRNA and ribosomal protein genes. A search for mutants that interrupted this repression revealed, surprisingly, that inactivation of RPL1B, one of a pair of genes encoding the 60S ribosomal protein L1, almost completely blocked the repression of rRNA and ribosomal protein gene transcription that usually follows a defect in the secretory pathway. Further experiments showed that almost any mutation leading to a defect in 60S subunit synthesis had the same effect, whereas mutations affecting 40S subunit synthesis did not. Although one might suspect that this effect would be due to a decrease in the initiation of translation or to the presence of half-mers, i.e., polyribosomes awaiting a 60S subunit, our data show that this is not the case. Rather, a variety of experiments suggest that some aspect of the production of defective 60S particles or, more likely, their breakdown suppresses the signal generated by a defect in the secretory pathway that represses ribosome synthesis}, keywords = {0,60S subunit,BIOLOGY,biosynthesis,BlottingNorthern,CEREVISIAE,Cytoplasm,Dna,DNA Primers,gene,Gene Deletion,Gene Expression RegulationFungal,GENE-TRANSCRIPTION,Genes,genetics,initiation,L1,La,metabolism,ModelsGenetic,MUTANTS,Mutation,MUTATIONS,nosource,PARTICLES,PATHWAY,pharmacology,Phenotype,Plasmids,Polyribosomes,protein,Protein Binding,Protein Biosynthesis,Proteins,repression,Ribosomal Proteins,RIBOSOMAL-PROTEIN,ribosome,RIBOSOME SYNTHESIS,Ribosomes,Rna,RNAMessenger,RNARibosomal,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,search,SIGNAL,SUBUNIT,Support,Temperature,Time Factors,transcription,TranscriptionGenetic,translation,Tunicamycin} } % == BibTeX quality report for zhaoAutoregulationBiosynthesisRibosomes2003: % ? unused Journal abbr (“Mol.Cell Biol”)

@article{zhouIncorporatingResidualDipolar1999, title = {Incorporating Residual Dipolar Couplings into the {{NMR}} Solution Structure Determination of Nucleic Acids}, author = {Zhou, H. and Vermeulen, A. and Jucker, F.M. and Pardi, A.}, year = 1999, journal = {Biopolymers}, volume = {52}, number = {4}, pages = {168–180}, publisher = {Wiley Online Library}, doi = {10.1002/1097-0282(1999)52:4<168::AID-BIP1002>3.0.CO;2-7}, url = {http://onlinelibrary.wiley.com/doi/10.1002/1097-0282(1999)52:4<168::AID-BIP1002>3.0.CO;2-7/pdf}, abstract = {NMR solution structures of nucleic acids are generally less well defined than similar-sized proteins. Most NMR structures of nucleic acids are defined only by short-range interactions, such as intrabase-pair or sequential nuclear Overhauser effects (NOEs), and J-coupling constants, and there are no long-range structural data on the tertiary structure. Residual dipolar couplings represent an extremely valuable source of distance and angle information for macromolecules but they average to zero in isotropic solutions. With the recent advent of general methods for partial alignment of macromolecules in solution, residual dipolar couplings are rapidly becoming indispensable constraints for solution NMR structural studies. These residual dipolar couplings give long-range global structural information and thus complement the strictly local structural data obtained from standard NOE and torsion angle constraints. Such global structural data are especially important in nucleic acids due to the more elongated, less-globular structure of many DNAs and RNAs. Here we review recent progress in application of residual dipolar couplings to structural studies of nucleic acids. We also present results showing how refinement procedures affect the final solution structures of nucleic acids.Copyright 2001 John Wiley & Sons, Inc}, keywords = {0,ACID,ACIDS,alignment,chemistry,Dna,Inovirus,La,metabolism,Methods,ModelsMolecular,NMR,NMR solution structure,nosource,Nuclear Magnetic ResonanceBiomolecular,Nucleic Acid Conformation,Nucleic Acids,protein,Proteins,Review,Rna,Solutions,Structural,structure,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.} }

@article{zhouPurificationFunctionalRNAprotein2003, title = {Purification of Functional {{RNA-protein}} Complexes Using {{MS2-MBP}}}, author = {Zhou, Z. and Reed, R.}, year = 2003, journal = {Curr.Protoc.Mol Biol}, volume = {Chapter 27}, pages = {Unit}, url = {PM:18265330}, abstract = {Biological machines composed of RNAs and proteins play essential roles in many biological processes. To better understand the mechanism and function of these machines, it is critical to isolate them in a highly purified and functional form. A method for isolating functional RNA-protein complexes assembled in vitro is described. The approach combines gel filtration and an affinity-chromatography strategy using the bacteriophage MS2 coat protein, which binds to a specific RNA-hairpin structure. Using this method, highly purified and functional human spliceosomes have been isolated. The purified spliceosome preparation is used to determine the protein components of the spliceosome by mass spectrometry and to examine the structure of the spliceosome by electron microscopy}, keywords = {0,Binding Sites,Capsid,capsid protein,Capsid Proteins,Carrier Proteins,Cell-Free System,chemistry,ChromatographyAffinity,ChromatographyGel,COAT PROTEIN,COMPLEX,COMPLEXES,COMPONENT,COMPONENTS,ELECTRON-MICROSCOPY,FORM,FUSION PROTEIN,genetics,Hela Cells,human,Humans,In Vitro,IN-VITRO,Indicators and Reagents,isolation & purification,La,Levivirus,Mass Spectrometry,MECHANISM,metabolism,Methods,No DOI found,nosource,Nucleic Acid Conformation,PRECURSOR,protein,Proteins,purification,Recombinant Fusion Proteins,RIBONUCLEOPROTEIN,Ribonucleoproteins,Rna,RNA Precursors,RNASmall Nuclear,Spliceosomes,structure,Substrate Specificity} } % == BibTeX quality report for zhouPurificationFunctionalRNAprotein2003: % ? Possibly abbreviated journal title Curr.Protoc.Mol Biol

@article{zhouravlevaTerminationTranslationEukaryotes1995, title = {Termination of Translation in Eukaryotes Is Governed by Two Interacting Polypeptide Chain Release Factors, {{eRF1}} and {{eRF3}}.}, author = {Zhouravleva, G. and Frolova, L. and LeGoff, X. and Le Guellec, R. and {Inge-Vechtomov}, S. and Kisselev, L. and Phillippe, M.}, year = 1995, journal = {EMBO J.}, volume = {14}, number = {16}, pages = {4065–4072}, publisher = {Nature Publishing Group}, doi = {10.1002/j.1460-2075.1995.tb00078.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC394485/}, keywords = {nosource,RELEASE FACTORS,sup35,sup45,termination,translation,yeast} } % == BibTeX quality report for zhouravlevaTerminationTranslationEukaryotes1995: % ? Possibly abbreviated journal title EMBO J.

@article{zollCharacterizationMammalianEIF2A2002, title = {Characterization of Mammalian {{eIF2A}} and Identification of the Yeast Homolog}, author = {Zoll, W.L. and Horton, L.E. and Komar, A.A. and Hensold, J.O. and Merrick, W.C.}, year = 2002, month = oct, journal = {Journal of Biological Chemistry}, volume = {277}, number = {40}, pages = {37079–37087}, publisher = {ASBMB}, doi = {10.1074/jbc.M207109200}, url = {http://www.jbc.org/content/277/40/37079.short}, abstract = {To begin the physical characterization of eukaryotic initiation factor (eIF) 2A, a translation initiation factor that binds Met-tRNA(i), tryptic peptides from rabbit reticulocyte eIF2A were analyzed to obtain amino acid sequence information. Sequences for 8 peptides were matched to three different expressed sequence tag clones. The sequence predicted for eIF2A is 585 amino acids. Matching of the cDNA sequence to the human genome revealed that the eIF2A mRNA is made up of 15 or 16 exons, and the gene is contained on chromosome 3. A homolog in Saccharomyces cerevisiae was identified, YGR054W, which is a non-essential gene. Hemagglutinin-tagged yeast eIF2A localizes on both 40 S and 80 S ribosomes. A knockout of both eIF2A and eIF5B yielded a “synthetically sick” yeast strain with a severe slow growth phenotype. The phenotype of this double mutant and the biochemical localization suggest that eIF2A participates in translation initiation. eIF2A does not appear to participate in re-initiation as the DeltaeIF2A strain shows the same level of GCN4 induction with amino acid starvation as seen in wild type yeast. The lack of any apparent phenotype in the DeltaeIF2A strain suggests that eIF2A functions in a minor pathway, perhaps internal initiation or in the translation of a small number of specific mRNAs}, keywords = {0,3,ACID,ACIDS,Amino Acid Sequence,Amino Acids,AMINO-ACID,AMINO-ACIDS,animal,Base Sequence,CEREVISIAE,chemistry,Chromosome Mapping,ChromosomesHumanPair 3,CloningMolecular,Dna,DNAComplementary,Escherichia coli,Eukaryotic Initiation Factor-2,EXON,Exons,Expressed Sequence Tags,FUSION PROTEIN,GCN4,gene,genetics,Genome,GenomeHuman,GROWTH,homolog,human,human genome,IDENTIFICATION,initiation,INITIATION-FACTOR,La,LOCALIZATION,Mammals,metabolism,Molecular Sequence Data,mRNA,nosource,PATHWAY,Peptide Fragments,Peptides,Phenotype,Poly U,Polyribosomes,Promoter Regions (Genetics),protein,Proteins,Recombinant Fusion Proteins,ribosome,Ribosomes,Rna,RNAMessenger,S,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,Sequence Alignment,Sequence HomologyAmino Acid,SEQUENCES,supportu.s.gov’tnon-p.h.s.,supportu.s.gov’tp.h.s.,translation,TRANSLATION INITIATION,WILD-TYPE,yeast} } % == BibTeX quality report for zollCharacterizationMammalianEIF2A2002: % ? unused Journal abbr (“J.Biol.Chem.”)

@article{zoubenkoNontoxicPokeweedAntivial2000, title = {A Nontoxic Pokeweed Antivial Protein Mutant Inhibits Pathogen Infection via a Novel Salicyclic Acid-Independent Pathway.}, author = {Zoubenko, O. and Hudak, K.A. and Tumer, N.E.}, year = {in press 2000}, journal = {Plant Molecular Biology}, doi = {10.1023/A:1006443626864}, keywords = {nosource,protein} }

@article{zukSingleAminoAcid1998, title = {A Single Amino Acid Substitution in Yeast {{eIF-5A}} Results in {{mRNA}} Stabilization}, author = {Zuk, D. and Jacobson, A.}, year = 1998, month = may, journal = {EMBO J.}, volume = {17}, number = {10}, pages = {2914–2925}, doi = {10.1093/emboj/17.10.2914}, url = {PM:9582285}, abstract = {Most factors known to function in mRNA turnover are not essential for cell viability. To identify essential factors, approximately 4000 temperature-sensitive yeast strains were screened for an increase in the level of the unstable CYH2 pre-mRNA. At the non-permissive temperature, five mutants exhibited decreased decay rates of the CYH2 pre-mRNA and mRNA, and the STE2, URA5 and PAB1 mRNAs. Of these, the mutant ts1159 had the most extensive phenotype. Expression of the TIF51A gene (encoding eIF-5A) complemented the temperature-sensitive growth and mRNA decay phenotypes of ts1159. The tif51A allele was rescued from these cells and shown to encode a serine to proline change within a predicted alpha-helical segment of the protein. ts1159 also exhibited an approximately 30% decrease in protein synthesis at the restrictive temperature. Measurement of amino acid incorporation in wild-type cells incubated with increasing amounts of cycloheximide demonstrated that a decrease in protein synthesis of this magnitude could not account for the full extent of the mRNA decay defects observed in ts1159. Interestingly, the ts1159 cells accumulated uncapped mRNAs at the non-permissive temperature. These results suggest that eIF-5A plays a role in mRNA turnover, perhaps acting downstream of decapping}, keywords = {0,ACID,Alleles,Amino Acid Sequence,Amino Acid Substitution,AMINO-ACID,Base Sequence,biosynthesis,CELLS,Cycloheximide,CYH2,DECAY,DOWNSTREAM,expression,Fungal Proteins,gene,GenesFungal,Genetic,genetics,GROWTH,IDENTIFY,initiation,INITIATION-FACTOR,La,Molecular Sequence Data,MOLECULAR-GENETICS,mRNA,mRNA decay,mRNA turnover,Mutagenesis,MUTANTS,nosource,Peptide Initiation Factors,Phenotype,PRECURSOR,Proline,protein,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Rna,RNA Precursors,RNAFungal,RNAMessenger,Serine,supportnon-u.s.gov’t,supportu.s.gov’tp.h.s.,Temperature,TranslationGenetic,turnover,WILD-TYPE,yeast,Yeasts} } % == BibTeX quality report for zukSingleAminoAcid1998: % ? Possibly abbreviated journal title EMBO J.

@article{zukTemperaturesensitiveMutationsSaccharomyces1999, title = {Temperature-Sensitive Mutations in the {{Saccharomyces}} Cerevisiae {{MRT4}}, {{GRC5}}, {{SLA2}} and {{THS1}} Genes Result in Defects in {{mRNA}} Turnover.}, author = {Zuk, D. and Belk, J.P. and Jacobson, A.}, year = 1999, journal = {Genetics}, volume = {153}, number = {1}, pages = {35–47}, publisher = {Genetics Soc America}, doi = {10.1093/genetics/153.1.35}, url = {http://www.genetics.org/content/153/1/35.short}, abstract = {In a screen for factors involved in mRNA turnover, four temperature- sensitive yeast strains (ts1189, ts942, ts817, and ts1100) exhibited defects in the decay of several mRNAs. Complementation of the growth and mRNA decay defects, and genetic experiments, revealed that ts1189 is mutated in the previously unknown MRT4 gene, ts942 is mutated in GRC5 (encoding the L9 ribosomal protein), ts817 contains a mutation in SLA2 (encoding a membrane protein), and ts1100 contains a mutation in THS1 (encoding the threonyl-tRNA synthetase). Three of the four mutants (mrt4, grc5, and sla2) were not defective in protein synthesis, suggesting that these strains contain mutations in factors that may play a specific role in mRNA decay. The mRNA stabilization observed in the ths1 strain, however, could be due to the significant drop in translation observed in this mutant at 37 degrees. While the three interesting mutants appear to encode novel mRNA decay factors, at least one could be linked to a previously characterized mRNA decay pathway. The growth and mRNA decay defects of ts942 (grc5) cells were suppressed by overexpression of the NMD3 gene, encoding a protein shown to participate in a two-hybrid interaction with the nonsense-mediated decay protein Upf1p}, keywords = {99402992,CEREVISIAE,DECAY,gene,Genes,Genetic,genetics,GRC5,microbiology,mRNA,mRNA decay,mRNA turnover,Mutation,MUTATIONS,nonsense-mediated decay,nosource,protein,protein synthesis,PROTEIN-SYNTHESIS,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,Temperature,translation,turnover,yeast} }

@article{zverevaRibosomalProteinTL52000a, title = {Ribosomal Protein {{TL5}} of {{T}}. Thermophilus Is Incorporated in the {{E}}. Coli {{50S}} Ribosomal Subunit}, author = {Zvereva, M.E. and Shpanchenko, O.V. and Nierhaus, K. and Dontsova, O.A.}, year = 2000, journal = {Dokl.Biochem.}, volume = {374}, number = {1-6}, pages = {199–201}, url = {PM:11109964}, keywords = {0,La,No DOI found,nosource,protein,RIBOSOMAL-SUBUNIT,SUBUNIT} } % == BibTeX quality report for zverevaRibosomalProteinTL52000a: % ? Possibly abbreviated journal title Dokl.Biochem.

@article{zverevaEffectPointMutations1998, title = {Effect of Point Mutations at Position 89 of the {{E}}. Coli {{5S rRNA}} on the Assembly and Activity of the Large Ribosomal Subunit}, author = {Zvereva, M.I. and Shpanchenko, O.V. and Dontsova, O.A. and Nierhaus, K.H. and Bogdanov, A.A.}, year = 1998, month = jan, journal = {FEBS letters}, volume = {421}, number = {3}, pages = {249–251}, publisher = {Elsevier}, doi = {10.1016/S0014-5793(97)01578-0}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579397015780}, abstract = {Nucleotide residue U89 in the D loop of Escherichia coli 5S rRNA is adjacent to two domains of 23S rRNA in the large ribosomal subunit [Dokudovskaya et al., RNA 2 (1996) 146-152]. 50S ribosomal subunits were reconstituted containing U89(C, G or A) mutants of 5S rRNAs and the activities of the corresponding 70S ribosomes were studied. The U89C mutant behaves similarly to the wild-type 5S rRNA. Replacement of the pyrimidine base at position U89 by more bulky purine bases impairs the incorporation of 5S rRNA into 50S subunits, whereas the particles formed showed full activities in poly(U)-dependent poly(Phe) synthesis in the presence of either U89G or U89A 5S rRNA mutants. The activity of the reconstituted particles depends on the incorporation of 5S rRNA in agreement with early observations}, keywords = {0,5S rRNA,assembly,Bacterial,Base Sequence,chemistry,Escherichia coli,ESCHERICHIA-COLI,genetics,La,metabolism,Molecular Sequence Data,Mutation,MUTATIONS,nosource,Nucleic Acid Conformation,Point Mutation,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,Rna,RNABacterial,RNARibosomal5S,rRNA,SUBUNIT,supportnon-u.s.gov’t} } % == BibTeX quality report for zverevaEffectPointMutations1998: % ? unused Journal abbr (“FEBS Lett.”)

@article{holcikSpuriousSplicingXIAP2005, title = {Spurious Splicing within the {{XIAP}} 5’ {{UTR}} Occurs in the {{Rluc}}/{{Fluc}} but Not the ~Gal/{{CAT}} Bicistronic Reporter System}, author = {Holcik, M.}, year = 2005, month = nov, journal = {RNA}, volume = {11}, number = {11}, pages = {1605–1609}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, doi = {10.1261/rna.2158605}, url = {http://www.rnajournal.org/cgi/doi/10.1261/rna.2158605}, keywords = {2004a,bicistronic reporter,ires,mrna,nosource,of strin-,recently proposed the use,rt-pcr,van eden et al} }

@article{rablCrystalStructureEukaryotic2010, title = {Crystal {{Structure}} of the {{Eukaryotic 40S Ribosomal Subunit}} in {{Complex}} with {{Initiation Factor}} 1}, author = {Rabl, J. and Leibundgut, M. and Ataide, S. F. and Haag, A. and Ban, N.}, year = 2010, month = dec, journal = {Science}, volume = {331}, number = {6018}, pages = {730–6}, publisher = {American Association for the Advancement of Science}, issn = {0036-8075}, doi = {10.1126/science.1198308}, url = {http://www.sciencemag.org/content/331/6018/730.short http://www.sciencemag.org/cgi/doi/10.1126/science.1198308 http://www.ncbi.nlm.nih.gov/pubmed/21205638}, urldate = {2011-01-10}, abstract = {Eukaryotic ribosomes are substantially larger and more complex than their bacterial counterparts. Although their core function is conserved, bacterial and eukaryotic protein synthesis differ considerably at the level of initiation. The eukaryotic small ribosomal subunit (40S) plays a central role in this process; it binds initiation factors that facilitate scanning of messenger RNAs and initiation of protein synthesis. We have determined the crystal structure of the Tetrahymena thermophila 40S ribosomal subunit in complex with eukaryotic initiation factor 1 (eIF1) at a resolution of 3.9 angstroms. The structure reveals the fold of the entire 18S ribosomal RNA and of all ribosomal proteins of the 40S subunit, and defines the interactions with eIF1. It provides insights into the eukaryotic-specific aspects of protein synthesis, including the function of eIF1 as well as signaling and regulation mediated by the ribosomal proteins RACK1 and rpS6e.}, pmid = {21205638}, keywords = {18S,18S: chemistry,Amino Acid Sequence,Crystallization,Crystallography,Eukaryotic,Eukaryotic Initiation Factor-1,Eukaryotic Initiation Factor-1: chemistry,Eukaryotic Initiation Factor-1: metabolism,Eukaryotic: chemistry,Eukaryotic: metabolism,Eukaryotic: ultrastructu,Messenger,Messenger: chemistry,Models,Molecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Protein Biosynthesis,Protein Conformation,Protein Folding,Protozoan,Protozoan Proteins,Protozoan Proteins: chemistry,Protozoan Proteins: metabolism,Protozoan: chemistry,Ribosomal,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: metabolism,Ribosome Subunits,RNA,Signal Transduction,Small,Tetrahymena thermophila,Tetrahymena thermophila: chemistry,Tetrahymena thermophila: ultrastructure,X-Ray} } % == BibTeX quality report for rablCrystalStructureEukaryotic2010: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“CrossRef”)

@article{heMicroRNAsSmallRNAs2004, title = {{{MicroRNAs}}: Small {{RNAs}} with a Big Role in Gene Regulation}, shorttitle = {{{MicroRNAs}}}, author = {He, Lin and Hannon, Gregory J.}, year = 2004, month = jul, journal = {Nature Reviews Genetics}, volume = {5}, number = {7}, pages = {522–531}, publisher = {Nature Publishing Group}, issn = {1471-0056}, doi = {10.1038/nrg1379}, url = {http://www.nature.com/nrg/journal/v5/n7/abs/nrg1379.html}, urldate = {2011-01-10}, keywords = {nosource} } % == BibTeX quality report for heMicroRNAsSmallRNAs2004: % ? unused Journal abbr (“Nat Rev Genet”) % ? unused Library catalog (“CrossRef”)

@article{ozsolakRNASequencingAdvances2010, title = {{{RNA}} Sequencing: Advances, Challenges and Opportunities}, shorttitle = {{{RNA}} Sequencing}, author = {Ozsolak, Fatih and Milos, Patrice M.}, year = 2010, month = dec, journal = {Nature Reviews Genetics}, volume = {12}, number = {2}, pages = {87–98}, publisher = {Nature Publishing Group}, issn = {1471-0056}, doi = {10.1038/nrg2934}, url = {http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg2934.html http://www.nature.com/nrg/journal/v12/n2/abs/nrg2934.html}, urldate = {2011-01-19}, keywords = {nosource} } % == BibTeX quality report for ozsolakRNASequencingAdvances2010: % ? unused Journal abbr (“Nat Rev Genet”) % ? unused Library catalog (“CrossRef”)

@article{kimMicroRNABiogenesisCoordinated2005, title = {{{MicroRNA}} Biogenesis: Coordinated Cropping and Dicing}, author = {Kim, V. Narry}, year = 2005, month = may, journal = {Nature Reviews Molecular Cell Biology}, volume = {6}, number = {5}, pages = {376–385}, publisher = {Nature Publishing Group}, issn = {1471-0072}, doi = {10.1038/nrm1644}, url = {http://www.nature.com/nrm/journal/v6/n5/abs/nrm1644.html}, keywords = {nosource} } % == BibTeX quality report for kimMicroRNABiogenesisCoordinated2005: % ? unused Journal abbr (“Nat Rev Mol Cell Biol”)

@article{winterManyRoadsMaturity2009a, title = {Many Roads to Maturity: {{microRNA}} Biogenesis Pathways and Their Regulation}, author = {Winter, Julia and Jung, Stephanie and Keller, Sarina and Gregory, Richard I. and Diederichs, Sven}, year = 2009, month = mar, journal = {Nature Cell Biology}, volume = {11}, number = {3}, pages = {228–234}, issn = {1465-7392}, doi = {10.1038/ncb0309-228}, url = {http://fbae.org/2009/FBAE/website/images/pdf/imporatant-publication/biogenesis_of_mi_rna.pdf}, keywords = {nosource} } % == BibTeX quality report for winterManyRoadsMaturity2009a: % ? unused Journal abbr (“Nat Cell Biol”)

@article{matthewmichaelNuclearExportSignal1995, title = {A Nuclear Export Signal in {{hnRNP A1}}: {{A}} Signal-Mediated, Temperature-Dependent Nuclear Protein Export Pathway}, author = {Matthewmichael, W}, year = 1995, month = nov, journal = {Cell}, volume = {83}, number = {3}, pages = {415–422}, issn = {00928674}, doi = {10.1016/0092-8674(95)90119-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867495901191}, keywords = {nosource} }

@article{fraserMinimalGeneComplement1995, title = {The {{Minimal Gene Complement}} of {{Mycoplasma}} Genitalium}, author = {Fraser, C. M. and Gocayne, J. D. and White, O. and Adams, M. D. and Clayton, R. A. and Fleischmann, R. D. and Bult, C. J. and Kerlavage, A. R. and Sutton, G. and Kelley, J. M. and Fritchman, J. L. and Weidman, J. F. and Small, K. V. and Sandusky, M. and Fuhrmann, J. and Nguyen, D. and Utterback, T. R. and Saudek, D. M. and Phillips, C. A. and Merrick, J. M. and Tomb, J.-F. and Dougherty, B. A. and Bott, K. F. and Hu, P.-C. and Lucier, T. S.}, year = 1995, month = oct, journal = {Science}, volume = {270}, number = {5235}, pages = {397–404}, publisher = {American Association for the Advancement of Science}, issn = {0036-8075}, doi = {10.1126/science.270.5235.397}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.270.5235.397}, urldate = {2011-02-23}, keywords = {nosource} } % == BibTeX quality report for fraserMinimalGeneComplement1995: % ? unused Library catalog (“CrossRef”)

@article{leontisAnnotationRNAMotifs2002, title = {The {{Annotation}} of {{RNA Motifs}}}, author = {Leontis, Neocles B. and Westhof, Eric}, year = 2002, journal = {Comparative and Functional Genomics}, volume = {3}, number = {6}, pages = {518–524}, publisher = {Wiley Online Library}, issn = {1531-6912}, doi = {10.1002/cfg.213}, url = {http://www.hindawi.com/journals/cfg/2002/426578.abs.html}, urldate = {2011-02-23}, keywords = {nosource} } % == BibTeX quality report for leontisAnnotationRNAMotifs2002: % ? Title looks like it was stored in title-case in Zotero % ? unused Journal abbr (“Comp. Funct. Genom.”) % ? unused Library catalog (“CrossRef”)

@article{leontisBuildingBlocksMotifs2006, title = {The Building Blocks and Motifs of {{RNA}} Architecture}, author = {Leontis, N and Lescoute, A and Westhof, E}, year = 2006, month = jun, journal = {Current Opinion in Structural Biology}, volume = {16}, number = {3}, pages = {279–287}, publisher = {Elsevier}, issn = {0959440X}, doi = {10.1016/j.sbi.2006.05.009}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0959440X06000807}, urldate = {2011-02-23}, keywords = {nosource} } % == BibTeX quality report for leontisBuildingBlocksMotifs2006: % ? unused Library catalog (“CrossRef”)

@misc{AnalysisRNAMotifs, title = {Analysis of {{RNA}} Motifs. [{{Curr Opin Struct Biol}}. 2003] - {{PubMed}} Result}, eprint = {12831880}, eprinttype = {pubmed}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12831880}, urldate = {2011-02-23}, keywords = {nosource}, file = {/home/trey/Zotero/storage/JNFEFZ22/12831880.html} }

@article{mittelstaetDistortionTRNANearcognate2011, title = {Distortion of {{tRNA}} upon Near-Cognate Codon Recognition on the Ribosome}, author = {Mittelstaet, J. and Konevega, A. L. and Rodnina, M. V.}, year = 2011, month = jan, journal = {Journal of Biological Chemistry}, volume = {286}, number = {10}, pages = {8158–64}, publisher = {ASBMB}, issn = {0021-9258}, doi = {10.1074/jbc.M110.210021}, url = {http://www.jbc.org/cgi/doi/10.1074/jbc.M110.210021}, urldate = {2011-02-24}, keywords = {nosource} } % == BibTeX quality report for mittelstaetDistortionTRNANearcognate2011: % ? unused Library catalog (“CrossRef”)

@article{martinezTelomericExtratelomericRoles2011, title = {Telomeric and Extra-Telomeric Roles for Telomerase and the Telomere-Binding Proteins}, author = {Mart{'i}nez, Paula and Blasco, Mar{'i}a A.}, year = 2011, month = mar, journal = {Nature Reviews Cancer}, volume = {11}, number = {3}, pages = {161–176}, publisher = {Nature Publishing Group}, issn = {1474-175X}, doi = {10.1038/nrc3025}, url = {http://www.nature.com/doifinder/10.1038/nrc3025 http://vetbiotech.um.ac.ir/parameters/vetbiotech/filemanager/new_admin/Selected Articles/series_3/nrc3025.pdf}, urldate = {2011-02-24}, keywords = {nosource} } % == BibTeX quality report for martinezTelomericExtratelomericRoles2011: % ? unused Journal abbr (“Nat Rev Cancer”) % ? unused Library catalog (“CrossRef”)

@article{bekaertRecode2NewDesign2009, title = {Recode-2: New Design, New Search Tools, and Many More Genes.}, shorttitle = {Recode-2}, author = {Bekaert, M. and Firth, A. E. and Zhang, Y. and Gladyshev, V. N. and Atkins, J. F. and Baranov, P. V.}, year = 2009, month = sep, journal = {Nucleic Acids Research}, volume = {38}, number = {Database issue}, pages = {D69-D74}, publisher = {Oxford Univ Press}, issn = {0305-1048}, doi = {10.1093/nar/gkp788}, url = {http://nar.oxfordjournals.org/content/38/suppl_1/D69.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2808893&tool=pmcentrez&rendertype=abstract}, urldate = {2011-04-25}, abstract = {‘Recoding’ is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frameshifting, stop codon readthrough, selenocysteine insertion and translational bypassing. Although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of ‘recoded’ genes lags far behind annotation of ‘standard’ genes. In order to address this issue, provide a service to researchers in the field, and offer training data for developers of gene-annotation software, we have gathered together known cases of recoding within the Recode database. Recode-2 is an improved and updated version of the database. It provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements. At present, the Recode-2 database stores information on approximately 1500 genes that are known to utilize recoding in their expression–a factor of approximately three increase over the previous version of the database. Recode-2 is available at http://recode.ucc.ie.}, pmid = {19783826}, keywords = {Algorithms,Animals,Base Sequence,Codon,Computational Biology,Computational Biology: methods,Computational Biology: trends,Databases,Frameshifting,Genetic,Humans,Information Storage and Retrieval,Information Storage and Retrieval: methods,Internet,Molecular Sequence Data,nosource,Protein,Protein Biosynthesis,Ribosomal,Software,Terminator} } % == BibTeX quality report for bekaertRecode2NewDesign2009: % ? unused Library catalog (“CrossRef”)

@misc{Recode2NewDesign, title = {Recode-2: New Design, New Search Tools, and Many More Genes}, url = {http://nar.oxfordjournals.org/content/38/suppl_1/D69.short}, urldate = {2011-04-25}, keywords = {nosource} }

@article{atkinsDistinctionRecodingCodon2010, title = {The {{Distinction Between Recoding}} and {{Codon Reassignment}}}, author = {Atkins, J. F. and Baranov, P. V.}, year = 2010, month = aug, journal = {Genetics}, volume = {1536}, number = {August}, pages = {1535–1536}, issn = {0016-6731}, doi = {10.1534/genetics.110.119016}, url = {http://www.genetics.org/cgi/doi/10.1534/genetics.110.119016}, urldate = {2011-04-25}, keywords = {Codon,Codon: genetics,Genetic Code,Genetic Code: genetics,Messenger,Messenger: genetics,nosource,Protein Biosynthesis,Protein Biosynthesis: genetics,RNA} } % == BibTeX quality report for atkinsDistinctionRecodingCodon2010: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“CrossRef”)

@article{johanssonAssociationYeastUpf1p2007, title = {Association of Yeast {{Upf1p}} with Direct Substrates of the {{NMD}} Pathway}, author = {Johansson, M. J. O. and He, F. and Spatrick, P. and Li, C. and Jacobson, A.}, year = 2007, month = dec, journal = {Proceedings of the National Academy of Sciences}, volume = {104}, number = {52}, pages = {20872–20877}, publisher = {National Acad Sciences}, issn = {0027-8424}, doi = {10.1073/pnas.0709257105}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0709257105}, urldate = {2011-04-28}, keywords = {nosource} } % == BibTeX quality report for johanssonAssociationYeastUpf1p2007: % ? unused Library catalog (“CrossRef”)

@article{behm-ansmantQualityControlGene2006, title = {Quality Control of Gene Expression: A Stepwise Assembly Pathway for the Surveillance Complex That Triggers Nonsense-Mediated {{mRNA}} Decay}, shorttitle = {Quality Control of Gene Expression}, author = {{Behm-Ansmant}, I.}, year = 2006, month = feb, journal = {Genes & Development}, volume = {20}, number = {4}, pages = {391–398}, publisher = {Cold Spring Harbor Lab}, issn = {0890-9369}, doi = {10.1101/gad.1407606}, url = {http://www.genesdev.org/cgi/doi/10.1101/gad.1407606}, urldate = {2011-04-28}, keywords = {nosource} } % == BibTeX quality report for behm-ansmantQualityControlGene2006: % ? unused Library catalog (“CrossRef”)

@article{filbinStructuralUnderstandingIRES2009, title = {Toward a Structural Understanding of {{IRES RNA}} Function}, author = {Filbin, Megan E and Kieft, Jeffrey S}, year = 2009, month = jun, journal = {Current Opinion in Structural Biology}, volume = {19}, number = {3}, pages = {267–276}, publisher = {Elsevier}, issn = {0959440X}, doi = {10.1016/j.sbi.2009.03.005}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0959440X09000384 http://www.sciencedirect.com/science/article/pii/S0959440X09000384}, urldate = {2011-04-28}, abstract = {Protein synthesis of an RNA template can start by two different known mechanisms: cap-dependent translation initiation and cap-independent translation initiation. The latter is driven by RNA sequences called internal ribosome entry sites (IRESs) that are found in both viral RNAs and cellular mRNAs. The diverse mechanisms used by IRESs are reflected in their structural diversity, and this structural diversity challenges us to develop a cohesive model linking IRES function to structure. With more direct structural information available for the viral IRESs, data suggest an inverse correlation between the degree to which an IRES RNA can form a stable structure on its own and the number of factors that it requires to function. Lessons learned from the viral IRESs may help understand the cellular IRESs, although more structural data are needed before any strong links can be made.}, pmid = {19362464}, keywords = {animals,base sequence,humans,molecular sequence data,nosource,ribosomal proteins,ribosomal proteins chemistry,ribosomal proteins metabolism,rna,rna chemistry,rna genetics,rna metabolism,viral proteins,viral proteins chemistry,viral proteins metabolism} } % == BibTeX quality report for filbinStructuralUnderstandingIRES2009: % ? unused Library catalog (“CrossRef”)

@article{zuoSolutionStructureCapindependent2010, title = {Solution Structure of the Cap-Independent Translational Enhancer and Ribosome-Binding Element in the 3’ {{UTR}} of Turnip Crinkle Virus}, author = {Zuo, X. and Wang, J. and Yu, P. and Eyler, D. and Xu, H. and Starich, M. R. and Tiede, D. M. and Simon, A. E. and Kasprzak, W. and Schwieters, C. D. and Shapiro, B. A. and Wang, Y.-X.}, year = 2010, month = jan, journal = {Proceedings of the National Academy of Sciences}, volume = {107}, number = {4}, pages = {1385–1390}, publisher = {National Acad Sciences}, issn = {0027-8424}, doi = {10.1073/pnas.0908140107}, url = {http://www.pnas.org/content/107/4/1385.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2803139&tool=pmcentrez&rendertype=abstract}, urldate = {2011-04-28}, abstract = {The 3(‘) untranslated region (3(’) UTR) of turnip crinkle virus (TCV) genomic RNA contains a cap-independent translation element (CITE), which includes a ribosome-binding structural element (RBSE) that participates in recruitment of the large ribosomal subunit. In addition, a large symmetric loop in the RBSE plays a key role in coordinating the incompatible processes of viral translation and replication, which require enzyme progression in opposite directions on the viral template. To understand the structural basis for the large ribosomal subunit recruitment and the intricate interplay among different parts of the molecule, we determined the global structure of the 102-nt RBSE RNA using solution NMR and small-angle x-ray scattering. This RNA has many structural features that resemble those of a tRNA in solution. The hairpins H1 and H2, linked by a 7-nucleotide linker, form the upper part of RBSE and hairpin H3 is relatively independent from the rest of the structure and is accessible to interactions. This global structure provides insights into the three-dimensional layout for ribosome binding, which may serve as a structural basis for its involvement in recruitment of the large ribosomal subunit and the switch between viral translation and replication. The experimentally determined three-dimensional structure of a functional element in the 3(‘) UTR of an RNA from any organism has not been previously reported. The RBSE structure represents a prototype structure of a new class of RNA structural elements involved in viral translation/replication processes.}, pmid = {20080629}, keywords = {3’ Untranslated Regions,Base Sequence,Carmovirus,Carmovirus: chemistry,Carmovirus: genetics,Carmovirus: metabolism,Enhancer Elements,Genetic,Models,Molecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Protein Biosynthesis,Ribosomes,Ribosomes: metabolism,RNA,Viral,Viral Proteins,Viral Proteins: biosynthesis,Viral Proteins: genetics,Viral: chemistry,Viral: metabolism} } % == BibTeX quality report for zuoSolutionStructureCapindependent2010: % ? unused Library catalog (“CrossRef”)

@article{hattaRegionRequiredProtein2009, title = {Region {{Required}} for {{Protein Expression}} from the {{Stop-Start Pentanucleotide}} in the {{M Gene}} of {{Influenza B Virus}}}, author = {Hatta, M. and Kohlmeier, C. K. and Hatta, Y. and Ozawa, M. and Kawaoka, Y.}, year = 2009, month = mar, journal = {Journal of Virology}, volume = {83}, number = {11}, pages = {5939–5942}, publisher = {Am Soc Microbiol}, issn = {0022-538X}, doi = {10.1128/JVI.00180-09}, url = {http://jvi.asm.org/cgi/content/abstract/83/11/5939}, urldate = {2011-04-28}, keywords = {nosource} } % == BibTeX quality report for hattaRegionRequiredProtein2009: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“CrossRef”)

@article{niuLipopolysaccharideinducedMiR1224Negatively2011, title = {Lipopolysaccharide-Induced {{miR-1224}} Negatively Regulates Tumour Necrosis Factor-{\(\alpha\)} Gene Expression by Modulating {{Sp1}}}, author = {Niu, Yuna and Mo, Delin and Qin, Limei and Wang, Chong and Li, Anning and Zhao, Xiao and Wang, Xiaoying and Xiao, Shuqi and Wang, Qiwei and Xie, Ying and He, Zuyong and Cong, Peiqing and Chen, Yaosheng}, year = 2011, month = may, journal = {Immunology}, volume = {133}, number = {1}, pages = {8–20}, publisher = {Wiley Online Library}, issn = {00192805}, doi = {10.1111/j.1365-2567.2010.03374.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2567.2010.03374.x/full}, urldate = {2011-05-09}, keywords = {nosource} } % == BibTeX quality report for niuLipopolysaccharideinducedMiR1224Negatively2011: % ? unused Library catalog (“CrossRef”)

@article{vila-coroHIV1InfectionCCR52000, title = {{{HIV-1}} Infection through the {{CCR5}} Receptor Is Blocked by Receptor Dimerization}, author = {{Vila-Coro}, A J and Mellado, M and {Mart{'i}n de Ana}, A and Lucas, P and {}{del Real}, G and {Mart{'i}nez-A}, C and {Rodr{'i}guez-Frade}, J M}, year = 2000, month = mar, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {7}, eprint = {10725362}, eprinttype = {pubmed}, pages = {3388–3393}, publisher = {National Acad Sciences}, issn = {0027-8424}, doi = {10.1073/pnas.050457797}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10725362}, urldate = {2011-05-09}, abstract = {The identification of the chemokine receptors as receptors for HIV-1 has boosted interest in these molecules, raising expectations for the development of new strategies to prevent HIV-1 infection. The discovery that chemokines block HIV-1 replication has focused attention on identifying their mechanism of action. Previous studies concluded that this inhibitory effect may be mediated by steric hindrance or by receptor down-regulation. We have identified a CCR5 receptor-specific mAb that neither competes with the chemokine for binding nor triggers signaling, as measured by Ca(2+) influx or chemotaxis. The antibody neither triggers receptor down-regulation nor interferes with the R5 JRFL viral strain gp120 binding to CCR5, but blocks HIV-1 replication in both in vitro assays using peripheral blood mononuclear cells as HIV-1 targets, as well as in vivo using human peripheral blood mononuclear cell-reconstituted SCID (severe combined immunodeficient) mice. Our evidence shows that the anti-CCR5 mAb efficiently prevents HIV-1 infection by inducing receptor dimerization. Chemokine receptor dimerization also is induced by chemokines and is required for their anti-HIV-1 activity. In addition to providing a molecular mechanism through which chemokines block HIV-1 infection, these results illustrate the prospects for developing new tools that possess HIV-1 suppressor activity, but lack the undesired inflammatory side effects of the chemokines.}, keywords = {Animals,Antibodies Monoclonal,Cell Line,Chemokine CCL5,Dimerization,Down-Regulation,HIV Infections,HIV-1,Humans,Mice,Mice SCID,nosource,Protein Binding,Receptors CCR5} } % == BibTeX quality report for vila-coroHIV1InfectionCCR52000: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A”) % ? unused Library catalog (“NCBI PubMed”)

@article{segererExpressionCCChemokine1999, title = {Expression of the {{C-C}} Chemokine Receptor 5 in Human Kidney Diseases 1}, author = {Segerer, Stephan and Mack, Matthias and Regele, Heinz and Kerjaschki, Dontscho and Schlondorff, Detlef}, year = 1999, month = jul, journal = {Kidney International}, volume = {56}, number = {1}, pages = {52–64}, publisher = {Nature Publishing Group}, issn = {0085-2538}, doi = {10.1046/j.1523-1755.1999.00544.x}, url = {http://www.nature.com/doifinder/10.1046/j.1523-1755.1999.00544.x http://www.nature.com/ki/journal/v56/n1/abs/4495523a.html}, urldate = {2011-05-09}, keywords = {nosource} } % == BibTeX quality report for segererExpressionCCChemokine1999: % ? unused Journal abbr (“Kidney Int”) % ? unused Library catalog (“CrossRef”)

@article{singhCompetitionStimulatorsAntagonists2008, title = {A {{Competition}} between {{Stimulators}} and {{Antagonists}} of {{Upf Complex Recruitment Governs Human Nonsense-Mediated mRNA Decay}}}, author = {Singh, Guramrit and Rebbapragada, Indrani and {Lykke-Andersen}, Jens}, editor = {Wickens, Marv}, year = 2008, journal = {PLoS Biology}, volume = {6}, number = {4}, pages = {e111}, issn = {1544-9173}, doi = {10.1371/journal.pbio.0060111}, url = {http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0060111}, urldate = {2011-05-09}, keywords = {nosource} } % == BibTeX quality report for singhCompetitionStimulatorsAntagonists2008: % ? Title looks like it was stored in title-case in Zotero % ? unused Journal abbr (“Plos Biol”) % ? unused Library catalog (“CrossRef”)

@article{nicholsonNonsensemediatedMRNADecay2009, title = {Nonsense-Mediated {{mRNA}} Decay in Human Cells: Mechanistic Insights, Functions beyond Quality Control and the Double-Life of {{NMD}} Factors}, shorttitle = {Nonsense-Mediated {{mRNA}} Decay in Human Cells}, author = {Nicholson, Pamela and Yepiskoposyan, Hasmik and Metze, Stefanie and Zamudio Orozco, Rodolfo and Kleinschmidt, Nicole and M{"u}hlemann, Oliver}, year = 2009, month = oct, journal = {Cellular and Molecular Life Sciences}, volume = {67}, number = {5}, pages = {677–700}, publisher = {Springer}, issn = {1420-682X}, doi = {10.1007/s00018-009-0177-1}, url = {http://www.springerlink.com/index/10.1007/s00018-009-0177-1 http://www.springerlink.com/index/c863461pp467727k.pdf}, urldate = {2011-05-09}, keywords = {nosource} } % == BibTeX quality report for nicholsonNonsensemediatedMRNADecay2009: % ? unused Journal abbr (“Cell. Mol. Life Sci.”) % ? unused Library catalog (“CrossRef”)

@article{kimArgonaute1DirectsSiRNAmediated2006, title = {Argonaute-1 Directs {{siRNA-mediated}} Transcriptional Gene Silencing in Human Cells}, author = {Kim, Daniel H and Villeneuve, Louisa M and Morris, Kevin V and Rossi, John J}, year = 2006, month = aug, journal = {Nature Structural &#38; Molecular Biology}, volume = {13}, number = {9}, pages = {793–797}, publisher = {Nature Publishing Group}, issn = {1545-9993}, doi = {10.1038/nsmb1142}, url = {http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb1142.html}, urldate = {2011-05-10}, keywords = {nosource} } % == BibTeX quality report for kimArgonaute1DirectsSiRNAmediated2006: % ? unused Journal abbr (“Nat Struct Mol Biol”) % ? unused Library catalog (“CrossRef”)

@article{meisterHumanArgonaute2Mediates2004, title = {Human {{Argonaute2 Mediates RNA Cleavage Targeted}} by {{miRNAs}} and {{siRNAs}}}, author = {Meister, Gunter and Landthaler, Markus and Patkaniowska, Agnieszka and Dorsett, Yair and Teng, Grace and Tuschl, Thomas}, year = 2004, month = jul, journal = {Molecular Cell}, volume = {15}, number = {2}, pages = {185–197}, publisher = {Elsevier}, issn = {10972765}, doi = {10.1016/j.molcel.2004.07.007}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276504004150}, urldate = {2011-05-10}, keywords = {nosource} } % == BibTeX quality report for meisterHumanArgonaute2Mediates2004: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“CrossRef”)

@inproceedings{bafnaNovoInterpretationTandem2003a, title = {On {} Interpretation of Tandem Mass Spectra for Peptide Identification}, booktitle = {Proceedings of the Seventh Annual International Conference on {{Computational}} Molecular Biology - {{RECOMB}} ’03}, author = {Bafna, Vineet and Edwards, Nathan}, year = 2003, pages = {9–18}, publisher = {ACM}, address = {Berlin, Germany}, doi = {10.1145/640075.640077}, url = {http://portal.acm.org/citation.cfm?doid=640075.640077}, urldate = {2011-05-10}, keywords = {nosource} } % == BibTeX quality report for bafnaNovoInterpretationTandem2003a: % ? Unsure about the formatting of the booktitle % ? unused Conference name (“the seventh annual international conference”) % ? unused Library catalog (“CrossRef”)

@article{huntProteinSequencingTandem1986, title = {Protein Sequencing by Tandem Mass Spectrometry}, author = {Hunt, D F and Yates, J R and Shabanowitz, J and Winston, S and Hauer, C R}, year = 1986, journal = {Proceedings of the National Academy of Sciences}, volume = {83}, number = {17}, pages = {6233–6237}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.83.17.6233}, url = {http://www.pnas.org/content/83/17/6233.abstract}, abstract = {Methodology for determining amino acid sequences of proteins by tandem mass spectrometry is described. The approach involves enzymatic and/or chemical degradation of the protein to a collection of peptides which are then fractionated by high-performance liquid chromatography. Each fraction, containing as many as 10-15 peptides, is then analyzed directly, without further purification, by a combination of liquid secondary-ion/collision-activated dissociation mass spectrometry on a multianalyzer instrument. Interpretation of collision-activated dissociation mass spectra is described, and results are presented from a study of soluble peptides produced by treatment of apolipoprotein B with cyanogen bromide and trypsin.}, keywords = {nosource} }

@article{udeshiAnalysisProteinsPeptides2007, title = {Analysis of Proteins and Peptides on a Chromatographic Timescale by Electron-Transfer Dissociation {{MS}}}, author = {Udeshi, Namrata D. and Shabanowitz, Jeffrey and Hunt, Donald F. and Rose, Kristie L.}, year = 2007, month = nov, journal = {FEBS Journal}, volume = {274}, number = {24}, pages = {071117034023003-???}, publisher = {Wiley Online Library}, issn = {1742-464X}, doi = {10.1111/j.1742-4658.2007.06148.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2007.06148.x/full}, urldate = {2011-05-10}, keywords = {nosource} } % == BibTeX quality report for udeshiAnalysisProteinsPeptides2007: % ? unused Library catalog (“CrossRef”)

@article{sykaPeptideProteinSequence2004, title = {Peptide and Protein Sequence Analysis by Electron Transfer Dissociation Mass Spectrometry}, author = {Syka, J. E. P.}, year = 2004, month = jun, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {26}, pages = {9528–9533}, publisher = {National Acad Sciences}, issn = {0027-8424}, doi = {10.1073/pnas.0402700101}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0402700101}, urldate = {2011-05-10}, abstract = {Peptide sequence analysis using a combination of gas-phase ion/ion chemistry and tandem mass spectrometry (MS/MS) is demonstrated. Singly charged anthracene anions transfer an electron to multiply protonated peptides in a radio frequency quadrupole linear ion trap (QLT) and induce fragmentation of the peptide backbone along pathways that are analogous to those observed in electron capture dissociation. Modifications to the QLT that enable this ion/ion chemistry are presented, and automated acquisition of high-quality, single-scan electron transfer dissociation MS/MS spectra of phosphopeptides separated by nanoflow HPLC is described.}, keywords = {nosource} } % == BibTeX quality report for sykaPeptideProteinSequence2004: % ? unused Journal abbr (“Proceedings of the National Academy of Sciences”) % ? unused Library catalog (“CrossRef”)

@article{schmittAffinityPurificationHistidinetagged1993, title = {Affinity Purification of Histidine-Tagged Proteins}, author = {Schmitt, Jacky and Hess, Heike and Stunnenberg, Hendrik G.}, year = 1993, month = oct, journal = {Molecular Biology Reports}, volume = {18}, number = {3}, pages = {223–230}, publisher = {Springer}, issn = {0301-4851}, doi = {10.1007/BF01674434}, url = {http://www.springerlink.com/index/X210537273436412.pdf}, urldate = {2011-05-10}, keywords = {nosource} } % == BibTeX quality report for schmittAffinityPurificationHistidinetagged1993: % ? unused Journal abbr (“Mol Biol Rep”) % ? unused Library catalog (“CrossRef”)

@article{oromIsolationMicroRNATargets2007, title = {Isolation of {{microRNA}} Targets Using Biotinylated Synthetic {{microRNAs}}.}, author = {Orom, U and Lund, A}, year = 2007, month = oct, journal = {Methods}, volume = {43}, number = {2}, pages = {162–165}, issn = {1046-2023}, doi = {10.1016/j.ymeth.2007.04.007}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1046202307000977}, urldate = {2011-05-10}, abstract = {MicroRNAs are small regulatory RNAs found in multicellular organisms where they post-transcriptionally regulate gene expression. In animals, microRNAs bind mRNAs via incomplete base pairings making the identification of microRNA targets inherently difficult. Here, we present a detailed method for experimental identification of microRNA targets based on affinity purification of tagged microRNAs associated with their targets.}, pmid = {17889804}, keywords = {Affinity,Affinity: methods,Animals,Base Sequence,Biotin,Cell Line,Chromatography,Drosophila,Drosophila Proteins,Drosophila Proteins: genetics,Drosophila: genetics,Genes,Humans,Insect,microrna,microrna target identification,microrna target isolation,MicroRNAs,MicroRNAs: chemical synthesis,MicroRNAs: genetics,MicroRNAs: isolation & purification,Neuropeptides,Neuropeptides: genetics,nosource,Transfection} } % == BibTeX quality report for oromIsolationMicroRNATargets2007: % ? unused Library catalog (“CrossRef”)

@article{ribardoDefiningMgaRegulon2006, title = {Defining the {{Mga}} Regulon: Comparative Transcriptome Analysis Reveals Both Direct and Indirect Regulation by {{Mga}} in the Group {{A}} Streptococcus}, shorttitle = {Defining the {{Mga}} Regulon}, author = {Ribardo, Deborah A. and McIver, Kevin S.}, year = 2006, month = oct, journal = {Molecular Microbiology}, volume = {62}, number = {2}, pages = {491–508}, publisher = {Wiley Online Library}, issn = {0950-382X}, doi = {10.1111/j.1365-2958.2006.05381.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2006.05381.x/full}, urldate = {2011-05-10}, keywords = {nosource} } % == BibTeX quality report for ribardoDefiningMgaRegulon2006: % ? unused Journal abbr (“Mol Microbiol”) % ? unused Library catalog (“CrossRef”)

@article{hammondArgonaute2LinkGenetic2001, title = {Argonaute2, a Link between Genetic and Biochemical Analyses of {{RNAi}}.}, author = {Hammond, S. M.}, year = 2001, month = aug, journal = {Science (New York, N.Y.)}, volume = {293}, number = {5532}, pages = {1146–1150}, issn = {0036-8075}, doi = {10.1126/science.1064023}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1064023}, urldate = {2011-05-16}, abstract = {Double-stranded RNA induces potent and specific gene silencing through a process referred to as RNA interference (RNAi) or posttranscriptional gene silencing (PTGS). RNAi is mediated by RNA-induced silencing complex (RISC), a sequence-specific, multicomponent nuclease that destroys messenger RNAs homologous to the silencing trigger. RISC is known to contain short RNAs ( approximately 22 nucleotides) derived from the double-stranded RNA trigger, but the protein components of this activity are unknown. Here, we report the biochemical purification of the RNAi effector nuclease from cultured Drosophila cells. The active fraction contains a ribonucleoprotein complex of approximately 500 kilodaltons. Protein microsequencing reveals that one constituent of this complex is a member of the Argonaute family of proteins, which are essential for gene silencing in Caenorhabditis elegans, Neurospora, and Arabidopsis. This observation begins the process of forging links between genetic analysis of RNAi from diverse organisms and the biochemical model of RNAi that is emerging from Drosophila in vitro systems.}, pmid = {11498593}, keywords = {Amino Acid Sequence,Animals,Argonaute Proteins,Cell Line,Double-Stranded,Double-Stranded: genetics,Double-Stranded: metabolism,Drosophila,Drosophila Proteins,Endoribonucleases,Endoribonucleases: metabolism,Gene Silencing,Genes,Insect,Insect Proteins,Insect Proteins: chemistry,Insect Proteins: genetics,Insect Proteins: isolation & purification,Insect Proteins: metabolism,Molecular Sequence Data,Multigene Family,nosource,Nucleic Acid,Protein Structure,Repetitive Sequences,Ribonuclease III,RNA,RNA-Induced Silencing Complex,Tertiary,Transfection} } % == BibTeX quality report for hammondArgonaute2LinkGenetic2001: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Library catalog (“CrossRef”)

@article{stanleySelectionCharacterizationEight1975, title = {Selection and Characterization of Eight Phenotypically Distinct Lines of Lectin-Resistant Chinese Hamster Ovary Cells}, author = {Stanley, Pamela and Caillibot, Velda and Siminovitch, Louis}, year = 1975, month = oct, journal = {Cell}, volume = {6}, number = {2}, pages = {121–128}, publisher = {Elsevier}, issn = {00928674}, doi = {10.1016/0092-8674(75)90002-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867475900021}, urldate = {2011-05-18}, keywords = {nosource} } % == BibTeX quality report for stanleySelectionCharacterizationEight1975: % ? unused Library catalog (“CrossRef”)

@article{kondrashovRibosomeMediatedSpecificityHox2011, title = {Ribosome-{{Mediated Specificity}} in {{Hox mRNA Translation}} and {{Vertebrate Tissue Patterning}}}, author = {Kondrashov, Nadya and Pusic, Aya and Stumpf, Craig R. and Shimizu, Kunihiko and Hsieh, Andrew~C. and Xue, Shifeng and Ishijima, Junko and Shiroishi, Toshihiko and Barna, Maria}, year = 2011, month = apr, journal = {Cell}, volume = {145}, number = {3}, pages = {383–397}, publisher = {Elsevier}, issn = {00928674}, doi = {10.1016/j.cell.2011.03.028}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867411003059}, urldate = {2011-05-19}, keywords = {nosource} } % == BibTeX quality report for kondrashovRibosomeMediatedSpecificityHox2011: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“CrossRef”)

@article{piekna-przybylska3DRRNAModification2007, title = {The {{3D rRNA}} Modification Maps Database: With Interactive Tools for Ribosome Analysis}, shorttitle = {The {{3D rRNA}} Modification Maps Database}, author = {{Piekna-Przybylska}, D. and Decatur, W. A. and Fournier, M. J.}, year = 2007, month = dec, journal = {Nucleic Acids Research}, volume = {36}, number = {Database}, pages = {D178-D183}, publisher = {Oxford Univ Press}, issn = {0305-1048}, doi = {10.1093/nar/gkm855}, url = {http://nar.oxfordjournals.org/content/36/suppl_1/D178.short http://www.nar.oxfordjournals.org/cgi/doi/10.1093/nar/gkm855}, urldate = {2011-05-19}, keywords = {nosource} } % == BibTeX quality report for piekna-przybylska3DRRNAModification2007: % ? unused Library catalog (“CrossRef”)

@article{suhGroupIntronNuclear1999, title = {A Group {{I}} Intron in the Nuclear Small Subunit {{rRNA}} Gene of {{Cryptendoxyla}} Hypophloia, an Ascomycetous Fungus: Evidence for a New Major Class of Group {{I}} Introns}, author = {Suh, S. O. and Jones, K. G. and Blackwell, M.}, year = 1999, journal = {Journal of molecular evolution}, volume = {48}, number = {5}, pages = {493–500}, publisher = {Springer}, url = {http://www.springerlink.com/index/d4h3b0438t0eutq9.pdf}, keywords = {nosource} }

@article{gutellCompilationLargeSubunit1993, title = {A Compilation of Large Subunit ({{23S}} and {{23S-like}}) Ribosomal {{RNA}} Structures: 1993.}, author = {Gutell, R. R. R. and Schnare, M. N. N. and Gray, M. W. W.}, year = 1993, journal = {Nucleic Acids Research}, volume = {21}, number = {13}, pages = {3055}, publisher = {Oxford University Press}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC309733/}, keywords = {nosource} }

@article{rajbhandaryNucleotideSequenceStudies1966a, title = {Nucleotide Sequence Studies on Yeast Phenylalanine {{sRNA}}.}, author = {RajBhandary, U. L. and Stuart, A. and Faulkner, R. D. and Chang, S. H. and Khorana, H. G.}, year = 1966, journal = {Cold Spring Harb Symp Quant Biol}, volume = {31}, pages = {425–434}, doi = {10.1101/SQB.1966.031.01.055}, keywords = {nosource} }

@article{holleyStructureRibonucleicAcid1965a, title = {Structure of a Ribonucleic Acid.}, author = {Holley, R. W. and Apgar, J. and Everett, G. A. and Madison, J. T. and Marquisee, M. and Merrill, S. H. and Penswick, J. R. and Zamir, A.}, year = 1965, journal = {Science}, volume = {147}, pages = {1462–1465}, doi = {10.1126/science.147.3664.1462}, url = {http://ukpmc.ac.uk/abstract/MED/14263761}, keywords = {nosource} }

@article{woeseBacterialEvolution1987, title = {Bacterial Evolution.}, author = {Woese, C. R.}, year = 1987, journal = {Microbiology and Molecular Biology Reviews}, volume = {51}, number = {2}, pages = {221–271}, publisher = {Am Soc Microbiol}, doi = {10.1128/mr.51.2.221-271.1987}, url = {http://mmbr.asm.org/cgi/reprint/51/2/221.pdf}, keywords = {nosource} }

@article{woeseArchaebacteria1978, title = {Archaebacteria.}, author = {Woese, C. R. and Magrum, L. J. and Fox, G. E.}, year = 1978, journal = {Journal of Molecular Evolution}, volume = {252}, pages = {245–251}, doi = {10.1007/BF01734485}, url = {http://link.springer.com/article/10.1007/BF01734485}, keywords = {a phylogenetically monolithic grouping,a s m a,archaebacteria -extreme halophiles -,bacteria do not constitute,based upon ribosomal,has revealed that the,m o p l,methanogens - progenote,molecular genealogical analysis -,nosource,o l o b,rna sequence homologies -,s u l f,t h e r,u s -} }

@article{cannoneComparativeRNAWeb2002, title = {The {{Comparative RNA Web}} ({{CRW}}) {{Site}}: An Online Database of Comparative Sequence and Structure Information for Ribosomal, Intron, and Other {{RNAs}}}, author = {Cannone, Jamie and Subramanian, Sankar and Schnare, Murray and Collett, James and D’Souza, Lisa and Du, Yushi and Feng, Brian and Lin, Nan and Madabusi, Lakshmi and Muller, Kirsten and Pande, Nupur and Shang, Zhidi and Yu, Nan and Gutell, Robin}, year = 2002, journal = {BMC Bioinformatics}, volume = {3}, number = {1}, pages = {2}, publisher = {BioMed Central Ltd}, url = {http://www.biomedcentral.com/1471-2105/3/2/}, abstract = {BACKGROUND:Comparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic tree. Underlying these accomplishments are very large, well-organized, and processed collections of RNA sequences. This data, starting with the sequences organized into a database management system and aligned to reveal their higher-order structure, and patterns of conservation and variation for organisms that span the phylogenetic tree, has been collected and analyzed. This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields.RESULTS:We have prepared a large web site that disseminates our comparative sequence and structure models and data. The four major types of comparative information and systems available for the three ribosomal RNAs (5S, 16S, and 23S rRNA), transfer RNA (tRNA), and two of the catalytic intron RNAs (group I and group II) are: (1) Current Comparative Structure Models; (2) Nucleotide Frequency and Conservation Information; (3) Sequence and Structure Data; and (4) Data Access Systems.CONCLUSIONS:This online RNA sequence and structure information, the result of extensive analysis, interpretation, data collection, and computer program and web development, is accessible at our Comparative RNA Web (CRW) Site http://www.rna.icmb.utexas.edu. In the future, more data and information will be added to these existing categories, new categories will be developed, and additional RNAs will be studied and presented at the CRW Site.}, keywords = {Multiple DOI,nonfile,nosource} }

@article{vanoppenEvidenceIndependentAcquisition1993, title = {Evidence for {{Independent Acquisition}} of {{Group I Introns}} in {{Green Algae}}.}, author = {Van Oppen, M. J. H. and Olsen, J. L. and Stam, W. T.}, year = 1993, journal = {Molecular biology and evolution}, volume = {10}, number = {6}, pages = {1317–1326}, publisher = {SMBE}, url = {http://mbe.oxfordjournals.org/content/10/6/1317.short}, keywords = {No DOI found,nosource} } % == BibTeX quality report for vanoppenEvidenceIndependentAcquisition1993: % ? Title looks like it was stored in title-case in Zotero

@article{zimmermanRibosomalRNAStructure1996, title = {Ribosomal {{RNA}}: {{Structure}}, {{Evolution}}, {{Processing}}, and {{Function}} in {{Protein Biosynthesis}}.}, author = {Zimmerman, R. A. and Dahlberg, A. E. and {editors}}, year = 1996, journal = {BocaRaton, CRC Press}, keywords = {No DOI found,nosource} } % == BibTeX quality report for zimmermanRibosomalRNAStructure1996: % ? Title looks like it was stored in title-case in Zotero

@article{hillRibosomeStructureFunction1990a, title = {The {{Ribosome}}: {{Structure}}, {{Function}}, and {{Evolution}}.}, author = {Hill, W. E. and Dahlberg, A. E. and Garrett, R. A. and Moore, P. B. and Schlessinger, D. and Warner, J. R. and {editors}}, year = 1990, journal = {Washington DC, American Society for Microbiology}, keywords = {No DOI found,nosource} } % == BibTeX quality report for hillRibosomeStructureFunction1990a: % ? Title looks like it was stored in title-case in Zotero

@article{cateCrystalStructureGroup1996, title = {Crystal Structure of a Group {{I}} Ribozyme Domain: Principles of {{RNA}} Packing.}, author = {Cate, J. H. and Gooding, A. R. and Podell, E. and Zhou, K. and Golden, B. L. and Kundrot, C. E. and Cech, T. R. and Doudna, J. A.}, year = 1996, month = sep, journal = {Science}, volume = {273}, number = {5282}, eprint = {8781224}, eprinttype = {pubmed}, pages = {1678–1685}, publisher = {American Association for the Advancement of Science}, issn = {0036-8075}, doi = {10.1126/science.273.5282.1678}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8781224 http://www.sciencemag.org/content/273/5282/1678.short}, abstract = {Group I self-splicing introns catalyze their own excision from precursor RNAs by way of a two-step transesterification reaction. The catalytic core of these ribozymes is formed by two structural domains. The 2.8-angstrom crystal structure of one of these, the P4-P6 domain of the Tetrahymena thermophila intron, is described. In the 160-nucleotide domain, a sharp bend allows stacked helices of the conserved core to pack alongside helices of an adjacent region. Two specific long-range interactions clamp the two halves of the domain together: a two-Mg2+-coordinated adenosine-rich corkscrew plugs into the minor groove of a helix, and a GAAA hairpin loop binds to a conserved 11-nucleotide internal loop. Metal- and ribose-mediated backbone contacts further stabilize the close side-by-side helical packing. The structure indicates the extent of RNA packing required for the function of large ribozymes, the spliceosome, and the ribosome.}, pmid = {8781224}, keywords = {Adenine,Adenine: chemistry,Animals,Base Composition,Base Sequence,Binding Sites,Catalysis,Catalytic,Catalytic: chemistry,Catalytic: metabolism,Crystallography,Hydrogen Bonding,Introns,Magnesium,Magnesium: chemistry,Models,Molecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Phosphates,Phosphates: chemistry,Phylogeny,Protozoan,Protozoan: chemistry,Protozoan: metabolism,Ribose,Ribose: chemistry,RNA,RNA Splicing,Tetrahymena thermophila,Tetrahymena thermophila: genetics,X-Ray} }

@article{gautheretIdentificationBasetriplesRNA1995, title = {Identification of Base-Triples in {{RNA}} Using Comparative Sequence Analysis.}, author = {Gautheret, D. and Damberger, S. H. and Gutell, R. R.}, year = 1995, journal = {Journal of molecular biology}, volume = {248}, number = {1}, pages = {27–43}, publisher = {Elsevier}, doi = {10.1006/jmbi.1995.0200}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283685702008}, keywords = {nosource} }

@article{gutellComparativeAnatomy16Slike1985, title = {Comparative {{Anatomy}} of 16-{{S-like Ribosomal RNA}}.}, author = {Gutell, R. R. and Weiser, B. and Woese, C. R. and Noller, H. F.}, year = 1985, journal = {Prog Nucleic Acid Res Mol Biol}, volume = {32}, pages = {155–216}, doi = {10.1016/S0079-6603(08)60348-7}, keywords = {nosource} } % == BibTeX quality report for gutellComparativeAnatomy16Slike1985: % ? Title looks like it was stored in title-case in Zotero

@article{bhattacharyaGroupIntronLateral2001, title = {Group {{I Intron Lateral Transfer Between Red}} and {{Brown Algal Ribosomal RNA}}.}, author = {Bhattacharya, D. and Cannone, J. J. and Gutell, R. R.}, year = 2001, journal = {Current Genetics}, volume = {40}, number = {1}, pages = {82–90}, publisher = {Springer}, doi = {10.1007/s002940100227}, url = {http://www.springerlink.com/index/UD05A6DFWP0028XN.pdf}, keywords = {nosource} } % == BibTeX quality report for bhattacharyaGroupIntronLateral2001: % ? Title looks like it was stored in title-case in Zotero

@article{koningsComparisonThermodynamicFoldings1995, title = {A Comparison of Thermodynamic Foldings with Comparatively Derived Structures of {{l6S}} and {{16S-like rRNAs}}.}, author = {Konings, D. A. M. and Gutell, R. R.}, year = 1995, journal = {RNA}, volume = {1}, pages = {559–574}, keywords = {No DOI found,nosource} }

@article{bensonGenBank2000, title = {{{GenBank}}.}, author = {Benson, D. A. and {Karsch-Mizrachi}, I. and Lipman, D. J. and Ostell, J. and Rapp, B. A. and Wheeler, D. L.}, year = 2000, journal = {Nucl Acids Res}, volume = {28}, pages = {15–18}, doi = {10.1093/nar/28.1.15}, keywords = {nosource} }

@article{huysmansCompilationSmallRibosomal1986, title = {Compilation of Small Ribosomal Subunit {{RNA}} Sequences.}, author = {Huysmans, E. and De Wachter, R.}, year = 1986, journal = {Nucleic Acids Res.}, volume = {14 Suppl}, pages = {r73 - 118}, doi = {10.1093/nar/14.suppl.r73}, keywords = {nosource} } % == BibTeX quality report for huysmansCompilationSmallRibosomal1986: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{maidakRDPIIRibosomalDatabase2001, title = {The {{RDP-II}} ({{Ribosomal Database Project}}).}, author = {Maidak, B. L. and Cole, J. R. and Lilbum, T. G. and Parker, C. T. and Saxman, P. R. and Farris, R. J. and Garrity, G. M. and Olsen, G. J. and Schmidt, T. M. and Tiedje, J. M.}, year = 2001, journal = {Nucleic Acids Research}, volume = {29}, number = {1}, pages = {173–174}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/29.1.173}, url = {http://nar.oxfordjournals.org/content/29/1/173.short}, keywords = {nosource} } % == BibTeX quality report for maidakRDPIIRibosomalDatabase2001: % ? Title looks like it was stored in title-case in Zotero

@article{schnareComprehensiveComparisonStructural1996a, title = {Comprehensive {{Comparison}} of {{Structural Characteristics}} in {{Eukaryotic Cytoplasmic Large Subunit}} ({{23S-like}}) {{Ribosomal RNA}}.}, author = {Schnare, M. N. and Damberger, S. H. and Gray, M. W. and Gutell, R. R.}, year = 1996, journal = {Journal of Molecular Biology}, volume = {256}, pages = {701–719}, doi = {10.1006/jmbi.1996.0119}, keywords = {nosource} } % == BibTeX quality report for schnareComprehensiveComparisonStructural1996a: % ? Title looks like it was stored in title-case in Zotero

@article{gutellCompilationLargeSubunit1990, title = {A Compilation of Large Subunit ({{23S-like}}) Ribosomal {{RNA}} Sequences Presented in a Secondary Structure Format.}, author = {Gutell, R. R. and Schnare, M. N. and Gray, M. W.}, year = 1990, journal = {Nucl Acids Res}, volume = {18 Suppl}, pages = {2319–2330}, doi = {10.1093/nar/18.suppl.2319}, keywords = {nosource} }

@article{gutellCollectionSmallSubunit1994a, title = {Collection of {{Small Subunit}} ({{16S-}} and {{16S-like}}) Ribosomal {{RNA}} Structures: 1994.}, author = {Gutell, R. R.}, year = 1994, journal = {Nucleic acids research}, volume = {22}, pages = {3502–3507}, doi = {10.1093/nar/22.17.3502}, url = {http://nar.oxfordjournals.org/content/22/17/3502.short}, keywords = {nosource} }

@article{zwiebStructureFunctionSignal1989, title = {Structure and Function of Signal Recognition Particle {{RNA}}.}, author = {Zwieb, C.}, year = 1989, journal = {Progress in nucleic acid research and molecular biology}, volume = {37}, pages = {207–234}, publisher = {Elsevier}, doi = {10.1016/S0079-6603(08)60699-6}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0079660308606996}, keywords = {nosource} }

@article{chenSecondaryStructureVertebrate2000, title = {Secondary Structure of Vertebrate Telomerase {{RNA}}.}, author = {Chen, J. L. and Blasco, M. A. and Greider, C. W.}, year = 2000, journal = {Cell}, volume = {100}, number = {5}, pages = {503–514}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(00)80687-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/S009286740080687X}, keywords = {nosource} }

@article{romeroConservedSecondaryStructure1991, title = {A Conserved Secondary Structure for Telomerase {{RNA}}.}, author = {Romero, D. P. and Blackburn, E. H.}, year = 1991, journal = {Cell}, volume = {67}, pages = {343–353}, doi = {10.1016/0092-8674(91)90186-3}, keywords = {Animals,Base Composition,Base Composition: genetics,Base Sequence,Blotting,Ciliophora,Ciliophora: enzymology,Ciliophora: genetics,Cloning,DNA Nucleotidylexotransferase,DNA Nucleotidylexotransferase: chemistry,DNA Nucleotidylexotransferase: genetics,Genetic Variation,Genetic Variation: genetics,Models,Molecular,Molecular Sequence Data,nosource,Nuclear,Nuclear: chemistry,Nuclear: genetics,Nucleic Acid Conformation,Polymerase Chain Reaction,Ribonucleoproteins,Ribonucleoproteins: chemistry,RNA,Sequence Alignment,Southern,Tetrahymena,Tetrahymena: enzymology,Tetrahymena: genetics} }

@article{jamesSecondaryStructureRibonuclease1988a, title = {The Secondary Structure of Ribonuclease {{P RNA}}, the Catalytic Element of a Ribonucleoprotein Enzyme.}, author = {James, B. D. and Olsen, G. J. and Liu, J. S. and Pace, N. R.}, year = 1988, journal = {Cell}, volume = {52}, pages = {19–26}, doi = {10.1016/0092-8674(88)90527-2}, keywords = {nosource} }

@article{woeseDetailedAnalysisHigherorder1983a, title = {Detailed Analysis of the Higher-Order Structure of {{16S-like}} Ribosomal Ribonucleic Acids.}, author = {Woese, C. R. and Gutell, R. and Gupta, R. and Noller, H. F.}, year = 1983, journal = {Microbiological reviews}, volume = {47}, pages = {621–669}, doi = {10.1128/mr.47.4.621-669.1983}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC283711/}, keywords = {nosource} }

@article{nollerSecondaryStructure16S1981, title = {Secondary {{Structure}} of {{16S Ribosomal RNA}}.}, author = {Noller, H. F. and Woese, C. R.}, year = 1981, journal = {Science}, volume = {212}, number = {4493}, pages = {403–411}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.6163215}, url = {http://www.sciencemag.org/content/212/4493/403.short}, keywords = {nosource} } % == BibTeX quality report for nollerSecondaryStructure16S1981: % ? Title looks like it was stored in title-case in Zotero

@article{glotzSecondaryStructureLarge1981, title = {Secondary Structure of the Large Subunit Ribosomal {{RNA}} from {{Escherichia}} Coli, {{Zea}} Mays Chloroplast, and Human and Mouse Mitochondrial Ribosomes.}, author = {Glotz, C. and Zwieb, C. and Brimacombe, R. and Edwards, K. and Kossel, H.}, year = 1981, journal = {Nucleic Acids Research}, volume = {9}, number = {14}, pages = {3287–3306}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/9.14.3287}, url = {http://nar.oxfordjournals.org/content/9/14/3287.short}, keywords = {nosource} }

@article{nollerSecondaryStructureModel1981, title = {Secondary Structure Model for {{23S}} Ribosomal {{RNA}}.}, author = {Noller, H. F. and Kop, J. and Wheaton, V. and Brosius, J. and Gutell, R. R. and Kopylov, A. M. and Dohme, F. and Herr, W. and Stahl, D. A. and Gupta, R. and Woese, C. R.}, year = 1981, journal = {Nucleic Acids Research}, volume = {9}, number = {22}, pages = {6167–6189}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/9.22.6167}, url = {http://nar.oxfordjournals.org/content/9/22/6167.short}, keywords = {nosource} }

@article{stieglerSecondaryTopographicStructure1980a, title = {[{{Secondary}} and Topographic Structure of Ribosomal {{RNA 16S}} of {{Escherichia}} Coli].}, author = {Stiegler, P. and Carbon, P. and Zuker, M. and Ebel, J. P. and Ehresmann, C.}, year = 1980, journal = {Comptes rendus des s'eances de l’Acad'emie des sciences. S'erie D, Sciences naturelles}, volume = {291}, number = {12}, eprint = {6784944}, eprinttype = {pubmed}, pages = {937–940}, url = {http://www.ncbi.nlm.nih.gov/pubmed/6784944}, keywords = {No DOI found,nosource} } % == BibTeX quality report for stieglerSecondaryTopographicStructure1980a: % ? Possibly abbreviated journal title Comptes rendus des séances de l’Académie des sciences. Série D, Sciences naturelles

@article{zwiebSecondaryStructureComparisons1981, title = {Secondary Structure Comparisons between Small Subunit Ribosomal {{RNA}} Molecules from Six Different Species.}, author = {Zwieb, C. and Glotz, C. and Brimacombe, R.}, year = 1981, journal = {Nucleic Acids Research}, volume = {9}, number = {15}, pages = {3621–3640}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/9.15.3621}, url = {http://nar.oxfordjournals.org/content/9/15/3621.short}, keywords = {nosource} }

@article{foxArchitecture5SRRNA1975, title = {The Architecture of {{5S rRNA}} and Its Relation to Function.}, author = {Fox, G. E. and Woese, C. R.}, year = 1975, journal = {Journal of Molecular Evolution}, volume = {6}, number = {1}, pages = {61–76}, publisher = {Springer}, doi = {10.1007/BF01732674}, url = {http://www.springerlink.com/index/R67126153N330577.pdf}, keywords = {nosource} }

@article{fox5SRNASecondary1975, title = {{{5S RNA}} Secondary Structure.}, author = {Fox, G. E. and Woese, C. R.}, year = 1975, journal = {Nature}, volume = {256}, pages = {505–507}, doi = {10.1038/256505a0}, keywords = {nosource} }

@article{robertusStructureYeastPhenylalanine1974a, title = {Structure of Yeast Phenylalanine {{tRNA}} at {{3A}} Resolution.}, author = {Robertus, J. D. and Ladner, J. E. and Finch, J. T. and Rhodes, D. and Brown, R. S. and Clark, B. F. and Klug, A.}, year = 1974, journal = {Nature}, volume = {250}, pages = {546–551}, doi = {10.1038/250546a0}, keywords = {nosource} }

@article{kimThreedimensionalTertiaryStructure1974a, title = {Three-Dimensional Tertiary Structure of Yeast Phenylalanine Transfer {{RNA}}.}, author = {Kim, S. H. and Suddath, F. L. and Quigley, G. J. and McPherson, A. and Sussman, J. L. and Wang, A. H. and Seeman, N. C. and Rich, A.}, year = 1974, journal = {Science}, volume = {185}, number = {4149}, pages = {435–440}, doi = {10.1126/science.185.4149.435}, url = {http://www.sciencemag.org/content/185/4149/435.short}, keywords = {nosource} }

@article{zachauSerineSpecificTransfer1966a, title = {Serine Specific Transfer Ribonucleic Acids. {{XIV}}. {{Comparison}} of Nucleotide Sequences and Secondary Structure Models.}, author = {Zachau, H. G. and Dutting, D. and Feldman, H. and Melchers, F. and Karau, W.}, year = 1966, journal = {Cold Spring Harb Symp Quant Biol}, volume = {31}, pages = {417–424}, doi = {10.1101/SQB.1966.031.01.054}, keywords = {nosource} }

@article{madisonNucleotideSequenceYeast1966, title = {On the Nucleotide Sequence of Yeast Tyrosine Transfer {{RNA}}.}, author = {Madison, J. T. and Everett, G. A. and Kung, H. K.}, year = 1966, journal = {Cold Spring Harb Symp Quant Biol}, volume = {31}, pages = {409–416}, doi = {10.1101/SQB.1966.031.01.053}, keywords = {nosource} }

@article{woesePhylogeneticStructureProkaryotic1977, title = {Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms.}, author = {Woese, C. R. and Fox, G. E.}, year = 1977, journal = {Proceedings of the National Academy of Sciences}, volume = {74}, number = {11}, pages = {5088–5090}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.74.11.5088}, url = {http://www.pnas.org/content/74/11/5088.short}, keywords = {nosource} }

@article{darwinOriginSpeciesMeans, title = {Origin of {{Species}} by {{Means}} of {{Natural Selection}}, or the {{Preservation}} of {{Favoured Races}} in the {{Struggle}} for {{Life}}.}, author = {Darwin, C.}, journal = {First edition, 1859; second edition, 1860; third edition, 1861; fourth edition, 1866; fifth edition, 1869; sixth and final edition, 1872. Amherst NY, Prometheus Books.}, keywords = {No DOI found,nosource} } % == BibTeX quality report for darwinOriginSpeciesMeans: % Missing required field ‘year’ % ? Possibly abbreviated journal title First edition, 1859; second edition, 1860; third edition, 1861; fourth edition, 1866; fifth edition, 1869; sixth and final edition, 1872. Amherst NY, Prometheus Books. % ? Title looks like it was stored in title-case in Zotero

@article{lutzoniMajorFungalLineages2001, title = {Major Fungal Lineages Are Derived from Lichen Symbiotic Ancestors.}, author = {Lutzoni, F. and Pagel, M. and Reeb, V.}, year = 2001, journal = {Nature}, volume = {411}, number = {6840}, pages = {937–940}, publisher = {Nature Publishing Group}, doi = {10.1038/35082053}, url = {http://www.nature.com/nature/journal/v411/n6840/abs/411937a0.html}, keywords = {nosource} }

@article{maidakRDPRibosomalDatabase1997a, title = {The {{RDP}} ({{Ribosomal Database Project}}).}, author = {Maidak, B. L. and Olsen, G. J. and Larsen, N. and Overbeek, R. and McCaughey, M. J. and Woese, C. R.}, year = 1997, journal = {Nucleic Acids Research}, volume = {25}, pages = {109–111}, doi = {10.1093/nar/25.1.109}, keywords = {nosource} } % == BibTeX quality report for maidakRDPRibosomalDatabase1997a: % ? Title looks like it was stored in title-case in Zotero

@article{bhattacharyaWidespreadOccurrenceSpliceosomal2000, title = {Widespread Occurrence of Spliceosomal Introns in the {{rDNA}} Genes of Ascomycetes.}, author = {Bhattacharya, D. and Lutzoni, F. and Reeb, V. and Simon, D. and Nason, J. and Fernandez, F.}, year = 2000, journal = {Molecular Biology and Evolution}, volume = {17}, number = {12}, pages = {1971–1984}, publisher = {SMBE}, doi = {10.1093/oxfordjournals.molbev.a026298}, url = {http://mbe.oxfordjournals.org/content/17/12/1971.short}, keywords = {nosource} }

@article{kjemsRibosomalRNAIntrons1991, title = {Ribosomal {{RNA}} Introns in Archaea and Evidence for {{RNA}} Conformational Changes Associated with Splicing.}, author = {Kjems, J. and Garrett, R. A.}, year = 1991, journal = {Proceedings of the National Academy of Sciences}, volume = {88}, number = {2}, pages = {439–443}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.88.2.439}, url = {http://www.pnas.org/content/88/2/439.short}, keywords = {nosource} }

@article{sprinzlCompilationTRNASequences1991a, title = {Compilation of {{tRNA}} Sequences and Sequences of {{tRNA}} Genes.}, author = {Sprinzl, M. and Dank, N. and Nock, S. and Schon, A.}, year = 1991, journal = {Nucleic Acids Research}, volume = {19 Suppl}, pages = {2127–2171}, doi = {10.1093/nar/19.suppl.2127}, keywords = {nosource} }

@article{woeseNaturalSystemOrganisms1990, title = {Towards a Natural System of Organisms: Proposal for the Domains {{Archaea}}, {{Bacteria}}, and {{Eucarya}}.}, author = {Woese, C. R. and Kandler, O. and Wheelis, M. L.}, year = 1990, journal = {Proceedings of the National Academy of Sciences}, volume = {87}, number = {12}, pages = {4576–4579}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.87.12.4576}, url = {http://www.pnas.org/content/87/12/4576.short}, keywords = {nosource} }

@article{neefsCompilationSmallRibosomal1990, title = {Compilation of Small Ribosomal Subunit {{RNA}} Sequences.}, author = {Neefs, J. M. and {Van de Peer}, Y. and Hendriks, L. and De Wachter, R.}, year = 1990, journal = {Nucleic Acids Research}, volume = {18 Suppl}, number = {Suppl}, pages = {2237–2317}, publisher = {Oxford University Press}, doi = {10.1093/nar/18.suppl.2237}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC331875/}, keywords = {nosource} }

@article{correllMetalsMotifsRecognition1997, title = {Metals, Motifs, and Recognition in the Crystal Structure of a {{5S rRNA}} Domain.}, author = {Correll, C. C. and Freeborn, B. and Moore, P. B. and Steitz, T. A.}, year = 1997, journal = {Cell}, volume = {91}, number = {5}, pages = {705–712}, publisher = {Elsevier}, doi = {10.1016/S0092-8674(00)80457-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867400804572}, keywords = {nosource} }

@article{chiuInferringConsensusStructure1991, title = {Inferring Consensus Structure from Nucleic Acid Sequences.}, author = {Chiu, D. K. and Kolodziejczak, T.}, year = 1991, journal = {Computer Applications in the Biosciences}, volume = {7}, number = {3}, pages = {347–352}, publisher = {Oxford Univ Press}, url = {http://bioinformatics.oxfordjournals.org/content/7/3/347.short}, keywords = {No DOI found,nosource} }

@article{olsenComparativeAnalysisNucleotide1983, title = {Comparative Analysis of Nucleotide Sequence Data.}, author = {Olsen, G. J.}, year = 1983, journal = {Ph.D. thesis, University of Colorado Health Sciences Center,}, keywords = {No DOI found,nosource} } % == BibTeX quality report for olsenComparativeAnalysisNucleotide1983: % ? Possibly abbreviated journal title Ph.D. thesis, University of Colorado Health Sciences Center,

@article{vernonAcceleratedEvolutionFunctional2001a, title = {Accelerated {{Evolution}} of {{Functional Plastid rRNA}} and {{Elongation Factor Genes Due}} to {{Reduced Protein Synthetic Load After}} the {{Loss}} of {{Photosynthesis}} in the {{Chlorophyte Alga Polytoma}}.}, author = {Vernon, D. and Gutell, R. R. and Cannone, J. J. and Rumpf, R. W. and Birky, C. W.}, year = 2001, journal = {Mol Biol Evol}, volume = {18}, pages = {1810–1822}, doi = {10.1093/oxfordjournals.molbev.a003968}, keywords = {nosource} } % == BibTeX quality report for vernonAcceleratedEvolutionFunctional2001a: % ? Title looks like it was stored in title-case in Zotero

@article{lydeardPhylogeneticAnalysisMolluscan2000, title = {Phylogenetic {{Analysis}} of {{Molluscan Mitochondrial LSU rDNA Sequences}} and {{Secondary Structures}}.}, author = {Lydeard, C. and Holznagel, W. E. and Schnare, M. N. and Gutell, R. R.}, year = 2000, journal = {Molecular Phylogenetics and Evolution}, volume = {15}, number = {1}, pages = {83–102}, publisher = {Elsevier}, doi = {10.1006/mpev.1999.0719}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790399907194}, keywords = {nosource} } % == BibTeX quality report for lydeardPhylogeneticAnalysisMolluscan2000: % ? Title looks like it was stored in title-case in Zotero

@article{fieldsAnalysisLargeRRNA1996, title = {An {{Analysis}} of {{Large rRNA Sequences Folded}} by a {{Thermodynamic Method}}.}, author = {Fields, D. S. and Gutell, R. R.}, year = 1996, journal = {Folding and Design}, volume = {1}, number = {6}, pages = {419–430}, publisher = {Elsevier}, doi = {10.1016/S1359-0278(96)00058-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1359027896000582}, keywords = {nosource} } % == BibTeX quality report for fieldsAnalysisLargeRRNA1996: % ? Title looks like it was stored in title-case in Zotero

@article{elgavishAAAGHelix2001a, title = {{{AA}}.{{AG}}@{Helix}.{{Ends}}: {{A}}:{{A}} and {{A}}:{{G Base-pairs}} at the {{Ends}} of 16 {{S}} and 23 {{S rRNA Helices}}.}, author = {Elgavish, T. and Cannone, J. J. and Lee, J. C. and Harvey, S. C. and Gutell, R. R.}, year = 2001, journal = {J Mol Biol}, volume = {310}, pages = {735–753}, doi = {10.1006/jmbi.2001.4807}, keywords = {16S,16S: chemistry,16S: genetics,23S,23S: chemistry,23S: genetics,Base Pairing,Base Sequence,Biomolecular,Computational Biology,Conserved Sequence,Conserved Sequence: genetics,Crystallography,Databases as Topic,Escherichia coli,Escherichia coli: genetics,Models,Molecular,Molecular Sequence Data,nosource,Nuclear Magnetic Resonance,Nucleic Acid Conformation,Ribosomal,RNA,Sequence Alignment,X-Ray} }

@article{gutellStoryUnpairedAdenosines2000a, title = {A {{Story}}: {{Unpaired Adenosines}} in {{Ribosomal RNAs}}.}, author = {Gutell, R. R. and Cannone, J. J. and Shang, Z. and Du, Y. and Serra, M.}, year = 2000, journal = {J Mol Biol}, volume = {304}, pages = {335–354}, doi = {10.1006/jmbi.2000.4172}, keywords = {nosource} } % == BibTeX quality report for gutellStoryUnpairedAdenosines2000a: % ? Title looks like it was stored in title-case in Zotero

@article{gutellPredictingUturnsRibosomal2000a, title = {Predicting {{U-turns}} in {{Ribosomal RNA}} with {{Comparative Sequence Analysis}}.}, author = {Gutell, R. R. and Cannone, J. J. and Konings, D. and Gautheret, D.}, year = 2000, journal = {J Mol Biol}, volume = {300}, pages = {791–803}, doi = {10.1006/jmbi.2000.3900}, keywords = {nosource} }

@article{wuytsEuropeanLargeSubunit2001, title = {The {{European Large Subunit Ribosomal RNA Database}}.}, author = {Wuyts, J. and De Rijk, P. and {Van de Peer}, Y. and Winkelmans, T. and De Wachter, R.}, year = 2001, journal = {Nucl Acids Res}, volume = {29}, pages = {175–177}, doi = {10.1093/nar/29.1.175}, keywords = {nosource} } % == BibTeX quality report for wuytsEuropeanLargeSubunit2001: % ? Title looks like it was stored in title-case in Zotero

@article{derijkDatabaseStructureLarge1994, title = {Database on the Structure of Large Ribosomal Subunit {{RNA}}.}, author = {De Rijk, P. and {Van de Peer}, Y. and Chapelle, S. and De Wachter, R.}, year = 1994, journal = {Nucleic Acids Research}, volume = {22}, number = {17}, pages = {3495–3501}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/22.17.3495}, url = {http://nar.oxfordjournals.org/content/22/17/3495.short}, keywords = {nosource} }

@article{vandepeerEuropeanSmallSubunit2000, title = {The {{European}} Small Subunit Ribosomal {{RNA}} Database.}, author = {{Van de Peer}, Y. and De Rijk, P. and Wuyts, J. and Winkelmans, T. and De Wachter, R.}, year = 2000, journal = {Nucleic Acids Research}, volume = {28}, number = {1}, pages = {175–176}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/28.1.175}, url = {http://nar.oxfordjournals.org/content/29/1/175.short http://nar.oxfordjournals.org/content/28/1/175.short}, keywords = {nosource} }

@article{erdmannCollectionPublished5S1983a, title = {Collection of Published {{5S}} and 5.{{8S}} Ribosomal {{RNA}} Sequences.}, author = {Erdmann, V. A. and Huysmans, E. and Vandenberghe, A. and De Wachter, R.}, year = 1983, journal = {Nucl Acids Res}, volume = {11}, pages = {rl05 - rl33}, doi = {10.1093/nar/11.1.235-b}, keywords = {nosource} }

@article{olsenRibosomalDatabaseProject1992, title = {The {{Ribosomal Database Project}}.}, author = {Olsen, G. J. and Overbeek, R. and Larsen, N. and Marsh, T. L. and McCaughey, M. J. and Maciukenas, M. A. and Kuan, W. M. and Macke, T. J. and Xing, Y. and Woese, C. R.}, year = 1992, journal = {Nucl Acids Res}, volume = {20 Suppl}, pages = {2199–2200}, doi = {10.1093/nar/20.suppl.2199}, keywords = {nosource} } % == BibTeX quality report for olsenRibosomalDatabaseProject1992: % ? Title looks like it was stored in title-case in Zotero

@article{gutellCompilationLargeSubunit1988, title = {A Compilation of Large Subunit {{RNA}} Sequences Presented in a Structural Format.}, author = {Gutell, R. R. and Fox, G. E.}, year = 1988, journal = {Nucl Acids Res}, volume = {16 Suppl}, pages = {rl75 - r269}, keywords = {No DOI found,nosource} }

@article{gutellCollectionSmallSubunit1993, title = {Collection of {{Small Subunit}} ({{16S-}} and {{16S-like}}) Ribosomal {{RNA}} Structures.}, author = {Gutell, R. R.}, year = 1993, journal = {Nucleic Acids Research}, volume = {21}, number = {13}, pages = {3051–3054}, publisher = {Oxford University Press}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC309732/}, keywords = {Multiple DOI,nonfile,nosource} }

@article{guthrieSpliceosomalSnRNAs1988, title = {Spliceosomal {{snRNAs}}.}, author = {Guthrie, C. and Patterson, B.}, year = 1988, month = jan, journal = {Annual review of genetics}, volume = {22}, eprint = {2977088}, eprinttype = {pubmed}, pages = {387–419}, issn = {0066-4197}, doi = {10.1146/annurev.ge.22.120188.002131}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2977088}, pmid = {2977088}, keywords = {Base Sequence,Molecular Sequence Data,nosource,Ribonucleoproteins,Ribonucleoproteins: genetics,RNA,RNA Splicing,Small Nuclear,Small Nuclear: genetics} } % == BibTeX quality report for guthrieSpliceosomalSnRNAs1988: % ? Title looks like it was stored in title-case in Zotero

@article{williamsPhylogeneticAnalysisTmRNA1996, title = {Phylogenetic Analysis of {{tmRNA}} Secondary Structure.}, author = {Williams, K. P. and Bartel, D. P.}, year = 1996, journal = {RNA}, volume = {2}, number = {2}, pages = {1306–1310}, publisher = {Proceedings of the National Academy of Sciences of the United States of America}, url = {http://rnajournal.cshlp.org/content/2/12/1306.short}, keywords = {No DOI found,nosource} }

@article{harrisNewInsightRNase2001, title = {New Insight into {{RNase P RNA}} Structure from Comparative Analysis of the Archaeal {{RNA}}.}, author = {Harris, J. K. and Haas, E. S. and Williams, D. and Frank, D. N. and Brown, J. W.}, year = 2001, journal = {RNA}, volume = {7}, number = {2}, pages = {220–232}, publisher = {Cold Spring Harbor Lab}, doi = {10.1017/S1355838201001777}, url = {http://rnajournal.cshlp.org/content/7/2/220.short}, keywords = {nosource} }

@article{brownPhylogeneticAnalysisEvolution1991, title = {Phylogenetic Analysis and Evolution of {{RNase P RNA}} in Proteobacteria.}, author = {Brown, J. W. and Haas, E. S. and James, B. D. and Hunt, D. A. and Liu, J. S. and Pace, N. R.}, year = 1991, journal = {Journal of bacteriology}, volume = {173}, number = {12}, pages = {3855–3863}, publisher = {Am Soc Microbiol}, doi = {10.1128/jb.173.12.3855-3863.1991}, url = {http://jb.asm.org/cgi/content/abstract/173/12/3855}, keywords = {nosource} }

@article{yuComparativeSequenceAnalysis2000, title = {Comparative {{Sequence Analysis}} of {{Group II Intron}} and {{tmRNA}} and {{Database}}.}, author = {Yu, N.}, year = 2000, journal = {M.A. thesis, University of Texas at Austin,}, keywords = {No DOI found,nosource} } % == BibTeX quality report for yuComparativeSequenceAnalysis2000: % ? Possibly abbreviated journal title M.A. thesis, University of Texas at Austin, % ? Title looks like it was stored in title-case in Zotero

@article{michelComparativeFunctionalAnatomy1989a, title = {Comparative and Functional Anatomy of Group {{II}} Catalytic Introns - a Review.}, author = {Michel, F. and Umesono, K. and Ozeki, H.}, year = 1989, journal = {Gene}, volume = {82}, pages = {5–30}, doi = {10.1016/0378-1119(89)90026-7}, keywords = {nosource} }

@article{dambergerComparativeDatabaseGroup1994, title = {A Comparative Database of Group {{I}} Intron Structures.}, author = {Damberger, S. H. and Gutell, R. R.}, year = 1994, journal = {Nucl Acids Res}, volume = {22}, pages = {3508–3510}, doi = {10.1093/nar/22.17.3508}, keywords = {nosource} }

@article{cechConservedSequencesStructures1988a, title = {Conserved Sequences and Structures of Group {{I}} Introns: Building an Active Site for {{RNA}} Catalysis-a Review.}, author = {Cech, T. R.}, year = 1988, journal = {Gene}, volume = {73}, pages = {259–271}, doi = {10.1016/0378-1119(88)90492-1}, keywords = {nosource} }

@article{michelComparisonFungalMitochondrial1982, title = {Comparison of Fungal Mitochondrial Introns Reveals Extensive Homologies in {{RNA}} Secondary Structure.}, author = {Michel, F. and Jacquier, A. and Dujon, B.}, year = 1982, journal = {Biochimie}, volume = {64}, number = {10}, pages = {867–881}, publisher = {Elsevier}, doi = {10.1016/S0300-9084(82)80349-0}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0300908482803490}, keywords = {nosource} }

@article{gutellComparativeSequenceAnalysis1996, title = {Comparative Sequence Analysis and the Structure of 16 {{S}} and 23 {{S rRNA}}.}, author = {Gutell, R. R.}, year = 1996, journal = {In: Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis}, pages = {111–128}, keywords = {No DOI found,nosource} }

@article{gutellLessonsEvolvingRRNA1994, title = {Lessons from an Evolving {{rRNA}}: {{16S}} and {{23S rRNA}} Structures from a Comparative Perspective.}, author = {Gutell, R. R. and Larsen, N. and Woese, C. R.}, year = 1994, journal = {Microbiology and Molecular Biology Reviews}, volume = {58}, number = {1}, pages = {10–26}, publisher = {Am Soc Microbiol}, doi = {10.1128/mr.58.1.10-26.1994}, url = {http://mmbr.asm.org/cgi/content/abstract/58/1/10}, keywords = {nosource} }

@article{larsenHigherOrderInteractions1992, title = {Higher Order Interactions in 23s {{rRNA}}.}, author = {Larsen, N.}, year = 1992, journal = {Proceedings of the National Academy of Sciences}, volume = {89}, number = {11}, pages = {5044–5048}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.89.11.5044}, url = {http://www.pnas.org/content/89/11/5044.short}, keywords = {nosource} }

@article{haselmanAdditionalWatsonCrickInteractions1989a, title = {Additional {{Watson-Crick}} Interactions Suggest a Structural Core in Large Subunit Ribosomal {{RNA}}.}, author = {Haselman, T. and Gutell, R. R. and Jurka, J. and Fox, G. E.}, year = 1989, journal = {Journal of biomolecular structure & dynamics}, volume = {7}, number = {1}, eprint = {2684221}, eprinttype = {pubmed}, pages = {181–186}, doi = {10.1080/07391102.1989.10507759}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2684221}, keywords = {nosource} }

@article{haselmanPhylogeneticEvidenceTertiary1989a, title = {Phylogenetic Evidence for Tertiary Interactions in {{16S-like}} Ribosomal {{RNA}}.}, author = {Haselman, T. and Camp, D. G. and Fox, G. E.}, year = 1989, journal = {Nucleic Acids Research}, volume = {17}, pages = {2215–2221}, doi = {10.1093/nar/17.6.2215}, keywords = {nosource} }

@article{nollerStructureRibosomalRNA1984, title = {Structure of Ribosomal {{RNA}}.}, author = {Noller, H. F.}, year = 1984, journal = {Annu Rev Biochem}, volume = {53}, pages = {119–162}, doi = {10.1146/annurev.bi.53.070184.001003}, keywords = {nosource} }

@article{branlantPrimarySecondaryStructures1981, title = {Primary and Secondary Structures of {{Escherichia}} Coli {{MRE}} 600 {{23S}} Ribosomal {{RNA}}. {{Comparison}} with Models of Secondary Structure for Maize Chloroplast {{23S rRNA}} and for Large Portions of Mouse and Human {{16S}} Mitochondrial {{rRNAs}}.}, author = {Branlant, C. and Krol, A. and Machatt, M. A. and Pouyet, J. and Ebel, J. P. and Edwards, K. and Kossel, H.}, year = 1981, journal = {Nucleic Acids Research}, volume = {9}, number = {17}, pages = {4303–4324}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/9/17/4303.short}, keywords = {Multiple DOI,nonfile,nosource} }

@article{brosiusCompleteNucleotideSequence1980, title = {Complete Nucleotide Sequence of a {{23S}} Ribosomal {{RNA}} Gene from {{Escherichia}} Coli.}, author = {Brosius, J. and Dull, T. J. and Noller, H. F.}, year = 1980, journal = {Proceedings of the National Academy of Sciences}, volume = {77}, number = {1}, pages = {201–204}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.77.1.201}, url = {http://www.pnas.org/content/77/1/201.short}, keywords = {nosource} }

@article{woeseSecondaryStructureModel1980, title = {Secondary Structure Model for Bacterial {{16S}} Ribosomal {{RNA}}: Phylogenetic, Enzymatic and Chemical Evidence.}, author = {Woese, C. R. and Magrum, L. J. and Gupta, R. and Siegel, R. B. and Stahl, D. A. and Kop, J. and Crawford, N. and Brosius, J. and Gutell, R. and Hogan, J. J. and Noller, H. F.}, year = 1980, journal = {Nucleic Acids Research}, volume = {8}, number = {10}, pages = {2275–2293}, publisher = {Oxford Univ Press}, doi = {10.1093/nar/8.10.2275}, url = {http://nar.oxfordjournals.org/content/8/10/2275.short}, keywords = {nosource} }

@article{brosiusCompleteNucleotideSequence1978, title = {Complete Nucleotide Sequence of a {{16S}} Ribosomal {{RNA}} Gene from {{Escherichia}} Coli.}, author = {Brosius, J. and Palmer, M. L. and Kennedy, P. J. and Noller, H. F.}, year = 1978, journal = {Proceedings of the National Academy of Sciences}, volume = {75}, number = {10}, pages = {4801–4805}, publisher = {National Acad Sciences}, doi = {10.1073/pnas.75.10.4801}, url = {http://www.pnas.org/content/75/10/4801.short}, keywords = {nosource} }

@article{levittDetailedMolecularModel1969a, title = {Detailed Molecular Model for Transfer Ribonucleic Acid.}, author = {Levitt, M.}, year = 1969, journal = {Nature}, volume = {224}, number = {5221}, pages = {759–763}, doi = {10.1038/224759a0}, url = {http://csb.stanford.edu/levitt/Levitt_NAT69_tRNA_model.pdf}, keywords = {nosource} }

@article{spicklerStreptomycinBindsDecoding1997, title = {Streptomycin Binds to the Decoding Center of 16 {{S}} Ribosomal {{RNA1}}}, author = {Spickler, Catherine and Brunelle, Marie-No{}lle and {Brakier-Gingras}, L{}a}, year = 1997, month = oct, journal = {Journal of Molecular Biology}, volume = {273}, number = {3}, pages = {586–599}, publisher = {Elsevier}, issn = {0022-2836}, doi = {10.1006/jmbi.1997.1323}, url = {http://www.sciencedirect.com/science/article/B6WK7-45RFG5T-88/2/4d2e20afc8f32829e49869dc850846d6}, keywords = {16 S rRNA,chemical probing,DECODING REGION,Neomycin,nonfile,nosource,Streptomycin} }

@article{sutcliffeImprovingNatureAntibiotics2005, title = {Improving on Nature: Antibiotics That Target the Ribosome}, shorttitle = {Improving on Nature}, author = {Sutcliffe, J}, year = 2005, month = oct, journal = {Current Opinion in Microbiology}, volume = {8}, number = {5}, pages = {534–542}, publisher = {Elsevier}, issn = {13695274}, doi = {10.1016/j.mib.2005.08.004}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1369527405001207}, urldate = {2011-05-20}, keywords = {nosource} } % == BibTeX quality report for sutcliffeImprovingNatureAntibiotics2005: % ? unused Library catalog (“CrossRef”)

@article{leshinHighThroughputStructural2011, title = {High Throughput Structural Analysis of Yeast Ribosomes Using {{hSHAPE}}.}, author = {Leshin, Jonathan A and Heselpoth, Ryan and Belew, Ashton Trey and Dinman, Jonathan D}, year = 2011, month = may, journal = {RNA Biology}, volume = {8}, number = {3}, eprint = {21508682}, eprinttype = {pubmed}, pages = {478–487}, issn = {1555-8584}, doi = {10.4161/rna.8.3.14453}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21508682 http://www.landesbioscience.com/journals/11/article/14453/}, urldate = {2011-05-20}, abstract = {Global mapping of rRNA structure by traditional methods is prohibitive in terms of time, labor and expense. High throughput selective 2’ hydroxyl acylation analyzed by primer extension (hSHAPE) bypasses these problems by using fluorescently labeled primers to perform primer extension reactions, the products of which can be separated by capillary electrophoresis, thus enabling long read lengths in a cost effective manner. The data so generated is analyzed in a quantitative fashion using SHAPEFinder. This approach was used to map the flexibility of nearly the entire sequences of the 3 largest rRNAs from intact, empty yeast ribosomes. Mapping of these data onto near-atomic resolution yeast ribosome structures revealed the binding sites of known trans-acting factors, as well as previously unknown highly flexible regions of yeast rRNA. Refinement of this technology will enable nucleotide-specific mapping of changes in rRNA structure depending on the status of tRNA occupancy, the presence or absence of other trans-acting factors, due to mutations of intrinsic ribosome components or extrinsic factors affecting ribosome biogenesis, or in the presence of translational inhibitors.}, pmid = {21508682}, keywords = {and large,be grown efficiently and,for the,hshape,inexpensively,nosource,quantities of cells can,ribosome,rrna,structure,these properties have made,unlike mammalian cells,yeast is genetically malleable,yeast the model organism} } % == BibTeX quality report for leshinHighThroughputStructural2011: % ? unused Journal abbr (“RNA Biol”) % ? unused Library catalog (“NCBI PubMed”)

@article{dunkleStructuresBacterialRibosome2011, title = {Structures of the {{Bacterial Ribosome}} in {{Classical}} and {{Hybrid States}} of {{tRNA Binding}}}, author = {Dunkle, J. A. and Wang, L. and Feldman, M. B. and Pulk, A. and Chen, V. B. and Kapral, G. J. and Noeske, J. and Richardson, J. S. and Blanchard, S. C. and Cate, J. H. D.}, year = 2011, month = may, journal = {Science}, volume = {332}, number = {6032}, pages = {981–984}, publisher = {American Association for the Advancement of Science}, issn = {0036-8075}, doi = {10.1126/science.1202692}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1202692}, urldate = {2011-05-23}, abstract = {During protein synthesis, the ribosome controls the movement of tRNA and mRNA by means of large-scale structural rearrangements. We describe structures of the intact bacterial ribosome from Escherichia coli that reveal how the ribosome binds tRNA in two functionally distinct states, determined to a resolution of 3.2 angstroms by means of x-ray crystallography. One state positions tRNA in the peptidyl-tRNA binding site. The second, a fully rotated state, is stabilized by ribosome recycling factor and binds tRNA in a highly bent conformation in a hybrid peptidyl/exit site. The structures help to explain how the ratchet-like motion of the two ribosomal subunits contributes to the mechanisms of translocation, termination, and ribosome recycling.}, keywords = {nosource} } % == BibTeX quality report for dunkleStructuresBacterialRibosome2011: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“CrossRef”)

@article{landgrafMammalianMicroRNAExpression2007, title = {A {{Mammalian microRNA Expression Atlas Based}} on {{Small RNA Library Sequencing}}}, author = {Landgraf, Pablo and Rusu, Mirabela and Sheridan, Robert and Sewer, Alain and Iovino, Nicola and Aravin, Alexei and Pfeffer, S{'e}bastien and Rice, Amanda and Kamphorst, Alice O. and Landthaler, Markus and Lin, Carolina and Socci, Nicholas D. and Hermida, Leandro and Fulci, Valerio and Chiaretti, Sabina and Fo{`a}, Robin and Schliwka, Julia and Fuchs, Uta and Novosel, Astrid and M{"u}ller, Roman-Ulrich and Schermer, Bernhard and Bissels, Ute and Inman, Jason and Phan, Quang and Chien, Minchen and Weir, David B. and Choksi, Ruchi and De Vita, Gabriella and Frezzetti, Daniela and Trompeter, Hans-Ingo and Hornung, Veit and Teng, Grace and Hartmann, Gunther and Palkovits, Miklos and Di Lauro, Roberto and Wernet, Peter and Macino, Giuseppe and Rogler, Charles E. and Nagle, James W. and Ju, Jingyue and Papavasiliou, F. Nina and Benzing, Thomas and Lichter, Peter and Tam, Wayne and Brownstein, Michael J. and Bosio, Andreas and Borkhardt, Arndt and Russo, James J. and Sander, Chris and Zavolan, Mihaela and Tuschl, Thomas}, year = 2007, month = jun, journal = {Cell}, volume = {129}, number = {7}, pages = {1401–1414}, issn = {00928674}, doi = {10.1016/j.cell.2007.04.040}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867407006046}, urldate = {2011-05-25}, keywords = {Animals,Base Sequence,Base Sequence: genetics,Cell Lineage,Cell Lineage: genetics,Conserved Sequence,Conserved Sequence: genetics,Gene Expression Profiling,Gene Expression Profiling: methods,Gene Expression Regulation,Gene Expression Regulation: genetics,Gene Library,Hematologic Neoplasms,Hematologic Neoplasms: genetics,Hematopoietic Stem Cells,Hematopoietic Stem Cells: metabolism,Humans,Messenger,Messenger: genetics,Mice,MicroRNAs,MicroRNAs: genetics,Molecular Sequence Data,nosource,Nucleic Acid,Phylogeny,Rats,RNA,Sequence Homology} } % == BibTeX quality report for landgrafMammalianMicroRNAExpression2007: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“CrossRef”)

@article{leidingerSpecificPeripheralMiRNA2011, title = {Specific Peripheral {{miRNA}} Profiles for Distinguishing Lung Cancer from {{COPD}}}, author = {Leidinger, Petra and Keller, Andreas and Borries, Anne and Huwer, Hanno and Rohling, Mareike and Huebers, Junko and Lenhof, Hans-Peter and Meese, Eckart}, year = 2011, month = mar, journal = {Lung Cancer}, publisher = {Elsevier}, issn = {01695002}, doi = {10.1016/j.lungcan.2011.02.003}, url = {http://linkinghub.elsevier.com/retrieve/pii/S016950021100105X}, urldate = {2011-05-25}, keywords = {nosource} } % == BibTeX quality report for leidingerSpecificPeripheralMiRNA2011: % ? unused Library catalog (“CrossRef”)

@article{usukiSpecificInhibitionNonsensemediated2006, title = {Specific Inhibition of Nonsense-Mediated {{mRNA}} Decay Components, {{SMG-1}} or {{Upf1}}, Rescues the Phenotype of Ullrich Disease Fibroblasts}, author = {Usuki, F and Yamashita, A and Kashima, I and Higuchi, I and Osame, M and Ohno, S}, year = 2006, month = sep, journal = {Molecular Therapy}, volume = {14}, number = {3}, pages = {351–360}, publisher = {Nature Publishing Group}, issn = {15250016}, doi = {10.1016/j.ymthe.2006.04.011}, url = {http://www.nature.com/mt/journal/v14/n3/abs/mt20061306a.html}, urldate = {2011-05-27}, keywords = {nosource} } % == BibTeX quality report for usukiSpecificInhibitionNonsensemediated2006: % ? unused Library catalog (“CrossRef”)

@article{sureauSC35AutoregulatesIts2001, title = {{{SC35}} Autoregulates Its Expression by Promoting Splicing Events That Destabilize Its {{mRNAs}}.}, author = {Sureau, A.}, year = 2001, month = apr, journal = {The EMBO Journal}, volume = {20}, number = {7}, pages = {1785–1796}, publisher = {European Molecular Biology Organization}, issn = {0261-4189}, doi = {10.1093/emboj/20.7.1785}, url = {http://www.nature.com/doifinder/10.1093/emboj/20.7.1785}, urldate = {2011-05-27}, abstract = {SC35 belongs to the family of SR proteins that regulate alternative splicing in a concentration-dependent manner in vitro and in vivo. We previously reported that SC35 is expressed through alternatively spliced mRNAs with differing 3’ untranslated sequences and stabilities. Here, we show that overexpression of SC35 in HeLa cells results in a significant decrease of endogenous SC35 mRNA levels along with changes in the relative abundance of SC35 alternatively spliced mRNAs. Remarkably, SC35 leads to both an exon inclusion and an intron excision in the 3’ untranslated region of its mRNAs. In vitro splicing experiments performed with recombinant SR proteins demonstrate that SC35, but not ASF/SF2 or 9G8, specifically activates these alternative splicing events. Interestingly, the resulting mRNA is very unstable and we present evidence that mRNA surveillance is likely to be involved in this instability. SC35 therefore constitutes the first example of a splicing factor that controls its own expression through activation of splicing events leading to expression of unstable mRNA.}, pmid = {11285241}, keywords = {Alternative Splicing,Down-Regulation,Gene Expression Profiling,Gene Expression Regulation,Hela Cells,Homeostasis,Humans,Messenger,nosource,Nuclear Proteins,Nuclear Proteins: genetics,Nuclear Proteins: metabolism,Phosphoproteins,Phosphoproteins: genetics,Phosphoproteins: metabolism,Ribonucleoproteins,RNA,RNA Precursors,RNA Stability} } % == BibTeX quality report for sureauSC35AutoregulatesIts2001: % ? unused Library catalog (“CrossRef”)

@article{janowskiInvolvementAGO1AGO22006, title = {Involvement of {{AGO1}} and {{AGO2}} in Mammalian Transcriptional Silencing}, author = {Janowski, Bethany A and Huffman, Kenneth E and Schwartz, Jacob C and Ram, Rosalyn and Nordsell, Robert and Shames, David S and Minna, John D and Corey, David R}, year = 2006, month = aug, journal = {Nature Structural &#38; Molecular Biology}, volume = {13}, number = {9}, pages = {787–792}, publisher = {Nature Publishing Group}, issn = {1545-9993}, doi = {10.1038/nsmb1140}, url = {http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb1140.html}, urldate = {2011-05-27}, keywords = {nosource} } % == BibTeX quality report for janowskiInvolvementAGO1AGO22006: % ? unused Journal abbr (“Nat Struct Mol Biol”) % ? unused Library catalog (“CrossRef”)

@article{mescalchinAntisenseToolsFunctional2010, title = {Antisense Tools for Functional Studies of Human {{Argonaute}} Proteins}, author = {Mescalchin, A. and Detzer, A. and Weirauch, U. and Hahnel, M. J. and Engel, C. and Sczakiel, G.}, year = 2010, month = oct, journal = {RNA}, volume = {16}, number = {12}, pages = {2529–2536}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, doi = {10.1261/rna.2204610}, url = {http://rnajournal.cshlp.org/cgi/doi/10.1261/rna.2204610}, urldate = {2011-05-27}, keywords = {nosource} } % == BibTeX quality report for mescalchinAntisenseToolsFunctional2010: % ? unused Library catalog (“CrossRef”)

@article{mcglincyExpressionProteomicsUPF12010, title = {Expression Proteomics of {{UPF1}} Knockdown in {{HeLa}} Cells Reveals Autoregulation of {{hnRNP A2}}/{{B1}} Mediated by Alternative Splicing Resulting in Nonsense-Mediated {{mRNA}} Decay.}, author = {McGlincy, Nicholas J and Tan, Lit-Yeen and Paul, Nicodeme and Zavolan, Mihaela and Lilley, Kathryn S and Smith, Christopher WJ}, year = 2010, journal = {BMC Genomics}, volume = {11}, number = {1}, pages = {565}, publisher = {BioMed Central Ltd}, issn = {1471-2164}, doi = {10.1186/1471-2164-11-565}, url = {http://www.doaj.org/doaj?func=abstract&id=642267 http://www.ncbi.nlm.nih.gov/pubmed/20946641}, urldate = {2011-05-27}, abstract = {In addition to acting as an RNA quality control pathway, nonsense-mediated mRNA decay (NMD) plays roles in regulating normal gene expression. In particular, the extent to which alternative splicing is coupled to NMD and the roles of NMD in regulating uORF containing transcripts have been a matter of debate.}, pmid = {20946641}, keywords = {nosource}, annotation = {Backup Publisher: Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK.} } % == BibTeX quality report for mcglincyExpressionProteomicsUPF12010: % ? unused Library catalog (“CrossRef”)

@article{qinEfficientMethodIdentify2008, title = {An Efficient Method to Identify Differentially Expressed Genes in Microarray Experiments.}, author = {Qin, H. and Feng, T. and Harding, S. A. and Tsai, C.-J. and Zhang, S.}, year = 2008, month = may, journal = {Bioinformatics}, volume = {24}, number = {14}, pages = {1583–1589}, publisher = {Oxford Univ Press}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btn215}, url = {http://www.bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btn215 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/14/1583}, urldate = {2011-05-31}, abstract = {MOTIVATION: Microarray experiments typically analyze thousands to tens of thousands of genes from small numbers of biological replicates. The fact that genes are normally expressed in functionally relevant patterns suggests that gene-expression data can be stratified and clustered into relatively homogenous groups. Cluster-wise dimensionality reduction should make it feasible to improve screening power while minimizing information loss. RESULTS: We propose a powerful and computationally simple method for finding differentially expressed genes in small microarray experiments. The method incorporates a novel stratification-based tight clustering algorithm, principal component analysis and information pooling. Comprehensive simulations show that our method is substantially more powerful than the popular SAM and eBayes approaches. We applied the method to three real microarray datasets: one from a Populus nitrogen stress experiment with 3 biological replicates; and two from public microarray datasets of human cancers with 10 to 40 biological replicates. In all three analyses, our method proved more robust than the popular alternatives for identification of differentially expressed genes. AVAILABILITY: The C++ code to implement the proposed method is available upon request for academic use.}, pmid = {18453554}, keywords = {nosource}, annotation = {Backup Publisher: Department of Mathematical Sciences, Biotechnology Research Center, School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.} } % == BibTeX quality report for qinEfficientMethodIdentify2008: % ? unused Library catalog (“CrossRef”)

@article{zaher2OHGroupPeptidyltRNA2011, title = {The 2{\(\prime\)}-{{OH}} Group of the Peptidyl-{{tRNA}} Stabilizes an Active Conformation of the Ribosomal {{PTC}}}, author = {Zaher, Hani S and Shaw, Jeffrey J and Strobel, Scott A and Green, Rachel}, year = 2011, month = may, journal = {The EMBO Journal}, eprint = {21552203}, eprinttype = {pubmed}, pages = {1–9}, publisher = {Nature Publishing Group}, issn = {0261-4189}, doi = {10.1038/emboj.2011.142}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21552203 http://dx.doi.org/10.1038/emboj.2011.142 http://onlinelibrary.wiley.com/doi/10.1038/emboj.2011.142/full}, urldate = {2011-06-02}, abstract = {The ribosome accelerates the rate of peptidyl transfer by {\(>\)}10(6)-fold relative to the background rate. A widely accepted model for this rate enhancement invokes entropic effects whereby the ribosome and the 2’-OH of the peptidyl-tRNA substrate precisely position the reactive moieties through an extensive network of hydrogen bonds that allows proton movement through them. Some studies, however, have called this model into question because they find the 2’-OH of the peptidyl-tRNA to be dispensable for catalysis. Here, we use an in vitro reconstituted translation system to resolve these discrepancies. We find that catalysis is at least 100-fold slower with the dA76-substituted peptidyl-tRNA substrate and that the peptidyl transferase centre undergoes a slow inactivation when the peptidyl-tRNA lacks the 2’-OH group. Additionally, the 2’-OH group was found to be critical for EFTu binding and peptide release. These findings reconcile the conflict in the literature, and support a model where interactions between active site residues and the 2’-OH of A76 of the peptidyl-tRNA are pivotal in orienting substrates in this active site for optimal catalysis.}, pmid = {21552203}, keywords = {mechanism,nosource,peptidyl transfer,peptidyl-trna} } % == BibTeX quality report for zaher2OHGroupPeptidyltRNA2011: % ? unused Journal abbr (“EMBO J”) % ? unused Library catalog (“CrossRef”)

@misc{centerforhistoryandnewmediaZoteroQuickStart, title = {Zotero {{Quick Start Guide}}}, author = {{Center for History and New Media}}, url = {http://zotero.org/support/quick_start_guide}, keywords = {nosource} } % == BibTeX quality report for centerforhistoryandnewmediaZoteroQuickStart: % ? Title looks like it was stored in title-case in Zotero

@article{zhaoCommonStressResponsive2016, title = {The Common Stress Responsive Transcription Factor {{ATF3}} Binds Genomic Sites Enriched with P300 and {{H3K27ac}} for Transcriptional Regulation}, author = {Zhao, Jonathan and Li, Xingyao and Guo, Mingxiong and Yu, Jindan and Yan, Chunhong}, year = 2016, journal = {BMC Genomics}, volume = {17}, number = {1}, pages = {1–14}, publisher = {BMC Genomics}, issn = {14712164}, doi = {10.1186/s12864-016-2664-8}, url = {http://dx.doi.org/10.1186/s12864-016-2664-8}, abstract = {Background: Dysregulation of the common stress responsive transcription factor ATF3 has been causally linked to many important human diseases such as cancer, atherosclerosis, infections, and hypospadias. Although it is believed that the ATF3 transcription activity is central to its cellular functions, how ATF3 regulates gene expression remains largely unknown. Here, we employed ATF3 wild-type and knockout isogenic cell lines to carry out the first comprehensive analysis of global ATF3-binding profiles in the human genome under basal and stressed (DNA damage) conditions. Results: Although expressed at a low basal level, ATF3 was found to bind a large number of genomic sites that are often associated with genes involved in cellular stress responses. Interestingly, ATF3 appears to bind a large portion of genomic sites distal to transcription start sites and enriched with p300 and H3K27ac. Global gene expression profiling analysis indicates that genes proximal to these genomic sites were often regulated by ATF3. While DNA damage elicited by camptothecin dramatically altered the ATF3 binding profile, most of the genes regulated by ATF3 upon DNA damage were pre-bound by ATF3 before the stress. Moreover, we demonstrated that ATF3 was co-localized with the major stress responder p53 at genomic sites, thereby collaborating with p53 to regulate p53 target gene expression upon DNA damage. Conclusions: These results suggest that ATF3 likely bookmarks genomic sites and interacts with other transcription regulators to control gene expression.}, pmid = {27146783}, keywords = {ATF3,ChIP-seq,Enhancer,H3K27ac,nosource,P300,P53} }

@article{cookTranscriptionFactorBhlhe402020, title = {Transcription {{Factor Bhlhe40}} in {{Immunity}} and {{Autoimmunity}}}, author = {Cook, Melissa E. and Jarjour, Nicholas N. and Lin, Chih Chung and Edelson, Brian T.}, year = 2020, journal = {Trends in Immunology}, volume = {41}, number = {11}, pages = {1023–1036}, publisher = {Elsevier Ltd}, issn = {14714981}, doi = {10.1016/j.it.2020.09.002}, url = {https://doi.org/10.1016/j.it.2020.09.002}, abstract = {The basic helix-loop-helix transcription factor (TF) Bhlhe40 is emerging as a key regulator of immunity during infection, autoimmunity, and inflammatory conditions. We describe the roles of Bhlhe40 in the circulating and tissue-resident arms of the immune system, with emphasis on recent work on the regulation of cytokine production and proliferation. We explore the mechanisms behind these functions in mouse models and human cells, including interactions with other TFs, and propose that Bhlhe40 is a central mediator of both inflammation and pathogen control, as well as a crucial regulator of a growing number of tissue-resident leukocyte populations. Finally, we suggest areas for further study that may advance our understanding of immunity and disease.}, pmid = {33039338}, keywords = {nosource} } % == BibTeX quality report for cookTranscriptionFactorBhlhe402020: % ? Title looks like it was stored in title-case in Zotero

@article{kessnerProteoWizardOpenSource2008, title = {{{ProteoWizard}}: {{Open}} Source Software for Rapid Proteomics Tools Development}, author = {Kessner, Darren and Chambers, Matt and Burke, Robert and Agus, David and Mallick, Parag}, year = 2008, journal = {Bioinformatics}, volume = {24}, number = {21}, pages = {2534–2536}, issn = {13674803}, doi = {10.1093/bioinformatics/btn323}, abstract = {Summary: The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library.nAvailability: Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.nContact: darren@proteowizard.org; parag@ucla.edunSupplementary information: Supplementary data are available at Bioinformatics online.}, isbn = {1367-4811 (Linking)}, pmid = {18606607}, keywords = {nosource} }

@article{rosenbergerALFQRpackageEstimating2014, title = {{{ALFQ}}: {{An R-package}} for Estimating Absolute Protein Quantities from Label-Free {{LC-MS}}/{{MS}} Proteomics Data}, author = {Rosenberger, George and Ludwig, Christina and R{"o}st, Hannes L. and Aebersold, Ruedi and Malmstr{"o}m, Lars}, year = 2014, journal = {Bioinformatics}, volume = {30}, number = {17}, pages = {2511–2513}, issn = {14602059}, doi = {10.1093/bioinformatics/btu200}, abstract = {MOTIVATION: The determination of absolute quantities of proteins in biological samples is necessary for multiple types of scientific inquiry. While relative quantification has been commonly used in proteomics, few proteomic datasets measuring absolute protein quantities have been reported to date. Various technologies have been applied using different types of input data, e.g. ion intensities or spectral counts, as well as different absolute normalization strategies. To date, a user-friendly and transparent software supporting large-scale absolute protein quantification has been lacking.nnRESULTS: We present a bioinformatics tool, termed aLFQ, which supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, together with validation algorithms enabling automated data analysis and error estimation.nnAVAILABILITY AND IMPLEMENTATION: aLFQ is written in R and freely available under the GPLv3 from CRAN (http://www.cran.r-project.org). Instructions and example data are provided in the R-package. The raw data can be obtained from the PeptideAtlas raw data repository (PASS00321).nnCONTACT: lars.malmstroem@imsb.biol.ethz.ch SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, isbn = {1367-4811}, pmid = {24753486}, keywords = {nosource} }

@article{choiMSstatsPackageStatistical2014, title = {{{MSstats}}: An {{R}} Package for Statistical Analysis of Quantitative Mass Spectrometry-Based Proteomic Experiments}, author = {Choi, Meena and Chang, Ching-Yun and Clough, Timothy and Broudy, Daniel and Killeen, Trevor and MacLean, Brendan and Vitek, Olga}, year = 2014, journal = {Bioinformatics}, volume = {30}, number = {17}, pages = {2524–2526}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btu305}, url = {https://academic.oup.com/bioinformatics/bioinformatics/article/2748156/MSstats:}, abstract = {Summary: MSstats is an R package for statistical relative quantification of proteins and peptides in mass spectrometry-based proteomics. Version 2.0 of MSstats supports label-free and label-based experimental workflows, and data dependent, targeted and data independent spectral acquisition. It takes as input identified and quantified spectral peaks, and outputs a list of differentially abundant peptides or proteins, or summaries of peptide or protein relative abundance. MSstats relies on a flexible family of linear mixed models.nAvailability: The code, the documentation, and example datasets are available open-source at www.msstats.org under the Artistic-2.0 license. The package can be downloaded from www.msstats.org or from Bioconductor www.bioconductor.org, and used in a R command line workflow. The package can also be accessed as an external tool in Skyline (Broudy et al., 2013) and used via graphical user interface.nContact: ovitekatpurdue.edu}, isbn = {1367-4811 (Electronic) 1367-4803 (Linking)}, pmid = {24794931}, keywords = {nosource} }

@article{blattmannSWATH2statsBioconductorPackage2016, title = {{{SWATH2stats}}: {{An R}}/Bioconductor Package to Process and Convert Quantitative {{SWATH-MS}} Proteomics Data for Downstream Analysis Tools}, author = {Blattmann, Peter and Heusel, Moritz and Aebersold, Ruedi}, year = 2016, journal = {PLoS ONE}, volume = {11}, number = {4}, pages = {1–7}, issn = {19326203}, doi = {10.1371/journal.pone.0153160}, abstract = {SWATH-MS is an acquisition and analysis technique of targeted proteomics that enables measuring several thousand proteins with high reproducibility and accuracy across many samples. OpenSWATH is popular open-source software for peptide identification and quan-tification from SWATH-MS data. For downstream statistical and quantitative analysis there exist different tools such as MSstats, mapDIA and aLFQ. However, the transfer of data from OpenSWATH to the downstream statistical tools is currently technically challenging. Here we introduce the R/Bioconductor package SWATH2stats, which allows convenient pro-cessing of the data into a format directly readable by the downstream analysis tools. In addi-tion, SWATH2stats allows annotation, analyzing the variation and the reproducibility of the measurements, FDR estimation, and advanced filtering before submitting the processed data to downstream tools. These functionalities are important to quickly analyze the quality of the SWATH-MS data. Hence, SWATH2stats is a new open-source tool that summarizes several practical functionalities for analyzing, processing, and converting SWATH-MS data and thus facilitates the efficient analysis of large-scale SWATH/DIA datasets.}, isbn = {1932-6203 (Electronic) 1932-6203 (Linking)}, pmid = {27054327}, keywords = {nosource} }

@article{telemanDIANAalgorithmicImprovementsAnalysis2015, title = {{{DIANA-algorithmic}} Improvements for Analysis of Data-Independent Acquisition {{MS}} Data}, author = {Teleman, Johan and R{"o}st, Hannes L. and Rosenberger, George and Schmitt, Uwe and Malmstr{"o}m, Lars and Malmstr{"o}m, Johan and Levander, Fredrik}, year = 2015, journal = {Bioinformatics}, volume = {31}, number = {4}, pages = {555–562}, issn = {14602059}, doi = {10.1093/bioinformatics/btu686}, abstract = {MOTIVATION:Data independent acquisition mass spectrometry has emerged as a reproducible and sensitive alternative in quantitative proteomics, where parsing the highly complex tandem mass spectra requires dedicated algorithms. Recently, targeted data extraction was proposed as a novel analysis strategy for this type of data, but it is important to further develop these concepts to provide quality-controlled, interference-adjusted and sensitive peptide quantification.nnRESULTS:We here present the algorithm DIANA and the classifier PyProphet, which are based on new probabilistic sub-scores to classify the chromatographic peaks in targeted data-independent acquisition data analysis. The algorithm is capable of providing accurate quantitative values and increased recall at a controlled false discovery rate, in a complex gold standard dataset. Importantly, we further demonstrate increased confidence gained by the use of two complementary data-independent acquisition targeted analysis algorithms, as well as increased numbers of quantified peptide precursors in complex biological samples. Availability and implementation: DIANA is implemented in scala and python and available as open source (Apache 2.0 license) or pre-compiled binaries from http://quantitativeproteomics.org/diana. PyProphet can be installed from PyPi (https://pypi.python.org/pypi/pyprophet). Supplementary information: Supplementary data are available at Bioinformatics online.}, isbn = {1367-4811 (Electronic)r1367-4803 (Linking)}, pmid = {25348213}, keywords = {nosource} }

@article{rostEfficientVisualizationHighthroughput2015, title = {Efficient Visualization of High-Throughput Targeted Proteomics Experiments: {{TAPIR}}}, author = {R{"o}st, Hannes L. and Rosenberger, George and Aebersold, Ruedi and Malmstr{"o}m, Lars}, year = 2015, journal = {Bioinformatics}, volume = {31}, number = {14}, pages = {2415–2417}, issn = {14602059}, doi = {10.1093/bioinformatics/btv152}, abstract = {Motivation: Targeted mass spectrometry comprises a set of powerful methods to obtain accurate and consistent protein quantification in complex samples. To fully exploit these techniques, a cross-platform and open-source software stack based on standardized data exchange formats is required. Results: We present TAPIR, a fast and efficient Python visualization software for chromatograms and peaks identified in targeted proteomics experiments. The input formats are open, community-driven standardized data formats (mzML for raw data storage and TraML encoding the hierarchical relationships between transitions, peptides and proteins). TAPIR is scalable to proteome-wide targeted proteomics studies (as enabled by SWATH-MS), allowing researchers to visualize high-throughput datasets. The framework integrates well with existing automated analysis pipelines and can be extended beyond targeted proteomics to other types of analyses. Availability: TAPIR is available for all computing platforms under the 3-clause BSD license at https://code.google.com/p/msproteomicstools. Contact: lars@imsb.biol.ethz.ch}, isbn = {1367-4811 (Electronic)r1367-4803 (Linking)}, pmid = {25788625}, keywords = {nosource} }

@article{engCometOpensourceMS2013, title = {Comet: {{An}} Open-Source {{MS}}/{{MS}} Sequence Database Search Tool}, author = {Eng, Jimmy K. and Jahan, Tahmina A. and Hoopmann, Michael R.}, year = 2013, journal = {Proteomics}, volume = {13}, number = {1}, pages = {22–24}, issn = {16159853}, doi = {10.1002/pmic.201200439}, abstract = {Proteomics research routinely involves identifying peptides and proteins via MS/MS sequence database search. Thus the database search engine is an integral tool in many proteomics research groups. Here, we introduce the Comet search engine to the existing landscape of commercial and open-source database search tools. Comet is open source, freely available, and based on one of the original sequence database search tools that has been widely used for many years.}, isbn = {1615-9861 (Electronic)r1615-9853 (Linking)}, pmid = {23148064}, keywords = {Bioinformatics,Identification,MS,nosource,Peptide,Protein} }

@article{VariantAnnotationBioconductorPackage, title = {{{VariantAnnotation}}: A {{Bioconductor}} Package for Exploration and Annotation of Genetic Variants}, doi = {10.1093/bioinformatics/btu168}, keywords = {nosource} } % == BibTeX quality report for VariantAnnotationBioconductorPackage: % Missing required field ‘author’ % Missing required field ‘journal’ % Missing required field ‘year’ % ? unused DOI (“https://doi.org/10.1093/bioinformatics/btu168”)

@article{narasimhanGeneticsPopulationAnalysis2016, title = {Genetics and Population Analysis {{BCFtools}}}, author = {Narasimhan, Vagheesh and Danecek, Petr and Scally, Aylwyn and Xue, Yali and {Tyler-smith}, Chris and Durbin, Richard}, year = 2016, journal = {Bioinformatics}, volume = {32}, number = {January}, pages = {1749–1751}, doi = {10.1093/bioinformatics/btw044}, keywords = {nosource} }

@article{brayNearoptimalRNASeqQuantification, title = {Near-Optimal {{RNA-Seq}} Quantification}, author = {Bray, Nicolas L. and Pimentel, Harold and Melsted, P{'a}ll and Pachter, Lior}, keywords = {nosource} } % == BibTeX quality report for brayNearoptimalRNASeqQuantification: % Missing required field ‘journal’ % Missing required field ‘year’

@article{liuImmuneActivationHost2016, title = {Immune Activation of the Host Cell Induces Drug Tolerance in {{{}}}{} Both in Vitro and in Vivo}, author = {Liu, Yancheng and Tan, Shumin and Huang, Lu and Abramovitch, Robert B. and Rohde, Kyle H. and Zimmerman, Matthew D. and Chen, Chao and Dartois, V{'e}ronique and VanderVen, Brian C. and Russell, David G.}, year = 2016, journal = {The Journal of Experimental Medicine}, pages = {jem.20151248}, issn = {0022-1007}, doi = {10.1084/jem.20151248}, url = {http://www.jem.org/lookup/doi/10.1084/jem.20151248}, abstract = {{\(<\)}p{\(>\)} Successful chemotherapy against {\(<\)}italic{\(>\)}Mycobacterium tuberculosis{\(<\)}/italic{\(>\)} (Mtb) must eradicate the bacterium within the context of its host cell. However, our understanding of the impact of this environment on antimycobacterial drug action remains incomplete. Intriguingly, we find that Mtb in myeloid cells isolated from the lungs of experimentally infected mice exhibit tolerance to both isoniazid and rifampin to a degree proportional to the activation status of the host cells. These data are confirmed by in vitro infections of resting versus activated macrophages where cytokine-mediated activation renders Mtb tolerant to four frontline drugs. Transcriptional analysis of intracellular Mtb exposed to drugs identified a set of genes common to all four drugs. The data imply a causal linkage between a loss of fitness caused by drug action and Mtb’s sensitivity to host-derived stresses. Interestingly, the environmental context exerts a more dominant impact on Mtb gene expression than the pressure on the drugs’ primary targets. Mtb’s stress responses to drugs resemble those mobilized after cytokine activation of the host cell. Although host-derived stresses are antimicrobial in nature, they negatively affect drug efficacy. Together, our findings demonstrate that the macrophage environment dominates Mtb’s response to drug pressure and suggest novel routes for future drug discovery programs. {\(<\)}/p{\(>\)}}, keywords = {nosource} }

@article{munchelDynamicProfilingMRNA2011, title = {Dynamic Profiling of {{mRNA}} Turnover Reveals Gene-Specific and System-Wide Regulation of {{mRNA}} Decay.}, author = {Munchel, Sarah E. and Shultzaberger, Ryan K. and Takizawa, Naoki and Weis, Karsten}, year = 2011, month = aug, journal = {Molecular biology of the cell}, volume = {22}, number = {15}, pages = {2787–95}, issn = {1939-4586}, doi = {10.1091/mbc.E11-01-0028}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3145553&tool=pmcentrez&rendertype=abstract http://www.ncbi.nlm.nih.gov/pubmed/21680716}, abstract = {RNA levels are determined by the rates of both transcription and decay, and a mechanistic understanding of the complex networks regulating gene expression requires methods that allow dynamic measurements of transcription and decay in living cells with minimal perturbation. Here, we describe a metabolic pulse-chase labeling protocol using 4-thiouracil combined with large-scale RNA sequencing to determine decay rates of all mRNAs in Saccharomyces cerevisiae. Profiling in various growth and stress conditions reveals that mRNA turnover is highly regulated both for specific groups of transcripts and at the system-wide level. For example, acute glucose starvation induces global mRNA stabilization but increases the degradation of all 132 detected ribosomal protein mRNAs. This effect is transient and can be mimicked by inhibiting the target-of-rapamycin kinase. Half-lives of mRNAs critical for galactose (GAL) metabolism are also highly sensitive to changes in carbon source. The fast reduction of GAL transcripts in glucose requires their dramatically enhanced turnover, highlighting the importance of mRNA decay in the control of gene expression. The approach described here provides a general platform for the global analysis of mRNA turnover and transcription and can be applied to dissect gene expression programs in a wide range of organisms and conditions.}, pmid = {21680716}, keywords = {Fungal,Fungal: genetics,Fungal: metabolism,Galactose,Galactose: metabolism,Gene Expression Regulation,Gene Library,Genetic,Genome,Genome-Wide Association Study,Glucose,Glucose: deficiency,Glucose: genetics,Half-Life,Messenger,Messenger: biosynthesis,Messenger: genetics,nosource,Ribosomal Proteins,Ribosomal Proteins: genetics,Ribosomal Proteins: metabolism,RNA,RNA Stability,RNA Stability: genetics,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Sequence Analysis,Thiouracil,Thiouracil: analogs & derivatives,Thiouracil: analysis,Thiouracil: metabolism,TOR Serine-Threonine Kinases,TOR Serine-Threonine Kinases: genetics,TOR Serine-Threonine Kinases: metabolism,Transcription} }

@article{lodesIncreasedExpressionLD11995, title = {Increased Expression of {{LD1}} Genes Transcribed by {{RNA}} Polymerase {{I}} in {{Leishmania}} Donovani as a Result of Duplication into the {{rRNA}} Gene Locus.}, author = {Lodes, Michael J. and Merlin, Gilles and {deVos}, T. and Ghosh, Anirban and Madhubala, R. and Myler, P. J. and Stuart, K.}, year = 1995, journal = {Molecular and cellular biology}, volume = {15}, number = {12}, pages = {6845–6853}, issn = {0270-7306}, abstract = {Eukaryotic protein-coding genes are generally transcribed by RNA polymerase II (Pol II), which has a lower transcription rate than that of Pol I. We report here the duplication of two LD1 genes into the rRNA locus and their resultant transcription by Pol I. The multigenic LD1 locus is present in a 2.2-Mb chromosome in all stocks of Leishmania spp. and is also present in multicopy 200- to 450-kb linear chromosomes or multicopy circular DNAs in over 15% of stocks examined. Genomic rearrangement in Leishmania donovani LSB-51.1 resulted in duplication of a 3.9-kb segment of LD1 containing two genes (orfF and orfG) and of a 1.3-kb segment from approximately 10 kb downstream into the rRNA gene repeat region of the 1.2-Mb chromosome. Short sequences (12 or 13 bp) common to the 2.2-Mb LD1 and 1.2-Mb rRNA loci suggest that this gene conversion occurred by homologous recombination. Transcription of the duplicated genes is alpha-amanitin resistant, indicating transcription by Pol I, in contrast to the alpha-amanitin-sensitive (Pol II) transcription of the genes in the 2.2-Mb LD1 locus. This results in higher transcript abundance than expected from the gene copy number in LSB-51.1 and in elevated expression of at least the orfF gene product.}, isbn = {0270-7306 (Print)r0270-7306 (Linking)}, pmid = {8524251}, keywords = {nosource} }

@article{davidPreferentialTranslationHsp832010, title = {Preferential Translation of {{Hsp83}} in {{Leishmania}} Requires a Thermosensitive Polypyrimidine-Rich Element in the 3{\(\prime\)} {{UTR}} and Involves Scanning of the 5{\(\prime\)} {{UTR}}}, author = {David, Maya and Gabdank, Idan and {Ben-David}, Miriam and Zilka, Alon and Orr, Irit and Barash, Danny and Shapira, Michal}, year = 2010, journal = {RNA}, volume = {16}, pages = {364–374}, issn = {1355-8382}, doi = {10.1261/rna.1874710}, url = {http://rnajournal.cshlp.org/content/16/2/364.short}, abstract = {Heat shock proteins (HSPs) provide a useful system for studying developmental patterns in the digenetic Leishmania parasites, since their expression is induced in the mammalian life form. Translation regulation plays a key role in control of protein coding genes in trypanosomatids, and is directed exclusively by elements in the 3’ untranslated region (UTR). Using sequential deletions of the Leishmania Hsp83 3’ UTR (888 nucleotides [nt]), we mapped a region of 150 nt that was required, but not sufficient for preferential translation of a reporter gene at mammalian-like temperatures, suggesting that changes in RNA structure could be involved. An advanced bioinformatics package for prediction of RNA folding (UNAfold) marked the regulatory region on a highly probable structural arm that includes a polypyrimidine tract (PPT). Mutagenesis of this PPT abrogated completely preferential translation of the fused reporter gene. Furthermore, temperature elevation caused the regulatory region to melt more extensively than the same region that lacked the PPT. We propose that at elevated temperatures the regulatory element in the 3’ UTR is more accessible to mediators that promote its interaction with the basal translation components at the 5’ end during mRNA circularization. Translation initiation of Hsp83 at all temperatures appears to proceed via scanning of the 5’ UTR, since a hairpin structure abolishes expression of a fused reporter gene.}, isbn = {1469-9001 (Electronic)r1355-8382 (Linking)}, pmid = {20040590}, keywords = {3 9 utr,39 utr,hsp83,leishmania,nosource,polypyrimidine tract,scanning of 5 9,scanning of 59 utr,translation regulation,utr} }

@article{humphreysMicroRNAsControlTranslation2005, title = {{{MicroRNAs}} Control Translation Initiation by Inhibiting Eukaryotic Initiation Factor {{4E}}/Cap and Poly ({{A}}) Tail Function}, author = {Humphreys, David T. DT and Westman, Belinda J. and Martin, David I. K. and Preiss, Thomas}, year = 2005, month = nov, journal = {Proceedings of the }, volume = {102}, number = {47}, pages = {16961–6}, publisher = {National Acad Sciences}, issn = {0027-8424}, doi = {10.1073/pnas.0506482102}, url = {http://www.pnas.org/content/102/47/16961.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1287990&tool=pmcentrez&rendertype=abstract}, abstract = {MicroRNAs (miRNAs) repress translation of target mRNAs by interaction with partially mismatched sequences in their 3’ UTR. The mechanism by which they act on translation has remained largely obscure. We examined the translation of mRNAs containing four partially mismatched miRNA-binding sites in the 3’ UTR in HeLa cells cotransfected with a cognate miRNA. The mRNAs were prepared by in vitro transcription and were engineered to employ different modes of translation initiation. We find that the 5’ cap structure and the 3’ poly(A) tail are each necessary but not sufficient for full miRNA-mediated repression of mRNA translation. Replacing the cap structure with an internal ribosome entry site from either the cricket paralysis virus or the encephalomyocarditis virus impairs miRNA-mediated repression. Collectively, these results demonstrate that miRNAs interfere with the initiation step of translation and implicate the cap-binding protein eukaryotic initiation factor 4E as a molecular target.}, pmid = {16287976}, keywords = {CXCR4,CXCR4: genetics,Eukaryotic Initiation Factor-4E,Eukaryotic Initiation Factor-4E: antagonists & inh,HeLa Cells,Humans,Messenger,Messenger: metabolism,MicroRNAs,MicroRNAs: physiology,nosource,Poly(A)-Binding Proteins,Poly(A)-Binding Proteins: antagonists & inhibitors,Receptors,Ribosomes,Ribosomes: physiology,RNA,RNA Caps,RNA Caps: antagonists & inhibitors} }

@article{kolevDevelopmentalProgressionInfectivity2012, title = {Developmental Progression to Infectivity in {{Trypanosoma}} Brucei Triggered by an {{RNA-binding}} Protein}, author = {Kolev, Nikolay G. NG and {Ramey-Butler}, Kiantra and Cross, GAM George a M. and Ullu, Elisabetta and Tschudi, Christian}, year = 2012, month = dec, journal = {Science}, volume = {338}, number = {6112}, pages = {1352–3}, issn = {1095-9203}, doi = {10.1126/science.1229641}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3664091&tool=pmcentrez&rendertype=abstract C http://www.sciencemag.org/content/338/6112/1352.short}, abstract = {Unraveling the intricate interactions between Trypanosoma brucei, the protozoan parasite causing African trypanosomiasis, and the tsetse (Glossina) vector remains a challenge. Metacyclic trypanosomes, which inhabit the tsetse salivary glands, transmit the disease and are produced through a complex differentiation and unknown program. By overexpressing a single RNA-binding protein, TbRBP6, in cultured noninfectious trypanosomes, we recapitulated the developmental stages that have been observed in tsetse, including the generation of infective metacyclic forms expressing the variant surface glycoprotein. Thus, events leading to acquisition of infectivity in the insect vector are now accessible to laboratory investigation, providing an opening for new intervention strategies.}, isbn = {1095-9203 (Electronic)r0036-8075 (Linking)}, pmid = {23224556}, keywords = {Animals,Base Sequence,Gene Expression Regulation,Molecular Sequence Data,nosource,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,RNA-Binding Proteins,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: growth & development,Trypanosoma brucei brucei: pathogenicity,Tsetse Flies,Tsetse Flies: parasitology} }

@article{ruanIterativeLoopMatching2003, title = {An Iterative Loop Matching Approach to the Prediction of {{RNA}} Secondary Structures with Pseudoknots}, author = {Ruan, J. and Stormo, G. D. D. and Zhang, W.}, year = 2003, journal = {Computational Systems Bioinformatics.}, pages = {519–520}, publisher = {IEEE Comput. Soc}, doi = {10.1109/CSB.2003.1227394}, url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=1227394}, isbn = {0-7695-2000-6}, keywords = {nosource} } % == BibTeX quality report for ruanIterativeLoopMatching2003: % ? Possibly abbreviated journal title Computational Systems Bioinformatics.

@article{robinsonIntegrativeGenomicsViewer2011, title = {Integrative Genomics Viewer}, author = {Robinson, JT James T. and Thorvaldsd{'o}ttir, Helga and Winckler, Wendy and Guttman, Mitchell and Lander, Eric S. and Getz, Gad and Mesirov, Jill P.}, year = 2011, journal = {Nature }, volume = {29}, number = {1}, pages = {24–26}, issn = {1087-0156}, doi = {10.1038/nbt0111-24}, url = {http://www.nature.com/nbt/journal/v29/n1/abs/nbt.1754.html}, abstract = {To the Editor:nRapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.nView full text}, isbn = {1546-1696 (Electronic) 1087-0156 (Linking)}, pmid = {21221095}, keywords = {nosource} }

@article{mathewsPredictionRNASecondary2006, title = {Prediction of {{RNA}} Secondary Structure by Free Energy Minimization}, author = {Mathews, D. H. H. and Turner, D. H. H.}, year = 2006, journal = {Current Opinion in Structural Biology}, volume = {16}, number = {3}, pages = {270–278}, publisher = {Elsevier}, issn = {1064-3745}, doi = {10.1016/j.sbi.2006.05.010}, url = {http://www.sciencedirect.com/science/article/pii/S0959440X06000819 http://www.springerlink.com/index/u618685313j54185.pdf http://www.sciencedirect.com/science/article/pii/s0959-440x(06)00081-9}, keywords = {Base Composition,Base Sequence,Consensus Sequence,DNA,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Repetitive Sequences- Nucleic Acid,RNA,Software,Thermodynamics} }

@article{lomakinInitiationMammalianProtein2013, title = {The Initiation of Mammalian Protein Synthesis and {{mRNA}} Scanning Mechanism.}, author = {Lomakin, Ivan B. and Steitz, Thomas A.}, year = 2013, month = aug, journal = {Nature}, volume = {500}, number = {7462}, eprint = {23873042}, eprinttype = {pubmed}, pages = {1–6}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature12355}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23873042 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3748252&tool=pmcentrez&rendertype=abstract}, abstract = {During translation initiation in eukaryotes, the small ribosomal subunit binds messenger RNA at the 5’ end and scans in the 5’ to 3’ direction to locate the initiation codon, form the 80S initiation complex and start protein synthesis. This simple, yet intricate, process is guided by multiple initiation factors. Here we determine the structures of three complexes of the small ribosomal subunit that represent distinct steps in mammalian translation initiation. These structures reveal the locations of eIF1, eIF1A, mRNA and initiator transfer RNA bound to the small ribosomal subunit and provide insights into the details of translation initiation specific to eukaryotes. Conformational changes associated with the captured functional states reveal the dynamics of the interactions in the P site of the ribosome. These results have functional implications for the mechanism of mRNA scanning.}, pmid = {23873042}, keywords = {Animals,Crystallography,Eukaryotic,Eukaryotic Initiation Factor-1,Eukaryotic Initiation Factor-1: chemistry,Eukaryotic Initiation Factor-1: metabolism,Eukaryotic: chemistry,Eukaryotic: metabolism,Humans,Messenger,Messenger: chemistry,Messenger: metabolism,Met,Met: chemistry,Met: metabolism,Models,Molecular,nosource,Protein Binding,Protein Biosynthesis,Protein Structure,Quaternary,Rabbits,Ribosome Subunits,Ribosomes,Ribosomes: metabolism,RNA,Small,Transfer,X-Ray} }

@article{budkevichStructureDynamicsMammalian2011, title = {Structure and Dynamics of the Mammalian Ribosomal Pretranslocation Complex}, author = {Budkevich, Tatyana and Giesebrecht, Jan and Altman, Roger B. RB and Munro, James B. and Mielke, Thorsten and Nierhaus, Knud H. and Blanchard, Scott C. and Spahn, Christian M. T.}, year = 2011, month = oct, journal = {Molecular cell}, volume = {44}, number = {2}, pages = {214–224}, publisher = {Elsevier Inc.}, issn = {1097-2765}, doi = {10.1016/j.molcel.2011.07.040}, url = {http://dx.doi.org/10.1016/j.molcel.2011.07.040 http://www.sciencedirect.com/science/article/pii/S109727651100757X}, abstract = {Although the structural core of the ribosome is conserved in all kingdoms of life, eukaryotic ribosomes are significantly larger and more complex than their bacterial counterparts. The extent to which these differences influence the molecular mechanism of translation remains elusive. Multiparticle cryo-electron microscopy and single-molecule FRET investigations of the mammalian pretranslocation complex reveal spontaneous, large-scale conformational changes, including an intersubunit rotation of the ribosomal subunits. Through structurally related processes, tRNA substrates oscillate between classical and at least two distinct hybrid configurations facilitated by localized changes in their L-shaped fold. Hybrid states are favored within the mammalian complex. However, classical tRNA positions can be restored by tRNA binding to the E site or by the eukaryotic-specific antibiotic and translocation inhibitor cycloheximide. These findings reveal critical distinctions in the structural and energetic features of bacterial and mammalian ribosomes, providing a mechanistic basis for divergent translation regulation strategies and species-specific antibiotic action.}, keywords = {nosource} }

@article{clarkKineticMechanismLuciferase1997, title = {Kinetic Mechanism of Luciferase Subunit Folding and Assembly.}, author = {Clark, a C. and Raso, S. W. and Sinclair, J. F. and Ziegler, M. M. and Chaffotte, a F. and Baldwin, T. O.}, year = 1997, month = feb, journal = {Biochemistry}, volume = {36}, number = {7}, eprint = {9048575}, eprinttype = {pubmed}, pages = {1891–9}, issn = {0006-2960}, doi = {10.1021/bi962477m}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9048575}, abstract = {The kinetic mechanism in vitro of the folding and assembly of the heterodimeric flavin monooxygenase bacterial luciferase has been defined by a unique set of rate constants which describe both the productive refolding pathway and competing off-pathway reactions in 50 mM phosphate, pH 7.0 at 18 degrees C. The individual alpha and beta subunits fold independently to form heterodimerization-competent species, alpha i and beta i. The alpha i beta i species can interact to form an inactive heterodimeric intermediate, [alpha beta ]i, which isomerizes to form the active alpha beta structure; the structure of the enzyme has been determined to 1.5 A resolution [Fisher, A. J., Thompson, T. B., Thoden, J. B., Baldwin, T. O., & Rayment, I. (1996) J. Biol. Chem. 271, 21956-21968]. In the absence of alpha i, beta i can form a kinetically trapped homodimer, beta 2, with a second-order rate constant of about 180 M-1 s-1 [Sinclair, J. F., Ziegler, M. M., & Baldwin, T. O. (1994) Nat. Struct. Biol. 1, 320-326]; the structure of beta 2 has recently been reported [Thoden. J. B., Holden, H. M., Fisher, A. J., Sinclair. J. F., Wesenberg, G., Baldwin, T.O., & Rayment, I. (1997) Protein Sci. 6, 13-23]. The beta i species, or some other form that precedes beta i on the refolding pathway, can also undergo a first-order conversion into a form (designated beta x) that cannot associate with alpha i to form the native enzyme. The rate constant for this process, assigned here, accounts well for the previously observed dependence of final yield on concentration of refolding species [Ziegler, M.M., Goldberg, M.E., Chaffotte, A. F., & Baldwin, T. O. (1993) J. Biol. Chem. 268, 10760-10765]. In simulations of the refolding reaction, all processes associated with the refolding of the individual subunits were combined into single first-order rate constants for each subunit which were consistent with the rate constants determined from stopped-flow circular dichroism studies. The first-order rate constant for the folding of the alpha subunit, estimated from the concentration-independent lag preceding the appearance of active enzyme, and the second-order rate constant for assembly of alpha i and beta i into the heterodimer, estimated from the concentration-dependent rate of appearance of active enzyme, were consistent with the rates of first- and second-order processes monitored by changes in fluorescence of an extrinsic probe [the product of modification with N-(4-anilino-1-naphthyl)maleimide] on the alpha subunit during refolding. The rate constant for the isomerization of [alpha beta]i to form the active heterodimer was estimated from the kinetic data of a secondary dilution experiment and from fluorescence measurements of protein diluted 20-fold from 2.1 M urea-containing buffer. The rate constants reported here for the kinetic mechanism of refolding permitted simulation of the time courses and yields for activity recovery during the refolding of luciferase from about 1 to 25 micrograms/mL which are in excellent agreement with our previously reported data.}, pmid = {9048575}, keywords = {Circular Dichroism,Enzyme Activation,Fluorescent Dyes,Kinetics,Luciferases,Luciferases: chemistry,Luciferases: metabolism,Maleimides,nosource,Protein Folding,Protein Structure,Secondary,Vibrio,Vibrio: enzymology} }

@article{juInhibitionEukaryoticTranslation2010, title = {Inhibition of Eukaryotic Translation Elongation by Cycloheximide and Lactimidomycin.}, author = {Ju, Jianhua and {Schneider-Poetsch}, Tilman and Ju, Jianhua and Eyler, Daniel E. and Dang, Yongjun and Bhat, Shridhar and Merrick, William C. and Green, Rachel and Shen, Ben and Liu, Jun O.}, year = 2010, month = mar, journal = {Nature chemical biology}, volume = {6}, number = {3}, pages = {209–217}, publisher = {Nature Publishing Group}, issn = {1552-4469}, doi = {10.1038/nchembio.304}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2831214&tool=pmcentrez&rendertype=abstract http://dx.doi.org/10.1038/nchembio.304}, abstract = {Although the protein synthesis inhibitor cycloheximide (CHX) has been known for decades, its precise mechanism of action remains incompletely understood. The glutarimide portion of CHX is seen in a family of structurally related natural products including migrastatin, isomigrastatin and lactimidomycin (LTM). We found that LTM, isomigrastatin and analogs have a potent antiproliferative effect on tumor cell lines and selectively inhibit translation. A systematic comparative study of the effects of CHX and LTM on protein synthesis revealed both similarities and differences between the two inhibitors. Both LTM and CHX were found to block the translocation step in elongation. Footprinting experiments revealed protection of a single cytidine nucleotide (C3993) in the E-site of the 60S ribosomal subunit, thus defining a common binding pocket for the two inhibitors in the ribosome. These results shed new light on the molecular mechanism of inhibition of translation elongation by both CHX and LTM.}, pmid = {20118940}, keywords = {nosource} }

@article{kellerHP1Swi6Mediates2012, title = {{{HP1 Swi6 Mediates}} the {{Recognition}} and {{Destruction}} of {{Heterochromatic RNA Transcripts}}}, author = {Keller, Claudia and Adaixo, Ricardo and Stunnenberg, Rieka and Woolcock, Katrina J. and Hiller, Sebastian and B{"u}hler, Marc}, year = 2012, month = jun, journal = {Molecular Cell}, pages = {215–227}, issn = {1097-4164}, doi = {10.1016/j.molcel.2012.05.009}, url = {http://www.sciencedirect.com/science/article/pii/S1097276512003929 http://www.ncbi.nlm.nih.gov/pubmed/22683269}, abstract = {HP1 proteins are major components of heterochromatin, which is generally perceived to be an inert and transcriptionally inactive chromatin structure. Yet, HP1 binding to chromatin is highly dynamic and robust silencing of heterochromatic genes can involve RNA processing. Here, we demonstrate by a combination of in vivo and in vitro experiments that the fission yeast HP1(Swi6) protein guarantees tight repression of heterochromatic genes through RNA sequestration and degradation. Stimulated by positively charged residues in the hinge region, RNA competes with methylated histone H3K9 for binding to the chromodomain of HP1(Swi6). Hence, HP1(Swi6) binding to RNA is incompatible with stable heterochromatin association. We propose a model in which an ensemble of HP1(Swi6) proteins functions as a heterochromatin-specific checkpoint, capturing and priming heterochromatic RNAs for the RNA degradation machinery. Sustaining a functional checkpoint requires continuous exchange of HP1(Swi6) within heterochromatin, which explains the dynamic localization of HP1 proteins on heterochromatin.}, pmid = {22683269}, keywords = {nosource} } % == BibTeX quality report for kellerHP1Swi6Mediates2012: % ? Title looks like it was stored in title-case in Zotero

@article{xueTranscriptomeBasedNetworkAnalysis2014, title = {Transcriptome-{{Based Network Analysis Reveals}} a {{Spectrum Model}} of {{Human Macrophage Activation}}}, author = {Xue, Jia and Schmidt, Susanne V. V. and Sander, Jil and Draffehn, Astrid and Krebs, Wolfgang and Quester, Inga and DeNardo, Dominic and Gohel, Trupti D. D. and Emde, Martina and Schmidleithner, Lisa and Ganesan, Hariharasudan and {Nino-Castro}, Andrea and Mallmann, Michael R. R. and Labzin, Larisa and Theis, Heidi and Kraut, Michael and Beyer, Marc and Latz, Eicke and Freeman, Tom C. C. and Ulas, Thomas and Schultze, Joachim L. L. and Nardo, Dominic De and Gohel, Trupti D. D. and Emde, Martina and Schmidleithner, Lisa and Ganesan, Hariharasudan and {Nino-Castro}, Andrea and Mallmann, Michael R. R. and Labzin, Larisa and Theis, Heidi and Kraut, Michael and Beyer, Marc and Latz, Eicke and Freeman, Tom C. C. and Ulas, Thomas and Schultze, Joachim L. L.}, year = 2014, month = feb, journal = {Immunity}, volume = {40}, number = {2}, pages = {274–288}, publisher = {Elsevier Inc.}, issn = {10747613}, doi = {10.1016/j.immuni.2014.01.006}, url = {http://linkinghub.elsevier.com/retrieve/pii/S107476131400034X http://dx.doi.org/10.1016/j.immuni.2014.01.006}, abstract = {Macrophage activation is associated with profound transcriptional reprogramming. Although much progress has been made in the understanding of macrophage activation, polarization, and function, the transcriptional programs regulating these processesremain poorly characterized. We stimulated human macrophages with diverse activation signals, acquiring a data set of 299 macrophage transcriptomes. Analysis of this data set revealed a spectrum of macrophage activation states extending the current M1 versus M2-polarization model. Network analyses identified central transcriptional regulators associated with all macrophage activation complemented by regulators related to stimulus-specific programs. Applying these transcriptional programs to human alveolar macrophages from smokers and patients with chronic obstructive pulmonary disease (COPD) revealed an unexpected loss of inflammatory signatures in COPD patients. Finally, by integrating murine data from the ImmGen project we propose a refined, activation-independent core signature for human and murine macrophages. This resource serves as a framework for future research into regulation of macrophage activation in health and disease. copy; 2014 Elsevier Inc.}, isbn = {1074-7613}, pmid = {24530056}, keywords = {nosource} } % == BibTeX quality report for xueTranscriptomeBasedNetworkAnalysis2014: % ? Title looks like it was stored in title-case in Zotero

@article{requenaMolecularChaperonesLeishmania2015, title = {Molecular {{Chaperones}} of {{Leishmania}}: {{Central Players}} in {{Many Stress-Related}} and -{{Unrelated Physiological Processes}}.}, author = {Requena, Jose M. and Montalvo, Ana M. and Fraga, Jorge}, year = 2015, journal = {BioMed research international}, volume = {2015}, pages = {301326}, issn = {2314-6141}, doi = {10.1155/2015/301326}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4488524&tool=pmcentrez&rendertype=abstract}, abstract = {Molecular chaperones are key components in the maintenance of cellular homeostasis and survival, not only during stress but also under optimal growth conditions. Folding of nascent polypeptides is supported by molecular chaperones, which avoid the formation of aggregates by preventing nonspecific interactions and aid, when necessary, the translocation of proteins to their correct intracellular localization. Furthermore, when proteins are damaged, molecular chaperones may also facilitate their refolding or, in the case of irreparable proteins, their removal by the protein degradation machinery of the cell. During their digenetic lifestyle, Leishmania parasites encounter and adapt to harsh environmental conditions, such as nutrient deficiency, hypoxia, oxidative stress, changing pH, and shifts in temperature; all these factors are potential triggers of cellular stress. We summarize here our current knowledge on the main types of molecular chaperones in Leishmania and their functions. Among them, heat shock proteins play important roles in adaptation and survival of this parasite against temperature changes associated with its passage from the poikilothermic insect vector to the warm-blooded vertebrate host. The study of structural features and the function of chaperones in Leishmania biology is providing opportunities (and challenges) for drug discovery and improving of current treatments against leishmaniasis.}, pmid = {26167482}, keywords = {nosource} } % == BibTeX quality report for requenaMolecularChaperonesLeishmania2015: % ? Title looks like it was stored in title-case in Zotero

@article{besteiroProteinTurnoverDifferentiation2007, title = {Protein Turnover and Differentiation in {{Leishmania}}}, author = {Besteiro, S{'e}bastien and Williams, R. A. M. and Coombs, Graham H. and Mottram, Jeremy C.}, year = 2007, journal = {International Journal for Parasitology}, volume = {37}, number = {10}, pages = {1063–1075}, issn = {00207519}, doi = {10.1016/j.ijpara.2007.03.008}, abstract = {Leishmania occurs in several developmental forms and thus undergoes complex cell differentiation events during its life-cycle. Those are required to allow the parasite to adapt to the different environmental conditions. The sequencing of the genome of L. major has facilitated the identification of the parasite’s vast arsenal of proteolytic enzymes, a few of which have already been carefully studied and found to be important for the development and virulence of the parasite. This review focuses on these peptidases and their role in the cellular differentiation of Leishmania through their key involvement in a variety of degradative pathways in the lysosomal and autophagy networks. 2007 Australian Society for Parasitology Inc.}, isbn = {0020-7519 (Print)r0020-7519}, pmid = {17493624}, keywords = {Differentiation,Genome,Leishmania,nosource,Peptidase,Protease} }

@article{mouraCloningCharacterizationDNA2009, title = {Cloning and {{Characterization}} of {{DNA Polymerase}} g {{fromTrypanosoma}} Cruzi: {{Roles}} for {{Translesion Bypass}} of {{Oxidative Damage}}}, author = {{}de Moura, Michelle and {Schamber-Reis}, Bruno and Silva, Danielle and Rajao, Matheus and Teixeira, Santuza and Machado, Carlos}, year = 2009, journal = {Environmental and molecular mutagenesis}, volume = {50}, pages = {375–386}, doi = {10.1002/em/em.20450}, keywords = {nosource} }

@article{rogersTransmissionCutaneousLeishmaniasis2004, title = {Transmission of Cutaneous Leishmaniasis by Sand Flies Is Enhanced by Regurgitation of {{fPPG}}.}, author = {Rogers, Matthew E. and Ilg, Thomas and Nikolaev, Andrei V. and Ferguson, Michael A. J. and Bates, Paul A.}, year = 2004, journal = {Nature}, volume = {430}, number = {6998}, pages = {463–7}, issn = {1476-4687}, doi = {10.1038/nature02675}, url = {http://dx.doi.org/10.1038/nature02675}, abstract = {Sand flies are the exclusive vectors of the protozoan parasite Leishmania, but the mechanism of transmission by fly bite has not been determined nor incorporated into experimental models of infection. In sand flies with mature Leishmania infections the anterior midgut is blocked by a gel of parasite origin, the promastigote secretory gel. Here we analyse the inocula from Leishmania mexicana-infected Lutzomyia longipalpis sand flies. Analysis revealed the size of the infectious dose, the underlying mechanism of parasite delivery by regurgitation, and the novel contribution made to infection by filamentous proteophosphoglycan (fPPG), a component of promastigote secretory gel found to accompany the parasites during transmission. Collectively these results have important implications for understanding the relationship between the parasite and its vector, the pathology of cutaneous leishmaniasis in humans and also the development of effective vaccines and drugs. These findings emphasize that to fully understand transmission of vector-borne diseases the interaction between the parasite, its vector and the mammalian host must be considered together.}, isbn = {1476-4687 (Electronic)n0028-0836 (Linking)}, pmid = {15269771}, keywords = {Animals,Cutaneous,Cutaneous: parasitology,Cutaneous: transmission,Diptera,Diptera: parasitology,Diptera: physiology,Disease Progression,Disease Vectors,Female,Gastroesophageal Reflux,Inbred BALB C,Inbred CBA,Leishmania mexicana,Leishmania mexicana: physiology,Leishmaniasis,Membrane Proteins,Membrane Proteins: chemistry,Membrane Proteins: metabolism,Mice,nosource,Proteoglycans,Proteoglycans: chemistry,Proteoglycans: metabolism,Protozoan Proteins,Protozoan Proteins: chemistry,Protozoan Proteins: metabolism,Rabbits,Saliva,Saliva: physiology,Salivary Glands,Salivary Glands: secretion} }

@article{pradelNIMArelatedKinaseTbNRKC2006, title = {{{NIMA-related}} Kinase {{TbNRKC}} Is Involved in Basal Body Separation in {{Trypanosoma}} Brucei.}, author = {Pradel, Lydie C. and Bonhivers, M{'e}lanie and Landrein, Nicolas and Robinson, Derrick R.}, year = 2006, journal = {Journal of cell science}, volume = {119}, number = {Pt 9}, pages = {1852–1863}, issn = {0021-9533}, doi = {10.1242/jcs.02900}, url = {papers2://publication/doi/10.1242/jcs.02900}, abstract = {The NIMA-related kinase 2 (NEK 2) has important cell cycle functions related to centriole integrity and splitting. Trypanosoma brucei does not possess centrioles, however, cytokinesis is coupled to basal body separation events. Here we report the first functional characterisation of a T. brucei basal body-cytoskeletal NIMA-related kinase (NRK) protein, TbNRKC. The TbNRKC kinase domain has high amino acid identity with the human NEK1 kinase domain (50%) but also shares 42% identity with human NEK2. TbNRKC is expressed in bloodstream and procyclic cells and functions as a bona fide kinase in vitro. Remarkably, RNAi knockdown of TbNRKC and overexpression of kinase-dead TbNRKC in procyclic forms induces the accumulation of cells with four basal bodies, whereas overexpression of active protein produces supernumary basal bodies and blocks cytokinesis. TbNRKC is located on mature and immature basal bodies and is the first T. brucei NRK to be found associated with the basal body cytokinesis pathway.}, isbn = {0021-9533}, pmid = {16608878}, keywords = {basal body,cell cycle,cytokinesis,nek,nosource,Trypanosoma brucei} }

@article{wieseMitogenactivatedProteinMAP1998, title = {A Mitogen-Activated Protein ({{MAP}}) Kinase Homologue of {{Leishmania}} Mexicana Is Essential for Parasite Survival in the Infected Host}, author = {Wiese, Martin}, year = 1998, journal = {EMBO Journal}, volume = {17}, number = {9}, pages = {2619–2628}, issn = {02614189}, doi = {10.1093/emboj/17.9.2619}, abstract = {The parasitic protozoon Leishmania mexicana undergoes two major developmental stages in its life cycle exhibiting profound physiological and morphological differences, the promastigotes in the insect vector and the amastigotes in mammalian macrophages. A deletion mutant, Deltalmsap1/2, for the secreted acid phosphatase (SAP) gene locus, comprising the two SAP genes separated by an intergenic region of approximately 11.5 kb, lost its ability to cause a progressive disease in Balb/c mice. While in vitro growth of promastigotes, invasion of host cells and differentiation from promastigotes to amastigotes was indistinguishable from the wild-type, the mutant parasites ceased to proliferate when transformed to amastigotes in infected macrophages or in a macrophage-free in vitro differentiation system, suggesting a stage-specific growth arrest. This phenotype could be reverted by complementation with 6 kb of the intergenic region of the SAP gene locus. Sequence analysis identified two open reading frames, both encoding single copy genes; one gene product shows high homology to mitogen-activated protein (MAP) kinases. Complementation experiments revealed that the MAP kinase homologue, designated LMPK, is required and is sufficient to restore the infectivity of the Deltalmsap1/2 mutant. Therefore, LMPK is a kinase that is essential for the survival of L.mexicana in the infected host by affecting the cell division of the amastigotes.}, isbn = {0261-4189 (Print)r0261-4189 (Linking)}, pmid = {9564044}, keywords = {Attenuated strain,Cell division,Deletion mutant,Leishmania mexicana,Mitogen-activated protein kinase,nosource} }

@article{holochRNAmediatedEpigeneticRegulation2015, title = {{{RNA-mediated}} Epigenetic Regulation of Gene Expression}, author = {Holoch, Daniel and Moazed, Danesh}, year = 2015, journal = {Nature Publishing Group}, volume = {16}, number = {2}, pages = {71–84}, publisher = {Nature Publishing Group}, issn = {1471-0056}, doi = {10.1038/nrg3863}, url = {http://dx.doi.org/10.1038/nrg3863}, keywords = {nosource} }

@article{fernandesDualTranscriptomeProfiling2016, title = {Dual {{Transcriptome Profiling}} of {{Leishmania}} -{{Infected Human Macrophages Reveals Distinct Reprogramming Signatures}}}, author = {Fernandes, Maria Cecilia and Dillon, Laura A. L. and Belew, Trey and Bravo, Corrada and Mosser, David M.}, year = 2016, journal = {mBIO}, volume = {7}, number = {3}, pages = {1–16}, doi = {10.1128/mBio.00027-16.Invited}, keywords = {nosource} } % == BibTeX quality report for fernandesDualTranscriptomeProfiling2016: % ? Title looks like it was stored in title-case in Zotero

@article{handmanLeishmaniaPromastigoteSurface1995, title = {The {{Leishmania}} Promastigote Surface Antigen 2 Complex Is Differentially Expressed during the Parasite Life Cycle}, author = {Handman, Emanuela and Osborn, Amelia H. and Symons, Fiona and {}van Driel, Rosemary and Cappai, Roberto}, year = 1995, journal = {Molecular and Biochemical Parasitology}, volume = {74}, number = {2}, pages = {189–200}, issn = {01666851}, doi = {10.1016/0166-6851(95)02500-6}, abstract = {The promastigote surface antigen 2 (PSA-2) complex comprises a family of antigenically similar polypeptides of Mr 96 000, 80 000 and 50 000, anchored to the membrane with glycosylphosphatidylinositol. Although PSA-2 was initially detected only in promastigotes, Northern blot analysis indicated that mRNA transcripts are also present in amastigotes. Unlike the situation in promastigotes, where at least four major transcripts (2.6-5.3 kb) were detected, only one major (2.6 kb) and two minor transcripts were present in amastigotes. A cDNA clone encoding a member of the PSA-2 family expressed in amastigotes was isolated using DNA probes. The predicted protein sequence of Mr 40 000 is distinct from promastigote sequences, but shows significant similarity to previously described members of the family from L. major and L. amazonensis. Antibodies to the carboxyl terminal sequence conserved in all L. major PSA-2 studied to date, as well as antibodies affinity purified on the amastigote cDNA-derived polypeptide recognized a major Mr 50 000 amastigote polypeptide. Immuno-electron microscopy localized both promastigote and amastigote PSA-2 to the cell surface. The expression of PSA-2 polypeptides during the transformation of amastigotes into promastigotes was ordered in a time-dependent manner, with the promastigote Mr 80 000 polypeptide appearing first, followed by the Mr 96 000 polypeptide. In contrast to the glycosylphosphatidylinositol anchor of promastigote PSA-2, which could be hydrolysed by phosphatidylinositol-specific phospholipase C, the amastigote form was resistant to this enzyme. ?? 1995.}, isbn = {0166-6851 (Print)r0166-6851 (Linking)}, pmid = {8719160}, keywords = {Amastigote,Leishmania major,N-Glycanase,nosource,Phosphatidylinositol specific phospholipase C,Promastigote surface antigen-2} }

@article{kuzmenokRetardationCellCycle2005, title = {Retardation of Cell Cycle Progression of Macrophages from {{G1}} to {{S}} Phase by {{ICAM-L}} from {{Leishmania}}}, author = {Kuzmenok, Oleg I. and Chiang, Su Chi and Lin, Yi Chun and Lee, Sho Tone}, year = 2005, journal = {International Journal for Parasitology}, volume = {35}, number = {14}, pages = {1547–1555}, issn = {00207519}, doi = {10.1016/j.ijpara.2005.08.006}, abstract = {Leishmania, an obligate intracellular parasite of host macrophages, infects the macrophage through receptor-mediated phagocytosis that either activates or deactivates macrophages to eliminate the parasite or allow the parasite to grow intracellularly. ICAM-L, an intercellular adhesion molecule from L. amazonensis, results in lower MTT tests and proliferative responses of macrophages when incubated in vitro. The inhibition of cell proliferation, however, results from temporary retardation of the cell cycle progression at the G1 to S phase transition rather than cell death. The retardation is due to the upregulation of two CKI proteins, p21 and p27, in a p53-independent manner which, control the G1 to S phase transition checkpoint. ?? 2005 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.}, isbn = {0020-7519 (Print)n0020-7519 (Linking)}, pmid = {16188262}, keywords = {Cell cycle progression,ICAM-L,Leishmania,Macrophages,nosource} }

@article{romiguierContrastingGCcontentDynamics2010, title = {Contrasting {{GC-content}} Dynamics across 33 Mammalian Genomes: {{Relationship}} with Life-History Traits and Chromosome Sizes}, author = {Romiguier, Jonathan and Ranwez, Vincent and Douzery, Emmanuel J. P. and Galtier, Nicolas}, year = 2010, journal = {Genome Research}, volume = {20}, number = {8}, pages = {1001–1009}, issn = {10889051}, doi = {10.1101/gr.104372.109}, abstract = {The origin, evolution, and functional relevance of genomic variations in GC content are a long-debated topic, especially in mammals. Most of the existing literature, however, has focused on a small number of model species and/or limited sequence data sets. We analyzed more than 1000 orthologous genes in 33 fully sequenced mammalian genomes, reconstructed their ancestral isochore organization in the maximum likelihood framework, and explored the evolution of third-codon position GC content in representatives of 16 orders and 27 families. We showed that the previously reported erosion of GC-rich isochores is not a general trend. Several species (e.g., shrew, microbat, tenrec, rabbit) have independently undergone a marked increase in GC content, with a widening gap between the GC-poorest and GC-richest classes of genes. The intensively studied apes and (especially) murids do not reflect the general placental pattern. We correlated GC-content evolution with species life-history traits and cytology. Significant effects of body mass and genome size were detected, with each being consistent with the GC-biased gene conversion model.}, isbn = {1088-9051}, pmid = {20530252}, keywords = {nosource} }

@article{cunninghamPteridineSalvageThroughout2001, title = {Pteridine Salvage throughout the {{Leishmania}} Infectious Cycle: Implications for Antifolate Chemotherapy}, author = {Cunningham, Mark L. and Beverley, Stephen M.}, year = 2001, journal = {Molecular and Biochemical Parasitology}, volume = {113}, number = {2}, pages = {199–213}, issn = {01666851}, doi = {10.1016/S0166-6851(01)00213-4}, url = {http://www.sciencedirect.com/science/article/pii/S0166685101002134}, abstract = {Protozoan parasites of the trypanosomatid genus Leishmania are pteridine auxotrophs, and have evolved an elaborate and versatile pteridine salvage network capable of accumulating and reducing pteridines. This includes biopterin and folate transporters (BT1 and FT1), pteridine reductase (PTR1), and dihydrofolate reductase–thymidylate synthase (DHFR-TS). Notably, PTR1 is a novel alternative pteridine reductase whose activity is resistant to inhibition by standard antifolates. In cultured promastigote parasites, PTR1 can function as a metabolic by-pass under conditions of DHFR inhibition and thus reduce the efficacy of chemotherapy. To test whether pteridine salvage occurred in the infectious stage of the parasite, we examined several pathogenic species of Leishmania and the disease-causing amastigote stage that resides within human macrophages. To accomplish this we developed a new sensitive HPLC-based assay for PTR1 activity. These studies established the existence of the pteridine salvage pathway throughout the infectious cycle of Leishmania, including amastigotes. In general, activities were not well correlated with RNA transcript levels, suggesting the occurrence of at least two different modes of post-transcriptional regulation. Thus, pteridine salvage by amastigotes may account for the clinical inefficacy of antifolates against leishmaniasis, and ultimately provide insights into how this may be overcome in the future.}, isbn = {0166-6851 (Print)r0166-6851 (Linking)}, pmid = {11295174}, keywords = {Biopterin transporter,biopterin transporter 1,BT1,Developmental regulation,DHFR-TS,dihydrobiopterin,dihydrofolate,Dihydrofolate reductase,dihydrofolate reductase-thymidylate synth,Folate transporter,folate transporter 1,FT1,H2-biopterin,H2-folate,H4-biopterin,H4-folate,HPLC biopterin assay,nosource,Pteridine reductase,pteridine reductase 1,PTR1,tetrahydrobiopterin,tetrahydrofolate} }

@article{deyCharacterizationLeishmaniaStagespecific2010, title = {Characterization of a {{Leishmania}} Stage-Specific Mitochondrial Membrane Protein That Enhances the Activity of Cytochrome c Oxidase and Its Role in Virulence}, author = {Dey, Ranadhir and Meneses, Claudio and Salotra, Poonam and Kamhawi, Shaden and Nakhasi, Hira L. and Duncan, Robert}, year = 2010, journal = {Molecular Microbiology}, volume = {77}, number = {2}, pages = {399–414}, issn = {0950382X}, doi = {10.1111/j.1365-2958.2010.07214.x}, abstract = {Leishmaniasis is caused by the dimorphic protozoan parasite Leishmania. Differentiation of the insect form, promastigotes, to the vertebrate form, amastigotes, and survival inside the vertebrate host accompanies a drastic metabolic shift. We describe a gene first identified in amastigotes that is essential for survival inside the host. Gene expression analysis identified a 27 kDa protein-encoding gene (Ldp27) that was more abundantly expressed in amastigotes and metacyclic promastigotes than in procyclic promastigotes. Immunofluorescence and biochemical analysis revealed that Ldp27 is a mitochondrial membrane protein. Co-immunoprecipitation using antibodies to the cytochrome c oxidase (COX) complex, present in the inner mitochondrial membrane, placed the p27 protein in the COX complex. Ldp27 gene-deleted parasites (Ldp27(-/-)) showed significantly less COX activity and ATP synthesis than wild type in intracellular amastigotes. Moreover, the Ldp27(-/-) parasites were less virulent both in human macrophages and in BALB/c mice. These results demonstrate that Ldp27 is an important component of an active COX complex enhancing oxidative phosphorylation specifically in infectious metacyclics and amastigotes and promoting parasite survival in the host. Thus, Ldp27 can be explored as a potential drug target and parasites devoid of the p27 gene could be considered as a live attenuated vaccine candidate against visceral leishmaniasis.}, isbn = {1047053508823}, pmid = {20497506}, keywords = {nosource} }

@article{pliufliuZeroInflatedPoissonModel2016, title = {A {{Zero-Inflated Poisson Model}} for {{Insertion Tolerance Analysis}} of {{Genes Based}} on {{Tn-seq Data}}}, author = {P Liu F Liu, C Wang, Z Wu, Q Zhang}, year = 2016, journal = {Bioinformatics}, keywords = {nosource} }

@article{dillonSimultaneousTranscriptionalProfiling2015, title = {Simultaneous Transcriptional Profiling of {{Leishmania}} Major and Its Murine Macrophage Host Cell Reveals Insights into Host-Pathogen Interactions}, author = {Dillon, Laura A. L. and Suresh, Rahul and Okrah, Kwame and Bravo, Hector Corrada and Mosser, David M.}, year = 2015, journal = {BMC Genomics}, pages = {1–15}, publisher = {BMC Genomics}, issn = {1471-2164}, doi = {10.1186/s12864-015-2237-2}, url = {http://dx.doi.org/10.1186/s12864-015-2237-2}, keywords = {correspondence,differentiation,Differentiation,edu,elsayed,H,host-pathogen interactions,leishmania,Leishmania,macrophage,mouse,nosource,rna-seq,RNA-seq,transcriptome,Transcriptome,umd} }

@article{grabherrFulllengthTranscriptomeAssembly2011, title = {Full-Length Transcriptome Assembly from {{RNA-Seq}} Data without a Reference Genome}, author = {Grabherr, Manfred G. and Haas, Brian J. and Yassour, Moran and Levin, Joshua Z. and Thompson, Dawn A. and Amit, Ido and Adiconis, Xian and Fan, Lin and Raychowdhury, Raktima and Zeng, Qiandong and Chen, Zehua and Mauceli, Evan and Hacohen, Nir and Gnirke, Andreas and Rhind, Nicholas and Palma, Federica and Birren, Bruce W. and Nusbaum, Chad and {Lindblad-toh}, Kerstin and Friedman, Nir and Regev, Aviv}, year = 2011, volume = {29}, number = {7}, doi = {10.1038/nbt.1883}, keywords = {nosource} } % == BibTeX quality report for grabherrFulllengthTranscriptomeAssembly2011: % Missing required field ‘journal’

@article{silvermanProteomicAnalysisSecretome2008, title = {Proteomic Analysis of the Secretome of {{Leishmania}} Donovani.}, author = {Silverman, J. Maxwell and Chan, Simon K. and Robinson, Dale P. and Dwyer, Dennis M. and Nandan, Devki and Foster, Leonard J. and Reiner, Neil E.}, year = 2008, journal = {Genome biology}, volume = {9}, number = {2}, pages = {R35}, issn = {1465-6906}, doi = {10.1186/gb-2008-9-2-r35}, abstract = {BACKGROUND: Leishmania and other intracellular pathogens have evolved strategies that support invasion and persistence within host target cells. In some cases the underlying mechanisms involve the export of virulence factors into the host cell cytosol. Previous work from our laboratory identified one such candidate leishmania effector, namely elongation factor-1alpha, to be present in conditioned medium of infectious leishmania as well as within macrophage cytosol after infection. To investigate secretion of potential effectors more broadly, we used quantitative mass spectrometry to analyze the protein content of conditioned medium collected from cultures of stationary-phase promastigotes of Leishmania donovani, an agent of visceral leishmaniasis. RESULTS: Analysis of leishmania conditioned medium resulted in the identification of 151 proteins apparently secreted by L. donovani. Ratios reflecting the relative amounts of each leishmania protein secreted, as compared to that remaining cell associated, revealed a hierarchy of protein secretion, with some proteins secreted to a greater extent than others. Comparison with an in silico approach defining proteins potentially exported along the classic eukaryotic secretion pathway suggested that few leishmania proteins are targeted for export using a classic eukaryotic amino-terminal secretion signal peptide. Unexpectedly, a large majority of known eukaryotic exosomal proteins was detected in leishmania conditioned medium, suggesting a vesicle-based secretion system. CONCLUSION: This analysis shows that protein secretion by L. donovani is a heterogeneous process that is unlikely to be determined by a classical amino-terminal secretion signal. As an alternative, L. donovani appears to use multiple nonclassical secretion pathways, including the release of exosome-like microvesicles.}, isbn = {1465-6914 (Electronic) 1465-6906 (Linking)}, pmid = {18282296}, keywords = {nosource} }

@article{kimaIdentificationLeishmaniaProteins2010, title = {Identification of {{Leishmania Proteins Preferentially Released}} in {{Infected Cells Using Change Mediated Antigen Technology}} ({{CMAT}})}, author = {Kima, Peter E. and Bonilla, J. Alfredo and Cho, Eumin and Ndjamen, Blaise and Canton, Johnathan and Leal, Nicole and Handfield, Martin}, year = 2010, journal = {PLoS neglected tropical diseases}, volume = {4}, number = {10}, pages = {19}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0000842}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2950143&tool=pmcentrez&rendertype=abstract}, abstract = {Although Leishmania parasites have been shown to modulate their host cell’s responses to multiple stimuli, there is limited evidence that parasite molecules are released into infected cells. In this study, we present an implementation of the change mediated antigen technology (CMAT) to identify parasite molecules that are preferentially expressed in infected cells. Sera from mice immunized with cell lysates prepared from L. donovani or L. pifanoi-infected macrophages were adsorbed with lysates of axenically grown amastigotes of L. donovani or L. pifanoi, respectively, as well as uninfected macrophages. The sera were then used to screen inducible parasite expression libraries constructed with genomic DNA. Eleven clones from the L. pifanoi and the L. donovani screen were selected to evaluate the characteristics of the molecules identified by this approach. The CMAT screen identified genes whose homologs encode molecules with unknown function as well as genes that had previously been shown to be preferentially expressed in the amastigote form of the parasite. In addition a variant of Tryparedoxin peroxidase that is preferentially expressed within infected cells was identified. Antisera that were then raised to recombinant products of the clones were used to validate that the endogenous molecules are preferentially expressed in infected cells. Evaluation of the distribution of the endogenous molecules in infected cells showed that some of these molecules are secreted into parasitophorous vacuoles (PVs) and that they then traffic out of PVs in vesicles with distinct morphologies. This study is a proof of concept study that the CMAT approach can be applied to identify putative Leishmania parasite effectors molecules that are preferentially expressed in infected cells. In addition we provide evidence that Leishmania molecules traffic out of the PV into the host cell cytosol and nucleus.}, isbn = {1935-2735 (Electronic)r1935-2727 (Linking)}, pmid = {20957202}, keywords = {animals,antibodies,antigens,cells,cultured,gene expression profiling,gene expression profiling methods,gene library,host parasite interactions,leishmania,leishmania genetics,leishmania pathogenicity,macrophages,macrophages parasitology,mice,nosource,protozoan,protozoan biosynthesis,protozoan genetics,protozoan immunology,protozoan proteins,protozoan proteins biosynthesis,protozoan proteins genetics} } % == BibTeX quality report for kimaIdentificationLeishmaniaProteins2010: % ? Title looks like it was stored in title-case in Zotero

@article{silvermanExosomesOtherMicrovesicles2011, title = {Exosomes and Other Microvesicles in Infection Biology: Organelles with Unanticipated Phenotypes}, author = {Silverman, Judith Maxwell and Reiner, Neil E.}, year = 2011, journal = {Cellular Microbiology}, volume = {13}, number = {1}, pages = {1–9}, issn = {14625814}, doi = {10.1111/j.1462-5822.2010.01537.x}, url = {http://doi.wiley.com/10.1111/j.1462-5822.2010.01537.x}, keywords = {nosource} }

@article{falconUsingGOstatsTest2007, title = {Using {{GOstats}} to Test Gene Lists for {{GO}} Term Association}, author = {Falcon, S. {~A} and Gentleman, R.}, year = 2007, month = jan, journal = {Bioinformatics (Oxford, England)}, volume = {23}, number = {2}, pages = {257–258}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btl567}, abstract = {MOTIVATION: Functional analyses based on the association of Gene Ontology (GO) terms to genes in a selected gene list are useful bioinformatic tools and the GOstats package has been widely used to perform such computations. In this paper we report significant improvements and extensions such as support for conditional testing. RESULTS: We discuss the capabilities of GOstats, a Bioconductor package written in R, that allows users to test GO terms for over or under-representation using either a classical hypergeometric test or a conditional hypergeometric that uses the relationships among GO terms to decorrelate the results. AVAILABILITY: GOstats is available as an R package from the Bioconductor project: http://bioconductor.org}, langid = {english}, pmid = {17098774}, keywords = {Algorithms,Data Interpretation Statistical,Database Management Systems,Databases Protein,Gene Expression Profiling,Information Storage and Retrieval,Natural Language Processing,Proteins,Software,Terminology as Topic}, file = {/home/trey/Zotero/storage/ST97B9VL/Falcon and Gentleman - 2007 - Using GOstats to test gene lists for GO term assoc.pdf} } % == BibTeX quality report for falconUsingGOstatsTest2007: % ? unused Journal abbr (“Bioinformatics”) % ? unused Library catalog (“PubMed”)

@article{ogataKEGGKyotoEncyclopedia1999, title = {{{KEGG}}: {{Kyoto}} Encyclopedia of Genes and Genomes}, author = {Ogata, Hiroyuki and Goto, Susumu and Sato, Kazushige and Fujibuchi, Wataru and Bono, Hidemasa and Kanehisa, Minoru}, year = 1999, journal = {Nucleic Acids Research}, volume = {27}, number = {1}, pages = {29–34}, issn = {03051048}, doi = {10.1093/nar/27.1.29}, abstract = {Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of biochemical pathways including most of the known metabolic pathways and some of the known regulatory pathways. The pathway information is also represented by the ortholog group tables summarizing orthologous and paralogous gene groups among different organisms. KEGG maintains the GENES database for the gene catalogs of all organisms with complete genomes and selected organisms with partial genomes, which are continuously re-annotated, as well as the LIGAND database for chemical compounds and enzymes. Each gene catalog is associated with the graphical genome map for chromosomal locations that is represented by Java applet. In addition to the data collection efforts, KEGG develops and provides various computational tools, such as for reconstructing biochemical pathways from the complete genome sequence and for predicting gene regulatory networks from the gene expression profiles. The KEGG databases are daily updated and made freely available (http://www.genome.ad.jp/kegg/).}, isbn = {0305-1048 (Print)r0305-1048 (Linking)}, pmid = {9847135}, keywords = {nosource} }

@article{williamsCharacterizationUnusualFamilies2009, title = {Characterization of Unusual Families of {{ATG8-like}} Proteins and {{ATG12}} in the Protozoan Parasite {{Leishmania}} Major}, author = {Williams, Roderick A. M. and Woods, Kerry L. and Juliano, Luiz and Mottram, Jeremy C. and Coombs, Graham H.}, year = 2009, journal = {Autophagy}, volume = {5}, number = {2}, pages = {159–172}, issn = {15548627}, doi = {10.4161/auto.5.2.7328}, abstract = {Leishmania major possesses, apparently uniquely, four families of ATG8-like genes, designated ATG8, ATG8A, ATG8B and ATG8C, and 25 genes in total. L. major ATG8 and examples from the ATG8A, ATG8B and ATG8C families are able to complement a Saccharomyces cerevisiae ATG8-deficient strain, indicating functional conservation. Whereas ATG8 has been shown to form putative autophagosomes during differentiation and starvation of L. major, ATG8A primarily form puncta in response to starvation-suggesting a role for ATG8A in starvation-induced autophagy. Recombinant ATG8A was processed at the scissile glycine by recombinant ATG4.2 but not ATG4.1 cysteine peptidases of L. major and, consistent with this, ATG4.2-deficient L. major mutants were unable to process ATG8A and were less able to withstand starvation than wild-type cells. GFP-ATG8-containing puncta were less abundant in ATG4.2 overexpression lines, in which unlipidated ATG8 predominated, which is consistent with ATG4.2 being an ATG8-deconjugating enzyme as well as an ATG8A-processing enzyme. In contrast, recombinant ATG8, ATG8B and ATG8C were all processed by ATG4.1, but not by ATG4.2. ATG8B and ATG8C both have a distinct subcellular location close to the flagellar pocket, but the occurrence of the GFP-labeled puncta suggest that they do not have a role in autophagy. L. major genes encoding possible ATG5, ATG10 and ATG12 homologues were found to complement their respective S. cerevisiae mutants, and ATG12 localized in part to ATG8-containing puncta, suggestive of a functional ATG5-ATG12 conjugation pathway in the parasite. L. major ATG12 is unusual as it requires C-terminal processing by an as yet unidentified peptidase.}, isbn = {0044141548}, pmid = {19066473}, keywords = {ATG12,ATG4,ATG8,Autophagy,Leishmania,nosource,Protozoan parasite} }

@article{dupeAlbadomainProteinContributes2013, title = {An {{Alba-domain}} Protein Contributes to the Stage-Regulated Stability of Amastin Transcripts in {{Leishmania}}}, author = {Dup{'e}, Aur{'e}lien and Dumas, Carole and Papadopoulou, Barbara}, year = 2013, journal = {Molecular Microbiology}, volume = {91}, number = {December 2013}, pages = {548–561}, issn = {0950382X}, doi = {10.1111/mmi.12478}, abstract = {Leishmania infantum promastigotes differentiate into amastigote forms within the phagolysosome of mammalian macrophages causing visceral leishmaniasis. Delta-amastins belong to a multigenic surface protein family of potential virulence factors that are specifically expressed in the amastigote life cycle stage through distinct regulatory elements in the 3’ UTR controlling either mRNA stability or translation. Here, we provide novel insights on trans-acting factors regulating amastin developmental gene expression. Using RNA affinity chromatography with a 300 nt regulatory region within the amastin 3’ UTR as bait, we identified an Alba-domain protein of 25 kDa (LiAlba20) as a specific amastin mRNA-binding partner. Genomic depletion of LiAlba20 results in amastin mRNA destabilization specifically in amastigotes, supporting a role of LiAlba20 in amastin gene regulation. As shown by comparative DNA microarray analysis, several delta-amastin transcripts but also other known developmentally regulated transcripts were downregulated in LiAlba20-/- knockout parasites. Inactivation of the second Alba-domain gene, LiAlba13, does not seem to affect amastin mRNA stability in either life stage of the parasite. These data indicate an important role of Alba-domain proteins in the regulation of Leishmania differentially expressed transcripts and open a new field of investigation for better understanding mechanisms contributing to post-transcriptional control in these parasites.}, pmid = {24620725}, keywords = {nosource} }

@article{tyersProteolysisCellCycle2000, title = {Proteolysis and the Cell Cycle: {{With}} This {{RING I}} Do Thee Destroy}, author = {Tyers, Mike and Jorgensen, Paul}, year = 2000, journal = {Current Opinion in Genetics and Development}, volume = {10}, number = {1}, pages = {54–64}, issn = {0959437X}, doi = {10.1016/S0959-437X(99)00049-0}, abstract = {The ubiquitin system drives the cell division cycle by the timely destruction of numerous regulatory proteins. Remarkably, the two main activities that catalyze substrate ubiquitination in the cell cycle, the Skp1-Cdc53/cullin-F-box protein (SCF) complexes and the anaphase-promoting complex/cyclosome (APC/C), define a new superfamily of E3 ubiquitin ligases, all based on related cullin and RING-H2 finger protein subunits. The circuits that interconnect the SCF, APC/C and cyclin-dependent kinase activities form a master oscillator that coordinates the replication and segregation of the genome.}, isbn = {0959-437X (Print)r0959-437X (Linking)}, pmid = {10679394}, keywords = {nosource} }

@article{williamsEndosomeSortingAutophagy2006, title = {Endosome {{Sorting}} and {{Autophagy Are Essential}} for {{Differentiation}} and {{Virulence}} of {{Leishmania}} Major}, author = {Williams, Roderick A. M. and Morrison, Lesley S. and Coombs, Graham H. and Mottram, Jeremy C.}, year = 2006, journal = {The Journal of biological chemistry}, volume = {281}, number = {16}, pages = {11384–11396}, doi = {10.1074/jbc.M512307200}, keywords = {nosource} }

@article{ilgProteophosphoglycansLeishmania2000, title = {Proteophosphoglycans of {{Leishmania}}}, author = {Ilg, Thomas}, year = 2000, journal = {Parasitology Today}, volume = {16}, number = {11}, pages = {489–497}, issn = {01694758}, doi = {10.1016/S0169-4758(00)01791-9}, url = {http://www.sciencedirect.com/science/article/pii/S0169475800017919}, abstract = {Proteophosphoglycans are an expanding family of highly glycosylated Leishmania proteins with many unusual and some unique structural features. The novel protein-glycan linkage in proteophosphoglycans - phosphoglycosylation of Ser by lipophosphoglycan-like structures - emerges as a major form of protein glycosylation in Leishmania. Here, Thomas Ilg reviews the chemical structure, the ultrastructure, the genes and the potential functions of different members of this novel family of parasite glycoproteins. Copyright (C) 2000 Elsevier Science Ltd.}, isbn = {0169-4758 (Print)}, pmid = {11063860}, keywords = {nosource} } % == BibTeX quality report for ilgProteophosphoglycansLeishmania2000: % ? Title looks like it was stored in title-case in Zotero

@article{kramerTransactingProteinsRegulating2011, title = {Trans-Acting Proteins Regulating {{mRNA}} Maturation, Stability and Translation in Trypanosomatids}, author = {Kramer, Susanne and Carrington, Mark}, year = 2011, journal = {Trends in Parasitology}, volume = {27}, number = {1}, pages = {23–30}, publisher = {Elsevier Ltd}, issn = {14714922}, doi = {10.1016/j.pt.2010.06.011}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1471492210001212}, keywords = {nosource} }

@article{huynhIronAcquisitionHost2008, title = {Iron Acquisition within Host Cells and the Pathogenicity of {{Leishmania}}}, author = {Huynh, Chau and Andrews, Norma W.}, year = 2008, journal = {Cellular Microbiology}, volume = {10}, number = {December 2007}, pages = {293–300}, issn = {14625814}, doi = {10.1111/j.1462-5822.2007.01095.x}, abstract = {Iron is an essential cofactor for several enzymes and metabolic pathways, in both microbes and in their eukaryotic hosts. To avoid toxicity, iron acquisition is tightly regulated. This represents a particular challenge for pathogens that reside within the endocytic pathway of mammalian cells, because endosomes and lysosomes are gradually depleted in iron by host transporters. An important player in this process is Nramp1 (Slc11a1), a proton efflux pump that translocates Fe(2+) and Mn(2+) ions from macrophage lysosomes/phagolysosomes into the cytosol. Mutations in Nramp1 cause susceptibility to infection with the bacteria Salmonella and Mycobacteria and the protozoan Leishmania, indicating that an available pool of intraphagosomal iron is critical for the intracellular survival and replication of these pathogens. Salmonella and Mycobacteria are known to express iron transporter systems that effectively compete with host transporters for iron. Until recently, however, very little was known about the molecular strategy used by Leishmania for survival in the iron-poor environment of macrophage phagolysosomes. It is now clear that intracellular residence induces Leishmania amazonensis to express LIT1, a ZIP family membrane Fe(2+) transporter that is required for intracellular growth and virulence.}, isbn = {1462-5822 (Electronic)r1462-5814 (Linking)}, pmid = {18070118}, keywords = {nosource} }

@article{dufernezPresenceFourIroncontaining2006, title = {The Presence of Four Iron-Containing Superoxide Dismutase Isozymes in {{Trypanosomatidae}}: {{Characterization}}, Subcellular Localization, and Phylogenetic Origin in {{Trypanosoma}} Brucei}, author = {Dufernez, Fabienne and Yernaux, C{'e}dric and Gerbod, Delphine and No{"e}l, Christophe and Chauvenet, M{'e}lanie and Wintjens, Ren{'e} and Edgcomb, Virginia P. and Capron, Monique and Opperdoes, Fred R. and Viscogliosi, Eric}, year = 2006, journal = {Free Radical Biology and Medicine}, volume = {40}, number = {2}, pages = {210–225}, issn = {08915849}, doi = {10.1016/j.freeradbiomed.2005.06.021}, abstract = {Metalloenzymes such as the superoxide dismutases (SODs) form part of a defense mechanism that helps protect obligate and facultative aerobic organisms from oxygen toxicity and damage. Here, we report the presence in the trypanosomatid genomes of four SOD genes: soda, sodb1, sodb2, and a newly identified sodc. All four genes of Trypanosoma brucei have been cloned (Tbsods), sequenced, and overexpressed in Escherichia coli and shown to encode active dimeric FeSOD isozymes. Homology modeling of the structures of all four enzymes using available X-ray crystal structures of homologs showed that the four TbSOD structures were nearly identical. Subcellular localization using GFP-fusion proteins in procyclic insect trypomastigotes shows that TbSODB1 is mainly cytosolic, with a minor glycosomal component, TbSODB2 is mainly glycosomal with some activity in the cytosol, and TbSODA and TbSODC are both mitochondrial isozymes. Phylogenetic studies of all available trypanosomatid SODs and 106 dimeric FeSODs and closely related cambialistic dimeric SOD sequences suggest that the trypanosomatid SODs have all been acquired by more than one event of horizontal gene transfer, followed by events of gene duplication. 2005 Elsevier Inc. All rights reserved.}, isbn = {0891-5849 (Print)r0891-5849 (Linking)}, pmid = {16413404}, keywords = {Antioxidant enzymes,Evolution,Free radical,nosource,Structural models,Subcellular localization,Superoxide dismutase,Trypanosoma} }

@article{rosenzweigRetoolingLeishmaniaMetabolism2007, title = {Retooling {{Leishmania}} Metabolism: From Sand Fly Gut to Human Macrophage}, author = {Rosenzweig, D. and Smith, D. and Opperdoes, F. and Stern, S. and Olafson, R. W. and Zilberstein, D.}, year = 2007, journal = {The FASEB Journal}, volume = {22}, number = {2}, pages = {590–602}, issn = {0892-6638}, doi = {10.1096/fj.07-9254com}, url = {http://www.fasebj.org/cgi/doi/10.1096/fj.07-9254com}, keywords = {gene expression,inside a specific host,intracellular differen-,intracellular parasitism is a,metabolomics,nosource,organism invades and proliferates,process in which an,proteomics,tiation} }

@article{plewesIronSuperoxideDismutases2003, title = {Iron {{Superoxide Dismutases Targeted}} to the {{Glycosomes}} of {{Leishmania}} Chagasi {{Are Important}} for {{Survival}}}, author = {{}a Plewes, Katherine and Barr, Stephen D. and Gedamu, Lashitew}, year = 2003, journal = {Infection and Immunity}, volume = {71}, number = {10}, pages = {5910–5920}, issn = {00199567}, doi = {10.1128/IAI.71.10.5910}, abstract = {Kinetoplastid glycosomes contain a variety of metabolic activities, such as glycolysis, beta-oxidation of fatty acids, lipid biosynthesis, and purine salvage. One advantage of sequestering metabolic activities is the avoidance of cellular oxidative damage by reactive oxygen species produced as a by-product of metabolism. Little is known about how glycosomes themselves withstand these toxic metabolites. We previously isolated an iron superoxide dismutase from Leishmania chagasi that is expressed at low levels in the early logarithmic promastigote stage and increases toward the stationary promastigote and amastigote stages. We have since identified a second highly homologous Lcfesodb gene that is expressed at high levels in the early logarithmic promastigote stage and decreases toward the stationary promastigote and amastigote stages. Localization studies using green fluorescent protein fusions have revealed that LcFeSODB1 and LcFeSODB2 are localized within the glycosomes by the last three amino acids of their carboxyl termini. To better understand the specific role that FeSODB plays in parasite growth and survival, a single-allele knockout of the Lcfesodb1 gene was generated. The parasites with these genes exhibited a significant reduction in growth when endogenous superoxide levels were increased with paraquat in culture. Furthermore, the FeSODB1-deficient parasites exhibited a significant reduction in survival within human macrophages. Our results suggest that LcFeSODB plays an important role in parasite growth and survival by protecting glycosomes from superoxide toxicity.}, isbn = {0019-9567 (Print)r0019-9567 (Linking)}, pmid = {14500512}, keywords = {00 0 doi,0019-9567,03,08,10,1128,2003,5910,5920,71,all rights reserved,american society for microbiology,are important for survival,barr and lashitew,chagasi,copyright,fection and i mmunity,iai,katherine a,n superoxide dismutases targeted,nosource,oct,p,plewes,stephen d,the glycosomes of leishmania,to} }

@article{agrawalTranscriptionalTranslationalRegulation1987, title = {Transcriptional and Translational Regulation of Ribosomal Protein Formation during Mouse Myoblast Differentiation.}, author = {Agrawal, M. G. and Bowman, L. H.}, year = 1987, journal = {The Journal of biological chemistry}, volume = {262}, number = {10}, pages = {4868–4875}, issn = {0021-9258}, abstract = {The metabolism of ribosomal proteins (r-proteins) and r-protein mRNAs was examined during mouse myoblast differentiation to identify the levels at which r-protein accumulation is regulated. Pulse-chase analyses of r-proteins in myoblasts and fibers indicate that the synthesis of r-proteins is coordinately reduced 2.0-fold following myoblast differentiation and that newly synthesized r-proteins do not turnover. This decreased synthesis of r-proteins in fibers is due to both a reduction in the steady-state levels of r-protein mRNAs and a decrease in the translational efficiency of r-protein mRNAs. Northern analyses of r-protein mRNA indicate that the steady-state levels of r-protein mRNAs S16, L18, and L32 are decreased 1.5-2.0-fold in fibers as compared to myoblasts. Analyses of the distribution of r-protein mRNAs in polysome gradients indicate that their translational efficiencies are reduced 1.3-1.6-fold in fibers as compared to myoblasts. To determine if the decrease in the steady-state levels of r-protein mRNAs is regulated at the level of transcription, the transcription of these genes was measured in isolated nuclei. These experiments show that the transcription of these r-protein genes is reduced 2-6-fold following myoblast differentiation. Thus, the production of r-proteins is regulated both at the level of transcription and translation during mouse myoblast differentiation.}, isbn = {0021-9258 (Print)}, pmid = {3558374}, keywords = {nosource} }

@article{liQuantifyingAbsoluteProtein2014, title = {Quantifying {{Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation}} of {{Cellular Resources}}}, author = {Li, Gene-Wei and Burkhardt, David and Gross, Carol and Weissman, Jonathan S.}, year = 2014, journal = {Cell}, volume = {157}, number = {3}, pages = {624–635}, publisher = {Elsevier}, issn = {00928674}, doi = {10.1016/j.cell.2014.02.033}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867414002323}, keywords = {nosource} } % == BibTeX quality report for liQuantifyingAbsoluteProtein2014: % ? Title looks like it was stored in title-case in Zotero

@article{bolgerTrimmomaticFlexibleTrimmer2014, title = {Trimmomatic: {{A}} Flexible Trimmer for {{Illumina}} Sequence Data}, shorttitle = {Trimmomatic}, author = {Bolger, Anthony M. and Lohse, Marc and Usadel, Bjoern}, year = 2014, month = aug, journal = {Bioinformatics}, volume = {30}, number = {15}, pages = {2114–2120}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btu170}, url = {https://doi.org/10.1093/bioinformatics/btu170}, abstract = {MOTIVATION: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. RESULTS: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. AVAILABILITY AND IMPLEMENTATION: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic CONTACT: usadel@bio1.rwth-aachen.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, isbn = {1367-4803}, pmid = {24695404}, file = {/home/trey/Zotero/storage/ZCAPFXLZ/Bolger et al. - 2014 - Trimmomatic a flexible trimmer for Illumina seque.pdf;/home/trey/Zotero/storage/CG7BLJAI/2390096.html} } % == BibTeX quality report for bolgerTrimmomaticFlexibleTrimmer2014: % ? unused Library catalog (“Silverchair”)

@article{longGeneEssentiality2015, title = {Gene {{Essentiality}}}, author = {Long, Jarukit E. and Dejesus, Michael and Ward, Doyle and Baker, Richard E. and Ioerger, Thomas and Sassetti, Christopher M.}, year = 2015, volume = {1279}, pages = {79–95}, doi = {10.1007/978-1-4939-2398-4}, url = {http://link.springer.com/10.1007/978-1-4939-2398-4}, isbn = {978-1-4939-2397-7}, keywords = {essentiality,himar1 mutagenesis,illumina next-generation sequencing,mycobacterium tuberculosis,nosource,tnseq,transposon sequencing} } % == BibTeX quality report for longGeneEssentiality2015: % Missing required field ‘journal’ % ? Title looks like it was stored in title-case in Zotero

@article{ridderExtracellularVesiclemediatedTransfer2015, title = {Extracellular Vesicle-Mediated Transfer of Functional {{RNA}} in the Tumor Microenvironment}, author = {Ridder, Kirsten and Sevko, Alexandra and Heide, Janina and Dams, Maria and Rupp, Anne-Kathleen and Macas, Jadranka and Starmann, Julia and Tjwa, Marc and Plate, Karl H. and S{"u}ltmann, Holger and Altevogt, Peter and Umansky, Viktor and Momma, Stefan}, year = 2015, journal = {OncoImmunology}, volume = {4}, number = {6}, pages = {e1008371}, issn = {2162-402X}, doi = {10.1080/2162402X.2015.1008371}, url = {http://www.tandfonline.com/doi/full/10.1080/2162402X.2015.1008371}, keywords = {nosource} }

@article{renCrystalStructureUnphosphorylated2008, title = {Crystal Structure of Unphosphorylated {{STAT3}} Core Fragment}, author = {Ren, Zhiyong and Mao, Xiang and Mertens, Claudia and Krishnaraj, Ravi and Qin, Jie and Mandal, Pijus K. and Romanowski, Michael J. and McMurray, John S. and Chen, Xiaomin}, year = 2008, journal = {Biochemical and Biophysical Research Communications}, volume = {374}, number = {1}, pages = {1–5}, issn = {0006291X}, doi = {10.1016/j.bbrc.2008.04.049}, abstract = {Signal transducers and activators of transcription (STATs) are latent cytoplasmic transcriptional factors that play an important role in cytokine and growth factor signaling. Here we report a 3.05 -resolution crystal structure of an unphosphorylated STAT3 core fragment. The overall monomeric structure is very similar to that of the phosphorylated STAT3 core fragment. However, the dimer interface observed in the unphosphorylated STAT1 core fragment structure is absent in the STAT3 structure. Solution studies further demonstrate that the core fragment of STAT3 is primarily monomeric. Mutations corresponding to those in STAT1, which lead to disruption of the core fragment interface and prolonged tyrosine phosphorylation, show little or no effect on the tyrosine phosphorylation kinetics of STAT3. These results highlight the structural and biochemical differences between STAT3 and STAT1, and suggest different regulation mechanisms of these two proteins. 2008 Elsevier Inc. All rights reserved.}, pmid = {18433722}, keywords = {Dimerization,nosource,Signal transduction,STAT} }

@article{beckerThreedimensionalStructureStat3beta1998, title = {Three-Dimensional Structure of the {{Stat3beta}} Homodimer Bound to {{DNA}}.}, author = {Becker, S. and Groner, B. and M{"u}ller, C. W.}, year = 1998, journal = {Nature}, volume = {394}, number = {6689}, pages = {145–151}, issn = {0028-0836}, doi = {10.1038/28101}, abstract = {STAT proteins are a family of eukaryotic transcription factors that mediate the response to a large number of cytokines and growth factors. Upon activation by cell-surface receptors or their associated kinases, STAT proteins dimerize, translocate to the nucleus and bind to specific promoter sequences on their target genes. Here we report the first crystal structure of a STAT protein bound to its DNA recognition site at 2.25 A resolution. The structure provides insight into the various steps by which STAT proteins deliver a response signal directly from the cell membrane to their target genes in the nucleus.}, isbn = {0028-0836 (Print)}, pmid = {9671298}, keywords = {nosource} }

@article{leekSVAPackageRemoving2012, title = {The {{SVA}} Package for Removing Batch Effects and Other Unwanted Variation in High-Throughput Experiments}, author = {Leek, Jeffrey T. and Johnson, W. Evan and Parker, Hilary S. and Jaffe, Andrew E. and Storey, John D.}, year = 2012, journal = {Bioinformatics}, volume = {28}, number = {6}, pages = {882–883}, issn = {13674803}, doi = {10.1093/bioinformatics/bts034}, abstract = {Heterogeneity and latent variables are now widely recognized as major sources of bias and variability in high-throughput experiments. The most well-known source of latent variation in genomic experiments are batch effects-when samples are processed on different days, in different groups or by different people. However, there are also a large number of other variables that may have a major impact on high-throughput measurements. Here we describe the sva package for identifying, estimating and removing unwanted sources of variation in high-throughput experiments. The sva package supports surrogate variable estimation with the sva function, direct adjustment for known batch effects with the ComBat function and adjustment for batch and latent variables in prediction problems with the fsva function.}, isbn = {1367480314602059}, pmid = {22257669}, keywords = {nosource} }

@article{andrewsEmergingEvidenceFunctional2014, title = {Emerging Evidence for Functional Peptides Encoded by Short Open Reading Frames.}, author = {Andrews, Shea J. and {}a Rothnagel, Joseph}, year = 2014, journal = {Nature reviews. Genetics}, volume = {15}, number = {3}, eprint = {24514441}, eprinttype = {pubmed}, pages = {193–204}, issn = {1471-0064}, doi = {10.1038/nrg3520}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24514441}, abstract = {Short open reading frames (sORFs) are a common feature of all genomes, but their coding potential has mostly been disregarded, partly because of the difficulty in determining whether these sequences are translated. Recent innovations in computing, proteomics and high-throughput analyses of translation start sites have begun to address this challenge and have identified hundreds of putative coding sORFs. The translation of some of these has been confirmed, although the contribution of their peptide products to cellular functions remains largely unknown. This Review examines this hitherto overlooked component of the proteome and considers potential roles for sORF-encoded peptides.}, isbn = {1471-0064 (Electronic)r1471-0056 (Linking)}, pmid = {24514441}, keywords = {Animals,Humans,Messenger,Messenger: genetics,nosource,Open Reading Frames,Peptides,Peptides: chemistry,Protein Biosynthesis,RNA,Untranslated,Untranslated: genetics} } % == BibTeX quality report for andrewsEmergingEvidenceFunctional2014: % ? Possibly abbreviated journal title Nature reviews. Genetics

@article{denekeComplexDegradationProcesses2013, title = {Complex {{Degradation Processes Lead}} to {{Non-Exponential Decay Patterns}} and {{Age-Dependent Decay Rates}} of {{Messenger RNA}}}, author = {Deneke, Carlus and Lipowsky, Reinhard and Valleriani, Angelo}, year = 2013, journal = {PLoS ONE}, volume = {8}, number = {2}, issn = {19326203}, doi = {10.1371/journal.pone.0055442}, abstract = {Experimental studies on mRNA stability have established several, qualitatively distinct decay patterns for the amount of mRNA within the living cell. Furthermore, a variety of different and complex biochemical pathways for mRNA degradation have been identified. The central aim of this paper is to bring together both the experimental evidence about the decay patterns and the biochemical knowledge about the multi-step nature of mRNA degradation in a coherent mathematical theory. We first introduce a mathematical relationship between the mRNA decay pattern and the lifetime distribution of individual mRNA molecules. This relationship reveals that the mRNA decay patterns at steady state expression level must obey a general convexity condition, which applies to any degradation mechanism. Next, we develop a theory, formulated as a Markov chain model, that recapitulates some aspects of the multi-step nature of mRNA degradation. We apply our theory to experimental data for yeast and explicitly derive the lifetime distribution of the corresponding mRNAs. Thereby, we show how to extract single-molecule properties of an mRNA, such as the age-dependent decay rate and the residual lifetime. Finally, we analyze the decay patterns of the whole translatome of yeast cells and show that yeast mRNAs can be grouped into three broad classes that exhibit three distinct decay patterns. This paper provides both a method to accurately analyze non-exponential mRNA decay patterns and a tool to validate different models of degradation using decay data.}, isbn = {1932-6203}, pmid = {23408982}, keywords = {nosource} } % == BibTeX quality report for denekeComplexDegradationProcesses2013: % ? Title looks like it was stored in title-case in Zotero

@article{chekanovaGenomeWideHighResolutionMapping2007, title = {Genome-{{Wide High-Resolution Mapping}} of {{Exosome Substrates Reveals Hidden Features}} in the {{Arabidopsis Transcriptome}}}, author = {{}a Chekanova, Julia and Gregory, Brian D. and Reverdatto, Sergei V. and Chen, Huaming and Kumar, Ravi and Hooker, Tanya and Yazaki, Junshi and Li, Pinghua and Skiba, Nikolai and Peng, Qian and Alonso, Jose and Brukhin, Vladimir and Grossniklaus, Ueli and Ecker, Joseph R. and {}a Belostotsky, Dmitry}, year = 2007, journal = {Cell}, volume = {131}, number = {7}, pages = {1340–1353}, issn = {00928674}, doi = {10.1016/j.cell.2007.10.056}, abstract = {The exosome complex plays a central and essential role in RNA metabolism. However, comprehensive studies of exosome substrates and functional analyses of its subunits are lacking. Here, we demonstrate that as opposed to yeast and metazoans the plant exosome core possesses an unanticipated functional plasticity and present a genome-wide atlas of Arabidopsis exosome targets. Additionally, our study provides evidence for widespread polyadenylation- and exosome-mediated RNA quality control in plants, reveals unexpected aspects of stable structural RNA metabolism, and uncovers numerous novel exosome substrates. These include a select subset of mRNAs, miRNA processing intermediates, and hundreds of noncoding RNAs, the vast majority of which have not been previously described and belong to a layer of the transcriptome that can only be visualized upon inhibition of exosome activity. These first genome-wide maps of exosome substrates will aid in illuminating new fundamental components and regulatory mechanisms of eukaryotic transcriptomes. 2007 Elsevier Inc. All rights reserved.}, isbn = {0092-8674 (Print)}, pmid = {18160042}, keywords = {CELLBIO,nosource,RNA,SYSBIO} } % == BibTeX quality report for chekanovaGenomeWideHighResolutionMapping2007: % ? Title looks like it was stored in title-case in Zotero

@article{faddaTranscriptomewideAnalysisTrypanosome2014, title = {Transcriptome-Wide Analysis of Trypanosome {{mRNA}} Decay Reveals Complex Degradation Kinetics and Suggests a Role for Co-Transcriptional Degradation in Determining {{mRNA}} Levels}, author = {Fadda, Abeer and Ryten, Mark and Droll, Dorothea and Rojas, Federico and F{"a}rber, Valentin and Haanstra, Jurgen R. and Merce, Clemetine and Bakker, Barbara M. and Matthews, Keith and Clayton, Christine}, year = 2014, journal = {Molecular Microbiology}, volume = {94}, number = {2}, pages = {307–326}, issn = {0950382X}, doi = {10.1111/mmi.12764}, url = {http://doi.wiley.com/10.1111/mmi.12764}, keywords = {nosource} }

@article{sternMultipleRolesPolypyrimidine2009, title = {Multiple Roles for Polypyrimidine Tract Binding ({{PTB}}) Proteins in Trypanosome {{RNA}} Metabolism.}, author = {Stern, Michael Zeev and Gupta, Sachin Kumar and {Salmon-Divon}, Mali and Haham, Tomer and Barda, Omer and Levi, Sarit and Wachtel, Chaim and Nilsen, Timothy W. and Michaeli, Shulamit}, year = 2009, journal = {RNA (New York, N.Y.)}, volume = {15}, number = {4}, pages = {648–665}, issn = {1355-8382}, doi = {10.1261/rna.1230209}, abstract = {Trypanosomatid genomes encode for numerous proteins containing an RNA recognition motif (RRM), but the function of most of these proteins in mRNA metabolism is currently unknown. Here, we report the function of two such proteins that we have named PTB1 and PTB2, which resemble the mammalian polypyrimidine tract binding proteins (PTB). RNAi silencing of these factors indicates that both are essential for life. PTB1 and PTB2 reside mostly in the nucleus, but are found in the cytoplasm, as well. Microarray analysis performed on PTB1 and PTB2 RNAi silenced cells indicates that each of these factors differentially affects the transcriptome, thus regulating a different subset of mRNAs. PTB1 and PTB2 substrates were categorized bioinformatically, based on the presence of PTB binding sites in their 5’ and 3’ flanking sequences. Both proteins were shown to regulate mRNA stability. Interestingly, PTB proteins are essential for trans-splicing of genes containing C-rich polypyrimidine tracts. PTB1, but not PTB2, also affects cis-splicing. The specificity of binding of PTB1 was established in vivo and in vitro using a model substrate. This study demonstrates for the first time that trans-splicing of only certain substrates requires specific factors such as PTB proteins for their splicing. The trypanosome PTB proteins, like their mammalian homologs, represent multivalent RNA binding proteins that regulate mRNAs from their synthesis to degradation.}, pmid = {19218552}, keywords = {nosource,ptb,sl rna,splicing,trans - and cis,trypanosoma brucei} } % == BibTeX quality report for sternMultipleRolesPolypyrimidine2009: % ? Possibly abbreviated journal title RNA (New York, N.Y.)

@article{dorsoTcUBP1DevelopmentallyRegulated2001, title = {{{TcUBP-1}}, a {{Developmentally Regulated U-rich RNA-binding Protein Involved}} in {{Selective mRNA Destabilization}} in {{Trypanosomes}}}, author = {D’Orso, Iv{'a}n and Frasch, Alberto C. C.}, year = 2001, journal = {Journal of Biological Chemistry}, volume = {276}, number = {37}, pages = {34801–34809}, issn = {00219258}, doi = {10.1074/jbc.M102120200}, abstract = {Developmental stages of the trypanosome life cycle differ in their morphology, biology, and biochemical properties. Consequently, several proteins have to be tightly regulated in their expression to allow trypanosomes to adapt rapidly to sudden environmental changes, a process that might be of central importance for parasite survival. However, in contrast to higher eukaryotic cells, trypanosomes do not seem to regulate gene expression through regulation of transcription initiation. These parasites make use of post-transcriptional regulatory mechanisms and modification of mRNA half-life is a relevant one. Trans-acting factors binding to cis-elements that affect mRNA stability of mature transcripts have not been identified in these cells. In this work, a novel U-rich RNA-binding protein (TcUBP-1) from Trypanosoma cruzi, the agent of Chagas disease, was identified. Its structure includes an RNA recognition motif, a nuclear export signal, and auxiliary domains with glycine- and glutamine-rich regions. TcUBP-1 recognizes the 44-nucleotide AU-rich RNA instability element located in the 3’-untranslated region of mucin SMUG mRNAs (Di Noia, J. M., D’Orso, I., Sanchez, D. O., and Frasch, A. C. (2000) J. Biol. Chem. 275, 10218-10227) as well as GU-rich sequences. Over-expression of TcUBP-1 in trypanosomes decreases the half-life of SMUG mucin mRNAs in vivo but does not affect the stability of other parasite mRNAs. Because TcUBP-1 is developmentally regulated, it might have a relevant role in regulating protein expression during trypanosome differentiation, allowing a correct expression pattern of U-rich-containing mRNAs.}, isbn = {0021-9258 (Print)r0021-9258 (Linking)}, pmid = {11435421}, keywords = {nosource} }

@article{keeneRNARegulonsCoordination2007, title = {{{RNA}} Regulons: Coordination of Post-Transcriptional Events.}, author = {Keene, Jack D.}, year = 2007, journal = {Nature reviews. Genetics}, volume = {8}, number = {7}, pages = {533–543}, issn = {1471-0056}, doi = {10.1038/nrg2111}, abstract = {Recent findings demonstrate that multiple mRNAs are co-regulated by one or more sequence-specific RNA-binding proteins that orchestrate their splicing, export, stability, localization and translation. These and other observations have given rise to a model in which mRNAs that encode functionally related proteins are coordinately regulated during cell growth and differentiation as post-transcriptional RNA operons or regulons, through a ribonucleoprotein-driven mechanism. Here I describe several recently discovered examples of RNA operons in budding yeast, fruitfly and mammalian cells, and their potential importance in processes such as immune response, oxidative metabolism, stress response, circadian rhythms and disease. I close by considering the evolutionary wiring and rewiring of these combinatorial post-transcriptional gene-expression networks.}, isbn = {1471-0056 (Print)r1471-0056 (Linking)}, pmid = {17572691}, keywords = {nosource} } % == BibTeX quality report for keeneRNARegulonsCoordination2007: % ? Possibly abbreviated journal title Nature reviews. Genetics

@article{fernandez-moyaShortRNAStemloop2014, title = {A Short {{RNA}} Stem-Loop Is Necessary and Sufficient for Repression of Gene Expression during Early Logarithmic Phase in Trypanosomes}, author = {{Fern{'a}ndez-Moya}, Sandra M. and Carrington, Mark and Est{'e}vez, Antonio M.}, year = 2014, journal = {Nucleic Acids Research}, volume = {42}, number = {11}, pages = {7201–7209}, issn = {13624962}, doi = {10.1093/nar/gku358}, abstract = {We have compared the transcriptomes of cultured procyclic Trypanosoma brucei cells in early and late logarithmic phases and found that {\(\sim\)}200 mRNAs were differentially regulated. In late log phase cells, the most upregulated mRNA encoded the nucleobase transporter NT8. The 3’ untranslated region (UTR) of NT8 contains a short stem-loop cis-element that is necessary for the regulation of NT8 expression in response to external purine levels. When placed in the 3’-UTR of an unregulated transcript, the cis-element is sufficient to confer regulation in response to purines. To our knowledge, this is the first example of a discrete RNA element that can autonomously regulate gene expression in trypanosomes in response to an external factor and reveals an unprecedented purine-dependent signaling pathway that controls gene expression in eukaryotes.}, pmid = {24813448}, keywords = {nosource} }

@article{quijadaExpressionHumanRNAbinding2002, title = {Expression of the Human {{RNA-binding}} Protein {{HuR}} in {{Trypanosoma}} Brucei Increases the Abundance of {{mRNAs}} Containing {{AU-rich}} Regulatory Elements.}, author = {Quijada, Luis and {Guerra-Giraldez}, Cristina and Drozdz, Maciej and Hartmann, Claudia and Irmer, Henriette and {Ben-Dov}, Claudia and Cristodero, Marina and Ding, Martina and Clayton, Christine}, year = 2002, journal = {Nucleic acids research}, volume = {30}, number = {20}, pages = {4414–4424}, issn = {1362-4962}, abstract = {The salivarian trypanosome Trypanosoma brucei infects mammals and is transmitted by tsetse flies. The mammalian ‘bloodstream form’ trypanosome has a variant surface glycoprotein coat and relies on glycolysis while the procyclic form from tsetse flies has EP protein on the surface and has a more developed mitochondrion. We show here that the mRNA for the procyclic-specific cytosolic phosphoglycerate kinase PGKB, like that for EP proteins, contains a regulatory AU-rich element (ARE) that destabilises the mRNA in bloodstream forms. The human HuR protein binds to, and stabilises, mammalian mRNAs containing AREs. Expression of HuR in bloodstream-form trypanosomes resulted in growth arrest and in stabilisation of the EP, PGKB and pyruvate, phosphate dikinase mRNAs, while three bloodstream-specific mRNAs were reduced in abundance. The synthesis and abundance of unregulated mRNAs and proteins were unaffected. Our results suggest that regulation of mRNA stability by AREs arose early in eukaryotic evolution.}, isbn = {0305-1048}, pmid = {12384588}, keywords = {nosource} }

@article{haileDeadenylationindependentStagespecificMRNA2008, title = {Deadenylation-Independent Stage-Specific {{mRNA}} Degradation in {{Leishmania}}}, author = {Haile, Simon and Dup{'e}, Aur{'e}lien and Papadopoulou, Barbara}, year = 2008, journal = {Nucleic Acids Research}, volume = {36}, number = {5}, pages = {1634–1644}, issn = {03051048}, doi = {10.1093/nar/gkn019}, abstract = {The life cycle of Leishmania alternates between developmental forms residing within the insect vector (e.g. promastigotes) and the mammalian host (amastigotes). In Leishmania nearly all control of gene expression is post-transcriptional and involves sequences in the 3’-untranslated regions (3’UTRs) of mRNAs. Very little is known as to how these cis-elements regulate RNA turnover and translation rates in trypanosomatids and nothing is known about mRNA degradation mechanisms in Leishmania in particular. Here, we use the amastin mRNA-an amastigote-specific transcript-as a model and show that a approximately 100 nt U-rich element (URE) within its 3’UTR significantly accounts for developmental regulation. RNase-H-RNA blot analysis revealed that a major part of the rapid promastigote-specific degradation of the amastin mRNA is not initiated by deadenylation. This is in contrast to the amastin mRNA in amastigotes and to reporter RNAs lacking the URE, which, in common with most eukaryotic mRNAs studied to-date, are deadenylated before being degraded. Moreover, our analysis did not reveal a role for decapping in the stage-specific degradation of the amastin mRNA. Overall, these results suggest that degradation of the amastin mRNA of Leishmania is likely to be bi-phasic, the first phase being stage-specific and dependent on an unusual URE-mediated pathway of mRNA degradation.}, isbn = {1362-4962 (Electronic)r0305-1048 (Linking)}, pmid = {18250085}, keywords = {nosource} }

@article{lemleyLeishmaniaDonovaniLD11999, title = {The {{Leishmania}} Donovani {{LD1}} Locus Gene {{ORFG}} Encodes a Biopterin Transporter ({{BT1}})}, author = {Lemley, Craig and Yan, Shaofeng and Dole, Vandana S. and Madhubala, Rentala and Cunningham, Mark L. and Beverley, Stephen M. and Myler, Peter J. and Stuart, Kenneth D.}, year = 1999, journal = {Molecular and Biochemical Parasitology}, volume = {104}, pages = {93–105}, issn = {01666851}, doi = {10.1016/S0166-6851(99)00132-2}, abstract = {We have previously described two genes, ORFF and ORFG, from the LD1 locus near one telomere of chromosome 35, which are frequently amplified in Leishmania isolates. In Leishmania donovani LSB-51.1, gene conversion of the rRNA gene locus on chromosome 27 with these two genes resulted in their over- expression, because of their transcription by the RNA polymerase I-mediated rRNA promoter. The predicted ORFG protein has substantial sequence homology to the ESAG10 gene product from the Trypanosoma brucei VSG expression site and both are putative membrane proteins. Using successive rounds of gene replacement of the three ORFG genes in L. donovani LSB-51.1, ORFG null mutants were obtained. These mutant cell lines show a direct relationship between ORFG mRNA, protein expression levels and active transport of biopterin into the cells. Transformation of the null mutant with a plasmid containing ORFG restores biopterin transport activity. In addition, the null mutants are unable to grow in the absence of supplemental biopterin. Thus, ORFG encodes a biopterin transporter and has been renamed BT1.}, isbn = {0166-6851 (Print)r0166-6851 (Linking)}, pmid = {10589984}, keywords = {Biopterin,Gene replacement,Leishmania donovani,nosource,Pteridines,Transporter} }

@article{martinez-calvilloTranscriptionLeishmaniaMajor2003, title = {Transcription of {{Leishmania}} Major {{Friedlin}} Chromosome 1 Initiates in Both Directions within a Single Region}, author = {{Mart{'i}nez-Calvillo}, Santiago and Yan, Shaofeng and Nguyen, Dan and Fox, Mark and Stuart, Kenneth and Myler, Peter J.}, year = 2003, journal = {Molecular Cell}, volume = {11}, pages = {1291–1299}, issn = {10972765}, doi = {10.1016/S1097-2765(03)00143-6}, abstract = {Almost nothing is known about the sequences involved in transcription initiation of protein-coding genes in the parasite Leishmania. We describe here the transcriptional analysis of chromosome 1 (chr1) from Leishmania major Friedlin (LmjF) which encodes the first 29 genes on one DNA strand, and the remaining 50 on the opposite strand. Strand-specific nuclear run-on assays showed that a low level of nonspecific transcription probably takes place over the entire chromosome, but an {\(\sim\)}10-fold higher level of coding strand-specific RNA polymerase II (Pol II)-mediated transcription initiates within the strand-switch region. 5{\(\prime\)} RACE studies localized the initiation sites to a {\(<\)}100 bp region. Transfection studies support the presence of a bidirectional promoter within the strand-switch region, but suggest that other factors are also involved in Pol II transcription. Thus, while in most eukaryotes each gene possesses its own promoter, a single region seems to drive the expression of the entire chr1 in LmjF.}, isbn = {1097-2765 (Print)r1097-2765 (Linking)}, pmid = {12769852}, keywords = {nosource} }

@article{contrerasStageSpecificGene1985, title = {Stage Specific Gene Expression Precedes Morphological Changes during {{Trypanosoma}} Cruzi Metacyclogenesis.}, author = {Contreras, V. T. and Morel, C. M. and Goldenberg, S.}, year = 1985, journal = {Molecular and biochemical parasitology}, volume = {14}, pages = {83–96}, issn = {01666851}, doi = {10.1016/0166-6851(85)90108-2}, abstract = {The transformation of epimastigotes to metacyclic trypomastigotes of the Trypanosoma cruzi clone Dm 28c has been studied in an in vitro system consisting of artificial triatomine urine supplemented with newborn calf serum. The comparison of morphological data with gene expression products, as judged by the proteins synthesized during differentiation, has shown that stage specific gene activation precedes by far the morphological changes of differentiating cells. Immunoprecipitation of differentiating cell antigens with a trypomastigote stage specific antiserum has shown that although the morphological differentiation process takes six days to be completed, epimastigotes start to express the Mr 86 000 and the 78 000 trypomastigote antigens within the first 12 h of induction.}, pmid = {3885031}, keywords = {cell differentiation,chagas,disease,gene expression,nosource,trypanosoma cruzi cloned strain} }

@article{durinckMappingIdentifiersIntegration2009, title = {Mapping Identifiers for the Integration of Genomic Datasets with the {{R}}/{{Bioconductor}} Package {{biomaRt}}}, author = {Durinck, S. and Spellman, P. T. and Birney, E. and Huber, W.}, year = 2009, journal = {Nature protocols}, volume = {4}, number = {8}, pages = {1184–1191}, doi = {10.1038/nprot.2009.97.Mapping}, url = {http://www.nature.com/nprot/journal/v4/n8/abs/nprot.2009.97.html}, keywords = {bioconductor,biomart,data integration,ensembl,identifiers,mapping,nosource} }

@article{eppleCellHostMicrobe2014, title = {Cell {{Host}} & {{Microbe Convergent}} Targeting of a Common Host Protein-Network by Pathogen Effectors from Three Kingdoms of Life}, author = {Epple, Petra M. and Mcdonald, Nathan and Bader, Kai Christian and Gl{"a}{\(\beta\)}er, Christine and Stephens, Amber E. and Ecker, Joseph R. and Jones, Jonathan D. G. and {Schulze-lefert}, Paul and Dangl, Jeffery L. and Hoffmann, Jules}, year = 2014, pages = {364–375}, issn = {19346069}, doi = {10.1016/j.chom.2014.08.004}, keywords = {-manuscript draft-,common host protein-network by,convergent targeting of a,l host,microbe,nosource,pathogen effectors from,three kingdoms of life} } % == BibTeX quality report for eppleCellHostMicrobe2014: % Missing required field ‘journal’

@article{alonsoGenomewideInsertionalMutagenesis2003, title = {Genome-Wide Insertional Mutagenesis of {{Arabidopsis}} Thaliana.}, author = {Alonso, Jos{'e} M. and Stepanova, Anna N. and Leisse, Thomas J. and Kim, Christopher J. and Chen, Huaming and Shinn, Paul and Stevenson, Denise K. and Zimmerman, Justin and Barajas, Pascual and Cheuk, Rosa and Gadrinab, Carmelita and Heller, Collen and Jeske, Albert and Koesema, Eric and Meyers, Cristina C. and Parker, Holly and Prednis, Lance and Ansari, Yasser and Choy, Nathan and Deen, Hashim and Geralt, Michael and Hazari, Nisha and Hom, Emily and Karnes, Meagan and Mulholland, Celene and Ndubaku, Ral and Schmidt, Ian and Guzman, Plinio and {Aguilar-Henonin}, Laura and Schmid, Markus and Weigel, Detlef and Carter, David E. and Marchand, Trudy and Risseeuw, Eddy and Brogden, Debra and Zeko, Albana and Crosby, William L. and Berry, Charles C. and Ecker, Joseph R.}, year = 2003, journal = {Science (New York, N.Y.)}, volume = {301}, number = {September}, pages = {653–657}, issn = {1095-9203}, doi = {10.1126/science.1086391}, abstract = {Over 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the approximately 29,454 predicted Arabidopsis genes. Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.}, isbn = {1095-9203 (Electronic)r0036-8075 (Linking)}, pmid = {12893945}, keywords = {nosource} } % == BibTeX quality report for alonsoGenomewideInsertionalMutagenesis2003: % ? Possibly abbreviated journal title Science (New York, N.Y.)

@article{parinovFunctionalGenomicsArabidopsis2000, title = {Functional Genomics in {{Arabidopsis}}: {{Large-scale}} Insertional Mutagenesis Complements the Genome Sequencing Project}, author = {Parinov, Serguei and Sundaresan, Venkatesan}, year = 2000, journal = {Current Opinion in Biotechnology}, volume = {11}, pages = {157–161}, issn = {09581669}, doi = {10.1016/S0958-1669(00)00075-6}, abstract = {The ultimate goal of genome research on the model flowering plant Arabidopsis thaliana is the identification of all of the genes and understanding their functions. A major step towards this goal, the genome sequencing project, is nearing completion; however, functional studies of newly discovered genes have not yet kept up to this pace. Recent progress in large-scale insertional mutagenesis opens new possibilities for functional genomics in Arabidopsis. The number of T-DNA and transposon insertion lines from different laboratories will soon represent insertions into most Arabidopsis genes. Vast resources of gene knockouts are becoming available that can be subjected to different types of reverse genetics screens to deduce the functions of the sequenced genes.}, isbn = {0958-1669 (Print)r0958-1669 (Linking)}, pmid = {10753770}, keywords = {nosource} }

@article{schoreyExosomesOtherExtracellular2015, title = {Exosomes and Other Extracellular Vesicles in Host – Pathogen Interactions}, author = {Schorey, Jeffrey S. and Cheng, Yong and Singh, Prachi P. and Smith, Victoria L.}, year = 2015, volume = {16}, number = {1}, pages = {24–44}, keywords = {15252,16,2014,201439363,2015,24,43,accepted 17 november 2014,doi 10,embo reports,embr,exosomes,extracellular vesicles,immunity,nosource,pathogens,published online 8 december,received 25 july 2014,revised 6 november} } % == BibTeX quality report for schoreyExosomesOtherExtracellular2015: % Missing required field ‘journal’

@article{rickl.pengCRISPRCas9MediatedSingleGeneGene2014, title = {{{CRISPR-Cas9-Mediated Single-Gene}} and {{Gene Family Disruption}} in {{Trypanosoma}} Cruzi}, author = {Rick L. Peng, Duo Kurup, Samarchith P. Yao, Phil Y. Minning, Todd A. Tarleton}, year = 2014, volume = {6}, number = {1}, pages = {1–11}, issn = {2150-7511}, doi = {10.1128/mBio.02097-14.Editor}, isbn = {2150-7511 (Electronic)}, pmid = {25550322}, keywords = {nosource} } % == BibTeX quality report for rickl.pengCRISPRCas9MediatedSingleGeneGene2014: % Missing required field ‘journal’

@article{zhouStructuralFunctionalEvidence2011, title = {Structural and Functional Evidence of High Specificity of {{Cbf5}} for {{ACA}} Trinucleotide}, author = {Zhou, Jing and Liang, B. O. and Li, Hong}, year = 2011, pages = {244–250}, doi = {10.1261/rna.2415811.Watson-Crick}, keywords = {nosource,protein interactions,pseudouridylase,ribosome biogenesis,rna,x-ray crystal structure} } % == BibTeX quality report for zhouStructuralFunctionalEvidence2011: % Missing required field ‘journal’

@article{faticaLongNoncodingRNAs2014, title = {Long Non-Coding {{RNAs}}: New Players in Cell Differentiation and Development.}, author = {Fatica, Alessandro and Bozzoni, Irene}, year = 2014, month = jan, journal = {Nature reviews. Genetics}, volume = {15}, number = {1}, eprint = {24296535}, eprinttype = {pubmed}, pages = {7–21}, publisher = {Nature Publishing Group}, issn = {1471-0064}, doi = {10.1038/nrg3606}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24296535}, abstract = {Genomes of multicellular organisms are characterized by the pervasive expression of different types of non-coding RNAs (ncRNAs). Long ncRNAs (lncRNAs) belong to a novel heterogeneous class of ncRNAs that includes thousands of different species. lncRNAs have crucial roles in gene expression control during both developmental and differentiation processes, and the number of lncRNA species increases in genomes of developmentally complex organisms, which highlights the importance of RNA-based levels of control in the evolution of multicellular organisms. In this Review, we describe the function of lncRNAs in developmental processes, such as in dosage compensation, genomic imprinting, cell differentiation and organogenesis, with a particular emphasis on mammalian development.}, pmid = {24296535}, keywords = {Animals,Cell Differentiation,Cell Differentiation: genetics,Cell Differentiation: physiology,Cytoplasm,Cytoplasm: genetics,Developmental,Developmental: genetic,Dosage Compensation,Gene Expression Regulation,Genetic,Genetic: genetics,Genomic Imprinting,Genomic Imprinting: genetics,Long Noncoding,Long Noncoding: genetics,Mammals,Mammals: genetics,Mammals: growth & development,Models,Molecular,Muscles,Muscles: physiology,nosource,Organogenesis,Organogenesis: genetics,RNA,Species Specificity} } % == BibTeX quality report for faticaLongNoncodingRNAs2014: % ? Possibly abbreviated journal title Nature reviews. Genetics

@article{wangIdentificationFunctionalCharacterization2013, title = {Identification and Functional Characterization of {{tRNA-derived RNA}} Fragments ({{tRFs}}) in Respiratory Syncytial Virus Infection.}, author = {Wang, Qingrong and Lee, Inhan and Ren, Junping and Ajay, Subramanian Shankar and Lee, Yong Sun and Bao, Xiaoyong}, year = 2013, month = feb, journal = {Molecular therapy : the journal of the American Society of Gene Therapy}, volume = {21}, number = {2}, pages = {368–79}, issn = {1525-0024}, doi = {10.1038/mt.2012.237}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3594034&tool=pmcentrez&rendertype=abstract}, abstract = {The discovery of small noncoding RNAs (sncRNAs) with regulatory functions is a recent breakthrough in biology. Among sncRNAs, microRNA (miRNA), derived from host or virus, has emerged as elements with high importance in control of viral replication and host responses. However, the expression pattern and functional aspects of other types of sncRNAs, following viral infection, are unexplored. In order to define expression patterns of sncRNAs, as well as to discover novel regulatory sncRNAs in response to viral infection, we applied deep sequencing to cells infected with human respiratory syncytial virus (RSV), the most common cause of bronchiolitis and pneumonia in babies. RSV infection leads to abundant production of transfer RNA (tRNA)-derived RNA Fragments (tRFs) that are 30 nucleotides (nts) long and correspond to the 5’-half of mature tRNAs. At least one tRF, which is derived from tRNA-Glu-CTC, represses target mRNA in the cytoplasm and promotes RSV replication. This demonstrates that this tRF is not a random by-product of tRNA degradation but a functional molecule. The biogenesis of this tRF is also specific, as it is mediated by the endonuclease angiogenin (ANG), not by other nucleases. In summary, our study presents novel information on the induction of a functional tRF by viral infection.}, pmid = {23183536}, keywords = {Biosensing Techniques,Blotting,Bronchiolitis,Bronchiolitis: genetics,Bronchiolitis: virology,Cell Differentiation,Cell Line,Chromosome Mapping,Cytoplasm,Cytoplasm: metabolism,Epithelial Cells,Epithelial Cells: cytology,Epithelial Cells: virology,Gene Expression Profiling,Gene Expression Regulation,High-Throughput Nucleotide Sequencing,High-Throughput Nucleotide Sequencing: methods,Human,Human: genetics,Human: physiology,Humans,Luciferases,Luciferases: genetics,Luciferases: metabolism,Messenger,Messenger: genetics,Messenger: metabolism,MicroRNAs,MicroRNAs: genetics,MicroRNAs: isolation & purification,Northern,nosource,Pancreatic,Pancreatic: genetics,Pancreatic: metabolism,Plasmids,Plasmids: genetics,Protein Biosynthesis,Real-Time Polymerase Chain Reaction,Respiratory Syncytial Virus,Respiratory Syncytial Virus Infections,Respiratory Syncytial Virus Infections: genetics,Respiratory Syncytial Virus Infections: metabolism,Ribonuclease,RNA,Small Interfering,Small Interfering: genetics,Small Interfering: isolation & purification,Small Untranslated,Small Untranslated: genetics,Small Untranslated: isolation & purification,Transfer,Transfer: genetics,Transfer: isolation & purification,Tumor,Viral,Virus Replication} }

@article{tuckRNAPieces2011, title = {{{RNA}} in Pieces.}, author = {Tuck, Alex C. and Tollervey, David}, year = 2011, month = oct, journal = {Trends in genetics : TIG}, volume = {27}, number = {10}, eprint = {21741109}, eprinttype = {pubmed}, pages = {422–32}, issn = {0168-9525}, doi = {10.1016/j.tig.2011.06.001}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21741109}, abstract = {Eukaryotic genomes accommodate numerous types of information within diverse DNA and RNA sequence elements. At many loci, these elements overlap and the same sequence is read multiple times during the production, processing, localization, function and turnover of a single transcript. Moreover, two or more transcripts from the same locus might use a common sequence in different ways, to perform distinct biological roles. Recent results show that many transcripts also undergo post-transcriptional cleavage to release specific fragments, which can then function independently. This phenomenon appears remarkably widespread, with even well-documented transcript classes such as messenger RNAs yielding fragments. RNA fragmentation significantly expands the already extraordinary spectrum of transcripts present within eukaryotic cells, and also calls into question how the ‘gene’ should be defined.}, pmid = {21741109}, keywords = {Alternative Splicing,Animals,DNA,DNA: genetics,Endoribonucleases,Endoribonucleases: metabolism,Genetic,Genetic Pleiotropy,Humans,Messenger,Messenger: chemistry,Messenger: genetics,Messenger: metabolism,MicroRNAs,MicroRNAs: chemistry,MicroRNAs: genetics,MicroRNAs: metabolism,nosource,Post-Transcriptional,Post-Transcriptional: genetics,RNA,RNA Folding,RNA Processing,Small Interfering,Small Interfering: chemistry,Small Interfering: genetics,Small Interfering: metabolism,Small Nucleolar,Small Nucleolar: chemistry,Small Nucleolar: genetics,Small Nucleolar: metabolism,Transcription,Transfer,Transfer: chemistry,Transfer: genetics,Transfer: metabolism} }

@article{yangFunctionalExpansionTRNA2011, title = {Functional Expansion of the {{tRNA}} World under Stress.}, author = {Yang, Xiang-Lei and Schimmel, Paul}, year = 2011, month = aug, journal = {Molecular cell}, volume = {43}, number = {4}, pages = {500–2}, publisher = {Elsevier Inc.}, issn = {1097-4164}, doi = {10.1016/j.molcel.2011.08.004}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3163667&tool=pmcentrez&rendertype=abstract}, pmid = {21855789}, keywords = {nosource} }

@article{siomiPIWIinteractingSmallRNAs2011, title = {{{PIWI-interacting}} Small {{RNAs}}: The Vanguard of Genome Defence.}, author = {Siomi, Mikiko C. and Sato, Kaoru and Pezic, Dubravka and {}a Aravin, Alexei}, year = 2011, month = apr, journal = {Nature reviews. Molecular cell biology}, volume = {12}, number = {4}, eprint = {21427766}, eprinttype = {pubmed}, pages = {246–58}, publisher = {Nature Publishing Group}, issn = {1471-0080}, doi = {10.1038/nrm3089}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21427766}, abstract = {PIWI-interacting RNAs (piRNAs) are a distinct class of small non-coding RNAs that form the piRNA-induced silencing complex (piRISC) in the germ line of many animal species. The piRISC protects the integrity of the genome from invasion by ‘genomic parasites’–transposable elements–by silencing them. Owing to their limited expression in gonads and their sequence diversity, piRNAs have been the most mysterious class of small non-coding RNAs regulating RNA silencing. Now, much progress is being made into our understanding of their biogenesis and molecular functions, including the specific subcellular compartmentalization of the piRNA pathway in granular cytoplasmic bodies.}, pmid = {21427766}, keywords = {Animals,DNA Transposable Elements,DNA Transposable Elements: genetics,Genetic,Genome,Genome: genetics,Insertional,Models,Mutagenesis,nosource,RNA,RNA Interference,Small Interfering,Small Interfering: genetics,Small Interfering: metabolism,Small Untranslated,Small Untranslated: genetics,Small Untranslated: metabolism} } % == BibTeX quality report for siomiPIWIinteractingSmallRNAs2011: % ? Possibly abbreviated journal title Nature reviews. Molecular cell biology

@article{teixeiraTrypanosomatidComparativeGenomics2012, title = {Trypanosomatid Comparative Genomics : {{Contributions}} to the Study of Parasite Biology and Different Parasitic Diseases}, author = {Teixeira, Santuza M. and M{'a}rcia, Rita and Paiva, Cardoso De and {Kangussu-marcolino}, Monica M. and Darocha, Wanderson D.}, year = 2012, volume = {17}, pages = {1–17}, keywords = {2011,accepted,august 8,genome,leishmania major,nosource,october 18,received,rnaseq,tri-tryp diseases and the,tri-tryp genomes,trypanosoma brucei,trypanosoma cruzi,trypanosoma cruzi and} } % == BibTeX quality report for teixeiraTrypanosomatidComparativeGenomics2012: % Missing required field ‘journal’

@article{garcia-silvaParticularSetSmall2014, title = {A Particular Set of Small Non-Coding {{RNAs}} Is Bound to the Distinctive {{Argonaute}} Protein of {{Trypanosoma}} Cruzi: Insights from {{RNA-interference}} Deficient Organisms.}, author = {{Garcia-Silva}, Maria Rosa and Sanguinetti, Julia and {Cabrera-Cabrera}, Florencia and Franz{'e}n, Oscar and Cayota, Alfonso}, year = 2014, month = apr, journal = {Gene}, volume = {538}, number = {2}, eprint = {24463018}, eprinttype = {pubmed}, pages = {379–84}, publisher = {Elsevier B.V.}, issn = {1879-0038}, doi = {10.1016/j.gene.2014.01.023}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24463018}, abstract = {The study of small RNAs and Argonaute proteins in eukaryotes that are deficient in functional RNA interference could provide insights into novel functions of small RNAs. In this study we describe small non-coding RNAs bound to a distinctive Argonaute protein of Trypanosoma cruzi, TcPIWI-tryp. Co-immunoprecipitation of TcPIWI-tryp followed by deep sequencing of isolated RNA identified abundant small RNAs derived from rRNAs and tRNAs. The small RNA repertoire differed from that of the canonical Argonaute in organisms with functional RNA interference, which could indicate novel biological functions for TcPIWI-tryp in T. cruzi and other members of the trypanosomatid clade.}, pmid = {24463018}, keywords = {Animals,Argonaute Proteins,Argonaute Proteins: metabolism,Base Sequence,Molecular Sequence Data,nosource,Post-Transcriptional,Protein Binding,Protozoan,Protozoan Proteins,Protozoan Proteins: metabolism,Protozoan: genetics,Protozoan: metabolism,Ribosomal,Ribosomal: genetics,Ribosomal: metabolism,RNA,RNA Interference,RNA Processing,Small Untranslated,Small Untranslated: genetics,Small Untranslated: metabolism,Transfer,Transfer: genetics,Transfer: metabolism,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosoma cruzi: metabolism} }

@article{mitaraiRibosomeCollisionsTranslation2008, title = {Ribosome Collisions and Translation Efficiency: Optimization by Codon Usage and {{mRNA}} Destabilization.}, author = {Mitarai, Namiko and Sneppen, Kim and Pedersen, Steen}, year = 2008, month = sep, journal = {Journal of molecular biology}, volume = {382}, number = {1}, eprint = {18619977}, eprinttype = {pubmed}, pages = {236–45}, issn = {1089-8638}, doi = {10.1016/j.jmb.2008.06.068}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18619977}, abstract = {Individual mRNAs are translated by multiple ribosomes that initiate translation with an interval of a few seconds. The ribosome speed is codon dependent, and ribosome queuing has been suggested to explain specific data for translation of some mRNAs in vivo. By modeling the stochastic translation process as a traffic problem, we here analyze conditions and consequences of collisions and queuing. The model allowed us to determine the on-rate (0.8 to 1.1 initiations/s) and the time (1 s) the preceding ribosome occludes initiation for Escherichia coli lacZ mRNA in vivo. We find that ribosome collisions and queues are inevitable consequences of a stochastic translation mechanism that reduce the translation efficiency substantially on natural mRNAs. The cells minimize collisions by having its mRNAs being unstable and by a highly selected codon usage in the start of the mRNA. The cost of mRNA breakdown is offset by the concomitant increase in translation efficiency.}, pmid = {18619977}, keywords = {beta-Galactosidase,beta-Galactosidase: metabolism,Biological,Codon,Codon: metabolism,Conserved Sequence,Escherichia coli,Escherichia coli: metabolism,Genetic Code,Kinetics,Messenger,Messenger: metabolism,Models,nosource,Protein Biosynthesis,Ribosomes,Ribosomes: metabolism,RNA,RNA Stability,Time Factors} }

@article{wenFollowingTranslationSingle2008, title = {Following Translation by Single Ribosomes One Codon at a Time.}, author = {Wen, Jin-Der and Lancaster, Laura and Hodges, Courtney and Zeri, Ana-Carolina and Yoshimura, Shige H. and Noller, Harry F. and Bustamante, Carlos and Tinoco, Ignacio}, year = 2008, month = apr, journal = {Nature}, volume = {452}, number = {7187}, pages = {598–603}, issn = {1476-4687}, doi = {10.1038/nature06716}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2556548&tool=pmcentrez&rendertype=abstract}, abstract = {We have followed individual ribosomes as they translate single messenger RNA hairpins tethered by the ends to optical tweezers. Here we reveal that translation occurs through successive translocation–and-pause cycles. The distribution of pause lengths, with a median of 2.8 s, indicates that at least two rate-determining processes control each pause. Each translocation step measures three bases–one codon-and occurs in less than 0.1 s. Analysis of the times required for translocation reveals, surprisingly, that there are three substeps in each step. Pause lengths, and thus the overall rate of translation, depend on the secondary structure of the mRNA; the applied force destabilizes secondary structure and decreases pause durations, but does not affect translocation times. Translocation and RNA unwinding are strictly coupled ribosomal functions.}, pmid = {18327250}, keywords = {Aminoacylation,Base Pairing,Codon,Codon: genetics,Kinetics,Messenger,Messenger: chemistry,Messenger: genetics,Messenger: metabolism,nosource,Optical Tweezers,Protein Biosynthesis,Protein Biosynthesis: physiology,Ribosomes,Ribosomes: metabolism,RNA,Time Factors,Transfer,Transfer: genetics,Transfer: metabolism} }

@article{kamhawiPhlebotomineSandFlies2006, title = {Phlebotomine Sand Flies and {{Leishmania}} Parasites: Friends or Foes?}, author = {Kamhawi, Shaden}, year = 2006, month = sep, journal = {Trends in parasitology}, volume = {22}, number = {9}, eprint = {16843727}, eprinttype = {pubmed}, pages = {439–45}, issn = {1471-4922}, doi = {10.1016/j.pt.2006.06.012}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16843727}, abstract = {Leishmania parasites need phlebotomine sand flies to complete their life cycle and to propagate. This review looks at Leishmania-sand fly interactions as the parasites develop from amastigotes to infectious metacyclics, highlighting recent findings concerning the evolutionary adaptations that ensure survival of the parasites. Such adaptations include secretion of phosphoglycans, which protect the parasite from digestive enzymes; production of chitinases that degrade the stomodeal valve of the sand fly; secretion of a neuropeptide that arrests midgut and hindgut peristalsis; and attaching to the midgut to avoid expulsion.}, pmid = {16843727}, keywords = {Adaptation,Animals,Galactosyltransferases,Galactosyltransferases: physiology,Glycosphingolipids,Glycosphingolipids: physiology,Host-Parasite Interactions,Insect Vectors,Insect Vectors: parasitology,Intestines,Intestines: parasitology,Leishmania,Leishmania: growth & development,Leishmania: physiology,Leishmaniasis,Leishmaniasis: parasitology,Leishmaniasis: transmission,Life Cycle Stages,nosource,Physiological,Psychodidae,Psychodidae: parasitology} }

@article{preusserGenomewideRNAbindingAnalysis2014, title = {Genome-Wide {{RNA-binding}} Analysis of the Trypanosome {{U1 snRNP}} Proteins {{U1C}} and {{U1-70K}} Reveals Cis/Trans-Spliceosomal Network.}, author = {Preu{}er, Christian and Rossbach, Oliver and Hung, Lee-Hsueh and Li, Dan and Bindereif, Albrecht}, year = 2014, month = jan, journal = {Nucleic acids research}, volume = {42}, number = {10}, pages = {6603–15}, issn = {1362-4962}, doi = {10.1093/nar/gku286}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4041458&tool=pmcentrez&rendertype=abstract}, abstract = {Trans-splicing in trypanosomes adds a 39-nucleotide mini-exon from the spliced leader (SL) RNA to the 5’ end of each protein-coding sequence. On the other hand, cis-splicing of the few intron-containing genes requires the U1 small nuclear ribonucleoprotein (snRNP) particle. To search for potential new functions of the U1 snRNP in Trypanosoma brucei, we applied genome-wide individual-nucleotide resolution crosslinking-immunoprecipitation (iCLIP), focusing on the U1 snRNP-specific proteins U1C and U1-70K. Surprisingly, U1C and U1-70K interact not only with the U1, but also with U6 and SL RNAs. In addition, mapping of crosslinks to the cis-spliced PAP [poly(A) polymerase] pre-mRNA indicate an active role of these proteins in 5’ splice site recognition. In sum, our results demonstrate that the iCLIP approach provides insight into stable and transient RNA-protein contacts within the spliceosomal network. We propose that the U1 snRNP may represent an evolutionary link between the cis- and trans-splicing machineries, playing a dual role in 5’ splice site recognition on the trans-spliceosomal SL RNP as well as on pre-mRNA cis-introns.}, pmid = {24748659}, keywords = {Cell Nucleus,Cell Nucleus: chemistry,Genome,Messenger,Messenger: metabolism,nosource,Protozoan,Protozoan Proteins,Protozoan Proteins: analysis,Protozoan Proteins: metabolism,Ribonucleoprotein,RNA,RNA Precursors,RNA Precursors: metabolism,RNA Splice Sites,RNA Splicing,Small Nuclear,Small Nuclear: metabolism,Spliceosomes,Spliceosomes: metabolism,Trans-Splicing,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: metabolism,U1 Small Nuclear,U1 Small Nuclear: analysis,U1 Small Nuclear: metabolism} }

@article{wangHydroxylRadicalFootprinting1989, title = {Hydroxyl Radical “Footprinting” of {{RNA}}: Application to Pre-{{mRNA}} Splicing Complexes.}, author = {Wang, X. D. and {}a Padgett, R.}, year = 1989, month = oct, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {86}, number = {20}, pages = {7795–9}, issn = {0027-8424}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=298157&tool=pmcentrez&rendertype=abstract}, abstract = {We present an adaptation of the hydroxyl radical DNA “footprinting” technique that permits high-resolution mapping of protected regions of RNA. Hydroxyl radical cleaves RNA independently of base sequence and secondary structure of the RNAs examined and allows resolution of protected regions at the single nucleotide level. By using this technique, we show that several regions of the 3’ splice site of mRNA precursors are protected during the formation of splicing-specific ribonucleoprotein complexes in an in vitro splicing system. These regions include the 3’ intron/exon junction and a portion of the adjacent exon, the polypyrimidine tract, and the site of branch formation. These protections appear to be due to splicing specific complexes since their formation is sensitive to point mutations at crucial residues and requires ATP and incubation. The formation of these protected regions is independent of the presence of a 5’ splice site.}, pmid = {2554290}, keywords = {Animals,Base Sequence,Cell Nucleus,Cell Nucleus: metabolism,Exons,Free Radicals,Genes,Genetic,Globins,Globins: genetics,HeLa Cells,HeLa Cells: metabolism,Humans,Hydroxides,Hydroxyl Radical,Introns,Molecular Sequence Data,nosource,Nucleotide Mapping,Plasmids,Rabbits,Restriction Mapping,RNA Precursors,RNA Precursors: genetics,RNA Splicing,Templates,Transcription} }

@article{belewRibosomalFrameshiftingCCR52014, title = {Ribosomal Frameshifting in the {{CCR5 mRNA}} Is Regulated by {{miRNAs}} and the {{NMD}} Pathway}, author = {Belew, Ashton Trey and Meskauskas, Arturas and Musalgaonkar, Sharmishtha and Advani, Vivek M. and Sulima, Sergey O. and Kasprzak, Wojciech K. and Shapiro, Bruce A. and Dinman, & Jonathan D.}, year = 2014, journal = {Nature}, volume = {doi:10.103}, abstract = {Programmed -1 ribosomal frameshift (-1 PRF) signals redirect translating ribosomes to slip back one base on messenger RNAs. Although well characterized in viruses, how these elements may regulate cellular gene expression is not understood. Here we describe a -1 PRF signal in the human mRNA encoding CCR5, the HIV-1 co-receptor. CCR5 mRNA-mediated -1 PRF is directed by an mRNA pseudoknot, and is stimulated by at least two microRNAs. Mapping the mRNA–miRNA interaction suggests that formation of a triplex RNA structure stimulates -1 PRF. A -1 PRF event on the CCR5 mRNA directs translating ribosomes to a premature termination codon, destabilizing it through the nonsense-mediated mRNA decay pathway. At least one additional mRNA decay pathway is also involved. Functional -1 PRF signals that seem to be regulated by miRNAs are also demonstrated in mRNAs encoding six other cytokine receptors, suggesting a novel mode through which immune responses may be fine-tuned in mammalian cells.}, keywords = {nosource} }

@article{messieresSinglemoleculeMeasurementsCCR52014, title = {Single-Molecule Measurements of the {{CCR5 mRNA}} Unfolding Pathways.}, author = {{}de Messieres, Michel and Chang, Jen-Chien and Belew, Ashton Trey and Meskauskas, Arturas and Dinman, Jonathan D. and Porta, Arthur La}, year = 2014, month = jan, journal = {Biophysical journal}, volume = {106}, number = {1}, eprint = {24411256}, eprinttype = {pubmed}, pages = {244–52}, publisher = {Biophysical Society}, issn = {1542-0086}, doi = {10.1016/j.bpj.2013.09.036}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24411256}, abstract = {Secondary or tertiary structure in an mRNA, such as a pseudoknot, can create a physical barrier that requires the ribosome to generate additional force to translocate. The presence of such a barrier can dramatically increase the probability that the ribosome will shift into an alternate reading frame, in which a different set of codons is recognized. The detailed biophysical mechanism by which frameshifting is induced remains unknown. Here we employ optical trapping techniques to investigate the structure of a -1 programmed ribosomal frameshift (-1 PRF) sequence element located in the CCR5 mRNA, which encodes a coreceptor for HIV-1 and is, to our knowledge, the first known human -1 PRF signal of nonviral origin. We begin by presenting a set of computationally predicted structures that include pseudoknots. We then employ what we believe to be new analytical techniques for measuring the effective free energy landscapes of biomolecules. We find that the -1 PRF element manifests several distinct unfolding pathways when subject to end-to-end force, one of which is consistent with a proposed pseudoknot conformation, and another of which we have identified as a folding intermediate. The dynamic ensemble of conformations that CCR5 mRNA exhibits in the single-molecule experiments may be a significant feature of the frameshifting mechanism.}, pmid = {24411256}, keywords = {Base Sequence,CCR5,CCR5: genetics,Humans,Messenger,Messenger: chemistry,Molecular Sequence Data,nosource,Nucleotide Motifs,Optical Tweezers,Receptors,RNA,RNA Folding,Thermodynamics} }

@article{barbosaGeneExpressionRegulation2013, title = {Gene Expression Regulation by Upstream Open Reading Frames and Human Disease.}, author = {Barbosa, Cristina and Peixeiro, Isabel and Rom{~a}o, Lu{'i}sa}, year = 2013, month = jan, journal = {PLoS genetics}, volume = {9}, number = {8}, pages = {e1003529}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1003529}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3738444&tool=pmcentrez&rendertype=abstract}, abstract = {Upstream open reading frames (uORFs) are major gene expression regulatory elements. In many eukaryotic mRNAs, one or more uORFs precede the initiation codon of the main coding region. Indeed, several studies have revealed that almost half of human transcripts present uORFs. Very interesting examples have shown that these uORFs can impact gene expression of the downstream main ORF by triggering mRNA decay or by regulating translation. Also, evidence from recent genetic and bioinformatic studies implicates disturbed uORF-mediated translational control in the etiology of many human diseases, including malignancies, metabolic or neurologic disorders, and inherited syndromes. In this review, we will briefly present the mechanisms through which uORFs regulate gene expression and how they can impact on the organism’s response to different cell stress conditions. Then, we will emphasize the importance of these structures by illustrating, with specific examples, how disturbed uORF-mediated translational control can be involved in the etiology of human diseases, giving special importance to genotype-phenotype correlations. Identifying and studying more cases of uORF-altering mutations will help us to understand and establish genotype-phenotype associations, leading to advancements in diagnosis, prognosis, and treatment of many human disorders.}, pmid = {23950723}, keywords = {5’ Untranslated Regions,5’ Untranslated Regions: genetics,Disease,Disease: genetics,Gene Expression Regulation,Genetic Association Studies,Humans,Mutation,nosource,Nucleic Acid,Nucleic Acid: genetics,Open Reading Frames,Open Reading Frames: genetics,Protein Biosynthesis,Protein Biosynthesis: genetics,Regulatory Sequences,RNA Stability} }

@article{rabaniMetabolicLabelingRNA2011, title = {Metabolic Labeling of {{RNA}} Uncovers Principles of {{RNA}} Production and Degradation Dynamics in Mammalian Cells.}, author = {Rabani, Michal and Levin, Joshua Z. and Fan, Lin and Adiconis, Xian and Raychowdhury, Raktima and Garber, Manuel and Gnirke, Andreas and Nusbaum, Chad and Hacohen, Nir and Friedman, Nir and Amit, Ido and Regev, Aviv}, year = 2011, month = may, journal = {Nature biotechnology}, volume = {29}, number = {5}, pages = {436–42}, publisher = {Nature Publishing Group}, issn = {1546-1696}, doi = {10.1038/nbt.1861}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3114636&tool=pmcentrez&rendertype=abstract}, abstract = {Cellular RNA levels are determined by the interplay of RNA production, processing and degradation. However, because most studies of RNA regulation do not distinguish the separate contributions of these processes, little is known about how they are temporally integrated. Here we combine metabolic labeling of RNA at high temporal resolution with advanced RNA quantification and computational modeling to estimate RNA transcription and degradation rates during the response of mouse dendritic cells to lipopolysaccharide. We find that changes in transcription rates determine the majority of temporal changes in RNA levels, but that changes in degradation rates are important for shaping sharp ‘peaked’ responses. We used sequencing of the newly transcribed RNA population to estimate temporally constant RNA processing and degradation rates genome wide. Degradation rates vary significantly between genes and contribute to the observed differences in the dynamic response. Certain transcripts, including those encoding cytokines and transcription factors, mature faster. Our study provides a quantitative approach to study the integrative process of RNA regulation.}, pmid = {21516085}, keywords = {Animals,Biotinylation,Biotinylation: methods,Cells,Computational Biology,Cultured,Dendritic Cells,Dendritic Cells: metabolism,Down-Regulation,Female,Genetic,Genetic Association Studies,Inbred C57BL,Lipopolysaccharides,Lipopolysaccharides: metabolism,Messenger,Messenger: biosynthesis,Messenger: genetics,Mice,Models,Molecular,nosource,RNA,RNA Polymerase II,RNA Polymerase II: metabolism,RNA: genetics,RNA: metabolism,RNA: methods,Sequence Analysis,Transcription,Transcription Factors,Transcription Factors: genetics,Transcription Factors: metabolism,Up-Regulation} }

@article{dolkenHighresolutionGeneExpression2008, title = {High-Resolution Gene Expression Profiling for Simultaneous Kinetic Parameter Analysis of {{RNA}} Synthesis and Decay.}, author = {D{"o}lken, Lars and Ruzsics, Zsolt and R{"a}dle, Bernd and Friedel, Caroline C. and Zimmer, Ralf and Mages, J{"o}rg and Hoffmann, Reinhard and Dickinson, Paul and Forster, Thorsten and Ghazal, Peter and Koszinowski, Ulrich H.}, year = 2008, month = sep, journal = {RNA (New York, N.Y.)}, volume = {14}, number = {9}, pages = {1959–72}, issn = {1469-9001}, doi = {10.1261/rna.1136108}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2525961&tool=pmcentrez&rendertype=abstract}, abstract = {RNA levels in a cell are determined by the relative rates of RNA synthesis and decay. State-of-the-art transcriptional analyses only employ total cellular RNA. Therefore, changes in RNA levels cannot be attributed to RNA synthesis or decay, and temporal resolution is poor. Recently, it was reported that newly transcribed RNA can be biosynthetically labeled for 1-2 h using thiolated nucleosides, purified from total cellular RNA and subjected to microarray analysis. However, in order to study signaling events at molecular level, analysis of changes occurring within minutes is required. We developed an improved approach to separate total cellular RNA into newly transcribed and preexisting RNA following 10-15 min of metabolic labeling. Employing new computational tools for array normalization and half-life determination we simultaneously study short-term RNA synthesis and decay as well as their impact on cellular transcript levels. As an example we studied the response of fibroblasts to type I and II interferons (IFN). Analysis of RNA transcribed within 15-30 min at different times during the first three hours of interferon-receptor activation resulted in a {\(>\)}10-fold increase in microarray sensitivity and provided a comprehensive profile of the kinetics of IFN-mediated changes in gene expression. We identify a previously undisclosed highly connected network of short-lived transcripts selectively down-regulated by IFNgamma in between 30 and 60 min after IFN treatment showing strong associations with cell cycle and apoptosis, indicating novel mechanisms by which IFNgamma affects these pathways.}, isbn = {4989516052}, pmid = {18658122}, keywords = {Animals,Fibroblasts,Fibroblasts: drug effects,Fibroblasts: metabolism,Gene Expression Profiling,Gene Expression Profiling: methods,Gene Expression Regulation,Genetic,Interferon Type I,Interferon Type I: pharmacology,Interferon-gamma,Interferon-gamma: pharmacology,Messenger,Messenger: analysis,Messenger: biosynthesis,Mice,NIH 3T3 Cells,nosource,RNA,RNA Stability,RNA Stability: genetics,Transcription} } % == BibTeX quality report for dolkenHighresolutionGeneExpression2008: % ? Possibly abbreviated journal title RNA (New York, N.Y.)

@article{haanstraControlRegulationGene2008, title = {Control and Regulation of Gene Expression: Quantitative Analysis of the Expression of Phosphoglycerate Kinase in Bloodstream Form {{Trypanosoma}} Brucei.}, author = {Haanstra, Jurgen R. and Stewart, Mhairi and Luu, Van-Duc and {}van Tuijl, Arjen and Westerhoff, Hans V. and Clayton, Christine and Bakker, Barbara M.}, year = 2008, month = feb, journal = {The Journal of biological chemistry}, volume = {283}, number = {5}, eprint = {17991737}, eprinttype = {pubmed}, pages = {2495–507}, issn = {0021-9258}, doi = {10.1074/jbc.M705782200}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17991737}, abstract = {Isoenzymes of phosphoglycerate kinase in Trypanosoma brucei are differentially expressed in its two main life stages. This study addresses how the organism manages to make sufficient amounts of the isoenzyme with the correct localization, which processes (transcription, splicing, and RNA degradation) control the levels of mRNAs, and how the organism regulates the switch in isoform expression. For this, we combined new quantitative measurements of phosphoglycerate kinase mRNA abundance, RNA precursor stability, trans splicing, and ribosome loading with published data and made a kinetic computer model. For the analysis of regulation we extended regulation analysis. Although phosphoglycerate kinase mRNAs are present at surprisingly low concentrations (e.g. 12 molecules per cell), its protein is highly abundant. Substantial control of mRNA and protein levels was exerted by both mRNA synthesis and degradation, whereas splicing and precursor degradation had little control on mRNA and protein concentrations. Yet regulation of mRNA levels does not occur by transcription, but by adjusting mRNA degradation. The contribution of splicing to regulation is negligible, as for all cases where splicing is faster than RNA precursor degradation.}, pmid = {17991737}, keywords = {Animals,Biological,Computer Simulation,Gene Expression Regulation,Genes,Genetic,Isoenzymes,Isoenzymes: genetics,Isoenzymes: metabolism,Kinetics,Messenger,Messenger: genetics,Messenger: metabolism,Models,nosource,Phosphoglycerate Kinase,Phosphoglycerate Kinase: genetics,Phosphoglycerate Kinase: metabolism,Protozoan,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Protozoan: genetics,Protozoan: metabolism,Ribosomes,Ribosomes: metabolism,RNA,RNA Splicing,Transcription,Trypanosoma brucei brucei,Trypanosoma brucei brucei: enzymology,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: growth & development} }

@article{nakatogawaRibosomalExitTunnel2002, title = {The Ribosomal Exit Tunnel Functions as a Discriminating Gate}, author = {Nakatogawa, Hitoshi and Ito, Koreaki}, year = 2002, journal = {Cell}, volume = {108}, pages = {629–636}, url = {http://www.sciencedirect.com/science/article/pii/S0092867402006499}, keywords = {nosource} }

@article{girnaryStructurefunctionAnalysisRibosomal2007, title = {Structure-Function Analysis of the Ribosomal Frameshifting Signal of Two Human Immunodeficiency Virus Type 1 Isolates with Increased Resistance to Viral Protease Inhibitors.}, author = {Girnary, Roseanne and King, Louise and Robinson, Laurence and Elston, Robert and Brierley, Ian}, year = 2007, month = jan, journal = {The Journal of general virology}, volume = {88}, number = {Pt 1}, eprint = {17170455}, eprinttype = {pubmed}, pages = {226–35}, issn = {0022-1317}, doi = {10.1099/vir.0.82064-0}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17170455}, abstract = {Expression of the pol-encoded proteins of human immunodeficiency virus type 1 (HIV-1) requires a programmed -1 ribosomal frameshift at the junction of the gag and pol coding sequences. Frameshifting takes place at a heptanucleotide slippery sequence, UUUUUUA, and is enhanced by a stimulatory RNA structure located immediately downstream. In patients undergoing viral protease (PR) inhibitor therapy, a p1/p6(gag) L449F cleavage site (CS) mutation is often observed in resistant isolates and frequently generates, at the nucleotide sequence level, a homopolymeric and potentially slippery sequence (UUUUCUU to UUUUUUU). The mutation is located within the stimulatory RNA downstream of the authentic slippery sequence and could act to augment levels of pol-encoded enzymes to counteract the PR deficit. Here, RNA secondary structure probing was employed to investigate the structure of a CS-containing frameshift signal, and the effect of this mutation on ribosomal frameshift efficiency in vitro and in tissue culture cells was determined. A second mutation, a GGG insertion in the loop of the stimulatory RNA that could conceivably lead to resistance by enhancing the activity of the structure, was also tested. It was found, however, that the CS and GGG mutations had only a very modest effect on the structure and activity of the HIV-1 frameshift signal. Thus the increased resistance to viral protease inhibitors seen with HIV-1 isolates containing mutations in the frameshifting signal is unlikely to be accounted for solely by enhancement of frameshift efficiency.}, pmid = {17170455}, keywords = {Drug Resistance,Frameshifting,Gene Expression Regulation,HIV Protease Inhibitors,HIV Protease Inhibitors: pharmacology,HIV-1,HIV-1: drug effects,HIV-1: genetics,HIV-1: isolation & purification,Humans,nosource,Nucleic Acid Conformation,Ribosomal,RNA,Viral,Viral: chemistry,Viral: genetics} }

@article{crickCodesCommas1957, title = {Codes without Commas}, author = {Crick, F. H. C. and Griffith, J. S. and Orgel, L. E.}, year = 1957, journal = { of Sciences of the United States }, volume = {64}, number = {x}, pages = {416–421}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528468/}, keywords = {nosource} }

@article{ibbaAdaptorHypothesisRevisited2000, title = {The Adaptor Hypothesis Revisited.}, author = {Ibba, M. and Becker, H. D. and Stathopoulos, C. and Tumbula, D. L. and S{"o}ll, D.}, year = 2000, month = jul, journal = {Trends in biochemical sciences}, volume = {25}, number = {7}, eprint = {16569314}, eprinttype = {pubmed}, pages = {311–6}, issn = {0968-0004}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16569314}, abstract = {As originally postulated in Crick’s Adaptor hypothesis, the faithful synthesis of proteins from messenger RNA is dependent on the presence of perfectly acylated tRNAs. The hypothesis also suggested that each aminoacyl-tRNA would be made by a unique enzyme. Recent data have now forced a revision of this latter point, with an increasingly diverse array of enzymes and pathways being implicated in aminoacyl-tRNA synthesis. These unexpected findings have far-reaching implications for our understanding of protein synthesis and its origins.}, pmid = {10871880}, keywords = {Amino Acid-Specific,Amino Acid-Specific: biosynthesis,Amino Acid-Specific: genetics,Amino Acid-Specific: metabolism,Amino Acyl-tRNA Synthetases,Amino Acyl-tRNA Synthetases: classification,Amino Acyl-tRNA Synthetases: genetics,Amino Acyl-tRNA Synthetases: metabolism,Archaeal Proteins,Archaeal Proteins: genetics,Archaeal Proteins: metabolism,Evolution,Genetic,Lysine-tRNA Ligase,Lysine-tRNA Ligase: classification,Lysine-tRNA Ligase: metabolism,Models,Molecular,nosource,Phylogeny,Protein Biosynthesis,RNA,Substrate Specificity,Transfer} }

@article{gamowPossibleRelationDeoxyribonucleic1954, title = {Possible Relation between Deoxyribonucleic Acid and Protein Structures}, author = {Gamow, G.}, year = 1954, journal = {Nature}, number = {173}, pages = {318}, url = {http://www.nature.com/nature/journal/v173/n4398/abs/173318a0.html}, keywords = {nosource} }

@article{lambertzSecretedVirulenceFactors2012, title = {Secreted Virulence Factors and Immune Evasion in Visceral Leishmaniasis.}, author = {Lambertz, Ulrike and Silverman, Judith Maxwell and Nandan, Devki and McMaster, W. Robert and Clos, Joachim and Foster, Leonard J. and Reiner, Neil E.}, year = 2012, month = jun, journal = {Journal of leukocyte biology}, volume = {91}, number = {6}, eprint = {22442494}, eprinttype = {pubmed}, pages = {887–99}, issn = {1938-3673}, doi = {10.1189/jlb.0611326}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22442494}, abstract = {Evasion or subversion of host immune responses is a well-established paradigm in infection with visceralizing leishmania. In this review, we summarize current findings supporting a model in which leishmania target host regulatory molecules and pathways, such as the PTP SHP-1 and the PI3K/Akt signaling cascade, to prevent effective macrophage activation. Furthermore, we describe how virulence factors, secreted by leishmania, interfere with macrophage intracellular signaling. Finally, we discuss mechanisms of secretion and provide evidence that leishmania use a remarkably adept, exosome-based secretion mechanism to export and deliver effector molecules to host cells. In addition to representing a novel mechanism for trafficking of virulence factors across membranes, recent findings indicate that leishmania exosomes may have potential as vaccine candidates.}, pmid = {22442494}, keywords = {Animals,Humans,Leishmania donovani,Leishmania donovani: immunology,Leishmania donovani: metabolism,Leishmaniasis,Non-Receptor Type 6,Non-Receptor Type 6:,nosource,Phosphatidylinositol 3-Kinases,Phosphatidylinositol 3-Kinases: immunology,Phosphatidylinositol 3-Kinases: metabolism,Protein Transport,Protein Transport: immunology,Protein Tyrosine Phosphatase,Proto-Oncogene Proteins c-akt,Proto-Oncogene Proteins c-akt: immunology,Proto-Oncogene Proteins c-akt: metabolism,Protozoan Proteins,Protozoan Proteins: immunology,Protozoan Proteins: secretion,Signal Transduction,Signal Transduction: immunology,Virulence Factors,Virulence Factors: immunology,Virulence Factors: metabolism,Visceral,Visceral: immunology,Visceral: metabolism} }

@article{yuClusterProfilerPackageComparing2012, title = {{{clusterProfiler}}: An {{R}} Package for Comparing Biological Themes among Gene Clusters.}, author = {Yu, Guangchuang and Wang, Li-Gen and Han, Yanyan and He, Qing-Yu}, year = 2012, month = may, journal = {Omics : a journal of integrative biology}, volume = {16}, number = {5}, pages = {284–7}, issn = {1557-8100}, doi = {10.1089/omi.2011.0118}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3339379&tool=pmcentrez&rendertype=abstract}, abstract = {Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.}, pmid = {22455463}, keywords = {Animals,Gene Expression Profiling,Gene Expression Profiling: methods,Humans,Mice,Multigene Family,nosource,Programming Languages,Proteomics,Proteomics: methods,Software,Transcriptome,Yeasts} }

@article{dilliesComprehensiveEvaluationNormalization2013, title = {A Comprehensive Evaluation of Normalization Methods for {{Illumina}} High-Throughput {{RNA}} Sequencing Data Analysis.}, author = {Dillies, Marie-Agn{`e}s and Rau, Andrea and Aubert, Julie and {Hennequet-Antier}, Christelle and Jeanmougin, Marine and Servant, Nicolas and Keime, C{'e}line and Marot, Guillemette and Castel, David and Estelle, Jordi and Guernec, Gregory and Jagla, Bernd and Jouneau, Luc and Lalo{"e}, Denis and Gall, Caroline Le and Scha{"e}ffer, Brigitte and Crom, St{'e}phane Le and Guedj, Micka{"e}l and Jaffr{'e}zic, Florence}, year = 2013, month = nov, journal = {Briefings in bioinformatics}, volume = {14}, number = {6}, eprint = {22988256}, eprinttype = {pubmed}, pages = {671–83}, issn = {1477-4054}, doi = {10.1093/bib/bbs046}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22988256}, abstract = {During the last 3 years, a number of approaches for the normalization of RNA sequencing data have emerged in the literature, differing both in the type of bias adjustment and in the statistical strategy adopted. However, as data continue to accumulate, there has been no clear consensus on the appropriate normalization method to be used or the impact of a chosen method on the downstream analysis. In this work, we focus on a comprehensive comparison of seven recently proposed normalization methods for the differential analysis of RNA-seq data, with an emphasis on the use of varied real and simulated datasets involving different species and experimental designs to represent data characteristics commonly observed in practice. Based on this comparison study, we propose practical recommendations on the appropriate normalization method to be used and its impact on the differential analysis of RNA-seq data.}, pmid = {22988256}, keywords = {High-Throughput Nucleotide Sequencing,High-Throughput Nucleotide Sequencing: methods,High-Throughput Nucleotide Sequencing: standards,nosource,RNA,RNA: methods,RNA: standards,Sequence Analysis} }

@techreport{loveModeratedEstimationFold2014, title = {Moderated Estimation of Fold Change and Dispersion for {{RNA-Seq}} Data with {{DESeq2}}}, author = {Love, Michael I. and Huber, Wolfgang and Anders, Simon}, year = 2014, journal = {bioRxiv}, issn = {1465-6906}, doi = {10.1101/002832}, isbn = {0-00-000000-0}, pmid = {1000006699}, keywords = {nosource} } % == BibTeX quality report for loveModeratedEstimationFold2014: % Missing required field ‘institution’

@article{mccarthyDifferentialExpressionAnalysis2012, title = {Differential Expression Analysis of Multifactor {{RNA-Seq}} Experiments with Respect to Biological Variation.}, author = {McCarthy, Davis J. and Chen, Yunshun and Smyth, Gordon K.}, year = 2012, month = may, journal = {Nucleic acids research}, volume = {40}, number = {10}, pages = {4288–97}, issn = {1362-4962}, doi = {10.1093/nar/gks042}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3378882&tool=pmcentrez&rendertype=abstract}, abstract = {A flexible statistical framework is developed for the analysis of read counts from RNA-Seq gene expression studies. It provides the ability to analyse complex experiments involving multiple treatment conditions and blocking variables while still taking full account of biological variation. Biological variation between RNA samples is estimated separately from the technical variation associated with sequencing technologies. Novel empirical Bayes methods allow each gene to have its own specific variability, even when there are relatively few biological replicates from which to estimate such variability. The pipeline is implemented in the edgeR package of the Bioconductor project. A case study analysis of carcinoma data demonstrates the ability of generalized linear model methods (GLMs) to detect differential expression in a paired design, and even to detect tumour-specific expression changes. The case study demonstrates the need to allow for gene-specific variability, rather than assuming a common dispersion across genes or a fixed relationship between abundance and variability. Genewise dispersions de-prioritize genes with inconsistent results and allow the main analysis to focus on changes that are consistent between biological replicates. Parallel computational approaches are developed to make non-linear model fitting faster and more reliable, making the application of GLMs to genomic data more convenient and practical. Simulations demonstrate the ability of adjusted profile likelihood estimators to return accurate estimators of biological variability in complex situations. When variation is gene-specific, empirical Bayes estimators provide an advantageous compromise between the extremes of assuming common dispersion or separate genewise dispersion. The methods developed here can also be applied to count data arising from DNA-Seq applications, including ChIP-Seq for epigenetic marks and DNA methylation analyses.}, pmid = {22287627}, keywords = {Algorithms,Bayes Theorem,Carcinoma,Gene Expression Profiling,Genetic Variation,High-Throughput Nucleotide Sequencing,Linear Models,Mouth Neoplasms,Mouth Neoplasms: genetics,Mouth Neoplasms: metabolism,nosource,RNA,Sequence Analysis,Squamous Cell,Squamous Cell: genetics,Squamous Cell: metabolism} }

@article{jhaDepletionTrypanosomePumilio2014, title = {Depletion of the {{Trypanosome Pumilio Domain Protein PUF2}} or of {{Some Other Essential Proteins Causes Transcriptome Changes Related}} to {{Coding Region Length}}.}, author = {Jha, Bhaskar Anand and Fadda, Abeer and Merce, Clementine and Mugo, Elisha and Droll, Dorothea and Clayton, Christine}, year = 2014, month = may, journal = {Eukaryotic cell}, volume = {13}, number = {5}, eprint = {24681684}, eprinttype = {pubmed}, pages = {664–74}, issn = {1535-9786}, doi = {10.1128/EC.00018-14}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24681684}, abstract = {Pumilio domain RNA-binding proteins are known mainly as posttranscriptional repressors of gene expression that reduce mRNA translation and stability. Trypanosoma brucei has 11 PUF proteins. We show here that PUF2 is in the cytosol, with roughly the same number of molecules per cell as there are mRNAs. Although PUF2 exhibits a low level of in vivo RNA binding, it is not associated with polysomes. PUF2 also decreased reporter mRNA levels in a tethering assay, consistent with a repressive role. Depletion of PUF2 inhibited growth of bloodstream-form trypanosomes, causing selective loss of mRNAs with long open reading frames and increases in mRNAs with shorter open reading frames. Reexamination of published RNASeq data revealed the same trend in cells depleted of some other proteins. We speculate that these length effects could be caused by inhibition of the elongation phase of transcription or by an influence of translation status or polysomal conformation on mRNA decay.}, pmid = {24681684}, keywords = {nosource} } % == BibTeX quality report for jhaDepletionTrypanosomePumilio2014: % ? Title looks like it was stored in title-case in Zotero

@article{noyesPreviouslyUnclassifiedTrypanosomatid2002, title = {A Previously Unclassified Trypanosomatid Responsible for Human Cutaneous Lesions in {{Martinique}} ({{French West Indies}}) Is the Most Divergent Member of the Genus {{Leishmania}} Ss.}, author = {Noyes, H. and Pratlong, F. and Chance, M. and Ellis, J. and Lanotte, G. and Dedet, J. P.}, year = 2002, month = jan, journal = {Parasitology}, volume = {124}, number = {Pt 1}, eprint = {11811799}, eprinttype = {pubmed}, pages = {17–24}, issn = {0031-1820}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11811799}, abstract = {Two cases of skin lesions similar to those caused by Leishmania parasites have been reported from Martinique. Parasites isolated from these lesions were unlike Leishmania reference strains by isoenzyme analysis and electron microscopy and were assumed to be monoxenous trypanosomatids which normally only infect invertebrates. Both strains have now been retyped by isoenzyme analysis and found to be identical to each other and distantly related to all other Leishmania species. The sequence of the 18S ribosomal RNA gene and partial sequences of the DNA polymerase alpha and RNA polymerase II largest subunit genes were obtained. These sequences indicated that the Martinique parasites clustered with L. enriettii and were basal to all other euleishmania. However, support for both the position basal to all euleishmania and the clustering with L. enriettii was low. The Martinique parasites may cluster with L. (Leishmania) or L. (Viannia) or form a novel clade within the euleishmania either with or without L. enriettii.}, pmid = {11811799}, keywords = {Animals,Cutaneous,Cutaneous: parasitology,Cutaneous: pathology,DNA,DNA Polymerase I,DNA Polymerase I: chemistry,DNA Polymerase I: genetics,Electrophoresis,Humans,Isoenzymes,Isoenzymes: metabolism,Leishmania,Leishmania: classification,Leishmania: enzymology,Leishmania: genetics,Leishmaniasis,Martinique,nosource,Nucleic Acid,Phylogeny,Polymerase Chain Reaction,Protozoan,Protozoan: chemistry,Protozoan: genetics,Protozoan: isolation & purification,Ribosomal,Ribosomal: chemistry,Ribosomal: genetics,Ribosomal: isolation & purification,RNA Polymerase II,RNA Polymerase II: chemistry,RNA Polymerase II: genetics,Sequence Alignment,Sequence Analysis,Sequence Homology,Starch Gel} }

@article{sieversFastScalableGeneration2011, title = {Fast, Scalable Generation of High-Quality Protein Multiple Sequence Alignments Using {{Clustal Omega}}.}, author = {Sievers, Fabian and Wilm, Andreas and Dineen, David and Gibson, Toby J. and Karplus, Kevin and Li, Weizhong and Lopez, Rodrigo and McWilliam, Hamish and Remmert, Michael and S{"o}ding, Johannes and Thompson, Julie D. and Higgins, Desmond G.}, year = 2011, month = jan, journal = {Molecular systems biology}, volume = {7}, number = {539}, pages = {539}, issn = {1744-4292}, doi = {10.1038/msb.2011.75}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3261699&tool=pmcentrez&rendertype=abstract}, abstract = {Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.}, pmid = {21988835}, keywords = {Algorithms,Amino Acid Sequence,Base Sequence,Data Mining,Data Mining: methods,Databases,Factual,Molecular Sequence Data,nosource,Protein,Protein: methods,Proteins,Proteins: analysis,Proteins: chemistry,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis,Software,Systems Biology,Systems Biology: instrumentation,Systems Biology: methods} }

@article{edgarMUSCLEMultipleSequence2004, title = {{{MUSCLE}}: Multiple Sequence Alignment with High Accuracy and High Throughput.}, author = {Edgar, Robert C.}, year = 2004, month = jan, journal = {Nucleic acids research}, volume = {32}, number = {5}, pages = {1792–7}, issn = {1362-4962}, doi = {10.1093/nar/gkh340}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=390337&tool=pmcentrez&rendertype=abstract}, abstract = {We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.}, pmid = {15034147}, keywords = {Algorithms,Amino Acid Motifs,Amino Acid Sequence,Internet,Molecular Sequence Data,nosource,Protein,Protein: methods,Reproducibility of Results,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis,Software,Time Factors} }

@article{castresanaSelectionConservedBlocks2000, title = {Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis.}, author = {Castresana, J.}, year = 2000, month = apr, journal = {Molecular biology and evolution}, volume = {17}, number = {4}, eprint = {10742046}, eprinttype = {pubmed}, pages = {540–52}, issn = {0737-4038}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10742046}, abstract = {The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not be homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of informative sites is presented here. The method is based on the selection of blocks of positions that fulfill a simple set of requirements with respect to the number of contiguous conserved positions, lack of gaps, and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. The percentages of removed positions were higher in the most divergent alignments. After removing divergent segments, the amino acid composition of the different sequences was more uniform, and pairwise distances became much smaller. Phylogenetic trees show that topologies can be different after removing conserved blocks, particularly when there are several poorly resolved nodes. Strong support was found for the grouping of animals and fungi but not for the position of more basal eukaryotes. The use of a computerized method such as the one presented here reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.}, pmid = {10742046}, keywords = {Amino Acid Sequence,Conserved Sequence,Conserved Sequence: genetics,DNA,Eukaryotic Cells,Likelihood Functions,Mitochondrial,Mitochondrial: analysis,Molecular Sequence Data,nosource,Phylogeny,Sequence Alignment,Sequence Alignment: methods,Software} }

@article{krzywinskiCircosInformationAesthetic2009, title = {Circos: {{An}} Information Aesthetic for Comparative Genomics}, shorttitle = {Circos}, author = {Krzywinski, Martin and Schein, Jacqueline and Birol, {.I}nan{} and Connors, Joseph and Gascoyne, Randy and Horsman, Doug and Jones, Steven J. and Marra, Marco A.}, year = 2009, month = jan, journal = {Genome Research}, volume = {19}, number = {9}, pages = {1639–1645}, publisher = {Cold Spring Harbor Lab}, issn = {1088-9051, 1549-5469}, doi = {10.1101/gr.092759.109}, url = {http://genome.cshlp.org/content/19/9/1639}, urldate = {2025-11-03}, abstract = {We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.}, langid = {english}, pmid = {19541911}, keywords = {Animals,Artificial,Bacterial,Chromosome Mapping,Chromosomes,Contig Mapping,Dogs,Follicular,Follicular: genetics,Gene Dosage,Gene Dosage: genetics,Genome,Genome: genetics,Genomics,Human,Humans,Lymphoma,Pair 17,Pair 17: genetics,Pair 6,Pair 6: genetics,Software}, file = {/home/trey/Zotero/storage/TV2C9CTH/Krzywinski et al. - 2009 - Circos An information aesthetic for comparative genomics.pdf} } % == BibTeX quality report for krzywinskiCircosInformationAesthetic2009: % ? unused Journal abbr (“Genome Res.”) % ? unused Library catalog (“genome.cshlp.org”)

@article{guydoshDom34RescuesRibosomes2014, title = {Dom34 Rescues Ribosomes in 3’ Untranslated Regions.}, author = {Guydosh, Nicholas R. and Green, Rachel}, year = 2014, month = feb, journal = {Cell}, volume = {156}, number = {5}, eprint = {24581494}, eprinttype = {pubmed}, pages = {950–62}, publisher = {Elsevier}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.02.006}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24581494}, abstract = {Ribosomes that stall before completing peptide synthesis must be recycled and returned to the cytoplasmic pool. The protein Dom34 and cofactors Hbs1 and Rli1 can dissociate stalled ribosomes in vitro, but the identity of targets in the cell is unknown. Here, we extend ribosome profiling methodology to reveal a high-resolution molecular characterization of Dom34 function in vivo. Dom34 removes stalled ribosomes from truncated mRNAs, but, in contrast, does not generally dissociate ribosomes on coding sequences known to trigger stalling, such as polyproline. We also show that Dom34 targets arrested ribosomes near the ends of 3’ UTRs. These ribosomes appear to gain access to the 3’ UTR via a mechanism that does not require decoding of the mRNA. These results suggest that ribosomes frequently enter downstream noncoding regions and that Dom34 carries out the important task of rescuing them.}, pmid = {24581494}, keywords = {nosource} }

@article{zhangInvolvementSRProteins2004, title = {Involvement of {{SR}} Proteins in {{mRNA}} Surveillance.}, author = {Zhang, Zuo and Krainer, Adrian R.}, year = 2004, month = nov, journal = {Molecular cell}, volume = {16}, number = {4}, eprint = {15546619}, eprinttype = {pubmed}, pages = {597–607}, issn = {1097-2765}, doi = {10.1016/j.molcel.2004.10.031}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15546619}, abstract = {Nonsense mutations influence several aspects of gene expression, including mRNA stability and splicing fidelity, but the mechanism by which premature termination codons (PTCs) can apparently affect splice-site selection remains elusive. We used a model human beta-globin gene with duplicated 5’ splice sites (5’ss) and found that PTCs inserted between the two 5’ss do not directly influence splicing in this system. Instead, their apparent effect on 5’ss selection in vivo is an indirect result of nonsense-mediated mRNA decay (NMD), as conditions that eliminated NMD also abrogated the effect on splicing. Remarkably, we found an unexpected function of SR proteins in targeting several mRNAs with PTCs to the NMD pathway. Overexpression of various SR proteins strongly enhanced NMD, and this effect required an RS domain. Our data argue against a universal role of PTCs in regulating pre-mRNA splicing and reveal an additional function of SR proteins in eukaryotic gene expression.}, pmid = {15546619}, keywords = {Animals,Blotting,Cercopithecus aethiops,Codon,COS Cells,Exons,Gene Expression Regulation,Globins,Globins: genetics,HeLa Cells,Humans,Introns,Messenger,Messenger: genetics,Messenger: metabolism,Nonsense,nosource,Nuclear Proteins,Nuclear Proteins: genetics,Nuclear Proteins: metabolism,Point Mutation,RNA,RNA Interference,RNA Precursors,RNA Precursors: metabolism,RNA Splicing,RNA Stability,RNA-Binding Proteins,Terminator,Western} }

@article{schuelerDifferentialProteinOccupancy2014, title = {Differential Protein Occupancy Profiling of the {{mRNA}} Transcriptome.}, author = {Schueler, Markus and Munschauer, Mathias and Gregersen, Lea Haarup and Finzel, Ana and Loewer, Alexander and Chen, Wei and Landthaler, Markus and Dieterich, Christoph}, year = 2014, month = jan, journal = {Genome biology}, volume = {15}, number = {1}, eprint = {24417896}, eprinttype = {pubmed}, pages = {R15}, issn = {1465-6914}, doi = {10.1186/gb-2014-15-1-r15}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24417896}, abstract = {BACKGROUND: RNA-binding proteins (RBPs) mediate mRNA biogenesis, translation and decay. We recently developed an approach to profile transcriptome-wide RBP contacts on polyadenylated transcripts by next-generation sequencing. A comparison of such profiles from different biological conditions has the power to unravel dynamic changes in protein-contacted cis-regulatory mRNA regions without a priori knowledge of the regulatory protein component. RESULTS: We compared protein occupancy profiles of polyadenylated transcripts in MCF7 and HEK293 cells. Briefly, we developed a bioinformatics workflow to identify differential crosslinking sites in cDNA reads of 4-thiouridine crosslinked polyadenylated RNA samples. We identified 30,000 differential crosslinking sites between MCF7 and HEK293 cells at an estimated false discovery rate of 10%. 73% of all reported differential protein-RNA contact sites cannot be explained by local changes in exon usage as indicated by complementary RNA-seq data. The majority of differentially crosslinked positions are located in 3’ UTRs, show distinct secondary-structure characteristics and overlap with binding sites of known RBPs, such as ELAVL1. Importantly, mRNA transcripts with the most significant occupancy changes show elongated mRNA half-lives in MCF7 cells. CONCLUSIONS: We present a global comparison of protein occupancy profiles from different cell types, and provide evidence for altered mRNA metabolism as a result of differential protein-RNA contacts. Additionally, we introduce POPPI, a bioinformatics workflow for the analysis of protein occupancy profiling experiments. Our work demonstrates the value of protein occupancy profiling for assessing cis-regulatory RNA sequence space and its dynamics in growth, development and disease.}, pmid = {24417896}, keywords = {nosource} }

@article{luiPatternsKnownNovel2007, title = {Patterns of Known and Novel Small {{RNAs}} in Human Cervical Cancer}, author = {Lui, W. O. and Pourmand, Nader and Patterson, B. K. and Fire, Andrew}, year = 2007, month = jul, journal = {Cancer research}, volume = {67}, number = {13}, eprint = {17616659}, eprinttype = {pubmed}, pages = {6031–43}, issn = {0008-5472}, doi = {10.1158/0008-5472.CAN-06-0561}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17616659 http://cancerres.aacrjournals.org/content/67/13/6031.short}, abstract = {Recent studies suggest that knowledge of differential expression of microRNAs (miRNA) in cancer may have substantial diagnostic and prognostic value. Here, we use a direct sequencing method to characterize the profiles of miRNAs and other small RNA segments for six human cervical carcinoma cell lines and five normal cervical samples. Of 166 miRNAs expressed in normal cervix and cancer cell lines, we observed significant expression variation of six miRNAs between the two groups. To further show the biological relevance of our findings, we examined the expression level of two significantly varying miRNAs in a panel of 29 matched pairs of human cervical cancer and normal cervical samples. Reduced expression of miR-143 and increased expression of miR-21 were reproducibly displayed in cancer samples, suggesting the potential value of these miRNAs as tumor markers. In addition to the known miRNAs, we found a number of novel miRNAs and an additional set of small RNAs that do not meet miRNA criteria.}, pmid = {17616659}, keywords = {Base Sequence,Cell Line,Cervix Uteri,Cervix Uteri: metabolism,Female,Gene Expression Profiling,Gene Expression Regulation,Humans,MicroRNAs,MicroRNAs: genetics,MicroRNAs: metabolism,Molecular Sequence Data,Neoplastic,nosource,Oligonucleotide Array Sequence Analysis,Prognosis,Tumor,Uterine Cervical Neoplasms,Uterine Cervical Neoplasms: diagnosis,Uterine Cervical Neoplasms: genetics,Uterine Cervical Neoplasms: metabolism} }

@article{michaelReducedAccumulationSpecific2003, title = {Reduced {{Accumulation}} of {{Specific MicroRNAs}} in {{Colorectal Neoplasia}}}, author = {Michael, Michael Z. and Connor, Susan M. O. and Pellekaan, Nicholas G. Van Holst and Young, Graeme P. and James, Robert J.}, year = 2003, journal = {Molecular Cancer }, pages = {882–891}, url = {http://mcr.aacrjournals.org/content/1/12/882.short}, keywords = {nosource} } % == BibTeX quality report for michaelReducedAccumulationSpecific2003: % ? Title looks like it was stored in title-case in Zotero

@article{lowIsolationIdentificationEukaryotic2007, title = {Isolation and Identification of Eukaryotic Initiation Factor {{4A}} as a Molecular Target for the Marine Natural Product {{Pateamine A}}.}, author = {Low, Woon-Kai and Dang, Yongjun and {Schneider-Poetsch}, Tilman and Shi, Zonggao and Choi, Nam Song and Rzasa, Robert M. and {}a Shea, Helene and Li, Shukun and Park, Kaapjoo and Ma, Gil and Romo, Daniel and Liu, Jun O.}, year = 2007, month = jan, journal = {Methods in enzymology}, volume = {431}, number = {07}, eprint = {17923240}, eprinttype = {pubmed}, pages = {303–24}, issn = {0076-6879}, doi = {10.1016/S0076-6879(07)31014-8}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17923240}, abstract = {Natural products continue to demonstrate their utility both as therapeutics and as molecular probes for the discovery and mechanistic deconvolution of various cellular processes. However, this utility is dampened by the inherent difficulties involved in isolating and characterizing new bioactive natural products, in obtaining sufficient quantities of purified compound for further biological studies, and in developing bioactive probes. Key to characterizing the biological activity of natural products is the identification of the molecular target(s) within the cell. The marine sponge-derived natural product Pateamine A (PatA) has been found to be an inhibitor of eukaryotic translation initiation. Herein, we describe the methods utilized for identification of the eukaryotic translation initiation factor 4A (eIF4A) as one of the primary protein targets of PatA. We begin by describing the synthesis of an active biotin conjugate of PatA (B-PatA), made possible by total synthesis, followed by its use for affinity purification of PatA binding proteins from cellular lysates. We have attempted to present the methodology as a general technique for the identification of protein targets for small molecules including natural products.}, pmid = {17923240}, keywords = {Affinity,Animals,Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: metabolism,Biological,Biotin,Biotin: chemistry,Biotin: metabolism,Chromatography,Cyclohexylamines,Cyclohexylamines: chemistry,Drug Design,Epoxy Compounds,Epoxy Compounds: chemistry,Epoxy Compounds: isolation & purification,Epoxy Compounds: metabolism,Epoxy Compounds: pharmacology,Eukaryotic Initiation Factor-4A,Eukaryotic Initiation Factor-4A: antagonists & inh,Eukaryotic Initiation Factor-4A: isolation & purif,Humans,Macrolides,Macrolides: chemical synthesis,Macrolides: chemistry,Macrolides: isolation & purification,Macrolides: metabolism,Macrolides: pharmacology,Models,nosource,Protein Binding,Sepharose,Sepharose: analogs & derivatives,Sepharose: chemistry,Sepharose: metabolism,Structure-Activity Relationship,Thiazoles,Thiazoles: chemistry,Thiazoles: isolation & purification,Thiazoles: metabolism,Thiazoles: pharmacology} }

@article{keeneTranscriptionalPauseArrest1999, title = {Transcriptional Pause, Arrest and Termination Sites for {{RNA}} Polymerase {{II}} in Mammalian {{N-}} and c-Myc Genes.}, author = {Keene, R. G. and Mueller, a and Landick, R. and London, L.}, year = 1999, month = aug, journal = {Nucleic acids research}, volume = {27}, number = {15}, pages = {3173–82}, issn = {1362-4962}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=148545&tool=pmcentrez&rendertype=abstract}, abstract = {Using either highly purified RNA polymerase II (pol II) elongation complexes assembled on oligo(dC)-tailed templates or promoter-initiated (extract-generated) pol II elongation complexes, the precise 3” ends of transcripts produced during transcription in vitro at several human c- and N- myc pause, arrest and termination sites were determined. Despite a low overall similarity between the entire c- and N- myc first exon sequences, many positions of pol II pausing, arrest or termination occurred within short regions of related sequence shared between the c- and N- myc templates. The c- and N- myc genes showed three general classes of sequence conservation near intrinsic pause, arrest or termination sites: (i) sites where arrest or termination occurred after the synthesis of runs of uridines (Us) preceding the transcript 3” end, (ii) sites downstream of potential RNA hairpins and (iii) sites after nucleotide addition following either a U or a C or following a combination of several pyrimidines near the transcript 3” end. The finding that regions of similarity occur near the sites of pol II pausing, arrest or termination suggests that the mechanism of c- and N- myc regulation at the level of transcript elongation may be similar and not divergent as previously proposed.}, pmid = {10454615}, keywords = {Bacterial,Bacterial: genetics,Base Sequence,Conserved Sequence,Conserved Sequence: genetics,Exons,Exons: genetics,Genes,Genetic,Genetic: genetics,HeLa Cells,Humans,Messenger,Messenger: analysis,Messenger: chemistry,Messenger: genetics,Molecular Sequence Data,Molecular Weight,myc,myc: genetics,nosource,Nucleic Acid Conformation,RNA,RNA Polymerase II,RNA Polymerase II: metabolism,Salmonella,Salmonella: genetics,Sarcosine,Sarcosine: analogs & derivatives,Templates,Terminator Regions,Time Factors,Transcription} }

@article{lyakhovPausingTerminationBacteriophage1998, title = {Pausing and Termination by Bacteriophage {{T7 RNA}} Polymerase.}, author = {Lyakhov, D. L. and He, B. and Zhang, X. and Studier, F. W. and Dunn, J. J. and McAllister, W. T.}, year = 1998, month = jul, journal = {Journal of molecular biology}, volume = {280}, number = {2}, eprint = {11124963}, eprinttype = {pubmed}, pages = {201–13}, issn = {0022-2836}, doi = {10.1006/jmbi.1998.1854}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11124963}, abstract = {Two types of sites are known to cause pausing and/or termination by bacteriophage T7 RNA polymerase (RNAP). Termination at class I sites (typified by the signal found in the late region of T7 DNA, TPhi) involves the formation of a stable stem-loop structure in the nascent RNA ahead of the point of termination, and results in termination near runs of U. Class II sites, typified by a signal first identified in the cloned human preproparathyroid hormone (PTH) gene, generate no evident structure in the RNA but contain a conserved sequence ahead of the point of termination, and also contain runs of U. Termination at class I and class II sites may involve non-equivalent mechanisms, as mutants of T7 RNA polymerase have been identified that fail to recognize class II sites yet continue to recognize class I sites. In this work, we have analyzed pausing and termination at several class II sites, and variants of them. We conclude that the 7 bp sequence ATCTGTT (5’ to 3’ in the non-template strand) causes transcribing T7 or T3 RNA polymerase to pause. Termination 6 to 8 bp past this sequence is favored by the presence of runs of U, perhaps because they destabilize an RNA:DNA hybrid. The effects of T7 lysozyme on pausing and termination are consistent with the idea that termination involves a reversion of the polymerase from the elongation to the initiation conformation, and that lysozyme inhibits the return to the elongation conformation. A kinetic model of pausing and termination is presented that provides a consistent interpretation of our results.}, pmid = {9654445}, keywords = {Bacteriophage T7,Bacteriophage T7: enzymology,Bacteriophage T7: genetics,Base Sequence,Conserved Sequence,DNA,DNA-Directed RNA Polymerases,DNA-Directed RNA Polymerases: metabolism,Genetic,Kinetics,Molecular Sequence Data,N-Acetylmuramoyl-L-alanine Amidase,N-Acetylmuramoyl-L-alanine Amidase: metabolism,nosource,Plasmids,Terminator Regions,Viral,Viral Proteins,Viral: genetics} }

@article{chenEffectsDNALesions1993, title = {Effects of {{DNA}} Lesions on Transcription Elongation by {{T7 RNA}} Polymerase.}, author = {Chen, Y. H. and Bogenhagen, D. F.}, year = 1993, journal = {Journal of Biological Chemistry}, volume = {268}, number = {8}, pages = {5849–5855}, url = {http://www.jbc.org/content/268/8/5849.short}, keywords = {nosource} }

@article{zilkaDevelopmentalRegulationHeat2001, title = {Developmental {{Regulation}} of {{Heat Shock Protein}} 83 in {{Leishmania}}: 3’ {{Processing AND mRNA Stability Control Transcript Abundance}} , and {{Translation}} Is {{Directed}} by a {{Determinant}} in the 3’-{{Untranslated Region}}}, author = {Zilka, a and Garlapati, S. and Dahan, E. and Yaolsky, V. and Shapira, M.}, year = 2001, month = dec, journal = {The Journal of biological chemistry}, volume = {276}, number = {51}, eprint = {11598129}, eprinttype = {pubmed}, pages = {47922–9}, issn = {0021-9258}, doi = {10.1074/jbc.M108271200}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11598129}, abstract = {Developmental gene regulation in trypanosomatids proceeds exclusively by post-transcriptional mechanisms. Stability and abundance of heat shock protein (HSP)70 and HSP83 transcripts in Leishmania increase at mammalian-like temperatures, and their translation is enhanced. Here we report that the 3’-untranslated region (UTR) of HSP83 (886 nucleotides) confers the temperature-dependent pattern of regulation on a chloramphenicol acetyltransferase (CAT) reporter transcript. We also show that the majority of the 3’-UTR sequences are required for increasing mRNA stability during heat shock. Processing of the HSP70 and HSP83 primary transcripts to poly(A)(+) mRNA was more efficient during heat shock; therefore, even when stability at 33 degrees C was reduced by deletions in the 3’-UTR, transcripts still accumulated to comparable and even higher levels. Translation of heat shock transcripts in Leishmania increases dramatically upon temperature elevation. Unlike in other eukaryotes in which the 5’-UTR confers preferential translation on heat shock transcripts, we show that translational control of HSP83 in Leishmania originates from its 3’-UTR. The 5’-UTR alone cannot induce translation during heat shock, but it has a minor contribution when combined with the HSP83 3’-UTR. We identified an element located between positions 201 and 472 of the 3’-UTR which is essential for increasing translation of the CAT-HSP83 reporter RNA at 33-37 degrees C. This region confers preferential translation during heat shock even in transcripts that were less stable. Thus, investigating the traditionally conserved heat shock response reveals that Leishmania parasites use unique pathways for translational control.}, pmid = {11598129}, keywords = {3’ Untranslated Regions,3’ Untranslated Regions: genetics,Animals,Base Sequence,Chloramphenicol O-Acetyltransferase,Chloramphenicol O-Acetyltransferase: genetics,Developmental,DNA Primers,Gene Expression Regulation,Heat-Shock Proteins,Heat-Shock Proteins: genetics,Leishmania,Leishmania: genetics,Leishmania: growth & development,Messenger,Messenger: genetics,Messenger: metabolism,Multigene Family,nosource,Post-Transcriptional,Protein Biosynthesis,Protozoan Proteins,RNA,RNA Processing,Sequence Deletion} }

@article{buchanHaltingCellularProduction2007, title = {Halting a Cellular Production Line: Responses to Ribosomal Pausing during Translation}, author = {Buchan, J. R. and Stansfield, Ian}, year = 2007, month = sep, journal = {Biology of the Cell}, volume = {99}, number = {9}, eprint = {17696878}, eprinttype = {pubmed}, pages = {475–87}, issn = {1768-322X}, doi = {10.1042/BC20070037}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17696878 http://onlinelibrary.wiley.com/doi/10.1042/BC20070037/full}, abstract = {Cellular protein synthesis is a complex polymerization process carried out by multiple ribosomes translating individual mRNAs. The process must be responsive to rapidly changing conditions in the cell that could cause ribosomal pausing and queuing. In some circumstances, pausing of a bacterial ribosome can trigger translational abandonment via the process of trans-translation, mediated by tmRNA (transfer-messenger RNA) and endonucleases. Together, these factors release the ribosome from the mRNA and target the incomplete polypeptide for destruction. In eukaryotes, ribosomal pausing can initiate an analogous process carried out by the Dom34p and Hbs1p proteins, which trigger endonucleolytic attack of the mRNA, a process termed mRNA no-go decay. However, ribosomal pausing can also be employed for regulatory purposes, and controlled translational delays are used to help co-translational folding of the nascent polypeptide on the ribosome, as well as a tactic to delay translation of a protein while its encoding mRNA is being localized within the cell. However, other responses to pausing trigger ribosomal frameshift events. Recent discoveries are thus revealing a wide variety of mechanisms used to respond to translational pausing and thus regulate the flow of ribosomal traffic on the mRNA population.}, pmid = {17696878}, keywords = {Codon,nosource,Protein Biosynthesis,Protein Biosynthesis: physiology,Ribosomes,Ribosomes: classification,Ribosomes: physiology,Terminator,Terminator: physiology,Time Factors} }

@article{rashmiComparativeGenomicsTrypanosomatid2013, title = {Comparative {{Genomics}} of {{Trypanosomatid Pathogens}} Using {{Codon Usage Bias}}}, author = {Rashmi, Mayank and Swati, D.}, year = 2013, journal = {Bioinformation}, volume = {9}, number = {18}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842577/}, keywords = {codon adaptation index,codon usage bias,essential genes,highly expressed genes,nosource,t-rna,translational selection} }

@article{hornCodonUsageSuggests2008, title = {Codon Usage Suggests That Translational Selection Has a Major Impact on Protein Expression in Trypanosomatids}, author = {Horn, David}, year = 2008, journal = {BMC genomics}, volume = {11}, pages = {1–11}, doi = {10.1186/1471-2164-9-2}, url = {http://www.biomedcentral.com/1471-2164/9/2/}, keywords = {nosource} }

@article{rogersRoleLeishmaniaProteophosphoglycans2012, title = {The Role of Leishmania Proteophosphoglycans in Sand Fly Transmission and Infection of the {{Mammalian}} Host.}, author = {Rogers, Matthew E.}, year = 2012, month = jan, journal = {Frontiers in microbiology}, volume = {3}, number = {June}, pages = {223}, issn = {1664-302X}, doi = {10.3389/fmicb.2012.00223}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3384971&tool=pmcentrez&rendertype=abstract}, abstract = {Leishmania are transmitted by the bite of their sand fly vector and this has a significant influence on the virulence of the resulting infection. From our studies into the interaction between parasite, vector, and host we have uncovered an important missing ingredient during Leishmania transmission. Leishmania actively adapt their sand fly hosts into efficient vectors by secreting Promastigote Secretory Gel (PSG), a proteophosphoglycan (PPG)-rich, mucin-like gel which accumulates in sand fly gut and mouthparts. This has the effect of blocking the fly, such that during bloodfeeding both parasites and gel are co-transmitted in an act of regurgitation. We are discovering that this has further implications for the mammalian infection, again, in favor of the parasite. Experimentally, PSG exacerbates cutaneous and visceral leishmaniasis and can promote the chronicity of Leishmania infection, even in mouse strains normally capable of controlling leishmaniasis. The underlying mechanism of PSG’s action is a major focus of our ongoing work. This review aims to synthesize what is known about the role and action of PSG and its constituent proteophosphoglycans, for parasite colonization of the sand fly, transmission, and mammalian infection. Lastly, we discuss potential exploitation of this important vector-transmitted product and future avenues of research.}, pmid = {22754550}, keywords = {leishmania,Leishmania,macrophage,nosource,promastigote secretory gel,proteophosphoglycan,saliva,sand fly,transmission,wound healing} }

@article{preusserMRNASplicingTrypanosomes2012, title = {{{mRNA}} Splicing in Trypanosomes.}, author = {Preu{}er, Christian and Ja{'e}, Nicolas and Bindereif, Albrecht}, year = 2012, month = oct, journal = {International journal of medical microbiology : IJMM}, volume = {302}, number = {4-5}, eprint = {22964417}, eprinttype = {pubmed}, pages = {221–4}, publisher = {Elsevier GmbH.}, issn = {1618-0607}, doi = {10.1016/j.ijmm.2012.07.004}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22964417}, abstract = {The parasitic unicellular trypanosomatids are responsible for several fatal diseases in humans and livestock. Regarding their biochemistry and molecular biology, they possess a multitude of special features such as polycistronic transcription of protein-coding genes. The resulting long primary transcripts need to be processed by coupled trans-splicing and polyadenylation reactions, thereby generating mature mRNAs. Catalyzed by a large ribonucleoprotein complex termed the spliceosome, trans-splicing attaches a 39-nucleotide leader sequence, which is derived from the Spliced Leader (SL) RNA, to each protein-coding gene. Recent genome-wide studies demonstrated that alternative trans-splicing increases mRNA and protein diversity in these organisms. In this mini-review we give an overview of the current state of research on trans-splicing.}, pmid = {22964417}, keywords = {Alternative Splicing,Genetic,Messenger,Messenger: genetics,Messenger: metabolism,nosource,Polyadenylation,Protein Binding,Protozoan,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Protozoan: genetics,Protozoan: metabolism,Ribonucleoproteins,RNA,RNA Stability,Small Nuclear,Small Nuclear: genetics,Small Nuclear: metabolism,Spliced Leader,Spliced Leader: genetics,Spliced Leader: metabolism,Spliceosomes,Spliceosomes: genetics,Spliceosomes: metabolism,Trans-Splicing,Transcription,Trypanosoma,Trypanosoma: genetics,Trypanosoma: metabolism} }

@article{blumenthalCisTransMRNA1988, title = {Cis and Trans {{mRNA}} Splicing in {{C}}. Elegans}, author = {Blumenthal, T. and Thomas, J.}, year = 1988, month = nov, journal = {Trends in Genetics}, volume = {4}, number = {11}, pages = {305–308}, issn = {01689525}, doi = {10.1016/0168-9525(88)90107-2}, url = {http://linkinghub.elsevier.com/retrieve/pii/0168952588901072}, keywords = {nosource} }

@article{gaudenziGenomewideAnalysisUntranslated2013, title = {Genome-Wide Analysis of 3’-Untranslated Regions Supports the Existence of Post-Transcriptional Regulons Controlling Gene Expression in Trypanosomes.}, author = {Gaudenzi, Javier G. De and Carmona, Santiago J. and Ag{"u}ero, Fern{'a}n and Frasch, Alberto C.}, year = 2013, month = jan, journal = {PeerJ}, volume = {1}, pages = {e118}, issn = {2167-8359}, doi = {10.7717/peerj.118}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3728762&tool=pmcentrez&rendertype=abstract}, abstract = {In eukaryotic cells, a group of messenger ribonucleic acids (mRNAs) encoding functionally interrelated proteins together with the trans-acting factors that coordinately modulate their expression is termed a post-transcriptional regulon, due to their partial analogy to a prokaryotic polycistron. This mRNA clustering is organized by sequence-specific RNA-binding proteins (RBPs) that bind cis-regulatory elements in the noncoding regions of genes, and mediates the synchronized control of their fate. These recognition motifs are often characterized by conserved sequences and/or RNA structures, and it is likely that various classes of cis-elements remain undiscovered. Current evidence suggests that RNA regulons govern gene expression in trypanosomes, unicellular parasites which mainly use post-transcriptional mechanisms to control protein synthesis. In this study, we used motif discovery tools to test whether groups of functionally related trypanosomatid genes contain a common cis-regulatory element. We obtained conserved structured RNA motifs statistically enriched in the noncoding region of 38 out of 53 groups of metabolically related transcripts in comparison with a random control. These motifs have a hairpin loop structure, a preferred sense orientation and are located in close proximity to the open reading frames. We found that 15 out of these 38 groups represent unique motifs in which most 3’-UTR signature elements were group-specific. Two extensively studied Trypanosoma cruzi RBPs, TcUBP1 and TcRBP3 were found associated with a few candidate RNA regulons. Interestingly, 13 motifs showed a strong correlation with clusters of developmentally co-expressed genes and six RNA elements were enriched in gene clusters affected after hyperosmotic stress. Here we report a systematic genome-wide in silico screen to search for novel RNA-binding sites in transcripts, and describe an organized network of several coordinately regulated cohorts of mRNAs in T. cruzi. Moreover, we found that structured RNA elements are also conserved in other human pathogens. These results support a model of regulation of gene expression by multiple post-transcriptional regulons in trypanosomes.}, pmid = {23904995}, keywords = {nosource} }

@article{stajichBioperlToolkitPerl2002, title = {The {{Bioperl}} Toolkit: {{Perl}} Modules for the Life Sciences.}, author = {Stajich, Jason E. and Block, David and Boulez, Kris and Brenner, Steven E. and {}a Chervitz, Stephen and Dagdigian, Chris and Fuellen, Georg and Gilbert, James G. R. and Korf, Ian and Lapp, Hilmar and Lehv{"a}slaiho, Heikki and Matsalla, Chad and Mungall, Chris J. and Osborne, Brian I. and Pocock, Matthew R. and Schattner, Peter and Senger, Martin and Stein, Lincoln D. and Stupka, Elia and Wilkinson, Mark D. and Birney, Ewan}, year = 2002, month = oct, journal = {Genome research}, volume = {12}, number = {10}, pages = {1611–8}, issn = {1088-9051}, doi = {10.1101/gr.361602}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=187536&tool=pmcentrez&rendertype=abstract}, abstract = {The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.}, pmid = {12368254}, keywords = {Algorithms,Animals,Biological Science Disciplines,Biological Science Disciplines: methods,Biological Science Disciplines: trends,Computational Biology,Computational Biology: methods,Computational Biology: trends,Computer Graphics,Database Management Systems,Databases,Genetic,Humans,Internet,nosource,Online Systems,Software,Software Design,Systems Integration} }

@article{SupplementaryFigureLegends2002, title = {Supplementary {{Figure Legends Figure S1 Characterization}} of {{4TU}} Labeling In}, year = 2002, keywords = {nosource} } % == BibTeX quality report for SupplementaryFigureLegends2002: % Missing required field ‘author’ % Missing required field ‘journal’

@article{leontisNonWatsonCrick2002, title = {The non-{{Watson}}–{{Crick}} Base Pairs and Their Associated Isostericity Matrices}, author = {Leontis, N. B. and Stombaugh, Jesse and Westhof, Eric}, year = 2002, journal = {Nucleic acids research}, volume = {30}, number = {16}, url = {http://nar.oxfordjournals.org/content/30/16/3497.short}, keywords = {nosource} }

@article{markoStretchingDNA1995, title = {Stretching {{DNA}}}, author = {Marko, John F. and Siggia, Eric D.}, year = 1995, month = dec, journal = {Macromolecules}, volume = {28}, number = {26}, pages = {8759–8770}, issn = {0024-9297}, doi = {10.1021/ma00130a008}, url = {http://pubs.acs.org/doi/abs/10.1021/ma00130a008}, keywords = {nosource} } % == BibTeX quality report for markoStretchingDNA1995: % ? Title looks like it was stored in title-case in Zotero

@article{maoGenomewideComputationalIdentification2009, title = {Genome-Wide Computational Identification of Functional {{RNA}} Elements in {{Trypanosoma}} Brucei.}, author = {Mao, Yuan and Najafabadi, Hamed Shateri and Salavati, Reza}, year = 2009, month = jan, journal = {BMC genomics}, volume = {10}, pages = {355}, issn = {1471-2164}, doi = {10.1186/1471-2164-10-355}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2907701&tool=pmcentrez&rendertype=abstract}, abstract = {Post-transcriptional regulation of gene expression is the dominant regulatory mechanism in trypanosomatids as their mRNAs are transcribed from polycistronic units. A few cis-acting RNA elements in 3’-untranslated regions of mRNAs have been identified in trypanosomatids, which affect the mRNA stability or translation rate in different life stages of these parasites. Other functional RNAs (fRNAs) also play essential roles in these organisms. However, there has been no genome-wide analysis for identification of fRNAs in trypanosomatids.}, isbn = {1471216410355}, pmid = {19653906}, keywords = {3’ Untranslated Regions,5’ Untranslated Regions,Animals,Computational Biology,Computational Biology: methods,Genome,Genome-Wide Association Study,Leishmania braziliensis,Leishmania braziliensis: genetics,nosource,Protozoan,Protozoan: genetics,Regulatory Sequences,Ribonucleic Acid,RNA,Sequence Analysis,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics} }

@article{holHUPF2SilencingIdentifies2006, title = {{{hUPF2}} Silencing Identifies Physiologic Substrates of Mammalian Nonsense-Mediated {{mRNA}} Decay}, author = {Hol, Elly M. E. M. M. and Ja, Hans-martin and Wittmann, J. and Jack, H. M. M.}, year = 2006, journal = {Molecular and Cellular Biology}, volume = {26}, number = {4}, pages = {1272}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.26.4.1272}, url = {http://mcb.asm.org/cgi/content/abstract/26/4/1272}, isbn = {4991318539343}, keywords = {nosource} }

@article{laurentImportanceSmallChanges2013, title = {On the Importance of Small Changes in {{RNA}} Expression.}, author = {Laurent, Georges St and Shtokalo, Dmitry and Tackett, Michael R. and Yang, Zhaoqing and Vyatkin, Yuri and Milos, Patrice M. and Seilheimer, Bernd and {}a McCaffrey, Timothy and Kapranov, Philipp}, year = 2013, month = sep, journal = {Methods (San Diego, Calif.)}, volume = {63}, number = {1}, eprint = {23563143}, eprinttype = {pubmed}, pages = {18–24}, publisher = {Elsevier Inc.}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2013.03.027}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23563143}, abstract = {The analysis of the differential expression of genes has been the key goal of many molecular biology methods for decades and will remain with us for decades to come. It constitutes a fundamental resource at our disposal for determining the relationship between products of transcription, biology and disease. The completed genome sequencing of many common species allowed microarrays and RNA sequencing (RNAseq) to become major tools in Systems Biology. However, we estimate that at least half of all experiments ignore transcripts that change less than some subjectively chosen threshold, typically around 2-3 fold. Here we show that a majority of the informative RNAs and differentially expressed transcripts can exhibit fold changes less than 2. We use highly quantitative single-molecule sequencing of total cellular RNA derived from a time course of inflammatory response, a process critical to a large number of diseases. Furthermore, we show that enrichment of biologically-relevant functions occurs even at very low fold changes in RNA levels. In addition, we show that most of the common statistical methods can reliably detect transcripts with low fold change when as few as 3 biological replicates are sequenced using single-molecule based RNAseq. In conclusion, given the prevalence of expression profiling in current research, the loss of data in half of all expression studies results in a significant, yet needless drain on the discovery process.}, pmid = {23563143}, keywords = {Differential gene expression,Inflammation,nosource,RNAseq,single molecule sequencing,Transcriptome} } % == BibTeX quality report for laurentImportanceSmallChanges2013: % ? Possibly abbreviated journal title Methods (San Diego, Calif.)

@article{franzenShotgunSequencingAnalysis2011, title = {Shotgun Sequencing Analysis of {{Trypanosoma}} Cruzi {{I Sylvio X10}}/1 and Comparison with {{T}}. Cruzi {{VI CL Brener}}.}, author = {Franz{'e}n, Oscar and Ochaya, Stephen and Sherwood, Ellen and Lewis, Michael D. and Llewellyn, Martin S. and {}a Miles, Michael and Andersson, Bj{"o}rn}, year = 2011, month = jan, journal = {PLoS neglected tropical diseases}, volume = {5}, number = {3}, pages = {e984}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0000984}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3050914&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanosoma cruzi is the causative agent of Chagas disease, which affects more than 9 million people in Latin America. We have generated a draft genome sequence of the TcI strain Sylvio X10/1 and compared it to the TcVI reference strain CL Brener to identify lineage-specific features. We found virtually no differences in the core gene content of CL Brener and Sylvio X10/1 by presence/absence analysis, but 6 open reading frames from CL Brener were missing in Sylvio X10/1. Several multicopy gene families, including DGF, mucin, MASP and GP63 were found to contain substantially fewer genes in Sylvio X10/1, based on sequence read estimations. 1,861 small insertion-deletion events and 77,349 nucleotide differences, 23% of which were non-synonymous and associated with radical amino acid changes, further distinguish these two genomes. There were 336 genes indicated as under positive selection, 145 unique to T. cruzi in comparison to T. brucei and Leishmania. This study provides a framework for further comparative analyses of two major T. cruzi lineages and also highlights the need for sequencing more strains to understand fully the genomic composition of this parasite.}, pmid = {21408126}, keywords = {DNA,Genome,Humans,Insertional,Latin America,Molecular Sequence Data,Mutagenesis,nosource,Protozoan,Protozoan: chemistry,Protozoan: genetics,Sequence Analysis,Sequence Deletion,Sequence Homology,Synteny,Trypanosoma cruzi,Trypanosoma cruzi: genetics} }

@article{freireFourTrypanosomatidEIF4E2011, title = {The Four Trypanosomatid {{eIF4E}} Homologues Fall into Two Separate Groups, with Distinct Features in Primary Sequence and Biological Properties.}, author = {Freire, Eden R. and Dhalia, Rafael and Moura, Danielle M. N. and Lima, Tamara D. da Costa and Lima, Rodrigo P. and Reis, Christian R. S. and Hughes, Katie and Figueiredo, Regina C. B. Q. and Standart, Nancy and Carrington, Mark and Neto, Osvaldo P. de Melo}, year = 2011, month = mar, journal = {Molecular and biochemical parasitology}, volume = {176}, number = {1}, eprint = {21111007}, eprinttype = {pubmed}, pages = {25–36}, publisher = {Elsevier B.V.}, issn = {1872-9428}, doi = {10.1016/j.molbiopara.2010.11.011}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21111007}, abstract = {Translation initiation in eukaryotes requires eIF4E, the cap binding protein, which mediates its function through an interaction with the scaffolding protein eIF4G, as part of the eIF4F complex. In trypanosomatids, four eIF4E homologues have been described but the specific function of each is not well characterized. Here, we report a study of these proteins in Trypanosoma brucei (TbEIF4E1 through 4). At the sequence level, they can be assigned to two groups: TbEIF4E1 and 2, similar in size to metazoan eIF4E1; and TbEIF4E3 and 4, with long N-terminal extensions. All are constitutively expressed, but whilst TbEIF4E1 and 2 localize to both the nucleus and cytoplasm, TbEIF4E3 and 4 are strictly cytoplasmic and are also more abundant. After knockdown through RNAi, TbEIF4E3 was the only homologue confirmed to be essential for viability of the insect procyclic form. In contrast, TbEIF4E1, 3 and 4 were all essential for the mammalian bloodstream form. Simultaneous RNAi knockdown of TbEIF4E1 and 2 caused cessation of growth and death in procyclics, but with a delayed impact on translation, whilst knockdown of TbEIF4E3 alone or a combined TbEIF4E1 and 4 knockdown led to substantial translation inhibition which preceded cellular death by several days, at least. Only TbEIF4E3 and 4 were found to interact with T. brucei eIF4G homologues; TbEIF4E3 bound both TbEIF4G3 and 4 whilst TbEIF4E4 bound only to TbEIF4G3. These results are consistent with TbEIF4E3 and 4 having distinct but relevant roles in initiation of protein synthesis.}, pmid = {21111007}, keywords = {Amino Acid Sequence,Cell Nucleus,Cell Nucleus: metabolism,Cell Proliferation,Cell Survival,Cytoplasm,Cytoplasm: metabolism,Eukaryotic Initiation Factor-4E,Eukaryotic Initiation Factor-4E: chemistry,Eukaryotic Initiation Factor-4E: genetics,Eukaryotic Initiation Factor-4E: metabolism,Gene Expression Regulation,Intracellular Space,Intracellular Space: metabolism,Molecular Sequence Data,nosource,Protein Binding,Protein Transport,Protein Transport: physiology,RNA Interference,Sequence Alignment,Trypanosoma,Trypanosoma: genetics,Trypanosoma: metabolism} }

@article{caruccioPreparationNextgenerationSequencing2011, title = {Preparation of Next-Generation Sequencing Libraries Using {{Nextera}}™ Technology: Simultaneous {{DNA}} Fragmentation and Adaptor Tagging by in Vitro Transposition}, author = {Caruccio, Nicholas}, editor = {Kwon, Young Min and Ricke, Steven C.}, year = 2011, journal = {High-Throughput Next Generation Sequencing}, volume = {733}, publisher = {Humana Press}, doi = {10.1007/978-1-61779-089-8}, url = {http://link.springer.com/10.1007/978-1-61779-089-8 http://link.springer.com/10.1007/978-1-61779-089-8_17}, isbn = {978-1-61779-088-1}, keywords = {454,dna library preparation,illumina,next-generation sequencing,nosource,roche,solexa} }

@article{keelingAutoregulatoryFrameshiftingAntizyme2010, title = {Autoregulatory Frameshifting in Antizyme Gene Expression Governs Polyamine Levels from Yeast to Mammals}, author = {Keeling, K. M. and Bedwell, D. M.}, year = 2010, journal = {Recoding: expansion of decoding rules enriches gene }, volume = {24}, pages = {123–146}, publisher = {Springer New York}, doi = {10.1007/978-0-387-89382-2}, url = {http://www.springerlink.com/index/t027340h6q1p32n8.pdf http://link.springer.com/chapter/10.1007/978-0-387-89382-2_20}, isbn = {978-0-387-89381-5}, keywords = {nosource} }

@article{huryTrypanosomeSplicedleaderassociatedRNA2009, title = {Trypanosome Spliced-Leader-Associated {{RNA}} ({{SLA1}}) Localization and Implications for Spliced-Leader {{RNA}} Biogenesis.}, author = {Hury, Avraham and Goldshmidt, Hanoch and Tkacz, Itai Dov and Michaeli, Shulamit}, year = 2009, month = jan, journal = {Eukaryotic cell}, volume = {8}, number = {1}, pages = {56–68}, issn = {1535-9786}, doi = {10.1128/EC.00322-08}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2620742&tool=pmcentrez&rendertype=abstract}, abstract = {Spliced-leader-associated RNA (SLA1) guides the pseudouridylation at position -12 (relative to the 5’ splice site) of the spliced-leader (SL) RNA in all trypanosomatid species. Nevertheless, the exact role of this RNA is currently unknown. Here, we demonstrate that the absence of pseudouridine on Leptomonas collosoma SL RNA has only a minor effect on the ability of this RNA to function in trans splicing in vivo. To investigate the possible role of SLA1 during SL RNA biogenesis, the structure of the SL RNA was examined in permeable Trypanosoma brucei cells depleted for CBF5, the H/ACA pseudouridine synthase, lacking SLA1. Our results suggest that in the absence of SLA1, the SL RNA secondary structure is changed, as was detected by differential sensitivity to oligonucleotide-directed RNase H cleavage, suggesting that the association of SLA1 maintains the SL RNA in a structural form which is distinct from the structure of the SL RNA in the steady state. In T. brucei cells depleted for the SL RNA core protein SmD1, SL RNA first accumulates in large amounts in the nucleus and then is expelled to the cytoplasm. Here, we demonstrate by in vivo aminomethyltrimethyl UV cross-linking studies that under SmD1 depletion, SLA1 remains bound to SL RNA and escorts the SL RNA to the cytoplasm. In situ hybridization with SLA1 and SL RNA demonstrates colocalization between SLA1 and the SL RNA transcription factor tSNAP42, as well as with Sm proteins, suggesting that SLA1 associates with SL RNA early in its biogenesis. These results demonstrate that SLA1 is a unique chaperonic RNA that functions during the early biogenesis of SL RNA to maintain a structure that is most probably suitable for cap 4 modification.}, pmid = {19028994}, keywords = {Animals,Base Sequence,Cell Nucleus,Cell Nucleus: metabolism,Cytoplasm,Cytoplasm: metabolism,Molecular Sequence Data,Mutation,nosource,Nucleic Acid Conformation,Protozoan,Protozoan: chemistry,Protozoan: genetics,Protozoan: metabolism,RNA,RNA Splicing,RNA Transport,Spliced Leader,Spliced Leader: chemistry,Spliced Leader: genetics,Spliced Leader: metabolism,Trypanosoma brucei brucei,Trypanosoma brucei brucei: chemistry,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: metabolism} }

@article{vagnerAttractingTranslationMachinery2001, title = {Attracting the Translation Machinery to Internal Ribosome Entry Sites}, author = {Vagner, St{'e}phan and Galy, Bruno and Pyronnet, St{'e}phane}, year = 2001, journal = {EMBO Reports}, volume = {2}, number = {10}, pages = {893–898}, keywords = {nosource} }

@article{bachmairVivoHalflifeProtein1986, title = {In Vivo Half-Life of a Protein Is a Function of Its Amino-Terminal Residue}, author = {Bachmair, a and Finley, D. and Varshavsky, a}, year = 1986, month = oct, journal = {Science}, volume = {234}, number = {4773}, pages = {179–186}, issn = {0036-8075}, doi = {10.1126/science.3018930}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.3018930}, keywords = {nosource} }

@article{liangGenomewideAnalysisACAlike2005, title = {A Genome-Wide Analysis of {{C}}/{{D}} and {{H}} /{{ACA-like}} Small Nucleolar {{RNAs}} in {{Trypanosoma}} Brucei Reveals a Trypanosome-Specific Pattern of {{rRNA}} Modification}, author = {Liang, Xue-hai and Uliel, Shai and Hury, Avraham and Barth, Sarit and Doniger, Tirza and Unger, R. O. N.}, year = 2005, journal = {RNA}, volume = {11}, pages = {619–645}, doi = {10.1261/rna.7174805.2}, keywords = {- o -methyls,2,aca,c,d,h,nosource,pseudouridines,snorna,trypanosomatids} }

@article{el-sayedComparativeGenomicsTrypanosomatid2005, title = {Comparative Genomics of Trypanosomatid Parasitic Protozoa.}, author = {{El-Sayed}, Najib M. and Myler, Peter J. and Blandin, Ga{"e}lle and Berriman, Matthew and Crabtree, Jonathan and Aggarwal, Gautam and Caler, Elisabet and Renauld, Hubert and {}a Worthey, Elizabeth and {Hertz-Fowler}, Christiane and Ghedin, Elodie and Peacock, Christopher and Bartholomeu, Daniella C. and Haas, Brian J. and Tran, Anh-Nhi and Wortman, Jennifer R. and Alsmark, U. Cecilia M. and Angiuoli, Samuel and Anupama, Atashi and Badger, Jonathan and Bringaud, Frederic and Cadag, Eithon and Carlton, Jane M. and Cerqueira, Gustavo C. and Creasy, Todd and Delcher, Arthur L. and Djikeng, Appolinaire and Embley, T. Martin and Hauser, Christopher and Ivens, Alasdair C. and Kummerfeld, Sarah K. and {Pereira-Leal}, Jose B. and Nilsson, Daniel and Peterson, Jeremy and Salzberg, Steven L. and Shallom, Joshua and Silva, Joana C. and Sundaram, Jaideep and Westenberger, Scott and White, Owen and Melville, Sara E. and Donelson, John E. and Andersson, Bj{"o}rn and Stuart, Kenneth D. and Hall, Neil}, year = 2005, month = jul, journal = {Science (New York, N.Y.)}, volume = {309}, number = {5733}, eprint = {16020724}, eprinttype = {pubmed}, pages = {404–9}, issn = {1095-9203}, doi = {10.1126/science.1112181}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16020724}, abstract = {A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that-along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions-have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.}, pmid = {16020724}, keywords = {Animals,Biological Evolution,Chromosomes,Chromosomes: genetics,Evolution,Gene Transfer,Genes,Genetic,Genome,Genomics,Horizontal,Leishmania major,Leishmania major: chemistry,Leishmania major: genetics,Leishmania major: metabolism,Molecular,Molecular Sequence Data,Multigene Family,Mutation,nosource,Phylogeny,Plastids,Plastids: genetics,Proteome,Protozoan,Protozoan Proteins,Protozoan Proteins: chemistry,Protozoan Proteins: genetics,Protozoan Proteins: physiology,Recombination,Retroelements,Species Specificity,Symbiosis,Synteny,Telomere,Telomere: genetics,Trypanosoma brucei brucei,Trypanosoma brucei brucei: chemistry,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: metabolism,Trypanosoma cruzi,Trypanosoma cruzi: chemistry,Trypanosoma cruzi: genetics,Trypanosoma cruzi: metabolism} } % == BibTeX quality report for el-sayedComparativeGenomicsTrypanosomatid2005: % ? Possibly abbreviated journal title Science (New York, N.Y.)

@article{smythLinearModelsEmpirical2004, title = {Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments.}, author = {Smyth, Gordon K.}, year = 2004, month = jan, journal = {Statistical applications in genetics and molecular biology}, volume = {3}, number = {1}, eprint = {16646809}, eprinttype = {pubmed}, pages = {Article3}, issn = {1544-6115}, doi = {10.2202/1544-6115.1027}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16646809}, abstract = {The problem of identifying differentially expressed genes in designed microarray experiments is considered. Lonnstedt and Speed (2002) derived an expression for the posterior odds of differential expression in a replicated two-color experiment using a simple hierarchical parametric model. The purpose of this paper is to develop the hierarchical model of Lonnstedt and Speed (2002) into a practical approach for general microarray experiments with arbitrary numbers of treatments and RNA samples. The model is reset in the context of general linear models with arbitrary coefficients and contrasts of interest. The approach applies equally well to both single channel and two color microarray experiments. Consistent, closed form estimators are derived for the hyperparameters in the model. The estimators proposed have robust behavior even for small numbers of arrays and allow for incomplete data arising from spot filtering or spot quality weights. The posterior odds statistic is reformulated in terms of a moderated t-statistic in which posterior residual standard deviations are used in place of ordinary standard deviations. The empirical Bayes approach is equivalent to shrinkage of the estimated sample variances towards a pooled estimate, resulting in far more stable inference when the number of arrays is small. The use of moderated t-statistics has the advantage over the posterior odds that the number of hyperparameters which need to estimated is reduced; in particular, knowledge of the non-null prior for the fold changes are not required. The moderated t-statistic is shown to follow a t-distribution with augmented degrees of freedom. The moderated t inferential approach extends to accommodate tests of composite null hypotheses through the use of moderated F-statistics. The performance of the methods is demonstrated in a simulation study. Results are presented for two publicly available data sets.}, pmid = {16646809}, keywords = {nosource} }

@article{vickersTrypanothioneStransferaseActivity2004, title = {Trypanothione {{S-transferase}} Activity in a Trypanosomatid Ribosomal Elongation Factor {{1B}}.}, author = {Vickers, Tim J. and Fairlamb, Alan H.}, year = 2004, month = jun, journal = {The Journal of biological chemistry}, volume = {279}, number = {26}, pages = {27246–56}, issn = {0021-9258}, doi = {10.1074/jbc.M311039200}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3428924&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanothione is a thiol unique to the Kinetoplastida and has been shown to be a vital component of their antioxidant defenses. However, little is known as to the role of trypanothione in xenobiotic metabolism. A trypanothione S-transferase activity was detected in extracts of Leishmania major, L. infantum, L. tarentolae, Trypanosoma brucei, and Crithidia fasciculata, but not Trypanosoma cruzi. No glutathione S-transferase activity was detected in any of these parasites. Trypanothione S-transferase was purified from C. fasciculata and shown to be a hexadecameric complex of three subunits with a relative molecular weight of 650,000. This enzyme complex was specific for the thiols trypanothione and glutathionylspermidine and only used 1-chloro-2,4-dinitrobenzene from a range of glutathione S-transferase substrates. Peptide sequencing revealed that the three components were the alpha, beta, and gamma subunits of ribosomal eukaryotic elongation factor 1B (eEF1B). Partial dissociation of the complex suggested that the S-transferase activity was associated with the gamma subunit. Moreover, Cibacron blue was found to be a tight binding inhibitor and reactive blue 4 an irreversible time-dependent inhibitor that covalently modified only the gamma subunit. The rate of inactivation by reactive blue 4 was increased more than 600-fold in the presence of trypanothione, and Cibacron blue protected the enzyme from inactivation by 1-chloro-2,4-dinitrobenzene, confirming that these dyes interact with the active site region. Two eEF1Bgamma genes were cloned from C. fasciculata, but recombinant C. fasciculata eEF1Bgamma had no S-transferase activity, suggesting that eEF1Bgamma is unstable in the absence of the other subunits.}, isbn = {4413823451}, pmid = {15073172}, keywords = {Amino Acid Sequence,Animals,Chromatography,Crithidia fasciculata,Crithidia fasciculata: enzymology,Cross-Linking Reagents,Cross-Linking Reagents: chemistry,Enzyme Inhibitors,Enzyme Inhibitors: pharmacology,Gel,Glutathione Transferase,Glutathione Transferase: metabolism,Molecular Sequence Data,NADH,NADPH Oxidoreductases,NADPH Oxidoreductases: metabolism,nosource,Peptide Elongation Factor 1,Peptide Elongation Factor 1: chemistry,Peptide Elongation Factor 1: genetics,Peptide Elongation Factor 1: metabolism,Protein Disulfide-Isomerases,Protein Disulfide-Isomerases: antagonists & inhibi,Protein Disulfide-Isomerases: chemistry,Protein Disulfide-Isomerases: isolation & purifica,Protein Disulfide-Isomerases: metabolism,Protein Subunits,Ribosomal Proteins,Ribosomal Proteins: metabolism,Sequence Alignment,Substrate Specificity,Triazines,Triazines: pharmacology,Trypanosomatina,Trypanosomatina: cytology,Trypanosomatina: enzymology,Trypanosomatina: metabolism} }

@article{varmusRetroviruses1988, title = {Retroviruses}, author = {Varmus, H.}, year = 1988, journal = {Science}, volume = {47}, eprint = {21433340}, eprinttype = {pubmed}, pages = {35–88}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21433340 http://www.sciencemag.org/content/240/4858/1427.short}, keywords = {nosource,oncogenes,Review,virus} }

@article{mccarthy-burkeCharacterizationSplicedLeader1989, title = {Characterization of the Spliced Leader Genes and Transcripts in {{Trypanosoma}} Cruzi.}, author = {{McCarthy-Burke}, C. and {}a Taylor, Z. and {}a Buck, G.}, year = 1989, month = oct, journal = {Gene}, volume = {82}, number = {1}, eprint = {2684773}, eprinttype = {pubmed}, pages = {177–89}, issn = {0378-1119}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2684773}, abstract = {Trypanosome mRNA is processed to maturity in a novel trans-splicing reaction during which a 35-nucleotide (nt) spliced leader (SL) is joined to the 5’ ends of most structural gene transcripts. We have examined this process in Trypanosoma cruzi, the causative agent of Chagas’ disease in Central and South America. In this communication, we characterize the genes encoding the SL (SL gene) in five different strains of T. cruzi by hybridization analysis and show that the genome of each of these strains contains numerous tandemly repeated copies of the SL gene. We demonstrate that the SL genes show remarkable intrastrain homogeneity, but significant interstrain heterogeneity. We have cloned and sequenced one of the SL repeats from T. cruzi strain CL and used synthetic oligodeoxyribonucleotides designed to hybridize to SL gene transcripts in Northern analyses of T. cruzi RNA to identify an approx. 110-nt putative SL primary transcript (SL-RNA). The 5’ end of the SL-RNA was mapped to the first nt of the SL by primer extension analyses. The sequence of the 110-nt SL-RNA was used to generate a predicted secondary structure, and this structure compared favorably to the predicted secondary structures of SL transcripts of other trypanosomatids.}, pmid = {2684773}, keywords = {Animals,Base Sequence,Caenorhabditis,Caenorhabditis: genetics,Genes,Messenger,Messenger: genetics,Messenger: metabolism,Molecular Sequence Data,nosource,Nucleic Acid,Nucleic Acid Conformation,Repetitive Sequences,RNA,RNA Splicing,Sequence Homology,Species Specificity,Trypanosoma,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosoma cruzi: growth & development,Trypanosoma: genetics} }

@article{rittigLeishmaniaHostcellInteraction2000, title = {Leishmania–{{Host-cell Interaction}}: {{Complexities}} and {{Alternative Views}}}, author = {Rittig, M. G. and Bogdan, C.}, year = 2000, journal = {Parasitology Today}, volume = {16}, number = {7}, url = {http://www.sciencedirect.com/science/article/pii/S0169475800016926}, keywords = {nosource} }

@article{borstControlVSGGene2001, title = {Control of {{VSG}} Gene Expression Sites.}, author = {Borst, P. and Ulbert, S.}, year = 2001, month = apr, journal = {Molecular and biochemical parasitology}, volume = {114}, number = {1}, eprint = {11356510}, eprinttype = {pubmed}, pages = {17–27}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11356510}, abstract = {Trypanosoma brucei survives in mammals by antigenic variation of its surface coat consisting of variant surface glycoprotein (VSG). Trypanosomes change coat mainly by replacing the transcribed VSG genes in an active telomeric expression site by a different VSG gene. There are about 20 different expression sites and trypanosomes can also change coat by switching the site that is active. This review summarizes recent work on the mechanism of site switching and on the way inactive expression sites are kept silent.}, pmid = {11356510}, keywords = {Animals,Gene Expression Regulation,Genes,Humans,nosource,Protozoan,Telomere,Telomere: genetics,Trypanosoma,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: physiology,Trypanosoma: geneti,Variant Surface Glycoproteins} }

@article{barryVSGGeneControl1998, title = {{{VSG}} Gene Control and Infectivity Strategy of Metacyclic Stage {{Trypanosoma}} Brucei.}, author = {Barry, J. D. and Graham, S. V. and Fotheringham, M. and Graham, V. S. and Kobryn, K. and Wymer, B.}, year = 1998, month = mar, journal = {Molecular and biochemical parasitology}, volume = {91}, number = {1}, eprint = {9574928}, eprinttype = {pubmed}, pages = {93–105}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9574928}, abstract = {As the metacyclic trypanosome stage develops in the tsetse fly salivary glands, it initiates expression of variant surface glycoproteins (VSGs) and does so by each cell activating, at random, one from a small subset of metacyclic VSG (M-VSG) genes. Whereas differential activation of individual VSG genes in the bloodstream occurs as a function of time, to evade waves of antibody, it is believed that the aim in the metacyclic stage is simultaneously to generate population diversity. M-VSG genes are activated in their telomeric loci and belong to monocistronic transcription units, unlike all other known trypanosome protein-coding genes, which appear to be transcribed polycistronically. The promoters of these metacyclic expression sites (M-ESs) have the unique property, in this organism, of being switched on and off in a life-cycle stage specific pattern. We have found that the 1.22 M-ES promoter is regulated according to life cycle stage, differential control being exerted through different elements of the promoter and under the influence of its genomic locus. We have characterized in detail the telomeres containing the 1.22 and 1.61 M-ESs. Upstream of the M-ES is a possibly haploid, non-transcribed region with some degenerate sequences homologous with expression site associated genes (ESAGs) that occur in bloodstream VSG expression sites. Further upstream (respectively, 22 and 13 kb upstream of the 1.22 and 1.61 VSG genes) are alpha-amanitin sensitive transcription units that may be polycistrons and are transcribed in all examined life cycle stages. They contain a number of genes. The differences between metacyclic and bloodstream ESs may have important consequences for life cycle regulation, genetic stability, phenotype complexity and adaptability of the metacyclic stage as it infects different host species.}, pmid = {9574928}, keywords = {African,African: parasitology,Animals,Gene Expression Regulation,Genes,Genetic,Host-Parasite Interactions,Life Cycle Stages,nosource,Promoter Regions,Protozoan,Trypanosoma,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: growth & development,Trypanosoma: geneti,Trypanosomiasis,Variant Surface Glycoproteins} }

@article{noiaAUrichElementsUntranslated2000, title = {{{AU-rich Elements}} in the 3’-{{Untranslated Region}} of a {{New Mucin-type Gene Family}} of {{Trypanosoma}} Cruzi {{Confers mRNA Instability}} and {{Modulates Translation Efficiency}}}, author = {Noia, J. M. Di}, year = 2000, month = mar, journal = {Journal of Biological Chemistry}, volume = {275}, number = {14}, pages = {10218–10227}, issn = {00219258}, doi = {10.1074/jbc.275.14.10218}, url = {http://www.jbc.org/cgi/doi/10.1074/jbc.275.14.10218}, keywords = {nosource} }

@article{alcoleaGenomewideAnalysisReveals2009, title = {Genome-Wide Analysis Reveals Increased Levels of Transcripts Related with Infectivity in Peanut Lectin Non-Agglutinated Promastigotes of {{Leishmania}} Infantum.}, author = {Alcolea, Pedro J. and Alonso, Ana and {S{'a}nchez-Gorostiaga}, Alicia and {Moreno-Paz}, Mercedes and G{'o}mez, Manuel J. and Ramos, Irene and Parro, V{'i}ctor and Larraga, Vicente}, year = 2009, month = jun, journal = {Genomics}, volume = {93}, number = {6}, eprint = {19442635}, eprinttype = {pubmed}, pages = {551–64}, publisher = {Elsevier Inc.}, issn = {1089-8646}, doi = {10.1016/j.ygeno.2009.01.007}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19442635}, abstract = {Metacyclic promastigotes are transmitted during bloodmeals after development inside the gut of the sandfly vector. The isolation from axenic cultures of procyclic and metacyclic promastigotes by peanut lectin agglutination followed by differential centrifugation is controversial in Leishmania infantum. The purpose of this study has been to isolate both fractions simultaneously from the same population in stationary phase of axenic culture and compare their expression profiles by whole-genome shotgun DNA microarrays. The 317 genes found with meaningful values of stage-specific regulation demonstrate that negative selection of metacyclic promastigotes by PNA agglutination is feasible in L. infantum and both fractions can be isolated. This subpopulation up-regulates a cysteine peptidase A and several genes involved in lipophosphoglycan, proteophosphoglycan and glycoprotein biosynthesis, all related with infectivity. In fact, we have confirmed the increased infection rate of PNA(-) promastigotes by U937 human cell line infection experiments. These data support that metacyclic promastigotes are related with infectivity and the lack of agglutination with PNA is a phenotypic marker for this subpopulation.}, pmid = {19442635}, keywords = {Agglutination,Amino Acids,Amino Acids: metabolism,Animals,Cell Line,Cysteine Endopeptidases,Cysteine Endopeptidases: metabolism,Fatty Acids,Fatty Acids: metabolism,Gene Expression Profiling,Gene Expression Regulation,Gene Expression Regulation: genetics,Genome,Humans,Leishmania infantum,Leishmania infantum: genetics,Leishmania infantum: pathogenicity,Life Cycle Stages,Life Cycle Stages: genetics,nosource,Oligonucleotide Array Sequence Analysis,Peanut Agglutinin,Peanut Agglutinin: metabolism,Protozoan,Protozoan: genetics,Virulence} }

@article{alcoleaTranscriptomicsThroughoutLife2010, title = {Transcriptomics throughout the Life Cycle of {{Leishmania}} Infantum: High down-Regulation Rate in the Amastigote Stage.}, author = {Alcolea, Pedro J. and Alonso, Ana and G{'o}mez, Manuel J. and Moreno, Inmaculada and Dom{'i}nguez, Mercedes and Parro, V{'i}ctor and Larraga, Vicente}, year = 2010, month = nov, journal = {International journal for parasitology}, volume = {40}, number = {13}, eprint = {20654620}, eprinttype = {pubmed}, pages = {1497–516}, publisher = {Australian Society for Parasitology Inc.}, issn = {1879-0135}, doi = {10.1016/j.ijpara.2010.05.013}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20654620}, abstract = {Leishmania infantum is the causative agent of zoonotic visceral leishmaniasis in the Mediterranean Basin. The promastigote and amastigote stages alternate in the life cycle of the parasite, developing inside the sand-fly gut and inside mammalian phagocytic cells, respectively. High-throughput genomic and proteomic analyses have not focused their attention on promastigote development, although partial approaches have been made in Leishmania major and Leishmania braziliensis. For this reason we have studied the expression modulation of an etiological agent of visceral leishmaniasis throughout the life cycle, which has been performed by means of complete genomic microarrays. In the context of constitutive genome expression in Leishmania spp. described elsewhere and confirmed here (5.7%), we found a down-regulation rate of 68% in the amastigote stage, which has been contrasted by binomial tests and includes the down-regulation of genes involved in translation and ribosome biogenesis. These findings are consistent with the hypothesis of pre-adaptation of the parasite to intracellular survival at this stage.}, pmid = {20654620}, keywords = {Adaptation,Animals,Cell Line,Down-Regulation,Gene Expression Profiling,Humans,Leishmania infantum,Leishmania infantum: genetics,Leishmania infantum: growth & development,Life Cycle Stages,Microarray Analysis,nosource,Oligonucleotide Array Sequence Analysis,Physiological,Protozoan Proteins,Protozoan Proteins: biosynthesis,Protozoan Proteins: genetics} }

@article{martinez-calvilloTranscriptionInitiationTermination2004, title = {Transcription Initiation and Termination on {{Leishmania}} Major Chromosome 3}, author = {{Mart{'i}nez-Calvillo}, S. and Nguyen, Dan and Stuart, Kenneth and Myler, P. J.}, year = 2004, journal = {Eukaryotic cell}, volume = {3}, number = {2}, doi = {10.1128/EC.3.2.506}, url = {http://ec.asm.org/content/3/2/506.short}, keywords = {nosource} }

@article{almeidaExpressionProfilingLeishmania2004, title = {Expression Profiling of the {{Leishmania}} Life Cycle: {{cDNA}} Arrays Identify Developmentally Regulated Genes Present but Not Annotated in the Genome.}, author = {Almeida, Renata and Gilmartin, Brian J. and McCann, Sharon H. and Norrish, Alan and Ivens, Alasdair C. and Lawson, Danial and Levick, Mark P. and Smith, Deborah F. and Dyall, Sabrina D. and Vetrie, David and Freeman, Tom C. and Coulson, Richard M. and Sampaio, Iracilda and Schneider, Horacio and Blackwell, Jenefer M.}, year = 2004, month = jul, journal = {Molecular and biochemical parasitology}, volume = {136}, number = {1}, eprint = {15138070}, eprinttype = {pubmed}, pages = {87–100}, issn = {0166-6851}, doi = {10.1016/j.molbiopara.2004.03.004}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15138070}, abstract = {As genomic sequencing of Leishmania nears completion, functional analyses that provide a global genetic perspective on biological processes are important. Despite polycistronic transcription, RNA transcript abundance can be measured using microarrays. To provide a resource to evaluate cDNA arrays, we undertook 5’ expressed sequence tag analysis of 2183 full-length randomly selected cDNAs from Leishmania major promastigote (days 3, 7, 10 of culture in vitro), and lesion-derived amastigote libraries. PCR-amplified inserts from 1830 of these cDNA representing 1001 unique genes were spotted onto microarrays, and compared internally with PCR-amplified open reading frames (ORFs) from 904 genes representing 842 unique genes annotated in the L. major genome. Microarrays were screened with RNA from procyclic, metacyclic and amastigote populations of L. major. Redundant clones on the array gave highly reproducible results, providing confidence in identification of stage-specific gene expression. Four hundred and thirty unique (i.e. non-redundant) stage-specific genes were identified. A higher percentage of stage-specific gene expression was observed in amastigotes ( approximately 35%) compared to metacyclics ( approximately 12%) for both cDNAs and ORFs, but cDNAs provided a richer source of regulated genes than currently annotated ORFs from the Leishmania genome. In mapping cDNAs onto the Leishmania genome, we noted that approximately 42% aligned to regions not recognised as genes using current predictive annotation tools. These genes are highly represented in our stage-specific genes, and therefore represent important drug targets and vaccine candidates. Careful annotation of cDNAs onto the Leishmania genome will be important before producing the next generation of oligonucleotide arrays based on annotated genes of the genomic sequencing project.}, pmid = {15138070}, keywords = {Animals,DNA,Expressed Sequence Tags,Gene Expression Profiling,Gene Expression Regulation,Leishmania,Leishmania major,Leishmania major: genetics,Leishmania major: growth & development,Leishmania major: metabolism,Leishmania: genetics,Leishmania: growth & development,Leishmania: metabolism,Life Cycle Stages,Molecular Sequence Data,nosource,Oligonucleotide Array Sequence Analysis,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Sequence Analysis} }

@article{shahGenomicOrganizationTranscription1999, title = {Genomic Organization, Transcription, Splicing and Gene Regulation in {{Leishmania}}}, author = {Shah, P. H. and Meade, J. C.}, year = 1999, journal = {Annals of tropical }, volume = {93}, number = {8}, pages = {781–808}, url = {http://www.ingentaconnect.com/content/routledg/catm/1999/00000093/00000008/art00001}, keywords = {nosource} }

@article{eliasTranscriptionRateModulation2001, title = {Transcription Rate Modulation through the {{Trypanosoma}} Cruzi Life Cycle Occurs in Parallel with Changes in Nuclear Organisation}, author = {Elias, {MCQB} and {Marques-Porto}, R.}, year = 2001, month = jan, journal = {Molecular and }, volume = {112}, number = {1}, eprint = {11166389}, eprinttype = {pubmed}, pages = {79–90}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11166389 http://www.sciencedirect.com/science/article/pii/S0166685100003492}, abstract = {In trypanosomes transcription occurs as large polycistronic units, with trans-splicing and polyadenylation generating each individual mRNA. There are no defined RNA polymerase II promoters and mRNA stabilisation is most likely the process controlling levels of differentially expressed mRNAs, since no selective modulation of gene activity has even been reported at the transcriptional level. Here, we show a large decrease in the transcription rates by RNA polymerases I and II when proliferative forms of Trypanosoma cruzi (epimastigotes and amastigotes) transform into non-proliferative and infective forms (trypomastigotes). We also show that these changes in transcription occur in parallel with modifications in the nuclear structure. While nuclei of proliferative forms are round, contain small amounts of peripheral heterochromatin and a large nucleolus, nuclei of trypomastigotes are elongated, the nucleolus disappears and the heterochromatin occupies most of the nuclear compartment. The decrease in the transcription parallels the nucleolus disassembly, as seen by the dispersion of nucleolar antigens. As T. cruzi cycles continuously through proliferative and infective forms, the molecular mechanisms involved in the control of nuclear organisation and chromatin remodelling can be revealed by this system.}, pmid = {11166389}, keywords = {Animals,Cell Line,Cell Nucleus,Cell Nucleus: ultrastructure,Chagas Disease,Chagas Disease: parasitology,Culture Media,Developmental,Electron,Fluorescent Antibody Technique,Gene Expression Regulation,Genetic,Immunoblotting,Life Cycle Stages,Microscopy,nosource,RNA Polymerase I,RNA Polymerase I: genetics,RNA Polymerase I: metabolism,RNA Polymerase II,RNA Polymerase II: genetics,RNA Polymerase II: metabolism,Transcription,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosoma cruzi: growth & development,Trypanosoma cruzi: metabolism} }

@article{smithTrypanosomesHomologLargest1989, title = {In Trypanosomes the Homolog of the Largest Subunit of {{RNA}} Polymerase {{II}} Is Encoded by Two Genes and Has a Highly Unusual {{C-terminal}} Domain Structure.}, author = {Smith, J. L. and Levin, J. R. and Ingles, C. J. and Agabian, N.}, year = 1989, month = mar, journal = {Cell}, volume = {56}, number = {5}, eprint = {2924350}, eprinttype = {pubmed}, pages = {815–27}, issn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2924350}, abstract = {We have isolated the genes encoding the largest subunit of all three classes of RNA polymerase from Trypanosoma brucei. While the pol II largest subunit is encoded by a single gene in all organisms examined to date, trypanosomes contain two copies of the gene. Both genes are expressed in the procyclic and bloodstream stages of the trypanosome life cycle. The two pol II genes differ from one another in their coding sequences by 21 silent substitutions and 4 amino acid substitutions. In the core part of the large subunit, the predicted polypeptides are similar to other eukaryotic RNA polymerases. Both trypanosome pol II polypeptides, like those of other eukaryotes, also have a unique C-terminal extension. However, this domain in the trypanosome polypeptides, unlike those of other eukaryotes, is not a tandemly repeated heptapeptide sequence.}, pmid = {2924350}, keywords = {Amino Acid Sequence,Animals,Base Sequence,Blotting,Cloning,Gene Expression Regulation,Genes,Messenger,Messenger: genetics,Molecular,Molecular Sequence Data,Northern,nosource,Restriction Mapping,RNA,RNA Polymerase II,RNA Polymerase II: genetics,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics} }

@article{leeTranscriptionProteincodingGenes1997, title = {Transcription of Protein-Coding Genes in Trypanosomes by {{RNA}} Polymerase {{I}}.}, author = {Lee, M. G. and {}der Ploeg, L. H. Van}, year = 1997, month = jan, journal = {Annual review of microbiology}, volume = {51}, eprint = {9343357}, eprinttype = {pubmed}, pages = {463–89}, issn = {0066-4227}, doi = {10.1146/annurev.micro.51.1.463}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9343357}, abstract = {In eukaryotes, RNA polymerase (pol) II transcribes the protein-coding genes, whereas RNA pol I transcribes the genes that encode the three RNA species of the ribosome [the ribosomal RNAs (rRNAs)] at the nucleolus. Protozoan parasites of the order Kinetoplastida may represent an exception, because pol I can mediate the expression of exogenously introduced protein-coding genes in these single-cell organisms. A unique molecular mechanism, which leads to pre-mRNA maturation by trans-splicing, facilitates pol I-mediated protein-coding gene expression in trypanosomes. Trans-splicing adds a capped 39-nucleotide mini-exon, or spliced leader transcript, to the 5’ end of the main coding exon posttranscriptionally. In other eukaryotes, the addition of a 5’ cap, which is essential for mRNA function, occurs exclusively as a result of RNA pol II-mediated transcription. Given the assumption that cap addition represents the limiting factor, trans-splicing may have uncoupled the requirement for RNA pol II-mediated mRNA production. A comparison of the alpha-amanitin sensitivity of transcription in naturally occurring trypanosome protein-coding genes reveals that a unique subset of protein-coding genes-the variant surface glycoprotein (VSG) expression sites and the procyclin or the procyclic acidic repetitive protein (PARP) genes-are transcribed by an RNA polymerase that is resistant to the mushroom toxin alpha-amanitin, a characteristic of transcription by RNA pol I. Promoter analysis and a pharmacological characterization of the RNA polymerase that transcribes these genes have strengthened the proposal that the VSG expression sites and the PARP genes represent naturally occurring protein-coding genes that are transcribed by RNA pol I.}, pmid = {9343357}, keywords = {Amanitins,Amanitins: genetics,Animals,Gene Expression Regulation,Genetic,Membrane Glycoproteins,Membrane Glycoproteins: genetics,Membrane Glycoproteins: metabolism,Messenger,Messenger: metabolism,nosource,Post-Transcriptional,Promoter Regions,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Ribosomal,Ribosomal: genetics,RNA,RNA Polymerase I,RNA Polymerase I: metabolism,RNA Processing,Transcription,Trypanosoma,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: metabolism,Trypanosoma: genetics,Trypanosoma: growth & development,Trypanosoma: metabolism} }

@article{grondalCharacterizationRNAPolymerases1989, title = {Characterization of the {{RNA}} Polymerases of {{Trypanosoma}} Brucei: Trypanosomal {{mRNAs}} Are Composed of Transcripts Derived from Both {{RNA}} Polymerase {{II}} and {{III}}.}, author = {Grondal, E. J. and Evers, R. and Kosubek, K. and Cornelissen, a W.}, year = 1989, month = nov, journal = {The EMBO journal}, volume = {8}, number = {11}, pages = {3383–9}, issn = {0261-4189}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=401483&tool=pmcentrez&rendertype=abstract}, abstract = {To analyze transcription in Typanosoma brucei, we have characterized the trypanosomal RNA polymerases. Here we present our results, which allow a discrimination between the different classes of RNA polymerases in nuclear run-on experiments by polymerase inhibitors and Mn2+ dependence. We also describe the separation of trypanosomal RNA polymerases by chromatography, demonstrating that T. brucei contains RNA polymerases I-III. The outcome of our experiments suggests that the VSG genes of T. brucei are not transcribed by RNA polymerase I, as previously reported, but by RNA polymerase II. We propose that an additional factor modifies RNA polymerase II, resulting in the alpha-amanitin-resistant transcription of VSG genes. Our data also suggest that the mini-exon genes, which encode the 5’ end of each trypanosomal mRNA, are probably transcribed by RNA polymerase III.}, pmid = {2583103}, keywords = {Amanitins,Amanitins: pharmacology,Animals,Antigens,Base Sequence,Chromatography,DNA-Directed RNA Polymerases,DNA-Directed RNA Polymerases: isolation & purifica,DNA-Directed RNA Polymerases: metabolism,Exons,Genes,Genetic,Ion Exchange,Manganese,Manganese: pharmacology,Messenger,Messenger: genetics,nosource,Protozoan,Protozoan: genetics,RNA,RNA Polymerase I,RNA Polymerase I: isolation & purification,RNA Polymerase I: metabolism,RNA Polymerase II,RNA Polymerase II: isolation & purification,RNA Polymerase II: metabolism,RNA Polymerase III,RNA Polymerase III: isolation & purification,RNA Polymerase III: metabolism,Surface,Surface: genetics,Transcription,Transfer,Transfer: genetics,Trypanosoma brucei brucei,Trypanosoma brucei brucei: enzymology,Trypanosoma brucei brucei: genetics} }

@article{greenbaumSolutionStructureDonor1996, title = {Solution Structure of the Donor Site of a Trans-Splicing {{RNA}}.}, author = {Greenbaum, N. L. and Radhakrishnan, I. and Patel, D. J. and Hirsh, D.}, year = 1996, month = jun, journal = {Structure (London, England : 1993)}, volume = {4}, number = {6}, eprint = {8805553}, eprinttype = {pubmed}, pages = {725–33}, issn = {0969-2126}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8805553}, abstract = {BACKGROUND: RNA splicing is both ubiquitous and essential for the maturation of precursor mRNA molecules in eukaryotes. The process of trans-splicing involves the transfer of a short spliced leader (SL) RNA sequence to a consensus acceptor site on a separate pre-mRNA transcript. In Caenorhabditis elegans, a majority of pre-mRNA transcripts receive the 22-nucleotide SL from the SL1 RNA. Very little is known about the various roles that RNA structures play in the complex conformational rearrangements and reactions involved in premRNA splicing. RESULTS: We have determined the solution structure of a domain of the first stem loop of the SL1 RNA of C. elegans, using homonuclear and heteronuclear NMR techniques; this domain contains the splice-donor site and a nine-nucleotide hairpin loop. In solution, the SL1 RNA fragment adopts a stem-loop structure: nucleotides in the stem region form a classical A-type helix while nucleotides in the hairpin loop specify a novel conformation that includes a helix, that extends for the first three residues; a syn guanosine nucleotide at the turn region; and an extrahelical adenine that defines a pocket with nucleotides at the base of the loop. CONCLUSION: The proximity of this pocket to the splice donor site, combined with the observation that the nucleotides in this motif are conserved among all nematode SL RNAs, suggests that this pocket may provide a recognition site for a protein or RNA molecule in the trans-splicing process.}, pmid = {8805553}, keywords = {Animals,Base Sequence,Caenorhabditis elegans,Caenorhabditis elegans: metabolism,Genetic,Genetic: genetics,Hydrogen Bonding,Magnetic Resonance Spectroscopy,Models,Molecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,RNA,RNA Precursors,RNA Precursors: metabolism,RNA Splicing,RNA Splicing: genetics,RNA: chemistry,Transcription} }

@article{abbinkHIV1LeaderRNA2005, title = {The {{HIV-1}} Leader {{RNA}} Conformational Switch Regulates {{RNA}} Dimerization but Does Not Regulate {{mRNA}} Translation.}, author = {Abbink, Truus E. M. and Ooms, Marcel and Haasnoot, P. C. Joost and Berkhout, Ben}, year = 2005, month = jun, journal = {Biochemistry}, volume = {44}, number = {25}, eprint = {15966729}, eprinttype = {pubmed}, pages = {9058–66}, issn = {0006-2960}, doi = {10.1021/bi0502588}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15966729}, abstract = {The untranslated leader RNA is the most conserved part of the human immunodeficiency virus type I (HIV-1) genome. It contains many regulatory motifs that mediate a variety of steps in the viral life cycle. Previous work showed that the full-length leader RNA can adopt two alternative structures: a long distance interaction (LDI) and a branched multiple-hairpin (BMH) structure. The BMH structure exposes the dimer initiation site (DIS) hairpin, whereas this motif is occluded in the LDI structure. Consequently, these structures differ in their capacity to form RNA dimers in vitro. The BMH structure is dimerization-competent, due to DIS hairpin formation, but also presents the splice donor (SD) and RNA packaging (Psi) hairpins. In the LDI structure, an extended RNA packaging (Psi(E)) hairpin is folded, which includes the splice donor site and gag coding sequences. The gag initiation codon is engaged in a long distance base pairing interaction with sequences in the upstream U5 region in the BMH structure, thus forming the evolutionarily conserved U5-AUG duplex. Therefore, the LDI-BMH equilibrium may affect not only the process of RNA dimer formation but also translation initiation. In this study, we designed mutations in the 3’-terminal region of the leader RNA that alter the equilibrium of the LDI-BMH structures. The mutant leader RNAs are affected in RNA dimer formation, but not in their translation efficiency. These results indicate that the LDI-BMH status does not regulate HIV-1 RNA translation, despite the differential presentation of the gag initiation codon in both leader RNA structures.}, pmid = {15966729}, keywords = {Base Sequence,Dimerization,Genetic,Genetic: genetics,HIV-1,HIV-1: genetics,Messenger,Messenger: genetics,Messenger: metabolism,Molecular Sequence Data,Mutation,Mutation: genetics,nosource,Nucleic Acid Conformation,Protein Biosynthesis,Protein Biosynthesis: genetics,RNA,Thermodynamics,Transcription,Viral,Viral: chemistry,Viral: genetics,Viral: metabolism} }

@article{liuStructureRNAPolymerase2010, title = {Structure of an {{RNA}} Polymerase {{II-TFIIB}} Complex and the Transcription Initiation Mechanism.}, author = {Liu, Xin and {}a Bushnell, David and Wang, Dong and Calero, Guillermo and Kornberg, Roger D.}, year = 2010, month = jan, journal = {Science (New York, N.Y.)}, volume = {327}, number = {5962}, pages = {206–9}, issn = {1095-9203}, doi = {10.1126/science.1182015}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2813267&tool=pmcentrez&rendertype=abstract}, abstract = {Previous x-ray crystal structures have given insight into the mechanism of transcription and the role of general transcription factors in the initiation of the process. A structure of an RNA polymerase II-general transcription factor TFIIB complex at 4.5 angstrom resolution revealed the amino-terminal region of TFIIB, including a loop termed the “B finger,” reaching into the active center of the polymerase where it may interact with both DNA and RNA, but this structure showed little of the carboxyl-terminal region. A new crystal structure of the same complex at 3.8 angstrom resolution obtained under different solution conditions is complementary with the previous one, revealing the carboxyl-terminal region of TFIIB, located above the polymerase active center cleft, but showing none of the B finger. In the new structure, the linker between the amino- and carboxyl-terminal regions can also be seen, snaking down from above the cleft toward the active center. The two structures, taken together with others previously obtained, dispel long-standing mysteries of the transcription initiation process.}, pmid = {19965383}, keywords = {Amino Acid,Amino Acid Sequence,Catalytic Domain,Crystallography,Genetic,Models,Molecular,Molecular Sequence Data,nosource,Protein Conformation,Protein Interaction Domains and Motifs,Protein Structure,Repetitive Sequences,RNA Polymerase II,RNA Polymerase II: chemistry,RNA Polymerase II: metabolism,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: chemistry,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: chemistry,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Secondary,Tertiary,Transcription,Transcription Factor TFIIB,Transcription Factor TFIIB: chemistry,Transcription Factor TFIIB: metabolism,X-Ray} } % == BibTeX quality report for liuStructureRNAPolymerase2010: % ? Possibly abbreviated journal title Science (New York, N.Y.)

@article{leibovichEfficientMotifSearch2012, title = {Efficient Motif Search in Ranked Lists and Applications to Variable Gap Motifs.}, author = {Leibovich, Limor and Yakhini, Zohar}, year = 2012, month = jul, journal = {Nucleic acids research}, volume = {40}, number = {13}, pages = {5832–47}, issn = {1362-4962}, doi = {10.1093/nar/gks206}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3401424&tool=pmcentrez&rendertype=abstract}, abstract = {Sequence elements, at all levels-DNA, RNA and protein, play a central role in mediating molecular recognition and thereby molecular regulation and signaling. Studies that focus on -measuring and investigating sequence-based recognition make use of statistical and computational tools, including approaches to searching sequence motifs. State-of-the-art motif searching tools are limited in their coverage and ability to address large motif spaces. We develop and present statistical and algorithmic approaches that take as input ranked lists of sequences and return significant motifs. The efficiency of our approach, based on suffix trees, allows searches over motif spaces that are not covered by existing tools. This includes searching variable gap motifs-two half sites with a flexible length gap in between-and searching long motifs over large alphabets. We used our approach to analyze several high-throughput measurement data sets and report some validation results as well as novel suggested motifs and motif refinements. We suggest a refinement of the known estrogen receptor 1 motif in humans, where we observe gaps other than three nucleotides that also serve as significant recognition sites, as well as a variable length motif related to potential tyrosine phosphorylation.}, pmid = {22416066}, keywords = {Algorithms,Amino Acid Motifs,Binding Sites,Chromatin Immunoprecipitation,Data Interpretation,DNA,Estrogen Receptor alpha,Estrogen Receptor alpha: metabolism,Heat-Shock Response,Heat-Shock Response: genetics,Humans,nosource,Nucleotide Motifs,Protein,RNA,RNA-Binding Proteins,RNA-Binding Proteins: metabolism,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Sequence Analysis,Statistical,Transcription Factors,Transcription Factors: metabolism,Tumor Suppressor Protein p53,Tumor Suppressor Protein p53: metabolism} }

@article{chaoHighresolutionDefinitionVibrio2013, title = {High-Resolution Definition of the {{Vibrio}} Cholerae Essential Gene Set with Hidden {{Markov}} Model-Based Analyses of Transposon-Insertion Sequencing Data.}, author = {Chao, Michael C. and Pritchard, Justin R. and Zhang, Yanjia J. and Rubin, Eric J. and Livny, Jonathan and Davis, Brigid M. and Waldor, Matthew K.}, year = 2013, month = oct, journal = {Nucleic acids research}, volume = {41}, number = {19}, pages = {9033–48}, issn = {1362-4962}, doi = {10.1093/nar/gkt654}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3799429&tool=pmcentrez&rendertype=abstract}, abstract = {The coupling of high-density transposon mutagenesis to high-throughput DNA sequencing (transposon-insertion sequencing) enables simultaneous and genome-wide assessment of the contributions of individual loci to bacterial growth and survival. We have refined analysis of transposon-insertion sequencing data by normalizing for the effect of DNA replication on sequencing output and using a hidden Markov model (HMM)-based filter to exploit heretofore unappreciated information inherent in all transposon-insertion sequencing data sets. The HMM can smooth variations in read abundance and thereby reduce the effects of read noise, as well as permit fine scale mapping that is independent of genomic annotation and enable classification of loci into several functional categories (e.g. essential, domain essential or ‘sick’). We generated a high-resolution map of genomic loci (encompassing both intra- and intergenic sequences) that are required or beneficial for in vitro growth of the cholera pathogen, Vibrio cholerae. This work uncovered new metabolic and physiologic requirements for V. cholerae survival, and by combining transposon-insertion sequencing and transcriptomic data sets, we also identified several novel noncoding RNA species that contribute to V. cholerae growth. Our findings suggest that HMM-based approaches will enhance extraction of biological meaning from transposon-insertion sequencing genomic data.}, pmid = {23901011}, keywords = {5’ Untranslated Regions,Bacterial,DNA,DNA Transposable Elements,Escherichia coli,Escherichia coli: genetics,Essential,Gene Library,Genes,Genetic Loci,High-Throughput Nucleotide Sequencing,Markov Chains,nosource,RNA,Sequence Analysis,Untranslated,Untranslated: genetics,Vibrio cholerae,Vibrio cholerae: genetics,Vibrio cholerae: growth & development} }

@article{dejesusReannotationTranslationalStart2013, title = {Reannotation of Translational Start Sites in the Genome of {{Mycobacterium}} Tuberculosis.}, author = {{}a DeJesus, Michael and Sacchettini, James C. and Ioerger, Thomas R.}, year = 2013, month = jan, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {93}, number = {1}, pages = {18–25}, publisher = {Elsevier Ltd}, issn = {1873-281X}, doi = {10.1016/j.tube.2012.11.012}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3582765&tool=pmcentrez&rendertype=abstract}, abstract = {Identification and correction of incorrect ORF start sites is important for a variety of experimental and analytical purposes, ranging from cloning to inference of operon structure. The genome of the H37Rv reference strain of Mycobacterium tuberculosis (Mtb) was originally annotated when it was first sequenced nearly 15 years ago. While this annotation has served the TB research community well as a standard of reference for over a decade, it has been demonstrated experimentally that the actual start sites for an estimated 5-10% of open reading frames differ from the annotation. In this paper, we present a comprehensive bioinformatic analysis of all 3989 ORFs (open reading frames) in the M. tuberculosis H37Rv genome. Our method combines information from comparative analysis (alignment to start sites of orthologs in other Actinobacteria), sequence conservation, “protein likeness”, putative ribosome binding sites, and other data to identify translational start sites. The features are combined in a linear model that is trained on dataset of known start sites verified by mass spectrometry, with a cross-validated accuracy of 94%. The method can be viewed as an augmentation of Hidden Markov Model-based tools such as Glimmer and GeneMark by incorporating more information than just the raw genomic sequence to decide which position is the legitimate translational start site for each ORF. Using this analysis, we identify 269 genes that most likely need to be re-annotated, and identify the best alterative translational start site for each. These revised ORF definitions could be used in the reannotation of the H37Rv genome, as well as to prioritize genes for experimental start-site validation.}, pmid = {23273318}, keywords = {Actinobacteria,Actinobacteria: genetics,Amino Acid Sequence,Bacterial,Codon,Computational Biology,Computational Biology: methods,Genome,Humans,Initiator,Initiator: genetics,Molecular Sequence Annotation,Molecular Sequence Annotation: methods,Molecular Sequence Data,Mycobacterium tuberculosis,Mycobacterium tuberculosis: genetics,nosource,Open Reading Frames,Open Reading Frames: genetics,Protein Biosynthesis,Ribosomes,Ribosomes: metabolism,Sequence Alignment} }

@article{bouvierPlasmidVectorsMolecular2013, title = {Plasmid Vectors and Molecular Building Blocks for the Development of Genetic Manipulation Tools for {{Trypanosoma}} Cruzi.}, author = {{}a Bouvier, Le{'o}n and C{'a}mara, Mar{'i}a De Los Milagros and Canepa, Gaspar E. and Miranda, Mariana R. and {}a Pereira, Claudio}, year = 2013, month = jan, journal = {PloS one}, volume = {8}, number = {10}, pages = {e80217}, issn = {1932-6203}, doi = {10.1371/journal.pone.0080217}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3812015&tool=pmcentrez&rendertype=abstract}, abstract = {The post genomic era revealed the need for developing better performing, easier to use and more sophisticated genetic manipulation tools for the study of Trypanosoma cruzi, the etiological agent of Chagas disease. In this work a series of plasmids that allow genetic manipulation of this protozoan parasite were developed. First of all we focused on useful tools to establish selection strategies for different strains and which can be employed as expression vectors. On the other hand molecular building blocks in the form of diverse selectable markers, modifiable fluorescent protein and epitope-tag coding sequences were produced. Both types of modules were harboured in backbone molecules conceived to offer multiple construction and sub-cloning strategies. These can be used to confer new properties to already available genetic manipulation tools or as starting points for whole novel designs. The performance of each plasmid and building block was determined independently. For illustration purposes, some simple direct practical applications were conducted.}, pmid = {24205392}, keywords = {nosource} }

@article{carboneCodonAdaptationIndex2003, title = {Codon Adaptation Index as a Measure of Dominating Codon Bias}, author = {Carbone, a and Zinovyev, a and Kepes, F.}, year = 2003, month = oct, journal = {Bioinformatics}, volume = {19}, number = {16}, pages = {2005–2015}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btg272}, url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btg272}, keywords = {nosource} }

@article{padmanabhanNovelFeaturesPIWIlike2012, title = {Novel Features of a {{PIWI-like}} Protein Homolog in the Parasitic Protozoan {{Leishmania}}.}, author = {Padmanabhan, Prasad K. and Dumas, Carole and Samant, Mukesh and Rochette, Annie and Simard, Martin J. and Papadopoulou, Barbara}, year = 2012, month = jan, journal = {PloS one}, volume = {7}, number = {12}, pages = {e52612}, issn = {1932-6203}, doi = {10.1371/journal.pone.0052612}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3528672&tool=pmcentrez&rendertype=abstract}, abstract = {In contrast to nearly all eukaryotes, the Old World Leishmania species L. infantum and L. major lack the bona fide RNAi machinery genes. Interestingly, both Leishmania genomes code for an atypical Argonaute-like protein that possesses a PIWI domain but lacks the PAZ domain found in Argonautes from RNAi proficient organisms. Using sub-cellular fractionation and confocal fluorescence microscopy, we show that unlike other eukaryotes, the PIWI-like protein is mainly localized in the single mitochondrion in Leishmania. To predict PIWI function, we generated a knockout mutant for the PIWI gene in both L. infantum (Lin) and L. major species by double-targeted gene replacement. Depletion of PIWI has no effect on the viability of insect promastigote forms but leads to an important growth defect of the mammalian amastigote lifestage in vitro and significantly delays disease pathology in mice, consistent with a higher expression of the PIWI transcript in amastigotes. Moreover, amastigotes lacking PIWI display a higher sensitivity to apoptosis inducing agents than wild type parasites, suggesting that PIWI may be a sensor for apoptotic stimuli. Furthermore, a whole-genome DNA microarray analysis revealed that loss of LinPIWI in Leishmania amastigotes affects mostly the expression of specific subsets of developmentally regulated genes. Several transcripts encoding surface and membrane-bound proteins were found downregulated in the LinPIWI((-/-)) mutant whereas all histone transcripts were upregulated in the null mutant, supporting the possibility that PIWI plays a direct or indirect role in the stability of these transcripts. Although our data suggest that PIWI is not involved in the biogenesis or the stability of small noncoding RNAs, additional studies are required to gain further insights into the role of this protein on RNA regulation and amastigote development in Leishmania.}, pmid = {23285111}, keywords = {Amino Acid Sequence,Animals,Apoptosis,Apoptosis: genetics,Argonaute Proteins,Argonaute Proteins: chemistry,Argonaute Proteins: genetics,Developmental,Gene Expression Regulation,Genetic,Leishmania,Leishmania infantum,Leishmania infantum: genetics,Leishmania major,Leishmania major: genetics,Leishmania: genetics,Leishmaniasis,Leishmaniasis: parasitology,Mice,Mitochondria,Mitochondria: genetics,Mitochondria: metabolism,Molecular Sequence Data,nosource,Protein Interaction Domains and Motifs,RNA,RNA Interference,Sequence Alignment,Small Untranslated,Small Untranslated: genetics,Small Untranslated: metabolism,Transcription} }

@article{langmeadUltrafastMemoryefficientAlignment2009, title = {Ultrafast and Memory-Efficient Alignment of Short {{DNA}} Sequences to the Human Genome.}, author = {Langmead, Ben and Trapnell, Cole and Pop, Mihai and Salzberg, Steven L.}, year = 2009, month = jan, journal = {Genome biology}, volume = {10}, number = {3}, pages = {R25}, issn = {1465-6914}, doi = {10.1186/gb-2009-10-3-r25}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2690996&tool=pmcentrez&rendertype=abstract}, abstract = {Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source (http://bowtie.cbcb.umd.edu).}, pmid = {19261174}, keywords = {Algorithms,Base Sequence,Genome,Human,Human: genetics,Humans,nosource,Sequence Alignment,Sequence Alignment: methods} }

@article{subramanianGSEAPDesktopApplication2007, title = {{{GSEA-P}}: A Desktop Application for {{Gene Set Enrichment Analysis}}.}, author = {Subramanian, Aravind and Kuehn, Heidi and Gould, Joshua and Tamayo, Pablo and Mesirov, Jill P.}, year = 2007, month = dec, journal = {Bioinformatics (Oxford, England)}, volume = {23}, number = {23}, eprint = {17644558}, eprinttype = {pubmed}, pages = {3251–3}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btm369}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17644558}, abstract = {UNLABELLED: Gene Set Enrichment Analysis (GSEA) is a computational method that assesses whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. We report the availability of a new version of the Java based software (GSEA-P 2.0) that represents a major improvement on the previous release through the addition of a leading edge analysis component, seamless integration with the Molecular Signature Database (MSigDB) and an embedded browser that allows users to search for gene sets and map them to a variety of microarray platform formats. This functionality makes it possible for users to directly import gene sets from MSigDB for analysis with GSEA. We have also improved the visualizations in GSEA-P 2.0 and added links to a new form of concise gene set annotations called Gene Set Cards. These additions, as well as other improvements suggested by over 3500 users who have downloaded the software over the past year have been incorporated into this new release of the GSEA-P Java desktop program. AVAILABILITY: GSEA-P 2.0 is freely available for academic and commercial users and can be downloaded from http://www.broad.mit.edu/GSEA}, pmid = {17644558}, keywords = {Algorithms,Biological,Computer Graphics,Computer Simulation,Gene Expression Profiling,Models,nosource,Programming Languages,Proteins,Proteins: metabolism,Signal Transduction,Signal Transduction: physiology,Software,User-Computer Interface} }

@article{harrisGeneOntologyGO2004, title = {The {{Gene Ontology}} ({{GO}}) Database and Informatics Resource.}, author = {{}a Harris, M. and Clark, J. and Ireland, a and Lomax, J. and Ashburner, M. and Foulger, R. and Eilbeck, K. and Lewis, S. and Marshall, B. and Mungall, C. and Richter, J. and Rubin, G. M. and {}a Blake, J. and Bult, C. and Dolan, M. and Drabkin, H. and Eppig, J. T. and Hill, D. P. and Ni, L. and Ringwald, M. and Balakrishnan, R. and Cherry, J. M. and Christie, K. R. and Costanzo, M. C. and Dwight, S. S. and Engel, S. and Fisk, D. G. and Hirschman, J. E. and Hong, E. L. and Nash, R. S. and Sethuraman, a and Theesfeld, C. L. and Botstein, D. and Dolinski, K. and Feierbach, B. and Berardini, T. and Mundodi, S. and Rhee, S. Y. and Apweiler, R. and Barrell, D. and Camon, E. and Dimmer, E. and Lee, V. and Chisholm, R. and Gaudet, P. and Kibbe, W. and Kishore, R. and Schwarz, E. M. and Sternberg, P. and Gwinn, M. and Hannick, L. and Wortman, J. and Berriman, M. and Wood, V. and {}de la Cruz, N. and Tonellato, P. and Jaiswal, P. and Seigfried, T. and White, R.}, year = 2004, month = jan, journal = {Nucleic acids research}, volume = {32}, number = {Database issue}, pages = {D258-61}, issn = {1362-4962}, doi = {10.1093/nar/gkh036}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=308770&tool=pmcentrez&rendertype=abstract}, abstract = {The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.}, pmid = {14681407}, keywords = {Animals,Bibliography as Topic,Databases,Electronic Mail,Genes,Genetic,Genomics,Humans,Information Storage and Retrieval,Internet,Molecular Biology,nosource,Proteins,Proteins: classification,Proteins: genetics,Software,Terminology as Topic} }

@article{subramanianGeneSetEnrichment2005, title = {Gene Set Enrichment Analysis : {{A}} Knowledge-Based Approach for Interpreting Genome-Wide}, author = {Subramanian, Aravind and Tamayo, Pablo and Mootha, Vamsi K. and Mukherjee, Sayan and Ebert, Benjamin L.}, year = 2005, keywords = {nosource} } % == BibTeX quality report for subramanianGeneSetEnrichment2005: % Missing required field ‘journal’

@article{rabhiComparativeAnalysisResistant2013, title = {Comparative Analysis of Resistant and Susceptible Macrophage Gene Expression Response to {{Leishmania}} Major Parasite.}, author = {Rabhi, Imen and Rabhi, Sameh and {Ben-Othman}, Rym and Aniba, Mohamed Radhouane and Trentin, Bernadette and Piquemal, David and Regnault, B{'e}atrice and {Guizani-Tabbane}, Lamia}, year = 2013, month = jan, journal = {BMC genomics}, volume = {14}, eprint = {24148319}, eprinttype = {pubmed}, pages = {723}, issn = {1471-2164}, doi = {10.1186/1471-2164-14-723}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24148319}, abstract = {BACKGROUND: Leishmania are obligated intracellular pathogens that replicate almost exclusively in macrophages. The outcome of infection depends largely on parasite pathogenicity and virulence but also on the activation status and genetic background of macrophages. Animal models are essential for a better understanding of pathogenesis of different microbes including Leishmania. RESULTS: Here we compared the transcriptional signatures of resistant (C57BL/6) and susceptible (BALB/c) mouse bone marrow-derived macrophages in response to Leishmania major (L. major) promastigotes infection.Microarray results were first analyzed for significant pathways using the Kyoto Encylopedia of Genes and Genomes (KEGG) database. The analysis revealed that a large set of the shared genes is involved in the immune response and that difference in the expression level of some chemokines and chemokine receptors could partially explain differences in resistance. We next focused on up-regulated genes unique to either BALB/c or C57BL/6 derived macrophages and identified, using KEGG database, signal transduction pathways among the most relevant pathways unique to both susceptible and resistant derived macrophages. Indeed, genes unique to C57BL/6 BMdMs were associated with target of rapamycin (mTOR) signaling pathway while a range of genes unique to BALB/c BMdMs, belong to p53 signaling pathway. We next investigated whether, in a given mice strain derived macrophages, the different up-regulated unique genes could be coordinately regulated. Using GeneMapp Cytoscape, we showed that the induced genes unique to BALB/c or C57BL/6 BMdMs are interconnected. Finally, we examined whether the induced pathways unique to BALB/c derived macrophages interfere with the ones unique to C57BL/6 derived macrophages. Protein-protein interaction analysis using String database highlights the existence of a cross-talk between p53 and mTOR signaling pathways respectively specific to susceptible and resistant BMdMs. CONCLUSIONS: Taken together our results suggest that strains specific pathogenesis may be due to a difference in the magnitude of the same pathways and/or to differentially expressed pathways in the two mouse strains derived macrophages. We identify signal transduction pathways among the most relevant pathways modulated by L. major infection, unique to BALB/c and C57BL/6 BMdM and postulate that the interplay between these potentially interconnected pathways could direct the macrophage response toward a given phenotype.}, pmid = {24148319}, keywords = {correspondence,gene expression,guizani,lamia,leishmania,macrophages,microarray,nosource,pasteur,rns,tn} }

@article{al-jubranVisualizationJoiningRibosomal2013, title = {Visualization of the Joining of Ribosomal Subunits Reveals the Presence of {{80S}} Ribosomes in the Nucleus.}, author = {{Al-Jubran}, Khalid and Wen, Jikai and Abdullahi, Akilu and Chaudhury, Subhendu Roy and Li, Min and Ramanathan, Preethi and Matina, Annunziata and De, Sandip and Piechocki, Kim and Rugjee, Kushal Nivriti and Brogna, Saverio}, year = 2013, month = dec, journal = {RNA (New York, N.Y.)}, volume = {19}, number = {12}, pages = {1669–83}, issn = {1469-9001}, doi = {10.1261/rna.038356.113}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3884666&tool=pmcentrez&rendertype=abstract}, abstract = {In eukaryotes the 40S and 60S ribosomal subunits are assembled in the nucleolus, but there appear to be mechanisms preventing mRNA binding, 80S formation, and initiation of translation in the nucleus. To visualize association between ribosomal subunits, we tagged pairs of Drosophila ribosomal proteins (RPs) located in different subunits with mutually complementing halves of fluorescent proteins. Pairs of tagged RPs expected to interact, or be adjacent in the 80S structure, showed strong fluorescence, while pairs that were not in close proximity did not. Moreover, the complementation signal is found in ribosomal fractions and it was enhanced by translation elongation inhibitors and reduced by initiation inhibitors. Our technique achieved 80S visualization both in cultured cells and in fly tissues in vivo. Notably, while the main 80S signal was in the cytoplasm, clear signals were also seen in the nucleolus and at other nuclear sites. Furthermore, we detected rapid puromycin incorporation in the nucleolus and at transcription sites, providing an independent indication of functional 80S in the nucleolus and 80S association with nascent transcripts.}, pmid = {24129492}, keywords = {Animals,Bacterial Proteins,Bacterial Proteins: biosynthesis,Cell Line,Cell Nucleolus,Cell Nucleolus: metabolism,Cell Nucleus,Cell Nucleus: metabolism,Drosophila melanogaster,Drosophila melanogaster: cytology,Drosophila melanogaster: genetics,Drosophila melanogaster: metabolism,Drosophila Proteins,Drosophila Proteins: metabolism,Fluorescence,Genetic,Luminescent Proteins,Luminescent Proteins: biosynthesis,Messenger,Messenger: genetics,Messenger: metabolism,Microscopy,nosource,Peptidyl Transferases,Peptidyl Transferases: metabolism,Polytene Chromosomes,Polytene Chromosomes: metabolism,Protein Binding,Recombinant Fusion Proteins,Recombinant Fusion Proteins: biosynthesis,Ribosomal Proteins,Ribosomal Proteins: metabolism,Ribosomes,Ribosomes: metabolism,RNA,Transcription} } % == BibTeX quality report for al-jubranVisualizationJoiningRibosomal2013: % ? Possibly abbreviated journal title RNA (New York, N.Y.)

@article{kramerHeatShockCauses2008, title = {Heat Shock Causes a Decrease in Polysomes and the Appearance of Stress Granules in Trypanosomes Independently of {{eIF2}}(Alpha) Phosphorylation at {{Thr169}}.}, author = {Kramer, Susanne and Queiroz, Rafael and Ellis, Louise and Webb, Helena and Hoheisel, J{"o}rg D. and Clayton, Christine and Carrington, Mark}, year = 2008, month = sep, journal = {Journal of cell science}, volume = {121}, number = {Pt 18}, pages = {3002–14}, issn = {0021-9533}, doi = {10.1242/jcs.031823}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2871294&tool=pmcentrez&rendertype=abstract}, abstract = {In trypanosomes there is an almost total reliance on post-transcriptional mechanisms to alter gene expression; here, heat shock was used to investigate the response to an environmental signal. Heat shock rapidly and reversibly induced a decrease in polysome abundance, and the consequent changes in mRNA metabolism were studied. Both heat shock and polysome dissociation were necessary for (1) a reduction in mRNA levels that was more rapid than normal turnover, (2) an increased number of P-body-like granules that contained DHH1, SCD6 and XRNA, (3) the formation of stress granules that remained largely separate from the P-body-like granules and localise to the periphery of the cell and, (4) an increase in the size of a novel focus located at the posterior pole of the cell that contain XRNA, but neither DHH1 nor SCD6. The response differed from mammalian cells in that neither the decrease in polysomes nor stress-granule formation required phosphorylation of eIF2alpha at the position homologous to that of serine 51 in mammalian eIF2alpha and in the occurrence of a novel XRNA-focus.}, pmid = {18713834}, keywords = {Animals,Cytoplasmic Granules,Cytoplasmic Granules: metabolism,DNA Damage,Eukaryotic Initiation Factor-2,Eukaryotic Initiation Factor-2: genetics,Eukaryotic Initiation Factor-2: metabolism,Gene Expression Regulation,Heat-Shock Response,Heat-Shock Response: physiology,Messenger,Messenger: metabolism,Microarray Analysis,nosource,Polyribosomes,Polyribosomes: metabolism,Protein Biosynthesis,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Recombinant Fusion Proteins,Recombinant Fusion Proteins: genetics,Recombinant Fusion Proteins: metabolism,RNA,Threonine,Threonine: metabolism,Trypanosoma brucei brucei,Trypanosoma brucei brucei: cytology,Trypanosoma brucei brucei: metabolism} }

@article{moreiraEvolutionEukaryoticTranslation2002, title = {Evolution of Eukaryotic Translation Elongation and Termination Factors: Variations of Evolutionary Rate and Genetic Code Deviations.}, author = {Moreira, David and Kervestin, St{'e}phanie and {Jean-Jean}, Olivier and Philippe, Herv{'e}}, year = 2002, month = feb, journal = {Molecular biology and evolution}, volume = {19}, number = {2}, eprint = {11801747}, eprinttype = {pubmed}, pages = {189–200}, issn = {0737-4038}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11801747}, abstract = {Translation is carried out by the ribosome and several associated protein factors through three consecutive steps: initiation, elongation, and termination. Termination remains the least understood of them, partly because of the nonuniversality of the factors involved. To get some insights on the evolution of eukaryotic translation termination, we have compared the phylogeny of the release factors eRF1 and eRF3 to that of the elongation factors EF-1alpha and EF-2, with special focus on ciliates. Our results show that these four translation proteins have experienced different modes of evolution. This is especially evident for the EF-1alpha, EF-2, and eRF1 ciliate sequences. Ciliates appear as monophyletic in the EF-2 phylogenetic tree but not in the EF-1alpha and eRF1 phylogenetic trees. This seems to be mainly because of phylogeny reconstruction artifacts (the long-branch attraction) produced by the acceleration of evolutionary rate of ciliate EF-1alpha and eRF1 sequences. Interaction with the highly divergent actin found in ciliates, or on the contrary, loss of interaction, could explain the acceleration of the evolutionary rate of the EF-1alpha sequences. In the case of ciliate eRF1 sequences, their unusually high evolutionary rate may be related to the deviations in the genetic code usage found in diverse ciliates. These deviations involve a relaxation (or even abolition) of the recognition of one or two stop codons by eRF1. To achieve this, structural changes in eRF1 are needed, and this may affect its evolutionary rate. Eukaryotic translation seems to have followed a mosaic evolution, with its different elements governed by different selective pressures. However, a correlation analysis shows that, beneath the disagreement shown by the different translation proteins, their concerted evolution can still be made apparent when they are compared with other proteins that are not involved in translation.}, pmid = {11801747}, keywords = {Animals,Ciliophora,Ciliophora: physiology,DNA,Eukaryotic Cells,Eukaryotic Cells: physiology,Evolution,Fungal Proteins,Fungal Proteins: genetics,Genetic Variation,GTP-Binding Proteins,HSP70 Heat-Shock Proteins,HSP70 Heat-Shock Proteins: genetics,Models,Molecular,nosource,Peptide Elongation Factor 2,Peptide Elongation Factor 2: genetics,Peptide Elongation Factors,Peptide Elongation Factors: genetics,Peptide Termination Factors,Peptide Termination Factors: genetics,Phylogeny,Protein Biosynthesis,Saccharomyces cerevisiae Proteins,Sequence Analysis} }

@article{thomasHistoneAcetylationsMark2009, title = {Histone Acetylations Mark Origins of Polycistronic Transcription in {{Leishmania}} Major}, author = {Thomas, Sean and Green, Amanda and Sturm, N. R.}, year = 2009, month = jan, journal = {BMC }, volume = {10}, pages = {152}, issn = {1471-2164}, doi = {10.1186/1471-2164-10-152}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2679053&tool=pmcentrez&rendertype=abstract http://www.biomedcentral.com/1471-2164/10/152}, abstract = {BACKGROUND: Many components of the RNA polymerase II transcription machinery have been identified in kinetoplastid protozoa, but they diverge substantially from other eukaryotes. Furthermore, protein-coding genes in these organisms lack individual transcriptional regulation, since they are transcribed as long polycistronic units. The transcription initiation sites are assumed to lie within the ‘divergent strand-switch’ regions at the junction between opposing polycistronic gene clusters. However, the mechanism by which Kinetoplastidae initiate transcription is unclear, and promoter sequences are undefined. RESULTS: The chromosomal location of TATA-binding protein (TBP or TRF4), Small Nuclear Activating Protein complex (SNAP50), and H3 histones were assessed in Leishmania major using microarrays hybridized with DNA obtained through chromatin immunoprecipitation (ChIP-chip). The TBP and SNAP50 binding patterns were almost identical and high intensity peaks were associated with tRNAs and snRNAs. Only 184 peaks of acetylated H3 histone were found in the entire genome, with substantially higher intensity in rapidly-dividing cells than stationary-phase. The majority of the acetylated H3 peaks were found at divergent strand-switch regions, but some occurred at chromosome ends and within polycistronic gene clusters. Almost all these peaks were associated with lower intensity peaks of TBP/SNAP50 binding a few kilobases upstream, evidence that they represent transcription initiation sites. CONCLUSION: The first genome-wide maps of DNA-binding protein occupancy in a kinetoplastid organism suggest that H3 histones at the origins of polycistronic transcription of protein-coding genes are acetylated. Global regulation of transcription initiation may be achieved by modifying the acetylation state of these origins.}, pmid = {19356248}, keywords = {Acetylation,Animals,Chromatin Immunoprecipitation,DNA-Binding Proteins,DNA-Binding Proteins: genetics,DNA-Binding Proteins: metabolism,Genetic,Histones,Histones: metabolism,Leishmania major,Leishmania major: genetics,nosource,Post-Translational,Promoter Regions,Protein Processing,RNA,Small Nuclear,Small Nuclear: metabolism,TATA-Box Binding Protein,TATA-Box Binding Protein: genetics,TATA-Box Binding Protein: metabolism,Transcription,Transfer,Transfer: metabolism} }

@article{sambrookIsolationDNAFragments2006, title = {Isolation of {{DNA}} Fragments from Polyacrylamide Gels by the Crush and Soak Method.}, author = {Sambrook, Joseph and Russell, David W.}, year = 2006, month = jan, journal = {CSH protocols}, volume = {2006}, number = {1}, eprint = {22485254}, eprinttype = {pubmed}, doi = {10.1101/pdb.prot2936}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22485254}, pmid = {22485254}, keywords = {nosource} }

@article{argamanExpressionHeatShock1994, title = {Expression of Heat Shock Protein 83 in {{Leishmania}} Is Regulated Post-Transcriptionally}, author = {Argaman, Miriam and Aly, Radi and Shapira, Michal}, year = 1994, journal = {Molecular and biochemical parasitology}, volume = {64}, pages = {95–110}, keywords = {heat shock protein 83,leishmania amazonensis,mrna stability,nosource,post-transcriptional regulation} }

@article{ashburnerGeneOntologyTool2000, title = {Gene {{Ontology}}: Tool for the Unification of Biology}, author = {Ashburner, Michael and Ball, C. A. and Blake, J. A. and Botstein, David}, year = 2000, journal = {Nature }, volume = {25}, number = {1}, pages = {25–29}, doi = {10.1038/75556.Gene}, url = {http://www.nature.com/ng/journal/v25/n1/abs/ng0500_25.html}, keywords = {nosource} }

@article{gingoldDeterminantsTranslationEfficiency2011, title = {Determinants of Translation Efficiency and Accuracy.}, author = {Gingold, Hila and Pilpel, Yitzhak}, year = 2011, month = apr, journal = {Molecular systems biology}, volume = {7}, number = {481}, pages = {481}, publisher = {Nature Publishing Group}, issn = {1744-4292}, doi = {10.1038/msb.2011.14}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3101949&tool=pmcentrez&rendertype=abstract}, abstract = {Proper functioning of biological cells requires that the process of protein expression be carried out with high efficiency and fidelity. Given an amino-acid sequence of a protein, multiple degrees of freedom still remain that may allow evolution to tune efficiency and fidelity for each gene under various conditions and cell types. Particularly, the redundancy of the genetic code allows the choice between alternative codons for the same amino acid, which, although ‘synonymous,’ may exert dramatic effects on the process of translation. Here we review modern developments in genomics and systems biology that have revolutionized our understanding of the multiple means by which translation is regulated. We suggest new means to model the process of translation in a richer framework that will incorporate information about gene sequences, the tRNA pool of the organism and the thermodynamic stability of the mRNA transcripts. A practical demonstration of a better understanding of the process would be a more accurate prediction of the proteome, given the transcriptome at a diversity of biological conditions.}, pmid = {21487400}, keywords = {Amino Acids,Amino Acids: genetics,Amino Acids: metabolism,Biological Evolution,Codon,Codon: genetics,Databases,Genetic,Genetic Code,Humans,Messenger,Messenger: genetics,Messenger: metabolism,nosource,Nucleic Acid Conformation,Protein Biosynthesis,Protein Modification,Proteome,Proteome: genetics,Proteome: metabolism,RNA,Transfer,Transfer: genetics,Transfer: metabolism,Translational} }

@article{atkinsonEvolutionNonstopNogo2008, title = {Evolution of Nonstop, No-Go and Nonsense-Mediated {{mRNA}} Decay and Their Termination Factor-Derived Components.}, author = {Atkinson, Gemma C. and Baldauf, Sandra L. and Hauryliuk, Vasili}, year = 2008, month = jan, journal = {BMC evolutionary biology}, volume = {8}, pages = {290}, issn = {1471-2148}, doi = {10.1186/1471-2148-8-290}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2613156&tool=pmcentrez&rendertype=abstract}, abstract = {BACKGROUND: Members of the eukaryote/archaea specific eRF1 and eRF3 protein families have central roles in translation termination. They are also central to various mRNA surveillance mechanisms, together with the eRF1 paralogue Dom34p and the eRF3 paralogues Hbs1p and Ski7p. We have examined the evolution of eRF1 and eRF3 families using sequence similarity searching, multiple sequence alignment and phylogenetic analysis. RESULTS: Extensive BLAST searches confirm that Hbs1p and eRF3 are limited to eukaryotes, while Dom34p and eRF1 (a/eRF1) are universal in eukaryotes and archaea. Ski7p appears to be restricted to a subset of Saccharomyces species. Alignments show that Dom34p does not possess the characteristic class-1 RF minidomains GGQ, NIKS and YXCXXXF, in line with recent crystallographic analysis of Dom34p. Phylogenetic trees of the protein families allow us to reconstruct the evolution of mRNA surveillance mechanisms mediated by these proteins in eukaryotes and archaea. CONCLUSION: We propose that the last common ancestor of eukaryotes and archaea possessed Dom34p-mediated no-go decay (NGD). This ancestral Dom34p may or may not have required a trGTPase, mostly like a/eEF1A, for its delivery to the ribosome. At an early stage in eukaryotic evolution, eEF1A was duplicated, giving rise to eRF3, which was recruited for translation termination, interacting with eRF1. eRF3 evolved nonsense-mediated decay (NMD) activity either before or after it was again duplicated, giving rise to Hbs1p, which we propose was recruited to assist eDom34p in eukaryotic NGD. Finally, a third duplication within ascomycete yeast gave rise to Ski7p, which may have become specialised for a subset of existing Hbs1p functions in non-stop decay (NSD). We suggest Ski7p-mediated NSD may be a specialised mechanism for counteracting the effects of increased stop codon read-through caused by prion-domain [PSI+] mediated eRF3 precipitation.}, pmid = {18947425}, keywords = {Amino Acid Sequence,Archaea,Archaea: classification,Archaea: genetics,Endoribonucleases,Endoribonucleases: chemistry,Endoribonucleases: genetics,Eukaryotic Cells,Eukaryotic Cells: classification,Evolution,GTP-Binding Proteins,GTP-Binding Proteins: genetics,Molecular,nosource,Peptide Termination Factors,Peptide Termination Factors: chemistry,Peptide Termination Factors: genetics,Phylogeny,Protein Structure,RNA Stability,RNA Stability: genetics,Sequence Alignment,Tertiary} }

@article{ulielSmallNucleolarRNAs2004, title = {Small Nucleolar {{RNAs}} That Guide Modification in Trypanosomatids: Repertoire, Targets, Genome Organisation, and Unique Functions.}, author = {Uliel, Shai and Liang, Xue-hai and Unger, Ron and Michaeli, Shulamit}, year = 2004, month = mar, journal = {International journal for parasitology}, volume = {34}, number = {4}, eprint = {15013734}, eprinttype = {pubmed}, pages = {445–54}, issn = {0020-7519}, doi = {10.1016/j.ijpara.2003.10.014}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15013734}, abstract = {Small nucleolar RNAs constitute a family of newly discovered non-coding small RNAs, most of which function in guiding RNA modifications. Two prevalent types of modifications are 2’-O-methylation and pseudouridylation. The modification is directed by the formation of a canonical small nucleolar RNA-target duplex. Initially, RNA-guided modification was shown to take place on rRNA, but recent studies suggest that small nuclear RNA, mRNA, tRNA, and the trypanosome spliced leader RNA also undergo guided modifications. Trypanosomes contain more modifications and potentially more small nucleolar RNAs than yeast, and the increased number of modifications may help to preserve ribosome function under adverse environmental conditions during the cycling between the insect and mammalian host. The genome organisation in clusters carrying the two types of small nucleolar RNAs, C/D and H/ACA-like RNAs, resembles that in plants. However, the trypanosomatid H/ACA RNAs are similar to those found in Archaea and are composed of a single hairpin that may represent the primordial H/ACA RNA. In this review we summarise this new field of trypanosome small nucleolar RNAs, emphasising the open questions regarding the number of small nucleolar RNAs, the repertoire, genome organisation, and the unique function of guided modifications in these protozoan parasites.}, pmid = {15013734}, keywords = {Animals,Conserved Sequence,Genes,Genetic,Genome,nosource,Protozoan,RNA,Small Nucleolar,Transcription,Trypanosoma,Trypanosoma: genetics} }

@article{dhaliaTwoEIF4AHelicases2006, title = {The Two {{eIF4A}} Helicases in {{Trypanosoma}} Brucei Are Functionally Distinct.}, author = {Dhalia, Rafael and Marinsek, Nina and Reis, Christian R. S. and Katz, Rodolfo and Muniz, Jo{~a}o R. C. and Standart, Nancy and Carrington, Mark and Neto, Osvaldo P. de Melo}, year = 2006, month = jan, journal = {Nucleic acids research}, volume = {34}, number = {9}, pages = {2495–507}, issn = {1362-4962}, doi = {10.1093/nar/gkl290}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1459412&tool=pmcentrez&rendertype=abstract}, abstract = {Protozoan parasites belonging to the family Trypanosomatidae are characterized by an unusual pathway for the production of mRNAs via polycistronic transcription and trans-splicing of a 5’ capped mini-exon which is linked to the 3’ cleavage and polyadenylation of the upstream transcript. However, little is known of the mechanism of protein synthesis in these organisms, despite their importance as agents of a number of human diseases. Here we have investigated the role of two Trypanosoma brucei homologues of the translation initiation factor eIF4A (in the light of subsequent experiments these were named as TbEIF4AI and TbEIF4AIII). eIF4A, a DEAD-box RNA helicase, is a subunit of the translation initiation complex eIF4F which binds to the cap structure of eukaryotic mRNA and recruits the small ribosomal subunit. TbEIF4AI is a very abundant predominantly cytoplasmic protein (over 1 x 10(5) molecules/cell) and depletion to approximately 10% of normal levels through RNA interference dramatically reduces protein synthesis one cell cycle following double-stranded RNA induction and stops cell proliferation. In contrast, TbEIF4AIII is a nuclear, moderately expressed protein (approximately 1-2 x 10(4) molecules/cell), and its depletion stops cellular proliferation after approximately four cell cycles. Ectopic expression of a dominant negative mutant of TbEIF4AI, but not of TbEIF4AIII, induced a slow growth phenotype in transfected cells. Overall, our results suggest that only TbEIF4AI is involved in protein synthesis while the properties and sequence of TbEIF4AIII indicate that it may be the orthologue of eIF4AIII, a component of the exon junction complex in mammalian cells.}, pmid = {16687655}, keywords = {Amino Acid,Amino Acid Sequence,Amino Acid Substitution,Animals,Eukaryotic Initiation Factor-4A,Eukaryotic Initiation Factor-4A: analysis,Eukaryotic Initiation Factor-4A: genetics,Eukaryotic Initiation Factor-4A: physiology,Isoenzymes,Isoenzymes: chemistry,Isoenzymes: genetics,Messenger,Messenger: metabolism,Models,Molecular,Molecular Sequence Data,Mutation,nosource,Protozoan Proteins,Protozoan Proteins: analysis,Protozoan Proteins: genetics,Protozoan Proteins: physiology,RNA,RNA Interference,Sequence Homology,Trypanosoma brucei brucei,Trypanosoma brucei brucei: enzymology,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: growth & development} }

@article{limaFunctionalCharacterizationThree2010, title = {Functional Characterization of Three Leishmania Poly(a) Binding Protein Homologues with Distinct Binding Properties to {{RNA}} and Protein Partners.}, author = {Lima, Tamara D. da Costa and Moura, Danielle M. N. and Reis, Christian R. S. and Vasconcelos, J. Ronnie C. and Ellis, Louise and Carrington, Mark and Figueiredo, Regina C. B. Q. and Neto, Osvaldo P. de Melo}, year = 2010, month = oct, journal = {Eukaryotic cell}, volume = {9}, number = {10}, pages = {1484–94}, issn = {1535-9786}, doi = {10.1128/EC.00148-10}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2950419&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanosomatid protozoans are reliant on posttranscriptional processes to control gene expression. Regulation occurs at the levels of mRNA processing, stability, and translation, events that may require the participation of the poly(A) binding protein (PABP). Here, we have undertaken a functional study of the three distinct Leishmania major PABP (LmPABP) homologues: the previously described LmPABP1; LmPABP2, orthologous to the PABP described from Trypanosoma species; and LmPABP3, unique to Leishmania. Sequence identity between the three PABPs is no greater than 40%. In assays measuring binding to A-rich sequences, LmPABP1 binding was poly(A) sensitive but heparin insensitive; LmPABP2 binding was heparin sensitive and less sensitive to poly(A), compatible with unique substitutions observed in residues implicated in poly(A) binding; and LmPABP3 displayed intermediate properties. All three homologues are simultaneously expressed as abundant cytoplasmic proteins in L. major promastigotes, but only LmPABP1 is present as multiple isoforms. Upon transcription inhibition, LmPABP2 and -3 migrated to the nucleus, while LmPABP1 remained predominantly cytoplasmic. Immunoprecipitation assays showed an association between LmPABP2 and -3. Although the three proteins bound to a Leishmania homologue of the translation initiation factor eukaryotic initiation factor 4G (eIF4G) (LmEIF4G3) in vitro, LmPABP1 was the only one to copurify with native LmEIF4G3 from cytoplasmic extracts. Functionality was tested using RNA interference (RNAi) in Trypanosoma brucei, where both orthologues to LmPABP1 and -2 are required for cellular viability. Our results indicate that these homologues have evolved divergent functions, some of which may be unique to the trypanosomatids, and reinforces a role for LmPABP1 in translation through its interaction with the eIF4G homologue.}, pmid = {20675580}, keywords = {Amino Acid,Amino Acid Sequence,Animals,Binding Sites,Cell Survival,Eukaryotic Initiation Factor-4G,Eukaryotic Initiation Factor-4G: metabolism,Leishmania major,Leishmania major: genetics,Leishmania major: growth & development,Leishmania major: metabolism,Messenger,Messenger: metabolism,Molecular Sequence Data,nosource,Poly A,Poly A: metabolism,Poly(A)-Binding Proteins,Poly(A)-Binding Proteins: chemistry,Poly(A)-Binding Proteins: genetics,Poly(A)-Binding Proteins: metabolism,Protein Binding,Protein Biosynthesis,RNA,RNA Interference,Sequence Homology,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: metabolism} }

@article{yoffeBindingSpecificitiesPotential2006, title = {Binding Specificities and Potential Roles of Isoforms of Eukaryotic Initiation Factor {{4E}} in {{Leishmania}}.}, author = {Yoffe, Yael and Zuberek, Joanna and Lerer, Asaf and Lewdorowicz, Magdalena and Stepinski, Janusz and Altmann, Michael and Darzynkiewicz, Edward and Shapira, Michal}, year = 2006, month = dec, journal = {Eukaryotic cell}, volume = {5}, number = {12}, pages = {1969–79}, issn = {1535-9778}, doi = {10.1128/EC.00230-06}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1694823&tool=pmcentrez&rendertype=abstract}, abstract = {The 5’ cap structure of trypanosomatid mRNAs, denoted cap 4, is a complex structure that contains unusual modifications on the first four nucleotides. We examined the four eukaryotic initiation factor 4E (eIF4E) homologues found in the Leishmania genome database. These proteins, denoted LeishIF4E-1 to LeishIF4E-4, are located in the cytoplasm. They show only a limited degree of sequence homology with known eIF4E isoforms and among themselves. However, computerized structure prediction suggests that the cap-binding pocket is conserved in each of the homologues, as confirmed by binding assays to m(7)GTP, cap 4, and its intermediates. LeishIF4E-1 and LeishIF4E-4 each bind m(7)GTP and cap 4 comparably well, and only these two proteins could interact with the mammalian eIF4E binding protein 4EBP1, though with different efficiencies. 4EBP1 is a translation repressor that competes with eIF4G for the same residues on eIF4E; thus, LeishIF4E-1 and LeishIF4E-4 are reasonable candidates for serving as translation factors. LeishIF4E-1 is more abundant in amastigotes and also contains a typical 3’ untranslated region element that is found in amastigote-specific genes. LeishIF4E-2 bound mainly to cap 4 and comigrated with polysomal fractions on sucrose gradients. Since the consensus eIF4E is usually found in 48S complexes, LeishIF4E-2 could possibly be associated with the stabilization of trypanosomatid polysomes. LeishIF4E-3 bound mainly m(7)GTP, excluding its involvement in the translation of cap 4-protected mRNAs. It comigrates with 80S complexes which are resistant to micrococcal nuclease, but its function is yet unknown. None of the isoforms can functionally complement the Saccharomyces cerevisiae eIF4E, indicating that despite their structural conservation, they are considerably diverged.}, pmid = {17041189}, keywords = {3’ Untranslated Regions,Animals,Binding Sites,Binding Sites: genetics,Eukaryotic Initiation Factor-4E,Eukaryotic Initiation Factor-4E: chemistry,Eukaryotic Initiation Factor-4E: genetics,Eukaryotic Initiation Factor-4E: metabolism,Gene Expression Regulation,Genes,Kinetics,Leishmania major,Leishmania major: genetics,Leishmania major: metabolism,Leishmania mexicana,Leishmania mexicana: genetics,Leishmania mexicana: metabolism,Models,Molecular,nosource,Protein Isoforms,Protein Isoforms: chemistry,Protein Isoforms: genetics,Protein Isoforms: metabolism,Protein Structure,Protozoan,Protozoan Proteins,Protozoan Proteins: chemistry,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Protozoan: genetics,Protozoan: metabolism,Recombinant Fusion Proteins,Recombinant Fusion Proteins: chemistry,Recombinant Fusion Proteins: genetics,Recombinant Fusion Proteins: metabolism,RNA,RNA Cap Analogs,RNA Cap Analogs: genetics,RNA Cap Analogs: metabolism,RNA Caps,RNA Caps: genetics,RNA Caps: metabolism,Species Specificity,Tertiary} }

@article{schwanhausserGlobalQuantificationMammalian2011, title = {Global Quantification of Mammalian Gene Expression Control.}, author = {Schwanh{"a}usser, Bj{"o}rn and Busse, Dorothea and Li, Na and Dittmar, Gunnar and Schuchhardt, Johannes and Wolf, Jana and Chen, Wei and Selbach, Matthias}, year = 2011, month = may, journal = {Nature}, volume = {473}, number = {7347}, eprint = {21593866}, eprinttype = {pubmed}, pages = {337–42}, issn = {1476-4687}, doi = {10.1038/nature10098}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21593866}, abstract = {Gene expression is a multistep process that involves the transcription, translation and turnover of messenger RNAs and proteins. Although it is one of the most fundamental processes of life, the entire cascade has never been quantified on a genome-wide scale. Here we simultaneously measured absolute mRNA and protein abundance and turnover by parallel metabolic pulse labelling for more than 5,000 genes in mammalian cells. Whereas mRNA and protein levels correlated better than previously thought, corresponding half-lives showed no correlation. Using a quantitative model we have obtained the first genome-scale prediction of synthesis rates of mRNAs and proteins. We find that the cellular abundance of proteins is predominantly controlled at the level of translation. Genes with similar combinations of mRNA and protein stability shared functional properties, indicating that half-lives evolved under energetic and dynamic constraints. Quantitative information about all stages of gene expression provides a rich resource and helps to provide a greater understanding of the underlying design principles.}, pmid = {21593866}, keywords = {Animals,Gene Expression Profiling,Gene Expression Profiling: methods,Gene Expression Regulation,Genetic,Half-Life,Mammals,Mammals: genetics,Messenger,Messenger: analysis,Messenger: biosynthesis,Messenger: genetics,Messenger: metabolism,Mice,Models,NIH 3T3 Cells,nosource,Protein Biosynthesis,Protein Biosynthesis: genetics,Proteins,Proteins: analysis,Proteins: genetics,Proteins: metabolism,Reproducibility of Results,RNA,Staining and Labeling} }

@article{cassolaRNAGranulesLiving2011, title = {{{RNA}} Granules Living a Post-Transcriptional Life: The Trypanosomes’ Case}, author = {Cassola, Alejandro}, year = 2011, journal = {Current chemical biology}, volume = {5}, number = {2}, pages = {108–117}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179377/}, keywords = {gene expression,granules,nosource,p bodies,post-transcriptional,rna granules,rna-binding protein,stress,trypanosoma} }

@article{djuranovicMiRNAmediatedGeneSilencing2012, title = {{{miRNA-mediated}} Gene Silencing by Translational Repression Followed by {{mRNA}} Deadenylation and Decay.}, author = {Djuranovic, Sergej and Nahvi, Ali and Green, Rachel}, year = 2012, month = apr, journal = {Science (New York, N.Y.)}, volume = {336}, number = {6078}, eprint = {22499947}, eprinttype = {pubmed}, pages = {237–40}, issn = {1095-9203}, doi = {10.1126/science.1215691}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22499947}, abstract = {microRNAs (miRNAs) regulate gene expression through translational repression and/or messenger RNA (mRNA) deadenylation and decay. Because translation, deadenylation, and decay are closely linked processes, it is important to establish their ordering and thus to define the molecular mechanism of silencing. We have investigated the kinetics of these events in miRNA-mediated gene silencing by using a Drosophila S2 cell-based controllable expression system and show that mRNAs with both natural and engineered 3’ untranslated regions with miRNA target sites are first subject to translational inhibition, followed by effects on deadenylation and decay. We next used a natural translational elongation stall to show that miRNA-mediated silencing inhibits translation at an early step, potentially translation initiation.}, pmid = {22499947}, keywords = {3’ Untranslated Regions,Animals,Cell Line,Drosophila melanogaster,Drosophila melanogaster: genetics,Drosophila melanogaster: metabolism,Drosophila Proteins,Drosophila Proteins: genetics,Gene Silencing,Kinetics,Messenger,Messenger: genetics,Messenger: metabolism,MicroRNAs,MicroRNAs: genetics,MicroRNAs: metabolism,nosource,Peptide Chain Elongation,Peptide Chain Initiation,Protein Biosynthesis,RNA,RNA Stability,Translational} } % == BibTeX quality report for djuranovicMiRNAmediatedGeneSilencing2012: % ? Possibly abbreviated journal title Science (New York, N.Y.)

@article{castelRNAInterferenceNucleus2013, title = {{{RNA}} Interference in the Nucleus: Roles for Small {{RNAs}} in Transcription, Epigenetics and Beyond.}, author = {Castel, Stephane E. and Martienssen, Robert A.}, year = 2013, month = feb, journal = {Nature reviews. Genetics}, volume = {14}, number = {2}, eprint = {23329111}, eprinttype = {pubmed}, pages = {100–12}, publisher = {Nature Publishing Group}, issn = {1471-0064}, doi = {10.1038/nrg3355}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23329111}, abstract = {A growing number of functions are emerging for RNA interference (RNAi) in the nucleus, in addition to well-characterized roles in post-transcriptional gene silencing in the cytoplasm. Epigenetic modifications directed by small RNAs have been shown to cause transcriptional repression in plants, fungi and animals. Additionally, increasing evidence indicates that RNAi regulates transcription through interaction with transcriptional machinery. Nuclear small RNAs include small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) and are implicated in nuclear processes such as transposon regulation, heterochromatin formation, developmental gene regulation and genome stability.}, pmid = {23329111}, keywords = {Animals,Arabidopsis,Arabidopsis: genetics,Arabidopsis: metabolism,Biological,Caenorhabditis elegans,Caenorhabditis elegans: genetics,Caenorhabditis elegans: metabolism,Cell Nucleus,Cell Nucleus: genetics,Cell Nucleus: metabolism,DNA Methylation,DNA Repair,Drosophila melanogaster,Drosophila melanogaster: genetics,Drosophila melanogaster: metabolism,Epigenesis,Female,Genetic,Germ Cells,Germ Cells: metabolism,Humans,Male,Mice,Models,nosource,RNA,RNA Interference,Schizosaccharomyces,Schizosaccharomyces: genetics,Schizosaccharomyces: metabolism,Small Interfering,Small Interfering: biosynthesis,Small Interfering: classification,Small Interfering: genetics,Transcription} } % == BibTeX quality report for castelRNAInterferenceNucleus2013: % ? Possibly abbreviated journal title Nature reviews. Genetics

@article{schoenbergRegulationCytoplasmicMRNA2012, title = {Regulation of Cytoplasmic {{mRNA}} Decay.}, author = {Schoenberg, Daniel R. and Maquat, Lynne E.}, year = 2012, month = apr, journal = {Nature reviews. Genetics}, volume = {13}, number = {4}, pages = {246–59}, issn = {1471-0064}, doi = {10.1038/nrg3160}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3351101&tool=pmcentrez&rendertype=abstract}, abstract = {Discoveries made over the past 20 years highlight the importance of mRNA decay as a means of modulating gene expression and thereby protein production. Up until recently, studies largely focused on identifying cis-acting sequences that serve as mRNA stability or instability elements, the proteins that bind these elements, how the process of translation influences mRNA decay and the ribonucleases that catalyse decay. Now, current studies have begun to elucidate how the decay process is regulated. This Review examines our current understanding of how mammalian cell mRNA decay is controlled by different signalling pathways and lays out a framework for future research.}, pmid = {22392217}, keywords = {Active Transport,Animals,Cell Nucleus,Cytoplasm,Cytoplasm: genetics,Cytoplasm: metabolism,Cytoplasmic and Nuclear,Cytoplasmic and Nuclear: metabolism,Histones,Histones: genetics,Histones: metabolism,Mammals,Mammals: genetics,nosource,Organ Specificity,Phosphorylation,Protein Biosynthesis,Receptors,RNA Stability,Signal Transduction} } % == BibTeX quality report for schoenbergRegulationCytoplasmicMRNA2012: % ? Possibly abbreviated journal title Nature reviews. Genetics

@article{norburyCytoplasmicRNACase2013, title = {Cytoplasmic {{RNA}}: A Case of the Tail Wagging the Dog.}, author = {Norbury, Chris J.}, year = 2013, month = oct, journal = {Nature reviews. Molecular cell biology}, volume = {14}, number = {10}, eprint = {23989958}, eprinttype = {pubmed}, pages = {643–53}, publisher = {Nature Publishing Group}, issn = {1471-0080}, doi = {10.1038/nrm3645}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23989958}, abstract = {The addition of poly(A) tails to eukaryotic nuclear mRNAs promotes their stability, export to the cytoplasm and translation. Subsequently, the balance between exonucleolytic deadenylation and selective re-establishment of translation-competent poly(A) tails by cytoplasmic poly(A) polymerases is essential for the appropriate regulation of gene expression from oocytes to neurons. In recent years, surprising roles for cytoplasmic poly(A) polymerase-related enzymes that add uridylyl, rather than adenylyl, residues to RNA 3’ ends have also emerged. These terminal uridylyl transferases promote the turnover of certain mRNAs but also modify microRNAs, their precursors and other small RNAs to modulate their stability or biological functions.}, pmid = {23989958}, keywords = {Cytoplasm,Cytoplasm: genetics,Messenger,Messenger: genetics,MicroRNAs,MicroRNAs: genetics,nosource,Nucleotidyltransferases,Nucleotidyltransferases: genetics,Nucleotidyltransferases: metabolism,Polyadenylation,Protein Biosynthesis,Protein Biosynthesis: genetics,RNA,RNA Stability,RNA Stability: genetics,RNA: genetics} } % == BibTeX quality report for norburyCytoplasmicRNACase2013: % ? Possibly abbreviated journal title Nature reviews. Molecular cell biology

@article{leeTranscriptionEukaryoticProteincoding2000, title = {Transcription of Eukaryotic Protein-Coding Genes}, author = {Lee, T. I. and Young, R. A.}, year = 2000, journal = {Annual review of genetics}, number = {34}, pages = {77–137}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.genet.34.1.77}, keywords = {about,activation and repression,chromatin modification,complex,decade has seen an,especially for protein-coding genes,explosive increase in information,gene expression,mediator,nosource,regulation of eukaryotic gene,rna polymerase ii holoenzyme,s abstract the past,srb,the,transcription} }

@article{makVersatileLentiviralExpression2012, title = {A Versatile Lentiviral Expression System to Identify Mammalian Protein-Protein Interactions.}, author = {Mak, Anthony B. and Moffat, Jason}, year = 2012, month = aug, journal = {Methods}, volume = {57}, number = {4}, eprint = {22713554}, eprinttype = {pubmed}, pages = {409–16}, publisher = {Elsevier Inc.}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2012.06.005}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22713554}, abstract = {Protein-protein interactions (PPIs) are central to our understanding of protein function, biological processes and signaling pathways. Affinity purification coupled with mass spectrometry (AP-MS) is a powerful approach for detecting PPIs and protein complexes and relies on the purification of bait proteins using bait-specific binding reagents. These binding reagents may recognize bait proteins directly or affinity tags that are fused to bait proteins. A limitation of the latter approach is that expression of affinity tagged baits is largely constrained to engineered or unnatural cell lines, which results in the AP-MS identification of PPIs that may not accurately reflect those seen in nature. Therefore, generating cell lines stably expressing affinity tagged bait proteins in a broad range of cell types and cell lines is important for identifying PPIs that are dependent on different contexts. To facilitate the identification of PPIs across many mammalian cell types, we developed the mammalian affinity purification and lentiviral expression (MAPLE) system. MAPLE uses recombinant lentiviral technology to stably and efficiently express affinity tagged complementary DNA (cDNA) in mammalian cells, including cells that are difficult to transfect and non-dividing cells. The MAPLE vectors contain a versatile affinity (VA) tag for multi-step protein purification schemes and subcellular localization studies. In this methods article, we present a step-by-step overview of the MAPLE system workflow.}, pmid = {22713554}, keywords = {Affinity,Affinity: methods,Amino Acid Sequence,Base Sequence,Cell Culture Techniques,Chromatography,Cloning,Gene Expression,Genetic Vectors,Humans,Lentivirus,Lentivirus: genetics,Molecular,Molecular Sequence Data,nosource,Protein Interaction Mapping,Protein Interaction Mapping: methods,Recombinant Fusion Proteins,Recombinant Fusion Proteins: biosynthesis,Recombinant Fusion Proteins: genetics,Recombinant Fusion Proteins: isolation & purificat,Tandem Mass Spectrometry} }

@article{varshavskyNendRulePathway1997, title = {The {{N-end}} Rule Pathway of Protein Degradation.}, author = {Varshavsky, a}, year = 1997, month = jan, journal = {Genes to cells : devoted to molecular & cellular mechanisms}, volume = {2}, number = {1}, eprint = {9112437}, eprinttype = {pubmed}, pages = {13–28}, issn = {1356-9597}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9112437}, abstract = {The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. Similar but distinct versions of the N-end rule operate in all organisms examined, from mammals to fungi and bacteria. In eukaryotes, the N-end rule pathway is a part of the ubiquitin system. Ubiquitin is a 76-residue protein whose covalent conjugation to other proteins plays a role in many biological processes, including cell growth and differentiation. I discuss the current understanding of the N-end rule pathway.}, pmid = {9112437}, keywords = {Amidohydrolases,Amidohydrolases: metabolism,Amino Acid Sequence,Animals,Binding Sites,Biological Transport,Cytosol,Cytosol: metabolism,DNA-Directed RNA Polymerases,DNA-Directed RNA Polymerases: metabolism,Evolution,Fungal Proteins,Fungal Proteins: metabolism,Genes,GTP-Binding Proteins,GTP-Binding Proteins: metabolism,Half-Life,Ligases,Molecular,Molecular Sequence Data,mos,nosource,Peptide Fragments,Peptide Fragments: chemistry,Peptide Fragments: metabolism,Proteins,Proteins: chemistry,Proteins: metabolism,Saccharomyces cerevisiae Proteins,Sindbis Virus,Sindbis Virus: genetics,Substrate Specificity,Ubiquitin-Protein Ligases,Ubiquitins,Ubiquitins: chemistry,Ubiquitins: metabolism} }

@article{vasquezComparativeRibosomeProfiling2014, title = {Comparative Ribosome Profiling Reveals Extensive Translational Complexity in Different {{Trypanosoma}} Brucei Life Cycle Stages.}, author = {Vasquez, Juan-Jos{'e} and Hon, Chung-Chau and Vanselow, Jens T. and Schlosser, Andreas and Siegel, T. Nicolai}, year = 2014, month = jan, journal = {Nucleic acids research}, eprint = {24442674}, eprinttype = {pubmed}, pages = {1–15}, issn = {1362-4962}, doi = {10.1093/nar/gkt1386}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24442674}, abstract = {While gene expression is a fundamental and tightly controlled cellular process that is regulated at multiple steps, the exact contribution of each step remains unknown in any organism. The absence of transcription initiation regulation for RNA polymerase II in the protozoan parasite Trypanosoma brucei greatly simplifies the task of elucidating the contribution of translation to global gene expression. Therefore, we have sequenced ribosome-protected mRNA fragments in T. brucei, permitting the genome-wide analysis of RNA translation and translational efficiency. We find that the latter varies greatly between life cycle stages of the parasite and {\(\sim\)}100-fold between genes, thus contributing to gene expression to a similar extent as RNA stability. The ability to map ribosome positions at sub-codon resolution revealed extensive translation from upstream open reading frames located within 5’ UTRs and enabled the identification of hundreds of previously un-annotated putative coding sequences (CDSs). Evaluation of existing proteomics and genome-wide RNAi data confirmed the translation of previously un-annotated CDSs and suggested an important role for {\(>\)}200 of those CDSs in parasite survival, especially in the form that is infective to mammals. Overall our data show that translational control plays a prevalent and important role in different parasite life cycle stages of T. brucei.}, pmid = {24442674}, keywords = {nosource} }

@article{zaborskeMultipleTranscriptsUTR2013, title = {Multiple {{Transcripts}} from a 3{\(\prime\)}-{{UTR Reporter Vary}} in {{Sensitivity}} to {{Nonsense-Mediated mRNA Decay}} in {{Saccharomyces}} Cerevisiae}, author = {Zaborske, J. M. and Zeitler, B. and Culbertson, M. R.}, year = 2013, journal = {PloS one}, number = {3650}, pages = {1–29}, url = {http://dx.plos.org/10.1371/journal.pone.0080981.g006}, keywords = {nosource} }

@article{metzeComparisonEJCenhancedEJCindependent2013, title = {Comparison of {{EJC-enhanced}} and {{EJC-independent NMD}} in Human Cells Reveals Two Partially Redundant Degradation Pathways}, author = {Metze, Stefanie and Herzog, V. A. and Ruepp, M. D. and M{"u}hlemann, Oliver}, year = 2013, journal = {RNA}, doi = {10.1261/rna.038893.113.by}, url = {http://rnajournal.cshlp.org/content/19/10/1432.short}, keywords = {degradation,endo- and exonucleolytic mrna,exon-,junction complex,mrna surveillance,mrna turnover,nonsense-mediated mrna decay,nosource,post-transcriptional gene regulation,smg1,smg5,smg6,smg7,upf1,upf2,upf3b} }

@article{farberTrypanosomeCNOT10Essential2013, title = {Trypanosome {{CNOT10}} Is Essential for the Integrity of the {{NOT}} Deadenylase Complex and for Degradation of Many {{mRNAs}}.}, author = {F{"a}rber, Valentin and Erben, Esteban and Sharma, Sahil and Stoecklin, Georg and Clayton, Christine}, year = 2013, month = jan, journal = {Nucleic acids research}, volume = {41}, number = {2}, pages = {1211–22}, issn = {1362-4962}, doi = {10.1093/nar/gks1133}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3553956&tool=pmcentrez&rendertype=abstract}, abstract = {The degradation of most eukaryotic mRNAs is initiated by removal of the poly(A) tail, and the major deadenylase activity is associated with the CCR4/CAF1/NOT complex (NOT complex). We here study the role of CNOT10, a protein that is found in human and trypanosome, but not in yeast, NOT complexes. Trypanosome (Tb) CNOT10 is essential for growth. TbCNOT10 interacted with the deadenylase TbCAF1 and the scaffold protein TbNOT1; TbCAF1 also interacted with TbNOT1 in a yeast two-hybrid assay. In both trypanosomes and human embryonic kidney cells, approximately half of CAF1 was associated with the NOT complex. Depletion of CNOT10 from human cells did not affect this association. In contrast, depletion of TbCNOT10 in trypanosomes caused a decrease in the level of TbNOT1, detachment of TbCAF1 from the complex and pronounced stabilization of most trypanosome mRNAs. Artificial tethering of TbCAF1 to a reporter mRNA in vivo resulted in mRNA degradation, and this was not affected by TbCNOT10 depletion. We conclude that in trypanosomes, TbCNOT10 may stabilize the interaction between TbCAF1 and the NOT complex. The results further suggest that TbCAF1 is only able to deadenylate mRNA in vivo if it is recruited to the mRNA through other NOT complex components.}, pmid = {23221646}, keywords = {HEK293 Cells,Humans,Messenger,Messenger: metabolism,nosource,Phylogeny,Protein Subunits,Protein Subunits: metabolism,Protein Subunits: physiology,Protozoan Proteins,Protozoan Proteins: classification,Protozoan Proteins: metabolism,Protozoan Proteins: physiology,Ribonucleases,Ribonucleases: metabolism,RNA,RNA Stability,Trypanosoma brucei brucei,Trypanosoma brucei brucei: enzymology,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: metabolism} }

@article{haileRoleExosomeVivo2003, title = {A Role for the Exosome in the in Vivo Degradation of Unstable {{mRNAs}}}, author = {Haile, S. and EST{'E}VEZ, {AM} and CLAYTON, C.}, year = 2003, journal = {Rna}, pages = {1491–1501}, doi = {10.1261/rna.5940703.Parker}, url = {http://rnajournal.cshlp.org/content/9/12/1491.short}, keywords = {degradation,exosome,mrna,nosource,trypanosoma,turnover} }

@article{singhActinlikeProteinInvolved2013, title = {An Actin-like Protein Is Involved in Regulation of Mitochondrial and Flagellar Functions as Well as in Intramacrophage Survival of {{Leishmania}} Donovani}, author = {Singh, Kuldeep and Veluru, Niranjan K. and Trivedi, Vishal and Gupta, Chhitar M. and {}a Sahasrabuddhe, Amogh}, year = 2013, month = dec, journal = {Molecular Microbiology}, pages = {n/a-n/a}, issn = {0950382X}, doi = {10.1111/mmi.12477}, url = {http://doi.wiley.com/10.1111/mmi.12477}, keywords = {nosource} }

@article{mullerSelectiveInactivationSIDER22010, title = {Selective Inactivation of {{SIDER2}} Retroposon-Mediated {{mRNA}} Decay Contributes to Stage- and Species-Specific Gene Expression in {{Leishmania}}.}, author = {M{"u}ller, Michaela and Padmanabhan, Prasad K. and Papadopoulou, Barbara}, year = 2010, month = jul, journal = {Molecular microbiology}, volume = {77}, number = {2}, eprint = {20497500}, eprinttype = {pubmed}, pages = {471–91}, issn = {1365-2958}, doi = {10.1111/j.1365-2958.2010.07226.x}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20497500}, abstract = {Despite their high genomic synteny, the Leishmania major and Leishmania infantum species exhibit extensive differences in mRNA expression patterns throughout the parasite’s development. Yet, the underlying mechanisms for this species-specific differential gene expression are largely unknown. Here we report that Short Interspersed DEgenerated Retroposons of the SIDER2 subfamily, shown previously to promote rapid mRNA turnover, confer differential regulation of orthologous transcripts resulting in a stage- and species-specific gene expression. We demonstrate that SIDER2-mediated decay of two L. major transcripts encoding a hypothetical protein and an aminomethyltransferase to a similar extent in promastigote and amastigote developmental forms results in a constitutive low expression of the corresponding proteins. In contrast, their L. infantum orthologs are differentially expressed due to the selective inactivation of SIDER2 in intracellular amastigotes. Inactivation of the SIDER2 function blocks the SIDER2-mediated deadenylation-independent decay pathway, and stabilized transcripts are degraded by a slower, deadenylation-dependent mechanism. Sequence variations in SIDER2 retroposons between orthologous transcripts do not contribute to SIDER2 inactivation. Our data suggest that SIDER2 inactivation is 3’-untranslated region context-dependent and that involves possibly species- and stage-specific trans-acting factor(s). These findings further emphasize the important contribution of SIDER retroposons in the control of gene expression across the Leishmania genus.}, pmid = {20497500}, keywords = {3’ Untranslated Regions,Gene Expression Regulation,Leishmania infantum,Leishmania infantum: genetics,Leishmania major,Leishmania major: genetics,nosource,Protozoan,Protozoan Proteins,Protozoan Proteins: metabolism,Protozoan: genetics,Protozoan: metabolism,Retroelements,RNA,RNA Stability,Species Specificity} }

@article{dhaliaTranslationInitiationLeishmania2005, title = {Translation Initiation in {{Leishmania}} Major: Characterisation of Multiple {{eIF4F}} Subunit Homologues.}, author = {Dhalia, Rafael and Reis, Christian R. S. and Freire, Eden R. and Rocha, Pollyanna O. and Katz, Rodolfo and Muniz, Jo{~a}o R. C. and Standart, Nancy and Neto, Osvaldo P. de Melo}, year = 2005, month = mar, journal = {Molecular and biochemical parasitology}, volume = {140}, number = {1}, eprint = {15694484}, eprinttype = {pubmed}, pages = {23–41}, issn = {0166-6851}, doi = {10.1016/j.molbiopara.2004.12.001}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15694484}, abstract = {In eukaryotes protein synthesis initiates with the binding of the multimeric translation initiation complex eIF4F - eIF4E, eIF4A and eIF4G - to the monomethylated cap present on the 5’ end of mRNAs. eIF4E interacts directly with the cap nucleotide, while eIF4A is a highly conserved RNA helicase and eIF4G acts as a scaffold for the complex with binding sites for both eIF4E and eIF4A. eIF4F binding to the mRNA recruits the small ribosomal subunit to its 5’ end. Little is known in detail of protein synthesis in the protozoan parasites belonging to the family Trypanosomatidae. However, the presence of the highly modified cap structure, cap4, and the spliced leader sequence on the 5’ ends of all mRNAs suggests possible differences in mRNA recruitment by ribosomes. We identified several potential eIF4F homologues by searching Leishmania major databases: four eIF4Es (LmEIF4E1-4), two eIF4As (LmEIF4A1-2) and five eIF4Gs (LmEIF4G1-5). We report the initial characterisation of LmEIF4E1-3, LmEIF4A1-2 and LmEIF4G3. First, the expression of these proteins in L. major promastigotes was quantitated by Western blotting using isoform specific antibodies. LmEIF4A1 and LmEIF4E3 are very abundant, LmEIF4G3 is moderately abundant and LmEIF4E1/LmEIF4E2/LmEIF4A2 are rare or not detected. In cap-binding assays, only LmEIF4E1 bound to the 7-methyl-GTP-Sepharose resin. Molecular modelling confirmed that LmEIF4E1 has all the structural features of a cap-binding protein. Finally, pull-down assays were used to investigate the potential interaction between the eIF4A (LmEIF4A1/LmEIF4A2) and eIF4G (LmEIF4G1-3) homologues. Only LmEIF4G3, via the HEAT domain, bound specifically both to LmEIF4A1 as well as to human eIF4A. Therefore for each factor, one of the L. major forms seems to fulfil, in part at least, the expected characteristics of a translational initiation factor.}, pmid = {15694484}, keywords = {Amino Acid Sequence,Animals,Cell Cycle Proteins,Cloning,Eukaryotic Initiation Factor-4F,Eukaryotic Initiation Factor-4F: biosynthesis,Eukaryotic Initiation Factor-4F: genetics,Intracellular Signaling Peptides and Proteins,Leishmania major,Leishmania major: genetics,Leishmania major: growth & development,Leishmania major: metabolism,Life Cycle Stages,Messenger,Messenger: metabolism,Molecular,Molecular Sequence Data,nosource,Protein Structure,Protein Subunits,Protein Subunits: biosynthesis,Protein Subunits: chemistry,Protein Subunits: genetics,Proteins,Protozoan,Protozoan: metabolism,RNA,Sequence Alignment,Tertiary,Tertiary: genetics} }

@article{aphasizhevaPentatricopeptideRepeatProteins2011, title = {Pentatricopeptide Repeat Proteins Stimulate {{mRNA}} Adenylation/Uridylation to Activate Mitochondrial Translation in Trypanosomes.}, author = {Aphasizheva, Inna and Maslov, Dmitri and Wang, Xiaorong and Huang, Lan and Aphasizhev, Ruslan}, year = 2011, month = apr, journal = {Molecular cell}, volume = {42}, number = {1}, pages = {106–17}, publisher = {Elsevier Inc.}, issn = {1097-4164}, doi = {10.1016/j.molcel.2011.02.021}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3073060&tool=pmcentrez&rendertype=abstract}, abstract = {The majority of trypanosomal mitochondrial pre-mRNAs undergo massive uridine insertion/deletion editing, which creates open reading frames. Although the pre-editing addition of short 3’ A tails is known to stabilize transcripts during and after the editing, the processing event committing the fully edited mRNAs to translation remained unknown. Here, we show that a heterodimer of pentatricopeptide repeat-containing (PPR) proteins, termed kinetoplast polyadenylation/uridylation factors (KPAFs) 1 and 2, induces the postediting addition of A/U heteropolymers by KPAP1 poly(A) polymerase and RET1 terminal uridyltransferase. Edited transcripts bearing 200- to 300-nucleotide-long A/U tails, but not short A tails, were enriched in translating ribosomal complexes and affinity-purified ribosomal particles. KPAF1 repression led to a selective loss of A/U-tailed mRNAs and concomitant inhibition of protein synthesis. These results establish A/U extensions as the defining cis-elements of translation-competent mRNAs. Furthermore, we demonstrate that A/U-tailed mRNA preferentially interacts with the small ribosomal subunit, whereas edited substrates and complexes bind to the large subunit.}, pmid = {21474072}, keywords = {Base Sequence,DNA,Kinetoplast,Kinetoplast: genetics,Kinetoplast: metabolism,Messenger,Messenger: genetics,Messenger: metabolism,Mitochondria,Mitochondria: genetics,Mitochondria: metabolism,Molecular Sequence Data,mRNA Cleavage and Polyadenylation Factors,mRNA Cleavage and Polyadenylation Factors: antagon,mRNA Cleavage and Polyadenylation Factors: genetic,mRNA Cleavage and Polyadenylation Factors: metabol,nosource,Protozoan,Protozoan Proteins,Protozoan Proteins: antagonists & inhibitors,Protozoan Proteins: biosynthesis,Protozoan Proteins: genetics,Protozoan: genetics,Protozoan: metabolism,Ribosomes,Ribosomes: genetics,Ribosomes: metabolism,RNA,RNA Editing,RNA Interference,RNA Precursors,RNA Precursors: genetics,RNA Precursors: metabolism,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: metabolism} }

@article{nunesTranscriptionPromoterSpliced1997, title = {The Transcription Promoter of the Spliced Leader Gene from {{Trypanosoma}} Cruzi.}, author = {Nunes, L. R. and Carvalho, M. R. and Shakarian, a M. and {}a Buck, G.}, year = 1997, month = apr, journal = {Gene}, volume = {188}, number = {2}, eprint = {9133587}, eprinttype = {pubmed}, pages = {157–68}, issn = {0378-1119}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9133587}, abstract = {A putative promoter element responsible for transcription of the spliced leader (SL) gene of Trypanosoma cruzi was identified by overlapping deletion and linker scanning analyses of the upstream flanking sequences using the bacterial chloramphenicol acetyltransferase (CAT) gene as a reporter in transient transfections of cultured epimastigotes. Deletion or substitution of a proximal sequence element (PSE) between positions -53 and -40 relative to the transcription start point eliminated CAT gene expression. Comparison of SL genes from several strains of T. cruzi revealed two alternative sequence patterns for the putative SL PSE, both composed of a short run of purines followed by a run of pyrimidines. Moreover, an examination of these sequences supports the subdivision of T. cruzi isolates into two divergent groups. Double-stranded oligonucleotides containing the sequence of the PSE exhibited specific gel mobility shifts after incubation with T. cruzi nuclear extracts, suggesting that a transcription factor binds this site. Finally, experiments designed to increase the level of CAT expression from the SL promoter suggest that it is not a strong promoter in cultured T. cruzi epimastigotes.}, pmid = {9133587}, keywords = {Animals,Base Sequence,DNA,Genes,Genetic,Messenger,Messenger: genetics,Molecular Sequence Data,nosource,Promoter Regions,Protozoan,Protozoan: genetics,RNA,RNA Splicing,Transcription,Transcription Factors,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosomatina,Trypanosomatina: genetics} }

@article{thomasIntragenomicSplicedLeader2005, title = {Intragenomic Spliced Leader {{RNA}} Array Analysis of Kinetoplastids Reveals Unexpected Transcribed Region Diversity in {{Trypanosoma}} Cruzi.}, author = {Thomas, Sean and Westenberger, Scott J. and {}a Campbell, David and Sturm, Nancy R.}, year = 2005, month = jun, journal = {Gene}, volume = {352}, eprint = {15925459}, eprinttype = {pubmed}, pages = {100–8}, issn = {0378-1119}, doi = {10.1016/j.gene.2005.04.002}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15925459}, abstract = {The spliced leader RNA gene (SL RNA) repeat is present in large multicopy arrays and has been used as a marker for the diversity of kinetoplastid protozoans. Intra-array variation could affect conclusions made using a randomly isolated repeat as a marker. We examined the Leishmania major (Friedlin) and Trypanosoma cruzi (CL Brener) genome projects for SL RNA repeat sequences in order to assess their homogeneity and the possible effects of sequence variation on taxonomic interpretation. Of the dozens of distinct sequence classes examined, no single copy would bias clustering analyses with regard to other closely related species or isolates. Six dimorphic sites within the T. cruzi transcribed region were found to be linked and are predicted to yield a heterogeneous SL RNA population. The variation that exists among the repeats paints a picture of the broad mechanisms of array maintenance and evolution where site-specific mutations in a single repeat may be spread throughout the array and recombined with existing repeats to create new sequence classes, all occurring under selective pressure to maintain or increase the fitness of the cell line in which these events occur.}, pmid = {15925459}, keywords = {Animals,Base Sequence,Evolution,Genetic Variation,Genome,Leishmania major,Leishmania major: genetics,Molecular,Molecular Sequence Data,Mutation,nosource,Polymorphism,Protozoan,RNA,Sequence Alignment,Sequence Alignment: methods,Single Nucleotide,Species Specificity,Spliced Leader,Spliced Leader: genetics,Trypanosoma cruzi,Trypanosoma cruzi: genetics} }

@article{ploegAntigenicVariationTrypanosoma1984, title = {Antigenic Variation in {{Trypanosoma}} Brucei Analyzed by Electrophoretic Separation of Chromosome-Sized {{DNA}} Molecules.}, author = {{}der Ploeg, L. H. Van and Schwartz, D. C. and Cantor, C. R. and Borst, P.}, year = 1984, month = may, journal = {Cell}, volume = {37}, number = {1}, eprint = {6202420}, eprinttype = {pubmed}, pages = {77–84}, issn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/6202420}, abstract = {Pulsed field gradient gel electrophoresis fractionates chromosome-sized DNA molecules from T. brucei. About 60% of the DNA remains in or close to the gel slot (large DNA). There are about three chromosomes of approximately 2 Mb, at least six chromosomes of 200-700 kb, and roughly a hundred mini-chromosomes of 50-150 kb. The basic copy genes for VSGs 118 and 221 reside in large DNA. Their activation by duplicative transposition leads to the appearance of an additional copy in the 2 Mb DNA, showing that activation involves an interchromosomal gene transposition. When gene 221 is activated without duplication, it remains in large DNA, proving that at least two sites for expression of VSG genes exist. In support of this, the mini-exons encoding the 5’ 35 nucleotides of VSG messenger RNAs are in large and 2 Mb DNA. The mini-chromosomes hybridize strongly to VSG gene probes and are absent in C. fasciculata. We suggest that their main function is to provide a large pool of telomeric VSG genes.}, pmid = {6202420}, keywords = {Animals,Chromosomes,Chromosomes: ultrastructure,DNA,DNA: genetics,DNA: immunology,DNA: isolation & purification,Electrophoresis,Electrophoresis: methods,Epitopes,Epitopes: analysis,Genes,Glycoproteins,Glycoproteins: genetics,Immune Sera,nosource,Nucleic Acid Hybridization,Trypanosoma,Trypanosoma brucei brucei,Trypanosoma brucei brucei: analysis,Trypanosoma brucei brucei: genetics,Variant Surface Glycoproteins} }

@article{marintchevTranslationInitiationStructures2004, title = {Translation Initiation: Structures, Mechanisms and Evolution.}, author = {Marintchev, Assen and Wagner, Gerhard}, year = 2004, journal = {Quarterly reviews of biophysics}, volume = {37}, number = {3-4}, eprint = {16194295}, eprinttype = {pubmed}, pages = {197–284}, issn = {0033-5835}, doi = {10.1017/S0033583505004026}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16194295}, abstract = {Translation, the process of mRNA-encoded protein synthesis, requires a complex apparatus, composed of the ribosome, tRNAs and additional protein factors, including aminoacyl tRNA synthetases. The ribosome provides the platform for proper assembly of mRNA, tRNAs and protein factors and carries the peptidyl-transferase activity. It consists of small and large subunits. The ribosomes are ribonucleoprotein particles with a ribosomal RNA core, to which multiple ribosomal proteins are bound. The sequence and structure of ribosomal RNAs, tRNAs, some of the ribosomal proteins and some of the additional protein factors are conserved in all kingdoms, underlying the common origin of the translation apparatus. Translation can be subdivided into several steps: initiation, elongation, termination and recycling. Of these, initiation is the most complex and the most divergent among the different kingdoms of life. A great amount of new structural, biochemical and genetic information on translation initiation has been accumulated in recent years, which led to the realization that initiation also shows a great degree of conservation throughout evolution. In this review, we summarize the available structural and functional data on translation initiation in the context of evolution, drawing parallels between eubacteria, archaea, and eukaryotes. We will start with an overview of the ribosome structure and of translation in general, placing emphasis on factors and processes with relevance to initiation. The major steps in initiation and the factors involved will be described, followed by discussion of the structure and function of the individual initiation factors throughout evolution. We will conclude with a summary of the available information on the kinetic and thermodynamic aspects of translation initiation.}, pmid = {16194295}, keywords = {Biological,Biophysical Phenomena,Biophysics,Codon,Evolution,Initiator,Initiator: chemistry,Initiator: genetics,Initiator: metabolism,Kinetics,Macromolecular Substances,Messenger,Messenger: chemistry,Messenger: genetics,Messenger: metabolism,Models,Molecular,nosource,Peptide Chain Initiation,Peptide Initiation Factors,Peptide Initiation Factors: chemistry,Peptide Initiation Factors: genetics,Peptide Initiation Factors: metabolism,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,RNA,Thermodynamics,Transfer,Transfer: chemistry,Transfer: genetics,Transfer: metabolism,Translational,Translational: physiolog} }

@article{rochetteGenomewideGeneExpression2008, title = {Genome-Wide Gene Expression Profiling Analysis of {{Leishmania}} Major and {{Leishmania}} Infantum Developmental Stages Reveals Substantial Differences between the Two Species.}, author = {Rochette, Annie and Raymond, Fr{'e}d{'e}ric and Ubeda, Jean-Michel and Smith, Martin and Messier, Nadine and Boisvert, S{'e}bastien and Rigault, Philippe and Corbeil, Jacques and Ouellette, Marc and Papadopoulou, Barbara}, year = 2008, month = jan, journal = {BMC genomics}, volume = {9}, pages = {255}, issn = {1471-2164}, doi = {10.1186/1471-2164-9-255}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2453527&tool=pmcentrez&rendertype=abstract}, abstract = {BACKGROUND: Leishmania parasites cause a diverse spectrum of diseases in humans ranging from spontaneously healing skin lesions (e.g., L. major) to life-threatening visceral diseases (e.g., L. infantum). The high conservation in gene content and genome organization between Leishmania major and Leishmania infantum contrasts their distinct pathophysiologies, suggesting that highly regulated hierarchical and temporal changes in gene expression may be involved. RESULTS: We used a multispecies DNA oligonucleotide microarray to compare whole-genome expression patterns of promastigote (sandfly vector) and amastigote (mammalian macrophages) developmental stages between L. major and L. infantum. Seven per cent of the total L. infantum genome and 9.3% of the L. major genome were differentially expressed at the RNA level throughout development. The main variations were found in genes involved in metabolism, cellular organization and biogenesis, transport and genes encoding unknown function. Remarkably, this comparative global interspecies analysis demonstrated that only 10-12% of the differentially expressed genes were common to L. major and L. infantum. Differentially expressed genes are randomly distributed across chromosomes further supporting a posttranscriptional control, which is likely to involve a variety of 3’UTR elements. CONCLUSION: This study highlighted substantial differences in gene expression patterns between L. major and L. infantum. These important species-specific differences in stage-regulated gene expression may contribute to the disease tropism that distinguishes L. major from L. infantum.}, pmid = {18510761}, keywords = {3’ Untranslated Regions,3’ Untranslated Regions: genetics,Animals,Cell Line,Developmental,Gene Expression Profiling,Gene Expression Regulation,Genome,Humans,Inbred A,Leishmania infantum,Leishmania infantum: genetics,Leishmania infantum: growth & development,Leishmania major,Leishmania major: genetics,Leishmania major: growth & development,Life Cycle Stages,Messenger,Messenger: isolation & purification,Mice,nosource,Oligonucleotide Array Sequence Analysis,Protozoan,Protozoan: isolation & purification,Retroelements,Reverse Transcriptase Polymerase Chain Reaction,RNA,Species Specificity} }

@article{efronTestingSignificanceSets2007, title = {On Testing the Significance of Sets of Genes}, author = {Efron, Bradley and Tibshirani, Robert}, year = 2007, month = jun, journal = {The Annals of Applied Statistics}, volume = {1}, number = {1}, pages = {107–129}, issn = {1932-6157}, doi = {10.1214/07-AOAS101}, url = {http://projecteuclid.org/euclid.aoas/1183143731}, keywords = {nosource} }

@article{liFastAccurateShort2009, title = {Fast and Accurate Short Read Alignment with {{Burrows-Wheeler}} Transform.}, author = {Li, Heng and Durbin, Richard}, year = 2009, month = jul, journal = {Bioinformatics (Oxford, England)}, volume = {25}, number = {14}, pages = {1754–60}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp324}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2705234&tool=pmcentrez&rendertype=abstract}, abstract = {MOTIVATION: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. RESULTS: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows-Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is approximately 10-20x faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. AVAILABILITY: http://maq.sourceforge.net.}, pmid = {19451168}, keywords = {Algorithms,DNA,DNA: methods,Genomics,Genomics: methods,nosource,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis,Software} }

@article{mullerRapidDecayUnstable2010, title = {Rapid Decay of Unstable {{Leishmania mRNAs}} Bearing a Conserved Retroposon Signature 3’-{{UTR}} Motif Is Initiated by a Site-Specific Endonucleolytic Cleavage without Prior Deadenylation.}, author = {M{"u}ller, Michaela and Padmanabhan, Prasad K. and Rochette, Annie and Mukherjee, Debdutta and Smith, Martin and Dumas, Carole and Papadopoulou, Barbara}, year = 2010, month = sep, journal = {Nucleic acids research}, volume = {38}, number = {17}, pages = {5867–83}, issn = {1362-4962}, doi = {10.1093/nar/gkq349}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2943621&tool=pmcentrez&rendertype=abstract}, abstract = {We have previously shown that the Leishmania genome possess two widespread families of extinct retroposons termed Short Interspersed DEgenerated Retroposons (SIDER1/2) that play a role in post-transcriptional regulation. Moreover, we have demonstrated that SIDER2 retroposons promote mRNA degradation. Here we provide new insights into the mechanism by which unstable Leishmania mRNAs harboring a SIDER2 retroposon in their 3’-untranslated region are degraded. We show that, unlike most eukaryotic transcripts, SIDER2-bearing mRNAs do not undergo poly(A) tail shortening prior to rapid turnover, but instead, they are targeted for degradation by a site-specific endonucleolytic cleavage. The main cleavage site was mapped in two randomly selected SIDER2-containing mRNAs in vivo between an AU dinucleotide at the 5’-end of the second 79-nt signature (signature II), which represents the most conserved sequence amongst SIDER2 retroposons. Deletion of signature II abolished endonucleolytic cleavage and deadenylation-independent decay and increased mRNA stability. Interestingly, we show that overexpression of SIDER2 anti-sense RNA can increase sense transcript abundance and stability, and that complementarity to the cleavage region is required for protecting SIDER2-containing transcripts from degradation. These results establish a new paradigm for how unstable mRNAs are degraded in Leishmania and could serve as the basis for a better understanding of mRNA decay pathways in general.}, pmid = {20453029}, keywords = {3’ Untranslated Regions,Antisense,Antisense: metabolism,Base Sequence,Conserved Sequence,Endoribonucleases,Endoribonucleases: metabolism,Leishmania major,Leishmania major: enzymology,Leishmania major: genetics,Messenger,Messenger: metabolism,Molecular Sequence Data,nosource,Retroelements,RNA,RNA Stability} }

@article{cloutierTranslationalControlEIF2alpha2012, title = {Translational Control through {{eIF2alpha}} Phosphorylation during the {{Leishmania}} Differentiation Process.}, author = {Cloutier, Serge and Laverdi{`e}re, Maxime and Chou, Marie-Noelle and Boilard, Nathalie and Chow, Conan and Papadopoulou, Barbara}, year = 2012, month = jan, journal = {PloS one}, volume = {7}, number = {5}, pages = {e35085}, issn = {1932-6203}, doi = {10.1371/journal.pone.0035085}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3365078&tool=pmcentrez&rendertype=abstract}, abstract = {The parasitic protozoan Leishmania alternates between an invertebrate and a mammalian host. Upon their entry to mammalian macrophages, Leishmania promastigotes differentiate into amastigote forms within the harsh environment of the phagolysosomal compartment. Here, we provide evidence for the importance of translational control during the Leishmania differentiation process. We find that exposure of promastigotes to a combined elevated temperature and acidic pH stress, a key signal triggering amastigote differentiation, leads to a marked decrease in global translation initiation, which is associated with eIF2{\(\alpha\)} phosphorylation. Interestingly, we show that amastigotes adapted to grow in a cell-free medium exhibit lower levels of protein synthesis in comparison to promastigotes, suggesting that amastigotes have to enter a slow growth state to adapt to the stressful conditions encountered inside macrophages. Reconversion of amastigotes back to promastigote growth results in upregulation of global translation and a decrease in eIF2{\(\alpha\)} phosphorylation. In addition, we show that while general translation is reduced during amastigote differentiation, translation of amastigote-specific transcripts such as A2 is preferentially upregulated. We find that A2 developmental gene regulation is triggered by temperature changes in the environment and that occurs mainly at the level of translation. Upon elevated temperature, the A2 transcript is stabilized through its association with polyribosomes leading to high levels of translation. When temperature decreases during amastigote to promastigote differentiation, the A2 transcript is not longer associated with translating polyribosomes and is being gradually degraded. Overall, these findings contribute to our better understanding of the adaptive responses of Leishmania to stress during its development and highlight the importance of translational control in promastigote to amastigote differentiation and vice-versa.}, pmid = {22693545}, keywords = {Adaptation,Animals,Developmental,Eukaryotic Initiation Factor-2,Eukaryotic Initiation Factor-2: metabolism,Gene Expression Regulation,Hydrogen-Ion Concentration,Leishmania infantum,Leishmania infantum: cytology,Leishmania infantum: genetics,Leishmania infantum: growth & development,Leishmania infantum: metabolism,Macrophages,Macrophages: parasitology,nosource,Phagosomes,Phagosomes: metabolism,Phosphorylation,Physiological,Physiological: genetics,Protein Biosynthesis,Stress,Temperature} }

@article{puigboECAINovelServer2008, title = {E-{{CAI}}: A Novel Server to Estimate an Expected Value of {{Codon Adaptation Index}} ({{eCAI}}).}, author = {Puigb{`o}, Pere and Bravo, Ignacio G. and {Garcia-Vallv{'e}}, Santiago}, year = 2008, month = jan, journal = {BMC bioinformatics}, volume = {9}, pages = {65}, issn = {1471-2105}, doi = {10.1186/1471-2105-9-65}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2246156&tool=pmcentrez&rendertype=abstract}, abstract = {BACKGROUND: The Codon Adaptation Index (CAI) is a measure of the synonymous codon usage bias for a DNA or RNA sequence. It quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. Extreme values in the nucleotide or in the amino acid composition have a large impact on differential preference for synonymous codons. It is thence essential to define the limits for the expected value of CAI on the basis of sequence composition in order to properly interpret the CAI and provide statistical support to CAI analyses. Though several freely available programs calculate the CAI for a given DNA sequence, none of them corrects for compositional biases or provides confidence intervals for CAI values. RESULTS: The E-CAI server, available at http://genomes.urv.es/CAIcal/E-CAI, is a web-application that calculates an expected value of CAI for a set of query sequences by generating random sequences with G+C and amino acid content similar to those of the input. An executable file, a tutorial, a Frequently Asked Questions (FAQ) section and several examples are also available. To exemplify the use of the E-CAI server, we have analysed the codon adaptation of human mitochondrial genes that codify a subunit of the mitochondrial respiratory chain (excluding those genes that lack a prokaryotic orthologue) and are encoded in the nuclear genome. It is assumed that these genes were transferred from the proto-mitochondrial to the nuclear genome and that its codon usage was then ameliorated. CONCLUSION: The E-CAI server provides a direct threshold value for discerning whether the differences in CAI are statistically significant or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences.}, isbn = {1471210596}, pmid = {18230160}, keywords = {Adaptation,Algorithms,Base Sequence,Codon,Codon: genetics,Computer Simulation,Data Interpretation,DNA,DNA: methods,Genetic,Genetic Variation,Genetic Variation: genetics,Internet,Models,Molecular Sequence Data,nosource,Physiological,Physiological: genetics,Sequence Analysis,Software,Statistical} }

@article{puigboCAIcalCombinedSet2008, title = {{{CAIcal}}: A Combined Set of Tools to Assess Codon Usage Adaptation.}, author = {Puigb{`o}, Pere and Bravo, Ignacio G. and {Garcia-Vallve}, Santiago}, year = 2008, month = jan, journal = {Biology direct}, volume = {3}, pages = {38}, issn = {1745-6150}, doi = {10.1186/1745-6150-3-38}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2553769&tool=pmcentrez&rendertype=abstract}, abstract = {BACKGROUND: The Codon Adaptation Index (CAI) was first developed to measure the synonymous codon usage bias for a DNA or RNA sequence. The CAI quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. RESULTS: We describe here CAIcal, a web-server available at http://genomes.urv.es/CAIcal that includes a complete set of utilities related with the CAI. The server provides useful important features, such as the calculation and graphical representation of the CAI along either an individual sequence or a protein multiple sequence alignment translated to DNA. The automated calculation of CAI and its expected value is also included as one of the CAIcal tools. The software is also free to be downloaded as a stand alone application for local use. CONCLUSION: The CAIcal server provides a complete set of tools to assess codon usage adaptation and to help in genome annotation.}, pmid = {18796141}, keywords = {Adaptation,Base Sequence,Codon,Codon: genetics,DNA,Evolution,Internet,Molecular,nosource,Physiological,Physiological: genetics,Sequence Alignment,Sequence Analysis,Software} }

@article{lemayNuclearPolyBinding2010, title = {The Nuclear Poly({{A}})-Binding Protein Interacts with the Exosome to Promote Synthesis of Noncoding Small Nucleolar {{RNAs}}.}, author = {Lemay, Jean-Fran{}ois and D’Amours, Annie and Lemieux, Caroline and Lackner, Daniel H. and {St-Sauveur}, Val{'e}rie G. and B{"a}hler, J{"u}rg and Bachand, Fran{}ois}, year = 2010, month = jan, journal = {Molecular cell}, volume = {37}, number = {1}, eprint = {20129053}, eprinttype = {pubmed}, pages = {34–45}, issn = {1097-4164}, doi = {10.1016/j.molcel.2009.12.019}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20129053}, abstract = {Poly(A)-binding proteins (PABPs) are important to eukaryotic gene expression. In the nucleus, the PABP PABPN1 is thought to function in polyadenylation of pre-mRNAs. Deletion of fission yeast pab2, the homolog of mammalian PABPN1, results in transcripts with markedly longer poly(A) tails, but the nature of the hyperadenylated transcripts and the mechanism that leads to RNA hyperadenylation remain unclear. Here we report that Pab2 functions in the synthesis of noncoding RNAs, contrary to the notion that PABPs function exclusively on protein-coding mRNAs. Accordingly, the absence of Pab2 leads to the accumulation of polyadenylated small nucleolar RNAs (snoRNAs). Our findings suggest that Pab2 promotes poly(A) tail trimming from pre-snoRNAs by recruiting the nuclear exosome. This work unveils a function for the nuclear PABP in snoRNA synthesis and provides insights into exosome recruitment to polyadenylated RNAs.}, pmid = {20129053}, keywords = {Cell Nucleus,Cell Nucleus: genetics,Cell Nucleus: metabolism,Exosomes,Exosomes: physiology,Fungal,Genome,nosource,Oligonucleotide Array Sequence Analysis,Poly(A)-Binding Protein II,Poly(A)-Binding Protein II: genetics,Poly(A)-Binding Protein II: physiology,Polyadenylation,RNA,Schizosaccharomyces,Schizosaccharomyces pombe Proteins,Schizosaccharomyces pombe Proteins: genetics,Schizosaccharomyces pombe Proteins: physiology,Schizosaccharomyces: genetics,Schizosaccharomyces: metabolism,Small Nucleolar,Small Nucleolar: biosynthesis} }

@article{ryvkinHAMRHighthroughputAnnotation2013, title = {{{HAMR}}: High-Throughput Annotation of Modified Ribonucleotides}, author = {Ryvkin, Paul and Leung, Y. Y. and Silverman, I. M.}, year = 2013, journal = {RNA}, pages = {1684–1692}, doi = {10.1261/rna.036806.112.8}, url = {http://rnajournal.cshlp.org/content/early/2013/10/22/rna.036806.112.short}, keywords = {nosource,rna modification,rna sequencing,trna} }

@article{yuStimulationRibosomalFrameshifting2013, title = {Stimulation of Ribosomal Frameshifting by {{RNA G-quadruplex}} Structures.}, author = {Yu, Chien-Hung and {Teulade-Fichou}, Marie-Paule and Olsthoorn, Ren{'e} C. L.}, year = 2013, month = oct, journal = {Nucleic acids research}, eprint = {24178029}, eprinttype = {pubmed}, pages = {1–6}, issn = {1362-4962}, doi = {10.1093/nar/gkt1022}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24178029}, abstract = {Guanine-rich sequences can fold into four-stranded structures of stacked guanine-tetrads, so-called G-quadruplexes (G4). These unique motifs have been extensively studied on the DNA level; however, exploration of the biological roles of G4s at the RNA level is just emerging. Here we show that G4 RNA when introduced within coding regions are capable of stimulating -1 ribosomal frameshifting (-1 FS) in vitro and in cultured cells. Systematic manipulation of the loop length between each G-tract revealed that the -1 FS efficiency positively correlates with G4 stability. Addition of a G4-stabilizing ligand, PhenDC3, resulted in higher -1 FS. Further, we demonstrated that the G4s can stimulate +1 FS and stop codon readthrough as well. These results suggest a potentially novel translational gene regulation mechanism mediated by G4 RNA.}, pmid = {24178029}, keywords = {nosource} }

@article{michaeliRNAseqAnalysisSmall2012, title = {{{RNA-seq}} Analysis of Small {{RNPs}} in {{Trypanosoma}} Brucei Reveals a Rich Repertoire of Non-Coding {{RNAs}}.}, author = {Michaeli, Shulamit and Doniger, Tirza and Gupta, Sachin Kumar and Wurtzel, Omri and Romano, Mali and Visnovezky, Damian and Sorek, Rotem and Unger, Ron and Ullu, Elisabetta}, year = 2012, month = feb, journal = {Nucleic acids research}, volume = {40}, number = {3}, pages = {1282–98}, issn = {1362-4962}, doi = {10.1093/nar/gkr786}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3273796&tool=pmcentrez&rendertype=abstract}, abstract = {The discovery of a plethora of small non-coding RNAs (ncRNAs) has fundamentally changed our understanding of how genes are regulated. In this study, we employed the power of deep sequencing of RNA (RNA-seq) to examine the repertoire of ncRNAs present in small ribonucleoprotein particles (RNPs) of Trypanosoma brucei, an important protozoan parasite. We identified new C/D and H/ACA small nucleolar RNAs (snoRNAs), as well as tens of putative novel non-coding RNAs; several of these are processed from trans-spliced and polyadenylated transcripts. The RNA-seq analysis provided information on the relative abundance of the RNAs, and their 5’- and 3’-termini. The study demonstrated that three highly abundant snoRNAs are involved in rRNA processing and highlight the unique trypanosome-specific repertoire of these RNAs. Novel RNAs were studied using in situ hybridization, association in RNP complexes, and ‘RNA walk’ to detect interaction with their target RNAs. Finally, we showed that the abundance of certain ncRNAs varies between the two stages of the parasite, suggesting that ncRNAs may contribute to gene regulation during the complex parasite’s life cycle. This is the first study to provide a whole-genome analysis of the large repertoire of small RNPs in trypanosomes.}, pmid = {21976736}, keywords = {Cells,Cultured,Gene Library,High-Throughput Nucleotide Sequencing,nosource,Nucleic Acid Conformation,Post-Transcriptional,Protozoan,Protozoan: chemistry,Protozoan: isolation & purification,Protozoan: metabolism,Ribonucleoproteins,Ribonucleoproteins: isolation & purification,Ribosomal,Ribosomal: metabolism,RNA,RNA Processing,Sequence Analysis,Small Nucleolar,Small Nucleolar: chemistry,Small Nucleolar: genetics,Small Nucleolar: metabolism,Small Untranslated,Small Untranslated: chemistry,Small Untranslated: isolation & purification,Small Untranslated: metabolism,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics} }

@article{hiraokaCodonUsageBias2009, title = {Codon Usage Bias Is Correlated with Gene Expression Levels in the Fission Yeast {{Schizosaccharomyces}} Pombe.}, author = {Hiraoka, Yasushi and Kawamata, Kenichi and Haraguchi, Tokuko and Chikashige, Yuji}, year = 2009, month = apr, journal = {Genes to cells}, volume = {14}, number = {4}, eprint = {19335619}, eprinttype = {pubmed}, pages = {499–509}, issn = {1365-2443}, doi = {10.1111/j.1365-2443.2009.01284.x}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19335619}, abstract = {Usage of synonymous codons represents a characteristic pattern of preference in each organism. It has been inferred that such bias of codon usage has evolved as a result of adaptation for efficient synthesis of proteins. Here we examined synonymous codon usage in genes of the fission yeast Schizosaccharomyces pombe, and compared codon usage bias with expression levels of the gene. In this organism, synonymous codon usage bias was correlated with expression levels of the gene; the bias was most obvious in two-codon amino acids. A similar pattern of the codon usage bias was also observed in Saccharomyces cerevisiae, Arabidopsis thaliana and Caenorhabditis elegans, but was not obvious in Oryza sativa, Drosophila melanogaster, Takifugu rubripes and Homo sapiens. As codons of the highly expressed genes have greater influence on translational efficiency than codons of genes expressed at lower levels, it is likely that codon usage in the S. pombe genome has been optimized by translational selection through evolution.}, pmid = {19335619}, keywords = {Algorithms,Animals,Arabidopsis,Arabidopsis: genetics,Base Sequence,Caenorhabditis elegans,Caenorhabditis elegans: genetics,Codon,Codon: genetics,Databases,Drosophila melanogaster,Drosophila melanogaster: genetics,Fungal Proteins,Fungal Proteins: genetics,Gene Expression Profiling,Genetic,Humans,Messenger,Messenger: genetics,Messenger: metabolism,nosource,Oligonucleotide Array Sequence Analysis,Open Reading Frames,Open Reading Frames: genetics,Oryza sativa,Oryza sativa: genetics,Ribosomal Proteins,Ribosomal Proteins: genetics,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Schizosaccharomyces,Schizosaccharomyces: genetics,Takifugu,Takifugu: genetics} }

@article{sandersEvaluationDigitalPCR2013, title = {Evaluation of Digital {{PCR}} for Absolute {{RNA}} Quantification.}, author = {Sanders, Rebecca and Mason, Deborah J. and {}a Foy, Carole and Huggett, Jim F.}, year = 2013, month = jan, journal = {PloS one}, volume = {8}, number = {9}, pages = {e75296}, issn = {1932-6203}, doi = {10.1371/journal.pone.0075296}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3779174&tool=pmcentrez&rendertype=abstract}, abstract = {Gene expression measurements detailing mRNA quantities are widely employed in molecular biology and are increasingly important in diagnostic fields. Reverse transcription (RT), necessary for generating complementary DNA, can be both inefficient and imprecise, but remains a quintessential RNA analysis tool using qPCR. This study developed a Transcriptomic Calibration Material and assessed the RT reaction using digital (d)PCR for RNA measurement. While many studies characterise dPCR capabilities for DNA quantification, less work has been performed investigating similar parameters using RT-dPCR for RNA analysis. RT-dPCR measurement using three, one-step RT-qPCR kits was evaluated using single and multiplex formats when measuring endogenous and synthetic RNAs. The best performing kit was compared to UV quantification and sensitivity and technical reproducibility investigated. Our results demonstrate assay and kit dependent RT-dPCR measurements differed significantly compared to UV quantification. Different values were reported by different kits for each target, despite evaluation of identical samples using the same instrument. RT-dPCR did not display the strong inter-assay agreement previously described when analysing DNA. This study demonstrates that, as with DNA measurement, RT-dPCR is capable of accurate quantification of low copy RNA targets, but the results are both kit and target dependent supporting the need for calibration controls.}, pmid = {24073259}, keywords = {nosource} }

@article{iyerAbsoluteMRNALevels1996, title = {Absolute {{mRNA}} Levels and Transcriptional Initiation Rates in {{Saccharomyces}} Cerevisiae}, author = {Iyer, Vishwanath and Struhl, K.}, year = 1996, journal = {Proceedings of the National Academy of }, volume = {93}, number = {May}, pages = {5208–5212}, url = {http://www.pnas.org/content/93/11/5208.short}, keywords = {nosource} }

@article{croanEvolutionGenusLeishmania1997, title = {Evolution of the Genus {{Leishmania}} Revealed by Comparison of {{DNA}} and {{RNA}} Polymerase Gene Sequences.}, author = {Croan, D. G. and {}a Morrison, D. and Ellis, J. T.}, year = 1997, month = nov, journal = {Molecular and biochemical parasitology}, volume = {89}, number = {2}, eprint = {9364962}, eprinttype = {pubmed}, pages = {149–59}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9364962}, abstract = {Previous hypotheses of Leishmania evolution are undermined by limitations in the phylogenetic reconstruction method employed or due to the omission of key parasites. In this experiment, sequences of the gene encoding the DNA polymerase alpha catalytic polypeptide (POLA) were analysed phylogenetically in combination with those encoding the RNA polymerase II largest subunit gene (RPOIILS) to infer a comprehensive phylogeny of Leishmania. Nineteen species of parasites were studied, comprising representatives of each Leishmania species-complex (Leishmania Leishmania tropica, Leishmania Leishmania donovani, Leishmania Leishmania mexicana, Leishmania Leishmania hertigi and Leishmania Viannia braziliensis), as well as parasites of questionable taxonomy (Leishmania herreri, Sauroleishmania adleri, Sauroleishmania deanei, Sauroleishmania gymnodactyli and Sauroleishmania tarentolae). The analyses presented here provide strong support for the hypothesis that the Leishmania that infect reptiles (also known as Sauroleishmania) evolved from mammalian Leishmania. One implication of this finding is that the taxonomic definition of Leishmania should be broadened to encompass characteristics of the reptilian parasites. However, this taxonomic revision is complicated in that Leishmania (L.) hertigi, Leishmania (L.) deanei and Leishmania herreri, which exhibit some biological properties of Leishmania, are more closely related to Endotrypanum on the basis of these sequence comparisons. Consequently, the taxonomic discrimination between Leishmania that infect mammals, Leishmania that infect reptiles and Endotrypanum may be more problematic than has been previously thought. Since our resulting phylogenetic hypothesis is supported by the analyses of two different genes, we speculate on the origin and evolutionary expansion of this lineage of kinetoplastid protozoa.}, pmid = {9364962}, keywords = {Animals,Biological Evolution,DNA,DNA Polymerase I,DNA Polymerase I: genetics,Genes,Humans,Leishmania,Leishmania: enzymology,Leishmania: genetics,Molecular Sequence Data,nosource,Phylogeny,Protozoan,Protozoan: genetics,RNA Polymerase II,RNA Polymerase II: genetics,Sequence Analysis} }

@article{loweTRNAscanSEProgramImproved1997, title = {{{tRNAscan-SE}}: A Program for Improved Detection of Transfer {{RNA}} Genes in Genomic Sequence.}, author = {Lowe, T. M. and Eddy, S. R.}, year = 1997, month = mar, journal = {Nucleic acids research}, volume = {25}, number = {5}, pages = {955–64}, issn = {0305-1048}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=146525&tool=pmcentrez&rendertype=abstract}, abstract = {We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.}, pmid = {9023104}, keywords = {Amino Acid-Specific,Amino Acid-Specific: genetics,Animals,Bacterial,Bacterial: analysis,Bacterial: genetics,Databases,Evaluation Studies as Topic,Factual,Genome,Introns,nosource,RNA,RNA: genetics,Software,Transfer,Transfer: analysis,Transfer: genetics} }

@article{sharpCodonAdaptationIndexa1987, title = {The Codon Adaptation Index-a Measure of Directional Synonymous Codon Usage Bias, and Its Potential Applications}, author = {Sharp, P. M. and Li, W. H.}, year = 1987, journal = {Nucleic acids research}, volume = {15}, number = {3}, pages = {1281–1295}, doi = {10.1093/nar/15.3.1281}, url = {http://nar.oxfordjournals.org/content/15/3/1281.short}, keywords = {nosource} }

@article{realGenomeSequenceLeishmania2013, title = {The {{Genome Sequence}} of {{Leishmania}} ({{Leishmania}}) Amazonensis: {{Functional Annotation}} and {{Extended Analysis}} of {{Gene Models}}.}, author = {Real, Fernando and Vidal, Ramon Oliveira and Carazzolle, Marcelo Falsarella and Mondego, Jorge Maur{'i}cio Costa and Costa, Gustavo Gilson Lacerda and Herai, Roberto Hirochi and W{"u}rtele, Martin and {}de Carvalho, Lucas Miguel and Ferreira, Renata Carmona E. and Mortara, Renato Arruda and Barbi{'e}ri, Clara Lucia and Mieczkowski, Piotr and {}da Silveira, Jos{'e} Franco and Briones, Marcelo Ribeiro Da Silva and Pereira, Gon{}alo Amarante Guimar{~a}es and Bahia, Diana}, year = 2013, month = jul, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, eprint = {23857904}, eprinttype = {pubmed}, pages = {1–15}, issn = {1756-1663}, doi = {10.1093/dnares/dst031}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23857904}, abstract = {We present the sequencing and annotation of the Leishmania (Leishmania) amazonensis genome, an etiological agent of human cutaneous leishmaniasis in the Amazon region of Brazil. L. (L.) amazonensis shares features with Leishmania (L.) mexicana but also exhibits unique characteristics regarding geographical distribution and clinical manifestations of cutaneous lesions (e.g. borderline disseminated cutaneous leishmaniasis). Predicted genes were scored for orthologous gene families and conserved domains in comparison with other human pathogenic Leishmania spp. Carboxypeptidase, aminotransferase, and 3’-nucleotidase genes and ATPase, thioredoxin, and chaperone-related domains were represented more abundantly in L. (L.) amazonensis and L. (L.) mexicana species. Phylogenetic analysis revealed that these two species share groups of amastin surface proteins unique to the genus that could be related to specific features of disease outcomes and host cell interactions. Additionally, we describe a hypothetical hybrid interactome of potentially secreted L. (L.) amazonensis proteins and host proteins under the assumption that parasite factors mimic their mammalian counterparts. The model predicts an interaction between an L. (L.) amazonensis heat-shock protein and mammalian Toll-like receptor 9, which is implicated in important immune responses such as cytokine and nitric oxide production. The analysis presented here represents valuable information for future studies of leishmaniasis pathogenicity and treatment.}, pmid = {23857904}, keywords = {amastin,genome,heat-shock protein,interactome,leishmania amazonensis,nosource} }

@article{koslowskyInsectphaseGRNATranscriptome2013, title = {The Insect-Phase {{gRNA}} Transcriptome in {{Trypanosoma}} Brucei.}, author = {Koslowsky, Donna and Sun, Yanni and Hindenach, Jordan and Theisen, Terence and Lucas, Jasmin}, year = 2013, month = oct, journal = {Nucleic acids research}, eprint = {24174546}, eprinttype = {pubmed}, pages = {1–14}, issn = {1362-4962}, doi = {10.1093/nar/gkt973}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24174546}, abstract = {One of the most striking examples of small RNA regulation of gene expression is the process of RNA editing in the mitochondria of trypanosomes. In these parasites, RNA editing involves extensive uridylate insertions and deletions within most of the mitochondrial messenger RNAs (mRNAs). Over 1200 small guide RNAs (gRNAs) are predicted to be responsible for directing the sequence changes that create start and stop codons, correct frameshifts and for many of the mRNAs generate most of the open reading frame. In addition, alternative editing creates the opportunity for unprecedented protein diversity. In Trypanosoma brucei, the vast majority of gRNAs are transcribed from minicircles, which are approximately one kilobase in size, and encode between three and four gRNAs. The large number (5000-10 000) and their concatenated structure make them difficult to sequence. To identify the complete set of gRNAs necessary for mRNA editing in T. brucei, we used Illumina deep sequencing of purified gRNAs from the procyclic stage. We report a near complete set of gRNAs needed to direct the editing of the mRNAs.}, pmid = {24174546}, keywords = {nosource} }

@book{schneiterGeneticsMolecularCell2004, title = {Genetics , {{Molecular}} and {{Cell Biology}} of {{Yeast}}}, author = {Schneiter, Roger}, year = 2004, number = {January}, keywords = {nosource} } % == BibTeX quality report for schneiterGeneticsMolecularCell2004: % Missing required field ‘publisher’ % ? Title looks like it was stored in title-case in Zotero

@article{tsengNovelMegaprimedLigasefree2008, title = {A Novel Megaprimed and Ligase-Free, {{PCR-based}}, Site-Directed Mutagenesis Method.}, author = {Tseng, Wen-Chi and Lin, Jing-Wei and Wei, Tsen-Yun and Fang, Tsuei-Yun}, year = 2008, month = apr, journal = {Anal. Biochem.}, volume = {375}, number = {2}, pages = {376–8}, issn = {0003-2697}, doi = {10.1016/j.ab.2007.12.013}, abstract = {In this study, we report a novel megaprimed and ligase-free, PCR-based, site-directed mutagenesis method modified from the QuikChange site-directed mutagenesis (QCM). One mutagenic oligonucleotide and one universal flanking primer were used to produce the complementary megaprimers that were then used to amplify the whole plasmid template. This method yields a mutagenesis efficiency ( approximately 90%) similar to that of QCM but uses only one mutagenic oligonucleotide instead of two of them, and the length of the oligonucleotide could be shorter. This method can be further extended to double mutations that are located at distant sites by using two mutagenic oligonucleotides and even to site saturation mutagenesis by introducing randomized codons.}, pmid = {18198125}, keywords = {Agar Gel,DNA Primers,DNA Primers: genetics,Electrophoresis,Ligases,Mutagenesis,Mutation,Mutation: genetics,nosource,Oligonucleotides,Oligonucleotides: genetics,Polymerase Chain Reaction,Polymerase Chain Reaction: methods,Site-Directed,Site-Directed: methods} } % == BibTeX quality report for tsengNovelMegaprimedLigasefree2008: % ? Possibly abbreviated journal title Anal. Biochem.

@article{klauckGeneticsAutismSpectrum2006, title = {Genetics of Autism Spectrum Disorder.}, author = {Klauck, Sabine M.}, year = 2006, month = jun, journal = {Eur. J. Hum. Genet.}, volume = {14}, number = {6}, pages = {714–20}, issn = {1018-4813}, doi = {10.1038/sj.ejhg.5201610}, abstract = {Autism is a highly heritable complex neurodevelopmental disorder characterized by distinct impairments of cognitive function in the field of social interaction and speech development. Different approaches have been undertaken worldwide to identify susceptibility loci or genes for autism spectrum disorders. No clear conclusions can be made today about genetic loci involved in these disorders. The review will focus on relevant results from the last decade of research with emphasis on whole genome screens and association studies.}, pmid = {16721407}, keywords = {Autistic Disorder,Autistic Disorder: genetics,Cognition Disorders,Cognition Disorders: genetics,Genetic Predisposition to Disease,Genome,Human,Human: genetics,Humans,nosource,Quantitative Trait Loci,Quantitative Trait Loci: genetics,Social Behavior,Speech} } % == BibTeX quality report for klauckGeneticsAutismSpectrum2006: % ? Possibly abbreviated journal title Eur. J. Hum. Genet.

@article{volkmarAutism2003, title = {Autism.}, author = {Volkmar, Fred R. and Pauls, David}, year = 2003, month = oct, journal = {Lancet}, volume = {362}, number = {9390}, pages = {1133–41}, issn = {1474-547X}, doi = {10.1016/S0140-6736(03)14471-6}, abstract = {Autism is a disorder characterised by severe difficulties in social interaction and communication, and with unusual behaviours. Once thought of as rare, autism is now recognised as being common. The role of CNS factors in pathogenesis is suggested by high rates of seizure disorder; research has highlighted the role of several specific brain regions in syndrome pathogenesis. Autism is a strongly genetic disorder and probably arises because of multiple genes; recurrence rates in families with one child are high. Early intervention with various techniques is helpful in many cases. Some pharmacological agents may help with certain problematic behaviours but do not address the underlying cause of the disorder.}, pmid = {14550703}, keywords = {Adult,Autistic Disorder,Autistic Disorder: diagnosis,Autistic Disorder: genetics,Autistic Disorder: therapy,Eye Movements,Humans,Infant,Magnetic Resonance Imaging,Newborn,nosource} }

@article{guptaHnRNPHomologueTrypanosoma2013, title = {The {{hnRNP F}}/{{H}} Homologue of {{Trypanosoma}} Brucei Is Differentially Expressed in the Two Life Cycle Stages of the Parasite and Regulates Splicing and {{mRNA}} Stability.}, author = {Gupta, Sachin Kumar and Kosti, Idit and Plaut, Guy and Pivko, Asher and Tkacz, Itai Dov and {Cohen-Chalamish}, Smadar and Biswas, Dipul Kumar and Wachtel, Chaim and {Ben-Asher}, Hiba Waldman and Carmi, Shai and Glaser, Fabian and {Mandel-Gutfreund}, Yael and Michaeli, Shulamit}, year = 2013, month = jul, journal = {Nucleic acids research}, volume = {41}, number = {13}, pages = {6577–94}, issn = {1362-4962}, doi = {10.1093/nar/gkt369}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3711420&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanosomes are protozoan parasites that cycle between a mammalian host (bloodstream form) and an insect host, the Tsetse fly (procyclic stage). In trypanosomes, all mRNAs are trans-spliced as part of their maturation. Genome-wide analysis of trans-splicing indicates the existence of alternative trans-splicing, but little is known regarding RNA-binding proteins that participate in such regulation. In this study, we performed functional analysis of the Trypanosoma brucei heterogeneous nuclear ribonucleoproteins (hnRNP) F/H homologue, a protein known to regulate alternative splicing in metazoa. The hnRNP F/H is highly expressed in the bloodstream form of the parasite, but is also functional in the procyclic form. Transcriptome analyses of RNAi-silenced cells were used to deduce the RNA motif recognized by this protein. A purine rich motif, AAGAA, was enriched in both the regulatory regions flanking the 3’ splice site and poly (A) sites of the regulated genes. The motif was further validated using mini-genes carrying wild-type and mutated sequences in the 3’ and 5’ UTRs, demonstrating the role of hnRNP F/H in mRNA stability and splicing. Biochemical studies confirmed the binding of the protein to this proposed site. The differential expression of the protein and its inverse effects on mRNA level in the two lifecycle stages demonstrate the role of hnRNP F/H in developmental regulation.}, pmid = {23666624}, keywords = {3’ Untranslated Regions,Amino Acid,Animals,Binding Sites,Cell Nucleus,Cell Nucleus: metabolism,Cytoplasm,Cytoplasm: metabolism,Developmental,Gene Expression Regulation,Heterogeneous-Nuclear Ribonucleoprotein Group F-H,Heterogeneous-Nuclear Ribonucleoprotein Group F-H:,Life Cycle Stages,Messenger,Messenger: metabolism,nosource,Protozoan Proteins,Protozoan Proteins: chemistry,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,RNA,RNA Interference,RNA Stability,Sequence Homology,Trans-Splicing,Transcriptome,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: growth & development,Trypanosoma brucei brucei: metabolism} }

@article{nagelSelfinducedStructuralSwitches2002, title = {Self-Induced Structural Switches in {{RNA}}.}, author = {{}a Nagel, Jord H. and {}a Pleij, Cornelis W.}, year = 2002, month = sep, journal = {Biochimie}, volume = {84}, number = {9}, eprint = {12458084}, eprinttype = {pubmed}, pages = {913–23}, issn = {0300-9084}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12458084}, abstract = {Many biologically active RNAs show a switch in their secondary structure, which is accompanied by changes in their function. Such changes in secondary structure often require trans-acting factors, e.g. RNA chaperones. However, several biologically active RNAs do not require trans-acting factors for this structural switch, which is therefore indicated here as a “self-induced switch”. These self-induced structural switches have several characteristics in common. They all start from a metastable structure, which is maintained for some time allowing or blocking a particular function of the RNA. Hereafter, a structural element becomes available, e.g. during transcription, triggering a rapid transition into a stable conformation, which again is accompanied by either a gain or loss of function. A further common element of this type of switches is the involvement of a branch migration or strand displacement reaction, which lowers the energy barrier of the reaction sufficiently to allow rapid refolding. Here, we review a number of these self-induced switches in RNA secondary structure as proposed for several systems. A general model for this type of switches is presented, showing its importance in the biology of functionally active RNAs.}, pmid = {12458084}, keywords = {Animals,Bacterial,Base Sequence,Catalytic,Catalytic: chemistry,Catalytic: genetics,Genetic,Genome,Introns,Models,Molecular Sequence Data,nosource,Nucleic Acid Conformation,RNA,RNA: chemistry,RNA: genetics,Structure-Activity Relationship,Thermodynamics,Transcription} }

@article{gongMRNAmRNADuplexesThat2013, title = {{{mRNA-mRNA}} Duplexes That Autoelicit {{Staufen1-mediated mRNA}} Decay.}, author = {Gong, Chenguang and Tang, Yalan and Maquat, Lynne E.}, year = 2013, month = sep, journal = {Nature structural & molecular biology}, volume = {20}, number = {10}, eprint = {24056942}, eprinttype = {pubmed}, issn = {1545-9985}, doi = {10.1038/nsmb.2664}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24056942}, abstract = {We report a new mechanism by which human mRNAs cross-talk: an Alu element in the 3’ untranslated region (3’ UTR) of one mRNA can base-pair with a partially complementary Alu element in the 3’ UTR of a different mRNA, thereby creating a Staufen1 (STAU1)-binding site (SBS). STAU1 binding to a 3’-UTR SBS was previously shown to trigger STAU1-mediated mRNA decay (SMD) by directly recruiting the ATP-dependent RNA helicase UPF1, which is also a key factor in the mechanistically related nonsense-mediated mRNA decay (NMD) pathway. In the case of a 3’-UTR SBS created by mRNA-mRNA base-pairing, we show that SMD targets both mRNAs in the duplex, provided that both mRNAs are translated. If only one mRNA is translated, then it alone is targeted for SMD. We demonstrate the functional importance of mRNA-mRNA-triggered SMD in cell migration and invasion.}, pmid = {24056942}, keywords = {nosource} }

@article{herasMicroprocessorControlsActivity2013, title = {The {{Microprocessor}} Controls the Activity of Mammalian Retrotransposons.}, author = {Heras, Sara R. and Macias, Sara and Plass, Mireya and Fernandez, Noem{'i} and Cano, David and Eyras, Eduardo and {Garcia-Perez}, Jos{'e} L. and C{'a}ceres, Javier F.}, year = 2013, month = sep, journal = {Nature structural & molecular biology}, volume = {20}, number = {10}, eprint = {23995758}, eprinttype = {pubmed}, issn = {1545-9985}, doi = {10.1038/nsmb.2658}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23995758}, abstract = {More than half of the human genome is made of transposable elements whose ongoing mobilization is a driving force in genetic diversity; however, little is known about how the host regulates their activity. Here, we show that the Microprocessor (Drosha-DGCR8), which is required for microRNA biogenesis, also recognizes and binds RNAs derived from human long interspersed element 1 (LINE-1), Alu and SVA retrotransposons. Expression analyses demonstrate that cells lacking a functional Microprocessor accumulate LINE-1 mRNA and encoded proteins. Furthermore, we show that structured regions of the LINE-1 mRNA can be cleaved in vitro by Drosha. Additionally, we used a cell culture-based assay to show that the Microprocessor negatively regulates LINE-1 and Alu retrotransposition in vivo. Altogether, these data reveal a new role for the Microprocessor as a post-transcriptional repressor of mammalian retrotransposons and a defender of human genome integrity.}, pmid = {23995758}, keywords = {nosource} }

@article{suzukiCharacterizationRNaseRdigested2006, title = {Characterization of {{RNase R-digested}} Cellular {{RNA}} Source That Consists of Lariat and Circular {{RNAs}} from Pre-{{mRNA}} Splicing.}, author = {Suzuki, Hitoshi and Zuo, Yuhong and Wang, Jinhua and Zhang, Michael Q. and Malhotra, Arun and Mayeda, Akila}, year = 2006, month = jan, journal = {Nucleic acids research}, volume = {34}, number = {8}, pages = {e63}, issn = {1362-4962}, doi = {10.1093/nar/gkl151}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1458517&tool=pmcentrez&rendertype=abstract}, abstract = {Besides linear RNAs, pre-mRNA splicing generates three forms of RNAs: lariat introns, Y-structure introns from trans-splicing, and circular exons through exon skipping. To study the persistence of excised introns in total cellular RNA, we used three Escherichia coli 3’ to 5’ exoribonucleases. Ribonuclease R (RNase R) thoroughly degrades the abundant linear RNAs and the Y-structure RNA, while preserving the loop portion of a lariat RNA. Ribonuclease II (RNase II) and polynucleotide phosphorylase (PNPase) also preserve the lariat loop, but are less efficient in degrading linear RNAs. RNase R digestion of the total RNA from human skeletal muscle generates an RNA pool consisting of lariat and circular RNAs. RT-PCR across the branch sites confirmed lariat RNAs and circular RNAs in the pool generated by constitutive and alternative splicing of the dystrophin pre-mRNA. Our results indicate that RNase R treatment can be used to construct an intronic cDNA library, in which majority of the intron lariats are represented. The highly specific activity of RNase R implies its ability to screen for rare intragenic trans-splicing in any target gene with a large background of cis-splicing. Further analysis of the intronic RNA pool from a specific tissue or cell will provide insights into the global profile of alternative splicing.}, pmid = {16682442}, keywords = {Dystrophin,Dystrophin: genetics,Dystrophin: metabolism,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: metabolism,Escherichia coli: enzymology,Exoribonucleases,Exoribonucleases: metabolism,Globins,Globins: genetics,Globins: metabolism,HeLa Cells,Humans,Introns,Messenger,Messenger: chemistry,Messenger: metabolism,nosource,Nucleic Acid Conformation,Polyribonucleotide Nucleotidyltransferase,Polyribonucleotide Nucleotidyltransferase: metabol,RNA,RNA Precursors,RNA Precursors: chemistry,RNA Precursors: metabolism,RNA Splicing,RNA: chemistry,RNA: metabolism} }

@article{grailleSurveillancePathwaysRescuing2012, title = {Surveillance Pathways Rescuing Eukaryotic Ribosomes Lost in Translation.}, author = {Graille, Marc and S{'e}raphin, Bertrand}, year = 2012, month = nov, journal = {Nature reviews. Molecular cell biology}, volume = {13}, number = {11}, eprint = {23072885}, eprinttype = {pubmed}, pages = {727–35}, publisher = {Nature Publishing Group}, issn = {1471-0080}, doi = {10.1038/nrm3457}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23072885}, abstract = {Living cells require the continuous production of proteins by the ribosomes. Any problem enforcing these protein factories to stall during mRNA translation may then have deleterious cellular effects. To minimize these defects, eukaryotic cells have evolved dedicated surveillance pathways: non-stop decay (NSD), no-go decay (NGD) and non-functional 18S-rRNA decay (18S-NRD). Recent studies support a general molecular framework for these surveillance pathways, the mechanisms of which are intimately related to translation termination.}, pmid = {23072885}, keywords = {Animals,Endoribonucleases,Endoribonucleases: metabolism,Eukaryotic Cells,Eukaryotic Cells: cytology,Humans,Messenger,Messenger: genetics,Messenger: metabolism,Nonsense Mediated mRNA Decay,nosource,Peptide Chain Termination,Peptide Elongation Factors,Peptide Elongation Factors: metabolism,Protein Biosynthesis,Ribosomes,Ribosomes: genetics,Ribosomes: metabolism,RNA,RNA Stability,RNA Stability: genetics,Translational} } % == BibTeX quality report for grailleSurveillancePathwaysRescuing2012: % ? Possibly abbreviated journal title Nature reviews. Molecular cell biology

@article{andreasenImprovedMicroRNAQuantification2010, title = {Improved {{microRNA}} Quantification in Total {{RNA}} from Clinical Samples.}, author = {Andreasen, Ditte and Fog, Jacob U. and Biggs, William and Salomon, Jesper and Dahslveen, Ina K. and Baker, Adam and Mouritzen, Peter}, year = 2010, month = apr, journal = {Methods (San Diego, Calif.)}, volume = {50}, number = {4}, eprint = {20215018}, eprinttype = {pubmed}, pages = {S6-9}, publisher = {Elsevier Inc.}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2010.01.006}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20215018}, abstract = {microRNAs are small regulatory RNAs that are currently emerging as new biomarkers for cancer and other diseases. In order for biomarkers to be useful in clinical settings, they should be accurately and reliably detected in clinical samples such as formalin fixed paraffin embedded (FFPE) sections and blood serum or plasma. These types of samples represent a challenge in terms of microRNA quantification. A newly developed method for microRNA qPCR using Locked Nucleic Acid (LNA)-enhanced primers enables accurate and reproducible quantification of microRNAs in scarce clinical samples. Here we show that LNA-based microRNA qPCR enables biomarker screening using very low amounts of total RNA from FFPE samples and the results are compared to microarray analysis data. We also present evidence that the addition of a small carrier RNA prior to total RNA extraction, improves microRNA quantification in blood plasma and laser capture microdissected (LCM) sections of FFPE samples.}, pmid = {20215018}, keywords = {Fixatives,Formaldehyde,Humans,Lasers,MicroRNAs,MicroRNAs: analysis,MicroRNAs: blood,MicroRNAs: genetics,nosource,Oligonucleotide Array Sequence Analysis,Oligonucleotide Array Sequence Analysis: methods,Paraffin Embedding,Polymerase Chain Reaction,Polymerase Chain Reaction: methods} } % == BibTeX quality report for andreasenImprovedMicroRNAQuantification2010: % ? Possibly abbreviated journal title Methods (San Diego, Calif.)

@article{liStressinducedTRNAderivedRNAs2008, title = {Stress-Induced {{tRNA-derived RNAs}}: A Novel Class of Small {{RNAs}} in the Primitive Eukaryote {{Giardia}} Lamblia.}, author = {Li, Yan and Luo, Jun and Zhou, Hui and Liao, Jian-You and Ma, Li-Ming and Chen, Yue-Qin and Qu, Liang-Hu}, year = 2008, month = nov, journal = {Nucleic acids research}, volume = {36}, number = {19}, pages = {6048–55}, issn = {1362-4962}, doi = {10.1093/nar/gkn596}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2577346&tool=pmcentrez&rendertype=abstract}, abstract = {Giardia lamblia is an early diverging and evolutionarily successful protozoan as it can enter into a dormant cyst stage from a vegetative trophozoite. During dormant stage, its metabolic rate decreases dramatically. However, to date, the regulatory molecules participating in the initiation and maintenance of this process have not been fully investigated. In this study, we have identified a class of abundant small RNAs named sitRNAs, which are approximately 46 nucleotides in length and accumulate in G. lamblia encysting cultures. Remarkably, they are derived from the 3’ portion of fully matured tRNAs by cleavage of the anticodon left arm, with the 3’ terminal CCA triplex still connected. During differentiation, only a limited portion of mature tRNAs is cleaved, but this cleavage occurs almost in the entire tRNA family. sitRNAs begin to accumulate as early as 3 h after initiation of encystation and are maintained at a relatively stable level during the whole process, exhibiting an expression peak at around 24 hr. Our studies further show that sitRNAs can be induced by several other stress factors, and in the case of serum deprivation, both tRNAs and sitRNAs degrade rapidly, with the accumulation of tRNA being halved. Our results may provide new insight into a novel mechanism for stressed G. lamblia to regulate gene expression globally.}, pmid = {18820301}, keywords = {Animals,Cells,Culture Media,Cultured,Giardia lamblia,Giardia lamblia: genetics,Giardia lamblia: growth & development,Giardia lamblia: metabolism,nosource,Protozoan,Protozoan: chemistry,Protozoan: classification,Protozoan: metabolism,RNA,Serum-Free,Temperature,Transfer,Transfer: chemistry,Transfer: metabolism,Trophozoites,Trophozoites: metabolism,Untranslated,Untranslated: chemistry,Untranslated: classification,Untranslated: metabolism} }

@article{marcotrigianoCocrystalStructureMessenger1997, title = {Cocrystal Structure of the Messenger {{RNA}} 5’ Cap-Binding Protein ({{eIF4E}}) Bound to 7-Methyl-{{GDP}}.}, author = {Marcotrigiano, J. and Gingras, a C. and Sonenberg, N. and Burley, S. K.}, year = 1997, month = jun, journal = {Cell}, volume = {89}, number = {6}, eprint = {9200613}, eprinttype = {pubmed}, pages = {951–61}, issn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9200613}, abstract = {The X-ray structure of the eukaryotic translation initiation factor 4E (eIF4E), bound to 7-methyl-GDP, has been determined at 2.2 A resolution. eIF4E recognizes 5’ 7-methyl-G(5’)ppp(5’)N mRNA caps during the rate-limiting initiation step of translation. The protein resembles a cupped hand and consists of a curved, 8-stranded antiparallel beta sheet, backed by three long alpha helices. 7-methyl-GDP binds in a narrow cap-binding slot on the molecule’s concave surface, where 7-methyl-guanine recognition is mediated by base sandwiching between two conserved tryptophans, plus formation of three hydrogen bonds and a van der Waals contact between its N7-methyl group and a third conserved tryptophan. The convex dorsal surface of the molecule displays a phylogenetically conserved hydrophobic/acidic portion, which may interact with other translation initiation factors and regulatory proteins.}, pmid = {9200613}, keywords = {Amino Acid,Binding Sites,Binding Sites: physiology,Conserved Sequence,Crystallography,Escherichia coli,Escherichia coli: genetics,Eukaryotic Cells,Eukaryotic Cells: physiology,Eukaryotic Initiation Factor-4E,Guanosine Diphosphate,Guanosine Diphosphate: analogs & derivatives,Guanosine Diphosphate: metabolism,Messenger,Messenger: chemistry,Messenger: metabolism,Methylation,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Peptide Initiation Factors,Peptide Initiation Factors: chemistry,Peptide Initiation Factors: genetics,Peptide Initiation Factors: metabolism,Protein Biosynthesis,Protein Biosynthesis: physiology,Protein Structure,RNA,RNA Cap Analogs,RNA Cap Analogs: metabolism,Secondary,Sequence Homology,Tertiary} }

@article{zikovaTrypanosomaBruceiMitochondrial2008, title = {Trypanosoma Brucei Mitochondrial Ribosomes: Affinity Purification and Component Identification by Mass Spectrometry.}, author = {Z{'i}kov{'a}, Alena and Panigrahi, Aswini K. and {}a Dalley, Rachel and Acestor, Nathalie and Anupama, Atashi and Ogata, Yuko and Myler, Peter J. and Stuart, Kenneth}, year = 2008, month = jul, journal = {Molecular & cellular proteomics : MCP}, volume = {7}, number = {7}, pages = {1286–96}, issn = {1535-9484}, doi = {10.1074/mcp.M700490-MCP200}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2493383&tool=pmcentrez&rendertype=abstract}, abstract = {Although eukaryotic mitochondrial (mt) ribosomes evolved from a putative prokaryotic ancestor their compositions vary considerably among organisms. We determined the protein composition of tandem affinity-purified Trypanosoma brucei mt ribosomes by mass spectrometry and identified 133 proteins of which 77 were associated with the large subunit and 56 were associated with the small subunit. Comparisons with bacterial and mammalian mt ribosomal proteins identified T. brucei mt homologs of L2-4, L7/12, L9, L11, L13-17, L20-24, L27-30, L33, L38, L43, L46, L47, L49, L52, S5, S6, S8, S9, S11, S15-18, S29, and S34, although the degree of conservation varied widely. Sequence characteristics of some of the component proteins indicated apparent functions in rRNA modification and processing, protein assembly, and mitochondrial metabolism implying possible additional roles for these proteins. Nevertheless most of the identified proteins have no homology outside Kinetoplastida implying very low conservation and/or a divergent function in kinetoplastid mitochondria.}, pmid = {18364347}, keywords = {Affinity,Algorithms,Animals,Cells,Chromatography,Cultured,Genetically Modified,Mass Spectrometry,Mitochondria,Mitochondria: chemistry,Mitochondria: metabolism,nosource,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosome Subunits,Ribosome Subunits: chemistry,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,Staining and Labeling,Staining and Labeling: methods,Trypanosoma brucei brucei,Trypanosoma brucei brucei: chemistry,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: metabolism} }

@article{gilingerTrypanosomeSplicedLeader2001, title = {Trypanosome Spliced Leader {{RNA}} Genes Contain the First Identified {{RNA}} Polymerase {{II}} Gene Promoter in These Organisms.}, author = {Gilinger, G. and Bellofatto, V.}, year = 2001, month = apr, journal = {Nucleic acids research}, volume = {29}, number = {7}, pages = {1556–64}, issn = {1362-4962}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=31286&tool=pmcentrez&rendertype=abstract}, abstract = {Typical general transcription factors, such as TATA binding protein and TFII B, have not yet been identified in any member of the Trypanosomatidae family of parasitic protozoa. Interestingly, mRNA coding genes do not appear to have discrete transcriptional start sites, although in most cases they require an RNA polymerase that has the biochemical properties of eukaryotic RNA polymerase II. A discrete transcription initiation site may not be necessary for mRNA synthesis since the sequences upstream of each transcribed coding region are trimmed from the nascent transcript when a short m(7)G-capped RNA is added during mRNA maturation. This short 39 nt m(7)G-capped RNA, the spliced leader (SL) sequence, is expressed as an approximately 100 nt long RNA from a set of reiterated, though independently transcribed, genes in the trypanosome genome. Punctuation of the 5’ end of mRNAs by a m(7)G cap-containing spliced leader is a developing theme in the lower eukaryotic world; organisms as diverse as EUGLENA: and nematode worms, including Caenorhabditis elegans, utilize SL RNA in their mRNA maturation programs. Towards understanding the coordination of SL RNA and mRNA expression in trypanosomes, we have begun by characterizing SL RNA gene expression in the model trypanosome Leptomonas seymouri. Using a homologous in vitro transcription system, we demonstrate in this study that the SL RNA is transcribed by RNA polymerase II. During SL RNA transcription, accurate initiation is determined by an initiator element with a loose consensus of CYAC/AYR(+1). This element, as well as two additional basal promoter elements, is divergent in sequence from the basal transcription elements seen in other eukaryotic gene promoters. We show here that the in vitro transcription extract contains a binding activity that is specific for the initiator element and thus may participate in recruiting RNA polymerase II to the SL RNA gene promoter.}, pmid = {11266558}, keywords = {Amino Acid,Amino Acid Sequence,Animals,Base Sequence,Binding Sites,Binding Sites: genetics,Binding Sites: immunology,Blotting,DNA,Genetic,Genetic: genetics,Molecular Sequence Data,nosource,Precipitin Tests,Promoter Regions,Protein Binding,Protein Subunits,Protozoan,Protozoan: chemistry,Protozoan: genetics,Protozoan: metabolism,Recombinant,Recombinant: genetics,Recombinant: metabolism,RNA,RNA Polymerase II,RNA Polymerase II: chemistry,RNA Polymerase II: genetics,RNA Polymerase II: metabolism,Sequence Analysis,Sequence Homology,Small Nuclear,Small Nuclear: genetics,Spliced Leader,Spliced Leader: genetics,Transcription,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosomatina,Trypanosomatina: enzymology,Trypanosomatina: genetics,Western} }

@article{bralyIsolationKinetoplastMitochondrial1974, title = {Isolation of {{Kinetoplast}}-{{Mitochondrial Complexes}} from {{Leishmania}} Tarentolae*}, author = {BRALY, P.}, year = 1974, journal = {Journal of Eukaryotic }, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1550-7408.1974.tb03752.x/full}, keywords = {nosource} }

@article{panigrahiComprehensiveAnalysisTrypanosoma2009, title = {A Comprehensive Analysis of {{Trypanosoma}} Brucei Mitochondrial Proteome}, author = {Panigrahi, A. K. and Ogata, Yuko and Z{'i}kov{'a}, Alena}, year = 2009, journal = {Proteomics}, volume = {9}, number = {2}, pages = {434–450}, doi = {10.1002/pmic.200800477.A}, url = {http://onlinelibrary.wiley.com/doi/10.1002/pmic.200800477/full}, isbn = {2062567316}, keywords = {database,mass spectrometry,mitochondrion,nosource,organelle fractionation,proteomics} }

@article{maslovMitochondrialTranslationTrypanosomatids2012, title = {Mitochondrial Translation in Trypanosomatids}, author = {Maslov, D. A. and Agrawal, R. K.}, editor = {Bindereif, Albrecht}, year = 2012, journal = {RNA Metabolism in Trypanosomes}, volume = {28}, pages = {215–236}, publisher = {Springer Berlin Heidelberg}, doi = {10.1007/978-3-642-28687-2}, url = {http://www.springerlink.com/index/10.1007/978-3-642-28687-2 http://link.springer.com/10.1007/978-3-642-28687-2_10}, isbn = {978-3-642-28686-5}, keywords = {nosource} }

@article{suzukiProteomicAnalysisMammalian2001, title = {Proteomic Analysis of the Mammalian Mitochondrial Ribosome. {{Identification}} of Protein Components in the 28 {{S}} Small Subunit.}, author = {Suzuki, T. and Terasaki, M. and {Takemoto-Hori}, C. and Hanada, T. and Ueda, T. and Wada, a and Watanabe, K.}, year = 2001, month = aug, journal = {The Journal of biological chemistry}, volume = {276}, number = {35}, eprint = {11402041}, eprinttype = {pubmed}, pages = {33181–95}, issn = {0021-9258}, doi = {10.1074/jbc.M103236200}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11402041}, abstract = {The mammalian mitochondrial ribosome (mitoribosome) has a highly protein-rich composition with a small sedimentation coefficient of 55 S, consisting of 39 S large and 28 S small subunits. In the previous study, we analyzed 39 S large subunit proteins from bovine mitoribosome (Suzuki, T., Terasaki, M., Takemoto-Hori, C., Hanada, T., Ueda, T., Wada, A., and Watanabe, K. (2001) J. Biol. Chem. 276, 21724-21736). The results suggested structural compensation for the rRNA deficit through proteins of increased molecular mass in the mitoribosome. We report here the identification of 28 S small subunit proteins. Each protein was separated by radical-free high-reducing two-dimensional polyacrylamide gel electrophoresis and analyzed by liquid chromatography/mass spectrometry/mass spectrometry using electrospray ionization/ion trap mass spectrometer to identify cDNA sequence by expressed sequence tag data base searches in silico. Twenty one proteins from the small subunit were identified, including 11 new proteins along with their complete cDNA sequences from human and mouse. In addition to these proteins, three new proteins were also identified in the 55 S mitoribosome. We have clearly identified a mitochondrial homologue of S12, which is a key regulatory protein of translation fidelity and a candidate for the autosomal dominant deafness gene, DFNA4. The apoptosis-related protein DAP3 was found to be a component of the small subunit, indicating a new function for the mitoribosome in programmed cell death. In summary, we have mapped a total of 55 proteins from the 55 S mitoribosome on the two-dimensional polyacrylamide gels.}, pmid = {11402041}, keywords = {Amino Acid Sequence,Animals,Bacteria,Bacteria: genetics,Caenorhabditis elegans,Caenorhabditis elegans: genetics,Cattle,Chromatography,Complementary,DNA,Drosophila melanogaster,Drosophila melanogaster: genetics,Humans,Liquid,Liver,Liver: chemistry,Liver: genetics,Mammals,Mass Spectrometry,Mice,Mitochondria,Models,Molecular,Molecular Sequence Data,Molecular Weight,nosource,Peptide Fragments,Peptide Fragments: chemistry,Phylogeny,Protein Structure,Proteome,Proteome: chemistry,Recombinant Proteins,Recombinant Proteins: chemistry,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: genetics,Ribosomal Proteins: isolation & purification,Ribosomes,Ribosomes: chemistry,Ribosomes: genetics,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Secondary} }

@article{campbellTranscriptionKinetoplastidProtozoa2003, title = {Transcription in Kinetoplastid Protozoa: Why Be Normal?}, author = {{}a Campbell, David and Thomas, Sean and Sturm, Nancy R.}, year = 2003, month = nov, journal = {Microbes and Infection}, volume = {5}, number = {13}, pages = {1231–1240}, issn = {12864579}, doi = {10.1016/j.micinf.2003.09.005}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1286457903002375}, keywords = {leishmania,nosource,polycistronic,promoter,trans splicing,transcription factor,trypanosoma} }

@article{bushnellStructuralBasisTranscription2002, title = {Structural Basis of Transcription: Alpha-Amanitin-{{RNA}} Polymerase {{II}} Cocrystal at 2.8 {{A}} Resolution.}, author = {{}a Bushnell, David and Cramer, Patrick and Kornberg, Roger D.}, year = 2002, month = feb, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {3}, pages = {1218–22}, issn = {0027-8424}, doi = {10.1073/pnas.251664698}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=122170&tool=pmcentrez&rendertype=abstract}, abstract = {The structure of RNA polymerase II in a complex with the inhibitor alpha-amanitin has been determined by x-ray crystallography. The structure of the complex indicates the likely basis of inhibition and gives unexpected insight into the transcription mechanism.}, pmid = {11805306}, keywords = {Amanitins,Amanitins: chemistry,Amino Acid Sequence,Animals,Binding Sites,Crystallography,Genetic,Hydrogen Bonding,Models,Molecular,nosource,Protein Conformation,Protein Structure,RNA Polymerase II,RNA Polymerase II: chemistry,Secondary,Transcription,X-Ray,X-Ray: methods} }

@article{jinekCoupled5Nucleotide2011, title = {Coupled 5’ Nucleotide Recognition and Processivity in {{Xrn1-mediated mRNA}} Decay.}, author = {Jinek, Martin and Coyle, Scott M. and {}a Doudna, Jennifer}, year = 2011, month = mar, journal = {Molecular cell}, volume = {41}, number = {5}, pages = {600–8}, publisher = {Elsevier Inc.}, issn = {1097-4164}, doi = {10.1016/j.molcel.2011.02.004}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3090138&tool=pmcentrez&rendertype=abstract}, abstract = {Messenger RNA decay plays a central role in the regulation and surveillance of eukaryotic gene expression. The conserved multidomain exoribonuclease Xrn1 targets cytoplasmic RNA substrates marked by a 5’ monophosphate for processive 5’-to-3’ degradation by an unknown mechanism. Here, we report the crystal structure of an Xrn1-substrate complex. The single-stranded substrate is held in place by stacking of the 5’-terminal trinucleotide between aromatic side chains while a highly basic pocket specifically recognizes the 5’ phosphate. Mutations of residues involved in binding the 5’-terminal nucleotide impair Xrn1 processivity. The substrate recognition mechanism allows Xrn1 to couple processive hydrolysis to duplex melting in RNA substrates with sufficiently long single-stranded 5’ overhangs. The Xrn1-substrate complex structure thus rationalizes the exclusive specificity of Xrn1 for 5’-monophosphorylated substrates, ensuring fidelity of mRNA turnover, and posits a model for translocation-coupled unwinding of structured RNA substrates.}, pmid = {21362555}, keywords = {Animals,Catalysis,Drosophila melanogaster,Drosophila Proteins,Drosophila Proteins: genetics,Exoribonucleases,Exoribonucleases: genetics,Hydrolysis,Magnesium,Magnesium: chemistry,Messenger,Messenger: metabolism,Mutation,nosource,Nucleic Acid Conformation,Nucleotides,Nucleotides: genetics,Phosphates,Phosphates: chemistry,Phosphorylation,Protein Conformation,Protein Structure,RNA,Tertiary} }

@article{haileDevelopmentalRegulationGene2007, title = {Developmental Regulation of Gene Expression in Trypanosomatid Parasitic Protozoa.}, author = {Haile, Simon and Papadopoulou, Barbara}, year = 2007, month = dec, journal = {Current opinion in microbiology}, volume = {10}, number = {6}, eprint = {18177626}, eprinttype = {pubmed}, pages = {569–77}, issn = {1369-5274}, doi = {10.1016/j.mib.2007.10.001}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18177626}, abstract = {Kinetoplastids branched early from the eukaryotic lineage and include several parasitic protozoan species. Up to several hundred kinetoplastid genes are co-transcribed into polycistronic RNAs and individual mRNAs are resolved by coupled co-transcriptional trans-splicing of a universal splice-leader RNA (SL-RNA) and 3’-end maturation processes. Protein-coding genes lack RNA polymerase II promoters. Consequently, most of gene regulation in these organisms occurs post-transcriptionally. Over the last few years, many more genes that are regulated at the mRNA stability level and a few at the translation level have been reported. Almost all major trypanosome homologues of yeast/mammalian mRNA degradation enzymes have been functionally characterized and major pathways identified. Novel paradigms have also recently emerged: regulated post-transcriptional processing of cytoplasmic RNAs, SL-RNA transcriptional silencing-mediated global stress response, and Leishmania-specific large-scale modulation of post-transcriptional gene expression via inactive degenerated retroelements. Several of these developments have greatly benefited from the recently completed genomic sequences and functional genomic studies.}, pmid = {18177626}, keywords = {Animals,Developmental,Gene Expression Regulation,Messenger,Messenger: genetics,Messenger: metabolism,nosource,Post-Transcriptional,Protozoan,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Protozoan: genetics,Protozoan: metabolism,RNA,RNA Processing,Trypanosomatina,Trypanosomatina: genetics,Trypanosomatina: growth & development,Trypanosomatina: metabolism} }

@article{ridlonImportance45SRibosomal2013, title = {The {{Importance}} of the {{45S Ribosomal Small Subunit-related Complex}} for {{Mitochondrial Translation}} in {{Trypanosoma}} Brucei.}, author = {Ridlon, Lucie and Skodova, Ingrid and Pan, Songqin and Lukes, Julius and {}a Maslov, Dmitri}, year = 2013, month = oct, journal = {The Journal of biological chemistry}, eprint = {24089529}, eprinttype = {pubmed}, issn = {1083-351X}, doi = {10.1074/jbc.M113.501874}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24089529}, abstract = {The mitochondrial 45S SSU* complex in Trypanosoma brucei contains the 9S SSU ribosomal RNA, a set of SSU ribosomal proteins, several pentatricopeptide repeat (PPR) proteins, and proteins not typically found in ribosomes, including rhodanese-domain protein (Rhod) and a 200 kDa coiled-coil protein. To investigate the function of this complex, PPR29, Rhod, 200 kDa proteins and mitochondrial ribosomal protein S17 were knocked-down by RNAi in procyclic T. brucei. A growth retardation phenotype, a reduction in the amount of the 45S SSU* complexes, and the preferential inhibition of synthesis of the cytochrome c oxidase subunit I (COI) over cytochrome b (Cyb) were observed as early as day 2 post induction of RNAi. On the contrary, the down-regulation of mitochondrial ribosomal protein L3 drastically reduced the amount of the large subunit and indiscriminately inhibited mitochondrial translation. The relative amount of translation-competent, long poly(AU)-tailed COI and edited Cyb mRNAs were selectively reduced by ablation of the 45S SSU* complex. The formation of the 80S translation complexes, identified by association of the long-tailed mRNAs with the mitoribosomes, was also disrupted. On the other hand, the relative amount of long-tailed edited RPS12 mRNA was not substantially affected, and there was no noticeable effect on the RPS12 translation complexes. In bloodstream trypanosomes the amount of the 45S complexes was drastically reduced compared to procyclics. We propose that the 45S SSU* complex represents a factor required for normal mitochondrial translation that may have selective effects on different mRNAs.}, pmid = {24089529}, keywords = {45s complex,kinetoplast,mitochondrial ribosome,mitochondrial translation,nosource,ssu} }

@article{laughreaSpeedaccuracyRelationshipsVitro1981, title = {Speed-Accuracy Relationships during in Vitro and in Vivo Protein Biosynthesis.}, author = {Laughrea, M.}, year = 1981, month = mar, journal = {Biochimie}, volume = {63}, number = {3}, eprint = {7013826}, eprinttype = {pubmed}, pages = {145–68}, issn = {0300-9084}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7013826}, abstract = {Poly U-directed incorporation of phenylalanine and leucine into polypeptide has been described in at least 50 papers since 1961. In general, high translation activities are associated with high accuracies, and vice-versa. Moreover, a vast body of independent experimental data (effect of ethanol, temperature, urea, aminoglycosides, etc… on protein synthesis) put together here suggests that, in many circumstances, speed and accuracy of elongation are correlated. This result is to be contrasted with the view that the speed and the fidelity of protein synthesis are two opposing parameters. In this report, recent experimental data on the nature and effect of ribosomal ambiguity (ram) and streptomycin resistance (Strr) mutations are reexamined. Models on the action of streptomycin and other misreading-inducing antibiotics, as well as long-standing ideas on the control of misreading in mammalian systems are critically evaluated. An explanation is provided for the long-befuddling data on the action of gentamicin.}, pmid = {7013826}, keywords = {Animals,Anti-Bacterial Agents,Anti-Bacterial Agents: pharmacology,Kinetics,Leucine,Leucine: genetics,Magnesium,Magnesium: pharmacology,Mutation,nosource,Peptide Chain Elongation,Phenylalanine,Phenylalanine: genetics,Poly U,Poly U: metabolism,Protein Biosynthesis,Protein Biosynthesis: drug effects,Ribosomal Proteins,Ribosomal Proteins: genetics,Streptomycin,Streptomycin: pharmacology,Translational,Translational: drug effe} }

@phdthesis{rhodinRibosomalProteinL112011, title = {Ribosomal Protein {{L11}}: A Cog in the Nanomachine ({{Doctoral}} Dissertation)}, author = {Rhodin, Michael H. J.}, year = 2011, school = {University of Maryland College Park}, keywords = {nosource} }

@article{lawVoomPrecisionWeights2013, title = {Voom! {{Precision}} Weights Unlock Linear Model Analysis Tools for {{RNA-seq}} Read Counts}, author = {Law, C. W. and Chen, Yunshun and Shi, W. and Smyth, G. K.}, year = 2013, journal = {Genome Biology}, volume = {15}, number = {2}, pages = {1–30}, doi = {10.1186/gb-2014-15-2-r29}, url = {http://www.statsci.org/smyth/pubs/VoomPreprint.pdf}, keywords = {nosource} }

@article{lopez-romeroProcessingAgilentMicroRNA2010, title = {Processing of {{Agilent microRNA}} Array Data.}, author = {{L{'o}pez-Romero}, Pedro and {}a Gonz{'a}lez, Manuel and Callejas, Sergio and Dopazo, Ana and {}a Irizarry, Rafael}, year = 2010, month = jan, journal = {BMC research notes}, volume = {3}, pages = {18}, issn = {1756-0500}, doi = {10.1186/1756-0500-3-18}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2823597&tool=pmcentrez&rendertype=abstract}, abstract = {BACKGROUND: The Agilent microRNA microarray platform interrogates each microRNA with several copies of distinct oligonucleotide probes and integrates the results into a total gene signal (TGS), using a proprietary algorithm that makes use of the background subtracted signal. The TGS can be normalized between arrays, and the Agilent recommendation is either not to normalize or to normalize to the 75th percentile signal intensity. The robust multiarray average algorithm (RMA) is an alternative method, originally developed to obtain a summary measure of mRNA Affymetrix gene expression arrays by using a linear model that takes into account the probe affinity effect. The RMA method has been shown to improve the accuracy and precision of expression measurements relative to other competing methods. There is also evidence that it might be preferable to use non-corrected signals for the processing of microRNA data, rather than background-corrected signals. In this study we assess the use of the RMA method to obtain a summarized microRNA signal for the Agilent arrays. FINDINGS: We have adapted the RMA method to obtain a processed signal for the Agilent arrays and have compared the RMA summarized signal to the TGS generated with the image analysis software provided by the vendor. We also compared the use of the RMA algorithm with uncorrected and background-corrected signals, and compared quantile normalization with the normalization method recommended by the vendor. The pre-processing methods were compared in terms of their ability to reduce the variability (increase precision) of the signals between biological replicates. Application of the RMA method to non-background corrected signals produced more precise signals than either the RMA-background-corrected signal or the quantile-normalized Agilent TGS. The Agilent TGS normalized to the 75% percentile showed more variation than the other measures. CONCLUSIONS: Used without background correction, a summarized signal that takes into account the probe effect might provide a more precise estimate of microRNA expression. The variability of quantile normalization was lower compared with the normalization method recommended by the vendor.}, pmid = {20205787}, keywords = {nosource} }

@article{dejesusBayesianAnalysisGene2013, title = {Bayesian Analysis of Gene Essentiality Based on Sequencing of Transposon Insertion Libraries.}, author = {{}a DeJesus, Michael and Zhang, Yanjia J. and Sassetti, Christopher M. and Rubin, Eric J. and Sacchettini, James C. and Ioerger, Thomas R.}, year = 2013, month = mar, journal = {Bioinformatics (Oxford, England)}, volume = {29}, number = {6}, eprint = {23361328}, eprinttype = {pubmed}, pages = {695–703}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btt043}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23361328}, abstract = {MOTIVATION: Next-generation sequencing affords an efficient analysis of transposon insertion libraries, which can be used to identify essential genes in bacteria. To analyse this high-resolution data, we present a formal Bayesian framework for estimating the posterior probability of essentiality for each gene, using the extreme-value distribution to characterize the statistical significance of the longest region lacking insertions within a gene. We describe a sampling procedure based on the Metropolis-Hastings algorithm to calculate posterior probabilities of essentiality while simultaneously integrating over unknown internal parameters. RESULTS: Using a sequence dataset from a transposon library for Mycobacterium tuberculosis, we show that this Bayesian approach predicts essential genes that correspond well with genes shown to be essential in previous studies. Furthermore, we show that by using the extreme-value distribution to characterize genomic regions lacking transposon insertions, this method is capable of identifying essential domains within genes. This approach can be used for analysing transposon libraries in other organisms and augmenting essentiality predictions with statistical confidence scores.}, pmid = {23361328}, keywords = {nosource} }

@article{bladesEstimatingNumberEssential2002, title = {Estimating the Number of Essential Genes in a Genome by Random Transposon Mutagenesis}, author = {Blades, N. J. and Broman, K. W.}, year = 2002, journal = {Technical Reports}, url = {http://biostats.bepress.com/jhubiostat/paper15/}, keywords = {nosource} }

@article{langridgeSimultaneousAssayEvery2009, title = {Simultaneous Assay of Every {{Salmonella Typhi}} Gene Using One Million Transposon Mutants.}, author = {Langridge, Gemma C. and Phan, Minh-Duy and Turner, Daniel J. and Perkins, Timothy T. and Parts, Leopold and Haase, Jana and Charles, Ian and Maskell, Duncan J. and Peters, Sarah E. and Dougan, Gordon and Wain, John and Parkhill, Julian and Turner, a Keith}, year = 2009, month = dec, journal = {Genome research}, volume = {19}, number = {12}, pages = {2308–16}, issn = {1549-5469}, doi = {10.1101/gr.097097.109}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2792183&tool=pmcentrez&rendertype=abstract}, abstract = {Very high-throughput sequencing technologies need to be matched by high-throughput functional studies if we are to make full use of the current explosion in genome sequences. We have generated a very large bacterial mutant pool, consisting of an estimated 1.1 million transposon mutants and we have used genomic DNA from this mutant pool, and Illumina nucleotide sequencing to prime from the transposon and sequence into the adjacent target DNA. With this method, which we have called TraDIS (transposon directed insertion-site sequencing), we have been able to map 370,000 unique transposon insertion sites to the Salmonella enterica serovar Typhi chromosome. The unprecedented density and resolution of mapped insertion sites, an average of one every 13 base pairs, has allowed us to assay simultaneously every gene in the genome for essentiality and generate a genome-wide list of candidate essential genes. In addition, the semiquantitative nature of the assay allowed us to identify genes that are advantageous and those that are disadvantageous for growth under standard laboratory conditions. Comparison of the mutant pool following growth in the presence or absence of ox bile enabled every gene to be assayed for its contribution toward bile tolerance, a trait required of any enteric bacterium and for carriage of S. Typhi in the gall bladder. This screen validated our hypothesis that we can simultaneously assay every gene in the genome to identify niche-specific essential genes.}, pmid = {19826075}, keywords = {Bacterial,Bacterial Proteins,Bacterial Proteins: genetics,Bacterial: genetics,Bile,Bile: physiology,Chromosome Mapping,Chromosomes,Computational Biology,Computational Biology: methods,DNA,DNA Transposable Elements,DNA Transposable Elements: genetics,Essential,Genes,Insertional,Mutagenesis,Mutation,nosource,Salmonella typhi,Salmonella typhi: drug effects,Salmonella typhi: genetics,Salmonella typhi: growth & development,Sequence Analysis} }

@article{narlaRibosomopathiesHumanDisorders2010, title = {Ribosomopathies: Human Disorders of Ribosome Dysfunction.}, author = {Narla, Anupama and Ebert, Benjamin L.}, year = 2010, month = apr, journal = {Blood}, volume = {115}, number = {16}, pages = {3196–205}, issn = {1528-0020}, doi = {10.1182/blood-2009-10-178129}, abstract = {Ribosomopathies compose a collection of disorders in which genetic abnormalities cause impaired ribosome biogenesis and function, resulting in specific clinical phenotypes. Congenital mutations in RPS19 and other genes encoding ribosomal proteins cause Diamond-Blackfan anemia, a disorder characterized by hypoplastic, macrocytic anemia. Mutations in other genes required for normal ribosome biogenesis have been implicated in other rare congenital syndromes, Schwachman-Diamond syndrome, dyskeratosis congenita, cartilage hair hypoplasia, and Treacher Collins syndrome. In addition, the 5q- syndrome, a subtype of myelodysplastic syndrome, is caused by a somatically acquired deletion of chromosome 5q, which leads to haploinsufficiency of the ribosomal protein RPS14 and an erythroid phenotype highly similar to Diamond-Blackfan anemia. Acquired abnormalities in ribosome function have been implicated more broadly in human malignancies. The p53 pathway provides a surveillance mechanism for protein translation as well as genome integrity and is activated by defects in ribosome biogenesis; this pathway appears to be a critical mediator of many of the clinical features of ribosomopathies. Elucidation of the mechanisms whereby selective abnormalities in ribosome biogenesis cause specific clinical syndromes will hopefully lead to novel therapeutic strategies for these diseases.}, pmid = {20194897}, keywords = {Genetic Diseases,Humans,Inborn,nosource,Ribosomes,Ribosomes: genetics,Ribosomes: metabolism,Ribosomes: pathology,Syndrome} }

@article{robertsonTelMarinerSuperfamily1995, title = {The {{Tel}} -Mariner {{Superfamily}} of {{Transposons}} in {{Animals}}}, author = {Robertson, M.}, year = 1995, journal = {J. Insect Physiol.}, volume = {41}, number = {2}, pages = {99–105}, keywords = {nosource} } % == BibTeX quality report for robertsonTelMarinerSuperfamily1995: % ? Possibly abbreviated journal title J. Insect Physiol.

@article{gazdaRibosomalProteinL52008, title = {Ribosomal Protein {{L5}} and {{L11}} Mutations Are Associated with Cleft Palate and Abnormal Thumbs in {{Diamond-Blackfan}} Anemia Patients.}, author = {Gazda, Hanna T. and Sheen, Mee Rie and Vlachos, Adrianna and Choesmel, Valerie and O’Donohue, Marie-Fran{}oise and Schneider, Hal and Darras, Natasha and Hasman, Catherine and Sieff, Colin A. and Newburger, Peter E. and Ball, Sarah E. and Niewiadomska, Edyta and Matysiak, Michal and Zaucha, Jan M. and Glader, Bertil and Niemeyer, Charlotte and Meerpohl, Joerg J. and Atsidaftos, Eva and Lipton, Jeffrey M. and Gleizes, Pierre-Emmanuel and Beggs, Alan H.}, year = 2008, month = dec, journal = {Am. J. Hum. Gen.}, volume = {83}, number = {6}, pages = {769–80}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2008.11.004}, abstract = {Diamond-Blackfan anemia (DBA), a congenital bone-marrow-failure syndrome, is characterized by red blood cell aplasia, macrocytic anemia, clinical heterogeneity, and increased risk of malignancy. Although anemia is the most prominent feature of DBA, the disease is also characterized by growth retardation and congenital anomalies that are present in approximately 30%-50% of patients. The disease has been associated with mutations in four ribosomal protein (RP) genes, RPS19, RPS24, RPS17, and RPL35A, in about 30% of patients. However, the genetic basis of the remaining 70% of cases is still unknown. Here, we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes, RPL5, RPL11, and RPS7. In addition, we identified rare variants of unknown significance in three other genes, RPL36, RPS15, and RPS27A. Remarkably, careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities, including craniofacial, thumb, and heart anomalies, whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11. We also demonstrate that mutations of RPL5, RPL11, or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway, expanding the repertoire of ribosomal RNA processing defects associated with DBA.}, pmid = {19061985}, keywords = {Anemia,Cleft Palate,Cleft Palate: genetics,Diamond-Blackfan,Diamond-Blackfan: genetics,Humans,Large,Large: genetics,Mutation,nosource,Ribosomal Proteins,Ribosomal Proteins: genetics,Ribosome Subunits,Small,Small: genetics,Thumb,Thumb: abnormalities} } % == BibTeX quality report for gazdaRibosomalProteinL52008: % ? Possibly abbreviated journal title Am. J. Hum. Gen.

@article{boriaRibosomalBasisDiamondBlackfan2010, title = {The Ribosomal Basis of {{Diamond-Blackfan Anemia}}: Mutation and Database Update.}, author = {Boria, Ilenia and Garelli, Emanuela and Gazda, Hanna T. and Aspesi, Anna and Quarello, Paola and Pavesi, Elisa and Ferrante, Daniela and Meerpohl, Joerg J. and Kartal, Mutlu and Costa, Lydie Da and Proust, Alexis and Leblanc, Thierry and Simansour, Maud and Dahl, Niklas and Fr{"o}jmark, Anne-Sophie and Pospisilova, Dagmar and Cmejla, Radek and Beggs, Alan H. and Sheen, Mee R. and Landowski, Michael and Buros, Christopher M. and Clinton, Catherine M. and Dobson, Lori J. and Vlachos, Adrianna and Atsidaftos, Eva and Lipton, Jeffrey M. and Ellis, Steven R. and Ramenghi, Ugo and Dianzani, Irma}, year = 2010, month = dec, journal = {Hum. Mut.}, volume = {31}, number = {12}, eprint = {20960466}, eprinttype = {pubmed}, pages = {1269–79}, issn = {1098-1004}, doi = {10.1002/humu.21383}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20960466}, abstract = {Diamond-Blackfan Anemia (DBA) is characterized by a defect of erythroid progenitors and, clinically, by anemia and malformations. DBA exhibits an autosomal dominant pattern of inheritance with incomplete penetrance. Currently nine genes, all encoding ribosomal proteins (RP), have been found mutated in approximately 50% of patients. Experimental evidence supports the hypothesis that DBA is primarily the result of defective ribosome synthesis. By means of a large collaboration among six centers, we report here a mutation update that includes nine genes and 220 distinct mutations, 56 of which are new. The DBA Mutation Database now includes data from 355 patients. Of those where inheritance has been examined, 125 patients carry a de novo mutation and 72 an inherited mutation. Mutagenesis may be ascribed to slippage in 65.5% of indels, whereas CpG dinucleotides are involved in 23% of transitions. Using bioinformatic tools we show that gene conversion mechanism is not common in RP genes mutagenesis, notwithstanding the abundance of RP pseudogenes. Genotype-phenotype analysis reveals that malformations are more frequently associated with mutations in RPL5 and RPL11 than in the other genes. All currently reported DBA mutations together with their functional and clinical data are included in the DBA Mutation Database.}, pmid = {20960466}, keywords = {Anemia,Base Sequence,Databases,Diamond-Blackfan,Diamond-Blackfan: diagnosis,Diamond-Blackfan: genetics,Genetic,Genetic Association Studies,Humans,Molecular Sequence Data,Mutagenesis,Mutagenesis: genetics,Mutation,Mutation: genetics,nosource,Ribosomal Proteins,Ribosomal Proteins: genetics,Ribosomes,Ribosomes: genetics} } % == BibTeX quality report for boriaRibosomalBasisDiamondBlackfan2010: % ? Possibly abbreviated journal title Hum. Mut.

@article{xueSpecializedRibosomesNew2012, title = {Specialized Ribosomes: A New Frontier in Gene Regulation and Organismal Biology.}, author = {Xue, Shifeng and Barna, Maria}, year = 2012, month = jun, journal = {Nat. Rev. Mol. Cell. Biol.}, volume = {13}, number = {6}, pages = {355–69}, issn = {1471-0080}, doi = {10.1038/nrm3359}, abstract = {Historically, the ribosome has been viewed as a complex ribozyme with constitutive rather than intrinsic regulatory capacity in mRNA translation. However, emerging studies reveal that ribosome activity may be highly regulated. Heterogeneity in ribosome composition resulting from differential expression and post-translational modifications of ribosomal proteins, ribosomal RNA (rRNA) diversity and the activity of ribosome-associated factors may generate ‘specialized ribosomes’ that have a substantial impact on how the genomic template is translated into functional proteins. Moreover, constitutive components of the ribosome may also exert more specialized activities by virtue of their interactions with specific mRNA regulatory elements such as internal ribosome entry sites (IRESs) or upstream open reading frames (uORFs). Here we discuss the hypothesis that intrinsic regulation by the ribosome acts to selectively translate subsets of mRNAs harbouring unique cis-regulatory elements, thereby introducing an additional level of regulation in gene expression and the life of an organism.}, pmid = {22617470}, keywords = {Animals,Biological,Cell Biology,Gene Expression Regulation,Humans,Messenger,Messenger: genetics,Messenger: metabolism,Models,nosource,Ribosomes,Ribosomes: metabolism,RNA} } % == BibTeX quality report for xueSpecializedRibosomesNew2012: % ? Possibly abbreviated journal title Nat. Rev. Mol. Cell. Biol.

@article{goodmanIdentifyingGeneticDeterminants2009, title = {Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat.}, author = {Goodman, Andrew L. and McNulty, Nathan P. and Zhao, Yue and Leip, Douglas and Mitra, Robi D. and {}a Lozupone, Catherine and Knight, Rob and Gordon, Jeffrey I.}, year = 2009, month = sep, journal = {Cell host & microbe}, volume = {6}, number = {3}, pages = {279–89}, publisher = {Elsevier Ltd}, issn = {1934-6069}, doi = {10.1016/j.chom.2009.08.003}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2895552&tool=pmcentrez&rendertype=abstract}, abstract = {The human gut microbiota is a metabolic organ whose cellular composition is determined by a dynamic process of selection and competition. To identify microbial genes required for establishment of human symbionts in the gut, we developed an approach (insertion sequencing, or INSeq) based on a mutagenic transposon that allows capture of adjacent chromosomal DNA to define its genomic location. We used massively parallel sequencing to monitor the relative abundance of tens of thousands of transposon mutants of a saccharolytic human gut bacterium, Bacteroides thetaiotaomicron, as they established themselves in wild-type and immunodeficient gnotobiotic mice, in the presence or absence of other human gut commensals. In vivo selection transforms this population, revealing functions necessary for survival in the gut: we show how this selection is influenced by community composition and competition for nutrients (vitamin B(12)). INSeq provides a broadly applicable platform to explore microbial adaptation to the gut and other ecosystems.}, pmid = {19748469}, keywords = {Animals,Bacteroides,Bacteroides: classification,Bacteroides: genetics,Bacteroides: physiology,Gastrointestinal Tract,Gastrointestinal Tract: microbiology,Gastrointestinal Tract: physiology,Germ-Free Life,Humans,Mice,nosource,Phylogeny,Symbiosis} }

@article{goodmanIdentifyingMicrobialFitness2011, title = {Identifying Microbial Fitness Determinants by Insertion Sequencing Using Genome-Wide Transposon Mutant Libraries.}, author = {Goodman, Andrew L. and Wu, Meng and Gordon, Jeffrey I.}, year = 2011, month = dec, journal = {Nature protocols}, volume = {6}, number = {12}, pages = {1969–80}, publisher = {Nature Publishing Group}, issn = {1750-2799}, doi = {10.1038/nprot.2011.417}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3310428&tool=pmcentrez&rendertype=abstract}, abstract = {Insertion sequencing (INSeq) is a method for determining the insertion site and relative abundance of large numbers of transposon mutants in a mixed population of isogenic mutants of a sequenced microbial species. INSeq is based on a modified mariner transposon containing MmeI sites at its ends, allowing cleavage at chromosomal sites 16-17 bp from the inserted transposon. Genomic regions adjacent to the transposons are amplified by linear PCR with a biotinylated primer. Products are bound to magnetic beads, digested with MmeI and barcoded with sample-specific linkers appended to each restriction fragment. After limited PCR amplification, fragments are sequenced using a high-throughput instrument. The sequence of each read can be used to map the location of a transposon in the genome. Read count measures the relative abundance of that mutant in the population. Solid-phase library preparation makes this protocol rapid (18 h), easy to scale up, amenable to automation and useful for a variety of samples. A protocol for characterizing libraries of transposon mutant strains clonally arrayed in a multiwell format is provided.}, pmid = {22094732}, keywords = {Bacterial,Bacterial: chemistry,DNA,DNA Transposable Elements,DNA Transposable Elements: genetics,DNA: methods,Gene Library,Insertional,Mutagenesis,Mutation,nosource,Polymerase Chain Reaction,Sequence Analysis} }

@article{shinIdentificationNovelVirulence2006, title = {Identification of Novel Virulence Determinants in {{Mycobacterium}} Paratuberculosis by Screening a Library of Insertional Mutants.}, author = {Shin, Sung Jae and Wu, Chia-Wei and Steinberg, Howard and Talaat, Adel M.}, year = 2006, month = jul, journal = {Infection and immunity}, volume = {74}, number = {7}, pages = {3825–33}, issn = {0019-9567}, doi = {10.1128/IAI.01742-05}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1489745&tool=pmcentrez&rendertype=abstract}, abstract = {Johne’s disease, caused by Mycobacterium paratuberculosis infection, is a worldwide problem for the dairy industry and has a possible involvement in Crohn’s disease in humans. To identify virulence determinants of this economically important pathogen, a library of 5,060 transposon mutants was constructed using Tn5367 insertion mutagenesis, followed by large-scale sequencing to identify disrupted genes. In this report, 1,150 mutants were analyzed and 970 unique insertion sites were identified. Sequence analysis of the disrupted genes indicated that the insertion of Tn5367 was more prevalent in genomic regions with G+C content (50.5 to 60.5%) lower than the average G+C content (69.3%) of the rest of the genome. Phenotypic screening of the library identified disruptions of genes involved in iron, tryptophan, or mycolic acid metabolic pathways that displayed unique growth characteristics. Bioinformatic analysis of disrupted genes identified a list of potential virulence determinants for further testing with animals. Mouse infection studies showed a significant decrease in tissue colonization by mutants with a disruption in the gcpE, pstA, kdpC, papA2, impA, umaA1, or fabG2_2 gene. Attenuation phenotypes were tissue specific (e.g., for the umaA1 mutant) as well as time specific (e.g., for the impA mutant), suggesting that those genes may be involved in different virulence mechanisms. The identified potential virulence determinants represent novel functional classes that could be necessary for mycobacterial survival during infection and could provide suitable targets for vaccine and drug development against Johne’s and Crohn’s diseases.}, pmid = {16790754}, keywords = {Animals,Gene Library,Inbred BALB C,Insertional,Mice,Mutagenesis,Mycobacterium avium subsp. paratuberculosis,Mycobacterium avium subsp. paratuberculosis: genet,Mycobacterium avium subsp. paratuberculosis: patho,nosource,Paratuberculosis,Paratuberculosis: immunology,Paratuberculosis: microbiology,Paratuberculosis: pathology,Virulence Factors,Virulence Factors: genetics,Virulence Factors: immunology} }

@article{scherensUsesGenomewideYeast2004, title = {The Uses of Genome-Wide Yeast Mutant Collections.}, author = {Scherens, Bart and Goffeau, Andre}, year = 2004, month = jan, journal = {Genome biology}, volume = {5}, number = {7}, pages = {229}, issn = {1465-6914}, doi = {10.1186/gb-2004-5-7-229}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=463272&tool=pmcentrez&rendertype=abstract}, abstract = {We assess five years of usage of the major genome-wide collections of mutants from Saccharomyces cerevisiae: single deletion mutants, double mutants conferring ‘synthetic’ lethality and the ‘TRIPLES’ collection of mutants obtained by random transposon insertion. Over 100 experimental conditions have been tested and more than 5,000 novel phenotypic traits have been assigned to yeast genes using these collections.}, pmid = {15239820}, keywords = {Fungal,Genetics,Genetics: trends,Genome,Humans,Mutation,Mutation: genetics,nosource,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics} }

@article{gawronskiTrackingInsertionMutants2009, title = {Tracking Insertion Mutants within Libraries by Deep Sequencing and a Genome-Wide Screen for {{Haemophilus}} Genes Required in the Lung.}, author = {Gawronski, Jeffrey D. and Wong, Sandy M. S. and Giannoukos, Georgia and Ward, Doyle V. and Akerley, Brian J.}, year = 2009, month = sep, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {38}, pages = {16422–7}, issn = {1091-6490}, doi = {10.1073/pnas.0906627106}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2752563&tool=pmcentrez&rendertype=abstract}, abstract = {Rapid genome-wide identification of genes required for infection would expedite studies of bacterial pathogens. We developed genome-scale “negative selection” technology that combines high-density transposon mutagenesis and massively parallel sequencing of transposon/chromosome junctions in a mutant library to identify mutants lost from the library after exposure to a selective condition of interest. This approach was applied to comprehensively identify Haemophilus influenzae genes required to delay bacterial clearance in a murine pulmonary model. Mutations in 136 genes resulted in defects in vivo, and quantitative estimates of fitness generated by this technique were in agreement with independent validation experiments using individual mutant strains. Genes required in the lung included those with characterized functions in other models of H. influenzae pathogenesis and genes not previously implicated in infection. Genes implicated in vivo have reported or potential roles in survival during nutrient limitation, oxidative stress, and exposure to antimicrobial membrane perturbations, suggesting that these conditions are encountered by H. influenzae during pulmonary infection. The results demonstrate an efficient means to identify genes required for bacterial survival in experimental models of pathogenesis, and this approach should function similarly well in selections conducted in vitro and in vivo with any organism amenable to insertional mutagenesis.}, pmid = {19805314}, keywords = {Animals,Bacterial,Bacterial: genetics,Chromosome Mapping,Chromosomes,DNA Transposable Elements,DNA Transposable Elements: genetics,Genes,Genome,Genome-Wide Association Study,Genomic Library,Haemophilus Infections,Haemophilus Infections: microbiology,Haemophilus influenzae,Haemophilus influenzae: genetics,Haemophilus influenzae: growth & development,Insertional,Insertional: methods,Lung,Lung: microbiology,Mice,Mutagenesis,Mutation,nosource} }

@article{beattieTranscriptomicNetworkIdentified2013, title = {A Transcriptomic Network Identified in Uninfected Macrophages Responding to Inflammation Controls Intracellular Pathogen Survival.}, author = {Beattie, Lynette and {}d’El-Rei Hermida, Micely and Moore, John W. J. and Maroof, Asher and Brown, Najmeeyah and Lagos, Dimitris and Kaye, Paul M.}, year = 2013, month = sep, journal = {Cell host & microbe}, volume = {14}, number = {3}, eprint = {24034621}, eprinttype = {pubmed}, pages = {357–68}, publisher = {Elsevier}, issn = {1934-6069}, doi = {10.1016/j.chom.2013.08.004}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24034621}, abstract = {Intracellular pathogens modulate host cell function to promote their survival. However, in vitro infection studies do not account for the impact of host-derived inflammatory signals. Examining the response of liver-resident macrophages (Kupffer cells) in mice infected with the parasite Leishmania donovani, we identified a transcriptomic network operating in uninfected Kupffer cells exposed to inflammation but absent from Kupffer cells from the same animal that contained intracellular Leishmania. To test the hypothesis that regulated expression of genes within this transcriptomic network might impact parasite survival, we pharmacologically perturbed the activity of retinoid X receptor alpha (RXR{\(\alpha\)}), a key hub within this network, and showed that this intervention enhanced the innate resistance of Kupffer cells to Leishmania infection. Our results illustrate a broadly applicable strategy for understanding the host response to infection in vivo and identify Rxra as the hub of a gene network controlling antileishmanial resistance.}, pmid = {24034621}, keywords = {nosource} }

@phdthesis{petrovWiringRibosomeFunctions2006, title = {Wiring the Ribosome: {{Functions}} of Ribosomal Proteins {{L3}} and {{L10}}, and {{5S rRNA}} ({{Doctoral}} Dissertation)}, author = {Petrov, Alexey N.}, year = 2006, school = {University of Maryland College Park}, keywords = {nosource} } % == BibTeX quality report for petrovWiringRibosomeFunctions2006: % ? unused Number of pages (“132-135”)

@article{sacksAnimalModelsAnalysis2001, title = {Animal Models for the Analysis of Immune Responses to Leishmaniasis.}, author = {Sacks, D. L. and Melby, P. C.}, year = 2001, month = may, journal = {Current protocols in immunology / edited by John E. Coligan … [et al.]}, volume = {Chapter 19}, eprint = {18432753}, eprinttype = {pubmed}, pages = {Unit 19.2}, issn = {1934-368X}, doi = {10.1002/0471142735.im1902s28}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18432753}, abstract = {This unit focuses on the murine model of cutaneous leishmaniasis and models of visceral leishmaniasis in mice and hamsters. Each basic protocol describes the methods used to inoculate parasites and to evaluate infections with regard to lesion progression and visceralization, and quantification of parasite load. Five support protocols are provided; two for the growth and isolation of metacyclic promastigotes from in vitro culture, one for isolation of tissue amastigotes from infected animals, one for cryopreservation of parasites, and one for the preparation of blood agar plates for quantitation of parasite numbers in infected tissue.}, pmid = {18432753}, keywords = {Animal,Animals,Culture Media,Cutaneous,Cutaneous: parasitology,Disease Models,Erythrocytes,Leishmania,Leishmania: growth & development,Leishmania: isolation & purification,Leishmaniasis,Life Cycle Stages,Mice,nosource} } % == BibTeX quality report for sacksAnimalModelsAnalysis2001: % ? Possibly abbreviated journal title Current protocols in immunology / edited by John E. Coligan … [et al.]

@article{hedgesMappingFunctionalDomains2006, title = {Mapping the Functional Domains of Yeast {{NMD3}}, the Nuclear Export Adapter for the 60 {{S}} Ribosomal Subunit.}, author = {Hedges, John and Chen, Yen-I. and West, Matthew and Bussiere, Cyril and Johnson, Arlen W.}, year = 2006, month = dec, journal = {J. Biol. Chem.}, volume = {281}, number = {48}, pages = {36579–87}, issn = {0021-9258}, doi = {10.1074/jbc.M606798200}, abstract = {Nuclear export of the large ribosomal subunit requires the adapter protein Nmd3p to provide a leucine-rich nuclear export signal that is recognized by the export receptor Crm1. Nmd3p binds to the pre-60 S subunit in the nucleus. After export to the cytoplasm, the release of Nmd3p depends on the ribosomal protein Rpl10p and the GTPase Lsg1p. Here, we have carried out a mutational analysis of Nmd3 to better define the domains responsible for nucleocytoplasmic shuttling and ribosome binding. We show that mutations in two regions of Nmd3p affect 60 S binding, suggesting that its binding to the subunit is multivalent.}, pmid = {17015443}, keywords = {Active Transport,Alleles,Amino Acid Sequence,Biological,Cell Nucleus,DNA Mutational Analysis,Gene Deletion,Genetic,Models,Molecular Sequence Data,Mutation,nosource,Plasmids,Plasmids: metabolism,Point Mutation,Protein Structure,Ribosomes,Ribosomes: chemistry,RNA-Binding Proteins,RNA-Binding Proteins: chemistry,RNA-Binding Proteins: genetics,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: chemistry,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae: metabolism,Tertiary} } % == BibTeX quality report for hedgesMappingFunctionalDomains2006: % ? Possibly abbreviated journal title J. Biol. Chem.

@article{vlachosIncidenceNeoplasiaDiamond2012, title = {Incidence of Neoplasia in {{Diamond Blackfan}} Anemia: A Report from the {{Diamond Blackfan Anemia Registry}}.}, author = {Vlachos, Adrianna and Rosenberg, Philip S. and Atsidaftos, Eva and Alter, Blanche P. and Lipton, Jeffrey M.}, year = 2012, month = apr, journal = {Blood}, volume = {119}, number = {16}, pages = {3815–9}, issn = {1528-0020}, doi = {10.1182/blood-2011-08-375972}, abstract = {Diamond Blackfan anemia (DBA) is an inherited bone marrow failure syndrome characterized by red cell aplasia and congenital anomalies. A predisposition to cancer has been suggested but not quantified by case reports. The DBA Registry of North America (DBAR) is the largest established DBA patient cohort, with prospective follow-up since 1991. This report presents the first quantitative assessment of cancer incidence in DBA. Among 608 patients with 9458 person-years of follow-up, 15 solid tumors, 2 acute myeloid leukemias, and 2 cases of myelodysplastic syndrome were diagnosed at a median age of 41 years in patients who had not received a bone marrow transplant. Cancer incidence in DBA was significantly elevated. The observed-to- expected ratio for all cancers combined was 5.4 (P {\(<\)} .05); significant observed-to-expected ratios were 287 for myelodysplastic syndrome, 28 for acute myeloid leukemia, 36 for colon carcinoma, 33 for osteogenic sarcoma, and 12 for female genital cancers. The median survival was 56 years, and the cumulative incidence of solid tumor/leukemia was approximately 20% by age 46 years. As in Fanconi anemia and dyskeratosis congenita, DBA is both an inherited bone marrow failure syndrome and a cancer predisposition syndrome; cancer risks appear lower in DBA than in Fanconi anemia or dyskeratosis congenita. This trial was registered at www.clinicaltrials.gov as #NCT00106015.}, pmid = {22362038}, keywords = {Adolescent,Adult,Aged,Anemia,Bone Marrow Transplantation,Child,Comorbidity,Diamond-Blackfan,Diamond-Blackfan: mortality,Diamond-Blackfan: therapy,Female,Follow-Up Studies,Hemoglobinuria,Humans,Incidence,Infant,Male,Middle Aged,Neoplasms,Neoplasms: mortality,nosource,Paroxysmal,Paroxysmal: mortality,Paroxysmal: therapy,Preschool,Registries,Registries: statistics & numerical data,Risk Factors,Young Adult} }

@article{vlierbergheMolecularBasisCell2012, title = {The Molecular Basis of {{T}} Cell Acute Lymphoblastic Leukemia.}, author = {Vlierberghe, Pieter Van and Ferrando, Adolfo and Vlierberghe, Pieter Van}, year = 2012, month = oct, journal = {J. Clin. Invest.}, volume = {122}, number = {10}, pages = {3398–406}, publisher = {American Society for Clinical Investigation}, issn = {1558-8238}, doi = {10.1172/JCI61269}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3461904/}, abstract = {T cell acute lymphoblastic leukemias (T-ALLs) arise from the malignant transformation of hematopoietic progenitors primed toward T cell development, as result of a multistep oncogenic process involving constitutive activation of NOTCH signaling and genetic alterations in transcription factors, signaling oncogenes, and tumor suppressors. Notably, these genetic alterations define distinct molecular groups of T-ALL with specific gene expression signatures and clinicobiological features. This review summarizes recent advances in our understanding of the molecular genetics of T-ALL.}, pmid = {23023710}, keywords = {Cell Cycle Proteins,Cell Cycle Proteins: genetics,Cell Cycle Proteins: physiology,Cell Lineage,Cell Transformation,Chromatin Assembly and Disassembly,Chromatin Assembly and Disassembly: genetics,Chromatin Assembly and Disassembly: physiology,Cyclin-Dependent Kinase Inhibitor p16,Cyclin-Dependent Kinase Inhibitor p16: physiology,Genes,Hematopoietic Stem Cells,Hematopoietic Stem Cells: pathology,Homeodomain Proteins,Homeodomain Proteins: genetics,Homeodomain Proteins: physiology,Humans,Molecular Targeted Therapy,Neoplasm Proteins,Neoplasm Proteins: genetics,Neoplasm Proteins: physiology,Neoplastic,Neoplastic: genetics,nosource,Notch,Notch: physiology,p16,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma:,Prognosis,Receptors,Signal Transduction,Signal Transduction: genetics,Signal Transduction: physiology,T-Lymphocytes,T-Lymphocytes: pathology,Transcription Factors,Transcription Factors: physiology,Transcriptome,Tumor Suppressor Proteins,Tumor Suppressor Proteins: genetics,Tumor Suppressor Proteins: physiology} } % == BibTeX quality report for vlierbergheMolecularBasisCell2012: % ? Possibly abbreviated journal title J. Clin. Invest.

@article{amsterdamManyRibosomalProtein2004, title = {Many Ribosomal Protein Genes Are Cancer Genes in Zebrafish.}, author = {Amsterdam, Adam and Sadler, Kirsten C. and Lai, Kevin and Farrington, Sarah and Bronson, Roderick T. and Lees, Jacqueline A. and Hopkins, Nancy}, year = 2004, month = may, journal = {PLoS Biol.}, volume = {2}, number = {5}, pages = {E139}, publisher = {Public Library of Science}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0020139}, abstract = {We have generated several hundred lines of zebrafish (Danio rerio), each heterozygous for a recessive embryonic lethal mutation. Since many tumor suppressor genes are recessive lethals, we screened our colony for lines that display early mortality and/or gross evidence of tumors. We identified 12 lines with elevated cancer incidence. Fish from these lines develop malignant peripheral nerve sheath tumors, and in some cases also other tumor types, with moderate to very high frequencies. Surprisingly, 11 of the 12 lines were each heterozygous for a mutation in a different ribosomal protein (RP) gene, while one line was heterozygous for a mutation in a zebrafish paralog of the human and mouse tumor suppressor gene, neurofibromatosis type 2. Our findings suggest that many RP genes may act as haploinsufficient tumor suppressors in fish. Many RP genes might also be cancer genes in humans, where their role in tumorigenesis could easily have escaped detection up to now.}, pmid = {15138505}, keywords = {Animals,Gene Expression Regulation,Genes,Heterozygote,Humans,Loss of Heterozygosity,Mutagenesis,Mutation,Neoplastic,Neurofibromin 2,Neurofibromin 2: genetics,nosource,Phenotype,Ribosomal,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal: chemistry,Ribosomes,Ribosomes: chemistry,RNA,RNA: chemistry,Tumor Suppressor,Zebrafish} } % == BibTeX quality report for amsterdamManyRibosomalProtein2004: % ? Possibly abbreviated journal title PLoS Biol.

@article{stumpfCancerousTranslationApparatus2011, title = {The Cancerous Translation Apparatus}, author = {Stumpf, Craig R. and Ruggero, Davide}, year = 2011, month = aug, journal = {Current opinion in genetics & development}, volume = {21}, number = {4}, pages = {474–483}, issn = {1879-0380}, doi = {10.1016/j.gde.2011.03.007.The}, url = {http://www.sciencedirect.com/science/article/pii/S0959437X11000670}, abstract = {Deregulations in translational control are critical features of cancer initiation and progression. Activation of key oncogenic pathways promotes rapid and dramatic translational reprogramming, not simply by increasing overall protein synthesis, but also by modulating specific mRNA networks that promote cellular transformation. Additionally, ribosomopathies caused by mutations in ribosome components alter translational regulation leading to specific pathological features, including cancer susceptibility. Exciting advances in our understanding of translational control in cancer have illuminated a striking specificity innate to the translational apparatus. Characterizing this specificity will provide novel insights into how cells normally utilize translational control to modulate gene expression, how it is deregulated in cancer, and how these processes can be targeted to develop new cancer therapies.}, pmid = {21543223}, keywords = {Animals,Gene Expression Regulation,Genetic Predisposition to Disease,Humans,Messenger,Messenger: genetics,Messenger: metabolism,Neoplasms,Neoplasms: genetics,Neoplasms: metabolism,Neoplasms: pathology,Neoplastic,nosource,Protein Biosynthesis,RNA,Signal Transduction} }

@article{leshinEnhancedPurityActivity2010, title = {Enhanced Purity, Activity and Structural Integrity of Yeast Ribosomes Purified Using a General Chromatographic Method.}, author = {Leshin, Jonathan A. and Rakauskait{.e}, Rasa and Dinman, Jonathan D. and Meskauskas, Arturas}, year = 2010, journal = {RNA Biol.}, volume = {7}, pages = {354–60}, issn = {1555-8584}, abstract = {One of the major challenges facing researchers working with eukaryotic ribosomes lies in their lability relative to their eubacterial and archael counterparts. In particular, lysis of cells and purification of eukaryotic ribosomes by conventional differential ultracentrifugation methods exposes them for long periods of time to a wide range of co-purifying proteases and nucleases, negatively impacting their structural integrity and functionality. A chromatographic method using a cysteine charged Sulfolink resin was adapted to address these problems. This fast and simple method significantly reduces co-purifying proteolytic and nucleolytic activities, producing good yields of highly biochemically active yeast ribosomes with fewer nicks in their rRNAs. In particular, the chromatographic purification protocol significantly improved the quality of ribosomes isolated from mutant cells. This method is likely applicable to mammalian ribosomes as well. The simplicity of the method, and the enhanced purity and activity of chromatographically purified ribosome represents a significant technical advancement for the study of eukaryotic ribosomes.}, pmid = {20404492}, keywords = {Binding Sites,Biological,Cell Fractionation,Cell Fractionation: methods,Chromatography,Chromatography: methods,Drug Contamination,Enzyme Assays,Models,nosource,Nucleic Acid Conformation,Peptide Hydrolases,Peptide Hydrolases: metabolism,Protein Conformation,Ribonucleases,Ribonucleases: metabolism,Ribosomal,Ribosomal: chemistry,Ribosomal: isolation & purification,Ribosomal: metabolism,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,Ribosomes: physiology,RNA,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: chemistry,Saccharomyces cerevisiae Proteins: isolation & pur,Saccharomyces cerevisiae Proteins: metabolism,Yeasts,Yeasts: chemistry,Yeasts: cytology} } % == BibTeX quality report for leshinEnhancedPurityActivity2010: % ? Possibly abbreviated journal title RNA Biol.

@article{ngConformationalFlexibilityMolecular2009, title = {Conformational Flexibility and Molecular Interactions of an Archaeal Homologue of the {{Shwachman-Bodian-Diamond}} Syndrome Protein.}, author = {Ng, C. Leong and Waterman, David G. and Koonin, Eugene V. and Walters, Alison D. and Chong, James P. J. and Isupov, Michail N. and Lebedev, Andrey A. and Bunka, David H. J. and Stockley, Peter G. and {Ortiz-Lombard{'i}a}, Miguel and Antson, Alfred A.}, year = 2009, month = jan, journal = {BMC Struct. Biol.}, volume = {9}, number = {1}, pages = {32–40}, issn = {1472-6807}, doi = {10.1186/1472-6807-9-32}, url = {http://www.biomedcentral.com/1472-6807/9/32}, abstract = {BACKGROUND: Defects in the human Shwachman-Bodian-Diamond syndrome (SBDS) protein-coding gene lead to the autosomal recessive disorder characterised by bone marrow dysfunction, exocrine pancreatic insufficiency and skeletal abnormalities. This protein is highly conserved in eukaryotes and archaea but is not found in bacteria. Although genomic and biophysical studies have suggested involvement of this protein in RNA metabolism and in ribosome biogenesis, its interacting partners remain largely unknown. RESULTS: We determined the crystal structure of the SBDS orthologue from Methanothermobacter thermautotrophicus (mthSBDS). This structure shows that SBDS proteins are highly flexible, with the N-terminal FYSH domain and the C-terminal ferredoxin-like domain capable of undergoing substantial rotational adjustments with respect to the central domain. Affinity chromatography identified several proteins from the large ribosomal subunit as possible interacting partners of mthSBDS. Moreover, SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments, combined with electrophoretic mobility shift assays (EMSA) suggest that mthSBDS does not interact with RNA molecules in a sequence specific manner. CONCLUSION: It is suggested that functional interactions of SBDS proteins with their partners could be facilitated by rotational adjustments of the N-terminal and the C-terminal domains with respect to the central domain. Examination of the SBDS protein structure and domain movements together with its possible interaction with large ribosomal subunit proteins suggest that these proteins could participate in ribosome function.}, pmid = {19454024}, keywords = {Amino Acid Sequence,Animals,Archaeal Proteins,Archaeal Proteins: chemistry,Archaeal Proteins: metabolism,Crystallography,Electrophoretic Mobility Shift Assay,Humans,Methanobacteriaceae,Methanobacteriaceae: metabolism,Molecular Sequence Data,nosource,Protein Binding,Proteins,Proteins: chemistry,Ribosomal Proteins,Ribosomal Proteins: metabolism,RNA,RNA: chemistry,RNA: metabolism,Sequence Alignment,X-Ray} } % == BibTeX quality report for ngConformationalFlexibilityMolecular2009: % ? Possibly abbreviated journal title BMC Struct. Biol.

@article{lebaronProofreadingPre40SRibosome2012, title = {Proofreading of Pre-{{40S}} Ribosome Maturation by a Translation Initiation Factor and {{60S}} Subunits}, author = {Lebaron, Simon and Schneider, Claudia and {}van Nues, Robert W. and Swiatkowska, Agata and Walsh, Dietrich and B{"o}ttcher, Bettina and Granneman, Sander and Watkins, Nicholas J. and Tollervey, David}, year = 2012, month = aug, journal = {Nature structural & }, volume = {19}, number = {8}, pages = {744–753}, issn = {1545-9985}, doi = {10.1038/nsmb.2308.Proof}, url = {http://www.nature.com/nsmb/journal/v19/n8/abs/nsmb.2308.html}, abstract = {In the final steps of yeast ribosome synthesis, immature translation-incompetent pre-40S particles that contain 20S pre-rRNA are converted to the mature translation-competent subunits containing the 18S rRNA. An assay for 20S pre-rRNA cleavage in purified pre-40S particles showed that cleavage by the PIN domain endonuclease Nob1 was strongly stimulated by the GTPase activity of Fun12, the yeast homolog of cytoplasmic translation initiation factor eIF5b. Cleavage of the 20S pre-rRNA was also inhibited in vivo and in vitro by blocking binding of Fun12 to the 25S rRNA through specific methylation of its binding site. Cleavage competent pre-40S particles stably associated with Fun12 and formed 80S complexes with 60S ribosomal subunits. We propose that recruitment of 60S subunits promotes GTP hydrolysis by Fun12, leading to structural rearrangements within the pre-40S particle that bring Nob1 and the pre-rRNA cleavage site together.}, pmid = {22751017}, keywords = {Adenosine Triphosphate,Adenosine Triphosphate: metabolism,Base Sequence,Binding Sites,Eukaryotic,Eukaryotic Initiation Factor-2,Eukaryotic Initiation Factor-2: chemistry,Eukaryotic Initiation Factor-2: metabolism,Eukaryotic: chemistry,Eukaryotic: metabolism,Fungal,Fungal: chemistry,Fungal: genetics,Fungal: metabolism,gtpase,Guanosine Triphosphate,Guanosine Triphosphate: metabolism,Large,Models,Molecular,Molecular Sequence Data,nosource,Nuclear Proteins,Nuclear Proteins: metabolism,nuclease,Nucleic Acid Conformation,pin domain,Post-Transcriptional,pre-rrna processing,Protein Conformation,Ribosomal,Ribosomal: chemistry,Ribosomal: genetics,Ribosomal: metabolism,Ribosome Subunits,ribosome synthesis,RNA,RNA Precursors,RNA Precursors: chemistry,RNA Precursors: genetics,RNA Precursors: metabolism,RNA Processing,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: chemistry,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Small,yeast} }

@article{gaoStructureRibosomeElongation2009, title = {The Structure of the Ribosome with Elongation Factor {{G}} Trapped in the Posttranslocational State.}, author = {Gao, Yong-Gui and Selmer, Maria and Dunham, Christine M. and Weixlbaumer, Albert and Kelley, Ann C. and Ramakrishnan, V.}, year = 2009, journal = {Science}, volume = {326}, pages = {694–699}, abstract = {Elongation factor G (EF-G) is a guanosine triphosphatase (GTPase) that plays a crucial role in the translocation of transfer RNAs (tRNAs) and messenger RNA (mRNA) during translation by the ribosome. We report a crystal structure refined to 3.6 angstrom resolution of the ribosome trapped with EF-G in the posttranslocational state using the antibiotic fusidic acid. Fusidic acid traps EF-G in a conformation intermediate between the guanosine triphosphate and guanosine diphosphate forms. The interaction of EF-G with ribosomal elements implicated in stimulating catalysis, such as the L10-L12 stalk and the L11 region, and of domain IV of EF-G with the tRNA at the peptidyl-tRNA binding site (P site) and with mRNA shed light on the role of these elements in EF-G function. The stabilization of the mobile stalks of the ribosome also results in a more complete description of its structure.}, pmid = {19833919}, keywords = {bacterial,bacterial chemistry,bacterial proteins,bacterial proteins chemistry,catalysis,crystallography,fusidic acid,fusidic acid chemistry,fusidic acid pharmacology,messenger,messenger chemistry,models,molecular,nosource,peptide elongation factor g,peptide elongation factor g chemistry,protein biosynthesis,protein conformation,protein structure,protein synthesis inhibitors,protein synthesis inhibitors chemistry,protein synthesis inhibitors pharmacology,ribosomes,ribosomes chemistry,rna,tertiary,thermus thermophilus,transfer,transfer chemistry,x ray} }

@article{ratjeHeadSwivelRibosome2010, title = {Head Swivel on the Ribosome Facilitates Translocation by Means of Intra-Subunit {{tRNA}} Hybrid Sites}, author = {Ratje, Andreas H. AH and Loerke, Justus and Mikolajka, Aleksandra and Br{"u}nner, Matthias and Hildebrand, Peter W. and Starosta, Agata L. and D{"o}nh{"o}fer, Alexandra and Connell, Sean R. and Fucini, Paola and Mielke, Thorsten and Whitford, Paul C. and Onuchic, Jos{'e} N. and Yu, Yanan and Sanbonmatsu, Karissa Y. and Hartmann, Roland K. and Penczek, Pawel A. and Wilson, Daniel N. and Spahn, Christian M. T.}, year = 2010, month = dec, journal = {Nature}, volume = {468}, number = {7324}, pages = {713–716}, publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.}, issn = {1476-4687}, doi = {10.1038/nature09547.Head}, url = {http://www.nature.com/nature/journal/v468/n7324/abs/nature09547.html}, abstract = {The elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer RNAs to the aminoacyl-tRNA-binding site (A site) of the ribosome, followed by peptide-bond formation and translocation of the tRNAs through the ribosome to reopen the A site. The translocation reaction is catalysed by elongation factor G (EF-G) in a GTP-dependent manner. Despite the availability of structures of various EF-G-ribosome complexes, the precise mechanism by which tRNAs move through the ribosome still remains unclear. Here we use multiparticle cryoelectron microscopy analysis to resolve two previously unseen subpopulations within Thermus thermophilus EF-G-ribosome complexes at subnanometre resolution, one of them with a partly translocated tRNA. Comparison of these substates reveals that translocation of tRNA on the 30S subunit parallels the swivelling of the 30S head and is coupled to unratcheting of the 30S body. Because the tRNA maintains contact with the peptidyl-tRNA-binding site (P site) on the 30S head and simultaneously establishes interaction with the exit site (E site) on the 30S platform, a novel intra-subunit ‘pe/E’ hybrid state is formed. This state is stabilized by domain IV of EF-G, which interacts with the swivelled 30S-head conformation. These findings provide direct structural and mechanistic insight into the ‘missing link’ in terms of tRNA intermediates involved in the universally conserved translocation process.}, pmid = {21124459}, keywords = {Bacterial,Bacterial: chemistry,Bacterial: metabolism,Bacterial: ultrastructur,Binding Sites,Cryoelectron Microscopy,Crystallography,Guanosine Diphosphate,Guanosine Diphosphate: chemistry,Guanosine Diphosphate: metabolism,Models,Molecular,Movement,nosource,Peptide Elongation Factor G,Peptide Elongation Factor G: chemistry,Peptide Elongation Factor G: metabolism,Protein Biosynthesis,Protein Conformation,Protein Subunits,Protein Subunits: chemistry,Protein Subunits: metabolism,Ribosome Subunits,RNA,Small,Thermus thermophilus,Thermus thermophilus: chemistry,Transfer,Transfer: chemistry,Transfer: metabolism,Transfer: ultrastructure,X-Ray} }

@article{gentlemanBioconductorOpenSoftware2004, title = {Bioconductor: Open Software Development for Computational Biology and Bioinformatics.}, author = {Gentleman, Robert C. and Carey, Vincent J. and Bates, Douglas M. and Bolstad, Ben and Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and Ge, Yongchao and Gentry, Jeff and Hornik, Kurt and Hothorn, Torsten and Huber, Wolfgang and Iacus, Stefano and Irizarry, Rafael and Leisch, Friedrich and Li, Cheng and Maechler, Martin and Rossini, Anthony J. and Sawitzki, Gunther and Smith, Colin and Smyth, Gordon and Tierney, Luke and Yang, Jean Y. H. and Zhang, Jianhua}, year = 2004, month = jan, journal = {Genome biology}, volume = {5}, number = {10}, pages = {R80}, issn = {1465-6914}, doi = {10.1186/gb-2004-5-10-r80}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=545600&tool=pmcentrez&rendertype=abstract}, abstract = {The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.}, pmid = {15461798}, keywords = {Computational Biology,Computational Biology: instrumentation,Computational Biology: methods,Internet,nosource,Reproducibility of Results,Software} }

@article{liSequenceAlignmentMap2009, title = {The {{Sequence Alignment}}/{{Map}} Format and {{SAMtools}}.}, author = {Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard}, year = 2009, month = aug, journal = {Bioinformatics (Oxford, England)}, volume = {25}, number = {16}, pages = {2078–9}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp352}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2723002&tool=pmcentrez&rendertype=abstract}, abstract = {SUMMARY: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. AVAILABILITY: http://samtools.sourceforge.net.}, pmid = {19505943}, keywords = {Algorithms,Base Sequence,Computational Biology,Computational Biology: methods,DNA,DNA: methods,Genome,Genomics,Molecular Sequence Data,nosource,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis,Software} }

@article{martinCutadaptRemovesAdapter2011, title = {Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads}, author = {Martin, Marcel}, year = 2011, journal = {EMBnet. journal}, pages = {10–12}, url = {http://journaldev.embnet.org/index.php/embnetjournal/article/view/200 https://code.google.com/p/cutadapt/}, keywords = {nosource} } % == BibTeX quality report for martinCutadaptRemovesAdapter2011: % ? Possibly abbreviated journal title EMBnet. journal

@article{aslettTriTrypDBFunctionalGenomic2010, title = {{{TriTrypDB}}: A Functional Genomic Resource for the {{Trypanosomatidae}}.}, author = {Aslett, Martin and Aurrecoechea, Cristina and Berriman, Matthew and Brestelli, John and Brunk, Brian P. and Carrington, Mark and Depledge, Daniel P. and Fischer, Steve and Gajria, Bindu and Gao, Xin and Gardner, Malcolm J. and Gingle, Alan and Grant, Greg and Harb, Omar S. and Heiges, Mark and {Hertz-Fowler}, Christiane and Houston, Robin and Innamorato, Frank and Iodice, John and Kissinger, Jessica C. and Kraemer, Eileen and Li, Wei and Logan, Flora J. and {}a Miller, John and Mitra, Siddhartha and Myler, Peter J. and Nayak, Vishal and Pennington, Cary and Phan, Isabelle and Pinney, Deborah F. and Ramasamy, Gowthaman and Rogers, Matthew B. and Roos, David S. and Ross, Chris and Sivam, Dhileep and Smith, Deborah F. and Srinivasamoorthy, Ganesh and Stoeckert, Christian J. and Subramanian, Sandhya and Thibodeau, Ryan and Tivey, Adrian and Treatman, Charles and Velarde, Giles and Wang, Haiming}, year = 2010, month = jan, journal = {Nucleic acids research}, volume = {38}, number = {Database issue}, pages = {D457-62}, issn = {1362-4962}, doi = {10.1093/nar/gkp851}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2808979&tool=pmcentrez&rendertype=abstract}, abstract = {TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. ‘User Comments’ may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate.}, pmid = {19843604}, keywords = {Animals,Computational Biology,Computational Biology: methods,Computational Biology: trends,Databases,Genetic,Genome,Information Storage and Retrieval,Information Storage and Retrieval: methods,Internet,Leishmania,Leishmania: genetics,nosource,Nucleic Acid,Protein,Protein Structure,Protozoan,Protozoan Proteins,Protozoan Proteins: genetics,Software,Tertiary,Trypanosoma,Trypanosoma: genetics,User-Computer Interface} }

@article{zinovievNovel4EinteractingProtein2011, title = {A Novel {{4E-interacting}} Protein in {{Leishmania}} Is Involved in Stage-Specific Translation Pathways.}, author = {Zinoviev, Alexandra and L{'e}ger, M{'e}lissa and Wagner, Gerhard and Shapira, Michal}, year = 2011, month = oct, journal = {Nucleic acids research}, volume = {39}, number = {19}, pages = {8404–15}, issn = {1362-4962}, doi = {10.1093/nar/gkr555}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3201875&tool=pmcentrez&rendertype=abstract}, abstract = {In eukaryotes, exposure to stress conditions causes a shift from cap-dependent to cap-independent translation. In trypanosomatids, environmental switches are the driving force of a developmental program of gene expression, but it is yet unclear how their translation machinery copes with their constantly changing environment. Trypanosomatids have a unique cap structure (cap-4) and encode four highly diverged paralogs of the cap-binding protein, eIF4E; none were found to genetically complement a yeast mutant failing to express eIF4E. Here we show that in promastigotes, a typical cap-binding complex is anchored through LeishIF4E-4, which associates with components of the cap-binding pre-initiation complex. In axenic amastigotes, expression of LeishIF4E-4 decreases and the protein does not bind the cap, whereas LeishIF4E-1 maintains its expression level and associates with the cap structure and with translation initiation factors. However, LeishIF4E-1 does not interact with eIF4G-like proteins in both life stages, excluding its involvement in cap-dependent translation. Using pull-down assays and mass-spectrometry, we identified a novel, non-conserved 4E-Interacting Protein (Leish4E-IP), which binds to LeishIF4E-1 in promastigotes, but not in amastigotes. Yeast two-hybrid and NMR spectroscopy confirmed the specificity of this interaction. We propose that Leish4E-IP is a translation regulator that is involved in switching between cap-dependent and alternative translation pathways.}, pmid = {21764780}, keywords = {Eukaryotic Initiation Factor-4E,Eukaryotic Initiation Factor-4E: metabolism,Eukaryotic Initiation Factor-4F,Eukaryotic Initiation Factor-4F: metabolism,Eukaryotic Initiation Factors,Eukaryotic Initiation Factors: metabolism,Leishmania,Leishmania: genetics,Leishmania: growth & development,Leishmania: metabolism,nosource,Peptide Chain Initiation,Protozoan Proteins,Protozoan Proteins: metabolism,Translational} }

@article{rakauskaiteMutationsHighlyConserved2011, title = {Mutations of Highly Conserved Bases in the Peptidyltransferase Center Induce Compensatory Rearrangements in Yeast Ribosomes.}, author = {Rakauskaite, Rasa and Dinman, Jonathan D.}, year = 2011, month = may, journal = {RNA}, volume = {17}, number = {5}, pages = {855–64}, issn = {1469-9001}, doi = {10.1261/rna.2593211}, abstract = {Molecular dynamics simulation identified three highly conserved rRNA bases in the large subunit of the ribosome that form a three-dimensional (3D) “gate” that induces pausing of the aa-tRNA acceptor stem during accommodation into the A-site. A nearby fourth base contacting the “tryptophan finger” of yeast protein L3, which is involved in the coordinating elongation factor recruitment to the ribosome with peptidyltransfer, is also implicated in this process. To better understand the functional importance of these bases, single base substitutions as well as deletions at all four positions were constructed and expressed as the sole forms of ribosomes in yeast Saccharomyces cerevisiae. None of the mutants had strong effects on cell growth, translational fidelity, or on the interactions between ribosomes and tRNAs. However, the mutants did promote strong effects on cell growth in the presence of translational inhibitors, and differences in viability between yeast and Escherichia coli mutants at homologous positions suggest new targets for antibacterial therapeutics. Mutant ribosomes also promoted changes in 25S rRNA structure, all localized to the core of peptidyltransferase center (i.e., the proto-ribosome area). We suggest that a certain degree of structural plasticity is built into the ribosome, enabling it to ensure accurate translation of the genetic code while providing it with the flexibility to adapt and evolve.}, pmid = {21441349}, keywords = {Base Sequence,Mutation,nosource,Nucleic Acid Conformation,Peptidyl Transferases,Peptidyl Transferases: genetics,Protein Binding,Protein Biosynthesis,Ribosomal,Ribosomal: chemistry,Ribosomal: genetics,Ribosomes,Ribosomes: chemistry,Ribosomes: genetics,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae: chemistry,Saccharomyces cerevisiae: enzymology} }

@article{vasaShapeFinderSoftwareSystem2008, title = {{{ShapeFinder}}: A Software System for High-Throughput Quantitative Analysis of Nucleic Acid Reactivity Information Resolved by Capillary Electrophoresis.}, author = {Vasa, Suzy M. and Guex, Nicolas and Wilkinson, Kevin A. and Weeks, Kevin M. and Giddings, Morgan C.}, year = 2008, month = oct, journal = {RNA}, volume = {14}, number = {10}, pages = {1979–90}, issn = {1469-9001}, doi = {10.1261/rna.1166808}, abstract = {Analysis of the long-range architecture of RNA is a challenging experimental and computational problem. Local nucleotide flexibility, which directly reports underlying base pairing and tertiary interactions in an RNA, can be comprehensively assessed at single nucleotide resolution using high-throughput selective 2’-hydroxyl acylation analyzed by primer extension (hSHAPE). hSHAPE resolves structure-sensitive chemical modification information by high-resolution capillary electrophoresis and typically yields quantitative nucleotide flexibility information for 300-650 nucleotides (nt) per experiment. The electropherograms generated in hSHAPE experiments provide a wealth of structural information; however, significant algorithmic analysis steps are required to generate quantitative and interpretable data. We have developed a set of software tools called ShapeFinder to make possible rapid analysis of raw sequencer data from hSHAPE, and most other classes of nucleic acid reactivity experiments. The algorithms in ShapeFinder (1) convert measured fluorescence intensity to quantitative cDNA fragment amounts, (2) correct for signal decay over read lengths extending to 600 nts or more, (3) align reactivity data to the known RNA sequence, and (4) quantify per nucleotide reactivities using whole-channel Gaussian integration. The algorithms and user interface tools implemented in ShapeFinder create new opportunities for tackling ambitious problems involving high-throughput analysis of structure-function relationships in large RNAs.}, pmid = {18772246}, keywords = {Algorithms,Base Sequence,Capillary,Computational Biology,Computational Biology: methods,Electrophoresis,nosource,Nucleic Acid Conformation,Nucleotides,Nucleotides: chemistry,RNA,RNA: chemistry,RNA: isolation & purification,RNA: methods,Sequence Analysis,Software} }

@article{chenCoordinatedConformationalCompositional2013, title = {Coordinated Conformational and Compositional Dynamics Drive Ribosome Translocation.}, author = {Chen, Jin and Petrov, Alexey and Tsai, Albert and O’Leary, Se{'a}n E. and Puglisi, Joseph D.}, year = 2013, month = jun, journal = {Nat. Struct. Mol. Biol.}, volume = {20}, number = {6}, pages = {718–27}, publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.}, issn = {1545-9985}, doi = {10.1038/nsmb.2567}, abstract = {During translation elongation, the ribosome compositional factors elongation factor G (EF-G; encoded by fusA) and tRNA alternately bind to the ribosome to direct protein synthesis and regulate the conformation of the ribosome. Here, we use single-molecule fluorescence with zero-mode waveguides to directly correlate ribosome conformation and composition during multiple rounds of elongation at high factor concentrations in Escherichia coli. Our results show that EF-G bound to GTP (EF-G-GTP) continuously samples both rotational states of the ribosome, binding with higher affinity to the rotated state. Upon successful accommodation into the rotated ribosome, the EF-G-ribosome complex evolves through several rate-limiting conformational changes and the hydrolysis of GTP, which results in a transition back to the nonrotated state and in turn drives translocation and facilitates release of both EF-G-GDP and E-site tRNA. These experiments highlight the power of tracking single-molecule conformation and composition simultaneously in real time.}, pmid = {23624862}, keywords = {nosource} } % == BibTeX quality report for chenCoordinatedConformationalCompositional2013: % ? Possibly abbreviated journal title Nat. Struct. Mol. Biol.

@article{shammasStructuralMutationalAnalysis2005, title = {Structural and Mutational Analysis of the {{SBDS}} Protein Family. {{Insight}} into the Leukemia-Associated {{Shwachman-Diamond Syndrome}}.}, author = {Shammas, Camille and Menne, Tobias F. and Hilcenko, Christine and Michell, Stephen R. and Goyenechea, Beatriz and Boocock, Graeme R. B. and Durie, Peter R. and Rommens, Johanna M. and Warren, Alan J.}, year = 2005, month = may, journal = {J. Biol. Chem.}, volume = {280}, number = {19}, pages = {19221–9}, issn = {0021-9258}, doi = {10.1074/jbc.M414656200}, abstract = {Shwachman-Diamond Syndrome (SDS) is an autosomal recessive disorder characterized by bone marrow failure with significant predisposition to the development of poor prognosis myelodysplasia and leukemia, exocrine pancreatic failure and metaphyseal chondrodysplasia. Although the SBDS gene mutated in this disorder is highly conserved in Archaea and all eukaryotes, the function is unknown. To interpret the molecular consequences of SDS-associated mutations, we have solved the crystal structure of the Archaeoglobus fulgidus SBDS protein orthologue at a resolution of 1.9 angstroms, revealing a three domain architecture. The N-terminal (FYSH) domain is the most frequent target for disease mutations and contains a novel mixed alpha/beta-fold identical to the single domain yeast protein Yhr087wp that is implicated in RNA metabolism. The central domain consists of a three-helical bundle, whereas the C-terminal domain has a ferredoxin-like fold. By genetic complementation analysis of the essential Saccharomyces cerevisiae SBDS orthologue YLR022C, we demonstrate an essential role in vivo for the FYSH domain and the central three-helical bundle. We further show that the common SDS-related K62X truncation is non-functional. Most SDS-related missense mutations that alter surface epitopes do not impair YLR022C function, but mutations affecting residues buried in the hydrophobic core of the FYSH domain severely impair or abrogate complementation. These data are consistent with absence of homozygosity for the common K62X truncation mutation in individuals with SDS, indicating that the SDS disease phenotype is a consequence of expression of hypomorphic SBDS alleles and that complete loss of SBDS function is likely to be lethal.}, pmid = {15701631}, keywords = {Alleles,Amino Acid,Amino Acid Sequence,Archaeoglobus fulgidus,Archaeoglobus fulgidus: metabolism,Blotting,Cell Cycle,Crystallography,DNA Mutational Analysis,Dose-Response Relationship,Drug,Electrophoresis,Epitopes,Epitopes: chemistry,Escherichia coli,Escherichia coli: metabolism,Flow Cytometry,Genetic Complementation Test,Guanidine,Guanidine: chemistry,Homozygote,Humans,Leukemia,Leukemia: genetics,Leukemia: metabolism,Messenger,Messenger: chemistry,Models,Molecular,Molecular Sequence Data,Mutation,nosource,Phenotype,Polyacrylamide Gel,Protein Binding,Protein Conformation,Protein Denaturation,Protein Folding,Protein Structure,Proteins,Proteins: chemistry,Proteins: genetics,RNA,RNA: chemistry,Saccharomyces cerevisiae,Saccharomyces cerevisiae: metabolism,Sequence Homology,Sodium Dodecyl Sulfate,Sodium Dodecyl Sulfate: chemistry,Syndrome,Tertiary,Time Factors,Western,X-Ray} } % == BibTeX quality report for shammasStructuralMutationalAnalysis2005: % ? Possibly abbreviated journal title J. Biol. Chem.

@article{armacheLocalizationEukaryotespecificRibosomal2010, title = {Localization of Eukaryote-Specific Ribosomal Proteins in a 5.5-{{}} Cryo-{{EM}} Map of the {{80S}} Eukaryotic Ribosome.}, author = {Armache, Jean-Paul and Jarasch, Alexander and Anger, Andreas M. and Villa, Elizabeth and Becker, Thomas and Bhushan, Shashi and Jossinet, Fabrice and Habeck, Michael and Dindar, G{"u}lcin and Franckenberg, Sibylle and Marquez, Viter and Mielke, Thorsten and Thomm, Michael and Berninghausen, Otto and Beatrix, Birgitta and S{"o}ding, Johannes and Westhof, Eric and Wilson, Daniel N. and Beckmann, Roland}, year = 2010, month = nov, journal = {PNAS}, volume = {107}, number = {46}, pages = {19754–9}, issn = {1091-6490}, doi = {10.1073/pnas.1010005107}, abstract = {Protein synthesis in all living organisms occurs on ribonucleoprotein particles, called ribosomes. Despite the universality of this process, eukaryotic ribosomes are significantly larger in size than their bacterial counterparts due in part to the presence of 80 r proteins rather than 54 in bacteria. Using cryoelectron microscopy reconstructions of a translating plant (Triticum aestivum) 80S ribosome at 5.5- resolution, together with a 6.1- map of a translating Saccharomyces cerevisiae 80S ribosome, we have localized and modeled 74/80 (92.5%) of the ribosomal proteins, encompassing 12 archaeal/eukaryote-specific small subunit proteins as well as the complete complement of the ribosomal proteins of the eukaryotic large subunit. Near-complete atomic models of the 80S ribosome provide insights into the structure, function, and evolution of the eukaryotic translational apparatus.}, pmid = {20974910}, keywords = {Cryoelectron Microscopy,Eukaryotic Cells,Eukaryotic Cells: metabolism,Eukaryotic Cells: ultrastructure,Evolution,Models,Molecular,nosource,Protein Transport,Ribosomal,Ribosomal Proteins,Ribosomal Proteins: metabolism,Ribosomal Proteins: ultrastructure,Ribosomal: chemistry,Ribosomal: genetics,Ribosomal: ultrastructure,Ribosomes,Ribosomes: metabolism,Ribosomes: ultrastructure,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae: metabolism,Saccharomyces cerevisiae: ultrastructure,Species Specificity,Triticum,Triticum: metabolism} }

@article{voorheesInsightsSubstrateStabilization2009, title = {Insights into Substrate Stabilization from Snapshots of the Peptidyl Transferase Center of the Intact {{70S}} Ribosome}, author = {Voorhees, RM Rebecca M. and Weixlbaumer, Albert and Loakes, David and Kelley, Ann C. and Ramakrishnan, V.}, year = 2009, month = may, journal = {Nature structural & }, volume = {16}, number = {5}, pages = {528–533}, issn = {1545-9985}, doi = {10.1038/nsmb.1577.Insights}, url = {http://www.nature.com/nsmb/journal/v16/n5/abs/nsmb.1577.html}, abstract = {Protein synthesis is catalyzed in the peptidyl transferase center (PTC), located in the large (50S) subunit of the ribosome. No high-resolution structure of the intact ribosome has contained a complete active site including both A- and P-site tRNAs. In addition, although past structures of the 50S subunit have found no ordered proteins at the PTC, biochemical evidence suggests that specific proteins are capable of interacting with the 3’ ends of tRNA ligands. Here we present structures, at 3.6-A and 3.5-A resolution respectively, of the 70S ribosome in complex with A- and P-site tRNAs that mimic pre- and post-peptidyl-transfer states. These structures demonstrate that the PTC is very similar between the 50S subunit and the intact ribosome. They also reveal interactions between the ribosomal proteins L16 and L27 and the tRNA substrates, helping to elucidate the role of these proteins in peptidyl transfer.}, pmid = {19363482}, keywords = {23S,23S: chemistry,23S: metabolism,Crystallography,Escherichia coli,nosource,Peptidyl Transferases,Peptidyl Transferases: metabolism,Protein Binding,Protein Structure,Ribosomal,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: metabolism,Ribosomes,Ribosomes: enzymology,RNA,Secondary,Static Electricity,Substrate Specificity,Thermus thermophilus,Thermus thermophilus: metabolism,Transfer,Transfer: chemistry,Transfer: metabolism,X-Ray} }

@article{bussiereIntegrityPsiteProbed2012, title = {Integrity of the {{P-site}} Is Probed during Maturation of the {{60S}} Ribosomal Subunit.}, author = {Bussiere, Cyril and Hashem, Yaser and Arora, Sucheta and Frank, Joachim and Johnson, Arlen W.}, year = 2012, month = jun, journal = {J. Cell Biol.}, volume = {197}, number = {6}, pages = {747–59}, issn = {1540-8140}, doi = {10.1083/jcb.201112131}, abstract = {Eukaryotic ribosomes are preassembled in the nucleus and mature in the cytoplasm. Release of the antiassociation factor Tif6 by the translocase-like guanosine triphosphatase Efl1 is a critical late maturation step. In this paper, we show that a loop of Rpl10 that embraces the P-site transfer ribonucleic acid was required for release of Tif6, 90 away. Mutations in this P-site loop blocked 60S maturation but were suppressed by mutations in Tif6 or Efl1. Molecular dynamics simulations of the mutant Efl1 proteins suggest that they promote a conformation change in Efl1 equivalent to changes that elongation factor G and eEF2 undergo during translocation. These results identify molecular signaling from the P-site to Tif6 via Efl1, suggesting that the integrity of the P-site is interrogated during maturation. We propose that Efl1 promotes a functional check of the integrity of the 60S subunit before its first round of translation.}, pmid = {22689654}, keywords = {Catalytic Domain,Cell Nucleus,Cell Nucleus: metabolism,Eukaryotic,Eukaryotic: metabolism,GTP Phosphohydrolases,GTP Phosphohydrolases: genetics,GTP Phosphohydrolases: metabolism,Large,Messenger,Messenger: metabolism,Models,Molecular,Molecular Dynamics Simulation,Mutation,nosource,Protein Conformation,Ribosomal Proteins,Ribosomal Proteins: genetics,Ribosomal Proteins: metabolism,Ribosome Subunits,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: metabolism} } % == BibTeX quality report for bussiereIntegrityPsiteProbed2012: % ? Possibly abbreviated journal title J. Cell Biol.

@article{hedgesReleaseExportAdapter2005, title = {Release of the Export Adapter, {{Nmd3p}}, from the {{60S}} Ribosomal Subunit Requires {{Rpl10p}} and the Cytoplasmic {{GTPase Lsg1p}}.}, author = {Hedges, John and West, Matthew and Johnson, Arlen W.}, year = 2005, month = feb, journal = {EMBO J.}, volume = {24}, number = {3}, pages = {567–79}, issn = {0261-4189}, doi = {10.1038/sj.emboj.7600547}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=548654&tool=pmcentrez&rendertype=abstract}, abstract = {In eukaryotes, nuclear export of the large (60S) ribosomal subunit requires the adapter protein Nmd3p to provide the nuclear export signal. Here, we show that in yeast release of Nmd3p from 60S subunits in the cytoplasm requires the ribosomal protein Rpl10p and the G-protein, Lsg1p. Mutations in LSG1 or RPL10 blocked Nmd3-GFP shuttling into the nucleus and export of pre-60S subunits from the nucleus. Overexpression of NMD3 alleviated the export defect, indicating that the block in 60S export in lsg1 and rpl10 mutants results indirectly from failing to recycle Nmd3p. The defect in Nmd3p recycling and the block in 60S export in both lsg1 and rpl10 mutants was also suppressed by mutant Nmd3 proteins that showed reduced binding to 60S subunits in vitro. We propose that the correct loading of Rpl10p into 60S subunits is required for the release of Nmd3p from subunits by Lsg1p. These results suggest a coupling between recycling the 60S export adapter and activation of 60S subunits for translation.}, pmid = {15660131}, keywords = {Active Transport,Base Sequence,Biological,Cell Nucleus,Cytoplasm,Cytoplasm: metabolism,DNA,Fungal,Fungal: genetics,Fungal: metabolism,Gene Dosage,Genes,Genetic,GTP-Binding Proteins,GTP-Binding Proteins: genetics,GTP-Binding Proteins: metabolism,Models,Mutation,nosource,Ribosomal Proteins,Ribosomal Proteins: genetics,Ribosomal Proteins: metabolism,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,RNA-Binding Proteins,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Suppression,Temperature} } % == BibTeX quality report for hedgesReleaseExportAdapter2005: % ? Possibly abbreviated journal title EMBO J.

@article{menneShwachmanBodianDiamondSyndromeProtein2007, title = {The {{Shwachman-Bodian-Diamond}} Syndrome Protein Mediates Translational Activation of Ribosomes in Yeast}, author = {Menne, Tobias F. and Goyenechea, Beatriz and {S{'a}nchez-Puig}, Nuria and Wong, Chi C. and Tonkin, Louise M. and Ancliff, Philip J. and Brost, Ren{'e}e L. and Costanzo, Michael and Boone, Charles and Warren, Alan J.}, year = 2007, month = mar, journal = {Nature Genet.}, volume = {39}, number = {4}, pages = {486–495}, issn = {1061-4036}, doi = {10.1038/ng1994}, abstract = {The autosomal recessive disorder Shwachman-Diamond syndrome, characterized by bone marrow failure and leukemia predisposition, is caused by deficiency of the highly conserved Shwachman-Bodian-Diamond syndrome (SBDS) protein. Here, we identify the function of the yeast SBDS ortholog Sdo1, showing that it is critical for the release and recycling of the nucleolar shuttling factor Tif6 from pre-60S ribosomes, a key step in 60S maturation and translational activation of ribosomes. Using genome-wide synthetic genetic array mapping, we identified multiple TIF6 gain-of-function alleles that suppressed the pre-60S nuclear export defects and cytoplasmic mislocalization of Tif6 observed in sdo1Delta cells. Sdo1 appears to function within a pathway containing elongation factor-like 1, and together they control translational activation of ribosomes. Thus, our data link defective late 60S ribosomal subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition.}, pmid = {17353896}, keywords = {Biological,Carrier Proteins,Carrier Proteins: genetics,Gene Deletion,Genetically Modified,GTP Phosphohydrolases,GTP Phosphohydrolases: genetics,GTP Phosphohydrolases: physiology,Intermediate Filament Proteins,Intermediate Filament Proteins: genetics,Models,Molecular,Mutation,nosource,Organisms,Peptide Elongation Factors,Peptide Elongation Factors: genetics,Peptide Elongation Factors: physiology,Phosphoproteins,Phosphoproteins: genetics,Protein Biosynthesis,Protein Biosynthesis: drug effects,Protein Biosynthesis: genetics,Protein Synthesis Inhibitors,Protein Synthesis Inhibitors: pharmacology,Ribosomal Proteins,Ribosomes,Ribosomes: metabolism,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: physiology,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: growth & development} } % == BibTeX quality report for menneShwachmanBodianDiamondSyndromeProtein2007: % ? Possibly abbreviated journal title Nature Genet.

@article{westDefiningOrderWhich2005, title = {Defining the Order in Which {{Nmd3p}} and {{Rpl10p}} Load onto Nascent {{60S}} Ribosomal Subunits.}, author = {West, Matthew and Hedges, John B. and Chen, Anthony and Johnson, Arlen W.}, year = 2005, month = may, journal = {Mol. Cell. Biol.}, volume = {25}, number = {9}, pages = {3802–13}, issn = {0270-7306}, doi = {10.1128/MCB.25.9.3802-3813.2005}, abstract = {The large ribosomal subunit protein Rpl10p is required for subunit joining and 60S export in yeast. We have recently shown that Rpl10p as well as the cytoplasmic GTPase Lsg1p are required for releasing the 60S nuclear export adapter Nmd3p from subunits in the cytoplasm. Here, we more directly address the order of Nmd3p and Rpl10p recruitment to the subunit. We show that Nmd3p can bind subunits in the absence of Rpl10p. In addition, we examined the basis of the previously reported dominant negative growth phenotype caused by overexpression of C-terminally truncated Rpl10p and found that these Rpl10p fragments are not incorporated into subunits in the nucleus but instead sequester the WD-repeat protein Sqt1p. Sqt1p is an Rpl10p binding protein that is proposed to facilitate loading of Rpl10p into the 60S subunit. Although Sqt1p normally only transiently binds 60S subunits, the levels of Sqt1p that can be coimmunoprecipitated by the 60S-associated GTPase Lsg1p are significantly increased by a dominant mutation in the Walker A motif of Lsg1p. This mutant Lsg1 protein also leads to increased levels of Sqt1p in complexes that are coimmunoprecipitated with Nmd3p. Furthermore, the dominant LSG1 mutant also traps a mutant Rpl10 protein that does not normally bind stably to the subunit. These results support the idea that Sqt1p loads Rpl10p onto the Nmd3p-bound subunit after export to the cytoplasm and that Rpl10p loading involves the GTPase Lsg1p.}, pmid = {15831484}, keywords = {Amino Acid Motifs,Cytoplasm,Cytoplasm: chemistry,GTP-Binding Proteins,GTP-Binding Proteins: metabolism,Immunoprecipitation,Mutation,Mutation: genetics,nosource,Protein Transport,Ribosomal Proteins,Ribosomal Proteins: analysis,Ribosomal Proteins: genetics,Ribosomal Proteins: metabolism,Ribosomes,Ribosomes: metabolism,Ribosomes: physiology,RNA-Binding Proteins,RNA-Binding Proteins: metabolism,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: analysis,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: metabolism} } % == BibTeX quality report for westDefiningOrderWhich2005: % ? Possibly abbreviated journal title Mol. Cell. Biol.

@article{darochaTestsCytoplasmicRNA2004, title = {Tests of Cytoplasmic {{RNA}} Interference ({{RNAi}}) and Construction of a Tetracycline-Inducible {{T7}} Promoter System in {{Trypanosoma}} Cruzi}, author = {DaRocha, Wanderson D. and Otsu, Keiko and Teixeira, Santuza M. R. and Donelson, John E.}, year = 2004, month = feb, journal = {Molecular and Biochemical Parasitology}, volume = {133}, number = {2}, pages = {175–186}, issn = {01666851}, doi = {10.1016/j.molbiopara.2003.10.005}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0166685103003025}, keywords = {amastin,double-stranded rna,flagellar adhesion protein,luciferase,nosource,proteins,red and green fluorescent,rna interference,rnai,trypanosoma cruzi,tubulin} }

@article{mengel-jorgensenDetectionPseudouridineOther2002, title = {Detection of Pseudouridine and Other Modifications in {{tRNA}} by Cyanoethylation and {{MALDI}} Mass Spectrometry}, author = {Mengel-J{}rgensen, J. and Kirpekar, Finn}, year = 2002, journal = {Nucleic acids research}, volume = {30}, number = {23}, url = {http://nar.oxfordjournals.org/content/30/23/e135.short}, keywords = {nosource} }

@article{kawashitaMaximumlikelihoodDivergenceDate2001, title = {Maximum-Likelihood Divergence Date Estimates Based on {{rRNA}} Gene Sequences Suggest Two Scenarios of {{Trypanosoma}} Cruzi Intraspecific Evolution.}, author = {Kawashita, S. Y. and Sanson, G. F. and Fernandes, O. and Zingales, B. and Briones, M. R.}, year = 2001, month = dec, journal = {Molecular biology and evolution}, volume = {18}, number = {12}, eprint = {11719574}, eprinttype = {pubmed}, pages = {2250–9}, issn = {0737-4038}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11719574}, abstract = {The phylogenetic relationships of Trypanosoma cruzi strains were inferred using maximum-likelihood from complete 18S rDNA sequences and D7-24Salpha rDNA regions from 20 representative strains of T. cruzi. For this we sequenced the 18S rDNA of 14 strains and the D7-24Salpha rDNA of four strains and aligned them to previously published sequences. Phylogenies inferred from these data sets identified four groups, named Riboclades 1, 2, 3, and 4, and a basal dichotomy that separated Riboclade 1 from Riboclades 2, 3, and 4. Substitution models and other parameters were optimized by hierarchical likelihood tests, and our analysis of the 18S rDNA molecular clock by the likelihood ratio test suggests that a taxa subset encompassing all 2,150 positions in the alignment supports rate constancy among lineages. The present analysis supports the notion that divergence dates of T. cruzi Riboclades can be estimated from 18S rDNA sequences and therefore, we present alternative evolutionary scenarios based on two different views of T. cruzi intraspecific divergence. The first assumes a faster evolutionary rate, which suggests that the divergence between T. cruzi I and II and the extant strains occurred in the Tertiary period (37-18 MYA). The other, which supports the hypothesis that the divergence between T. cruzi I and II occurred in the Cretaceous period (144-65 MYA) and the divergence of the extant strains occurred in the Tertiary period of the Cenozoic era (65-1.8 MYA), is consistent with our previously proposed hypothesis of divergence by geographical isolation and mammalian host coevolution.}, pmid = {11719574}, keywords = {Animals,Biological Evolution,DNA,Genes,Likelihood Functions,nosource,Phylogeny,Ribosomal,Ribosomal: genetics,rRNA,Trypanosoma cruzi,Trypanosoma cruzi: classification,Trypanosoma cruzi: genetics} }

@article{inouyeDetectionInosinecontainingTransfer1973, title = {Detection of Inosine-Containing Transfer Ribonucleic Acid Species by Affinity Chromatography on Columns of Anti-Inosine Antibodies}, author = {Inouye, Hiroshi and Fuchs, Sara and Sela, Michael and Littauer, U. Z.}, year = 1973, journal = {Journal of Biological Chemistry}, url = {http://www.jbc.org/content/248/23/8125.short}, keywords = {nosource} }

@article{jackowiakRNADegradomeIts2011, title = {{{RNA}} Degradome–Its Biogenesis and Functions.}, author = {Jackowiak, Paulina and Nowacka, Martyna and Strozycki, Pawel M. and Figlerowicz, Marek}, year = 2011, month = sep, journal = {Nucleic acids research}, volume = {39}, number = {17}, pages = {7361–70}, issn = {1362-4962}, doi = {10.1093/nar/gkr450}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3177198&tool=pmcentrez&rendertype=abstract}, abstract = {RNA degradation is among the most fundamental processes that occur in living cells. The continuous decay of RNA molecules is associated not only with nucleotide turnover, but also with transcript maturation and quality control. The efficiency of RNA decay is ensured by a broad spectrum of both specific and non-specific ribonucleases. Some of these ribonucleases participate mainly in processing primary transcripts and in RNA quality control. Others preferentially digest mature, functional RNAs to yield a variety of molecules that together constitute the RNA degradome. Recently, it has become increasingly clear that the composition of the cellular RNA degradome can be modulated by numerous endogenous and exogenous factors (e.g. by stress). In addition, instead of being hydrolyzed to single nucleotides, some intermediates of RNA degradation can accumulate and function as signalling molecules or participate in mechanisms that control gene expression. Thus, RNA degradation appears to be not only a process that contributes to the maintenance of cellular homeostasis but also an underestimated source of regulatory molecules.}, pmid = {21653558}, keywords = {Messenger,Messenger: metabolism,nosource,Ribonucleases,Ribonucleases: metabolism,RNA,RNA Stability,RNA: metabolism,RNA: physiology} }

@article{zingalesEpidemiologyBiochemistryEvolution1999, title = {Epidemiology, Biochemistry and Evolution of {{Trypanosoma}} Cruzi Lineages Based on Ribosomal {{RNA}} Sequences.}, author = {Zingales, B. and Stolf, B. S. and Souto, R. P. and Fernandes, O. and Briones, M. R.}, year = 1999, month = jan, journal = {Mem'orias do Instituto Oswaldo Cruz}, volume = {94 Suppl 1}, eprint = {10677706}, eprinttype = {pubmed}, pages = {159–64}, issn = {0074-0276}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10677706}, pmid = {10677706}, keywords = {Animals,Chagas Disease,Chagas Disease: epidemiology,Genes,Humans,nosource,Phylogeny,Protozoan,Protozoan: genetics,Ribosomal,Ribosomal: genetics,RNA,Species Specificity,Trypanosoma cruzi,Trypanosoma cruzi: chemistry,Trypanosoma cruzi: classification,Trypanosoma cruzi: genetics} }

@article{thompsonTRNACleavageConserved2008, title = {{{tRNA}} Cleavage Is a Conserved Response to Oxidative Stress in Eukaryotes.}, author = {Thompson, Debrah M. and Lu, Cheng and Green, Pamela J. and Parker, Roy}, year = 2008, month = oct, journal = {RNA (New York, N.Y.)}, volume = {14}, number = {10}, pages = {2095–103}, issn = {1469-9001}, doi = {10.1261/rna.1232808}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2553748&tool=pmcentrez&rendertype=abstract}, abstract = {Recent results have identified a diversity of small RNAs in a wide range of organisms. In this work, we demonstrate that Saccharomyces cerevisiae contains a small RNA population consisting primarily of tRNA halves and rRNA fragments. Both 5’ and 3’ fragments of tRNAs are detectable by Northern blot analysis, suggesting a process of endonucleolytic cleavage. tRNA and rRNA fragment production in yeast is most pronounced during oxidative stress conditions, especially during entry into stationary phase. Similar tRNA fragments are also observed in human cell lines and in plants during oxidative stress. These results demonstrate that tRNA cleavage is a conserved aspect of the response to oxidative stress.}, pmid = {18719243}, keywords = {Fungal,Fungal: metabolism,Humans,nosource,Oxidative Stress,Ribosomal,Ribosomal: metabolism,RNA,RNA Stability,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Transfer,Transfer: metabolism} } % == BibTeX quality report for thompsonTRNACleavageConserved2008: % ? Possibly abbreviated journal title RNA (New York, N.Y.)

@article{alcoleaProteomeProfilingLeishmania2011, title = {Proteome Profiling of {{Leishmania}} Infantum Promastigotes.}, author = {Alcolea, Pedro J. and Alonso, Ana and Larraga, Vicente}, year = 2011, journal = {The Journal of eukaryotic microbiology}, volume = {58}, number = {4}, eprint = {21569158}, eprinttype = {pubmed}, pages = {352–8}, issn = {1550-7408}, doi = {10.1111/j.1550-7408.2011.00549.x}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21569158}, abstract = {A proteome analysis of the promastigote stage of the trypanosomatid parasite Leishmania infantum (MON-1 zymodeme) is described here for the first time. Total protein extracts were prepared at early logarithmic and stationary phases of replicate axenic cultures and processed by 2D electrophoresis (pH 3-10). A total of 28 differentially regulated proteins were identified by matrix-assisted laser desorption/ionization-tandem time of flight mass spectrometry. This approach has revealed that the electron transfer flavoprotein (ETF) and the eukaryotic elongation factor 1{\(\alpha\)} (eEF1{\(\alpha\)}) subunit have the same differential expression pattern at the protein and mRNA levels, up-regulation in the stationary phase. A low-molecular-weight isoform and an alternatively processed form of the eEF1{\(\alpha\)} subunit have been detected. A 51 kDa subunit of replication factor A is up-regulated in dividing logarithmic promastigotes. None of the proteins described here shows opposite differential regulation values with the corresponding mRNA levels. Taken together with previous approaches to the proteome and the transcriptome, this report contributes to the elucidation of the differential regulation patterns of the ETF, the eEF1{\(\alpha\)} subunit, the 40S ribosomal protein S12, {\(\alpha\)}-tubulin and the T-complex protein 1 subunit {\(\gamma\)} throughout the life cycle of the parasites from the genus Leishmania.}, pmid = {21569158}, keywords = {Animals,Chaperonin Containing TCP-1,Chaperonin Containing TCP-1: genetics,Chaperonin Containing TCP-1: metabolism,Electron-Transferring Flavoproteins,Electron-Transferring Flavoproteins: biosynthesis,Electron-Transferring Flavoproteins: genetics,Leishmania infantum,Leishmania infantum: genetics,Leishmania infantum: metabolism,Life Cycle Stages,Mass,Matrix-Assisted Laser Desorpti,Messenger,Messenger: analysis,Messenger: genetics,nosource,Protein Isoforms,Protein Isoforms: genetics,Protein Isoforms: metabolism,Proteome,Proteome: genetics,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Psychodidae,Psychodidae: parasitology,Ribosomal,Ribosomal: genetics,RNA,Spectrometry,Tubulin,Tubulin: genetics,Tubulin: metabolism,Up-Regulation} }

@article{menezesProteomicAnalysisReveals2013, title = {Proteomic Analysis Reveals Differentially Expressed Proteins in Macrophages Infected with {{Leishmania}} Amazonensis or {{Leishmania}} Major.}, author = {Menezes, J. P. B. and Almeida, T. F. and {}a Petersen, a L. O. and Guedes, C. E. S. and Mota, M. S. V. and Lima, J. G. B. and Palma, L. C. and {}a Buck, G. and {}a Krieger, M. and Probst, C. M. and Veras, P. S. T.}, year = 2013, journal = {Microbes and infection / Institut Pasteur}, volume = {15}, number = {8-9}, eprint = {23628411}, eprinttype = {pubmed}, pages = {579–91}, publisher = {Elsevier Masson SAS}, issn = {1769-714X}, doi = {10.1016/j.micinf.2013.04.005}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23628411}, abstract = {CBA macrophages effectively control Leishmania major infection, yet are permissive to Leishmania amazonensis. Employing a transcriptomic approach, we previously showed the up-regulation of the genes involved in the classical pathway of macrophage activation in resistant mice. However, microarray analyses do not evaluate changes in gene expression that occur after translation. To circumvent this analytical limitation, we employed a proteomics approach to increase our understanding of the modulations that occur during infection and identify novel targets for the control of Leishmania infection. To identify proteins whose expression changes in CBA macrophages infected with L. major or L. amazonensis, protein extracts were obtained and digested and the peptides were characterized using multi-dimensional liquid chromatography coupled with tandem mass spectrometry analyses. A total of 162 proteins were selected as potentially modulated. Using biological network analyses, these proteins were classified as primarily involved in cellular metabolism and grouped into cellular development biological networks. This study is the first to use a proteomics approach to describe the protein modulations involved in cellular metabolism during the initial events of Leishmania-macrophage interaction. Based on these findings, we hypothesize that these differentially expressed proteins likely play a pivotal role in determining the course of infection.}, pmid = {23628411}, keywords = {leishmania amazonensis,leishmania major,macrophages,nosource,proteomics} }

@article{lynnDifferentialQuantitativeProteomic2013, title = {Differential Quantitative Proteomic Profiling of {{Leishmania}} Infantum and {{Leishmania}} Mexicana Density Gradient Separated Membranous Fractions.}, author = {{}a Lynn, Miriam and Marr, Alexandra K. and McMaster, W. Robert}, year = 2013, month = apr, journal = {Journal of proteomics}, volume = {82}, eprint = {23466312}, eprinttype = {pubmed}, pages = {179–92}, publisher = {Elsevier B.V.}, issn = {1876-7737}, doi = {10.1016/j.jprot.2013.02.010}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23466312}, abstract = {UNLABELLED: Leishmaniasis, caused by infection with Leishmania, is a major public health concern affecting more than 20million people globally. Leishmania has a digenetic lifecycle consisting of an extracellular flagellated promastigote, adapted to live in the mid-gut of the sand fly host and an aflagellated intracellular amastigote that resides within the macrophage of the mammalian host. Leishmania mexicana and Leishmania infantum are causative agents of cutaneous and visceral leishmaniasis, respectively. Membrane proteins play a pivotal role in host-pathogen interactions and in regulatory pathways. As the genome of Leishmania is essentially constitutively expressed, regulation of protein expression during differentiation occurs post-transcriptionally and/or post-translationally. Quantitative mass spectrometry using iTRAQ labeling identified differences in the proteomes of density gradient separated membranous fractions of promastigote and amastigote life-stages. We identified 189 L. infantum and 107 L. mexicana non-redundant proteins of which 20-40% showed differential expression levels between promastigote and amastigote lifecycle stages. Differentially expressed proteins mapped to several pathways including cell motility, metabolism, and infectivity as well as virulence factors such as eEF-1{\(\alpha\)}, amastin and leishmanolysin (GP63). Western blot analysis validated iTRAQ quantitation for leishmanolysin. Focusing on differentially expressed proteins essential for pathogenesis, may ultimately lead to the identification of novel potential therapeutic targets. BIOLOGICAL SIGNIFICANCE: Leishmania, protozoan parasites of the Trypanosomatidae family, are the causative agents of leishmaniasis that represents a major public health concern affecting more than 20million people globally Membrane associated proteins play a pivotal role in host-pathogen interactions and in regulatory pathways. Quantitative proteomic analysis of the membranous fractions from L. mexicana and L. infantum (causative agents of cutaneous and visceral leishmaniasis, respectively) identified a number of proteins that may have important stage-specific functions in either the sand fly or mammalian host. The function of these proteins includes roles in virulence, as well as differences in metabolic process between life stages. Many of the proteins identified may act as virulence factors playing significant roles in parasite invasion, host-parasite interaction or parasite survival and thus may have therapeutic potential as drug target candidates.}, pmid = {23466312}, keywords = {iTRAQ,Leishmania infantum,Leishmania mexicana,nosource,Quantitative protein profiling,Stable isotope labeling} }

@article{lahavMultipleLevelsGene2011, title = {Multiple Levels of Gene Regulation Mediate Differentiation of the Intracellular Pathogen {{Leishmania}}.}, author = {Lahav, T. and Sivam, D. and Volpin, H. and Ronen, M. and Tsigankov, P. and Green, a and Holland, N. and Kuzyk, M. and Borchers, C. and Zilberstein, D. and Myler, P. J.}, year = 2011, month = feb, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {25}, number = {2}, eprint = {20952481}, eprinttype = {pubmed}, pages = {515–25}, issn = {1530-6860}, doi = {10.1096/fj.10-157529}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20952481}, abstract = {For many years, mRNA abundance has been used as the surrogate measure of gene expression in biological systems. However, recent genome-scale analyses in both bacteria and eukaryotes have revealed that mRNA levels correlate with steady-state protein abundance for only 50-70% of genes, indicating that translation and post-translation processes also play important roles in determining gene expression. What is not yet clear is whether dynamic processes such as cell cycle progression, differentiation, or response to environmental changes change the relationship between mRNA and protein abundance. Here, we describe a systems approach to interrogate promastigote-to-amastigote differentiation in the obligatory intracellular parasitic protozoan Leishmania donovani. Our results indicate that regulation of mRNA levels plays a major role early in the differentiation process, while translation and post-translational regulation are more important in the latter part. In addition, it appears that the differentiation signal causes a transient global increase in the rate of protein synthesis, which is subsequently down-regulated by phosphorylation of {\(\alpha\)}-subunit of translation initiation factor 2. Thus, Leishmania dynamically changes the relationship between mRNA and protein abundance as it adapts to new environmental circumstances. It is likely that similar mechanisms play a more important role than previously recognized in regulation of gene expression in other organisms.}, pmid = {20952481}, keywords = {Animals,Cell Differentiation,Gene Expression Regulation,Gene Expression Regulation: physiology,Leishmania donovani,Leishmania donovani: genetics,Leishmania donovani: metabolism,Messenger,Messenger: genetics,Messenger: metabolism,nosource,Oligonucleotide Array Sequence Analysis,Protein Folding,Protozoan,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Protozoan: genetics,Protozoan: metabolism,RNA,Time Factors} }

@article{agamiNucleotideSequenceSpliced1992, title = {Nucleotide Sequence of the Spliced Leader {{RNA}} Gene from {{Leishmania}} Mexicana Amazonensis.}, author = {Agami, R. and Shapira, M.}, year = 1992, month = apr, journal = {Nucleic acids research}, volume = {20}, number = {7}, pages = {1804}, issn = {0305-1048}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=312276&tool=pmcentrez&rendertype=abstract}, pmid = {1579474}, keywords = {Animals,Base Sequence,Blotting,Deoxyribonucleases,DNA,Leishmania mexicana,Leishmania mexicana: genetics,Messenger,Messenger: genetics,Molecular Sequence Data,Multigene Family,Multigene Family: genetics,nosource,Protozoan,Protozoan: genetics,Protozoan: metabolism,RNA,RNA Splicing,RNA Splicing: genetics,Southern,Type II Site-Specific,Type II Site-Specific: metabol} }

@article{parsonsTrypanosomeMRNAsShare1984, title = {Trypanosome {{mRNAs}} Share a Common 5’ Spliced Leader Sequence.}, author = {Parsons, M. and Nelson, R. G. and Watkins, K. P. and Agabian, N.}, year = 1984, month = aug, journal = {Cell}, volume = {38}, number = {1}, eprint = {6088073}, eprinttype = {pubmed}, pages = {309–16}, issn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/6088073}, abstract = {A 5’-terminal leader sequence of 35 nucleotides was found to be present on multiple trypanosome RNAs. Based on its representation in cDNA libraries, we estimate that many, if not all, trypanosome mRNAs contain this leader. This same leader was originally identified on mRNAs encoding the molecules responsible for antigenic variation, variant surface glycoproteins. Studies of selected cDNAs containing this leader sequence revealed that leader-containing transcripts can be stage-specific, stage-regulated, or constitutive. They can be abundant or rare, and transcribed from single or multigene families. No linkage between the genomic leader sequences and the structural gene exons was observed. Possible mechanisms by which the leader sequences are added to trypanosome mRNAs are discussed.}, pmid = {6088073}, keywords = {Amino Acid Sequence,Animals,Base Sequence,Cloning,DNA,DNA Restriction Enzymes,DNA: analysis,Genes,Genetic,Genetic Linkage,Messenger,Messenger: genetics,Molecular,nosource,Nucleic Acid Hybridization,RNA,RNA Splicing,Transcription,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics} }

@article{milhausenIdentificationSmallRNA1984, title = {Identification of a Small {{RNA}} Containing the Trypanosome Spliced Leader: A Donor of Shared 5’ Sequences of Trypanosomatid {{mRNAs}}?}, author = {Milhausen, M. and Nelson, R. G. and Sather, S. and Selkirk, M. and Agabian, N.}, year = 1984, month = oct, journal = {Cell}, volume = {38}, number = {3}, eprint = {6091897}, eprinttype = {pubmed}, pages = {721–9}, issn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/6091897}, abstract = {The 35 nucleotide spliced leader (SL) sequence is found on the 5’ end of numerous trypanosome mRNAs, yet the tandemly organized reiteration units encoding this leader are not detectably linked to any of these structural genes. Here we report the presence of a class of discrete small SL RNA molecules that are derived from the genomic SL reiteration units of Trypanosoma brucei, Trypanosoma cruzi, and Leptomonas collosoma. These small SL RNAs are 135, 105, and 95 nucleotides, respectively, and contain a 5’-terminal SL or SL-like sequence. S1 nuclease analyses demonstrate that these small SL RNAs are transcribed from continuous sequence within the respective SL reiteration units. With the exception of the SL sequence and a concensus donor splice site immediately following it, these small RNAs are not well conserved. We suggest that the small SL RNAs may function as a donor of the SL sequence in an intermolecular process that places the SL at the 5’ terminus of many trypanosomatid mRNAs.}, pmid = {6091897}, keywords = {Animals,Base Sequence,Cloning,DNA,DNA: analysis,Endonucleases,Genetic,Messenger,Messenger: genetics,Molecular,nosource,Nucleic Acid Hybridization,RNA,RNA Splicing,Single-Strand Specific DNA and RNA Endonucleases,Transcription,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics} }

@article{ivensGenomeKinetoplastidParasite2005, title = {The Genome of the Kinetoplastid Parasite, {{Leishmania}} Major.}, author = {Ivens, Alasdair C. and Peacock, Christopher S. and {}a Worthey, Elizabeth and Murphy, Lee and Aggarwal, Gautam and Berriman, Matthew and Sisk, Ellen and Rajandream, Marie-Adele and Adlem, Ellen and Aert, Rita and Anupama, Atashi and Apostolou, Zina and Attipoe, Philip and Bason, Nathalie and Bauser, Christopher and Beck, Alfred and Beverley, Stephen M. and Bianchettin, Gabriella and Borzym, Katja and Bothe, Gordana and Bruschi, Carlo V. and Collins, Matt and Cadag, Eithon and Ciarloni, Laura and Clayton, Christine and Coulson, Richard M. R. and Cronin, Ann and Cruz, Angela K. and Davies, Robert M. and Gaudenzi, Javier De and Dobson, Deborah E. and Duesterhoeft, Andreas and Fazelina, Gholam and Fosker, Nigel and Frasch, Alberto Carlos and Fraser, Audrey and Fuchs, Monika and Gabel, Claudia and Goble, Arlette and Goffeau, Andr{'e} and Harris, David and {Hertz-Fowler}, Christiane and Hilbert, Helmut and Horn, David and Huang, Yiting and Klages, Sven and Knights, Andrew and Kube, Michael and Larke, Natasha and Litvin, Lyudmila and Lord, Angela and Louie, Tin and Marra, Marco and Masuy, David and Matthews, Keith and Michaeli, Shulamit and Mottram, Jeremy C. and {M{"u}ller-Auer}, Silke and Munden, Heather and Nelson, Siri and Norbertczak, Halina and Oliver, Karen and O’neil, Susan and Pentony, Martin and Pohl, Thomas M. and Price, Claire and Purnelle, B{'e}n{'e}dicte and {}a Quail, Michael and Rabbinowitsch, Ester and Reinhardt, Richard and Rieger, Michael and Rinta, Joel and Robben, Johan and Robertson, Laura and Ruiz, Jeronimo C. and Rutter, Simon and Saunders, David and Sch{"a}fer, Melanie and Schein, Jacquie and Schwartz, David C. and Seeger, Kathy and Seyler, Amber and Sharp, Sarah and Shin, Heesun and Sivam, Dhileep and Squares, Rob and Squares, Steve and Tosato, Valentina and Vogt, Christy and Volckaert, Guido and Wambutt, Rolf and Warren, Tim and Wedler, Holger and Woodward, John and Zhou, Shiguo and Zimmermann, Wolfgang and Smith, Deborah F. and Blackwell, Jenefer M. and Stuart, Kenneth D. and Barrell, Bart and Myler, Peter J.}, year = 2005, month = jul, journal = {Science (New York, N.Y.)}, volume = {309}, number = {5733}, pages = {436–42}, issn = {1095-9203}, doi = {10.1126/science.1112680}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1470643&tool=pmcentrez&rendertype=abstract}, abstract = {Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The organization of protein-coding genes into long, strand-specific, polycistronic clusters and lack of general transcription factors in the L. major, Trypanosoma brucei, and Trypanosoma cruzi (Tritryp) genomes suggest that the mechanisms regulating RNA polymerase II-directed transcription are distinct from those operating in other eukaryotes, although the trypanosomatids appear capable of chromatin remodeling. Abundant RNA-binding proteins are encoded in the Tritryp genomes, consistent with active posttranscriptional regulation of gene expression.}, pmid = {16020728}, keywords = {Animals,Chromatin,Chromatin: genetics,Chromatin: metabolism,Cutaneous,Cutaneous: parasitology,DNA,Gene Expression Regulation,Genes,Genetic,Genome,Glycoconjugates,Glycoconjugates: biosynthesis,Glycoconjugates: metabolism,Leishmania major,Leishmania major: chemistry,Leishmania major: genetics,Leishmania major: metabolism,Leishmaniasis,Lipid Metabolism,Membrane Proteins,Membrane Proteins: biosynthesis,Membrane Proteins: chemistry,Membrane Proteins: genetics,Membrane Proteins: metabolism,Molecular Sequence Data,Multigene Family,nosource,Post-Transcriptional,Post-Translational,Protein Biosynthesis,Protein Processing,Protozoan,Protozoan Proteins,Protozoan Proteins: biosynthesis,Protozoan Proteins: chemistry,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Protozoan: genetics,Protozoan: metabolism,RNA,RNA Processing,RNA Splicing,rRNA,Sequence Analysis,Transcription} } % == BibTeX quality report for ivensGenomeKinetoplastidParasite2005: % ? Possibly abbreviated journal title Science (New York, N.Y.)

@article{mottaPredictingProteinsAngomonas2013, title = {Predicting the Proteins of {{Angomonas}} Deanei, {{Strigomonas}} Culicis and Their Respective Endosymbionts Reveals New Aspects of the Trypanosomatidae Family.}, author = {Motta, Maria Cristina Machado and Martins, Allan Cezar De Azevedo and {}de Souza, Silvana Sant’Anna and {Catta-Preta}, Carolina Moura Costa and Silva, Rosane and Klein, Cecilia Coimbra and {}de Almeida, Luiz Gonzaga Paula and Cunha, Oberdan de Lima and Ciapina, Luciane Prioli and Brocchi, Marcelo and Colabardini, Ana Cristina and Lima, Bruna de Araujo and Machado, Carlos Renato and Soares, C{'e}lia Maria de Almeida and Probst, Christian Macagnan and {}de Menezes, Claudia Beatriz Afonso and Thompson, Claudia Elizabeth and Bartholomeu, Daniella Castanheira and Gradia, Daniela Fiori and Pavoni, Daniela Parada and Grisard, Edmundo C. and {Fantinatti-Garboggini}, Fabiana and Marchini, Fabricio Klerynton and {Rodrigues-Luiz}, Gabriela Fl{'a}via and Wagner, Glauber and Goldman, Gustavo Henrique and Fietto, Juliana Lopes Rangel and Elias, Maria Carolina and Goldman, Maria Helena S. and Sagot, Marie-France and Pereira, Maristela and Stoco, Patr{'i}cia H. and {}de {Mendon{}a-Neto}, Rondon Pessoa and Teixeira, Santuza Maria Ribeiro and Maciel, Talles Eduardo Ferreira and Mendes, Tiago Ant{^o}nio de Oliveira and {"U}rm{'e}nyi, Tur{'a}n P. and {}de Souza, Wanderley and Schenkman, Sergio and {}de Vasconcelos, Ana Tereza Ribeiro}, year = 2013, month = jan, journal = {PloS one}, volume = {8}, number = {4}, pages = {e60209}, issn = {1932-6203}, doi = {10.1371/journal.pone.0060209}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3616161&tool=pmcentrez&rendertype=abstract}, abstract = {Endosymbiont-bearing trypanosomatids have been considered excellent models for the study of cell evolution because the host protozoan co-evolves with an intracellular bacterium in a mutualistic relationship. Such protozoa inhabit a single invertebrate host during their entire life cycle and exhibit special characteristics that group them in a particular phylogenetic cluster of the Trypanosomatidae family, thus classified as monoxenics. In an effort to better understand such symbiotic association, we used DNA pyrosequencing and a reference-guided assembly to generate reads that predicted 16,960 and 12,162 open reading frames (ORFs) in two symbiont-bearing trypanosomatids, Angomonas deanei (previously named as Crithidia deanei) and Strigomonas culicis (first known as Blastocrithidia culicis), respectively. Identification of each ORF was based primarily on TriTrypDB using tblastn, and each ORF was confirmed by employing getorf from EMBOSS and Newbler 2.6 when necessary. The monoxenic organisms revealed conserved housekeeping functions when compared to other trypanosomatids, especially compared with Leishmania major. However, major differences were found in ORFs corresponding to the cytoskeleton, the kinetoplast, and the paraflagellar structure. The monoxenic organisms also contain a large number of genes for cytosolic calpain-like and surface gp63 metalloproteases and a reduced number of compartmentalized cysteine proteases in comparison to other TriTryp organisms, reflecting adaptations to the presence of the symbiont. The assembled bacterial endosymbiont sequences exhibit a high A+T content with a total of 787 and 769 ORFs for the Angomonas deanei and Strigomonas culicis endosymbionts, respectively, and indicate that these organisms hold a common ancestor related to the Alcaligenaceae family. Importantly, both symbionts contain enzymes that complement essential host cell biosynthetic pathways, such as those for amino acid, lipid and purine/pyrimidine metabolism. These findings increase our understanding of the intricate symbiotic relationship between the bacterium and the trypanosomatid host and provide clues to better understand eukaryotic cell evolution.}, pmid = {23560078}, keywords = {nosource} }

@article{guttmanRibosomeProfilingProvides2013, title = {Ribosome {{Profiling Provides Evidence}} That {{Large Noncoding RNAs Do Not Encode Proteins}}.}, author = {Guttman, Mitchell and Russell, Pamela and Ingolia, Nicholas T. and Weissman, Jonathan S. and Lander, Eric S.}, year = 2013, month = jul, journal = {Cell}, volume = {154}, number = {1}, eprint = {23810193}, eprinttype = {pubmed}, pages = {240–51}, publisher = {Elsevier Inc.}, issn = {1097-4172}, doi = {10.1016/j.cell.2013.06.009}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23810193}, abstract = {Large noncoding RNAs are emerging as an important component in cellular regulation. Considerable evidence indicates that these transcripts act directly as functional RNAs rather than through an encoded protein product. However, a recent study of ribosome occupancy reported that many large intergenic ncRNAs (lincRNAs) are bound by ribosomes, raising the possibility that they are translated into proteins. Here, we show that classical noncoding RNAs and 5’ UTRs show the same ribosome occupancy as lincRNAs, demonstrating that ribosome occupancy alone is not sufficient to classify transcripts as coding or noncoding. Instead, we define a metric based on the known property of translation whereby translating ribosomes are released upon encountering a bona fide stop codon. We show that this metric accurately discriminates between protein-coding transcripts and all classes of known noncoding transcripts, including lincRNAs. Taken together, these results argue that the large majority of lincRNAs do not function through encoded proteins.}, pmid = {23810193}, keywords = {nosource} }

@article{uphoffDetectionMycoplasmaContaminations2013, title = {Detection of {{Mycoplasma Contaminations}}}, author = {Uphoff, Cord C. and Drexler, Hans G.}, editor = {Helgason, Cheryl D. and Miller, Cindy L.}, year = 2013, volume = {946}, pages = {1–13}, publisher = {Humana Press}, doi = {10.1007/978-1-62703-128-8}, url = {http://www.springerlink.com/index/10.1007/978-1-62703-128-8}, isbn = {978-1-62703-127-1}, keywords = {bacteria,cell lines,contamination,mycoplasma,nosource,pcr} } % == BibTeX quality report for uphoffDetectionMycoplasmaContaminations2013: % Missing required field ‘journal’ % ? Title looks like it was stored in title-case in Zotero

@article{parkinsonPreparationHighqualityNextgeneration2012, title = {Preparation of High-Quality next-Generation Sequencing Libraries from Picogram Quantities of Target {{DNA}}}, author = {Parkinson, N. J. and Maslau, Siarhei}, year = 2012, journal = {Genome }, pages = {125–133}, doi = {10.1101/gr.124016.111.Freely}, url = {http://genome.cshlp.org/content/22/1/125.short}, keywords = {nosource} }

@book{millerBasicCellCulture1997, title = {Basic Cell Culture Protocols}, author = {Miller, C. Helgason; C.}, year = 1997, url = {http://books.google.com/books?hl=en&lr=&id=cql_pf8ZBs4C&oi=fnd&pg=PR7&dq=Basic+Cell+Culture+Protocols&ots=jqHRlhpZFn&sig=UlEqsIEjjeL7BJq2U7OZdxNoZ_U}, isbn = {978-1-62703-127-1}, keywords = {nosource} } % == BibTeX quality report for millerBasicCellCulture1997: % Missing required field ‘publisher’

@article{bretonDistributionDiversityMycoplasma2012, title = {Distribution and Diversity of Mycoplasma Plasmids: Lessons from Cryptic Genetic Elements.}, author = {Breton, Marc and Tardy, Florence and {Dordet-Frisoni}, Emilie and Sagne, Eveline and Mick, Virginie and Renaudin, Jo{"e}l and {Sirand-Pugnet}, Pascal and Citti, Christine and Blanchard, Alain}, year = 2012, month = jan, journal = {BMC microbiology}, volume = {12}, number = {1}, pages = {257}, publisher = {BMC Microbiology}, issn = {1471-2180}, doi = {10.1186/1471-2180-12-257}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3541243&tool=pmcentrez&rendertype=abstract}, abstract = {BACKGROUND: The evolution of mycoplasmas from a common ancestor with Firmicutes has been characterized not only by genome down-sizing but also by horizontal gene transfer between mycoplasma species sharing a common host. The mechanisms of these gene transfers remain unclear because our knowledge of the mycoplasma mobile genetic elements is limited. In particular, only a few plasmids have been described within the Mycoplasma genus. RESULTS: We have shown that several species of ruminant mycoplasmas carry plasmids that are members of a large family of elements and replicate via a rolling-circle mechanism. All plasmids were isolated from species that either belonged or were closely related to the Mycoplasma mycoides cluster; none was from the Mycoplasma bovis-Mycoplasma agalactiae group. Twenty one plasmids were completely sequenced, named and compared with each other and with the five mycoplasma plasmids previously reported. All plasmids share similar size and genetic organization, and present a mosaic structure. A peculiar case is that of the plasmid pMyBK1 from M. yeatsii; it is larger in size and is predicted to be mobilizable. Its origin of replication and replication protein were identified. In addition, pMyBK1 derivatives were shown to replicate in various species of the M. mycoides cluster, and therefore hold considerable promise for developing gene vectors. The phylogenetic analysis of these plasmids confirms the uniqueness of pMyBK1 and indicates that the other mycoplasma plasmids cluster together, apart from the related replicons found in phytoplasmas and in species of the clade Firmicutes. CONCLUSIONS: Our results unraveled a totally new picture of mycoplasma plasmids. Although they probably play a limited role in the gene exchanges that participate in mycoplasma evolution, they are abundant in some species. Evidence for the occurrence of frequent genetic recombination strongly suggests they are transmitted between species sharing a common host or niche.}, pmid = {23145790}, keywords = {Animals,Bacterial,Bacterial: chemistry,Bacterial: genetics,Cluster Analysis,DNA,Gene Order,Gene Transfer,Genetic,Genetic Variation,Horizontal,Molecular Sequence Data,Mycoplasma Infections,Mycoplasma Infections: microbiology,Mycoplasma Infections: veterinary,Mycoplasma mycoides,Mycoplasma mycoides: genetics,Mycoplasma mycoides: isolation & purification,nosource,Phylogeny,Plasmids,Recombination,Ruminants,Sequence Analysis} }

@article{kervestinNMDMultifacetedResponse2012, title = {{{NMD}}: A Multifaceted Response to Premature Translational Termination.}, author = {Kervestin, Stephanie and Jacobson, Allan}, year = 2012, month = nov, journal = {Nature reviews. Molecular cell biology}, volume = {13}, number = {11}, eprint = {23072888}, eprinttype = {pubmed}, pages = {700–12}, publisher = {Nature Publishing Group}, issn = {1471-0080}, doi = {10.1038/nrm3454}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23072888}, abstract = {Although most mRNA molecules derived from protein-coding genes are destined to be translated into functional polypeptides, some are eliminated by cellular quality control pathways that collectively perform the task of mRNA surveillance. In the nonsense-mediated decay (NMD) pathway premature translation termination promotes the recruitment of a set of factors that destabilize a targeted mRNA. The same factors also seem to have key roles in repressing the translation of the mRNA, dissociating its terminating ribosome and messenger ribonucleoproteins (mRNPs), promoting the degradation of its truncated polypeptide product and possibly even feeding back to the site of transcription to interfere with splicing of the primary transcript.}, pmid = {23072888}, keywords = {Codon,Humans,Messenger,Messenger: genetics,Messenger: metabolism,Nonsense,Nonsense Mediated mRNA Decay,nosource,Peptide Chain Termination,Peptide Termination Factors,Peptide Termination Factors: genetics,Peptide Termination Factors: metabolism,Protein Biosynthesis,Ribonucleoproteins,Ribonucleoproteins: genetics,Ribonucleoproteins: metabolism,Ribosomes,Ribosomes: genetics,Ribosomes: metabolism,RNA,RNA Stability,RNA Stability: genetics,RNA-Binding Proteins,RNA-Binding Proteins: metabolism,Trans-Activators,Trans-Activators: metabolism,Transcription Factors,Transcription Factors: metabolism,Translational,Translational: genetics} } % == BibTeX quality report for kervestinNMDMultifacetedResponse2012: % ? Possibly abbreviated journal title Nature reviews. Molecular cell biology

@article{wortheyLeishmaniaMajorChromosome2003, title = {Leishmania Major Chromosome 3 Contains Two Long Convergent Polycistronic Gene Clusters Separated by a {{tRNA}} Gene}, author = {{}a Worthey, E.}, year = 2003, month = jul, journal = {Nucleic Acids Research}, volume = {31}, number = {14}, pages = {4201–4210}, issn = {1362-4962}, doi = {10.1093/nar/gkg469}, url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkg469}, keywords = {nosource} }

@article{leibundgutSelenocysteineTRNAspecificElongation2005, title = {Selenocysteine {{tRNA-specific}} Elongation Factor {{SelB}} Is a Structural Chimaera of Elongation and Initiation Factors}, author = {Leibundgut, Marc and Frick, Christian and Thanbichler, Martin and B{"o}ck, August and Ban, Nenad}, year = 2005, journal = {EMBO J.}, volume = {24}, pages = {11–22}, doi = {10.1038/sj.emboj.7600505}, abstract = {In all three kingdoms of life, SelB is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop. Here, we present the X-ray structures of SelB from the archaeon Methanococcus maripaludis in the apo-, GDP- and GppNHp-bound form and use mutational analysis to investigate the role of individual amino acids in its aminoacyl-binding pocket. All three SelB structures reveal an EF-Tu:GTP-like domain arrangement. Upon binding of the GTP analogue GppNHp, a conformational change of the Switch 2 region in the GTPase domain leads to the exposure of SelB residues involved in clamping the 5 phosphate of the tRNA. A conserved extended loop in domain III of SelB may be responsible for specific interactions with tRNASec and act as a ruler for measuring the extra long acceptor arm. Domain IV of SelB adopts a {\(\beta\)} barrel fold and is flexibly tethered to domain III. The overall domain arrangement of SelB resembles a chalice’ observed so far only for initiation factor IF2/eIF5B. In our model of SelB bound to the ribosome, domain IV points towards the 3 mRNA entrance cleft ready to interact with the downstream secondary structure element.}, pmid = {15616587}, keywords = {amino acid sequence,archaeal proteins,archaeal proteins chemistry,archaeal proteins genetics,archaeal proteins metabolism,binding sites,crystallography,dna mutational analysis,eukaryotic initiation factors,eukaryotic initiation factors chemistry,guanosine diphosphate,guanosine diphosphate metabolism,guanosine triphosphate,guanosine triphosphate analogs & derivatives,guanosine triphosphate metabolism,methanococcus,methanococcus chemistry,methanococcus metabolism,models,molecular,molecular sequence data,nosource,nucleic acid conformation,peptide elongation factors,peptide elongation factors chemistry,peptide elongation factors genetics,peptide elongation factors metabolism,prokaryotic initiation factors,prokaryotic initiation factors chemistry,prokaryotic initiation factors genetics,prokaryotic initiation factors metabolism,protein binding,protein conformation,rna,sequence alignment,transfer,transfer metabolism,x ray} } % == BibTeX quality report for leibundgutSelenocysteineTRNAspecificElongation2005: % ? Possibly abbreviated journal title EMBO J.

@article{schomburgSeleniumSelenoproteinsMammals2004, title = {Selenium and Selenoproteins in Mammals: Extraordinary, Essential, Enigmatic.}, author = {Schomburg, L. and Schweizer, U. and K{"o}hrle, J.}, year = 2004, journal = {Cell. Mol. Life Sci.}, volume = {61}, pages = {1988–1995}, abstract = {Selenium (Se), once known only for its potential toxicity, is now well established as an essential trace element for mammals. Insufficient Se intake predisposes to and manifests in a variety of diseases. Recent studies have proven that it is the synthesis of selenocysteine (Sec)-containing proteins, designated selenoproteins, which represents an essential prerequisite for regular development and a long and healthy life. New transgenic mouse models analysing those selenoproteins with proven enzymatic functions displayed particular phenotypes and highlighted essential Se-dependent processes in development, growth or against specific challenges. While there is a growing molecular understanding of and general agreement on the importance of sufficiently high Se intake and undisturbed selenoprotein biosynthesis, many of the recently identified selenoproteins are still uncharacterised, and the effects and consequences of supra-physiological Se dosages are not biochemically understood. With the recent definition of the human and mouse selenoproteomes and a growing number of available tools, the Se field is now geared for a great leap forward. Se biology has already broadened our knowledge about the genetic code and about protein translation. It now holds great promises also for a better understanding of some key aspects of cancer, inflammation, fertility and prevention of age-associated diseases.}, pmid = {15316649}, keywords = {animals,enzymes,enzymes physiology,mice,nosource,protein biosynthesis,proteins,proteins physiology,selenium,selenium compounds,selenium compounds metabolism,selenium physiology,selenoproteins} } % == BibTeX quality report for schomburgSeleniumSelenoproteinsMammals2004: % ? Possibly abbreviated journal title Cell. Mol. Life Sci.

@article{yoshinakaMurineLeukemiaVirus1985, title = {Murine Leukemia Virus Protease Is Encoded by the Gag-Pol Gene and Is Synthesized through Suppression of an Amber Termination Codon.}, author = {Yoshinaka, Y. and Katoh, I. and Copeland, T. D. and Oroszlan, S.}, year = 1985, journal = {PNAS}, volume = {82}, pages = {1618–1622}, abstract = {We have purified from Moloney murine leukemia virus (Mo-MuLV) a protease that has the capacity of accurately cleaving the polyprotein precursor Pr65gag into the mature viral structural proteins. Both the NH2- and COOH-terminal amino acid sequences have been determined and aligned with the amino acid sequence deduced from the DNA sequence of Mo-MuLV by other workers. The results show that: (i) the protease is located at the 5’ end of the pol gene, and the first four amino acids are overlapped with the 3’ end of the gag gene; (ii) the fifth amino acid residue is glutamine, which is inserted by suppression of the UAG termination codon at the gag-pol junction; and (iii) the protease is composed of 125 amino acids with calculated Mr = 13,315, and the COOH terminus of the protease is adjacent to the NH2 terminus of reverse transcriptase. The map order of the gag-pol gene is proposed to be 5’-p15-p12-p30-p10-protease-reverse transcriptase-endonuclease-3’. Images:}, pmid = {3885215}, keywords = {amino acid sequence,codon,codon genetics,genes,genetic,moloney murine leukemia virus,moloney murine leukemia virus enzymology,moloney murine leukemia virus genetics,nosource,peptide hydrolases,peptide hydrolases biosynthesis,peptide hydrolases genetics,peptide hydrolases isolation & purification,protein biosynthesis,suppression,viral} }

@article{adamskiCompetitionFrameshiftingTermination1993, title = {Competition between Frameshifting, Termination and Suppression at the Frameshift Site in the {{Escherichia}} Coli Release Factor-2 {{mRNA}}.}, author = {Adamski, F. M. and Donly, B. C. and Tate, W. P.}, year = 1993, journal = {Nucleic Acids Res.}, volume = {21}, pages = {5074–5078}, abstract = {Competition between frameshifting, termination, and suppression at the frameshifting site in the release factor-2 (RF-2) mRNA was determined in vitro using a coupled transcription-translation system by adding a UGA suppressor tRNA. The expression system was programmed with a plasmid containing a trpE-prfB fusion gene so that each of the products of the competing events could be measured. With increasing concentrations of suppressor tRNA the readthrough product increased at the expense of both the termination and the frameshifting product indicating all three processes are in direct competition. The readthrough at the internal UGA termination codon was greater than that at the natural UGA termination codon at the end of the coding sequence. The results suggest that this enhanced suppression may reflect slower decoding of the internal stop codon by the release factor giving suppression a competitive advantage. The internal UGAC stop signal at the frameshift site has been proposed to be a relatively poor signal, but in addition the release factor may be less able to recognise the signal with the mRNA in such a constrained state. Consequently, the frameshifting event itself will be more competitive with termination in vivo because of this longer pause as the release factor is decoding the stop signal. Images:}, pmid = {7504811}, keywords = {nosource} } % == BibTeX quality report for adamskiCompetitionFrameshiftingTermination1993: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{advaniYeastTelomereMaintenance2013, title = {Yeast Telomere Maintenance Is Globally Controlled by Programmed Ribosomal Frameshifting and the Nonsense-Mediated {{mRNA}} Decay Pathway}, author = {Advani, V. and Belew, Ashton Trey and Dinman, Jonathan D.}, year = 2013, journal = {Translation}, volume = {1}, pages = {1–10}, keywords = {nosource} }

@article{schwartzNucleotideSequenceRous1983, title = {Nucleotide Sequence of {{Rous}} Sarcoma Virus.}, author = {Schwartz, D. E. and Tizard, R. and Gilbert, W.}, year = 1983, journal = {Cell}, volume = {32}, pages = {853–869}, abstract = {We present the 9312 nucleotide sequence of the Prague C (Pr-C) strain of Rous sarcoma virus (RSV). A comparison of known protein sequences with the nucleotide sequence allows assignment of the coding regions for the gag, pol, env and src genes. The gag gene is terminated by an amber stop codon and is contained within a different reading frame than is the pol gene. The pol and env genes overlap. The sequences surrounding the src gene in the Pr-C and Schmidt-Ruppin (SR-A) strains of RSV have been compared, and they reveal that an element, E, of approximately 153 nucleotides is present on the 3’ side of the src gene in Pr-C, and on the 5’ side in SR-A. We hypothesize that E was part of a duplicated region of over 250 nucleotides flanking the src gene in an ancestral RSV, and that differential deletion of one copy of E led to its positional difference in Pr-C and SR-A.}, pmid = {6299578}, keywords = {amino acid sequence,avian sarcoma viruses,avian sarcoma viruses genetics,base sequence,dna,dna biosynthesis,dna restriction enzymes,dna restriction enzymes metabolism,nosource,viral,viral analysis} }

@article{dinmanMechanismsImplicationsProgrammed2012, title = {Mechanisms and Implications of Programmed Translational Frameshifting.}, author = {Dinman, Jonathan D.}, year = 2012, journal = {RNA}, volume = {3}, pages = {661–73}, issn = {17577012}, doi = {10.1002/wrna.1126}, abstract = {While ribosomes must maintain translational reading frame in order to translate primary genetic information into polypeptides, cis-acting signals located in mRNAs represent higher order information content that can be used to fine-tune gene expression. Classes of signals have been identified that direct a fraction of elongating ribosomes to shift reading frame by one base in the 5’ (-1) or 3’ (+1) direction. This is called programmed ribosomal frameshifting (PRF). Although mechanisms of PRF differ, a common feature is induction of ribosome pausing, which alters kinetic partitioning rates between in-frame and out-of-frame codons at specific ‘slippery’ sequences. Many viruses use PRF to ensure synthesis of the correct ratios of virus-encoded proteins required for proper viral particle assembly and maturation, thus identifying PRF as an attractive target for antiviral therapeutics. In contrast, recent studies indicate that PRF signals may primarily function as mRNA destabilizing elements in cellular mRNAs. These studies suggest that PRF may be used to fine-tune gene expression through mRNA decay pathways. The possible regulation of PRF by noncoding RNAs is also discussed. WIREs RNA 2012 doi: 10.1002/wrna.1126 For further resources related to this article, please visit the WIREs website.}, pmid = {22715123}, keywords = {nosource} }

@article{eylerDistinctResponseYeast2011, title = {Distinct Response of Yeast Ribosomes to a Miscoding Event during Translation.}, author = {Eyler, Daniel E. and Green, Rachel}, year = 2011, journal = {RNA}, volume = {17}, pages = {925–932}, abstract = {Numerous mechanisms have evolved to control the accuracy of translation, including a recently discovered retrospective quality control mechanism in bacteria. This quality control mechanism is sensitive to perturbations in the codon:anticodon interaction in the P site of the ribosome that trigger a dramatic loss of fidelity in subsequent tRNA and release factor selection events in the A site. These events ultimately lead to premature termination of translation in response to an initial miscoding error. In this work, we extend our investigations of this mechanism to an in vitro reconstituted Saccharomyces cerevisiae translation system. We report that yeast ribosomes do not respond to mismatches in the P site by loss of fidelity in subsequent substrate recognition events. We conclude that retrospective editing, as initially characterized in Escherichia coli, does not occur in S. cerevisiae. These results highlight potential mechanistic differences in the functional core of highly conserved ribosomes.}, pmid = {21415142}, keywords = {mutation,nosource,paromomycin,paromomycin pharmacology,protein biosynthesis,ribosomes,ribosomes genetics,ribosomes metabolism,rna,saccharomyces cerevisiae,saccharomyces cerevisiae drug effects,saccharomyces cerevisiae genetics,saccharomyces cerevisiae metabolism,thermodynamics,transfer,transfer genetics} }

@article{sohmenSnapShotAntiobioticInhibition2009, title = {{{SnapShot}}: {{Antiobiotic}} Inhibition of Protein Synthesis {{I}}}, author = {Sohmen, D. and Harms, J. M. and Schlunzen, F. and Wilson, D. N.}, year = 2009, journal = {Cell}, volume = {18}, pages = {1248.e1}, keywords = {nosource} }

@article{bulkleyRevisitingStructuresSeveral2010, title = {Revisiting the Structures of Several Antibiotics Bound to the Bacterial Ribosome.}, author = {Bulkley, David and Innis, C. Axel and Blaha, Gregor and Steitz, Thomas A.}, year = 2010, journal = {PNAS}, volume = {107}, pages = {17158–17163}, doi = {10.1073/pnas.1008685107}, abstract = {The increasing prevalence of antibiotic-resistant pathogens reinforces the need for structures of antibiotic-ribosome complexes that are accurate enough to enable the rational design of novel ribosome-targeting therapeutics. Structures of many antibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepancies between several of these models have raised the question of whether these differences arise from species-specific variations or from experimental problems. Our structure of chloramphenicol in complex with the 70S ribosome from Thermus thermophilus suggests a model for chloramphenicol bound to the large subunit of the bacterial ribosome that is radically different from the prevailing model. Further, our structures of the macrolide antibiotics erythromycin and azithromycin in complex with a bacterial ribosome are indistinguishable from those determined of complexes with the 50S subunit of Haloarcula marismortui, but differ significantly from the models that have been published for 50S subunit complexes of the eubacterium Deinococcus radiodurans. Our structure of the antibiotic telithromycin bound to the T. thermophilus ribosome reveals a lactone ring with a conformation similar to that observed in the H. marismortui and D. radiodurans complexes. However, the alkyl-aryl moiety is oriented differently in all three organisms, and the contacts observed with the T. thermophilus ribosome are consistent with biochemical studies performed on the Escherichia coli ribosome. Thus, our results support a mode of macrolide binding that is largely conserved across species, suggesting that the quality and interpretation of electron density, rather than species specificity, may be responsible for many of the discrepancies between the models.}, pmid = {20876130}, keywords = {nosource} }

@article{zhouDesignAtomicLevel2008, title = {Design at the Atomic Level: Generation of Novel Hybrid Biaryloxazolidinones as Promising New Antibiotics.}, author = {Zhou, Jiacheng and Bhattacharjee, Ashoke and Chen, Shili and Chen, Yi and Duffy, Erin and Farmer, Jay and Goldberg, Joel and Hanselmann, Roger and Ippolito, Joseph A. and Lou, Rongliang and Orbin, Alia and Oyelere, Ayomi and Salvino, Joe and Springer, Dane and Tran, Jennifer and Wang, Deping and Wu, Yusheng and Johnson, Graham}, year = 2008, journal = {Bioorg. Med. Chem. Lett.}, volume = {18}, pages = {6179–83}, issn = {14643405}, doi = {10.1016/j.bmcl.2008.10.014}, pmid = {18951792}, keywords = {nosource} } % == BibTeX quality report for zhouDesignAtomicLevel2008: % ? Possibly abbreviated journal title Bioorg. Med. Chem. Lett.

@article{tensonAntibioticsRibosome2006, title = {Antibiotics and the Ribosome.}, author = {Tenson, Tanel and Mankin, Alexander}, year = 2006, journal = {Mol. Micro.}, volume = {59}, pages = {1664–1677}, abstract = {The ribosome is one of the main antibiotic targets in the cell. Recent years brought important insights into the mode of interaction of antibiotics with the ribosome and mechanisms of antibiotic action. Ribosome crystallography provided a detailed view of the interactions between antibiotics and rRNA. Advances in biochemical techniques let us better understand how the binding of small organic molecules can interfere with functions of an enzyme four orders of magnitude larger than the inhibitor. These and other achievements paved the way for the development of new ribosome-targeting antibiotics, some of which have already entered medical practice. The recent progress, problems and new directions of research of ribosome-targeting antibiotics are discussed in this review.}, pmid = {16553874}, keywords = {anti bacterial agents,anti bacterial agents pharmacology,drug resistance,microbial,microbial genetics,mitochondrial proteins,mitochondrial proteins biosynthesis,mitochondrial proteins drug effects,nosource,protein biosynthesis,protein biosynthesis drug effects,protein synthesis inhibitors,protein synthesis inhibitors pharmacology,ribosomes,ribosomes chemistry,ribosomes drug effects,ribosomes genetics} } % == BibTeX quality report for tensonAntibioticsRibosome2006: % ? Possibly abbreviated journal title Mol. Micro.

@article{longResistanceLinezolidCaused2011, title = {Resistance to Linezolid Caused by Modifications at Its Binding Site on the Ribosome.}, author = {Long, Katherine S. and Vester, Birte}, year = 2011, journal = {Antimicrob. Agents Chemoth.}, volume = {56}, pages = {603–12}, issn = {10986596}, abstract = {Linezolid is an oxazolidinone antibiotic in clinical use for the treatment of serious infections of resistant gram-positive bacteria. It inhibits protein synthesis by binding to the peptidyl transferase center on the ribosome. Almost all known resistance mechanisms involve small alterations to the linezolid binding site, so this review will therefore focus on the various changes that can adversely affect drug binding and confer resistance. High-resolution structures of linezolid bound to the ribosomal 50S subunit show that it binds in a deep cleft that is surrounded by 23S rRNA nucleotides. Mutation of 23S rRNA has for some time been established as a linezolid resistance mechanism. Although ribosomal proteins L3 and L4 are located further away from the bound drug, mutations in specific regions of these proteins are increasingly being associated with linezolid resistance. However, very little evidence has been presented to confirm this. Furthermore, recent findings on the Cfr methyltransferase underscore the modification of 23S rRNA as a highly effective and transferable form of linezolid resistance. On a positive note, detailed knowledge of the linezolid binding site has facilitated the design of a new generation of oxazolidinones that show improved properties against the known resistance mechanisms.}, pmid = {22143525}, keywords = {nosource} } % == BibTeX quality report for longResistanceLinezolidCaused2011: % ? Possibly abbreviated journal title Antimicrob. Agents Chemoth.

@article{lambertAntibioticsThatAffect2012, title = {Antibiotics That Affect the Ribosome.}, author = {Lambert, T.}, year = 2012, journal = {Rev. Sci. Tech.}, volume = {31}, pages = {57–64}, issn = {02531933}, abstract = {The ribosome is a major bacterial target for antibiotics. Drugs inhibit ribosome function either by interfering in messenger RNA translation or by blocking the formation of peptide bonds at the peptidyl transferase centre. These effects are the consequence of the binding of drugs to the ribosomal subunits. Various mechanisms, including enzymatic detoxification, target alteration (ribosomal rRNAs and ribosomal proteins) and reduced accumulation (impermeability and efflux) are involved in bacterial resistance to protein synthesis inhibitors. The fact that some positions in rRNA participate in the binding of antibiotics belonging to distinct families explains why bacteria have developed mechanisms that can lead to cross-resistance.}, pmid = {22849268}, keywords = {16s rrna,23s rrna,aminoglycoside,fusidic acid,macrolide,nosource,orthosomycin,oxazolidinone,phenicol,pleuromutilin,protein synthesis,ribosomal protein,ribosome,tetracycline} } % == BibTeX quality report for lambertAntibioticsThatAffect2012: % ? Possibly abbreviated journal title Rev. Sci. Tech.

@article{kannanSelectiveProteinSynthesis2012, title = {Selective Protein Synthesis by Ribosomes with a Drug-Obstructed Exit Tunnel}, author = {Kannan, K. and {Vazquez-Laslop}, Nora and Mankin, A. S.}, year = 2012, journal = {Cell}, volume = {151}, pages = {508–520}, keywords = {nosource} }

@article{uchidaNovelRoleMammalian2002, title = {A Novel Role of the Mammalian {{GSPT}}/{{eRF3}} Associating with Poly({{A}})-Binding Protein in {{Cap}}/{{Poly}}({{A}})-Dependent Translation.}, author = {Uchida, Naoyuki and Hoshino, Shin-Ichi and Imataka, Hiroaki and Sonenberg, Nahum and Katada, Toshiaki}, year = 2002, journal = {J. Biol. Chem.}, volume = {277}, pages = {6700–6707}, abstract = {We have previously described the purification of a myelin basis protein (MBP) kinase from maturing sea star oocytes (Sanghera, J. S., Paddon, H. B., Bader, S. A., and Pelech, S. L. (1990) J. Biol. Chem. 265, 52-57). The ability of the purified 44-kDa protein to bind azido-ATP and undergo autophosphorylation on the serine residue implied that it is a protein kinase. Furthermore, partial amino acid sequence data has revealed that it is a novel protein kinase, which we have provisionally designated p44mpk. Autophosphorylation of p44mpk to 0.7 mol of phosphate/mol of enzyme was correlated with a modest (approximately 17%) increase in the MBP-phosphorylating activity of the kinase. Rabbit polyclonal antibody raised against purified p44mpk recognized on immunoblots the protein in highly purified preparations as well as crude oocyte extracts. The affinity-purified anti-p44mpk antibody could immunoprecipitate active kinase, but a subpopulation of the antibody also appeared to be inhibitory. Using this antibody, we have demonstrated that the up to 12-fold stimulation of the cytosolic MBP-phosphorylating activity of this kinase that occurs during sea star oocyte maturation is not due to an increase in the amount of enzyme protein, either from a redistribution within the oocyte or protein synthesis. A slight retardation of the migration of the activated p44mpk on sodium dodecyl sulfate-polyacrylamide gels and its tighter interaction with a MonoQ column is consistent with phosphorylation of the kinase during maturation. p44mpk underwent enhanced phosphorylation when oocytes prelabeled with 32Porthophosphate were induced to mature with 1-methyladenine. The stimulated MBP-phosphorylating activity of p44mpk in cytosols from maturing oocytes was partly stabilized by the presence of the phosphatase inhibitor beta-glycerol phosphate. Furthermore, treatment of purified p44mpk with protein phosphatase 2A and alkaline phosphatase resulted in 56 and 86% decreases, respectively, in the activity of the kinase. Together, these findings strongly implicate a role for phosphorylation of p44mpk in its activation during sea star oocyte maturation.}, pmid = {12381739}, keywords = {animals,binding sites,cercopithecus aethiops,cos cells,glutathione transferase,glutathione transferase genetics,glutathione transferase metabolism,hela cells,humans,kinetics,mutagenesis,nosource,peptide termination factors,peptide termination factors chemistry,peptide termination factors genetics,peptide termination factors metabolism,poly(a) binding proteins,poly(a) binding proteins chemistry,poly(a) binding proteins metabolism,protein biosynthesis,recombinant fusion proteins,recombinant fusion proteins metabolism,sequence deletion,transfection} } % == BibTeX quality report for uchidaNovelRoleMammalian2002: % ? Possibly abbreviated journal title J. Biol. Chem.

@article{khoshnevisNovelInsightsArchitecture2012, title = {Novel Insights into the Architecture and Protein Interaction Network of Yeast {{eIF3}}.}, author = {Khoshnevis, Sohail and Hauer, Florian and Mil{'o}n, Pohl and Stark, Holger and Ficner, Ralf}, year = 2012, journal = {RNA}, volume = {18}, pages = {2306–19}, issn = {14699001}, abstract = {Translation initiation in eukaryotes is a multistep process requiring the orchestrated interaction of several eukaryotic initiation factors (eIFs). The largest of these factors, eIF3, forms the scaffold for other initiation factors, promoting their binding to the 40S ribosomal subunit. Biochemical and structural studies on eIF3 need highly pure eIF3. However, natively purified eIF3 comprise complexes containing other proteins such as eIF5. Therefore we have established in vitro reconstitution protocols for Saccharomyces cerevisiae eIF3 using its five recombinantly expressed and purified subunits. This reconstituted eIF3 complex (eIF3(rec)) exhibits the same size and activity as the natively purified eIF3 (eIF3(nat)). The homogeneity and stoichiometry of eIF3(rec) and eIF3(nat) were confirmed by analytical size exclusion chromatography, mass spectrometry, and multi-angle light scattering, demonstrating the presence of one copy of each subunit in the eIF3 complex. The reconstituted and native eIF3 complexes were compared by single-particle electron microscopy showing a high degree of structural conservation. The interaction network between eIF3 proteins was studied by means of limited proteolysis, analytical size exclusion chromatography, in vitro binding assays, and isothermal titration calorimetry, unveiling distinct protein domains and subcomplexes that are critical for the integrity of the protein network in yeast eIF3. Taken together, the data presented here provide a novel procedure to obtain highly pure yeast eIF3, suitable for biochemical and structural analysis, in addition to a detailed picture of the network of protein interactions within this complex.}, keywords = {nosource} }

@article{karimiNovelRolesClassical1999, title = {Novel Roles for Classical Factors at the Interface between Translation Termination and Initiation.}, author = {Karimi, R. and Pavlov, M. Y. and Buckingham, R. H. and Ehrenberg, M.}, year = 1999, journal = {Mol. Cell}, volume = {3}, pages = {601–609}, abstract = {The pathway of bacterial ribosome recycling following translation termination has remained obscure. Here, we elucidate two essential steps and describe the roles played by the three translation factors EF-G, RRF, and IF3. Release factor RF3 is known to catalyze the dissociation of RF1 or RF2 from ribosomes after polypeptide release. We show that the next step is dissociation of 50S subunits from the 70S posttermination complex and that it is catalyzed by RRF and EF-G and requires GTP hydrolysis. Removal of deacylated tRNA from the resulting 30S:mRNA:tRNA posttermination complex is then necessary to permit rapid 30S subunit recycling. We show that this step requires initiation factor IF3, whose role was previously thought to be restricted to promoting specific 30S initiation complex formation from free 30S subunits.}, pmid = {10360176}, keywords = {acetylation,bacterial,base sequence,codon,escherichia coli,eukaryotic initiation factor 3,gene expression regulation,guanine,guanine pharmacology,guanosine triphosphate,guanosine triphosphate metabolism,hydrolysis,initiator,molecular sequence data,nosource,peptide elongation factor g,peptide elongation factors,peptide elongation factors genetics,peptide initiation factors,peptide initiation factors genetics,protein biosynthesis,protein biosynthesis drug effects,protein biosynthesis genetics,protein synthesis inhibitors,protein synthesis inhibitors pharmacology,proteins,proteins genetics,puromycin,puromycin pharmacology,ribosomal proteins,ribosomal proteins genetics,ribosomes,ribosomes genetics,ribosomes metabolism,rna,transfer,transfer genetics} } % == BibTeX quality report for karimiNovelRolesClassical1999: % ? Possibly abbreviated journal title Mol. Cell

@article{moraEssentialRoleInvariant2003, title = {The Essential Role of the Invariant {{GGQ}} Motif in the Function and Stability in Vivo of Bacterial Release Factors {{RF1}} and {{RF2}}}, author = {Mora, Liliana and {Heurgu{'e}-hamard}, Val{'e}rie and Champ, St{'e}phanie and Ehrenberg, M{}ns and Kisselev, Lev L. and Buckingham, Richard H.}, year = 2003, journal = {Mol. Micro.}, volume = {47}, pages = {267–275}, issn = {0950382X}, abstract = {Release factors RF1 and RF2 are required in bacteria for the cleavage of peptidyl-tRNA. A single sequence motif, GGQ, is conserved in all eubacterial, archaebacterial and eukaryotic release factors and may mimic the CCA end of tRNA, although the position of the motif in the crystal structures of human eRF1 and Escherichia coli RF2 is strikingly different. Mutations have been introduced at each of the three conserved positions. Changing the Gln residue to Ala or Glu allowed the factors to retain about 22% of tetrapeptide release activity in vitro, but these mutants could not complement thermosensitive RF mutants in vivo. None of several mutants with altered Gly residues retained activity in vivo or in vitro. Many GGQ mutants were poorly expressed and are presumably unstable; many were also toxic to the cell. The toxic mutant factors or their degradation products may bind to ribosomes inhibiting the action of the normal factor. These data are consistent with a common role for the GGQ motif in bacterial and eukaryotic release factors, despite strong divergence in primary, secondary and tertiary structure, but are difficult to reconcile with the hypothesis that the amide nitrogen of the Gln plays a vital role in peptidyl-tRNA hydrolysis.}, keywords = {nosource} } % == BibTeX quality report for moraEssentialRoleInvariant2003: % ? Possibly abbreviated journal title Mol. Micro.

@article{seit-nebiClass1TranslationTermination2001, title = {Class-1 Translation Termination Factors: Invariant {{GGQ}} Minidomain Is Essential for Release Activity and Ribosome Binding but Not for Stop Codon Recognition}, author = {{Seit-Nebi}, Alim and Frolova, Ludmila and Justesen, Just and Kisselev, Lev}, year = 2001, journal = {Nucleic Acids Res.}, volume = {29}, pages = {3982–3987}, abstract = {Previously, we have shown that all class-1 polypeptide release factors (RFs) share a common glycine-glycine-glutamine (GGQ) motif, which is critical for RF activity. Here, we subjected to site-directed mutagenesis two invariant amino acids, Gln185 and Arg189, situated in the GGQ minidomain of human eRF1, followed by determination of RF activity and the ribosome binding capacity for mutant eRF1. We show that replacement of Gln185 with polar amino acid residues causes partial inactivation of RF activity; Gln185Ile, Arg189Ala and Arg189Gln mutants are completely inactive; all mutants that retain partial RF activity respond similarly to three stop codons. We suggest that loss of RF activity for Gln185 and Arg189 mutants is caused by distortion of the conformation of the GGQ minidomain but not by damage of the stop codon recognition site of eRF1. Our data are inconsistent with the model postulating direct involvement of Gln185 side chain in orientation of water molecule toward peptidyl-tRNA ester bond at the ribosomal peptidyl transferase centre. Most of the Gln185 mutants exhibit reduced ability to bind to the ribosome, probably, to rRNA and/or (peptidyl)-tRNA(s). The data suggest that the GGQ motif is implicated both in promoting peptidyl-tRNA hydrolysis and binding to the ribosome.}, pmid = {11574680}, keywords = {nosource} } % == BibTeX quality report for seit-nebiClass1TranslationTermination2001: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{frolovaMutationsHighlyConserved1999, title = {Mutations in the Highly Conserved {{GGQ}} Motif of Class 1 Polypeptide Release Factors Abolish Ability of Human {{eRF1}} to Trigger Peptidyl-{{tRNA}} Hydrolysis.}, author = {Frolova, L. Y. and Tsivkovskii, R. Y. and Sivolobova, G. F. and Oparina, N. Y. and Serpinsky, O. I. and Blinov, V. M. and Tatkov, S. I. and Kisselev, L. L.}, year = 1999, journal = {RNA}, volume = {5}, pages = {1014–1020}, abstract = {Although the primary structures of class 1 polypeptide release factors (RF1 and RF2 in prokaryotes, eRF1 in eukaryotes) are known, the molecular basis by which they function in translational termination remains obscure. Because all class 1 RFs promote a stop-codon-dependent and ribosome-dependent hydrolysis of peptidyl-tRNAs, one may anticipate that this common function relies on a common structural motif(s). We have compared amino acid sequences of the available class 1 RFs and found a novel, common, unique, and strictly conserved GGQ motif that should be in a loop (coil) conformation as deduced by programs predicting protein secondary structure. Site-directed mutagenesis of the human eRF1 as a representative of class 1 RFs shows that substitution of both glycyl residues in this motif, G183 and G184, causes complete inactivation of the protein as a release factor toward all three stop codons, whereas two adjacent amino acid residues, G181 and R182, are functionally nonessential. Inactive human eRF1 mutants compete in release assays with wild-type eRF1 and strongly inhibit their release activity. Mutations of the glycyl residues in this motif do not affect another function, the ability of eRF1 together with the ribosome to induce GTPase activity of human eRF3, a class 2 RF. We assume that the novel highly conserved GGQ motif is implicated directly or indirectly in the activity of class 1 RFs in translation termination.}, pmid = {10445876}, keywords = {amino acid,amino acid sequence,amino acyl,amino acyl metabolism,bacterial proteins,bacterial proteins genetics,bacterial proteins metabolism,conserved sequence,gtp phosphohydrolases,gtp phosphohydrolases metabolism,guanosine diphosphate,guanosine diphosphate metabolism,guanosine triphosphate,guanosine triphosphate metabolism,humans,hydrolysis,molecular sequence data,mutagenesis,nosource,peptide chain termination,peptide termination factors,peptide termination factors antagonists & inhibit,peptide termination factors metabolism,rna,sequence homology,site directed,trans activators,trans activators genetics,trans activators metabolism,transfer,translational} }

@article{chavatteInvariantUridineStop2002, title = {The Invariant Uridine of Stop Codons Contacts the Conserved {{NIKSR}} Loop of Human {{eRF1}} in the Ribosome}, author = {Chavatte, Laurent and {Seit-Nebi}, Alim and Dubovaya, Vera and Favre, Alain}, year = 2002, journal = {Euro. Mol. Biol. Org. J.}, volume = {21}, pages = {5302–5311}, doi = {10.1093/emboj/cdf484}, abstract = {To unravel the region of human eukaryotic release factor 1 (eRF1) that is close to stop codons within the ribosome, we used mRNAs containing a single photoactivatable 4-thiouridine (s(4)U) residue in the first position of stop or control sense codons. Accurate phasing of these mRNAs onto the ribosome was achieved by the addition of tRNA(Asp). Under these conditions, eRF1 was shown to crosslink exclusively to mRNAs containing a stop or s(4)UGG codon. A procedure that yielded (32)P-labeled eRF1 deprived of the mRNA chain was developed; analysis of the labeled peptides generated after specific cleavage of both wild-type and mutant eRF1s maps the crosslink in the tripeptide KSR (positions 63-65 of human eRF1) and points to K63 located in the conserved NIKS loop as the main crosslinking site. These data directly show the interaction of the N-terminal (N) domain of eRF1 with stop codons within the 40S ribosomal subunit and provide strong support for the positioning of the eRF1 middle (M) domain on the 60S subunit. Thus, the N and M domains mimic the tRNA anticodon and acceptor arms, respectively.}, pmid = {12356746}, keywords = {amino acid sequence,base sequence,cloning,codon,conserved sequence,cross linking reagents,genetic,humans,messenger,messenger genetics,models,molecular,molecular sequence data,nosource,nucleic acid conformation,peptide termination factors,peptide termination factors chemistry,peptide termination factors genetics,peptide termination factors metabolism,protein conformation,recombinant proteins,recombinant proteins chemistry,recombinant proteins metabolism,ribosomes,ribosomes metabolism,rna,terminator,transcription,transfer,transfer chemistry,transfer genetics,uridine} } % == BibTeX quality report for chavatteInvariantUridineStop2002: % ? Possibly abbreviated journal title Euro. Mol. Biol. Org. J.

@article{songCrystalStructureHuman2000, title = {The Crystal Structure of Human Eukaryotic Release Factor {{eRF1}} - {{Mechanism}} of Stop Codon Recognition and Peptidyl-{{tRNA}} Hydrolysis}, author = {Song, H. W. and Mugnier, P. and Das, A. K. and Webb, H. M. and Evans, D. R. and Tuite, M. F. and Hemmings, B. A. and Barford, D.}, year = 2000, journal = {Cell}, volume = {100}, pages = {311–321}, doi = {10.1016/S0092-8674(00)80667-4}, pmid = {10676813}, keywords = {nosource} }

@article{opijnenTransposonInsertionSequencing2013, title = {Transposon Insertion Sequencing: A New Tool for Systems-Level Analysis of Microorganisms}, author = {{}van Opijnen, Tim and Camilli, Andrew}, year = 2013, month = may, journal = {Nature Reviews Microbiology}, volume = {11}, number = {7}, pages = {435–442}, publisher = {Nature Publishing Group}, issn = {1740-1526}, doi = {10.1038/nrmicro3033}, url = {http://www.nature.com/doifinder/10.1038/nrmicro3033}, keywords = {nosource} }

@article{schaackPromiscuousDNAHorizontal2010, title = {Promiscuous {{DNA}}: Horizontal Transfer of Transposable Elements and Why It Matters for Eukaryotic Evolution.}, author = {Schaack, Sarah and Gilbert, Cl{'e}ment and Feschotte, C{'e}dric}, year = 2010, month = sep, journal = {Trends in ecology & evolution}, volume = {25}, number = {9}, pages = {537–46}, issn = {0169-5347}, doi = {10.1016/j.tree.2010.06.001}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2940939&tool=pmcentrez&rendertype=abstract}, abstract = {Horizontal transfer is the passage of genetic material between genomes by means other than parent-to-offspring inheritance. Although the transfer of genes is thought to be crucial in prokaryotic evolution, few instances of horizontal gene transfer have been reported in multicellular eukaryotes; instead, most cases involve transposable elements. With over 200 cases now documented, it is possible to assess the importance of horizontal transfer for the evolution of transposable elements and their host genomes. We review criteria for detecting horizontal transfers and examine recent examples of the phenomenon, shedding light on its mechanistic underpinnings, including the role of host-parasite interactions. We argue that the introduction of transposable elements by horizontal transfer in eukaryotic genomes has been a major force propelling genomic variation and biological innovation.}, pmid = {20591532}, keywords = {Adaptation,Animals,Bacteria,Bacteria: genetics,DNA,DNA Transposable Elements,DNA Transposable Elements: genetics,DNA Transposable Elements: physiology,DNA: genetics,Evolution,Molecular,nosource,Physiological,Physiological: genetics,Plants,Plants: genetics} }

@article{gallagherGenomescaleIdentificationResistance2011, title = {Genome-Scale Identification of Resistance Functions in {{Pseudomonas}} Aeruginosa Using {{Tn-seq}}}, author = {Gallagher, L. A. and Shendure, Jay and Manoil, Colin}, year = 2011, journal = {MBio}, volume = {2}, number = {1}, pages = {1–8}, doi = {10.1128/mBio.00315-10.Editor}, url = {http://mbio.asm.org/content/2/1/e00315-10.short}, keywords = {nosource} }

@article{copelandHarnessingTransposonsCancer2010, title = {Harnessing Transposons for Cancer Gene Discovery.}, author = {Copeland, Neal G. and {}a Jenkins, Nancy}, year = 2010, month = oct, journal = {Nature reviews. Cancer}, volume = {10}, number = {10}, eprint = {20844553}, eprinttype = {pubmed}, pages = {696–706}, publisher = {Nature Publishing Group}, issn = {1474-1768}, doi = {10.1038/nrc2916}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20844553}, abstract = {Recently, it has become possible to mobilize the Tc1/mariner transposon, Sleeping Beauty (SB), in mouse somatic cells at frequencies high enough to induce cancer. Tumours result from SB insertional mutagenesis of cancer genes, thus facilitating the identification of the genes and signalling pathways that drive tumour formation. A conditional SB transposition system has also been developed that makes it possible to limit where SB mutagenesis occurs, providing a means to selectively model many types of human cancer. SB mutagenesis has already identified a large collection of known cancer genes in addition to a plethora of new candidate cancer genes and potential drug targets.}, pmid = {20844553}, keywords = {Animals,DNA Transposable Elements,Genes,Humans,Insertional,Mice,Mutagenesis,Neoplasm,Neoplasms,Neoplasms: genetics,nosource} } % == BibTeX quality report for copelandHarnessingTransposonsCancer2010: % ? Possibly abbreviated journal title Nature reviews. Cancer

@article{sinzelleMolecularDomesticationTransposable2009, title = {Molecular Domestication of Transposable Elements: From Detrimental Parasites to Useful Host Genes.}, author = {Sinzelle, L. and Izsv{'a}k, Z. and Ivics, Z.}, year = 2009, month = mar, journal = {Cellular and molecular life sciences : CMLS}, volume = {66}, number = {6}, eprint = {19132291}, eprinttype = {pubmed}, pages = {1073–93}, issn = {1420-9071}, doi = {10.1007/s00018-009-8376-3}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19132291}, abstract = {Transposable elements (TEs) are commonly viewed as molecular parasites producing mainly neutral or deleterious effects in host genomes through their ability to move. However, during the past two decades, major interest has been focusing on the positive contribution of these elements in the evolution of gene regulation and in the creation of diverse structural host genes. Indeed, DNA transposons carry an attractive and elaborate enzymatic machinery as well as DNA components that have been co-opted in several cases by the host genome via an evolutionary process referred to as molecular domestication. A large number of transposon-derived genes known to date have been recruited by the host to function as transcriptional regulators; however, the biological role of the majority of them remains undetermined. Our knowledge on the structure, distribution, evolution and mechanism of transposons will continue to provide important contributions to our understanding of host genome functions.}, isbn = {3094062547}, pmid = {19132291}, keywords = {Animals,Apoptosis,Apoptosis: physiology,Cell Cycle,Cell Cycle: physiology,DNA Transposable Elements,DNA Transposable Elements: genetics,DNA Transposable Elements: physiology,DNA-Binding Proteins,DNA-Binding Proteins: genetics,DNA-Binding Proteins: metabolism,Evolution,Genome,Humans,Molecular,nosource,Transcription Factors,Transcription Factors: genetics,Transcription Factors: metabolism} }

@article{lampeHyperactiveTransposaseMutants1999, title = {Hyperactive Transposase Mutants of the {{Himar1}} Mariner Transposon.}, author = {Lampe, D. J. and Akerley, B. J. and Rubin, E. J. and Mekalanos, J. J. and Robertson, H. M.}, year = 1999, month = sep, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {96}, number = {20}, pages = {11428–33}, issn = {0027-8424}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=18050&tool=pmcentrez&rendertype=abstract}, abstract = {Mariner-family transposable elements are active in a wide variety of organisms and are becoming increasingly important genetic tools in species lacking sophisticated genetics. The Himar1 element, isolated from the horn fly, Haematobia irritans, is active in Escherichia coli when expressed appropriately. We used this fact to devise a genetic screen for hyperactive mutants of Himar1 transposase that enhance overall transposition from approximately 4- to 50-fold as measured in an E. coli assay. Purified mutant transposases retain their hyperactivity, although to a lesser degree, in an in vitro transposition assay. Mutants like those described herein should enable sophisticated analysis of the biochemistry of mariner transposition and should improve the use of these elements as genetic tools, both in vivo and in vitro.}, pmid = {10500193}, keywords = {Animals,DNA,DNA Transposable Elements,DNA: metabolism,Muscidae,Muscidae: genetics,Mutation,nosource,Transposases,Transposases: genetics} }

@article{febrerAdvancesBacterialTranscriptome2011, title = {Advances in Bacterial Transcriptome and Transposon Insertion-Site Profiling Using Second-Generation Sequencing.}, author = {Febrer, Melanie and McLay, Kirsten and Caccamo, Mario and Twomey, Kate B. and Ryan, Robert P.}, year = 2011, month = nov, journal = {Trends in biotechnology}, volume = {29}, number = {11}, eprint = {21764162}, eprinttype = {pubmed}, pages = {586–94}, publisher = {Elsevier Ltd}, issn = {1879-3096}, doi = {10.1016/j.tibtech.2011.06.004}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21764162}, abstract = {The arrival of second-generation sequencing has revolutionized the study of bacteria within a short period. The sequence information generated from these platforms has helped in our understanding of bacterial development, adaptation and diversity and how bacteria cause disease. Furthermore, these technologies have quickly been adapted for high-throughput studies that were previously performed using DNA cloning or microarray-based applications. This has facilitated a more comprehensive study of bacterial transcriptomes through RNA sequencing (RNA-Seq) and the systematic determination of gene function by ‘transposon monitoring’. In this review, we provide an outline of these powerful tools and the in silico analyses used in their application, and also highlight the biological questions being addressed in these approaches.}, pmid = {21764162}, keywords = {Bacteria,Bacteria: genetics,Computer Simulation,DNA Transposable Elements,DNA Transposable Elements: genetics,High-Throughput Nucleotide Sequencing,High-Throughput Nucleotide Sequencing: methods,nosource,RNA,RNA: methods,Sequence Analysis,Transcriptome,Transcriptome: genetics} }

@article{henrasPosttranscriptionalStepsEukaryotic2008, title = {The Post-Transcriptional Steps of Eukaryotic Ribosome Biogenesis.}, author = {Henras, A. K. and Soudet, J. and G{'e}rus, M. and Lebaron, S. and {Caizergues-Ferrer}, M. and Mougin, A. and Henry, Y.}, year = 2008, journal = {Cell. Mol. Life Sci.}, volume = {65}, pages = {2334–2359}, abstract = {One of the most important tasks of any cell is to synthesize ribosomes. In eukaryotes, this process occurs sequentially in the nucleolus, the nucleoplasm and the cytoplasm. It involves the transcription and processing of pre-ribosomal RNAs, their proper folding and assembly with ribosomal proteins and the transport of the resulting pre-ribosomal particles to the cytoplasm where final maturation events occur. In addition to the protein and RNA constituents of the mature cytoplasmic ribosomes, this intricate process requires the intervention of numerous protein and small RNA trans-acting factors. These transiently interact with pre-ribosomal particles at various stages of their maturation. Most of the constituents of pre-ribosomal particles have probably now been identified and research in the field is starting to unravel the timing of their intervention and their precise mode of action. Moreover, quality control mechanisms are being discovered that monitor ribosome synthesis and degrade the RNA components of defective pre-ribosomal particles.}, pmid = {18408888}, keywords = {animals,eukaryotic cells,eukaryotic cells metabolism,genetic,humans,nosource,ribosomal,ribosomal metabolism,ribosomal proteins,ribosomal proteins metabolism,ribosomes,ribosomes metabolism,rna,rna precursors,rna precursors metabolism,transcription} } % == BibTeX quality report for henrasPosttranscriptionalStepsEukaryotic2008: % ? Possibly abbreviated journal title Cell. Mol. Life Sci.

@article{kresslerDrivingRibosomeAssembly2010, title = {Driving Ribosome Assembly.}, author = {Kressler, Dieter and Hurt, Ed and Bassler, Jochen}, year = 2010, journal = {Biochim. Biophys. Acta}, volume = {1803}, pages = {673–683}, abstract = {Ribosome biogenesis is a fundamental process that provides cells with the molecular factories for cellular protein production. Accordingly, its misregulation lies at the heart of several hereditary diseases (e.g., Diamond-Blackfan anemia). The process of ribosome assembly comprises the processing and folding of the pre-rRNA and its concomitant assembly with the ribosomal proteins. Eukaryotic ribosome biogenesis relies on a large number ({\(>\)}200) of non-ribosomal factors, which confer directionality and accuracy to this process. Many of these non-ribosomal factors fall into different families of energy-consuming enzymes, notably including ATP-dependent RNA helicases, AAA-ATPases, GTPases, and kinases. Ribosome biogenesis is highly conserved within eukaryotic organisms; however, due to the combination of powerful genetic and biochemical methods, it is best studied in the yeast Saccharomyces cerevisiae. This review summarizes our current knowledge on eukaryotic ribosome assembly, with particular focus on the molecular role of the involved energy-consuming enzymes.}, pmid = {19879902}, keywords = {adenosine triphosphatases,adenosine triphosphatases metabolism,biochemistry,biochemistry methods,biological,cell nucleolus,cell nucleolus metabolism,cell nucleus,cell nucleus metabolism,cytoplasm,cytoplasm metabolism,eukaryotic,eukaryotic chemistry,gtp phosphohydrolases,gtp phosphohydrolases metabolism,large,models,nosource,protein conformation,protein structure,quality control,ribosomal,ribosomal genetics,ribosome subunits,ribosomes,ribosomes metabolism,rna,saccharomyces cerevisiae,saccharomyces cerevisiae genetics,saccharomyces cerevisiae metabolism,small,tertiary} } % == BibTeX quality report for kresslerDrivingRibosomeAssembly2010: % ? Possibly abbreviated journal title Biochim. Biophys. Acta

@article{chenUnravelingDynamicsRibosome2012, title = {Unraveling the Dynamics of Ribosome Translocation}, author = {Chen, J. and Tsai, A. and O’Leary, S. E. and Petrov, A. and Puglisi, J. D.}, year = 2012, journal = {Curr. Opin. Struct. Biol.}, volume = {22}, pages = {804–814}, abstract = {Translocation is one of the key events in translation, requiring large-scale conformational changes in the ribosome, movements of two transfer RNAs (tRNAs) across a distance of more than 20 and the coupled movement of the messenger RNA (mRNA) by one codon, completing one cycle of peptide-chain elongation. Translocation is catalyzed by elongation factor G (EF-G in bacteria), which hydrolyzes GTP in the process. However, how the conformational rearrangements of the ribosome actually drive the movements of the tRNAs and how EF-G GTP hydrolysis plays a role in this process are still unclear. Fluorescence methods, both single-molecule and bulk, have provided a dynamic view of translocation, allowing us to follow the different conformational changes of the ribosome in real-time. The application of electron microscopy has revealed new conformational intermediates during translocation and important structural rearrangements in the ribosome that drive tRNA movement, while computational approaches have added quantitative views of the translational pathway. These recent advances shed light on the process of translocation, providing insight on how to resolve the different descriptions of translocation in the current literature.}, keywords = {nosource} } % == BibTeX quality report for chenUnravelingDynamicsRibosome2012: % ? Possibly abbreviated journal title Curr. Opin. Struct. Biol.

@article{spiegelElongationFactorStabilizes2007, title = {Elongation Factor {{G}} Stabilizes the Hybrid-State Conformation of the {{70S}} Ribosome}, author = {Spiegel, P. Clint and Ermolenko, Dmitri N. and Noller, Harry F.}, year = 2007, journal = {RNA}, volume = {13}, pages = {1473–1482}, doi = {10.1261/rna.601507}, abstract = {Following peptide bond formation, transfer RNAs (tRNAs) and messenger RNA (mRNA) are translocated through the ribosome, a process catalyzed by elongation factor EF-G. Here, we have used a combination of chemical footprinting, peptidyl transferase activity assays, and mRNA toeprinting to monitor the effects of EF-G on the positions of tRNA and mRNA relative to the A, P, and E sites of the ribosome in the presence of GTP, GDP, GDPNP, and fusidic acid. Chemical footprinting experiments show that binding of EF-G in the presence of the non-hydrolyzable GTP analog GDPNP or GDPfusidic acid induces movement of a deacylated tRNA from the classical P/P state to the hybrid P/E state. Furthermore, stabilization of the hybrid P/E state by EF-G compromises P-site codonanticodon interaction, causing frame-shifting. A deacylated tRNA bound to the P site and a peptidyl-tRNA in the A site are completely translocated to the E and P sites, respectively, in the presence of EF-G with GTP or GDPNP but not with EF-GGDP. Unexpectedly, translocation with EF-GGTP leads to dissociation of deacylated tRNA from the E site, while tRNA remains bound in the presence of EF-GGDPNP, suggesting that dissociation of tRNA from the E site is promoted by GTP hydrolysis and/or EF-G release. Our results show that binding of EF-G in the presence of GDPNP or GDPfusidic acid stabilizes the ribosomal intermediate hybrid state, but that complete translocation is supported only by EF-GGTP or EF-GGDPNP.}, pmid = {17630323}, keywords = {chemical footprinting,elongation factor g,hybrid states,nosource,ribosome,translocation} }

@article{agirrezabalaVisualizationHybridState2008, title = {Visualization of the Hybrid State of {{tRNA}} Binding Promoted by Spontaneous Ratcheting of the Ribosome.}, author = {Agirrezabala, Xabier and Lei, Jianlin and Brunelle, Julie L. and {Ortiz-Meoz}, Rodrigo F. and Green, Rachel and Frank, Joachim}, year = 2008, journal = {Mol. Cell}, volume = {32}, pages = {190–197}, abstract = {A crucial step in translation is the translocation of tRNAs through the ribosome. In the transition from one canonical site to the other, the tRNAs acquire intermediate configurations, so-called hybrid states. At this stage, the small subunit is rotated with respect to the large subunit, and the anticodon stem loops reside in the A and P sites of the small subunit, while the acceptor ends interact with the P and E sites of the large subunit. In this work, by means of cryo-EM and particle classification procedures, we visualize the hybrid state of both A/P and P/E tRNAs in an authentic factor-free ribosome complex during translocation. In addition, we show how the repositioning of the tRNAs goes hand in hand with the change in the interplay between S13, L1 stalk, L5, H68, H69, and H38 that is caused by the ratcheting of the small subunit.}, pmid = {18951087}, keywords = {bacterial,bacterial chemistry,bacterial physiology,bacterial ultrastructur,binding sites,cryoelectron microscopy,large,models,molecular,nosource,nucleic acid conformation,peptide chain elongation,protein biosynthesis,protein subunits,protein subunits metabolism,ribosome subunits,rna,small,transfer,transfer chemistry,transfer metabolism,transfer ultrastructure,translational} } % == BibTeX quality report for agirrezabalaVisualizationHybridState2008: % ? Possibly abbreviated journal title Mol. Cell

@article{zhangStructuresRibosomeIntermediate2009, title = {Structures of the {{Ribosome}} in {{Intermediate States}} of {{Ratcheting}}}, author = {Zhang, W. and Dunkle, J. A. and Cate, J. H. D.}, year = 2009, journal = {Science}, volume = {325}, pages = {1014–1017}, issn = {00368075}, doi = {10.1126/science.1175275}, abstract = {Protein biosynthesis on the ribosome requires repeated cycles of ratcheting, which couples rotation of the two ribosomal subunits with respect to each other, and swiveling of the head domain of the small subunit. However, the molecular basis for how the two ribosomal subunits rearrange contacts with each other during ratcheting while remaining stably associated is not known. Here, we describe x-ray crystal structures of the intact Escherichia coli ribosome, either in the apo-form (3.5 angstrom resolution) or with one (4.0 angstrom resolution) or two (4.0 angstrom resolution) anticodon stem-loop tRNA mimics bound, that reveal intermediate states of intersubunit rotation. In the structures, the interface between the small and large ribosomal subunits rearranges in discrete steps along the ratcheting pathway. Positioning of the head domain of the small subunit is controlled by interactions with the large subunit and with the tRNA bound in the peptidyl-tRNA site. The intermediates observed here provide insight into how tRNAs move into the hybrid state of binding that precedes the final steps of mRNA and tRNA translocation.}, keywords = {70s ribosome,angstrom resolution,binding,complex,crystal structure,hybrid state,messenger rna,movement,nosource,transfer rna translocation,translation termination} } % == BibTeX quality report for zhangStructuresRibosomeIntermediate2009: % ? Title looks like it was stored in title-case in Zotero

@article{robertsMechanismActionRibonuclease1969, title = {The Mechanism of Action of Ribonuclease}, author = {Roberts, G. C. K.}, year = 1969, journal = {Proceedings of the }, pages = {1151–1158}, url = {http://www.pnas.org/content/62/4/1151.short}, keywords = {nosource} }

@article{spahrPurificationMechanismAction1961, title = {Purification and Mechanism of Action of Ribonuclease from {{Escherichia}} Coli Ribosomes}, author = {Spahr, P. F. and Hollingworth, B. R.}, year = 1961, journal = {Journal of Biological Chemistry}, url = {http://www.jbc.org/content/236/3/823.short}, keywords = {nosource} }

@article{delcardayreExtentWhichRibonucleases1995, title = {The Extent to Which Ribonucleases Cleave Ribonucleic Acid}, author = {Delcardayre, S. B. and Raines, R. T.}, year = 1995, journal = {Analytical biochemistry}, url = {http://www.sciencedirect.com/science/article/pii/S0003269785711323}, keywords = {nosource} }

@article{zhuangStructuralBiasT42012, title = {Structural Bias in {{T4 RNA}} Ligase-Mediated 3’-Adapter Ligation.}, author = {Zhuang, Fanglei and Fuchs, Ryan T. and Sun, Zhiyi and Zheng, Yu and Robb, G. Brett}, year = 2012, month = apr, journal = {Nucleic acids research}, volume = {40}, number = {7}, pages = {e54}, issn = {1362-4962}, doi = {10.1093/nar/gkr1263}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3326334&tool=pmcentrez&rendertype=abstract}, abstract = {T4 RNA ligases are commonly used to attach adapters to RNAs, but large differences in ligation efficiency make detection and quantitation problematic. We developed a ligation selection strategy using random RNAs in combination with high-throughput sequencing to gain insight into the differences in efficiency of ligating pre-adenylated DNA adapters to RNA 3’-ends. After analyzing biases in RNA sequence, secondary structure and RNA-adapter cofold structure, we conclude that T4 RNA ligases do not show significant primary sequence preference in RNA substrates, but are biased against structural features within RNAs and adapters. Specifically, RNAs with less than three unstructured nucleotides at the 3’-end and RNAs that are predicted to cofold with an adapter in unfavorable structures are likely to be poorly ligated. The effect of RNA-adapter cofold structures on ligation is supported by experiments where the ligation efficiency of specific miRNAs was changed by designing adapters to alter cofold structure. In addition, we show that using adapters with randomized regions results in higher ligation efficiency and reduced ligation bias. We propose that using randomized adapters may improve RNA representation in experiments that include a 3’-adapter ligation step.}, pmid = {22241775}, keywords = {Animals,High-Throughput Nucleotide Sequencing,Mice,MicroRNAs,MicroRNAs: chemistry,MicroRNAs: metabolism,nosource,Nucleic Acid Conformation,Oligonucleotides,Oligonucleotides: chemistry,RNA,RNA Folding,RNA Ligase (ATP),RNA Ligase (ATP): metabolism,RNA: chemistry,RNA: metabolism,Sequence Analysis,Viral Proteins,Viral Proteins: metabolism} }

@article{lingAminoacyltRNASynthesisTranslational2009, title = {Aminoacyl-{{tRNA}} Synthesis and Translational Quality Control.}, author = {Ling, Jiqiang and Reynolds, Noah and Ibba, Michael}, year = 2009, journal = {Ann. Rev. Microbiol.}, volume = {63}, pages = {61–78}, abstract = {Translating the 4-letter code of RNA into the 22-letter alphabet of proteins is a central feature of cellular life. The fidelity with which mRNA is translated during protein synthesis is determined by two factors: the availability of aminoacyl-tRNAs composed of cognate amino acid:tRNA pairs and the accurate selection of aminoacyl-tRNAs on the ribosome. The role of aminoacyl-tRNA synthetases in translation is to define the genetic code by accurately pairing cognate tRNAs with their corresponding amino acids. Synthetases achieve the amino acid substrate specificity necessary to keep errors in translation to an acceptable level in two ways: preferential binding of the cognate amino acid and selective editing of near-cognate amino acids. Editing significantly decreases the frequency of errors and is important for translational quality control, and many details of the various editing mechanisms and their effect on different cellular systems are now starting to emerge.}, pmid = {19379069}, keywords = {amino acyl,amino acyl biosynthesis,amino acyl trna synthetases,amino acyl trna synthetases metabolism,biological,messenger,messenger metabolism,models,nosource,protein biosynthesis,rna,transfer} } % == BibTeX quality report for lingAminoacyltRNASynthesisTranslational2009: % ? Possibly abbreviated journal title Ann. Rev. Microbiol.

@article{dock-bregeonAchievingErrorfreeTranslation2004, title = {Achieving Error-Free Translation; the Mechanism of Proofreading of Threonyl-{{tRNA}} Synthetase at Atomic Resolution.}, author = {{Dock-Bregeon}, Anne-Catherine and Rees, Bernard and {Torres-Larios}, Alfredo and Bey, Gilbert and Caillet, Joel and Moras, Dino}, year = 2004, journal = {Mol. Cell}, volume = {16}, pages = {375–386}, abstract = {The fidelity of aminoacylation of tRNA(Thr) by the threonyl-tRNA synthetase (ThrRS) requires the discrimination of the cognate substrate threonine from the noncognate serine. Misacylation by serine is corrected in a proofreading or editing step. An editing site has been located 39 A away from the aminoacylation site. We report the crystal structures of this editing domain in its apo form and in complex with the serine product, and with two nonhydrolyzable analogs of potential substrates: the terminal tRNA adenosine charged with serine, and seryl adenylate. The structures show how serine is recognized, and threonine rejected, and provide the structural basis for the editing mechanism, a water-mediated hydrolysis of the mischarged tRNA. When the adenylate analog binds in the editing site, a phosphate oxygen takes the place of one of the catalytic water molecules, thereby blocking the reaction. This rules out a correction mechanism that would occur before the binding of the amino acid on the tRNA.}, pmid = {15525511}, keywords = {amino acid,amino acid sequence,aminoacylation,binding sites,escherichia coli,escherichia coli chemistry,escherichia coli genetics,escherichia coli metabolism,hydrolysis,molecular sequence data,mutagenesis,nosource,oxygen,oxygen chemistry,phosphates,phosphates chemistry,protein biosynthesis,rna,rna editing,sequence homology,ser,ser chemistry,ser metabolism,site directed,thr,thr chemistry,thr metabolism,threonine trna ligase,threonine trna ligase chemistry,threonine trna ligase genetics,threonine trna ligase metabolism,transfer} } % == BibTeX quality report for dock-bregeonAchievingErrorfreeTranslation2004: % ? Possibly abbreviated journal title Mol. Cell

@article{nurekiEnzymeStructureTwo1998, title = {Enzyme Structure with Two Catalytic Sites for Double-Sieve Selection of Substrate.}, author = {Nureki, O. and Vassylyev, D. G. and Tateno, M. and Shimada, A. and Nakama, T. and Fukai, S. and Konno, M. and Hendrickson, T. L. and Schimmel, P. and Yokoyama, S.}, year = 1998, journal = {Science}, volume = {280}, pages = {578–582}, abstract = {High-fidelity transfers of genetic information in the central dogma can be achieved by a reaction called editing. The crystal structure of an enzyme with editing activity in translation is presented here at 2.5 angstroms resolution. The enzyme, isoleucyl-transfer RNA synthetase, activates not only the cognate substrate L-isoleucine but also the minimally distinct L-valine in the first, aminoacylation step. Then, in a second, “editing” step, the synthetase itself rapidly hydrolyzes only the valylated products. For this two-step substrate selection, a “double-sieve” mechanism has already been proposed. The present crystal structures of the synthetase in complexes with L-isoleucine and L-valine demonstrate that the first sieve is on the aminoacylation domain containing the Rossmann fold, whereas the second, editing sieve exists on a globular beta-barrel domain that protrudes from the aminoacylation domain.}, pmid = {9554847}, keywords = {nosource} }

@article{fershtEnzymeHyperspecificityRejection1976, title = {Enzyme Hyperspecificity. {{Rejection}} of Threonine by the Valyl-{{tRNA}} Synthetase by Misacylation and Hydrolytic Editing.}, author = {Fersht, A. R. and Kaethner, M. M.}, year = 1976, journal = {Biochem.}, volume = {15}, pages = {3342–3346}, abstract = {Valyl-tRNA synthetase from Bacillus stearothermophilus activates thereonine and forms a 1:1 complex with threonyl adenylate, but it does not catalyze the net formation of threonyl-tRNAVal at pH 7.78 and 25 degrees C in the quenched flow apparatus it decomposes at a rate constant of 36s-1. During this process there is a transient formation of Thr-tRNAVal reaching a maximum at 25 ms and rapidly falling to zero after 150 ms. At the peak, 22% of the (14C) threonine from the complex is present as (14C) Thr-tRNA. The reaction may be quenched with phenol and the partially mischarged tRNA isolated. The enzyme catalyzes its hydrolysis with a rate constant of 40s-1. The data fit a kinetic scheme in which 62% of the threonine from the threonyl adenylate is transferred to the tRNA. This may be compared with the rate constant of 12s-1 at which 84% of the valine is transferred to tRNAVal from the enzyme-bound valyl adenylate, and the rate constant of 0.015s-1 for the subsequent hydrolysis of Val-tRNAVal. Inhibition studies indicate a distinct second site for hydrolysis. The translocation of the aminoacyl moiety between the two sites could be mediated by a transfer between the 2’-and 3’-OH groups of the terminal adenosine fo the tRNA. The hyperspecificity of the enzyme is based on discriminating between the two competing substrates twice: once against the undesired substrate in the synthetic step, and once against the desired substrate in the destructive step.}, pmid = {182209}, keywords = {adenosine monophosphate,adenosine monophosphate metabolism,adenosine triphosphate,adenosine triphosphate metabolism,amino acyl trna synthetases,amino acyl trna synthetases metabolism,binding sites,chemical,diphosphates,diphosphates metabolism,geobacillus stearothermophilus,geobacillus stearothermophilus enzymology,hydrolysis,kinetics,models,nosource,phenols,phenols pharmacology,rna,temperature,threonine,threonine metabolism,transfer,transfer metabolism,transfer rna aminoacylation,valine,valine metabolism,valine trna ligase,valine trna ligase metabolism} } % == BibTeX quality report for fershtEnzymeHyperspecificityRejection1976: % ? Possibly abbreviated journal title Biochem.

@article{erianiPartitionTRNASynthetases1990, title = {Partition of {{tRNA}} Synthetases into Two Classes Based on Mutually Exclusive Sets of Sequence Motifs}, author = {Eriani, Gilbert and Delarue, Marc and Poch, Olivier and Gangloff, Jean and Moras, Dino}, year = 1990, journal = {Nature}, volume = {347}, pages = {203–206}, issn = {00280836}, doi = {10.1038/347203a0}, abstract = {The aminoacyl-transfer RNA synthetases (aaRS) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology. Out of the 18 known aaRS, only 9 referred to as class I synthetases (GlnRS, TyrRS, MetRS, GluRS, ArgRS, ValRS, IleRS, LeuRS, TrpRS), display two short common consensus sequences (‘HIGH’ and ‘KMSKS’) which indicate, as observed in three crystal structures, the presence of a structural domain (the Rossman fold) that binds ATP. We report here the sequence of Escherichia coli ProRS, a dimer of relative molecular mass 127,402, which is homologous to both ThrRS and SerRS. These three latter aaRS share three new sequence motifs with AspRS, AsnRS, LysRS, HisRS and the beta subunit of PheRS. These three motifs (motifs 1, 2 and 3), in a search through the entire data bank, proved to be specific for this set of aaRS (referred to as class II). Class II may also contain AlaRS and GlyRS, because these sequences have a typical motif 3. Surprisingly, this partition of aaRS in two classes is found to be strongly correlated on the functional level with the acylation occurring either on the 2’ OH (class I) or 3’ OH (class II) of the ribose of the last nucleotide of tRNA.}, pmid = {2203971}, keywords = {nosource} }

@book{bergBiochemistry5thEdition2002, title = {Biochemistry, 5th Edition}, author = {Berg, Jeremy M. and Tymoczko, John L. and Stryer, Lubert}, editor = {Freeman, W. H.}, year = 2002, edition = {Fifth}, publisher = {New York: W. H. Freeman}, keywords = {nosource} } % == BibTeX quality report for bergBiochemistry5thEdition2002: % ? unused Edition (“5th”)

@article{markhamStructureRibonucleicAcids1952, title = {The Structure of Ribonucleic Acids. 1. {{Cyclic}} Nucleotides Produced by Ribonuclease and by Alkaline Hydrolysis}, author = {Markham, R. and Smith, J. D.}, year = 1952, journal = {Biochemical Journal}, pages = {552–557}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1198056/}, keywords = {nosource} }

@article{leeRNaseIIIT4Polynucleotide2013, title = {{{RNaseIII}} and {{T4 Polynucleotide Kinase}} Sequence Biases and Solutions during {{RNA-seq}} Library Construction.}, author = {Lee, Changhoon and Harris, R. Adron and Wall, Jason K. and Mayfield, R. Dayne and Wilke, Claus O.}, year = 2013, month = jan, journal = {Biology direct}, volume = {8}, number = {1}, pages = {16}, publisher = {Biology Direct}, issn = {1745-6150}, doi = {10.1186/1745-6150-8-16}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3710281&tool=pmcentrez&rendertype=abstract}, abstract = {BACKGROUND: RNA-seq is a next generation sequencing method with a wide range of applications including single nucleotide polymorphism (SNP) detection, splice junction identification, and gene expression level measurement. However, the RNA-seq sequence data can be biased during library constructions resulting in incorrect data for SNP, splice junction, and gene expression studies. Here, we developed new library preparation methods to limit such biases. RESULTS: A whole transcriptome library prepared for the SOLiD system displayed numerous read duplications (pile-ups) and gaps in known exons. The pile-ups and gaps of the whole transcriptome library caused a loss of SNP and splice junction information and reduced the quality of gene expression results. Further, we found clear sequence biases for both 5’ and 3’ end reads in the whole transcriptome library. To remove this bias, RNaseIII fragmentation was replaced with heat fragmentation. For adaptor ligation, T4 Polynucleotide Kinase (T4PNK) was used following heat fragmentation. However, its kinase and phosphatase activities introduced additional sequence biases. To minimize them, we used OptiKinase before T4PNK. Our study further revealed the specific target sequences of RNaseIII and T4PNK. CONCLUSIONS: Our results suggest that the heat fragmentation removed the RNaseIII sequence bias and significantly reduced the pile-ups and gaps. OptiKinase minimized the T4PNK sequence biases and removed most of the remaining pile-ups and gaps, thus maximizing the quality of RNA-seq data. REVIEWERS: This article was reviewed by Dr. A. Kolodziejczyk (nominated by Dr. Sarah Teichmann), Dr. Eugene Koonin, and Dr. Christoph Adami. For the full reviews, see the Reviewers’ Comments section.}, pmid = {23826734}, keywords = {heat fragmentation,nosource,optikinase,rna-seq,rnaseiii,sequence bias,t4pnk} }

@article{hellenInternalRibosomeEntry2001, title = {Internal Ribosome Entry Sites in Eukaryotic {{mRNA}} Molecules.}, author = {Hellen, C. U. and Sarnow, P.}, year = 2001, journal = {Genes & Dev.}, volume = {15}, pages = {1593–1612}, abstract = {Initiation of translation of most eukaryotic mRNAs commences with 5 enddependent recruitment of 40S ribosomal subunits to the mRNA. The 40S subunit car- rying the initiator methionine-tRNA and certain eukary- otic initiation factors (eIFs) is thought to scan themRNA ina5 to 3 direction until an appropriate start codon is encountered at which stage a 60S subunit joins to form an 80S ribosome that can decode the RNA into protein (Kozak 1989; Hershey and Merrick 2000). A subset of mRNAs contains internal ribosomal entry sites (IRESs), usually in the 5 NTR, that enable end-independent ini- tiation to occur. IRES-containing mRNAs are not sub- jected to many of the regulatory mechanisms that con- trol recruitment of most mRNAs to the translation ap- paratus. In this review, we briefly provide an introduction to the known mechanisms of translation initiation. Then, we discuss in detail the molecular mechanisms of IRES-mediated initiation and how they are used by specific mRNAs to permit translation under physiological circumstances such as mitosis, apoptosis, hypoxia, and some viral infections when translation of most mRNAs is repressed.}, pmid = {11445534}, keywords = {animals,apoptosis,base sequence,binding sites,codon,eukaryotic cells,gene expression regulation,hepacivirus,hepacivirus genetics,humans,initiator,messenger,messenger metabolism,molecular sequence data,nosource,peptide chain initiation,picornaviridae,picornaviridae genetics,ribosomes,ribosomes metabolism,rna,transfer,translational} } % == BibTeX quality report for hellenInternalRibosomeEntry2001: % ? Possibly abbreviated journal title Genes & Dev.

@article{lopez-lastraProteinSynthesisEukaryotes2005, title = {Protein Synthesis in Eukaryotes: The Growing Biological Relevance of Cap-Independent Translation Initiation.}, author = {{L{'o}pez-Lastra}, Marcelo and Rivas, Andrea and Barr{'i}a, Mar{'i}a In{'e}s}, year = 2005, journal = {Biol. Res.}, volume = {38}, pages = {121–146}, abstract = {Ribosome recruitment to eukaryotic mRNAs is generally thought to occur by a scanning mechanism, whereby the 40S ribosomal subunit binds in the vicinity of the 5’cap structure of the mRNA and scans until an AUG codon is encountered in an appropriate sequence context. Study of the picornaviruses allowed the characterization of an alternative mechanism of translation initiation. Picornaviruses can initiate translation via an internal ribosome entry segment (IRES), an RNA structure that directly recruits the 40S ribosomal subunits in a cap and 5’ end independent fashion. Since its discovery, the notion of IRESs has extended to a number of different virus families and cellular RNAs. This review summarizes features of both cap-dependent and IRES-dependent mechanisms of translation initiation and discusses the role of cis-acting elements, which include the 5’ cap, the 5’-untranslated region (UTR) and the poly(A) tail as well as the possible roles of IRESs as part of a cellular stress response mechanism and in the virus replication cycle.}, pmid = {16238092}, keywords = {5 untranslated regions,5 untranslated regions genetics,5 untranslated regions metabolism,animals,cells,cultured,eukaryotic cells,eukaryotic cells metabolism,messenger,nosource,picornaviridae,picornaviridae genetics,picornaviridae metabolism,poly(a) binding proteins,poly(a) binding proteins metabolism,protein biosynthesis,protein biosynthesis genetics,rna,rna cap binding proteins,rna cap binding proteins metabolism,rna caps,rna caps genetics,rna caps metabolism,virus replication} } % == BibTeX quality report for lopez-lastraProteinSynthesisEukaryotes2005: % ? Possibly abbreviated journal title Biol. Res.

@article{thompsonTricksIRESUses2012, title = {Tricks an {{IRES}} Uses to Enslave Ribosomes.}, author = {Thompson, Sunnie R.}, year = 2012, journal = {Trends Microbiol.}, volume = {20}, pages = {1–9}, issn = {18784380}, keywords = {3,4,can recruit ribosomes,dicistroviridae,does not,fact,igr ires,internally mrna,ires,ires able,iress,nosource,recruit ribosome internally,ribosome,translation initiation,viral rnas,were first discovered} } % == BibTeX quality report for thompsonTricksIRESUses2012: % ? Possibly abbreviated journal title Trends Microbiol.

@article{thakorIRESmediatedTranslationCellular2011, title = {{{IRES-mediated}} Translation of Cellular Messenger {{RNA}} Operates in {{eIF2alpha-}} Independent Manner during Stress.}, author = {Thakor, Nehal and Holcik, Martin}, year = 2011, journal = {Nucleic Acids Res.}, volume = {40}, pages = {1–12}, issn = {13624962}, doi = {10.1093/nar/gkr701}, abstract = {Physiological and pathophysiological stress attenuates global translation via phosphorylation of eIF2{\(\alpha\)}. This in turn leads to the reprogramming of gene expression that is required for adaptive stress response. One class of cellular messenger RNAs whose translation was reported to be insensitive to eIF2{\(\alpha\)} phosphorylation-mediated repression of translation is that harboring an Internal Ribosome Entry Site (IRES). IRES-mediated translation of several apoptosis-regulating genes increases in response to hypoxia, serum deprivation or gamma irradiation and promotes tumor cell survival and chemoresistance. However, the molecular mechanism that allows IRES-mediated translation to continue in an eIF2{\(\alpha\)}-independent manner is not known. Here we have used the X-chromosome linked Inhibitor of Apoptosis, XIAP, IRES to address this question. Using toeprinting assay, western blot analysis and polysomal profiling we show that the XIAP IRES supports cap-independent translation when eIF2{\(\alpha\)} is phosphorylated both in vitro and in vivo. During normal growth condition eIF2{\(\alpha\)}-dependent translation on the IRES is preferred. However, IRES-mediated translation switches to eIF5B-dependent mode when eIF2{\(\alpha\)} is phosphorylated as a consequence of cellular stress.}, pmid = {21917851}, keywords = {nosource} } % == BibTeX quality report for thakorIRESmediatedTranslationCellular2011: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{goodfellowIdentificationCisactingReplication2000, title = {Identification of a Cis-Acting Replication Element within the Poliovirus Coding Region}, author = {Goodfellow, I. and Chaudhry, Y. and Richardson, A. and Meredith, J. and Almond, J. W. and Barclay, W. and Evans, D. J.}, year = 2000, journal = {J. Virol.}, volume = {74}, pages = {4590-600.}, abstract = {The replication of poliovirus, a positive-stranded RNA virus, requires translation of the infecting genome followed by virus-encoded VPg and 3D polymerase-primed synthesis of a negative-stranded template. RNA sequences involved in the latter process are poorly defined. Since many sequences involved in picornavirus replication form RNA structures, we searched the genome, other than the untranslated regions, for predicted local secondary structural elements and identified a 61-nucleotide (nt) stem-loop in the region encoding the 2C protein. Covariance analysis suggested the structure was well conserved in the Enterovirus genus of the Picornaviridae. Site-directed mutagenesis, disrupting the structure without affecting the 2C product, destroyed genome viability and suggested that the structure was required in the positive sense for function. Recovery of revertant viruses suggested that integrity of the structure was critical for function, and analysis of replication demonstrated that nonviable mutants did not synthesize negative strands. Our conclusion, that this RNA secondary structure constitutes a novel poliovirus cis-acting replication element (CRE), is supported by the demonstration that subgenomic replicons bearing lethal mutations in the native structure can be restored to replication competence by the addition of a second copy of the 61-nt wild-type sequence at another location within the genome. This poliovirus CRE functionally resembles an element identified in rhinovirus type 14 (K. L. McKnight and S. M. Lemon, RNA 4:1569-1584, 1998) and the cardioviruses (P. E. Lobert, N. Escriou, J. Ruelle, and T. Michiels, Proc. Natl. Acad. Sci. USA 96:11560-11565, 1999) but differs in sequence, structure, and location. The functional role and evolutionary significance of CREs in the replication of positive-sense RNA viruses is discussed.}, pmid = {10775595}, keywords = {chemistry,genetics,analysis variance,base sequence,carrier proteins,chemistry,gene deletion,genetic,genetics,human,m,metabolism,molecular sequence data,non u.s. gov t,nosource,nucleic acid conformation,physiology,polioviruses,replicon,rna,structure activity relationship,support,transfection,translation,viral,viral nonstructural proteins,virus replication} } % == BibTeX quality report for goodfellowIdentificationCisactingReplication2000: % ? Possibly abbreviated journal title J. Virol.

@article{flaneganCovalentLinkageProtein1977, title = {Covalent Linkage of a Protein to a Defined Nucleotide Sequence at the 5’-Terminus of Virion and Replicative Intermediate {{RNAs}} of Poliovirus.}, author = {Flanegan, J. B. and Petterson, R. F. and Ambros, V. and Hewlett, N. J. and Baltimore, D.}, year = 1977, journal = {PNAS}, volume = {74}, pages = {961–965}, abstract = {The 5’-terminus of poliovirus polyribosomal RNA is pUp. A candidate for the 5’-terminus of poliovirion RNA was recovered as a compound migrating toward the cathode when 32P-labeled virion RNA was completely digested with ribonucleases T1, T2 and A and analyzed by paper ionophoresis at pH 3.5. Treatment with proteinase K reversed its direction of migration, indicating the presence of protein. Treatment with venom phosphodiesterase liberated all of the radioactivity as pUp, suggesting that poliovirion RNA has a protein-pUp 5’-terminus. Treatment of virion RNA with T1 ribonuclease alone generated a proteinase K-sensitive oligoribonucleotide. Analysis of the oligoribonucleotide using ribonucleases A and U2 showed its structure to be protein-pU-U-A-A-A-A-C-A-G. Digests of replicative intermediate RNA contained sufficient protein-pUp to suggest that this structure is at the 5’-end of most nascent poliovirus RNA molecules. We suggest that a protein-nucleotide structure acts as a primer for initiating synthesis of poliovirus RNA.}, pmid = {191841}, keywords = {nosource} }

@article{pathakPicornavirusGenomeReplication2007, title = {Picornavirus Genome Replication: Assembly and Organization of the {{VPg}} Uridylylation Ribonucleoprotein (Initiation) Complex.}, author = {Pathak, Harsh B. and Arnold, Jamie J. and Wiegand, Phillip N. and Hargittai, Michele R. S. and Cameron, Craig E.}, year = 2007, journal = {The Journal of biological chemistry}, volume = {282}, pages = {16202–16213}, abstract = {All picornaviruses have a protein, VPg, covalently linked to the 5’-ends of their genomes. Uridylylated VPg (VPg-pUpU) is thought to serve as the protein primer for RNA synthesis. VPg-pUpU can be produced in vitro by the viral polymerase, 3Dpol, in a reaction in which a single adenylate residue of a stem-loop structure, termed oriI, templates processive incorporation of UMP into VPg by using a “slide-back” mechanism. This reaction is greatly stimulated by viral precursor protein 3CD or its processed derivative, 3C; both contain RNA-binding and protease activities. We show that the 3C domain encodes specificity for oriI, and the 3D domain enhances the overall affinity for oriI. Thus, 3C(D) stimulation exhibits an RNA length dependence. By using a minimal system to evaluate the mechanism of VPg uridylylation, we show that the active complex contains polymerase, oriI, and 3C(D) at stoichiometry of 1:1:2. Dimerization of 3C(D) is supported by physical and structural data. Polymerase recruitment to and retention in this complex require a protein-protein interaction between the polymerase and 3C(D). Physical and functional data for this interaction are provided for three picornaviruses. VPg association with this complex is weak, suggesting that formation of a complex containing all necessary components of the reaction is rate-limiting for the reaction. We suggest that assembly of this complex in vivo would be facilitated by use of precursor proteins instead of processed proteins. These data provide a glimpse into the organization of the ribonucleoprotein complex that catalyzes this key step in picornavirus genome replication.}, keywords = {nosource} }

@article{asanoMultifactorComplexEukaryotic2000, title = {A Multifactor Complex of Eukaryotic Initiation Factors, {{eIF1}}, {{eIF2}}, {{eIF3}}, {{eIF5}}, and Initiator {{tRNA}}({{Met}}) Is an Important Translation Initiation Intermediate in Vivo.}, author = {Asano, Katsura and Clayton, Jason and Shalev, Anath and Hinnebusch, Alan G.}, year = 2000, journal = {Genes & Dev.}, volume = {14}, pages = {2534–2546}, abstract = {Translation initiation factor 2 (eIF2) bound to GTP transfers the initiator methionyl tRNA to the 40S ribosomal subunit. The eIF5 stimulates GTP hydrolysis by the eIF2/GTP/Met-tRNAi Met ternary complex on base-pairing between Met-tRNAi Met and the start codon. The eIF2, eIF5, and eIF1 all have been implicated in stringent selection of AUG as the start codon. The eIF3 binds to the 40S ribosome and promotes recruitment of the ternary complex; however, physical contact between eIF3 and eIF2 has not been observed. We show that yeast eIF5 can bridge interaction in vitro between eIF3 and eIF2 by binding simultaneously to the amino terminus of eIF3 subunit NIP1 and the amino-terminal half of eIF2{\(\beta\)}, dependent on a conserved bipartite motif in the carboxyl terminus of eIF5. Additionally, the amino terminus of NIP1 can bind concurrently to eIF5 and eIF1. These findings suggest the occurrence of an eIF3/eIF1/eIF5/eIF2 multifactor complex, which was observed in cell extracts free of 40S ribosomes and found to contain stoichiometric amounts of tRNAi Met. The multifactor complex was disrupted by the tif5-7A mutation in the bipartite motif of eIF5. Importantly, the tif5-7A mutant is temperature sensitive and displayed a substantial reduction in translation initiation at the restrictive temperature. We propose that the multifactor complex is an important intermediate in translation initiation in vivo.}, pmid = {11018020}, keywords = {2000,8,aug,eif,eukaryotic translation initiation factor,gap,initiation involves forma,met trna imet binding,nosource,process translation,received july 5,revised version accepted august,ribosomal preinitiation complex,selection} } % == BibTeX quality report for asanoMultifactorComplexEukaryotic2000: % ? Possibly abbreviated journal title Genes & Dev.

@article{krupkinVestigePrebioticBonding2011, title = {A Vestige of a Prebiotic Bonding Machine Is Functioning within the Contemporary Ribosome.}, author = {Krupkin, Miri and Matzov, Donna and Tang, Hua and Metz, Markus and Kalaora, Rinat and Belousoff, Matthew J. and Zimmerman, Ella and Bashan, Anat and Yonath, Ada}, year = 2011, journal = {Phil. Trans. R. Soc. Lond. B}, volume = {366}, pages = {2972–8}, issn = {14712970}, doi = {10.1098/rstb.2011.0146}, abstract = {Based on the presumed capability of a prebiotic pocket-like entity to accommodate substrates whose stereochemistry enables the creation of chemical bonds, it is suggested that a universal symmetrical region identified within all contemporary ribosomes originated from an entity that we term the ‘proto-ribosome’. This ‘proto-ribosome’ could have evolved from an earlier machine that was capable of performing essential tasks in the RNA world, called here the ‘pre-proto-ribosome’, which was adapted for producing proteins.}, pmid = {21930590}, keywords = {amino acids,amino acids chemistry,binding sites,catalysis,catalytic,catalytic chemistry,evolution,messenger,messenger chemistry,molecular,nosource,protein biosynthesis,ribosomal,ribosomal chemistry,ribosomes,ribosomes chemistry,ribosomes genetics,rna,rna folding,rna stability,stereoisomerism,transfer,transfer chemistry} } % == BibTeX quality report for krupkinVestigePrebioticBonding2011: % ? Possibly abbreviated journal title Phil. Trans. R. Soc. Lond. B

@article{djuranovicParsimoniousModelGene2011, title = {A Parsimonious Model for Gene Regulation by {{miRNAs}}.}, author = {Djuranovic, Sergej and Nahvi, Ali and Green, Rachel}, year = 2011, month = feb, journal = {Science (New York, N.Y.)}, volume = {331}, number = {6017}, eprint = {21292970}, eprinttype = {pubmed}, pages = {550–3}, issn = {1095-9203}, doi = {10.1126/science.1191138}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21292970}, abstract = {MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) act with the Argonaute family of proteins to regulate target messenger RNAs (mRNAs) posttranscriptionally. SiRNAs typically induce endonucleolytic cleavage of mRNA with near-perfect complementarity. For targets with less complementarity, both translational repression and mRNA destabilization mechanisms have been implicated in miRNA-mediated gene repression, although the timing, coupling, and relative importance of these events have not been determined. Here, we review gene-specific and global approaches that probe miRNA function and mechanism, looking for a unifying model. More systematic analyses of the molecular specificities of the core components coupled with analysis of the relative timing of the different events will ultimately shed light on the mechanism of miRNA-mediated repression.}, pmid = {21292970}, keywords = {Animals,Eukaryotic Initiation Factors,Eukaryotic Initiation Factors: chemistry,Eukaryotic Initiation Factors: metabolism,Gene Expression Regulation,Genetic,Humans,Messenger,Messenger: genetics,Messenger: metabolism,MicroRNAs,MicroRNAs: genetics,MicroRNAs: metabolism,Models,nosource,Protein Biosynthesis,Ribonucleoproteins,Ribonucleoproteins: metabolism,RNA,RNA Interference,RNA Stability} } % == BibTeX quality report for djuranovicParsimoniousModelGene2011: % ? Possibly abbreviated journal title Science (New York, N.Y.)

@article{diasCapsnatchingEndonucleaseInfluenza2009, title = {The Cap-Snatching Endonuclease of Influenza Virus Polymerase Resides in the {{PA}} Subunit.}, author = {Dias, Alexandre and Bouvier, Denis and Cr{'e}pin, Thibaut and McCarthy, Andrew A. and Hart, Darren J. and Baudin, Florence and Cusack, Stephen and Ruigrok, Rob W. H.}, year = 2009, journal = {Nature}, volume = {458}, pages = {914–918}, abstract = {The influenza virus polymerase, a heterotrimer composed of three subunits, PA, PB1 and PB2, is responsible for replication and transcription of the eight separate segments of the viral RNA genome in the nuclei of infected cells. The polymerase synthesizes viral messenger RNAs using short capped primers derived from cellular transcripts by a unique ‘cap-snatching’ mechanism. The PB2 subunit binds the 5’ cap of host pre-mRNAs, which are subsequently cleaved after 10-13 nucleotides by the viral endonuclease, hitherto thought to reside in the PB2 (ref. 5) or PB1 (ref. 2) subunits. Here we describe biochemical and structural studies showing that the amino-terminal 209 residues of the PA subunit contain the endonuclease active site. We show that this domain has intrinsic RNA and DNA endonuclease activity that is strongly activated by manganese ions, matching observations reported for the endonuclease activity of the intact trimeric polymerase. Furthermore, this activity is inhibited by 2,4-dioxo-4-phenylbutanoic acid, a known inhibitor of the influenza endonuclease. The crystal structure of the domain reveals a structural core closely resembling resolvases and type II restriction endonucleases. The active site comprises a histidine and a cluster of three acidic residues, conserved in all influenza viruses, which bind two manganese ions in a configuration similar to other two-metal-dependent endonucleases. Two active site residues have previously been shown to specifically eliminate the polymerase endonuclease activity when mutated. These results will facilitate the optimisation of endonuclease inhibitors as potential new anti-influenza drugs.}, pmid = {19194459}, keywords = {amino acid sequence,animals,catalytic domain,endonucleases,endonucleases chemistry,endonucleases metabolism,enzyme stability,h3n2 subtype,h3n2 subtype enzymology,h5n1 subtype,h5n1 subtype enzymology,histidine,histidine metabolism,humans,influenza a virus,influenzavirus c,influenzavirus c enzymology,manganese,manganese metabolism,manganese pharmacology,models,molecular,molecular sequence data,nosource,protein subunits,protein subunits chemistry,protein subunits metabolism,rna caps,rna caps metabolism,rna replicase,rna replicase chemistry,rna replicase metabolism,viral proteins,viral proteins chemistry,viral proteins metabolism} }

@article{hinnebuschMolecularMechanismScanning2011, title = {Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes.}, author = {Hinnebusch, Alan G.}, year = 2011, journal = {Microbiol. Mol. Biol. Rev.}, volume = {75}, pages = {434–467}, abstract = {Summary: The correct translation of mRNA depends critically on the ability to initiate at the right AUG codon. For most mRNAs in eukaryotic cells, this is accomplished by the scanning mechanism, wherein the small (40S) ribosomal subunit attaches to the 5’ end of the mRNA and then inspects the leader base by base for an AUG in a suitable context, using complementarity with the anticodon of methionyl initiator tRNA (Met-tRNA(i)(Met)) as the key means of identifying AUG. Over the past decade, a combination of yeast genetics, biochemical analysis in reconstituted systems, and structural biology has enabled great progress in deciphering the mechanism of ribosomal scanning. A robust molecular model now exists, describing the roles of initiation factors, notably eukaryotic initiation factor 1 (eIF1) and eIF1A, in stabilizing an “open” conformation of the 40S subunit with Met-tRNA(i)(Met) bound in a low-affinity state conducive to scanning and in triggering rearrangement into a “closed” conformation incompatible with scanning, which features Met-tRNA(i)(Met) more tightly bound to the “P” site and base paired with AUG. It has also emerged that multiple DEAD-box RNA helicases participate in producing a single-stranded “landing pad” for the 40S subunit and in removing the secondary structure to enable the mRNA to traverse the 40S mRNA-binding channel in the single-stranded form for base-by-base inspection in the P site.}, pmid = {21885680}, keywords = {nosource} } % == BibTeX quality report for hinnebuschMolecularMechanismScanning2011: % ? Possibly abbreviated journal title Microbiol. Mol. Biol. Rev.

@article{keersmaeckerExomeSequencingIdentifies2012, title = {Exome Sequencing Identifies Mutation in {{CNOT3}} and Ribosomal Genes {{RPL5}} and {{RPL10}} in {{T-cell}} Acute Lymphoblastic Leukemia.}, author = {Keersmaecker, Kim De and Atak, Zeynep Kalender and Li, Ning and Vicente, Carmen and Patchett, Stephanie and Girardi, Tiziana and Gianfelici, Valentina and Geerdens, Ellen and Clappier, Emmanuelle and Porcu, Micha{"e}l and Lahortiga, Idoya and Luc{`a}, Rossella and Yan, Jiekun and Hulselmans, Gert and Vranckx, Hilde and Vandepoel, Roel and Sweron, Bram and Jacobs, Kris and Mentens, Nicole and Wlodarska, Iwona and Cauwelier, Barbara and Cloos, Jacqueline and Soulier, Jean and Uyttebroeck, Anne and Bagni, Claudia and Hassan, Bassem A. and Vandenberghe, Peter and Johnson, Arlen W. and Aerts, Stein and Cools, Jan}, year = 2012, journal = {Nature Genet.}, volume = {45}, pages = {186–190}, issn = {15461718}, abstract = {T-cell acute lymphoblastic leukemia (T-ALL) is caused by the cooperation of multiple oncogenic lesions. We used exome sequencing on 67 T-ALLs to gain insight into the mutational spectrum in these leukemias. We detected protein-altering mutations in 508 genes, with an average of 8.2 mutations in pediatric and 21.0 mutations in adult T-ALL. Using stringent filtering, we predict seven new oncogenic driver genes in T-ALL. We identify CNOT3 as a tumor suppressor mutated in 7 of 89 (7.9%) adult T-ALLs, and its knockdown causes tumors in a sensitized Drosophila melanogaster model. In addition, we identify mutations affecting the ribosomal proteins RPL5 and RPL10 in 12 of 122 (9.8%) pediatric T-ALLs, with recurrent alterations of Arg98 in RPL10. Yeast and lymphoid cells expressing the RPL10 Arg98Ser mutant showed a ribosome biogenesis defect. Our data provide insights into the mutational landscape of pediatric versus adult T-ALL and identify the ribosome as a potential oncogenic factor.}, keywords = {nosource} } % == BibTeX quality report for keersmaeckerExomeSequencingIdentifies2012: % ? Possibly abbreviated journal title Nature Genet.

@article{tronQSR1EssentialYeast1995, title = {{{QSR1}}, an Essential Yeast Gene with a Genetic Relationship to a Subunit of the Mitochondrial Cytochrome Bc1 Complex, Is Homologous to a Gene Implicated in Eukaryotic Cell Differentiation.}, author = {Tron, T. and Yang, M. and Dick, F. A. and Schmitt, M. E. and Trumpower, B. L.}, year = 1995, journal = {J. Biol. Chem.}, volume = {270}, pages = {9961–9970}, abstract = {Subunit 6 of the mitochondrial cytochrome bc1 complex regulates the activity of the bc1 complex in Saccharomyces cerevisiae but is not essential for respiration. To test whether QCR6, the nuclear gene which encodes subunit 6, might be functionally redundant with any other gene(s), we screened for mutations in yeast genes which are essential when the otherwise non-essential QCR6 is deleted from the yeast chromosome. We obtained such quinolcytochrome c reductase subunit-requiring mutants in two complementation groups, which we named qsr1 and qsr2. The qsr mutants require QCR6 for viability on fermentable and non-fermentable carbon sources, indicating that QCR6 is covering lethal mutations in qsr1 and qsr2, even when the yeast do not require respiration. QSR1 was cloned by rescuing the synthetic lethality of a qsr1-1 mutant. QSR1 encodes a 25.4-kDa protein which is 65% identical to a protein encoded by QM, a highly conserved human gene which has been implicated in tumorigenesis. In mammals QM is down-regulated during adipocyte, kidney, and heart differentiation, and in Nicotiana the homolog of QM is also down-regulated during differentiation. When one chromosomal copy of QSR1 was deleted in a diploid yeast strain, haploid spores derived therefrom and carrying the deletion were unable to grow on fermentable or non-fermentable carbon sources. Although QCR6 allows the qsr1-1 mutant to grow, it will not substitute for QSR1, since the deletion of QSR1 is lethal even if QCR6 is present. These results indicate a novel genetic relationship between a subunit of the mitochondrial respiratory chain and an essential gene in yeast which is homologous to a gene implicated in differentiation in other eukaryotes.}, pmid = {7730379}, keywords = {nosource} } % == BibTeX quality report for tronQSR1EssentialYeast1995: % ? Possibly abbreviated journal title J. Biol. Chem.

@article{radzickaProficientEnzyme1995, title = {A Proficient Enzyme.}, author = {Radzicka, A. and Wolfenden, R.}, year = 1995, journal = {Science}, volume = {267}, pages = {90–93}, abstract = {Orotic acid is decarboxylated with a half-time (t1/2) of 78 million years in neutral aqueous solution at room temperature, as indicated by reactions in quartz tubes at elevated temperatures. Spontaneous hydrolysis of phosphodiester bonds, such as those present in the backbone of DNA, proceeds even more slowly at high temperatures, but the heat of activation is less positive, so that dimethyl phosphate is hydrolyzed with a t1/2 of 130,000 years in neutral solution at room temperature. These values extend the known range of spontaneous rate constants for reactions that are also susceptible to catalysis by enzymes to more than 14 orders of magnitude. Values of the second-order rate constant kcat/Km for the corresponding enzyme reactions are confined to a range of only 600-fold, in contrast. Orotidine 5’-phosphate decarboxylase, an extremely proficient enzyme, enhances the rate of reaction by a factor of 10(17) and is estimated to bind the altered substrate in the transition state with a dissociation constant of less than 5 x 10(-24) M.}, pmid = {7809611}, keywords = {catalysis,decarboxylation,hydrogen ion concentration,hydrolysis,kinetics,micrococcal nuclease,micrococcal nuclease metabolism,nosource,organophosphorus compounds,organophosphorus compounds chemistry,orotic acid,orotic acid analogs & derivatives,orotic acid chemistry,orotidine 5 phosphate decarboxylase,orotidine 5 phosphate decarboxylase metabolism,temperature,thermodynamics} }

@article{sieversRibosomeEntropyTrap2004, title = {The Ribosome as an Entropy Trap}, author = {Sievers, A. and Beringer, M. and Rodnina, M. V. and Wolfenden, R.}, year = 2004, journal = {PNAS}, volume = {101}, pages = {7897–7901}, abstract = {15141076 To determine the effectiveness of the ribosome as a catalyst, we compared the rate of uncatalyzed peptide bond formation, by the reaction of the ethylene glycol ester of N-formylglycine with with the rate of peptidyl transfer by the ribosome. Activation parameters were also determined for both reactions, from the temperature dependence of their second-order rate constants. In contrast with most protein enzymes, the enthalpy of activation is slightly less favorable on the ribosome than in solution. The 2 x 10(7)-fold rate enhancement produced by the ribosome is achieved entirely by lowering the entropy of activation. These results are consistent with the view that the ribosome enhances the rate of peptide bond formation mainly by positioning the substrates and/or water exclusion within the active site, rather than by conventional chemical catalysis}, keywords = {aminoacyl trna,catalytic trna,nosource,ribosome,trna} }

@article{ben-shemCrystalStructureEukaryotic2010, title = {Crystal Structure of the Eukaryotic Ribosome.}, author = {{Ben-Shem}, Adam and Jenner, Lasse and Yusupova, Gulnara and Yusupov, Marat}, year = 2010, journal = {Science}, volume = {330}, pages = {1203–1209}, abstract = {Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the yeast 80S ribosome determined at 4.15 angstrom resolution reveals the higher complexity of eukaryotic ribosomes, which are 40% larger than their bacterial counterparts. Our model shows how eukaryote-specific elements considerably expand the network of interactions within the ribosome and provides insights into eukaryote-specific features of protein synthesis. Our crystals capture the ribosome in the ratcheted state, which is essential for translocation of mRNA and transfer RNA (tRNA), and in which the small ribosomal subunit has rotated with respect to the large subunit. We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation.}, pmid = {21109664}, keywords = {nosource} }

@article{huloViralZoneKnowledgeResource2011, title = {{{ViralZone}}: A Knowledge Resource to Understand Virus Diversity.}, author = {Hulo, Chantal and Castro, Edouard De and Masson, Patrick and Bougueleret, Lydie and Bairoch, Amos and Xenarios, Ioannis and Mercier, Philippe Le}, year = 2011, journal = {Nucleic Acids Res.}, volume = {39}, pages = {D576-D582}, doi = {10.1093/nar/gkq901}, abstract = {The molecular diversity of viruses complicates the interpretation of viral genomic and proteomic data. To make sense of viral gene functions, investigators must be familiar with the virus host range, replication cycle and virion structure. Our aim is to provide a comprehensive resource bridging together textbook knowledge with genomic and proteomic sequences. ViralZone web resource (www.expasy.org/viralzone/) provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.}, pmid = {20947564}, keywords = {nosource} } % == BibTeX quality report for huloViralZoneKnowledgeResource2011: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{zaherFidelityMolecularLevel2009, title = {Fidelity at the {{Molecular Level}} : {{Lessons}} from {{Protein Synthesis}}}, author = {Zaher, Hani S. and Green, Rachel}, year = 2009, journal = {Cell}, volume = {136}, pages = {746–762}, issn = {00928674}, doi = {10.1016/j.cell.2009.01.036}, keywords = {nosource} } % == BibTeX quality report for zaherFidelityMolecularLevel2009: % ? Title looks like it was stored in title-case in Zotero

@article{finchUncouplingGTPHydrolysis2011, title = {Uncoupling of {{GTP}} Hydrolysis from {{eIF6}} Release on the Ribosome Causes {{Shwachman-Diamond}} Syndrome.}, author = {Finch, Andrew J. and Hilcenko, Christine and Basse, Nicolas and Drynan, Lesley F. and Goyenechea, Beatriz and Menne, Tobias F. and Fern{'a}ndez, Africa Gonz{'a}lez and Simpson, Paul and D’Santos, Clive S. and Arends, Mark J. and Donadieu, Jean and {Bellann{'e}-Chantelot}, Christine and Costanzo, Michael and Boone, Charles and McKenzie, Andrew N. and Freund, Stefan M. V. and Warren, Alan J.}, year = 2011, journal = {Genes & Dev.}, volume = {25}, pages = {917–929}, abstract = {Removal of the assembly factor eukaryotic initiation factor 6 (eIF6) is critical for late cytoplasmic maturation of 60S ribosomal subunits. In mammalian cells, the current model posits that eIF6 release is triggered following phosphorylation of Ser 235 by activated protein kinase C. In contrast, genetic studies in yeast indicate a requirement for the ortholog of the SBDS (Shwachman-Bodian-Diamond syndrome) gene that is mutated in the inherited leukemia predisposition disorder Shwachman-Diamond syndrome (SDS). Here, by isolating late cytoplasmic 60S ribosomal subunits from Sbds-deleted mice, we show that SBDS and the GTPase elongation factor-like 1 (EFL1) directly catalyze eIF6 removal in mammalian cells by a mechanism that requires GTP binding and hydrolysis by EFL1 but not phosphorylation of eIF6 Ser 235. Functional analysis of disease-associated missense variants reveals that the essential role of SBDS is to tightly couple GTP hydrolysis by EFL1 on the ribosome to eIF6 release. Furthermore, complementary NMR spectroscopic studies suggest unanticipated mechanistic parallels between this late step in 60S maturation and aspects of bacterial ribosome disassembly. Our findings establish a direct role for SBDS and EFL1 in catalyzing the translational activation of ribosomes in all eukaryotes, and define SDS as a ribosomopathy caused by uncoupling GTP hydrolysis from eIF6 release.}, pmid = {21536732}, keywords = {nosource} } % == BibTeX quality report for finchUncouplingGTPHydrolysis2011: % ? Possibly abbreviated journal title Genes & Dev.

@article{daiInhibitionMDM2mediatedP532004, title = {Inhibition of {{MDM2-mediated}} P53 {{Ubiquitination}} and {{Degradation}} by {{Ribosomal Protein L5}}}, author = {Dai, Mu-Shui and Lu, Hua}, year = 2004, journal = {J. Biol. Chem.}, volume = {279}, pages = {44475–44482}, issn = {00219258}, doi = {10.1074/jbc.M403722200}, abstract = {The oncoprotein MDM2 associates with ribosomal proteins L5, L11, and L23. Both L11 and L23 have been shown to activate p53 by inhibiting MDM2-mediated p53 suppression. Here we have shown that L5 also activates p53. Overexpression of L5 stabilized ectopic p53 in H1299 cells and endogenous p53 in U2OS cells. Consequently, L5 enhanced p53 transcriptional activity and induced p53-dependent G1 cell cycle arrest. Furthermore, like L11 and L23, L5 also remarkably inhibited MDM2-mediated p53 ubiquitination. The interaction of L5 with MDM2 was also enhanced by treatment with a low dose of actinomycin D. Actinomycin D-induced p53 was inhibited by small interference RNA against L5. By reciprocal co-immunoprecipitation, we further showed that there were at least two MDM2-ribosomal protein complexes in cells: MDM2-L5-L11-L23 and p53-MDM2-L5-L11-L23. We propose that the MDM2-L5-L11-L23 complex functions to inhibit MDM2-mediated p53 ubiquitination and thus activates p53.}, pmid = {15308643}, keywords = {nosource} } % == BibTeX quality report for daiInhibitionMDM2mediatedP532004: % ? Possibly abbreviated journal title J. Biol. Chem.

@article{constantinouActivationP53Stimulates2008, title = {Activation of P53 Stimulates Proteasome-Dependent Truncation of {{eIF4E-binding}} Protein 1 ({{4E-BP1}}).}, author = {Constantinou, Constantina and Elia, Androulla and Clemens, Michael J.}, year = 2008, journal = {Biol. Cell}, volume = {100}, pages = {279–289}, abstract = {BACKGROUND INFORMATION: The translational inhibitor protein 4E-BP1 eIF4E (eukaryotic initiation factor 4E)-binding protein 1 regulates the availability of polypeptide chain initiation factor eIF4E for protein synthesis. Initiation factor eIF4E binds the 5’ cap structure present on all cellular mRNAs. Its ability to associate with initiation factors eIF4G and eIF4A, forming the eIF4F complex, brings the mRNA to the 43S complex during the initiation of translation. Binding of eIF4E to eIF4G is inhibited in a competitive manner by 4E-BP1. Phosphorylation of 4E-BP1 decreases the affinity of this protein for eIF4E, thus favouring the binding of eIF4G and enhancing translation. We have previously shown that induction or activation of the tumour suppressor protein p53 rapidly leads to 4E-BP1 dephosphorylation, resulting in sequestration of eIF4E, decreased formation of the eIF4F complex and inhibition of protein synthesis. RESULTS: We now report that activation of p53 also results in modification of 4E-BP1 to a truncated form. Unlike full-length 4E-BP1, which is reversibly phosphorylated at multiple sites, the truncated protein is almost completely unphosphorylated. Moreover, the latter interacts with eIF4E in preference to full-length 4E-BP1. Inhibitor studies indicate that the p53-induced cleavage of 4E-BP1 is mediated by the proteasome and is blocked by conditions that inhibit the dephosphorylation of full-length 4E-BP1. Measurements of the turnover of 4E-BP1 indicate that the truncated form is much more stable than the full-length protein. CONCLUSIONS: The results suggest a model in which proteasome activity gives rise to a stable, hypophosphorylated and truncated form of 4E-BP1, which may exert a long-term inhibitory effect on the availability of eIF4E, thus contributing to the inhibition of protein synthesis and the growth-inhibitory and pro-apoptotic effects of p53.}, pmid = {18021075}, keywords = {acute,acute metabolism,adaptor proteins,animals,cell line,erythroblastic,leukemia,mice,nosource,phosphoproteins,phosphoproteins drug effects,phosphoproteins metabolism,phosphorylation,proteasome endopeptidase complex,proteasome endopeptidase complex metabolism,signal transducing,signal transducing drug effects,signal transducing metabolism,tumor,tumor suppressor protein p53,tumor suppressor protein p53 metabolism,tumor suppressor protein p53 pharmacology} } % == BibTeX quality report for constantinouActivationP53Stimulates2008: % ? Possibly abbreviated journal title Biol. Cell

@article{ebertIdentificationRPS145q2008, title = {Identification of {{RPS14}} as a 5q- Syndrome Gene by {{RNA}} Interference Screen.}, author = {Ebert, Benjamin L. and Pretz, Jennifer and Bosco, Jocelyn and Chang, Cindy Y. and Tamayo, Pablo and Galili, Naomi and Raza, Azra and Root, David E. and Attar, Eyal and Ellis, Steven R. and Golub, Todd R.}, year = 2008, journal = {Nature}, volume = {451}, pages = {335–339}, abstract = {Somatic chromosomal deletions in cancer are thought to indicate the location of tumour suppressor genes, by which a complete loss of gene function occurs through biallelic deletion, point mutation or epigenetic silencing, thus fulfilling Knudson’s two-hit hypothesis. In many recurrent deletions, however, such biallelic inactivation has not been found. One prominent example is the 5q- syndrome, a subtype of myelodysplastic syndrome characterized by a defect in erythroid differentiation. Here we describe an RNA-mediated interference (RNAi)-based approach to discovery of the 5q- disease gene. We found that partial loss of function of the ribosomal subunit protein RPS14 phenocopies the disease in normal haematopoietic progenitor cells, and also that forced expression of RPS14 rescues the disease phenotype in patient-derived bone marrow cells. In addition, we identified a block in the processing of pre-ribosomal RNA in RPS14-deficient cells that is functionally equivalent to the defect in Diamond-Blackfan anaemia, linking the molecular pathophysiology of the 5q- syndrome to a congenital syndrome causing bone marrow failure. These results indicate that the 5q- syndrome is caused by a defect in ribosomal protein function and suggest that RNAi screening is an effective strategy for identifying causal haploinsufficiency disease genes.}, pmid = {18202658}, keywords = {18s,18s genetics,anemia,cell differentiation,cells,chromosome deletion,chromosomes,cultured,diamond blackfan,diamond blackfan genetics,diamond blackfan physiopathology,erythroid cells,erythroid cells cytology,erythroid cells metabolism,genetic predisposition disease,genetic predisposition disease genetics,hematopoietic stem cells,hematopoietic stem cells metabolism,human,humans,linkage (genetics),linkage (genetics) genetics,nosource,pair 5,pair 5 genetics,phenotype,ribosomal,ribosomal genetics,ribosomal metabolism,ribosomal proteins,ribosomal proteins deficiency,ribosomal proteins genetics,ribosomal proteins metabolism,ribosomes,ribosomes chemistry,ribosomes genetics,ribosomes metabolism,rna,rna interference,rna precursors,rna precursors genetics,rna precursors metabolism,syndrome} }

@article{draptchinskaiaGeneEncodingRibosomal1999, title = {The Gene Encoding Ribosomal Protein {{S19}} Is Mutated in {{Diamond-Blackfan}} Anaemia}, author = {Draptchinskaia, N. and Gustavsson, P. and Andersson, B. and Pettersson, M. and Willig, T. N. and Dianzani, I. and Ball, S. and Tchernia, G. and Klar, J. and Matsson, H. and Tentler, D. and Mohandas, N. and Carlsson, B. and Dahl, N.}, year = 1999, journal = {Nature Genet.}, volume = {21}, pages = {169–175}, abstract = {Diamond-Blackfan anaemia (DBA) is a constitutional erythroblastopenia characterized by absent or decreased erythroid precursors. The disease, previously mapped to human chromosome 19q13, is frequently associated with a variety of malformations. To identify the gene involved in DBA, we cloned the chromosome 19q13 breakpoint in a patient with a reciprocal X;19 chromosome translocation. The breakpoint occurred in the gene encoding ribosomal protein S19. Furthermore, we identified mutations in RPS19 in 10 of 40 unrelated DBA patients, including nonsense, frameshift, splice site and missense mutations, as well as two intragenic deletions. These mutations are associated with clinical features that suggest a function for RPS19 in erythropoiesis and embryogenesis.}, keywords = {genetic,genetics,*mutation,amino acid sequence,biosynthesis,chemistry,chromosomes,cosmids,dna,fanconi s anemia,female,genetics,human,male,molecular sequence data,non u.s. gov t,nosource,p.h.s.,pair 19,pedigree,ribosomal proteins,sequence analysis,support,translocation (genetics),u.s. gov t,x chromosome} } % == BibTeX quality report for draptchinskaiaGeneEncodingRibosomal1999: % ? Possibly abbreviated journal title Nature Genet.

@article{tengGrowthControlRibosomopathies2013, title = {Growth Control and Ribosomopathies.}, author = {Teng, Teng and Thomas, George and Mercer, Carol A.}, year = 2013, journal = {Curr. Opin. Gen. Dev.}, volume = {23}, pages = {63–71}, issn = {18790380}, doi = {10.1016/j.gde.2013.02.001}, pmid = {23490481}, keywords = {nosource} } % == BibTeX quality report for tengGrowthControlRibosomopathies2013: % ? Possibly abbreviated journal title Curr. Opin. Gen. Dev.

@article{strunkTranslationlikeCycleQuality2012, title = {A Translation-like Cycle Is a Quality Control Checkpoint for Maturing {{40S}} Ribosome Subunits.}, author = {Strunk, Bethany S. and Novak, Megan N. and Young, Crystal L. and Karbstein, Katrin}, year = 2012, journal = {Cell}, volume = {150}, pages = {111–21}, issn = {10974172}, doi = {10.1016/j.cell.2012.04.044}, pmid = {22770215}, keywords = {nosource} }

@article{loDefiningPathwayCytoplasmic2010, title = {Defining the Pathway of Cytoplasmic Maturation of the {{60S}} Ribosomal Subunit.}, author = {Lo, Kai-Yin and Li, Zhihua and Bussiere, Cyril and Bresson, Stefan and Marcotte, Edward M. and Johnson, Arlen W.}, year = 2010, journal = {Mol. Cell}, volume = {39}, pages = {196–208}, abstract = {In eukaryotic cells the final maturation of ribosomes occurs in the cytoplasm, where trans-acting factors are removed and critical ribosomal proteins are added for functionality. Here, we have carried out a comprehensive analysis of cytoplasmic maturation, ordering the known steps into a coherent pathway. Maturation is initiated by the ATPase Drg1. Downstream, assembly of the ribosome stalk is essential for the release of Tif6. The stalk recruits GTPases during translation. Because the GTPase Efl1, which is required for the release of Tif6, resembles the translation elongation factor eEF2, we suggest that assembly of the stalk recruits Efl1, triggering a step in 60S biogenesis that mimics aspects of translocation. Efl1 could thereby provide a mechanism to functionally check the nascent subunit. Finally, the release of Tif6 is a prerequisite for the release of the nuclear export adaptor Nmd3. Establishing this pathway provides an important conceptual framework for understanding ribosome maturation.}, pmid = {20670889}, keywords = {nosource} } % == BibTeX quality report for loDefiningPathwayCytoplasmic2010: % ? Possibly abbreviated journal title Mol. Cell

@article{strunkPoweringRibosomeAssembly2009, title = {Powering through Ribosome Assembly}, author = {Strunk, Bethany S. and Karbstein, Katrin}, year = 2009, journal = {RNA}, volume = {15}, pages = {2083–2104}, doi = {10.1261/rna.1792109}, abstract = {Ribosome assembly is required for cell growth in all organisms. Classic in vitro work in bacteria has led to a detailed understanding of the biophysical, thermodynamic, and structural basis for the ordered and correct assembly of ribosomal proteins on ribosomal RNA. Furthermore, it has enabled reconstitution of active subunits from ribosomal RNA and proteins in vitro. Nevertheless, recent work has shown that eukaryotic ribosome assembly requires a large macromolecular machinery in vivo. Many of these assembly factors such as ATPases, GTPases, and kinases hydrolyze nucleotide triphosphates. Because these enzymes are likely regulatory proteins, much work to date has focused on understanding their role in the assembly process. Here, we review these factors, as well as other sources of energy, and their roles in the ribosome assembly process. In addition, we propose roles of energy-releasing enzymes in the assembly process, to explain why energy is used for a process that occurs largely spontaneously in bacteria. Finally, we use literature data to suggest testable models for how these enzymes could be used as targets for regulation of ribosome assembly.}, pmid = {19850913}, keywords = {animals,humans,nosource,nucleic acid conformation,protein multimerization,ribosomal,ribosomal chemistry,ribosomal metabolism,ribosomal proteins,ribosomal proteins metabolism,ribosomes,ribosomes metabolism,rna} }

@article{griffiths-jonesRfamAnnotatingNoncoding2005, title = {Rfam: Annotating Non-Coding {{RNAs}} in Complete Genomes}, author = {{Griffiths-Jones}, Sam and Moxon, Simon and Marshall, Mhairi and Khanna, Ajay and Eddy, Sean R. and Bateman, Alex}, year = 2005, journal = {Nucleic Acids Res.}, volume = {33}, pages = {D121-D124}, doi = {10.1093/nar/gki081}, abstract = {Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the identification and classification of new members of known sequence families, and distributes annotation of ncRNAs in over 200 complete genome sequences. The data provide the first glimpses of conservation of multiple ncRNA families across a wide taxonomic range. A small number of large families are essential in all three kingdoms of life, with large numbers of smaller families specific to certain taxa. Recent improvements in the database are discussed, together with challenges for the future. Rfam is available on the Web at http://www.sanger.ac.uk/Software/Rfam/ and http://rfam.wustl.edu/.}, pmid = {15608160}, keywords = {animals,base sequence,databases,genome,humans,nosource,nucleic acid,rna,sequence alignment,untranslated,untranslated chemistry,untranslated classification} } % == BibTeX quality report for griffiths-jonesRfamAnnotatingNoncoding2005: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{angerStructuresHumanDrosophila2013, title = {Structures of the Human and {{Drosophila 80S}} Ribosome}, author = {Anger, Andreas M. and Armache, Jean-Paul and Berninghausen, Otto and Habeck, O. and Subklewe, M. and Wilson, D. N. and Beckmann, Roland}, year = 2013, journal = {Nature}, volume = {497}, number = {7447}, pages = {80–85}, keywords = {nosource} }

@article{giegeUniversalRulesIdiosyncratic1998, title = {Universal Rules and Idiosyncratic Features in {{tRNA}} Identity.}, author = {Giege, R. and Sissler, M. and Florentz, C.}, year = 1998, journal = {Nucleic Acids Res.}, volume = {26}, pages = {5017–5035}, abstract = {Correct expression of the genetic code at translation is directly correlated with tRNA identity. This survey describes the molecular signals in tRNAs that trigger specific aminoacylations. For most tRNAs, determinants are located at the two distal extremities: the anticodon loop and the amino acid accepting stem. In a few tRNAs, however, major identity signals are found in the core of the molecule. Identity elements have different strengths, often depend more on k cat effects than on K m effects and exhibit additive, cooperative or anti-cooperative interplay. Most determinants are in direct contact with cognate synthetases, and chemical groups on bases or ribose moieties that make functional interactions have been identified in several systems. Major determinants are conserved in evolution; however, the mechanisms by which they are expressed are species dependent. Recent studies show that alternate identity sets can be recognized by a single synthetase, and emphasize the importance of tRNA architecture and anti-determinants preventing false recognition. Identity rules apply to tRNA-like molecules and to minimalist tRNAs. Knowledge of these rules allows the manipulation of identity elements and engineering of tRNAs with switched, altered or multiple specificities. References: 280}, keywords = {aminoacyl trna,aminoacyl trna synthetase,nosource,recognition,structure,trna} } % == BibTeX quality report for giegeUniversalRulesIdiosyncratic1998: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{mooreStructuralMotifsRNA1999, title = {Structural Motifs in {{RNA}}}, author = {Moore, P. B.}, year = 1999, journal = {Ann. Rev. Biochem.}, volume = {68}, pages = {287–300}, issn = {00664154}, abstract = {An RNA motif is a discrete sequence or combination of base juxtapositions found in naturally occurring RNAs in unexpectedly high abundance. Because all the motifs examined so far have three-dimensional structures independent of the context in which they are embedded, they are important components of the “kit” of structural elements from which RNAs are constructed. This review discusses the structures of the motifs that have been identified so far and speculates on the importance of their role in determining RNA conformation and their evolutionary origin.}, keywords = {nosource} } % == BibTeX quality report for mooreStructuralMotifsRNA1999: % ? Possibly abbreviated journal title Ann. Rev. Biochem.

@article{agrawalStructuralAspectsMitochondrial2012, title = {Structural Aspects of Mitochondrial Translational Apparatus}, author = {Agrawal, R. K. and Sharma, M. R.}, year = 2012, journal = {Curr. Opin. Struct. Biol.}, volume = {22}, pages = {797–803}, abstract = {During the last decade groundbreaking progress has been made towards the understanding of structure and function of cell’s translational machinery. Cryo-electron microscopic (cryo-EM) and X-ray crystallographic structures of cytoplasmic ribosomes from several bacterial and eukaryotic species are now available in various ligand-bound states. Significant advances have also been made in structural studies on ribosomes of the cellular organelles, such as those present in the chloroplasts and mitochondria, using cryo-EM techniques. Here we review the progress made in structure determination of the mitochondrial ribosomes, with an emphasis on the mammalian mitochondrial ribosome and one of its translation initiation factors, and discuss challenges that lie ahead in obtaining their high-resolution structures.}, keywords = {nosource} } % == BibTeX quality report for agrawalStructuralAspectsMitochondrial2012: % ? Possibly abbreviated journal title Curr. Opin. Struct. Biol.

@article{sharmaStructureMitochondrialRibosome2009, title = {Structure of a Mitochondrial Ribosome with Minimal {{RNA}}.}, author = {Sharma, Manjuli R. and Booth, Timothy M. and Simpson, Larry and Maslov, Dmitri A. and Agrawal, Rajendra K.}, year = 2009, journal = {PNAS}, volume = {106}, pages = {9637–9642}, doi = {10.1073/pnas.0901631106}, abstract = {The Leishmania tarentolae mitochondrial ribosome (Lmr) is a minimal ribosomal RNA (rRNA)-containing ribosome. We have obtained a cryo-EM map of the Lmr. The map reveals several features that have not been seen in previously-determined structures of eubacterial or eukaryotic (cytoplasmic or organellar) ribosomes to our knowledge. Comparisons of the Lmr map with X-ray crystallographic and cryo-EM maps of the eubacterial ribosomes and a cryo-EM map of the mammalian mitochondrial ribosome show that (i) the overall structure of the Lmr is considerably more porous, (ii) the topology of the intersubunit space is significantly different, with fewer intersubunit bridges, but more tunnels, and (iii) several of the functionally-important rRNA regions, including the {\(\alpha\)}-sarcin-ricin loop, have different relative positions within the structure. Furthermore, the major portions of the mRNA channel, the tRNA passage, and the nascent polypeptide exit tunnel contain Lmr-specific proteins, suggesting that the mechanisms for mRNA recruitment, tRNA interaction, and exiting of the nascent polypeptide in Lmr must differ markedly from the mechanisms deduced for ribosomes in other organisms. Our study identifies certain structural features that are characteristic solely of mitochondrial ribosomes and other features that are characteristic of both mitochondrial and chloroplast ribosomes (i.e., organellar ribosomes).}, pmid = {19497863}, keywords = {animals,cryoelectron microscopy,leishmania,leishmania genetics,messenger,messenger metabolism,mitochondria,mitochondria chemistry,mitochondria metabolism,models,molecular,nosource,ribosomes,ribosomes chemistry,ribosomes metabolism,ribosomes ultrastructure,rna,transfer,transfer metabolism} }

@article{wittmannArchitectureProkaryoticRibosomes1983, title = {Architecture of Prokaryotic Ribosomes}, author = {Wittmann, H. G.}, year = 1983, journal = {Ann. Rev. Biochem.}, volume = {52}, pages = {35–65}, keywords = {nosource} } % == BibTeX quality report for wittmannArchitectureProkaryoticRibosomes1983: % ? Possibly abbreviated journal title Ann. Rev. Biochem.

@article{wittmannStructureEvolutionRibosomes1982, title = {Structure and Evolution of Ribosomes.}, author = {Wittmann, H. G.}, year = 1982, journal = {Proceedings of the Royal Society of London Series B Containing papers of a Biological character Royal Society Great Britain}, volume = {216}, pages = {117–135}, abstract = {Ribosomes are the only cell organelles occurring in all organisms. E. coli ribosomes, which are the best characterized particles, consist of three RNAs and 53 proteins. All components have been isolated and characterized by chemical, physical and immunological methods. The primary structures of the RNAs and of all the proteins are known. Information about the secondary structure of the proteins derives from circular dichroism measurements and from secondary structure prediction methods. The tertiary structure is being studied by limited proteolysis, proton magnetic resonance and crystallization followed by X-ray analysis. Various methods are being used to elucidate the architecture of the ribosomal particle: three-dimensional image reconstruction of crystals of bacterial ribosomes and/or their subunits; immune electron microscopy; neutron scattering; protein-protein, protein-RNA and RNA-RNA crosslinking; total reconstitution of ribosomal subunits. The results from these studies yield valuable information on the architecture of the ribosomal particle. Many mutants have been isolated in which one or a few ribosomal proteins are altered or even deleted. The genetic and biochemical characterization of these mutants allows conclusions about the importance of these proteins for the function of the ribosome. Ribosomal proteins from various prokaryotic and eukaryotic species have been compared by two-dimensional gel electrophoresis, immunological methods, reconstitution and amino acid sequence analysis. These studies show a strong homology among prokaryotic ribosomal proteins but only a weak homology between proteins from prokaryotic and eukaryotic ribosomes. Comparison of the primary and secondary structures of the ribosomal RNAs from various organisms shows that the secondary structure of the RNA molecules has been strongly conserved throughout evolution.}, pmid = {6129626}, keywords = {nosource} }

@book{robertsMicrosomalParticlesProtein1958, title = {Microsomal Particles and Protein Synthesis}, author = {Roberts, R. B.}, year = 1958, publisher = {Pergamon Press}, keywords = {nosource} } % == BibTeX quality report for robertsMicrosomalParticlesProtein1958: % ? unused Number of pages (“vii-viii”)

@article{kellerTurnoverProteinsCell1951, title = {Turnover of Proteins of Cell Fractions of Adult Rat Liver in Vivo}, author = {Keller, E. B.}, year = 1951, journal = {Fed. Proc.}, volume = {10}, pages = {206–210}, keywords = {nosource} } % == BibTeX quality report for kellerTurnoverProteinsCell1951: % ? Possibly abbreviated journal title Fed. Proc.

@article{zamecnikRelationPhosphateEnergy1954, title = {Relation between Phosphate Energy Donors and Incorporation of Labelled Amino Acids into Proteins}, author = {Zamecnik, P. C. and Keller, E. B.}, year = 1954, journal = {J. Biol. Chem}, volume = {209}, pages = {337–354}, keywords = {nosource} } % == BibTeX quality report for zamecnikRelationPhosphateEnergy1954: % ? Possibly abbreviated journal title J. Biol. Chem

@article{claudeConstitutionProtoplasm1943, title = {The Constitution of Protoplasm}, author = {Claude, Albert}, year = 1943, journal = {Science}, volume = {97}, pages = {451–456}, keywords = {nosource} }

@article{documentsGettingStartedMendeley2011, title = {Getting {{Started}} with {{Mendeley}}}, author = {Documents, Sharing and Team, The Mendeley Support}, year = 2011, journal = {Mendeley Desktop}, number = {January}, pages = {1–16}, publisher = {Mendeley Ltd.}, url = {http://www.mendeley.com}, abstract = {A quick introduction to Mendeley. Learn how Mendeley creates your personal digital library, how to organize and annotate documents, how to collaborate and share with colleagues, and how to generate citations and bibliographies.}, keywords = {how-to,Mendeley,nosource,user manual} } % == BibTeX quality report for documentsGettingStartedMendeley2011: % ? Title looks like it was stored in title-case in Zotero

@article{paladeSmallParticulateComponent1955, title = {A Small Particulate Component of the Cytoplasm}, author = {Palade, G. E.}, year = 1955, journal = {J. Biophys. Biochem. Cyt.}, volume = {1}, pages = {59–68}, issn = {00959901}, abstract = {A particulate component of small dimensions (100 to 150 A) and high density is described in the ground substance of the cytoplasm of mammalian and avian cells. In many cell types that seem to have in common a high degree of differentiation, the new component is preferentially associated with the membrane of the endoplasmic reticulum; whereas in other cell types, characterized by rapid proliferation, it occurs more or less freely distributed in the ground substance of the cytoplasm. In the Discussion an attempt is made to integrate the observations presented in this paper with the already available cytological, histochemical, and cytochemical information.}, pmid = {14381428}, keywords = {nosource} } % == BibTeX quality report for paladeSmallParticulateComponent1955: % ? Possibly abbreviated journal title J. Biophys. Biochem. Cyt.

@article{paladeEndoplasmicReticulum1956, title = {The Endoplasmic Reticulum.}, author = {Palade, G. E.}, year = 1956, journal = {The Journal of biophysical and biochemical cytology}, volume = {2}, pages = {85–98}, abstract = {The Endoplasmic Reticulum (ER) organelle is made up of two types, smooth and rough endoplasmic reticulum, which carry out different functions in the cell.}, pmid = {13357527}, keywords = {electron,microscopy,nosource,protoplasm} }

@article{paladeSTUDIESENDOPLASMICRETICULUM1960, title = {{{STUDIES ON THE ENDOPLASMIC RETICULUM}}}, author = {Palade, George E. and Porter, Keith R.}, year = 1960, journal = {The Journal of biophysical and biochemical cytology}, volume = {3}, pages = {167–180}, abstract = {Several types of striated muscle have been examined by the technics of electron microscopy and the findings in myotome fibers of Amblystoma larvae, the sartorius, and cardiac muscle of the rat are reported on in some detail. Particular attention has been given to structural components of the interfibrillar sarcoplasm and most especially to a finely divided, vacuolar system known as the sarcoplasmic reticulum. This consists of membrane-limited vesicles, tubules, and cisternae associated in a continuous reticular structure which forms lace-like sleeves around the myofibrils. It shows a definable organization which repeats with each sarcomere of the fiber so that the entire system is segmented in phase with the striations of the associated myofibrils. Details of these repetitive patterns are presented diagrammatically in Text-figs. 1, 2, and 3 on pages 279, 283, and 288 respectively. The system is continuous across the fiber at the H band level and largely discontinuous longitudinally because of interruptions in the structure at the I and Z band levels. The structure of the system relates it to the endoplasmic reticulum of other cell types. The precise morphological relation of the reticulum to the myofibrils, with specializations opposite the different bands, prompts the supposition that the system is functionally important in muscle contraction. In this regard it is proposed that the membrane limiting the system is polarized like the sarcolemma and that the corresponding potential difference is utilized in the intracellular distribution of the excitatory impulse.}, keywords = {nosource} } % == BibTeX quality report for paladeSTUDIESENDOPLASMICRETICULUM1960: % ? Title looks like it was stored in title-case in Zotero

@article{paladeIntracellularAspectsProcess1975, title = {Intracellular Aspects of the Process of Protein Sy… [{{Science}}. 1975] - {{PubMed}} Result}, author = {Palade, G.}, year = 1975, journal = {Science}, volume = {189}, pages = {867}, issn = {00368075}, doi = {10.1126/science.189.4206.867-b}, abstract = {The title of the Nobel Lecture of George Palade (1 August, p. 347) should have been “Intracellular aspects of the process of protein secretion.”}, pmid = {17812524}, keywords = {nosource,undefined} }

@article{allfreySynthesisProteinPancreas1953, title = {Synthesis of Protein in the Pancreas. {{II}}. {{The}} Role of Ribonucleoprotein in Protein Synthesis.}, author = {Allfrey, V. and Daly, M. M. and Mirsky, A. E.}, year = 1953, journal = {J. Gen. Physiol.}, volume = {37}, pages = {157–175}, abstract = {1. The ribonucleoprotein of the microsome fraction which sediments at 40,000 R.P.M. as a pellet (and which is referred to as the pellet material) has been studied with reference to its role in protein synthesis in the pancreas. 2. In pellet material nucleic acid and protein form a definite complex as shown by its electrophoretic behavior and unchanging composition under various conditions. 3. Protein of pellet material is not especially rich in the diamino acids. 4. Evidence is brought forward indicating that the protein component of pellet material takes part in the general process of protein synthesis in the cell. (a) The well known correlation between quantity of RNA and rate of protein synthesis in a tissue implicates the protein of the pellet material, for most of the RNA in the pancreas and other tissues is in this material. (b) Uptake of isotopically labelled glycine by the pellet material, confirming results of previous workers, is for short periods greater than in other protein fractions. (c) Comparing the pellet materials of pancreas, liver, and kidney-three tissues with vastly different rates of protein synthesis, in the sequence given-there is a correlation between the quantity of RNA in the pellet and the rate of protein synthesis in the tissue; a similar correlation between quantity of RNA in the pellet material and rate of N(15)-glycine uptake by the protein component of the pellet; and finally, the level of uptake by total protein varies with the tissue and is related to the uptake of N(15)-glycine by protein of the pellet. 5. In the pancreas a distinction can be made between proteins synthesized for secretion and the nucleoprotein of the pellet (not found in the secretion) which, however, takes part in the synthetic process, as shown by the fact that the N(15) uptake by protein of the pellet is increased when the synthesis of digestive enzymes is stimulated by secretion. 6. The time course of N(15) uptake by proteins of the pancreas indicates that pellet protein serves as precursor material in the synthesis of the secretory proteins. 7. Rate of uptake of N(15)-glycine by the purines of RNA of the pellet material is not correlated with uptake by the protein. 8. The uptake of C(14)-alanine by an in vitro system of microsomes + mitochondria is impaired by preincubation of the microsomes with ribonuclease. This is direct experimental evidence for the dependence of protein synthesis upon the presence or intactness of ribonucleic acid in the microsomes.}, pmid = {13109153}, keywords = {metabolism,nosource,nucleoproteins,pancreas,physiology,proteins} } % == BibTeX quality report for allfreySynthesisProteinPancreas1953: % ? Possibly abbreviated journal title J. Gen. Physiol.

@article{hultinIncorporationVivo15Nlabeled1950, title = {Incorporation in Vivo of {{15N-labeled}} Glycine into Liver Fractions of Newly Hatched Chicks.}, author = {Hultin, T.}, year = 1950, journal = {Experim. Cell. Res.}, volume = {1}, pages = {372–376}, abstract = {In the livers of newly hatched chicks, 15N from labeled glycine is incorporated in vivo into the microsome proteins earlier and at a more rapid rate than into the proteins of any other cell fraction isolated by differential centrifugation. The microsomes, moreover, probably contribute in a high degree to the surprisingly high isotope level of the considerable amounts of cell fluid proteins. Since the microsomes are especially rich in ribonucleic acid, and the production of phosphate-bound energy is centered in the mitochondria, the experiments indicate that the immediate availability of ribonucleic acid is more important for the formation of proteins than a close proximity to energy-producing enzyme systems.}, keywords = {nosource} } % == BibTeX quality report for hultinIncorporationVivo15Nlabeled1950: % ? Possibly abbreviated journal title Experim. Cell. Res.

@article{claudeConstitutionMitochondriaMicrosomes1944, title = {The Constitution of Mitochondria and Microsomes}, author = {Claude, Albert}, year = 1944, journal = {J. Exp. Med.}, volume = {80}, pages = {19–29}, abstract = {1. Rat tumor extracts, containing chiefly the cytoplasmic constituents of leukemic cells, were fractionated into three main portions, the different components separating in the centrifuge according to size. 2. Mitochondria were isolated by centrifugation at relatively low speed. Elementary composition of purified mitochondria was found to correspond to about 11.5 per cent nitrogen, 1.6 per cent phosphorus, and 27 per cent lipids. Phosphorus and nitrogen content of the lipid portion suggests that as much as 75 to 80 per cent of the lipids of mitochondria is represented by phospholipids. Tests for ribose nucleic acid were positive. 3. Microsomes were separated by means of centrifugation at 18,000 x g. A relation between the high phosphorus content of the microsomes and the marked basophilia of the cytoplasm of leukemic cells is suggested. 4. Phosphorus distribution in the tumor extract, and light absorption analysis of the third fraction, seem to demonstrate that nucleic acid was not present either in a free condition, or in the form of nucleoprotein of relatively low molecular weight. The nature of the results suggests that ribose nucleic acid occurs in the cytoplasm of leukemic cells only in association with formed elements of relatively large size, namely microsomes, and mitochondria.}, pmid = {19871395}, keywords = {nosource} } % == BibTeX quality report for claudeConstitutionMitochondriaMicrosomes1944: % ? Possibly abbreviated journal title J. Exp. Med.

@article{claudeFRACTIONATIONMAMMALIANLIVER1946, title = {{{FRACTIONATION OF MAMMALIAN LIVER CELLS BY DIFFERENTIAL CENTRIFUGATION}}}, author = {Claude, Albert}, year = 1946, journal = {The Journal of Experimental Medicine}, volume = {84}, pages = {61–89}, abstract = {1. A method is described whereby the major components of liver suspensions are segregated according to size into three main fractions: (a) a large granule fraction composed of elements approximately 0.5 to 2 in diameter; (b) a microsome fraction composed of submicroscopic elements approximately 80 to 150 m in diameter; and, (c) a supernate fraction containing the soluble components of the extract. 2. The nature and origin of the constituents of liver extract is discussed. The large granule fraction is deemed to consist mostly of mitochondria and liver secretory granules, whereas the microsome fraction corresponds to the chromophilic ground substance of the hepatic cell. Phosphorus distribution in the supernate fraction, and ultraviolet absorption of the solution suggests that practically all the ribose nucleoproteins of liver extract are sedimentable, and occur in association with the large granules and microsomes. 3. The method of fractionation of liver suspension by differential centrifugation is being used as a means to investigate the chemical constitution of the morphological constituents of cytoplasm, and the distribution of biochemical activities in the cytoplasm of the hepatic cell. 4. The method of differential centrifugation is found to be applicable not only to the fractionation of cells but also, with the aid of auxiliary techniques, to the fractionation of much smaller elements, such as mitochondria.}, pmid = {19871554}, keywords = {nosource} } % == BibTeX quality report for claudeFRACTIONATIONMAMMALIANLIVER1946: % ? Title looks like it was stored in title-case in Zotero

@article{faddaRoles3exoribonucleasesExosome2013, title = {The Roles of 3{\(\prime\)}-Exoribonucleases and the Exosome in Trypanosome {{mRNA}} Degradation}, author = {Fadda, Abeer and F{"a}rber, Valentin and Droll, Dorothea and Clayton, Christine}, year = 2013, month = may, journal = {RNA}, eprint = {23697549}, eprinttype = {pubmed}, pages = {937–947}, issn = {1469-9001}, doi = {10.1261/rna.038430.113.2}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23697549}, abstract = {The degradation of eukaryotic mRNAs can be initiated by deadenylation, decapping, or endonuclease cleavage. This is followed by 5’-3’ degradation by homologs of Xrn1, and/or 3’-5’ degradation by the exosome. We previously reported that, in African trypanosome Trypanosoma brucei, most mRNAs are deadenylated prior to degradation, and that depletion of the major 5’-3’ exoribonuclease XRNA preferentially stabilizes unstable mRNAs. We now show that depletion of either CAF1 or CNOT10, two components of the principal deadenylation complex, strongly inhibits degradation of most mRNAs. RNAi targeting another deadenylase, PAN2, or RRP45, a core component of the exosome, preferentially stabilized mRNAs with intermediate half-lives. RRP45 depletion resulted in a 5’ bias of mRNA sequences, suggesting action by a distributive 3’-5’ exoribonuclease. Results suggested that the exosome is involved in the processing of trypanosome snoRNAs. There was no correlation between effects on half-lives and on mRNA abundance.}, pmid = {23697549}, keywords = {caf1,deadenylation,exosome,mrna decay,mrna degradation,nosource,pan2,trypanosoma} }

@article{rayCompendiumRNAbindingMotifs2013, title = {A Compendium of {{RNA-binding}} Motifs for Decoding Gene Regulation}, author = {Ray, Debashish and Kazan, Hilal and Cook, Kate B. and Weirauch, Matthew T. and Najafabadi, Hamed S. and Li, Xiao and Gueroussov, Serge and Albu, Mihai and Zheng, Hong and Yang, Ally and Na, Hong and Irimia, Manuel and Matzat, Leah H. and Dale, Ryan K. and {}a Smith, Sarah and {}a Yarosh, Christopher and Kelly, Seth M. and Nabet, Behnam and Mecenas, Desirea and Li, Weimin and Laishram, Rakesh S. and Qiao, Mei and Lipshitz, Howard D. and Piano, Fabio and Corbett, Anita H. and Carstens, Russ P. and Frey, Brendan J. and {}a Anderson, Richard and Lynch, Kristen W. and Penalva, Luiz O. F. and Lei, Elissa P. and Fraser, Andrew G. and Blencowe, Benjamin J. and Morris, Quaid D. and Hughes, Timothy R.}, year = 2013, month = jul, journal = {Nature}, volume = {499}, number = {7457}, pages = {172–177}, publisher = {Nature Publishing Group}, issn = {0028-0836}, doi = {10.1038/nature12311}, url = {http://www.nature.com/doifinder/10.1038/nature12311}, keywords = {nosource} }

@article{shahRateLimitingStepsYeast2013, title = {Rate-{{Limiting Steps}} in {{Yeast Protein Translation}}}, author = {Shah, Premal and Ding, Yang and Niemczyk, Malwina and Kudla, Grzegorz and Plotkin, Joshua B.}, year = 2013, month = jun, journal = {Cell}, volume = {153}, number = {7}, pages = {1589–1601}, publisher = {Elsevier Inc.}, issn = {00928674}, doi = {10.1016/j.cell.2013.05.049}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867413006557}, keywords = {nosource} } % == BibTeX quality report for shahRateLimitingStepsYeast2013: % ? Title looks like it was stored in title-case in Zotero

@article{kumarHighThroughputMethodIllumina2012, title = {A {{High-Throughput Method}} for {{Illumina RNA-Seq Library Preparation}}.}, author = {Kumar, Ravi and Ichihashi, Yasunori and Kimura, Seisuke and Chitwood, Daniel H. and Headland, Lauren R. and Peng, Jie and Maloof, Julin N. and Sinha, Neelima R.}, year = 2012, month = jan, journal = {Frontiers in plant science}, volume = {3}, number = {August}, pages = {202}, issn = {1664-462X}, doi = {10.3389/fpls.2012.00202}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3428589&tool=pmcentrez&rendertype=abstract}, abstract = {With the introduction of cost effective, rapid, and superior quality next generation sequencing techniques, gene expression analysis has become viable for labs conducting small projects as well as large-scale gene expression analysis experiments. However, the available protocols for construction of RNA-sequencing (RNA-Seq) libraries are expensive and/or difficult to scale for high-throughput applications. Also, most protocols require isolated total RNA as a starting point. We provide a cost-effective RNA-Seq library synthesis protocol that is fast, starts with tissue, and is high-throughput from tissue to synthesized library. We have also designed and report a set of 96 unique barcodes for library adapters that are amenable to high-throughput sequencing by a large combination of multiplexing strategies. Our developed protocol has more power to detect differentially expressed genes when compared to the standard Illumina protocol, probably owing to less technical variation amongst replicates. We also address the problem of gene-length biases affecting differential gene expression calls and demonstrate that such biases can be efficiently minimized during mRNA isolation for library preparation.}, pmid = {22973283}, keywords = {cdna fragmentation,cDNA fragmentation,have contributed equally to,high-throughput,ichihashi,illumina,Illumina,mRN,mrna isolation,multiplexing,nosource,ravi kumar and yasunori,rna-seq,sequencing,this work} } % == BibTeX quality report for kumarHighThroughputMethodIllumina2012: % ? Title looks like it was stored in title-case in Zotero

@article{plotkinSynonymousNotSame2011, title = {Synonymous but Not the Same: The Causes and Consequences of Codon Bias.}, author = {Plotkin, Joshua B. and Kudla, Grzegorz}, year = 2011, month = jan, journal = {Nature reviews. Genetics}, volume = {12}, number = {1}, pages = {32–42}, publisher = {Nature Publishing Group}, issn = {1471-0064}, doi = {10.1038/nrg2899}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3074964&tool=pmcentrez&rendertype=abstract}, abstract = {Despite their name, synonymous mutations have significant consequences for cellular processes in all taxa. As a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology. Although recent advances in sequencing and synthetic biology have helped to resolve longstanding questions about codon bias, they have also uncovered striking patterns that suggest new hypotheses about protein synthesis. Ongoing work to quantify the dynamics of initiation and elongation is as important for understanding natural synonymous variation as it is for designing transgenes in applied contexts.}, pmid = {21102527}, keywords = {Animals,Codon,Codon: genetics,Drosophila Proteins,Drosophila Proteins: genetics,Gene Expression,Genome,Humans,Mice,Mutation,nosource,Protein Biosynthesis} } % == BibTeX quality report for plotkinSynonymousNotSame2011: % ? Possibly abbreviated journal title Nature reviews. Genetics

@article{capewellRegulationTrypanosomaBrucei2013, title = {Regulation of {{Trypanosoma}} Brucei {{Total}} and {{Polysomal mRNA}} during {{Development}} within {{Its Mammalian Host}}}, author = {Capewell, Paul and Monk, Stephanie and Ivens, Alasdair and MacGregor, Paula and Fenn, Katelyn and Walrad, Pegine and Bringaud, Frederic and Smith, Terry K. and Matthews, Keith R.}, editor = {Elias, M. Carolina}, year = 2013, month = jun, journal = {PLoS ONE}, volume = {8}, number = {6}, pages = {e67069}, issn = {1932-6203}, doi = {10.1371/journal.pone.0067069}, url = {http://dx.plos.org/10.1371/journal.pone.0067069}, keywords = {nosource} }

@article{laiBiochemicalCharacterizationATPdependent2002, title = {Biochemical Characterization of an {{ATP-dependent DNA}} Ligase from the Hyperthermophilic Crenarchaeon {{Sulfolobus}} Shibatae}, author = {Lai, X. and Shao, H. and Hao, F. and Huang, L.}, year = 2002, journal = {Extremophiles}, pages = {469–477}, url = {http://link.springer.com/article/10.1007/s00792-002-0284-5}, keywords = {atp,crenarchaeota,dna ligase,metal cofactor,nosource,shibatae,sulfolobus,thermostability} }

@article{nakasugiNovoTranscriptomeSequence2013, title = {De {{Novo Transcriptome Sequence}} Assembly and Analysis of {{RNA}} Silencing Genes of {{Nicotiana}} Benthamiana}, author = {Nakasugi, Kenlee and Crowhurst, R. N. and Bally, Julia}, year = 2013, journal = {PloS one}, volume = {8}, number = {3}, doi = {10.1371/journal.pone.0059534}, url = {http://dx.plos.org/10.1371/journal.pone.0059534.g009}, keywords = {nosource} }

@article{liRSEMAccurateTranscript2011, title = {{{RSEM}}: Accurate Transcript Quantification from {{RNA-Seq}} Data with or without a Reference Genome}, author = {Li, Bo and Dewey, C. N.}, year = 2011, journal = {BMC bioinformatics}, doi = {10.1186/1471-2105-12-323}, url = {http://www.biomedcentral.com/1471-2105/12/323/}, keywords = {nosource} }

@article{pandyaSilencingSubtelomericVSGs2013, title = {Silencing Subtelomeric {{VSGs}} by {{Trypanosoma}} Brucei {{RAP1}} at the Insect Stage Involves Chromatin Structure Changes}, author = {Pandya, U. M. and Sandhu, Ranjodh and Li, Bibo}, year = 2013, journal = {Nucleic acids research}, pages = {1–10}, doi = {10.1093/nar/gkt562}, url = {http://nar.oxfordjournals.org/content/41/16/7673.short}, keywords = {nosource} }

@article{linigerOverlappingSenseAntisense2001, title = {Overlapping Sense and Antisense Transcription Units in {{Trypanosoma}} Brucei}, author = {Liniger, Matthias and Bodenm{"u}ller, K.}, year = 2001, journal = {Molecular }, volume = {40}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02426.x/full}, keywords = {nosource} }

@article{tateEvaluationCircularDNA2012, title = {Evaluation of Circular {{DNA}} Substrates for Whole Genome Amplification Prior to Forensic Analysis.}, author = {Tate, Courtney M. and Nu{~n}ez, Ada N. and {}a Goldstein, Cori and Gomes, Iva and Robertson, James M. and Kavlick, Mark F. and Budowle, Bruce}, year = 2012, month = mar, journal = {Forensic science international. Genetics}, volume = {6}, number = {2}, eprint = {21570374}, eprinttype = {pubmed}, pages = {185–90}, issn = {1878-0326}, doi = {10.1016/j.fsigen.2011.04.011}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21570374}, abstract = {Forensic biological evidence often contains low quantities of DNA or substantially degraded DNA which makes samples refractory to genotype analysis. One approach that shows promise to overcome the limited quantity of DNA is whole genome amplification (WGA). One WGA technique, termed rolling circle amplification (RCA), involves the amplification of circular DNA fragments and this study evaluates a single-stranded (ss) DNA ligase enzyme for generating circular DNA templates for RCA WGA. Fast, efficient ligation of several sizes of ssDNA templates was achieved. The enzyme also ligated double-stranded (ds) DNA templates, a novel activity not previously reported. Adapter sequences containing optimal terminal nucleotide ends for increased ligation efficiency were designed and ligation of adapters to template DNA was optimized. Increased amplification of DNA templates was observed following WGA; however, no amplification advantage for ssDNA ligase treatment of templates was evident compared to linear templates. A multi-step process to utilize ssDNA ligase prior to WGA was developed and short tandem repeat (STR) analysis of simulated low template (LT) and fragmented DNA was evaluated. The process resulted in the loss of template DNA and failed STR analysis whereas input of linear genomic DNA template directly into WGA prior to STR analysis improved STR genotyping results compared to non-WGA treated samples. Inclusion of an extreme thermostable single-stranded DNA binding protein (SSB) during WGA also increased DNA yields. While STR artifacts such as peak imbalance, drop-in, and dropout persisted, WGA shows potential for successful genetic profiling of LT and fragmented DNA samples. Further research and development is warranted prior to use of WGA in forensic casework.}, pmid = {21570374}, keywords = {DNA,DNA Degradation,DNA Fingerprinting,DNA Fingerprinting: methods,DNA Ligases,DNA: analysis,Genetic,Genome,Genotype,Human,Humans,Microsatellite Repeats,Necrotic,nosource,Nucleic Acid Amplification Techniques,Nucleic Acid Amplification Techniques: methods,Templates} } % == BibTeX quality report for tateEvaluationCircularDNA2012: % ? Possibly abbreviated journal title Forensic science international. Genetics

@article{deanRapidAmplificationPlasmid2001, title = {Rapid Amplification of Plasmid and Phage {{DNA}} Using {{Phi}} 29 {{DNA}} Polymerase and Multiply-Primed Rolling Circle Amplification.}, author = {Dean, F. B. and Nelson, J. R. and Giesler, T. L. and Lasken, R. S.}, year = 2001, month = jun, journal = {Genome research}, volume = {11}, number = {6}, pages = {1095–9}, issn = {1088-9051}, doi = {10.1101/gr.180501}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=311129&tool=pmcentrez&rendertype=abstract}, abstract = {We describe a simple method of using rolling circle amplification to amplify vector DNA such as M13 or plasmid DNA from single colonies or plaques. Using random primers and phi29 DNA polymerase, circular DNA templates can be amplified 10,000-fold in a few hours. This procedure removes the need for lengthy growth periods and traditional DNA isolation methods. Reaction products can be used directly for DNA sequencing after phosphatase treatment to inactivate unincorporated nucleotides. Amplified products can also be used for in vitro cloning, library construction, and other molecular biology applications.}, pmid = {11381035}, keywords = {Bacillus Phages,Bacillus Phages: enzymology,Bacillus Phages: genetics,Base Sequence,Circular,Circular: genetics,DNA,DNA Primers,DNA Primers: genetics,DNA Primers: metabolism,DNA-Directed DNA Polymerase,DNA-Directed DNA Polymerase: metabolism,Exonucleases,Exonucleases: metabolism,Genetic,Molecular Sequence Data,nosource,Nucleic Acid Amplification Techniques,Nucleic Acid Amplification Techniques: methods,Plasmids,Plasmids: genetics,Sequence Analysis,Templates,Viral,Viral Proteins,Viral Proteins: metabolism,Viral: genetics} }

@article{kaurInhibitionChikungunyaVirus2013, title = {Inhibition of Chikungunya Virus Replication by Harringtonine, a Novel Antiviral That Suppresses Viral Protein Expression.}, author = {Kaur, Parveen and Thiruchelvan, Meerra and Lee, Regina Ching Hua and Chen, Huixin and Chen, Karen Caiyun and Ng, Mah Lee and Chu, Justin Jang Hann}, year = 2013, month = jan, journal = {Antimicrobial agents and chemotherapy}, volume = {57}, number = {1}, eprint = {23275491}, eprinttype = {pubmed}, pages = {155–67}, issn = {1098-6596}, doi = {10.1128/AAC.01467-12}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23275491}, abstract = {Chikungunya virus (CHIKV) is a mosquito-transmitted virus that has reemerged as a significant public health threat in the last decade. Since the 2005-2006 chikungunya fever epidemic in the Indian Ocean island of La R'eunion, millions of people in more than 40 countries have been infected. Despite this, there is currently no antiviral treatment for chikungunya infection. In this study, an immunofluorescence-based screening platform was developed to identify potential inhibitors of CHIKV infection. A primary screen was performed using a highly purified natural product compound library, and 44 compounds exhibiting {\(\geq\)}70% inhibition of CHIKV infection were identified as positive hits. Among these, four were selected for dose-dependent inhibition assays to confirm their anti-CHIKV activity. Harringtonine, a cephalotaxine alkaloid, displayed potent inhibition of CHIKV infection (50% effective concentration [EC(50)] = 0.24 {\(\mu\)}M) with minimal cytotoxicity and was selected for elucidation of its antiviral mechanism. Time-of-addition studies, cotreatment assays, and direct transfection of viral genomic RNA indicated that harringtonine inhibited an early stage of the CHIKV replication cycle which occurred after viral entry into cells. In addition, quantitative reverse transcription-PCR (qRT-PCR) and Western blot analyses indicated that harringtonine affects CHIKV RNA production as well as viral protein expression. Treatment of harringtonine against Sindbis virus, a related alphavirus, suggested that harringtonine could inhibit other alphaviruses. This study suggests for the first time that harringtonine exerts its antiviral effects by inhibiting CHIKV viral protein synthesis.}, pmid = {23275491}, keywords = {Aedes,Animals,Antiviral Agents,Antiviral Agents: isolation & purification,Antiviral Agents: pharmacology,Biological Agents,Biological Agents: isolation & purification,Biological Agents: pharmacology,Cell Line,Chikungunya virus,Chikungunya virus: drug effects,Chikungunya virus: genetics,Chikungunya virus: growth & development,Cricetinae,Dose-Response Relationship,Drug,Fluorescent Antibody Technique,Gene Expression,Gene Expression: drug effects,Genetic,Harringtonines,Harringtonines: isolation & purification,Harringtonines: pharmacology,High-Throughput Screening Assays,Humans,nosource,Protein Biosynthesis,Protein Biosynthesis: drug effects,RNA,Sindbis Virus,Sindbis Virus: drug effects,Sindbis Virus: genetics,Sindbis Virus: growth & development,Small Molecule Libraries,Small Molecule Libraries: isolation & purification,Small Molecule Libraries: pharmacology,Transduction,Viral,Viral: antagonists & inhibitors,Viral: genetics,Virus Replication,Virus Replication: drug effects} }

@article{huynhLeishmaniaAmazonensisZIP2006, title = {A {{Leishmania}} Amazonensis {{ZIP}} Family Iron Transporter Is Essential for Parasite Replication within Macrophage Phagolysosomes.}, author = {Huynh, Chau and Sacks, David L. and Andrews, Norma W.}, year = 2006, month = oct, journal = {The Journal of experimental medicine}, volume = {203}, number = {10}, pages = {2363–75}, issn = {0022-1007}, doi = {10.1084/jem.20060559}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2118100&tool=pmcentrez&rendertype=abstract}, abstract = {Infection of mammalian hosts with Leishmania amazonensis depends on the remarkable ability of these parasites to replicate within macrophage phagolysosomes. A critical adaptation for survival in this harsh environment is an efficient mechanism for gaining access to iron. In this study, we identify and characterize LIT1, a novel L. amazonensis membrane protein with extensive similarity to IRT1, a ZIP family ferrous iron transporter from Arabidopsis thaliana. The ability of LIT1 to promote iron transport was demonstrated after expression in yeast and in L. amazonensis LIT1-null amastigotes. Endogenous LIT1 was only detectable in amastigotes replicating intracellularly, and its intracellular expression was accelerated under conditions predicted to result in iron deprivation. Although L. amazonensis lacking LIT1 grew normally in axenic culture and had no defects differentiating into infective forms, replication within macrophages was abolished. Consistent with an essential role for LIT1 in intracellular growth as amastigotes, Deltalit1 parasites were avirulent. After inoculation into highly susceptible mice, no lesions were detected, even after extensive periods of time. Despite the absence of pathology, viable Deltalit1 parasites were recovered from the original sites of inoculation, indicating that L. amazonensis can persist in vivo independently of the ability to grow in macrophages. Our findings highlight the essential role played by intracellular iron acquisition in Leishmania virulence and identify this pathway as a promising target for therapeutic intervention.}, pmid = {17000865}, keywords = {Amino Acid Sequence,Animals,Base Sequence,Cation Transport Proteins,Cation Transport Proteins: genetics,Cation Transport Proteins: metabolism,DNA,DNA Primers,Fluorescence,Iron,Iron: metabolism,Leishmania,Leishmania: metabolism,Leishmania: pathogenicity,Leishmania: physiology,Lysosomes,Lysosomes: parasitology,Macrophages,Macrophages: parasitology,Mice,Microscopy,Molecular Sequence Data,nosource,Reproduction,Reproduction: physiology,Sequence Alignment,Sequence Analysis,Virulence,Yeasts} }

@article{akinboyeBiologicalActivitiesEmetine2011, title = {Biological Activities of Emetine}, author = {Akinboye, E. S. and Bakare, Oladapo}, year = 2011, journal = {The Open Natural Products Journal}, pages = {8–15}, url = {http://www.benthamscience.com/open/tonpj/articles/V004/8TONPJ.pdf}, keywords = {alkaloid,biological activity,dna,emetine,entamoeba histolytica,ipecac,nosource,protein synthesis,rna} }

@article{dangInhibitionEukaryoticTranslation2011, title = {Inhibition of Eukaryotic Translation Elongation by the Antitumor Natural Product {{Mycalamide B}}}, author = {Dang, Y. and {Schneider-Poetsch}, T. and Eyler, D. E. and Jewett, J. C. and Bhat, S. and Rawal, V. H. and Green, R. and Liu, J. O.}, year = 2011, month = jun, journal = {Rna}, volume = {17}, number = {8}, pages = {1578–1588}, issn = {1355-8382}, doi = {10.1261/rna.2624511}, url = {http://rnajournal.cshlp.org/cgi/doi/10.1261/rna.2624511}, keywords = {eukaryotic ribosome,mycalamide b,nosource,translation elongation,trna} }

@article{shalekSinglecellTranscriptomicsReveals2013, title = {Single-Cell Transcriptomics Reveals Bimodality in Expression and Splicing in Immune Cells.}, author = {Shalek, Alex K. and Satija, Rahul and Adiconis, Xian and Gertner, Rona S. and Gaublomme, Jellert T. and Raychowdhury, Raktima and Schwartz, Schragi and Yosef, Nir and Malboeuf, Christine and Lu, Diana and Trombetta, John T. and Gennert, Dave and Gnirke, Andreas and Goren, Alon and Hacohen, Nir and Levin, Joshua Z. and Park, Hongkun and Regev, Aviv}, year = 2013, month = may, journal = {Nature}, eprint = {23685454}, eprinttype = {pubmed}, pages = {1–5}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature12172}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23685454}, abstract = {Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels and phenotypic output, with important functional consequences. Existing studies of cellular heterogeneity, however, have typically measured only a few pre-selected RNAs or proteins simultaneously, because genomic profiling methods could not be applied to single cells until very recently. Here we use single-cell RNA sequencing to investigate heterogeneity in the response of mouse bone-marrow-derived dendritic cells (BMDCs) to lipopolysaccharide. We find extensive, and previously unobserved, bimodal variation in messenger RNA abundance and splicing patterns, which we validate by RNA-fluorescence in situ hybridization for select transcripts. In particular, hundreds of key immune genes are bimodally expressed across cells, surprisingly even for genes that are very highly expressed at the population average. Moreover, splicing patterns demonstrate previously unobserved levels of heterogeneity between cells. Some of the observed bimodality can be attributed to closely related, yet distinct, known maturity states of BMDCs; other portions reflect differences in the usage of key regulatory circuits. For example, we identify a module of 137 highly variable, yet co-regulated, antiviral response genes. Using cells from knockout mice, we show that variability in this module may be propagated through an interferon feedback circuit, involving the transcriptional regulators Stat2 and Irf7. Our study demonstrates the power and promise of single-cell genomics in uncovering functional diversity between cells and in deciphering cell states and circuits.}, pmid = {23685454}, keywords = {nosource} }

@article{opijnenTnseqHighthroughputParallel2009, title = {Tn-Seq: High-Throughput Parallel Sequencing for Fitness and Genetic Interaction Studies in Microorganisms.}, author = {{}van Opijnen, Tim and Bodi, Kip L. and Camilli, Andrew}, year = 2009, month = oct, journal = {Nature methods}, volume = {6}, number = {10}, pages = {767–72}, publisher = {Nature Publishing Group}, issn = {1548-7105}, doi = {10.1038/nmeth.1377}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2957483&tool=pmcentrez&rendertype=abstract}, abstract = {Biological pathways are structured in complex networks of interacting genes. Solving the architecture of such networks may provide valuable information, such as how microorganisms cause disease. Here we present a method (Tn-seq) for accurately determining quantitative genetic interactions on a genome-wide scale in microorganisms. Tn-seq is based on the assembly of a saturated Mariner transposon insertion library. After library selection, changes in frequency of each insertion mutant are determined by sequencing the flanking regions en masse. These changes are used to calculate each mutant’s fitness. Using this approach, we determined fitness for each gene of Streptococcus pneumoniae, a causative agent of pneumonia and meningitis. A genome-wide screen for genetic interactions of five query genes identified both alleviating and aggravating interactions that could be divided into seven distinct categories. Owing to the wide activity of the Mariner transposon, Tn-seq has the potential to contribute to the exploration of complex pathways across many different species.}, pmid = {19767758}, keywords = {Bacterial,Bacterial: genetics,Chromosome Mapping,Chromosome Mapping: methods,Computer Simulation,DNA,DNA: methods,Genetic,Models,nosource,Proteome,Proteome: genetics,Sequence Analysis,Signal Transduction,Signal Transduction: genetics,Streptococcus pneumoniae,Streptococcus pneumoniae: genetics} }

@article{daveyGenomewideGeneticMarker2011, title = {Genome-Wide Genetic Marker Discovery and Genotyping Using next-Generation Sequencing.}, author = {Davey, John W. and {}a Hohenlohe, Paul and Etter, Paul D. and Boone, Jason Q. and Catchen, Julian M. and Blaxter, Mark L.}, year = 2011, month = jul, journal = {Nature reviews. Genetics}, volume = {12}, number = {7}, eprint = {21681211}, eprinttype = {pubmed}, pages = {499–510}, publisher = {Nature Publishing Group}, issn = {1471-0064}, doi = {10.1038/nrg3012}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21681211}, abstract = {The advent of next-generation sequencing (NGS) has revolutionized genomic and transcriptomic approaches to biology. These new sequencing tools are also valuable for the discovery, validation and assessment of genetic markers in populations. Here we review and discuss best practices for several NGS methods for genome-wide genetic marker development and genotyping that use restriction enzyme digestion of target genomes to reduce the complexity of the target. These new methods – which include reduced-representation sequencing using reduced-representation libraries (RRLs) or complexity reduction of polymorphic sequences (CRoPS), restriction-site-associated DNA sequencing (RAD-seq) and low coverage genotyping – are applicable to both model organisms with high-quality reference genome sequences and, excitingly, to non-model species with no existing genomic data.}, pmid = {21681211}, keywords = {Algorithms,Animals,Biological,Chromosome Mapping,Chromosome Mapping: methods,Genetic Association Studies,Genetic Association Studies: methods,Genetic Association Studies: trends,Genetic Markers,Genetic Markers: genetics,Genetic Markers: physiology,Genome,Genome: genetics,Genomics,Genomics: methods,Genomics: trends,Genotype,High-Throughput Nucleotide Sequencing,High-Throughput Nucleotide Sequencing: methods,High-Throughput Nucleotide Sequencing: trends,Humans,Models,nosource} } % == BibTeX quality report for daveyGenomewideGeneticMarker2011: % ? Possibly abbreviated journal title Nature reviews. Genetics

@article{zomerESSENTIALSSoftwareRapid2012, title = {{{ESSENTIALS}}: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data.}, author = {Zomer, Aldert and Burghout, Peter and Bootsma, Hester J. and Hermans, Peter W. M. and {}van Hijum, Sacha a F. T.}, year = 2012, month = jan, journal = {PloS one}, volume = {7}, number = {8}, pages = {e43012}, issn = {1932-6203}, doi = {10.1371/journal.pone.0043012}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3416827&tool=pmcentrez&rendertype=abstract}, abstract = {High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon insertions by mutant-specific amplification and sequence readout of DNA flanking the transposon insertions site, assigning a measure of essentiality based on the number of reads per insertion site flanking sequence or per gene. However, analysis of these large and complex datasets is hampered by the lack of an easy to use and automated tool for transposon insertion sequencing data. To fill this gap, we developed ESSENTIALS, an open source, web-based software tool for researchers in the genomics field utilizing transposon insertion sequencing analysis. It accurately predicts (conditionally) essential genes and offers the flexibility of using different sample normalization methods, genomic location bias correction, data preprocessing steps, appropriate statistical tests and various visualizations to examine the results, while requiring only a minimum of input and hands-on work from the researcher. We successfully applied ESSENTIALS to in-house and published Tn-seq, TraDIS and HITS datasets and we show that the various pre- and post-processing steps on the sequence reads and count data with ESSENTIALS considerably improve the sensitivity and specificity of predicted gene essentiality.}, pmid = {22900082}, keywords = {Algorithms,Computational Biology,Computational Biology: methods,DNA,DNA Transposable Elements,DNA: methods,Essential,Genes,Genomics,Genomics: methods,High-Throughput Nucleotide Sequencing,High-Throughput Nucleotide Sequencing: methods,Insertional,Internet,Mutagenesis,nosource,Sequence Analysis,Software} }

@article{snyderFunctionalCharacterizationAlphavirus2013, title = {Functional {{Characterization}} of the {{Alphavirus TF Protein}}.}, author = {Snyder, Jonathan E. and {}a Kulcsar, Kirsten and Schultz, Kimberly L. W. and Riley, Catherine P. and Neary, Jacob T. and Marr, Scott and Jose, Joyce and Griffin, Diane E. and Kuhn, Richard J.}, year = 2013, month = may, journal = {Journal of virology}, number = {May}, eprint = {23720714}, eprinttype = {pubmed}, issn = {1098-5514}, doi = {10.1128/JVI.00449-13}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23720714}, abstract = {Alphavirus dogma has long dictated the production of a discrete set of structural proteins during infection of a cell: capsid, pE2, 6K, and E1. However, bioinformatic analyses of alphavirus genomes (1) suggested that a ribosomal frameshifting event occurs during translation of the alphavirus structural polyprotein. Specifically, a frameshift event is suggested to occur during translation of the 6K gene, yielding production of a novel protein, termed transframe (TF), comprised of a C-terminal extension of the 6K protein in the -1 open reading frame (ORF). Here, we validate the findings of Firth and colleagues with respect to the production of the TF protein, and begin to characterize the function of TF. Using a mass spectrometry-based approach, we identified TF in purified preparations of both Sindbis and Chikungunya virus particles. We next constructed a panel of Sindbis virus mutants, which alter the production, size, or sequence of TF. We demonstrate that TF is not absolutely required in culture, although disrupting TF production leads to a decrease in virus particle release in both mammalian and insect cells. In a mouse neuropathogenesis model, mortality was {\(<\)} 15% in animals infected with the TF mutants compared to 95% mortality with the wild type virus. Using a variety of additional assays, we demonstrate that TF retains ion-channel activity analogous to 6K, and that lack of production of TF does not affect genome replication, particle infectivity, or envelope protein transit to the cell surface. The TF protein therefore represents a previously uncharacterized factor important for alphavirus assembly.}, pmid = {23720714}, keywords = {nosource} } % == BibTeX quality report for snyderFunctionalCharacterizationAlphavirus2013: % ? Title looks like it was stored in title-case in Zotero

@article{kayeLeishmaniasisComplexityHostpathogen2011, title = {Leishmaniasis: Complexity at the Host-Pathogen Interface.}, author = {Kaye, Paul and Scott, Phillip}, year = 2011, month = aug, journal = {Nature reviews. Microbiology}, volume = {9}, number = {8}, eprint = {21747391}, eprinttype = {pubmed}, pages = {604–15}, publisher = {Nature Publishing Group}, issn = {1740-1534}, doi = {10.1038/nrmicro2608}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21747391}, abstract = {Leishmania is a genus of protozoan parasites that are transmitted by the bite of phlebotomine sandflies and give rise to a range of diseases (collectively known as leishmaniases) that affect over 150 million people worldwide. Cellular immune mechanisms have a major role in the control of infections with all Leishmania spp. However, as discussed in this Review, recent evidence suggests that each host-pathogen combination evokes different solutions to the problems of parasite establishment, survival and persistence. Understanding the extent of this diversity will be increasingly important in ensuring the development of broadly applicable vaccines, drugs and immunotherapeutic interventions.}, pmid = {21747391}, keywords = {Animals,Biological,Cellular,Host-Pathogen Interactions,Humans,Immunity,Leishmania,Leishmania: immunology,Leishmania: pathogenicity,Leishmaniasis,Leishmaniasis: immunology,Leishmaniasis: parasitology,Leishmaniasis: pathology,Models,nosource,Phagosomes,Phagosomes: immunology,Phagosomes: parasitology,Psychodidae,Psychodidae: parasitology} } % == BibTeX quality report for kayeLeishmaniasisComplexityHostpathogen2011: % ? Possibly abbreviated journal title Nature reviews. Microbiology

@article{forestierImagingHostCellLeishmania2011, title = {Imaging Host Cell-{{Leishmania}} Interaction Dynamics Implicates Parasite Motility, Lysosome Recruitment, and Host Cell Wounding in the Infection Process.}, author = {Forestier, Claire-Lise and Machu, Christophe and Loussert, Celine and Pescher, Pascale and Sp{"a}th, Gerald F.}, year = 2011, month = apr, journal = {Cell host & microbe}, volume = {9}, number = {4}, eprint = {21501831}, eprinttype = {pubmed}, pages = {319–30}, issn = {1934-6069}, doi = {10.1016/j.chom.2011.03.011}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21501831}, abstract = {Leishmania donovani causes human visceral leishmaniasis. The parasite infectious cycle comprises extracellular flagellated promastigotes that proliferate inside the insect vector, and intracellular nonmotile amastigotes that multiply within infected host cells. Using primary macrophages infected with virulent metacyclic promastigotes and high spatiotemporal resolution microscopy, we dissect the dynamics of the early infection process. We find that motile promastigotes enter macrophages in a polarized manner through their flagellar tip and are engulfed into host lysosomal compartments. Persistent intracellular flagellar activity leads to reorientation of the parasite flagellum toward the host cell periphery and results in oscillatory parasite movement. The latter is associated with local lysosomal exocytosis and host cell plasma membrane wounding. These findings implicate lysosome recruitment followed by lysosome exocytosis, consistent with parasite-driven host cell injury, as key cellular events in Leishmania host cell infection. This work highlights the role of promastigote polarity and motility during parasite entry.}, pmid = {21501831}, keywords = {Animals,Cell Membrane,Cell Membrane: pathology,Cell Movement,Cells,Confocal,Cultured,Electron,Eukaryotic Cells,Eukaryotic Cells: parasitology,Exocytosis,Exocytosis: physiology,Flagella,Host-Parasite Interactions,Humans,Leishmania donovani,Leishmania donovani: physiology,Lysosomes,Lysosomes: metabolism,Macrophages,Macrophages: immunology,Macrophages: parasitology,Mice,Microscopy,nosource,Phagocytosis,Phagocytosis: immunology,Phagocytosis: physiology,Phase-Contrast,Transmission} }

@article{melloRevealingWorldRNA2004, title = {Revealing the World of {{RNA}} Interference.}, author = {Mello, Craig C. and Conte, Darryl}, year = 2004, month = sep, journal = {Nature}, volume = {431}, number = {7006}, eprint = {15372040}, eprinttype = {pubmed}, pages = {338–42}, issn = {1476-4687}, doi = {10.1038/nature02872}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15372040}, abstract = {The recent discoveries of RNA interference and related RNA silencing pathways have revolutionized our understanding of gene regulation. RNA interference has been used as a research tool to control the expression of specific genes in numerous experimental organisms and has potential as a therapeutic strategy to reduce the expression of problem genes. At the heart of RNA interference lies a remarkable RNA processing mechanism that is now known to underlie many distinct biological phenomena.}, pmid = {15372040}, keywords = {Animals,Caenorhabditis elegans,Caenorhabditis elegans: genetics,Double-Stranded,Double-Stranded: genetics,Double-Stranded: metabolism,nosource,RNA,RNA Interference,RNA Interference: physiology,Transgenes,Transgenes: genetics} }

@article{maslovDiversityPhylogenyInsect2013, title = {Diversity and Phylogeny of Insect Trypanosomatids: All That Is Hidden Shall Be Revealed.}, author = {{}a Maslov, Dmitri and Vot{'y}pka, Jan and Yurchenko, Vyacheslav and Luke{}, Julius}, year = 2013, month = jan, journal = {Trends in parasitology}, volume = {29}, number = {1}, eprint = {23246083}, eprinttype = {pubmed}, pages = {43–52}, issn = {1471-5007}, doi = {10.1016/j.pt.2012.11.001}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23246083}, abstract = {Monoxenous trypanosomatids, which are usually regarded as benign dwellers of the insect alimentary tract, represent a relatively obscure group within the family Trypanosomatidae. This field of study has long been in disarray with the genus level taxonomy of this group remaining artificial, species criteria elusive, host specificity and occurrence poorly known, and their diversity mostly unexplored. The time has arrived to remedy this situation: a phylogenetic approach has been applied to taxa recognition and description, and a culture-independent (PCR-based) approach for detection and identification of organisms in nature has made it feasible to study the diversity of the group. Although more than 100 typing units have been discovered recently, these appear to represent a small segment of trypanosomatid biodiversity, which still remains to be uncovered.}, pmid = {23246083}, keywords = {Animals,Biodiversity,nosource,Phylogeny,Species Specificity,Trypanosomatina,Trypanosomatina: classification,Trypanosomatina: cytology,Trypanosomatina: genetics,Trypanosomatina: ultrastructure} }

@article{kolevTranscriptomeHumanPathogen2010, title = {The Transcriptome of the Human Pathogen {{Trypanosoma}} Brucei at Single-Nucleotide Resolution.}, author = {Kolev, Nikolay G. and Franklin, Joseph B. and Carmi, Shai and Shi, Huafang and Michaeli, Shulamit and Tschudi, Christian}, year = 2010, month = jan, journal = {PLoS pathogens}, volume = {6}, number = {9}, pages = {e1001090}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1001090}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2936537&tool=pmcentrez&rendertype=abstract}, abstract = {The genome of Trypanosoma brucei, the causative agent of African trypanosomiasis, was published five years ago, yet identification of all genes and their transcripts remains to be accomplished. Annotation is challenged by the organization of genes transcribed by RNA polymerase II (Pol II) into long unidirectional gene clusters with no knowledge of how transcription is initiated. Here we report a single-nucleotide resolution genomic map of the T. brucei transcriptome, adding 1,114 new transcripts, including 103 non-coding RNAs, confirming and correcting many of the annotated features and revealing an extensive heterogeneity of 5’ and 3’ ends. Some of the new transcripts encode polypeptides that are either conserved in T. cruzi and Leishmania major or were previously detected in mass spectrometry analyses. High-throughput RNA sequencing (RNA-Seq) was sensitive enough to detect transcripts at putative Pol II transcription initiation sites. Our results, as well as recent data from the literature, indicate that transcription initiation is not solely restricted to regions at the beginning of gene clusters, but may occur at internal sites. We also provide evidence that transcription at all putative initiation sites in T. brucei is bidirectional, a recently recognized fundamental property of eukaryotic promoters. Our results have implications for gene expression patterns in other important human pathogens with similar genome organization (Trypanosoma cruzi, Leishmania sp.) and revealed heterogeneity in pre-mRNA processing that could potentially contribute to the survival and success of the parasite population in the insect vector and the mammalian host.}, pmid = {20838601}, keywords = {African,African: genetics,African: microbiology,Bacterial,Bacterial: genetics,Base Sequence,beet,Catalytic,Catalytic: chemistry,Gene Expression Profiling,Genetic,Genome,hepatitis delta virus,Hepatitis Delta Virus,Hepatitis Delta Virus: genetics,High-Throughput Nucleotide Sequencing,Humans,ing,Molecular Sequence Data,mouse mammary tumor virus,nmr,nosource,Nucleic Acid,Nucleic Acid Conformation,pseudoknot,ribozyme,rna,RNA,RNA Polymerase II,RNA Polymerase II: genetics,RNA Precursors,RNA Precursors: genetics,RNA: chemistry,Sequence Homology,simian retrovirus type-1,Structure-Activity Relationship,Transcription,Transcription Initiation Site,translational frameshift-,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: pathogenicity,Trypanosomiasis,turnip yellow mosaic virus,western yellows virus,x-ray diffraction} }

@article{vazquezFunctionalCharacterizationProtein2009, title = {Functional Characterization and Protein–Protein Interactions of Trypanosome Splicing Factors {{U2AF35}}, {{U2AF65}} and {{SF1}}}, author = {Vazquez, Martin P. and Mualem, David and Bercovich, Natalia and Stern, Michael Zeev and Nyambega, Benson and Barda, Omer and Masiga, Dan and Gupta, Sachin Kumar and Michaeli, Shulamit and Levin, Mariano J.}, year = 2009, month = apr, journal = {Molecular and Biochemical Parasitology}, volume = {164}, number = {2}, pages = {137–146}, issn = {01666851}, doi = {10.1016/j.molbiopara.2008.12.009}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0166685109000024}, keywords = {nosource} }

@article{liangTransCisSplicing2003, title = {Trans and Cis Splicing in Trypanosomatids: {{Mechanism}}, Factors, and Regulation}, author = {Liang, Xue-hai and Haritan, Asaf and Uliel, Shai and Michaeli, S.}, year = 2003, journal = {Eukaryotic cell}, volume = {2}, number = {5}, doi = {10.1128/EC.2.5.830}, url = {http://ec.asm.org/content/2/5/830.short}, keywords = {nosource} }

@article{ambrosioSpliceosomalProteomicsTrypanosoma2009, title = {Spliceosomal Proteomics in {{Trypanosoma}} Brucei Reveal New {{RNA}} Splicing Factors.}, author = {Ambr{'o}sio, Daniela Luz and Lee, Ju Huck and Panigrahi, Aswini K. and Nguyen, Tu Ngoc and Cicarelli, Regina Maria Barretto and G{"u}nzl, Arthur}, year = 2009, month = jul, journal = {Eukaryotic cell}, volume = {8}, number = {7}, pages = {990–1000}, issn = {1535-9786}, doi = {10.1128/EC.00075-09}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2708463&tool=pmcentrez&rendertype=abstract}, abstract = {In trypanosomatid parasites, spliced leader (SL) trans splicing is an essential nuclear mRNA maturation step which caps mRNAs posttranscriptionally and, in conjunction with polyadenylation, resolves individual mRNAs from polycistronic precursors. While all trypanosomatid mRNAs are trans spliced, intron removal by cis splicing is extremely rare and predicted to occur in only four pre-mRNAs. trans- and cis-splicing reactions are carried out by the spliceosome, which consists of U-rich small nuclear ribonucleoprotein particles (U snRNPs) and of non-snRNP factors. Mammalian and yeast spliceosome complexes are well characterized and found to be associated with up to 170 proteins. Despite the central importance of trans splicing in trypanosomatid gene expression, only the core RNP proteins and a few snRNP-specific proteins are known. To characterize the trypanosome spliceosomal protein repertoire, we conducted a proteomic analysis by tagging and tandem affinity-purifying the canonical core RNP protein SmD1 in Trypanosoma brucei and by identifying copurified proteins by mass spectrometry. The set of 47 identified proteins harbored nearly all spliceosomal snRNP factors characterized in trypanosomes thus far and 21 proteins lacking a specific annotation. A bioinformatic analysis combined with protein pull-down assays and immunofluorescence microscopy identified 10 divergent orthologues of known splicing factors, including the missing U1-specific protein U1A. In addition, a novel U5-specific, and, as we show, an essential splicing factor was identified that shares a short, highly conserved N-terminal domain with the yeast protein Cwc21p and was thus tentatively named U5-Cwc21. Together, these data strongly indicate that most of the identified proteins are components of the spliceosome.}, pmid = {19429779}, keywords = {Animals,Computational Biology,Computational Biology: methods,Conserved Sequence,Conserved Sequence: physiology,Evolution,Mass Spectrometry,Messenger,Messenger: biosynthesis,Messenger: genetics,Molecular,nosource,Protein Structure,Proteome,Proteome: analysis,Proteome: genetics,Proteome: metabolism,Proteomics,Protozoan Proteins,Protozoan Proteins: analysis,Protozoan Proteins: metabolism,Ribonucleoprotein,Ribonucleoproteins,Ribonucleoproteins: analysis,Ribonucleoproteins: genetics,Ribonucleoproteins: metabolism,RNA,RNA Splicing,RNA Splicing: physiology,RNA-Binding Proteins,RNA-Binding Proteins: analysis,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism,snRNP Core Proteins,snRNP Core Proteins: genetics,snRNP Core Proteins: metabolism,Species Specificity,Spliceosomes,Spliceosomes: genetics,Spliceosomes: metabolism,Tertiary,Tertiary: physiology,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: metabolism,U1 Small Nuclear,U1 Small Nuclear: genetics,U1 Small Nuclear: metabolism} }

@article{tkaczAnalysisSpliceosomalProteins2010, title = {Analysis of Spliceosomal Proteins in {{Trypanosomatids}} Reveals Novel Functions in {{mRNA}} Processing.}, author = {Tkacz, Itai Dov and Gupta, Sachin Kumar and Volkov, Vadim and Romano, Mali and Haham, Tomer and Tulinski, Pawel and Lebenthal, Ilana and Michaeli, Shulamit}, year = 2010, month = sep, journal = {The Journal of biological chemistry}, volume = {285}, number = {36}, pages = {27982–99}, issn = {1083-351X}, doi = {10.1074/jbc.M109.095349}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2934664&tool=pmcentrez&rendertype=abstract}, abstract = {In trypanosomatids, all mRNAs are processed via trans-splicing, although cis-splicing also occurs. In trans-splicing, a common small exon, the spliced leader (SL), which is derived from a small SL RNA species, is added to all mRNAs. Sm and Lsm proteins are core proteins that bind to U snRNAs and are essential for both these splicing processes. In this study, SmD3- and Lsm3-associated complexes were purified to homogeneity from Leishmania tarentolae. The purified complexes were analyzed by mass spectrometry, and 54 and 39 proteins were purified from SmD3 and Lsm complexes, respectively. Interestingly, among the proteins purified from Lsm3, no mRNA degradation factors were detected, as in Lsm complexes from other eukaryotes. The U1A complex was purified and mass spectrometry analysis identified, in addition to U1 small nuclear ribonucleoprotein (snRNP) proteins, additional co-purified proteins, including the polyadenylation factor CPSF73. Defects observed in cells silenced for U1 snRNP proteins suggest that the U1 snRNP functions exclusively in cis-splicing, although U1A also participates in polyadenylation and affects trans-splicing. The study characterized several trypanosome-specific nuclear factors involved in snRNP biogenesis, whose function was elucidated in Trypanosoma brucei. Conserved factors, such as PRP19, which functions at the heart of every cis-spliceosome, also affect SL RNA modification; GEMIN2, a protein associated with SMN (survival of motor neurons) and implicated in selective association of U snRNA with core Sm proteins in trypanosomes, is a master regulator of snRNP assembly. This study demonstrates the existence of trypanosomatid-specific splicing factors but also that conserved snRNP proteins possess trypanosome-specific functions.}, pmid = {20592024}, keywords = {Biological Transport,Cell Line,Leishmania,Leishmania: cytology,Leishmania: genetics,Mass Spectrometry,Messenger,Messenger: genetics,Messenger: metabolism,nosource,Polyadenylation,Protozoan Proteins,Protozoan Proteins: isolation & purification,Protozoan Proteins: metabolism,Ribonucleoproteins,RNA,RNA Splicing,Small Nuclear,Small Nuclear: metabolism,Species Specificity,Spliced Leader,Spliced Leader: biosynthesis,Spliceosomes,Spliceosomes: metabolism} }

@article{kielkopfU2AFHomologyMotifs2004, title = {{{U2AF}} Homology Motifs: Protein Recognition in the {{RRM}} World.}, author = {Kielkopf, Clara L. and L{"u}cke, Stephan and Green, Michael R.}, year = 2004, month = jul, journal = {Genes & development}, volume = {18}, number = {13}, pages = {1513–26}, issn = {0890-9369}, doi = {10.1101/gad.1206204}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2043112&tool=pmcentrez&rendertype=abstract}, abstract = {Recent structures of the heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) have revealed two unexpected examples of RNA recognition motif (RRM)-like domains with specialized features for protein recognition. These unusual RRMs, called U2AF homology motifs (UHMs), represent a novel class of protein recognition motifs. Defining a set of rules to distinguish traditional RRMs from UHMs is key to identifying novel UHM family members. Here we review the critical sequence features necessary to mediate protein-UHM interactions, and perform comprehensive database searches to identify new members of the UHM family. The resulting implications for the functional and evolutionary relationships among candidate UHM family members are discussed.}, pmid = {15231733}, keywords = {Amino Acid,Amino Acid Sequence,Binding Sites,Molecular Sequence Data,nosource,Nuclear Proteins,Nuclear Proteins: chemistry,Nuclear Proteins: metabolism,Ribonucleoproteins,Ribonucleoproteins: chemistry,Ribonucleoproteins: metabolism,RNA,RNA: metabolism,Sequence Homology} }

@article{willSpliceosomeStructureFunction2011, title = {Spliceosome Structure and Function.}, author = {Will, Cindy L. and L{"u}hrmann, Reinhard}, year = 2011, month = jul, journal = {Cold Spring Harbor perspectives in biology}, volume = {3}, number = {7}, eprint = {21441581}, eprinttype = {pubmed}, issn = {1943-0264}, doi = {10.1101/cshperspect.a003707}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21441581}, abstract = {Pre-mRNA splicing is catalyzed by the spliceosome, a multimegadalton ribonucleoprotein (RNP) complex comprised of five snRNPs and numerous proteins. Intricate RNA-RNA and RNP networks, which serve to align the reactive groups of the pre-mRNA for catalysis, are formed and repeatedly rearranged during spliceosome assembly and catalysis. Both the conformation and composition of the spliceosome are highly dynamic, affording the splicing machinery its accuracy and flexibility, and these remarkable dynamics are largely conserved between yeast and metazoans. Because of its dynamic and complex nature, obtaining structural information about the spliceosome represents a major challenge. Electron microscopy has revealed the general morphology of several spliceosomal complexes and their snRNP subunits, and also the spatial arrangement of some of their components. X-ray and NMR studies have provided high resolution structure information about spliceosomal proteins alone or complexed with one or more binding partners. The extensive interplay of RNA and proteins in aligning the pre-mRNA’s reactive groups, and the presence of both RNA and protein at the core of the splicing machinery, suggest that the spliceosome is an RNP enzyme. However, elucidation of the precise nature of the spliceosome’s active site, awaits the generation of a high-resolution structure of its RNP core.}, pmid = {21441581}, keywords = {Biomolecular,Catalytic Domain,Crystallography,Genetic,Humans,Models,Molecular,nosource,Nuclear Magnetic Resonance,Nucleic Acid Conformation,Post-Translational,Protein Processing,Protein Structure,Ribonucleoproteins,Ribonucleoproteins: chemistry,Ribonucleoproteins: physiology,RNA Precursors,RNA Precursors: metabolism,RNA Splicing,RNA Splicing: physiology,Small Nuclear,Small Nuclear: chemistry,Small Nuclear: physiology,Spliceosomes,Spliceosomes: chemistry,Spliceosomes: physiology,Spliceosomes: ultrastructure,Tertiary,X-Ray} }

@article{kruseRNAHelicasesInvolved2013, title = {{{RNA}} Helicases Involved in {{U-insertion}}/Deletion-Type {{RNA}} Editing.}, author = {Kruse, Elisabeth and Voigt, Christin and Leeder, W.-Matthias and G{"o}ringer, H. Ulrich}, year = 2013, month = apr, journal = {Biochimica et biophysica acta}, eprint = {23587716}, eprinttype = {pubmed}, issn = {0006-3002}, doi = {10.1016/j.bbagrm.2013.04.003}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23587716}, abstract = {Mitochondrial pre-messenger RNAs in kinetoplastid protozoa such as the disease-causing African trypanosomes are substrates of a unique RNA editing reaction. The process is characterized by the site-specific insertion and deletion of exclusively U nucleotides and converts nonfunctional pre-mRNAs into translatable transcripts. Similar to other RNA-based metabolic pathways, RNA editing is catalyzed by a macromolecular protein complex, the editosome. Editosomes provide a reactive surface for the individual steps of the catalytic cycle and involve as key players a specific class of small, non-coding RNAs termed guide (g)RNAs. gRNAs basepair proximal to an editing site and act as quasi templates in the U-insertion/deletion reaction. Next to the editosome several accessory proteins and complexes have been identified, which contribute to different steps of the reaction. This includes matchmaking-type RNA/RNA annealing factors as well as RNA helicases of the archetypical DEAD- and DExH/D-box families. Here we summarize the current structural, genetic and biochemical knowledge of the two characterized “editing RNA helicases” and provide an outlook onto dynamic processes within the editing reaction cycle. This article is part of a Special Issue entitled: The Biology of RNA helicases - Modulation for Life.}, pmid = {23587716}, keywords = {nosource} }

@article{buarqueDifferentialExpressionProfiles2013, title = {Differential {{Expression Profiles}} in the {{Midgut}} of {{Triatoma}} Infestans {{Infected}} with {{Trypanosoma}} Cruzi.}, author = {Buarque, Diego S. and Braz, Gl{'o}ria R. C. and Martins, Rafael M. and {Tanaka-Azevedo}, Anita M. and Gomes, C{'i}cera M. and {}a a Oliveira, Felipe and Schenkman, Sergio and Tanaka, Aparecida S.}, year = 2013, month = jan, journal = {PloS one}, volume = {8}, number = {5}, pages = {e61203}, issn = {1932-6203}, doi = {10.1371/journal.pone.0061203}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3642171&tool=pmcentrez&rendertype=abstract}, abstract = {Chagas disease, or American trypanosomiasis, is a parasitic disease caused by the protozoan Trypanosoma cruzi and is transmitted by insects from the Triatominae subfamily. To identify components involved in the protozoan-vector relationship, we constructed and analyzed cDNA libraries from RNA isolated from the midguts of uninfected and T. cruzi-infected Triatoma infestans, which are major vectors of Chagas disease. We generated approximately 440 high-quality Expressed Sequence Tags (ESTs) from each T. infestans midgut cDNA library. The sequences were grouped in 380 clusters, representing an average length of 664.78 base pairs (bp). Many clusters were not classified functionally, representing unknown transcripts. Several transcripts involved in different processes (e.g., detoxification) showed differential expression in response to T. cruzi infection. Lysozyme, cathepsin D, a nitrophorin-like protein and a putative 14 kDa protein were significantly upregulated upon infection, whereas thioredoxin reductase was downregulated. In addition, we identified several transcripts related to metabolic processes or immunity with unchanged expressions, including infestin, lipocalins and defensins. We also detected ESTs encoding juvenile hormone binding protein (JHBP), which seems to be involved in insect development and could be a target in control strategies for the vector. This work demonstrates differential gene expression upon T. cruzi infection in the midgut of T. infestans. These data expand the current knowledge regarding vector-parasite interactions for Chagas disease.}, pmid = {23658688}, keywords = {nosource} }

@article{shlensTutorialPrincipalComponent2005, title = {A Tutorial on Principal Component Analysis}, author = {Shlens, Jonathon}, year = 2005, journal = { Neurobiology Laboratory, University of California at }, url = {http://www.brainmapping.org/NITP/PNA/Readings/pca.pdf}, keywords = {nosource} }

@article{zouSparsePrincipalComponent2006, title = {Sparse {{Principal Component Analysis}}}, author = {Zou, Hui and Hastie, Trevor and Tibshirani, Robert}, year = 2006, month = jun, journal = {Journal of Computational and Graphical Statistics}, volume = {15}, number = {2}, pages = {265–286}, issn = {1061-8600}, doi = {10.1198/106186006X113430}, url = {http://www.tandfonline.com/doi/abs/10.1198/106186006X113430}, isbn = {106186006X}, keywords = {nosource} } % == BibTeX quality report for zouSparsePrincipalComponent2006: % ? Title looks like it was stored in title-case in Zotero

@article{mcgwireInteractionsAntimicrobialPeptides2010, title = {Interactions of Antimicrobial Peptides with {{Leishmania}} and Trypanosomes and Their Functional Role in Host Parasitism.}, author = {McGwire, Bradford S. and Kulkarni, Manjusha M.}, year = 2010, month = nov, journal = {Experimental parasitology}, volume = {126}, number = {3}, eprint = {20159013}, eprinttype = {pubmed}, pages = {397–405}, publisher = {Elsevier Inc.}, issn = {1090-2449}, doi = {10.1016/j.exppara.2010.02.006}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20159013}, abstract = {Antimicrobial peptides (AMPs) are multifunctional components of the innate systems of both insect and mammalian hosts of the pathogenic trypanosomatids Leishmania and Trypanosoma species. Structurally diverse AMPs from a wide range of organisms have in vitro activity against these parasites acting mainly to disrupt surface-membranes. In some cases AMPs also localize intracellularly to affect calcium levels, mitochondrial function and induce autophagy, necrosis and apoptosis. In this review we discuss the work done in the area of AMP interactions with trypanosomatid protozoa, propose potential targets of AMP activity at the cellular level and discuss how AMPs might influence parasite growth and differentiation in their hosts to determine the outcome of natural infection.}, pmid = {20159013}, keywords = {Animals,Antimicrobial Cationic Peptides,Antimicrobial Cationic Peptides: immunology,Antimicrobial Cationic Peptides: pharmacology,Antimicrobial Cationic Peptides: physiology,Euglenozoa Infections,Euglenozoa Infections: immunology,Euglenozoa Infections: parasitology,Host-Parasite Interactions,Host-Parasite Interactions: drug effects,Host-Parasite Interactions: immunology,Humans,Immunity,Innate,Insects,Insects: immunology,Insects: parasitology,Leishmania,Leishmania: drug effects,Leishmania: growth & development,Leishmania: immunology,Life Cycle Stages,Life Cycle Stages: drug effects,Life Cycle Stages: physiology,nosource,Trypanosoma brucei brucei,Trypanosoma brucei brucei: drug effects,Trypanosoma brucei brucei: growth & development,Trypanosoma brucei brucei: immunology,Trypanosoma cruzi,Trypanosoma cruzi: drug effects,Trypanosoma cruzi: growth & development,Trypanosoma cruzi: immunology,Trypanosomatina,Trypanosomatina: drug effects,Trypanosomatina: growth & development,Trypanosomatina: immunology} }

@article{couvillionSequenceBiogenesisFunction2009, title = {Sequence, Biogenesis, and Function of Diverse Small {{RNA}} Classes Bound to the {{Piwi}} Family Proteins of {{Tetrahymena}} Thermophila}, author = {Couvillion, MT Mary T. and Lee, Suzanne R. SR and Hogstad, Brandon and Malone, Colin D. and Tonkin, Leath A. and Hannon, Gregory J. and Collins, Kathleen and Sachidanandam, Ravi}, year = 2009, month = sep, journal = {Genes & }, volume = {3}, number = {17}, pages = {2016–32}, issn = {1549-5477}, doi = {10.1101/gad.1821209}, url = {http://genesdev.cshlp.org/content/23/17/2016.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2751968&tool=pmcentrez&rendertype=abstract}, abstract = {PAZ/PIWI domain (PPD) proteins carrying small RNAs (sRNAs) function in gene and genome regulation. The ciliate Tetrahymena thermophila encodes numerous PPD proteins exclusively of the Piwi clade. We show that the three Tetrahymena Piwi family proteins (Twis) preferentially expressed in growing cells differ in their genetic essentiality and subcellular localization. Affinity purification of all eight distinct Twi proteins revealed unique properties of their bound sRNAs. Deep sequencing of Twi-bound and total sRNAs in strains disrupted for various silencing machinery uncovered an unanticipated diversity of 23- to 24-nt sRNA classes in growing cells, each with distinct genetic requirements for accumulation. Altogether, Twis distinguish sRNAs derived from loci of pseudogene families, three types of DNA repeats, structured RNAs, and EST-supported loci with convergent or paralogous transcripts. Most surprisingly, Twi7 binds complementary strands of unequal length, while Twi10 binds a specific permutation of the guanosine-rich telomeric repeat. These studies greatly expand the structural and functional repertoire of endogenous sRNAs and RNPs.}, pmid = {19656801}, keywords = {Animals,Developmental,Expressed Sequence Tags,Gene Expression Regulation,MicroRNAs,MicroRNAs: chemistry,MicroRNAs: genetics,MicroRNAs: metabolism,Microsatellite Repeats,Microsatellite Repeats: genetics,Molecular Sequence Data,nosource,Protein Binding,Protozoan,Protozoan Proteins,Protozoan Proteins: metabolism,Protozoan: chemistry,Protozoan: genetics,Protozoan: metabolism,RNA,Sequence Analysis,Tetrahymena thermophila,Tetrahymena thermophila: genetics,Tetrahymena thermophila: metabolism,Twist Transcription Factor,Twist Transcription Factor: metabolism} }

@article{hassaniImmunomodulatoryImpactLeishmaniainduced2013, title = {Immunomodulatory Impact of Leishmania-Induced Macrophage Exosomes: A Comparative Proteomic and Functional Analysis.}, author = {Hassani, Kasra and Olivier, Martin}, year = 2013, month = may, journal = {PLoS neglected tropical diseases}, volume = {7}, number = {5}, pages = {e2185}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0002185}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3642089&tool=pmcentrez&rendertype=abstract}, abstract = {Released by many eukaryotic cells, the exosomes are 40-100 nm vesicles shown to operate over the complex processes of cell-cell communication. Among the metazoan cell lineages known to generate exosomes is the mononuclear phagocyte lineage, a lineage that parasites such as Leishmania are known to subvert as host cells. We previously reported that mouse macrophage signaling and functions are modified once co-incubated with exoproteome of Leishmania promastigotes. Using mass spectrometry analysis, we were curious to further compare the content of purified exosomes released by the J774 mouse macrophage cell line exposed or not to either LPS or to stationary phase Leishmania mexicana promastigotes. Collectively, our analyses resulted in detection of 248 proteins, {\(\sim\)}50-80% of which were shared among the three sources studied. Using exponentially modified protein abundance index (emPAI) and network analyses, we found that the macrophage exosomes display unique signatures with respect to composition and abundance of many functional groups of proteins, such as plasma membrane-associated proteins, chaperones and metabolic enzymes. Moreover, for the first time, L. mexicana surface protease GP63 is shown to be present in exosomes released from J774 macrophages exposed to stationary phase promastigotes. We observed that macrophage exosomes are able to induce signaling molecules and transcription factors in naive macrophages. Finally, using qRT-PCR, we monitored modulation of expression of multiple immune-related genes within macrophages exposed to exosomes. We found all three groups of exosomes to induce expression of immune-related genes, the ones collected from macrophages exposed to L. mexicana sharing properties with exosomes collected from macrophage left unexposed to any agonist. Overall, our results allowed depicting that protein sorting into macrophage-derived exosomes depends upon the cell status and how such distinct protein sorting can in turn impact the functions of naive J774 cells.}, pmid = {23658846}, keywords = {nosource} }

@article{buscagliaTrypanosomaCruziClonal2003, title = {Trypanosoma Cruzi Clonal Diversity and the Epidemiology of {{Chagas}}’ Disease.}, author = {{}a Buscaglia, Carlos and Noia, Javier M. Di}, year = 2003, month = apr, journal = {Microbes and infection / Institut Pasteur}, volume = {5}, number = {5}, eprint = {12737998}, eprinttype = {pubmed}, pages = {419–27}, issn = {1286-4579}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12737998}, abstract = {Chagas’ disease is caused by the protozoan Trypanosoma cruzi and it has a variable clinical outcome. The basis for this variability relies in part on the complexity of the parasite population consisting of multiple clones displaying distinct biological properties. A major current challenge is to correlate parasite genetic variability with pathogenesis.}, pmid = {12737998}, keywords = {Animals,Chagas Disease,Chagas Disease: epidemiology,Chagas Disease: parasitology,Genetic Variation,Humans,nosource,Trypanosoma cruzi,Trypanosoma cruzi: classification,Trypanosoma cruzi: genetics,Trypanosoma cruzi: pathogenicity} }

@article{leyAmastigotesTrypanosomaCruzi1988, title = {Amastigotes of {{Trypanosoma}} Cruzi Sustain an Infective Cycle in Mammalian Cells.}, author = {Ley, V. and Andrews, N. W.}, year = 1988, journal = {The Journal of }, volume = {168}, number = {August}, url = {http://jem.rupress.org/content/168/2/649.abstract}, keywords = {nosource} }

@book{ruleFundamentalsProteinNMR2006, title = {Fundamentals of Protein {{NMR}} Spectrosopy}, author = {Rule, G. S. and Hitchens, T. K.}, year = 2006, volume = {5}, publisher = {Springer-Verlag}, doi = {10.1007/1-4020-3500-4}, url = {http://www.springerlink.com/index/10.1007/1-4020-3500-4 http://books.google.com/books?hl=en&lr=&id=pB-hsMnPy60C&oi=fnd&pg=PR25&dq=Fundamentals+of+Protein+NMR+Spectroscopy&ots=3QkbR-xqpu&sig=HVPgHNp1CfeYRgnuPV0OwZBGgmY}, isbn = {1-4020-3499-7}, keywords = {nosource} }

@article{choRegulationProgrammedRibosomal2013, title = {Regulation of Programmed Ribosomal Frameshifting by Co-Translational Refolding {{RNA}} Hairpins.}, author = {Cho, Che-Pei and Lin, Szu-Chieh and Chou, Ming-Yuan and Hsu, Hsiu-Ting and Chang, Kung-Yao}, year = 2013, month = jan, journal = {PloS ONE}, volume = {8}, number = {4}, pages = {e62283}, issn = {1932-6203}, doi = {10.1371/journal.pone.0062283}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3639245&tool=pmcentrez&rendertype=abstract}, abstract = {RNA structures are unwound for decoding. In the process, they can pause the elongating ribosome for regulation. An example is the stimulation of -1 programmed ribosomal frameshifting, leading to 3’ direction slippage of the reading-frame during elongation, by specific pseudoknot stimulators downstream of the frameshifting site. By investigating a recently identified regulatory element upstream of the SARS coronavirus (SARS-CoV) -1 frameshifting site, it is shown that a minimal functional element with hairpin forming potential is sufficient to down-regulate-1 frameshifting activity. Mutagenesis to disrupt or restore base pairs in the potential hairpin stem reveals that base-pair formation is required for-1 frameshifting attenuation in vitro and in 293T cells. The attenuation efficiency of a hairpin is determined by its stability and proximity to the frameshifting site; however, it is insensitive to E site sequence variation. Additionally, using a dual luciferase assay, it can be shown that a hairpin stimulated +1 frameshifting when placed upstream of a +1 shifty site in yeast. The investigations indicate that the hairpin is indeed a cis-acting programmed reading-frame switch modulator. This result provides insight into mechanisms governing-1 frameshifting stimulation and attenuation. Since the upstream hairpin is unwound (by a marching ribosome) before the downstream stimulator, this study’s findings suggest a new mode of translational regulation that is mediated by the reformed stem of a ribosomal unwound RNA hairpin during elongation.}, pmid = {23638024}, keywords = {nosource} }

@article{boomRapidSimpleMethod1990, title = {Rapid and Simple Method for Purification of Nucleic Acids.}, author = {Boom, R. and Sol, C. J. and Salimans, M. M. and Jansen, C. L. and Dillen, P. M. Wertheim-van and {}van der Noordaa, J.}, year = 1990, month = mar, journal = {Journal of clinical microbiology}, volume = {28}, number = {3}, pages = {495–503}, issn = {0095-1137}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=269651&tool=pmcentrez&rendertype=abstract}, abstract = {We have developed a simple, rapid, and reliable protocol for the small-scale purification of DNA and RNA from, e.g., human serum and urine. The method is based on the lysing and nuclease-inactivating properties of the chaotropic agent guanidinium thiocyanate together with the nucleic acid-binding properties of silica particles or diatoms in the presence of this agent. By using size-fractionated silica particles, nucleic acids (covalently closed circular, relaxed circular, and linear double-stranded DNA; single-stranded DNA; and rRNA) could be purified from 12 different specimens in less than 1 h and were recovered in the initial reaction vessel. Purified DNA (although significantly sheared) was a good substrate for restriction endonucleases and DNA ligase and was recovered with high yields (usually over 50%) from the picogram to the microgram level. Copurified rRNA was recovered almost undegraded. Substituting size-fractionated silica particles for diatoms (the fossilized cell walls of unicellular algae) allowed for the purification of microgram amounts of genomic DNA, plasmid DNA, and rRNA from cell-rich sources, as exemplified for pathogenic gram-negative bacteria. In this paper, we show representative experiments illustrating some characteristics of the procedure which may have wide application in clinical microbiology.}, pmid = {1691208}, keywords = {Agar Gel,Circular,Circular: blood,Circular: isolation & purification,DNA,DNA: blood,DNA: isolation & purification,DNA: urine,Electrophoresis,Eukaryota,Glass,Humans,Microspheres,nosource,Ribosomal,Ribosomal: isolation & purification,Ribosomal: urine,RNA,RNA: blood,RNA: isolation & purification,RNA: urine,Silicon Dioxide,Single-Stranded,Single-Stranded: blood,Single-Stranded: isolation & purification} }

@article{tumaCharacterizationSYBRGold1999, title = {Characterization of {{SYBR Gold}} Nucleic Acid Gel Stain: A Dye Optimized for Use with 300-Nm Ultraviolet Transilluminators.}, author = {Tuma, R. S. and Beaudet, M. P. and Jin, X. and Jones, L. J. and Cheung, C. Y. and Yue, S. and Singer, V. L.}, year = 1999, month = mar, journal = {Analytical biochemistry}, volume = {268}, number = {2}, eprint = {10075818}, eprinttype = {pubmed}, pages = {278–88}, issn = {0003-2697}, doi = {10.1006/abio.1998.3067}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10075818}, abstract = {The highest sensitivity nucleic acid gel stains developed to date are optimally excited using short-wavelength ultraviolet or visible light. This is a disadvantage for laboratories equipped only with 306- or 312-nm UV transilluminators. We have developed a new unsymmetrical cyanine dye that overcomes this problem. This new dye, SYBR Gold nucleic acid gel stain, has two fluorescence excitation maxima when bound to DNA, one centered at approximately 300 nm and one at approximately 495 nm. We found that when used with 300-nm transillumination and Polaroid black-and-white photography, SYBR Gold stain is more sensitive than ethidium bromide, SYBR Green I stain, and SYBR Green II stain for detecting double-stranded DNA, single-stranded DNA, and RNA. SYBR Gold stain’s superior sensitivity is due to the high fluorescence quantum yield of the dye-nucleic acid complexes ( approximately 0.7), the dye’s large fluorescence enhancement upon binding to nucleic acids ( approximately 1000-fold), and its capacity to more fully penetrate gels than do the SYBR Green gel stains. We found that SYBR Gold stain is as sensitive as silver staining for detecting DNA-with a single-step staining procedure. Finally, we found that staining nucleic acids with SYBR Gold stain does not interfere with subsequent molecular biology protocols.}, pmid = {10075818}, keywords = {Animals,Cattle,DNA,DNA: analysis,Ethidium,Evaluation Studies as Topic,Fluorescein,Fluorescent Dyes,Mice,nosource,Nucleic Acids,Nucleic Acids: analysis,Organic Chemicals,Photography,RNA,RNA: analysis,Sensitivity and Specificity,Staining and Labeling,Staining and Labeling: methods,Staining and Labeling: statistics & numerical data,Ultraviolet Rays,Viral,Viral: analysis} }

@article{siegelGeneExpressionTrypanosoma2011, title = {Gene Expression in {{Trypanosoma}} Brucei: Lessons from High-Throughput {{RNA}} Sequencing.}, author = {Siegel, T. Nicolai and Gunasekera, Kapila and Cross, George a M. and Ochsenreiter, Torsten}, year = 2011, month = oct, journal = {Trends in parasitology}, volume = {27}, number = {10}, pages = {434–41}, publisher = {Elsevier Ltd}, issn = {1471-5007}, doi = {10.1016/j.pt.2011.05.006}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3178736&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanosoma brucei undergoes major biochemical and morphological changes during its development from the bloodstream form in the mammalian host to the procyclic form in the midgut of its insect host. The underlying regulation of gene expression, however, is poorly understood. More than 60% of the predicted genes remain annotated as hypothetical, and the 5’ and 3’ untranslated regions important for regulation of gene expression are unknown for {\(>\)}90% of the genes. In this review, we compare the data from four recently published high-throughput RNA sequencing studies in light of the different experimental setups and discuss how these data can enhance genome annotation and give insights into the regulation of gene expression in T. brucei.}, pmid = {21737348}, keywords = {Animals,Gene Expression Profiling,Gene Expression Profiling: methods,Gene Expression Regulation,Genetic,High-Throughput Nucleotide Sequencing,Humans,nosource,Polyadenylation,RNA,RNA Splice Sites,RNA Splicing,RNA Stability,RNA: methods,Sequence Analysis,Transcription,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Tsetse Flies,Tsetse Flies: parasitology,Untranslated Regions} }

@article{shinCardiacSystemsBiology2008, title = {Cardiac Systems Biology and Parameter Sensitivity Analysis: Intracellular {{Ca2}}+ Regulatory Mechanisms in Mouse Ventricular Myocytes}, author = {Shin, S. Y. and Choo, S. M. and Woo, S. H. and Cho, K. H.}, year = 2008, journal = {Protein–Protein Interaction}, url = {http://link.springer.com/chapter/10.1007/10_2007_093}, keywords = {nosource} }

@book{designProteomicsProteinProteinInteractions2005, title = {Proteomics and {{Protein-Protein Interactions}}}, author = {Design, Drug}, editor = {Waksman, Gabriel}, year = 2005, volume = {3}, publisher = {Springer US}, doi = {10.1007/b105866}, url = {http://www.springerlink.com/index/10.1007/b105866}, isbn = {978-0-387-24531-7}, keywords = {nosource} } % == BibTeX quality report for designProteomicsProteinProteinInteractions2005: % ? Title looks like it was stored in title-case in Zotero

@article{kumarPharmacologicalPotentialP382005, title = {Pharmacological Potential of P38 {{MAPK}} Inhibitors}, author = {Kumar, S. and Blake, S. M.}, year = 2005, journal = {Inhibitors of protein kinases and protein phosphates}, pages = {65–83}, url = {http://link.springer.com/chapter/10.1007/3-540-26670-4_4}, keywords = {nosource} }

@article{gasselInhibitorsPKARelated2005, title = {Inhibitors of {{PKA}} and Related Protein Kinases}, author = {Gassel, M. and Breitenlechner, C. and Herrero, S.}, year = 2005, journal = {Inhibitors of Protein }, volume = {3}, url = {http://link.springer.com/chapter/10.1007/3-540-26670-4_5}, keywords = {nosource} }

@article{battistuttaInhibitorsProteinKinase2005, title = {Inhibitors of Protein Kinase {{CK2}}: Structural Aspects}, author = {Battistutta, R. and Sarno, S. and Zanotti, G.}, year = 2005, journal = {Inhibitors of Protein Kinases and Protein }, volume = {1}, pages = {125–155}, url = {http://link.springer.com/chapter/10.1007/3-540-26670-4_6}, keywords = {nosource} }

@article{fongAminoglycosideKinasesAntibiotic2005, title = {Aminoglycoside Kinases and Antibiotic Resistance}, author = {Fong, D. H. and Burk, D. L. and Berghuis, A. M.}, year = 2005, journal = {Inhibitors of Protein Kinases and Protein }, volume = {2}, url = {http://link.springer.com/chapter/10.1007/3-540-26670-4_7}, keywords = {nosource} }

@article{chengProteinTyrosinePhosphatases2005, title = {Protein Tyrosine Phosphatases as Therapeutic Targets}, author = {Cheng, A. and Uetani, N.}, year = 2005, journal = {Inhibitors of Protein }, pages = {191–214}, url = {http://link.springer.com/chapter/10.1007/3-540-26670-4_8}, keywords = {nosource} }

@article{mollerStructurebasedDesignProtein2005, title = {Structure-Based Design of Protein Tyrosine Phosphatase Inhibitors}, author = {M{}ller, N. P. H. and Andersen, H. S.}, year = 2005, journal = {Inhibitors of Protein }, volume = {1}, pages = {215–262}, url = {http://link.springer.com/chapter/10.1007/3-540-26670-4_9}, keywords = {nosource} }

@article{alexanderBiologicalValidationCD452005, title = {Biological Validation of the {{CD45}} Tyrosine Phosphatase as a Pharmaceutical Target}, author = {Alexander, D. R.}, year = 2005, journal = {Inhibitors of Protein Kinases and Protein Phosphates}, pages = {263–293}, url = {http://link.springer.com/chapter/10.1007/3-540-26670-4_10}, keywords = {nosource} }

@article{honkanenSerineThreonineProtein2005, title = {Serine/Threonine Protein Phosphatase Inhibitors with Antitumor Activity}, author = {Honkanen, R. E.}, year = 2005, journal = {Inhibitors of Protein Kinases and Protein Phosphates}, pages = {295–318}, url = {http://link.springer.com/chapter/10.1007/3-540-26670-4_11}, keywords = {nosource} }

@article{bannerClinicalImmunosuppressionUsing2005, title = {Clinical Immunosuppression Using the Calcineurin-Inhibitors Ciclosporin and Tacrolimus}, author = {Banner, N. R. and Lyster, H. and Yacoub, M. H.}, year = 2005, journal = {Inhibitors of Protein Kinases and }, pages = {321–359}, url = {http://link.springer.com/chapter/10.1007/3-540-26670-4_12}, keywords = {nosource} }

@article{fabbroTargetedTherapyImatinib2005, title = {Targeted Therapy with Imatinib: {{An}} Exception or a Rule?}, author = {Fabbro, D. and Fendrich, G. and Guez, V. and Meyer, T.}, year = 2005, journal = {Inhibitors of Protein }, volume = {1}, pages = {361–389}, url = {http://link.springer.com/chapter/10.1007/3-540-26670-4_13}, keywords = {nosource} }

@article{drukerClinicalAspectsImatinib2005, title = {Clinical Aspects of Imatinib Therapy}, author = {Druker, B. J.}, year = 2005, journal = {Inhibitors of Protein Kinases and Protein Phosphates}, pages = {391–410}, url = {http://link.springer.com/chapter/10.1007/3-540-26670-4_14}, keywords = {nosource} }

@article{hidakaIsoquinolinesulfonamideSpecificInhibitor2005, title = {Isoquinolinesulfonamide: {{A}} Specific Inhibitor of {{Rho-kinase}} and the Clinical Aspect of Anti-{{Rho-kinase}} Therapy}, author = {Hidaka, H. and Suzuki, Y. and Shibuya, M. and Sasaki, Y.}, year = 2005, journal = {Inhibitors of Protein Kinases }, pages = {411–432}, url = {http://link.springer.com/chapter/10.1007/3-540-26670-4_15}, keywords = {nosource} }

@article{wakelingDiscoveryDevelopmentIressa2005, title = {Discovery and Development of {{Iressa}}: The First in a New Class of Drugs Targeted at the Epidermal Growth Factor Receptor Tyrosine Kinase}, author = {Wakeling, A. E.}, year = 2005, journal = {Inhibitors of Protein Kinases and Protein Phosphates}, pages = {433–450}, url = {http://link.springer.com/chapter/10.1007/3-540-26670-4_16}, keywords = {nosource} }

@article{rastrojoTranscriptomeLeishmaniaMajor2013, title = {The Transcriptome of {{Leishmania}} Major in the Axenic Promastigote Stage: Transcript Annotation and Relative Expression Levels by {{RNA-seq}}.}, author = {Rastrojo, Alberto and {Carrasco-Ramiro}, Fernando and Mart{'i}n, Diana and Crespillo, Antonio and Reguera, Rosa M. and Aguado, Bego{~n}a and Requena, Jose M.}, year = 2013, month = jan, journal = {BMC genomics}, volume = {14}, number = {1}, pages = {223}, issn = {1471-2164}, doi = {10.1186/1471-2164-14-223}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3637525&tool=pmcentrez&rendertype=abstract}, abstract = {BACKGROUND: Although the genome sequence of the protozoan parasite Leishmania major was determined several years ago, the knowledge of its transcriptome was incomplete, both regarding the real number of genes and their primary structure. RESULTS: Here, we describe the first comprehensive transcriptome analysis of a parasite from the genus Leishmania. Using high-throughput RNA sequencing (RNA-seq), a total of 10285 transcripts were identified, of which 1884 were considered novel, as they did not match previously annotated genes. In addition, our data indicate that current annotations should be modified for many of the genes. The detailed analysis of the transcript processing sites revealed extensive heterogeneity in the spliced leader (SL) and polyadenylation addition sites. As a result, around 50% of the genes presented multiple transcripts differing in the length of the UTRs, sometimes in the order of hundreds of nucleotides. This transcript heterogeneity could provide an additional source for regulation as the different sizes of UTRs could modify RNA stability and/or influence the efficiency of RNA translation. In addition, for the first time for the Leishmania major promastigote stage, we are providing relative expression transcript levels. CONCLUSIONS: This study provides a concise view of the global transcriptome of the L. major promastigote stage, providing the basis for future comparative analysis with other development stages or other Leishmania species.}, pmid = {23557257}, keywords = {gene expression,leishmania,mrnas,nosource,rna-seq,transcript annotation,trypanosomatids} }

@article{wagnerSmallRegulatoryRNAs2006, title = {Small Regulatory {{RNAs}} in Bacteria}, author = {Wagner, E. G. H. and Darfeuille, F.}, year = 2006, journal = {Small RNAs}, volume = {17}, number = {1961}, url = {http://link.springer.com/chapter/10.1007/978-3-540-28130-6_1}, keywords = {nosource} }

@article{alfonzoEditingTRNAStructure2008, title = {Editing of {{tRNA}} for {{Structure}} and {{Function}}}, author = {Alfonzo, J. D.}, year = 2008, journal = {RNA editing}, url = {http://link.springer.com/chapter/10.1007/978-3-540-73787-2_2}, keywords = {nosource} } % == BibTeX quality report for alfonzoEditingTRNAStructure2008: % ? Title looks like it was stored in title-case in Zotero

@article{bassRNAEditingAdenosine2001, title = {{{RNA}} Editing by Adenosine Deaminases That Act on {{RNA}}.}, author = {Bass, B. L.}, year = 2001, journal = {Annual review of biochemistry}, volume = {1}, pages = {51–84}, url = {http://europepmc.org/articles/PMC1823043}, keywords = {nosource} }

@article{gottInsertionDeletionEditing2008, title = {Insertion/Deletion Editing in {{Physarum}} Polycephalum}, author = {Gott, J. M. and Rhee, A. C.}, year = 2008, journal = {RNA editing}, pages = {85–104}, url = {http://link.springer.com/chapter/10.1007/978-3-540-73787-2_4}, keywords = {nosource} }

@article{carnesWorkingTogetherRNA2008, title = {Working Together: The {{RNA}} Editing Machinery in {{Trypanosoma}} Brucei}, author = {Carnes, Jason and Stuart, Kenneth}, year = 2008, journal = {RNA editing}, url = {http://link.springer.com/chapter/10.1007/978-3-540-73787-2_7}, keywords = {nosource} }

@article{goringerRNAEditingAccessory2008, title = {{{RNA}} Editing Accessory Factors—the Example of {{mHel61p}}}, author = {G{"o}ringer, H. U. and Brecht, Michael and B{"o}hm, Cordula and Kruse, Elisabeth}, year = 2008, journal = {RNA Editing}, pages = {165–179}, url = {http://link.springer.com/chapter/10.1007/978-3-540-73787-2_8}, keywords = {nosource} }

@article{ochsenreiterFunctionRNAEditing2008, title = {The Function of {{RNA}} Editing in {{Trypanosomes}}}, author = {Ochsenreiter, Torsten and Hajduk, Stephen}, year = 2008, journal = {RNA editing}, url = {http://link.springer.com/chapter/10.1007/978-3-540-73787-2_9}, keywords = {nosource} }

@article{homannEditingReactionsPerspective2008, title = {Editing Reactions from the Perspective of {{RNA}} Structure}, author = {Homann, Matthias}, year = 2008, journal = {RNA editing}, pages = {1–32}, url = {http://link.springer.com/chapter/10.1007/978-3-540-73787-2_1}, keywords = {nosource} }

@book{davidovichTargetingFunctionalCenters2011, title = {Targeting {{Functional Centers}} of the {{Ribosome}}}, author = {Davidovich, Chen}, year = 2011, publisher = {Springer Berlin Heidelberg}, doi = {10.1007/978-3-642-16931-1}, url = {http://www.springerlink.com/index/10.1007/978-3-642-16931-1 http://books.google.com/books?hl=en&lr=&id=Z_iH32Fz4oYC&oi=fnd&pg=PR6&dq=Targeting+Functional+Centers+of+the+Ribosome&ots=QfefOEdz63&sig=1yrHVnfaA60Bk1gdyIltRrHic3w}, isbn = {978-3-642-16930-4}, keywords = {nosource} } % == BibTeX quality report for davidovichTargetingFunctionalCenters2011: % ? Title looks like it was stored in title-case in Zotero

@article{ayubCterminalEndProteins2008, title = {The {{C-terminal}} End of {{P}} Proteins Mediates Ribosome Inactivation by Trichosanthin but Does Not Affect the Pokeweed Antiviral Protein Activity.}, author = {Ayub, Maximiliano Juri and Smulski, Cristian R. and Ma, Kit-Wan and Levin, Mariano J. and Shaw, Pang-Chui and Wong, Kam-Bo}, year = 2008, month = may, journal = {Biochemical and biophysical research communications}, volume = {369}, number = {2}, eprint = {18282466}, eprinttype = {pubmed}, pages = {314–9}, issn = {1090-2104}, doi = {10.1016/j.bbrc.2008.01.170}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18282466}, abstract = {Ribosome inactivating proteins (RIPs) inhibit protein synthesis depurinating a conserved residue in the sarcin/ricin loop of ribosomes. Some RIPs are only active against eukaryotic ribosomes, but other RIPs inactivate with similar efficiency prokaryotic and eukaryotic ribosomes, suggesting that different RIPs would interact with different proteins. The SRL in Trypanosoma cruzi ribosomes is located on a 178b RNA molecule named 28Sdelta. In addition, T. cruzi ribosomes are remarkably resistant to TCS. In spite of these peculiarities, we show that TCS specifically depurinate the predicted A(51) residue on 28Sdelta. We also demonstrated that the C-terminal end of ribosomal P proteins is needed for full activity of the toxin. In contrast to TCS, PAP inactivated efficiently T.cruzi ribosomes, and most importantly, does not require from the C-terminal end of P proteins. These results could explain, at least partially, the different selectivity of these toxins against prokaryotic and eukaryotic ribosomes.}, isbn = {1047053422723}, pmid = {18282466}, keywords = {Binding Sites,Chemical,Computer Simulation,DNA-Binding Proteins,DNA-Binding Proteins: chemistry,Models,Molecular,nosource,Plant Proteins,Plant Proteins: chemistry,Protein Binding,Protein Structure,Ribosome Inactivating Proteins,Ribosome Inactivating Proteins: chemistry,Ribosomes,Ribosomes: chemistry,Tertiary,Trichosanthin,Trichosanthin: chemistry,Type 1,Type 1: chemistry} }

@article{saccoNonCodingRNAs2011, title = {Non {{Coding RNAs}} in {{Plants}}}, author = {Sacco, Letizia Da and Palma, Alessia and Lam, Bernard Chi-hang and {Haj-ahmad}, Yousef and Rghei, Nezar and Masotti, Andrea}, editor = {Erdmann, Volker A. and Barciszewski, Jan}, year = 2011, publisher = {Springer Berlin Heidelberg}, doi = {10.1007/978-3-642-19454-2}, url = {http://link.springer.com/10.1007/978-3-642-19454-2}, isbn = {978-3-642-19453-5}, keywords = {nosource} } % == BibTeX quality report for saccoNonCodingRNAs2011: % Missing required field ‘journal’ % ? Title looks like it was stored in title-case in Zotero

@article{ayubTrypanosomaCruziHigh2008, title = {Trypanosoma Cruzi: High Ribosomal Resistance to Trichosanthin Inactivation.}, author = {Ayub, Maximiliano Juri and Ma, Kit-Wan and Shaw, Pang-Chui and Wong, Kam-Bo}, year = 2008, month = mar, journal = {Experimental parasitology}, volume = {118}, number = {3}, eprint = {17949717}, eprinttype = {pubmed}, pages = {442–7}, issn = {0014-4894}, doi = {10.1016/j.exppara.2007.09.002}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17949717}, abstract = {Trypanosoma cruzi is the parasite causing Chagas Disease. Several results already published suggest that T. cruzi ribosomes have remarkable differences with their mammalian counterparts. In the present work, we showed that trypanosomatid (T. cruzi and Crithidia fasciculata) ribosomes are highly resistant to inactivation by trichosanthin (TCS), which is active against mammalian ribosomes. Differential resistance is an intrinsic feature of the ribosomal particles, as demonstrated by using assays where the only variable was the ribosomes source. Because we have recently described that TCS interacts with the acidic C-terminal end of mammalian ribosomal P proteins, we assayed the effect of a TCS variant, which is unable to interact with P proteins, on trypanosomatid ribosomes. This mutant showed similar shifting of IC(50) values on rat, T. cruzi and C. fasciculata ribosomes, suggesting that the resistance mechanism might involve other ribosomal components rather than the C-terminal end of P proteins.}, pmid = {17949717}, keywords = {Animals,Antiparasitic Agents,Antiparasitic Agents: pharmacology,Crithidia fasciculata,Crithidia fasciculata: drug effects,Crithidia fasciculata: ultrastructure,Drug Resistance,Liver,Liver: ultrastructure,nosource,Protein Biosynthesis,Protein Biosynthesis: drug effects,Rats,Ribosomes,Ribosomes: drug effects,Trichosanthin,Trichosanthin: pharmacology,Trypanosoma cruzi,Trypanosoma cruzi: drug effects,Trypanosoma cruzi: ultrastructure} }

@article{jouannetLongNonproteincodingRNAs2011, title = {Long Nonprotein-Coding {{RNAs}} in Plants}, author = {Jouannet, V. and Crespi, M.}, editor = {Ugarkovic, Durdica}, year = 2011, journal = {Long Non-Coding RNAs}, volume = {51}, pages = {1–27}, publisher = {Springer Berlin Heidelberg}, doi = {10.1007/978-3-642-16502-3}, url = {http://link.springer.com/10.1007/978-3-642-16502-3 http://link.springer.com/chapter/10.1007/978-3-642-16502-3_9}, isbn = {978-3-642-16501-6}, keywords = {nosource} }

@article{greifTranscriptomeAnalysisBloodstream2013, title = {Transcriptome Analysis of the Bloodstream Stage from the Parasite {{Trypanosoma}} Vivax}, author = {Greif, Gonzalo and {}de Leon, Miguel Ponce and Lamolle, Guillermo and Rodriguez, Mat{'i}as and Pi{~n}eyro, Dolores and {Tavares-Marques}, Lucinda M. and {Reyna-Bello}, Armando and Robello, Carlos and Valin, Fernando Alvarez}, year = 2013, journal = {BMC Genomics}, volume = {14}, number = {1}, pages = {149}, issn = {1471-2164}, doi = {10.1186/1471-2164-14-149}, url = {http://www.biomedcentral.com/1471-2164/14/149}, keywords = {nosource} }

@article{guptaBasalSplicingFactors2013, title = {Basal {{Splicing Factors Regulate}} the {{Stability}} of {{Mature mRNAs}} in {{Trypanosomes}}.}, author = {Gupta, Sachin Kumar and Carmi, Shai and {Ben-Asher}, Hiba Waldman and Tkacz, Itai Dov and Naboishchikov, Ilana and Michaeli, Shulamit}, year = 2013, month = feb, journal = {The Journal of biological chemistry}, volume = {288}, number = {7}, eprint = {23283975}, eprinttype = {pubmed}, pages = {4991–5006}, issn = {1083-351X}, doi = {10.1074/jbc.M112.416578}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23283975}, abstract = {Gene expression in trypanosomes is mainly regulated post-transcriptionally. Genes are transcribed as polycistronic mRNAs that are dissected by the concerted action of trans-splicing and polyadenylation. In trans-splicing, a common exon, the spliced leader, is added to all mRNAs from a small RNA. In this study, we examined by microarray analysis the transcriptome following RNAi silencing of the basal splicing factors U2AF65, SF1, and U2AF35. The transcriptome data revealed correlations between the affected genes and their splicing and polyadenylation signaling properties, suggesting that differential binding of these factors to pre-mRNA regulates trans-splicing and hence expression of specific genes. Surprisingly, all these factors were shown to affect not only splicing but also mRNA stability. Affinity purification of SF1 and U2AF35 complexes supported their role in mRNA stability. U2AF35 but not SF1 was shown to bind to ribosomes. To examine the role of splicing factors in mRNA stability, mutations were introduced into the polypyrimidine tract located in the 3’ UTR of a mini-gene, and the results demonstrate that U2AF65 binds to such a site and controls the mRNA stability. We propose that transcripts carrying splicing signals in their 3’ UTR bind the splicing factors and control their stability.}, pmid = {23283975}, keywords = {nosource} } % == BibTeX quality report for guptaBasalSplicingFactors2013: % ? Title looks like it was stored in title-case in Zotero

@article{hoareDevelopmentalStagesTrypanosomatid1966, title = {Developmental Stages of Trypanosomatid Flagellates: A New Terminology}, author = {Hoare, C. A. and Wallace, F. G.}, year = 1966, journal = {Nature}, url = {http://www.nature.com/nature/journal/v212/n5068/abs/2121385a0.html}, keywords = {nosource} }

@article{darnellReflectionsHistoryPremRNA2013, title = {Reflections on the History of Pre-{{mRNA}} Processing and Highlights of Current Knowledge: A Unified Picture}, author = {Darnell, J. E.}, year = 2013, journal = {RNA}, pages = {443–460}, doi = {10.1261/rna.038596.113.1}, url = {http://rnajournal.cshlp.org/content/19/4/443.short}, keywords = {nosource,pre-mrna processing} }

@article{salzmanCircularRNAsAre2012, title = {Circular {{RNAs}} Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types.}, author = {Salzman, Julia and Gawad, Charles and Wang, Peter Lincoln and Lacayo, Norman and Brown, Patrick O.}, year = 2012, month = jan, journal = {PloS one}, volume = {7}, number = {2}, pages = {e30733}, issn = {1932-6203}, doi = {10.1371/journal.pone.0030733}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3270023&tool=pmcentrez&rendertype=abstract}, abstract = {Most human pre-mRNAs are spliced into linear molecules that retain the exon order defined by the genomic sequence. By deep sequencing of RNA from a variety of normal and malignant human cells, we found RNA transcripts from many human genes in which the exons were arranged in a non-canonical order. Statistical estimates and biochemical assays provided strong evidence that a substantial fraction of the spliced transcripts from hundreds of genes are circular RNAs. Our results suggest that a non-canonical mode of RNA splicing, resulting in a circular RNA isoform, is a general feature of the gene expression program in human cells.}, pmid = {22319583}, keywords = {Base Sequence,Exons,Gene Expression,Humans,nosource,Protein Isoforms,RNA,RNA Precursors,RNA Precursors: genetics,RNA Splicing,RNA: genetics} }

@article{dananTranscriptomewideDiscoveryCircular2012, title = {Transcriptome-Wide Discovery of Circular {{RNAs}} in {{Archaea}}.}, author = {Danan, Miri and Schwartz, Schraga and Edelheit, Sarit and Sorek, Rotem}, year = 2012, month = apr, journal = {Nucleic acids research}, volume = {40}, number = {7}, pages = {3131–42}, issn = {1362-4962}, doi = {10.1093/nar/gkr1009}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3326292&tool=pmcentrez&rendertype=abstract}, abstract = {Circular RNA forms had been described in all domains of life. Such RNAs were shown to have diverse biological functions, including roles in the life cycle of viral and viroid genomes, and in maturation of permuted tRNA genes. Despite their potentially important biological roles, discovery of circular RNAs has so far been mostly serendipitous. We have developed circRNA-seq, a combined experimental/computational approach that enriches for circular RNAs and allows profiling their prevalence in a whole-genome, unbiased manner. Application of this approach to the archaeon Sulfolobus solfataricus P2 revealed multiple circular transcripts, a subset of which was further validated independently. The identified circular RNAs included expected forms, such as excised tRNA introns and rRNA processing intermediates, but were also enriched with non-coding RNAs, including C/D box RNAs and RNase P, as well as circular RNAs of unknown function. Many of the identified circles were conserved in Sulfolobus acidocaldarius, further supporting their functional significance. Our results suggest that circular RNAs, and particularly circular non-coding RNAs, are more prevalent in archaea than previously recognized, and might have yet unidentified biological roles. Our study establishes a specific and sensitive approach for identification of circular RNAs using RNA-seq, and can readily be applied to other organisms.}, pmid = {22140119}, keywords = {Archaeal,Archaeal: chemistry,Archaeal: classification,Archaeal: metabolism,Gene Expression Profiling,Introns,nosource,Ribosomal,Ribosomal: chemistry,Ribosomal: metabolism,RNA,RNA: chemistry,RNA: classification,RNA: metabolism,Sequence Analysis,Sulfolobus acidocaldarius,Sulfolobus acidocaldarius: genetics,Sulfolobus solfataricus,Sulfolobus solfataricus: genetics,Transcriptome,Transfer,Transfer: chemistry,Transfer: metabolism,Untranslated,Untranslated: chemistry,Untranslated: metabolism} }

@article{graurImmortalityTelevisionSets2013, title = {On the Immortality of Television Sets: “Function” in the Human Genome According to the Evolution-Free Gospel of {{ENCODE}}.}, author = {Graur, Dan and Zheng, Yichen and Price, Nicholas and Azevedo, Ricardo B. R. and {}a Zufall, Rebecca and Elhaik, Eran}, year = 2013, month = feb, journal = {Genome biology and evolution}, eprint = {23431001}, eprinttype = {pubmed}, pages = {1–43}, issn = {1759-6653}, doi = {10.1093/gbe/evt028}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23431001}, abstract = {A recent slew of ENCODE Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is under 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 - 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions, or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly (1) by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as “affirming the consequent,” (3) by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.}, pmid = {23431001}, keywords = {nosource} }

@article{chenDynamicsTranslationSingle2013, title = {Dynamics of Translation by Single Ribosomes through {{mRNA}} Secondary Structures.}, author = {Chen, Chunlai and Zhang, Haibo and Broitman, Steven L. and Reiche, Michael and Farrell, Ian and Cooperman, Barry S. and Goldman, Yale E.}, year = 2013, month = mar, journal = {Nature structural & molecular biology}, number = {February}, eprint = {23542154}, eprinttype = {pubmed}, pages = {1–8}, publisher = {Nature Publishing Group}, issn = {1545-9985}, doi = {10.1038/nsmb.2544}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23542154}, abstract = {During protein synthesis, the ribosome translates nucleotide triplets in single-stranded mRNA into polypeptide sequences. Strong downstream mRNA secondary structures, which must be unfolded for translation, can slow or even halt protein synthesis. Here we used single-molecule fluorescence resonance energy transfer to determine reaction rates for specific steps within the elongation cycle as the Escherichia coli ribosome encounters stem-loop or pseudoknot mRNA secondary structures. Downstream stem-loops containing 100% GC base pairs decrease the rates of both tRNA translocation within the ribosome and deacylated tRNA dissociation from the ribosomal exit site (E site). Downstream stem-loops or pseudoknots containing both GC and AU pairs also decrease the rate of tRNA dissociation, but they have little effect on tRNA translocation rate. Thus, somewhat unexpectedly, unfolding of mRNA secondary structures is more closely coupled to E-site tRNA dissociation than to tRNA translocation.}, pmid = {23542154}, keywords = {nosource} }

@article{krebsThreedimensionalStructureBovine2003, title = {The Three-Dimensional Structure of Bovine Rhodopsin Determined by Electron Cryomicroscopy}, author = {Krebs, A. and Edwards, P. C. and Villa, C.}, year = 2003, month = dec, journal = {Journal of Biological }, volume = {278}, number = {50}, pages = {50217–50225}, publisher = {AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC}, doi = {10.1074/jbc.M307995200}, url = {http://www.jbc.org/content/278/50/50217.short}, abstract = {G-protein-coupled receptors are integral membrane proteins that respond to environmental signals and initiate signal transduction pathways, which activate cellular processes. Rhodopsin, a well known member of the G-protein-coupled receptor family, is located in the disk membranes of the rod outer segment, where it is responsible for the visualization of dim light. Rhodopsin is the most extensively studied G-protein-coupled receptor, and knowledge about its structure serves as a template for other related receptors. We have gained detailed structural knowledge from the crystal structure ( 1), which was solved by x-ray crystallography in 2000 using three-dimensional crystals. Here we report a three-dimensional density map of bovine rhodopsin determined by electron cryomicroscopy of two-dimensional crystals with p22(1)2(1) symmetry. The usage of relatively small and disordered crystals made the process of structure determination challenging. Special attention was paid to the extraction of amplitudes and phases, since usable raw data were limited to a maximum tilt of 45degrees. In the refinement process, an improved unbending procedure was applied. This led to a final resolution of 5.5 Angstrom in the membrane plane and similar to 13 Angstrom perpendicular to it, making our electron density map the most accurate map of a G-protein-coupled receptor currently available by electron microscopy. Most important is the information we gain about the center of the membrane plane and the orientation of the molecule relative to the bilayer. This information cannot be retrieved from the three-dimensional crystals. In our electron density map, all seven transmembrane helices were identified, and their arrangement is in agreement with the arrangement known from the crystal structure ( 1). In the retinal binding pocket, a density peak adjacent to helix 3 suggests the position of the beta-ionine ring of the chromophore, and in its vicinity several of the bigger amino acids can be identified.}, keywords = {nosource} }

@article{wlodawerProteinCrystallographyNon2008, title = {Protein Crystallography for Non-crystallographers, or How to Get the Best (but Not More) from Published Macromolecular Structures}, author = {Wlodawer, Alexander and Minor, Wladek and Dauter, Zbigniew and Jaskolski, Mariusz}, year = 2008, month = jan, journal = {Febs Journal}, volume = {275}, number = {1}, pages = {1–21}, doi = {10.1111/j.1742-4658.2007.06178.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2007.06178.x/full}, abstract = {The number of macromolecular structures deposited in the Protein Data Bank now exceeds 45,000, with the vast majority determined using crystallographic methods. Thousands of studies describing such structures have been published in the scientific literature, and 14 Nobel prizes in chemistry or medicine have been awarded to protein crystallographers. As important as these structures are for understanding the processes that take place in living organisms and also for practical applications such as drug design, many non-crystallographers still have problems with critical evaluation of the structural literature data. This review attempts to provide a brief outline of technical aspects of crystallography and to explain the meaning of some parameters that should be evaluated by users of macromolecular structures in order to interpret, but not over-interpret, the information present in the coordinate files and in their description. A discussion of the extent of the information that can be gleaned from the coordinates of structures solved at different resolution, as well as problems and pitfalls encountered in structure determination and interpretation are also covered.}, keywords = {nosource} }

@article{georgeGproteincoupledReceptorOligomerization2002, title = {G-Protein-Coupled Receptor Oligomerization and Its Potential for Drug Discovery}, author = {George, S. R. and O’Dowd, B. F. and Lee, S. P.}, year = 2002, month = oct, journal = {Nature Reviews Drug Discovery}, volume = {1}, number = {10}, pages = {808–20}, doi = {10.1038/nrd913}, url = {http://www.nature.com/nrd/journal/v1/n10/abs/nrd913.html}, abstract = {G-protein-coupled receptors (GPCRs) represent by far the largest class of targets for modern drugs. Virtually all therapeutics that are directed towards GPCRs have been designed using assays that presume that these receptors are monomeric. The recent realization that these receptors form homo-oligomeric and hetero-oligomeric complexes has added a new dimension to rational drug design. However, this important aspect of GPCR biology remains largely unincorporated into schemes to search for new therapeutics. This review provides a synopsis of the current thinking surrounding GPCR homo-oligomerization and hetero-oligomerization and shows how new models point towards unexplored avenues in the development of new therapies.}, keywords = {nosource} }

@article{gingrichAffinityChromatographyD11988, title = {Affinity Chromatography of the {{D1}} Dopamine Receptor from Rat Corpus Striatum}, author = {Gingrich, J. A. and Amlaiky, N. and Senogles, S. E.}, year = 1988, journal = {Biochemistry}, volume = {27}, number = {11}, pages = {3907–3912}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00411a003}, abstract = {The D1 dopamine receptor from rat corpus striatum has been purified 200-250-fold by using a newly developed biospecific affinity chromatography matrix based on a derivative of the D1 selective antagonist SCH 23390. This compound, (RS)-5-(4-aminophenyl)-8-chloro-2,3,4,5-tetrahydro-3-methyl-1H-3-benz azepin-7-o l (SCH 39111), possesses high affinity for the D1 receptor and, when immobilized on Sepharose 6B through an extended spacer arm, was able to adsorb digitonin-solubilized D1 receptors. The interaction between the solubilized receptor and the affinity matrix was biospecific. Adsorption of receptor activity could be blocked in a stereoselective fashion SCH 23390 greater than SCH 23388; (+)-butaclamol greater than (-)-butaclamol. The elution of 3HSCH 23390 activity from the gel demonstrated similar stereoselectivity for antagonist ligands. Agonists eluted receptor activity with a rank order of potency consistent with that of a D1 receptor apomorphine greater than dopamine greater than (-)-epinephrine much greater than LY 171555 greater than serotonin. SCH 39111-Sepharose absorbed 75-85% of the soluble receptor activity, and after the gel was washed extensively, 35-55% of the absorbed receptor activity could be eluted with 100 microM (+)-butaclamol with specific activities ranging from 250 to 450 pmol/mg of protein. The affinity-purified receptor retains the ligand binding characteristics of a D1 dopamine receptor. This affinity chromatography procedure should prove valuable in the isolation and molecular characterization of the D1 dopamine receptor.}, keywords = {nosource} }

@article{karmaliModelbuildingStrategiesLowresolution2009, title = {Model-Building Strategies for Low-Resolution {{X-ray}} Crystallographic Data}, author = {Karmali, A. M. and Blundell, T. L. and Furnham, Nicholas}, year = 2009, month = feb, journal = { D: Biological Crystallography}, volume = {65}, number = {Pt 2}, pages = {121–7}, doi = {10.1107/S0907444908040006}, url = {http://scripts.iucr.org/cgi-bin/paper?s0907444908040006}, abstract = {The interpretation of low-resolution X-ray crystallographic data proves to be challenging even for the most experienced crystallographer. Ambiguity in the electron-density map makes main-chain tracing and side-chain assignment difficult. However, the number of structures solved at resolutions poorer than 3.5 A is growing rapidly and the structures are often of high biological interest and importance. Here, the challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The methods employed in model generation from electron microscopy, which share many of the same challenges in providing high-confidence models of macromolecular structures and assemblies, are also considered.}, keywords = {nosource} }

@article{tiberiDifferentialRegulationDopamine1996, title = {Differential Regulation of Dopamine {{D1A}} Receptor Responsiveness by Various {{G}} Protein-Coupled Receptor Kinases}, author = {Tiberi, M. and Nash, S. R. and Bertrand, L.}, year = 1996, journal = {Journal of Biological }, volume = {271}, number = {7}, pages = {3771–3778}, url = {http://www.jbc.org/content/271/7/3771.short}, abstract = {The role of G protein-coupled receptor kinases (GRKs) in the regulation of dopamine D1A receptor responsiveness is poorly understood. To explore the potential role played by the GRKs in the regulation of the rat dopamine D1A receptor, we performed whole cell phosphorylation experiments and cAMP assays in 293 cells cotransfected with the receptor alone or with various GRKs (GRK2, GRK3, and GRK5). The agonist-dependent phosphorylation of the rat D1A receptor was substantially increased in cells overexpressing GRK2, GRK3, or GRK5. Moreover, we report that cAMP formation upon receptor activation was differentially regulated in cells overexpressing either GRK2, GRK3, and GRK5 under conditions that elicited similar levels of GRK-mediated receptor phosphorylation. Cells expressing the rat D1A receptor with GRK2 and GRK3 displayed a rightward shift of the dopamine dose-response curve with little effect on the maximal activation when compared with cells expressing the receptor alone. In contrast, cells expressing GRK5 displayed a rightward shift in the EC50 value with an additional 40% reduction in the maximal activation when compared with cells expressing the receptor alone. Thus, we show that the dopamine D1A receptor can serve as a substrate for various GRKs and that GRK-phosphorylated D1A receptors display a differential reduction of functional coupling to adenylyl cyclase. These results suggest that the cellular complement of G protein-coupled receptor kinases may determine the properties and extent of agonist-mediated responsiveness and desensitization.}, keywords = {nosource} }

@article{ericksenLigandSelectivityD22009, title = {Ligand Selectivity of {{D2}} Dopamine Receptors Is Modulated by Changes in Local Dynamics Produced by Sodium Binding}, author = {Ericksen, S. S. and Cummings, D. F.}, year = 2009, journal = {Journal of Pharmacology }, volume = {328}, number = {1}, pages = {40–54}, publisher = {{American Society for Pharmacology and Experimental Therapeutics}}, url = {http://jpet.aspetjournals.org/content/328/1/40.short}, abstract = {We have uncovered a significant allosteric response of the D2 dopamine receptor to physiologically relevant concentrations of sodium (140 mM), characterized by a sodium-enhanced binding affinity for a D4-selective class of agonists and antagonists. This enhancement is significantly more pronounced in a D2-V2.61(91)F mutant and cannot be mimicked by an equivalent concentration of the sodium replacement cation N-methyl-d-glucamine. This phenomenon was explored computationally at the molecular level by analyzing the effect of sodium binding on the dynamic properties of D2 receptor model constructs. Normal mode analysis identified one mode (M19), which is involved in the open/closed motions of the binding cleft as being particularly sensitive to the sodium effect. To examine the consequences for D2 receptor ligand recognition, one of the ligands, L-745,870 3-4-(4-chlorophenyl) piperazin-1-yl-methyl-1H-pyrrolo2,3-bpyridine or CPPMA, chlorophenylpiperazinyl methylazaindole, was docked into conformers along the M19 trajectory. Structurally and pharmacologically well established ligand-receptor interactions, including the ionic interaction with D3.32(114) and interactions between the ligand aryl moieties and V2.61(91)F, were achieved only in open phase conformers. The docking of (-)-raclopride 3,5-dichloro-N-(1-ethylpyrrolidin-2-ylmethyl)-2-hydroxy-6-methoxybenzamide suggests that the same binding cleft changes in response to sodium-binding perturbation account as well for the enhancements in binding affinity for substituted benzamides in the wild-type D2 receptor. Our findings demonstrate how key interactions can be modulated by occupancy at an allosteric site and are consistent with a mechanism in which sodium binding enhances the affinity of selected ligands through dynamic changes that increase accessibility of substituted benzamides and 1,4-DAP ligands to the orthosteric site and accessibility of 1,4-DAPs to V2.61(91)F.}, keywords = {nosource} }

@article{senoglesAffinityChromatographyAnterior1986, title = {Affinity Chromatography of the Anterior Pituitary {{D2-dopamine}} Receptor}, author = {Senogles, S. E. and Amlaiky, N. and Johnson, A. L. and Caron, M. G.}, year = 1986, journal = {Biochemistry}, volume = {25}, number = {4}, pages = {749–753}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00352a002}, abstract = {The D2-dopamine receptor from bovine anterior pituitary has been solubilized with digitonin and purified approximately 1000-fold by affinity chromatography on a new affinity support. This support consists of a (carboxymethylene)oximino derivative of the D2-selective antagonist spiperone (CMOS) covalently attached to Sepharose 4B through a long side chain. The interaction of the solubilized receptor activity with the affinity gel was biospecific. Dopaminergic drugs blocked adsorption of solubilized receptor activity to the CMOS-Sepharose with the appropriate D2-dopaminergic potency and stereoselectivity. For agonists, (-)-N-n-propylnorapomorphine greater than 2-amino-6,7-dihydroxytetrahydronaphthalene approximately equal to apomorphine greater than dopamine, whereas for antagonists (+)-butaclamol much greater than (-)-butaclamol. The same D2-dopaminergic specificity was observed for elution of receptor activity from the gel. To observe eluted receptor binding activity, reconstitution of the eluted material into phospholipid vesicles was necessary. Typically, 70-80% of the solubilized receptor was adsorbed by CMOS-Sepharose, and 40-50% of the adsorbed activity could be recovered after reconstitution of the eluted material. The overall recovery of D2-receptor activity from bovine anterior pituitary membranes was 12-15% with specific binding activity of approximately 150 pmol/mg. The reconstituted affinity-purified receptor bound ligands with the expected D2-dopaminergic specificity, stereoselectivity, and rank order of potency.}, keywords = {nosource} }

@article{evansIntroductionMolecularReplacement2007, title = {An Introduction to Molecular Replacement}, author = {Evans, Philip and McCoy, Airlie}, year = 2007, month = jan, journal = {Acta Crystallographica Section D: Biological }, volume = {64}, number = {Pt 1}, pages = {1–10}, publisher = {International Union of Crystallography}, doi = {10.1107/S0907444907051554}, url = {http://scripts.iucr.org/cgi-bin/paper?S0907444907051554}, abstract = {Molecular replacement is fundamentally a simple trial-and-error method of solving crystal structures when a suitable related model is available. The underlying simplicity of the method is often obscured by the mathematical trickery required to make the searches computationally tractable. This introduction sketches the essential issues in molecular replacement without going into technical details. General search strategies are discussed and the alternative Patterson and likelihood approaches are outlined.}, keywords = {nosource} }

@article{odowdTwoAminoAcids2012, title = {Two Amino Acids in Each of {{D1}} and {{D2}} Dopamine Receptor Cytoplasmic Regions Are Involved in {{D1-D2}} Heteromer Formation.}, author = {O’Dowd, Brian F. and Ji, Xiaodong and Nguyen, Tuan and George, Susan R.}, year = 2012, journal = {Biochemical and Biophysical Research Communications}, volume = {417}, number = {1}, pages = {23–8}, publisher = {Elsevier Inc.}, doi = {10.1016/j.bbrc.2011.11.027}, abstract = {D(1) and D(2) dopamine receptors exist as heteromers in cells and brain tissue and are dynamically regulated and separated by agonist concentrations at the cell surface. We determined that these receptor pairs interact primarily through discrete amino acids in the cytoplasmic regions of each receptor, with no evidence of any D(1)-D(2) receptor transmembrane interaction found. Specifically involved in heteromer formation we identified, in intracellular loop 3 of the D(2) receptor, two adjacent arginine residues. Substitution of one of the arginine pair prevented heteromer formation. Also involved in heteromer formation we identified, in the carboxyl tail of the D(1) receptor, two adjacent glutamic acid residues. Substitution of one of the glutamic acid pair prevented heteromer formation. These amino acid pairs in D(1) and D(2) receptors are oppositely charged, and presumably interact directly by electrostatic interactions.}, keywords = {nosource} }

@article{kobilkaProteinCoupledReceptor2007, title = {G Protein Coupled Receptor Structure and Activation}, author = {Kobilka, B. K.}, year = 2007, month = apr, journal = {Biochimica et Biophysica Acta (BBA)-Biomembranes}, volume = {1768}, number = {4}, pages = {794–807}, doi = {10.1016/j.bbamem.2006.10.021}, url = {http://www.sciencedirect.com/science/article/pii/S0005273606003981}, abstract = {G protein coupled receptors (GPCRs) are remarkably versatile signaling molecules. The members of this large family of membrane proteins are activated by a spectrum of structurally diverse ligands, and have been shown to modulate the activity of different signaling pathways in a ligand specific manner. In this manuscript I will review what is known about the structure and mechanism of activation of GPCRs focusing primarily on two model systems, rhodopsin and the beta(2) adrenoceptor.}, keywords = {nosource} }

@article{mottolaFunctionalSelectivityDopamine2002, title = {Functional Selectivity of Dopamine Receptor Agonists. {{I}}. {{Selective}} Activation of Postsynaptic Dopamine {{D2}} Receptors Linked to Adenylate Cyclase}, author = {Mottola, D. M. and Kilts, J. D. and Lewis, M. M.}, year = 2002, month = jun, journal = { of Pharmacology and }, volume = {301}, number = {3}, pages = {1166–1178}, publisher = {AMER SOC PHARMACOLOGY EXPERIMENTAL THERAPEUTICS}, doi = {10.1124/jpet.301.3.1166}, url = {http://jpet.aspetjournals.org/content/301/3/1166.short}, abstract = {Dihydrexidine (DHX), the first high-affinity D-1 dopamine receptor full agonist, is only 10-fold selective for D-1 versus D-2 receptors, having D-2 affinity similar to the prototypical agonist quinpirole. The D-2 functional properties of DHX and its more D-2 selective analog N-n-propyl-dihydrexidine (PrDHX) were explored in rat brain and pituitary. DHX and PrDHX had binding characteristics to D-2 receptors in rat striatum typical of D-2 agonists, binding to both high- and low-affinity sites and being sensitive to guanine-nucleotides. Consistent with these binding data, both DHX and PrDHX inhibited forskolin-stimulated cAMP synthesis in striatum with a potency and intrinsic activity equivalent to that of quinpirole. Unexpectedly, however, DHX and PrDHX had little functional effect at D-2 receptors expressed on dopaminergic neurons that mediate inhibition of cell firing, dopamine release, or dopamine synthesis. Quantitative receptor competition autoradiography demonstrated that DHX bound to D-2 receptors in striatum (predominantly postsynaptic receptor sites) with equal affinity as D-2 sites in the substantia nigra (autoreceptor sites). The data from these experiments, coupled with what is known about the location of specific dopamine receptor isoforms, lead to the hypothesis that DHX, after binding to D-2L and D-2S receptors, causes agonist-typical functional changes only at some of these receptors. This phenomenon (herein termed ``functional selectivity’’) suggests that drugs may be targeted not only at specific receptor isoforms but also at separate functions mediated by a single isoform, yielding novel approaches to drug discovery.}, keywords = {nosource} }

@article{senoglesD2dopamineReceptorAnterior1987, title = {The {{D2-dopamine}} Receptor of Anterior Pituitary Is Functionally Associated with a Pertussis Toxin-Sensitive Guanine Nucleotide Binding Protein.}, author = {Senogles, S. E. and Benovic, J. L. and Amlaiky, N.}, year = 1987, month = apr, journal = {Journal of Biological }, volume = {262}, number = {10}, pages = {4860–7}, url = {http://www.jbc.org/content/262/10/4860.short}, abstract = {Dopaminergic inhibition of prolactin release from the anterior pituitary may be mediated through both the adenylate cyclase and Ca2+ mobilization/phosphoinositide pathways. The D2-dopamine receptor of the bovine anterior pituitary has been partially purified by affinity chromatography on CMOS-Sepharose (immobilized carboxymethyleneoximinospiperone). Reinsertion of these partially purified receptor preparations into phospholipid vesicles reconstituted guanine nucleotide-sensitive high affinity agonist binding, agonist-promoted GTPase and 35S-labeled guanosine 5’-O-(thiotriphosphate) [( 35S]GTP gamma S) binding activity in these preparations. Pertussis toxin treatment of the purified receptor preparation abolished agonist-stimulated GTPase and guanine nucleotide-sensitive high affinity agonist binding. These observations suggest that the receptor copurifies with an endogenous, pertussis toxin-sensitive guanine nucleotide binding protein (N). [32P]ADP-ribosylation of affinity-purified D2 receptor preparations by pertussis toxin revealed the presence of a substrate of Mr 39,000-40,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Peptide maps generated using elastase of the [32P]ADP-ribosylated endogenous N protein, transducin, and Ni and No from brain revealed similarities but not identity between the endogenous pituitary N protein and brain Ni and No. Immunoblotting of the partially purified D2 receptor preparations showed an Mr 39,000-40,000 band with an Ni-specific antiserum raised against a synthetic peptide, and with RV3, an No-specific anti-serum, but not with CW6, an antiserum strongly reactive with brain Ni. Several lines of evidence indicate that endogenous pituitary N protein is functionally coupled to the D2 receptor. As measured by [35S]GTP gamma S binding, ratios of 0.2-0.6 mol N protein/mol receptor were observed. Association of N protein with the D2 receptor was increased by agonist pretreatment and decreased by guanine nucleotides. These results suggest that No and/or a form of Ni distinct from the Mr 41,000 pertussis toxin substrate (Ni) is the predominant N protein functionally coupled with the D2-dopamine receptor of anterior pituitary.}, keywords = {nosource} }

@article{palczewskiCrystalStructureRhodopsin2000, title = {Crystal Structure of Rhodopsin: {{AG}} Protein-Coupled Receptor}, author = {Palczewski, K. and Kumasaka, T. and Hori, T.}, year = 2000, month = aug, journal = {science}, volume = {289}, number = {5480}, pages = {739–745}, doi = {10.1126/science.289.5480.739}, url = {http://www.sciencemag.org/content/289/5480/739.short}, keywords = {nosource} }

@article{maggioImpactProteinCoupled2005, title = {The Impact of {{G}}-protein-coupled Receptor Hetero-oligomerization on Function and Pharmacology}, author = {Maggio, Roberto and Novi, Francesca and Scarselli, Marco and Corsini, G. U.}, year = 2005, month = jun, journal = {Febs Journal}, volume = {272}, number = {12}, pages = {2939–46}, doi = {10.1111/j.1742-4658.2005.04729.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2005.04729.x/full}, abstract = {Although highly controversial just a few years ago, the idea that G-protein-coupled receptors (GPCRs) may undergo homo-oligomerization or hetero-oligomerization has recently gained considerable attention. The recognition that GPCRs may exhibit either dimeric or oligomeric structures is based on a number of different biochemical and biophysical approaches. Although much effort has been spent to demonstrate the mechanism(s) by which GPCRs interact with each other, the physiological relevance of this phenomenon remains elusive. An additional source of uncertainty stems from the realization that homo-oligomerization and hetero-oligomerization of GPCRs may affect receptor binding and activity in different ways, depending on the type of interacting receptors. In this brief review, the functional and pharmacological effects of the hetero-oligomerization of GPCR on binding and cell signaling are critically analyzed.}, keywords = {nosource} }

@article{kiltsFunctionalSelectivityDopamine2002, title = {Functional Selectivity of Dopamine Receptor Agonists. {{II}}. {{Actions}} of Dihydrexidine in {{D2L}} Receptor-Transfected {{MN9D}} Cells and Pituitary Lactotrophs}, author = {Kilts, J. D. and Connery, H. S. and Arrington, E. G.}, year = 2002, month = jun, journal = { of Pharmacology and }, volume = {301}, number = {3}, pages = {1179–1189}, publisher = {AMER SOC PHARMACOLOGY EXPERIMENTAL THERAPEUTICS}, doi = {10.1124/jpet.301.3.1179}, url = {http://jpet.aspetjournals.org/content/301/3/1179.short}, abstract = {D(2)-like dopamine receptors mediate functional changes via activation of inhibitory G proteins, including those that affect adenylate cyclase activity, and potassium and calcium channels. Although it is assumed that the binding of a drug to a single isoform of a D(2)-like receptor will cause similar changes in all receptor-mediated functions, it has been demonstrated in brain that the dopamine agonists dihydrexidine (DHX) and N-n-propyl-DHX are functionally selective\textbraceleft ''\textbraceright. The current study explores the underlying mechanism using transfected MN9D cells and D(2)-producing anterior pituitary lactotrophs. Both dopamine and DHX inhibited adenylate cyclase activity in a concentration-dependent manner in both systems, effects blocked by D(2), but not D(1), antagonists. In the MN9D cells, quinpirole and R-(-) N- propylnorapomorphine (NPA) also inhibited the K(+) stimulated release of \textbraceleft [\textbraceright (3)H] dopamine in a concentration-responsive, antagonist-reversible manner. Conversely, neither DHX, nor its analogs, inhibited K(+)-stimulated \textbraceleft [\textbraceright (3)H] dopamine release, although they antagonized the effects of quinpirole. S-(+)-NPA actually had the reverse functional selectivity profile from DHX (i.e., it was a full agonist at D(2L) receptors coupled to inhibition of dopamine release, but a weak partial agonist at D(2L) receptor-mediated inhibition of adenylate cyclase). In lactotrophs, DHX had little intrinsic activity at D(2) receptors coupled to G protein-coupled inwardly rectifying potassium channels, and actually antagonized the effects of dopamine at these D(2) receptors. Together, these findings provide compelling evidence for agonist-induced functional selectivity with the D(2L) receptor. Although the underlying molecular mechanism is controversial (e.g.,conformational induction’‘ versus drug-active state selection\textbraceleft ''\textbraceright ), such data are irreconcilable with the widely held view that drugs haveintrinsic efficacy’’.}, keywords = {nosource} }

@article{straussmanDevelopmentalProgrammingCpG2009, title = {Developmental Programming of {{CpG}} Island Methylation Profiles in the Human Genome.}, author = {Straussman, Ravid and Nejman, Deborah and Roberts, Douglas and Steinfeld, Israel and Blum, Barak and Benvenisty, Nissim and Simon, Itamar and Yakhini, Zohar and Cedar, Howard}, year = 2009, month = may, journal = {Nature structural & molecular biology}, volume = {16}, number = {5}, eprint = {19377480}, eprinttype = {pubmed}, pages = {564–71}, issn = {1545-9985}, doi = {10.1038/nsmb.1594}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19377480}, abstract = {CpG island-like sequences are commonly thought to provide the sole signals for designating constitutively unmethylated regions in the genome, thus generating open chromatin domains within a sea of global repression. Using a new database obtained from comprehensive microarray analysis, we show that unmethylated regions (UMRs) seem to be formed during early embryogenesis, not as a result of CpG-ness, but rather through the recognition of specific sequence motifs closely associated with transcription start sites. This same system probably brings about the resetting of pluripotency genes during somatic cell reprogramming. The data also reveal a new class of nonpromoter UMRs that become de novo methylated in a tissue-specific manner during development, and this process may be involved in gene regulation. In short, we show that UMRs are an important aspect of genome structure that have a dynamic role in development.}, pmid = {19377480}, keywords = {Algorithms,CpG Islands,CpG Islands: genetics,DNA Methylation,Embryonic Development,Embryonic Development: genetics,Genome,Human,Human: genetics,Humans,nosource,Nucleic Acid,Nucleic Acid: genetics,Oligonucleotide Array Sequence Analysis,Organ Specificity,Organ Specificity: genetics,Pluripotent Stem Cells,Pluripotent Stem Cells: metabolism,Regulatory Sequences,Transcription Initiation Site} }

@article{cedarProgrammingDNAMethylation2012, title = {Programming of {{DNA}} Methylation Patterns}, author = {Cedar, Howard and Bergman, Yehudit}, year = 2012, journal = {Annual review of biochemistry}, doi = {10.1146/annurev-biochem-052610}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev-biochem-052610-091920}, keywords = {chromatin,development,maintenance,nosource,repression,reprogramming} }

@article{hermannBiochemistryBiologyMammalian2004, title = {Biochemistry and Biology of Mammalian {{DNA}} Methyltransferases.}, author = {Hermann, a and Gowher, H. and Jeltsch, a}, year = 2004, month = oct, journal = {Cellular and molecular life sciences : CMLS}, volume = {61}, number = {19-20}, eprint = {15526163}, eprinttype = {pubmed}, pages = {2571–87}, issn = {1420-682X}, doi = {10.1007/s00018-004-4201-1}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15526163}, abstract = {DNA methylation is a stable but not irreversible epigenetic signal that silences gene expression. It has a variety of important functions in mammals, including control of gene expression, cellular differentiation and development, preservation of chromosomal integrity, parental imprinting and X-chromosome inactivation. In addition, it has been implicated in brain function and the development of the immune system. Somatic alterations in genomic methylation patterns contribute to the etiology of human cancers and ageing. It is tightly interwoven with the modification of histone tails and other epigenetic signals. Here we review our current understanding of the molecular enzymology of the mammalian DNA methyltransferases Dnmt1, Dnmt3a, Dnmt3b and Dnmt2 and the roles of the enzymes in the above-mentioned biological processes.}, isbn = {0001800442}, pmid = {15526163}, keywords = {Animals,DNA (Cytosine-5-)-Methyltransferase,DNA (Cytosine-5-)-Methyltransferase: chemistry,DNA (Cytosine-5-)-Methyltransferase: metabolism,DNA (Cytosine-5-)-Methyltransferase: physiology,DNA Methylation,Enzymologic,Gene Expression Regulation,Genetic,Humans,Models,nosource,Signal Transduction} }

@article{gruenbaumSubstrateSequenceSpecificity1982, title = {Substrate and Sequence Specificity of a Eukaryotic {{DNA}} Methylase}, author = {Gruenbaum, Y. and Cedar, H. and Razin, A.}, year = 1982, journal = {Science}, url = {http://www.nature.com/nature/journal/v295/n5850/abs/295620a0.html}, keywords = {nosource} }

@article{pesoleUTRdbUTRsiteSpecialized2002, title = {{{UTRdb}} and {{UTRsite}}: Specialized Databases of Sequences and Functional Elements of 5’ and 3’ Untranslated Regions of Eukaryotic {{mRNAs}}. {{Update}} 2002.}, author = {Pesole, Graziano and Liuni, Sabino and Grillo, Giorgio and Licciulli, Flavio and Mignone, Flavio and Gissi, Carmela and Saccone, Cecilia}, year = 2002, month = jan, journal = {Nucleic acids research}, volume = {30}, number = {1}, pages = {335–40}, issn = {1362-4962}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=99102&tool=pmcentrez&rendertype=abstract}, abstract = {The 5’- and 3’-untranslated regions (5’- and 3’-UTRs) of eukaryotic mRNAs are known to play a crucial role in post-transcriptional regulation of gene expression modulating nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and stability. UTRdb is a specialized database of 5’ and 3’ untranslated sequences of eukaryotic mRNAs cleaned from redundancy. UTRdb entries are enriched with specialized information not present in the primary databases including the presence of nucleotide sequence patterns already demonstrated by experimental analysis to have some functional role. All these patterns have been collected in the UTRsite database so that it is possible to search any input sequence for the presence of annotated functional motifs. Furthermore, UTRdb entries have been annotated for the presence of repetitive elements. All Internet resources we implemented for retrieval and functional analysis of 5’- and 3’-UTRs of eukaryotic mRNAs are accessible at http://bighost.area.ba.cnr.it/BIG/UTRHome/.}, pmid = {11752330}, keywords = {3’ Untranslated Regions,5’ Untranslated Regions,Animals,Database Management Systems,Databases,Eukaryotic Cells,Eukaryotic Cells: metabolism,Humans,Information Storage and Retrieval,Internet,Messenger,Messenger: genetics,nosource,Nucleic Acid,Regulatory Sequences,Repetitive Sequences,Response Elements,RNA} }

@article{ganTertiaryStructurebasedAnalysis2013, title = {Tertiary Structure-Based Analysis of {{microRNA}}–Target Interactions}, author = {Gan, H. H. and Gunsalus, K. C.}, year = 2013, journal = {RNA}, pages = {539–551}, doi = {10.1261/rna.035691.112.3}, url = {http://rnajournal.cshlp.org/content/19/4/539.short}, keywords = {argonaute,duplex binding free energy,entropy of duplex formation,microrna,mirna,mirna tertiary structures,nosource} }

@article{liGlobalProfilingMiRNAs2013, title = {Global Profiling of {{miRNAs}} and the Hairpin Precursors: Insights into {{miRNA}} Processing and Novel {{miRNA}} Discovery.}, author = {Li, Na and You, Xintian and Chen, Tao and Mackowiak, Sebastian D. and Friedl{"a}nder, Marc R. and Weigt, Martina and Du, Hang and {Gogol-D{"o}ring}, Andreas and Chang, Zisong and Dieterich, Christoph and Hu, Yuhui and Chen, Wei}, year = 2013, month = feb, journal = {Nucleic acids research}, volume = {41}, number = {6}, eprint = {23396444}, eprinttype = {pubmed}, pages = {3619–3634}, issn = {1362-4962}, doi = {10.1093/nar/gkt072}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23396444}, abstract = {MicroRNAs (miRNAs) constitute an important class of small regulatory RNAs that are derived from distinct hairpin precursors (pre-miRNAs). In contrast to mature miRNAs, which have been characterized in numerous genome-wide studies of different organisms, research on global profiling of pre-miRNAs is limited. Here, using massive parallel sequencing, we have performed global characterization of both mouse mature and precursor miRNAs. In total, 87 369 704 and 252 003 sequencing reads derived from 887 mature and 281 precursor miRNAs were obtained, respectively. Our analysis revealed new aspects of miRNA/pre-miRNA processing and modification, including eight Ago2-cleaved pre-miRNAs, eight new instances of miRNA editing and exclusively 5’ tailed mirtrons. Furthermore, based on the sequences of both mature and precursor miRNAs, we developed a miRNA discovery pipeline, miRGrep, which does not rely on the availability of genome reference sequences. In addition to 239 known mouse pre-miRNAs, miRGrep predicted 41 novel ones with high confidence. Similar as known ones, the mature miRNAs derived from most of these novel loci showed both reduced abundance following Dicer knockdown and the binding with Argonaute2. Evaluation on data sets obtained from Caenorhabditis elegans and Caenorhabditis sp.11 demonstrated that miRGrep could be widely used for miRNA discovery in metazoans, especially in those without genome reference sequences.}, pmid = {23396444}, keywords = {nosource} }

@book{careyTranscriptionalRegulationEukaryotes2000, title = {Transcriptional Regulation in Eukaryotes}, author = {Carey, Michael and Smale, S. T.}, year = 2000, url = {http://download.nehudlit.ru/area001/self0008/carey.rar}, isbn = {0-87969-537-4}, keywords = {nosource} } % == BibTeX quality report for careyTranscriptionalRegulationEukaryotes2000: % Missing required field ‘publisher’

@article{liWidespreadRNADNA2011, title = {Widespread {{RNA}} and {{DNA}} Sequence Differences in the Human Transcriptome.}, author = {Li, Mingyao and Wang, Isabel X. and Li, Yun and Bruzel, Alan and Richards, Allison L. and Toung, Jonathan M. and Cheung, Vivian G.}, year = 2011, month = jul, journal = {Science (New York, N.Y.)}, volume = {333}, number = {6038}, pages = {53–8}, issn = {1095-9203}, doi = {10.1126/science.1207018}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3204392&tool=pmcentrez&rendertype=abstract}, abstract = {The transmission of information from DNA to RNA is a critical process. We compared RNA sequences from human B cells of 27 individuals to the corresponding DNA sequences from the same individuals and uncovered more than 10,000 exonic sites where the RNA sequences do not match that of the DNA. All 12 possible categories of discordances were observed. These differences were nonrandom as many sites were found in multiple individuals and in different cell types, including primary skin cells and brain tissues. Using mass spectrometry, we detected peptides that are translated from the discordant RNA sequences and thus do not correspond exactly to the DNA sequences. These widespread RNA-DNA differences in the human transcriptome provide a yet unexplored aspect of genome variation.}, pmid = {21596952}, keywords = {Adult,Aged,Amino Acid Sequence,B-Lymphocytes,Base Sequence,Cell Line,Cerebral Cortex,Cerebral Cortex: cytology,DNA,DNA: chemistry,DNA: genetics,Exons,Expressed Sequence Tags,Fibroblasts,Gene Expression Profiling,Genetic Variation,Genome,Genotype,Human,Humans,Mass Spectrometry,Messenger,Messenger: chemistry,Messenger: genetics,Middle Aged,Molecular Sequence Data,nosource,Polymorphism,Protein Biosynthesis,Proteins,Proteins: chemistry,Proteome,Proteome: chemistry,RNA,Sequence Analysis,Single Nucleotide,Skin,Skin: cytology,Untranslated Regions} } % == BibTeX quality report for liWidespreadRNADNA2011: % ? Possibly abbreviated journal title Science (New York, N.Y.)

@article{khairulinaEukaryotespecificMotifRibosomal2010, title = {Eukaryote-Specific Motif of Ribosomal Protein {{S15}} Neighbors {{A}} Site Codon during Elongation and Termination of Translation.}, author = {Khairulina, Julia and Graifer, Dmitri and Bulygin, Konstantin and Ven’yaminova, Aliya and Frolova, Ludmila and Karpova, Galina}, year = 2010, month = jul, journal = {Biochimie}, volume = {92}, number = {7}, eprint = {20206660}, eprinttype = {pubmed}, pages = {820–825}, publisher = {Elsevier Masson SAS}, issn = {1638-6183}, doi = {10.1016/j.biochi.2010.02.031}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20206660}, abstract = {The eukaryotic ribosomal protein S15 is a key component of the decoding site in contrast to its prokaryotic counterpart, S19p, which is located away from the mRNA binding track on the ribosome. Here, we determined the oligopeptide of S15 neighboring the A site mRNA codon on the human 80S ribosome with the use of mRNA analogues bearing perfluorophenyl azide-modified nucleotides in the sense or stop codon targeted to the 80S ribosomal A site. The protein was cross-linked to mRNA analogues in specific ribosomal complexes that were obtained in the presence of eRF1 in the experiments with mRNAs bearing stop codon. Digestion of modified S15 with various specific proteolytic agents followed by identification of the resulting modified oligopeptides showed that cross-link was in C-terminal fragment in positions 131-145, most probably, in decapeptide 131-PGIGATHSSR-140. The position of cross-linking site on the S15 protein did not depend on the nature of the A site-bound codon (sense or stop codon) and on the presence of polypeptide chain release factor eRF1 in the ribosomal complexes with mRNA analogues bearing a stop codon. The results indicate an involvement of the mentioned decapeptide in the formation of the ribosomal decoding site during elongation and termination of translation. Alignment of amino acid sequences of eukaryotic S15 and its prokaryotic counterpart, S19p from eubacteria and archaea, revealed that decapeptide PGIGATHSSR in positions 131-140 is strongly conserved in eukaryotes and has minor variations in archaea but has no homology with any sequence in C-terminal part of eubacterial S19p, which suggests involvement of the decapeptide in the translation process in a eukaryote-specific manner.}, pmid = {20206660}, keywords = {Amino Acid,Amino Acid Motifs,Amino Acid Sequence,Animals,Archaea,Codon,Codon: genetics,Codon: metabolism,Cyanogen Bromide,Cyanogen Bromide: metabolism,Eukaryota,Humans,Messenger,Messenger: genetics,Messenger: metabolism,Models,Molecular,Molecular Sequence Data,nosource,Oligopeptides,Oligopeptides: chemistry,Oligopeptides: metabolism,Peptide Fragments,Peptide Fragments: chemistry,Peptide Fragments: metabolism,Protein Biosynthesis,Protein Conformation,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: metabolism,RNA,Sequence Homology,Species Specificity} }

@article{pavon-eternodOverexpressionInitiatorMethionine2013, title = {Overexpression of Initiator Methionine {{tRNA}} Leads to Global Reprogramming of {{tRNA}} Expression and Increased Proliferation in Human Epithelial Cells}, author = {{Pavon-Eternod}, M. and Gomes, Suzana and Rosner, M. R. and Pan, T.}, year = 2013, journal = {RNA}, pages = {461–466}, doi = {10.1261/rna.037507.112.malignant}, url = {http://rnajournal.cshlp.org/content/early/2013/02/18/rna.037507.112.short}, keywords = {initiator methionine trna,nosource,trna,trna microarrays} }

@article{gloverDNABreakSite2013, title = {{{DNA Break Site}} at {{Fragile Subtelomeres Determines Probability}} and {{Mechanism}} of {{Antigenic Variation}} in {{African Trypanosomes}}}, author = {Glover, Lucy and Alsford, Sam and Horn, David}, editor = {Hill, Kent L.}, year = 2013, month = mar, journal = {PLoS Pathogens}, volume = {9}, number = {3}, pages = {e1003260}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1003260}, url = {http://dx.plos.org/10.1371/journal.ppat.1003260}, keywords = {nosource} } % == BibTeX quality report for gloverDNABreakSite2013: % ? Title looks like it was stored in title-case in Zotero

@article{memczakCircularRNAsAre2013, title = {Circular {{RNAs}} Are a Large Class of Animal {{RNAs}} with Regulatory Potency}, author = {Memczak, Sebastian and Jens, Marvin and Elefsinioti, Antigoni and Torti, Francesca and Krueger, Janna and Rybak, Agnieszka and Maier, Luisa and Mackowiak, Sebastian D. and Gregersen, Lea H. and Munschauer, Mathias and Loewer, Alexander and Ziebold, Ulrike and Landthaler, Markus and Kocks, Christine and {}le Noble, Ferdinand and Rajewsky, Nikolaus}, year = 2013, month = feb, journal = {Nature}, volume = {495}, number = {7441}, pages = {333–338}, publisher = {Nature Publishing Group}, issn = {0028-0836}, doi = {10.1038/nature11928}, url = {http://www.nature.com/doifinder/10.1038/nature11928}, keywords = {nosource} }

@article{seidlCircularizedSyntheticOligodeoxynucleotides2013, title = {Circularized Synthetic Oligodeoxynucleotides Serve as Promoterless {{RNA}} Polymerase {{III}} Templates for Small {{RNA}} Generation in Human Cells.}, author = {Seidl, Christine I. and Lama, Lodoe and Ryan, Kevin}, year = 2013, month = feb, journal = {Nucleic acids research}, volume = {41}, number = {4}, pages = {2552–64}, issn = {1362-4962}, doi = {10.1093/nar/gks1334}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3575851&tool=pmcentrez&rendertype=abstract}, abstract = {Synthetic RNA formulations and viral vectors are the two main approaches for delivering small therapeutic RNA to human cells. Here we report findings supporting an alternative strategy in which an endogenous human RNA polymerase (RNAP) is harnessed to make RNA hairpin-containing small RNA from synthetic single-stranded DNA oligonucleotides. We report that circularizing a DNA template strand encoding a pre-microRNA hairpin mimic can trigger its circumtranscription by human RNAP III in vitro and in human cells. Sequence and secondary structure preferences that appear to promote productive transcription are described. The circular topology of the template is required for productive transcription, at least in part, to stabilize the template against exonucleases. In contrast to bacteriophage and Escherichia coli RNAPs, human RNAPs do not carry out rolling circle transcription on circularized templates. While transfected DNA circles distribute between the nucleus and cytosol, their transcripts are found mainly in the cytosol. Circularized oligonucleotides are synthetic, free of the hazards of viral vectors and maintain small RNA information in a stable form that RNAP III can access in a cellular context with, in some cases, near promoter-like precision and biologically relevant efficiency.}, pmid = {23275570}, keywords = {nosource} }

@article{waldmannMultifacetedRegulationInterleukin151999, title = {The Multifaceted Regulation of Interleukin-15 Expression and the Role of This Cytokine in {{NK}} Cell Differentiation and Host Response to Intracellular Pathogens.}, author = {{}a Waldmann, T. and Tagaya, Y.}, year = 1999, month = jan, journal = {Annual review of immunology}, volume = {17}, eprint = {10358752}, eprinttype = {pubmed}, pages = {19–49}, issn = {0732-0582}, doi = {10.1146/annurev.immunol.17.1.19}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10358752}, abstract = {Interleukin-15 (IL-15) is a 14- to 15-kDa member of the 4 alpha-helix bundle family of cytokines. IL-15 expression is controlled at the levels of transcription, translation, and intracellular trafficking. In particular, IL-15 protein is posttranscriptionally regulated by multiple controlling elements that impede translation, including 12 upstream AUGs of the 5’ UTR, 2 unusual signal peptides, and the C-terminus of the mature protein. IL-15 uses two distinct receptor and signaling pathways. In T and NK cells the IL-15 receptor includes IL-2/15R beta and gamma c subunits, which are shared with IL-2, and an IL-15-specific receptor subunit, IL-15R alpha. Mast cells respond to IL-15 with a receptor system that does not share elements with the IL-2 receptor but uses a novel 60- to 65-kDa IL-15RX subunit. In mast cells IL-15 signaling involves Jak2/STAT5 activation rather than the Jak1/Jak3 and STAT5/STAT3 system used in activated T cells. In addition to its other functional activities in immune and nonimmune cells, IL-15 plays a pivotal role in the development, survival, and function of NK cells. Abnormalities of IL-15 expression have been described in patients with rheumatoid arthritis or inflammatory bowel disease and in diseases associated with the retroviruses HIV and HTLV-I. New approaches directed toward IL-15, its receptor, or its signaling pathway may be of value in the therapy of these disorders.}, pmid = {10358752}, keywords = {Animals,Autoimmune Diseases,Autoimmune Diseases: immunology,Base Sequence,Cell Differentiation,Complementary,Complementary: genetics,DNA,Gene Expression Regulation,Humans,Immunosuppression,Immunotherapy,Inflammation,Inflammation: immunology,Interleukin-15,Interleukin-15: genetics,Interleukin-15: physiology,Interleukin-2,Interleukin-2: physiology,Killer Cells,Natural,Natural: cytology,Natural: immunology,Neoplasms,Neoplasms: immunology,nosource,Receptors,Retroviridae Infections,Retroviridae Infections: immunology,Signal Transduction} }

@article{bartholomeuGenomicOrganizationExpression2009, title = {Genomic Organization and Expression Profile of the Mucin-Associated Surface Protein (Masp) Family of the Human Pathogen {{Trypanosoma}} Cruzi}, author = {Bartholomeu, D. C. and Cerqueira, G. C.}, year = 2009, month = jun, journal = {Nucleic acids Research}, volume = {37}, number = {10}, pages = {3407–17}, issn = {1362-4962}, doi = {10.1093/nar/gkp172}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2691823&tool=pmcentrez&rendertype=abstract http://nar.oxfordjournals.org/content/37/10/3407.short}, abstract = {A novel large multigene family was recently identified in the human pathogen Trypanosoma cruzi, causative agent of Chagas disease, and corresponds to approximately 6% of the parasite diploid genome. The predicted gene products, mucin-associated surface proteins (MASPs), are characterized by highly conserved N- and C-terminal domains and a strikingly variable and repetitive central region. We report here an analysis of the genomic organization and expression profile of masp genes. Masps are not randomly distributed throughout the genome but instead are clustered with genes encoding mucin and other surface protein families. Masp transcripts vary in size, are preferentially expressed during the trypomastigote stage and contain highly conserved 5’ and 3’ untranslated regions. A sequence analysis of a trypomastigote cDNA library reveals the expression of multiple masp variants with a bias towards a particular masp subgroup. Immunofluorescence assays using antibodies generated against a MASP peptide reveals that the expression of particular MASPs at the cell membrane is limited to subsets of the parasite population. Western blots of phosphatidylinositol-specific phospholipase C (PI-PLC)-treated parasites suggest that MASP may be GPI-anchored and shed into the medium culture, thus contributing to the large repertoire of parasite polypeptides that are exposed to the host immune system.}, pmid = {19336417}, keywords = {3’ Flanking Region,5’ Flanking Region,Amino Acid Sequence,Animals,Base Sequence,Conserved Sequence,Gene Expression Profiling,Genes,Genome,Membrane Proteins,Membrane Proteins: chemistry,Membrane Proteins: genetics,Membrane Proteins: metabolism,Messenger,Messenger: chemistry,Messenger: metabolism,Molecular Sequence Data,Mucins,Mucins: genetics,Multigene Family,nosource,Protozoan,Protozoan Proteins,Protozoan Proteins: chemistry,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,RNA,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosoma cruzi: growth & development,Trypanosoma cruzi: metabolism} }

@article{sultanSimpleStrandspecificRNASeq2012, title = {A Simple Strand-Specific {{RNA-Seq}} Library Preparation Protocol Combining the {{Illumina TruSeq RNA}} and the {{dUTP}} Methods.}, author = {Sultan, Marc and D{"o}kel, Simon and Amstislavskiy, Vyacheslav and Wuttig, Daniela and S{"u}ltmann, Holger and Lehrach, Hans and Yaspo, Marie-Laure}, year = 2012, month = jun, journal = {Biochemical and biophysical research communications}, volume = {422}, number = {4}, eprint = {22609201}, eprinttype = {pubmed}, pages = {643–6}, publisher = {Elsevier Inc.}, issn = {1090-2104}, doi = {10.1016/j.bbrc.2012.05.043}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22609201}, abstract = {Preserving the original RNA orientation information in RNA-Sequencing (RNA-Seq) experiment is essential to the analysis and understanding of the complexity of mammalian transcriptomes. We describe herein a simple, robust, and time-effective protocol for generating strand-specific RNA-seq libraries suited for the Illumina sequencing platform. We modified the Illumina TruSeq RNA sample preparation by implementing the strand specificity feature using the dUTP method. This protocol uses low amounts of starting material and allows a fast processing within two days. It can be easily implemented and requires only few additional reagents to the original Illumina kit.}, pmid = {22609201}, keywords = {Deoxyuracil Nucleotides,Deoxyuracil Nucleotides: chemistry,Deoxyuracil Nucleotides: genetics,Gene Expression Profiling,Gene Expression Profiling: methods,Gene Library,Humans,nosource,RNA,RNA: methods,Sequence Analysis,Transcriptome} }

@article{roblesEfficientExperimentalDesign2012, title = {Efficient Experimental Design and Analysis Strategies for the Detection of Differential Expression Using {{RNA-Sequencing}}}, author = {Robles, J. A. and Qureshi, S. E. and Stephen, S. J.}, year = 2012, month = sep, journal = {BMC }, volume = {13}, number = {1}, pages = {484}, doi = {10.1186/1471-2164-13-484}, url = {http://www.biomedcentral.com/1471-2164/13/484}, abstract = {ABSTRACT: BACKGROUND: RNA sequencing (RNA-Seq) has emerged as a powerful approach for the detection of differential gene expression with both high-throughput and high resolution capabilities possible depending upon the experimental design chosen. Multiplex experimental designs are now readily available, these can be utilised to increase the numbers of samples or replicates profiled at the cost of decreased sequencing depth generated per sample. These strategies impact on the power of the approach to accurately identify differential expression. This study presents a detailed analysis of the power to detect differential expression in a range of scenarios including simulated null and differential expression distributions with varying numbers of biological or technical replicates, sequencing depths and analysis methods. RESULTS: Differential and non-differential expression datasets were simulated using a combination of negative binomial and exponential distributions derived from real RNA-Seq data. These datasets were used to evaluate the performance of three commonly used differential expression analysis algorithms and to quantify the changes in power with respect to true and false positive rates when simulating variations in sequencing depth, biological replication and multiplex experimental design choices. CONCLUSIONS: This work quantitatively explores comparisons between contemporary analysis tools and experimental design choices for the detection of differential expression using RNA-Seq. We found that the DESeq algorithm performs more conservatively than edgeR and NBPSeq. With regard to testing of various experimental designs, this work strongly suggests that greater power is gained through the use of biological replicates relative to library (technical) replicates and sequencing depth. Strikingly, sequencing depth could be reduced as low as 15% without substantial impacts on false positive or true positive rates.}, keywords = {nosource} }

@article{claytonChagasDisease1012010, title = {Chagas Disease 101}, author = {Clayton, Julie}, year = 2010, journal = {Nature}, pages = {S4 - S5}, url = {http://www.nature.com/nature/journal/v465/n7301_supp/full/nature09220.html}, keywords = {nosource} }

@article{araujoRegulatoryElementsInvolved2011, title = {Regulatory Elements Involved in the Post-Transcriptional Control of Stage-Specific Gene Expression in {{Trypanosoma}} Cruzi: A Review}, author = {Ara{'u}jo, P. R. and Teixeira, S. M.}, year = 2011, month = may, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {106}, number = {3}, pages = {257–66}, url = {http://www.scielo.br/scielo.php?pid=S0074-02762011000300002&script=sci_arttext}, abstract = {Trypanosoma cruzi, a protozoan parasite that causes Chagas disease, exhibits unique mechanisms for gene expression such as constitutive polycistronic transcription of protein-coding genes, RNA editing and trans-splicing. In the absence of mechanism controlling transcription initiation, organized subsets of T. cruzi genes must be post-transcriptionally co-regulated in response to extracellular signals. The mechanisms that regulate stage-specific gene expression in this parasite have become much clearer through sequencing its whole genome as well as performing various proteomic and microarray analyses, which have demonstrated that at least half of the T. cruzi genes are differentially regulated during its life cycle. In this review, we attempt to highlight the recent advances in characterising cis and trans-acting elements in the T. cruzi genome that are involved in its post-transcriptional regulatory machinery.}, keywords = {nosource} }

@article{caradonnaHostMetabolismRegulates2013, title = {Host Metabolism Regulates Intracellular Growth of {{Trypanosoma}} Cruzi.}, author = {Caradonna, Kacey L. and Engel, Juan C. and Jacobi, David and Lee, Chih-Hao and {}a Burleigh, Barbara}, year = 2013, month = jan, journal = {Cell host & microbe}, volume = {13}, number = {1}, eprint = {23332160}, eprinttype = {pubmed}, pages = {108–17}, publisher = {Elsevier Inc.}, issn = {1934-6069}, doi = {10.1016/j.chom.2012.11.011}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23332160}, abstract = {Metabolic coupling of intracellular pathogens with host cells is essential for successful colonization of the host. Establishment of intracellular infection by the protozoan Trypanosoma cruzi leads to the development of human Chagas’ disease, yet the functional contributions of the host cell toward the infection process remain poorly characterized. Here, a genome-scale functional screen identified interconnected metabolic networks centered around host energy production, nucleotide metabolism, pteridine biosynthesis, and fatty acid oxidation as key processes that fuel intracellular T. cruzi growth. Additionally, the host kinase Akt, which plays essential roles in various cellular processes, was critical for parasite replication. Targeted perturbations in these host metabolic pathways or Akt-dependent signaling pathways modulated the parasite’s replicative capacity, highlighting the adaptability of this intracellular pathogen to changing conditions in the host. These findings identify key cellular process regulating intracellular T. cruzi growth and illuminate the potential to leverage host pathways to limit T. cruzi infection.}, pmid = {23332160}, keywords = {nosource} }

@article{dasEssentialPolysomeassociatedRNAbinding2012, title = {The Essential Polysome-Associated {{RNA-binding}} Protein {{RBP42}} Targets {{mRNAs}} Involved in {{Trypanosoma}} Brucei Energy Metabolism.}, author = {Das, Anish and Morales, Rachel and Banday, Mahrukh and Garcia, Stacey and Hao, Li and Cross, George a M. and Estevez, Antonio M. and Bellofatto, Vivian}, year = 2012, month = nov, journal = {RNA}, volume = {18}, number = {11}, eprint = {22966087}, eprinttype = {pubmed}, pages = {1968–83}, issn = {1469-9001}, doi = {10.1261/rna.033829.112}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22966087}, abstract = {RNA-binding proteins that target mRNA coding regions are emerging as regulators of post-transcriptional processes in eukaryotes. Here we describe a newly identified RNA-binding protein, RBP42, which targets the coding region of mRNAs in the insect form of the African trypanosome, Trypanosoma brucei. RBP42 is an essential protein and associates with polysome-bound mRNAs in the cytoplasm. A global survey of RBP42-bound mRNAs was performed by applying HITS-CLIP technology, which captures protein-RNA interactions in vivo using UV light. Specific RBP42-mRNA interactions, as well as mRNA interactions with a known RNA-binding protein, were purified using specific antibodies. Target RNA sequences were identified and quantified using high-throughput RNA sequencing. Analysis revealed that RBP42 bound mainly within the coding region of mRNAs that encode proteins involved in cellular energy metabolism. Although the mechanism of RBP42’s function is unclear at present, we speculate that RBP42 plays a critical role in modulating T. brucei energy metabolism.}, pmid = {22966087}, keywords = {3’ Untranslated Regions,Amino Acid,Amino Acid Sequence,Binding Sites,Energy Metabolism,Energy Metabolism: genetics,Gene Expression Regulation,Gene Knockdown Techniques,Messenger,Messenger: metabolism,Molecular Sequence Data,nosource,Open Reading Frames,Polyribosomes,Polyribosomes: metabolism,Protein Binding,Protein Structure,Protozoan,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: isolation & purification,Protozoan Proteins: metabolism,Protozoan: metabolism,RNA,RNA Interference,RNA-Binding Proteins,RNA-Binding Proteins: genetics,RNA-Binding Proteins: isolation & purification,RNA-Binding Proteins: metabolism,Sequence Homology,Tertiary,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: growth & development,Trypanosoma brucei brucei: metabolism} }

@article{patelNGSQCToolkit2012, title = {{{NGS QC Toolkit}}: A Toolkit for Quality Control of next Generation Sequencing Data.}, author = {Patel, Ravi K. and Jain, Mukesh}, year = 2012, month = jan, journal = {PloS one}, volume = {7}, number = {2}, pages = {e30619}, issn = {1932-6203}, doi = {10.1371/journal.pone.0030619}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3270013&tool=pmcentrez&rendertype=abstract}, abstract = {Next generation sequencing (NGS) technologies provide a high-throughput means to generate large amount of sequence data. However, quality control (QC) of sequence data generated from these technologies is extremely important for meaningful downstream analysis. Further, highly efficient and fast processing tools are required to handle the large volume of datasets. Here, we have developed an application, NGS QC Toolkit, for quality check and filtering of high-quality data. This toolkit is a standalone and open source application freely available at http://www.nipgr.res.in/ngsqctoolkit.html. All the tools in the application have been implemented in Perl programming language. The toolkit is comprised of user-friendly tools for QC of sequencing data generated using Roche 454 and Illumina platforms, and additional tools to aid QC (sequence format converter and trimming tools) and analysis (statistics tools). A variety of options have been provided to facilitate the QC at user-defined parameters. The toolkit is expected to be very useful for the QC of NGS data to facilitate better downstream analysis.}, pmid = {22312429}, keywords = {Data Compression,DNA Primers,DNA Primers: genetics,High-Throughput Nucleotide Sequencing,nosource,Polymerization,Quality Control,Sequence Analysis,Sequence Analysis: methods,Sequence Analysis: standards,Statistics as Topic} }

@article{liFindingConsistentPatterns2011, title = {Finding Consistent Patterns: {{A}} Nonparametric Approach for Identifying Differential Expression in {{RNA-Seq}} Data.}, author = {Li, Jun and Tibshirani, Robert}, year = 2011, month = nov, journal = {Statistical methods in medical research}, eprint = {22127579}, eprinttype = {pubmed}, pages = {1–26}, issn = {1477-0334}, doi = {10.1177/0962280211428386}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22127579}, abstract = {We discuss the identification of features that are associated with an outcome in RNA-Sequencing (RNA-Seq) and other sequencing-based comparative genomic experiments. RNA-Seq data takes the form of counts, so models based on the normal distribution are generally unsuitable. The problem is especially challenging because different sequencing experiments may generate quite different total numbers of reads, or ‘sequencing depths’. Existing methods for this problem are based on Poisson or negative binomial models: they are useful but can be heavily influenced by ‘outliers’ in the data. We introduce a simple, non-parametric method with resampling to account for the different sequencing depths. The new method is more robust than parametric methods. It can be applied to data with quantitative, survival, two-class or multiple-class outcomes. We compare our proposed method to Poisson and negative binomial-based methods in simulated and real data sets, and find that our method discovers more consistent patterns than competing methods.}, pmid = {22127579}, keywords = {differential expression,fdr,nonparametric,nosource,resampling,rna-seq} }

@article{dnaSTRUCTUREREPLICATIONKinetoplast1995, title = {{{THE STRUCTURE AND REPLICATION OF}} Kinetoplast Dna}, author = {Dna, Kinetoplast and Shapiro, Theresa A. TA and Englund, Paul T. PT}, year = 1995, journal = {Annual Reviews in Microbiology}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.mi.49.100195.001001}, keywords = {nosource} }

@article{lopesTrypanosomatidsOddOrganisms2010, title = {Trypanosomatids: Odd Organisms, Devastating Diseases}, author = {Lopes, A. H. and {Souto-Padr{'o}n}, T.}, year = 2010, journal = {Open }, number = {1}, pages = {30–59}, url = {http://benthamscience.com/open/toparaj/articles/V004/SI0029TOPARAJ/30TOPARAJ.pdf http://benthamsciencepublisher.com/open/toparaj/articles/V004/SI0029TOPARAJ/30TOPARAJ.pdf}, keywords = {herpetomonas,leishmania,nosource,phytomonas,trypanosoma,trypanosomatids} }

@article{maretti-miraTranscriptomePatternsPrimary2012, title = {Transcriptome Patterns from Primary Cutaneous {{Leishmania}} Braziliensis Infections Associate with Eventual Development of Mucosal Disease in Humans.}, author = {{Maretti-Mira}, Ana Claudia and Bittner, Jaime and {Oliveira-Neto}, Manoel Paes and Liu, Minghsun and Kang, Dezhi and Li, Huiying and Pirmez, Claude and Craft, Noah}, year = 2012, month = jan, journal = {PLoS neglected tropical diseases}, volume = {6}, number = {9}, pages = {e1816}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0001816}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3441406&tool=pmcentrez&rendertype=abstract}, abstract = {Localized Cutaneous Leishmaniasis (LCL) and Mucosal Leishmaniasis (ML) are two extreme clinical forms of American Tegumentary Leishmaniasis that usually begin as solitary primary cutaneous lesions. Host and parasite factors that influence the progression of LCL to ML are not completely understood. In this manuscript, we compare the gene expression profiles of primary cutaneous lesions from patients who eventually developed ML to those that did not.}, pmid = {23029578}, keywords = {Adolescent,Adult,Aged,Cutaneous,Cutaneous: parasitology,Cutaneous: pathology,Female,Host-Pathogen Interactions,Humans,Leishmania braziliensis,Leishmania braziliensis: genetics,Leishmania braziliensis: pathogenicity,Leishmaniasis,Male,Middle Aged,nosource,Transcriptome,Young Adult} }

@article{parkhomchukTranscriptomeAnalysisStrandspecific2009, title = {Transcriptome Analysis by Strand-Specific Sequencing of Complementary {{DNA}}.}, author = {Parkhomchuk, Dmitri and Borodina, Tatiana and Amstislavskiy, Vyacheslav and Banaru, Maria and Hallen, Linda and Krobitsch, Sylvia and Lehrach, Hans and Soldatov, Alexey}, year = 2009, month = oct, journal = {Nucleic acids research}, volume = {37}, number = {18}, pages = {e123}, issn = {1362-4962}, doi = {10.1093/nar/gkp596}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2764448&tool=pmcentrez&rendertype=abstract}, abstract = {High-throughput complementary DNA sequencing (RNA-Seq) is a powerful tool for whole-transcriptome analysis, supplying information about a transcript’s expression level and structure. However, it is difficult to determine the polarity of transcripts, and therefore identify which strand is transcribed. Here, we present a simple cDNA sequencing protocol that preserves information about a transcript’s direction. Using Saccharomyces cerevisiae and mouse brain transcriptomes as models, we demonstrate that knowing the transcript’s orientation allows more accurate determination of the structure and expression of genes. It also helps to identify new genes and enables studying promoter-associated and antisense transcription. The transcriptional landscapes we obtained are available online.}, pmid = {19620212}, keywords = {Animals,Antisense,Antisense: biosynthesis,Complementary,Complementary: chemistry,Deoxyuracil Nucleotides,Deoxyuracil Nucleotides: metabolism,DNA,DNA: methods,Fungal,Gene Expression Profiling,Genes,Genetic,Mice,nosource,Promoter Regions,Reproducibility of Results,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Sequence Analysis,Transcription} }

@article{protoCellDeathParasitic2013, title = {Cell Death in Parasitic Protozoa: Regulated or Incidental?}, author = {Proto, William R. and Coombs, Graham H. and Mottram, Jeremy C.}, year = 2013, month = jan, journal = {Nature reviews. Microbiology}, volume = {11}, number = {1}, eprint = {23202528}, eprinttype = {pubmed}, pages = {58–66}, publisher = {Nature Publishing Group}, issn = {1740-1534}, doi = {10.1038/nrmicro2929}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23202528}, abstract = {Apoptosis and other types of regulated cell death have been defined as fundamental processes in plant and animal development, but the occurrence of, and possible roles for, regulated cell death in parasitic protozoa remain controversial. A key problem has been the difficulty in reconciling the presence of apparent morphological markers of apoptosis and the notable absence of some of the key executioners functioning in higher eukaryotes. Here, we review the evidence for regulated cell death pathways in selected parasitic protozoa and propose that cell death in these organisms be classified into just two primary types: necrosis and incidental death. It is our opinion that dedicated molecular machinery required for the initiation and execution of regulated cell death has yet to be convincingly identified.}, pmid = {23202528}, keywords = {Animals,Biological,Cell Death,Gene Expression Regulation,Leishmania,Leishmania: genetics,Leishmania: physiology,Models,nosource,Parasites,Parasites: genetics,Parasites: physiology,Plasmodium,Plasmodium: genetics,Plasmodium: physiology,Trypanosoma,Trypanosoma: genetics,Trypanosoma: physiology} } % == BibTeX quality report for protoCellDeathParasitic2013: % ? Possibly abbreviated journal title Nature reviews. Microbiology

@article{mottaBacteriumEndosymbiontCrithidia2010, title = {The Bacterium Endosymbiont of {{Crithidia}} Deanei Undergoes Coordinated Division with the Host Cell Nucleus.}, author = {Motta, Maria Cristina Machado and {Catta-Preta}, Carolina Moura Costa and Schenkman, Sergio and Martins, Allan Cezar de Azevedo and Miranda, Kildare and {}de Souza, Wanderley and Elias, Maria Carolina}, year = 2010, month = jan, journal = {PloS one}, volume = {5}, number = {8}, pages = {e12415}, issn = {1932-6203}, doi = {10.1371/journal.pone.0012415}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2932560&tool=pmcentrez&rendertype=abstract}, abstract = {In trypanosomatids, cell division involves morphological changes and requires coordinated replication and segregation of the nucleus, kinetoplast and flagellum. In endosymbiont-containing trypanosomatids, like Crithidia deanei, this process is more complex, as each daughter cell contains only a single symbiotic bacterium, indicating that the prokaryote must replicate synchronically with the host protozoan. In this study, we used light and electron microscopy combined with three-dimensional reconstruction approaches to observe the endosymbiont shape and division during C. deanei cell cycle. We found that the bacterium replicates before the basal body and kinetoplast segregations and that the nucleus is the last organelle to divide, before cytokinesis. In addition, the endosymbiont is usually found close to the host cell nucleus, presenting different shapes during the protozoan cell cycle. Considering that the endosymbiosis in trypanosomatids is a mutualistic relationship, which resembles organelle acquisition during evolution, these findings establish an excellent model for the understanding of mechanisms related with the establishment of organelles in eukaryotic cells.}, pmid = {20865129}, keywords = {Bacteria,Bacteria: cytology,Bacteria: genetics,Bacterial Physiological Phenomena,Cell Division,Cell Nucleus,Cell Nucleus: microbiology,Crithidia,Crithidia: cytology,Crithidia: microbiology,Crithidia: physiology,DNA Replication,nosource,Symbiosis} }

@article{notredameTCoffeeNovelMethod2000, title = {T-{{Coffee}}: {{A}} Novel Method for Fast and Accurate Multiple Sequence Alignment.}, author = {Notredame, C. and Higgins, D. G. and Heringa, J.}, year = 2000, month = sep, journal = {Journal of molecular biology}, volume = {302}, number = {1}, eprint = {10964570}, eprinttype = {pubmed}, pages = {205–17}, issn = {0022-2836}, doi = {10.1006/jmbi.2000.4042}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10964570}, abstract = {We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives. The method is broadly based on the popular progressive approach to multiple alignment but avoids the most serious pitfalls caused by the greedy nature of this algorithm. With T-Coffee we pre-process a data set of all pair-wise alignments between the sequences. This provides us with a library of alignment information that can be used to guide the progressive alignment. Intermediate alignments are then based not only on the sequences to be aligned next but also on how all of the sequences align with each other. This alignment information can be derived from heterogeneous sources such as a mixture of alignment programs and/or structure superposition. Here, we illustrate the power of the approach by using a combination of local and global pair-wise alignments to generate the library. The resulting alignments are significantly more reliable, as determined by comparison with a set of 141 test cases, than any of the popular alternatives that we tried. The improvement, especially clear with the more difficult test cases, is always visible, regardless of the phylogenetic spread of the sequences in the tests.}, pmid = {10964570}, keywords = {Algorithms,Amino Acid,Amino Acid Motifs,Amino Acid Sequence,Animals,Computational Biology,Computational Biology: methods,Databases as Topic,Humans,Molecular Sequence Data,nosource,Protein-Serine-Threonine Kinases,Protein-Serine-Threonine Kinases: chemistry,Reproducibility of Results,Sensitivity and Specificity,Sequence Alignment,Sequence Alignment: methods,Sequence Homology,Software} }

@article{lipmanRapidSensitiveProtein1985, title = {Rapid and Sensitive Protein Similarity Searches}, author = {Lipman, D. J. and Pearson, W. R.}, year = 1985, journal = {Science}, url = {http://www.faculty.virginia.edu/wrpearson/papers/lipman_pearson_sci85.pdf}, keywords = {nosource} }

@article{andradeDifferentialTissueTropism2010, title = {Differential Tissue Tropism of {{Trypanosoma}} Cruzi Strains: An in Vitro Study.}, author = {Andrade, Luciana O. and Galv{~a}o, L{'u}cia M. C. and Meirelles, Maria De Nazareth S. L. and Chiari, Egler and Pena, Sergio D. J. and Macedo, Andrea M.}, year = 2010, month = sep, journal = {Mem'orias do Instituto Oswaldo Cruz}, volume = {105}, number = {6}, eprint = {20945002}, eprinttype = {pubmed}, pages = {834–7}, issn = {1678-8060}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20945002}, abstract = {We have previously demonstrated selection favoring the JG strain of Trypanosoma cruzi in hearts of BALB/c mice that were chronically infected with an equal mixture of the monoclonal JG strain and a clone of the Colombian strain, Col1.7G2. To evaluate whether cell invasion efficiency drives this selection, we infected primary cultures of BALB/c cardiomyocytes using these same T. cruzi populations. Contrary to expectation, Col1.7G2 parasites invaded heart cell cultures in higher numbers than JG parasites; however, intracellular multiplication of JG parasites was more efficient than that of Col1.7G2 parasites. This phenomenon was only observed for cardiomyocytes and not for cultured Vero cells. Double infections (Col1.7G2 + JG) showed similar results. Even though invasion might influence tissue selection, our data strongly suggest that intracellular development is important to determine parasite tissue tropism.}, pmid = {20945002}, keywords = {Animals,Cardiac,Cardiac: parasitology,Female,Host-Parasite Interactions,Inbred BALB C,Inbred DBA,Mice,Myocytes,nosource,Time Factors,Tropism,Tropism: physiology,Trypanosoma cruzi,Trypanosoma cruzi: classification,Trypanosoma cruzi: genetics,Trypanosoma cruzi: growth & development} }

@article{telleriaTrypanosomaCruziSequence2006, title = {Trypanosoma Cruzi: {{Sequence}} Analysis of the Variable Region of Kinetoplast Minicircles}, author = {Telleria, Jenny and Lafay, B{'e}n{'e}dicte and Virreira, Myrna}, year = 2006, journal = {Experimental }, volume = {114}, pages = {279–288}, doi = {10.1016/j.exppara.2006.04.005}, url = {http://www.sciencedirect.com/science/article/pii/S0014489406001007}, keywords = {nosource} }

@article{freitasAncestralGenomesSex2006, title = {Ancestral Genomes, Sex, and the Population Structure of {{Trypanosoma}} Cruzi.}, author = {{}de Freitas, Jorge M. and {Augusto-Pinto}, Luiz and Pimenta, Juliana R. and {Bastos-Rodrigues}, Luciana and Gon{}alves, Vanessa F. and Teixeira, Santuza M. R. and Chiari, Egler and Junqueira, Angela C. V. and Fernandes, Octavio and Macedo, Andr{'e}a M. and Machado, Carlos Renato and Pena, S{'e}rgio D. J.}, year = 2006, month = mar, journal = {PLoS pathogens}, volume = {2}, number = {3}, pages = {e24}, issn = {1553-7374}, doi = {10.1371/journal.ppat.0020024}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1434789&tool=pmcentrez&rendertype=abstract}, abstract = {Acquisition of detailed knowledge of the structure and evolution of Trypanosoma cruzi populations is essential for control of Chagas disease. We profiled 75 strains of the parasite with five nuclear microsatellite loci, 24Salpha RNA genes, and sequence polymorphisms in the mitochondrial cytochrome oxidase subunit II gene. We also used sequences available in GenBank for the mitochondrial genes cytochrome B and NADH dehydrogenase subunit 1. A multidimensional scaling plot (MDS) based in microsatellite data divided the parasites into four clusters corresponding to T. cruzi I (MDS-cluster A), T. cruzi II (MDS-cluster C), a third group of T. cruzi strains (MDS-cluster B), and hybrid strains (MDS-cluster BH). The first two clusters matched respectively mitochondrial clades A and C, while the other two belonged to mitochondrial clade B. The 24Salpha rDNA and microsatellite profiling data were combined into multilocus genotypes that were analyzed by the haplotype reconstruction program PHASE. We identified 141 haplotypes that were clearly distributed into three haplogroups (X, Y, and Z). All strains belonging to T. cruzi I (MDS-cluster A) were Z/Z, the T. cruzi II strains (MDS-cluster C) were Y/Y, and those belonging to MDS-cluster B (unclassified T. cruzi) had X/X haplogroup genotypes. The strains grouped in the MDS-cluster BH were X/Y, confirming their hybrid character. Based on these results we propose the following minimal scenario for T. cruzi evolution. In a distant past there were at a minimum three ancestral lineages that we may call, respectively, T. cruzi I, T. cruzi II, and T. cruzi III. At least two hybridization events involving T. cruzi II and T. cruzi III produced evolutionarily viable progeny. In both events, the mitochondrial recipient (as identified by the mitochondrial clade of the hybrid strains) was T. cruzi II and the mitochondrial donor was T. cruzi III.}, pmid = {16609729}, keywords = {Animals,Base Sequence,Biological Evolution,Genes,Genetic Markers,Genetics,Genome,Genotype,Microsatellite Repeats,Mitochondrial,Molecular Sequence Data,nosource,Phylogeny,Population,Protozoan,Sex Factors,Trypanosoma cruzi,Trypanosoma cruzi: genetics} }

@article{morriswoodNovelBilobeComponents2013, title = {Novel {{Bilobe Components}} in {{Trypanosoma}} Brucei {{Identified Using Proximity-Dependent Biotinylation}}.}, author = {Morriswood, Brooke and Havlicek, Katharina and Demmel, Lars and Yavuz, Sevil and {Sealey-Cardona}, Marco and Vidilaseris, Keni and Anrather, Dorothea and Kostan, Julius and {Djinovic-Carugo}, Kristina and Roux, Kyle J. and Warren, Graham}, year = 2013, month = feb, journal = {Eukaryotic cell}, volume = {12}, number = {2}, eprint = {23264645}, eprinttype = {pubmed}, pages = {356–67}, issn = {1535-9786}, doi = {10.1128/EC.00326-12}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23264645}, abstract = {The trypanosomes are a family of parasitic protists of which the African trypanosome, Trypanosoma brucei, is the best characterized. The complex and highly ordered cytoskeleton of T. brucei has been shown to play vital roles in its biology but remains difficult to study, in large part owing to the intractability of its constituent proteins. Existing methods of protein identification, such as bioinformatic analysis, generation of monoclonal antibody panels, proteomics, affinity purification, and yeast two-hybrid screens, all have drawbacks. Such deficiencies-troublesome proteins and technical limitations-are common not only to T. brucei but also to many other protists, many of which are even less well studied. Proximity-dependent biotin identification (BioID) is a recently developed technique that allows forward screens for interaction partners and near neighbors in a native environment with no requirement for solubility in nonionic detergent. As such, it is extremely well suited to the exploration of the cytoskeleton. In this project, BioID was adapted for use in T. brucei. The trypanosome bilobe, a discrete cytoskeletal structure with few known protein components, represented an excellent test subject. Use of the bilobe protein TbMORN1 as a probe resulted in the identification of seven new bilobe constituents and two new flagellum attachment zone proteins. This constitutes the first usage of BioID on a largely uncharacterized structure, and demonstrates its utility in identifying new components of such a structure. This remarkable success validates BioID as a new tool for the study of unicellular eukaryotes in particular and the eukaryotic cytoskeleton in general.}, pmid = {23264645}, keywords = {nosource} }

@article{picottiCompleteMassspectrometricMap2013, title = {A Complete Mass-Spectrometric Map of the Yeast Proteome Applied to Quantitative Trait Analysis.}, author = {Picotti, Paola and {Cl{'e}ment-Ziza}, Mathieu and Lam, Henry and Campbell, David S. and Schmidt, Alexander and Deutsch, Eric W. and R{"o}st, Hannes and Sun, Zhi and Rinner, Oliver and Reiter, Lukas and Shen, Qin and Michaelson, Jacob J. and Frei, Andreas and Alberti, Simon and Kusebauch, Ulrike and Wollscheid, Bernd and Moritz, Robert L. and Beyer, Andreas and Aebersold, Ruedi}, year = 2013, month = jan, journal = {Nature}, volume = {494}, number = {7436}, eprint = {23334424}, eprinttype = {pubmed}, pages = {266–70}, issn = {1476-4687}, doi = {10.1038/nature11835}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23334424}, abstract = {Experience from different fields of life sciences suggests that accessible, complete reference maps of the components of the system under study are highly beneficial research tools. Examples of such maps include libraries of the spectroscopic properties of molecules, or databases of drug structures in analytical or forensic chemistry. Such maps, and methods to navigate them, constitute reliable assays to probe any sample for the presence and amount of molecules contained in the map. So far, attempts to generate such maps for any proteome have failed to reach complete proteome coverage. Here we use a strategy based on high-throughput peptide synthesis and mass spectrometry to generate an almost complete reference map (97% of the genome-predicted proteins) of the Saccharomyces cerevisiae proteome. We generated two versions of this mass-spectrometric map, one supporting discovery-driven (shotgun) and the other supporting hypothesis-driven (targeted) proteomic measurements. Together, the two versions of the map constitute a complete set of proteomic assays to support most studies performed with contemporary proteomic technologies. To show the utility of the maps, we applied them to a protein quantitative trait locus (QTL) analysis, which requires precise measurement of the same set of peptides over a large number of samples. Protein measurements over 78 S. cerevisiae strains revealed a complex relationship between independent genetic loci, influencing the levels of related proteins. Our results suggest that selective pressure favours the acquisition of sets of polymorphisms that adapt protein levels but also maintain the stoichiometry of functionally related pathway members.}, pmid = {23334424}, keywords = {Genetic,Mass Spectrometry,nosource,Peptide Library,Polymorphism,Proteome,Proteome: analysis,Proteome: genetics,Proteomics,Proteomics: methods,Quantitative Trait Loci,Quantitative Trait Loci: genetics,Reference Values,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: analysis,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae: chemistry,Saccharomyces cerevisiae: genetics,Selection} }

@article{malonePreparationSmallRNA2012, title = {Preparation of Small {{RNA}} Libraries for High-Throughput Sequencing.}, author = {Malone, Colin and Brennecke, Julius and Czech, Ben and Aravin, Alexei and Hannon, Gregory J.}, year = 2012, month = oct, journal = {Cold Spring Harbor protocols}, volume = {2012}, number = {10}, eprint = {23028068}, eprinttype = {pubmed}, pages = {1067–77}, issn = {1559-6095}, doi = {10.1101/pdb.prot071431}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23028068}, abstract = {This protocol details the process of small RNA cloning for sequencing on the Illumina/Solexa sequencing platform, but it can be easily modified for use on other next-generation platforms (e.g., SOLiD, 454). This procedure is designed to clone canonical small RNA molecules with 5’-monophosphate and 3’-hydroxyl termini. Modifications, such as the presence of a 2’-O-methyl group, can reduce efficiency, although not sufficiently to negate the utility of the approach. Other termini modifications, such as a 5’ triphosphate or a 3’ phosphate, can be altered by enzymatic treatment before cloning.}, pmid = {23028068}, keywords = {nosource} }

@article{vedelCharacterizationRNALeishmania1987, title = {Characterization of {{RNA}} from {{Leishmania}} Tropica and {{Leishmania}} d.Donovani Promastigotes.}, author = {Vedel, M. and {Robert-G{'e}ro}, M.}, year = 1987, month = may, journal = {Molecular and biochemical parasitology}, volume = {24}, number = {1}, eprint = {2441255}, eprinttype = {pubmed}, pages = {81–7}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2441255}, abstract = {RNA has been prepared from promastigotes of Leishmania tropica and Leishmania d.donovani using three different methods. Extraction by hot phenol/isothiocyanate gave the best quantitative and qualitative results. The analysis of total RNA on methyl mercuric agarose gels shows that the large rRNA species is nicked: it is composed of a 630 and a 560 kDa molecule. The small rRNA species has a molecular weight of 800,000. Poly(A+) RNA can be translated in a rabbit reticulocyte lysate system. The newly synthesized products comprise high molecular weight proteins and show different patterns using RNA from L. tropica or from L. d. donovani promastigotes.}, pmid = {2441255}, keywords = {Agar Gel,Animals,Electrophoresis,Leishmania donovani,Leishmania donovani: genetics,Leishmania tropica,Leishmania tropica: genetics,Messenger,Messenger: analysis,Messenger: genetics,Messenger: isolation & purification,nosource,Poly A,Poly A: analysis,Poly A: genetics,Poly A: isolation & purification,Polyacrylamide Gel,Protein Biosynthesis,Ribosomal,Ribosomal: analysis,RNA,RNA: analysis,RNA: genetics,RNA: isolation & purification} }

@article{hashemHighresolutionCryoelectronMicroscopy2013, title = {High-Resolution Cryo-Electron Microscopy Structure of the {{Trypanosoma}} Brucei Ribosome}, author = {Hashem, Yaser and {}des Georges, Amedee and Fu, Jie and Buss, Sarah N. and Jossinet, Fabrice and Jobe, Amy and Zhang, Qin and Liao, Hstau Y. and {}a Grassucci, Robert and Bajaj, Chandrajit and Westhof, Eric and {Madison-Antenucci}, Susan and Frank, Joachim}, year = 2013, month = feb, journal = {Nature}, publisher = {Nature Publishing Group}, issn = {0028-0836}, doi = {10.1038/nature11872}, url = {http://www.nature.com/doifinder/10.1038/nature11872}, keywords = {nosource} }

@article{trapnellDifferentialAnalysisGene2012, title = {Differential Analysis of Gene Regulation at Transcript Resolution with {{RNA-seq}}.}, author = {Trapnell, Cole and Hendrickson, David G. and Sauvageau, Martin and Goff, Loyal and Rinn, John L. and Pachter, Lior}, year = 2012, month = dec, journal = {Nature biotechnology}, volume = {31}, number = {1}, eprint = {23222703}, eprinttype = {pubmed}, pages = {46–53}, publisher = {Nature Publishing Group}, issn = {1546-1696}, doi = {10.1038/nbt.2450}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23222703}, abstract = {Differential analysis of gene and transcript expression using high-throughput RNA sequencing (RNA-seq) is complicated by several sources of measurement variability and poses numerous statistical challenges. We present Cuffdiff 2, an algorithm that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries. Cuffdiff 2 robustly identifies differentially expressed transcripts and genes and reveals differential splicing and promoter-preference changes. We demonstrate the accuracy of our approach through differential analysis of lung fibroblasts in response to loss of the developmental transcription factor HOXA1, which we show is required for lung fibroblast and HeLa cell cycle progression. Loss of HOXA1 results in significant expression level changes in thousands of individual transcripts, along with isoform switching events in key regulators of the cell cycle. Cuffdiff 2 performs robust differential analysis in RNA-seq experiments at transcript resolution, revealing a layer of regulation not readily observable with other high-throughput technologies.}, pmid = {23222703}, keywords = {nosource} }

@article{ahmedFrameshiftSignalsGenes2007, title = {Frameshift Signals in Genes Associated with the Circular Code}, author = {Ahmed, Ahmed and Frey, Gabriel and Michel, C. J.}, year = 2007, month = jan, journal = {In silico biology}, volume = {7}, number = {2}, eprint = {17688441}, eprinttype = {pubmed}, pages = {155–68}, issn = {1386-6338}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17688441 http://iospress.metapress.com/index/K5674JP74708078W.pdf}, abstract = {Three sets of 20 trinucleotides are preferentially associated with the reading frames and their 2 shifted frames of both eukaryotic and prokaryotic genes. These 3 sets are circular codes. They allow retrieval of any frame in genes (containing these circular code words), locally anywhere in the 3 frames and in particular without start codons in the reading frame, and automatically with the reading of a few nucleotides. The circular code in the reading frame, noted X, which can deduce the 2 other circular codes in the shifted frames by permutation, is the information used for analysing frameshift genes, i. e. genes with a change of reading frame during translation. This work studies the circular code signal around their frameshift sites. Two scoring methods are developed, a function P based on this code X and a function Q based both on this code X and the 4 trinucleotides with identical nucleotides. They detect a significant correlation between the code X and the -1 frameshift signals in both eukaryotic and prokaryotic genes, and the +1 frameshift signals in eukaryotic genes.}, pmid = {17688441}, keywords = {Animals,Codon,Codon: genetics,DNA,DNA: genetics,Eukaryotic Cells,Eukaryotic Cells: physiology,Frameshifting,Genes,Genes: physiology,Genetic,Genetic Code,Humans,Models,nosource,Prokaryotic Cells,Prokaryotic Cells: physiology,Ribosomal} }

@article{eigenHypercycle1978, title = {The Hypercycle}, author = {Eigen, Manfred and Chemie, Max-planck-institut and Schuster, Peter}, year = 1978, journal = {Naturwissenschaften}, url = {http://link.springer.com/article/10.1007/BF00420631}, keywords = {nosource} }

@article{schmeingWhatRecentRibosome2009, title = {What Recent Ribosome Structures Have Revealed about the Mechanism of Translation.}, author = {Schmeing, T. Martin and Ramakrishnan, V.}, year = 2009, month = oct, journal = {Nature}, volume = {461}, number = {7268}, eprint = {19838167}, eprinttype = {pubmed}, pages = {1234–42}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature08403}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19838167}, abstract = {The high-resolution structures of ribosomal subunits published in 2000 have revolutionized the field of protein translation. They facilitated the determination and interpretation of functional complexes of the ribosome by crystallography and electron microscopy. Knowledge of the precise positions of residues in the ribosome in various states has facilitated increasingly sophisticated biochemical and genetic experiments, as well as the use of new methods such as single-molecule kinetics. In this review, we discuss how the interaction between structural and functional studies over the last decade has led to a deeper understanding of the complex mechanisms underlying translation.}, pmid = {19838167}, keywords = {Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: metabolism,Biocatalysis,nosource,Protein Biosynthesis,Protein Biosynthesis: physiology,Ribosomal Proteins,Ribosomal Proteins: metabolism,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,Structure-Activity Relationship} }

@article{brookmanImmunologicalAnalysisTy11995, title = {An Immunological Analysis of {{Ty1}} Virus-like Particle Structure}, author = {Brookman, J. L. and Stott, A. J. and Cheeseman, P. J.}, year = 1995, journal = {Virology}, url = {http://www.sciencedirect.com/science/article/pii/S0042682285710513}, keywords = {nosource} }

@article{neuNucleotideSequenceAnalysis1964, title = {Nucleotide {{Sequence Analysis}} of {{Polyribonucleotides By Means}} of {{Periodate Oxidation Followed By Cleavage With}} an {{Amine}}.}, author = {Neu, H. C. and {}a Heppel, L.}, year = 1964, month = sep, journal = {The Journal of biological chemistry}, volume = {239}, number = {9}, eprint = {14217878}, eprinttype = {pubmed}, pages = {2927–34}, issn = {0021-9258}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14217878}, pmid = {14217878}, keywords = {Amines,Chemical Phenomena,Chemistry,Chromatography,Cyclohexanes,Escherichia coli,Esterases,Glycine,Lysine,nosource,Nucleosides,Oxidation-Reduction,Periodic Acid,Phosphates,Phosphoric Monoester Hydrolases,Polynucleotides,Research,Swine} } % == BibTeX quality report for neuNucleotideSequenceAnalysis1964: % ? Title looks like it was stored in title-case in Zotero

@article{changCorrelationDeformabilityTRNA1999, title = {Correlation of Deformability at a {{tRNA}} Recognition Site and Aminoacylation Specificity.}, author = {Chang, K. Y. and Varani, G. and Bhattacharya, S. and Choi, H. and McClain, W. H.}, year = 1999, month = oct, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {96}, number = {21}, pages = {11764–9}, issn = {0027-8424}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=18360&tool=pmcentrez&rendertype=abstract}, abstract = {The fidelity of protein synthesis depends on specific tRNA aminoacylation by aminoacyl-tRNA synthetase enzymes, which in turn depends on the recognition of the identity of particular nucleotides and structural features in the substrate tRNA. These features generally reside within the acceptor helix, the anticodon stem-loop, and in some systems the variable pocket of the tRNA. In the alanine system, fidelity is ensured by a G.U wobble base pair located at the third position within the acceptor helix of alanine tRNA. We have investigated the activity of mutant alanine tRNAs to explore the mechanism of enzyme recognition. Here we show that the mismatched pair C-C is an excellent substitute for G.U in alanine-tRNA-knockout cells. A structural investigation by NMR spectroscopy of the C-C RNA acceptor end reveals that the two cytosines are intercalated into the helix, and that C-C exists in multiple conformations. Structural heterogeneity also is present in the wild-type G.U RNA, whereas inactive Watson-Crick helices are structurally rigid. The correlation between functional and structural data suggests that the G.U pair provides a distinctive structure and a point of deformability that allow the tRNA acceptor end to fit into the active site of the alanyl-tRNA synthetase. Fidelity is ensured because noncognate and inactive mutant tRNAs are bound in the active site in an incorrect conformation that reduces enzymatic activity.}, pmid = {10518524}, keywords = {Acylation,Adenine,Adenine: metabolism,Ala,Ala: chemistry,Ala: metabolism,Base Pairing,Blotting,Catalysis,Cytosine,Cytosine: metabolism,Escherichia coli,Escherichia coli: genetics,Guanine,Guanine: metabolism,Magnetic Resonance Spectroscopy,Molecular Sequence Data,Mutagenesis,nosource,Nucleic Acid Conformation,Protein Biosynthesis,RNA,RNA: chemistry,Transfer,Uracil,Uracil: metabolism,Western} }

@article{patrickDistinctOverlappingRoles2009, title = {Distinct and Overlapping Roles for Two {{Dicer-like}} Proteins in the {{RNA}} Interference Pathways of the Ancient Eukaryote {{Trypanosoma}} Brucei.}, author = {Patrick, Kristin L. and Shi, Huafang and Kolev, Nikolay G. and Ersfeld, Klaus and Tschudi, Christian and Ullu, Elisabetta}, year = 2009, month = oct, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {42}, pages = {17933–8}, issn = {1091-6490}, doi = {10.1073/pnas.0907766106}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2764927&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanosoma brucei is one of the most ancient eukaryotes where RNA interference (RNAi) is operational and is the only single-cell pathogen where RNAi has been extensively studied and used as a tool for functional analyses. Here, we report that the T. brucei RNAi pathway, although relying on a single Argonaute protein (AGO1), is initiated by the activities of two distinct Dicer-like enzymes. Both TbDCL1, a mostly cytoplasmic protein, and the previously undescribed nuclear enzyme TbDCL2 contribute to the biogenesis of siRNAs from retroposons. However, TbDCL2 has a predominant role in generating siRNAs from chromosomal internal repeat transcripts that accumulate at the nucleolus in RNAi-deficient cells and in initiating the endogenous RNAi response against retroposons and repeats alike. Moreover, siRNAs generated by both TbDCL1 and TbDCL2 carry a 5’-monophosphate and a blocked 3’ terminus, suggesting that 3’ end modification is an ancient trait of siRNAs. We thus propose a model whereby TbDCL2 fuels the T. brucei nuclear RNAi pathway and TbDCL1 patrols the cytoplasm, posttranscriptionally silencing potentially harmful nucleic acid parasites that may access the cytoplasm. Nevertheless, we also provide evidence for cross-talk between the two Dicer-like enzymes, because TbDCL2 is implicated in the generation of 35- to 65-nucleotide intermediate transcripts that appear to be substrates for TbDCL1. Our finding that dcl2KO cells are more sensitive to RNAi triggers than wild-type cells has significant implications for reverse genetic analyses in this important human pathogen.}, pmid = {19815526}, keywords = {Animals,Genetic,Humans,nosource,Protozoan,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Protozoan: genetics,Retroelements,Retroelements: genetics,Ribonuclease III,Ribonuclease III: genetics,Ribonuclease III: metabolism,RNA,RNA Interference,Small Interfering,Small Interfering: genetics,Transcription,Trypanosoma brucei rhodesiense,Trypanosoma brucei rhodesiense: genetics,Trypanosoma brucei rhodesiense: metabolism,Trypanosoma brucei rhodesiense: pathogenicity} }

@article{aravinPiwipiRNAPathwayProvides2007, title = {The {{Piwi-piRNA}} Pathway Provides an Adaptive Defense in the Transposon Arms Race}, author = {Aravin, A. A. and Hannon, G. J. and Brennecke, Julius}, year = 2007, month = nov, journal = {Science}, volume = {318}, number = {5851}, eprint = {17975059}, eprinttype = {pubmed}, pages = {761–4}, issn = {1095-9203}, doi = {10.1126/science.1146484}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17975059 http://www.sciencemag.org/content/318/5851/761.short}, abstract = {Increasingly complex networks of small RNAs act through RNA-interference (RNAi) pathways to regulate gene expression, to mediate antiviral responses, to organize chromosomal domains, and to restrain the spread of selfish genetic elements. Historically, RNAi has been defined as a response to double-stranded RNA. However, some small RNA species may not arise from double-stranded RNA precursors. Yet, like microRNAs and small interfering RNAs, such species guide Argonaute proteins to silencing targets through complementary base-pairing. Silencing can be achieved by corecruitment of accessory factors or through the activity of Argonaute itself, which often has endonucleolytic activity. As a specific and adaptive regulatory system, RNAi is used throughout eukarya, which indicates a long evolutionary history. A likely function of RNAi throughout that history is to protect the genome from both pathogenic and parasitic invaders.}, pmid = {17975059}, keywords = {Adaptation,Animals,Argonaute Proteins,Base Sequence,Biological,DNA Transposable Elements,Drosophila Proteins,Evolution,Gene Silencing,Molecular,Molecular Sequence Data,nosource,Proteins,Proteins: genetics,Proteins: physiology,RNA,RNA-Binding Proteins,RNA-Binding Proteins: genetics,RNA-Binding Proteins: physiology,RNA-Induced Silencing Complex,Small Interfering} }

@article{meisterMechanismsGeneSilencing2004, title = {Mechanisms of Gene Silencing by Double-Stranded {{RNA}}.}, author = {Meister, Gunter and Tuschl, Thomas}, year = 2004, month = sep, journal = {Nature}, volume = {431}, number = {7006}, eprint = {15372041}, eprinttype = {pubmed}, pages = {343–9}, issn = {1476-4687}, doi = {10.1038/nature02873}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15372041}, abstract = {Double-stranded RNA (dsRNA) is an important regulator of gene expression in many eukaryotes. It triggers different types of gene silencing that are collectively referred to as RNA silencing or RNA interference. A key step in known silencing pathways is the processing of dsRNAs into short RNA duplexes of characteristic size and structure. These short dsRNAs guide RNA silencing by specific and distinct mechanisms. Many components of the RNA silencing machinery still need to be identified and characterized, but a more complete understanding of the process is imminent.}, pmid = {15372041}, keywords = {Animals,Double-Stranded,Double-Stranded: genetics,Double-Stranded: metabolism,Gene Silencing,Messenger,Messenger: genetics,Messenger: metabolism,nosource,Post-Transcriptional,Protein Biosynthesis,Ribonucleoproteins,Ribonucleoproteins: chemistry,Ribonucleoproteins: metabolism,RNA,RNA Processing} }

@article{kimBiogenesisSmallRNAs2009, title = {Biogenesis of Small {{RNAs}} in Animals.}, author = {Kim, V. Narry and Han, Jinju and Siomi, Mikiko C.}, year = 2009, month = mar, journal = {Nature reviews. Molecular cell biology}, volume = {10}, number = {2}, eprint = {19165215}, eprinttype = {pubmed}, pages = {126–39}, issn = {1471-0080}, doi = {10.1038/nrm2632}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19165215}, abstract = {Small RNAs of 20-30 nucleotides can target both chromatin and transcripts, and thereby keep both the genome and the transcriptome under extensive surveillance. Recent progress in high-throughput sequencing has uncovered an astounding landscape of small RNAs in eukaryotic cells. Various small RNAs of distinctive characteristics have been found and can be classified into three classes based on their biogenesis mechanism and the type of Argonaute protein that they are associated with: microRNAs (miRNAs), endogenous small interfering RNAs (endo-siRNAs or esiRNAs) and Piwi-interacting RNAs (piRNAs). This Review summarizes our current knowledge of how these intriguing molecules are generated in animal cells.}, pmid = {19165215}, keywords = {Animals,Eukaryotic Initiation Factors,Eukaryotic Initiation Factors: chemistry,Eukaryotic Initiation Factors: genetics,Eukaryotic Initiation Factors: metabolism,Gene Expression Regulation,Humans,MicroRNAs,MicroRNAs: genetics,MicroRNAs: metabolism,Models,Molecular,nosource,Protein Conformation,Protein Isoforms,Protein Isoforms: chemistry,Protein Isoforms: genetics,Protein Isoforms: metabolism,Ribonuclease III,Ribonuclease III: chemistry,Ribonuclease III: genetics,Ribonuclease III: metabolism,RNA,Small Interfering,Small Interfering: genetics,Small Interfering: metabolism} } % == BibTeX quality report for kimBiogenesisSmallRNAs2009: % ? Possibly abbreviated journal title Nature reviews. Molecular cell biology

@article{chapmanSpecializationEvolutionEndogenous2007, title = {Specialization and Evolution of Endogenous Small {{RNA}} Pathways.}, author = {Chapman, Elisabeth J. and Carrington, James C.}, year = 2007, month = nov, journal = {Nature reviews. Genetics}, volume = {8}, number = {11}, eprint = {17943195}, eprinttype = {pubmed}, pages = {884–96}, issn = {1471-0064}, doi = {10.1038/nrg2179}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17943195}, abstract = {The specificity of RNA silencing is conferred by small RNA guides that are processed from structured RNA or dsRNA. The core components for small RNA biogenesis and effector functions have proliferated and specialized in eukaryotic lineages, resulting in diversified pathways that control expression of endogenous and exogenous genes, invasive elements and viruses, and repeated sequences. Deployment of small RNA pathways for spatiotemporal regulation of the transcriptome has shaped the evolution of eukaryotic genomes and contributed to the complexity of multicellular organisms.}, pmid = {17943195}, keywords = {Animals,Evolution,Humans,MicroRNAs,MicroRNAs: physiology,Molecular,nosource,Plants,Plants: genetics,RNA,RNA Interference,RNA Interference: physiology,Signal Transduction,Signal Transduction: genetics,Small Interfering,Small Interfering: physiology} } % == BibTeX quality report for chapmanSpecializationEvolutionEndogenous2007: % ? Possibly abbreviated journal title Nature reviews. Genetics

@article{dunkleRibosomeStructureDynamics2010, title = {Ribosome Structure and Dynamics during Translocation and Termination.}, author = {Dunkle, Jack and Cate, Jamie H.}, year = 2010, month = jan, journal = {Annu. Rev. Biophys.}, volume = {39}, eprint = {20192776}, eprinttype = {pubmed}, pages = {227–44}, issn = {1936-1238}, doi = {10.1146/annurev.biophys.37.032807.125954}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20192776}, abstract = {Protein biosynthesis, or translation, occurs on the ribosome, a large RNA-protein assembly universally conserved in all forms of life. Over the last decade, structures of the small and large ribosomal subunits and of the intact ribosome have begun to reveal the molecular details of how the ribosome works. Both cryo-electron microscopy and X-ray crystallography continue to provide fresh insights into the mechanism of translation. In this review, we describe the most recent structural models of the bacterial ribosome that shed light on the movement of messenger RNA and transfer RNA on the ribosome after each peptide bond is formed, a process termed translocation. We also discuss recent structures that reveal the molecular basis for stop codon recognition during translation termination. Finally, we review recent advances in understanding how bacteria handle errors in both translocation and termination.}, pmid = {20192776}, keywords = {Animals,Codon,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: metabolism,GTP Phosphohydrolase-Linked Elongation Factors,GTP Phosphohydrolase-Linked Elongation Factors: me,Humans,Messenger,Messenger: chemistry,Messenger: metabolism,nosource,Peptide Chain Elongation,Peptide Chain Termination,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,RNA,Terminator,Transfer,Transfer: chemistry,Transfer: metabolism,Translational} } % == BibTeX quality report for dunkleRibosomeStructureDynamics2010: % ? Possibly abbreviated journal title Annu. Rev. Biophys.

@article{bernfieldRNACodewordsProtein1965, title = {{{RNA}} Codewords and Protein Synthesis, {{VII}}. {{On}} the {{General Nature}} of the {{RNA Code}}}, author = {Bernfield, M. R. and Nirenberg, M. W.}, year = 1965, journal = {Science}, volume = {53}, number = {1962}, pages = {1161–1168}, url = {http://adsabs.harvard.edu/abs/1965Sci…147..479B}, keywords = {nosource} }

@article{flanneryLFR1FerricIron2011, title = {{{LFR1}} Ferric Iron Reductase of {{Leishmania}} Amazonensis Is Essential for the Generation of Infective Parasite Forms.}, author = {Flannery, Andrew R. and Huynh, Chau and Mittra, Bidyottam and {}a Mortara, Renato and Andrews, Norma W.}, year = 2011, month = jul, journal = {The Journal of biological chemistry}, volume = {286}, number = {26}, pages = {23266–79}, issn = {1083-351X}, doi = {10.1074/jbc.M111.229674}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3123093&tool=pmcentrez&rendertype=abstract}, abstract = {The protozoan parasite Leishmania is the causative agent of serious human infections worldwide. The parasites alternate between insect and vertebrate hosts and cause disease by invading macrophages, where they replicate. Parasites lacking the ferrous iron transporter LIT1 cannot grow intracellularly, indicating that a plasma membrane-associated mechanism for iron uptake is essential for the establishment of infections. Here, we identify and functionally characterize a second member of the Leishmania iron acquisition pathway, the ferric iron reductase LFR1. The LFR1 gene is up-regulated under iron deprivation and accounts for all the detectable ferric reductase activity exposed on the surface of Leishmania amazonensis. LFR1 null mutants grow normally as promastigote insect stages but are defective in differentiation into the vertebrate infective forms, metacyclic promastigotes and amastigotes. LFR1 overexpression partially restores the abnormal morphology of infective stages but markedly reduces parasite viability, precluding its ability to rescue LFR1 null replication in macrophages. However, LFR1 overexpression is not toxic for amastigotes lacking the ferrous iron transporter LIT1 and rescues their growth defect. In addition, the intracellular growth of both LFR1 and LIT1 null parasites is rescued in macrophages loaded with exogenous iron. This indicates that the Fe(3+) reductase LFR1 functions upstream of LIT1 and suggests that LFR1 overexpression results in excessive Fe(2+) production, which impairs parasite viability after intracellular transport by LIT1.}, pmid = {21558274}, keywords = {Amino Acid Sequence,Animals,Cells,Cultured,Enzymologic,Enzymologic: physiolog,FMN Reductase,FMN Reductase: biosynthesis,FMN Reductase: genetics,Gene Expression Regulation,Humans,Inbred BALB C,Iron,Iron: metabolism,Leishmania,Leishmania: enzymology,Leishmania: genetics,Leishmania: pathogenicity,Leishmaniasis,Leishmaniasis: enzymology,Leishmaniasis: genetics,Macrophages,Macrophages: metabolism,Macrophages: parasitology,Mice,Molecular Sequence Data,nosource,Protozoan Proteins,Protozoan Proteins: biosynthesis,Protozoan Proteins: genetics} }

@article{wangAssociationNovelPreribosomal2012, title = {Association of a Novel Pre-Ribosomal Complex in {{T}}. Brucei Determined by Fluorescence Resonance Energy Transfer.}, author = {Wang, Lei and Ciganda, Martin and Williams, Noreen}, year = 2012, month = dec, journal = {Eukaryotic cell}, number = {December}, eprint = {23264640}, eprinttype = {pubmed}, issn = {1535-9786}, doi = {10.1128/EC.00316-12}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23264640}, abstract = {We have previously reported that the trypanosome-specific proteins P34 and P37 form a unique pre-ribosomal complex with ribosomal protein L5 and 5S rRNA in the nucleoplasm. We hypothesize that this novel tri-molecular complex is necessary for stabilizing 5S rRNA in T. brucei and is essential for the survival of the parasite. In vitro quantitative analysis of the association between the proteins, L5 and P34, is fundamental to our understanding of this novel complex and thus, our ability to exploit its unique characteristics. Here we used in vitro fluorescence resonance energy transfer (FRET) to analyze the association between L5 and P34. First, we demonstrated that FRET can be used to confirm the association between L5 and P34. We then determined that the binding constant for L5 and P34 is 0.60 {\(\mu\)}M 0.03 {\(\mu\)}M, which is in the range of protein-protein binding constants for RNA binding proteins. In addition, we used FRET to identify the critical regions of L5 and P34 involved in the protein-protein association. We found that the N-terminal APK rich domain and RNA recognition motif (RRM) of P34 and the L18 domain of L5 are important for the association of the two proteins with each other. These results provide us with the framework for the discovery of ways to disrupt this essential complex.}, pmid = {23264640}, keywords = {nosource} }

@article{lovenRevisitingGlobalGene2012, title = {Revisiting Global Gene Expression Analysis.}, author = {Lov{'e}n, Jakob and {}a Orlando, David and {}a Sigova, Alla and Lin, Charles Y. and Rahl, Peter B. and Burge, Christopher B. and Levens, David L. and Lee, Tong Ihn and {}a Young, Richard}, year = 2012, month = oct, journal = {Cell}, volume = {151}, number = {3}, eprint = {23101621}, eprinttype = {pubmed}, pages = {476–82}, issn = {1097-4172}, doi = {10.1016/j.cell.2012.10.012}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23101621}, abstract = {Gene expression analysis is a widely used and powerful method for investigating the transcriptional behavior of biological systems, for classifying cell states in disease, and for many other purposes. Recent studies indicate that common assumptions currently embedded in experimental and analytical practices can lead to misinterpretation of global gene expression data. We discuss these assumptions and describe solutions that should minimize erroneous interpretation of gene expression data from multiple analysis platforms.}, pmid = {23101621}, keywords = {Gene Expression Profiling,Gene Expression Profiling: methods,Genetic,Genome-Wide Association Study,Humans,nosource,Oligonucleotide Array Sequence Analysis,Proto-Oncogene Proteins c-myc,Proto-Oncogene Proteins c-myc: genetics,RNA,Sequence Analysis,Transcription} }

@article{zookSyntheticSpikeinStandards2012, title = {Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for {{DNA}} and {{RNA}} Sequencing.}, author = {Zook, Justin M. and Samarov, Daniel and McDaniel, Jennifer and Sen, Shurjo K. and Salit, Marc}, year = 2012, month = jan, journal = {PloS one}, volume = {7}, number = {7}, pages = {e41356}, issn = {1932-6203}, doi = {10.1371/journal.pone.0041356}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3409179&tool=pmcentrez&rendertype=abstract}, abstract = {While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants. These SSEs can cause base quality scores to underestimate the probability of error at certain genomic positions, resulting in false positive variant calls, particularly in mixtures such as samples with RNA editing, tumors, circulating tumor cells, bacteria, mitochondrial heteroplasmy, or pooled DNA. Most algorithms proposed for correction of SSEs require a data set used to calculate association of SSEs with various features in the reads and sequence context. This data set is typically either from a part of the data set being “recalibrated” (Genome Analysis ToolKit, or GATK) or from a separate data set with special characteristics (SysCall). Here, we combine the advantages of these approaches by adding synthetic RNA spike-in standards to human RNA, and use GATK to recalibrate base quality scores with reads mapped to the spike-in standards. Compared to conventional GATK recalibration that uses reads mapped to the genome, spike-ins improve the accuracy of Illumina base quality scores by a mean of 5 Phred-scaled quality score units, and by as much as 13 units at CpG sites. In addition, since the spike-in data used for recalibration are independent of the genome being sequenced, our method allows run-specific recalibration even for the many species without a comprehensive and accurate SNP database. We also use GATK with the spike-in standards to demonstrate that the Illumina RNA sequencing runs overestimate quality scores for AC, CC, GC, GG, and TC dinucleotides, while SOLiD has less dinucleotide SSEs but more SSEs for certain cycles. We conclude that using these DNA and RNA spike-in standards with GATK improves base quality score recalibration.}, pmid = {22859977}, keywords = {nosource} }

@article{ataydeStructureRepertoireSmall2013, title = {The Structure and Repertoire of Small Interfering {{RNAs}} in {{Leishmania}} ({{Viannia}}) Braziliensis Reveal Diversification in the Trypanosomatid {{RNAi}} Pathway}, author = {Atayde, Vanessa D. VD and Shi, Huafang and Franklin, JB Joseph B. and Carriero, Nicholas and Notton, Timothy and Lye, Lon-Fye and Owens, Katherine and Beverley, Stephen M. and Tschudi, Christian and Ullu, Elisabetta}, year = 2013, month = mar, journal = {Molecular }, volume = {87}, number = {3}, eprint = {23217017}, eprinttype = {pubmed}, pages = {580–93}, issn = {1365-2958}, doi = {10.1111/mmi.12117}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23217017 http://onlinelibrary.wiley.com/doi/10.1111/mmi.12117/full}, abstract = {Among trypanosomatid protozoa the mechanism of RNA interference (RNAi) has been investigated in Trypanosoma brucei and to a lesser extent in Leishmania braziliensis. Although these two parasitic organisms belong to the same family, they are evolutionarily distantly related raising questions about the conservation of the RNAi pathway. Here we carried out an in-depth analysis of small interfering RNAs (siRNAs) associated with L. braziliensis Argonaute1 (LbrAGO1). In contrast to T. brucei, Leishmania siRNAs are sensitive to 3’ end oxidation, indicating the absence of blocking groups, and the Leishmania genome does not code for a HEN1 RNA 2’-O-methyltransferase, which modifies small RNA 3’ ends. Consistent with this observation, {\(\sim\)} 20% of siRNA 3’ ends carry non-templated uridines. Thus siRNA biogenesis, and most likely their metabolism, is different in these organisms. Similarly to T. brucei, putative mobile elements and repeats constitute the major Leishmania siRNA-producing loci and AGO1 ablation leads to accumulation of long transcripts derived from putative mobile elements. However, contrary to T. brucei, no siRNAs were detected from other genomic regions with the potential to form double-stranded RNA, namely sites of convergent transcription and inverted repeats. Thus, our results indicate that organism-specific diversification has occurred in the RNAi pathway during evolution of the trypanosomatid lineage.}, pmid = {23217017}, keywords = {nosource} }

@article{hardwickRarelyRestRNA2012, title = {Rarely at Rest: {{RNA}} Helicases and Their Busy Contributions to {{RNA}} Degradation, Regulation and Quality Control}, author = {Hardwick, S. W. and Luisi, B. F.}, year = 2012, journal = {RNA biology}, number = {January}, pages = {1–16}, url = {http://www.landesbioscience.com/journals/rna/article/22270/}, keywords = {nosource} }

@article{fernandesExtracellularAmastigotesTrypanosoma2012, title = {Extracellular Amastigotes of {{Trypanosoma}} Cruzi Are Potent Inducers of Phagocytosis in Mammalian Cells.}, author = {Fernandes, Maria Cecilia and Flannery, Andrew R. and Andrews, Norma and {}a Mortara, Renato}, year = 2012, month = dec, journal = {Cellular microbiology}, eprint = {23241026}, eprinttype = {pubmed}, issn = {1462-5822}, doi = {10.1111/cmi.12090}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23241026}, abstract = {The protozoan parasite Trypanosoma cruzi, the aetiological agent of Chagas’ disease, has two infective life cycle stages, trypomastigotes and amastigotes. While trypomastigotes actively enter mammalian cells, highly infective extracellular amastigotes (type I T. cruzi) rely on actin-mediated uptake, which is generally inefficient in non-professional phagocytes. We found that extracellular amastigotes (EAs) of T. cruzi G strain (type I), but not Y strain (type II), were taken up 100-fold more efficiently than inert particles. Mammalian cell lines showed levels of parasite uptake comparable to macrophages, and extensive actin recruitment and polymerization was observed at the site of entry. EA uptake was not dependent on parasite-secreted molecules and required the same molecular machinery utilized by professional phagocytes during large particle phagocytosis. Transcriptional silencing of synaptotagmin VII and CD63 significantly inhibited EA internalization, demonstrating that delivery of supplemental lysosomal membrane to form the phagosome is involved in parasite uptake. Importantly, time-lapse live imaging using fluorescent reporters revealed phagosome-associated modulation of phosphoinositide metabolism during EA uptake that closely resembles what occurs during phagocytosis by macrophages. Collectively, our results demonstrate that T. cruzi EAs are potent inducers of phagocytosis in non-professional phagocytes, a process that may facilitate parasite persistence in infected hosts.}, pmid = {23241026}, keywords = {nosource} }

@article{maedaCellSignalingTrypanosoma2012, title = {Cell Signaling during {{Trypanosoma}} Cruzi Invasion.}, author = {Maeda, Fernando Y. and Cortez, Cristian and Yoshida, Nobuko}, year = 2012, month = jan, journal = {Frontiers in immunology}, volume = {3}, number = {November}, pages = {361}, issn = {1664-3224}, doi = {10.3389/fimmu.2012.00361}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3515895&tool=pmcentrez&rendertype=abstract}, abstract = {Cell signaling is an essential requirement for mammalian cell invasion by Trypanosoma cruzi. Depending on the parasite strain and the parasite developmental form, distinct signaling pathways may be induced. In this short review, we focus on the data coming from studies with metacyclic trypomastigotes (MT) generated in vitro and tissue culture-derived trypomastigotes (TCT), used as counterparts of insect-borne and bloodstream parasites, respectively. During invasion of host cells by MT or TCT, intracellular Ca(2) (+) mobilization and host cell lysosomal exocytosis are triggered. Invasion mediated by MT surface molecule gp82 requires the activation of mammalian target of rapamycin (mTOR), phosphatidylinositol 3-kinase (PI3K), and protein kinase C (PKC) in the host cell, associated with Ca(2) (+)-dependent disruption of the actin cytoskeleton. In MT, protein tyrosine kinase, PI3K, phospholipase C, and PKC appear to be activated. TCT invasion, on the other hand, does not rely on mTOR activation, rather on target cell PI3K, and may involve the host cell autophagy for parasite internalization. Enzymes, such as oligopeptidase B and the major T. cruzi cysteine proteinase cruzipain, have been shown to generate molecules that induce target cell Ca(2) (+) signal. In addition, TCT may trigger host cell responses mediated by transforming growth factor {\(\beta\)} receptor or integrin family member. Further investigations are needed for a more complete and detailed picture of T. cruzi invasion.}, pmid = {23230440}, keywords = {ca 2,cell invasion,cell signaling,culture trypomastigote,metacyclic rypomastigote,mobilization,nosource,tissue,trypanosoma cruzi,Trypanosoma cruzi} }

@article{mittalUniquePosttranslationalModifications2012, title = {Unique {{Posttranslational Modifications}} in {{Eukaryotic Translation Factors}} and Their {{Roles}} in {{Protozoan Parasite Viability}} and {{Pathogenesis}}.}, author = {Mittal, Nimisha and Subramanian, Gowri and B{"u}tikofer, Peter and Madhubala, Rentala}, year = 2012, month = nov, journal = {Molecular and biochemical parasitology}, volume = {187}, number = {1}, eprint = {23201129}, eprinttype = {pubmed}, pages = {21–31}, publisher = {Elsevier B.V.}, issn = {1872-9428}, doi = {10.1016/j.molbiopara.2012.11.001}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23201129}, abstract = {Protozoan parasites are one of the major causes of diseases worldwide. The vector transmitted parasites exhibit complex life cycles involving interactions between humans, protozoa, and arthropods. In order to adapt themselves to the changing microenvironments, they have to undergo complex morphological and metabolic changes. These changes can be brought about by expressing a new pool of proteins in the cell or by modifying the existing repertoire of proteins via posttranslational modifications (PTMs). PTMs involve covalent modification and processing of proteins thereby modulating their functions. Some of these changes may involve PTMs of parasite proteins to help the parasite survive within the host and the vector. Out of many PTMs known, three are unique since they occur only on single proteins: ethanolamine phosphoglycerol (EPG) glutamate, hypusine and diphthamide. These modifications occur on eukaryotic elongation factor 1A (eEF1A), eukaryotic initiation factor 5A (eIF5A) and eukaryotic elongation factor 2 (eEF2), respectively. Interestingly, the proteins carrying these unique modifications are all involved in the elongation steps of translation. Here we review these unique PTMs, which are well conserved in protozoan parasites, and discuss their roles in viability and pathogenesis of parasites. Characterization of these modifications and studying their roles in physiology as well as pathogenesis will provide new insights in parasite biology, which may also help in developing new therapeutic interventions.}, pmid = {23201129}, keywords = {eukaryotic elongation factor 1a,eukaryotic elongation factor 2,eukaryotic initiation factor 5a,nosource} }

@article{moorthieReviewMassivelyParallel2011, title = {Review of Massively Parallel {{DNA}} Sequencing Technologies.}, author = {Moorthie, Sowmiya and Mattocks, Christopher J. and Wright, Caroline F.}, year = 2011, month = dec, journal = {The HUGO journal}, volume = {5}, number = {1-4}, pages = {1–12}, issn = {1877-6566}, doi = {10.1007/s11568-011-9156-3}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3238019&tool=pmcentrez&rendertype=abstract}, abstract = {Since the development of technologies that can determine the base-pair sequence of DNA, the ability to sequence genes has contributed much to science and medicine. However, it has remained a relatively costly and laborious process, hindering its use as a routine biomedical tool. Recent times are seeing rapid developments in this field, both in the availability of novel sequencing platforms, as well as supporting technologies involved in processes such as targeting and data analysis. This is leading to significant reductions in the cost of sequencing a human genome and the potential for its use as a routine biomedical tool. This review is a snapshot of this rapidly moving field examining the current state of the art, forthcoming developments and some of the issues still to be resolved prior to the use of new sequencing technologies in routine clinical diagnosis.}, pmid = {23205160}, keywords = {next generation sequencing a,nosource,targeting a} }

@article{liuContributionIntersubunitBridges2012, title = {Contribution of Intersubunit Bridges to the Energy Barrier of Ribosomal Translocation.}, author = {Liu, Qi and Fredrick, Kurt}, year = 2012, month = nov, journal = {Nucleic acids research}, volume = {41}, number = {1}, eprint = {23161696}, eprinttype = {pubmed}, pages = {565–574}, issn = {1362-4962}, doi = {10.1093/nar/gks1074}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23161696}, abstract = {In every round of translation elongation, EF-G catalyzes translocation, the movement of tRNAs (and paired codons) to their adjacent binding sites in the ribosome. Previous kinetic studies have shown that the rate of tRNA-mRNA movement is limited by a conformational change in the ribosome termed ‘unlocking’. Although structural studies offer some clues as to what unlocking might entail, the molecular basis of this conformational change remains an open question. In this study, the contribution of intersubunit bridges to the energy barrier of translocation was systematically investigated. Unlike those targeting B2a and B3, mutations that disrupt bridges B1a, B4, B7a and B8 increased the maximal rate of both forward (EF-G dependent) and reverse (spontaneous) translocation. As bridge B1a is predicted to constrain 30S head movement and B4, B7a and B8 are predicted to constrain intersubunit rotation, these data provide evidence that formation of the unlocked (transition) state involves both 30S head movement and intersubunit rotation.}, pmid = {23161696}, keywords = {nosource} }

@article{cigandaCharacterizationNovelAssociation2012, title = {Characterization of a Novel Association between Two Trypanosome-Specific Proteins and {{5S rRNA}}.}, author = {Ciganda, Martin and Williams, Noreen}, year = 2012, month = jan, journal = {PloS one}, volume = {7}, number = {1}, pages = {e30029}, issn = {1932-6203}, doi = {10.1371/journal.pone.0030029}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3257258&tool=pmcentrez&rendertype=abstract}, abstract = {P34 and P37 are two previously identified RNA binding proteins in the flagellate protozoan Trypanosoma brucei. RNA interference studies have determined that the proteins are essential and are involved in ribosome biogenesis. Here, we show that these proteins interact in vitro with the 5S rRNA with nearly identical binding characteristics in the absence of other cellular factors. The T. brucei 5S rRNA has a complex secondary structure and presents four accessible loops (A to D) for interactions with RNA-binding proteins. In other eukaryotes, loop C is bound by the L5 ribosomal protein and loop A mainly by TFIIIA. The binding of P34 and P37 to T. brucei 5S rRNA involves the LoopA region of the RNA, but these proteins also protect the L5 binding site located on LoopC.}, pmid = {22253864}, keywords = {5S,5S: chemistry,5S: metabolism,Base Sequence,Molecular Sequence Data,Mutation,Mutation: genetics,nosource,Nucleic Acid Conformation,Protein Binding,Protozoan Proteins,Protozoan Proteins: metabolism,Ribonuclease H,Ribonuclease H: metabolism,Ribosomal,RNA,RNA-Binding Proteins,RNA-Binding Proteins: metabolism,Species Specificity,Trypanosoma brucei brucei,Trypanosoma brucei brucei: metabolism} }

@article{shapiraPhysicalRegulatoryMap2009, title = {A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in {{H1N1}} Infection.}, author = {Shapira, Sagi D. and {Gat-Viks}, Irit and Shum, Bennett O. V. and Dricot, Amelie and {}de Grace, Marciela M. and Wu, Liguo and Gupta, Piyush B. and Hao, Tong and Silver, Serena J. and Root, David E. and Hill, David E. and Regev, Aviv and Hacohen, Nir}, year = 2009, month = dec, journal = {Cell}, volume = {139}, number = {7}, pages = {1255–67}, publisher = {Elsevier Ltd}, issn = {1097-4172}, doi = {10.1016/j.cell.2009.12.018}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2892837&tool=pmcentrez&rendertype=abstract}, abstract = {During the course of a viral infection, viral proteins interact with an array of host proteins and pathways. Here, we present a systematic strategy to elucidate the dynamic interactions between H1N1 influenza and its human host. A combination of yeast two-hybrid analysis and genome-wide expression profiling implicated hundreds of human factors in mediating viral-host interactions. These factors were then examined functionally through depletion analyses in primary lung cells. The resulting data point to potential roles for some unanticipated host and viral proteins in viral infection and the host response, including a network of RNA-binding proteins, components of WNT signaling, and viral polymerase subunits. This multilayered approach provides a comprehensive and unbiased physical and regulatory model of influenza-host interactions and demonstrates a general strategy for uncovering complex host-pathogen relationships.}, pmid = {20064372}, keywords = {Apoptosis,Epithelial Cells,Epithelial Cells: virology,Gene Expression Profiling,H1N1 Subtype,H1N1 Subtype: immunology,H1N1 Subtype: metabolism,H1N1 Subtype: pathogenicity,Host-Pathogen Interactions,Humans,Influenza A Virus,Interferons,Interferons: metabolism,Lung,Lung: cytology,Lung: virology,nosource,Proteomics,RNA,Small Interfering,Small Interfering: metabolism,Two-Hybrid System Techniques,Viral,Viral Nonstructural Proteins,Viral Nonstructural Proteins: metabolism,Viral Proteins,Viral Proteins: metabolism,Viral: metabolism,Wnt Proteins,Wnt Proteins: metabolism} }

@article{mchardyRoleGenomicsTracking2009, title = {The Role of Genomics in Tracking the Evolution of Influenza {{A}} Virus.}, author = {McHardy, Alice Carolyn and Adams, Ben}, year = 2009, month = oct, journal = {PLoS pathogens}, volume = {5}, number = {10}, pages = {e1000566}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1000566}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2739293&tool=pmcentrez&rendertype=abstract}, abstract = {Influenza A virus causes annual epidemics and occasional pandemics of short-term respiratory infections associated with considerable morbidity and mortality. The pandemics occur when new human-transmissible viruses that have the major surface protein of influenza A viruses from other host species are introduced into the human population. Between such rare events, the evolution of influenza is shaped by antigenic drift: the accumulation of mutations that result in changes in exposed regions of the viral surface proteins. Antigenic drift makes the virus less susceptible to immediate neutralization by the immune system in individuals who have had a previous influenza infection or vaccination. A biannual reevaluation of the vaccine composition is essential to maintain its effectiveness due to this immune escape. The study of influenza genomes is key to this endeavor, increasing our understanding of antigenic drift and enhancing the accuracy of vaccine strain selection. Recent large-scale genome sequencing and antigenic typing has considerably improved our understanding of influenza evolution: epidemics around the globe are seeded from a reservoir in East-Southeast Asia with year-round prevalence of influenza viruses; antigenically similar strains predominate in epidemics worldwide for several years before being replaced by a new antigenic cluster of strains. Future in-depth studies of the influenza reservoir, along with large-scale data mining of genomic resources and the integration of epidemiological, genomic, and antigenic data, should enhance our understanding of antigenic drift and improve the detection and control of antigenically novel emerging strains.}, pmid = {19855818}, keywords = {Antigens,Evolution,Genomics,Human,Human: epidemiology,Human: immunology,Human: virology,Humans,Influenza,Influenza A virus,Influenza A virus: genetics,Influenza A virus: immunology,Molecular,nosource,Viral,Viral: genetics} }

@article{ghedinLargescaleSequencingHuman2005, title = {Large-Scale Sequencing of Human Influenza Reveals the Dynamic Nature of Viral Genome Evolution.}, author = {Ghedin, Elodie and {}a Sengamalay, Naomi and Shumway, Martin and Zaborsky, Jennifer and Feldblyum, Tamara and Subbu, Vik and Spiro, David J. and Sitz, Jeff and Koo, Hean and Bolotov, Pavel and Dernovoy, Dmitry and Tatusova, Tatiana and Bao, Yiming and George, Kirsten St and Taylor, Jill and Lipman, David J. and Fraser, Claire M. and Taubenberger, Jeffery K. and Salzberg, Steven L.}, year = 2005, month = oct, journal = {Nature}, volume = {437}, number = {7062}, eprint = {16208317}, eprinttype = {pubmed}, pages = {1162–6}, issn = {1476-4687}, doi = {10.1038/nature04239}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16208317}, abstract = {Influenza viruses are remarkably adept at surviving in the human population over a long timescale. The human influenza A virus continues to thrive even among populations with widespread access to vaccines, and continues to be a major cause of morbidity and mortality. The virus mutates from year to year, making the existing vaccines ineffective on a regular basis, and requiring that new strains be chosen for a new vaccine. Less-frequent major changes, known as antigenic shift, create new strains against which the human population has little protective immunity, thereby causing worldwide pandemics. The most recent pandemics include the 1918 ‘Spanish’ flu, one of the most deadly outbreaks in recorded history, which killed 30-50 million people worldwide, the 1957 ‘Asian’ flu, and the 1968 ‘Hong Kong’ flu. Motivated by the need for a better understanding of influenza evolution, we have developed flexible protocols that make it possible to apply large-scale sequencing techniques to the highly variable influenza genome. Here we report the results of sequencing 209 complete genomes of the human influenza A virus, encompassing a total of 2,821,103 nucleotides. In addition to increasing markedly the number of publicly available, complete influenza virus genomes, we have discovered several anomalies in these first 209 genomes that demonstrate the dynamic nature of influenza transmission and evolution. This new, large-scale sequencing effort promises to provide a more comprehensive picture of the evolution of influenza viruses and of their pattern of transmission through human and animal populations. All data from this project are being deposited, without delay, in public archives.}, pmid = {16208317}, keywords = {20th Century,21st Century,Animals,Evolution,Genome,Hemagglutinin Glycoproteins,History,Human,Human: epidemiology,Human: transmission,Human: veterinary,Human: virology,Humans,Influenza,Influenza A virus,Influenza A virus: classification,Influenza A virus: genetics,Influenza A virus: isolation & purification,Influenza A virus: physiology,Influenza Vaccines,Influenza Vaccines: history,Influenza Vaccines: immunology,Influenza Virus,Influenza Virus: gene,Influenza Virus: immu,Molecular,Mutagenesis,Mutagenesis: genetics,Mutation,Mutation: genetics,Neuraminidase,Neuraminidase: genetics,Neuraminidase: metabolism,New York,New York: epidemiology,nosource,Phylogeny,Public Sector,Reassortant Viruses,Reassortant Viruses: genetics,Sequence Analysis,Time Factors,Viral,Virus Replication} }

@article{wilsonStructuralBasisImmune1990, title = {Structural Basis of Immune Recognition of Influenza Virus Hemagglutinin}, author = {Wilson, I. A. and Cox, N. J.}, year = 1990, journal = {Annual review of immunology}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.iy.08.040190.003513}, keywords = {antigenic variation,immune response,influenza hemagglutinin,nosource,synthetic peptides,vaccines} }

@article{holmesWholegenomeAnalysisHuman2005, title = {Whole-Genome Analysis of Human Influenza {{A}} Virus Reveals Multiple Persistent Lineages and Reassortment among Recent {{H3N2}} Viruses.}, author = {Holmes, Edward C. and Ghedin, Elodie and Miller, Naomi and Taylor, Jill and Bao, Yiming and George, Kirsten St and Grenfell, Bryan T. and Salzberg, Steven L. and Fraser, Claire M. and Lipman, David J. and Taubenberger, Jeffery K.}, year = 2005, month = sep, journal = {PLoS biology}, volume = {3}, number = {9}, pages = {e300}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0030300}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1180517&tool=pmcentrez&rendertype=abstract}, abstract = {Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2 influenza A viruses collected between 1999 and 2004 from New York State, United States, and observed multiple co-circulating clades with different population frequencies. Strikingly, phylogenies inferred for individual gene segments revealed that multiple reassortment events had occurred among these clades, such that one clade of H3N2 viruses present at least since 2000 had provided the hemagglutinin gene for all those H3N2 viruses sampled after the 2002-2003 influenza season. This reassortment event was the likely progenitor of the antigenically variant influenza strains that caused the A/Fujian/411/2002-like epidemic of the 2003-2004 influenza season. However, despite sharing the same hemagglutinin, these phylogenetically distinct lineages of viruses continue to co-circulate in the same population. These data, derived from the first large-scale analysis of H3N2 viruses, convincingly demonstrate that multiple lineages can co-circulate, persist, and reassort in epidemiologically significant ways, and underscore the importance of genomic analyses for future influenza surveillance.}, pmid = {16026181}, keywords = {Evolution,Genes,Genetic,Genetic Variation,Genome,H3N2 Subtype,H3N2 Subtype: classification,H3N2 Subtype: genetics,Humans,Influenza A Virus,Molecular,nosource,Phylogeny,Reassortant Viruses,Reassortant Viruses: genetics,Recombination,Viral} }

@article{jeckCircularRNAsAre2012, title = {Circular {{RNAs}} Are Abundant, Conserved, and Associated with {{ALU}} Repeats.}, author = {Jeck, William R. and {}a Sorrentino, Jessica and Wang, Kai and Slevin, Michael K. and Burd, Christin E. and Liu, Jinze and Marzluff, William F. and Sharpless, Norman E.}, year = 2012, month = dec, journal = {RNA}, eprint = {23249747}, eprinttype = {pubmed}, pages = {141–157}, issn = {1469-9001}, doi = {10.1261/rna.035667.112}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23249747}, abstract = {Circular RNAs composed of exonic sequence have been described in a small number of genes. Thought to result from splicing errors, circular RNA species possess no known function. To delineate the universe of endogenous circular RNAs, we performed high-throughput sequencing (RNA-seq) of libraries prepared from ribosome-depleted RNA with or without digestion with the RNA exonuclease, RNase R. We identified {\(>\)}25,000 distinct RNA species in human fibroblasts that contained non-colinear exons (a “backsplice”) and were reproducibly enriched by exonuclease degradation of linear RNA. These RNAs were validated as circular RNA (ecircRNA), rather than linear RNA, and were more stable than associated linear mRNAs in vivo. In some cases, the abundance of circular molecules exceeded that of associated linear mRNA by {\(>\)}10-fold. By conservative estimate, we identified ecircRNAs from 14.4% of actively transcribed genes in human fibroblasts. Application of this method to murine testis RNA identified 69 ecircRNAs in precisely orthologous locations to human circular RNAs. Of note, paralogous kinases HIPK2 and HIPK3 produce abundant ecircRNA from their second exon in both humans and mice. Though HIPK3 circular RNAs contain an AUG translation start, it and other ecircRNAs were not bound to ribosomes. Circular RNAs could be degraded by siRNAs and, therefore, may act as competing endogenous RNAs. Bioinformatic analysis revealed shared features of circularized exons, including long bordering introns that contained complementary ALU repeats. These data show that ecircRNAs are abundant, stable, conserved and nonrandom products of RNA splicing that could be involved in control of gene expression.}, pmid = {23249747}, keywords = {exon shuffling,missplicing,noncoding rna,nosource,trans-splicing} }

@article{canavaciVitroVivoHighthroughput2010, title = {In Vitro and in Vivo High-Throughput Assays for the Testing of Anti-{{Trypanosoma}} Cruzi Compounds.}, author = {Canavaci, Adriana M. C. and Bustamante, Juan M. and Padilla, Angel M. and Brandan, Cecilia M. Perez and Simpson, Laura J. and Xu, Dan and Boehlke, Courtney L. and Tarleton, Rick L.}, year = 2010, month = jan, journal = {PLoS neglected tropical diseases}, volume = {4}, number = {7}, pages = {e740}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0000740}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2903469&tool=pmcentrez&rendertype=abstract}, abstract = {The two available drugs for treatment of T. cruzi infection, nifurtimox and benznidazole (BZ), have potential toxic side effects and variable efficacy, contributing to their low rate of use. With scant economic resources available for antiparasitic drug discovery and development, inexpensive, high-throughput and in vivo assays to screen potential new drugs and existing compound libraries are essential.}, pmid = {20644616}, keywords = {Animal,Animals,Antiprotozoal Agents,Antiprotozoal Agents: pharmacology,Chagas Disease,Chagas Disease: drug therapy,Disease Models,Drug Evaluation,Firefly,Firefly: genetics,Firefly: metabolism,Foot,Foot: parasitology,Genes,High-Throughput Screening Assays,High-Throughput Screening Assays: methods,Inbred BALB C,Inhibitory Concentration 50,Luciferases,Luminescent Proteins,Luminescent Proteins: genetics,Luminescent Proteins: metabolism,Mice,nosource,Plant Proteins,Plant Proteins: genetics,Plant Proteins: metabolism,Preclinical,Preclinical: methods,Reporter,Reproducibility of Results,Sensitivity and Specificity,Staining and Labeling,Trypanosoma cruzi,Trypanosoma cruzi: drug effects,Trypanosoma cruzi: genetics} }

@article{tardieuxLysosomeRecruitmentFusion1992, title = {Lysosome Recruitment and Fusion Are Early Events Required for Trypanosome Invasion of Mammalian Cells.}, author = {Tardieux, I. and Webster, P. and Ravesloot, J. and Boron, W. and {}a Lunn, J. and Heuser, J. E. and Andrews, N. W.}, year = 1992, month = dec, journal = {Cell}, volume = {71}, number = {7}, eprint = {1473148}, eprinttype = {pubmed}, pages = {1117–30}, issn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/1473148}, abstract = {Trypanosoma cruzi invades most nucleated cells by a mechanism distinct from classical phagocytosis. Although parasites enter at the lysosome-poor peripheral cell margins, lysosomal markers are immediately incorporated into the parasitophorous vacuole. No accumulation of polymerized actin was detected around recently internalized parasites, and disruption of microfilaments significantly facilitated invasion. Lysosomes were observed to aggregate at the sites of trypanosome attachment and to fuse with the vacuole at early stages of its formation. Experimentally induced, microtubule-dependent movement of lysosomes from the perinuclear area to the cell periphery enhanced entry. Conditions that deplete cells of peripheral lysosomes or interfere with lysosomal fusion capacity inhibited invasion. These observations reveal a novel mechanism for cell invasion:recruitment of lysosomes for fusion at the site of parasite internalization.}, pmid = {1473148}, keywords = {Animals,Cell Line,Cell Membrane,Cell Membrane: parasitology,Host-Parasite Interactions,Lysosomes,Lysosomes: parasitology,Microtubules,Microtubules: physiology,nosource,Rats,Signal Transduction,Sucrose,Sucrose: pharmacology,Trypanosoma cruzi,Trypanosoma cruzi: physiology,Vacuoles,Vacuoles: parasitology} }

@article{costalesCytokinedependentAndindependentGene2009, title = {Cytokine-Dependent and-Independent Gene Expression Changes and Cell Cycle Block Revealed in {{Trypanosoma}} Cruzi-Infected Host Cells by Comparative {{mRNA}} Profiling.}, author = {{}a Costales, Jaime and Daily, Johanna P. and {}a Burleigh, Barbara}, year = 2009, month = jan, journal = {BMC genomics}, volume = {10}, pages = {252}, issn = {1471-2164}, doi = {10.1186/1471-2164-10-252}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2709661&tool=pmcentrez&rendertype=abstract}, abstract = {The requirements for growth and survival of the intracellular pathogen Trypanosoma cruzi within mammalian host cells are poorly understood. Transcriptional profiling of the host cell response to infection serves as a rapid read-out for perturbation of host physiology that, in part, reflects adaptation to the infective process. Using Affymetrix oligonucleotide array analysis we identified common and disparate host cell responses triggered by T. cruzi infection of phenotypically diverse human cell types.}, pmid = {19480704}, keywords = {Animals,Cell Cycle,Cell Line,Cell Proliferation,Chagas Disease,Chagas Disease: genetics,Chagas Disease: immunology,Cytokines,Cytokines: genetics,Cytokines: immunology,Gene Expression Profiling,Gene Expression Regulation,Host-Pathogen Interactions,Humans,Messenger,Messenger: genetics,nosource,Oligonucleotide Array Sequence Analysis,RNA,Trypanosoma cruzi,Trypanosoma cruzi: immunology} }

@article{lauAbundantClassTiny2001, title = {An Abundant Class of Tiny {{RNAs}} with Probable Regulatory Roles in {{Caenorhabditis}} Elegans.}, author = {Lau, N. C. and Lim, L. P. and Weinstein, E. G. and Bartel, D. P.}, year = 2001, month = oct, journal = {Science (New York, N.Y.)}, volume = {294}, number = {5543}, eprint = {11679671}, eprinttype = {pubmed}, pages = {858–62}, issn = {0036-8075}, doi = {10.1126/science.1065062}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11679671}, abstract = {Two small temporal RNAs (stRNAs), lin-4 and let-7, control developmental timing in Caenorhabditis elegans. We find that these two regulatory RNAs are members of a large class of 21- to 24-nucleotide noncoding RNAs, called microRNAs (miRNAs). We report on 55 previously unknown miRNAs in C. elegans. The miRNAs have diverse expression patterns during development: a let-7 paralog is temporally coexpressed with let-7; miRNAs encoded in a single genomic cluster are coexpressed during embryogenesis; and still other miRNAs are expressed constitutively throughout development. Potential orthologs of several of these miRNA genes were identified in Drosophila and human genomes. The abundance of these tiny RNAs, their expression patterns, and their evolutionary conservation imply that, as a class, miRNAs have broad regulatory functions in animals.}, pmid = {11679671}, keywords = {Animals,Base Sequence,Blotting,Caenorhabditis elegans,Caenorhabditis elegans: genetics,Cloning,Conserved Sequence,Developmental,Endoribonucleases,Endoribonucleases: metabolism,Gene Expression Regulation,Genes,Genetic,Genome,Helminth,Helminth: chemistry,Helminth: genetics,Helminth: physiology,Humans,Molecular,Molecular Sequence Data,Multigene Family,Northern,nosource,Nucleic Acid Conformation,Ribonuclease III,RNA,RNA Precursors,RNA Precursors: genetics,RNA Precursors: metabolism,Transcription,Untranslated,Untranslated: chemistry,Untranslated: genetics,Untranslated: physiology} } % == BibTeX quality report for lauAbundantClassTiny2001: % ? Possibly abbreviated journal title Science (New York, N.Y.)

@article{nagalakshmiRNASeqMethodComprehensive2010, title = {{{RNA-Seq}}: A Method for Comprehensive Transcriptome Analysis.}, author = {Nagalakshmi, Ugrappa and Waern, Karl and Snyder, Michael}, year = 2010, month = jan, journal = {Current protocols in molecular biology / edited by Frederick M. Ausubel … [et al.]}, volume = {Chapter 4}, number = {January}, eprint = {20069539}, eprinttype = {pubmed}, pages = {Unit 4.11.1-13}, issn = {1934-3647}, doi = {10.1002/0471142727.mb0411s89}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20069539}, abstract = {A recently developed technique called RNA Sequencing (RNA-Seq) uses massively parallel sequencing to allow transcriptome analyses of genomes at a far higher resolution than is available with Sanger sequencing- and microarray-based methods. In the RNA-Seq method, complementary DNAs (cDNAs) generated from the RNA of interest are directly sequenced using next-generation sequencing technologies. The reads obtained from this can then be aligned to a reference genome in order to construct a whole-genome transcriptome map. RNA-Seq has been used successfully to precisely quantify transcript levels, confirm or revise previously annotated 5’ and 3’ ends of genes, and map exon/intron boundaries. This unit describes protocols for performing RNA-Seq using the Illumina sequencing platform.}, isbn = {0471142727}, pmid = {20069539}, keywords = {Complementary,Complementary: genetics,Complementary: metabolism,DNA,Gene Expression Profiling,Gene Expression Profiling: methods,Genetic,Humans,nosource,RNA,RNA: methods,Sequence Analysis,Transcription} } % == BibTeX quality report for nagalakshmiRNASeqMethodComprehensive2010: % ? Possibly abbreviated journal title Current protocols in molecular biology / edited by Frederick M. Ausubel … [et al.]

@article{minenoExpressionProfileMicroRNAs2006, title = {The Expression Profile of {{microRNAs}} in Mouse Embryos.}, author = {Mineno, Junichi and Okamoto, Sachiko and Ando, Tatsuya and Sato, Masahiro and Chono, Hideto and Izu, Hiroyuki and Takayama, Masanori and Asada, Kiyozo and Mirochnitchenko, Oleg and Inouye, Masayori and Kato, Ikunoshin}, year = 2006, month = jan, journal = {Nucleic acids research}, volume = {34}, number = {6}, pages = {1765–71}, issn = {1362-4962}, doi = {10.1093/nar/gkl096}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1421506&tool=pmcentrez&rendertype=abstract}, abstract = {MicroRNAs (miRNAs), which are non-coding RNAs 18-25 nt in length, regulate a variety of biological processes, including vertebrate development. To identify new species of miRNA and to simultaneously obtain a comprehensive quantitative profile of small RNA expression in mouse embryos, we used the massively parallel signature sequencing technology that potentially identifies virtually all of the small RNAs in a sample. This approach allowed us to detect a total of 390 miRNAs, including 195 known miRNAs covering approximately 80% of previously registered mouse miRNAs as well as 195 new miRNAs, which are so far unknown in mouse. Some of these miRNAs showed temporal expression profiles during prenatal development (E9.5, E10.5 and E11.5). Several miRNAs were positioned in polycistron clusters, including one particular large transcription unit consisting of 16 known and 23 new miRNAs. Our results indicate existence of a significant number of new miRNAs expressed at specific stages of mammalian embryonic development and which were not detected by earlier methods.}, pmid = {16582102}, keywords = {Animals,Cluster Analysis,Developmental,Embryo,Embryonic Development,Embryonic Development: genetics,Gene Expression Profiling,Gene Expression Regulation,Gene Library,Genomics,Inbred BALB C,Mammalian,Mammalian: metabolism,Mice,MicroRNAs,MicroRNAs: analysis,MicroRNAs: genetics,MicroRNAs: metabolism,nosource,RNA,Small Interfering,Small Interfering: analysis} }

@article{kuhnTemplateindependentLigationSinglestranded2005, title = {Template-Independent Ligation of Single-Stranded {{DNA}} by {{T4 DNA}} Ligase.}, author = {Kuhn, Heiko and {Frank-Kamenetskii}, Maxim D.}, year = 2005, month = dec, journal = {The FEBS journal}, volume = {272}, number = {23}, eprint = {16302964}, eprinttype = {pubmed}, pages = {5991–6000}, issn = {1742-464X}, doi = {10.1111/j.1742-4658.2005.04954.x}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16302964}, abstract = {T4 DNA ligase is one of the workhorses of molecular biology and used in various biotechnological applications. Here we report that this ligase, unlike Escherichia coli DNA ligase, Taq DNA ligase and Ampligase, is able to join the ends of single-stranded DNA in the absence of any duplex DNA structure at the ligation site. Such nontemplated ligation of DNA oligomers catalyzed by T4 DNA ligase occurs with a very low yield, as assessed by quantitative competitive PCR, between 10(-6) and 10(-4) at oligonucleotide concentrations in the range 0.1-10 nm, and thus is insignificant in many molecular biological applications of T4 DNA ligase. However, this side reaction may be of paramount importance for diagnostic detection methods that rely on template-dependent or target-dependent DNA probe ligation in combination with amplification techniques, such as PCR or rolling-circle amplification, because it can lead to nonspecific background signals or false positives. Comparison of ligation yields obtained with substrates differing in their strandedness at the terminal segments involved in ligation shows that an acceptor duplex DNA segment bearing a 3’-hydroxy end, but lacking a 5’-phosphate end, is sufficient to play a role as a cofactor in blunt-end ligation.}, pmid = {16302964}, keywords = {Circular,Circular: chemistry,Circular: metabolism,DNA,DNA Ligases,DNA Ligases: metabolism,nosource,Oligonucleotides,Oligonucleotides: genetics,Oligonucleotides: metabolism,Polymerase Chain Reaction,Single-Stranded,Single-Stranded: chemistry,Single-Stranded: metabolism} }

@article{jayaprakashIdentificationRemediationBiases2011, title = {Identification and Remediation of Biases in the Activity of {{RNA}} Ligases in Small-{{RNA}} Deep Sequencing.}, author = {Jayaprakash, Anitha D. and Jabado, Omar and Brown, Brian D. and Sachidanandam, Ravi}, year = 2011, month = nov, journal = {Nucleic acids research}, volume = {39}, number = {21}, pages = {e141}, issn = {1362-4962}, doi = {10.1093/nar/gkr693}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3241666&tool=pmcentrez&rendertype=abstract}, abstract = {Deep sequencing of small RNAs (sRNA-seq) is now the gold standard for small RNA profiling and discovery. Biases in sRNA-seq have been reported, but their etiology remains unidentified. Through a comprehensive series of sRNA-seq experiments, we establish that the predominant cause of the bias is the RNA ligases. We further demonstrate that RNA ligases have strong sequence-specific biases which distort the small RNA profiles considerably. We have devised a pooled adapter strategy to overcome this bias, and validated the method through data derived from microarray and qPCR. In light of our findings, published small RNA profiles, as well as barcoding strategies using adapter-end modifications, may need to be revisited. Importantly, by providing a wide spectrum of substrate for the ligase, the pooled-adapter strategy developed here provides a means to overcome issues of bias, and generate more accurate small RNA profiles.}, pmid = {21890899}, keywords = {Animals,Bias (Epidemiology),Gene Expression Profiling,HEK293 Cells,High-Throughput Nucleotide Sequencing,High-Throughput Nucleotide Sequencing: methods,Humans,Mice,nosource,RNA,RNA Ligase (ATP),RNA: methods,Sequence Analysis,Small Untranslated,Small Untranslated: chemistry,Small Untranslated: metabolism} }

@article{levinComprehensiveComparativeAnalysis2010, title = {Comprehensive Comparative Analysis of Strand-Specific {{RNA}} Sequencing Methods.}, author = {Levin, Joshua Z. and Yassour, Moran and Adiconis, Xian and Nusbaum, Chad and Thompson, Dawn Anne and Friedman, Nir and Gnirke, Andreas and Regev, Aviv}, year = 2010, month = sep, journal = {Nature methods}, volume = {7}, number = {9}, pages = {709–15}, publisher = {Nature Publishing Group}, issn = {1548-7105}, doi = {10.1038/nmeth.1491}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3005310&tool=pmcentrez&rendertype=abstract}, abstract = {Strand-specific, massively parallel cDNA sequencing (RNA-seq) is a powerful tool for transcript discovery, genome annotation and expression profiling. There are multiple published methods for strand-specific RNA-seq, but no consensus exists as to how to choose between them. Here we developed a comprehensive computational pipeline to compare library quality metrics from any RNA-seq method. Using the well-annotated Saccharomyces cerevisiae transcriptome as a benchmark, we compared seven library-construction protocols, including both published and our own methods. We found marked differences in strand specificity, library complexity, evenness and continuity of coverage, agreement with known annotations and accuracy for expression profiling. Weighing each method’s performance and ease, we identified the dUTP second-strand marking and the Illumina RNA ligation methods as the leading protocols, with the former benefitting from the current availability of paired-end sequencing. Our analysis provides a comprehensive benchmark, and our computational pipeline is applicable for assessment of future protocols in other organisms.}, pmid = {20711195}, keywords = {Complementary,Complementary: genetics,Computational Biology,DNA,Gene Expression Profiling,Gene Expression Profiling: methods,Gene Library,nosource,RNA,RNA: methods,Sequence Analysis,Substrate Specificity} }

@article{contrerasBiologicalAspectsDM28C1988, title = {Biological Aspects of the {{DM28C}} Clone of {{Trypanosoma}} Cruzi after Metacylogenesis in Chemically Defined Media}, author = {Contreras, V. T. and {Ara{'u}jo-Jorge}, T. C. and Bonaldo, M. and Thomaz, N. and Barbosa, H. and Nazareth, M. and Goldenberg, Samuel}, year = 1988, journal = {Memorias do Instituto }, url = {http://www.scielo.br/scielo.php?pid=S0074-02761988000100016&script=sci_arttext}, keywords = {nosource} }

@article{brechtChangesPolysomeProfiles1998, title = {Changes in Polysome Profiles Accompany Trypanosome Development.}, author = {Brecht, M. and Parsons, M.}, year = 1998, month = nov, journal = {Molecular and biochemical parasitology}, volume = {97}, number = {1-2}, eprint = {9879897}, eprinttype = {pubmed}, pages = {189–98}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9879897}, abstract = {Development of the protozoan pathogen Trypanosoma brucei involves regulated changes in parasite structure, biochemistry, and the cell cycle. The transition of slender blood forms into stumpy bloodforms includes cell cycle arrest and a decrease in protein synthesis. The next stage in the development cycle, the procyclic form, shows increased protein synthesis and proliferates. To address the mechanism of the cyclical changes in protein synthesis, we examined two parameters: polyadenylation of mRNA and ribosome loading. We developed a method for analytical polyribosome analysis in T. brucei which provided excellent results with regard to reproducibility, yield of mRNA densely loaded with ribosomes, and separation of mRNA associated with different numbers of polyribosomes. Use of this technique allowed us to determine that the polysome profiles of the different developmental stages are distinctly different, with higher ribosome loading in the proliferating stages. The lengths of the poly(A) tails on the total population of RNA from the different developmental stages showed no significant variation. These data indicate that changes in polysome loading of mRNAs accompany development, and that they do not reflect bulk changes in polyadenylation. We speculate that developmental changes in translation reflect reduced translational initiation.}, pmid = {9879897}, keywords = {Animals,Blotting,Genetic,Genetic Techniques,Helminth,Helminth Proteins,Helminth Proteins: analysis,Helminth: analysis,Helminth: genetics,Hybridization,Life Cycle Stages,Male,Northern,nosource,Polyribosomes,Polyribosomes: chemistry,Polyribosomes: genetics,Rats,RNA,Trypanosoma brucei brucei,Trypanosoma brucei brucei: growth & development,Trypanosoma brucei brucei: metabolism,Wistar} }

@article{parsonsElevatedPhosphoglycerateKinase1989, title = {Elevated Phosphoglycerate Kinase {{mRNA}} but Not Protein in Monomorphic {{Trypanosoma}} Brucei: Implications for Stage-Regulation and Post-Transcriptional Control.}, author = {Parsons, M. and Hill, T.}, year = 1989, month = mar, journal = {Molecular and biochemical parasitology}, volume = {33}, number = {3}, eprint = {2704387}, eprinttype = {pubmed}, pages = {215–27}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2704387}, abstract = {Phosphoglycerate kinase (PGK) is present in high levels in the glycosomes of bloodstream stage Trypanosoma brucei, but is virtually absent in procyclic stage glycosomes. Glycosomes isolated from slender and stumpy stage bloodforms show similar levels of PGK, although levels are slightly lower in stumpy forms. Lower levels of glycosomal PGK transcripts are observed in stumpy form RNA, paralleling the decrease in glycosomal PGK activity. Monomorphic strains and pleiomorphic strains show similar glycosomal PGK activity, but monomorphic strains have much higher levels of the glycosomal PGK transcript. In three separate cases, predominantly monomorphic strains derived from highly pleiomorphic strains showed increased levels of glycosomal PGK (gPGK) mRNA. gPGK synthesis rates in monomorphic and pleiomorphic strains were similar, and no significant differences in turnover were observed. These data suggest the possibility of translational control of gPGK protein levels in trypanosome bloodforms. The data also indicate that the metabolism of gPGK mRNA in highly passaged laboratory strains is altered, and counsel caution when attributing differences in transcript levels to stage-specific regulation.}, pmid = {2704387}, keywords = {Animals,Blotting,Electrophoresis,Genetic,Messenger,Messenger: analysis,Northern,nosource,Nucleic Acid Hybridization,Phosphoglycerate Kinase,Phosphoglycerate Kinase: biosynthesis,Phosphoglycerate Kinase: genetics,Phosphoglycerate Kinase: metabolism,Polyacrylamide Gel,Post-Transcriptional,RNA,RNA Processing,Transcription,Trypanosoma brucei brucei,Trypanosoma brucei brucei: enzymology,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: pathogenicity,Virulence} }

@article{boucherCommonMechanismStageregulated2002, title = {A Common Mechanism of Stage-Regulated Gene Expression in {{Leishmania}} Mediated by a Conserved 3’-Untranslated Region Element.}, author = {Boucher, Nathalie and Wu, Ying and Dumas, Carole and Dube, Marthe and Sereno, Denis and Breton, Marie and Papadopoulou, Barbara}, year = 2002, month = may, journal = {The Journal of biological chemistry}, volume = {277}, number = {22}, eprint = {11912202}, eprinttype = {pubmed}, pages = {19511–20}, issn = {0021-9258}, doi = {10.1074/jbc.M200500200}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11912202}, abstract = {Developmental regulation of mRNA levels in trypanosomatid protozoa is determined post-transcriptionally and often involves sequences located in the 3’-untranslated regions (3’-UTR) of the mRNAs. We have previously identified a developmentally regulated gene family in Leishmania encoding the amastin surface proteins and showed that stage-specific accumulation of the amastin mRNA is mediated by sequences within the 3’-UTR. Here we identified a 450-nt region within the amastin 3’-UTR that can confer amastigote-specific gene expression by a novel mechanism that increases mRNA translation without an increase in mRNA stability. Remarkably, this 450-nt 3’-UTR element is highly conserved among a large number of Leishmania mRNAs in several Leishmania species. Here we show that several of these mRNAs are differentially expressed in the intracellular amastigote stage of the parasite and that the 450-nt conserved element in their 3’-UTRs is responsible for stage-specific gene regulation. We propose that the 450-nt conserved element, which is unlike any other regulatory element identified thus far, is part of a common mechanism of stage-regulated gene expression in Leishmania that regulates mRNA translation in response to intracellular stresses.}, pmid = {11912202}, keywords = {3’ Untranslated Regions,Animals,Base Sequence,Conserved Sequence,DNA,DNA: metabolism,Gene Deletion,Gene Expression Regulation,Genes,Inbred BALB C,Kinetics,Leishmania,Leishmania: genetics,Messenger,Messenger: metabolism,Mice,Molecular Sequence Data,nosource,Open Reading Frames,Protein Biosynthesis,Reporter,RNA,Time Factors,Transfection} }

@article{galeTranslationalControlMediates1994, title = {Translational Control Mediates the Developmental Regulation of the {{Trypanosoma}} Brucei {{Nrk}} Protein Kinase.}, author = {Gale, M. and Carter, V. and Parsons, M.}, year = 1994, month = dec, journal = {The Journal of biological chemistry}, volume = {269}, number = {50}, eprint = {7989338}, eprinttype = {pubmed}, pages = {31659–65}, issn = {0021-9258}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7989338}, abstract = {The expression and function of eukaryotic protein kinases is highly regulated, primarily through transcriptional and post-translational processes. In this report we demonstrate an unusual mechanism for controlling protein kinase function, translational control. The Trypanosoma brucei Nrk loci encode predicted protein kinases. Here we show that Nrk has protein serine-threonine kinase activity and examine the expression and activity of Nrk during parasite development. While Nrk transcripts were previously found to be constitutively expressed throughout the life cycle, we now find that expression of Nrk protein is highly stage-regulated. Immunoblot analysis revealed that Nrk expression dramatically increased as the parasites differentiated from proliferative slender bloodforms to the non-proliferative stumpy bloodforms. Procyclic form organisms expressed moderate levels of Nrk. Analysis of Nrk activity demonstrated that it too was highest in stumpy bloodforms. Metabolic labeling and pulse-chase analysis demonstrated that Nrk accumulation was highest in stumpy bloodforms and indicated that Nrk abundance is primarily controlled at the level of biosynthesis rather than turnover. All Nrk mRNA was contained in the poly(A)+ fraction, and the 5’ ends of the transcript were the same in each developmental stage. Thus, Nrk is under translational control. The strict developmental regulation of the Nrk enzymes within the trypanosome life cycle suggests that the Nrk protein kinase may play a role in parasite differentiation.}, isbn = {2062848846}, pmid = {7989338}, keywords = {Animals,Base Sequence,Blotting,Developmental,DNA Primers,DNA Primers: chemistry,Gene Expression Regulation,Genes,Intracellular Signaling Peptides and Proteins,Messenger,Messenger: genetics,Molecular Sequence Data,nosource,Protein Biosynthesis,Protein-Serine-Threonine Kinases,Protein-Serine-Threonine Kinases: genetics,Protein-Serine-Threonine Kinases: metabolism,Protozoan,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,RNA,Substrate Specificity,Trypanosoma brucei brucei,Trypanosoma brucei brucei: enzymology,Western} }

@article{jagerMRNAMaturationTwostep2007, title = {{{mRNA}} Maturation by Two-Step Trans-Splicing/Polyadenylation Processing in Trypanosomes.}, author = {J{"a}ger, Adriana V. and Gaudenzi, Javier G. De and Cassola, Alejandro and D’Orso, Iv{'a}n and Frasch, Alberto C.}, year = 2007, month = feb, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {7}, pages = {2035–42}, issn = {0027-8424}, doi = {10.1073/pnas.0611125104}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1892994&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanosomes are unique eukaryotic cells, in that they virtually lack mechanisms to control gene expression at the transcriptional level. These microorganisms mostly control protein synthesis by posttranscriptional regulation processes, like mRNA stabilization and degradation. Transcription in these cells is polycistronic. Tens to hundreds of protein-coding genes of unrelated function are arrayed in long clusters on the same DNA strand. Polycistrons are cotranscriptionally processed by trans-splicing at the 5’ end and polyadenylation at the 3’ end, generating monocistronic units ready for degradation or translation. In this work, we show that some trans-splicing/polyadenylation sites may be skipped during normal polycistronic processing. As a consequence, dicistronic units or monocistronic transcripts having long 3’ UTRs are produced. Interestingly, these unspliced transcripts can be processed into mature mRNAs by the conventional trans-splicing/polyadenylation events leading to translation. To our knowledge, this is a previously undescribed mRNA maturation by trans-splicing uncoupled from transcription. We identified an RNA-recognition motif-type protein, homologous to the mammalian polypyrimidine tract-binding protein, interacting with one of the partially processed RNAs analyzed here that might be involved in exon skipping. We propose that splice-site skipping might be part of a posttranscriptional mechanism to regulate gene expression in trypanosomes, through the generation of premature nontranslatable RNA molecules.}, isbn = {1047053507093}, pmid = {17267594}, keywords = {3’ Untranslated Regions,Animals,Gene Expression Regulation,Genes,nosource,Polyadenylation,Post-Transcriptional,Protozoan,Protozoan: genetics,RNA,RNA Processing,Trans-Splicing,Trypanosoma,Trypanosoma: genetics} }

@article{jensenWidespreadVariationTranscript2009, title = {Widespread Variation in Transcript Abundance within and across Developmental Stages of {{Trypanosoma}} Brucei.}, author = {Jensen, Bryan C. and Sivam, Dhileep and Kifer, Charles T. and Myler, Peter J. and Parsons, Marilyn}, year = 2009, month = jan, journal = {BMC genomics}, volume = {10}, pages = {482}, issn = {1471-2164}, doi = {10.1186/1471-2164-10-482}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2771046&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanosoma brucei, the causative agent of African sleeping sickness, undergoes a complex developmental cycle that takes place in mammalian and insect hosts and is accompanied by changes in metabolism and cellular morphology. While differences in mRNA expression have been described for many genes, genome-wide expression analyses have been largely lacking. Trypanosomatids represent a unique case in eukaryotes in that they transcribe protein-coding genes as large polycistronic units, and rarely regulate gene expression at the level of transcription initiation.}, pmid = {19840382}, keywords = {Animals,Cluster Analysis,Developmental,Gene Expression Profiling,Gene Expression Regulation,Genome,Messenger,Messenger: genetics,nosource,Oligonucleotide Array Sequence Analysis,Protozoan,Protozoan: genetics,Rats,RNA,Trypanosoma,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: growth & development,Trypanosoma: geneti,Variant Surface Glycoproteins,Wistar} }

@article{mcnicollCombinedProteomicTranscriptomic2006, title = {A Combined Proteomic and Transcriptomic Approach to the Study of Stage Differentiation in {{Leishmania}} Infantum.}, author = {McNicoll, Fran{}ois and Drummelsmith, Jolyne and M{"u}ller, Michaela and Madore, Eric and Boilard, Nathalie and Ouellette, Marc and Papadopoulou, Barbara}, year = 2006, month = jun, journal = {Proteomics}, volume = {6}, number = {12}, eprint = {16705753}, eprinttype = {pubmed}, pages = {3567–81}, issn = {1615-9853}, doi = {10.1002/pmic.200500853}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16705753}, abstract = {Protozoan parasites of the genus Leishmania are found as promastigotes in the sandfly vector and as amastigotes in mammalian macrophages. Mechanisms controlling stage-regulated gene expression in these organisms are poorly understood. Here, we applied a comprehensive approach consisting of protein prefractionation, global proteomics and targeted DNA microarray analysis to the study of stage differentiation in Leishmania. By excluding some abundant structural proteins and reducing complexity, we detected and identified numerous novel differentially expressed protein isoforms in L. infantum. Using 2-D gels, over 2200 protein isoforms were visualized in each developmental stage. Of these, 6.1% were strongly increased or appeared unique in the promastigote stage, while the relative amounts of 12.4% were increased in amastigotes. Amastigote-specific protein isoform and mRNA expression trends correlated modestly (53%), while no correlation was found for promastigote-specific spots. Even where direction of regulation was similar, fold-changes were more modest at the RNA than protein level. Many proteins were present in multiple spots, suggesting that PTM is extensive in this organism. In several cases, different isoforms appeared to be specific to different life stages. Our results suggest that post-transcriptional controls at translational and post-translational levels could play major roles in differentiation in Leishmania parasites.}, pmid = {16705753}, keywords = {Animals,Developmental,Electrophoresis,Gel,Gene Expression Regulation,Gene Targeting,Genes,Genetic,Leishmania infantum,Leishmania infantum: chemistry,Leishmania infantum: genetics,Leishmania infantum: growth & development,Leishmania infantum: metabolism,Life Cycle Stages,Messenger,Messenger: metabolism,nosource,Oligonucleotide Array Sequence Analysis,Peptide Fragments,Peptide Fragments: chemistry,Peptide Mapping,Protein Isoforms,Protein Isoforms: genetics,Protein Isoforms: metabolism,Proteome,Proteome: analysis,Proteomics,Proteomics: methods,Protozoan,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,RNA,Transcription,Two-Dimensional} }

@book{mathersGlobalBurdenDisease2008, title = {The Global Burden of Disease: 2004 Update}, author = {Mathers, C. and Fat, D. M. and Boerma, J. T.}, year = 2008, url = {http://books.google.com/books?hl=en&lr=&id=xrYYZ6Jcfv0C&oi=fnd&pg=PR5&dq=The+global+burden+of+disease+2004&ots=t9_zZh45tp&sig=j_X8B-sp4EXwz9w9uJADBYJO_YE}, keywords = {nosource} } % == BibTeX quality report for mathersGlobalBurdenDisease2008: % Missing required field ‘publisher’

@article{restringidaESTIMACiONCUANTITATIVAENFERMEDAD, title = {{{ESTIMACi'ON CUANTITATIVA DE LA ENFERMEDAD DE CHAGAS EN LAS AM'ERICAS}}}, author = {Restringida, C.}, journal = {bvsops.org.uy}, url = {http://www.bvsops.org.uy/pdf/chagas19.pdf}, keywords = {nosource} } % == BibTeX quality report for restringidaESTIMACiONCUANTITATIVAENFERMEDAD: % Missing required field ‘year’ % ? Possibly abbreviated journal title bvsops.org.uy % ? Title looks like it was stored in title-case in Zotero

@article{luenenGlucosylatedHydroxymethyluracilDNA2012, title = {Glucosylated Hydroxymethyluracil, {{DNA}} Base {{J}}, Prevents Transcriptional Readthrough in {{Leishmania}}.}, author = {{}van Luenen, Henri G. a M. and Farris, Carol and Jan, Sabrina and Genest, Paul-Andre and Tripathi, Pankaj and Velds, Arno and Kerkhoven, Ron M. and Nieuwland, Marja and Haydock, Andrew and Ramasamy, Gowthaman and Vainio, Saara and Heidebrecht, Tatjana and Perrakis, Anastassis and Pagie, Ludo and {}van Steensel, Bas and Myler, Peter J. and Borst, Piet}, year = 2012, month = aug, journal = {Cell}, volume = {150}, number = {5}, eprint = {22939620}, eprinttype = {pubmed}, pages = {909–21}, issn = {1097-4172}, doi = {10.1016/j.cell.2012.07.030}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22939620}, abstract = {Some Ts in nuclear DNA of trypanosomes and Leishmania are hydroxylated and glucosylated to yield base J ({\(\beta\)}-D-glucosyl-hydroxymethyluracil). In Leishmania, about 99% of J is located in telomeric repeats. We show here that most of the remaining J is located at chromosome-internal RNA polymerase II termination sites. This internal J and telomeric J can be reduced by a knockout of J-binding protein 2 (JBP2), an enzyme involved in the first step of J biosynthesis. J levels are further reduced by growing Leishmania JBP2 knockout cells in BrdU-containing medium, resulting in cell death. The loss of internal J in JBP2 knockout cells is accompanied by massive readthrough at RNA polymerase II termination sites. The readthrough varies between transcription units but may extend over 100 kb. We conclude that J is required for proper transcription termination and infer that the absence of internal J kills Leishmania by massive readthrough of transcriptional stops.}, pmid = {22939620}, keywords = {Double-Stranded,Double-Stranded: metabolism,Gene Knockout Techniques,Genetic,Glucosides,Glucosides: metabolism,Leishmania,Leishmania: genetics,Leishmania: metabolism,nosource,RNA,RNA Polymerase II,RNA Polymerase II: metabolism,Transcription,Uracil,Uracil: analogs & derivatives,Uracil: metabolism} }

@article{tomasStageregulatedExpressionCruzipain1996, title = {Stage-Regulated Expression of Cruzipain, the Major Cysteine Protease of {{Trypanosoma}} Cruzi Is Independent of the Level of {{RNA1}}.}, author = {Tom{'a}s, a M. and Kelly, J. M.}, year = 1996, journal = {Molecular and biochemical parasitology}, volume = {76}, number = {1-2}, eprint = {8919998}, eprinttype = {pubmed}, pages = {91–103}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8919998}, abstract = {The genes that encode cruzipain, the major cysteine protease of Trypanosoma cruzi are known to be arranged in tandem arrays. To gain a detailed insight into how these arrays are organised at the chromosomal level we have isolated clones from a cosmid library constructed with DNA from the X10.6 strain. In this strain we found that cruzipain is encoded by two allelic clusters composed of approximately 14 and 23 tandemly repeated genes which are located on homologous chromosomes of 650 and 670 kb. With the exception of the 3’-proximal genes, the cruzipain genes were all of identical or very similar sequence. An unusual feature of the 3’-proximal genes is that they lack the sequences that encode the 130 amino acid carboxyl terminal extension which is characteristic of cruzipain. Both gene clusters are situated in a similar chromosomal environment and are flanked by sequences which have the potential to form Z-DNA. In other eukaryotes, these motifs have been associated with recombinational hotspots and have been demonstrated to enhance gene conversion. The cruzipain genes are transcribed to produce a 1.8-kb transcript which is present at the same steady-state level in each of the parasite life cycle stages. However, protein levels and activity are 4-5-times higher in the insect epimastigote stage than in the trypomastigote and amastigote stages. By implication developmental regulation of cruzipain expression occurs predominantly at the translational and/or post-translational levels.}, pmid = {8919998}, keywords = {Amino Acid Sequence,Animals,Base Sequence,Blotting,Cloning,Cosmids,Cysteine Endopeptidases,Cysteine Endopeptidases: genetics,Cysteine Endopeptidases: metabolism,Gene Expression Regulation,Gene Library,Molecular,Molecular Sequence Data,Multigene Family,nosource,Polymerase Chain Reaction,Protozoan,Protozoan: biosynthesis,RNA,Southern,Trypanosoma cruzi,Trypanosoma cruzi: enzymology,Trypanosoma cruzi: genetics,Western} }

@article{gonzalez-pinoExpressionAlphaBetatubulin1999, title = {Expression of Alpha- and Beta-Tubulin Genes during Growth of {{Trypanosoma}} Cruzi Epimastigotes.}, author = {{Gonz{'a}lez-Pino}, M. J. and {Rangel-Aldao}, R. and Slezynger, T. C.}, year = 1999, month = jun, journal = {DNA and cell biology}, volume = {18}, number = {6}, eprint = {10390153}, eprinttype = {pubmed}, pages = {449–55}, issn = {1044-5498}, doi = {10.1089/104454999315169}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10390153}, abstract = {The expression of tubulin genes was studied during the growth of epimastigotes of Trypanosoma cruzi. Northern blot analysis showed that there was a decrease in the levels of alpha- and beta-tubulin mRNAs as epimastigotes changed from the logarithmic to the stationary phase. The changes were associated with a similar decrease in the rates of transcription for both of these genes as measured by run-on assays using permeabilized parasites. In contrast to these results, ubiquitin transcription increased slightly. The levels of alpha-tubulin protein per parasite also decreased in stationary compared with logarithmic phase epimastigotes, in close agreement with the decrease in transcription. However, beta-tubulin protein levels did not change significantly. Our results thus indicated that during the growth of epimastigotes, the expression of alpha-tubulin is controlled partially at the transcriptional level. On the other hand, the experiments also suggested that beta-tubulin expression is controlled at a post-transcriptional level.}, pmid = {10390153}, keywords = {Animals,Blotting,Cell Membrane Permeability,Cell Membrane Permeability: genetics,Developmental,Gene Expression Regulation,Genetic,Messenger,Messenger: metabolism,nosource,RNA,Transcription,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosoma cruzi: growth & development,Tubulin,Tubulin: biosynthesis,Tubulin: genetics,Tubulin: isolation & purification,Western} }

@article{pabaProteomicAnalysisTrypanosoma2004, title = {Proteomic Analysis of {{Trypanosoma}} Cruzi Developmental Stages Using Isotope-Coded Affinity Tag Reagents}, author = {Paba, Jaime and Ricart, Carlos A. O. and Fontes, Wagner and Santana, Jaime M. and Teixeira, Antonio R. L. and Marchese, Jason and Williamson, Brian and Hunt, Tony and Karger, Barry L. and Sousa, Marcelo V.}, year = 2004, journal = { of proteome research}, pages = {517–524}, url = {http://pubs.acs.org/doi/abs/10.1021/pr034075o}, keywords = {icat reagents,isotope-coded affinity tag,nosource,proteome,proteomics,trypanosoma cruzi} }

@article{gasconChagasDiseaseSpain2010, title = {Chagas Disease in {{Spain}}, the {{United States}} and Other Non-Endemic Countries.}, author = {Gascon, Joaquim and Bern, Caryn and Pinazo, Mar{'i}a-Jes{'u}s}, year = 2010, journal = {Acta tropica}, volume = {115}, number = {1-2}, eprint = {19646412}, eprinttype = {pubmed}, pages = {22–7}, issn = {1873-6254}, doi = {10.1016/j.actatropica.2009.07.019}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19646412}, abstract = {Due to recent trends in migration, there are millions of people from Chagas disease-endemic countries now living in North America, Europe, Australia and Japan, including thousands of people with Trypanosoma cruzi infection. Most infected individuals are not aware of their status. Congenital, transfusion- and/or transplant-associated transmission has been documented in the United States, Spain, Canada and Switzerland; most instances likely go undetected. High priorities include the implementation of appropriate screening, evaluation and clinical management, and better assessment of the true burden associated with this disease.}, pmid = {19646412}, keywords = {Australia,Australia: epidemiology,Chagas Disease,Chagas Disease: diagnosis,Chagas Disease: epidemiology,Chagas Disease: transmission,Communicable Disease Control,Communicable Disease Control: methods,Developed Countries,Emigration and Immigration,Europe,Europe: epidemiology,Humans,Japan,Japan: epidemiology,Mass Screening,Mass Screening: methods,North America,North America: epidemiology,nosource,Trypanosoma cruzi,Trypanosoma cruzi: isolation & purification} }

@article{caldasBenznidazoleTherapyAcute2008, title = {Benznidazole Therapy during Acute Phase of {{Chagas}} Disease Reduces Parasite Load but Does Not Prevent Chronic Cardiac Lesions.}, author = {Caldas, Ivo Santana and Talvani, Andr{'e} and Caldas, S{'e}rgio and Carneiro, Cl{'a}udia Martins and {}de Lana, Marta and Guedes, Paulo Marcos da Matta and Bahia, Maria Terezinha}, year = 2008, month = jul, journal = {Parasitology research}, volume = {103}, number = {2}, eprint = {18454349}, eprinttype = {pubmed}, pages = {413–21}, issn = {0932-0113}, doi = {10.1007/s00436-008-0992-6}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18454349}, abstract = {The goals of this study were to evaluate the efficacy of benznidazole (Bz) treatment in decreasing of the parasitic load during the acute phase of experimental Chagas disease and to analyze its influence in the development of cardiac chronic alterations in mice inoculated with drug-resistant Trypanosoma cruzi strains. Our results showed that the early Bz treatment (started at 4th day of infection) was efficient in reducing the parasite load in animals from both acute and chronic phase of the infection. Moreover, this reduction in the parasite load could not be associated with the intensity of the cardiac chronic lesions. The histopathological evaluation of cardiac tissue of Bz-treated mice showed three different patterns of response: (1) presence of a small number of inflammatory cells and fibrotic area similar to noninfected mice; (2) similar intensity of inflammatory infiltrate and smaller fibrotic area in relation to nontreated animals; (3) similar intensity of inflammatory infiltrated and fibrosis area among the Bz-treated and nontreated animals. Each specific pattern was obtained with different T. cruzi strain, suggesting that the pattern of the heart lesions in chronic phase of Bz-treated animals was T. cruzi strain dependent but not related with drug resistance levels.}, pmid = {18454349}, keywords = {Acute Disease,Animals,Chagas Disease,Chagas Disease: drug therapy,Chagas Disease: mortality,Chagas Disease: parasitology,Chagas Disease: pathology,Chronic Disease,Drug Resistance,Heart,Heart: parasitology,Humans,Mice,Myocardium,Myocardium: pathology,Nitroimidazoles,Nitroimidazoles: pharmacology,Nitroimidazoles: therapeutic use,nosource,Parasitemia,Parasitemia: drug therapy,Parasitemia: mortality,Parasitemia: parasitology,Trypanocidal Agents,Trypanocidal Agents: pharmacology,Trypanocidal Agents: therapeutic use,Trypanosoma cruzi,Trypanosoma cruzi: drug effects,Trypanosoma cruzi: isolation & purification,Trypanosoma cruzi: pathogenicity} }

@article{diasImpactChagasDisease2002, title = {The Impact of {{Chagas}} Disease Control in {{Latin America}}: A Review.}, author = {Dias, J. C. P. and Silveira, a C. and Schofield, C. J.}, year = 2002, month = jul, journal = {Mem'orias do Instituto Oswaldo Cruz}, volume = {97}, number = {5}, eprint = {12219120}, eprinttype = {pubmed}, pages = {603–12}, issn = {0074-0276}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12219120}, abstract = {Discovered in 1909, Chagas disease was progressively shown to be widespread throughout Latin America, affecting millions of rural people with a high impact on morbidity and mortality. With no vaccine or specific treatment available for large-scale public health interventions, the main control strategy relies on prevention of transmission, principally by eliminating the domestic insect vectors and control of transmission by blood transfusion. Vector control activities began in the 1940s, initially by means of housing improvement and then through insecticide spraying following successful field trials in Brazil (Bambui Research Centre), with similar results soon reproduced in S~ao Paulo, Argentina, Venezuela and Chile. But national control programmes only began to be implemented after the 1970s, when technical questions were overcome and the scientific demonstration of the high social impact of Chagas disease was used to encourage political determination in favour of national campaigns (mainly in Brazil). Similarly, large-scale screening of infected blood donors in Latin America only began in the 1980s following the emergence of AIDS. By the end of the last century it became clear that continuous control in contiguous endemic areas could lead to the elimination of the most highly domestic vector populations - especially Triatoma infestans and Rhodnius prolixus - as well as substantial reductions of other widespread species such as T. brasiliensis, T. sordida, and T. dimidiata, leading in turn to interruption of disease transmission to rural people. The social impact of Chagas disease control can now be readily demonstrated by the disappearance of acute cases and of new infections in younger age groups, as well as progressive reductions of mortality and morbidity rates in controlled areas. In economic terms, the cost-benefit relationship between intervention (insecticide spraying, serology in blood banks) and the reduction of Chagas disease (in terms of medical and social care and improved productivity) is highly positive. Effective control of Chagas disease is now seen as an attainable goal that depends primarily on maintaining political will, so that the major constraints involve problems associated with the decentralisation of public health services and the progressive political disinterest in Chagas disease. Counterbalancing this are the political and technical cooperation strategies such as the “Southern Cone Initiative” launched in 1991. This international approach, coordinated by PAHO, has been highly successful, already reaching elimination of Chagas disease transmission in Uruguay, Chile, and large parts of Brazil and Argentina. The Southern Cone Initiative also helped to stimulate control campaigns in other countries of the region (Paraguay, Bolivia, Peru) which have also reached tangible regional successes. This model of international activity has been shown to be feasible and effective, with similar initiatives developed since 1997 in the Andean Region and in Central America. At present, Mexico and the Amazon Region remain as the next major challenges. With consolidation of operational programmes in all endemic countries, the future focus will be on epidemiological surveillance and care of those people already infected. In political terms, the control of Chagas disease in Latin America can be considered, so far, as a victory for international scientific cooperation, but will require continuing political commitment for sustained success.}, pmid = {12219120}, keywords = {Animals,Chagas Disease,Chagas Disease: epidemiology,Chagas Disease: prevention & control,Chagas Disease: transmission,Humans,Insect Control,Insect Vectors,Latin America,Latin America: epidemiology,nosource,Trypanosoma cruzi} }

@article{bernEstimateBurdenChagas2009, title = {An Estimate of the Burden of {{Chagas}} Disease in the {{United States}}.}, author = {Bern, Caryn and Montgomery, Susan P.}, year = 2009, month = sep, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {49}, number = {5}, eprint = {19640226}, eprinttype = {pubmed}, pages = {e52-4}, issn = {1537-6591}, doi = {10.1086/605091}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19640226}, abstract = {Chagas disease causes the highest burden of any parasitic disease in the Western hemisphere. By applying published seroprevalence figures to immigrant populations, we estimate that 300,167 individuals with Trypanosoma cruzi infection live in the United States, with 30,000-45,000 cardiomyopathy cases and 63-315 congenital infections annually. T. cruzi causes a substantial disease burden in the United States.}, pmid = {19640226}, keywords = {Animals,Antibodies,Chagas Cardiomyopathy,Chagas Cardiomyopathy: epidemiology,Chagas Cardiomyopathy: parasitology,Chagas Disease,Chagas Disease: epidemiology,Cost of Illness,Emigration and Immigration,Humans,nosource,Protozoan,Protozoan: blood,Sentinel Surveillance,Seroepidemiologic Studies,Severity of Illness Index,Trypanosoma cruzi,Trypanosoma cruzi: immunology,United States,United States: epidemiology} }

@article{moncayoGlobalBurdenChagas2002, title = {The {{Global Burden}} of {{Chagas}}’ {{Disease}} in the {{Year}} 2000}, author = {Moncayo, A. and Guhl, F. and Stein, C.}, year = 2002, pages = {1–13}, url = {http://www.who.int/entity/healthinfo/statistics/bod_chagas.pdf}, keywords = {nosource} } % == BibTeX quality report for moncayoGlobalBurdenChagas2002: % Missing required field ‘journal’ % ? Title looks like it was stored in title-case in Zotero

@article{kingAsymmetriesPovertyWhy2008, title = {Asymmetries of Poverty: Why Global Burden of Disease Valuations Underestimate the Burden of Neglected Tropical Diseases.}, author = {King, Charles H. and Bertino, Anne-Marie}, year = 2008, month = jan, journal = {PLoS neglected tropical diseases}, volume = {2}, number = {3}, pages = {e209}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0000209}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2267491&tool=pmcentrez&rendertype=abstract}, abstract = {The disability-adjusted life year (DALY) initially appeared attractive as a health metric in the Global Burden of Disease (GBD) program, as it purports to be a comprehensive health assessment that encompassed premature mortality, morbidity, impairment, and disability. It was originally thought that the DALY would be useful in policy settings, reflecting normative valuations as a standardized unit of ill health. However, the design of the DALY and its use in policy estimates contain inherent flaws that result in systematic undervaluation of the importance of chronic diseases, such as many of the neglected tropical diseases (NTDs), in world health. The conceptual design of the DALY comes out of a perspective largely focused on the individual risk rather than the ecology of disease, thus failing to acknowledge the implications of context on the burden of disease for the poor. It is nonrepresentative of the impact of poverty on disability, which results in the significant underestimation of disability weights for chronic diseases such as the NTDs. Finally, the application of the DALY in policy estimates does not account for the nonlinear effects of poverty in the cost-utility analysis of disease control, effectively discounting the utility of comprehensively treating NTDs. The present DALY framework needs to be substantially revised if the GBD is to become a valid and useful system for determining health priorities.}, pmid = {18365036}, keywords = {Communicable Diseases,Communicable Diseases: epidemiology,Humans,Models,nosource,Poverty,Quality-Adjusted Life Years,Theoretical,Tropical Medicine,World Health} }

@article{hotezControlNeglectedTropical2007, title = {Control of Neglected Tropical Diseases}, author = {Hotez, P. J. and Molyneux, D. H.}, year = 2007, journal = { England Journal of }, pages = {1018–1027}, url = {http://www.nejm.org/doi/full/10.1056/NEJMra064142}, keywords = {nosource} }

@article{aufderheide9000yearRecordChagas2004, title = {A 9,000-Year Record of {{Chagas}}’ Disease.}, author = {Aufderheide, Arthur C. and Salo, Wilmar and Madden, Michael and Streitz, John and Buikstra, Jane and Guhl, Felipe and Arriaza, Bernardo and Renier, Colleen and Wittmers, Lorentz E. and Fornaciari, Gino and Allison, Marvin}, year = 2004, month = feb, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {7}, pages = {2034–9}, issn = {0027-8424}, doi = {10.1073/pnas.0307312101}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=357047&tool=pmcentrez&rendertype=abstract}, abstract = {Tissue specimens from 283 principally spontaneously (naturally) desiccated human mummies from coastal and low valley sites in northern Chile and southern Peru were tested with a DNA probe directed at a kinetoplast DNA segment of Trypanosoma cruzi. The time interval spanned by the eleven major cultural groups represented in the sample ranged from approximately 9,000 years B.P. (7050 B.C.) to approximately the time of the Spanish conquest, approximately 450 B.P. ( approximately 1500 A.D.). Forty-one percent of the tissue extracts, amplified by the PCR reacted positively (i.e., hybridized) with the probe. Prevalence patterns demonstrated no statistically significant differences among the individual cultural groups, nor among subgroups compared on the basis of age, sex, or weight of specimen tested. These results suggest that the sylvatic (animal-infected) cycle of Chagas’ disease was probably well established at the time that the earliest humans (members of the Chinchorro culture) first peopled this segment of the Andean coast and inadvertently joined the many other mammal species acting as hosts for this parasite.}, pmid = {14766963}, keywords = {Adult,Age Factors,Ancient,Animals,Chagas Disease,Chagas Disease: epidemiology,Chagas Disease: history,Chagas Disease: parasitology,Chagas Disease: transmission,Chile,Chile: epidemiology,Ethnic Groups,Female,History,Humans,Male,Mummies,Mummies: parasitology,Muscles,Muscles: parasitology,nosource,Organ Size,Organ Specificity,Prevalence,Research Design,Sex Factors,Time Factors,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosoma cruzi: isolation & purification} }

@article{lutonComparisonsRibosomalInternal1992, title = {Comparisons of Ribosomal Internal Transcribed Spacers from Two Congeneric Species of Flukes ({{Platyhelminthes}}: {{Trematoda}}: {{Digenea}}).}, author = {Luton, K. and Walker, D. and Blair, D.}, year = 1992, month = dec, journal = {Molecular and biochemical parasitology}, volume = {56}, number = {2}, eprint = {1484553}, eprinttype = {pubmed}, pages = {323–7}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/1484553}, pmid = {1484553}, keywords = {Animals,Base Sequence,Cloning,DNA,Genetic,Genetic Variation,Molecular,Molecular Sequence Data,nosource,Nucleic Acid,Ribosomal,Ribosomal: genetics,Sequence Homology,Species Specificity,Transcription,Trematoda,Trematoda: classification,Trematoda: genetics} }

@article{danaDeterminantsTranslationElongation2012, title = {Determinants of {{Translation Elongation Speed}} and {{Ribosomal Profiling Biases}} in {{Mouse Embryonic Stem Cells}}}, author = {Dana, Alexandra and Tuller, Tamir}, editor = {Teichmann, Sarah A.}, year = 2012, month = nov, journal = {PLoS Computational Biology}, volume = {8}, number = {11}, pages = {e1002755}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002755}, url = {http://dx.plos.org/10.1371/journal.pcbi.1002755}, keywords = {nosource} } % == BibTeX quality report for danaDeterminantsTranslationElongation2012: % ? Title looks like it was stored in title-case in Zotero

@article{steitzPolypeptideChainInitiation1969, title = {Polypeptide Chain Initiation: Nucleotide Sequences of the Three Ribosomal Binding Sites in Bacteriophage {{R17 RNA}}}, author = {Steitz, J. A.}, year = 1969, journal = {Nature}, volume = {224}, number = {06}, pages = {957–964}, doi = {doi:10.1038/224957a0}, url = {http://adsabs.harvard.edu/abs/1969Natur.224..957S}, keywords = {nosource} }

@article{kuerstenEliminatingUltracentrifugationDeep2012, title = {Eliminating {{Ultracentrifugation}} in the {{Deep Sequencing}} of {{Ribosome-Protected mRNA Fragments Using Polysomes}} and {{Monosomes}}}, author = {Kuersten, Scott and Radek, Agnes and Swami, Sajani}, year = 2012, journal = {Journal of }, pages = {6}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3630598/}, keywords = {nosource} } % == BibTeX quality report for kuerstenEliminatingUltracentrifugationDeep2012: % ? Title looks like it was stored in title-case in Zotero

@article{collartPreparationYeastRNA2001, title = {Preparation of Yeast {{RNA}}}, author = {Collart, M. A. and Oliviero, S.}, year = 2001, journal = {Current protocols in molecular biology}, number = {1993}, pages = {1–5}, url = {http://onlinelibrary.wiley.com/doi/10.1002/0471142727.mb1312s23/full}, keywords = {nosource} }

@article{greeneChartingHIVRemarkable2002, title = {Charting {{HIV}}’s Remarkable Voyage through the Cell: {{Basic}} Science as a Passport to Future Therapy}, author = {Greene, W. C. and Peterlin, B. M.}, year = 2002, journal = {Nature medicine}, pages = {673–680}, url = {http://www.gladstone.ucsf.edu/gladstone/files/greene/nat med.pdf http://search.ebscohost.com/login.aspx?direct=true&profile=ehost&scope=site&authtype=crawler&jrnl=10788956&AN=9511374&h=bsCzPfsZgOiRKmeiuYPgIKi480TTiF8Y29Re3pbmB264zNg27nLsfBKjFpz0CQ4KJTDssKXD0CAdw4PmYKzQFA==&crl=c}, keywords = {nosource} }

@article{schererViralMultiplicationStable1953, title = {Viral Multiplication in a Stable Strain of Human Malignant Epithelial Cells (Strain {{HeLa}}) Derived from an Epidermoid Carcinoma of the Cervix}, author = {Scherer, W. F. and Syverton, J. T. and Gey, G. O.}, year = 1953, journal = {J. Exp. Med}, url = {http://www.cabdirect.org/abstracts/19660306320.html http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Viral+Multiplication+in+a+Stable+Strain+of+Human+Malignant+Epithelial+Cells+(Strain+HeLa)+Derived+from+an+Epidermoid+Carcinoma+of+the+Cervix.#5}, keywords = {nosource} } % == BibTeX quality report for schererViralMultiplicationStable1953: % ? Possibly abbreviated journal title J. Exp. Med

@article{yokoyamaStructuralInsightsInitial2012, title = {Structural Insights into Initial and Intermediate Steps of the Ribosome-recycling Process}, author = {Yokoyama, Takeshi and Shaikh, T. R. and Iwakura, Nobuhiro}, year = 2012, journal = {The EMBO }, pages = {1–11}, publisher = {Nature Publishing Group}, issn = {0261-4189}, doi = {10.1038/emboj.2012.22}, url = {http://dx.doi.org/10.1038/emboj.2012.22 http://onlinelibrary.wiley.com/doi/10.1038/emboj.2012.22/full}, keywords = {conformation of elongation factor,Cryoelectron Microscopy,during,ef-g,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: metabolism,Escherichia coli: metabolism,Escherichia coli: ultrastructure,g,nosource,Peptide Elongation Factor G,Peptide Elongation Factor G: metabolism,Protein Binding,Protein Conformation,reverse ratcheting of the,Ribosomal,Ribosomal Proteins,Ribosomal Proteins: metabolism,Ribosomal: metabolism,ribosome,ribosome recycling,ribosome-recycling factor,Ribosomes,Ribosomes: metabolism,RNA,rrf} }

@article{davidNuclearTranslationVisualized2012, title = {Nuclear Translation Visualized by Ribosome-Bound Nascent Chain Puromycylation}, author = {David, Alexandre and Dolan, B. P.}, year = 2012, journal = {The Journal of cell }, volume = {197}, number = {1}, doi = {10.1083/jcb.201112145}, url = {http://jcb.rupress.org/content/197/1/45.short}, keywords = {nosource} }

@article{siegelCancerStatistics20112011, title = {Cancer Statistics, 2011: The Impact of Eliminating Socioeconomic and Racial Disparities on Premature Cancer Deaths}, author = {Siegel, Rebecca and Ward, E.}, year = 2011, journal = {CA Cancer J Clin}, doi = {10.3322/caac.20121}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Cancer+Statistics,+2011:+The+Impact+of+Eliminating+Socioeconomic+and+Racial+Disparities+on+Premature+Cancer+Deaths#6}, keywords = {nosource} }

@article{petersenSignalP40Discriminating2011, title = {{{SignalP}} 4.0: Discriminating Signal Peptides from Transmembrane Regions}, author = {Petersen, T. N. and Brunak, S{}ren and Heijne, Gunnar Von and Nielsen, Henrik}, year = 2011, journal = {Nature methods}, volume = {8}, number = {10}, pages = {785–786}, publisher = {Nature Publishing Group}, issn = {1548-7091}, doi = {10.1038/nmeth.1701}, url = {http://dx.doi.org/10.1038/nmeth.1701 http://www.nature.com/nmeth/journal/v8/n10/abs/nmeth.1701.html}, keywords = {nosource} }

@article{arias-palomoNonsensemediatedMRNADecay2011, title = {The Nonsense-Mediated {{mRNA}} Decay {{SMG-1}} Kinase Is Regulated by Large-Scale Conformational Changes Controlled by {{SMG-8}}}, author = {{Arias-Palomo}, E.}, year = 2011, journal = {Genes & }, volume = {10}, pages = {153–164}, doi = {10.1101/gad.606911.harboring}, url = {http://genesdev.cshlp.org/content/25/2/153.short}, keywords = {2010,29,cryo-em,eukaryotic gene expression is,exquisitely regulated at,for this article,nmd,nonsense-mediated mrna decay,nosource,received august 30,revised version accepted november,smg-1,smg-8,smg-9,supplemental material is available} }

@article{nakamuraTRNAMimicryTranslation2011, title = {{{tRNA}} Mimicry in Translation Termination and Beyond}, author = {Nakamura, Yoshikazu and Ito, Koichi}, year = 2011, journal = {Wiley Interdisciplinary Reviews: RNA}, number = {Dc}, doi = {10.1002/wrna.81}, url = {http://onlinelibrary.wiley.com/doi/10.1002/wrna.81/full}, keywords = {nosource} }

@article{chakrabartiMolecularMechanismsRNAdependent2011, title = {Molecular Mechanisms for the {{RNA-dependent ATPase}} Activity of {{Upf1}} and Its Regulation by {{Upf2}}}, author = {Chakrabarti, Sutapa and Jayachandran, Uma and Bonneau, Fabien}, year = 2011, journal = {Molecular cell}, pages = {693–703}, doi = {10.1016/j.molcel.2011.02.010}, url = {http://www.sciencedirect.com/science/article/pii/S1097276511000931}, keywords = {nosource} }

@article{ben-shemStructureEukaryoticRibosome2012, title = {The {{Structure}} of the {{Eukaryotic Ribosome}} at 3.0 {{Resolution}}}, author = {{Ben-shem}, Adam}, year = 2012, journal = {Science}, volume = {1524}, number = {2011}, doi = {10.1126/science.1212642}, keywords = {Cryoelectron Microscopy,Crystallography,DNA-Binding Proteins,DNA-Binding Proteins: ultrastructure,Fungal,Fungal: ultrastructure,Models,Molecular,nosource,Ribosomal,Ribosomal: ultrastructure,Ribosomes,Ribosomes: ultrastructure,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: ultrastructure,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: ultrastructure,X-Ray} } % == BibTeX quality report for ben-shemStructureEukaryoticRibosome2012: % ? Title looks like it was stored in title-case in Zotero

@article{alsfordHighthroughputPhenotypingUsing2011, title = {High-Throughput Phenotyping Using Parallel Sequencing of {{RNA}} Interference Targets in the {{African}} Trypanosome}, author = {Alsford, Sam and Turner, D. J.}, year = 2011, journal = {Genome }, pages = {915–924}, doi = {10.1101/gr.115089.110}, url = {http://genome.cshlp.org/content/21/6/915.short}, keywords = {nosource} }

@article{uemuraRealtimeTRNATransit2010, title = {Real-Time {{tRNA}} Transit on Single Translating Ribosomes at Codon Resolution}, author = {Uemura, Sotaro and Aitken, C. E. and Korlach, Jonas}, year = 2010, journal = {Nature}, volume = {464}, number = {April}, doi = {10.1038/nature08925}, url = {http://www.nature.com/nature/journal/v464/n7291/abs/nature08925.html}, keywords = {nosource} }

@article{gunzlPremRNASplicingMachinery2010, title = {The Pre-{{mRNA}} Splicing Machinery of Trypanosomes: Complex or Simplified?}, author = {G{"u}nzl, Arthur}, year = 2010, journal = {Eukaryotic cell}, volume = {9}, number = {June}, doi = {10.1128/EC.00113-10}, url = {http://ec.asm.org/content/9/8/1159.short}, keywords = {nosource} }

@article{oromMicroRNA10aBindsUTR2008, title = {{{MicroRNA-10a}} Binds the 5{\(\prime\)} {{UTR}} of Ribosomal Protein {{mRNAs}} and Enhances Their Translation}, author = {{}rom, U. A. and Nielsen, F. C. and Lund, A. H.}, year = 2008, journal = {Molecular cell}, pages = {460–471}, doi = {10.1016/j.molcel.2008.05.001}, url = {http://www.sciencedirect.com/science/article/pii/S1097276508003286}, keywords = {5’ Untranslated Regions,Amino Acids,Amino Acids: metabolism,Animals,Base Sequence,Binding Sites,Cell Transformation,Hela Cells,Humans,Immunologic,Immunologic: genetics,Immunologic: metabolism,Membrane Glycoproteins,Membrane Glycoproteins: genetics,Membrane Glycoproteins: metabolism,Mice,Molecular Sequence Data,Neoplastic,NIH 3T3 Cells,nosource,Protein Biosynthesis,Rats,Receptors,Ribosomal Proteins,Ribosomal Proteins: genetics,Ribosomal Proteins: metabolism} }

@book{haynesRNAproteinInteractionProtocols1999, title = {{{RNA-protein}} Interaction Protocols}, author = {Haynes, S. R.}, editor = {Lin, Ren-Jang}, year = 1999, journal = {RNA protein interaction protocols}, volume = {488}, publisher = {Humana Press}, doi = {10.1007/978-1-60327-475-3}, url = {http://www.springerlink.com/index/10.1007/978-1-60327-475-3 http://link.springer.com/content/pdf/10.1385/1592596762.pdf http://books.google.com/books?hl=en&lr=&id=oLHI585bHYgC&oi=fnd&pg=PR5&dq=RNA-protein+Interaction+Protocols&ots=yWcx3LN9ef&sig=vmiRgahZ7r6h1VGBmUe5Fq0B6WI}, isbn = {978-1-58829-419-7}, keywords = {aptamer,nosource,ribonucleoprotein,rna,rnp isolation,selex,sephadex,streptavidin} } % == BibTeX quality report for haynesRNAproteinInteractionProtocols1999: % ? unused Issue (“1”) % ? unused Number of pages (“1-16”)

@article{sturmKinetoplastidGenomicsThin2008, title = {Kinetoplastid Genomics: The Thin End of the Wedge}, author = {Sturm, N. R. and Martinez, L. L. and Thomas, Sean}, year = 2008, journal = {Infection, Genetics and Evolution}, volume = {8}, pages = {901–906}, doi = {10.1016/j.meegid.2008.07.001}, url = {http://www.sciencedirect.com/science/article/pii/S1567134808001354}, keywords = {nosource} }

@article{stapleGuanidinoneomycinRecognitionHIV2008, title = {Guanidinoneomycin {{B Recognition}} of an {{HIV}}-1 {{RNA Helix}}}, author = {Staple, D. W. and Venditti, V.}, year = 2008, journal = {Chembiochem}, volume = {9}, number = {1}, pages = {93–102}, doi = {10.1002/cbic.200700251.Guanidinoneomycin}, url = {http://onlinelibrary.wiley.com/doi/10.1002/cbic.200700251/full}, keywords = {antibiotics,guanidinoglycosides,nmr spectroscopy,nosource,rna recognition,rna structures} } % == BibTeX quality report for stapleGuanidinoneomycinRecognitionHIV2008: % ? Title looks like it was stored in title-case in Zotero

@article{firthDiscoveryFrameshiftingAlphavirus2008, title = {Discovery of Frameshifting in {{Alphavirus 6K}} Resolves a 20-Year Enigma}, author = {Firth, A. E. and Chung, B. Y. and Fleeton, M. N. and Atkins, J. F.}, year = 2008, journal = {Virol J}, volume = {19}, pages = {1–19}, doi = {10.1186/1743-422X-5-108}, url = {http://www.biomedcentral.com/content/pdf/1743-422X-5-108.pdf}, keywords = {Amino Acid Sequence,Animals,Base Sequence,Cell Line,Conserved Sequence,Cricetinae,Fluorescent Antibody Technique,Frameshifting,Gene Order,Immunoprecipitation,Isotope Labeling,Mass Spectrometry,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Ribosomal,RNA,Semliki forest virus,Semliki forest virus: genetics,Semliki forest virus: physiology,Viral,Viral Structural Proteins,Viral Structural Proteins: biosynthesis,Viral Structural Proteins: chemistry,Viral: chemistry,Virion,Virion: chemistry} }

@article{chandramouliStructureMammalian80S2008, title = {Structure of the Mammalian {{80S}} Ribosome at 8.7 {{}} Resolution}, author = {Chandramouli, Preethi and Topf, Maya and M{'e}n{'e}tret, J. F.}, year = 2008, journal = {Structure}, number = {April}, pages = {535–548}, doi = {10.1016/j.str.2008.01.007}, url = {http://www.sciencedirect.com/science/article/pii/S0969212608000543}, keywords = {Animals,Cell Surface,Cell Surface: chemistry,Computer-Assisted,Cryoelectron Microscopy,Dogs,Eukaryotic,Eukaryotic: chemistry,Image Processing,Models,Molecular,nosource,Protein Biosynthesis,Receptors,Ribosomal,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal: chemistry,Ribosome Subunits,Ribosomes,Ribosomes: chemistry,RNA,Small,Transfer,Transfer: chemistry} }

@article{waisbergMicroarrayAnalysisGene2007, title = {Microarray Analysis of Gene Expression Induced by Sexual Contact in {{Schistosoma}} Mansoni}, author = {Waisberg, Michael and Lobo, F. P.}, year = 2007, journal = {BMC }, volume = {14}, pages = {1–14}, doi = {10.1186/1471-2164-8-181}, url = {http://www.biomedcentral.com/1471-2164/8/181}, keywords = {Animal,Animals,Cloning,Complementary,DNA,Female,Gene Expression Profiling,Gene Expression Regulation,Genes,Genetic,Helminth,Male,Messenger,Messenger: metabolism,Models,Molecular,nosource,Nucleic Acid Hybridization,Oligonucleotide Array Sequence Analysis,Oligonucleotide Array Sequence Analysis: methods,Reverse Transcriptase Polymerase Chain Reaction,RNA,Schistosoma mansoni,Schistosoma mansoni: genetics,Sexual Behavior} }

@article{simonSpecificRoleCterminal2007, title = {A Specific Role for the {{C-terminal}} Region of the {{Poly}} ({{A}})-Binding Protein in {{mRNA}} Decay}, author = {Sim{'o}n, E. and S{'e}raphin, B.}, year = 2007, journal = {Nucleic acids research}, pages = {1–12}, doi = {10.1093/nar/gkm452}, url = {http://nar.oxfordjournals.org/content/35/18/6017.short}, keywords = {Codon,Endoribonucleases,Endoribonucleases: genetics,Messenger,Messenger: chemistry,Messenger: metabolism,Nonsense,nosource,Poly A,Poly A: metabolism,Poly(A)-Binding Proteins,Poly(A)-Binding Proteins: chemistry,Poly(A)-Binding Proteins: genetics,Poly(A)-Binding Proteins: metabolism,Protein Biosynthesis,Protein Structure,Ribonucleases,Ribonucleases: genetics,Ribonucleases: metabolism,RNA,RNA Cap-Binding Proteins,RNA Stability,RNA Transport,RNA-Binding Proteins,RNA-Binding Proteins: genetics,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: chemistry,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Sequence Deletion,Tertiary} }

@article{sonenbergTranslationalControlGene2000, title = {Translational Control of Gene Expression}, author = {Sonenberg, N. and Hershey, J. W. B. and Mathews, M.}, year = 2000, number = {2000}, pages = {2001}, url = {http://www.lavoisier.fr/livre/notice.asp?ouvrage=1729269}, keywords = {nosource} } % == BibTeX quality report for sonenbergTranslationalControlGene2000: % Missing required field ‘journal’

@article{westenbergerTrypanosomaCruziMitochondrial2006, title = {Trypanosoma Cruzi Mitochondrial Maxicircles Display Species-and Strain-Specific Variation and a Conserved Element in the Non-Coding Region}, author = {Westenberger, S. J. and Cerqueira, G. C.}, year = 2006, journal = {BMC }, volume = {18}, pages = {1–18}, doi = {10.1186/1471-2164-7-60}, url = {http://www.biomedcentral.com/1471-2164/7/60}, keywords = {Amino Acid,Amino Acid Sequence,Animals,Base Composition,Biological,Conserved Sequence,Conserved Sequence: genetics,DNA,Frameshifting,Gene Deletion,Gene Order,Genetic Variation,Inbred Strains,Kinetoplast,Kinetoplast: genetics,Leishmania,Leishmania: genetics,Models,Molecular Sequence Data,Muscle Proteins,Muscle Proteins: genetics,NADH Dehydrogenase,NADH Dehydrogenase: genetics,nosource,Open Reading Frames,Open Reading Frames: genetics,Regulatory Elements,Ribosomal,Ribosomal: genetics,RNA Editing,RNA Editing: genetics,Sequence Homology,Species Specificity,Transcriptional,Transcriptional: genetics,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Ubiquitin-Protein Ligases,Ubiquitin-Protein Ligases: genetics,Untranslated Regions,Untranslated Regions: genetics} }

@article{wheelerDatabaseResourcesNational2007, title = {Database Resources of the National Center for Biotechnology Information}, author = {Wheeler, D. L. and Barrett, Tanya}, year = 2007, journal = {Nucleic acids }, volume = {35}, number = {December 2006}, pages = {5–12}, doi = {10.1093/nar/gkl1031}, url = {http://nar.oxfordjournals.org/content/35/suppl_1/D5.short}, keywords = {nosource} }

@article{dinmanProgrammedRibosomalFrameshifting2006, title = {Programmed {{Ribosomal Frameshifting Goes}} beyond {{Viruses}}}, author = {Dinman, Jonathan D.}, year = 2006, volume = {1}, number = {11}, pages = {521–527}, keywords = {nosource} } % == BibTeX quality report for dinmanProgrammedRibosomalFrameshifting2006: % Missing required field ‘journal’ % ? Title looks like it was stored in title-case in Zotero

@article{gietzTransformationYeastLithium2005, title = {Transformation of Yeast by Lithium Acetate/Single-Stranded Carrier {{DNA}}/Polyethylene Glycol Method}, author = {Gietz, R. Daniel and Woods, R. A.}, year = 2005, month = jan, journal = {Methods in enzymology}, volume = {402}, number = {05}, pages = {245–289}, issn = {0076-6879}, doi = {10.1016/S0076-6879(05)02008-2}, url = {http://www.sciencedirect.com/science/article/pii/S0076687902509575}, abstract = {Proteomics is the measurement of one or more protein populations or proteomes, preferably in a quantitative manner. A protein population may be the set of proteins found in an organism, in a tissue or biofluid, in a cell, or in a subcellular compartment. A population also may be the set of proteins with a common characteristic, for example, those that interact with each other in molecular complexes, those involved in the same process such as signal transduction or cell cycle control, or those that share a common posttranslational modification such as phosphorylation or glycosylation. Proteomics experiments that involve mass spectrometry are divided into five categories: (1) protein identification, (2) protein quantitation or differential analysis, (3) protein-protein interactions, (4) post-translational modifications, and (5) structural proteomics. Each of these proteomics categories is reviewed. Examples are given for quantitative experiments involving two-dimensional gel electrophoresis, and for gel-free analysis using isotope-coded affinity tags. The impact of proteomics on biological research and on drug development is discussed. Challenges for further development in proteomics are presented, including sample preparation, sensitivity, dynamic range, and automation.}, pmid = {16401512}, keywords = {Animals,Electrophoresis,Gel,Humans,Mass,Matrix-Assisted Laser Desorpti,nosource,Proteins,Proteins: chemistry,Proteins: genetics,Proteins: isolation & purification,Proteins: metabolism,Proteomics,Proteomics: methods,Spectrometry,Two-Dimensional,Two-Dimensional: methods} }

@article{dinmanRapidEfficientPurification2009, title = {Rapid and Efficient Purification of {{RNA-binding}} Proteins: {{Application}} to {{HIV-1 Rev}}}, author = {Dinman, Jonathan D. and Manuscript, Author}, year = 2009, month = feb, journal = {Protein Expression and Purification}, volume = {63}, number = {1}, pages = {112–119}, publisher = {Elsevier}, doi = {10.1016/j.pep.2008.09.010.Rapid}, url = {http://www.sciencedirect.com/science/article/pii/S1046592808002349 http://linkinghub.elsevier.com/retrieve/pii/S1046592808002349}, abstract = {Non-specifically bound nucleic acid contaminants are an unwanted feature of recombinant RNA-binding proteins purified from Escherichia coli (E. coli). Removal of these contaminants represents an important step for the proteins’ application in several biological assays and structural studies. The method described in this paper is a one-step protocol which is effective at removing tightly bound nucleic acids from overexpressed tagged HIV-1 Rev in E. coli. We combined affinity chromatography under denaturing conditions with subsequent on-column refolding, to prevent self-association of Rev while removing the nucleic acid contaminants from the end product. We compare this purification method with an established, multi-step protocol involving precipitation with polyethyleneimine (PEI). As our tailored protocol requires only one-step to simultaneously purify tagged proteins and eliminate bound cellular RNA and DNA, it represents a substantial advantage in time, effort, and expense}, keywords = {5s,antibiotics,cryo-electron microscopy,drugs,fidelity,frameshifting,guanidinoglycosides,hiv-1,immobilized metal affinity chromatography,luteovirus,nmr,nmr spectroscopy,nosource,on-column,pseudoknot,rev,ribosomal recoding,ribosome,rna recognition,rna structures,rre,rrna,solution structure,structure,translation,translational regulation,trna,urea denaturation,virus} }

@article{marvinFidelityProteinSynthesis1968, title = {Fidelity in Protein Synthesis}, author = {Marvin, S. and Berezny, R. and Weinstein, R.}, year = 1968, journal = {The Journal of Biological Chemistry}, volume = {243}, number = {19}, pages = {5044–5048}, keywords = {nosource} }

@article{andradeTrypanosomaCruziHostcell2005, title = {The {{Trypanosoma}} Cruzi–Host-Cell Interplay: Location, Invasion, Retention}, author = {Andrade, L. O. and Andrews, N. W.}, year = 2005, journal = {Nature Reviews Microbiology}, number = {September}, pages = {1–5}, doi = {10.1038/nrmicro1249}, url = {http://www.nature.com/nrmicro/journal/v3/n10/abs/nrmicro1249.html}, keywords = {Animals,Chagas Disease,Chagas Disease: parasitology,Chagas Disease: physiopathology,Fibroblasts,Fibroblasts: parasitology,Host-Parasite Interactions,Humans,Lysosomes,Lysosomes: physiology,Movement,nosource,Phagocytes,Phagocytes: parasitology,Trypanosoma cruzi,Trypanosoma cruzi: physiology} }

@article{gomesTcRRMsTcp28Genes2004, title = {{{TcRRMs}} and {{Tcp28}} Genes Are Intercalated and Differentially Expressed in {{Trypanosoma}} Cruzi Life Cycle.}, author = {Gomes, GG Giselle Guimar{~a}es and {"U}rm{'e}nyi, T. Peter and Urm{'e}nyi, Tur{'a}n Peter and Rondinelli, Edson and Williams, Noreen and Silva, Rosane and Guimara, Giselle}, year = 2004, month = sep, journal = {Biochemical and biophysical research communications}, volume = {322}, number = {3}, eprint = {15336561}, eprinttype = {pubmed}, pages = {985–92}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2004.08.026}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15336561 http://www.sciencedirect.com/science/article/pii/S0006291X04017565}, abstract = {The identification and characterization of RNA binding proteins in Trypanosoma cruzi are particularly relevant as they play key roles in the regulatory mechanisms of gene expression. In this work, we have identified coding sequences for the proteins, named TcRRM1 and TcRRM2, in the EST database generated by the T. cruzi genomic initiative. TcRRM1 and TcRRM2 contain two RNA binding domains (RRM) and are very similar to two Trypanosoma brucei RNA binding proteins previously reported, Tbp34 and Tbp37, and to a not yet annotated ORF in Leishmania major genome project. The T. cruzi RRM genes are organized in tandem, alternating with copies of Tcp28, a gene of unknown function. However, TcRRM transcript accumulation is higher in the spheromastigote stage, while Tcp28 transcripts accumulate more in the trypomastigote stage suggesting developmental regulation.}, pmid = {15336561}, keywords = {a member of the,Amino Acid,Amino Acid Sequence,Animals,Base Sequence,differential gene expression,Expressed Sequence Tags,Genes,idae family,is the etiological agent,Leishmania,Leishmania: genetics,Life Cycle Stages,Life Cycle Stages: genetics,Molecular Sequence Data,nosource,of chagaso disease,people in latin america,post-transcriptional gene regulation,Protozoan,Protozoan Proteins,Protozoan Proteins: chemistry,Protozoan Proteins: genetics,Protozoan: genetics,Restriction Mapping,rna binding proteins,RNA-Binding Proteins,RNA-Binding Proteins: chemistry,RNA-Binding Proteins: genetics,Sequence Alignment,Sequence Homology,tbp34,tbp37,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosoma cruzi: growth & development,trypanosomat-,which affects 18 million} }

@article{bringaudIngiRIMENonLTR2004, title = {The Ingi and {{RIME}} Non-{{LTR}} Retrotransposons Are Not Randomly Distributed in the Genome of {{Trypanosoma}} Brucei}, author = {Bringaud, F. and Biteau, Nicolas and Zuiderwijk, Eduard}, year = 2004, journal = {Molecular biology and }, pages = {520–528}, doi = {10.1093/molbev/msh045}, url = {http://mbe.oxfordjournals.org/content/21/3/520.short}, keywords = {nosource} }

@article{cartlidgeFrancisCrick19162004, title = {Francis {{Crick}}, 1916–2004}, author = {Cartlidge, E.}, year = 2004, journal = {Current Biology}, volume = {14}, number = {16}, pages = {642–645}, url = {http://physicsworldarchive.iop.org/index.cfm?action=summary&doc=17%2F9%2Fphwv17i9a20%40pwa-xml&qt=}, keywords = {nosource} } % == BibTeX quality report for cartlidgeFrancisCrick19162004: % ? Title looks like it was stored in title-case in Zotero

@article{ruanIteratedLoopMatching2004, title = {An Iterated Loop Matching Approach to the Prediction of {{RNA}} Secondary Structures with Pseudoknots}, author = {Ruan, Jianhua and Stormo, G. D. and Zhang, Weixiong}, year = 2004, journal = {Bioinformatics}, volume = {20}, number = {1}, pages = {58–66}, doi = {10.1093/bioinformatics/btg373}, url = {http://bioinformatics.oxfordjournals.org/content/20/1/58.short}, keywords = {nosource} }

@article{strobelBiochemicalIdentificationAminor2002, title = {Biochemical Identification of {{A-minor}} Motifs within {{RNA}} Tertiary Structure by Interference Analysis.}, author = {Strobel, S. A.}, year = 2002, journal = {Biochemical Society Transactions}, volume = {30}, pages = {1126–1131}, url = {http://europepmc.org/abstract/MED/12440988}, keywords = {nosource} }

@article{shirleyNuclearImportUpf3p2002a, title = {Nuclear Import of {{Upf3p}} Is Mediated by Importin-{\(\alpha\)}/-{\(\beta\)} and Export to the Cytoplasm Is Required for a Functional Nonsense-Mediated {{mRNA}} Decay Pathway in Yeast}, author = {Shirley, R. L. and Ford, A. S. and Richards, M. R.}, year = 2002, journal = {}, volume = {1482}, number = {August}, pages = {1465–1482}, url = {http://www.genetics.org/content/161/4/1465.short}, keywords = {nosource} }

@article{haoNewUAGEncodedResidue2012, title = {A {{New UAG-Encoded Residue}} in the {{Structure}} of a {{Methanogen Methyltransferase}}}, author = {Hao, Bing}, year = 2012, volume = {1462}, number = {2002}, doi = {10.1126/science.1069556}, keywords = {Archaeal,Archaeal Proteins,Archaeal Proteins: chemistry,Archaeal Proteins: metabolism,Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: metabolism,Codon,Crystallization,Crystallography,Dimerization,Electrospray Ionization,Genes,Hydrogen Bonding,Lysine,Lysine: analogs & derivatives,Lysine: chemistry,Lysine: genetics,Mass,Methanosarcina barkeri,Methanosarcina barkeri: enzymology,Methanosarcina barkeri: genetics,Methylamines,Methylamines: metabolism,Methyltransferases,Methyltransferases: chemistry,Methyltransferases: genetics,Methyltransferases: metabolism,Models,Molecular,Molecular Weight,nosource,Protein Conformation,Protein Structure,Quaternary,Secondary,Spectrometry,Tertiary,X-Ray} } % == BibTeX quality report for haoNewUAGEncodedResidue2012: % Missing required field ‘journal’ % ? Title looks like it was stored in title-case in Zotero

@article{tolmanProteins2001, title = {For {{Proteins}}}, author = {Tolman, Joel R. and {Al-hashimi}, Hashim M. and Kay, Lewis E. and Prestegard, James H.}, year = 2001, number = {14}, pages = {6360–6368}, keywords = {nosource} } % == BibTeX quality report for tolmanProteins2001: % Missing required field ‘journal’

@article{kebaaraAnalysisNonsensemediatedMRNA2012, title = {Analysis of Nonsense-Mediated {{mRNA}} Decay in {{Saccharomyces}} Cerevisiae.}, author = {Kebaara, Bessie W. and Baker, Kristian E. and Patefield, Krista D. and Atkin, Audrey L.}, year = 2012, month = mar, journal = {Current protocols in cell biology / editorial board, Juan S. Bonifacino … [et al.]}, volume = {Chapter 27}, eprint = {22422476}, eprinttype = {pubmed}, pages = {Unit 27.3}, issn = {1934-2616}, doi = {10.1002/0471143030.cb2703s54}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22422476}, abstract = {Nonsense-mediated mRNA decay is a highly conserved pathway that degrades mRNAs with premature termination codons. These mRNAs include mRNAs transcribed from nonsense or frameshift alleles as well as wild-type mRNA with signals that direct ribosomes to terminate prematurely. This unit describes techniques to monitor steady-state mRNA levels, decay rates, and structural features of mRNAs targeted by this pathway, as well as in vivo analysis of nonsense suppression and allosuppression in the yeast Saccharomyces cerevisiae. Protocols for the structural features of mRNA include analysis of cap status, 5’ and 3’ untranslated region (UTR) lengths, and poly(A) tail length.}, pmid = {22422476}, keywords = {Fungal,Fungal: chemistry,Genetic Techniques,Nonsense Mediated mRNA Decay,nosource,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics} } % == BibTeX quality report for kebaaraAnalysisNonsensemediatedMRNA2012: % ? Possibly abbreviated journal title Current protocols in cell biology / editorial board, Juan S. Bonifacino … [et al.]

@article{breakRNASurveillanceWatching1999, title = {{{RNA}} Surveillance: Watching the Defectives. {{Detecting}} Premature Stop Codons in {{mRNA}} Halts the Production of Dangerous Truncated Proteins}, author = {Break, Coffee}, year = 1999, pages = {1–3}, keywords = {nosource} } % == BibTeX quality report for breakRNASurveillanceWatching1999: % Missing required field ‘journal’

@article{biologyUKARYOTES1999, title = {{{IN E UKARYOTES}}}, author = {Biology, Cellular}, year = 1999, keywords = {a defining aspect of,exists in eukaryotic cells,kinetic proofreading,lance,mrna biogenesis,mrna degradation system,mrnp remodeling,nonsense decay,nosource,referred to as mrna,s abstract a conserved,surveil-,termination,to degrade aberrant mrnas,translation} } % == BibTeX quality report for biologyUKARYOTES1999: % Missing required field ‘journal’ % ? Title looks like it was stored in title-case in Zotero

@article{sambrookRapidEfficientSitedirected2006, title = {Rapid and {{Efficient Site-directed Mutagenesis}} by the {{Single-tube Megaprimer PCR Method}}.}, author = {Sambrook, Joseph and Russell, David W.}, year = 2006, month = jan, journal = {CSH protocols}, volume = {2006}, number = {1}, eprint = {22485268}, eprinttype = {pubmed}, pages = {181–182}, doi = {10.1101/pdb.prot3467}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22485268}, pmid = {22485268}, keywords = {nosource} }

@article{muhlradTurnoverMechanismsStable1995a, title = {Turnover Mechanisms of the Stable Yeast {{PGK1 mRNA}} . {{These}} Include : {{Turnover Mechanisms}} of the {{Stable Yeast PGK1 mRNA}}}, author = {Muhlrad, Denise and Decker, Carolyn J. and Parker, R. O. Y.}, year = 1995, volume = {15}, number = {4}, keywords = {nosource} } % == BibTeX quality report for muhlradTurnoverMechanismsStable1995a: % Missing required field ‘journal’

@article{komineTRNAlikeStructurePresent1994, title = {A {{tRNA-like}} Structure Is Present in {{10Sa RNA}}, a Small Stable {{RNA}} from {{Escherichia}} Coli}, author = {KoMINE, Y. and Kitabatake, Makoto}, year = 1994, journal = {Proceedings of the }, volume = {91}, number = {September}, pages = {9223–9227}, url = {http://www.pnas.org/content/91/20/9223.short}, keywords = {nosource} }

@article{riles1993, title = {Of 2.6}, author = {Riles, Linda and Dutchik, James E. and Baktha, Amara and Mccauley, Brigid K. and Thayer, Edward C. and Leckiet, Mary P. and Braden, Valerie V. and Depketv, Julie E. and Olsontvs, Maynard V.}, year = 1993, volume = {150}, pages = {81–150}, keywords = {nosource} } % == BibTeX quality report for riles1993: % Missing required field ‘journal’

@article{widner20SRNANaked1991, title = {Is {{20S RNA}} Naked?}, author = {Widner, W. R.}, year = 1991, journal = {Molecular and cellular }, volume = {11}, number = {5}, doi = {10.1128/MCB.11.5.2905.Updated}, url = {http://mcb.asm.org/content/11/5/2905.short}, keywords = {nosource} }

@article{brierleyMutationalAnalysisSlipperysequence1992, title = {Mutational Analysis of the ``Slippery-Sequence’’ Component of a Coronavirus Ribosomal Frameshifting Signal}, author = {Brierley, I. and Jenner, A. J. and Inglis, S. C.}, year = 1992, journal = {Journal of molecular biology}, url = {http://www.sciencedirect.com/science/article/pii/002228369290901U}, keywords = {nosource} }

@article{diffleyProteinDNAInteractionsYeast1992, title = {Protein-{{DNA}} Interactions at a Yeast Replication Origin}, author = {Diffley, J. F. X. and Cocker, J. H.}, year = 1992, journal = {Nature}, volume = {357}, url = {http://www.nature.com/nature/journal/v357/n6374/abs/357169a0.html}, keywords = {nosource} }

@article{macejakInternalInitiationTranslation1991, title = {Internal Initiation of Translation Mediated by the 5{\(\prime\)} Leader of a Cellular {{mRNA}}}, author = {Macejak, D. G. and Sarnow, P.}, year = 1991, journal = {Nature}, url = {http://www.nature.com/nature/journal/v353/n6339/abs/353090a0.html}, keywords = {nosource} }

@article{srivastavaMechanismRegulationBacterial1990, title = {Mechanism and Regulation of Bacterial Ribosomal {{RNA}} Processing}, author = {Srivastava, A. K. and Schlessinger, David}, year = 1990, journal = {Annual Reviews in Microbiology}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.mi.44.100190.000541}, keywords = {16s rrna,2 3 s rrna,nosource,precursor rna,ribosome formation,rnases,trna in ribosome biosynthesis} }

@article{yungShortExposureActinomycin1990, title = {Short Exposure to Actinomycin {{D}} Induces Reversible'' Translocation of Protein {{B23}} as Well asReversible’’ Inhibition of Cell Growth and {{RNA}} Synthesis in {{HeLa}} Cells}, author = {Yung, B. Y. M. and Bor, A. M. S. and Chan, P. K.}, year = 1990, journal = {Cancer research}, pages = {5987–5991}, url = {http://cancerres.aacrjournals.org/content/50/18/5987.short}, keywords = {nosource} }

@article{danonLightRegulatedTranslational1991, title = {Light Regulated Translational Activators: Identification of Chloroplast Gene Specific {{mRNA}} Binding Proteins.}, author = {Danon, Avihai and Mayfield, S. P.}, year = 1991, journal = {The EMBO journal}, volume = {1}, number = {1}, pages = {3993–4001}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC453146/}, keywords = {chloroplast light regulation,mrna-binding,nosource,proteins,translational regulation} }

@article{christiansenEnzymaticChemicalProbing1988, title = {Enzymatic and Chemical Probing of Ribosomal {{RNA-protein}} Interactions.}, author = {Christiansen, J. and Garrett, R.}, year = 1988, journal = {Methods in enzymology}, volume = {59}, eprint = {3071676}, eprinttype = {pubmed}, pages = {456–468}, url = {http://www.ncbi.nlm.nih.gov/pubmed/3071676}, keywords = {nosource} }

@article{rivest3DeazaguanineInhibitionInitiation1982, title = {3-{{Deazaguanine}}: Inhibition of Initiation of Translation in {{L1210}} Cells}, author = {Rivest, R. S. and Irwin, David and Mandel, H. G.}, year = 1982, journal = {Cancer research}, pages = {4039–4044}, url = {http://cancerres.aacrjournals.org/content/42/10/4039.short}, keywords = {nosource} }

@article{robertusStructureYeastPhenylalanine1974, title = {Structure of Yeast Phenylalanine {{tRNA}} at 3 {{}} Resolution}, author = {Robertus, J. D. and Ladner, J. E. and Finch, J. T.}, year = 1974, journal = {Nature}, url = {http://adsabs.harvard.edu/abs/1974Natur.250..546R}, keywords = {nosource} }

@article{kankiFrequencyErrorsProtein1972, title = {The {{Frequency}} of {{Errors}} in {{Protein}} Biosynthesis}, author = {Kanki, Tatsuo and Iuchi, Satoru and Ogata, Mitoshi and Ikemizu, Kiyoshi and Shinohara, Hisashi}, year = 1972, journal = {Chemical engineering}, volume = {36}, number = {4}, pages = {442–447,a1}, issn = {0375-9253}, doi = {10.1252/kakoronbunshu1953.36.442}, url = {http://joi.jlc.jst.go.jp/JST.Journalarchive/kakoronbunshu1953/36.442?from=CrossRef}, keywords = {nosource} }

@article{crickCodonAnticodonPairing1966, title = {Codon—Anticodon Pairing: The Wobble Hypothesis}, author = {Crick, F. H. C.}, year = 1966, journal = {Journal of molecular biology}, volume = {19}, pages = {548–555}, url = {http://www.sciencedirect.com/science/article/pii/S0022283666800220}, keywords = {nosource} }

@article{atkinsLowActivityVgalactosidase1972, title = {Low Activity of {\(\beta\)}-Galactosidase in Frameshift Mutants of {{Escherichia}} Coli}, author = {Atkins, J. F. and Elseviers, Dirk and Gorini, L.}, year = 1972, journal = {Proceedings of the }, volume = {69}, number = {5}, pages = {1192–1195}, url = {http://www.pnas.org/content/69/5/1192.short}, keywords = {nosource} }

@article{puckGeneticsSomaticMammalian1958, title = {Genetics of Somatic Mammalian Cells {{III}}. {{Long-term}} Cultivation of Euploid Cells from Human and Animal Subjects}, author = {Puck, T. T. and Cieciura, S. J. and Robinson, A.}, year = 1958, journal = {The Journal of experimental }, number = {77}, url = {http://jem.rupress.org/content/108/6/945.abstract}, keywords = {nosource} }

@book{darwinOriginSpeciesMeans1859, title = {On the {{Origin}} of {{Species}} by {{Means}} of {{Natural Selection}} , or the {{Preservation}} of {{Favoured Races}} in the {{Struggle}} for {{Life}}}, author = {Darwin, Charles}, year = 1859, number = {February 2009}, keywords = {nosource} } % == BibTeX quality report for darwinOriginSpeciesMeans1859: % Missing required field ‘publisher’ % ? Title looks like it was stored in title-case in Zotero % ? unused Number of pages (“204-208”)

@article{geyTissueCultureStudies1952, title = {Tissue Culture Studies of the Proliferative Capacity of Cervical Carcinoma and Normal Epithelium}, author = {Gey, G. O.}, year = 1952, journal = {Cancer }, pages = {5}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:TISSUE+CULTURE+STUDIES+OF+THE+PROLIFERATIVE+CAPACITY+OF+CERVICAL+CARCINOMA+AND+NORMAL+EPITHELIUM#0}, keywords = {nosource} }

@article{lewenhoeckObservationesAnthoniiLewenhoeck1677, title = {Observationes {{D}}. {{Anthonii Lewenhoeck}}, {{De Natis E Semine Genitali Animalculis}}}, author = {Lewenhoeck, D. Anthonii}, year = 1677, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, volume = {12}, pages = {1040–1046}, keywords = {nosource} } % == BibTeX quality report for lewenhoeckObservationesAnthoniiLewenhoeck1677: % ? Possibly abbreviated journal title Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences % ? Title looks like it was stored in title-case in Zotero

@article{youngGeneOntologyAnalysis2010, title = {Gene Ontology Analysis for {{RNA-seq}}: Accounting for Selection Bias.}, shorttitle = {Gene Ontology Analysis for {{RNA-seq}}}, author = {Young, Matthew D. and Wakefield, Matthew J. and Smyth, Gordon K. and Oshlack, Alicia}, year = 2010, month = feb, journal = {Genome biology}, volume = {11}, number = {2}, pages = {R14}, issn = {1465-6906}, doi = {10.1186/gb-2010-11-2-r14}, url = {http://www.biomedcentral.com/content/pdf/gb-2010-11-2-r14.pdf}, abstract = {We present GOseq, an application for performing Gene Ontology (GO) analysis on RNA-seq data. GO analysis is widely used to reduce complexity and highlight biological processes in genome-wide expression studies, but standard methods give biased results on RNA-seq data due to over-detection of differential expression for long and highly expressed transcripts. Application of GOseq to a prostate cancer data set shows that GOseq dramatically changes the results, highlighting categories more consistent with the known biology.}, isbn = {1465-6906}, pmid = {20132535}, keywords = {Androgen,Differentially Express,Differentially Express Gene,Gene Ontology,LNCaP Cell}, file = {/home/trey/Zotero/storage/H2X5ETMS/Young et al. - 2010 - Gene ontology analysis for RNA-seq accounting for.pdf;/home/trey/Zotero/storage/SVF8DH6W/gb-2010-11-2-r14.html} } % == BibTeX quality report for youngGeneOntologyAnalysis2010: % ? unused Library catalog (“BioMed Central”)

@article{spahnThrowingSpannerWorks1996, title = {Throwing a Spanner in the Works: Antibiotics and the Translation Apparatus}, author = {Spahn, T. and Prescott, D. and The, Abstract and Rna, Ribosomal and Elongation, Abbreviations E. F. and Initiation, I. F. and Termination, R. F.}, year = 1996, journal = {Journal of Molecular Medicine}, pages = {423–439}, keywords = {nosource} }

@article{fresnoInhibitionTranslationEukaryotic1977, title = {Inhibition of Translation in Eukaryotic Systems by Harringtonine}, author = {Fresno, Manuel and Jimenez, Antonio and Vazquez, David}, year = 1977, journal = {European journal of }, volume = {330}, number = {72}, pages = {323–330}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1977.tb11256.x/full}, keywords = {nosource} }

@article{palczewskiOligomericFormsProteincoupled2010, title = {Oligomeric Forms of {{G}} Protein-Coupled Receptors ({{GPCRs}}).}, author = {Palczewski, Krzysztof}, year = 2010, month = nov, journal = {Trends in biochemical sciences}, volume = {35}, number = {11}, pages = {595–600}, publisher = {Elsevier Ltd}, issn = {0968-0004}, doi = {10.1016/j.tibs.2010.05.002}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2937196&tool=pmcentrez&rendertype=abstract}, abstract = {Oligomerization is a general characteristic of cell membrane receptors that is shared by G protein-coupled receptors (GPCRs) together with their G protein partners. Recent studies of these complexes, both in vivo and in purified reconstituted forms, unequivocally support this contention for GPCRs, perhaps with only rare exceptions. As evidence has evolved from experimental cell lines to more relevant in vivo studies and from indirect biophysical approaches to well defined isolated complexes of dimeric receptors alone and complexed with G proteins, there is an expectation that the structural basis of oligomerization and the functional consequences for membrane signaling will be elucidated. Oligomerization of cell membrane receptors is fully supported by both thermodynamic calculations and the selectivity and duration of signaling required to reach targets located in various cellular compartments.}, pmid = {20538466}, keywords = {Animals,G-Protein-Coupled,G-Protein-Coupled: chemistry,G-Protein-Coupled: metabolism,GTP-Binding Proteins,GTP-Binding Proteins: metabolism,Humans,nosource,Protein Binding,Protein Multimerization,Receptors,Signal Transduction,Thermodynamics} }

@article{urizarCODARETRevealsFunctional2011, title = {{{CODA-RET}} Reveals Functional Selectivity as a Result of {{GPCR}} Heteromerization.}, author = {Urizar, Eneko and Yano, Hideaki and Kolster, Rachel and Gal{'e}s, C{'e}line and Lambert, Nevin and {}a Javitch, Jonathan}, year = 2011, month = sep, journal = {Nature chemical biology}, volume = {7}, number = {9}, pages = {624–630}, issn = {1552-4469}, doi = {10.1038/nchembio.623}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3158273&tool=pmcentrez&rendertype=abstract}, abstract = {Here we present a new method that combines protein complementation with resonance energy transfer to study conformational changes in response to activation of a defined G protein-coupled receptor heteromer, and we apply the approach to the putative dopamine D1-D2 receptor heteromer. Remarkably, the potency of the D2 dopamine receptor (D2R) agonist R-(-)-10,11-dihydroxy-N-n-propylnoraporphine (NPA) to change the G{\(\alpha\)}(i) conformation via the D2R protomer in the D1-D2 heteromer was enhanced ten-fold relative to its potency in the D2R homomer. In contrast, the potencies of the D2R agonists dopamine and quinpirole were the same in the homomer and heteromer. Thus, we have uncovered a molecular mechanism for functional selectivity in which a drug acts differently at a G protein-coupled receptor (GPCR) protomer depending on the identity of the second protomer participating in the formation of the signaling unit–opening the door to enhancing pharmacological specificity by targeting differences between homomeric and heteromeric signaling.}, pmid = {21785426}, keywords = {Apomorphine,Apomorphine: analogs & derivatives,Apomorphine: chemistry,Apomorphine: pharmacology,Dopamine,Dopamine Agonists,Dopamine Agonists: chemistry,Dopamine Agonists: pharmacology,Dopamine D1,Dopamine D1: agonists,Dopamine D1: chemistry,Dopamine D2,Dopamine D2: agonists,Dopamine D2: chemistry,Dopamine: chemistry,Dopamine: pharmacology,Fluorescence Resonance Energy Transfer,Fluorescence Resonance Energy Transfer: methods,Humans,nosource,Protein Conformation,Protein Multimerization,Quinpirole,Quinpirole: chemistry,Quinpirole: pharmacology,Receptors} }

@article{mustafaIdentificationProfilingNovel2012, title = {Identification and Profiling of Novel {{$\(1A-adrenoceptor-CXC}} Chemokine Receptor 2 Heteromer.}, author = {Mustafa, Sanam and See, Heng B. and Seeber, Ruth M. and Armstrong, Stephen P. and White, Carl W. and Ventura, Sabatino and Ayoub, Mohammed Akli and Pfleger, Kevin D. G.}, year = 2012, month = apr, journal = {The Journal of biological chemistry}, volume = {287}, number = {16}, pages = {12952--12965}, issn = {1083-351X}, doi = {10.1074/jbc.M111.322834}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3340001&tool=pmcentrez&rendertype=abstract}, abstract = {We have provided the first evidence for specific heteromerization between the {\)\(}(1A)-adrenoceptor ({\)\(}(1A)AR) and CXC chemokine receptor 2 (CXCR2) in live cells. {\)\(}(1A)AR and CXCR2 are both expressed in areas such as the stromal smooth muscle layer of the prostate. By utilizing the G protein-coupled receptor (GPCR) heteromer identification technology on the live cell-based bioluminescence resonance energy transfer (BRET) assay platform, our studies in human embryonic kidney 293 cells have identified norepinephrine-dependent {\)\(}-arrestin recruitment that was in turn dependent upon co-expression of {\)\(}(1A)AR with CXCR2. These findings have been supported by co-localization observed using confocal microscopy. This norepinephrine-dependent {\)\(}-arrestin recruitment was inhibited not only by the {\)\(}(1)AR antagonist Terazosin but also by the CXCR2-specific allosteric inverse agonist SB265610. Furthermore, Labetalol, which is marketed for hypertension as a nonselective {\)\(}-adrenoceptor antagonist with {\)\(}(1)AR antagonist properties, was identified as a heteromer-specific-biased agonist exhibiting partial agonism for inositol phosphate production but essentially full agonism for {\)\(}-arrestin recruitment at the {\)\(}(1A)AR-CXCR2 heteromer. Finally, bioluminescence resonance energy transfer studies with both receptors tagged suggest that {\)$}(1A)AR-CXCR2 heteromerization occurs constitutively and is not modulated by ligand. These findings support the concept of GPCR heteromer complexes exhibiting distinct pharmacology, thereby providing additional mechanisms through which GPCRs can potentially achieve their diverse biological functions. This has important implications for the use and future development of pharmaceuticals targeting these receptors.}, pmid = {22371491}, keywords = {Adrenergic,Adrenergic alpha-1 Receptor Antagonists,Adrenergic alpha-1 Receptor Antagonists: pharmacol,Adrenergic alpha-Agonists,Adrenergic alpha-Agonists: pharmacology,Allosteric Regulation,Allosteric Regulation: physiology,alpha-1,alpha-1: chemistry,alpha-1: metabolism,Animals,Arrestins,Arrestins: metabolism,Chemokines,Chemokines: metabolism,CHO Cells,Cricetinae,G-Protein-Coupled,G-Protein-Coupled: chemistry,G-Protein-Coupled: metabolism,HEK293 Cells,Humans,Inbred C57BL,Inositol Phosphates,Inositol Phosphates: metabolism,Interleukin-8B,Interleukin-8B: chemistry,Interleukin-8B: metabolism,Labetalol,Labetalol: pharmacology,Male,Mice,Norepinephrine,Norepinephrine: pharmacology,nosource,Prazosin,Prazosin: analogs & derivatives,Prazosin: pharmacology,Prostate,Prostate: metabolism,Protein Structure,Quaternary,Receptors} }

@article{wangTelomereandTelomeraseinteractingProtein2012, title = {Telomere-and Telomerase-Interacting Protein That Unfolds Telomere {{G-quadruplex}} and Promotes Telomere Extension in Mammalian Cells}, author = {Wang, Feng and Tang, Ming-liang and Zeng, Zhi-xiong and Wu, Ren-yi}, year = 2012, journal = {Proceedings of the }, pages = {1–6}, doi = {10.1073/pnas.1200232109}, url = {http://www.pnas.org/content/109/50/20413.short}, keywords = {nosource} }

@article{leeuwenLocalizationModifiedBase1997, title = {Localization of the Modified Base {{J}} in Telomeric {{VSG}} Gene Expression Sites of {{Trypanosoma}} Brucei.}, author = {{}van Leeuwen, F. and Wijsman, E. R. and Kieft, R. and {}a van der Marel, G. and {}van Boom, J. H. and Borst, P.}, year = 1997, month = dec, journal = {Genes & development}, volume = {11}, number = {23}, pages = {3232–41}, issn = {0890-9369}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=316749&tool=pmcentrez&rendertype=abstract}, abstract = {African trypanosomes such as Trypanosoma brucei undergo antigenic variation in the bloodstream of their mammalian hosts by regularly changing the variant surface glycoprotein (VSG) gene expressed. The transcribed VSG gene is invariably located in a telomeric expression site. There are multiple expression sites and one way to change the VSG gene expressed is by activating a new site and inactivating the previously active one. The mechanisms that control expression site switching are unknown, but have been suggested to involve epigenetic regulation. We have found previously that VSG genes in silent (but not active) expression sites contain modified restriction endonuclease cleavage sites, and we have presented circumstantial evidence indicating that this is attributable to the presence of a novel modified base beta-D-glucosyl-hydroxymethyluracil, or J. To directly test this, we have generated antisera that specifically recognize J-containing DNA and have used these to determine the precise location of this modified thymine in the telomeric VSG expression sites. By anti J-DNA immunoprecipitations, we found that J is present in telomeric VSG genes in silenced expression sites and not in actively transcribed telomeric VSG genes. J was absent from inactive chromosome-internal VSG genes. DNA modification was also found at the boundaries of expression sites. In the long 50-bp repeat arrays upstream of the promoter and in the telomeric repeat arrays downstream of the VSG gene, J was found both in silent and active expression sites. This suggests that silencing results in a gradient of modification spreading from repetitive DNA flanks into the neighboring expression site sequences. In this paper, we discuss the possible role of J in silencing of expression sites.}, pmid = {9389654}, keywords = {Animals,Antibodies,Binding Sites,Deoxyribonucleases,DNA,Gene Expression,Genes,Genetic,Glucosides,Glucosides: analysis,nosource,Nucleic Acid,Precipitin Tests,Promoter Regions,Protozoan,Protozoan: immunology,Protozoan: metabolism,Rabbits,Repetitive Sequences,Telomere,Trypanosoma,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma: geneti,Type II Site-Specific,Type II Site-Specific: metabol,Uracil,Uracil: analogs & derivatives,Uracil: analysis,Variant Surface Glycoproteins} }

@article{shiArgonauteProteinEarly2004, title = {Argonaute Protein in the Early Divergent Eukaryote {{Trypanosoma}} Brucei: Control of Small Interfering {{RNA}} Accumulation and Retroposon Transcript Abundance}, author = {Shi, Huafang and Djikeng, Appolinaire and Tschudi, Christian and Ullu, Elisabetta}, year = 2004, journal = {Molecular and cellular }, volume = {24}, number = {1}, pages = {420–427}, doi = {10.1128/MCB.24.1.420}, url = {http://mcb.asm.org/content/24/1/420.short}, keywords = {nosource} }

@article{logan-klumplerGeneDBAnnotationDatabase2012, title = {{{GeneDB}}–an Annotation Database for Pathogens.}, author = {{Logan-Klumpler}, Flora J. and Silva, Nishadi De and Boehme, Ulrike and Rogers, Matthew B. and Velarde, Giles and {}a McQuillan, Jacqueline and Carver, Tim and Aslett, Martin and Olsen, Christian and Subramanian, Sandhya and Phan, Isabelle and Farris, Carol and Mitra, Siddhartha and Ramasamy, Gowthaman and Wang, Haiming and Tivey, Adrian and Jackson, Andrew and Houston, Robin and Parkhill, Julian and Holden, Matthew and Harb, Omar S. and Brunk, Brian P. and Myler, Peter J. and Roos, David and Carrington, Mark and Smith, Deborah F. and {Hertz-Fowler}, Christiane and Berriman, Matthew}, year = 2012, month = jan, journal = {Nucleic acids research}, volume = {40}, number = {Database issue}, pages = {D98-108}, issn = {1362-4962}, doi = {10.1093/nar/gkr1032}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3245030&tool=pmcentrez&rendertype=abstract}, abstract = {GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and closely related organisms. The resource provides a portal to genome sequence and annotation data, which is primarily generated by the Pathogen Genomics group at the Wellcome Trust Sanger Institute. It combines data from completed and ongoing genome projects with curated annotation, which is readily accessible from a web based resource. The development of the database in recent years has focused on providing database-driven annotation tools and pipelines, as well as catering for increasingly frequent assembly updates. The website has been significantly redesigned to take advantage of current web technologies, and improve usability. The current release stores 41 data sets, of which 17 are manually curated and maintained by biologists, who review and incorporate data from the scientific literature, as well as other sources. GeneDB is primarily a production and annotation database for the genomes of predominantly pathogenic organisms.}, pmid = {22116062}, keywords = {Animals,Arthropods,Arthropods: genetics,Bacterial,Controlled,Databases,Genetic,Genome,Genomics,Helminth,Internet,Molecular Sequence Annotation,nosource,Protozoan,Vocabulary} }

@article{ritchieProgrammed1Frameshifting2012, title = {Programmed -1 Frameshifting Efficiency Correlates with {{RNA}} Pseudoknot Conformational Plasticity, Not Resistance to Mechanical Unfolding}, author = {Ritchie, DB Dustin B. and Foster, Daniel a N. and Woodside, Michael T.}, year = 2012, month = oct, journal = {Proceedings of the }, volume = {109}, number = {40}, pages = {1–6}, issn = {1091-6490}, doi = {10.1073/pnas.1204114109}, url = {http://www.pnas.org/content/109/40/16167.short http://www.pnas.org/content/early/2012/09/11/1204114109.short http://www.ncbi.nlm.nih.gov/pubmed/22988073 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3479558&tool=pmcentrez&rendertype=abstract}, abstract = {Programmed -1 frameshifting, whereby the reading frame of a ribosome on messenger RNA is shifted in order to generate an alternate gene product, is often triggered by a pseudoknot structure in the mRNA in combination with an upstream slippery sequence. The efficiency of frameshifting varies widely for different sites, but the factors that determine frameshifting efficiency are not yet fully understood. Previous work has suggested that frameshifting efficiency is related to the resistance of the pseudoknot against mechanical unfolding. We tested this hypothesis by studying the mechanical properties of a panel of pseudoknots with frameshifting efficiencies ranging from 2% to 30%: four pseudoknots from retroviruses, two from luteoviruses, one from a coronavirus, and a nonframeshifting bacteriophage pseudoknot. Using optical tweezers to apply tension across the RNA, we measured the distribution of forces required to unfold each pseudoknot. We found that neither the average unfolding force, nor the unfolding kinetics, nor the parameters describing the energy landscape for mechanical unfolding of the pseudoknot (energy barrier height and distance to the transition state) could be correlated to frameshifting efficiency. These results indicate that the resistance of pseudoknots to mechanical unfolding is not a primary determinant of frameshifting efficiency. However, increased frameshifting efficiency was correlated with an increased tendency to form alternate, incompletely folded structures, suggesting a more complex picture of the role of the pseudoknot involving the conformational dynamics.}, pmid = {22988073}, keywords = {Biomechanical Phenomena,Biophysics,Frameshifting,Messenger,Messenger: genetics,nosource,Nucleic Acid Conformation,Optical Tweezers,Ribosomal,Ribosomal: genetics,Ribosomal: physiology,RNA,Spectrum Analysis,Spectrum Analysis: methods} }

@article{thoreenUnifyingModelMTORC1mediated2012, title = {A Unifying Model for {{mTORC1-mediated}} Regulation of {{mRNA}} Translation.}, author = {Thoreen, Carson C. and Chantranupong, Lynne and Keys, Heather R. and Wang, Tim and Gray, Nathanael S. and Sabatini, David M.}, year = 2012, month = may, journal = {Nature}, volume = {485}, number = {7396}, eprint = {22552098}, eprinttype = {pubmed}, pages = {109–13}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature11083}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22552098}, abstract = {The mTOR complex 1 (mTORC1) kinase nucleates a pathway that promotes cell growth and proliferation and is the target of rapamycin, a drug with many clinical uses. mTORC1 regulates messenger RNA translation, but the overall translational program is poorly defined and no unifying model exists to explain how mTORC1 differentially controls the translation of specific mRNAs. Here we use high-resolution transcriptome-scale ribosome profiling to monitor translation in mouse cells acutely treated with the mTOR inhibitor Torin 1, which, unlike rapamycin, fully inhibits mTORC1 (ref. 2). Our data reveal a surprisingly simple model of the mRNA features and mechanisms that confer mTORC1-dependent translation control. The subset of mRNAs that are specifically regulated by mTORC1 consists almost entirely of transcripts with established 5’ terminal oligopyrimidine (TOP) motifs, or, like Hsp90ab1 and Ybx1, with previously unrecognized TOP or related TOP-like motifs that we identified. We find no evidence to support proposals that mTORC1 preferentially regulates mRNAs with increased 5’ untranslated region length or complexity. mTORC1 phosphorylates a myriad of translational regulators, but how it controls TOP mRNA translation is unknown. Remarkably, loss of just the 4E-BP family of translational repressors, arguably the best characterized mTORC1 substrates, is sufficient to render TOP and TOP-like mRNA translation resistant to Torin 1. The 4E-BPs inhibit translation initiation by interfering with the interaction between the cap-binding protein eIF4E and eIF4G1. Loss of this interaction diminishes the capacity of eIF4E to bind TOP and TOP-like mRNAs much more than other mRNAs, explaining why mTOR inhibition selectively suppresses their translation. Our results clarify the translational program controlled by mTORC1 and identify 4E-BPs and eIF4G1 as its master effectors.}, pmid = {22552098}, keywords = {5’ Untranslated Regions,5’ Untranslated Regions: genetics,Animals,Base Sequence,Biological,Cell Line,Eukaryotic Initiation Factor-4E,Eukaryotic Initiation Factor-4E: metabolism,Eukaryotic Initiation Factor-4G,Eukaryotic Initiation Factor-4G: metabolism,Gene Expression Regulation,Gene Expression Regulation: drug effects,Humans,Male,Messenger,Messenger: genetics,Messenger: metabolism,Mice,Models,Naphthyridines,Naphthyridines: pharmacology,nosource,Nucleotide Motifs,Phosphorylation,Prostatic Neoplasms,Prostatic Neoplasms: genetics,Prostatic Neoplasms: pathology,Protein Binding,Protein Biosynthesis,Protein Biosynthesis: drug effects,Proteins,Proteins: antagonists & inhibitors,Proteins: metabolism,Ribosomes,Ribosomes: metabolism,RNA,Tumor} }

@article{leekTacklingWidespreadCritical2010, title = {Tackling the Widespread and Critical Impact of Batch Effects in High-Throughput Data.}, author = {Leek, Jeffrey T. and Scharpf, Robert B. and Bravo, H{'e}ctor Corrada and Simcha, David and Langmead, Benjamin and Johnson, W. Evan and Geman, Donald and Baggerly, Keith and {}a Irizarry, Rafael}, year = 2010, month = oct, journal = {Nature reviews. Genetics}, volume = {11}, number = {10}, eprint = {20838408}, eprinttype = {pubmed}, pages = {733–9}, publisher = {Nature Publishing Group}, issn = {1471-0064}, doi = {10.1038/nrg2825}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20838408}, abstract = {High-throughput technologies are widely used, for example to assay genetic variants, gene and protein expression, and epigenetic modifications. One often overlooked complication with such studies is batch effects, which occur because measurements are affected by laboratory conditions, reagent lots and personnel differences. This becomes a major problem when batch effects are correlated with an outcome of interest and lead to incorrect conclusions. Using both published studies and our own analyses, we argue that batch effects (as well as other technical and biological artefacts) are widespread and critical to address. We review experimental and computational approaches for doing so.}, pmid = {20838408}, keywords = {Biotechnology,Biotechnology: methods,Biotechnology: standards,Biotechnology: statistics & numerical data,Computational Biology,Computational Biology: methods,DNA,DNA: methods,DNA: standards,DNA: statistics & numerical dat,Genomics,Genomics: methods,Genomics: standards,Genomics: statistics & numerical data,nosource,Oligonucleotide Array Sequence Analysis,Oligonucleotide Array Sequence Analysis: methods,Oligonucleotide Array Sequence Analysis: standards,Oligonucleotide Array Sequence Analysis: statistic,Periodicals as Topic,Periodicals as Topic: standards,Research Design,Research Design: standards,Research Design: statistics & numerical data,Sequence Analysis} } % == BibTeX quality report for leekTacklingWidespreadCritical2010: % ? Possibly abbreviated journal title Nature reviews. Genetics

@article{varshavskyNendRulePathway2011, title = {The {{N-end}} Rule Pathway and Regulation by Proteolysis.}, author = {Varshavsky, Alexander}, year = 2011, month = jun, journal = {Protein science : a publication of the Protein Society}, volume = {20}, pages = {1298–1345}, issn = {1469-896X}, doi = {10.1002/pro.666}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3189519&tool=pmcentrez&rendertype=abstract}, abstract = {The N-end rule relates the regulation of the in vivo half-life of a protein to the identity of its N-terminal residue. Degradation signals (degrons) that are targeted by the N-end rule pathway include a set called N-degrons. The main determinant of an N-degron is a destabilizing N-terminal residue of a protein. In eukaryotes, the N-end rule pathway is a part of the ubiquitin system and consists of two branches, the Ac/N-end rule and the Arg/N-end rule pathways. The Ac/N-end rule pathway targets proteins containing N({\(\alpha\)}) -terminally acetylated (Nt-acetylated) residues. The Arg/N-end rule pathway recognizes unacetylated N-terminal residues and involves N-terminal arginylation. Together, these branches target for degradation a majority of cellular proteins. For example, more than 80% of human proteins are cotranslationally Nt-acetylated. Thus most proteins harbor a specific degradation signal, termed (Ac) N-degron, from the moment of their birth. Specific N-end rule pathways are also present in prokaryotes and in mitochondria. Enzymes that produce N-degrons include methionine-aminopeptidases, caspases, calpains, Nt-acetylases, Nt-amidases, arginyl-transferases and leucyl-transferases. Regulated degradation of specific proteins by the N-end rule pathway mediates a legion of physiological functions, including the sensing of heme, oxygen, and nitric oxide; selective elimination of misfolded proteins; the regulation of DNA repair, segregation and condensation; the signaling by G proteins; the regulation of peptide import, fat metabolism, viral and bacterial infections, apoptosis, meiosis, spermatogenesis, neurogenesis, and cardiovascular development; and the functioning of adult organs, including the pancreas and the brain. Discovered 25 years ago, this pathway continues to be a fount of biological insights.}, pmid = {21633985}, keywords = {arginylation,leucylation,n-degron,n-end rule,nosource,proteolysis,ubiquitin} }

@article{ammermanArchitectureTrypanosomeRNA2012, title = {Architecture of the Trypanosome {{RNA}} Editing Accessory Complex, {{MRB1}}.}, author = {Ammerman, Michelle L. and Downey, Kurtis M. and Hashimi, Hassan and Fisk, John C. and Tomasello, Danielle L. and Faktorov{'a}, Drahom{'i}ra and Kafkov{'a}, Lucie and King, Tony and Lukes, Julius and Read, Laurie K.}, year = 2012, month = jul, journal = {Nucleic acids research}, volume = {40}, number = {12}, pages = {5637–50}, issn = {1362-4962}, doi = {10.1093/nar/gks211}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3384329&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanosoma brucei undergoes an essential process of mitochondrial uridine insertion and deletion RNA editing catalyzed by a 20S editosome. The multiprotein mitochondrial RNA-binding complex 1 (MRB1) is emerging as an equally essential component of the trypanosome RNA editing machinery, with additional functions in gRNA and mRNA stabilization. The distinct and overlapping protein compositions of reported MRB1 complexes and diverse MRB1 functions suggest that the complex is composed of subcomplexes with RNA-dependent and independent interactions. To determine the architecture of the MRB1 complex, we performed a comprehensive yeast two-hybrid analysis of 31 reported MRB1 proteins. We also used in vivo analyses of tagged MRB1 components to confirm direct and RNA-mediated interactions. Here, we show that MRB1 contains a core complex comprised of six proteins and maintained by numerous direct interactions. The MRB1 core associates with multiple subcomplexes and proteins through RNA-enhanced or RNA-dependent interactions. These findings provide a framework for interpretation of previous functional studies and suggest that MRB1 is a dynamic complex that coordinates various aspects of mitochondrial gene regulation.}, pmid = {22396527}, keywords = {Mitochondrial Proteins,Mitochondrial Proteins: metabolism,nosource,Protein Subunits,Protein Subunits: metabolism,Protozoan,Protozoan Proteins,Protozoan Proteins: metabolism,Protozoan: metabolism,RNA,RNA Editing,RNA-Binding Proteins,RNA-Binding Proteins: metabolism,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: metabolism,Two-Hybrid System Techniques} }

@article{aphasizhevMitochondrialRNAProcessing2011, title = {Mitochondrial {{RNA}} Processing in Trypanosomes.}, author = {Aphasizhev, Ruslan and Aphasizheva, Inna}, year = 2011, month = sep, journal = {Research in microbiology}, volume = {162}, number = {7}, pages = {655–63}, publisher = {Elsevier Masson SAS}, issn = {1769-7123}, doi = {10.1016/j.resmic.2011.04.015}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3148333&tool=pmcentrez&rendertype=abstract}, abstract = {The mitochondrial genome of trypanosomes is composed of {\(\sim\)}50 maxicircles and thousands of minicircles. Maxi-({\(\sim\)}25 kb) and mini-({\(\sim\)}1 kb)circles are catenated and packed into a dense structure called a kinetoplast. Both types of circular DNA are transcribed by a phage-like RNA polymerase: maxicircles yield multicistronic rRNA and mRNA precursors, while guide RNA (gRNA) precursors are produced from minicircles. To function in mitochondrial translation, pre-mRNAs must undergo a nucleolytic processing and 3’ modifications, and often uridine insertion/deletion editing. gRNAs, which represent short (50-60 nt) RNAs directing editing reactions, are produced by 3’ nucleolytic processing of a much longer precursor followed by 3’ uridylation. Ribosomal RNAs are excised from precursors and their 3’ ends are also trimmed and uridylated. All tRNAs are imported from the cytoplasm and some are further modified and edited in the mitochondrial matrix. Historically, the fascinating phenomenon of RNA editing has been extensively studied as an isolated pathway in which nuclear-encoded proteins mediate interactions of maxi- and minicircle transcripts to create open reading frames. However, recent studies unraveled a highly integrated network of mitochondrial genome expression including critical pre- and post-editing 3’ mRNA processing, and gRNA and rRNA maturation steps. Here we focus on RNA 3’ adenylation and uridylation as processes essential for biogenesis, stability and functioning of mitochondrial RNAs.}, pmid = {21596134}, keywords = {nosource,Post-Transcriptional,Protozoan,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Protozoan: genetics,Protozoan: metabolism,RNA,RNA Processing,RNA: genetics,RNA: metabolism,Trypanosoma,Trypanosoma: genetics,Trypanosoma: metabolism} }

@article{estevezUridineInsertionDeletion1999, title = {Uridine Insertion/Deletion {{RNA}} Editing in Trypanosome Mitochondria–a Review.}, author = {Est{'e}vez, a M. and Simpson, L.}, year = 1999, month = nov, journal = {Gene}, volume = {240}, number = {2}, eprint = {10580144}, eprinttype = {pubmed}, pages = {247–60}, issn = {0378-1119}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10580144}, abstract = {The uridine insertion/deletion RNA editing in trypanosome mitochondria is a unique posttranscriptional RNA maturation process that involves the addition or removal of uridine residues at precise sites usually within the coding regions of mitochondrial transcripts. This process creates initiation and termination codons, corrects frameshifts and even builds entire open-reading frames from nonsense sequences. The development of several in-vitro editing assays has provided much insight into the molecular mechanism of RNA editing, which appears to involve cleavage, U addition, exonuclease trimming and ligation, essentially as proposed in the original ‘enzyme cascade’ model (Blum, B., Bakalara, N., Simpson, L., 1990. A model for RNA editing in kinetoplastid mitochondria: ‘Guide’ RNA molecules transcribed from maxicircle DNA provide the edited information. Cell 60, 189-198). However, little is known about the biochemical properties of the proteins involved and the significance and role of this process. This article is a review of recent findings on uridine-insertion/deletion editing in trypanosome mitochondria, with an emphasis on the proteins isolated and characterized that may have a role in this process.}, pmid = {10580144}, keywords = {Animals,Base Sequence,Guide,Guide: genetics,Guide: metabolism,Insertional,Mitochondria,Mitochondria: genetics,Molecular Sequence Data,Mutagenesis,nosource,Protozoan,Protozoan Proteins,Protozoan Proteins: metabolism,Protozoan: genetics,Protozoan: metabolism,RNA,RNA Editing,Sequence Deletion,Trypanosomatina,Trypanosomatina: genetics,Uridine,Uridine: genetics} }

@article{maslovEvolutionRNAEditing1994, title = {Evolution of {{RNA}} Editing in Kinetoplastid Protozoa}, author = {Maslov, D. A. and Avila, H. A. and Lake, J. A. and Simpson, L.}, year = 1994, journal = {Nature}, url = {http://dna.kdna.ucla.edu/simpsonlab/Lab publications/maslov evol 1994.pdf}, keywords = {nosource} }

@article{soutoDNAMarkersDefine1996, title = {{{DNA}} Markers Define Two Major Phylogenetic Lineages of {{Trypanosoma}} Cruzi}, author = {Souto, R. P. and Fernandes, O.}, year = 1996, journal = {Molecular and }, volume = {83}, pages = {141–152}, url = {http://www.sciencedirect.com/science/article/pii/S0166685196027557}, keywords = {nosource} }

@article{zavala-castroStageSpecificKinetoplast2000, title = {Stage Specific Kinetoplast {{DNA-binding}} Proteins in {{Trypanosoma}} Cruzi.}, author = {{Zavala-Castro}, J. E. and {Acosta-Viana}, K. and {Guzm{'a}n-Mar{'i}n}, E. and {Rosado-Barrera}, M. E. and {Rosales-Encina}, J. L.}, year = 2000, month = sep, journal = {Acta tropica}, volume = {76}, number = {2}, eprint = {10936573}, eprinttype = {pubmed}, pages = {139–46}, issn = {0001-706X}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10936573}, abstract = {Knowledge regarding kinetoplast DNA organization in all members of the Trypanosomatid family is incomplete. Recently, the presence of kinetoplast-associated proteins in condensing kDNA networks in Crithidia fasciculata has been described and a role for these proteins in the maintenance of these complex structures was suggested. To investigate the presence of protein components in Trypanosoma cruzi kinetoplast, we previously described seven epimastigote kinetoplast-associated proteins. We report here the existence of kinetoplast binding proteins in amastigote and trypomastigote stages of T. cruzi, which could bind both mini and maxicircles components with a stage specific elements for every infective form of the parasite. We propose three major classes of kinetoplast-associated proteins related to the basic processes of this intricate disc structure and suggest a possible function of these binding proteins in the T. cruzi mitochondrial DNA organization.}, isbn = {5299246412}, pmid = {10936573}, keywords = {Animals,Bacterial Proteins,Blotting,Deoxyribonucleases,DNA,DNA Probes,DNA Probes: chemistry,DNA-Binding Proteins,DNA-Binding Proteins: chemistry,Electrophoresis,Humans,Kinetoplast,Kinetoplast: chemistry,Kinetoplast: isolation & purification,nosource,Polyacrylamide Gel,Protozoan Proteins,Protozoan Proteins: chemistry,Trypanosoma cruzi,Trypanosoma cruzi: chemistry,Trypanosoma cruzi: genetics,Type II Site-Specific,Type II Site-Specific: chemist,Western} }

@article{deanaLostTranslationInfluence2005, title = {Lost in Translation: The Influence of Ribosomes on Bacterial {{mRNA}} Decay.}, author = {Deana, Atilio and Belasco, Joel G.}, year = 2005, month = nov, journal = {Genes & development}, volume = {19}, number = {21}, eprint = {16264189}, eprinttype = {pubmed}, pages = {2526–33}, issn = {0890-9369}, doi = {10.1101/gad.1348805}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16264189}, abstract = {The lifetimes of bacterial mRNAs are strongly affected by their association with ribosomes. Events occurring at any stage during translation, including ribosome binding, polypeptide elongation, or translation termination, can influence the susceptibility of mRNA to ribonuclease attack. Ribosomes usually act as protective barriers that impede mRNA cleavage, but in some instances they can instead trigger the decay of the mRNA to which they are bound or send a signal that leads to widespread mRNA destabilization within a cell. The influence of translation on mRNA decay provides a quality-control mechanism for minimizing the use of poorly or improperly translated mRNAs as templates for the production of abnormal proteins that might be toxic to bacteria.}, pmid = {16264189}, keywords = {Bacteria,Bacteria: metabolism,Bacterial,Bacterial Physiological Phenomena,Bacterial: metabolism,Messenger,Messenger: metabolism,nosource,Peptide Chain Elongation,Peptide Chain Termination,Ribosomes,Ribosomes: metabolism,RNA,RNA Stability,RNA Stability: physiology,Translational,Translational: physiolo,Translational: physiolog} }

@article{figueiredoDifferentiationTrypanosomaCruzi2000, title = {Differentiation of {{Trypanosoma}} Cruzi Epimastigotes: Metacyclogenesis and Adhesion to Substrate Are Triggered by Nutritional Stress}, author = {Figueiredo, {RCBQ}}, year = 2000, journal = {Journal of }, volume = {86}, number = {6}, pages = {1213–1218}, url = {http://www.journalofparasitology.org/doi/full/10.1645/0022-3395(2000)086[1213:DOTCEM]2.0.CO;2}, keywords = {nosource} }

@article{ingoliaRibosomeProfilingStrategy2012, title = {The Ribosome Profiling Strategy for Monitoring Translation in Vivo by Deep Sequencing of Ribosome-Protected {{mRNA}} Fragments.}, author = {Ingolia, Nicholas T. and {}a Brar, Gloria and Rouskin, Silvia and McGeachy, Anna M. and Weissman, Jonathan S.}, year = 2012, month = aug, journal = {Nature protocols}, volume = {7}, number = {8}, eprint = {22836135}, eprinttype = {pubmed}, pages = {1534–50}, issn = {1750-2799}, doi = {10.1038/nprot.2012.086}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22836135}, abstract = {Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. We present a protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing. This ribosome profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. In addition, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, we describe an adaptation that reveals the sites of translation initiation by pretreating cells with harringtonine to immobilize initiating ribosomes. The protocol we describe requires 5-7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis require a further 4-5 days.}, pmid = {22836135}, keywords = {nosource} }

@article{kafkovaFunctionalCharacterizationTwo2012, title = {Functional Characterization of Two Paralogs That Are Novel {{RNA}} Binding Proteins Influencing Mitochondrial Transcripts of {{Trypanosoma}} Brucei.}, author = {Kafkov{'a}, Lucie and Ammerman, ML Michelle L. and Faktorov{'a}, Drahom{'i}ra and Fisk, John C. and Zimmer, Sara L. and Sobotka, Roman and Read, Laurie K. and Lukes, Julius and Hashimi, Hassan}, year = 2012, month = oct, journal = {RNA}, volume = {18}, number = {10}, eprint = {22898985}, eprinttype = {pubmed}, pages = {1846–61}, issn = {1469-9001}, doi = {10.1261/rna.033852.112}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22898985 http://rnajournal.cshlp.org/content/18/10/1846.short}, abstract = {A majority of Trypanosoma brucei proteins have unknown functions, a consequence of its independent evolutionary history within the order Kinetoplastida that allowed for the emergence of several unique biological properties. Among these is RNA editing, needed for expression of mitochondrial-encoded genes. The recently discovered mitochondrial RNA binding complex 1 (MRB1) is composed of proteins with several functions in processing organellar RNA. We characterize two MRB1 subunits, referred to herein as MRB8170 and MRB4160, which are paralogs arisen from a large chromosome duplication occurring only in T. brucei. As with many other MRB1 proteins, both have no recognizable domains, motifs, or orthologs outside the order. We show that they are both novel RNA binding proteins, possibly representing a new class of these proteins. They associate with a similar subset of MRB1 subunits but not directly with each other. We generated cell lines that either individually or simultaneously target the mRNAs encoding both proteins using RNAi. Their dual silencing results in a differential effect on moderately and pan-edited RNAs, suggesting a possible functional separation of the two proteins. Cell growth persists upon RNAi silencing of each protein individually in contrast to the dual knockdown. Yet, their apparent redundancy in terms of cell viability is at odds with the finding that only one of these knockdowns results in the general degradation of pan-edited RNAs. While MRB8170 and MRB4160 share a considerable degree of conservation, our results suggest that their recent sequence divergence has led to them influencing mitochondrial mRNAs to differing degrees.}, pmid = {22898985}, keywords = {Biological,Cloning,Conserved Sequence,Macromolecular Substances,Macromolecular Substances: metabolism,Messenger,Messenger: metabolism,Models,Molecular,nosource,Protein Binding,Protein Subunits,Protein Subunits: genetics,Protein Subunits: metabolism,Protozoan Proteins,Protozoan Proteins: chemistry,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Protozoan Proteins: physiology,RNA,RNA-Binding Proteins,RNA-Binding Proteins: chemistry,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism,RNA-Binding Proteins: physiology,RNA: metabolism,Sequence Homology,Substrate Specificity,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: metabolism} }

@article{swiderskiSequentialSepharoseChromatographic1979, title = {Sequential {{Sepharose}} Chromatographic Isolation of Polysomes and Polysomal {{RNAs}} Depleted in Nuclear {{RNA}} from {{Xenopus}}}, author = {Swiderski, RE Ruth E. and Johnson, SA Steven A. and Larkins, Brian A. and Graham, Dale E.}, year = 1979, journal = {Nucleic acids }, volume = {6}, number = {11}, pages = {3685–3701}, url = {http://nar.oxfordjournals.org/content/6/11/3685.short}, keywords = {nosource} }

@article{liskaCombiningMassSpectrometry2003, title = {Combining Mass Spectrometry with Database Interrogation Strategies in Proteomics}, author = {Liska, Adam J. and Shevchenko, Andrej}, year = 2003, month = may, journal = {TrAC Trends in Analytical Chemistry}, volume = {22}, number = {5}, pages = {291–298}, issn = {01659936}, doi = {10.1016/S0165-9936(03)00507-7}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0165993603005077}, keywords = {2-d,abbreviations,bioinformatics,cdna,complementary,database,databases,db,dna,electrospray ionization,esi,est,expressed sequence tag,ft-,gel electrophoresis,mass spectrometry,ms,nosource,proteomics,spectra interpretation,two-dimensional} }

@article{tschudiSmallInterferingRNAproducing2012, title = {Small Interfering {{RNA-producing}} Loci in the Ancient Parasitic Eukaryote {{Trypanosoma}} Brucei.}, author = {Tschudi, Christian and Shi, Huafang and Franklin, Joseph B. and Ullu, Elisabetta}, year = 2012, month = jan, journal = {BMC genomics}, volume = {13}, number = {1}, pages = {427}, publisher = {BMC Genomics}, issn = {1471-2164}, doi = {10.1186/1471-2164-13-427}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3447711&tool=pmcentrez&rendertype=abstract}, abstract = {ABSTRACT:}, pmid = {22925482}, keywords = {argonaute,convergent transcription,Convergent transcription unit,dicer-deficient,inverted repeat,nosource,retrotransposon,siRNA,trypanosome} }

@article{cabanskiReQONBioconductorPackage2012, title = {{{ReQON}}: A {{Bioconductor}} Package for Recalibrating Quality Scores from next-Generation Sequencing Data.}, author = {Cabanski, Christopher R. and Cavin, Keary and Bizon, Chris and Wilkerson, Matthew D. and Parker, Joel S. and Wilhelmsen, Kirk C. and Perou, Charles M. and Marron, Js and Hayes, D. Neil}, year = 2012, month = jan, journal = {BMC bioinformatics}, volume = {13}, number = {1}, eprint = {22946927}, eprinttype = {pubmed}, pages = {221}, issn = {1471-2105}, doi = {10.1186/1471-2105-13-221}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22946927}, abstract = {ABSTRACT:}, pmid = {22946927}, keywords = {bioconductor,bioinformatics,next-generation sequencing,nosource,quality score,recalibration} }

@article{gygiMassSpectrometryProteomics2000, title = {Mass Spectrometry and Proteomics.}, author = {Gygi, S. P. and Aebersold, R.}, year = 2000, month = oct, journal = {Current opinion in chemical biology}, volume = {4}, number = {5}, eprint = {11006534}, eprinttype = {pubmed}, pages = {489–94}, issn = {1367-5931}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11006534}, abstract = {Proteomics is the systematic analysis of the proteins expressed by a cell or tissue, and mass spectrometry is its essential analytical tool. In the past two years, incremental advances in standard proteome technology have increased the speed of protein identification with higher levels of automation and sensitivity. Furthermore, new approaches have provided landmark advances in determining functionally relevant properties of proteins, including their quantity and involvement within protein complexes.}, pmid = {11006534}, keywords = {Mass Spectrometry,Mass Spectrometry: methods,nosource,Proteome} }

@article{zirbelClassificationEnergeticsBasephosphate2009, title = {Classification and Energetics of the Base-Phosphate Interactions in {{RNA}}}, author = {Zirbel, Craig L. CL and Sponer, Judit E. Jiri and Stombaugh, Jesse and Leontis, Neocles B. and Jiri, S. and {}poner, J. E.}, year = 2009, month = aug, journal = {Nucleic acids }, volume = {37}, number = {15}, pages = {4898–4918}, issn = {1362-4962}, doi = {10.1093/nar/gkp468}, url = {http://nar.oxfordjournals.org/content/37/15/4898.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2731888&tool=pmcentrez&rendertype=abstract}, abstract = {Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of the bases in structured RNA molecules in the Protein Data Bank (PDB) hydrogen-bond with phosphates of other nucleotides. By extracting and superimposing base-phosphate (BPh) interactions from a reduced-redundancy subset of 3D structures from the PDB, we identified recurrent phosphate-binding sites on the RNA bases. Quantum chemical calculations were carried out on model systems representing each BPh interaction. The calculations show that the centers of each cluster obtained from the structure superpositions correspond to energy minima on the potential energy hypersurface. The calculations also show that the most stable phosphate-binding sites occur on the Watson-Crick edge of guanine and the Hoogsteen edge of cytosine. We modified the ‘Find RNA 3D’ (FR3D) software suite to automatically find and classify BPh interactions. Comparison of the 3D structures of the 16S and 23S rRNAs of Escherichia coli and Thermus thermophilus revealed that most BPh interactions are phylogenetically conserved and they occur primarily in hairpin, internal or junction loops or as part of tertiary interactions. Bases that form BPh interactions, which are conserved in the rRNA 3D structures are also conserved in homologous rRNA sequence alignments.}, pmid = {19528080}, keywords = {Adenine,Adenine: chemistry,Base Pairing,Base Sequence,Binding Sites,Conserved Sequence,Cytosine,Cytosine: chemistry,Guanine,Guanine: chemistry,Hydrogen Bonding,Models,Molecular,Molecular Sequence Data,nosource,Nucleic Acid,Nucleic Acid Conformation,Phosphates,Phosphates: chemistry,Quantum Theory,Ribosomal,Ribosomal: chemistry,RNA,RNA: chemistry,Sequence Homology,Uracil,Uracil: chemistry} }

@article{almakaremComprehensiveSurveyGeometric2012, title = {Comprehensive Survey and Geometric Classification of Base Triples in {{RNA}} Structures.}, author = {Almakarem, Amal S. Abu and Petrov, Anton I. and Stombaugh, Jesse and Zirbel, Craig L. and Leontis, Neocles B. and Almakarem, Amal S. Abu}, year = 2012, month = feb, journal = {Nucleic acids research}, volume = {40}, number = {4}, pages = {1407–23}, issn = {1362-4962}, doi = {10.1093/nar/gkr810}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3287178&tool=pmcentrez&rendertype=abstract}, abstract = {Base triples are recurrent clusters of three RNA nucleobases interacting edge-to-edge by hydrogen bonding. We find that the central base in almost all triples forms base pairs with the other two bases of the triple, providing a natural way to geometrically classify base triples. Given 12 geometric base pair families defined by the Leontis-Westhof nomenclature, combinatoric enumeration predicts 108 potential geometric base triple families. We searched representative atomic-resolution RNA 3D structures and found instances of 68 of the 108 predicted base triple families. Model building suggests that some of the remaining 40 families may be unlikely to form for steric reasons. We developed an on-line resource that provides exemplars of all base triples observed in the structure database and models for unobserved, predicted triples, grouped by triple family, as well as by three-base combination (http://rna.bgsu.edu/Triples). The classification helps to identify recurrent triple motifs that can substitute for each other while conserving RNA 3D structure, with applications in RNA 3D structure prediction and analysis of RNA sequence evolution.}, pmid = {22053086}, keywords = {Base Pairing,Cluster Analysis,Hydrogen Bonding,Models,Molecular,nosource,Nucleotide Motifs,Ribosomal,Ribosomal: chemistry,RNA,RNA: chemistry} }

@article{avessonMicroRNAsAmoebozoaDeep2012, title = {{{MicroRNAs}} in {{Amoebozoa}}: Deep Sequencing of the Small {{RNA}} Population in the Social Amoeba {{Dictyostelium}} Discoideum Reveals Developmentally Regulated {{microRNAs}}.}, author = {Avesson, Lotta and Reimeg{}rd, Johan and Wagner, EGH Gerhart H. and S{"o}derbom, Fredrik and Reimegard, J. and Soderbom, F.}, year = 2012, month = oct, journal = {RNA (New York, N.Y.)}, volume = {18}, number = {10}, pages = {1771–82}, issn = {1469-9001}, doi = {10.1261/rna.033175.112}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3446702&tool=pmcentrez&rendertype=abstract http://www.ncbi.nlm.nih.gov/pubmed/22875808 http://rnajournal.cshlp.org/cgi/doi/10.1261/rna.033175.112 http://rnajournal.cshlp.org/content/18/10/1771.shor}, abstract = {The RNA interference machinery has served as a guardian of eukaryotic genomes since the divergence from prokaryotes. Although the basic components have a shared origin, silencing pathways directed by small RNAs have evolved in diverse directions in different eukaryotic lineages. Micro (mi)RNAs regulate protein-coding genes and play vital roles in plants and animals, but less is known about their functions in other organisms. Here, we report, for the first time, deep sequencing of small RNAs from the social amoeba Dictyostelium discoideum. RNA from growing single-cell amoebae as well as from two multicellular developmental stages was sequenced. Computational analyses combined with experimental data reveal the expression of miRNAs, several of them exhibiting distinct expression patterns during development. To our knowledge, this is the first report of miRNAs in the Amoebozoa supergroup. We also show that overexpressed miRNA precursors generate miRNAs and, in most cases, miRNA* sequences, whose biogenesis is dependent on the Dicer-like protein DrnB, further supporting the presence of miRNAs in D. discoideum. In addition, we find miRNAs processed from hairpin structures originating from an intron as well as from a class of repetitive elements. We believe that these repetitive elements are sources for newly evolved miRNAs.}, pmid = {22875808}, keywords = {Amoebozoa,Amoebozoa: genetics,Animals,Base Sequence,Cluster Analysis,development,Developmental,Dictyostelium,dictyostelium discoideum,Dictyostelium: genetics,Dictyostelium: growth & development,Gene Expression Regulation,Genome,High-Throughput Nucleotide Sequencing,High-Throughput Nucleotide Sequencing: methods,high-throughput sequencing,microrna,MicroRNAs,MicroRNAs: chemistry,MicroRNAs: genetics,MicroRNAs: isolation & purification,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Protozoan,Protozoan: genetics,RNA,small rna,Transfection,Validation Studies as Topic} } % == BibTeX quality report for avessonMicroRNAsAmoebozoaDeep2012: % ? Possibly abbreviated journal title RNA (New York, N.Y.)

@article{bellaviaHomemadeDeviceLinear2008, title = {A Homemade Device for Linear Sucrose Gradients.}, author = {Bellavia, Daniele and Cellura, Doriana and Sisino, Giorgia and Barbieri, Rainer}, year = 2008, month = aug, journal = {Analytical biochemistry}, volume = {379}, number = {2}, eprint = {18533103}, eprinttype = {pubmed}, pages = {211–2}, issn = {1096-0309}, doi = {10.1016/j.ab.2008.05.010}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18533103}, abstract = {We have developed a simple and inexpensive device to obtain linear sucrose gradients with commonly used laboratory materials–a syringe, a flask, a plastic tube, and a piece of Pongo (Play-Doh). Refractive index values measured on sucrose fractions collected using our system demonstrate both the linearity and reliability of the gradients obtained.}, pmid = {18533103}, keywords = {Centrifugation,Costs and Cost Analysis,Density Gradient,Density Gradient: economics,Density Gradient: instrumentation,Laboratories,nosource,Reproducibility of Results} }

@article{preusserSpecialSmCore2009, title = {Special {{Sm}} Core Complex Functions in Assembly of the {{U2}} Small Nuclear Ribonucleoprotein of {{Trypanosoma}} Brucei.}, author = {Preusser, Christian and Palfi, Zsofia and Bindereif, Albrecht and Preu{}er, Christian}, year = 2009, month = aug, journal = {Eukaryotic cell}, volume = {8}, number = {8}, pages = {1228–34}, issn = {1535-9786}, doi = {10.1128/EC.00090-09}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2725569&tool=pmcentrez&rendertype=abstract}, abstract = {The processing of polycistronic pre-mRNAs in trypanosomes requires the spliceosomal small ribonucleoprotein complexes (snRNPs) U1, U2, U4/U6, U5, and SL, each of which contains a core of seven Sm proteins. Recently we reported the first evidence for a core variation in spliceosomal snRNPs; specifically, in the trypanosome U2 snRNP, two of the canonical Sm proteins, SmB and SmD3, are replaced by two U2-specific Sm proteins, Sm15K and Sm16.5K. Here we identify the U2-specific, nuclear-localized U2B’’ protein from Trypanosoma brucei. U2B’’ interacts with a second U2 snRNP protein, U2-40K (U2A’), which in turn contacts the U2-specific Sm16.5K/15K subcomplex. Together they form a high-affinity, U2-specific binding complex. This trypanosome-specific assembly differs from the mammalian system and provides a functional role for the Sm core variation found in the trypanosomal U2 snRNP.}, pmid = {19542313}, keywords = {Amino Acid Sequence,Animals,Molecular Sequence Data,nosource,Protein Binding,Protozoan Proteins,Protozoan Proteins: chemistry,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Ribonucleoprotein,RNA,Sequence Alignment,Small Nuclear,Small Nuclear: genetics,snRNP Core Proteins,snRNP Core Proteins: chemistry,snRNP Core Proteins: genetics,snRNP Core Proteins: metabolism,Trypanosoma brucei brucei,Trypanosoma brucei brucei: chemistry,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: metabolism,U2 Small Nuclear,U2 Small Nuclear: chemistry,U2 Small Nuclear: genetics,U2 Small Nuclear: metabolism} }

@article{hsuUniqueRibosomeStructure1990, title = {Unique Ribosome Structure of {{Leptospira}} Interrogans Is Composed of Four {{rRNA}} Components.}, author = {Hsu, D. and Pan, M. J. and Zee, Y. C. and LeFebvre, R. B.}, year = 1990, month = jun, journal = {Journal of bacteriology}, volume = {172}, number = {6}, pages = {3478–80}, issn = {0021-9193}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=209161&tool=pmcentrez&rendertype=abstract}, abstract = {All known ribosomes of procaryotic organisms are made up of three rRNA components that are 23, 16, and 5S in size. We now report that in some Leptospira interrogans strains, the classical 23S rRNA is further processed to generate 14 and 17S rRNAs. This processing step was previously known to occur only in some eucaryotes and in a small group of procaryotes. The implications of this finding are discussed.}, pmid = {2345155}, keywords = {23S,23S: analysis,Leptospira interrogans,Leptospira interrogans: genetics,nosource,Ribosomal,Ribosomal: analysis,Ribosomes,Ribosomes: analysis,RNA} }

@phdthesis{chiouRoleRibosomalStalk2011, title = {The Role of the Ribosomal Stalk in the Activity of Ricin, {{Shiga-like}} Toxin 1 and {{Shiga-like}} Toxin 2 in {{Saccharomyces}} Cerevisiae}, author = {Chiou, J.}, year = 2011, url = {http://mss3.libraries.rutgers.edu/dlr/showfed.php?pid=rutgers-lib:31029 http://mss3.libraries.rutgers.edu/dlr/outputds.php?pid=rutgers-lib:31029&ds=PDF-1}, keywords = {nosource} } % == BibTeX quality report for chiouRoleRibosomalStalk2011: % Missing required field ‘school’

@article{serganovLongShortRiboswitches2009, title = {The Long and the Short of Riboswitches.}, author = {Serganov, Alexander}, year = 2009, month = jun, journal = {Current opinion in structural biology}, volume = {19}, number = {3}, pages = {251–9}, issn = {1879-033X}, doi = {10.1016/j.sbi.2009.02.002}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2762789&tool=pmcentrez&rendertype=abstract}, abstract = {Regulatory mRNA elements or riboswitches specifically control the expression of a large number of genes in response to various cellular metabolites. The basis for selectivity of regulation is programmed in the evolutionarily conserved metabolite-sensing regions of riboswitches, which display a plethora of sequence and structural variants. Recent X-ray structures of two distinct SAM riboswitches and the sensing domains of the Mg(2+), lysine, and FMN riboswitches have uncovered novel recognition principles and provided molecular details underlying the exquisite specificity of metabolite binding by RNA. These and earlier structures constitute the majority of widespread riboswitch classes and, together with riboswitch folding studies, improve our understanding of the mechanistic principles involved in riboswitch-mediated gene expression control.}, pmid = {19303767}, keywords = {Gene Expression Regulation,Ligands,Messenger,Messenger: chemistry,Messenger: metabolism,Models,Molecular,nosource,Nucleic Acid Conformation,RNA,Substrate Specificity} }

@article{garcia-silvaPopulationTRNAderivedSmall2010, title = {A Population of {{tRNA-derived}} Small {{RNAs}} Is Actively Produced in {{Trypanosoma}} Cruzi and Recruited to Specific Cytoplasmic Granules.}, author = {{Garcia-Silva}, Maria Rosa and Frugier, Magali and Pablo, Juan and {Correa-dominguez}, Alejandro and {Ronalte-alves}, Lysangela and {Parodi-Talice}, Adriana and Rovira, Carlos and Robello, Carlos and Goldenberg, Samuel and Cayota, Alfonso and Tosar, Juan Pablo}, year = 2010, month = jun, journal = {Molecular and biochemical parasitology}, volume = {171}, number = {2}, pages = {64–73}, publisher = {Elsevier B.V.}, issn = {1872-9428}, doi = {10.1016/j.molbiopara.2010.02.003}, url = {http://dx.doi.org/10.1016/j.molbiopara.2010.02.003 http://www.ncbi.nlm.nih.gov/pubmed/20156490 http://www.sciencedirect.com/science/article/pii/S0166685110000356}, abstract = {Over the last years an expanding family of small RNAs (i.e. microRNAs, siRNAs and piRNAs) was recognized as key players in diverse forms of gene silencing and chromatin organization. Effectors functions of these small RNAs are achieved through ribonucleoprotein (RNP) complexes containing at their center an Argonaute/Piwi protein. Although these proteins and their small RNA-associated machinery can be traced back to the common ancestor of eukaryotes, this machinery seems to be entirely lost or extensively simplified in some unicellular organisms including Trypanosoma cruzi, which are unable to trigger RNAi related phenomena. Speculating about the presence of alternate small RNA-mediated pathways in these organisms, we constructed and analyzed a size-fractionated cDNA library (20-35 nt) from epimastigotes forms of T. cruzi. Our results showed the production of an abundant class of tRNA-derived small RNAs preferentially restricted to specific isoacceptors and whose production was more accentuated under nutritional stress. These small tRNAs derived preferentially from the 5’ halves of mature tRNAs and were recruited to distinctive cytoplasmic granules. Our data favor the idea that tRNA cleavage is unlikely to be the consequence of non-specific degradation but a controlled process, whose biological significance remains to be elucidated.}, pmid = {20156490}, keywords = {Cytoplasmic Granules,Cytoplasmic Granules: chemistry,Cytoplasmic Granules: metabolism,nosource,Protozoan,Protozoan: genetics,Protozoan: metabolism,RNA,Transfer,Transfer: genetics,Transfer: metabolism,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosoma cruzi: metabolism,Untranslated,Untranslated: genetics,Untranslated: metabolism} }

@article{rettigDualTargetingIsoleucyltRNA2012, title = {Dual Targeting of Isoleucyl-{{tRNA}} Synthetase in {{Trypanosoma}} Brucei Is Mediated through Alternative Trans-Splicing.}, author = {Rettig, Jochen and Wang, Yimu and Schneider, Andr{'e} and Ochsenreiter, Torsten}, year = 2012, month = feb, journal = {Nucleic acids research}, volume = {40}, number = {3}, pages = {1299–306}, issn = {1362-4962}, doi = {10.1093/nar/gkr794}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3273800&tool=pmcentrez&rendertype=abstract}, abstract = {Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNAs with their cognate amino acids. They are an essential part of each translation system and in eukaryotes are therefore found in both the cytosol and mitochondria. Thus, eukaryotes either have two distinct genes encoding the cytosolic and mitochondrial isoforms of each of these enzymes or a single gene encoding dually localized products. Trypanosomes require trans-splicing of a cap containing leader sequence onto the 5’-untranslated region of every mRNA. Recently we speculated that alternative trans-splicing could lead to the expression of proteins having amino-termini of different lengths that derive from the same gene. We now demonstrate that alternative trans-splicing, creating a long and a short spliced variant, is the mechanism for dual localization of trypanosomal isoleucyl-tRNA synthetase (IleRS). The protein product of the longer spliced variant possesses an amino-terminal presequence and is found exclusively in mitochondria. In contrast, the shorter spliced variant is translated to a cytosol-specific isoform lacking the presequence. Furthermore, we show that RNA stability is one mechanism determining the differential abundance of the two spliced isoforms.}, pmid = {21976735}, keywords = {Alternative Splicing,Amino Acid Sequence,Cells,Cultured,Cytosol,Cytosol: enzymology,Isoleucine-tRNA Ligase,Isoleucine-tRNA Ligase: analysis,Isoleucine-tRNA Ligase: genetics,Isoleucine-tRNA Ligase: metabolism,Messenger,Messenger: metabolism,Mitochondria,Mitochondria: enzymology,Mitochondrial Proteins,Mitochondrial Proteins: genetics,Mitochondrial Proteins: metabolism,Molecular Sequence Data,nosource,Protein Isoforms,Protein Isoforms: analysis,Protein Isoforms: genetics,Protein Isoforms: metabolism,Protozoan Proteins,Protozoan Proteins: analysis,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,RNA,RNA Stability,Trans-Splicing,Trypanosoma brucei brucei,Trypanosoma brucei brucei: enzymology,Trypanosoma brucei brucei: genetics} }

@article{yoffeEvolutionaryChangesLeishmania2009, title = {Evolutionary Changes in the {{Leishmania eIF4F}} Complex Involve Variations in the {{eIF4E-eIF4G}} Interactions.}, author = {Yoffe, Yael and L{'e}ger, M{'e}lissa and Zinoviev, Alexandra and Zuberek, Joanna and Darzynkiewicz, Edward and Wagner, Gerhard and Shapira, Michal}, year = 2009, month = jun, journal = {Nucleic acids research}, volume = {37}, number = {10}, pages = {3243–53}, issn = {1362-4962}, doi = {10.1093/nar/gkp190}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2691829&tool=pmcentrez&rendertype=abstract}, abstract = {Translation initiation in eukaryotes is mediated by assembly of the eIF4F complex over the m(7)GTP cap structure at the 5’-end of mRNAs. This requires an interaction between eIF4E and eIF4G, two eIF4F subunits. The Leishmania orthologs of eIF4E are structurally diverged from their higher eukaryote counterparts, since they have evolved to bind the unique trypanosomatid cap-4 structure. Here, we characterize a key eIF4G candidate from Leishmania parasites (LeishIF4G-3) that contains a conserved MIF4G domain. LeishIF4G-3 was found to coelute with the parasite eIF4F subunits from an m(7)GTP-Sepharose column and to bind directly to LeishIF4E. In higher eukaryotes the eIF4E-eIF4G interaction is based on a conserved peptide signature [Y(X(4))Lphi], where X is any amino acid and Phi is a hydrophobic residue. A parallel eIF4E-binding peptide was identified in LeishIF4G-3 (20-YPGFSLDE-27). However, the binding motif varies extensively: in addition to Y20 and L25, binding strictly requires the presence of F23, whereas the hydrophobic amino acid (Phi) is dispensable. The LeishIF4E-LeishIF4G-3 interaction was also confirmed by nuclear magnetic resonance (NMR) studies. In view of these diversities, the characterization of the parasite eIF4E-eIF4G interaction may not only serve as a novel target for inhibiting Leishmaniasis but also provide important insight for future drug discovery.}, pmid = {19321500}, keywords = {Agarose,Animals,Binding Sites,Biological Evolution,Centrifugation,Chromatography,Density Gradient,Eukaryotic Initiation Factor-4E,Eukaryotic Initiation Factor-4E: isolation & purif,Eukaryotic Initiation Factor-4E: metabolism,Eukaryotic Initiation Factor-4F,Eukaryotic Initiation Factor-4F: metabolism,Eukaryotic Initiation Factor-4G,Eukaryotic Initiation Factor-4G: chemistry,Eukaryotic Initiation Factor-4G: isolation & purif,Eukaryotic Initiation Factor-4G: metabolism,Leishmania major,Leishmania major: metabolism,nosource,Peptides,Peptides: chemistry,Peptides: metabolism,Protozoan Proteins,Protozoan Proteins: metabolism,RNA Cap Analogs,RNA Cap Analogs: metabolism} }

@article{queirozTranscriptomeAnalysisDifferentiating2009, title = {Transcriptome Analysis of Differentiating Trypanosomes Reveals the Existence of Multiple Post-Transcriptional Regulons.}, author = {Queiroz, Rafael and Benz, Corinna and Fellenberg, Kurt and Hoheisel, J{"o}rg D. and Clayton, Christine}, year = 2009, month = jan, journal = {BMC genomics}, volume = {10}, pages = {495}, issn = {1471-2164}, doi = {10.1186/1471-2164-10-495}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2772864&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanosome gene expression is regulated almost exclusively at the post-transcriptional level, with mRNA degradation playing a decisive role. When trypanosomes are transferred from the blood of a mammal to the midgut of a Tsetse fly, they transform to procyclic forms: gene expression is reprogrammed, changing the cell surface and switching the mode of energy metabolism. Within the blood, trypanosomes can pre-adapt for Tsetse transmission, becoming growth-arrested stumpy forms. We describe here the transitions in gene expression that occur during differentiation of in-vitro cultured bloodstream forms to procyclic forms.}, pmid = {19857263}, keywords = {Cluster Analysis,Developmental,Gene Expression Profiling,Gene Expression Regulation,Messenger,Messenger: metabolism,nosource,Oligonucleotide Array Sequence Analysis,Post-Transcriptional,Protozoan,Protozoan: metabolism,Regulon,RNA,RNA Processing,Trypanosoma,Trypanosoma: genetics,Trypanosoma: growth & development,Trypanosoma: metabolism} }

@article{zinovievEvolutionaryConservationDiversification2012, title = {Evolutionary Conservation and Diversification of the Translation Initiation Apparatus in Trypanosomatids.}, author = {Zinoviev, Alexandra and Shapira, Michal}, year = 2012, month = jan, journal = {Comparative and functional genomics}, volume = {2012}, pages = {813718}, issn = {1532-6268}, doi = {10.1155/2012/813718}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3399392&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanosomatids are ancient eukaryotic parasites that migrate between insect vectors and mammalian hosts, causing a range of diseases in humans and domestic animals. Trypanosomatids feature a multitude of unusual molecular features, including polycistronic transcription and subsequent processing by trans-splicing and polyadenylation. Regulation of protein coding genes is posttranscriptional and thus, translation regulation is fundamental for activating the developmental program of gene expression. The spliced-leader RNA is attached to all mRNAs. It contains an unusual hypermethylated cap-4 structure in its 5’ end. The cap-binding complex, eIF4F, has gone through evolutionary changes in accordance with the requirement to bind cap-4. The eIF4F components in trypanosomatids are highly diverged from their orthologs in higher eukaryotes, and their potential functions are discussed. The cap-binding activity in all eukaryotes is a target for regulation and plays a similar role in trypanosomatids. Recent studies revealed a novel eIF4E-interacting protein, involved in directing stage-specific and stress-induced translation pathways. Translation regulation during stress also follows unusual regulatory cues, as the increased translation of Hsp83 following heat stress is driven by a defined element in the 3’ UTR, unlike higher eukaryotes. Overall, the environmental switches experienced by trypanosomatids during their life cycle seem to affect their translational machinery in unique ways.}, pmid = {22829751}, keywords = {nosource} }

@article{quRibosomalProteinS12012, title = {Ribosomal Protein {{S1}} Unwinds Double-Stranded {{RNA}} in Multiple Steps.}, author = {Qu, Xiaohui and Lancaster, Laura and Noller, Harry F. and Bustamante, Carlos and Tinoco, Ignacio}, year = 2012, month = aug, journal = {Proceedings of the National Academy of Sciences of the United States of America}, eprint = {22908248}, eprinttype = {pubmed}, issn = {1091-6490}, doi = {10.1073/pnas.1208950109}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22908248}, abstract = {The sequence and secondary structure of the 5’-end of mRNAs regulate translation by controlling ribosome initiation on the mRNA. Ribosomal protein S1 is crucial for ribosome initiation on many natural mRNAs, particularly for those with structured 5’-ends, or with no or weak Shine-Dalgarno sequences. Besides a critical role in translation, S1 has been implicated in several other cellular processes, such as transcription recycling, and the rescuing of stalled ribosomes by tmRNA. The mechanisms of S1 functions are still elusive but have been widely considered to be linked to the affinity of S1 for single-stranded RNA and its corresponding destabilization of mRNA secondary structures. Here, using optical tweezers techniques, we demonstrate that S1 promotes RNA unwinding by binding to the single-stranded RNA formed transiently during the thermal breathing of the RNA base pairs and that S1 dissociation results in RNA rezipping. We measured the dependence of the RNA unwinding and rezipping rates on S1 concentration, and the force applied to the ends of the RNA. We found that each S1 binds 10 nucleotides of RNA in a multistep fashion implying that S1 can facilitate ribosome initiation on structured mRNA by first binding to the single strand next to an RNA duplex structure (“stand-by site”) before subsequent binding leads to RNA unwinding. Unwinding by multiple small substeps is much less rate limited by thermal breathing than unwinding in a single step. Thus, a multistep scheme greatly expedites S1 unwinding of an RNA structure compared to a single-step mode.}, pmid = {22908248}, keywords = {nosource} }

@article{palencharGeneTranscriptionTrypanosomes2006, title = {Gene Transcription in Trypanosomes.}, author = {Palenchar, Jennifer B. and Bellofatto, Vivian}, year = 2006, month = apr, journal = {Molecular and biochemical parasitology}, volume = {146}, number = {2}, eprint = {16427709}, eprinttype = {pubmed}, pages = {135–41}, issn = {0166-6851}, doi = {10.1016/j.molbiopara.2005.12.008}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16427709}, abstract = {Trypanosoma brucei and the other members of the trypanosomatid family of parasitic protozoa, contain an unusual RNA polymerase II enzyme, uncoordinated mRNA 5’ capping and transcription initiation events, and most likely contain an abridged set of transcription factors. Pre-mRNA start sites remain elusive. In addition, two important life cycle stage-specific mRNAs are transcribed by RNA polymerase I. This review interprets these unusual transcription traits in the context of parasite biology.}, pmid = {16427709}, keywords = {Animals,Genetic,Messenger,Messenger: biosynthesis,nosource,Protozoan,Protozoan: biosynthesis,RNA,RNA Polymerase I,RNA Polymerase I: metabolism,RNA Polymerase II,RNA Polymerase II: metabolism,Transcription,Transcription Initiation Site,Trypanosoma brucei brucei,Trypanosoma brucei brucei: enzymology,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: growth & development} }

@article{billaut-mulotNucleotideSequenceTrypanosoma1993, title = {Nucleotide Sequence of a {{Trypanosoma}} Cruzi {{cDNA}} Encoding a Protein Homologous to Mammalian {{EF1}} Gamma.}, author = {{Billaut-Mulot}, O. and Pommier, V. and Sch{"o}neck, R. and {Plumas-Marty}, B. and Taibi, A. and Loyens, M. and Capron, A. and {}a Ouaissi, M.}, year = 1993, month = aug, journal = {Nucleic acids research}, volume = {21}, number = {16}, pages = {3901}, issn = {0305-1048}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=309928&tool=pmcentrez&rendertype=abstract}, pmid = {8367313}, keywords = {Animals,Base Sequence,DNA,Humans,Mammals,Molecular Sequence Data,nosource,Peptide Elongation Factor 1,Peptide Elongation Factors,Peptide Elongation Factors: genetics,Protozoan,Protozoan Proteins,Protozoan Proteins: genetics,Sequence Homology,Trypanosoma cruzi,Trypanosoma cruzi: genetics} }

@article{jaramilloLeishmaniaRepressionHost2011, title = {Leishmania {{Repression}} of {{Host Translation}} through {{mTOR Cleavage Is Required}} for {{Parasite Survival}} and {{Infection}}}, author = {Jaramillo, Maritza and Gomez, Maria Adelaida and Larsson, Ola and Shio, Marina Tiemi and Topisirovic, Ivan and Luxenburg, Randi and Rosenfeld, Amy and Colina, Rodney and McMaster, Robert W. and Olivier, Martin and {Costa-mattioli}, Mauro and Contreras, Iraz{'u} and Sonenberg, Nahum}, year = 2011, month = apr, journal = {Cell host & }, volume = {9}, number = {4}, eprint = {21501832}, eprinttype = {pubmed}, pages = {331–341}, issn = {1934-6069}, doi = {10.1016/j.chom.2011.03.008}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21501832 http://www.sciencedirect.com/science/article/pii/S1931312811000953}, abstract = {The protozoan parasite Leishmania alters the activity of its host cell, the macrophage. However, little is known about the effect of Leishmania infection on host protein synthesis. Here, we show that the Leishmania protease GP63 cleaves the mammalian/mechanistic target of rapamycin (mTOR), a serine/threonine kinase that regulates the translational repressor 4E-BP1. mTOR cleavage results in the inhibition of mTOR complex 1 (mTORC1) and concomitant activation of 4E-BP1 to promote Leishmania proliferation. Consistent with these results, pharmacological activation of 4E-BPs with rapamycin, results in a dramatic increase in parasite replication. In contrast, genetic deletion of 4E-BP1/2 reduces parasite load in macrophages ex vivo and decreases susceptibility to cutaneous leishmaniasis in vivo. The parasite resistant phenotype of 4E-BP1/2 double-knockout mice involves an enhanced type I IFN response. This study demonstrates that Leishmania evolved a survival mechanism by activating 4E-BPs, which serve as major targets for host translational control.}, pmid = {21501832}, keywords = {Animals,Carrier Proteins,Carrier Proteins: genetics,Carrier Proteins: metabolism,Cell Line,Cutaneous,Cutaneous: metabolism,Cutaneous: parasitology,Host-Parasite Interactions,Leishmania major,Leishmania major: physiology,Leishmaniasis,Macrophages,Macrophages: metabolism,Macrophages: parasitology,Metalloendopeptidases,Metalloendopeptidases: metabolism,Mice,nosource,Phosphoproteins,Phosphoproteins: genetics,Phosphoproteins: metabolism,Polymerase Chain Reaction,Protein Biosynthesis,Proteins,Proteins: metabolism,Sequence Deletion,Signal Transduction,Signal Transduction: genetics,Sirolimus,Sirolimus: pharmacology,TOR Serine-Threonine Kinases,TOR Serine-Threonine Kinases: metabolism} } % == BibTeX quality report for jaramilloLeishmaniaRepressionHost2011: % ? Title looks like it was stored in title-case in Zotero

@article{thermannDrosophilaMiR2Induces2007, title = {Drosophila {{miR2}} Induces Pseudo-Polysomes and Inhibits Translation Initiation.}, author = {Thermann, Rolf and Hentze, Matthias W.}, year = 2007, month = jun, journal = {Nature}, volume = {447}, number = {7146}, eprint = {17507927}, eprinttype = {pubmed}, pages = {875–8}, issn = {1476-4687}, doi = {10.1038/nature05878}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17507927}, abstract = {MicroRNAs (miRs) inhibit protein synthesis by mechanisms that are as yet unresolved. We developed a cell-free system from Drosophila melanogaster embryos that faithfully recapitulates miR2-mediated translational control by means of the 3’ untranslated region of the D. melanogaster reaper messenger RNA. Here we show that miR2 inhibits translation initiation without affecting mRNA stability. Surprisingly, miR2 induces the formation of dense (heavier than 80S) miRNPs (‘pseudo-polysomes’) even when polyribosome formation and 60S ribosomal subunit joining are blocked. An mRNA bearing an ApppG instead of an m7GpppG cap structure escapes the miR2-mediated translational block. These results directly show the inhibition of m7GpppG cap-mediated translation initiation as the mechanism of miR2 function, and uncover pseudo-polysomal messenger ribonucleoprotein assemblies that may help to explain earlier findings.}, pmid = {17507927}, keywords = {3’ Untranslated Regions,3’ Untranslated Regions: genetics,3’ Untranslated Regions: metabolism,Animals,Base Sequence,Cell-Free System,Drosophila melanogaster,Drosophila melanogaster: embryology,Drosophila melanogaster: genetics,Drosophila Proteins,Drosophila Proteins: genetics,Genes,MicroRNAs,MicroRNAs: genetics,MicroRNAs: metabolism,nosource,Polyribosomes,Polyribosomes: genetics,Polyribosomes: metabolism,Protein Biosynthesis,Reporter,Reporter: genetics,Ribonucleoproteins,Ribonucleoproteins: biosynthesis,Ribonucleoproteins: genetics,Ribonucleoproteins: metabolism,Ribosomes,Ribosomes: chemistry,Ribosomes: genetics,Ribosomes: metabolism,RNA Caps,RNA Caps: genetics,RNA Caps: metabolism,RNA Stability} }

@article{bonaldoCellsubstrateAdhesionTrypanosoma1988, title = {Cell-Substrate Adhesion during {{Trypanosoma}} Cruzi Differentiation.}, author = {Bonaldo, M. C. and {Souto-Padron}, T. and {}de Souza, W. and Goldenberg, S.}, year = 1988, month = apr, journal = {The Journal of cell biology}, volume = {106}, number = {4}, eprint = {11191893}, eprinttype = {pubmed}, pages = {1349–58}, issn = {0021-9525}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11191893}, abstract = {The transformation of Trypanosoma cruzi epimastigotes to the mammal infective metacyclic trypomastigotes (metacyclogenesis) can be performed in vitro under chemically defined conditions. Under these conditions, differentiating epimastigotes adhere to a surface before their transformation into metacyclic trypomastigotes. Scanning and transmission electron microscopy of adhered and non-adhered parasites during the metacyclogenesis process show that only epimastigotes and few transition forms are found in the first population, whereas metacyclic trypomastigotes are exclusively found in the cell culture supernatant. PAGE analysis of the [35S]methionine metabolic labeling products of adhered and non-adhered parasites shows that although most of the polypeptides are conserved, adhered parasites express specifically four polypeptides in the range of 45-50 kD with an isoelectric point of 4.8. These proteins might be involved in the adhesion process and are recognized by an antiserum against total adhered parasite proteins. This antiserum also recognized a group of 45-50 kD in the iodine-radiolabeled surface proteins of differentiating cells, providing direct evidence that these components are indeed surface antigens. The results suggest that epimastigotes must adhere to a substrate before their transformation to metacyclic trypomastigotes, being released to the medium as the metacyclogenesis process is accomplished. This could correspond to the process naturally occurring within the triatomine invertebrate host.}, pmid = {3283152}, keywords = {Animals,Cell Adhesion,Cell Movement,Electron,Electrophoresis,Immunoassay,Membrane Proteins,Membrane Proteins: analysis,Microscopy,nosource,Peptide Biosynthesis,Polyacrylamide Gel,Scanning,Trypanosoma cruzi,Trypanosoma cruzi: growth & development,Trypanosoma cruzi: physiology,Trypanosoma cruzi: ultrastructure} }

@article{nardelliSmallsubunitRRNAProcessome2007, title = {Small-Subunit {{rRNA}} Processome Proteins Are Translationally Regulated during Differentiation of {{Trypanosoma}} Cruzi.}, author = {Nardelli, Sheila Cristina SC and {'A}vila, AR Andr{'e}a Rodrigues and Freund, Aline and Motta, Maria Cristina and Manh{~a}es, Lauro and Jesus, Cristina Leandro De and Schenkman, Sergio and Fragoso, Perdig{~a}o and Krieger, Marco Aur{'e}lio and Dallagiovanna, Bruno and Cristina, Teresa and Jesus, Leandro De and Avila, Andr{'e}a Rodrigues and {}de Jesus, Teresa Cristina Leandro and Fragoso, Stenio Perdig{~a}o and Goldenberg, Samuel}, year = 2007, month = feb, journal = {Eukaryotic cell}, volume = {6}, number = {2}, pages = {337–45}, issn = {1535-9778}, doi = {10.1128/EC.00279-06}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1797946&tool=pmcentrez&rendertype=abstract http://ec.asm.org/content/6/2/337.short}, abstract = {We used differential display to select genes differentially expressed during differentiation of epimastigotes into metacyclic trypomastigotes in the protozoan parasite Trypanosoma cruzi. One of the selected clones had a sequence similar to that of the small-subunit (SSU) processome protein Sof1p, which is involved in rRNA processing. The corresponding T. cruzi protein, TcSof1, displayed a nuclear localization and is downregulated during metacyclogenesis. Heterologous RNA interference assays showed that depletion of this protein impaired growth but did not affect progression through the cell cycle, suggesting that ribosome synthesis regulation and the cell cycle are uncoupled in this parasite. Quantitative PCR (qPCR) assays of several SSU processome-specific genes in T. cruzi also showed that most of them were regulated posttranscriptionally. This process involves the accumulation of mRNA in the polysome fraction of metacyclic trypomastigotes, where TcSof1 cannot be detected. Metacyclic trypomastigote polysomes were purified and separated by sucrose gradient sedimentation. Northern blot analysis of the sucrose gradient fractions showed the association of TcSof1 mRNA with polysomes, confirming the qPCR data. The results suggest that the mechanism of regulation involves the blocking of translation elongation and/or termination.}, pmid = {17158738}, keywords = {Animals,Blotting,Cell Differentiation,Fluorescent Antibody Technique,Gene Expression Profiling,Gene Expression Regulation,Immunoprecipitation,Messenger,Messenger: genetics,Messenger: metabolism,Mutation,Northern,nosource,Protein Biosynthesis,Protozoan,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Protozoan: genetics,Protozoan: metabolism,Reverse Transcriptase Polymerase Chain Reaction,Ribonucleoproteins,Ribosomal,Ribosomal: metabolism,RNA,RNA Precursors,RNA Precursors: metabolism,Saccharomyces cerevisiae Proteins,Small Nuclear,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosoma cruzi: growth & development} }

@article{junqueiraTrypanosomaCruziEffective2011, title = {Trypanosoma Cruzi as an Effective Cancer Antigen Delivery Vector.}, author = {Junqueira, Caroline and Santos, Luara I. and {Galv{~a}o-Filho}, Bruno and Teixeira, Santuza M. and Rodrigues, Fl{'a}via G. and DaRocha, Wanderson D. and Chiari, Egler and {}a Jungbluth, Achim and Ritter, Gerd and Gnjatic, Sacha and Old, Lloyd J. and Gazzinelli, Ricardo T.}, year = 2011, month = dec, journal = {Proceedings of the National Academy of Sciences}, volume = {108}, number = {49}, pages = {19695–700}, issn = {1091-6490}, doi = {10.1073/pnas.1110030108}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3241774&tool=pmcentrez&rendertype=abstract}, abstract = {One of the main challenges in cancer research is the development of vaccines that induce effective and long-lived protective immunity against tumors. Significant progress has been made in identifying members of the cancer testis antigen family as potential vaccine candidates. However, an ideal form for antigen delivery that induces robust and sustainable antigen-specific T-cell responses, and in particular of CD8(+) T lymphocytes, remains to be developed. Here we report the use of a recombinant nonpathogenic clone of Trypanosoma cruzi as a vaccine vector to induce vigorous and long-term T cell-mediated immunity. The rationale for using the highly attenuated T. cruzi clone was (i) the ability of the parasite to persist in host tissues and therefore to induce a long-term antigen-specific immune response; (ii) the existence of intrinsic parasite agonists for Toll-like receptors and consequent induction of highly polarized T helper cell type 1 responses; and (iii) the parasite replication in the host cell cytoplasm, leading to direct antigen presentation through the endogenous pathway and consequent induction of antigen-specific CD8(+) T cells. Importantly, we found that parasites expressing a cancer testis antigen (NY-ESO-1) were able to elicit human antigen-specific T-cell responses in vitro and solid protection against melanoma in a mouse model. Furthermore, in a therapeutic protocol, the parasites expressing NY-ESO-1 delayed the rate of tumor development in mice. We conclude that the T. cruzi vector is highly efficient in inducing T cell-mediated immunity and protection against cancer cells. More broadly, this strategy could be used to elicit a long-term T cell-mediated immunity and used for prophylaxis or therapy of chronic infectious diseases.}, pmid = {22114198}, keywords = {Animals,Antigens,Blotting,Cancer Vaccines,Cancer Vaccines: administration & dosage,Cancer Vaccines: immunology,CD4-Positive T-Lymphocytes,CD4-Positive T-Lymphocytes: immunology,CD4-Positive T-Lymphocytes: parasitology,CD8-Positive T-Lymphocytes,CD8-Positive T-Lymphocytes: immunology,CD8-Positive T-Lymphocytes: parasitology,Cell Line,Cells,Chagas Disease,Chagas Disease: immunology,Chagas Disease: parasitology,Chagas Disease: prevention & control,Cultured,Enzyme-Linked Immunosorbent Assay,Experimental,Experimental: immunology,Experimental: pathology,Experimental: prevention & control,Genetic Vectors,Genetic Vectors: administration & dosage,Genetic Vectors: immunology,Humans,Immunization,Immunization: methods,Inbred BALB C,Inbred C57BL,Knockout,Male,Membrane Proteins,Membrane Proteins: genetics,Membrane Proteins: immunology,Membrane Proteins: metabolism,Mice,Neoplasm,Neoplasm: genetics,Neoplasm: immunology,Neoplasm: metabolism,Neoplasms,nosource,Transfection,Transfection: methods,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosoma cruzi: immunology,Trypanosoma cruzi: metabolism,Tumor,Western} }

@article{hobbieGeneticReconstructionProtozoan2011, title = {Genetic Reconstruction of Protozoan {{rRNA}} Decoding Sites Provides a Rationale for Paromomycin Activity against {{Leishmania}} and {{Trypanosoma}}.}, author = {Hobbie, Sven N. and Kaiser, Marcel and Schmidt, Sebastian and Shcherbakov, Dmitri and Janusic, Tanja and Brun, Reto and B{"o}ttger, Erik C.}, year = 2011, month = may, journal = {PLoS neglected tropical diseases}, volume = {5}, number = {5}, pages = {e1161}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0001161}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3101183&tool=pmcentrez&rendertype=abstract}, abstract = {Aminoglycoside antibiotics target the ribosomal decoding A-site and are active against a broad spectrum of bacteria. These compounds bind to a highly conserved stem-loop-stem structure in helix 44 of bacterial 16S rRNA. One particular aminoglycoside, paromomycin, also shows potent antiprotozoal activity and is used for the treatment of parasitic infections, e.g. by Leishmania spp. The precise drug target is, however, unclear; in particular whether aminoglycoside antibiotics target the cytosolic and/or the mitochondrial protozoan ribosome. To establish an experimental model for the study of protozoan decoding-site function, we constructed bacterial chimeric ribosomes where the central part of bacterial 16S rRNA helix 44 has been replaced by the corresponding Leishmania and Trypanosoma rRNA sequences. Relating the results from in-vitro ribosomal assays to that of in-vivo aminoglycoside activity against Trypanosoma brucei, as assessed in cell cultures and in a mouse model of infection, we conclude that aminoglycosides affect cytosolic translation while the mitochondrial ribosome of trypanosomes is not a target for aminoglycoside antibiotics.}, pmid = {21629725}, keywords = {African,African: drug therapy,African: parasitology,Animal,Animals,Antiprotozoal Agents,Antiprotozoal Agents: pharmacology,Bacterial,Bacterial: genetics,Bacterial: metabolism,Disease Models,Female,Genetic,Leishmania,Leishmania: drug effects,Mice,nosource,Parasitic Sensitivity Tests,Paromomycin,Paromomycin: pharmacology,Protein Biosynthesis,Protein Biosynthesis: drug effects,Protozoan,Protozoan: genetics,Protozoan: metabolism,Recombination,Ribosomal,Ribosomal: genetics,Ribosomal: metabolism,RNA,Rodent Diseases,Rodent Diseases: drug therapy,Rodent Diseases: parasitology,Trypanosoma brucei brucei,Trypanosoma brucei brucei: drug effects,Trypanosomiasis} }

@article{scoryDifferentialToxicityRicin1997, title = {Differential Toxicity of Ricin and Diphtheria Toxin for Bloodstream Forms of {{Trypanosoma}} Brucei.}, author = {Scory, S. and Steverding, D.}, year = 1997, month = dec, journal = {Molecular and biochemical parasitology}, volume = {90}, number = {1}, eprint = {9497050}, eprinttype = {pubmed}, pages = {289–95}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9497050}, abstract = {The cytotoxicity of ricin and diphtheria toxin was studied in culture-adapted bloodstream forms of Trypanosoma brucei. Although ricin is endocytosed at a rate comparable to that of other internalized macromolecules, it is nontoxic to bloodstream-form trypanosomes. The resistance lies partly in low susceptibility of the targeted ribosomes: T. brucei cell-free protein biosynthesis is only partially inhibited by ricin A chain. In addition, ricin is degraded before it reaches the ribosomes, as the toxin is delivered to lysosomes. In contrast, diphtheria toxin shows similar cytotoxicities for bloodstream-form trypanosomes and mouse myeloma cells. Both trypanosome and myeloma cells are more than 1000-fold less sensitive to the action of the toxin than most other mammalian cell lines, although nicked reduced diphtheria toxin inhibits cell-free protein synthesis of T. brucei and myeloma cells to the same extent as that of a rabbit reticulocyte lysate. The effect of diphtheria toxin on T. brucei in vitro translation is NAD+ dependent, suggesting that ADP-ribosylation of elongation factor 2 could be the cause of the inhibition as it is in mammalian cells. Thus, the toxic moiety of diphtheria toxin is suitable for preparation of cell-type-specific cytotoxic reagents directed towards trypanosomes.}, pmid = {9497050}, keywords = {Animals,Cell-Free System,Cultured,Diphtheria Toxin,Diphtheria Toxin: metabolism,Diphtheria Toxin: toxicity,Endocytosis,Mice,nosource,Protease Inhibitors,Protease Inhibitors: pharmacology,Protein Biosynthesis,Protozoan Proteins,Protozoan Proteins: biosynthesis,Rabbits,Ricin,Ricin: metabolism,Ricin: toxicity,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: growth & development,Trypanosoma brucei brucei: metabolism,Tumor Cells} }

@article{martinsQuantitativeProteomicsTrypanosoma2012, title = {Quantitative {{Proteomics}} of {{Trypanosoma}} Cruzi {{During Metacyclogenesis}}.}, author = {Martins, Lyris and Godoy, Franco De and Marchini, Fabricio Klerynton and Pavoni, Daniela Parada and {}de Godoy, Lyris Martins Franco and Rampazzo, Rita de C{'a}ssia Pontello and Probst, Christian Macagnan and Goldenberg, Samuel and Krieger, Marco Aurelio}, year = 2012, month = jul, journal = {Proteomics}, eprint = {22761176}, eprinttype = {pubmed}, pages = {1–31}, issn = {1615-9861}, doi = {10.1002/pmic.201200078}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22761176}, abstract = {Trypanosoma cruzi is the etiologic agent of Chagas disease, which is estimated to affect over 8 million people around the world. T. cruzi has a complex life cycle, involving insect and mammalian hosts and four distinct developmental stages: epimastigotes, metacyclic trypomastigotes, amastigotes and bloodstream trypomastigotes. Metacyclogenesis is the process by which T. cruzi epimastigotes differentiate into metacyclic trypomastigotes and acquire infectivity, and involves differential gene expression associated with acquisition of virulence. In T. cruzi, gene expression regulation is achieved mainly post transcriptionally. Therefore, proteomics-based approaches are extremely useful for gaining a better understanding of the changes that occur in the stage-regulated gene expression program of the parasite at the molecular level. Here, we performed an in-depth quantitative MS-based proteomic study of T. cruzi metacyclogenesis and quantified almost three thousand proteins expressed during the process of differentiation. To the best of our knowledge, this work is the most comprehensive quantitative proteomics study of different cell populations of T. cruzi available so far. We identified relevant proteins and pathways involved in the parasites differentiation and infectivity acquisition, opening new perspectives for further studies which could, ultimately, lead to the identification of new targets for chemotherapy.}, pmid = {22761176}, keywords = {2012,cellular differentiation,february 24,label free quantification,mass spectrometry-based,mass spectrometry-based pro-,metacyclogenesis,nosource,proteomics,received,teomics,trypanosoma cruzi} }

@article{probstComparisonTwoDistinct2012, title = {A Comparison of Two Distinct Murine Macrophage Gene Expression Profiles in Response to {{Leishmania}} Amazonensis Infection.}, author = {Probst, Christian M. and {}a Silva, Rodrigo and Menezes, Juliana P. B. and Almeida, Tais F. and Gomes, Ivana N. and Dallabona, Andr{'e}ia C. and Ozaki, Luiz S. and {}a Buck, Gregory and Pavoni, Daniela P. and {}a Krieger, Marco and Veras, Patr{'i}cia S. T.}, year = 2012, month = jan, journal = {BMC microbiology}, volume = {12}, number = {1}, pages = {22}, publisher = {BioMed Central Ltd}, issn = {1471-2180}, doi = {10.1186/1471-2180-12-22}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3313874&tool=pmcentrez&rendertype=abstract}, abstract = {The experimental murine model of leishmaniasis has been widely used to characterize the immune response against Leishmania. CBA mice develop severe lesions, while C57BL/6 present small chronic lesions under L. amazonensis infection. Employing a transcriptomic approach combined with biological network analysis, the gene expression profiles of C57BL/6 and CBA macrophages, before and after L. amazonensis infection in vitro, were compared. These strains were selected due to their different degrees of susceptibility to this parasite.}, pmid = {22321871}, keywords = {Animals,Cells,Cultured,Female,Gene Expression Profiling,Host-Pathogen Interactions,Inbred C57BL,Inbred CBA,Leishmania mexicana,Leishmania mexicana: immunology,Leishmania mexicana: pathogenicity,Macrophages,Macrophages: immunology,Macrophages: parasitology,Male,Mice,Microarray Analysis,nosource,Real-Time Polymerase Chain Reaction} }

@article{nikolicModulationRibosomalFrameshifting2012, title = {Modulation of Ribosomal Frameshifting Frequency and Its Effect on the Replication of {{Rous}} Sarcoma Virus.}, author = {Nikolic, Emily I. C. and King, Louise M. LM and Vidakovic, Marijana and Irigoyen, Nerea and Brierley, Ian and Nikoli{"A}{}, E. I. C.}, year = 2012, month = aug, journal = {Journal of virology}, number = {August}, issn = {1098-5514}, doi = {10.1128/JVI.01846-12}, url = {http://jvi.asm.org/content/early/2012/08/09/JVI.01846-12.short http://www.ncbi.nlm.nih.gov/pubmed/22896611}, abstract = {Programmed -1 ribosomal frameshifting is widely used in the expression of RNA virus replicases and represents a potential target for antiviral intervention. There is interest in determining the extent to which frameshifting efficiency can be modulated before virus replication is compromised and we have addressed this question using the alpharetrovirus Rous sarcoma virus (RSV) as a model system. In RSV, frameshifting is essential in the production of the Gag-Pol polyprotein from the overlapping gag and pol coding sequences. The frameshift signal is composed of two elements, a heptanucleotide slippery sequence followed by a stimulatory RNA structure that has been proposed to be an RNA pseudoknot. Point mutations were introduced into the frameshift signal of an infectious RSV clone and virus replication monitored following transfection and subsequent infection of susceptible cells. The introduced mutations were designed to generate a range of frameshifting efficiencies yet with minimal impact on encoded amino acids. Our results reveal that point mutations leading to a 3-fold decrease in frameshifting efficiency noticeably reduce virus replication, and that further reduction is severely inhibitory. In contrast, a 3-fold stimulation of frameshifting is well-tolerated. These observations suggest that small molecule inhibitors of frameshifting are likely to have potential as agents for antiviral intervention. During the course of this work, we were able to confirm, for the first time in vivo, that the RSV stimulatory RNA is indeed an RNA pseudoknot but that the pseudoknot per se is not absolutely required for virus viability.}, pmid = {22896611}, keywords = {nosource} }

@article{englundStructureBiosynthesisGlycosyl1993, title = {The Structure and Biosynthesis of Glycosyl Phosphatidylinositol Protein Anchors}, author = {Englund, P. T.}, year = 1993, journal = {Annual review of biochemistry}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.bi.62.070193.001005}, keywords = {acetylcholinesterase,nosource,paroxysmal nocturnal hemoglobinuria,thy-i,trypanosome,variant surface glycoprotein} }

@article{poissonFragAnchorLargescalePredictor2007, title = {{{FragAnchor}}: A Large-Scale Predictor of Glycosylphosphatidylinositol Anchors in Eukaryote Protein Sequences by Qualitative Scoring.}, author = {Poisson, Guylaine and Chauve, Cedric and Chen, Xin and Bergeron, Anne}, year = 2007, month = may, journal = {Genomics, proteomics & bioinformatics / Beijing Genomics Institute}, volume = {5}, number = {2}, eprint = {17893077}, eprinttype = {pubmed}, pages = {121–30}, issn = {1672-0229}, doi = {10.1016/S1672-0229(07)60022-9}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17893077}, abstract = {A glycosylphosphatidylinositol (GPI) anchor is a common but complex C-terminal post-translational modification of extracellular proteins in eukaryotes. Here we investigate the problem of correctly annotating GPI-anchored proteins for the growing number of sequences in public databases. We developed a computational system, called FragAnchor, based on the tandem use of a neural network (NN) and a hidden Markov model (HMM). Firstly, NN selects potential GPI-anchored proteins in a dataset, then HMM parses these potential GPI signals and refines the prediction by qualitative scoring. FragAnchor correctly predicted 91% of all the GPI-anchored proteins annotated in the Swiss-Prot database. In a large-scale analysis of 29 eukaryote proteomes, FragAnchor predicted that the percentage of highly probable GPI-anchored proteins is between 0.21% and 2.01%. The distinctive feature of FragAnchor, compared with other systems, is that it targets only the C-terminus of a protein, making it less sensitive to the background noise found in databases and possible incomplete protein sequences. Moreover, FragAnchor can be used to predict GPI-anchored proteins in all eukaryotes. Finally, by using qualitative scoring, the predictions combine both sensitivity and information content. The predictor is publicly available at [see text].}, pmid = {17893077}, keywords = {Amino Acid Sequence,Computational Biology,Computational Biology: methods,Databases,Eukaryotic Cells,Eukaryotic Cells: chemistry,Genetic,Glycosylphosphatidylinositols,Glycosylphosphatidylinositols: chemistry,Glycosylphosphatidylinositols: isolation & purific,Glycosylphosphatidylinositols: metabolism,Humans,Hydrophobic and Hydrophilic Interactions,Markov Chains,Models,Molecular Sequence Data,Neural Networks (Computer),nosource,Post-Translational,Predictive Value of Tests,Protein,Protein Processing,Proteome,Proteome: analysis,Sensitivity and Specificity,Sequence Analysis} }

@article{veldmanPrimarySecondaryStructure1981, title = {The Primary and Secondary Structure of Yeast {{26S rRNA}}}, author = {Veldman, G. M. and Klootwijk, J.}, year = 1981, journal = {Nucleic Acids }, volume = {9}, number = {24}, pages = {6935–6952}, url = {http://nar.oxfordjournals.org/content/9/24/6935.short}, keywords = {nosource} }

@article{vonlaufenStressResponsePathways2008, title = {Stress Response Pathways in Protozoan Parasites}, author = {Vonlaufen, Nathalie and Kanzok, SM Stefan M. and Wek, Ronald C. and Sullivan, William J. and Jr, William J. Sullivan}, year = 2008, month = dec, journal = {Cellular }, volume = {10}, number = {August}, eprint = {18647172}, eprinttype = {pubmed}, pages = {2387–2399}, issn = {1462-5822}, doi = {10.1111/j.1462-5822.2008.01210.x}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18647172 http://onlinelibrary.wiley.com/doi/10.1111/j.1462-5822.2008.01210.x/full}, abstract = {Diseases caused by protozoan parasites have a dramatic impact on world health. Emerging drug resistance and a general lack of experimental understanding has created a void in the medicine cabinet used to treat these widespread infections. A novel therapeutic idea that is receiving more attention is centred on targeting the microbe’s response to the multitude of environmental stresses it encounters. Protozoan pathogens have complex life cycles, often having to transition from one host to another, or survive in a cyst form in the environment until a new host arrives. The need to respond to environmental cues and stress, and endure in less than optimal conditions, is paramount to their viability and successful progression through their life cycle. This review summarizes the research on parasitic stress responses for Apicomplexa, kinetoplastids and anaerobic protozoa, with an eye towards how these processes may be exploited therapeutically.}, pmid = {18647172}, keywords = {Adaptation,Animals,Cell Survival,Eukaryota,Eukaryota: physiology,nosource,Parasites,Parasites: physiology,Physiological} }

@article{abuinExpressionTranssialidase85kDa1999, title = {Expression of Trans-Sialidase and 85-{{kDa}} Glycoprotein Genes in {{Trypanosoma}} Cruzi Is Differentially Regulated at the Post-Transcriptional Level by Labile Protein Factors.}, author = {Abuin, G. and {Freitas-Junior}, L. H. and Colli, W. and Alves, M. J. and Schenkman, S.}, year = 1999, month = may, journal = {The Journal of biological chemistry}, volume = {274}, number = {19}, eprint = {10224055}, eprinttype = {pubmed}, pages = {13041–7}, issn = {0021-9258}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10224055}, abstract = {To adapt to different environments, Trypanosoma cruzi, the protozoan parasite that causes Chagas’ disease, expresses a different set of proteins during development. To begin to understand the mechanism that controls this differential gene expression, we have analyzed the levels of amastin and trans-sialidase mRNAs and the mRNAs encoding members of the 85-kDa glycoprotein gene family, which are differentially expressed in the T. cruzi stages found in the mammalian host. Amastin mRNA is expressed predominantly in intracellular and proliferative amastigotes. trans-Sialidase mRNAs are found mostly in forms undergoing transformation from amastigotes to trypomastigotes inside infected cells, whereas mRNAs encoding the 85-kDa glycoproteins appear only in the infective trypomastigotes released from the cells. The genes coding for these mRNA species are constitutively transcribed in all stages of T. cruzi cells, suggesting that expression is controlled post-transcriptionally during differentiation. Inhibition of transcription by actinomycin D revealed that each mRNA species has a relatively long half-life in stages where it accumulates. In the case of the trans-sialidase and 85-kDa glycoprotein genes, mRNA accumulation was induced by treatment with the protein synthesis inhibitor cycloheximide at the stages that preceded the normal accumulation. Therefore, mRNA stabilization may account for mRNA accumulation. mRNA degradation could be promoted by proteins with high turnover, or stabilization could be promoted by forming a complex with the translational machinery at defined times in development. Identification of the factors that induce mRNA degradation or stabilization is essential to the understanding of control of gene expression in these organisms.}, pmid = {10224055}, keywords = {Animals,Base Sequence,Cycloheximide,Cycloheximide: pharmacology,Dactinomycin,Dactinomycin: pharmacology,DNA Primers,Gene Expression Regulation,Genetic,Genetic: drug effects,Glycoproteins,Glycoproteins: genetics,Messenger,Messenger: genetics,Messenger: metabolism,Neuraminidase,Neuraminidase: genetics,nosource,Post-Transcriptional,Protein Synthesis Inhibitors,Protein Synthesis Inhibitors: pharmacology,Protozoan,Protozoan: genetics,Protozoan: metabolism,RNA,RNA Processing,Transcription,Trypanosoma cruzi,Trypanosoma cruzi: enzymology,Trypanosoma cruzi: genetics,Trypanosoma cruzi: metabolism} }

@article{maiInternalTranscribedSpacer1997, title = {The Internal Transcribed Spacer 2 Exhibits a Common Secondary Structure in Green Algae and Flowering Plants.}, author = {Mai, J. C. and Coleman, a W.}, year = 1997, month = mar, journal = {Journal of molecular evolution}, volume = {44}, number = {3}, eprint = {9060392}, eprinttype = {pubmed}, pages = {258–71}, issn = {0022-2844}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9060392}, abstract = {Sequences of the Internal Transcribed Spacer 2 (ITS-2) regions of the nuclear rDNA repeats from 111 organisms of the family Volvocaceae (Chlorophyta) and unicellular organisms of the Volvocales, including Chlamydomonas reinhardtii, were determined. The use of thermodynamic energy optimization to generate secondary structures and phylogenetic comparative analysis of the spacer regions revealed a common secondary structure that is conserved despite wide intra- and interfamilial primary sequence divergence. The existence of this conserved higher-order structure is supported by the presence of numerous compensating basepair changes as well as by an evolutionary history of insertions and deletions that nevertheless maintains major aspects of the overall structure. Furthermore, this general structure is preserved across broad phylogenetic lines, as it is observed in the ITS-2s of other chlorophytes, including flowering plants; previous reports of common ITS-2 secondary structures in other eukaryotes were restricted to the order level. The reported ITS-2 structure possesses important conserved structural motifs which may help to mediate cleavages in the ITS-2 that occur during rRNA transcript processing. Their recognition can guide further studies of eukaryotic rRNA processing, and their application to sequence alignments may contribute significantly to the value of ITS-2 sequences in phylogenetic analyses at several taxonomic levels, but particularly in characterizing populations and species.}, pmid = {9060392}, keywords = {Base Sequence,Chlorophyta,Chlorophyta: classification,Chlorophyta: genetics,DNA,Evolution,Molecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Phylogeny,Plants,Plants: classification,Plants: genetics,Ribosomal,Ribosomal: chemistry} }

@article{bucknerEfficientTechniqueScreening1996, title = {Efficient Technique for Screening Drugs for Activity against {{Trypanosoma}} Cruzi Using Parasites Expressing Beta-Galactosidase.}, author = {Buckner, F. S. and Verlinde, C. L.}, year = 1996, journal = {Antimicrobial agents }, volume = {40}, number = {11}, url = {http://aac.asm.org/content/40/11/2592.short}, keywords = {nosource} }

@article{kinnamonActivityAntitumorDrugs1979, title = {Activity of Antitumor Drugs against {{African}} Trypanosomes.}, author = {Kinnamon, KE E. and {}a Steck, {EA} and Rane, DS S.}, year = 1979, month = feb, journal = {Antimicrobial agents and }, volume = {15}, number = {2}, pages = {157–60}, issn = {0066-4804}, doi = {10.1128/AAC.15.2.157.Updated}, url = {http://aac.asm.org/content/15/2/157.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=352625&tool=pmcentrez&rendertype=abstract}, abstract = {Of 49 compounds known to have antitumor properties, 6 were found to have significant activity against Trypanosoma rhodesiense infections in mice. Activity against the African trypanosomes has not been reported previously for any of these six compounds. In order of decreasing activity these compounds were: (i) imidazole-4-carboxamide, 5-(3,3-dimethyl-1,1-triazene), (ii) inosine diglycolaldehyde, (iii) cis-diamminedichloro-platinum, (iv) streptozotocin, (v) coralyne sulfate, and (vi) 5-fluoro-2’-deoxyuridine. The percentage of “hits” (12.2%) from these known antitumor agents was approximately twice as great as when other means are employed for the selection of compounds for this test system.}, pmid = {426509}, keywords = {African,African: drug therapy,Animals,Antineoplastic Agents,Antineoplastic Agents: therapeutic use,Female,Inbred ICR,Male,Mice,nosource,Structure-Activity Relationship,Trypanosomiasis} }

@article{kinnamonActivityAnticancerCompounds1998, title = {Activity of Anticancer Compounds against {{Trypanosoma}} Cruzi-Infected Mice.}, author = {Kinnamon, K. E. and Poon, B. T. and Hanson, W. L. and Waits, V. B.}, year = 1998, month = jun, journal = {The American journal of tropical medicine and hygiene}, volume = {58}, number = {6}, eprint = {9660468}, eprinttype = {pubmed}, pages = {804–6}, issn = {0002-9637}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9660468}, abstract = {Chagas’ disease, which is caused by Trypanosoma cruzi, remains essentially incurable. Due principally to a lack of profit incentive, the pharmaceutical industry has had limited interest in developing new antichagasic drugs. Thus, a search for agents that exhibit activity against T. cruzi, although medicaments have been developed for the treatment of other diseases, seems justifiable. Responding to evidence that the principal biochemical differences between mammalian cells and African trypanosomes apply equally to T. cruzi, our evaluations were conducted. Previous work showed the effectiveness of anticancer agents against T. rhodesiense. In the present studies, 76 anticancer compounds were assessed for their ability to suppress the trypomastigotes of T. cruzi- infected mice. Five compounds were found to be active. The most effective was cycloheximide, which was more than six times as effective as the standard, nifurtimox.}, pmid = {9660468}, keywords = {Animal,Animals,Antineoplastic Agents,Antineoplastic Agents: therapeutic use,Berberine Alkaloids,Berberine Alkaloids: therapeutic use,Chagas Disease,Chagas Disease: drug therapy,Cycloheximide,Cycloheximide: therapeutic use,Disease Models,Female,Mice,Nifurtimox,Nifurtimox: therapeutic use,nosource,Quinolinium Compounds,Quinolinium Compounds: therapeutic use,Reserpine,Reserpine: therapeutic use,Streptozocin,Streptozocin: therapeutic use} }

@article{arrudaSequence24SAlpha1990, title = {Sequence of the {{24S}} Alpha Ribosomal {{RNA}} Gene and Characterization of a Corresponding Pseudogene from {{Trypanosoma}} Cruzi.}, author = {{}de Arruda, M. V. and Reinach, F. C. and Colli, W. and Zingales, B.}, year = 1990, month = apr, journal = {Molecular and biochemical parasitology}, volume = {40}, number = {1}, eprint = {2190086}, eprinttype = {pubmed}, pages = {35–41}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2190086}, abstract = {Two genomic clones which cover a 30-kb region containing the ribosomal RNA cistron from Trypanosoma cruzi have been isolated. The location of the 18S, 24S alpha and 24S beta RNA species within the cistron was determined. The complete sequences of the genes corresponding to the 24S alpha RNA and to a small RNA (S1), as well as two internal transcribed spacers were obtained by sequencing a cDNA and a genomic fragment. A locus containing sequences related to the 24S alpha RNA has been determined. Sequence data and structural characterization of this locus strongly suggest that this region contains a 24S alpha RNA pseudogene.}, pmid = {2190086}, keywords = {Animals,Base Sequence,Blotting,DNA,Genes,Molecular Sequence Data,Northern,nosource,Nucleic Acid,Pseudogenes,Restriction Mapping,Ribosomal,Ribosomal: genetics,RNA,Sequence Homology,Southern,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosoma cruzi: growth & development} }

@article{kuhnGlobalSpecificTranslational2001, title = {Global and Specific Translational Regulation in the Genomic Response of {{Saccharomyces}} Cerevisiae to a Rapid Transfer from a Fermentable to a Nonfermentable Carbon Source}, author = {Kuhn, Kenneth M. KM and Derisi, JL Joseph L. and Brown, Patrick O. and Risi, Joseph L. D. E.}, year = 2001, journal = {Molecular and cellular }, doi = {10.1128/MCB.21.3.916}, url = {http://mcb.asm.org/content/21/3/916.short}, keywords = {nosource} }

@article{millerInducibleResistanceOxidant2000, title = {Inducible Resistance to Oxidant Stress in the Protozoan {{Leishmania}} Chagasi.}, author = {{}a Miller, M. and McGowan, S. E. and Gantt, K. R. and Champion, M. and Novick, S. L. and {}a Andersen, K. and Bacchi, C. J. and Yarlett, N. and Britigan, B. E. and Wilson, M. E.}, year = 2000, month = oct, journal = {The Journal of biological chemistry}, volume = {275}, number = {43}, eprint = {10931831}, eprinttype = {pubmed}, pages = {33883–9}, issn = {0021-9258}, doi = {10.1074/jbc.M003671200}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10931831}, abstract = {Leishmania sp. protozoa are introduced into a mammalian skin by a sandfly vector, whereupon they encounter increased temperature and toxic oxidants generated during phagocytosis. We studied the effects of 37 degrees C “heat shock” or sublethal menadione, which generates superoxide and hydrogen peroxide, on Leishmania chagasi virulence. Both heat and menadione caused parasites to become more resistant to H(2)O(2)-mediated toxicity. Peroxide resistance was also induced as promastigotes developed in culture from logarithmic to their virulent stationary phase form. Peroxide resistance was not associated with an increase in reduced thiols (trypanothione and glutathione) or increased activity of ornithine decarboxylase, which is rate-limiting in trypanothione synthesis. Membrane lipophosphoglycan increased in size as parasites developed to stationary phase but not after environmental exposures. Instead, parasites underwent a heat shock response upon exposure to heat or sublethal menadione, detected by increased levels of HSP70. Transfection of promastigotes with L. chagasi HSP70 caused a heat-inducible increase in resistance to peroxide, implying it is involved in antioxidant defense. We conclude that leishmania have redundant mechanisms for resisting toxic oxidants. Some are induced during developmental change and others are induced in response to environmental stress.}, isbn = {3193847208}, pmid = {10931831}, keywords = {Animals,Antioxidants,Antioxidants: pharmacology,Glycosphingolipids,Glycosphingolipids: metabolism,HSP70 Heat-Shock Proteins,HSP70 Heat-Shock Proteins: biosynthesis,Hydrogen Peroxide,Hydrogen Peroxide: toxicity,Leishmania infantum,Leishmania infantum: drug effects,Leishmania infantum: metabolism,nosource,Ornithine Decarboxylase,Ornithine Decarboxylase: biosynthesis,Oxidative Stress,Sulfhydryl Compounds,Sulfhydryl Compounds: metabolism} }

@article{alcinaHeatshockResponseTrypanosoma1988, title = {The Heat-Shock Response in {{Trypanosoma}} Cruzi.}, author = {Alcina, a and Urzainqui, A. and Carrasco, L.}, year = 1988, month = feb, journal = {European journal of biochemistry / FEBS}, volume = {172}, number = {1}, eprint = {3278903}, eprinttype = {pubmed}, pages = {121–7}, issn = {0014-2956}, url = {http://www.ncbi.nlm.nih.gov/pubmed/3278903}, abstract = {When Trypanosoma cruzi epimastigotes are exposed to temperatures of 37-41 degrees C there is a drastic decline in total protein synthesis. Analysis of the proteins synthesized at 41 degrees C by one-dimensional gel electrophoresis showed three major bands of Mr 83,000, 70,000 and 60,000. A similar pattern of heat-shock proteins was found in two different strains of T. cruzi (Tulahuen and GM strains) and in exponentially growing or in stationary epimastigotes. Actinomycin D prevented the appearance of these polypeptide bands, suggesting that the heat-shock proteins in T. cruzi epimastigotes are induced at the level of transcription. Analysis of the proteins synthesized by metacyclic forms at different temperatures suggests that heat-shock proteins in these cells are already synthesized at 27 degrees C. Elevation of temperature above 37 degrees C blocks the synthesis of most proteins in metacyclic forms except for major bands of Mr 83,000, 70,000, 60,000 and 55,000. More detailed analyses by high-resolution two-dimensional gel electrophoresis of the proteins synthesized at 27 degrees C or 37 degrees C by epimastigotes indicates that the heat-shock protein pattern is more complex than that demonstrated by one dimension, and at least ten new polypeptides are identified in two-dimensional gels. A similar analysis of metacyclic forms shows that most if not all the proteins present at 39 degrees C are also present at 27 degrees C. This result led us to the suggestion that the differentiation of T. cruzi to metacyclic forms involves the induction of heat-shock proteins, which prepares the parasite to infect the mammalian host.}, pmid = {3278903}, keywords = {Animals,Dactinomycin,Dactinomycin: pharmacology,Electrophoresis,Heat-Shock Proteins,Heat-Shock Proteins: analysis,Heat-Shock Proteins: biosynthesis,Hot Temperature,nosource,Polyacrylamide Gel,Species Specificity,Trypanosoma cruzi,Trypanosoma cruzi: growth & development,Trypanosoma cruzi: metabolism} }

@article{alvesProteomicAnalysisReveals2010, title = {Proteomic Analysis Reveals the Dynamic Association of Proteins with Translated {{mRNAs}} in {{Trypanosoma}} Cruzi.}, author = {Alves, Lysangela R. and Avila, Andr{'e}a R. and Correa, Alejandro and Holetz, Fab{'i}ola B. and Mansur, Fernanda C. B. and {}a Manque, Patr{'i}cio and {}de Menezes, Juliana P. B. and {}a Buck, Gregory and {}a Krieger, Marco and Goldenberg, Samuel}, year = 2010, month = mar, journal = {Gene}, volume = {452}, number = {2}, eprint = {20060445}, eprinttype = {pubmed}, pages = {72–8}, publisher = {Elsevier B.V.}, issn = {1879-0038}, doi = {10.1016/j.gene.2009.12.009}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20060445}, abstract = {Gene regulation is mainly post-transcriptional in trypanosomatids. The stability of mRNA and access to polysomes are thought to be tightly regulated, allowing Trypanosoma cruzi to adapt to the different environmental conditions during its life cycle. Post-transcriptional regulation requires the association between mRNAs and certain proteins to form mRNP complexes. We investigated the dynamic association between proteins and mRNAs, using poly(T) beads to isolate and characterize proteins and protein complexes bound to poly-A+ mRNAs. The protein content of these fractions was analyzed by mass spectrometry (LC-MS/MS). We identified 542 protein component of the mRNP complexes associated with mRNAs. Twenty-four of the proteins obtained were present in all fractions, whereas some other proteins were exclusive to a particular fraction: epimastigote polysomal (0.37%) and post-polysomal (2.95%) fractions; stress polysomal (13.8%) and post-polysomal (40.78%) fractions. Several proteins known to be involved in mRNA metabolism were identified, and this was considered important as it made it possible to confirm the reliability of our mRNP isolation approach. This procedure allowed us to have a first insight into the composition and dynamics of mRNPs in T. cruzi.}, pmid = {20060445}, keywords = {Animals,Messenger,Messenger: genetics,Messenger: metabolism,nosource,Polyribosomes,Polyribosomes: chemistry,Protein Binding,Protein Biosynthesis,Proteome,Proteome: analysis,Proteome: genetics,Proteome: metabolism,Protozoan Proteins,Protozoan Proteins: analysis,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Ribonucleoproteins,Ribonucleoproteins: analysis,Ribonucleoproteins: genetics,Ribonucleoproteins: metabolism,RNA,Trypanosoma cruzi,Trypanosoma cruzi: chemistry,Trypanosoma cruzi: genetics,Trypanosoma cruzi: metabolism} }

@article{whiteThreeSmallRNAs1986, title = {Three Small {{RNAs}} within the 10 Kb Trypanosome {{rRNA}} Transcription Unit Are Analogous to {{Doman VII}} of Other Eukaryotic {{28S rRNAs}}}, author = {White, Theodore TC and Rudenko, Gloria and Borst, Piet}, year = 1986, journal = {Nucleic acids research}, volume = {14}, number = {23}, pages = {9471–9489}, doi = {doi: 10.1093/nar/14.23.9471}, url = {http://nar.oxfordjournals.org/content/14/23/9471.short}, keywords = {nosource} }

@article{turmelAnalysisChloroplastLarge1993, title = {Analysis of the {{Chloroplast Large Subunit Ribosomal RNA Gene}} from 17 {{Chlamydomonas Taxa}}:: {{Three Internal Transcribed Spacers}} and 12 {{Group I Intron Insertion}}}, author = {Turmel, M. and Gutell, R. R. and Mercier, J. P.}, year = 1993, journal = {Journal of molecular }, volume = {232}, pages = {446–467}, url = {http://www.sciencedirect.com/science/article/pii/s0022-2836(83)71402-6 http://www.sciencedirect.com/science/article/pii/S0022283683714026}, keywords = {nosource} } % == BibTeX quality report for turmelAnalysisChloroplastLarge1993: % ? Title looks like it was stored in title-case in Zotero

@article{edwardsRRNAOperonZea1981, title = {The {{rRNA}} Operon from {{Zea}} Mays Chloroplasts: Nucleotide Sequence of {{23S rDNA}} and Its Homology with {{E}}. Coli {{23S rDNA}}}, author = {Edwards, K. and Freiburg, Universitlt}, year = 1981, journal = {Nucleic acids research}, volume = {9}, number = {12}, pages = {2853–2869}, doi = {10.1093/nar/9.12.2853}, url = {http://nar.oxfordjournals.org/content/9/12/2853.short}, keywords = {nosource} }

@article{machadoCCR5PlaysCritical2005, title = {{{CCR5}} Plays a Critical Role in the Development of Myocarditis and Host Protection in Mice Infected with {{Trypanosoma}} Cruzi.}, author = {Machado, Fabiana S. and Koyama, Natalia S. and Carregaro, Vanessa and Ferreira, Beatriz R. and Milanezi, Cristiane M. and Teixeira, Mauro M. and {}a Rossi, Marcos and Silva, Jo{~a}o S.}, year = 2005, month = feb, journal = {The Journal of infectious diseases}, volume = {191}, number = {4}, eprint = {15655788}, eprinttype = {pubmed}, pages = {627–36}, issn = {0022-1899}, doi = {10.1086/427515}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15655788}, abstract = {The pathogenesis of myocarditis during Trypanosoma cruzi infection is poorly understood. We investigated the role played by chemokine receptor 5 (CCR5) in the influx of T cells to the cardiac tissue of T. cruzi-infected mice. mRNA and protein for the CCR5 ligands CCL3, CCL4, and CCL5 were detected in the hearts of infected mice in association with CD4+ and CD8+ T cells. There was a high level of CCR5 expression on CD8+ T cells in the hearts of infected mice. Moreover, CCR5 expression on CD8+ T cells was positively modulated by T. cruzi infection. CCR5-deficient mice infected with T. cruzi experienced a dramatically inhibited migration of T cells to the heart and were also more susceptible to infection. These results suggest that CCR5 and its ligands play a central role in the control of T cell influx in T. cruzi-infected mice. Knowledge of the mechanisms that trigger and control the migration of cells to the heart in patients with Chagas disease may help in the design of drugs that prevent myocarditis and protect against the development of severe disease.}, pmid = {15655788}, keywords = {Animal,Animals,CC,CC: analysis,CC: genetics,CCR5,CCR5: analysis,CCR5: physiology,CD4-Positive T-Lymphocytes,CD4-Positive T-Lymphocytes: immunology,CD8-Positive T-Lymphocytes,CD8-Positive T-Lymphocytes: immunology,Chagas Cardiomyopathy,Chagas Cardiomyopathy: immunology,Chagas Cardiomyopathy: parasitology,Chagas Cardiomyopathy: pathology,Chemokine CCL3,Chemokine CCL4,Chemokines,Disease Models,Inbred C57BL,Knockout,Macrophage Inflammatory Proteins,Macrophage Inflammatory Proteins: analysis,Macrophage Inflammatory Proteins: genetics,Messenger,Messenger: analysis,Mice,Myocardium,Myocardium: immunology,Myocardium: pathology,nosource,Receptors,RNA,T-Lymphocyte Subsets,T-Lymphocyte Subsets: immunology,Trypanosoma cruzi,Trypanosoma cruzi: immunology} }

@article{zingalesTrypanosomaCruziGenome1997, title = {Trypanosoma Cruzi Genome Project: Biological Characteristics and Molecular Typing of Clone {{CL Brener}}.}, author = {Zingales, B. and Pereira, M. E. and Oliveira, R. P. and {}a Almeida, K. and Umezawa, E. S. and Souto, R. P. and Vargas, N. and Cano, M. I. and {}da Silveira, J. F. and Nehme, N. S. and Morel, C. M. and Brener, Z. and Macedo, A.}, year = 1997, month = nov, journal = {Acta tropica}, volume = {68}, number = {2}, eprint = {9386791}, eprinttype = {pubmed}, pages = {159–73}, issn = {0001-706X}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9386791}, abstract = {Clone CL Brener is the reference organism used in the Trypanosoma cruzi Genome Project. CL Brener was obtained by cloning procedures from bloodstream trypomastigotes isolated from mice infected with the CL strain. The doubling time of CL Brener epimastigotes cultured at 28 degrees C in liver infusion-tryptose (LIT) medium is 58 +/- 13 h. Differentiation to metacyclic forms is induced by incubation of epimastigotes in LIT-20% Grace’s medium. Metacyclics give very low parasitemia in mice, contrary to what is observed for blood forms which promote 100% mortality of the animals with inocula of 5 x 10(3) parasites. CL Brener blood forms are highly susceptible to nifurtimox, benznidazole and ketoconazole. Allopurinol is inefficient in the treatment of mice experimental infection. The clone infects mammalian cultured cells and performs the complete intracellular cycle at 33 and 37 degrees C. The molecular typing of CL Brener has been done by isoenzymatic profiles; sequencing of a 24S alpha ribosomal RNA gene domain and by schizodeme, randomly amplified polymorphic DNA and DNA fingerprinting analyses. For each typing approach the patterns obtained do not change after prolonged parasite subcultivation in LIT medium (up to 100 generations). The stability of the molecular karyotype of the clone was also confirmed.}, pmid = {9386791}, keywords = {Animals,DNA,Genome,Inbred BALB C,Male,Mice,nosource,Protozoan,Protozoan: analysis,Trypanosoma cruzi,Trypanosoma cruzi: classification,Trypanosoma cruzi: drug effects,Trypanosoma cruzi: genetics} }

@article{preteIsolationPolysomeboundMRNA2007, title = {Isolation of Polysome-Bound {{mRNA}} from Solid Tissues Amenable for {{RT-PCR}} and Profiling Experiments}, author = {Prete, MJ Del Julieta Del and Vernal, Rolando and Dolznig, Helmut and {}del Prete, M. Julieta and M{"u}llner, Ernst W. and {}a {Garcia-Sanz}, Jose}, year = 2007, month = mar, journal = {Rna}, volume = {13}, number = {3}, pages = {414–421}, issn = {1355-8382}, doi = {10.1261/rna.79407}, url = {http://rnajournal.cshlp.org/content/13/3/414.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1800518&tool=pmcentrez&rendertype=abstract}, abstract = {Using cell lines and primary cells, it has been shown that translation control plays a key role regulating gene expression during physiological and pathological conditions. The relevance of this type of regulation in vivo (tissues, organs) remains to be elucidated, due to the lack of an efficient method for polysome-bound fractionation of solid tissue RNA samples. A simple and efficient method is described, in which tissue samples were pulverized in liquid nitrogen and lysed with NP40-lysis buffer in the presence of the RNAse inhibitors RNAsin and vanadyl-ribonucleoside complex. After cell lysis, the cytoplasmic extract was loaded into sucrose gradients, fractionated, and RNA prepared from each fraction. The obtained RNA was reverse transcribed with a low efficiency, a problem that was overcome by purifying polyA+ RNA. Aiming to use small quantities of solid tissue samples (10-20 mg/sample), polyA+ RNA purification was discarded, and the different components were individually screened for a negative effect on reverse transcription. The polysaccharide heparin, which is present as a nonspecific RNAse inhibitor, inhibits reverse transcriptase activity, and must be removed from RNA samples for an efficient reaction. Heparin was successfully removed by precipitation of the RNA with lithium chloride, as demonstrated by the reversal of the inhibition on RT-PCR reactions. In summary, we present a reliable method allowing us to prepare high-quality polysome-bound mRNA from small quantities of liquid-nitrogen-frozen solid tissue samples from both human and mouse origin, amenable for Northern blotting, RT-PCR reactions, and expression profiling analyses.}, pmid = {17237355}, keywords = {Analytic Sample Preparation Methods,Animals,Blotting,Cell Fractionation,expression profiling,Heparin,Heparin: chemistry,Humans,Lithium Chloride,Lithium Chloride: chemistry,Messenger,Messenger: analysis,Messenger: chemistry,Messenger: isolation & purification,Mice,Northern,nosource,Polyribosomes,Polyribosomes: chemistry,polysome fractionation,Reverse Transcriptase Inhibitors,Reverse Transcriptase Inhibitors: chemistry,Reverse Transcriptase Polymerase Chain Reaction,RNA,RNA-Directed DNA Polymerase,RNA-Directed DNA Polymerase: chemistry,rt-pcr,sucrose gradients,tissue samples} }

@article{oleinickInitiationElongationProtein1977, title = {Initiation and Elongation of Protein Synthesis in Growing Cells: Differential Inhibition by Cycloheximide and Emetine}, author = {Oleinick, N. L.}, year = 1977, journal = {Archives of Biochemistry and Biophysics}, url = {http://www.sciencedirect.com/science/article/pii/000398617790296X}, keywords = {nosource} }

@article{gayAutoregulatoryControlBetatubulin1989, title = {Autoregulatory Control of Beta-Tubulin {{mRNA}} Stability Is Linked to Translation Elongation.}, author = {{}a Gay, D. and Sisodia, S. S. and Cleveland, D. W.}, year = 1989, month = aug, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {86}, number = {15}, pages = {5763–7}, issn = {0027-8424}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=297710&tool=pmcentrez&rendertype=abstract}, abstract = {Tubulin synthesis in animal cells is controlled in part by an autoregulatory mechanism that modulates the stability of ribosome-bound tubulin mRNAs. For beta tubulin, the initial recognition event for this selective RNA instability has previously been shown to be a cotranslational binding (presumably by tubulin itself) to the nascent amino-terminal beta-tubulin tetrapeptide just after it emerges from the ribosome. Although this “autoregulation” of tubulin expression is thus obligatorily linked to the translation process, the mechanism of how a cotranslational protein-protein binding event ultimately triggers RNA degradation is unknown. Using protein synthesis inhibitors to slow and ultimately to block translation elongation, we now show that the mRNA destabilization pathway requires ongoing ribosome translocation.}, pmid = {2762294}, keywords = {Animals,Anisomycin,Anisomycin: pharmacology,Colchicine,Colchicine: pharmacology,Cycloheximide,Cycloheximide: pharmacology,Emetine,Emetine: pharmacology,Genes,Homeostasis,Kinetics,L Cells (Cell Line),L Cells (Cell Line): metabolism,Messenger,Messenger: genetics,Mice,nosource,Peptide Chain Elongation,Polyribosomes,Polyribosomes: drug effects,Polyribosomes: metabolism,Regulator,RNA,Translational,Translational: drug effe,Tubulin,Tubulin: biosynthesis,Tubulin: genetics} }

@article{luccaVitroTransferReactivity1982, title = {In Vitro Transfer of Reactivity to {{Trypanosoma}} Cruzi Antigens from Rat Cells to Human Cells with Immune {{RNA}}.}, author = {Lucca, F. L. De and Bertolini, M. C. and Zini, M. N.}, year = 1982, month = feb, journal = {The Journal of infectious diseases}, volume = {145}, number = {2}, eprint = {6172524}, eprinttype = {pubmed}, pages = {148–51}, issn = {0022-1899}, url = {http://www.ncbi.nlm.nih.gov/pubmed/6172524}, abstract = {The immunologic activity of polysomal RNA isolated from the spleens of rats infected with Trypanosoma cruzi was assessed by the leukocyte migration-inhibition assay as an in vitro correlate of delayed hypersensitivity. This RNA preparation transferred reactivity to T. cruzi antigens to nonsensitized human lymphocytes from peripheral blood. This transfer of reactivity was abolished by treatment of the RNA preparation with ribonuclease. The transfer of delayed hypersensitivity in vitro from rat cells to human cells was antigen-specific. Polysomal RNA also conferred significant protection against infection with T. cruzi in mice, as evaluated by the level of parasitemia and the survival rate of mice challenged with virulent strain of Y of T. cruzi.}, pmid = {6172524}, keywords = {Animals,Antigens,Antigens: immunology,Chagas Disease,Chagas Disease: immunology,Delayed,Delayed: immunology,Humans,Hypersensitivity,Immunity,Immunologic Techniques,Lymphocytes,Lymphocytes: immunology,Maternally-Acquired,Maternally-Acquired: drug effects,Mice,nosource,Rats,Ribonucleases,Ribonucleases: pharmacology,RNA,RNA: immunology} }

@article{tanowitzStudiesRibosomalRNA1975, title = {Studies of Ribosomal {{RNA}} of {{Trypanosoma}} Cruzi.}, author = {Tanowitz, H. and Wittner, M. and Sveda, M. and Soeiro, R.}, year = 1975, month = dec, journal = {The Journal of parasitology}, volume = {61}, number = {6}, eprint = {1104797}, eprinttype = {pubmed}, pages = {1065–9}, issn = {0022-3395}, url = {http://www.ncbi.nlm.nih.gov/pubmed/1104797}, pmid = {1104797}, keywords = {Animals,HeLa Cells,HeLa Cells: analysis,Humans,Molecular Weight,nosource,Nucleic Acid Precursors,Nucleic Acid Precursors: isolation & purification,Ribosomal,Ribosomal: analysis,Ribosomal: biosynthesis,RNA,Tritium,Trypanosoma cruzi,Trypanosoma cruzi: analysis,Trypanosoma cruzi: ultrastructure,Uridine,Uridine: metabolism} }

@article{hernandezSmallsizeRibosomalRNA1983, title = {Small-Size Ribosomal {{RNA}} Species in {{Trypanosoma}} Cruzi}, author = {Hern{'a}ndez, R. and Nava, Gabriel and Casta{~n}eda, M.}, year = 1983, journal = {Molecular and Biochemical }, volume = {8}, pages = {297–304}, url = {http://www.sciencedirect.com/science/article/pii/0166685183900762}, keywords = {8 s and 5,nosource,pseudo 5,rrna,s rna,small-size rrna species,trypanosoma cruzi} }

@article{stolfTwoTypesRibosomal2003, title = {Two Types of Ribosomal {{RNA}} Genes in Hybrid {{Trypanosoma}} Cruzi Strains.}, author = {Stolf, Beatriz S. and Souto, Ricardo P. and Pedroso, Aur{'e}lio and Zingales, Bianca}, year = 2003, month = jan, journal = {Molecular and biochemical parasitology}, volume = {126}, number = {1}, eprint = {12554086}, eprinttype = {pubmed}, pages = {73–80}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12554086}, abstract = {Trypanosoma cruzi isolates can be divided into two major phylogenetic lineages-T. cruzi I and T. cruzi II. The population structure is predominantly clonal, with sexuality having no or limited influence on the evolution of the parasite. Isoenzymes and nuclear gene sequences have provided evidence that some T. cruzi strains are hybrids. Previous work of our group has shown that the putative hybrid strains designated as group 1/2 contain two types of rDNA units, corresponding to those found in T. cruzi I and T. cruzi II. In this study, the presence and transcription of the two types of ribosomal RNA (rRNA) cistrons were investigated in epimastigotes, metacyclic and tissue culture trypomastigotes of group 1/2 isolates. PCR and RT-PCR assays indicate that both types of cistrons are present in group 1/2 strains, but only type-2 genes are transcribed in all developmental stages. The structure of the promoter regions of group 1/2 was compared to reference T. cruzi I and T. cruzi II strains. In all cases, the transcription start point was mapped to a conserved A residue located approximately 1800 bp upstream the 18S rRNA gene. The distribution of rDNA clusters in chromosomal bands of group 1/2 was evaluated by pulsed-field gel electrophoresis (PFGE). The majority of type-2 rDNA genes are localized in a 1.5 Mbp band, whereas type-1 cistrons are mostly concentrated in a 1.1 Mbp band. The structural and functional studies of group 1/2 ribosomal cistrons described here may shed light on the evolutionary processes that took place during the generation of such hybrid organisms.}, pmid = {12554086}, keywords = {Animals,Base Sequence,Chromosome Mapping,Cloning,Genes,Genetic,Genetic Variation,Genetic: genetics,Hybridization,Molecular,Molecular Sequence Data,nosource,Promoter Regions,Protozoan,Ribosomal,Ribosomal: analysis,Ribosomal: classification,Ribosomal: genetics,Ribosomal: metabolism,RNA,rRNA,Sequence Alignment,Species Specificity,Transcription,Trypanosoma cruzi,Trypanosoma cruzi: classification,Trypanosoma cruzi: genetics} }

@article{linSpacerlengthDependenceProgrammed2012, title = {Spacer-Length Dependence of Programmed -1 or -2 Ribosomal Frameshifting on a {{U6A}} Heptamer Supports a Role for Messenger {{RNA}} ({{mRNA}}) Tension in Frameshifting.}, author = {Lin, Zhaoru and Gilbert, Robert J. C. and Brierley, Ian}, year = 2012, month = jun, journal = {Nucleic acids research}, eprint = {22743270}, eprinttype = {pubmed}, pages = {1–16}, issn = {1362-4962}, doi = {10.1093/nar/gks629}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22743270}, abstract = {Programmed -1 ribosomal frameshifting is employed in the expression of a number of viral and cellular genes. In this process, the ribosome slips backwards by a single nucleotide and continues translation of an overlapping reading frame, generating a fusion protein. Frameshifting signals comprise a heptanucleotide slippery sequence, where the ribosome changes frame, and a stimulatory RNA structure, a stem-loop or RNA pseudoknot. Antisense oligonucleotides annealed appropriately 3’ of a slippery sequence have also shown activity in frameshifting, at least in vitro. Here we examined frameshifting at the U(6)A slippery sequence of the HIV gag/pol signal and found high levels of both -1 and -2 frameshifting with stem-loop, pseudoknot or antisense oligonucleotide stimulators. By examining -1 and -2 frameshifting outcomes on mRNAs with varying slippery sequence-stimulatory RNA spacing distances, we found that -2 frameshifting was optimal at a spacer length 1-2 nucleotides shorter than that optimal for -1 frameshifting with all stimulatory RNAs tested. We propose that the shorter spacer increases the tension on the mRNA such that when the tRNA detaches, it more readily enters the -2 frame on the U(6)A heptamer. We propose that mRNA tension is central to frameshifting, whether promoted by stem-loop, pseudoknot or antisense oligonucleotide stimulator.}, pmid = {22743270}, keywords = {nosource} }

@article{dorsoFunctionallyDifferentAU2001, title = {Functionally Different {{AU-}} and {{G-rich}} Cis-Elements Confer Developmentally Regulated {{mRNA}} Stability in {{Trypanosoma}} Cruzi by Interaction with Specific {{RNA-binding}} Proteins.}, author = {D’Orso, I. and Frasch, a C.}, year = 2001, month = may, journal = {The Journal of biological chemistry}, volume = {276}, number = {19}, eprint = {11278796}, eprinttype = {pubmed}, pages = {15783–93}, issn = {0021-9258}, doi = {10.1074/jbc.M010959200}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11278796}, abstract = {Post-transcriptional regulatory mechanisms have been suggested to be the main point of control of gene expression in kinetoplastid parasites. We have previously shown that Trypanosoma cruzi SMUG mucin mRNA steady-state level is developmentally regulated by post-transcriptional mechanisms, being stable in the epimastigote insect vector stage, but unstable in the trypomastigote infective stage of the parasite. Its turnover is controlled by an AU-rich element (ARE) localized in the 3’-untranslated region, since a reporter gene lacking this sequence was stable in the trypomastigote stage (Di Noia, J. M., D’Orso, I., Sanchez, D. O., and Frasch, A. C. (2000) J. Biol. Chem. 275, 10218-10227). Here, we show by gel mobility shift assay that the 44-nt ARE sequence interacts with a set of stage-specific AU-rich element RNA-binding proteins (ARE-BPs). The epimastigote stage AU-rich element RNA-binding protein, named E-ARE-BP, and the trypomastigote stage ARE-BPs, named T-ARE-BPs, are efficiently competed by poly(U). UV cross-linking analysis showed that E-ARE-BP has an apparent molecular mass of 100 kDa and is different from the 45-50-kDa ARE-BPs present in other stages of the parasite. Transfection experiments allowed the identification of a novel cis-element that might be responsible for a positive effect on mRNA stability. It is a G-rich element, named GRE, composed by two contiguous CGGGG pentamers. The factors that recognize GRE were different from the ones that bind to ARE, in both molecular masses and subcellular localization. Thus, ARE and GRE are functionally different cis-elements, which might regulate mucin expression throughout the parasite life cycle.}, isbn = {5411458072}, pmid = {11278796}, keywords = {Adenine,Animals,Base Composition,Base Sequence,Binding Sites,Chloramphenicol O-Acetyltransferase,Chloramphenicol O-Acetyltransferase: genetics,Chloramphenicol O-Acetyltransferase: metabolism,Developmental,Gene Expression Regulation,Guanine,Messenger,Messenger: genetics,Molecular Sequence Data,nosource,Protozoan,Protozoan: genetics,RNA,RNA-Binding Proteins,RNA-Binding Proteins: metabolism,Transfection,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosoma cruzi: growth & development,Uracil} }

@article{castroTrypanosomaCruziRibosomal1981, title = {Trypanosoma Cruzi Ribosomal {{RNA}}: Internal Break in the Large-Molecular-Mass Species and Number of Genes.}, author = {Castro, C. and Hern{'a}ndez, R. and Casta{~n}eda, M.}, year = 1981, month = feb, journal = {Molecular and biochemical parasitology}, volume = {2}, number = {3-4}, eprint = {7012618}, eprinttype = {pubmed}, pages = {219–33}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7012618}, abstract = {The large-molecular-mass ribosomal ribonucleic acid from Trypanosoma cruzi probably contains an internal break. The molecule can be obtained in its intact form or in its two fragments depending on the denaturing agents used for its purification and/or display. This break appears to be an in vivo late processing step rather than a random nucleolytic cleavage during in vitro manipulations. Calculations of mass, from gel electrophoretograms, for the large and small main ribosomal ribonucleic acid species and for the two chains derived from the large species gave values of 1.37, 0.84, 0.70 and 0.57 X 10(6) daltons, respectively. Sedimentation velocity measurements in sucrose gradients and in the analytical ultracentrifuge indicated sedimentation coefficients of 24 and 18 S for the large and small main species, respectively. Saturation hybridization curves showed that the nuclear genome, quantified by chemical analysis, contains about 114 ribosomal ribonucleic acid gene copies.}, pmid = {7012618}, keywords = {Animals,Centrifugation,Density Gradient,Genes,Molecular Weight,nosource,Nucleic Acid Denaturation,Nucleic Acid Hybridization,Ribosomal,Ribosomal: genetics,RNA,Trypanosoma cruzi,Trypanosoma cruzi: analysis,Trypanosoma cruzi: genetics} }

@article{hernandezMolecularCloningPartial1988, title = {Molecular Cloning and Partial Characterization of Ribosomal {{RNA}} Genes from {{Trypanosoma}} Cruzi.}, author = {Hern{'a}ndez, R. and L{'e}on, F. D{'i}az-de and Casta{~n}eda, M.}, year = 1988, month = jan, journal = {Molecular and biochemical parasitology}, volume = {27}, number = {2-3}, eprint = {3278230}, eprinttype = {pubmed}, pages = {275–9}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/3278230}, abstract = {To further analyze the organization of the nuclear rDNA locus in Trypanosoma cruzi, genomic recombinant plasmid clones were constructed and isolated after hybridization with rRNA molecules as hybridization probes. Approximately 11 kilobase pairs from the cistron were cloned in three recombinant plasmids carrying adjacent genomic fragments. Restriction mapping and Southern hybridization experiments performed on these clones indicate the following relative arrangement of the mature rRNA coding sequences: 18S (2.46 kb), S3 (197 b), 24S alpha (2.02 kb), S1 (261 b), 24 beta (1.66 kb), S2 (217 b) and S6 (90 b). Neither S4 (141 b) nor S5 (110 b) sequences were found within these genomic clones. Nevertheless genomic Southerns suggest a linkage of S4 towards the 3’ end of this genetic system.}, pmid = {3278230}, keywords = {Animals,DNA,Genes,nosource,Recombinant,Ribosomal,Ribosomal: genetics,RNA,Trypanosoma cruzi,Trypanosoma cruzi: genetics} }

@article{lowInhibitionEukaryoticTranslation2005, title = {Inhibition of Eukaryotic Translation Initiation by the Marine Natural Product Pateamine {{A}}.}, author = {Low, Woon-Kai and Dang, Yongjun and {Schneider-Poetsch}, Tilman and Shi, Zonggao and Choi, Nam Song and Merrick, William C. and Romo, Daniel and Liu, Jun O.}, year = 2005, month = dec, journal = {Molecular cell}, volume = {20}, number = {5}, eprint = {16337595}, eprinttype = {pubmed}, pages = {709–22}, issn = {1097-2765}, doi = {10.1016/j.molcel.2005.10.008}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16337595}, abstract = {Translation initiation in eukaryotes is accomplished through the coordinated and orderly action of a large number of proteins, including the eIF4 initiation factors. Herein, we report that pateamine A (PatA), a potent antiproliferative and proapoptotic marine natural product, inhibits cap-dependent eukaryotic translation initiation. PatA bound to and enhanced the intrinsic enzymatic activities of eIF4A, yet it inhibited eIF4A-eIF4G association and promoted the formation of a stable ternary complex between eIF4A and eIF4B. These changes in eIF4A affinity for its partner proteins upon binding to PatA caused the stalling of initiation complexes on mRNA in vitro and induced stress granule formation in vivo. These results suggest that PatA will be a valuable molecular probe for future studies of eukaryotic translation initiation and may serve as a lead compound for the development of anticancer agents.}, pmid = {16337595}, keywords = {Epoxy Compounds,Epoxy Compounds: chemistry,Epoxy Compounds: pharmacology,Eukaryotic Cells,Eukaryotic Cells: drug effects,Eukaryotic Cells: metabolism,Eukaryotic Initiation Factor-4A,Eukaryotic Initiation Factor-4A: drug effects,Eukaryotic Initiation Factor-4A: metabolism,Eukaryotic Initiation Factor-4G,Eukaryotic Initiation Factor-4G: drug effects,Eukaryotic Initiation Factor-4G: metabolism,Eukaryotic Initiation Factors,Eukaryotic Initiation Factors: antagonists & inhib,Eukaryotic Initiation Factors: drug effects,Eukaryotic Initiation Factors: metabolism,HeLa Cells,Humans,Macrolides,Molecular Structure,nosource,Protein Biosynthesis,Protein Biosynthesis: drug effects,Protein Biosynthesis: physiology,Thiazoles,Thiazoles: chemistry,Thiazoles: pharmacology} }

@article{meissnerGenomescaleDNAMethylation2008, title = {Genome-Scale {{DNA}} Methylation Maps of Pluripotent and Differentiated Cells.}, author = {Meissner, Alexander and Mikkelsen, Tarjei S. and Gu, Hongcang and Wernig, Marius and Hanna, Jacob and Sivachenko, Andrey and Zhang, Xiaolan and Bernstein, Bradley E. and Nusbaum, Chad and Jaffe, David B. and Gnirke, Andreas and Jaenisch, Rudolf and Lander, Eric S.}, year = 2008, month = aug, journal = {Nature}, volume = {454}, number = {7205}, pages = {766–70}, issn = {1476-4687}, doi = {10.1038/nature07107}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2896277&tool=pmcentrez&rendertype=abstract}, abstract = {DNA methylation is essential for normal development and has been implicated in many pathologies including cancer. Our knowledge about the genome-wide distribution of DNA methylation, how it changes during cellular differentiation and how it relates to histone methylation and other chromatin modifications in mammals remains limited. Here we report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput reduced representation bisulphite sequencing and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of embryonic-stem-cell-derived and primary cells reveals that ‘weak’ CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumours. More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.}, pmid = {18600261}, keywords = {Animals,Cell Differentiation,Cells,Conserved Sequence,CpG Islands,CpG Islands: genetics,Cultured,DNA Methylation,Embryonic Stem Cells,Embryonic Stem Cells: cytology,Embryonic Stem Cells: metabolism,Fibroblasts,Fibroblasts: cytology,Genome,Genome: genetics,Genomics,Histones,Histones: genetics,Histones: metabolism,Male,Mice,Neurons,Neurons: cytology,nosource,Pluripotent Stem Cells,Pluripotent Stem Cells: cytology,Pluripotent Stem Cells: metabolism} }

@article{sandmeyerIntegrationSpecificityRetrotransposons1990, title = {Integration Specificity of Retrotransposons and Retroviruses}, author = {Sandmeyer, SB Suzanne B. and Hansen, Lori J. and Chalker, Douglas L.}, year = 1990, journal = {Annual review of }, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.ge.24.120190.002423}, keywords = {nosource,polymerase iii,retroelements,transposable elements,ty elements} }

@article{patnaikAutonomouslyReplicatingSinglecopy1993, title = {Autonomously Replicating Single-Copy Episomes in {{Trypanosoma}} Brucei Show Unusual Stability.}, author = {Patnaik, P. K. and Kulkarni, S. K. and Cross, G. A.}, year = 1993, journal = {The EMBO journal}, volume = {12}, number = {6}, pages = {2529–2538}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC413491/}, keywords = {ars element,dna replication,kinetoplastid,nosource} }

@article{alsfordIdentificationCircularExtrachromosomal2003, title = {The Identification of Circular Extrachromosomal {{DNA}} in the Nuclear Genome of {{Trypanosoma}} Brucei.}, author = {Alsford, N. S. and Navarro, M. and Jamnadass, H. R. and Dunbar, H. and Ackroyd, M. and Murphy, N. B. and Gull, K. and Ersfeld, K.}, year = 2003, month = jan, journal = {Molecular microbiology}, volume = {47}, number = {2}, eprint = {12519183}, eprinttype = {pubmed}, pages = {277–89}, issn = {0950-382X}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12519183}, abstract = {Nuclear extrachromosomal DNA elements have been identified in several kinetoplastids such as Leishmania and Trypanosoma cruzi, but never in Trypanosoma brucei. They can occur naturally or arise spontaneously as the result of sublethal drug exposure of parasites. In most cases, they are represented as circular elements and are mitotically unstable. In this study we describe the presence of circular DNA in the nucleus of Trypanosoma brucei. This novel type of DNA was termed NR-element (NlaIII repeat element). In contrast to drug-induced episomes in other kinetoplastids, the T. brucei extrachromosomal NR-element is not generated by drug selection. Furthermore, the element is stable during mitosis over many generations. Restriction analysis of tagged NR-element DNA, unusual migration patterns during pulsed field gel electrophoresis (PFGE) and CsCl/ethidium bromide equilibrium centrifugation demonstrates that the NR-element represents circular DNA. Whereas it has been found in all field isolates of the parasites we analysed, it is not detectable in some laboratory strains notably the genome reference strain 927. The DNA sequence of this element is related to a 29 bp repeat present in the subtelomeric region of VSG-bearing chromosomes of T. brucei. It has been suggested that this subtelomeric region is part of a transition zone on chromosomes separating the relatively stable telomeric repeats from the recombinationaly active region downstream of VSG genes. Therefore, we discuss a functional connection between the occurrence of this circular DNA and subtelomeric recombination events in T. brucei.}, pmid = {12519183}, keywords = {Animals,Base Sequence,Bovine,Bovine: parasitology,Cattle,Cell Nucleus,Cell Nucleus: genetics,Circular,Circular: chemistry,Circular: genetics,Deoxyribonucleases,DNA,Electrophoresis,Gel,Genome,Molecular Sequence Data,nosource,Protozoan,Protozoan: chemistry,Protozoan: genetics,Pulsed-Field,Sequence Analysis,Telomere,Telomere: genetics,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosomiasis,Type II Site-Specific,Type II Site-Specific: metabol} }

@article{respuelaHistoneAcetylationMethylation2008, title = {Histone Acetylation and Methylation at Sites Initiating Divergent Polycistronic Transcription in {{Trypanosoma}} Cruzi.}, author = {Respuela, Patricia and Ferella, Marcela and {Rada-Iglesias}, Alvaro and Aslund, Lena}, year = 2008, month = jun, journal = {The Journal of biological chemistry}, volume = {283}, number = {23}, pages = {15884–92}, issn = {0021-9258}, doi = {10.1074/jbc.M802081200}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3259629&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanosomes are ancient eukaryotic parasites in which the protein-coding genes, organized in large polycistronic clusters on both strands, are transcribed from as yet unidentified promoters. In an effort to reveal transcriptional initiation sites, we examined the Trypanosoma cruzi genome for histone modification patterns shown to be linked to active genes in various organisms. Here, we show that acetylated and methylated histones were found to be enriched at strand switch regions of divergent gene arrays, not at convergent clusters or intra- and intergenic regions within clusters. The modified region showed a bimodular profile with two peaks centered over the 5’-regions of the gene pair flanking the strand switch region. This pattern, which demarcates polycistronic transcription units originating from bidirectional initiation sites, is likely to be common in kinetoplastid parasites as well as in other organisms with polycistronic transcription. In contrast, no acetylation was found at promoters of the highly expressed rRNA and spliced leader genes or satellite DNA or at tested retrotransposonal elements. These results reveal, for the first time, the presence of specific epigenetic marks in T. cruzi with potential implications for transcriptional regulation; they indicate that both histone modifications and bidirectional transcription are evolutionarily conserved.}, pmid = {18400752}, keywords = {Acetylation,Animals,DNA,Evolution,Genetic,Genetic: physiology,Genome,Histones,Histones: metabolism,Methylation,Molecular,nosource,Post-Translational,Post-Translational: physiology,Promoter Regions,Protein Processing,Protozoan,Protozoan Proteins,Protozoan Proteins: metabolism,Protozoan: biosynthesis,Protozoan: physiology,Ribosomal,Ribosomal: biosynthesis,RNA,Satellite,Satellite: metabolism,Transcription,Trypanosoma cruzi,Trypanosoma cruzi: physiology} }

@article{gaoStructure80SRibosome2005, title = {The Structure of the {{80S}} Ribosome from {{Trypanosoma}} Cruzi Reveals Unique {{rRNA}} Components.}, author = {Gao, Haixiao and Ayub, Maximiliano Juri and Levin, Mariano J. and Frank, Joachim}, year = 2005, month = jul, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {29}, pages = {10206–11}, issn = {0027-8424}, doi = {10.1073/pnas.0500926102}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1174928&tool=pmcentrez&rendertype=abstract}, abstract = {We present analysis, by cryo-electron microscopy and single-particle reconstruction, of the structure of the 80S ribosome from Trypanosoma cruzi, the kinetoplastid protozoan pathogen that causes Chagas disease. The density map of the T. cruzi 80S ribosome shows the phylogenetically conserved eukaryotic rRNA core structure, together with distinctive structural features in both the small and large subunits. Remarkably, a previously undescribed helical structure appears in the small subunit in the vicinity of the mRNA exit channel. We propose that this rRNA structure likely participates in the recruitment of ribosome onto the 5’ end of mRNA, in facilitating and modulating the initiation of translation that is unique to the trypanosomes.}, pmid = {16014419}, keywords = {Animals,Base Pairing,Computer-Assisted,Cryoelectron Microscopy,Image Processing,Models,Molecular,nosource,Ribosomal,Ribosomal: genetics,Ribosomes,Ribosomes: chemistry,RNA,Trypanosoma cruzi,Trypanosoma cruzi: genetics} }

@article{salmonAdenylateCyclasesTrypanosoma2012, title = {Adenylate {{Cyclases}} of {{Trypanosoma}} Brucei {{Inhibit}} the {{Innate Immune Response}} of the {{Host}}}, author = {Salmon, Didier and Vanwalleghem, Gilles}, year = 2012, journal = {Science }, volume = {337}, number = {July}, pages = {463–466}, url = {http://stke.sciencemag.org/cgi/content/abstract/sci;337/6093/463}, keywords = {nosource} }

@article{tsaiHeterogeneousPathwaysTiming2012, title = {Heterogeneous Pathways and Timing of Factor Departure during Translation Initiation}, author = {Tsai, Albert and Petrov, Alexey and Marshall, RA Andrew and Korlach, Jonas and Uemura, Sotaro and Puglisi, Joseph D.}, year = 2012, month = jun, journal = {Nature}, volume = {487}, number = {7407}, eprint = {22722848}, eprinttype = {pubmed}, pages = {390–393}, publisher = {Nature Publishing Group}, issn = {0028-0836}, doi = {10.1038/nature11172}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22722848 http://dx.doi.org/10.1038/nature11172 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11172.html?WT.ec_id=NATURE-20120621}, abstract = {The initiation of translation establishes the reading frame for protein synthesis and is a key point of regulation. Initiation involves factor-driven assembly at a start codon of a messenger RNA of an elongation-competent 70S ribosomal particle (in bacteria) from separated 30S and 50S subunits and initiator transfer RNA. Here we establish in Escherichia coli, using direct single-molecule tracking, the timing of initiator tRNA, initiation factor 2 (IF2; encoded by infB) and 50S subunit joining during initiation. Our results show multiple pathways to initiation, with orders of arrival of tRNA and IF2 dependent on factor concentration and composition. IF2 accelerates 50S subunit joining and stabilizes the assembled 70S complex. Transition to elongation is gated by the departure of IF2 after GTP hydrolysis, allowing efficient arrival of elongator tRNAs to the second codon presented in the aminoacyl-tRNA binding site (A site). These experiments highlight the power of single-molecule approaches to delineate mechanisms in complex multicomponent systems.}, pmid = {22722848}, keywords = {nosource} }

@article{dorsoRNAbindingProteinsMRNA2003, title = {{{RNA-binding}} Proteins and {{mRNA}} Turnover in Trypanosomes.}, author = {D’Orso, Iv{'a}n and Gaudenzi, Javier G. De and Frasch, Alberto C. C.}, year = 2003, month = apr, journal = {Trends in parasitology}, volume = {19}, number = {4}, eprint = {12689640}, eprinttype = {pubmed}, pages = {151–5}, issn = {1471-4922}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12689640}, abstract = {Trypanosomes, protozoan parasites of the order Kinetoplastida, control gene expression essentially through post-transcriptional mechanisms. Several motifs located mainly in the 3’ untranslated region, such as AU-rich elements (AREs), were recently shown to modulate mRNA half-life, and are able to modify mRNA abundance in vivo through the interaction with specific RNA-binding proteins. Along with the detection of an active exosome, decapping activities and a regulated 3’ to 5’ exonuclease activity stimulated by AREs, these results suggest that modulation of mRNA stability is essential in trypanosomes. These regulatory processes are specific for different developmental stages and thus relevant for allowing trypanosomes to adapt to variable environmental conditions.}, pmid = {12689640}, keywords = {Animals,Gene Expression Regulation,Genetic,Genetic: genetics,Messenger,Messenger: genetics,Messenger: metabolism,Models,nosource,Protozoan,Protozoan: metabolism,RNA,RNA Stability,RNA-Binding Proteins,RNA-Binding Proteins: classification,RNA-Binding Proteins: physiology,Transcription,Trypanosoma,Trypanosoma: classification,Trypanosoma: genetics,Trypanosoma: metabolism} }

@article{fernandesEvolutionNuclearRibosomal1993, title = {Evolution of Nuclear Ribosomal {{RNAs}} in Kinetoplastid Protozoa: Perspectives on the Age and Origins of Parasitism.}, author = {Fernandes, a P. and Nelson, K. and Beverley, S. M.}, year = 1993, month = dec, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {90}, number = {24}, pages = {11608–12}, issn = {0027-8424}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=48033&tool=pmcentrez&rendertype=abstract}, abstract = {Molecular evolutionary relationships within the protozoan order Kinetoplastida were deduced from comparisons of the nuclear small and large subunit ribosomal RNA (rRNA) gene sequences. These studies show that relationships among the trypanosomatid protozoans differ from those previously proposed from studies of organismal characteristics or mitochondrial rRNAs. The genera Leishmania, Endotrypanum, Leptomonas, and Crithidia form a closely related group, which shows progressively more distant relationships to Phytomonas and Blastocrithidia, Trypanosoma cruzi, and lastly Trypanosoma brucei. The rooting of the trypanosomatid tree was accomplished by using Bodo caudatus (family Bodonidae) as an outgroup, a status confirmed by molecular comparisons with other eukaryotes. The nuclear rRNA tree agrees well with data obtained from comparisons of other nuclear genes. Differences with the proposed mitochondrial rRNA tree probably reflect the lack of a suitable outgroup for this tree, as the topologies are otherwise similar. Small subunit rRNA divergences within the trypanosomatids are large, approaching those among plants and animals, which underscores the evolutionary antiquity of the group. Analysis of the distribution of different parasitic life-styles of these species in conjunction with a probable timing of evolutionary divergences suggests that vertebrate parasitism arose multiple times in the trypanosomatids.}, pmid = {8265597}, keywords = {Animals,Base Sequence,Biological Evolution,Cell Nucleus,Cell Nucleus: metabolism,DNA,DNA Primers,Eukaryota,Eukaryota: genetics,Eukaryota: metabolism,Host-Parasite Interactions,Molecular Sequence Data,nosource,Phylogeny,Polymerase Chain Reaction,Protozoan,Protozoan: genetics,Protozoan: metabolism,Ribosomal,Ribosomal: genetics,RNA,Species Specificity} }

@article{iiiTrypanosomaCruziProteome2005, title = {The {{Trypanosoma}} Cruzi Proteome}, author = {III, JA Atwood and Weatherly, D. B. and Minning, T. A. and Atwood, J. A.}, year = 2005, month = jul, journal = {Science}, volume = {309}, number = {5733}, pages = {473–6}, issn = {1095-9203}, doi = {10.1126/science.1110289}, url = {http://www.sciencemag.org/content/309/5733/473.short http://www.ncbi.nlm.nih.gov/pubmed/16020736}, abstract = {To complement the sequencing of the three kinetoplastid genomes reported in this issue, we have undertaken a whole-organism, proteomic analysis of the four life-cycle stages of Trypanosoma cruzi. Peptides mapping to 2784 proteins in 1168 protein groups from the annotated T. cruzi genome were identified across the four life-cycle stages. Protein products were identified from {\(>\)}1000 genes annotated as “hypothetical” in the sequenced genome, including members of a newly defined gene family annotated as mucin-associated surface proteins. The four parasite stages appear to use distinct energy sources, including histidine for stages present in the insect vectors and fatty acids by intracellular amastigotes.}, pmid = {16020736}, keywords = {Adaptation,Animals,Antigens,Chromatography,Computational Biology,Databases,Energy Metabolism,Enzymes,Enzymes: genetics,Enzymes: metabolism,Genes,Genetic,Genome,Glycoproteins,Glycoproteins: analysis,Glycoproteins: genetics,Histidine,Histidine: metabolism,Life Cycle Stages,Liquid,Mass Spectrometry,Membrane Proteins,Membrane Proteins: analysis,Membrane Proteins: genetics,Mucins,Mucins: analysis,Multigene Family,Neuraminidase,Neuraminidase: analysis,Neuraminidase: genetics,nosource,Peptides,Peptides: analysis,Physiological,Protein Transport,Proteome,Protozoan,Protozoan Proteins,Protozoan Proteins: analysis,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Protozoan: analysis,Trypanosoma cruzi,Trypanosoma cruzi: chemistry,Trypanosoma cruzi: genetics,Trypanosoma cruzi: growth & development,Trypanosoma cruzi: metabolism} }

@article{loEvidenceSupportingMajor2003, title = {Evidence Supporting a Major Promoter in the {{Trypanosoma}} Cruzi {{rRNA}} Gene}, author = {Lo, Imelda and {Figueroa-Angulo}, Elisa and Mart, Santiago and Herna, Roberto and {Mart{"A}{}{`I}nez-Calvillo}, Santiago and {L{~A}{\(^3\)}pez-Villase{~A}{}or}, Imelda and Hern{~A}{}ndez, Roberto}, year = 2003, month = aug, journal = {FEMS Microbiology Letters}, volume = {225}, number = {2}, pages = {221–225}, issn = {03781097}, doi = {10.1016/S0378-1097(03)00516-0}, url = {http://doi.wiley.com/10.1016/S0378-1097(03)00516-0}, keywords = {nosource,rna polymerase i,rrna gene promoter,transcription,trypanosoma cruzi} }

@article{glassEssentialGenesMinimal2006, title = {Essential Genes of a Minimal Bacterium.}, author = {Glass, John I. and {Assad-Garcia}, Nacyra and Alperovich, Nina and Yooseph, Shibu and Lewis, Matthew R. and Maruf, Mahir and {}a Hutchison, Clyde and Smith, Hamilton O. and Venter, J. Craig}, year = 2006, month = jan, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {2}, pages = {425–30}, issn = {0027-8424}, doi = {10.1073/pnas.0510013103}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1324956&tool=pmcentrez&rendertype=abstract}, abstract = {Mycoplasma genitalium has the smallest genome of any organism that can be grown in pure culture. It has a minimal metabolism and little genomic redundancy. Consequently, its genome is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. Using global transposon mutagenesis, we isolated and characterized gene disruption mutants for 100 different nonessential protein-coding genes. None of the 43 RNA-coding genes were disrupted. Herein, we identify 382 of the 482 M. genitalium protein-coding genes as essential, plus five sets of disrupted genes that encode proteins with potentially redundant essential functions, such as phosphate transport. Genes encoding proteins of unknown function constitute 28% of the essential protein-coding genes set. Disruption of some genes accelerated M. genitalium growth.}, pmid = {16407165}, keywords = {Bacterial,Bacterial: genetics,Essential,Essential: genetics,Genes,Genome,Molecular Sequence Data,Mutation,Mutation: genetics,Mycoplasma genitalium,Mycoplasma genitalium: genetics,nosource} }

@article{guerra-slompoMolecularCharacterizationTrypanosoma2012, title = {Molecular Characterization of the {{Trypanosoma}} Cruzi Specific {{RNA}} Binding Protein {{TcRBP40}} and Its Associated {{mRNAs}}.}, author = {{Guerra-slompo}, EP Eloise P. and Probst, CM Christian M. and Pavoni, Daniela P. and Goldenberg, Samuel and {}a Krieger, Marco and Dallagiovanna, Bruno}, year = 2012, month = apr, journal = {Biochemical and biophysical research communications}, volume = {420}, number = {2}, pages = {302–7}, publisher = {Elsevier Inc.}, issn = {1090-2104}, doi = {10.1016/j.bbrc.2012.02.154}, url = {http://dx.doi.org/10.1016/j.bbrc.2012.02.154 http://www.ncbi.nlm.nih.gov/pubmed/22425988 http://www.sciencedirect.com/science/article/pii/S0006291X12004287}, abstract = {Trypanosoma cruzi is the causative agent of Chagas disease, a neglected disorder that affects millions of people in the Americas. T. cruzi relies mostly upon post-transcriptional regulation to control stage specific gene expression. RNA binding proteins (RBPs) associate with functionally related mRNAs forming ribonucleoprotein complexes that define post-transcriptional operons. The RNA Recognition Motif (RRM) is the most common and ancient family of RBPs. This family of RBPs has been identified in trypanosomatid parasites and only a few of them have been functionally characterized. We describe here the functional characterization of TcRBP40, a T. cruzi specific RBP, and its associated mRNAs. We used a modified version of the recombinant RIP-Chip assay to identify the mRNAs with which it associates and in vivo TAP-tag assays to confirm these results. TcRBP40 binds to an AG-rich sequence in the 3’UTR of the associated mRNAs, which were found to encode mainly putative transmembrane proteins. TcRBP40 is differentially expressed in metacyclogenesis. Surprisingly, in epimastigotes, it is dispersed in the cytoplasm but is concentrated in the reservosomes, a T. cruzi specific organelle, which suggests a putative new function for this parasite organelle.}, pmid = {22425988}, keywords = {Base Sequence,Messenger,Messenger: metabolism,nosource,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Recombinant Proteins,Recombinant Proteins: genetics,Recombinant Proteins: metabolism,RNA,RNA-Binding Proteins,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism,Trypanosoma cruzi,Trypanosoma cruzi: metabolism} }

@article{perez-diazTrypanosomaCruziMolecular2007, title = {Trypanosoma Cruzi: {{Molecular}} Characterization of an {{RNA}} Binding Protein Differentially Expressed in the Parasite Life Cycle}, author = {{P{'e}rez-D{'i}az}, Leticia and Duhagon, Mar{'i}a Ana and Smircich, Pablo and {Sotelo-Silveira}, Jos{'e} and Robello, Carlos and Krieger, Marco Aurelio and Goldenberg, Samuel and Williams, Noreen and Dallagiovanna, Bruno and Garat, Beatriz and Pe, Leticia}, year = 2007, month = sep, journal = {Experimental }, volume = {117}, number = {1}, pages = {99–105}, issn = {0014-4894}, doi = {10.1016/j.exppara.2007.03.010}, url = {http://www.sciencedirect.com/science/article/pii/S0014489407000847 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2020836&tool=pmcentrez&rendertype=abstract}, abstract = {Molecular studies have shown several peculiarities in the regulatory mechanisms of gene expression in trypanosomatids. Protein coding genes are organized in long polycistronic units that seem to be constitutively transcribed. Therefore, post-transcriptional regulation of gene expression is considered to be the main point for control of transcript abundance and functionality. Here we describe the characterization of a 17 kDa RNA-binding protein from Trypanosoma cruzi (TcRBP19) containing an RNA recognition motive (RRM). This protein is coded by a single copy gene located in a high molecular weight chromosome of T. cruzi. Orthologous genes are present in the TriTryp genomes. TcRBP19 shows target selectivity since among the different homoribopolymers it preferentially binds polyC. TcRBP19 is a low expression protein only barely detected at the amastigote stage localizing in a diffuse pattern in the cytoplasm.}, pmid = {17475252}, keywords = {a protozoan parasite of,Amino Acid Sequence,Animals,Blotting,central america and mexico,chagas,Consensus Sequence,disease affecting several million,Electroporation,Gene Expression Regulation,Gene Expression Regulation: genetics,is the causative agent,kinetoplastida,Life Cycle Stages,Life Cycle Stages: genetics,Life Cycle Stages: physiology,Molecular Sequence Data,Molecular Weight,nosource,of,people along south and,Poly C,Poly C: metabolism,Post-Transcriptional,Post-Transcriptional: genetics,Protozoan Proteins,Protozoan Proteins: chemistry,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Rabbits,rna binding proteins,RNA Processing,RNA-Binding Proteins,RNA-Binding Proteins: chemistry,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism,rrm protein,Southern,tcrbp19,the order kinetoplastida,trypanosoma cruzi,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosoma cruzi: growth & development,Trypanosoma cruzi: metabolism,Western} }

@article{claytonPosttranscriptionalRegulationGene2007, title = {Post-Transcriptional Regulation of Gene Expression in Trypanosomes and Leishmanias.}, author = {Clayton, Christine and Shapira, Michal}, year = 2007, month = dec, journal = {Molecular and biochemical parasitology}, volume = {156}, number = {2}, eprint = {17765983}, eprinttype = {pubmed}, pages = {93–101}, issn = {0166-6851}, doi = {10.1016/j.molbiopara.2007.07.007}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17765983}, abstract = {Gene expression in Kinetoplastids is very unusual in that the open reading frames are arranged in long polycistronic arrays, monocistronic mRNAs being created by post-transcriptional processing. Thus the regulation of gene expression is post-transcriptional. We here discuss recent results concerning the enzymes required for mRNA degradation, and components of the translation initiation machinery, and how both are regulated.}, pmid = {17765983}, keywords = {Animals,Gene Expression Regulation,Leishmania,Leishmania: genetics,Messenger,Messenger: metabolism,nosource,Post-Transcriptional,Protein Biosynthesis,Protozoan,Protozoan: metabolism,RNA,RNA Processing,Trypanosoma,Trypanosoma: genetics} }

@article{holetzEvidencePbodylikeStructures2007, title = {Evidence of {{P-body-like}} Structures in {{Trypanosoma}} Cruzi.}, author = {Holetz, Fab{'i}ola Barbieri FB and Correa, Alejandro and {'A}vila, A. R. and Avila, Andrea Rodrigues and Nakamura, Celso Vataru and Krieger, Marco Aur{'e}lio and Goldenberg, Samuel}, year = 2007, month = may, journal = {Biochemical and biophysical research communications}, volume = {356}, number = {4}, eprint = {17399688}, eprinttype = {pubmed}, pages = {1062–7}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2007.03.104}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17399688 http://www.sciencedirect.com/science/article/pii/S0006291X0700589X}, abstract = {Gene expression in trypanosomatids is mainly regulated post-transcriptionally. One of the mechanisms involves the differential stability of mRNAs. However, the existence of other mechanisms involving the accessibility of mRNAs to the translation machinery cannot be ruled out. Defined cytoplasmic foci containing non-translating mRNPs, known as P-bodies, have been discovered in recent years. P-bodies are sites where mRNA can be decapped and 5’-3’ degraded or stored for subsequent return to polysomes. The highly conserved DEAD box helicase Dhh1p is a marker protein of P-body functions. Here, we report the identification and cloning of a Trypanosoma cruzi Dhh1 homolog gene. TcDhh1 expression is not regulated through the parasite life cycle or under stress conditions. We show that TcDhh1 is present in polysome-independent complexes and is localized to discrete cytoplasmic foci, resembling P-bodies; these foci vary in number according to nutritional stress conditions and cycloheximide/puromycin treatment.}, isbn = {1047053506959}, pmid = {17399688}, keywords = {Animals,causative agent of chagas,Cells,Cultured,Cytoplasmic Structures,Cytoplasmic Structures: metabolism,DEAD-box RNA Helicases,DEAD-box RNA Helicases: metabolism,Developmental,Developmental: physiol,disease,gene expression is pri-,Gene Expression Regulation,in trypanosomatids,including trypanosoma cruzi the,marily regulated post-transcriptionally,mature mrnas,Messenger,nosource,p-bodies,polysomes,RNA,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: metabolism,Stored,Stored: metabolism,tcdhh1,trypanosoma cruzi,Trypanosoma cruzi,Trypanosoma cruzi: growth & development,Trypanosoma cruzi: metabolism} }

@article{porcileRefinedMolecularKaryotype2003, title = {A Refined Molecular Karyotype for the Reference Strain of the {{Trypanosoma}} Cruzi Genome Project (Clone {{CL Brener}}) by Assignment of Chromosome Markers}, author = {Porcile, Patricio E. and Santos, M{'a}rcia R. M. and Souza, Renata T. and Verbisck, Newton V. and Brand{~a}o, Adeilton and Urmenyi, Turan and Silva, Rosane and Rondinelli, Edson and Lorenzi, Herman and Levin, Mariano J. and Degrave, Wim and {}da Silveira, Jos{'e} Franco}, year = 2003, month = apr, journal = {Gene}, volume = {308}, pages = {53–65}, issn = {03781119}, doi = {10.1016/S0378-1119(03)00489-X}, url = {http://linkinghub.elsevier.com/retrieve/pii/S037811190300489X}, isbn = {5511557110}, keywords = {chromosome specific marker,expressed sequence tag,linkage group,nosource,repetitive sequence,yeast artificial chromosome contig} }

@article{soutoSensitiveDetectionStrain1993, title = {Sensitive Detection and Strain Classification of {{Trypanosoma}} Cruzi by Amplification of a Ribosomal {{RNA}} Sequence.}, author = {Souto, R. P. and Zingales, B.}, year = 1993, month = nov, journal = {Molecular and biochemical parasitology}, volume = {62}, number = {1}, eprint = {8114825}, eprinttype = {pubmed}, pages = {45–52}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8114825}, abstract = {A sequence of about 100 bp of the 24S alpha ribosomal RNA was investigated for sensitive detection of Trypanosoma cruzi. It was shown that the target sequence is specific for this parasite and no cross-reactivity was observed with different species of pathogenic Leishmania, two strains of Trypanosoma rangeli or human RNA. Amplification of the sequence was obtained by reverse transcription coupled to polymerase chain reaction. Following this procedure the equivalent to 0.1% of the nucleic acid content of a single parasite cell could be detected either by ethidium staining or blot hybridization. The distribution of the target sequence in sixteen strains of T. cruzi was investigated. Positive amplification was obtained for all samples employing the same oligonucleotides as primers. However, amplified fragments of 125 bp were obtained in eight strains, while fragments of 110 bp were detected in the remaining eight isolates. No amplification of both classes of fragments has been detected in any of the strains examined. Dimorphism in the target region was confirmed by hybridization to specific internal probes and sequencing, allowing the division of T. cruzi strains in two groups. It is proposed that sensitive parasite detection could be achieved by rRNA amplification followed by hybridization to two probes derived from the target sequences of both groups of T. cruzi strains. Furthermore, the sequence dimorphism found in this sequence opens the perspective of strain typing simultaneous with parasite detection.}, pmid = {8114825}, keywords = {Animals,Base Sequence,Chagas Disease,Chagas Disease: diagnosis,DNA,DNA Primers,DNA Primers: genetics,Gene Amplification,Genes,Humans,Molecular Sequence Data,nosource,Polymerase Chain Reaction,Polymerase Chain Reaction: statistics & numerical,Protozoan,Protozoan: genetics,Ribosomal,Ribosomal: genetics,RNA,Sensitivity and Specificity,Species Specificity,Trypanosoma cruzi,Trypanosoma cruzi: classification,Trypanosoma cruzi: genetics} }

@article{franzenShortNoncodingTranscriptome2011, title = {The Short Non-Coding Transcriptome of the Protozoan Parasite {{Trypanosoma}} Cruzi.}, author = {Franz{'e}n, Oscar and Arner, Erik and Ferella, Marcela and Nilsson, Daniel and Respuela, Patricia and Carninci, Piero and Hayashizaki, Yoshihide and Aslund, Lena and Andersson, Bj{"o}rn and Daub, Carsten O.}, year = 2011, month = aug, journal = {PLoS neglected tropical diseases}, volume = {5}, number = {8}, pages = {e1283}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0001283}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3166047&tool=pmcentrez&rendertype=abstract}, abstract = {The pathway for RNA interference is widespread in metazoans and participates in numerous cellular tasks, from gene silencing to chromatin remodeling and protection against retrotransposition. The unicellular eukaryote Trypanosoma cruzi is missing the canonical RNAi pathway and is unable to induce RNAi-related processes. To further understand alternative RNA pathways operating in this organism, we have performed deep sequencing and genome-wide analyses of a size-fractioned cDNA library (16-61 nt) from the epimastigote life stage. Deep sequencing generated 582,243 short sequences of which 91% could be aligned with the genome sequence. About 95-98% of the aligned data (depending on the haplotype) corresponded to small RNAs derived from tRNAs, rRNAs, snRNAs and snoRNAs. The largest class consisted of tRNA-derived small RNAs which primarily originated from the 3’ end of tRNAs, followed by small RNAs derived from rRNA. The remaining sequences revealed the presence of 92 novel transcribed loci, of which 79 did not show homology to known RNA classes.}, pmid = {21912713}, keywords = {DNA,Gene Library,High-Throughput Nucleotide Sequencing,nosource,RNA,Sequence Analysis,Transcriptome,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Untranslated,Untranslated: genetics} }

@article{berrimanGenomeBloodFluke2009, title = {The Genome of the Blood Fluke {{Schistosoma}} Mansoni}, author = {Berriman, Matthew and Haas, B. J. and LoVerde, P. T.}, year = 2009, journal = {Nature}, volume = {460}, number = {July}, doi = {10.1038/nature08160}, url = {http://www.nature.com/nature/journal/v460/n7253/abs/nature08160.html}, keywords = {nosource} }

@article{cerqueiraSequenceDiversityEvolution2008, title = {Sequence Diversity and Evolution of Multigene Families in {{Trypanosoma}} Cruzi}, author = {Cerqueira, G. C. and Bartholomeu, D. C.}, year = 2008, journal = {Molecular and }, volume = {157}, pages = {65–72}, doi = {10.1016/j.molbiopara.2007.10.002}, url = {http://www.sciencedirect.com/science/article/pii/S0166685107002769}, keywords = {amastin,gene conversion,genetic diversity,multigene families,nosource,trypanosoma cruzi} }

@article{bringaudRoleTransposableElements2008, title = {Role of Transposable Elements in Trypanosomatids.}, author = {Bringaud, Fr{'e}d{'e}ric and Ghedin, Elodie and {}a {El-Sayed}, Najib M. and Papadopoulou, Barbara}, year = 2008, month = may, journal = {Microbes and infection / Institut Pasteur}, volume = {10}, number = {6}, eprint = {18467144}, eprinttype = {pubmed}, pages = {575–81}, issn = {1286-4579}, doi = {10.1016/j.micinf.2008.02.009}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18467144}, abstract = {Transposable elements constitute 2-5% of the genome content in trypanosomatid parasites. Some of them are involved in critical cellular functions, such as the regulation of gene expression in Leishmania spp. In this review, we highlight the remarkable role extinct transposable elements can play as the source of potential new functions.}, pmid = {18467144}, keywords = {Animals,DNA,DNA Transposable Elements,DNA Transposable Elements: physiology,Evolution,Gene Expression Regulation,Gene Expression Regulation: physiology,Genome,Host-Parasite Interactions,Host-Parasite Interactions: physiology,Intergenic,Intergenic: genetics,Leishmania,Leishmania: genetics,Leishmania: physiology,Molecular,nosource,Protozoan,Protozoan: genetics,Trypanosoma} }

@article{stelterExpressionPlanttypeFerredoxin2007, title = {The Expression of a Plant-Type Ferredoxin Redox System Provides Molecular Evidence for a Plastid in the Early Dinoflagellate {{Perkinsus}} Marinus.}, author = {Stelter, Kathrin and {El-Sayed}, Najib M. and Seeber, Frank}, year = 2007, month = jan, journal = {Protist}, volume = {158}, number = {1}, eprint = {17123864}, eprinttype = {pubmed}, pages = {119–30}, issn = {1434-4610}, doi = {10.1016/j.protis.2006.09.003}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17123864}, abstract = {Perkinsus marinus is a parasitic protozoan with a phylogenetic positioning between Apicomplexa and dinoflagellates. It is thus of interest for reconstructing the early evolution of eukaryotes, especially with regard to the acquisition of secondary plastids in these organisms. It is also an important pathogen of oysters, and the definition of parasite-specific metabolic pathways would be beneficial for the identification of efficient treatments for infected mollusks. Although these different scientific interests have resulted in the start of a genome project for this organism, it is still unknown whether P. marinus contains a plastid or plastid-like organelle like the related dinoflagellates and Apicomplexa. Here, we show that in vitro-cultivated parasites contain transcripts of the plant-type ferredoxin and its associated reductase. Both proteins are nuclear-encoded and possess N-terminal targeting sequences similar to those characterized in dinoflagellates. Since this redox pair is exclusively found in cyanobacteria and plastid-harboring organisms its presence also in P. marinus is highly indicative of a plastid. We also provide additional evidence for such an organelle by demonstrating pharmacological sensitivity to inhibitors of plastid-localized enzymes involved in fatty acid biosynthesis (e.g. acetyl-CoA carboxylase) and by detection of genes for three enzymes of plastid-localized isoprenoid biosynthesis (1-deoxy-D-xylulose 5-phosphate reductoisomerase, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase, and (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate synthase).}, pmid = {17123864}, keywords = {Amino Acid Sequence,Animals,Base Sequence,Dinoflagellida,Dinoflagellida: enzymology,Dinoflagellida: genetics,Dinoflagellida: growth & development,Dinoflagellida: ultrastructure,Fatty Acids,Fatty Acids: biosynthesis,Ferredoxins,Ferredoxins: chemistry,Ferredoxins: genetics,Ferredoxins: metabolism,Molecular Sequence Data,nosource,Oxidation-Reduction,Phylogeny,Plant Proteins,Plant Proteins: chemistry,Plant Proteins: genetics,Plant Proteins: metabolism,Plastids,Plastids: metabolism,Plastids: ultrastructure,Terpenes,Terpenes: metabolism} }

@article{djikengCofactorindependentPhosphoglycerateMutase2007, title = {Cofactor-Independent Phosphoglycerate Mutase Is an Essential Gene in Procyclic Form {{Trypanosoma}} Brucei.}, author = {Djikeng, Appolinaire and Raverdy, Sylvine and Foster, Jeremy and Bartholomeu, Daniella and Zhang, Yinhua and {El-Sayed}, Najib M. and Carlow, Clotilde}, year = 2007, month = mar, journal = {Parasitology research}, volume = {100}, number = {4}, eprint = {17024352}, eprinttype = {pubmed}, pages = {887–92}, issn = {0932-0113}, doi = {10.1007/s00436-006-0332-7}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17024352}, abstract = {Glycolysis and gluconeogenesis are, in part, driven by the interconversion of 3- and 2-phosphoglycerate (3-PG and 2-PG) which is performed by phosphoglycerate mutases (PGAMs) which can be cofactor dependant (dPGAM) or cofactor independent (iPGAM). The African trypanosome, Trypanosoma brucei, possesses the iPGAM form which is thought to play an important role in glycolysis. Here, we report on the use of RNA interference to down-regulate the T. brucei iPGAM in procyclic form T. brucei and evaluation of the resulting phenotype. We first demonstrated biochemically that depletion of the steady state levels of iPGM mRNA correlates with a marked reduction of enzyme activity. We further show that iPGAM is required for cell growth in procyclic T. brucei.}, isbn = {0043600603}, pmid = {17024352}, keywords = {Animals,Coenzymes,Essential,Essential: genetics,Genes,nosource,Phosphoglycerate Mutase,Phosphoglycerate Mutase: genetics,Time Factors,Trypanosoma brucei brucei,Trypanosoma brucei brucei: enzymology,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: growth & development} }

@article{souzaNewTrypanosomaCruzi2007, title = {New {{Trypanosoma}} Cruzi Repeated Element That Shows Site Specificity for Insertion}, author = {Souza, Renata T. RT and Santos, MRM M{'a}rcia R. M. and Lima, F{'a}bio M. FM and {El-Sayed}, Najib M. and Myler, Peter J. and Ruiz, Jeronimo C. and {}da Silveira, Jos{'e} Franco and Santos, R. M.}, year = 2007, month = jul, journal = {Eukaryotic }, volume = {6}, number = {7}, pages = {1228–38}, issn = {1535-9778}, doi = {10.1128/EC.00036-07}, url = {http://ec.asm.org/content/6/7/1228.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1951114&tool=pmcentrez&rendertype=abstract}, abstract = {A new family of site-specific repeated elements identified in Trypanosoma cruzi, which we named TcTREZO, is described here. TcTREZO appears to be a composite repeated element, since three subregions may be defined within it on the basis of sequence similarities with other T. cruzi sequences. Analysis of the distribution of TcTREZO in the genome clearly indicates that it displays site specificity for insertion. Most TcTREZO elements are flanked by conserved sequences. There is a highly conserved 68-bp sequence at the 5’ end of the element and a sequence domain of approximately 500 bp without a well-defined borderline at the 3’ end. Northern blot hybridization and reverse transcriptase PCR analyses showed that TcTREZO transcripts are expressed as oligo(A)-terminated transcripts whose length corresponds to the unit size of the element (1.6 kb). Transcripts of approximately 0.2 kb derived from a small part of TcTREZO are also detected in steady-state RNA. TcTREZO transcripts are unspliced and not translated. The copy number of TcTREZO sequences was estimated to be approximately 173 copies per haploid genome. TcTREZO appears to have been assembled by insertions of sequences into a progenitor element. Once associated with each other, these subunits were amplified as a new transposable element. TcTREZO shows site specificity for insertion, suggesting that a sequence-specific endonuclease could be responsible for its insertion at a unique site.}, isbn = {5511557110}, pmid = {17526721}, keywords = {Animals,Base Sequence,DNA Transposable Elements,Molecular Sequence Data,nosource,Nucleic Acid,Repetitive Sequences,Retroelements,Sequence Alignment,Trypanosoma cruzi,Trypanosoma cruzi: genetics} }

@article{muMembersLargeRetroposon2007, title = {Members of a Large Retroposon Family Are Determinants of Post-Transcriptional Gene Expression in {{Leishmania}}.}, author = {Mu, Michaela and Cerqueira, Gustavo Coutinho and Smith, Martin and Rochette, Annie and Bringaud, Fr{'e}d{'e}ric and M{"u}ller, Michaela and {}a {El-Sayed}, Najib M. and Papadopoulou, Barbara and Ghedin, Elodie}, year = 2007, month = sep, journal = {PLoS pathogens}, volume = {3}, number = {9}, pages = {1291–307}, issn = {1553-7374}, doi = {10.1371/journal.ppat.0030136}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2323293&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanosomatids are unicellular protists that include the human pathogens Leishmania spp. (leishmaniasis), Trypanosoma brucei (sleeping sickness), and Trypanosoma cruzi (Chagas disease). Analysis of their recently completed genomes confirmed the presence of non-long-terminal repeat retrotransposons, also called retroposons. Using the 79-bp signature sequence common to all trypanosomatid retroposons as bait, we identified in the Leishmania major genome two new large families of small elements–LmSIDER1 (785 copies) and LmSIDER2 (1,073 copies)–that fulfill all the characteristics of extinct trypanosomatid retroposons. LmSIDERs are approximately 70 times more abundant in L. major compared to T. brucei and are found almost exclusively within the 3’-untranslated regions (3’UTRs) of L. major mRNAs. We provide experimental evidence that LmSIDER2 act as mRNA instability elements and that LmSIDER2-containing mRNAs are generally expressed at lower levels compared to the non-LmSIDER2 mRNAs. The considerable expansion of LmSIDERs within 3’UTRs in an organism lacking transcriptional control and their role in regulating mRNA stability indicate that Leishmania have probably recycled these short retroposons to globally modulate the expression of a number of genes. To our knowledge, this is the first example in eukaryotes of the domestication and expansion of a family of mobile elements that have evolved to fulfill a critical cellular function.}, pmid = {17907803}, keywords = {3’ Untranslated Regions,3’ Untranslated Regions: chemistry,Animals,Base Sequence,Biological Evolution,Down-Regulation,Gene Expression Regulation,Gene Expression Regulation: physiology,Genome,Leishmania,Leishmania major,Leishmania major: genetics,Leishmania: genetics,Leishmania: physiology,Messenger,Messenger: metabolism,Molecular Sequence Data,nosource,Protozoan,Protozoan: genetics,Retroelements,Retroelements: physiology,RNA,Sequence Alignment,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma cruzi,Trypanosoma cruzi: genetics} }

@article{attardoAnalysisFatBody2006, title = {Analysis of Fat Body Transcriptome from the Adult Tsetse Fly, {{Glossina}} Morsitans Morsitans.}, author = {Attardo, G. M. and {Strickler-Dinglasan}, P. and Perkin, S. a H. and Caler, E. and Bonaldo, M. F. and Soares, M. B. and {El-Sayeed}, N. and Aksoy, S.}, year = 2006, month = aug, journal = {Insect molecular biology}, volume = {15}, number = {4}, eprint = {16907828}, eprinttype = {pubmed}, pages = {411–24}, issn = {0962-1075}, doi = {10.1111/j.1365-2583.2006.00649.x}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16907828}, abstract = {Tsetse flies (Diptera: Glossinidia) are vectors of pathogenic African trypanosomes. To develop a foundation for tsetse physiology, a normalized expressed sequence tag (EST) library was constructed from fat body tissue of immune-stimulated Glossina morsitans morsitans. Analysis of 20,257 high-quality ESTs yielded 6372 unique genes comprised of 3059 tentative consensus (TC) sequences and 3313 singletons (available at http://aksoylab.yale.edu). We analysed the putative fat body transcriptome based on homology to other gene products with known functions available in the public domain. In particular, we describe the immune-related products, reproductive function related yolk proteins and milk-gland protein, iron metabolism regulating ferritins and transferrin, and tsetse’s major energy source proline biosynthesis. Expression analysis of the three yolk proteins indicates that all are detected in females, while only the yolk protein with similarity to lipases, is expressed in males. Milk gland protein, apparently important for larval nutrition, however, is primarily synthesized by accessory milk gland tissue.}, pmid = {16907828}, keywords = {Adipose Tissue,Adipose Tissue: metabolism,Animals,Base Sequence,Computational Biology,DNA,DNA Primers,Egg Proteins,Egg Proteins: metabolism,Expressed Sequence Tags,Female,Gene Expression Profiling,Insect Vectors,Insect Vectors: genetics,Insect Vectors: metabolism,Male,Molecular Sequence Data,nosource,Reverse Transcriptase Polymerase Chain Reaction,Sequence Analysis,Sex Factors,Tsetse Flies,Tsetse Flies: genetics,Tsetse Flies: metabolism} }

@article{ouhammouchPromoterArchitectureResponse2005, title = {Promoter Architecture and Response to a Positive Regulator of Archaeal Transcription.}, author = {Ouhammouch, Mohamed and Langham, Geoffrey E. and Hausner, Winfried and Simpson, Anjana J. and {}a {El-Sayed}, Najib M. and Geiduschek, E. Peter}, year = 2005, month = may, journal = {Molecular microbiology}, volume = {56}, number = {3}, eprint = {15819620}, eprinttype = {pubmed}, pages = {625–37}, issn = {0950-382X}, doi = {10.1111/j.1365-2958.2005.04563.x}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15819620}, abstract = {The archaeal transcription apparatus is chimeric: its core components (RNA polymerase and basal factors) closely resemble those of eukaryotic RNA polymerase II, but the putative archaeal transcriptional regulators are overwhelmingly of bacterial type. Particular interest attaches to how these bacterial-type effectors, especially activators, regulate a eukaryote-like transcription system. The hyperthermophilic archaeon Methanocaldococcus jannaschii encodes a potent transcriptional activator, Ptr2, related to the Lrp/AsnC family of bacterial regulators. Ptr2 activates rubredoxin 2 (rb2) transcription through a bipartite upstream activating site (UAS), and conveys its stimulatory effects on its cognate transcription machinery through direct recruitment of the TATA binding protein (TBP). A functional dissection of the highly constrained architecture of the rb2 promoter shows that a ‘one-site’ minimal UAS suffices for activation by Ptr2, and specifies the required placement of this site. The presence of such a simplified UAS upstream of the natural rubrerythrin (rbr) promoter also suffices for positive regulation by Ptr2 in vitro, and TBP recruitment remains the primary means of transcriptional activation at this promoter.}, pmid = {15819620}, keywords = {Archaeal,Archaeal Proteins,Archaeal Proteins: genetics,Archaeal Proteins: metabolism,Bacterial Proteins,Bacterial Proteins: genetics,Bacterial Proteins: metabolism,DNA-Binding Proteins,DNA-Binding Proteins: genetics,DNA-Binding Proteins: metabolism,Ferredoxins,Ferredoxins: genetics,Ferredoxins: metabolism,Gene Expression Regulation,Genetic,Genetic: genetics,Hemerythrin,Methanococcales,Methanococcales: genetics,Methanococcales: metabolism,nosource,Promoter Regions,Rubredoxins,Rubredoxins: genetics,Rubredoxins: metabolism,TATA Box,TATA-Box Binding Protein,Transcription,Transcription Initiation Site} }

@article{zanforlinMolecularCharacterizationTrypanosoma2013, title = {Molecular {{Characterization}} of {{Trypanosoma}} Cruzi {{SAP Proteins}} with {{Host-Cell Lysosome Exocytosis-Inducing Activity Required}} for {{Parasite Invasion}}}, author = {Zanforlin, T. and {Bayer-Santos}, E. and Cortez, C.}, year = 2013, journal = {PloS one}, volume = {74}, number = {3}, pages = {1537–1546}, doi = {10.1128/IAI.74.3.1537}, url = {http://dx.plos.org/10.1371/journal.pone.0083864.g005}, isbn = {5511557110}, keywords = {nosource} }

@article{loftusGenomeProtistParasite2005, title = {The Genome of the Protist Parasite {{Entamoeba}} Histolytica.}, author = {Loftus, Brendan and Anderson, Iain and Davies, Rob and Alsmark, U. Cecilia M. and Samuelson, John and Amedeo, Paolo and Roncaglia, Paola and Berriman, Matt and Hirt, Robert P. and Mann, Barbara J. and Nozaki, Tomo and Suh, Bernard and Pop, Mihai and Duchene, Michael and Ackers, John and Tannich, Egbert and Leippe, Matthias and Hofer, Margit and Bruchhaus, Iris and Willhoeft, Ute and Bhattacharya, Alok and Chillingworth, Tracey and Churcher, Carol and Hance, Zahra and Harris, Barbara and Harris, David and Jagels, Kay and Moule, Sharon and Mungall, Karen and Ormond, Doug and Squares, Rob and Whitehead, Sally and {}a Quail, Michael and Rabbinowitsch, Ester and Norbertczak, Halina and Price, Claire and Wang, Zheng and Guill{'e}n, Nancy and Gilchrist, Carol and Stroup, Suzanne E. and Bhattacharya, Sudha and Lohia, Anuradha and Foster, Peter G. and {Sicheritz-Ponten}, Thomas and Weber, Christian and Singh, Upinder and Mukherjee, Chandrama and {El-Sayed}, Najib M. and {}a Petri, William and Clark, C. Graham and Embley, T. Martin and Barrell, Bart and Fraser, Claire M. and Hall, Neil}, year = 2005, month = feb, journal = {Nature}, volume = {433}, number = {7028}, eprint = {15729342}, eprinttype = {pubmed}, pages = {865–8}, issn = {1476-4687}, doi = {10.1038/nature03291}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15729342}, abstract = {Entamoeba histolytica is an intestinal parasite and the causative agent of amoebiasis, which is a significant source of morbidity and mortality in developing countries. Here we present the genome of E. histolytica, which reveals a variety of metabolic adaptations shared with two other amitochondrial protist pathogens: Giardia lamblia and Trichomonas vaginalis. These adaptations include reduction or elimination of most mitochondrial metabolic pathways and the use of oxidative stress enzymes generally associated with anaerobic prokaryotes. Phylogenomic analysis identifies evidence for lateral gene transfer of bacterial genes into the E. histolytica genome, the effects of which centre on expanding aspects of E. histolytica’s metabolic repertoire. The presence of these genes and the potential for novel metabolic pathways in E. histolytica may allow for the development of new chemotherapeutic agents. The genome encodes a large number of novel receptor kinases and contains expansions of a variety of gene families, including those associated with virulence. Additional genome features include an abundance of tandemly repeated transfer-RNA-containing arrays, which may have a structural function in the genome. Analysis of the genome provides new insights into the workings and genome evolution of a major human pathogen.}, pmid = {15729342}, keywords = {Animals,Entamoeba histolytica,Entamoeba histolytica: genetics,Entamoeba histolytica: metabolism,Entamoeba histolytica: pathogenicity,Evolution,Fermentation,Gene Transfer,Genome,Glycolysis,Horizontal,Horizontal: genetics,Molecular,nosource,Oxidative Stress,Oxidative Stress: genetics,Parasites,Parasites: genetics,Parasites: metabolism,Parasites: pathogenicity,Phylogeny,Protozoan,Signal Transduction,Virulence,Virulence: genetics} }

@article{macleodGeneticMapComparative2005, title = {The Genetic Map and Comparative Analysis with the Physical Map of {{Trypanosoma}} Brucei.}, author = {MacLeod, Annette and Tweedie, Alison and McLellan, Sarah and Taylor, Sonya and Hall, Neil and Berriman, Matthew and {El-Sayed}, Najib M. and Hope, Michelle and Turner, C. Michael R. and Tait, Andy}, year = 2005, month = jan, journal = {Nucleic acids research}, volume = {33}, number = {21}, pages = {6688–93}, issn = {1362-4962}, doi = {10.1093/nar/gki980}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1297707&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanosoma brucei is the causative agent of African sleeping sickness in humans and contributes to the debilitating disease ‘Nagana’ in cattle. To date we know little about the genes that determine drug resistance, host specificity, pathogenesis and virulence in these parasites. The availability of the complete genome sequence and the ability of the parasite to undergo genetic exchange have allowed genetic investigations into this parasite and here we report the first genetic map of T.brucei for the genome reference stock TREU 927, comprising of 182 markers and 11 major linkage groups, that correspond to the 11 previously identified chromosomes. The genetic map provides 90% probability of a marker being 11 cM from any given locus. Its comparison to the available physical map has revealed the average physical size of a recombination unit to be 15.6 Kb/cM. The genetic map coupled with the genome sequence and the ability to undertake crosses presents a new approach to identifying genes relevant to the disease and its prevention in this important pathogen through forward genetic analysis and positional cloning.}, pmid = {16314301}, keywords = {Animals,Chromosome Mapping,Chromosomes,Genetic Linkage,Genome,nosource,Physical Chromosome Mapping,Protozoan,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics} }

@article{el-sayedGenomeSequenceTrypanosoma2005, title = {The Genome Sequence of {{Trypanosoma}} Cruzi, Etiologic Agent of {{Chagas}} Disease.}, author = {{El-Sayed}, Najib M. and Myler, Peter J. and Bartholomeu, Daniella C. and Nilsson, Daniel and Aggarwal, Gautam and Tran, Anh-Nhi and Ghedin, Elodie and {}a Worthey, Elizabeth and Delcher, Arthur L. and Blandin, Ga{"e}lle and Westenberger, Scott J. and Caler, Elisabet and Cerqueira, Gustavo C. and Branche, Carole and Haas, Brian and Anupama, Atashi and Arner, Erik and Aslund, Lena and Attipoe, Philip and Bontempi, Esteban and Bringaud, Fr{'e}d{'e}ric and Burton, Peter and Cadag, Eithon and {}a Campbell, David and Carrington, Mark and Crabtree, Jonathan and Darban, Hamid and {}da Silveira, Jose Franco and {}de Jong, Pieter and Edwards, Kimberly and Englund, Paul T. and Fazelina, Gholam and Feldblyum, Tamara and Ferella, Marcela and Frasch, Alberto Carlos and Gull, Keith and Horn, David and Hou, Lihua and Huang, Yiting and Kindlund, Ellen and Klingbeil, Michele and Kluge, Sindy and Koo, Hean and Lacerda, Daniela and Levin, Mariano J. and Lorenzi, Hernan and Louie, Tin and Machado, Carlos Renato and McCulloch, Richard and McKenna, Alan and Mizuno, Yumi and Mottram, Jeremy C. and Nelson, Siri and Ochaya, Stephen and Osoegawa, Kazutoyo and Pai, Grace and Parsons, Marilyn and Pentony, Martin and Pettersson, Ulf and Pop, Mihai and Ramirez, Jose Luis and Rinta, Joel and Robertson, Laura and Salzberg, Steven L. and Sanchez, Daniel O. and Seyler, Amber and Sharma, Reuben and Shetty, Jyoti and Simpson, Anjana J. and Sisk, Ellen and Tammi, Martti T. and Tarleton, Rick and Teixeira, Santuza and Aken, Susan Van and Vogt, Christy and Ward, Pauline N. and Wickstead, Bill and Wortman, Jennifer and White, Owen and Fraser, Claire M. and Stuart, Kenneth D. and Andersson, Bj{"o}rn}, year = 2005, month = jul, journal = {Science}, volume = {309}, number = {5733}, eprint = {16020725}, eprinttype = {pubmed}, pages = {409–15}, issn = {1095-9203}, doi = {10.1126/science.1112631}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16020725}, abstract = {Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family ({\(>\)}1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.}, pmid = {16020725}, keywords = {Animals,Chagas Disease,Chagas Disease: drug therapy,Chagas Disease: parasitology,DNA,DNA Repair,DNA Replication,Genes,Genetic,Genome,Humans,Meiosis,Membrane Proteins,Membrane Proteins: chemistry,Membrane Proteins: genetics,Membrane Proteins: physiology,Mitochondrial,Mitochondrial: genetics,Multigene Family,nosource,Nucleic Acid,Protozoan,Protozoan Proteins,Protozoan Proteins: chemistry,Protozoan Proteins: genetics,Protozoan Proteins: physiology,Protozoan: genetics,Recombination,Repetitive Sequences,Retroelements,Sequence Analysis,Signal Transduction,Telomere,Telomere: genetics,Trypanocidal Agents,Trypanocidal Agents: pharmacology,Trypanocidal Agents: therapeutic use,Trypanosoma cruzi,Trypanosoma cruzi: chemistry,Trypanosoma cruzi: genetics,Trypanosoma cruzi: physiology} }

@article{bringaudEvolutionNonLTRRetrotransposons2006, title = {Evolution of Non-{{LTR}} Retrotransposons in the Trypanosomatid Genomes: {{Leishmania}} Major Has Lost the Active Elements.}, author = {Bringaud, Fr{'e}d{'e}ric and Ghedin, Elodie and Blandin, Ga{"e}lle and Bartholomeu, Daniella C. and Caler, Elisabet and Levin, Mariano J. and Baltz, Th{'e}o and {El-Sayed}, Najib M.}, year = 2006, month = feb, journal = {Molecular and biochemical parasitology}, volume = {145}, number = {2}, eprint = {16257065}, eprinttype = {pubmed}, pages = {158–70}, issn = {0166-6851}, doi = {10.1016/j.molbiopara.2005.09.017}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16257065}, abstract = {The ingi and L1Tc non-LTR retrotransposons–which constitute the ingi clade–are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5’-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs.}, pmid = {16257065}, keywords = {Amino Acid,Animals,Base Sequence,Computational Biology,Conserved Sequence,Evolution,Frameshift Mutation,Genome,Leishmania major,Leishmania major: genetics,Molecular,Molecular Sequence Data,nosource,Nucleic Acid,Nucleic Acid Conformation,Phylogeny,Protozoan,Retroelements,Retroelements: genetics,Sequence Homology,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma cruzi,Trypanosoma cruzi: genetics} }

@article{berrimanGenomeAfricanTrypanosome2005, title = {The Genome of the {{African}} Trypanosome {{Trypanosoma}} Brucei.}, author = {Berriman, Matthew and Ghedin, Elodie and {Hertz-Fowler}, Christiane and Blandin, Ga{"e}lle and Renauld, Hubert and Bartholomeu, Daniella C. and Lennard, Nicola J. and Caler, Elisabet and Hamlin, Nancy E. and Haas, Brian and B{"o}hme, Ulrike and Hannick, Linda and Aslett, Martin A. and Shallom, Joshua and Marcello, Lucio and Hou, Lihua and Wickstead, Bill and Alsmark, U. Cecilia M. and Arrowsmith, Claire and Atkin, Rebecca J. and Barron, Andrew J. and Bringaud, Frederic and Brooks, Karen and Carrington, Mark and Cherevach, Inna and Chillingworth, Tracey-jane and Churcher, Carol and Clark, Louise N. and Corton, Craig H. and Cronin, Ann and Davies, Rob M. and Doggett, Jonathon and Djikeng, Appolinaire and Feldblyum, Tamara and Field, Mark C. and Fraser, Audrey and Goodhead, Ian and Hance, Zahra and Harper, David and Harris, Barbara R. and Hauser, Heidi and Hostetler, Jessica and Ivens, Al and Jagels, Kay and Johnson, David and Johnson, Justin and Jones, Kristine and Kerhornou, Arnaud X. and Koo, Hean and Larke, Natasha and Landfear, Scott and Larkin, Christopher and Leech, Vanessa and Line, Alexandra and Lord, Angela and Macleod, Annette and Mooney, Paul J. and Moule, Sharon and {}a Martin, David M. and Morgan, Gareth W. and Mungall, Karen and Norbertczak, Halina and Ormond, Doug and Pai, Grace and Peacock, Chris S. and Peterson, Jeremy and {}a Quail, Michael and Rabbinowitsch, Ester and Rajandream, Marie-adele and Reitter, Chris and Salzberg, Steven L. and Sanders, Mandy and Schobel, Seth and Sharp, Sarah and Simmonds, Mark and Simpson, Anjana J. and Tallon, Luke and Turner, C. Michael R. and Tait, Andrew and Tivey, Adrian R. and Aken, Susan Van and Walker, Danielle and Wanless, David and Wang, Shiliang and White, Brian and White, Owen and Whitehead, Sally and Woodward, John and Wortman, Jennifer and Adams, Mark D. and Embley, T. Martin and Gull, Keith and Ullu, Elisabetta and Barry, J. David and Fairlamb, Alan H. and Opperdoes, Fred and Barrell, Barclay G. and Donelson, John E. and Hall, Neil and Fraser, Claire M. and Melville, Sara E. and {El-Sayed}, Najib M. and Bo, Ulrike and Aken, Susan Van}, year = 2005, month = jul, journal = {Science (New York, N.Y.)}, volume = {309}, number = {5733}, eprint = {16020726}, eprinttype = {pubmed}, pages = {416–22}, issn = {1095-9203}, doi = {10.1126/science.1112642}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16020726}, abstract = {African trypanosomes cause human sleeping sickness and livestock trypanosomiasis in sub-Saharan Africa. We present the sequence and analysis of the 11 megabase-sized chromosomes of Trypanosoma brucei. The 26-megabase genome contains 9068 predicted genes, including approximately 900 pseudogenes and approximately 1700 T. brucei-specific genes. Large subtelomeric arrays contain an archive of 806 variant surface glycoprotein (VSG) genes used by the parasite to evade the mammalian immune system. Most VSG genes are pseudogenes, which may be used to generate expressed mosaic genes by ectopic recombination. Comparisons of the cytoskeleton and endocytic trafficking systems with those of humans and other eukaryotic organisms reveal major differences. A comparison of metabolic pathways encoded by the genomes of T. brucei, T. cruzi, and Leishmania major reveals the least overall metabolic capability in T. brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified.}, pmid = {16020726}, keywords = {African,African: parasitology,Amino Acids,Amino Acids: metabolism,Animals,Antigenic Variation,Antigens,Carbohydrate Metabolism,Chromosomes,Chromosomes: genetics,Cytoskeleton,Cytoskeleton: chemistry,Cytoskeleton: genetics,Cytoskeleton: physiology,DNA,Ergosterol,Ergosterol: biosynthesis,Genes,Genetic,Genome,Glutathione,Glutathione: analogs & derivatives,Glutathione: metabolism,Glycosylphosphatidylinositols,Glycosylphosphatidylinositols: biosynthesis,Humans,Lipid Metabolism,Molecular Sequence Data,nosource,Protein Transport,Protozoan,Protozoan Proteins,Protozoan Proteins: chemistry,Protozoan Proteins: genetics,Protozoan Proteins: metabolism,Protozoan: chemistry,Protozoan: genetics,Protozoan: immunology,Pseudogenes,Purines,Purines: metabolism,Pyrimidines,Pyrimidines: biosynthesis,Recombination,Sequence Analysis,Spermidine,Spermidine: analogs & derivatives,Spermidine: metabolism,Trypanosoma brucei brucei,Trypanosoma brucei brucei: chemistry,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: immunology,Trypanosoma brucei brucei: metabolism,Trypanosomiasis} } % == BibTeX quality report for berrimanGenomeAfricanTrypanosome2005: % ? Possibly abbreviated journal title Science (New York, N.Y.)

@article{ghedinGeneSyntenyEvolution2004, title = {Gene Synteny and Evolution of Genome Architecture in Trypanosomatids.}, author = {Ghedin, Elodie and Bringaud, Frederic and Peterson, Jeremy and Myler, Peter and Berriman, Matthew and Ivens, Alasdair and Andersson, Bj{"o}rn and Bontempi, Esteban and Eisen, Jonathan and Angiuoli, Sam and Wanless, David and Arx, Anna Von and Murphy, Lee and Lennard, Nicola and Salzberg, Steven and Adams, Mark D. and White, Owen and Hall, Neil and Stuart, Kenneth and Fraser, Claire M. and {}a {El-Sayed}, Najib M.}, year = 2004, month = apr, journal = {Molecular and biochemical parasitology}, volume = {134}, number = {2}, eprint = {15003838}, eprinttype = {pubmed}, pages = {183–91}, issn = {0166-6851}, doi = {10.1016/j.molbiopara.2003.11.012}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15003838}, abstract = {The trypanosomatid protozoa Trypanosoma brucei, Trypanosoma cruzi and Leishmania major are related human pathogens that cause markedly distinct diseases. Using information from genome sequencing projects currently underway, we have compared the sequences of large chromosomal fragments from each species. Despite high levels of divergence at the sequence level, these three species exhibit a striking conservation of gene order, suggesting that selection has maintained gene order among the trypanosomatids over hundreds of millions of years of evolution. The few sites of genome rearrangement between these species are marked by the presence of retrotransposon-like elements, suggesting that retrotransposons may have played an important role in shaping trypanosomatid genome organization. A degenerate retroelement was identified in L. major by examining the regions near breakage points of the synteny. This is the first such element found in L. major suggesting that retroelements were found in the common ancestor of all three species.}, isbn = {1301838020}, pmid = {15003838}, keywords = {Animals,Computational Biology,Evolution,Gene Order,Genetic,Genome,Genomics,Leishmania major,Leishmania major: genetics,Molecular,Multigene Family,nosource,Protozoan,Recombination,Retroelements,Retroelements: physiology,Selection,Synteny,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosomatina,Trypanosomatina: genetics} }

@article{el-sayedSequenceAnalysisTrypanosoma2003, title = {The Sequence and Analysis of {{Trypanosoma}} Brucei Chromosome {{II}}}, author = {{}a {El-Sayed}, N. M.}, year = 2003, month = aug, journal = {Nucleic Acids Research}, volume = {31}, number = {16}, pages = {4856–4863}, issn = {1362-4962}, doi = {10.1093/nar/gkg673}, url = {http://www.nar.oupjournals.org/cgi/doi/10.1093/nar/gkg673}, keywords = {nosource} }

@article{bringaudIdentificationNonautonomousNonLTR2002, title = {Identification of Non-Autonomous Non-{{LTR}} Retrotransposons in the Genome of {{Trypanosoma}} Cruzi.}, author = {Bringaud, Fr{'e}d{'e}ric and {Garc{'i}a-P{'e}rez}, Jos{'e} Luis and Heras, Sara R. and Ghedin, Elodie and {El-Sayed}, Najib M. and Andersson, Bj{"o}rn and Baltz, Th{'e}o and Lopez, Manuel C.}, year = 2002, journal = {Molecular and biochemical parasitology}, volume = {124}, number = {1-2}, eprint = {12387852}, eprinttype = {pubmed}, pages = {73–8}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12387852}, abstract = {As observed for most eukaryotic cells, trypanosomatids contains non-LTR retrotransposons randomly inserted in the nuclear genome. Autonomous retroelements which, code for their own transposition, have been characterized in Trypanosoma brucei (ingi) and Trypanosoma cruzi (L1Tc), whereas non-autonomous retroelements have only been characterized in T. brucei (RIME). Here, we have characterized in the genome of Trypanosoma cruzi four complete copies of a non-autonomous non-LTR retrotransposon, called NARTc. This 0.26 kb NARTc element has the characteristics of non-LTR retrotransposons: the presence a poly(dA) tail and of a short flanking duplicated motif. Analysis of the Genome Survey Sequence databases indicated that the Trypanosoma cruzi haploid genome contains about 140 NARTc copies and about twice as many L1Tc copies. Interestingly, the NARTc and L1Tc retroelements share, with the Trypanosoma brucei ingi and RIME retrotransposons, a common sequence (the first 45 bp with 91% identity), whereas the remaining sequences are very divergent. This suggests that these four trypanosome non-LTR retrotransposons were derived from the same common ancester and the sequence of their 5’-extremity may have a functional role. In addition, the genome of Leishmania major contains the same conserved motif present in the trypanosome retroelements, whicle no transposable elements have been detected so far in Leishmania sp.}, pmid = {12387852}, keywords = {Animals,Base Sequence,Computational Biology,Genome,Long Interspersed Nucleotide Elements,Long Interspersed Nucleotide Elements: genetics,Molecular Sequence Data,nosource,Protozoan,Retroelements,Retroelements: genetics,Short Interspersed Nucleotide Elements,Short Interspersed Nucleotide Elements: genetics,Trypanosoma cruzi,Trypanosoma cruzi: genetics} }

@article{bringaudNewExpressedMultigene2002, title = {A New, Expressed Multigene Family Containing a Hot Spot for Insertion of Retroelements Is Associated with Polymorphic Subtelomeric Regions of {{Trypanosoma}} Brucei}, author = {Bringaud, Fr{'e}d{'e}ric and Biteau, Nicolas and Melville, SE Sara E. and Hez, St{'e}phanie and {El-sayed}, Najib M. and Leech, Vanessa and Berriman, Matthew and Hall, Neil and Donelson, John E. and Baltz, Th{'e}o}, year = 2002, journal = {Eukaryotic }, volume = {1}, number = {1}, pages = {137–151}, doi = {10.1128/EC.1.1.137}, url = {http://ec.asm.org/content/1/1/137.short}, keywords = {nosource} }

@article{bartholomeuTrypanosomaCruziRNA2002, title = {Trypanosoma Cruzi: {{RNA}} Structure and Post-Transcriptional Control of Tubulin Gene Expression}, author = {Bartholomeu, Daniella C. and {}a Silva, Rosiane and Galv{~a}o, Lucia M. C. and Sayed, Najib M. a El- and Donelson, John E. and Teixeira, Santuza M. R.}, year = 2002, month = nov, journal = {Experimental Parasitology}, volume = {102}, number = {3-4}, pages = {123–133}, issn = {00144894}, doi = {10.1016/S0014-4894(03)00034-1}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014489403000341}, keywords = {nosource} }

@article{el-sayedAfricanTrypanosomeGenome2000, title = {The {{African}} Trypanosome Genome.}, author = {{El-Sayed}, N. M. and Hegde, P. and Quackenbush, J. and Melville, S. E. and Donelson, J. E.}, year = 2000, month = apr, journal = {International journal for parasitology}, volume = {30}, number = {4}, eprint = {10731558}, eprinttype = {pubmed}, pages = {329–45}, issn = {0020-7519}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10731558}, abstract = {The haploid nuclear genome of the African trypanosome, Trypanosoma brucei, is about 35 Mb and varies in size among different trypanosome isolates by as much as 25%. The nuclear DNA of this diploid organism is distributed among three size classes of chromosomes: the megabase chromosomes of which there are at least 11 pairs ranging from 1 Mb to more than 6 Mb (numbered I-XI from smallest to largest); several intermediate chromosomes of 200-900 kb and uncertain ploidy; and about 100 linear minichromosomes of 50-150 kb. Size differences of as much as four-fold can occur, both between the two homologues of a megabase chromosome pair in a specific trypanosome isolate and among chromosome pairs in different isolates. The genomic DNA sequences determined to date indicated that about 50% of the genome is coding sequence. The chromosomal telomeres possess TTAGGG repeats and many, if not all, of the telomeres of the megabase and intermediate chromosomes are linked to expression sites for genes encoding variant surface glycoproteins (VSGs). The minichromosomes serve as repositories for VSG genes since some but not all of their telomeres are linked to unexpressed VSG genes. A gene discovery program, based on sequencing the ends of cloned genomic DNA fragments, has generated more than 20 Mb of discontinuous single-pass genomic sequence data during the past year, and the complete sequences of chromosomes I and II (about 1 Mb each) in T. brucei GUTat 10.1 are currently being determined. It is anticipated that the entire genomic sequence of this organism will be known in a few years. Analysis of a test microarray of 400 cDNAs and small random genomic DNA fragments probed with RNAs from two developmental stages of T. brucei demonstrates that the microarray technology can be used to identify batteries of genes differentially expressed during the various life cycle stages of this parasite.}, isbn = {3198380200}, pmid = {10731558}, keywords = {Animals,Antigenic Variation,Expressed Sequence Tags,Genome,Karyotyping,nosource,Protozoan,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics} }

@article{donelsonMoreSurprisesKinetoplastida1999, title = {More Surprises from {{Kinetoplastida}}}, author = {Donelson, J. E.}, year = 1999, journal = {Proceedings of the }, volume = {96}, number = {March}, pages = {2579–2581}, url = {http://www.pnas.org/content/96/6/2579.short}, keywords = {nosource} }

@article{morganDifferentialExpressionExpression1996, title = {Differential Expression of the Expression Site-Associated Gene {{I}} Family in {{African}} Trypanosomes.}, author = {Morgan, R. W. and {El-Sayed}, N. M. and Kepa, J. K. and Pedram, M. and Donelson, J. E.}, year = 1996, month = apr, journal = {The Journal of biological chemistry}, volume = {271}, number = {16}, eprint = {8621657}, eprinttype = {pubmed}, pages = {9771–7}, issn = {0021-9258}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8621657}, abstract = {A minimum of 20 different mRNA species encoding related members of the expression site-associated gene I (ESAG-I) family occur in metacyclic variant antigen type 4 bloodstream trypanosomes. None of these ESAG-I mRNAs are derived from the metacyclic variant antigen type 4 variant surface glycoprotein (VSG) gene expression site, and some appear to come from pseudogenes. The ESAG-Is are transcribed in both procyclic and bloodstream trypanosomes, but their mRNAs accumulate to a detectable steady state level only in bloodstream trypanosomes. At least five different groups of 3’-untranslated regions (3’-UTRs) are represented among these ESAG-I mRNAs, suggesting that the 3’-UTR does not contribute to their differential expression. Some ESAG-I mRNAs completely lack a 3’-UTR or have only a single nucleotide as a 3’-UTR. Transcription of the ESAG-Is is sensitive to alpha-amanitin, indicating that they are transcribed by a different RNA polymerase than the VSG genes. These results collectively demonstrate that ESAG-I’s are a heterogeneous population that can be expressed independently of VSG genes, but like the VSG genes, their mRNAs are present in the bloodstream stage of the parasite and not in the procyclic stage.}, pmid = {8621657}, keywords = {Amanitins,Amanitins: pharmacology,Amino Acid,Amino Acid Sequence,Animals,Blotting,Cell Nucleus,Cell Nucleus: metabolism,Gene Expression,Gene Library,Genes,Genetic,Genetic: drug effects,Messenger,Messenger: analysis,Messenger: biosynthesis,Molecular Sequence Data,Multigene Family,Northern,nosource,Protein Biosynthesis,Protozoan,Protozoan Proteins,Protozoan: analysis,Protozoan: biosynthesis,Rats,RNA,Sequence Homology,Transcription,Trypanosoma,Trypanosoma brucei rhodesiense,Trypanosoma brucei rhodesiense: genetics,Trypanosoma brucei rhodesiense: metabolism,Trypanosoma: biosyn,Variant Surface Glycoproteins} }

@article{kimTelomereSubtelomereTrypanosoma2005, title = {Telomere and Subtelomere of {{Trypanosoma}} Cruzi Chromosomes Are Enriched in (Pseudo)Genes of Retrotransposon Hot Spot and Trans-Sialidase-like Gene Families: The Origins of {{T}}. Cruzi Telomeres.}, author = {Kim, Dong and Chiurillo, Miguel Angel and {El-Sayed}, Najib and Jones, Kristin and Santos, M{'a}rcia R. M. and Porcile, Patricio E. and Andersson, Bjorn and Myler, Peter and {}da Silveira, Jos{'e} Franco and Ram{'i}rez, Jos{'e} Luis}, year = 2005, month = feb, journal = {Gene}, volume = {346}, eprint = {15716016}, eprinttype = {pubmed}, pages = {153–61}, issn = {0378-1119}, doi = {10.1016/j.gene.2004.10.014}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15716016}, abstract = {Here, we sequenced two large telomeric regions obtained from the pathogen protozoan Trypanosoma cruzi. These sequences, together with in silico assembled contigs, allowed us to establish the general features of telomeres and subtelomeres of this parasite. Our findings can be summarized as follows: We confirmed the presence of two types of telomeric ends; subtelomeric regions appeared to be enriched in (pseudo)genes of RHS (retrotransposon hot spot), TS (trans-sialidase)-like proteins, and putative surface protein DGF-1 (dispersed gene family-1). Sequence analysis of the ts-like genes located at the telomeres suggested that T. cruzi chromosomal ends could have been the site for generation of new gp85 variants, an important adhesin molecule involved in the invasion of mammalian cells by T. cruzi. Finally, a mechanism for generation of T. cruzi telomere by chromosome breakage and telomere healing is proposed.}, pmid = {15716016}, keywords = {Amino Acid,Amino Acid Sequence,Animals,Artificial,Bacterial,Base Sequence,Chromosomes,DNA,Genes,Glycoproteins,Glycoproteins: chemistry,Glycoproteins: genetics,Molecular Sequence Data,Multigene Family,Neuraminidase,Neuraminidase: chemistry,Neuraminidase: genetics,nosource,Nucleic Acid,Protozoan,Protozoan: genetics,Pseudogenes,Retroelements,Sequence Homology,Telomere,Trypanosoma cruzi,Trypanosoma cruzi: genetics} }

@article{freitas-juniorTwoDistinctGroups1998, title = {Two Distinct Groups of Mucin-like Genes Are Differentially Expressed in the Developmental Stages of {{Trypanosoma}} Cruzi.}, author = {{Freitas-Junior}, L. H. and Briones, M. R. and Schenkman, S.}, year = 1998, month = may, journal = {Molecular and biochemical parasitology}, volume = {93}, number = {1}, eprint = {9662032}, eprinttype = {pubmed}, pages = {101–14}, issn = {0166-6851}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9662032}, abstract = {Sialic acid acceptors of Trypanosoma cruzi are abundant mucin-like glycoproteins linked to the parasite membrane by a glycosylphosphatidyl inositol (GPI) anchor. They are heterogeneous and variable in different parasite stages. The protein portion of these mucins contains many threonine residues, and is thought to be encoded by a heterogeneous gene family. To investigate whether the high degree of heterogeneity in the mucin gene family is responsible for the diversity of mucins expressed on the parasite surface, we have studied the expression of mucin genes in several developmental stages of T. cruzi. We have found that mucins are expressed in all parasite stages. By using conserved sequences at 3’ end of translated sequences of the gene family and the splice leader sequence, we have isolated 120 mucin-like cDNAs by RT-PCR from epimastigote and trypomastigote mRNAs. All transcribed genes contain conserved 5’ and 3’ regions, which code for the signal peptide, the sequence for GPI anchor addition, and a conserved domain rich in threonine residues. The internal portions of these genes are highly variable in size and sequence, and can be grouped in two major categories. One group contains KP(1-2)T(6-8) repeats, a motif found in mammalian mucins in the central region. This group is expressed preferentially in the trypomastigote forms ready to be released from the infected mammalian cell. The other has highly variable sequences in the central portion, and is expressed in all parasite stages. Because the number of synonymous substitutions is equivalent to the non-synonymous substitutions in the second group, they are probably evolving neutrally. On the other hand, the KP(1-2)T(6-8) containing genes have more synonymous substitutions and are most likely under a strong selective pressure. We propose that the group of KP(1-2)T(6-8) motif corresponds to the highly glycosylated mucins of the trypomastigote stages. In the other group proteolysis may remove the central domain yielding small mucins, such as the mucins found in insect derived stages of T. cruzi.}, pmid = {9662032}, keywords = {Animals,Base Sequence,Cell Differentiation,Cell Differentiation: genetics,Cloning,Complementary,Complementary: genetics,Conserved Sequence,Cosmids,DNA,Gene Expression Regulation,Genes,Genetic,Genomic Library,Likelihood Functions,Molecular,Molecular Sequence Data,Mucins,Mucins: classification,Mucins: genetics,Multigene Family,nosource,Nucleic Acid,Protozoan,Repetitive Sequences,Sequence Analysis,Transcription,Trypanosoma cruzi,Trypanosoma cruzi: cytology,Trypanosoma cruzi: genetics} }

@article{el-sayedSurveyTrypanosomaBrucei1997, title = {A Survey of the {{Trypanosoma}} Brucei Rhodesiense Genome Using Shotgun Sequencing}, author = {{El-Sayed}, N. and Donelson, J. E.}, year = 1997, journal = {Molecular and biochemical parasitology}, volume = {84}, pages = {167–178}, url = {http://www.sciencedirect.com/science/article/pii/S0166685196027922}, keywords = {abbre6iations,est,expressed sequence tag,genome,genome survey sequence,gss,nosource,trypanosoma brucei rhodesiense} }

@article{el-sayedCDNAExpressedSequence1995, title = {{{cDNA}} Expressed Sequence Tags of {{Trypanosoma}} Brucei Rhodesiense Provide New Insights into the Biology of the Parasite.}, author = {{}{el-Sayed}, N. M. and Alarcon, C. M. and Beck, J. C. and Sheffield, V. C. and Donelson, J. E.}, year = 1995, month = jul, journal = {Molecular and biochemical parasitology}, volume = {73}, number = {1-2}, pages = {75–90}, issn = {0166-6851}, doi = {10.1016/0166-6851(95)00098-L}, url = {https://www.sciencedirect.com/science/article/pii/016668519500098L}, abstract = {A total of 518 expressed sequence tags (ESTS) have been generated from clones randomly selected from a cDNA library and a spliced leader sub-library of a Z’ryunosoma brucei rhodesiense bloodstream clone. 205 (39%) of the clones were identified based on matches to 113 unique genes in the public databases. Of these, 71 cDNAs display significant similarities to genes in unrelated organisms encoding metabolic enzymes, signal transduction proteins, transcription factors, ribosomal proteins, histones, a proliferation-associated protein and thimet oligopeptidase, among others. 313 of the cDNAs are not related to any other sequences in the databases. These cDNA ESTs provide new avenues of research for exploring both the novel trypanosome-specific genes and the genome organization of this parasite, as well as a resource for identifying trypanosome homologs to genes expressed in other organisms.}, langid = {english}, pmid = {8577350}, keywords = {Amino Acid,Amino Acid Sequence,Animals,Base Sequence,cDNA,Cloning,Complementary,Complementary: genetics,Databases,DNA,DNA Primers,DNA Primers: genetics,Expressed sequence tag,Factual,Gene Expression,Gene Library,Genes,GTP-Binding Proteins,GTP-Binding Proteins: genetics,Humans,Molecular,Molecular Sequence Data,Nucleic Acid,Protozoan,Protozoan Proteins,Protozoan Proteins: genetics,Protozoan: genetics,Repetitive Sequences,Sequence Homology,Trypanosoma brucei rhodesiense,Trypanosoma brucei rhodesiense: genetics}, file = {/home/trey/Zotero/storage/CAMBPL97/El-Sayed et al. - 1995 - cDNA expressed sequence tags of Trypanosoma brucei.pdf;/home/trey/Zotero/storage/23M5JX9F/016668519500098L.html;/home/trey/Zotero/storage/AK9H4AXQ/016668519500098L.html;/home/trey/Zotero/storage/GQ9UC7NY/016668519500098L.html;/home/trey/Zotero/storage/I5ZLB3EY/016668519500098L.html;/home/trey/Zotero/storage/ISFMW8M9/016668519500098L.html;/home/trey/Zotero/storage/NT7QXMSX/016668519500098L.html} } % == BibTeX quality report for el-sayedCDNAExpressedSequence1995: % ? unused Library catalog (“DOI.org (Crossref)”)

@article{dallagiovannaTrypanosomaCruziGene2001, title = {Trypanosoma Cruzi: A Gene Family Encoding Chitin-Binding-like Proteins Is Posttranscriptionally Regulated during Metacyclogenesis.}, author = {Dallagiovanna, B. and {Plazanet-Menut}, C. and Ogatta, S. F. and Avila, a R. and {}a Krieger, M. and Goldenberg, S.}, year = 2001, month = sep, journal = {Experimental parasitology}, volume = {99}, number = {1}, eprint = {11708829}, eprinttype = {pubmed}, pages = {7–16}, issn = {0014-4894}, doi = {10.1006/expr.2001.4628}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11708829}, abstract = {The development of the representation of differential expression method has lead to the cloning of Trypanosoma cruzi stage-specific genes. We used this method to characterize a multicopy gene family differentially expressed during metacyclogenesis. The genomic and cDNA clones sequenced encoded three short cysteine-rich polypeptides, of two types, with predicted molecular masses of 7.1, 10.4, and 10.8 kDa. We searched GenBank for similar sequences and found that the sequences of these clones were similar to that encoding the wheat germ agglutinin protein. The region of similarity corresponds to the chitin-binding domain, with eight similarly positioned half-cysteines and conserved aromatic residues involved in chitin recognition. Multiple copies of the genes of this family are present on a high- molecular-mass chromosome. We studied the expression of genes of this family during metacyclogenesis by determining messenger RNA (mRNA) levels. The mRNAs for the members of this gene family were present in the total RNA fraction but were mobilized to the polysomal fraction of adhered (differentiating) epimastigotes during metacyclogenesis, with a peak of accumulation at 24 of differentiation. Polyclonal antisera were raised against a recombinant protein and a synthetic peptide. The specific sera obtained detected 7- and 11-kDa proteins in T. cruzi total protein extracts. The 11-kDa protein was present in similar amounts in the various cell populations, whereas the 7-kDa protein displayed differential synthesis during metacyclogenesis, with maximal levels in 24-h-adhered (differentiating) epimastigotes.}, pmid = {11708829}, keywords = {Amino Acid Sequence,Animals,Blotting,Carrier Proteins,Carrier Proteins: biosynthesis,Carrier Proteins: chemistry,Carrier Proteins: genetics,Cell Adhesion,Chitin,Chitin: metabolism,Cloning,DNA,Gene Expression,Genome,Immune Sera,Immune Sera: chemistry,Molecular,Molecular Sequence Data,Multigene Family,Multigene Family: physiology,Northern,nosource,Protein Structure,Protozoan,Protozoan Proteins,Protozoan Proteins: biosynthesis,Protozoan Proteins: chemistry,Protozoan Proteins: genetics,Protozoan: analysis,Protozoan: chemistry,Rabbits,RNA,Southern,Tertiary,Trypanosoma cruzi,Trypanosoma cruzi: chemistry,Trypanosoma cruzi: genetics,Trypanosoma cruzi: physiology,Western} }

@article{diehlAnalysisStagespecificGene2002, title = {Analysis of Stage-Specific Gene Expression in the Bloodstream and the Procyclic Form of {{Trypanosoma}} Brucei Using a Genomic {{DNA-microarray}}}, author = {Diehl, S. and Diehl, Frank and {El-Sayed}, N. M.}, year = 2002, month = aug, journal = {Molecular and Biochemical Parasitology}, volume = {123}, number = {2}, pages = {115–123}, issn = {0166-6851}, doi = {10.1016/S0166-6851(02)00138-X}, url = {https://www.sciencedirect.com/science/article/pii/S016668510200138X}, abstract = {A microarray comprising 21,024 different PCR products spotted on glass slides was constructed for gene expression studies on Trypanosoma brucei. The arrayed fragments were generated from a T. brucei shotgun clone library, which had been prepared from randomly sheared and size-fractionated genomic DNA. For the identification of stage-specific gene activity, total RNA from in vitro cultures of the human, long slender form and the insect, procyclic form of the parasite was labelled and hybridised to the microarray. Approximately 75% of the genomic fragments produced a signal and about 2% exhibited significant differences between the transcript levels in the bloodstream and procyclic forms. A few results were confirmed by Northern blot analysis or reverse-transcription and PCR. Three hundred differentially regulated clones have been selected for sequencing. So far, of 33 clones that showed about 2-fold or more over-expression in bloodstream forms, 15 contained sequences similar to those of VSG expression sites and at least six others appeared non-protein-coding. Of 29 procyclic-specific clones, at least eight appeared not to be protein-coding. A surprisingly large proportion of known regulated genes was already identified in this small sample, and some new ones were found, illustrating the utility of genomic arrays.}, pmid = {12270627}, keywords = {Animals,Blotting,Escherichia coli,Escherichia coli: genetics,Expression,Gene,Gene Expression,Gene Expression Profiling,Genes,Genetic,Humans,Life Cycle Stages,Microarray,Molecular Sequence Data,Northern,Oligonucleotide Array Sequence Analysis,Polymerase Chain Reaction,Protozoan,Regulation,Transcription,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: isolation & purificatio}, file = {/home/trey/Zotero/storage/MDDHM9JF/Diehl et al. - 2002 - Analysis of stage-specific gene expression in the .pdf;/home/trey/Zotero/storage/2KBU52WB/S016668510200138X.html;/home/trey/Zotero/storage/BZ8Y4R5J/S016668510200138X.html;/home/trey/Zotero/storage/L5HSWEFN/S016668510200138X.html;/home/trey/Zotero/storage/MWWTX86V/S016668510200138X.html} } % == BibTeX quality report for diehlAnalysisStagespecificGene2002: % ? unused Library catalog (“ScienceDirect”)

@article{lacountAnalysisDonorGene2001, title = {Analysis of a Donor Gene Region for a Variant Surface Glycoprotein and Its Expression Site in {{African}} Trypanosomes.}, author = {LaCount, D. J. and {El-Sayed}, N. M. and Kaul, S. and Wanless, D. and Turner, C. M. and Donelson, J. E.}, year = 2001, month = may, journal = {Nucleic acids research}, volume = {29}, number = {10}, pages = {2012–9}, issn = {1362-4962}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=55451&tool=pmcentrez&rendertype=abstract}, abstract = {African trypanosomes evade the immune response of their mammalian hosts by sequentially expressing genes for different variant surface glycoproteins (VSGs) from telomere-linked VSG expression sites. In the Trypanosoma brucei clone whose genome is being sequenced (GUTat 10.1), we show that the expressed VSG (VSG 10.1) is duplicated from a silent donor VSG located at another telomere-linked site. We have determined two 130 kb sequences representing the VSG 10.1 donor and expression sites. The telomere-linked donor VSG 10.1 resembles metacyclic VSG expression sites, and is preceded by a cluster of 35 or more tandem housekeeping genes, all of which are transcribed away from the telomere. The 45 kb telomere-linked VSG 10.1 expression site contains a promoter followed by seven expression site-associated genes (ESAGs), three pseudo ESAGs, two pseudo VSGs and VSG 10.1. The 80 kb preceding the expression site has few, if any, functional ORFs, but contains 50 bp repeats, INGI retrotransposon-like elements, and novel 4-12 kb repeats found near other telomeres. This analysis provides the first look over a 130 kb range of a telomere-linked donor VSG and its corresponding telomere-linked VSG expression site and forms the basis for studies on antigenic variation in the context of a completely sequenced genome.}, pmid = {11353069}, keywords = {Amino Acid Sequence,Animals,Artificial,Bacterial,Bacterial: genetics,Base Sequence,Chromosomes,Cloning,Complementary,Complementary: genetics,DNA,Duplicate,Duplicate: genetics,Gene Expression Regulation,Gene Order,Gene Order: genetics,Genes,Genetic,Genetic Linkage,Genetic Linkage: genetics,Genetic: genetics,Messenger,Messenger: genetics,Messenger: metabolism,Molecular,Molecular Sequence Data,Multigene Family,Multigene Family: genetics,nosource,Open Reading Frames,Open Reading Frames: genetics,Promoter Regions,Protozoan,Protozoan: genetics,Pseudogenes,Pseudogenes: genetics,Retroelements,Retroelements: genetics,RNA,Sequence Analysis,Tandem Repeat Sequences,Tandem Repeat Sequences: genetics,Telomere,Telomere: genetics,Trypanosoma,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: immunology,Trypanosoma: geneti,Variant Surface Glycoproteins} }

@article{garberComputationalMethodsTranscriptome2011, title = {Computational Methods for Transcriptome Annotation and Quantification Using {{RNA-seq}}.}, author = {Garber, Manuel and Grabherr, Manfred G. and Guttman, Mitchell and Trapnell, Cole}, year = 2011, month = jun, journal = {Nature methods}, volume = {8}, number = {6}, eprint = {21623353}, eprinttype = {pubmed}, pages = {469–77}, publisher = {Nature Publishing Group}, issn = {1548-7105}, doi = {10.1038/nmeth.1613}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21623353}, abstract = {High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all genes and their isoforms across samples. Realizing this promise requires increasingly complex computational methods. These computational challenges fall into three main categories: (i) read mapping, (ii) transcriptome reconstruction and (iii) expression quantification. Here we explain the major conceptual and practical challenges, and the general classes of solutions for each category. Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications.}, pmid = {21623353}, keywords = {Animals,Computational Biology,Computational Biology: methods,Gene Expression Profiling,Gene Expression Profiling: statistics & numerical,Genomics,Genomics: statistics & numerical data,High-Throughput Nucleotide Sequencing,High-Throughput Nucleotide Sequencing: statistics,Humans,nosource,RNA,RNA: statistics & numerical dat,Sequence Alignment,Sequence Alignment: statistics & numerical data,Sequence Analysis} }

@article{wangRNASeqRevolutionaryTool2009, title = {{{RNA-Seq}}: A Revolutionary Tool for Transcriptomics.}, author = {Wang, Zhong and Gerstein, Mark and Snyder, Michael}, year = 2009, month = jan, journal = {Nature Reviews Genetics}, volume = {10}, number = {1}, pages = {57–63}, issn = {1471-0064}, doi = {10.1038/nrg2484}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2949280&tool=pmcentrez&rendertype=abstract}, abstract = {RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far more precise measurement of levels of transcripts and their isoforms than other methods. This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes.}, pmid = {19015660}, keywords = {Animals,Base Sequence,Chromosome Mapping,Exons,Gene Expression Profiling,Gene Expression Profiling: methods,Genetic,Humans,Models,Molecular Sequence Data,nosource,RNA,RNA: analysis,RNA: methods,Sequence Analysis,Transcription} }

@article{mardisNextgenerationDNASequencing2008, title = {Next-Generation {{DNA}} Sequencing Methods.}, author = {Mardis, Elaine R.}, year = 2008, month = jan, journal = {Annual Review of Genomics and Human Genetics}, volume = {9}, eprint = {18576944}, eprinttype = {pubmed}, pages = {387–402}, issn = {1527-8204}, doi = {10.1146/annurev.genom.9.081307.164359}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18576944}, abstract = {Recent scientific discoveries that resulted from the application of next-generation DNA sequencing technologies highlight the striking impact of these massively parallel platforms on genetics. These new methods have expanded previously focused readouts from a variety of DNA preparation protocols to a genome-wide scale and have fine-tuned their resolution to single base precision. The sequencing of RNA also has transitioned and now includes full-length cDNA analyses, serial analysis of gene expression (SAGE)-based methods, and noncoding RNA discovery. Next-generation sequencing has also enabled novel applications such as the sequencing of ancient DNA samples, and has substantially widened the scope of metagenomic analysis of environmentally derived samples. Taken together, an astounding potential exists for these technologies to bring enormous change in genetic and biological research and to enhance our fundamental biological knowledge.}, pmid = {18576944}, keywords = {Chromatin Immunoprecipitation,Chromatin Immunoprecipitation: methods,DNA,DNA: instrumentation,DNA: methods,DNA: trends,Fossils,Gene Expression Profiling,Gene Expression Profiling: methods,Genome,Genomics,Genomics: methods,Human,Humans,nosource,RNA,Sequence Analysis,Untranslated,Untranslated: genetics} }

@article{trapnellDifferentialGeneTranscript2012, title = {Differential Gene and Transcript Expression Analysis of {{RNA-seq}} Experiments with {{TopHat}} and {{Cufflinks}}}, author = {Trapnell, Cole and Roberts, Adam and Goff, Loyal and Pertea, Geo and Kim, Daehwan and Kelley, David R. and Pimentel, Harold and Salzberg, Steven L. and Rinn, John L. and Pachter, Lior}, year = 2012, month = mar, journal = {Nature Protocols}, volume = {7}, number = {3}, pages = {562–578}, publisher = {Nature Publishing Group}, issn = {1754-2189}, doi = {10.1038/nprot.2012.016}, url = {http://www.nature.com/doifinder/10.1038/nprot.2012.016}, keywords = {nosource} }

@article{martinNextgenerationTranscriptomeAssembly2011, title = {Next-Generation Transcriptome Assembly}, author = {{}a Martin, JA Jeffrey and Wang, Zhong}, year = 2011, month = oct, journal = {Nature Reviews Genetics}, volume = {12}, number = {10}, pages = {671–82}, publisher = {Nature Publishing Group}, issn = {1471-0064}, doi = {10.1038/nrg3068}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3707877&tool=pmcentrez&rendertype=abstract http://www.ncbi.nlm.nih.gov/pubmed/21897427 http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg3068.html}, abstract = {Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalogue of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies - along with some perspectives on transcriptome assembly in the near future.}, pmid = {21897427}, keywords = {Animals,assembly,Base Sequence,Biological,Cloning,DNA,DNA: methods,DNA: trends,Gene Expression Profiling,Gene Expression Profiling: methods,Gene Expression Profiling: trends,Gene Library,Humans,Models,Molecular,Molecular Sequence Annotation,Molecular Sequence Annotation: methods,Molecular Sequence Annotation: trends,Molecular Sequence Data,next-generation,nosource,RNA,RNA: methods,RNA: trends,rnas,Sequence Analysis,transcriptome} }

@article{loughranRibosomalFrameshiftingOverlapping2011, title = {Ribosomal Frameshifting into an Overlapping Gene in the {{2B-encoding}} Region of the Cardiovirus Genome.}, author = {Loughran, Gary and Firth, Andrew E. and Atkins, John F.}, year = 2011, month = nov, journal = {Proceedings of the National Academy of Sciences}, volume = {108}, number = {46}, pages = {E1111-9}, issn = {1091-6490}, doi = {10.1073/pnas.1102932108}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3219106&tool=pmcentrez&rendertype=abstract}, abstract = {The genus Cardiovirus (family Picornaviridae) currently comprises the species Encephalomyocarditis virus (EMCV) and Theilovirus. Cardioviruses have a positive-sense, single-stranded RNA genome that encodes a large polyprotein (L-1ABCD-2ABC-3ABCD) that is cleaved to produce approximately 12 mature proteins. We report on a conserved ORF that overlaps the 2B-encoding sequence of EMCV in the +2 reading frame. The ORF is translated as a 128-129 amino acid transframe fusion (2B) with the N-terminal 11-12 amino acids of 2B, via ribosomal frameshifting at a conserved GGUUUUY motif. Mutations that knock out expression of 2B result in a small-plaque phenotype. Curiously, although theilovirus sequences lack a long ORF in the +2 frame at this genomic location, they maintain a conserved GGUUUUU motif just downstream of the 2A-2B junction, and a highly localized peak in conservation at polyprotein-frame synonymous sites suggests that theiloviruses also utilize frameshifting here, albeit into a very short +2-frame ORF. Unlike previous cases of programmed -1 frameshifting, here frameshifting is modulated by virus infection, thus suggesting a novel regulatory role for frameshifting in these viruses.}, isbn = {1102932108}, pmid = {22025686}, keywords = {5’ Untranslated Regions,Amino Acid Motifs,Amino Acid Sequence,Animals,Base Sequence,Cardiovirus,Cardiovirus: genetics,Cricetinae,Cricetulus,Encephalomyocarditis virus,Encephalomyocarditis virus: genetics,Frameshifting,Genome,Molecular Sequence Data,nosource,Nucleic Acid,Nucleic Acid Conformation,Open Reading Frames,Phylogeny,Polyproteins,Polyproteins: chemistry,Ribosomal,Ribosomes,Ribosomes: chemistry,RNA,Sequence Homology,Theilovirus,Theilovirus: genetics,Viral,Viral Proteins,Viral Proteins: genetics,Viral: metabolism} }

@article{wuStudyCCR5Analogs2012, title = {Study on {{CCR5}} Analogs and Affinity Peptides.}, author = {Wu, Yingping and Deng, Riqiang and Wu, Wenyan}, year = 2012, month = mar, journal = {Protein engineering, design & selection : PEDS}, volume = {25}, number = {3}, eprint = {22238429}, eprinttype = {pubmed}, pages = {97–105}, issn = {1741-0134}, doi = {10.1093/protein/gzr062}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22238429}, abstract = {The G protein-coupled receptor of human chemokine receptor 5 (CCR5) is a key target in the human immunodeficiency virus (HIV) infection process due to its major involvement in binding to the HIV type 1 (HIV-1) envelope glycoprotein gp120 and facilitating virus entry into the cells. The identification of naturally occurring CCR5 mutations (especially CCR5 delta-32) has allowed us to address the CCR5 molecule as a promising target to prevent or resist HIV infection in vivo. To obtain high-affinity peptides that can be used to block CCR5, CCR5 analogs with high conformational similarity are required. In this study, two recombinant proteins named CCR5 N-Linker-E2 and CCR5 mN-E1-E2 containing the fragments of the CCR5 N-terminal, the first extracellular loop or the second extracellular loop are cloned from a full-length human CCR5 cDNA. The recombinant human CCR5 analogs with self-cleavage activity of the intein Mxe or Ssp in the vector pTwinI were then produced with a high-yield expression and purification system in Escherichia coli. Experiments of extracellular epitope-activity identification (such as immunoprecipitation and indirective/competitive enzyme-linked immunosorbent assay) confirmed the close similarity between the epitope activity of the CCR5 analogs and that of the natural CCR5, suggesting the applicability of the recombinant CCR5 analogs as antagonists of the chemokine ligands. Subsequent screening of high-affinity peptides from the phage random-peptides library acquired nine polypeptides, which could be used as CCR5 peptide antagonists. The CCR5 analogs and affinity peptides elucidated in this paper provide us with a basis for further study of the mechanism of inhibition of HIV-1 infection.}, pmid = {22238429}, keywords = {Amino Acid Sequence,Binding,CCR5,CCR5: antagonists & inhibitors,CCR5: chemistry,CCR5: immunology,CCR5: isolation & purification,Chemokine CCL5,Chemokine CCL5: metabolism,Chromatography,Competitive,Complementary,Complementary: genetics,DNA,Drug Design,Enzyme-Linked Immunosorbent Assay,Epitopes,Epitopes: immunology,Escherichia coli,Genetic Vectors,High Pressure Liquid,HIV-1,HIV-1: physiology,Humans,Mass,Matrix-Assisted Laser Desorpti,Models,Molecular,Molecular Sequence Data,nosource,Peptide Fragments,Peptide Fragments: chemistry,Peptide Fragments: immunology,Peptide Fragments: isolation & purification,Peptide Fragments: pharmacology,Peptide Library,Protein Conformation,Protein Structure,Receptors,Recombinant Fusion Proteins,Recombinant Fusion Proteins: antagonists & inhibit,Recombinant Fusion Proteins: immunology,Recombinant Fusion Proteins: isolation & purificat,Spectrometry,Tertiary,Virus Attachment,Virus Attachment: drug effects} }

@article{rassiChagasDisease2010, title = {Chagas Disease.}, author = {Rassi, Anis and {Marin-Neto}, Jos{'e} Antonio}, year = 2010, month = apr, journal = {Lancet}, volume = {375}, number = {9723}, eprint = {20399979}, eprinttype = {pubmed}, pages = {1388–402}, publisher = {Elsevier Ltd}, issn = {1474-547X}, doi = {10.1016/S0140-6736(10)60061-X}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20399979}, abstract = {Chagas disease is a chronic, systemic, parasitic infection caused by the protozoan Trypanosoma cruzi, and was discovered in 1909. The disease affects about 8 million people in Latin America, of whom 30-40% either have or will develop cardiomyopathy, digestive megasyndromes, or both. In the past three decades, the control and management of Chagas disease has undergone several improvements. Large-scale vector control programmes and screening of blood donors have reduced disease incidence and prevalence. Although more effective trypanocidal drugs are needed, treatment with benznidazole (or nifurtimox) is reasonably safe and effective, and is now recommended for a widened range of patients. Improved models for risk stratification are available, and certain guided treatments could halt or reverse disease progression. By contrast, some challenges remain: Chagas disease is becoming an emerging health problem in non-endemic areas because of growing population movements; early detection and treatment of asymptomatic individuals are underused; and the potential benefits of novel therapies (eg, implantable cardioverter defibrillators) need assessment in prospective randomised trials.}, pmid = {20399979}, keywords = {Acute Disease,Chagas Cardiomyopathy,Chagas Cardiomyopathy: diagnosis,Chagas Cardiomyopathy: drug therapy,Chagas Disease,Chagas Disease: diagnosis,Chagas Disease: drug therapy,Chagas Disease: epidemiology,Chagas Disease: transmission,Chronic Disease,Humans,nosource,Trypanosoma cruzi,Trypanosoma cruzi: physiology} }

@article{burleighCellSignallingTrypanosoma2002, title = {Cell Signalling and {{Trypanosoma}} Cruzi Invasion}, author = {Burleigh, Barbara A. and Woolsey, AM Aaron M.}, year = 2002, journal = {Cellular Microbiology}, volume = {4}, pages = {701–711}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1462-5822.2002.00226.x/full}, keywords = {nosource} }

@article{vanhammeControlGeneExpression1995, title = {Control of Gene Expression in Trypanosomes.}, author = {Vanhamme, L. and Pays, E.}, year = 1995, month = jun, journal = {Microbiological Reviews}, volume = {59}, number = {2}, pages = {223–40}, issn = {0146-0749}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=239361&tool=pmcentrez&rendertype=abstract}, abstract = {Trypanosomes are protozoan agents of major parasitic diseases such as Chagas’ disease in South America and sleeping sickness of humans and nagana disease of cattle in Africa. They are transmitted to mammalian hosts by specific insect vectors. Their life cycle consists of a succession of differentiation and growth phases requiring regulated gene expression to adapt to the changing extracellular environment. Typical of such stage-specific expression is that of the major surface antigens of Trypanosoma brucei, procyclin in the procyclic (insect) form and the variant surface glycoprotein (VSG) in the bloodstream (mammalian) form. In trypanosomes, the regulation of gene expression is effected mainly at posttranscriptional levels, since primary transcription of most of the genes occurs in long polycistronic units and is constitutive. The transcripts are processed by transsplicing and polyadenylation under the influence of intergenic polypyrimidine tracts. These events show some developmental regulation. Untranslated sequences of the mRNAs seem to play a prominent role in the stage-specific control of individual gene expression, through a modulation of mRNA abundance. The VSG and procyclin transcription units exhibit particular features that are probably related to the need for a high level of expression. The promoters and RNA polymerase driving the expression of these units resemble those of the ribosomal genes. Their mutually exclusive expression is ensured by controls operating at several levels, including RNA elongation. Antigenic variation in the bloodstream is achieved through DNA rearrangements or alternative activation of the telomeric VSG gene expression sites. Recent discoveries, such as the existence of a novel nucleotide in telomeric DNA and the generation of point mutations in VSG genes, have shed new light on the mechanisms and consequences of antigenic variation.}, pmid = {7603410}, keywords = {Animals,Base Sequence,Developmental,Gene Expression Regulation,Genes,Molecular Sequence Data,nosource,Protozoan,Trypanosoma,Trypanosoma: genetics} }

@article{fraschFunctionalDiversityTranssialidase2000, title = {Functional Diversity in the Trans-Sialidase and Mucin Families in {{Trypanosoma}} Cruzi.}, author = {Frasch, a C.}, year = 2000, month = jul, journal = {Parasitology Today}, volume = {16}, number = {7}, eprint = {10858646}, eprinttype = {pubmed}, pages = {282–6}, issn = {0169-4758}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10858646}, abstract = {Trypanosomes are unable to synthesize the monosaccharide sialic acid, but some African trypanosomes and the American Trypanosoma cruzi can incorporate sialic acid derived from the host. To do so, T. cruzi expresses a trans-sialidase, an enzyme that catalyzes the transfer of sialic acid from host glycoconjugates to mucin-like molecules located on the parasite surface membrane. The importance of the process is indicated by the fact that T. cruzi has hundreds of genes encoding trans-sialidase, trans-sialidase-like proteins and mucin core proteins. Sequence divergence of members of these families has resulted in some molecules having functions unrelated to the acquisition of sialic acid. In this article, Alberto Frasch reviews the structure and possible function of the proteins making up these families.}, pmid = {10858646}, keywords = {Animals,Chagas Disease,Chagas Disease: parasitology,Humans,Mucins,Mucins: chemistry,Mucins: genetics,Mucins: metabolism,Neuraminidase,Neuraminidase: chemistry,Neuraminidase: genetics,Neuraminidase: metabolism,nosource,Trypanosoma cruzi,Trypanosoma cruzi: enzymology,Trypanosoma cruzi: genetics} }

@article{tarletonParasitePersistenceAetiology2001, title = {Parasite Persistence in the Aetiology of {{Chagas}} Disease.}, author = {Tarleton, R. L.}, year = 2001, month = may, journal = {International Journal for Parasitology}, volume = {31}, number = {5-6}, eprint = {11334941}, eprinttype = {pubmed}, pages = {550–4}, issn = {0020-7519}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11334941}, abstract = {Two primary hypotheses are proposed to account for pathogenesis in chronic Trypanosoma cruzi infections: that the persistence of T. cruzi at specific sites in the infected host results in chronic inflammatory reactivity and that T. cruzi infection induces immune responses which are targetted at self tissues. The data supporting parasite persistence as the primary cause of disease in T. cruzi infection have been recently reviewed and the reader is referred to this review for extensive documentation of most of the arguments outlined herein. This manuscript will briefly reiterate the main points of this previous review, adding additional data that have been presented since its publication. Then, philosophical and practical arguments on why Chagas disease should be investigated and treated as a parasitic infection and not as an autoimmune disease are presented. This is admittedly an ‘opinion piece’ and not a balanced review of the literature on Chagas disease. There are substantial data other than those reviewed here, which have been presented in support of the autoimmunity hypothesis. It is left to others to review that body of literature.}, pmid = {11334941}, keywords = {Animals,Autoimmunity,Autoimmunity: immunology,Chagas Disease,Chagas Disease: immunology,Chagas Disease: parasitology,Humans,nosource,Trypanosoma cruzi,Trypanosoma cruzi: immunology} }

@article{brenerBiologyTrypanosomaCruzi1973, title = {Biology of {{Trypanosoma}} Cruzi}, author = {Brener, Zigman}, year = 1973, journal = {Annual Reviews in Microbiology}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.mi.27.100173.002023}, keywords = {nosource} }

@article{colliTranssialidaseUniqueEnzyme1993, title = {Trans-Sialidase: A Unique Enzyme Activity Discovered in the Protozoan {{Trypanosoma}} Cruzi}, author = {Colli, Walter}, year = 1993, journal = {The FASEB journal}, number = {4}, pages = {1257–1264}, url = {http://www.fasebj.org/content/7/13/1257.short}, keywords = {nosource} }

@article{danielsCellBiologyTrypanosome2010, title = {Cell Biology of the Trypanosome Genome.}, author = {Daniels, JP Jan-Peter and Gull, Keith and Wickstead, Bill}, year = 2010, month = dec, journal = {Microbiology and Molecular Biology Reviews}, volume = {74}, number = {4}, pages = {552–69}, issn = {1098-5557}, doi = {10.1128/MMBR.00024-10}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3008170&tool=pmcentrez&rendertype=abstract http://mmbr.asm.org/content/74/4/552.short}, abstract = {Trypanosomes are a group of protozoan eukaryotes, many of which are major parasites of humans and livestock. The genomes of trypanosomes and their modes of gene expression differ in several important aspects from those of other eukaryotic model organisms. Protein-coding genes are organized in large directional gene clusters on a genome-wide scale, and their polycistronic transcription is not generally regulated at initiation. Transcripts from these polycistrons are processed by global trans-splicing of pre-mRNA. Furthermore, in African trypanosomes, some protein-coding genes are transcribed by a multifunctional RNA polymerase I from a specialized extranucleolar compartment. The primary DNA sequence of the trypanosome genomes and their cellular organization have usually been treated as separate entities. However, it is becoming increasingly clear that in order to understand how a genome functions in a living cell, we will need to unravel how the one-dimensional genomic sequence and its trans-acting factors are arranged in the three-dimensional space of the eukaryotic nucleus. Understanding this cell biology of the genome will be crucial if we are to elucidate the genetic control mechanisms of parasitism. Here, we integrate the concepts of nuclear architecture, deduced largely from studies of yeast and mammalian nuclei, with recent developments in our knowledge of the trypanosome genome, gene expression, and nuclear organization. We also compare this nuclear organization to those in other systems in order to shed light on the evolution of nuclear architecture in eukaryotes.}, pmid = {21119017}, keywords = {Cell Biology,Cell Nucleus,Cell Nucleus: genetics,Cell Nucleus: metabolism,Chromatin,Chromatin: genetics,Evolution,Gene Expression Regulation,Genome,Humans,Molecular,nosource,Nuclear Matrix,Protozoan,Trypanosoma,Trypanosoma: genetics} }

@article{noiaTrypanosomaCruziSurface2006, title = {Trypanosoma Cruzi Surface Mucins: Host-Dependent Coat Diversity.}, author = {Noia, Javier M. Di and {}a Buscaglia, Carlos and {}a Campo, Vanina and Frasch, Alberto C. C. and Noia, Javier M. Di}, year = 2006, month = mar, journal = {Nature Reviews Microbiology}, volume = {4}, number = {3}, eprint = {16489349}, eprinttype = {pubmed}, pages = {229–36}, issn = {1740-1526}, doi = {10.1038/nrmicro1351}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16489349}, abstract = {The surface of the protozoan parasite Trypanosoma cruzi is covered in mucins, which contribute to parasite protection and to the establishment of a persistent infection. Their importance is highlighted by the fact that the approximately 850 mucin-encoding genes comprise approximately 1% of the parasite genome and approximately 6% of all predicted T. cruzi genes. The coordinate expression of a large repertoire of mucins containing variable regions in the mammal-dwelling stages of the T. cruzi life cycle suggests a possible strategy to thwart the host immune response. Here, we discuss the expression profiling of T. cruzi mucins, the mechanisms leading to the acquisition of mucin diversity and the possible consequences of a mosaic surface coat in the interplay between parasite and host.}, pmid = {16489349}, keywords = {Animals,Chagas Disease,Chagas Disease: parasitology,Evolution,Genes,Host-Parasite Interactions,Humans,Molecular,Mucins,Mucins: chemistry,Mucins: genetics,Mucins: physiology,nosource,Protozoan,Protozoan Proteins,Protozoan Proteins: chemistry,Protozoan Proteins: genetics,Protozoan Proteins: physiology,Protozoan: genetics,Trypanosoma cruzi,Trypanosoma cruzi: chemistry,Trypanosoma cruzi: pathogenicity,Trypanosoma cruzi: physiology,Virulence} }

@article{claytonLifeTranscriptionalControl2002, title = {Life without Transcriptional Control? {{From}} Fly to Man and Back Again}, author = {Clayton, CE Christine E.}, year = 2002, journal = {The EMBO Journal}, volume = {21}, number = {8}, pages = {1881–1888}, url = {http://onlinelibrary.wiley.com/doi/10.1093/emboj/21.8.1881/full}, keywords = {leishmania,nosource,rna degradation,transcription} }

@article{ulluRNAInterferenceProtozoan2004, title = {{{RNA}} Interference in Protozoan Parasites}, author = {Ullu, Elisabetta and Tschudi, Christian and Chakraborty, Tirtha}, year = 2004, month = jun, journal = {Cellular microbiology}, volume = {6}, number = {6}, eprint = {15104593}, eprinttype = {pubmed}, pages = {509–519}, issn = {1462-5814}, doi = {10.1111/j.1462-5822.2004.00399.x}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15104593 http://onlinelibrary.wiley.com/doi/10.1111/j.1462-5822.2004.00399.x/full}, abstract = {RNA interference or RNAi is defined as the mechanism through which gene-specific, double-stranded RNA (dsRNA) triggers degradation of homologous transcripts. Besides providing an invaluable tool to downregulate gene expression in a variety of organisms, it is now evident that RNAi extends its tentacles into both the nucleus and the cytoplasm and is involved in a variety of gene silencing phenomena. Here we review the current status of RNAi in protozoan parasites that cause diseases of considerable medical and veterinary importance throughout Africa, Asia and the Americas. RNAi was first discovered in Trypanosoma brucei, a species of the family Trypanosomatidae, and it rapidly became the method of choice to downregulate gene expression in these organisms. At the same time, mechanistic studies exposed a role for RNAi in the control of retroposon transcript abundance. Whereas RNAi is also present in T. congolense, other members of the same family of organisms, namely T. cruzi and Leishmania major, are RNAi-negative. In apicomplexan parasites, there is experimental evidence for RNAi in Plasmodium, but this is not supported by their genetic make up. In contrast, the genome of Toxoplasma gondii harbours gene candidates with convincing similarity to ‘classical’ RNAi genes. Thus, as previously shown in fungi, protozoan parasites are genetically heterogeneous as far as the RNAi pathway is concerned. Finally, database mining predicts that Entamoeba histolytica and Giardia intestinalis have an RNAi pathway and the presence of RNAi genes in Giardia supports the view that gene silencing by dsRNA appeared very early during evolution of the eukaryotic lineage.}, pmid = {15104593}, keywords = {Animals,Entamoeba histolytica,Entamoeba histolytica: genetics,Eukaryota,Eukaryota: genetics,Eukaryota: metabolism,Gene Expression Regulation,Giardia lamblia,Giardia lamblia: genetics,Leishmania major,Leishmania major: genetics,Leishmania major: metabolism,nosource,Plasmodium,Plasmodium: genetics,Plasmodium: metabolism,RNA Interference,Toxoplasma,Toxoplasma: genetics,Toxoplasma: metabolism,Trypanosoma brucei brucei,Trypanosoma brucei brucei: genetics,Trypanosoma brucei brucei: metabolism,Trypanosoma cruzi,Trypanosoma cruzi: genetics,Trypanosoma cruzi: metabolism} }

@article{berrizNextGenerationSoftware2009, title = {Next Generation Software for Functional Trend Analysis.}, author = {Berriz, Gabriel F. and Beaver, John E. and Cenik, Can and Tasan, Murat and Roth, Frederick P.}, year = 2009, month = nov, journal = {Bioinformatics}, volume = {25}, number = {22}, pages = {3043–4}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp498}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2800365&tool=pmcentrez&rendertype=abstract}, abstract = {FuncAssociate is a web application that discovers properties enriched in lists of genes or proteins that emerge from large-scale experimentation. Here we describe an updated application with a new interface and several new features. For example, enrichment analysis can now be performed within multiple gene- and protein-naming systems. This feature avoids potentially serious translation artifacts to which other enrichment analysis strategies are subject. AVAILABILITY: The FuncAssociate web application is freely available to all users at http://llama.med.harvard.edu/funcassociate.}, isbn = {0000011541}, pmid = {19717575}, keywords = {Computational Biology,Computational Biology: methods,Databases,Factual,nosource,Proteins,Proteins: chemistry,Software,User-Computer Interface} }

@article{spencerSilentSubstitutionsPredictably2012, title = {Silent Substitutions Predictably Alter Translation Elongation Rates and Protein Folding Efficiencies}, author = {Spencer, Paige S. and Siller, Efra{'i}n and Anderson, John F. and Barral, Jos{'e} M.}, year = 2012, month = jun, journal = {Journal of Molecular Biology}, publisher = {Elsevier B.V.}, issn = {00222836}, doi = {10.1016/j.jmb.2012.06.010}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283612004834}, keywords = {nosource,protein folding,protein synthesis,sequence engineering,synonymous substitutions,tRNA} }

@article{mirzabekovEnhancedExpressionNative1999, title = {Enhanced Expression, Native Purification, and Characterization of {{CCR5}}, a Principal {{HIV-1}} Coreceptor.}, author = {Mirzabekov, T. and Bannert, N. and Farzan, M. and Hofmann, W. and Kolchinsky, P. and Wu, L. and Wyatt, R. and Sodroski, J.}, year = 1999, month = oct, journal = {The Journal of biological chemistry}, volume = {274}, number = {40}, eprint = {10497246}, eprinttype = {pubmed}, pages = {28745–50}, issn = {0021-9258}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10497246}, abstract = {Seven-transmembrane segment, G protein-coupled receptors (GPCRs) play important roles in many biological processes in which pharmaceutical intervention may be useful. High level expression and native purification of GPCRs are important steps in the biochemical and structural characterization of these molecules. Here, we describe enhanced mammalian cell expression and purification of a codon-optimized variant of the chemokine receptor CCR5, a GPCR that plays a central role in the entry of the human immunodeficiency virus-1 (HIV-1) into immune cells. CCR5 could be solubilized in its native state as determined by its ability to be precipitated by 2D7, a conformation-dependent anti-CCR5 antibody, and by the HIV-1 gp120 envelope glycoprotein. The 2D7 antibody recognized immature and mature forms of CCR5 equally, whereas gp120 preferentially recognized the mature form, a result that underscores a role for posttranslational modification of CCR5 in its HIV-1 coreceptor function. The methods described herein contribute to the analysis of CCR5 and are likely to be applicable to many other GPCRs.}, isbn = {6176323371}, pmid = {10497246}, keywords = {Amino Acid Sequence,Animals,Base Sequence,CCR5,CCR5: genetics,CCR5: isolation & purification,CCR5: metabolism,Cell Line,Cloning,DNA Primers,Electrophoresis,HIV Envelope Protein gp120,HIV Envelope Protein gp120: metabolism,Humans,Molecular,nosource,Polyacrylamide Gel,Protein Binding,Receptors} }

@article{langmeadFastGappedreadAlignment2012, title = {Fast Gapped-Read Alignment with {{Bowtie}} 2}, author = {Langmead, Ben and Salzberg, Steven L.}, year = 2012, month = mar, journal = {Nature Methods}, volume = {9}, number = {4}, pages = {357–360}, issn = {1548-7091}, doi = {10.1038/nmeth.1923}, url = {http://www.nature.com/doifinder/10.1038/nmeth.1923}, keywords = {nosource} }

@article{langmeadAligningShortSequencing2010, title = {Aligning Short Sequencing Reads with {{Bowtie}}}, author = {Langmead, B.}, year = 2010, journal = {Current protocols in bioinformatics}, pages = {1–24}, doi = {10.1002/0471250953.bi1107s32.Aligning}, url = {http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1107s32/full?globalMessage=0 http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1107s32/full}, isbn = {0471250953}, keywords = {alignment,comparative,genome indexing,genomics,mapping,nosource,read alignment,read mapping,short reads,software package} }

@article{fujitaUCSCGenomeBrowser2011, title = {The {{UCSC}} Genome Browser Database: Update 2011}, author = {Fujita, P. A. and Rhead, B. and Zweig, A. S.}, year = 2011, month = jan, journal = {Nucleic acids }, volume = {31}, number = {1}, pages = {51–54}, issn = {13624962}, doi = {10.1093/nar/gkg129}, url = {http://www.nar.oupjournals.org/cgi/doi/10.1093/nar/gkg129 http://nar.oxfordjournals.org/content/39/suppl_1/D876.short}, keywords = {nosource} }

@article{templeCompletionMammalianGene2009, title = {The Completion of the {{Mammalian Gene Collection}} ({{MGC}}).}, author = {Temple, Gary and Gerhard, Daniela S. DS and Rasooly, Rebekah and {}a Feingold, Elise and Good, Peter J. and Robinson, Cristen and Mandich, Allison and Derge, Jeffrey G. and Lewis, Jeanne and Shoaf, Debonny and Collins, Francis S. and Jang, Wonhee and Wagner, Lukas and Shenmen, Carolyn M. and Misquitta, Leonie and Schaefer, Carl F. and Buetow, Kenneth H. and Bonner, Tom I. and Yankie, Linda and Ward, Ming and Phan, Lon and Astashyn, Alex and Brown, Garth and Farrell, Catherine and Hart, Jennifer and Landrum, Melissa and Maidak, Bonnie L. and Murphy, Michael and Murphy, Terence and Rajput, Bhanu and Riddick, Lillian and Webb, David and Weber, Janet and Wu, Wendy and Pruitt, Kim D. and Maglott, Donna and Siepel, Adam and Brejova, Brona and Diekhans, Mark and Harte, Rachel and Baertsch, Robert and Kent, Jim and Haussler, David and Brent, Michael and Langton, Laura and Comstock, Charles L. G. and Stevens, Michael and Wei, Chaochun and {}van Baren, Marijke J. and {Salehi-Ashtiani}, Kourosh and Murray, Ryan R. and Ghamsari, Lila and Mello, Elizabeth and Lin, Chenwei and Pennacchio, Christa and Schreiber, Kirsten and Shapiro, Nicole and Marsh, Amber and Pardes, Elizabeth and Moore, Troy and Lebeau, Anita and Muratet, Mike and Simmons, Blake and Kloske, David and Sieja, Stephanie and Hudson, James and Sethupathy, Praveen and Brownstein, Michael and Bhat, Narayan and Lazar, Joseph and Jacob, Howard and Gruber, Chris E. and Smith, Mark R. and McPherson, John and Garcia, Angela M. and Gunaratne, Preethi H. and Wu, Jiaqian and Muzny, Donna and {}a Gibbs, Richard and Young, Alice C. and Bouffard, Gerard G. and Blakesley, Robert W. and Mullikin, Jim and Green, Eric D. and Dickson, Mark C. and Rodriguez, Alex C. and Grimwood, Jane and Schmutz, Jeremy and Myers, Richard M. and Hirst, Martin and Zeng, Thomas and Tse, Kane and Moksa, Michelle and Deng, Merinda and Ma, Kevin and Mah, Diana and Pang, Johnson and Taylor, Greg and Chuah, Eric and Deng, Athena and Fichter, Keith and Go, Anne and Lee, Stephanie and Wang, Jing and Griffith, Malachi and Morin, Ryan and {}a Moore, Richard and Mayo, Michael and Munro, Sarah and Wagner, Susan and Jones, Steven J. M. and {}a Holt, Robert and {}a Marra, Marco and Lu, Sun and Yang, Shuwei and Hartigan, James and Graf, Marcus and Wagner, Ralf and Letovksy, Stanley and Pulido, Jacqueline C. and Robison, Keith and Esposito, Dominic and Hartley, James and Wall, Vanessa E. and Hopkins, Ralph F. and Ohara, Osamu and Wiemann, Stefan}, year = 2009, month = dec, journal = {Genome research}, volume = {19}, number = {12}, pages = {2324–2333}, issn = {1549-5469}, doi = {10.1101/gr.095976.109}, url = {http://www.wsjsw.gov.cn:8089/gate/big5/genome.cshlp.org/content/19/12/2324.full http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2792178&tool=pmcentrez&rendertype=abstract}, abstract = {Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide.}, pmid = {19767417}, keywords = {Animals,Cloning,Complementary,Complementary: genetics,Computational Biology,Computational Biology: methods,DNA,DNA: biosynthesis,Gene Library,Genes,Genes: genetics,Humans,Mammals,Mammals: genetics,Mice,Molecular,Molecular: methods,National Institutes of Health (U.S.),nosource,Rats,Reverse Transcriptase Polymerase Chain Reaction,United States} }

@article{barrettNCBIGEOArchive2009, title = {{{NCBI GEO}}: Archive for High-Throughput Functional Genomic Data.}, author = {Barrett, Tanya and Troup, Dennis B. and Wilhite, Stephen E. and Ledoux, Pierre and Rudnev, Dmitry and Evangelista, Carlos and Kim, Irene F. and Soboleva, Alexandra and Tomashevsky, Maxim and {}a Marshall, Kimberly and Phillippy, Katherine H. and Sherman, Patti M. and Muertter, Rolf N. and Edgar, Ron}, year = 2009, month = jan, journal = {Nucleic acids research}, volume = {37}, number = {Database issue}, pages = {D885-90}, issn = {1362-4962}, doi = {10.1093/nar/gkn764}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2686538&tool=pmcentrez&rendertype=abstract}, abstract = {The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest public repository for high-throughput gene expression data. Additionally, GEO hosts other categories of high-throughput functional genomic data, including those that examine genome copy number variations, chromatin structure, methylation status and transcription factor binding. These data are generated by the research community using high-throughput technologies like microarrays and, more recently, next-generation sequencing. The database has a flexible infrastructure that can capture fully annotated raw and processed data, enabling compliance with major community-derived scientific reporting standards such as ‘Minimum Information About a Microarray Experiment’ (MIAME). In addition to serving as a centralized data storage hub, GEO offers many tools and features that allow users to effectively explore, analyze and download expression data from both gene-centric and experiment-centric perspectives. This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.}, pmid = {18940857}, keywords = {Computer Graphics,Databases,Gene Expression Profiling,Genetic,Genomics,nosource,Oligonucleotide Array Sequence Analysis,Software} }

@article{hsiehTranslationalLandscapeMTOR2012, title = {The Translational Landscape of {{mTOR}} Signalling Steers Cancer Initiation and Metastasis.}, author = {Hsieh, Andrew C. and Liu, Yi and Edlind, Merritt P. and Ingolia, Nicholas T. and Janes, Matthew R. and Sher, Annie and Shi, Evan Y. and Stumpf, Craig R. and Christensen, Carly and Bonham, Michael J. and Wang, Shunyou and Ren, Pingda and Martin, Michael and Jessen, Katti and Feldman, Morris E. and Weissman, Jonathan S. and Shokat, Kevan M. and Rommel, Christian and Ruggero, Davide}, year = 2012, month = feb, journal = {Nature}, volume = {485}, number = {7396}, eprint = {22367541}, eprinttype = {pubmed}, pages = {55–61}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature10912}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22367541}, abstract = {The mammalian target of rapamycin (mTOR) kinase is a master regulator of protein synthesis that couples nutrient sensing to cell growth and cancer. However, the downstream translationally regulated nodes of gene expression that may direct cancer development are poorly characterized. Using ribosome profiling, we uncover specialized translation of the prostate cancer genome by oncogenic mTOR signalling, revealing a remarkably specific repertoire of genes involved in cell proliferation, metabolism and invasion. We extend these findings by functionally characterizing a class of translationally controlled pro-invasion messenger RNAs that we show direct prostate cancer invasion and metastasis downstream of oncogenic mTOR signalling. Furthermore, we develop a clinically relevant ATP site inhibitor of mTOR, INK128, which reprograms this gene expression signature with therapeutic benefit for prostate cancer metastasis, for which there is presently no cure. Together, these findings extend our understanding of how the ‘cancerous’ translation machinery steers specific cancer cell behaviours, including metastasis, and may be therapeutically targeted.}, pmid = {22367541}, keywords = {nosource} }

@article{guindonNewAlgorithmsMethods2010, title = {New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of {{PhyML}} 3.0.}, author = {Guindon, St{'e}phane and Dufayard, Jean-Fran{}ois and Lefort, Vincent and Anisimova, Maria and Hordijk, Wim and Gascuel, Olivier and Uindon, Phane G. and Ranc, J. E. A. N.}, year = 2010, month = may, journal = {Systematic biology}, volume = {59}, number = {3}, eprint = {20525638}, eprinttype = {pubmed}, pages = {307–21}, issn = {1076-836X}, doi = {10.1093/sysbio/syq010}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20525638}, abstract = {PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used ({\(>\)}2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.}, pmid = {20525638}, keywords = {Algorithms,Classification,Classification: methods,Likelihood Functions,nosource,Phylogeny,Software} }

@article{gascuelBIONJImprovedVersion1997, title = {{{BIONJ}}: An Improved Version of the {{NJ}} Algorithm Based on a Simple Model of Sequence Data.}, author = {Gascuel, O.}, year = 1997, month = jul, journal = {Molecular biology and evolution}, volume = {14}, number = {7}, eprint = {9254330}, eprinttype = {pubmed}, pages = {685–95}, issn = {0737-4038}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9254330}, abstract = {We propose an improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei. This new algorithm, BIONJ, follows the same agglomerative scheme as NJ, which consists of iteratively picking a pair of taxa, creating a new mode which represents the cluster of these taxa, and reducing the distance matrix by replacing both taxa by this node. Moreover, BIONJ uses a simple first-order model of the variances and covariances of evolutionary distance estimates. This model is well adapted when these estimates are obtained from aligned sequences. At each step it permits the selection, from the class of admissible reductions, of the reduction which minimizes the variance of the new distance matrix. In this way, we obtain better estimates to choose the pair of taxa to be agglomerated during the next steps. Moreover, in comparison with NJ’s estimates, these estimates become better and better as the algorithm proceeds. BIONJ retains the good properties of NJ–especially its low run time. Computer simulations have been performed with 12-taxon model trees to determine BIONJ’s efficiency. When the substitution rates are low (maximum pairwise divergence approximately 0.1 substitutions per site) or when they are constant among lineages, BIONJ is only slightly better than NJ. When the substitution rates are higher and vary among lineages,BIONJ clearly has better topological accuracy. In the latter case, for the model trees and the conditions of evolution tested, the topological error reduction is on the average around 20%. With highly-varying-rate trees and with high substitution rates (maximum pairwise divergence approximately 1.0 substitutions per site), the error reduction may even rise above 50%, while the probability of finding the correct tree may be augmented by as much as 15%.}, pmid = {9254330}, keywords = {Algorithms,Biological,Biological Evolution,Models,nosource,Phylogeny,Sequence Analysis,Sequence Analysis: methods,Software} }

@article{gouySeaViewVersion42010, title = {{{SeaView}} Version 4: {{A}} Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building.}, author = {Gouy, Manolo and Guindon, St{'e}phane and Gascuel, Olivier and Lyon, De}, year = 2010, month = feb, journal = {Molecular biology and evolution}, volume = {27}, number = {2}, pages = {221–4}, issn = {1537-1719}, doi = {10.1093/molbev/msp259}, url = {http://mbe.oxfordjournals.org/content/27/2/221.short http://www.ncbi.nlm.nih.gov/pubmed/19854763}, abstract = {We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees. In relation to the wide present offer of tools and algorithms for phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available at http://pbil.univ-lyon1.fr/software/seaview.}, pmid = {19854763}, keywords = {are key tasks for,Computer Graphics,from molecular sequence data,graphical user interface,lecular evolution analyses,many mo-,molecular phylogeny,multiple alignment and phylogenetic,multiple sequence alignment,nosource,Phylogeny,phyml,seaview,Sequence Alignment,Sequence Alignment: methods,Software,they involve the sequential,tree reconstruction,use,User-Computer Interface} }

@article{zhangSequenceEvolutionCCR51999, title = {Sequence Evolution of the {{CCR5}} Chemokine Receptor Gene in Primates.}, author = {Zhang, Y. W. and {}a Ryder, O. and Zhang, Y. P.}, year = 1999, month = sep, journal = {Molecular Biology and Evolution}, volume = {16}, number = {9}, eprint = {10486970}, eprinttype = {pubmed}, pages = {1145–54}, issn = {0737-4038}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10486970}, abstract = {The chemokine receptor CCR5 can serve as a coreceptor for M-tropic HIV-1 infection and both M-tropic and T-tropic SIV infection. We sequenced the entire CCR5 gene from 10 nonhuman primates: Pongo pygmaeus, Hylobates leucogenys, Trachypithecus francoisi, Trachypithecus phayrei, Pygathrix nemaeus, Rhinopithecus roxellanae, Rhinopithecus bieti, Rhinopithecus avunculus, Macaca assamensis, and Macaca arctoides. When compared with CCR5 sequences from humans and other primates, our results demonstrate that: (1) nucleotide and amino acid sequences of CCR5 among primates are highly homologous, with variations slightly concentrated on the amino and carboxyl termini; and (2) site Asp13, which is critical for CD4-independent binding of SIV gp120 to Macaca mulatta CCR5, was also present in all other nonhuman primates tested here, suggesting that those nonhuman primate CCR5s might also bind SIV gp120 without the presence of CD4. The topologies of CCR5 gene trees constructed here conflict with the putative opinion that the snub-nosed langurs compose a monophyletic group, suggesting that the CCR5 gene may not be a good genetic marker for low-level phylogenetic analysis. The evolutionary rate of CCR5 was calculated, and our results suggest a slowdown in primates after they diverged from rodents. The synonymous mutation rate of CCR5 in primates is constant, about 1.1 x 10(-9) synonymous mutations per site per year. Comparisons of Ka and Ks suggest that the CCR5 genes have undergone negative or purifying selection. Ka/Ks ratios from cercopithecines and colobines are significantly different, implying that selective pressures have played different roles in the two lineages.}, pmid = {10486970}, keywords = {Animals,Base Sequence,CCR5,CCR5: genetics,DNA,DNA Primers,DNA Primers: genetics,DNA: genetics,Evolution,HIV-1,HIV-1: pathogenicity,Humans,Molecular,Mutation,nosource,Nucleic Acid,Phylogeny,Primates,Primates: genetics,Receptors,Sequence Homology,Simian immunodeficiency virus,Simian immunodeficiency virus: pathogenicity,Species Specificity,Time Factors} }

@article{rocca-serraSharingArchivingNucleic2011, title = {Sharing and Archiving Nucleic Acid Structure Mapping Data.}, author = {{Rocca-serra}, Philippe and Bellaousov, Stanislav and Birmingham, Amanda and Chen, Chunxia and Cordero, Pablo and Das, Rhiju and {Davis-neulander}, Lauren and Duncan, Caia D. S. and Halvorsen, Matthew and Knight, Rob O. B. and Leontis, Neocles B. and Mathews, David H. and Ritz, Justin and Stombaugh, Jesse and Weeks, Kevin M. and Zirbel, Craig L. and Laederach, Alain}, year = 2011, month = jul, journal = {RNA}, volume = {17}, number = {7}, pages = {1204–12}, issn = {1469-9001}, doi = {10.1261/rna.2753211}, url = {http://rnajournal.cshlp.org/content/17/7/1204.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3138558&tool=pmcentrez&rendertype=abstract}, abstract = {Nucleic acids are particularly amenable to structural characterization using chemical and enzymatic probes. Each individual structure mapping experiment reveals specific information about the structure and/or dynamics of the nucleic acid. Currently, there is no simple approach for making these data publically available in a standardized format. We therefore developed a standard for reporting the results of single nucleotide resolution nucleic acid structure mapping experiments, or SNRNASMs. We propose a schema for sharing nucleic acid chemical probing data that uses generic public servers for storing, retrieving, and searching the data. We have also developed a consistent nomenclature (ontology) within the Ontology of Biomedical Investigations (OBI), which provides unique identifiers (termed persistent URLs, or PURLs) for classifying the data. Links to standardized data sets shared using our proposed format along with a tutorial and links to templates can be found at http://snrnasm.bio.unc.edu.}, pmid = {21610212}, keywords = {Algorithms,Archives,Base Sequence,Chromosome Mapping,Chromosome Mapping: classification,Chromosome Mapping: methods,Databases,Humans,Information Dissemination,Molecular Sequence Data,nosource,Nucleic Acid,Nucleic Acid Conformation,Nucleic Acids,Nucleic Acids: analysis,Nucleic Acids: chemistry,Research Design,RNA,RNA: analysis,RNA: chemistry,Validation Studies as Topic} }

@article{mcginnisMechanismsRNASHAPE2012, title = {The Mechanisms of {{RNA SHAPE}} Chemistry.}, author = {McGinnis, Jennifer L. and {}a Dunkle, Jack and Cate, Jamie H. D. and Weeks, Kevin M.}, year = 2012, month = apr, journal = {Journal of the American Chemical Society}, volume = {134}, number = {15}, eprint = {22475022}, eprinttype = {pubmed}, pages = {6617–24}, issn = {1520-5126}, doi = {10.1021/ja2104075}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22475022}, abstract = {The biological functions of RNA are ultimately governed by the local environment at each nucleotide. Selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry is a powerful approach for measuring nucleotide structure and dynamics in diverse biological environments. SHAPE reagents acylate the 2’-hydroxyl group at flexible nucleotides because unconstrained nucleotides preferentially sample rare conformations that enhance the nucleophilicity of the 2’-hydroxyl. The critical corollary is that some constrained nucleotides must be poised for efficient reaction at the 2’-hydroxyl group. To identify such nucleotides, we performed SHAPE on intact crystals of the Escherichia coli ribosome, monitored the reactivity of 1490 nucleotides in 16S rRNA, and examined those nucleotides that were hyper-reactive toward SHAPE and had well-defined crystallographic conformations. Analysis of these conformations revealed that 2’-hydroxyl reactivity is broadly facilitated by general base catalysis involving multiple RNA functional groups and by two specific orientations of the bridging 3’-phosphate group. Nucleotide analog studies confirmed the contributions of these mechanisms to SHAPE reactivity. These results provide a strong mechanistic explanation for the relationship between SHAPE reactivity and local RNA dynamics and will facilitate interpretation of SHAPE information in the many technologies that make use of this chemistry.}, pmid = {22475022}, keywords = {nosource} }

@article{michelObservationDuallyDecoded2012, title = {Observation of Dually Decoded Regions of the Human Genome Using Ribosome Profiling Data.}, author = {Michel, Audrey M. and Choudhury, Kingshuk Roy and Firth, Andrew E. and Ingolia, Nicholas T. and Atkins, John F. and Baranov, Pavel V.}, year = 2012, month = may, journal = {Genome research}, eprint = {22593554}, eprinttype = {pubmed}, issn = {1549-5469}, doi = {10.1101/gr.133249.111}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22593554}, abstract = {The recently developed ribosome profiling technique (Ribo-Seq) allows mapping of the locations of translating ribosomes on mRNAs with sub-codon precision. When ribosome protected fragments (RPFs) are aligned to mRNA, a characteristic triplet periodicity pattern is revealed. We utilized the triplet periodicity of RPFs to develop a computational method for detecting transitions between reading frames that occur during programmed ribosomal frameshifting or in dual coding regions where the same nucleotide sequence codes for multiple proteins in different reading frames. Application of this method to ribosome profiling data obtained for human cells allowed us to detect several human genes where the same genomic segment is translated in more than one reading frame (from different transcripts as well as from the same mRNA) and revealed the translation of hitherto unpredicted coding open reading frames.}, pmid = {22593554}, keywords = {nosource} }

@article{huMAGI2InhibitsCell2007, title = {{{MAGI-2 Inhibits}} Cell Migration and Proliferation via {{PTEN}} in Human Hepatocarcinoma Cells.}, author = {Hu, Yali and Li, Zengxia and Guo, Liang and Wang, Liying and Zhang, Lineng and Cai, Xiumei and Zhao, Hongbo and Zha, Xiliang}, year = 2007, month = nov, journal = {Archives of biochemistry and biophysics}, volume = {467}, number = {1}, eprint = {17880912}, eprinttype = {pubmed}, pages = {1–9}, issn = {1096-0384}, doi = {10.1016/j.abb.2007.07.027}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17880912}, abstract = {MAGI-2, a multidomain scaffolding protein, contains nine potential protein-protein interaction modules, including a GuK domain, two WW domains and six PDZ domains. In this study, we examined eight human hepatocarcinoma cell lines (HHCCs) and found that MAGI-2 was expressed only in 7721 cells. After 7721, 7404 and 97H cells were transfected with myc-MAGI-2 plasmid, their migration and proliferation was significantly inhibited, which was associated with downregulation of p-FAK and p-Akt. It is known that p-FAK is a substrate of PTEN and p-Akt can be regulated by PTEN via PIP(3). We demonstrated that PTEN was upregulated after myc-MAGI-2 transfection, which was due to the enhancement of PTEN protein stability rather than mRNA levels. Furthermore, MAGI-2-induced inhibition of cell migration and proliferation was attenuated in 7721 cells with PTEN silence or in PTEN-null cell line U87MG, and PTEN transfection could restore the effect of MAGI-2 in U87MG cells. Finally, the molecular association between PTEN and MAGI-2 was confirmed. Our results suggested that PTEN played a critical role in MAGI-2-induced inhibition of cell migration and proliferation in HHCCs.}, pmid = {17880912}, keywords = {Biological,Carcinoma,Carrier Proteins,Cell Movement,Cell Proliferation,Cyclin-Dependent Kinase Inhibitor p27,Cyclin-Dependent Kinase Inhibitor p27: metabolism,Gene Expression Regulation,Hepatocellular,Hepatocellular: metabolism,Humans,Liver Neoplasms,Liver Neoplasms: metabolism,Messenger,Messenger: metabolism,Models,Neoplastic,nosource,Phosphorylation,Plasmids,Plasmids: metabolism,Protein Structure,Proteins,Proteins: metabolism,Proteins: physiology,PTEN Phosphohydrolase,PTEN Phosphohydrolase: metabolism,RNA,Tertiary,Transfection} }

@article{gomaaHepatocellularCarcinomaEpidemiology2008, title = {Hepatocellular Carcinoma: {{Epidemiology}}, Risk Factors and Pathogenesis}, author = {Gomaa, Asmaa-Ibrahim}, year = 2008, journal = {World Journal of Gastroenterology}, volume = {14}, number = {27}, pages = {4300}, issn = {1007-9327}, doi = {10.3748/wjg.14.4300}, url = {http://www.wjgnet.com/1007-9327/14/4300.asp}, keywords = {100-2647 willow street,aetiology,department of medicine,epidemiology,eric m yoshida,hepatocellular carcinoma,md,nosource,pathogenesis,peer reviewer,risk factors,university of british columbia} }

@article{brandaSignalTransductionCascades2006, title = {Signal Transduction Cascades and Hepatitis {{B}} and {{C}} Related Hepatocellular Carcinoma.}, author = {Branda, Mark and Wands, JR Jack R.}, year = 2006, month = may, journal = {Hepatology}, volume = {43}, number = {5}, pages = {891–902}, issn = {0270-9139}, doi = {10.1002/hep.21196}, url = {http://onlinelibrary.wiley.com/doi/10.1002/hep.21196/full http://www.ncbi.nlm.nih.gov/pubmed/16628664}, pmid = {16628664}, keywords = {beta Catenin,beta Catenin: physiology,Carcinoma,Chronic,Chronic: complications,Chronic: metabolism,Frizzled Receptors,Frizzled Receptors: physiology,Hepatitis B,Hepatitis C,Hepatitis C Antigens,Hepatitis C Antigens: physiology,Hepatocellular,Hepatocellular: etiology,Humans,Liver Neoplasms,Liver Neoplasms: etiology,nosource,Signal Transduction,Signal Transduction: physiology,Trans-Activators,Trans-Activators: physiology,Wnt Proteins,Wnt Proteins: physiology} }

@article{el-seragHepatocellularCarcinomaEpidemiology2007, title = {Hepatocellular Carcinoma: Epidemiology and Molecular Carcinogenesis}, author = {{El–Serag}, H. B. and Rudolph, KL Lenhard and {El-Serag}, Hashem B.}, year = 2007, month = jun, journal = {Gastroenterology}, volume = {132}, number = {Figure 1}, eprint = {17570226}, eprinttype = {pubmed}, pages = {2557–2576}, issn = {0016-5085}, doi = {10.1053/j.gastro.2007.04.061}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17570226 http://www.sciencedirect.com/science/article/pii/S0016508507007998}, abstract = {Primary liver cancer, which consists predominantly of hepatocellular carcinoma (HCC), is the fifth most common cancer worldwide and the third most common cause of cancer mortality. HCC has several interesting epidemiologic features including dynamic temporal trends; marked variations among geographic regions, racial and ethnic groups, and between men and women; and the presence of several well-documented environmental potentially preventable risk factors. Moreover, there is a growing understanding on the molecular mechanisms inducing hepatocarcinogenesis, which almost never occurs in healthy liver, but the cancer risk increases sharply in response to chronic liver injury at the cirrhosis stage. A detailed understanding of epidemiologic factors and molecular mechanisms associated with HCC ultimately could improve our current concepts for screening and treatment of this disease.}, pmid = {17570226}, keywords = {Age Distribution,Carcinoma,Continental Population Groups,Diabetes Complications,Hepatocellular,Hepatocellular: chemically induced,Hepatocellular: epidemiology,Hepatocellular: etiology,Hepatocellular: genetics,Humans,Incidence,Liver Cirrhosis,Liver Cirrhosis: complications,Liver Diseases,Liver Diseases: complications,Liver Neoplasms,Liver Neoplasms: epidemiology,Liver Neoplasms: genetics,nosource,Obesity,Obesity: complications,Risk Factors,Sex Distribution,United States,World Health} }

@article{perzContributionsHepatitisVirus2006, title = {The Contributions of Hepatitis {{B}} Virus and Hepatitis {{C}} Virus Infections to Cirrhosis and Primary Liver Cancer Worldwide.}, author = {Perz, Joseph F. and Armstrong, Gregory L. and {}a Farrington, Leigh and Hutin, Yvan J. F. and Bell, Beth P.}, year = 2006, month = oct, journal = {Journal of hepatology}, volume = {45}, number = {4}, eprint = {16879891}, eprinttype = {pubmed}, pages = {529–38}, issn = {0168-8278}, doi = {10.1016/j.jhep.2006.05.013}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16879891}, abstract = {End-stage liver disease accounts for one in forty deaths worldwide. Chronic infections with hepatitis B virus (HBV) and hepatitis C virus (HCV) are well-recognized risk factors for cirrhosis and liver cancer, but estimates of their contributions to worldwide disease burden have been lacking.}, pmid = {16879891}, keywords = {Adult,Chronic,Chronic: mortality,Female,Hepatitis B,Hepatitis C,Humans,Liver Cirrhosis,Liver Cirrhosis: mortality,Liver Cirrhosis: virology,Liver Neoplasms,Liver Neoplasms: mortality,Liver Neoplasms: virology,Male,Middle Aged,nosource,Prevalence,Risk Factors,World Health,World Health Organization} }

@article{tsaiViralHepatocarcinogenesis2010, title = {Viral Hepatocarcinogenesis.}, author = {Tsai, WL W.-L. and Chung, RT T.}, year = 2010, month = apr, journal = {Oncogene}, volume = {29}, number = {16}, pages = {2309–24}, publisher = {Nature Publishing Group}, issn = {1476-5594}, doi = {10.1038/onc.2010.36}, url = {http://www.nature.com/onc/journal/v29/n16/abs/onc201036a.html http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3148694&tool=pmcentrez&rendertype=abstract}, abstract = {Hepatocellular carcinoma (HCC) is the fifth most common cancer and the third leading cause of cancer death worldwide. Despite recent advances in the diagnosis and treatment of HCC, its prognosis remains dismal. Infection with hepatitis B virus (HBV) and hepatitis C virus (HCV) are the major risk factors for HCC. Although both are hepatotropic viral infections, there are important differences between the oncogenic mechanisms of these two viruses. In addition to the oncogenic potential of its viral proteins, HBV, as a DNA virus, can integrate into host DNA and directly transform hepatocytes. In contrast, HCV, an RNA virus, is unable to integrate into the host genome, and viral protein expression has a more critical function in hepatocarcinogenesis. Both HBV and HCV proteins have been implicated in disrupting cellular signal transduction pathways that lead to unchecked cell growth. Most HCC develops in the cirrhotic liver, but the linkage between cirrhosis and HCC is likely multifactorial. In this review, we summarize current knowledge regarding the pathogenetic mechanisms of viral HCC.}, pmid = {20228847}, keywords = {Animals,Fatty Liver,Fatty Liver: etiology,genomics,Hepatitis B,hepatitis b virus,Hepatitis B virus,Hepatitis B virus: genetics,Hepatitis B: complications,Hepatitis C,hepatitis c virus,Hepatitis C: complications,hepatocellular carcinoma,Humans,Liver Cirrhosis,Liver Cirrhosis: complications,Liver Neoplasms,Liver Neoplasms: etiology,Liver Neoplasms: virology,Mutation,nosource,Oxidative Stress,signaling pathways,Trans-Activators,Trans-Activators: physiology,Viral Load,Virus Integration} }

@article{ferlayEstimatesWorldwideBurden2010, title = {Estimates of Worldwide Burden of Cancer in 2008: {{GLOBOCAN}} 2008}, author = {Ferlay, Jacques and Shin, HR Hai-Rim and Bray, Freddie and Forman, David and Mathers, Colin and Parkin, Donald Maxwell}, year = 2010, month = dec, journal = { journal of cancer}, volume = {127}, number = {12}, eprint = {21351269}, eprinttype = {pubmed}, pages = {2893–917}, issn = {1097-0215}, doi = {10.1002/ijc.25516}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21351269 http://onlinelibrary.wiley.com/doi/10.1002/ijc.25516/full}, abstract = {Estimates of the worldwide incidence and mortality from 27 cancers in 2008 have been prepared for 182 countries as part of the GLOBOCAN series published by the International Agency for Research on Cancer. In this article, we present the results for 20 world regions, summarizing the global patterns for the eight most common cancers. Overall, an estimated 12.7 million new cancer cases and 7.6 million cancer deaths occur in 2008, with 56% of new cancer cases and 63% of the cancer deaths occurring in the less developed regions of the world. The most commonly diagnosed cancers worldwide are lung (1.61 million, 12.7% of the total), breast (1.38 million, 10.9%) and colorectal cancers (1.23 million, 9.7%). The most common causes of cancer death are lung cancer (1.38 million, 18.2% of the total), stomach cancer (738,000 deaths, 9.7%) and liver cancer (696,000 deaths, 9.2%). Cancer is neither rare anywhere in the world, nor mainly confined to high-resource countries. Striking differences in the patterns of cancer from region to region are observed.}, pmid = {21351269}, keywords = {10,1002,25516,accepted 1 jun 2010,Adolescent,Adult,Aged,cancer,Child,doi,Female,global estimates,history,Humans,ijc,incidence,Infant,Male,Middle Aged,mortality,Neoplasms,Neoplasms: classification,Neoplasms: epidemiology,Newborn,nosource,online 17 jun,Preschool,Prognosis,received 26 may 2010,Registries,Risk Factors,Survival Rate,Time Factors,World Health,Young Adult} }

@article{leonardiTumorMicroenvironmentHepatocellular2012, title = {The Tumor Microenvironment in Hepatocellular Carcinoma ({{Review}}).}, author = {Leonardi, Giulia Costanza and Candido, Saverio and Cervello, Melchiorre and Nicolosi, Daria and Raiti, Fabio and Travali, Salvatore and {}a Spandidos, Demetrios and Libra, Massimo}, year = 2012, month = mar, journal = {International journal of oncology}, eprint = {22447316}, eprinttype = {pubmed}, pages = {1733–1747}, issn = {1791-2423}, doi = {10.3892/ijo.2012.1408}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22447316}, abstract = {The tumor microenvironment has been largely studied as a dynamic system orchestrated by inflammatory cells, including cancer cells, stroma as well as the extracellular matrix. It is useful to describe and predict the phenotypic characteristics of cancer. Furthermore, a better understanding of its interplay with the various aspects of the tumor cells may be utilized for the discovery of novel molecular targets. Liver cancer is considered a model of the relation occurring between the tumor micro-environment and tumor development. The chronic inflammatory status of the liver, sustained by the infection of hepatitis viruses, as well as the production of cytokines and growth factors within the parenchyma, lead to an intricate microenvironment. The identification of novel molecular therapeutic targets may improve the outcome of patients with liver cancer as it remains the third leading cause of cancer death worldwide. In the present study, the tumor microenvironment in hepatocellular carcinoma (HCC) was explored by a review of the literature. Studies on hepatitis virus infections and the consequent chronic inflammatory status were examined. In this context, immune-mediated and/or virus-related molecular mechanisms have been hypothesized as being responsible for liver cancer development. The interlink among HCC microenvironment components, comprising cellular elements, cytokines, growth factors and several proteins is also described together with the role of matrix metalloproteinases in HCC development. Finally, the rationale for targeting tumor-stromal interface is summarized in the context of new therapeutic opportunities.}, pmid = {22447316}, keywords = {nosource} }

@article{ludlamCrystalStructureRibosomal2004, title = {The Crystal Structure of Ribosomal Chaperone Trigger Factor from {{Vibrio}} Cholerae}, author = {Ludlam, A. V. and Moore, B. A. and Xu, Z.}, year = 2004, journal = { Academy of Sciences of the }, volume = {2004}, url = {http://www.pnas.org/content/101/37/13436.short}, keywords = {nosource} }

@article{wangConservedProlineSwitch2012, title = {A Conserved Proline Switch on the Ribosome Facilitates the Recruitment and Binding of {{trGTPases}}.}, author = {Wang, Li and Yang, Fang and Zhang, Dejiu and Chen, Zhi and Xu, Rui-Ming and Nierhaus, Knud H. and Gong, Weimin and Qin, Yan}, year = 2012, month = mar, journal = {Nature Structural & Molecular Biology}, volume = {19}, number = {4}, eprint = {22407015}, eprinttype = {pubmed}, pages = {403–410}, publisher = {Nature Publishing Group}, issn = {1545-9985}, doi = {10.1038/nsmb.2254}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22407015}, abstract = {When elongation factor G (EF-G) binds to the ribosome, it first makes contact with the C-terminal domain (CTD) of L12 before interacting with the N-terminal domain (NTD) of L11. Here we have identified a universally conserved residue, Pro22 of L11, that functions as a proline switch (PS22), as well as the corresponding center of peptidyl-prolyl cis-trans isomerase (PPIase) activity on EF-G that drives the cis-trans isomerization of PS22. Only the cis configuration of PS22 allows direct contact between the L11 NTD and the L12 CTD. Mutational analyses of both PS22 and the residues of the EF-G PPIase center reveal their function in translational GTPase (trGTPase) activity, protein synthesis and cell survival in Escherichia coli. Finally, we demonstrate that all known universal trGTPases contain an active PPIase center. Our observations suggest that the cis-trans isomerization of the L11 PS22 is a universal event required for an efficient turnover of trGTPases throughout the translation process.}, pmid = {22407015}, keywords = {nosource} }

@article{limRhphen2phi3ShapeselectiveProbe1998, title = {Rh(Phen)2phi3+ as a Shape-Selective Probe of Triple Helices.}, author = {Lim, a C. and Barton, J. K.}, year = 1998, month = jun, journal = {Biochemistry}, volume = {37}, number = {25}, eprint = {9636060}, eprinttype = {pubmed}, pages = {9138–46}, issn = {0006-2960}, doi = {10.1021/bi980509v}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9636060}, abstract = {RNA purpur-pyr and pyrpur-pyr (pur = purine, pyr = pyrimidine) triple helices consisting of a Watson-Crick base-paired 28mer hairpin duplex and a Hoogsteen base-paired purine or pyrimidine 12mer are targeted with photoactivated cleavage by the metal complex Rh(phen)2phi3+ (phen = phenanthroline, phi = 9, 10-phenanthrenequinone diimine). The metal complex interacts with these triple helices in a structure-specific manner. Different cleavage patterns are seen with the pyrpur-pyr and purpur-pyr motifs. Cleavage is seen on both of the Watson-Crick strands of the former motif and primarily on the purine Watson-Crick strand of the latter motif. Little cleavage is seen on the Hoogsteen strand for either motif. Importantly, the metal complex shows no detectable cleavage on the A-form RNA duplex in the absence of the third Hoogsteen strand. The cleavage patterns are consistent with an intercalated model for the metal complex in the triple helix. Similar cleavage is seen on DNA triple helices, but over a background of duplex cleavage. Targeting of synthetic RNA triple helices, but not duplex regions, by Rh(phen)2phi3+ provides a basis for the chemical probing of triply bonded sites in folded RNA molecules.}, pmid = {9636060}, keywords = {Base Composition,Hydrolysis,Intercalating Agents,Intercalating Agents: chemistry,nosource,Nucleic Acid Conformation,Organometallic Compounds,Organometallic Compounds: chemistry,Phenanthrenes,Phenanthrenes: chemistry,Phenanthrolines,Phenanthrolines: chemistry,Photochemistry,Purine Nucleotides,Purine Nucleotides: chemistry,Pyrimidine Nucleotides,Pyrimidine Nucleotides: chemistry,RNA,RNA Probes,RNA Probes: chemistry,RNA: chemistry,Salts} }

@article{yinglingPredictionWildtypeTelomerase2006, title = {The Prediction of the Wild-Type Telomerase {{RNA}} Pseudoknot Structure and the Pivotal Role of the Bulge in Its Formation.}, author = {Yingling, Yaroslava G. and {}a Shapiro, Bruce}, year = 2006, month = oct, journal = {Journal of molecular graphics & modelling}, volume = {25}, number = {2}, eprint = {16481205}, eprinttype = {pubmed}, pages = {261–74}, issn = {1093-3263}, doi = {10.1016/j.jmgm.2006.01.003}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16481205}, abstract = {In this study, the three-dimensional structure of the wild-type human telomerase RNA pseudoknot was predicted via molecular modeling. The wild-type pseudoknot structure is then compared to the recent NMR solution structure of the telomerase pseudoknot, which does not contain the U177 bulge. The removal of the bulge from the pseudoknot structure results in higher stability and significant reduction of activity of telomerase. We show that the effect of the bulge on the structure results in a significant transformation of the pseudoknot junction region where the starting base pairs are disrupted and unique triple base pairs are formed. We found that the formation of the junction region is greatly influenced by interactions of the U177 bulge with loop residues and rotation of residue A174. Moreover, this is the first study to our knowledge where a structure as complex as the pseudoknot has been solved by purely theoretical methods.}, pmid = {16481205}, keywords = {Base Pairing,Base Pairing: genetics,Base Sequence,Computer Simulation,Humans,Hydrogen Bonding,Models,Molecular,nosource,Nucleic Acid Conformation,RNA,RNA: chemistry,RNA: genetics,Telomerase,Telomerase: chemistry,Telomerase: genetics,Thermodynamics} }

@article{wainGuidelinesHumanGene2002, title = {Guidelines for Human Gene Nomenclature.}, author = {Wain, Hester M. and {}a Bruford, Elspeth and Lovering, Ruth C. and Lush, Michael J. and Wright, Mathew W. and Povey, Sue}, year = 2002, month = apr, journal = {Genomics}, volume = {79}, number = {4}, eprint = {11944974}, eprinttype = {pubmed}, pages = {464–70}, issn = {0888-7543}, doi = {10.1006/geno.2002.6748}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11944974}, pmid = {11944974}, keywords = {Genes,Guidelines as Topic,Humans,nosource,Terminology as Topic} }

@techreport{cherrySaccharomycesCerevisiaeGene1998, title = {Saccharomyces Cerevisiae {{Gene Nomenclature Conventions}}}, author = {Cherry, J. M.}, year = 1998, journal = {Trends in Genetics}, volume = {1}, number = {c}, pages = {10–11}, url = {http://www.yeastgenome.org/help/community/nomenclature-conventions}, keywords = {nosource} } % == BibTeX quality report for cherrySaccharomycesCerevisiaeGene1998: % Missing required field ‘institution’

@article{nickersonNullHypothesisSignificance2000, title = {Null Hypothesis Significance Testing: A Review of an Old and Continuing Controversy.}, author = {Nickerson, R. S.}, year = 2000, journal = {Psychological methods}, volume = {5}, number = {2}, pages = {241–301}, url = {http://psycnet.apa.org/journals/met/5/2/241/}, keywords = {nosource} }

@article{bentlerCovarianceStructureAnalysis1996, title = {Covariance Structure Analysis: {{Statistical}} Practice, Theory, and Directions}, author = {Bentler, P. M. and Dudgeon, Paul}, year = 1996, journal = {Annual review of psychology}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.psych.47.1.563}, keywords = {eqs,latent variables,lisrel,multivariate analysis,nosource,structural modeling} }

@article{taylorPracticalApproachRTqPCRPublishing2010, title = {A Practical Approach to {{RT-qPCR-Publishing}} Data That Conform to the {{MIQE}} Guidelines.}, author = {Taylor, Sean and Wakem, Michael and Dijkman, Greg and Alsarraj, Marwan and Nguyen, Marie}, year = 2010, month = apr, journal = {Methods (San Diego, Calif.)}, volume = {50}, number = {4}, eprint = {20215014}, eprinttype = {pubmed}, pages = {S1-5}, publisher = {Elsevier Inc.}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2010.01.005}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20215014}, abstract = {Given the highly dynamic nature of mRNA transcription and the potential variables introduced in sample handling and in the downstream processing steps (Garson et al. (2009)), a standardized approach to each step of the RT-qPCR workflow is critical for reliable and reproducible results. The MIQE provides this approach with a checklist that contains 85 parameters to assure quality results that will meet the acceptance criteria of any journal (Bustin et al. (2009)). In this paper we demonstrate how to apply the MIQE guidelines (www.rdml.org/miqe) to establish a solid experimental approach.}, pmid = {20215014}, keywords = {Guidelines as Topic,nosource,Publishing,Publishing: standards,Quality Control,Research Design,Research Design: standards,Reverse Transcriptase Polymerase Chain Reaction,Reverse Transcriptase Polymerase Chain Reaction: m,Reverse Transcriptase Polymerase Chain Reaction: s,RNA,RNA: standards,Validation Studies as Topic} } % == BibTeX quality report for taylorPracticalApproachRTqPCRPublishing2010: % ? Possibly abbreviated journal title Methods (San Diego, Calif.)

@article{kalynaAlternativeSplicingNonsensemediated2011, title = {Alternative Splicing and Nonsense-Mediated Decay Modulate Expression of Important Regulatory Genes in {{Arabidopsis}}.}, author = {Kalyna, Maria and Simpson, Craig G. CG and Syed, Naeem H. and Lewandowska, Dominika and Marquez, Yamile and Kusenda, Branislav and Marshall, Jacqueline and Fuller, John and Cardle, Linda and McNicol, Jim and Dinh, Huy Q. and Barta, Andrea and Brown, John W. S.}, year = 2011, month = dec, journal = {Nucleic acids research}, volume = {40}, number = {6}, pages = {2454–2469}, issn = {1362-4962}, doi = {10.1093/nar/gkr932}, url = {http://nar.oxfordjournals.org/content/40/6/2454.short http://www.ncbi.nlm.nih.gov/pubmed/22127866}, abstract = {Alternative splicing (AS) coupled to nonsense-mediated decay (NMD) is a post-transcriptional mechanism for regulating gene expression. We have used a high-resolution AS RT-PCR panel to identify endogenous AS isoforms which increase in abundance when NMD is impaired in the Arabidopsis NMD factor mutants, upf1-5 and upf3-1. Of 270 AS genes (950 transcripts) on the panel, 102 transcripts from 97 genes (32%) were identified as NMD targets. Extrapolating from these data around 13% of intron-containing genes in the Arabidopsis genome are potentially regulated by AS/NMD. This cohort of naturally occurring NMD-sensitive AS transcripts also allowed the analysis of the signals for NMD in plants. We show the importance of AS in introns in 5’ or 3’UTRs in modulating NMD-sensitivity of mRNA transcripts. In particular, we identified upstream open reading frames overlapping the main start codon as a new trigger for NMD in plants and determined that NMD is induced if 3’-UTRs were {\(>\)}350 nt. Unexpectedly, although many intron retention transcripts possess NMD features, they are not sensitive to NMD. Finally, we have shown that AS/NMD regulates the abundance of transcripts of many genes important for plant development and adaptation including transcription factors, RNA processing factors and stress response genes.}, pmid = {22127866}, keywords = {nosource} }

@article{kortmannBacterialRNAThermometers2012, title = {Bacterial {{RNA}} Thermometers: Molecular Zippers and Switches}, author = {Kortmann, Jens and Narberhaus, Franz}, year = 2012, month = mar, journal = {Nature Reviews Microbiology}, volume = {10}, number = {4}, pages = {255–265}, publisher = {Nature Publishing Group}, issn = {1740-1526}, doi = {10.1038/nrmicro2730}, url = {http://www.nature.com/doifinder/10.1038/nrmicro2730}, keywords = {nosource} }

@article{antoineIdentificationUnconventionalNuclear2005, title = {Identification of an Unconventional Nuclear Localization Signal in Human Ribosomal Protein {{S2}}.}, author = {Antoine, M. and Reimers, K. and Wirz, W. and Gressner, a M. and M{"u}ller, R. and Kiefer, P.}, year = 2005, month = sep, journal = {Biochemical and biophysical research communications}, volume = {335}, number = {1}, eprint = {16061210}, eprinttype = {pubmed}, pages = {146–53}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2005.07.069}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16061210}, abstract = {Ribosomal proteins must be imported into the nucleus after being synthesized in the cytoplasm. Since the rpS2 amino acid sequence does not contain a typical nuclear localization signal, we used deletion mutant analysis and rpS2-beta-galactosidase chimeric proteins to identify the nuclear targeting domains in rpS2. Nuclear rpS2 is strictly localized in the nucleoplasm and is not targeted to the nucleoli. Subcellular localization analysis of deletion mutants of rpS2-beta-galactosidase chimeras identified a central domain comprising 72 amino acids which is necessary and sufficient to target the chimeric beta-galactosidase to the nucleus. The nuclear targeting domain shares no significant similarity to already characterized nuclear localization signals in ribosomal proteins or other nuclear proteins. Although a Nup153 fragment containing the importinbeta binding site fused to VP22 blocks nuclear import of rpS2-beta-galactosidase fusion proteins, nuclear uptake of rpS2 could be mediated by several import receptors since it binds to importinalpha/beta and transportin.}, pmid = {16061210}, keywords = {Active Transport,Amino Acid Sequence,Animals,beta-Galactosidase,beta-Galactosidase: genetics,beta-Galactosidase: metabolism,Cell Nucleolus,Cell Nucleolus: metabolism,Cell Nucleus,Cell Nucleus: metabolism,Cercopithecus aethiops,COS Cells,Cytoplasm,Cytoplasm: metabolism,Humans,Molecular Sequence Data,Mutation,Mutation: genetics,nosource,Nuclear Localization Signals,Nuclear Localization Signals: physiology,Protein Binding,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: genetics,Ribosomal Proteins: metabolism,Sequence Alignment} }

@article{yeACAGuideRNAs2007, title = {H/{{ACA}} Guide {{RNAs}}, Proteins and Complexes.}, author = {Ye, Keqiong}, year = 2007, month = jun, journal = {Current opinion in structural biology}, volume = {17}, number = {3}, eprint = {17574834}, eprinttype = {pubmed}, pages = {287–92}, issn = {0959-440X}, doi = {10.1016/j.sbi.2007.05.012}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17574834}, abstract = {H/ACA guide RNAs direct site-specific pseudouridylation of substrate RNAs by forming ribonucleoprotein (RNP) complexes with pseudouridine synthase Cbf5 and three accessory proteins. Recently determined crystal structures of H/ACA protein complexes and a fully assembled H/ACA RNP complex have provided significant insights into the architecture, assembly and mechanism of action of RNA-guided pseudouridine synthase. The binding of guide RNA is directed by its conserved secondary structure and sequence motifs, which enables guide RNA with different sequences to be incorporated into the same protein complex. Accessory proteins and peripheral domains crucially coordinate the position of guide RNA, and possibly regulate the reaction process.}, pmid = {17574834}, keywords = {Animals,Guide,Guide: chemistry,Guide: physiology,Humans,nosource,Pseudouridine,Pseudouridine: biosynthesis,Ribonucleoproteins,Ribonucleoproteins: chemistry,Ribonucleoproteins: physiology,RNA} }

@article{duanStructuralMechanismSubstrate2009, title = {Structural Mechanism of Substrate {{RNA}} Recruitment in {{H}}/{{ACA RNA-guided}} Pseudouridine Synthase.}, author = {Duan, Jingqi and Li, Ling and Lu, Jing and Wang, Wei and Ye, Keqiong}, year = 2009, month = may, journal = {Molecular cell}, volume = {34}, number = {4}, eprint = {19481523}, eprinttype = {pubmed}, pages = {427–39}, publisher = {Elsevier Ltd}, issn = {1097-4164}, doi = {10.1016/j.molcel.2009.05.005}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19481523 http://dx.doi.org/10.1016/j.molcel.2009.05.005 http://www.sciencedirect.com/science/article/pii/S1097276509003128}, abstract = {H/ACA RNAs form ribonucleoprotein complex (RNP) with proteins Cbf5, Nop10, L7Ae, and Gar1 and guide site-specific conversion of uridine into pseudouridine in cellular RNAs. The crystal structures of H/ACA RNP with substrate bound at the active site cleft reveal that the substrate is recruited through sequence-specific pairing with guide RNA and essential protein contacts. Substrate binding leads to a reorganization of a preset pseudouridylation pocket and an adaptive movement of the PUA domain and the lower stem of the H/ACA RNA. Moreover, a thumb loop flips from the Gar1-bound state in the substrate-free RNP structure to tightly associate with the substrate. Mutagenesis and enzyme kinetics analysis suggest a critical role of Gar1 and the thumb in substrate turnover, particularly in product release. Comparison with tRNA Psi55 synthase TruB reveals the structural conservation and adaptation between an RNA-guided and stand-alone pseudouridine synthase and provides insight into the guide-independent activity of Cbf5.}, pmid = {19481523}, keywords = {Amino Acid Sequence,Base Sequence,Catalytic Domain,Crystallography,Intramolecular Transferases,Intramolecular Transferases: genetics,Intramolecular Transferases: metabolism,Macromolecular Substances,Macromolecular Substances: chemistry,Macromolecular Substances: metabolism,Models,Molecular,Molecular Sequence Data,Mutagenesis,nosource,Nucleic Acid Conformation,Protein Conformation,Ribonucleoproteins,RNA,RNA: chemistry,RNA: genetics,RNA: metabolism,Site-Directed,Small Nucleolar,Small Nucleolar: chemistry,Small Nucleolar: genetics,Small Nucleolar: metabolism,X-Ray} }

@article{demeshkinaNewUnderstandingDecoding2012, title = {A New Understanding of the Decoding Principle on the Ribosome}, author = {Demeshkina, Natalia and Jenner, Lasse and Westhof, Eric and Yusupov, Marat and Yusupova, Gulnara}, year = 2012, journal = {Nature}, volume = {484}, pages = {256–259}, publisher = {Nature Publishing Group}, issn = {0028-0836}, keywords = {nosource} }

@article{hermannApramycinRecognitionHuman2007, title = {Apramycin Recognition by the Human Ribosomal Decoding Site.}, author = {Hermann, Thomas and Tereshko, Valentina and Skripkin, Eugene and Patel, Dinshaw J.}, year = 2007, journal = {Blood cells, molecules & diseases}, volume = {38}, number = {3}, eprint = {17258916}, eprinttype = {pubmed}, pages = {193–8}, issn = {1079-9796}, doi = {10.1016/j.bcmd.2006.11.006}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17258916}, abstract = {Aminoglycoside antibiotics bind specifically to the bacterial ribosomal decoding-site RNA and thereby interfere with fidelity but not efficiency of translation. Apramycin stands out among aminoglycosides for its mechanism of action which is based on blocking translocation and its ability to bind also to the eukaryotic decoding site despite differences in key residues required for apramycin recognition by the bacterial target. To elucidate molecular recognition of the eukaryotic decoding site by apramycin we have determined the crystal structure of an oligoribonucleotide containing the human sequence free and in complex with the antibiotic at 1.5 A resolution. The drug binds in the deep groove of the RNA which forms a continuously stacked helix comprising non-canonical C.A and G.A base pairs and a bulged-out adenine. The binding mode of apramycin at the human decoding-site RNA is distinct from aminoglycoside recognition of the bacterial target, suggesting a molecular basis for the actions of apramycin in eukaryotes and bacteria.}, pmid = {17258916}, keywords = {Binding Sites,Humans,Models,Molecular,Molecular Structure,Nebramycin,Nebramycin: analogs & derivatives,Nebramycin: chemistry,Nebramycin: metabolism,nosource,Nucleic Acid Conformation,Ribosomal,Ribosomal: chemistry,Ribosomal: metabolism,RNA,Structure-Activity Relationship} }

@article{ledouxDifferentAatRNAsAre2008, title = {Different Aa-{{tRNAs}} Are Selected Uniformly on the Ribosome}, author = {Ledoux, Sarah and Uhlenbeck, Olke C. OC}, year = 2008, month = jul, journal = {Molecular cell}, volume = {31}, number = {Figure 1}, pages = {114–123}, issn = {1097-4164}, doi = {10.1016/j.molcel.2008.04.026}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2709977&tool=pmcentrez&rendertype=abstract http://www.sciencedirect.com/science/article/pii/S1097276508003353}, abstract = {Ten E. coli aminoacyl-tRNAs (aa-tRNAs) were assessed for their ability to decode cognate codons on E. coli ribosomes by using three assays that evaluate the key steps in the decoding pathway. Despite a wide variety of structural features, each aa-tRNA exhibited similar kinetic and thermodynamic properties in each assay. This surprising kinetic and thermodynamic uniformity is likely to reflect the importance of ribosome conformational changes in defining the rates and affinities of the decoding process as well as the evolutionary “tuning” of each aa-tRNA sequence to modify their individual interactions with the ribosome at each step.}, pmid = {18614050}, keywords = {Amino Acyl,Amino Acyl: chemistry,Amino Acyl: genetics,Amino Acyl: metabolism,Base Sequence,Escherichia coli,Escherichia coli: metabolism,Guanosine Triphosphate,Guanosine Triphosphate: metabolism,Hydrolysis,Kinetics,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Peptides,Peptides: metabolism,Protein Binding,Ribosomes,Ribosomes: metabolism,RNA,Transfer} }

@article{sunOligonucleotideDirectedTriple1996, title = {Oligonucleotide Directed Triple Helix Formation.}, author = {Sun, J. S. and Garestier, T. and H{'e}l{`e}ne, C.}, year = 1996, month = jun, journal = {Current opinion in structural biology}, volume = {6}, number = {3}, eprint = {12240328}, eprinttype = {pubmed}, pages = {327–33}, issn = {0959-440X}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12240328}, abstract = {Oligonucleotide directed triple helix formation allows the sequence-specific recognition of the major groove of double-helical DNA. Recently synthesized base analogs and backbones, such as N3’–{\(>\)}P5’ phosphoramidates, allow stable triplexes to be formed under physiological conditions. However, it remains a challenge to design new oligomers that would extend the range of recognition sequences (which are still limited to oligopurine-rich tracts). Oligonucleotide directed triple helix formation could be used to control biological processes such as transcription and replication. Three-stranded structures formed during recombination processes have been further characterized.}, pmid = {8804836}, keywords = {Base Composition,DNA,DNA: chemistry,Kinetics,nosource,Nucleic Acid Conformation,Rec A Recombinases,Rec A Recombinases: chemistry,Rec A Recombinases: genetics,RNA,RNA: chemistry,Thermodynamics} }

@article{peralesCotranscriptionalityTranscriptionElongation2009, title = {“{{Cotranscriptionality}}”: The Transcription Elongation Complex as a Nexus for Nuclear Transactions.}, author = {Perales, Roberto and Bentley, David}, year = 2009, month = oct, journal = {Molecular cell}, volume = {36}, number = {2}, pages = {178–91}, publisher = {Elsevier Ltd}, issn = {1097-4164}, doi = {10.1016/j.molcel.2009.09.018}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2770090&tool=pmcentrez&rendertype=abstract http://dx.doi.org/10.1016/j.molcel.2009.09.018}, abstract = {Much of the complex process of RNP biogenesis takes place at the gene cotranscriptionally. The target for RNA binding and processing factors is, therefore, not a solitary RNA molecule but, rather, a transcription elongation complex (TEC) comprising the growing nascent RNA and RNA polymerase traversing a chromatin template with associated passenger proteins. RNA maturation factors are not the only nuclear machines whose work is organized cotranscriptionally around the TEC scaffold. Additionally, DNA repair, covalent chromatin modification, “gene gating” at the nuclear pore, Ig gene hypermutation, and sister chromosome cohesion have all been demonstrated or suggested to involve a cotranscriptional component. From this perspective, TECs can be viewed as potent “community organizers” within the nucleus.}, pmid = {19854129}, keywords = {Alternative Splicing,Alternative Splicing: genetics,Cell Nucleus,Cell Nucleus: genetics,Chromatin,Chromatin: metabolism,Genetic,Humans,nosource,RNA 3’ End Processing,RNA Polymerase II,RNA Polymerase II: metabolism,Transcription} }

@article{weisblumBackCamelotDefining1999, title = {Back to {{Camelot}}: Defining the Specific Role of {{tRNA}} in Protein Synthesis.}, author = {Weisblum, B.}, year = 1999, month = jun, journal = {Trends in biochemical sciences}, volume = {24}, number = {6}, eprint = {10366855}, eprinttype = {pubmed}, pages = {247–50}, issn = {0968-0004}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10366855}, pmid = {10366855}, keywords = {20th Century,Alanine,Alanine: metabolism,Alleles,Biological,Cysteine,Cysteine: metabolism,Escherichia coli,Escherichia coli: genetics,Genetic Code,Hemoglobins,Hemoglobins: genetics,History,Models,Molecular Biology,Molecular Biology: history,nosource,Protein Biosynthesis,Protein Biosynthesis: physiology,RNA,Transfer,Transfer: physiology} }

@article{borerMajorNucleolarProteins1989, title = {Major Nucleolar Proteins Shuttle between Nucleus and Cytoplasm.}, author = {{}a Borer, R. and Lehner, C. F. and Eppenberger, H. M. and {}a Nigg, E.}, year = 1989, month = feb, journal = {Cell}, volume = {56}, number = {3}, eprint = {2914325}, eprinttype = {pubmed}, pages = {379–90}, issn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2914325}, abstract = {Nucleolin is a 92 kd nucleolar protein implicated in regulating polymerase I transcription and binding of preribosomal RNA. Another abundant nucleolar protein of 38 kd (B23/No38) is thought to be involved in intranuclear packaging of preribosomal particles. Although both proteins have previously been detected only in nuclei, we conclude that they shuttle constantly between nucleus and cytoplasm. This conclusion is based on monitoring the equilibration of these proteins between nuclei present in interspecies heterokaryons, and on observing the antigen-mediated nuclear accumulation of cytoplasmically injected antibodies. Our unexpected results suggest a role for these major nucleolar proteins in the nucleocytoplasmic transport of ribosomal components. Moreover, they suggest that transient exposure of shuttling proteins to the cytoplasm may provide a mechanism for cytoplasmic regulation of nuclear activities.}, pmid = {2914325}, keywords = {Amino Acid Sequence,Animals,Base Sequence,Cell Line,Cell Nucleolus,Cell Nucleolus: metabolism,Cell Nucleus,Cell Nucleus: metabolism,Chick Embryo,Chickens,Cloning,Cytoplasm,Cytoplasm: metabolism,Mice,Molecular,Molecular Sequence Data,nosource,Nuclear Proteins,Nuclear Proteins: genetics,Nuclear Proteins: metabolism,Phosphoproteins,Phosphoproteins: genetics,Phosphoproteins: metabolism,RNA-Binding Proteins,Species Specificity,Xenopus} }

@article{bashanCorrelatingRibosomeFunction2008, title = {Correlating Ribosome Function with High-Resolution Structures.}, author = {Bashan, Anat and Yonath, Ada}, year = 2008, month = jul, journal = {Trends in microbiology}, volume = {16}, number = {7}, eprint = {18547810}, eprinttype = {pubmed}, pages = {326–35}, issn = {0966-842X}, doi = {10.1016/j.tim.2008.05.001}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18547810}, abstract = {Ribosome research has undergone astonishing progress in recent years. Crystal structures have shed light on the functional properties of the translation machinery and revealed how the striking architecture of the ribosome is ingeniously designed as the framework for its unique capabilities: precise decoding, substrate-mediated peptide-bond formation and efficient polymerase activity. New findings include the two concerted elements of tRNA translocation: sideways shift and a ribosomal-navigated rotatory motion; the dynamics of the nascent-chain exit tunnel and the shelter formed by the ribosome-bound trigger-factor, which acts as a chaperone to prevent nascent-chain aggregation and misfolding. The availability of these structures has also illuminated the action, selectivity, resistance and synergism of antibiotics that target ribosomes.}, pmid = {18547810}, keywords = {Animals,Base Sequence,Cryoelectron Microscopy,Crystallography,Eukaryotic Cells,Eukaryotic Cells: ultrastructure,Humans,Models,Molecular,Molecular Sequence Data,nosource,Prokaryotic Cells,Prokaryotic Cells: ultrastructure,Protein Biosynthesis,Ribosomal Proteins,Ribosomes,Ribosomes: chemistry,Ribosomes: genetics,Ribosomes: metabolism,Ribosomes: ultrastructure,RNA,Transfer,X-Ray} }

@article{matthewsOriginsPrinciplesTranslational2000, title = {Origins and {{Principles}} of {{Translational Control}}}, author = {Matthews, M. and Sonenberg, N. and J, Hershey and Mathews, M. B.}, year = 2000, journal = {COLD SPRING }, url = {http://faculty.washington.edu/dmorris/conjoint/Lecture1/Papers/csh-1.pdf}, keywords = {nosource} } % == BibTeX quality report for matthewsOriginsPrinciplesTranslational2000: % ? Title looks like it was stored in title-case in Zotero

@article{kimuraPrimaryStructuresThree1987, title = {Primary Structures of Three Highly Acidic Ribosomal Proteins {{S6}}, {{S12}} and {{S15}} from the Archaebacterium {{Halobacterium}} Marismortui.}, author = {Kimura, J. and Arndt, E. and Kimura, M.}, year = 1987, month = nov, journal = {FEBS letters}, volume = {224}, number = {1}, eprint = {3315748}, eprinttype = {pubmed}, pages = {65–70}, issn = {0014-5793}, url = {http://www.ncbi.nlm.nih.gov/pubmed/3315748}, abstract = {The amino acid sequences of three extremely acidic ribosomal proteins, S6, S12, and S15, from Halobacterium marismortui have been determined. The sequences were obtained by the sequence analysis of peptides derived by enzymatic digestion with trypsin. Stapylococcus aureus protease and chymotrypsin, as well as by cleavage with dilute HCl. The proteins, S6, S12 and S15, consist of 116, 147 and 102 amino acid residues, and have molecular masses of 12,251, 16,440 and 11,747 Da, respectively. Comparison of the amino acid sequences of these proteins with ribosomal protein sequences of other organisms revealed that halobacterial protein S12 has homology with the eukaryotic protein S16A from Saccharomyces cerevisiae, while S15 is significantly related to the Xenopus laevis S19 protein. No homology was found between these halobacterial proteins and any eubacterial ribosomal proteins.}, pmid = {3315748}, keywords = {Amino Acid Sequence,Animals,Bacterial Proteins,Bacterial Proteins: genetics,Escherichia coli,Escherichia coli: genetics,Fungal Proteins,Fungal Proteins: genetics,Halobacterium,Halobacterium: genetics,Molecular Sequence Data,nosource,Nucleic Acid,Ribosomal Protein S6,Ribosomal Proteins,Ribosomal Proteins: genetics,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Sequence Homology,Xenopus laevis,Xenopus laevis: genetics} }

@article{badhaiRibosomalProteinS192009, title = {Ribosomal Protein {{S19}} and {{S24}} Insufficiency Cause Distinct Cell Cycle Defects in {{Diamond}}–{{Blackfan}} Anemia}, author = {Badhai, Jitendra and Fr{"o}jmark, AS Anne-sophie and Davey, Edward J. and Schuster, Jens and Dahl, Niklas and Davey, Edward J. EJ}, year = 2009, month = oct, journal = {Biochimica et Biophysica }, volume = {1792}, number = {10}, pages = {1036–1042}, publisher = {Elsevier B.V.}, issn = {0925-4439}, doi = {10.1016/j.bbadis.2009.08.002}, url = {http://dx.doi.org/10.1016/j.bbadis.2009.08.002 http://www.sciencedirect.com/science/article/pii/S0925443909001690 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2759502&tool=pmcentrez&rendertype=abstract}, abstract = {Diamond-Blackfan anemia (DBA) is a severe congenital anemia characterized by a specific decrease of erythroid precursors. The disease is also associated with growth retardation, congenital malformations, a predisposition for malignant disease and heterozygous mutations in either of the ribosomal protein (RP) genes RPS7, RPS17, RPS19, RPS24, RPL5, RPL11 and RPL35a. We show herein that primary fibroblasts from DBA patients with truncating mutations in RPS19 or in RPS24 have a marked reduction in proliferative capacity. Mutant fibroblasts are associated with extended cell cycles and normal levels of p53 when compared to w.t. cells. RPS19 mutant fibroblasts accumulate in the G1 phase, whereas the RPS24 mutant cells show an altered progression in the S phase resulting in reduced levels in the G2/M phase. RPS19 deficient cells exhibit reduced levels of Cyclin-E, CDK2 and retinoblastoma (Rb) protein supporting a cell cycle arrest in the G1 phase. In contrast, RPS24 deficient cells show increased levels of the cell cycle inhibitor p21 and a seemingly opposing increase in Cyclin-E, CDK4 and CDK6. In combination, our results show that RPS19 and RPS24 insufficient fibroblasts have an impaired growth caused by distinct blockages in the cell cycle. We suggest this proliferative constraint to be an important contributing mechanism for the complex extra-hematological features observed in DBA.}, pmid = {19689926}, keywords = {Anemia,Blotting,Cell Cycle,Cell Cycle Proteins,Cell Cycle Proteins: metabolism,Cell Proliferation,Cells,Cultured,Diamond-Blackfan,Diamond-Blackfan: metabolism,Diamond-Blackfan: pathology,Down-Regulation,Fibroblasts,Fibroblasts: metabolism,Fibroblasts: pathology,Humans,Mutation,Mutation: genetics,nosource,Ribosomal,Ribosomal Proteins,Ribosomal Proteins: metabolism,Ribosomal: metabolism,RNA,Western} }

@article{greenPathPerditionPaved2002, title = {The Path to Perdition Is Paved with Protons.}, author = {Green, Rachel and Lorsch, Jon R.}, year = 2002, month = sep, journal = {Cell}, volume = {110}, number = {6}, eprint = {12297040}, eprinttype = {pubmed}, pages = {665–8}, issn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12297040}, abstract = {Recent studies are beginning to shed light on the mechanism of ribosome-catalyzed peptide bond formation.}, pmid = {12297040}, keywords = {Animals,Catalysis,Hydrogen Bonding,Hydrogen-Ion Concentration,Kinetics,Molecular Structure,nosource,Peptide Biosynthesis,Peptides,Peptides: chemistry,Peptidyl Transferases,Peptidyl Transferases: chemistry,Protons,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism} }

@article{simonovicStructuralViewMechanism2009, title = {A Structural View on the Mechanism of the Ribosome-Catalyzed Peptide Bond Formation.}, author = {Simonovi{'c}, Miljan and Steitz, Thomas A.}, year = 2009, journal = {Biochimica et biophysica acta}, volume = {1789}, number = {9-10}, pages = {612–23}, publisher = {Elsevier B.V.}, issn = {0006-3002}, doi = {10.1016/j.bbagrm.2009.06.006}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2783306&tool=pmcentrez&rendertype=abstract http://dx.doi.org/10.1016/j.bbagrm.2009.06.006}, abstract = {The ribosome is a large ribonucleoprotein particle that translates genetic information encoded in mRNA into specific proteins. Its highly conserved active site, the peptidyl-transferase center (PTC), is located on the large (50S) ribosomal subunit and is comprised solely of rRNA, which makes the ribosome the only natural ribozyme with polymerase activity. The last decade witnessed a rapid accumulation of atomic-resolution structural data on both ribosomal subunits as well as on the entire ribosome. This has allowed studies on the mechanism of peptide bond formation at a level of detail that surpasses that for the classical protein enzymes. A current understanding of the mechanism of the ribosome-catalyzed peptide bond formation is the focus of this review. Implications on the mechanism of peptide release are discussed as well.}, pmid = {19595805}, keywords = {Amino Acids,Amino Acids: chemistry,Binding Sites,Catalysis,Chemical,Crystallography,Guanosine Triphosphate,Guanosine Triphosphate: chemistry,Kinetics,Messenger,Messenger: metabolism,Models,Molecular Conformation,nosource,Nucleic Acid Conformation,Peptides,Peptides: chemistry,Peptidyl Transferases,Peptidyl Transferases: chemistry,Ribosomes,Ribosomes: chemistry,RNA,Thermus,Thermus: metabolism,Transfer,Transfer: chemistry,X-Ray,X-Ray: methods} }

@article{tohIndigenousPosttranscriptionalModification2008, title = {An Indigenous Posttranscriptional Modification in the Ribosomal Peptidyl Transferase Center Confers Resistance to an Array of Protein Synthesis Inhibitors.}, author = {Toh, Seok-Ming and Mankin, Alexander S.}, year = 2008, month = jul, journal = {Journal of molecular biology}, volume = {380}, number = {4}, eprint = {18554609}, eprinttype = {pubmed}, pages = {593–7}, issn = {1089-8638}, doi = {10.1016/j.jmb.2008.05.027}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18554609}, abstract = {A number of nucleotide residues in ribosomal RNA (rRNA) undergo specific posttranscriptional modifications. The roles of most modifications are unclear, but their clustering in functionally important regions of rRNA suggests that they might either directly affect the activity of the ribosome or modulate its interactions with ligands. Of the 25 modified nucleotides in Escherichia coli 23S rRNA, 14 are located in the peptidyl transferase center, the main antibiotic target in the large ribosomal subunit. Since nucleotide modifications have been closely associated with both antibiotic sensitivity and antibiotic resistance, loss of some of these posttranscriptional modifications may affect the susceptibility of bacteria to antibiotics. We investigated the antibiotic sensitivity of E. coli cells in which the genes of 8 rRNA-modifying enzymes targeting the peptidyl transferase center were individually inactivated. The lack of pseudouridine at position 2504 of 23S rRNA was found to significantly increase the susceptibility of bacteria to peptidyl transferase inhibitors. Therefore, this indigenous posttranscriptional modification may have evolved as an intrinsic resistance mechanism protecting bacteria against natural antibiotics.}, pmid = {18554609}, keywords = {23S,23S: chemistry,23S: genetics,Bacterial,Base Sequence,Drug Resistance,Escherichia coli,Escherichia coli: genetics,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Peptidyl Transferases,Peptidyl Transferases: chemistry,Peptidyl Transferases: genetics,Peptidyl Transferases: metabolism,Post-Transcriptional,Protein Synthesis Inhibitors,Protein Synthesis Inhibitors: chemistry,Protein Synthesis Inhibitors: metabolism,Ribosomal,Ribosomes,Ribosomes: enzymology,RNA,RNA Processing} }

@article{klossResistanceMutations231999, title = {Resistance Mutations in 23 {{S rRNA}} Identify the Site of Action of the Protein Synthesis Inhibitor Linezolid in the Ribosomal Peptidyl Transferase Center.}, author = {Kloss, P. and Xiong, L. and Shinabarger, D. L. and Mankin, a S.}, year = 1999, month = nov, journal = {Journal of molecular biology}, volume = {294}, number = {1}, eprint = {10556031}, eprinttype = {pubmed}, pages = {93–101}, issn = {0022-2836}, doi = {10.1006/jmbi.1999.3247}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10556031}, abstract = {Oxazolidinones represent a novel class of antibiotics that inhibit protein synthesis in sensitive bacteria. The mechanism of action and location of the binding site of these drugs is not clear. A new representative of oxazolidinone antibiotics, linezolid, was found to be active against bacteria and against the halophilic archaeon Halobacterium halobium. The use of H. halobium, which possess only one chromosomal copy of rRNA operon, allowed isolation of a number of linezolid-resistance mutations in rRNA. Four types of linezolid-resistant mutants were isolated by direct plating of H. halobium cells on agar medium containing antibiotic. In addition, three more linezolid-resistant mutants were identified among the previously isolated mutants of H. halobium containing mutations in either 16 S or 23 S rRNA genes. All the isolated mutants were found to contain single-point mutations in 23 S rRNA. Seven mutations affecting six different positions in the central loop of domain V of 23 S rRNA were found to confer resistance to linezolid. Domain V of 23 S rRNA is known to be a component of the ribosomal peptidyl transferase center. Clustering of linezolid-resistance mutations within this region strongly suggests that the binding site of the drug is located in the immediate vicinity of the peptidyl transferase center. However, the antibiotic failed to inhibit peptidyl transferase activity of the H. halobium ribosome, supporting the previous conclusion that linezolid inhibits translation at a step different from the catalysis of the peptide bond formation.}, pmid = {10556031}, keywords = {23S,23S: genetics,Acetamides,Acetamides: pharmacology,Binding Sites,Drug Resistance,Halobacterium salinarum,Halobacterium salinarum: genetics,Met,Met: metabolism,Microbial,Microbial: genetics,Mutation,nosource,Nucleic Acid Conformation,Oxazoles,Oxazoles: pharmacology,Oxazolidinones,Peptide Chain Initiation,Peptidyl Transferases,Peptidyl Transferases: metabolism,Protein Synthesis Inhibitors,Protein Synthesis Inhibitors: pharmacology,Ribosomal,Ribosomes,Ribosomes: drug effects,RNA,Transfer,Translational,Translational: drug effe} }

@article{srisawatRNAAffinityTags2002, title = {{{RNA}} Affinity Tags for Purification of {{RNAs}} and Ribonucleoprotein Complexes.}, author = {Srisawat, Chatchawan and Engelke, David R.}, year = 2002, month = feb, journal = {Methods}, volume = {26}, number = {2}, eprint = {12054892}, eprinttype = {pubmed}, pages = {156–61}, issn = {1046-2023}, doi = {10.1016/S1046-2023(02)00018-X}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12054892}, abstract = {Intrinsic affinity tags are useful tools for the study of macromolecular targets. Although polypeptide affinity tags are routinely used in purification and detection of protein complexes, there has been a relative lack of powerful RNA affinity tags that can be embedded within RNA sequences. Here, the preparation and use of two RNA affinity tags against Sephadex or streptavidin are described. The two tags have different strengths that make them appropriate for slightly different uses. One is a high-affinity ligand for streptavidin that can be specifically eluted by competition with biotin under otherwise native binding conditions. The other tag binds selectively to Sephadex beads, and can be eluted by competition with the soluble dextran that composes Sephadex. When properly placed within another RNA molecule, the tags can be used to effect dramatic purification of RNA or ribonucleoprotein complexes from complex mixtures of cellular RNA.}, pmid = {12054892}, keywords = {Amino Acid Motifs,Base Sequence,Blotting,Catalytic,Catalytic: metabolism,Endoribonucleases,Endoribonucleases: metabolism,Genetic Techniques,Ligands,Molecular Sequence Data,Northern,nosource,Ribonuclease P,Ribonucleoproteins,Ribonucleoproteins: isolation & purification,RNA,RNA: isolation & purification,RNA: metabolism,Streptavidin,Streptavidin: chemistry} }

@article{beillardMiRSensARetroviralDualluciferase2012, title = {{{miR-Sens}}–{{A}} Retroviral Dual-Luciferase Reporter to Detect {{microRNA}} Activity in Primary Cells.}, author = {Beillard, Emmanuel and Ong, Siau Chi H. I. and Giannakakis, Antonis and Guccione, Ernesto and Vardy, Leah A. and Voorhoeve, P. Mathijs}, year = 2012, month = mar, journal = {RNA}, volume = {18}, number = {5}, eprint = {22417692}, eprinttype = {pubmed}, pages = {1091–100}, issn = {1469-9001}, doi = {10.1261/rna.031831.111}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22417692 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3334695&tool=pmcentrez&rendertype=abstract}, abstract = {MicroRNA-mRNA interactions are commonly validated and deconstructed in cell lines transfected with luciferase reporters. However, due to cell type-specific variations in microRNA or RNA-binding protein abundance, such assays may not reliably reflect microRNA activity in other cell types that are less easily transfected. In order to measure miRNA activity in primary cells, we constructed miR-Sens, a MSCV-based retroviral vector that encodes both a Renilla luciferase reporter gene controlled by microRNA binding sites in its 3’ UTR and a Firefly luciferase normalization gene. miR-Sens sensors can be efficiently transduced in primary cells such as human fibroblasts and mammary epithelial cells, and allow the detection of overexpressed and, more importantly, endogenous microRNAs. Notably, we find that the relative luciferase activity is correlated to the miRNA expression, allowing quantitative measurement of microRNA activity. We have subsequently validated the miR-Sens 3’ UTR vectors with known human miRNA-372, miRNA-373, and miRNA-31 targets (LATS2 and TXNIP). Overall, we observe that miR-Sens-based assays are highly reproducible, allowing detection of the independent contribution of multiple microRNAs to 3’ UTR-mediated translational control of LATS2. In conclusion, miR-Sens is a new tool for the efficient study of microRNA activity in primary cells or panels of cell lines. This vector will not only be useful for studies on microRNA biology, but also more broadly on other factors influencing the translation of mRNAs.}, pmid = {22417692}, keywords = {3’ Untranslated Regions,Animals,Argonaute Proteins,Argonaute Proteins: metabolism,Base Sequence,Cell Line,dual luciferase,Gene Expression,Gene Order,Genes,Genetic Vectors,Humans,Luciferases,Luciferases: genetics,Luciferases: metabolism,Messenger,Messenger: metabolism,Mice,microrna,MicroRNAs,MicroRNAs: metabolism,Molecular Sequence Data,nosource,Poly A,Poly A: chemistry,primary cells,Protein Biosynthesis,Reporter,Retroviridae,Retroviridae: genetics,retrovirus,RNA,utr} }

@article{chenDifferentialRegulationAREmediated2006, title = {Differential Regulation of {{ARE-mediated TNF\(\alpha\)}} and {{IL-1beta mRNA}} Stability by Lipopolysaccharide in {{RAW264}}.7 Cells}, author = {Chen, Yu-Ling and Huang, Ya-Lin and Lin, Nien-Yi and Chen, Hui-Chen and Chiu, Wan-Chih and Chang, Ching-Jin}, year = 2006, month = jul, journal = {Biochemical and Biophysical Research Communications}, volume = {346}, number = {1}, eprint = {16759646}, eprinttype = {pubmed}, pages = {160–168}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2006.05.093}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16759646}, abstract = {Messenger RNA degradation is a mechanism by which eukaryotic cells regulate gene expression and influence cell growth and differentiation. Many protooncogene, cytokine, and growth factor RNAs contain AU-rich element (AREs) in the 3’untranslated regions which enable them to be targeted for rapid degradation. To investigate the mechanism of ARE-mediated RNA stability, we demonstrate the expression and regulation of TNFalpha and IL-1beta mRNAs in LPS-stimulated macrophages. TNFalpha mRNA was rapidly induced by LPS and showed short half-life at 2-h induction, whereas IL-1beta mRNA was induced slowly and had longer half-life. Electrophoretic mobility shift assays showed that the LPS-induced destabilization factor tristetraprolin (TTP) could bind to TNFalpha ARE with higher affinity than to IL-1beta ARE. HuR was identified to interact with TNFalpha ARE to exert RNA stabilization activity. The expression and phosphorylation of TTP could be activated by p38 MAPK pathway during LPS stimulation. Moreover, ectopic expression with TTP and kinases in p38 pathway followed by biochemical assays showed that the activation of p38 pathway resulted in the phosphorylation of TTP and a decrease in its RNA-binding activity. The ARE-containing reporter assay presented that the p38 signal could reverse the inhibitory activity of TTP on IL-1beta ARE but not on TNFalpha ARE. The present results indicate that the heterogeneity of AREs from TNFalpha and IL-1beta could reflect distinct ARE-binding proteins to modulate their RNA expression.}, pmid = {16759646}, keywords = {Animals,Antigens,Base Sequence,Cell Line,Gene Expression Regulation,Heterogeneous-Nuclear Ribonucleoprotein D,Heterogeneous-Nuclear Ribonucleoprotein D: drug ef,Heterogeneous-Nuclear Ribonucleoprotein D: physiol,Humans,hur,il-1b,inflam-,Interleukin-1,Interleukin-1: genetics,lipopolysaccharide,Lipopolysaccharides,Lipopolysaccharides: pharmacology,many cases by interactions,matory response are potentially,Messenger,Messenger: metabolism,Mice,Molecular Sequence Data,mrna is determined in,nosource,p38 Mitogen-Activated Protein Kinases,p38 Mitogen-Activated Protein Kinases: physiology,regulatory proteins of the,RNA,RNA-Binding Proteins,RNA-Binding Proteins: metabolism,Signal Transduction,Surface,Surface: metabolism,the mrnas of many,the stability of,tnfa,tristetraprolin,Tristetraprolin,Tristetraprolin: metabolism,Tumor Necrosis Factor-alpha,Tumor Necrosis Factor-alpha: genetics,unstable} }

@article{muhlemannPrecursorRNAsHarboring2001, title = {Precursor {{RNAs}} Harboring Nonsense Codons Accumulate near the Site of Transcription}, author = {M{"u}hlemann, O. and {Mock-Casagrande}, C. S. and Wang, Jun}, year = 2001, journal = {Molecular cell}, volume = {8}, pages = {33–43}, url = {http://www.sciencedirect.com/science/article/pii/S109727650100288X}, keywords = {nosource} }

@article{dreumontCytoplasmicNonsensemediatedMRNA2004, title = {Cytoplasmic Nonsense-Mediated {{mRNA}} Decay for a Nonsense ({{W262X}}) Transcript of the Gene Responsible for Hereditary Tyrosinemia, Fumarylacetoacetate Hydrolase.}, author = {Dreumont, Natacha and Maresca, Antonella and Khandjian, Edward W. and Baklouti, Faouzi and Tanguay, Robert M.}, year = 2004, month = nov, journal = {Biochemical and biophysical research communications}, volume = {324}, number = {1}, eprint = {15465000}, eprinttype = {pubmed}, pages = {186–92}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2004.09.041}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15465000}, abstract = {Messenger RNAs containing premature stop codons are generally targeted for degradation through the nonsense-mediated mRNA decay (NMD) pathway. The subcellular localization of the NMD process in higher eukaryotes remains controversial. While many mRNAs are subjected to NMD prior to their release from the nucleus, a few display cytoplasmic NMD. To understand the possible impact of NMD on the pathogenesis of hereditary tyrosinemia type I, a severe metabolic disease caused by fumarylacetoacetate hydrolase (FAH) deficiency, we examined the metabolism of FAH mRNA harboring a nonsense mutation, W262X, in lymphoblastoid cell lines derived from patients and their parents. W262X-FAH transcripts show a approximately 20-fold reduction in abundance in mutant cells, which is translation-dependent. Cellular fractionation shows that this down-regulation of the W262X transcript occurs in the cytoplasm. Thus, the W262X FAH is another example of nonsense mRNAs subjected to the NMD pathway in the cytoplasm.}, pmid = {15465000}, keywords = {Cell Line,Codon,Gene Expression Regulation,Humans,Hydrolases,Hydrolases: genetics,Hydrolases: metabolism,Messenger,Messenger: genetics,Messenger: metabolism,Mutation,Nonsense,nosource,Protein Biosynthesis,RNA,RNA Stability,Subcellular Fractions,Subcellular Fractions: chemistry,Tyrosinemias,Tyrosinemias: genetics,Tyrosinemias: metabolism} }

@article{feiCouplingRibosomalL12008, title = {Coupling of Ribosomal {{L1}} Stalk and {{tRNA}} Dynamics during Translation Elongation}, author = {Fei, Jingyi and Kosuri, Pallav and MacDougall, DD Daniel D. and Gonzalez, Ruben L. and Jr, RL Gonzalez}, year = 2008, month = may, journal = {Molecular cell}, volume = {30}, number = {3}, pages = {348–359}, issn = {1097-4164}, doi = {10.1016/j.molcel.2008.03.012}, url = {http://www.sciencedirect.com/science/article/pii/S1097276508002128 http://www.ncbi.nlm.nih.gov/pubmed/18471980}, abstract = {By using single-molecule fluorescence resonance energy transfer (smFRET), we observe the real-time dynamic coupling between the ribosome, labeled at the L1 stalk, and transfer RNA (tRNA). We find that an interaction between the ribosomal L1 stalk and the newly deacylated tRNA is established spontaneously upon peptide bond formation; this event involves coupled movements of the L1 stalk and tRNAs as well as ratcheting of the ribosome. In the absence of elongation factor G, the entire pretranslocation ribosome fluctuates between just two states: a nonratcheted state, with tRNAs in their classical configuration and no L1 stalk-tRNA interaction, and a ratcheted state, with tRNAs in an intermediate hybrid configuration and a direct L1 stalk-tRNA interaction. We demonstrate that binding of EF-G shifts the equilibrium toward the ratcheted state. Real-time smFRET experiments reveal that the L1 stalk-tRNA interaction persists throughout the translocation reaction, suggesting that the L1 stalk acts to direct tRNA movements during translocation.}, pmid = {18471980}, keywords = {Carbocyanines,Carbocyanines: metabolism,Fluorescence Resonance Energy Transfer,Fluorescent Dyes,Fluorescent Dyes: metabolism,Macromolecular Substances,Macromolecular Substances: chemistry,Macromolecular Substances: metabolism,Models,Molecular,nosource,Nucleic Acid Conformation,Peptide Chain Elongation,Protein Conformation,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: genetics,Ribosomal Proteins: metabolism,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,RNA,Transfer,Transfer: chemistry,Transfer: metabolism,Translational} }

@article{altuntopSinglemoleculeStudyRibosome2010, title = {Single-Molecule Study of Ribosome Hierarchic Dynamics at the Peptidyl Transferase Center.}, author = {Altuntop, Mediha Esra and Ly, Cindy Tu and Wang, Yuhong}, year = 2010, month = nov, journal = {Biophysical journal}, volume = {99}, number = {9}, pages = {3002–9}, publisher = {Biophysical Society}, issn = {1542-0086}, doi = {10.1016/j.bpj.2010.08.037}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2966008&tool=pmcentrez&rendertype=abstract}, abstract = {During protein biosynthesis the ribosome moves along mRNA in steps of precisely three nucleotides. The mechanism for this ribosome motion remains elusive. Using a classification algorithm to sort single-molecule fluorescence resonance energy transfer data into subpopulations, we found that the ribosome dynamics detected at the peptidyl transferase center are highly inhomogeneous. The pretranslocation complex has at least four subpopulations that sample two hybrid states, whereas the posttranslocation complex is mainly static. We observed transitions among the ribosome subpopulations under various conditions, including 1), in the presence of EF-G; 2), spontaneously; 3), in different buffers, and 4), bound to antibiotics. Therefore, these subpopulations represent biologically active ribosomes. One key observation indicates that the Hy2 hybrid state only exists in a fluctuating ribosome subpopulation, which prompts us to propose that ribosome dynamics are hierarchically arranged. This proposal may have important implications for the regulation of cellular translation rates.}, pmid = {21044598}, keywords = {Algorithms,Biophysical Phenomena,Fluorescence Resonance Energy Transfer,Kinetics,Messenger,Messenger: genetics,Messenger: metabolism,Models,Molecular,nosource,Peptide Elongation Factor G,Peptide Elongation Factor G: metabolism,Peptidyl Transferases,Peptidyl Transferases: chemistry,Peptidyl Transferases: metabolism,Protein Biosynthesis,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: metabolism,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,RNA,Thermodynamics} }

@article{peskeSequenceStepsRibosome2005, title = {Sequence of Steps in Ribosome Recycling as Defined by Kinetic Analysis.}, author = {Peske, Frank and Rodnina, M. V. and Wintermeyer, Wolfgang}, year = 2005, month = may, journal = {Molecular cell}, volume = {18}, number = {4}, eprint = {15893724}, eprinttype = {pubmed}, pages = {403–12}, issn = {1097-2765}, doi = {10.1016/j.molcel.2005.04.009}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15893724}, abstract = {After termination of protein synthesis in bacteria, ribosomes are recycled from posttermination complexes by the combined action of elongation factor G (EF-G), ribosome recycling factor (RRF), and initiation factor 3 (IF3). The functions of the factors and the sequence in which ribosomal subunits, tRNA, and mRNA are released from posttermination complexes are unclear and, in part, controversial. Here, we study the reaction by rapid kinetics monitoring fluorescence. We show that RRF and EF-G with GTP, but not with GDPNP, promote the dissociation of 50S subunits from the posttermination complex without involving translocation or a translocation-like event. IF3 does not affect subunit dissociation but prevents reassociation, thereby masking the dissociating effect of EF-G-RRF under certain experimental conditions. IF3 is required for the subsequent ejection of tRNA and mRNA from the small subunit. The latter step is slower than subunit dissociation and constitutes the rate-limiting step of ribosome recycling.}, pmid = {15893724}, keywords = {Escherichia coli,Escherichia coli: genetics,Escherichia coli: metabolism,Fluorescence Resonance Energy Transfer,Kinetics,Messenger,Messenger: metabolism,nosource,Peptide Elongation Factor G,Peptide Elongation Factor G: metabolism,Protein Biosynthesis,Protein Biosynthesis: physiology,Ribosomal Proteins,Ribosomal Proteins: metabolism,Ribosomes,Ribosomes: metabolism,RNA,Transfer,Transfer: metabolism} }

@article{neumannEncodingMultipleUnnatural2010, title = {Encoding Multiple Unnatural Amino Acids via Evolution of a Quadruplet-Decoding Ribosome.}, author = {Neumann, Heinz and Wang, Kaihang and Davis, Lloyd and {Garcia-Alai}, Maria and Chin, Jason W.}, year = 2010, month = mar, journal = {Nature}, volume = {464}, number = {7287}, eprint = {20154731}, eprinttype = {pubmed}, pages = {441–4}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature08817}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20154731}, abstract = {The in vivo, genetically programmed incorporation of designer amino acids allows the properties of proteins to be tailored with molecular precision. The Methanococcus jannaschii tyrosyl-transfer-RNA synthetase-tRNA(CUA) (MjTyrRS-tRNA(CUA)) and the Methanosarcina barkeri pyrrolysyl-tRNA synthetase-tRNA(CUA) (MbPylRS-tRNA(CUA)) orthogonal pairs have been evolved to incorporate a range of unnatural amino acids in response to the amber codon in Escherichia coli. However, the potential of synthetic genetic code expansion is generally limited to the low efficiency incorporation of a single type of unnatural amino acid at a time, because every triplet codon in the universal genetic code is used in encoding the synthesis of the proteome. To encode efficiently many distinct unnatural amino acids into proteins we require blank codons and mutually orthogonal aminoacyl-tRNA synthetase-tRNA pairs that recognize unnatural amino acids and decode the new codons. Here we synthetically evolve an orthogonal ribosome (ribo-Q1) that efficiently decodes a series of quadruplet codons and the amber codon, providing several blank codons on an orthogonal messenger RNA, which it specifically translates. By creating mutually orthogonal aminoacyl-tRNA synthetase-tRNA pairs and combining them with ribo-Q1 we direct the incorporation of distinct unnatural amino acids in response to two of the new blank codons on the orthogonal mRNA. Using this code, we genetically direct the formation of a specific, redox-insensitive, nanoscale protein cross-link by the bio-orthogonal cycloaddition of encoded azide- and alkyne-containing amino acids. Because the synthetase-tRNA pairs used have been evolved to incorporate numerous unnatural amino acids, it will be possible to encode more than 200 unnatural amino acid combinations using this approach. As ribo-Q1 independently decodes a series of quadruplet codons, this work provides foundational technologies for the encoded synthesis and synthetic evolution of unnatural polymers in cells.}, pmid = {20154731}, keywords = {Alkynes,Alkynes: metabolism,Amino Acids,Amino Acids: genetics,Amino Acids: metabolism,Amino Acyl-tRNA Synthetases,Amino Acyl-tRNA Synthetases: genetics,Amino Acyl-tRNA Synthetases: metabolism,Azides,Azides: metabolism,Biocatalysis,Biocatalysis: drug effects,Calmodulin,Calmodulin: chemistry,Calmodulin: genetics,Calmodulin: metabolism,Codon,Codon: genetics,Copper,Copper: metabolism,Copper: pharmacology,Cyclization,Cyclization: drug effects,Directed Molecular Evolution,Genetic Code,Genetic Code: genetics,Genetic Engineering,Genetic Engineering: methods,Messenger,Messenger: genetics,Messenger: metabolism,Methanococcus,Models,Molecular,nosource,Protein Biosynthesis,Protein Biosynthesis: genetics,Protein Biosynthesis: physiology,Protein Conformation,Protein Engineering,Protein Engineering: methods,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,RNA,Transfer,Transfer: genetics,Transfer: metabolism} }

@article{songMultipleMRNADecapping2010, title = {Multiple {{mRNA}} Decapping Enzymes in Mammalian Cells.}, author = {Song, Man-gen and Li, You and Kiledjian, Megerditch}, year = 2010, month = nov, journal = {Molecular cell}, volume = {40}, number = {3}, pages = {423–32}, publisher = {Elsevier Inc.}, issn = {1097-4164}, doi = {10.1016/j.molcel.2010.10.010}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2982215&tool=pmcentrez&rendertype=abstract http://dx.doi.org/10.1016/j.molcel.2010.10.010}, abstract = {Regulation of RNA degradation plays an important role in the control of gene expression. One mechanism of eukaryotic mRNA decay proceeds through an initial deadenylation followed by 5’ end decapping and exonucleolytic decay. Dcp2 is currently believed to be the only cytoplasmic decapping enzyme responsible for decapping of all mRNAs. Here we report that Dcp2 protein modestly contributes to bulk mRNA decay and surprisingly is not detectable in a subset of mouse and human tissues. Consistent with these findings, a hypomorphic knockout of Dcp2 had no adverse consequences in mice. In contrast, the previously reported Xenopus nucleolar decapping enzyme, Nudt16, is an ubiquitous cytoplasmic decapping enzyme in mammalian cells. Like Dcp2, Nudt16 also regulates the stability of a subset of mRNAs including a member of the motin family of proteins involved in angiogenesis, Angiomotin-like 2. These data demonstrate mammalian cells possess multiple mRNA decapping enzymes, including Nudt16 to regulate mRNA turnover.}, pmid = {21070968}, keywords = {Animals,Cell Line,Endoribonucleases,Endoribonucleases: metabolism,Gene Expression Profiling,Gene Expression Regulation,Homozygote,Humans,Insertional,Insertional: genetics,Mammals,Mammals: metabolism,Messenger,Messenger: genetics,Messenger: metabolism,Mice,Mutagenesis,nosource,Organ Specificity,Organ Specificity: genetics,Pyrophosphatases,Pyrophosphatases: genetics,Pyrophosphatases: metabolism,RNA,RNA Caps,RNA Caps: metabolism,RNA Stability,RNA Stability: genetics,Transfection} }

@article{nissanDecappingActivatorsSaccharomyces2010, title = {Decapping Activators in {{Saccharomyces}} Cerevisiae Act by Multiple Mechanisms.}, author = {Nissan, Tracy and Rajyaguru, Purusharth and She, Meipei and Song, Haiwei and Parker, Roy}, year = 2010, month = sep, journal = {Molecular cell}, volume = {39}, number = {5}, pages = {773–83}, publisher = {Elsevier Ltd}, issn = {1097-4164}, doi = {10.1016/j.molcel.2010.08.025}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2946179&tool=pmcentrez&rendertype=abstract http://dx.doi.org/10.1016/j.molcel.2010.08.025}, abstract = {Eukaryotic mRNA degradation often occurs in a process whereby translation initiation is inhibited and the mRNA is targeted for decapping. In yeast cells, Pat1, Scd6, Edc3, and Dhh1 all function to promote decapping by an unknown mechanism(s). We demonstrate that purified Scd6 and a region of Pat1 directly repress translation in vitro by limiting the formation of a stable 48S preinitiation complex. Moreover, while Pat1, Edc3, Dhh1, and Scd6 all bind the decapping enzyme, only Pat1 and Edc3 enhance its activity. We also identify numerous direct interactions between Pat1, Dcp1, Dcp2, Dhh1, Scd6, Edc3, Xrn1, and the Lsm1-7 complex. These observations identify three classes of decapping activators that function to directly repress translation initiation and/or stimulate Dcp1/2. Moreover, Pat1 is identified as critical in mRNA decay by first inhibiting translation initiation, then serving as a scaffold to recruit components of the decapping complex, and finally activating Dcp2.}, pmid = {20832728}, keywords = {Fungal,Fungal: genetics,Fungal: metabolism,Messenger,Messenger: genetics,Messenger: metabolism,nosource,Peptide Chain Initiation,RNA,RNA Stability,RNA Stability: physiology,RNA-Binding Proteins,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Translational,Translational: physiolog} }

@article{geislerAlternateEndingsNew2010, title = {Alternate Endings: A New Story for {{mRNA}} Decapping.}, author = {Geisler, Sarah and Coller, Jeff}, year = 2010, month = nov, journal = {Molecular cell}, volume = {40}, number = {3}, pages = {349–50}, publisher = {Elsevier Inc.}, issn = {1097-4164}, doi = {10.1016/j.molcel.2010.10.025}, url = {http://dx.doi.org/10.1016/j.molcel.2010.10.025 http://www.ncbi.nlm.nih.gov/pubmed/21070961}, abstract = {With most of the important players identified, the process of decapping is thought, for the most part, to be well understood. In this issue of Molecular Cell, Song et al. (2010) challenge this notion with the identification of a previously uncharacterized mRNA decapping enzyme.}, pmid = {21070961}, keywords = {nosource} }

@article{sanbonmatsuComputationalStudiesMolecular2012, title = {Computational Studies of Molecular Machines: The Ribosome.}, author = {Sanbonmatsu, Karissa Y.}, year = 2012, month = feb, journal = {Current opinion in structural biology}, eprint = {22336622}, eprinttype = {pubmed}, pages = {1–7}, publisher = {Elsevier Ltd}, issn = {1879-033X}, doi = {10.1016/j.sbi.2012.01.008}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22336622}, abstract = {The past decade has produced an avalanche of experimental data on the structure and dynamics of the ribosome. Groundbreaking studies in structural biology and kinetics have placed important constraints on ribosome structural dynamics. However, a gulf remains between static structures and time dependent data. In particular, X-ray crystallography and cryo-EM studies produce static models of the ribosome in various states, but lack dynamic information. Single molecule studies produce information on the rates of transitions between these states but do not have high-resolution spatial information. Computational studies have aided in bridging this gap by providing atomic resolution simulations of structural fluctuations and transitions between configurations.}, pmid = {22336622}, keywords = {nosource} }

@article{mcdevittRequirementDownstreamSequence1984, title = {Requirement of a Downstream Sequence for Generation of a Poly({{A}}) Addition Site.}, author = {{}a McDevitt, M. and Imperiale, M. J. and Ali, H. and Nevins, J. R.}, year = 1984, month = jul, journal = {Cell}, volume = {37}, number = {3}, eprint = {6744418}, eprinttype = {pubmed}, pages = {993–9}, issn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/6744418}, abstract = {The 3’ terminus of most, if not all, eucaryotic polyadenylated mRNAs is formed as a result of endonucleolytic cleavage of a larger precursor RNA. That is, transcription does not terminate at the mRNA 3’ sequence but rather proceeds through this site, terminating at some distance downstream. Using a plasmid containing the adenovirus E2A transcriptional unit, we have investigated the sequence requirement for the formation of a mature mRNA 3’ terminus, focusing on the role of sequences immediately distal to the poly(A) addition site. Deletion mutants were constructed in the region distal to the poly(A) addition site and assayed by transfection into human 293 cells. The results demonstrate that 35 nucleotides distal to the site of poly(A) addition are sufficient for the formation of a mature E2 mRNA. However, removal of an additional 15 nucleotides, leaving 20 nucleotides distal to the poly(A) site, abolished the ability to produce functional E2A mRNA. The defect in the production of functional mRNA from such a mutant appears to be in the proper cleavage of the primary transcript at the poly(A) addition site. It would thus appear that sequences immediately distal to the site of poly(A) addition do not contribute to the mature mRNA but are essential for the formation of mature mRNA.}, pmid = {6744418}, keywords = {Adenoviruses,Base Sequence,DNA,Endoribonucleases,Endoribonucleases: genetics,Human,Human: genetics,Humans,Messenger,Messenger: genetics,nosource,Poly A,Poly A: genetics,Post-Transcriptional,RNA,RNA Processing,Viral,Viral: genetics} }

@article{kesslerHrp1SequencespecificRNAbinding1997, title = {Hrp1, a Sequence-Specific {{RNA-binding}} Protein That Shuttles between the Nucleus and the Cytoplasm, Is Required for {{mRNA}} 3’-End Formation in Yeast}, author = {Kessler, M. M. and Henry, M. F. and Shen, E. and Zhao, J. and Gross, S. and {}a Silver, P. and Moore, C. L.}, year = 1997, month = oct, journal = {Genes & Development}, volume = {11}, number = {19}, pages = {2545–2556}, issn = {0890-9369}, doi = {10.1101/gad.11.19.2545}, url = {http://www.genesdev.org/cgi/doi/10.1101/gad.11.19.2545}, keywords = {1997,31,a,hnrnp,hrp1,most mrna precursors undergo,mrna export,mrna polyadenylation,nosource,prior to moving into,received july 3,revised version accepted july,rna processing,series of processing events,the cy-,while in the nucleus} }

@article{linSua5ProteinEssential2010, title = {The {{Sua5}} Protein Is Essential for Normal Translational Regulation in Yeast.}, author = {{}a Lin, Changyi and Ellis, Steven R. and True, Heather L.}, year = 2010, month = jan, journal = {Molecular and cellular biology}, volume = {30}, number = {1}, pages = {354–63}, issn = {1098-5549}, doi = {10.1128/MCB.00754-09}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2798302&tool=pmcentrez&rendertype=abstract}, abstract = {The anticodon stem-loop of tRNAs requires extensive posttranscriptional modifications in order to maintain structure and stabilize the codon-anticodon interaction. These modifications also play a role in accommodating wobble, allowing a limited pool of tRNAs to recognize degenerate codons. Of particular interest is the formation of a threonylcarbamoyl group on adenosine 37 (t(6)A(37)) of tRNAs that recognize ANN codons. Located adjacent and 3’ to the anticodon, t(6)A(37) is a conserved modification that is critical for reading frame maintenance. Recently, the highly conserved YrdC/Sua5 family of proteins was shown to be required for the formation of t(6)A(37). Sua5 was originally identified in a screen by virtue of its ability to affect expression from an aberrant upstream AUG codon in the cyc1 transcript. Together, these findings implicate Sua5 in protein translation at the level of codon recognition. Here, we show that Sua5 is critical for normal translation. The loss of SUA5 causes increased leaky scanning through AUG codons, +1 frameshifting, and nonsense suppression. In addition, the loss of SUA5 amplifies the 20S RNA virus found in Saccharomyces cerevisiae, possibly through an internal ribosome entry site-mediated mechanism. This study reveals a critical role for Sua5 and the t(6)A(37) modification in translational fidelity.}, pmid = {19884342}, keywords = {Basic-Leucine Zipper Transcription Factors,Basic-Leucine Zipper Transcription Factors: biosyn,Basic-Leucine Zipper Transcription Factors: geneti,Codon,DNA-Binding Proteins,DNA-Binding Proteins: genetics,DNA-Binding Proteins: physiology,Frameshifting,Initiator,nosource,Open Reading Frames,Protein Biosynthesis,Ribosomal,RNA,RNA Viruses,RNA Viruses: genetics,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: biosynthesis,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: physiology,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Saccharomyces cerevisiae: virology,Terminator,Transfer,Transfer: genetics,Viral,Viral: biosynthesis} }

@article{sonenbergRegulationTranslationInitiation2009, title = {Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets.}, author = {Sonenberg, Nahum and Hinnebusch, Alan G.}, year = 2009, month = feb, journal = {Cell}, volume = {136}, number = {4}, eprint = {19239892}, eprinttype = {pubmed}, pages = {731–45}, publisher = {Elsevier Inc.}, issn = {1097-4172}, doi = {10.1016/j.cell.2009.01.042}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19239892 http://dx.doi.org/10.1016/j.cell.2009.01.042}, abstract = {Translational control in eukaryotic cells is critical for gene regulation during nutrient deprivation and stress, development and differentiation, nervous system function, aging, and disease. We describe recent advances in our understanding of the molecular structures and biochemical functions of the translation initiation machinery and summarize key strategies that mediate general or gene-specific translational control, particularly in mammalian systems.}, pmid = {19239892}, keywords = {Animals,Gene Expression Regulation,Humans,Models,Molecular,nosource,Peptide Chain Initiation,Peptide Initiation Factors,Peptide Initiation Factors: chemistry,Peptide Initiation Factors: metabolism,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,Translational} }

@article{congHumanTelomeraseIts2002, title = {Human {{Telomerase}} and {{Its Regulation}}}, author = {Cong, Yu-sheng and Wright, Woodring E. and Shay, Jerry W.}, year = 2002, journal = {Microbiology and Molecular Biology Reviews}, volume = {66}, number = {3}, pages = {407–425}, doi = {10.1128/MMBR.66.3.407}, keywords = {nosource} } % == BibTeX quality report for congHumanTelomeraseIts2002: % ? Title looks like it was stored in title-case in Zotero

@article{ruggeroDoesRibosomeTranslate2003, title = {Does the Ribosome Translate Cancer?}, author = {Ruggero, Davide and Pandolfi, Pier Paolo}, year = 2003, month = mar, journal = {Nat. Rev. Cancer}, volume = {3}, number = {3}, eprint = {12612653}, eprinttype = {pubmed}, pages = {179–92}, issn = {1474-175X}, doi = {10.1038/nrc1015}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12612653}, abstract = {Ribosome biogenesis and translation control are essential cellular processes that are governed at numerous levels. Several tumour suppressors and proto-oncogenes have been found either to affect the formation of the mature ribosome or to regulate the activity of proteins known as translation factors. Disruption in one or more of the steps that control protein biosynthesis has been associated with alterations in the cell cycle and regulation of cell growth. Therefore, certain tumour suppressors and proto-oncogenes might regulate malignant progression by altering the protein synthesis machinery. Although many studies have correlated deregulation of protein biosynthesis with cancer, it remains to be established whether this translates directly into an increase in cancer susceptibility, and under what circumstances.}, pmid = {12612653}, keywords = {Biological,cdc,Cell Cycle Proteins,Cell Cycle Proteins: genetics,Cell Cycle Proteins: physiology,Cell Nucleolus,Cell Nucleolus: physiology,Cell Size,Cell Transformation,Forecasting,Genes,Hereditary,Hereditary: genetics,Models,Neoplasms,Neoplasms: genetics,Neoplasms: metabolism,Neoplasms: therapy,Neoplastic,Neoplastic Syndromes,Neoplastic: genetics,nosource,Phosphoric Monoester Hydrolases,Phosphoric Monoester Hydrolases: physiology,Protein Biosynthesis,Proto-Oncogene Proteins,Proto-Oncogene Proteins c-myc,Proto-Oncogene Proteins c-myc: physiology,Proto-Oncogene Proteins: physiology,Proto-Oncogenes,PTEN Phosphohydrolase,Retinoblastoma Protein,Retinoblastoma Protein: physiology,Ribosomal,Ribosomal Proteins,Ribosomal Proteins: physiology,Ribosomal: biosynthesis,Ribosomes,Ribosomes: physiology,RNA,Tumor Suppressor,Tumor Suppressor Protein p53,Tumor Suppressor Protein p53: physiology,Tumor Suppressor Proteins,Tumor Suppressor Proteins: physiology} } % == BibTeX quality report for ruggeroDoesRibosomeTranslate2003: % ? Possibly abbreviated journal title Nat. Rev. Cancer

@article{lafontaineGarbageCanRibosomes2010, title = {A ‘garbage Can’ for Ribosomes: How Eukaryotes Degrade Their Ribosomes.}, author = {Lafontaine, Denis L. J.}, year = 2010, month = may, journal = {Trends in Biochemical Sciences}, volume = {35}, number = {5}, eprint = {20097077}, eprinttype = {pubmed}, pages = {267–77}, publisher = {Elsevier Ltd}, issn = {0968-0004}, doi = {10.1016/j.tibs.2009.12.006}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20097077}, abstract = {Ribosome synthesis is a major metabolic activity that involves hundreds of individual reactions, each of which is error-prone. Ribosomal insults occur in cis (alteration in rRNA sequences) and in trans (failure to bind to, or loss of, an assembly factor or ribosomal protein). In addition, specific growth conditions, such as starvation, require that excess ribosomes are turned over efficiently. Recent work indicates that cells evolved multiple strategies to recognize specifically, and target for clearance, ribosomes that are structurally and/or functionally deficient, as well as in excess. This surveillance is active at every step of the ribosome synthesis pathway and on mature ribosomes, involves nearly entirely different mechanisms for the small and large subunits, and requires specialized subcellular organelles.}, pmid = {20097077}, keywords = {Base Sequence,Eukaryota,nosource,Ribosomal,Ribosomal Proteins,Ribosomal Proteins: genetics,Ribosomal Proteins: metabolism,Ribosomal: genetics,Ribosomal: metabolism,Ribosomes,Ribosomes: genetics,Ribosomes: metabolism,RNA} }

@article{shoemakerDom34Hbs1Promotes2010, title = {Dom34:{{Hbs1}} Promotes Subunit Dissociation and Peptidyl-{{tRNA}} Drop-off to Initiate No-Go Decay.}, author = {Shoemaker, Christopher J. and Eyler, Daniel E. and Green, Rachel}, year = 2010, month = oct, journal = {Science}, volume = {330}, number = {6002}, eprint = {20947765}, eprinttype = {pubmed}, pages = {369–72}, issn = {1095-9203}, doi = {10.1126/science.1192430}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20947765}, abstract = {No-go decay (NGD) is one of several messenger RNA (mRNA) surveillance systems dedicated to the removal of defective mRNAs from the available pool. Two interacting factors, Dom34 and Hbs1, are genetically implicated in NGD in yeast. Using a reconstituted yeast translation system, we show that Dom34:Hbs1 interacts with the ribosome to promote subunit dissociation and peptidyl-tRNA drop-off. Our data further indicate that these recycling activities are shared by the homologous translation termination factor complex eRF1:eRF3, suggesting a common ancestral function. Because Dom34:Hbs1 activity exhibits no dependence on either peptide length or A-site codon identity, we propose that this quality-control system functions broadly to recycle ribosomes throughout the translation cycle whenever stalls occur.}, pmid = {20947765}, keywords = {Amino Acyl,Amino Acyl: genetics,Amino Acyl: metabolism,Cell Cycle Proteins,Cell Cycle Proteins: genetics,Cell Cycle Proteins: metabolism,Codon,Endoribonucleases,Endoribonucleases: genetics,Endoribonucleases: metabolism,Fungal,Fungal: genetics,Fungal: metabolism,GTP-Binding Proteins,GTP-Binding Proteins: genetics,GTP-Binding Proteins: metabolism,Guanosine Triphosphate,Guanosine Triphosphate: metabolism,HSP70 Heat-Shock Proteins,HSP70 Heat-Shock Proteins: genetics,HSP70 Heat-Shock Proteins: metabolism,Kinetics,Messenger,Messenger: genetics,Messenger: metabolism,nosource,Peptide Chain Termination,Peptide Elongation Factors,Peptide Elongation Factors: genetics,Peptide Elongation Factors: metabolism,Peptide Termination Factors,Peptide Termination Factors: metabolism,Protein Biosynthesis,Recombinant Proteins,Recombinant Proteins: metabolism,Ribosome Subunits,Ribosome Subunits: metabolism,RNA,RNA Stability,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Terminator,Transfer,Translational} }

@article{warneckeUniqueCostDynamics2010, title = {Unique Cost Dynamics Elucidate the Role of Frameshifting Errors in Promoting Translational Robustness.}, author = {Warnecke, Tobias and Huang, Yang and Przytycka, Teresa M. and Hurst, Laurence D.}, year = 2010, month = jan, journal = {Genome Biology and Evolution}, volume = {2}, pages = {636–45}, issn = {1759-6653}, doi = {10.1093/gbe/evq049}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2941156&tool=pmcentrez&rendertype=abstract}, abstract = {There is now considerable evidence supporting the view that codon usage is frequently under selection for translational accuracy. There are, however, multiple forms of inaccuracy (missense, premature termination, and frameshifting errors) and pinpointing a particular error process behind apparently adaptive mRNA anatomy is rarely straightforward. Understanding differences in the fitness costs associated with different types of translational error can help us devise critical tests that can implicate one error process to the exclusion of others. To this end, we present a model that captures distinct features of frameshifting cost and apply this to 641 prokaryotic genomes. We demonstrate that, although it is commonly assumed that the ribosome encounters an off-frame stop codon soon after the frameshift and costs of mis-elongation are therefore limited, genomes with high GC content typically incur much larger per-error costs. We go on to derive the prediction, unique to frameshifting errors, that differences in translational robustness between the 5’ and 3’ ends of genes should be less pronounced in genomes with higher GC content. This prediction we show to be correct. Surprisingly, this does not mean that GC-rich organisms necessarily carry a greater fitness burden as a consequence of accidental frameshifting. Indeed, increased per-error costs are often more than counterbalanced by lower predicted error rates owing to more diverse anticodon repertoires in GC-rich genomes. We therefore propose that selection on tRNA repertoires may operate to reduce frameshifting errors.}, pmid = {20688751}, keywords = {Base Composition,Base Composition: genetics,Frameshift Mutation,Frameshift Mutation: genetics,Genetic,Models,nosource,Protein Biosynthesis,Protein Biosynthesis: genetics,RNA,Transfer,Transfer: genetics} }

@article{drummondEvolutionaryConsequencesErroneous2009, title = {The Evolutionary Consequences of Erroneous Protein Synthesis}, author = {Drummond, D. A. and Wilke, C. O.}, year = 2009, journal = {Nature Reviews Genetics}, volume = {10}, number = {10}, pages = {715–724}, doi = {10.1038/nrg2662.The}, url = {http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg2662.html}, keywords = {nosource} }

@article{anderssonCodonPreferencesFreeliving1990, title = {Codon Preferences in Free-Living Microorganisms.}, author = {Andersson, S. G. and Kurland, C. G.}, year = 1990, month = jun, journal = {Microbiological reviews}, volume = {54}, number = {2}, pages = {198–210}, issn = {0146-0749}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=372768&tool=pmcentrez&rendertype=abstract}, abstract = {A popular interpretation of the major codon preference is that it reflects the operation of a regulatory device that controls the expression of individual proteins. In this popular model, rapidly translated codons are thought to promote the accumulation of the highly expressed proteins and slowly translated codons are thought to retard the expression of poorly expressed proteins. However, this widely accepted model is not supported by kinetic theory or by experimental results. A less fashionable model in which the major codon preference has nothing to do with the expression level of the individual proteins is forwarded. In this model, the major codon preference is viewed as a global strategy to support the efficient function of the translation system and thereby to maximize the growth rates of cells under favorable conditions.}, pmid = {2194095}, keywords = {Animals,Bacteria,Bacteria: genetics,Bacterial Proteins,Bacterial Proteins: biosynthesis,Codon,Codon: genetics,Eukaryota,Eukaryota: genetics,Gene Expression Regulation,Messenger,Messenger: genetics,nosource,Protein Biosynthesis,Protozoan Proteins,Protozoan Proteins: biosynthesis,RNA} }

@article{buskePotentialVivoRoles2011, title = {Potential in Vivo Roles of Nucleic Acid Triple-Helices}, author = {{}a Buske, Fabian and Mattick, John S. and Bailey, Timothy L. and Rules, P.}, year = 2011, month = may, journal = {RNA biology}, volume = {8}, number = {June}, pages = {427–439}, issn = {1547-6286}, doi = {10.4161/rna.8.3.14999}, url = {http://www.landesbioscience.com/journals/rnabiology/BuskeRNA8-3.pdf http://www.landesbioscience.com/journals/rnabiology/article/14999/}, keywords = {abbreviations,dna to form a,ncrna,non-protein-coding rna,nosource,rna-dna interaction,sequence-specific,tf,tfo,the ability of double-stranded,transcription factor,transcriptional regulation,triple-helical,triple-helix,triplex target site,triplex-forming oligonucleotide,tts} }

@article{lujambioMicrocosmosCancer2012, title = {The Microcosmos of Cancer.}, author = {Lujambio, Amaia and Lowe, Scott W.}, year = 2012, month = feb, journal = {Nature}, volume = {482}, number = {7385}, eprint = {22337054}, eprinttype = {pubmed}, pages = {347–55}, issn = {1476-4687}, doi = {10.1038/nature10888}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22337054}, abstract = {The discovery of microRNAs (miRNAs) almost two decades ago established a new paradigm of gene regulation. During the past ten years these tiny non-coding RNAs have been linked to virtually all known physiological and pathological processes, including cancer. In the same way as certain key protein-coding genes, miRNAs can be deregulated in cancer, in which they can function as a group to mark differentiation states or individually as bona fide oncogenes or tumour suppressors. Importantly, miRNA biology can be harnessed experimentally to investigate cancer phenotypes or used therapeutically as a target for drugs or as the drug itself.}, pmid = {22337054}, keywords = {nosource} }

@article{landerInitialSequencingAnalysis2001, title = {Initial Sequencing and Analysis of the Human Genome}, author = {Lander, ES S. and Linton, LM M. and Birren, B. and Nusbaum, C. and Zody, M. C. and Baldwin, J. and Devon, K. and Dewar, K. and Doyle, M. and FitzHugh, W. and Funke, R. and Gage, D. and Harris, K. and Heaford, a and Howland, J. and Kann, L. and Lehoczky, J. and LeVine, R. and McEwan, P. and McKernan, K. and Meldrim, J. and Mesirov, J. P. and Miranda, C. and Morris, W. and Naylor, J. and Raymond, C. and Rosetti, M. and Santos, R. and Sheridan, a and Sougnez, C. and {Stange-Thomann}, N. and Stojanovic, N. and Subramanian, a and Wyman, D. and Rogers, J. and Sulston, J. and Ainscough, R. and Beck, S. and Bentley, D. and Burton, J. and Clee, C. and Carter, N. and Coulson, a and Deadman, R. and Deloukas, P. and Dunham, a and Dunham, I. and Durbin, R. and French, L. and Grafham, D. and Gregory, S. and Hubbard, T. and Humphray, S. and Hunt, a and Jones, M. and Lloyd, C. and McMurray, a and Matthews, L. and Mercer, S. and Milne, S. and Mullikin, J. C. and Mungall, a and Plumb, R. and Ross, M. and Shownkeen, R. and Sims, S. and Waterston, R. H. and Wilson, R. K. and Hillier, L. W. and McPherson, J. D. and {}a Marra, M. and Mardis, E. R. and {}a Fulton, L. and Chinwalla, a T. and Pepin, K. H. and Gish, W. R. and Chissoe, S. L. and Wendl, M. C. and Delehaunty, K. D. and Miner, T. L. and Delehaunty, a and Kramer, J. B. and Cook, L. L. and Fulton, R. S. and Johnson, D. L. and Minx, P. J. and Clifton, S. W. and Hawkins, T. and Branscomb, E. and Predki, P. and Richardson, P. and Wenning, S. and Slezak, T. and Doggett, N. and Cheng, J. F. and Olsen, a and Lucas, S. and Elkin, C. and Uberbacher, E. and Frazier, M. and {}a Gibbs, R. and Muzny, D. M. and Scherer, S. E. and Bouck, J. B. and Sodergren, E. J. and Worley, K. C. and Rives, C. M. and Gorrell, J. H. and Metzker, M. L. and Naylor, S. L. and Kucherlapati, R. S. and Nelson, D. L. and Weinstock, G. M. and Sakaki, Y. and Fujiyama, a and Hattori, M. and Yada, T. and Toyoda, a and Itoh, T. and Kawagoe, C. and Watanabe, H. and Totoki, Y. and Taylor, T. and Weissenbach, J. and Heilig, R. and Saurin, W. and Artiguenave, F. and Brottier, P. and Bruls, T. and Pelletier, E. and Robert, C. and Wincker, P. and Smith, D. R. and {Doucette-Stamm}, L. and Rubenfield, M. and Weinstock, K. and Lee, H. M. and Dubois, J. and Rosenthal, a and Platzer, M. and Nyakatura, G. and Taudien, S. and Rump, a and Yang, H. and Yu, J. and Wang, J. and Huang, G. and Gu, J. and Hood, L. and Rowen, L. and Madan, a and Qin, S. and Davis, R. W. and {}a Federspiel, N. and Abola, a P. and Proctor, M. J. and Myers, R. M. and Schmutz, J. and Dickson, M. and Grimwood, J. and Cox, D. R. and Olson, M. V. and Kaul, R. and Shimizu, N. and Kawasaki, K. and Minoshima, S. and {}a Evans, G. and Athanasiou, M. and Schultz, R. and {}a Roe, B. and Chen, F. and Pan, H. and Ramser, J. and Lehrach, H. and Reinhardt, R. and McCombie, W. R. and {}de la Bastide, M. and Dedhia, N. and Bl{"o}cker, H. and Hornischer, K. and Nordsiek, G. and Agarwala, R. and Aravind, L. and {}a Bailey, J. and Bateman, a and Batzoglou, S. and Birney, E. and Bork, P. and Brown, D. G. and Burge, C. B. and Cerutti, L. and Chen, H. C. and Church, D. and Clamp, M. and Copley, R. R. and Doerks, T. and Eddy, S. R. and Eichler, E. E. and Furey, T. S. and Galagan, J. and Gilbert, J. G. and Harmon, C. and Hayashizaki, Y. and Haussler, D. and Hermjakob, H. and Hokamp, K. and Jang, W. and Johnson, L. S. and {}a Jones, T. and Kasif, S. and Kaspryzk, a and Kennedy, S. and Kent, W. J. and Kitts, P. and Koonin, E. V. and Korf, I. and Kulp, D. and Lancet, D. and Lowe, T. M. and McLysaght, a and Mikkelsen, T. and Moran, J. V. and Mulder, N. and Pollara, V. J. and Ponting, C. P. and Schuler, G. and Schultz, J. and Slater, G. and Smit, a F. and Stupka, E. and Szustakowski, J. and {Thierry-Mieg}, D. and {Thierry-Mieg}, J. and Wagner, L. and Wallis, J. and Wheeler, R. and Williams, a and Wolf, Y. I. and Wolfe, K. H. and Yang, S. P. and Yeh, R. F. and Collins, F. and Guyer, M. S. and Peterson, J. and Felsenfeld, a and {}a Wetterstrand, K. and Patrinos, a and Morgan, M. J. and {}de Jong, P. and Catanese, J. J. and Osoegawa, K. and Shizuya, H. and Choi, S. and Chen, Y. J. and Szustakowki, J.}, year = 2001, month = feb, journal = {Nature}, volume = {409}, number = {6822}, pages = {860–921}, issn = {0028-0836}, doi = {10.1038/35057062}, url = {http://www.nature.com/nature/journal/v409/n6822/abs/409860a0.html http://www.ncbi.nlm.nih.gov/pubmed/11237011}, abstract = {The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.}, pmid = {11237011}, keywords = {Animals,Chromosome Mapping,Conserved Sequence,CpG Islands,Databases,DNA,DNA Transposable Elements,DNA: methods,Drug Industry,Evolution,Factual,Forecasting,GC Rich Sequence,Gene Duplication,Genes,Genetic Diseases,Genetics,Genome,Human,Human Genome Project,Humans,Inborn,Medical,Molecular,Mutation,nosource,Nucleic Acid,Private Sector,Proteins,Proteins: genetics,Proteome,Public Sector,Repetitive Sequences,RNA,RNA: genetics,Sequence Analysis,Species Specificity} }

@article{beckerStructuralBasisHighly2012, title = {Structural Basis of Highly Conserved Ribosome Recycling in Eukaryotes and Archaea.}, author = {Becker, Thomas and Franckenberg, Sibylle and Wickles, Stephan and Shoemaker, Christopher J. and Anger, Andreas M. and Armache, Jean-Paul and Sieber, Heidemarie and Ungewickell, Charlotte and Berninghausen, Otto and Daberkow, Ingo and Karcher, Annette and Thomm, Michael and Hopfner, Karl-Peter and Green, Rachel and Beckmann, Roland}, year = 2012, month = feb, journal = {Nature}, volume = {482}, number = {7386}, eprint = {22358840}, eprinttype = {pubmed}, pages = {501–6}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature10829}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22358840}, abstract = {Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation factor G, and several structures of bacterial recycling complexes have been determined. In the eukaryotic and archaeal kingdoms, however, recycling involves the ABC-type ATPase ABCE1 and little is known about its structural basis. Here we present cryo-electron microscopy reconstructions of eukaryotic and archaeal ribosome recycling complexes containing ABCE1 and the termination factor paralogue Pelota. These structures reveal the overall binding mode of ABCE1 to be similar to canonical translation factors. Moreover, the iron-sulphur cluster domain of ABCE1 interacts with and stabilizes Pelota in a conformation that reaches towards the peptidyl transferase centre, thus explaining how ABCE1 may stimulate peptide-release activity of canonical termination factors. Using the mechanochemical properties of ABCE1, a conserved mechanism in archaea and eukaryotes is suggested that couples translation termination to recycling, and eventually to re-initiation.}, pmid = {22358840}, keywords = {ATP-Binding Cassette Transporters,ATP-Binding Cassette Transporters: chemistry,ATP-Binding Cassette Transporters: metabolism,Cell Cycle Proteins,Cell Cycle Proteins: chemistry,Cell Cycle Proteins: metabolism,Cryoelectron Microscopy,Endoribonucleases,Endoribonucleases: chemistry,Endoribonucleases: metabolism,Evolution,Iron-Sulfur Proteins,Iron-Sulfur Proteins: chemistry,Iron-Sulfur Proteins: metabolism,Models,Molecular,Movement,Multiprotein Complexes,Multiprotein Complexes: chemistry,Multiprotein Complexes: metabolism,nosource,Nuclear Proteins,Nuclear Proteins: chemistry,Nuclear Proteins: metabolism,Peptide Termination Factors,Peptide Termination Factors: chemistry,Peptide Termination Factors: metabolism,Protein Binding,Protein Stability,Protein Structure,Pyrococcus furiosus,Pyrococcus furiosus: chemistry,Pyrococcus furiosus: metabolism,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,Ribosomes: ultrastructure,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: chemistry,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: chemistry,Saccharomyces cerevisiae: metabolism,Tertiary} }

@article{choderEukaryoticTranslationInitiation2001, title = {Eukaryotic {{Translation Initiation Factor 4E-Dependent Translation Is Not Essential}} for {{Survival}} of {{Starved Yeast Cells}}}, author = {Choder, Mordechai}, year = 2001, journal = {Journal of Bacteriology}, volume = {183}, number = {15}, pages = {4477–4483}, doi = {10.1128/JB.183.15.4477}, keywords = {nosource} } % == BibTeX quality report for choderEukaryoticTranslationInitiation2001: % ? Title looks like it was stored in title-case in Zotero

@article{dunnT7EarlyRNAs1973, title = {T7 {{Early RNAs}} Are {{Generated}} by {{Site-Specific Cleavages}}}, author = {Dunn, John J. and Studier, F. William}, year = 1973, journal = {Proceedings of the National Academy of Sciences}, volume = {70}, number = {5}, pages = {1559–1563}, keywords = {nosource} }

@article{gagnonIntronsRibosomalProtein2011, title = {Introns within Ribosomal Protein Genes Regulate the Production and Function of Yeast Ribosomes}, author = {Gagnon, Jules and Parenteau, Julie and Durand, Mathieu and Wellinger, Raymund J. and Chabot, Benoit and Elela, Sherif Abou and Morin, Genevi{`e}ve and Lucier, Jean-Fran{}ois}, year = 2011, month = oct, journal = {Cell}, volume = {147}, number = {2}, pages = {320–31}, issn = {1097-4172}, doi = {10.1016/j.cell.2011.08.044}, url = {http://www.sciencedirect.com/science/article/pii/S0092867411010658 http://www.ncbi.nlm.nih.gov/pubmed/22000012}, abstract = {In budding yeast, the most abundantly spliced pre-mRNAs encode ribosomal proteins (RPs). To investigate the contribution of splicing to ribosome production and function, we systematically eliminated introns from all RP genes to evaluate their impact on RNA expression, pre-rRNA processing, cell growth, and response to stress. The majority of introns were required for optimal cell fitness or growth under stress. Most introns are found in duplicated RP genes, and surprisingly, in the majority of cases, deleting the intron from one gene copy affected the expression of the other in a nonreciprocal manner. Consistently, 70% of all duplicated genes were asymmetrically expressed, and both introns and gene deletions displayed copy-specific phenotypic effects. Together, our results indicate that splicing in yeast RP genes mediates intergene regulation and implicate the expression ratio of duplicated RP genes in modulating ribosome function.}, pmid = {22000012}, keywords = {Fungal,Gene Duplication,Gene Expression Regulation,Introns,Microbial Viability,nosource,Physiological,Protein Biosynthesis,Ribosomal Proteins,Ribosomal Proteins: genetics,Ribosomal Proteins: metabolism,Ribosomes,Ribosomes: metabolism,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: cytology,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: physiology,Stress} }

@article{zhangPurificationCharacterizationCDNA1993, title = {Purification, Characterization, and {{cDNA}} Cloning of an {{AU-rich}} Element {{RNA-binding}} Protein, {{AUF1}}.}, author = {Zhang, W. and Wagner, B. J. and Crater, Dinene and Dehaven, Kristin and Long, Laura and Brewer, Gary and Demaria, Christine T. and Carolina, North}, year = 1993, month = dec, journal = { and Cellular Biology}, volume = {13}, number = {12}, pages = {7652–65}, issn = {0270-7306}, doi = {10.1128/​MCB.13.12.7652}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=364837&tool=pmcentrez&rendertype=abstract http://mcb.asm.org/content/13/12/7652.short}, abstract = {The degradation of some proto-oncogene and lymphokine mRNAs is controlled in part by an AU-rich element (ARE) in the 3’ untranslated region. It was shown previously (G. Brewer, Mol. Cell. Biol. 11:2460-2466, 1991) that two polypeptides (37 and 40 kDa) copurified with fractions of a 130,000 x g postribosomal supernatant (S130) from K562 cells that selectively accelerated degradation of c-myc mRNA in a cell-free decay system. These polypeptides bound specifically to the c-myc and granulocyte-macrophage colony-stimulating factor 3’ UTRs, suggesting they are in part responsible for selective mRNA degradation. In the present work, we have purified the RNA-binding component of this mRNA degradation activity, which we refer to as AUF1. Using antisera specific for these polypeptides, we demonstrate that the 37- and 40-kDa polypeptides are immunologically cross-reactive and that both polypeptides are phosphorylated and can be found in a complex(s) with other polypeptides. Immunologically related polypeptides are found in both the nucleus and the cytoplasm. The antibodies were also used to clone a cDNA for the 37-kDa polypeptide. This cDNA contains an open reading frame predicted to produce a protein with several features, including two RNA recognition motifs and domains that potentially mediate protein-protein interactions. These results provide further support for a role of this protein in mediating ARE-directed mRNA degradation.}, pmid = {8246982}, keywords = {Amino Acid,Amino Acid Sequence,Base Sequence,Cloning,Complementary,Complementary: genetics,DNA,Genes,Heterogeneous-Nuclear Ribonucleoprotein D,Humans,Immunochemistry,Messenger,Messenger: genetics,Messenger: metabolism,Molecular,Molecular Sequence Data,myc,nosource,RNA,RNA-Binding Proteins,RNA-Binding Proteins: genetics,RNA-Binding Proteins: immunology,RNA-Binding Proteins: isolation & purification,Sequence Homology,Subcellular Fractions,Subcellular Fractions: metabolism} }

@article{houseleyRNAqualityControlExosome2006, title = {{{RNA-quality}} Control by the Exosome.}, author = {Houseley, Jonathan and LaCava, John and Tollervey, David}, year = 2006, month = jul, journal = {Nature Reviews Molecular Cell Biology}, volume = {7}, number = {7}, eprint = {16829983}, eprinttype = {pubmed}, pages = {529–39}, issn = {1471-0072}, doi = {10.1038/nrm1964}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16829983}, abstract = {The exosome complex of 3’–{\(>\)}5’ exonucleases is an important component of the RNA-processing machinery in eukaryotes. This complex functions in the accurate processing of nuclear RNA precursors and in the degradation of RNAs in both the nucleus and the cytoplasm. However, it has been unclear how different classes of substrate are distinguished from one another. Recent studies now provide insights into the regulation and structure of the exosome, and they reveal striking similarities between the process of RNA degradation in bacteria and eukaryotes.}, pmid = {16829983}, keywords = {Animals,Archaeal Proteins,Archaeal Proteins: chemistry,Archaeal Proteins: genetics,Archaeal Proteins: metabolism,Cell Nucleus,Cell Nucleus: genetics,Enzyme Activation,Exoribonucleases,Exoribonucleases: chemistry,Exoribonucleases: genetics,Exoribonucleases: metabolism,Fungal Proteins,Fungal Proteins: chemistry,Fungal Proteins: genetics,Fungal Proteins: metabolism,Models,Molecular,nosource,Polyadenylation,Polyribonucleotide Nucleotidyltransferase,Polyribonucleotide Nucleotidyltransferase: chemist,Polyribonucleotide Nucleotidyltransferase: metabol,Post-Transcriptional,RNA,RNA Precursors,RNA Precursors: genetics,RNA Precursors: metabolism,RNA Processing,RNA Stability,RNA: genetics,RNA: metabolism} }

@article{symmonsDuplicatedFoldStructural2000, title = {A Duplicated Fold Is the Structural Basis for Polynucleotide Phosphorylase Catalytic Activity, Processivity, and Regulation.}, author = {Symmons, M. F. and Jones, G. H. and Luisi, B. F.}, year = 2000, month = nov, journal = {Structure}, volume = {8}, number = {11}, eprint = {11080643}, eprinttype = {pubmed}, pages = {1215–26}, issn = {0969-2126}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11080643}, abstract = {Polynucleotide phosphorylase (PNPase) is a polyribonucleotide nucleotidyl transferase (E.C.2.7.7.8) that degrades mRNA in prokaryotes. Streptomyces antibioticus PNPase also assays as a guanosine 3’-diphosphate 5’-triphosphate (pppGpp) synthetase (E.C.2.7.6.5). It may function to coordinate changes in mRNA lifetimes with pppGpp levels during the Streptomyces lifecycle.}, pmid = {11080643}, keywords = {Amino Acid,Amino Acid Sequence,Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: metabolism,Binding Sites,Catalysis,Crystallography,Ligases,Ligases: chemistry,Ligases: metabolism,Models,Molecular,Molecular Sequence Data,nosource,Polyribonucleotide Nucleotidyltransferase,Polyribonucleotide Nucleotidyltransferase: chemist,Polyribonucleotide Nucleotidyltransferase: metabol,Protein Conformation,Protein Folding,Protein Structure,Recombinant Fusion Proteins,Recombinant Fusion Proteins: chemistry,Sequence Alignment,Sequence Homology,Streptococcus,Streptococcus: enzymology,Structure-Activity Relationship,Tertiary,Tungsten Compounds,Tungsten Compounds: metabolism,X-Ray} }

@article{buttnerStructuralFrameworkMechanism2005, title = {Structural Framework for the Mechanism of Archaeal Exosomes in {{RNA}} Processing}, author = {B{"u}ttner, Katharina and Wenig, Katja and Hopfner, Karl-Peter KP and Bu, Katharina}, year = 2005, month = nov, journal = {Molecular cell}, volume = {20}, number = {3}, pages = {461–471}, issn = {1097-2765}, doi = {10.1016/j.molcel.2005.10.018}, url = {http://www.sciencedirect.com/science/article/pii/S1097276505017132 http://www.ncbi.nlm.nih.gov/pubmed/16285927}, abstract = {Exosomes emerge as central 3’–{\(>\)}5’ RNA processing and degradation machineries in eukaryotes and archaea. We determined crystal structures of two 230 kDa nine subunit archaeal exosome isoforms. Both exosome isoforms contain a hexameric ring of RNase phosphorolytic (PH) domain subunits with a central chamber. Tungstate soaks identified three phosphorolytic active sites in this processing chamber. A trimer of Csl4 or Rrp4 subunits forms a multidomain macromolecular interaction surface on the RNase-PH domain ring with central S1 domains and peripheral KH and zinc-ribbon domains. Structural and mutational analyses suggest that the S1 domains and a subsequent neck in the RNase-PH domain ring form an RNA entry pore to the processing chamber that only allows access of unstructured RNA. This structural framework can mechanistically unify observed features of exosomes, including processive degradation of unstructured RNA, the requirement for regulatory factors to degrade structured RNA, and left-over tails in rRNA trimming.}, pmid = {16285927}, keywords = {Archaeal,Archaeal Proteins,Archaeal Proteins: chemistry,Archaeal Proteins: genetics,Archaeal: chemistry,Archaeal: genetics,Archaeal: metabolism,Archaeoglobus fulgidus,Archaeoglobus fulgidus: enzymology,Archaeoglobus fulgidus: genetics,Crystallography,Multienzyme Complexes,Multienzyme Complexes: chemistry,Multienzyme Complexes: genetics,Multienzyme Complexes: metabolism,nosource,Protein Structure,Quaternary,Ribonucleases,Ribonucleases: chemistry,Ribonucleases: genetics,Ribonucleases: metabolism,Ribosomal,Ribosomal: chemistry,Ribosomal: genetics,Ribosomal: metabolism,RNA,RNA Stability,RNA Stability: physiology,Tertiary,X-Ray} }

@article{huangSelectionMinimizationTranslational2009, title = {Selection for Minimization of Translational Frameshifting Errors as a Factor in the Evolution of Codon Usage.}, author = {Huang, Yang and Koonin, Eugene V. and Lipman, David J. and Przytycka, Teresa M.}, year = 2009, month = nov, journal = {Nucleic Acids Research}, volume = {37}, number = {20}, eprint = {19745054}, eprinttype = {pubmed}, pages = {6799–6810}, issn = {1362-4962}, doi = {10.1093/nar/gkp712}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19745054}, abstract = {In a wide range of genomes, it was observed that the usage of synonymous codons is biased toward specific codons and codon patterns. Factors that are implicated in the selection for codon usage include facilitation of fast and accurate translation. There are two types of translational errors: missense errors and processivity errors. There is considerable evidence in support of the hypothesis that codon usage is optimized to minimize missense errors. In contrast, little is known about the relationship between codon usage and frameshifting errors, an important form of processivity errors, which appear to occur at frequencies comparable to the frequencies of missense errors. Based on the recently proposed pause-and-slip model of frameshifting, we developed Frameshifting Robustness Score (FRS). We used this measure to test if the pattern of codon usage indicates optimization against frameshifting errors. We found that the FRS values of protein-coding sequences from four analyzed genomes (the bacteria Bacillus subtilis and Escherichia coli, and the yeasts Saccharomyces cerevisiae and Schizosaccharomyce pombe) were typically higher than expected by chance. Other properties of FRS patterns observed in B. subtilis, S. cerevisiae and S. pombe, such as the tendency of FRS to increase from the 5’- to 3’-end of protein-coding sequences, were also consistent with the hypothesis of optimization against frameshifting errors in translation. For E. coli, the results of different tests were less consistent, suggestive of a much weaker optimization, if any. Collectively, the results fit the concept of selection against mistranslation-induced protein misfolding being one of the factors shaping the evolution of both coding and non-coding sequences.}, pmid = {19745054}, keywords = {Codon,Evolution,Frameshift Mutation,Genetic,Models,Molecular,nosource,Protein Biosynthesis} }

@article{percudaniTransferRNAGene1997, title = {Transfer {{RNA}} Gene Redundancy and Translational Selection in {{Saccharomyces}} Cerevisiae1}, author = {Percudani, R. and Pavesi, A. and Ottonello, S.}, year = 1997, month = may, journal = {Journal of molecular biology}, volume = {268}, number = {2}, pages = {322–330}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283697909426}, abstract = {A total of 274 transfer RNA genes, representing the entire tRNA gene set of the yeast Saccharomyces cerevisiae, has been extracted from the whole genome sequence of this organism using a dedicated search algorithm (Pol3scan). All tRNA genes were assigned to 42 classes of distinct codon specificity. Accordingly, four deviations from previously proposed rules for third position wobble pairing in yeast, three G:U and one A:I codon-anticodon pairings, were found to be required to account for the reading of 61 coding triplets. The gene copy number for individual tRNA species, which ranges from one to 16, correlates well with both the frequency of codon occurrence in a sample of 1756 distinct protein coding sequences (r = 0.82) and the previously measured intracellular content of 21 tRNA species. A close link between tRNA gene redundancy and the overall amino acid composition of yeast proteins was also observed. Regression analysis values for individual protein coding sequences proved to be effective descriptions of the translational selective pressure operating on a particular gene. A significantly stronger co-adaptation between codon choice and tRNA gene copy number was observed in highly expressed genes. These observations strongly support the notion that intracellular tRNA levels in normally growing yeast cells are mainly determined by gene copy number, which, along with codon choice, is the key parameter acted upon by translational selection}, keywords = {0,ACID,AMINO-ACID,analysis,Anticodon,CELLS,CEREVISIAE,coding sequence,Codon,gene,Gene Expression Regulation-Fungal,Genes,Genes-Fungal,genetics,Genome,La,nosource,POSITION,protein,Protein Biosynthesis,Proteins,Rna,RNA-Fungal,RNA-Transfer,RULES,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,search,SELECTION,sequence,Sequence Analysis,SEQUENCES,Software,SPECIFICITY,Support,TRANSFER-RNA,tRNA,yeast,YEAST-CELLS} }

@article{matadeenEscherichiaColiLarge1999, title = {The {{Escherichia}} Coli Large Ribosomal Subunit at 7.5 {{resolution}}}, author = {Matadeen, R. and Patwardhan, A. and Gowen, B. and Orlova, E. V. and Pape, T. and Cuff, M. and Mueller, F. and Brimacombe, R. and {}van Heel, M.}, year = 1999, month = dec, journal = {Structure}, volume = {7}, number = {12}, pages = {1575–1583}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0969212600883483}, abstract = {BACKGROUND: In recent years, the three-dimensional structure of the ribosome has been visualised in different functional states by single- particle cryo-electron microscopy (cryo-EM) at 13-25 A resolution. Even more recently, X-ray crystallography has achieved resolution levels better than 10 A for the ribosomal structures of thermophilic and halophilic organisms. We present here the 7.5 A solution structure of the 50S large subunit of the Escherichia coli ribosome, as determined by cryo-EM and angular reconstitution. RESULTS: The reconstruction reveals a host of new details including the long alpha helix connecting t}, keywords = {0,Bacterial,Bacterial Proteins,chemistry,Cryoelectron Microscopy,Crystallography,elongation,Escherichia coli,ESCHERICHIA-COLI,Image Processing-Computer-Assisted,La,Methods,Models-Molecular,nosource,Peptide Elongation Factor Tu,protein,Protein Conformation,Protein Structure-Secondary,Proteins,Ribosomal Proteins,RIBOSOMAL-SUBUNIT,ribosome,Ribosomes,structure,SUBUNIT,support-non-u.s.gov’t,ultrastructure} }

@article{shirleyNuclearImportUpf3p2002, title = {Nuclear {{Import}} of {{Upf3p Is Mediated}} by {{Importin-\(\alpha\)}}/-SSand{{Export}}t to the{{Cytoplasm Is Required}}d fo a {{Functional Nonsense-Mediated mRNA Decay Pathway}}y in{{Yeast}}}, author = {Shirley, R. L. and Ford, A. S. and Richards, M. R. and Albertini, Markus and Culbertson, M. R.}, year = 2002, journal = {Genetics}, volume = {161}, number = {4}, pages = {1465}, publisher = {Genetics Soc America}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Nuclear+Import+of+Upf3p+Is+Mediated+by+Importin-alpha/-beta+and+Export+to+the+Cytoplasm+Is+Required+for+a+Functional+Nonsense-Mediated+mRNA+Decay+Pathway+in+Yeast#1 http://www.genetics.org/content/161/4/1465.short}, abstract = {Upf3p, which is required for nonsense-mediated mRNA decay (NMD) in yeast, is primarily cytoplasmic but accumulates inside the nucleus when UPF3 is overexpressed or when upf3 mutations prevent nuclear export. Upf3p physically interacts with Srp1p (importin-alpha). Upf3p fails to be imported into the nucleus in a temperature-sensitive srp1-31 strain, indicating that nuclear import is mediated by the importin-alpha/beta heterodimer. Nuclear export of Upf3p is mediated by a leucine-rich nuclear export sequence (NES-A), but export is not dependent on the Crm1p exportin. Mutations identified in NES-A prevent nuclear export and confer an Nmd(-) phenotype. The addition of a functional NES element to an export-defective upf(-) allele restores export and partially restores an Nmd(+) phenotype. Our findings support a model in which the movement of Upf3p between the nucleus and the cytoplasm is required for a fully functional NMD pathway. We also found that overexpression of Upf2p suppresses the Nmd(-) phenotype in mutant strains carrying nes-A alleles but has no effect on the localization of Upf3p. To explain these results, we suggest that the mutations in NES-A that impair nuclear export cause additional defects in the function of Upf3p that are not rectified by restoration of export alone}, keywords = {Alleles,Cytoplasm,DECAY,Genetic,genetics,La,Movement,mRNA,mRNA decay,Mutation,MUTATIONS,NMD,nosource,Phenotype,sequence,Support,UPF3,yeast} }

@article{clemonsStructureBacterial30S1999, title = {Structure of a Bacterial {{30S}} Ribosomal Subunit at 5.5 {{resolution}}}, author = {Clemons, W. M. and May, J. L. C. and Wimberly, B. T. and McCutcheon, J. P. and Capel, M. S. and Ramakrishnan, V.}, year = 1999, journal = {Nature}, volume = {400}, number = {6747}, pages = {833–840}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/nature/journal/v400/n6747/abs/400833a0.html}, abstract = {The 30S ribosomal subunit binds messenger RNA and the anticodon stem- loop of transfer RNA during protein synthesis. A crystallographic analysis of the structure of the subunit from the bacterium Thermus thermophilus is presented. At a resolution of 5.5 A, the phosphate backbone of the ribosomal RNA is visible, as are the alpha-helices of the ribosomal proteins, enabling double-helical regions of RNA to be identified throughout the subunit, all seven of the small-subunit proteins of known crystal structure to be positioned in the electron density map, and the fold of the entire central domain of the small- subunit ribosomal RNA to be determined}, keywords = {99404610,analysis,Anticodon,Bacteria,Bacterial,Bacterial Proteins,chemistry,Crystallography-X-Ray,MESSENGER-RNA,Models-Molecular,nosource,Nucleic Acid Conformation,protein,Protein Conformation,protein synthesis,PROTEIN-SYNTHESIS,Proteins,Ribosomal Proteins,Ribosomes,Rna,RNA-Bacterial,RNA-Ribosomal,structure,SUBUNIT,support-non-u.s.gov’t,support-u.s.gov’t-non-p.h.s.,support-u.s.gov’t-p.h.s.,Thermus,Thermus thermophilus,ultrastructure} }

@article{gomez-lorenzoThreedimensionalCryoelectronMicroscopy2000, title = {Three-Dimensional Cryo-Electron Microscopy Localization of {{EF2}} in the {{Saccharomyces}} Cerevisiae {{80S}} Ribosome at 17.5 {{resolution}}}, author = {{Gomez-Lorenzo}, M. G. and Spahn, C. M. T. and Agrawal, R. K. and Grassucci, R. A. and Penczek, P. and Chakraburtty, K. and Ballesta, J. P. G. and Lavandera, J. L. and {Garcia-Bustos}, J. F. and Frank, J.}, year = 2000, month = jun, journal = {The EMBO journal}, volume = {19}, number = {11}, pages = {2710–2718}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/emboj/journal/v19/n11/abs/7593094a.html}, abstract = {Using a sordarin derivative, an antifungal drug, it was possible to determine the structure of a eukaryotic ribosome small middle dotEF2 complex at 17.5 A resolution by three-dimensional (3D) cryo-electron microscopy. EF2 is directly visible in the 3D map and the overall arrangement of the complex from Saccharomyces cerevisiae corresponds to that previously seen in Escherichia coli. However, pronounced differences were found in two prominent regions. First, in the yeast system the interaction between the elongation factor and the stalk region of the large subunit is much more extensive. Secondly, domain IV of EF2 contains additional mass that appears to interact with the head of the 40S subunit and the region of the main bridge of the 60S subunit. The shape and position of domain IV of EF2 suggest that it might interact directly with P-site-bound tRNA}, keywords = {20296695,60S subunit,analysis,chemistry,COMPLEX,COMPLEXES,Cryoelectron Microscopy,elongation,Escherichia coli,ESCHERICHIA-COLI,Fungal Proteins,Macromolecular Systems,metabolism,Models-Molecular,nosource,Nucleic Acid Conformation,Peptide Elongation Factor 2,Protein Conformation,Protein Structure-Tertiary,ribosome,Ribosomes,RNA-Fungal,RNA-Transfer,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,structure,SUBUNIT,support-non-u.s.gov’t,support-u.s.gov’t-p.h.s.,SYSTEM,tRNA,ultrastructure,yeast} }

@article{valencia-sanchezControlTranslationMRNA2006, title = {Control of Translation and {{mRNA}} Degradation by {{miRNAs}} and {{siRNAs}}.}, author = {{Valencia-Sanchez}, Marco Antonio and Liu, Jidong and Hannon, Gregory J. and Parker, Roy}, year = 2006, month = mar, journal = {Genes & Development}, volume = {20}, number = {5}, eprint = {16510870}, eprinttype = {pubmed}, pages = {515–524}, issn = {0890-9369}, doi = {10.1101/gad.1399806}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16510870}, abstract = {The control of translation and mRNA degradation is an important part of the regulation of gene expression. It is now clear that small RNA molecules are common and effective modulators of gene expression in many eukaryotic cells. These small RNAs that control gene expression can be either endogenous or exogenous micro RNAs (miRNAs) and short interfering RNAs (siRNAs) and can affect mRNA degradation and translation, as well as chromatin structure, thereby having impacts on transcription rates. In this review, we discuss possible mechanisms by which miRNAs control translation and mRNA degradation. An emerging theme is that miRNAs, and siRNAs to some extent, target mRNAs to the general eukaryotic machinery for mRNA degradation and translation control.}, pmid = {16510870}, keywords = {Animals,Eukaryotic Cells,Eukaryotic Cells: metabolism,Gene Expression,Genetic,Messenger,Messenger: metabolism,MicroRNAs,MicroRNAs: genetics,MicroRNAs: metabolism,nosource,Post-Transcriptional,Protein Biosynthesis,RNA,RNA Processing,Small Interfering,Small Interfering: genetics,Small Interfering: metabolism,Transcription} }

@article{varshavskyNendRuleFunctions1996, title = {The {{N-end}} Rule: Functions, Mysteries, Uses}, author = {Varshavsky, A.}, year = 1996, month = may, journal = {Proceedings of the National Academy of }, volume = {60}, number = {5}, pages = {461}, publisher = {Cold Spring Harbor Laboratory Press}, url = {http://symposium.cshlp.org/content/60/461.short PM:1317266 http://www.pnas.org/content/93/22/12142.short}, keywords = {0,Amino Acid Sequence,Animals,BIOLOGY,chemistry,Escherichia coli,La,metabolism,Molecular Sequence Data,nosource,protein,Protein Processing-Post-Translational,Proteins,Research Support-U.S.Gov’t-P.H.S.,Review,Saccharomyces cerevisiae,Ubiquitin,Ubiquitins} }

@article{nambaVisualizationProteinnucleicAcid1989, title = {Visualization of Protein-Nucleic Acid Interactions in a Virus: {{Refined}} Structure of Intact Tobacco Mosaic Virus at 2.9 {{resolution}} by {{X-ray}} Fiber Diffraction}, author = {Namba, K. and Pattanayek, R. and Stubbs, G.}, year = 1989, month = jul, journal = {Journal of molecular biology}, volume = {208}, number = {2}, pages = {307–325}, publisher = {Elsevier}, issn = {0022-2836}, url = {http://linkinghub.elsevier.com/retrieve/pii/0022283689903914 http://www.ncbi.nlm.nih.gov/pubmed/2769760}, abstract = {The structure of tobacco mosaic virus (TMV) has been determined by fiber diffraction methods at 2.9 A resolution, and refined by restrained least-squares to an R-factor of 0.096. Protein-nucleic acid interactions are clearly visible. The final model contains all of the non-hydrogen atoms of the RNA and the protein, 71 water molecules, and two calcium-binding sites. Viral disassembly is driven by electrostatic repulsions between the charges in two carboxyl-carboxylate pairs and a phosphate-carboxylate pair. The phosphate-carboxylate pair and at least one of the carboxyl-carboxylate pairs appear to be calcium-binding sites. Nucleotide specificity, enabling TMV to recognize its own RNA by a repeating pattern of guanine residues, is provided by two guanine-specific hydrogen bonds in one of the three base-binding sites}, pmid = {2769760}, keywords = {0,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,Binding Sites,BIOLOGY,Calcium,Calcium: metabolism,genetics,Guanine,Hydrogen Bonding,La,metabolism,Methods,MODEL,Models,Models-Molecular,Models-Structural,Molecular,Molecular Conformation,MOSAIC-VIRUS,nosource,protein,Proteins,RESIDUES,RESOLUTION,Rna,Rna-Viral,SITE,SITES,SPECIFICITY,Structural,structure,support-u.s.gov’t-p.h.s.,Tobacco,Tobacco Mosaic Virus,Tobacco Mosaic Virus: genetics,Viral,Viral Proteins,Viral Proteins: genetics,Viral: genetics,virus,Water,X-Ray Diffraction} }

@article{kawashimaStructureEscherichiaColi1996, title = {The Structure of the {{Escherichia}} Coli {{EF-Tu}}{\(\cdot\)} {{EF-Ts}} Complex at 2.5 {{}} Resolution}, author = {Kawashima, T. and {Berthet-Colominas}, C. and Wulff, M.}, year = 1996, month = feb, journal = {Nature}, volume = {379}, number = {8}, pages = {511–518}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/nature/journal/v379/n6565/abs/379511a0.html}, keywords = {BINDING,COMPLEX,COMPLEXES,EFTu,elongation,Escherichia coli,ESCHERICHIA-COLI,Guanine,nosource,Nucleotides,structure,SUBUNIT} }

@article{tsuiMolecularDynamicsSimulations2000, title = {Molecular {{Dynamics Simulations}} of {{Nucleic Acids}} with a {{Generalized Born Solvation Mode}}}, author = {Tsui, Vickie and Case, David A.}, year = 2000, journal = {J.Am.Chem.Soc.}, volume = {122}, number = {24}, pages = {2489–2498}, url = {http://pubs.acs.org/doi/abs/10.1021/ja9939385}, keywords = {nosource} } % == BibTeX quality report for tsuiMolecularDynamicsSimulations2000: % ? Possibly abbreviated journal title J.Am.Chem.Soc. % ? Title looks like it was stored in title-case in Zotero

@article{haarPurificationAminoacyltRNASynthetases1979, title = {Purification of Aminoacyl-{{tRNA}} Synthetases.}, author = {{}der Haar, F. Von and {}der Haar, F. Von and {}von der Haar, F.}, year = 1979, journal = {Methods in enzymology}, volume = {LIX}, eprint = {374941}, eprinttype = {pubmed}, pages = {257–267}, url = {http://www.ncbi.nlm.nih.gov/pubmed/374941}, isbn = {0121819590}, keywords = {AMINOACYL-TRANSFER RNA,nosource,purification} }

@article{bensonGenBank2008, title = {{{GenBank}}}, author = {Benson, Dennis A. DA A. and {Karsch-Mizrachi}, Ilene and Lipman, David J. and Ostell, James and Wheeler, David L.}, year = 2008, month = jan, journal = {Nucleic Acids Research}, volume = {36}, number = {suppl 1}, pages = {25–30}, publisher = {Oxford Univ Press}, issn = {1362-4962}, doi = {10.1093/nar/gkm929}, url = {http://nar.oxfordjournals.org/content/36/suppl_1/D25.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2238942&tool=pmcentrez&rendertype=abstract}, abstract = {GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI’s retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.}, pmid = {18073190}, keywords = {Complementary,Complementary: chemistry,Databases,DNA,Expressed Sequence Tags,Expressed Sequence Tags: chemistry,Genomics,Internet,National Library of Medicine (U.S.),nosource,Nucleic Acid,Sequence Analysis,United States,User-Computer Interface} }

@article{masisonDecoyingCapmRNADegradation1995, title = {Decoying the Cap-{{mRNA}} Degradation System by a Double-Stranded {{RNA}} Virus and Poly ({{A}})-{{mRNA}} Surveillance by a Yeast Antiviral System.}, author = {Masison, D. C. and Blanc, Antony and Ribas, JC C. and Masison, d C. and Carroll, K. and Sonenberg, N. and Wickner, R. B.}, year = 1995, journal = { and cellular biology}, volume = {15}, number = {5}, pages = {2763}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/15/5/2763 http://mcb.asm.org/content/15/5/2763.short}, abstract = {The major coat protein of the L-A double-stranded RNA virus of Saccharomyces cerevisiae covalently binds m7 GMP from 5’ capped mRNAs in vitro. We show that this cap binding also occurs in vivo and that, while this activity is required for expression of viral information (killer toxin mRNA level and toxin production) in a wild-type strain, this requirement is suppressed by deletion of SKI1/XRN1/SEP1. We propose that the virus creates decapped cellular mRNAs to decoy the 5’–{\(>\)}3’ exoribonuclease specific for cap- RNA encoded by XRN1. The SKI2 antiviral gene represses the copy numbers of the L-A and L-BC viruses and the 20S RNA replicon, apparently by specifically blocking translation of viral RNA. We show that SKI2, SKI3, and SKI8 inhibit translation of electroporated luciferase and beta-glucuronidase mRNAs in vivo, but only if they lack the 3’ poly(A) structure. Thus, L-A decoys the SKI1/XRN1/SEP1 exonuclease directed at 5’ uncapped ends, but translation of the L-A poly(A)- mRNA is repressed by Ski2,3,8p. The SKI2-SKI3-SKI8 system is more effective against cap+ poly(A)- mRNA, suggesting a (nonessential) role in blocking translation of fragmented cellular mRNAs.}, keywords = {3,antiviral,BINDING,Cap,Cap binding,CEREVISIAE,COAT PROTEIN,degradation,DOUBLE-STRANDED-RNA,expression,gene,In Vitro,IN-VITRO,IN-VIVO,INFORMATION,killer,killer toxin,L-A,L-BC,La,luciferase,mRNA,nosource,poly(A),protein,Rna,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SKI,SKI2,structure,SYSTEM,toxin,translation,VIRAL-RNA,virus,Viruses,WILD-TYPE,XRN1,yeast} }

@article{hookTwoYeastPUF2007, title = {Two Yeast {{PUF}} Proteins Negatively Regulate a Single {{mRNA}}.}, author = {Hook, Brad A. and Goldstrohm, Aaron C. and Seay, Daniel J. and Wickens, Marvin}, year = 2007, month = may, journal = {The Journal of Biological Chemistry}, volume = {282}, number = {21}, eprint = {17389596}, eprinttype = {pubmed}, pages = {15430–8}, issn = {0021-9258}, doi = {10.1074/jbc.M611253200}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17389596}, abstract = {mRNA stability and translation are regulated by protein repressors that bind 3’-untranslated regions. PUF proteins provide a paradigm for these regulatory molecules: like other repressors, they inhibit translation, enhance mRNA decay, and promote poly(A) removal. Here we show that a single mRNA in Saccharomyces cerevisiae, encoding the HO endonuclease, is regulated by two distinct PUF proteins, Puf4p and Mpt5p. These proteins bind to adjacent sites and can co-occupy the mRNA. Both proteins are required for full repression and deadenylation in vivo; their removal dramatically stabilizes the mRNA. The two proteins act through overlapping but non-identical mechanisms: repression by Puf4p is dependent on deadenylation, whereas repression by Mpt5p can occur through additional mechanisms. Combinatorial action of the two regulatory proteins may allow responses to specific environmental cues and be common in 3’-untranslated region-mediated control.}, isbn = {6082629108}, pmid = {17389596}, keywords = {3’ Untranslated Regions,3’ Untranslated Regions: genetics,3’ Untranslated Regions: metabolism,Cell Cycle Proteins,Cell Cycle Proteins: genetics,Cell Cycle Proteins: metabolism,nosource,Poly A,Poly A: genetics,Poly A: metabolism,Protein Binding,Protein Binding: physiology,Protein Biosynthesis,Protein Biosynthesis: physiology,Repressor Proteins,Repressor Proteins: genetics,Repressor Proteins: metabolism,RNA Stability,RNA Stability: physiology,RNA-Binding Proteins,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism} }

@article{mayrWidespreadShortening3UTRs2009, title = {Widespread Shortening of 3’{{UTRs}} by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells.}, author = {Mayr, Christine and Bartel, David P.}, year = 2009, month = aug, journal = {Cell}, volume = {138}, number = {4}, pages = {673–84}, publisher = {Elsevier Ltd}, issn = {1097-4172}, doi = {10.1016/j.cell.2009.06.016}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2819821&tool=pmcentrez&rendertype=abstract http://www.sciencedirect.com/science/article/pii/S0092867409007168}, abstract = {In cancer cells, genetic alterations can activate proto-oncogenes, thereby contributing to tumorigenesis. However, the protein products of oncogenes are sometimes overexpressed without alteration of the proto-oncogene. Helping to explain this phenomenon, we found that when compared to similarly proliferating nontransformed cell lines, cancer cell lines often expressed substantial amounts of mRNA isoforms with shorter 3’ untranslated regions (UTRs). These shorter isoforms usually resulted from alternative cleavage and polyadenylation (APA). The APA had functional consequences, with the shorter mRNA isoforms exhibiting increased stability and typically producing ten-fold more protein, in part through the loss of microRNA-mediated repression. Moreover, expression of the shorter mRNA isoform of the proto-oncogene IGF2BP1/IMP-1 led to far more oncogenic transformation than did expression of the full-length, annotated mRNA. The high incidence of APA in cancer cells, with consequent loss of 3’UTR repressive elements, suggests a pervasive role for APA in oncogene activation without genetic alteration.}, pmid = {19703394}, keywords = {3’ Untranslated Regions,3’ Untranslated Regions: metabolism,Alternative Splicing,Cell Line,Cell Transformation,Cyclin D2,Cyclins,Cyclins: genetics,Cyclins: metabolism,Gene Expression Regulation,Humans,Mutation,Neoplastic,nosource,Oncogenes,Polyadenylation,RNA Stability,RNA-Binding Proteins,RNA-Binding Proteins: metabolism,S Phase,Tumor} }

@article{giedrocFrameshiftingRNAPseudoknots2009, title = {Frameshifting {{RNA}} Pseudoknots: Structure and Mechanism}, author = {Giedroc, DP David P. and Cornish, Peter V. PV}, year = 2009, month = feb, journal = {Virus research}, volume = {139}, number = {2}, pages = {193–208}, issn = {0168-1702}, doi = {10.1016/j.virusres.2008.06.008.Frameshifting}, url = {http://www.sciencedirect.com/science/article/pii/S0168170208002323 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2670756&tool=pmcentrez&rendertype=abstract}, abstract = {Programmed ribosomal frameshifting (PRF) is one of the multiple translational recoding processes that fundamentally alters triplet decoding of the messenger RNA by the elongating ribosome. The ability of the ribosome to change translational reading frames in the -1 direction (-1 PRF) is employed by many positive strand RNA viruses, including economically important plant viruses and many human pathogens, such as retroviruses, e.g., HIV-1, and coronaviruses, e.g., the causative agent of severe acute respiratory syndrome (SARS), in order to properly express their genomes. -1 PRF is programmed by a bipartite signal embedded in the mRNA and includes a heptanucleotide “slip site” over which the paused ribosome “backs up” by one nucleotide, and a downstream stimulatory element, either an RNA pseudoknot or a very stable RNA stem-loop. These two elements are separated by six to eight nucleotides, a distance that places the 5’ edge of the downstream stimulatory element in direct contact with the mRNA entry channel of the 30S ribosomal subunit. The precise mechanism by which the downstream RNA stimulates -1 PRF by the translocating ribosome remains unclear. This review summarizes the recent structural and biophysical studies of RNA pseudoknots and places this work in the context of our evolving mechanistic understanding of translation elongation. Support for the hypothesis that the downstream stimulatory element provides a kinetic barrier to the ribosome-mediated unfolding is discussed.}, isbn = {1812856571}, pmid = {18621088}, keywords = {cryo-electron microscopy,frameshifting,Frameshifting,hiv-1,luteovirus,Messenger,Messenger: chemistry,Models,Molecular,nmr,nosource,Nucleic Acid Conformation,Peptide Chain Elongation,pseudoknot,Ribosomal,ribosomal recoding,RNA,RNA Viruses,RNA Viruses: genetics,solution structure,Translational,translational regulation,Viral,Viral: chemistry} }

@article{andersonExploringLimitsCodon2002, title = {Exploring the Limits of Codon and Anticodon Size.}, author = {Anderson, J. Christopher and Magliery, Thomas J. and Schultz, Peter G.}, year = 2002, month = feb, journal = {Chemistry & Biology}, volume = {9}, number = {2}, eprint = {11880038}, eprinttype = {pubmed}, pages = {237–44}, issn = {1074-5521}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11880038}, abstract = {We previously employed a combinatorial approach to identify the most efficient suppressors of four-base codons in E. coli. We have now examined the suppression of two-, three-, four-, five-, and six-base codons with tRNAs containing 6-10 nt in their anticodon loops. We found that the E. coli translational machinery tolerates codons of 3-5 bases and that tRNAs with 6-10 nt anticodon loops can suppress these codons. However, N-length codons were found to prefer N + 4-length anticodon loops. Additionally, sequence preferences, including the requirement of Watson-Crick complementarity to the codon, were evident in the loops. These selections have yielded efficient suppressors of four-base and five-base codons for our ongoing efforts to expand the genetic code. They also highlight some of the parameters that underlie the fidelity of frame maintenance.}, pmid = {11880038}, keywords = {Anticodon,Anticodon: genetics,Bacterial,Codon,Codon: genetics,Escherichia coli,Escherichia coli: genetics,Frameshifting,Gene Expression Regulation,Gene Library,Genetic,Genetic Code,Genetic Code: genetics,nosource,Protein Biosynthesis,Ribosomal,RNA,Suppression,Transfer,Transfer: genetics} }

@article{xieExpandingGeneticCode2005, title = {An Expanding Genetic Code.}, author = {Xie, Jianming and Schultz, Peter G.}, year = 2005, month = jul, journal = {Methods}, volume = {36}, number = {3}, eprint = {16076448}, eprinttype = {pubmed}, pages = {227–38}, issn = {1046-2023}, doi = {10.1016/j.ymeth.2005.04.010}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16076448}, abstract = {A general method was recently developed that makes it possible to genetically encode unnatural amino acids (UAAs) with diverse physical, chemical or biological properties in Escherichia coli, yeast, and mammalian cells. Over 30 UAAs have been cotranslationally incorporated into proteins with high fidelity and efficiency by means of a unique codon and corresponding tRNA-synthetase pair. A key feature of this methodology is the orthogonality between the new translational components and their endogenous host counterparts. Specifically, the codon for the UAA should not encode a common amino acid; neither the new tRNA nor cognate aminoacyl tRNA synthetase should cross-react with any endogenous tRNA-synthetase pairs; and the new synthetase should recognize only the UAA and not any of the 20 common amino acids. This methodology provides a powerful tool for exploring protein structure and function both in vitro and in vivo, as well as generating proteins with new or enhanced properties.}, pmid = {16076448}, keywords = {Amino Acids,Amino Acids: chemistry,Amino Acids: genetics,Base Sequence,Genetic Code,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Protein Biosynthesis,Protein Biosynthesis: genetics,Protein Engineering,Protein Engineering: methods,Proteins,Proteins: chemistry,RNA,Transfer,Transfer: chemistry,Transfer: genetics} }

@article{suMicroRNA101DownregulatedHepatocellular2009, title = {{{MicroRNA-101}}, down-Regulated in Hepatocellular Carcinoma, Promotes Apoptosis and Suppresses Tumorigenicity.}, author = {Su, Hang and Yang, Jian-Rong and Xu, Teng and Huang, Jun and Xu, Li and Yuan, Yunfei and Zhuang, Shi-Mei}, year = 2009, month = feb, journal = {Cancer Research}, volume = {69}, number = {3}, eprint = {19155302}, eprinttype = {pubmed}, pages = {1135–42}, issn = {1538-7445}, doi = {10.1158/0008-5472.CAN-08-2886}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19155302}, abstract = {Although aberrant microRNA (miRNA) expressions have been observed in different types of cancer, their pathophysiologic role and their relevance to tumorigenesis are still largely unknown. In this study, we first evaluated the expression of 308 miRNAs in human hepatocellular carcinoma (HCC) and normal hepatic tissues and identified 29 differentially expressed miRNAs in HCC tissues. miR-101, a significantly down-regulated miRNA, was further studied in greater detail because the signal pathway(s) regulated by miR-101 and the role of miR-101 in tumorigenesis have not yet been elucidated. Interestingly, decreased expression of miR-101 was found in all six hepatoma cell lines examined and in as high as 94.1% of HCC tissues, compared with their nontumor counterparts. Furthermore, ectopic expression of miR-101 dramatically suppressed the ability of hepatoma cells to form colonies in vitro and to develop tumors in nude mice. We also found that miR-101 could sensitize hepatoma cell lines to both serum starvation- and chemotherapeutic drug-induced apoptosis. Further investigation revealed that miR-101 significantly repressed the expression of luciferase carrying the 3’-untranslated region of Mcl-1 and reduced the endogenous protein level of Mcl-1, whereas the miR-101 inhibitor obviously up-regulated Mcl-1 expression and inhibited cell apoptosis. Moreover, silencing of Mcl-1 phenocopied the effect of miR-101 and forced expression of Mcl-1 could reverse the proapoptotic effect of miR-101. These results indicate that miR-101 may exert its proapoptotic function via targeting Mcl-1. Taken together, our data suggest an important role of miR-101 in the molecular etiology of cancer and implicate the potential application of miR-101 in cancer therapy.}, isbn = {8620873431}, pmid = {19155302}, keywords = {Animals,Apoptosis,Apoptosis: genetics,Carcinoma,Cell Line,Cell Transformation,Down-Regulation,Hela Cells,Hepatocellular,Hepatocellular: genetics,Hepatocellular: metabolism,Hepatocellular: pathology,Humans,Liver Neoplasms,Liver Neoplasms: genetics,Liver Neoplasms: metabolism,Liver Neoplasms: pathology,Mice,MicroRNAs,MicroRNAs: biosynthesis,MicroRNAs: genetics,Neoplastic,Neoplastic: genetics,Neoplastic: metabolism,NIH 3T3 Cells,nosource,Nude,Proto-Oncogene Proteins c-bcl-2,Proto-Oncogene Proteins c-bcl-2: genetics,Transfection,Tumor} }

@article{horowitzSubtelomericRegionsYeast1984, title = {Subtelomeric Regions of Yeast Chromosomes Contain a 36 Base-Pair Tandemly Repeated Sequence.}, author = {Horowitz, H. and Haber, J. E.}, year = 1984, month = sep, journal = {Nucleic Acids Research}, volume = {12}, number = {18}, pages = {7105–21}, abstract = {We have determined the nucleotide sequence of a region of DNA derived from the end of one chromosome of the yeast, Saccharomyces cerevisiae. Inspection of the sequence reveals the presence of 12 tandem direct repeats, each 36 nucleotides long and having nearly identical sequence. Each 36 base-pair repeat can be further subdivided into three tandem sub-repeats of a similar 12 base-pair sequence. Analysis of total genomic yeast DNA from several strains by Southern hybridization suggests that the number of tandem 36 base-pair repeat units may vary from approximately 8 to 25 among different telomeric regions. Differences in the number of repeats may have arisen by unequal crossing over between them. Furthermore, the finding that the pattern of bases at multiple variable positions within the repeat unit is not random suggests that these regions may undergo gene conversion events that render them homogeneous.}, keywords = {nosource} }

@article{hoshidaIntegrativeTranscriptomeAnalysis2009, title = {Integrative Transcriptome Analysis Reveals Common Molecular Subclasses of Human Hepatocellular Carcinoma.}, author = {Hoshida, Yujin and Nijman, Sebastian M. B. and Kobayashi, Masahiro and {}a Chan, Jennifer and Brunet, Jean-Philippe and Chiang, Derek Y. and Villanueva, Augusto and Newell, Philippa and Ikeda, Kenji and Hashimoto, Masaji and Watanabe, Goro and Gabriel, Stacey and Friedman, Scott L. and Kumada, Hiromitsu and Llovet, Josep M. and Golub, Todd R.}, year = 2009, month = sep, journal = {Cancer Research}, volume = {69}, number = {18}, eprint = {19723656}, eprinttype = {pubmed}, pages = {7385–92}, issn = {1538-7445}, doi = {10.1158/0008-5472.CAN-09-1089}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19723656}, abstract = {Hepatocellular carcinoma (HCC) is a highly heterogeneous disease, and prior attempts to develop genomic-based classification for HCC have yielded highly divergent results, indicating difficulty in identifying unified molecular anatomy. We performed a meta-analysis of gene expression profiles in data sets from eight independent patient cohorts across the world. In addition, aiming to establish the real world applicability of a classification system, we profiled 118 formalin-fixed, paraffin-embedded tissues from an additional patient cohort. A total of 603 patients were analyzed, representing the major etiologies of HCC (hepatitis B and C) collected from Western and Eastern countries. We observed three robust HCC subclasses (termed S1, S2, and S3), each correlated with clinical parameters such as tumor size, extent of cellular differentiation, and serum alpha-fetoprotein levels. An analysis of the components of the signatures indicated that S1 reflected aberrant activation of the WNT signaling pathway, S2 was characterized by proliferation as well as MYC and AKT activation, and S3 was associated with hepatocyte differentiation. Functional studies indicated that the WNT pathway activation signature characteristic of S1 tumors was not simply the result of beta-catenin mutation but rather was the result of transforming growth factor-beta activation, thus representing a new mechanism of WNT pathway activation in HCC. These experiments establish the first consensus classification framework for HCC based on gene expression profiles and highlight the power of integrating multiple data sets to define a robust molecular taxonomy of the disease.}, pmid = {19723656}, keywords = {beta Catenin,beta Catenin: genetics,beta Catenin: metabolism,Carcinoma,Cell Line,Cohort Studies,Gene Expression Profiling,Hepatocellular,Hepatocellular: classification,Hepatocellular: genetics,Hepatocellular: metabolism,Hepatocellular: pathology,Humans,Liver Neoplasms,Liver Neoplasms: classification,Liver Neoplasms: genetics,Liver Neoplasms: metabolism,Liver Neoplasms: pathology,nosource,Signal Transduction,Transforming Growth Factor beta,Transforming Growth Factor beta: metabolism,Tumor,Wnt Proteins,Wnt Proteins: metabolism} }

@article{guoMammalianMicroRNAsPredominantly2010, title = {Mammalian {{microRNAs}} Predominantly Act to Decrease Target {{mRNA}} Levels.}, author = {Guo, Huili and Ingolia, Nicholas T. and Weissman, Jonathan S. and Bartel, David P.}, year = 2010, month = aug, journal = {Nature}, volume = {466}, number = {7308}, pages = {835–840}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature09267}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2990499&tool=pmcentrez&rendertype=abstract}, abstract = {MicroRNAs (miRNAs) are endogenous approximately 22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most ({\(>\)}/=84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output.}, pmid = {20703300}, keywords = {3’ Untranslated Regions,3’ Untranslated Regions: genetics,Animals,Down-Regulation,Down-Regulation: genetics,Genetic,Hela Cells,Humans,Mammals,Mammals: genetics,Messenger,Messenger: analysis,Messenger: genetics,Messenger: metabolism,Mice,MicroRNAs,MicroRNAs: genetics,MicroRNAs: metabolism,Models,nosource,Open Reading Frames,Open Reading Frames: genetics,Post-Transcriptional,Post-Transcriptional: genetics,Protein Biosynthesis,Protein Biosynthesis: genetics,Ribosomes,Ribosomes: genetics,Ribosomes: metabolism,RNA,RNA Processing,RNA Stability,RNA Stability: genetics} }

@article{ingoliaRibosomeProfilingMouse2011, title = {Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes.}, author = {Ingolia, Nicholas T. and Lareau, Liana F. and Weissman, Jonathan S.}, year = 2011, month = nov, journal = {Cell}, volume = {147}, number = {4}, pages = {789–802}, publisher = {Elsevier Inc.}, issn = {1097-4172}, doi = {10.1016/j.cell.2011.10.002}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3225288&tool=pmcentrez&rendertype=abstract}, abstract = {The ability to sequence genomes has far outstripped approaches for deciphering the information they encode. Here we present a suite of techniques, based on ribosome profiling (the deep sequencing of ribosome-protected mRNA fragments), to provide genome-wide maps of protein synthesis as well as a pulse-chase strategy for determining rates of translation elongation. We exploit the propensity of harringtonine to cause ribosomes to accumulate at sites of translation initiation together with a machine learning algorithm to define protein products systematically. Analysis of translation in mouse embryonic stem cells reveals thousands of strong pause sites and unannotated translation products. These include amino-terminal extensions and truncations and upstream open reading frames with regulatory potential, initiated at both AUG and non-AUG codons, whose translation changes after differentiation. We also define a class of short, polycistronic ribosome-associated coding RNAs (sprcRNAs) that encode small proteins. Our studies reveal an unanticipated complexity to mammalian proteomes.}, pmid = {22056041}, keywords = {Algorithms,Animals,Artificial Intelligence,Embryoid Bodies,Embryoid Bodies: cytology,Embryoid Bodies: metabolism,Embryonic Stem Cells,Embryonic Stem Cells: metabolism,Genomics,Genomics: methods,Harringtonines,Harringtonines: pharmacology,High-Throughput Nucleotide Sequencing,High-Throughput Nucleotide Sequencing: methods,Kinetics,Mice,nosource,Open Reading Frames,Peptide Chain Initiation,Protein Biosynthesis,Ribosomes,Ribosomes: chemistry,Ribosomes: drug effects,RNA,RNA: analysis,RNA: methods,Sequence Analysis,Translational} }

@article{caliSmg7RequiredMRNA1999, title = {Smg-7 {{Is Required}} for {{mRNA Surveillance}} in {{Caenorhabditis}} Elegans}, author = {Cali, Brian M. and Kuchma, Sherry L. and Latham, Jonathan and Anderson, Philip}, year = 1999, journal = {Genetics}, number = {151}, pages = {605–616}, keywords = {nosource} }

@article{wiedenheftRNAguidedGeneticSilencing2012, title = {{{RNA-guided}} Genetic Silencing Systems in Bacteria and Archaea}, author = {Wiedenheft, Blake and Sternberg, Samuel H. and {}a Doudna, Jennifer}, year = 2012, month = feb, journal = {Nature}, volume = {482}, number = {7385}, pages = {331–338}, issn = {0028-0836}, doi = {10.1038/nature10886}, url = {http://www.nature.com/doifinder/10.1038/nature10886}, keywords = {nosource} }

@article{guttmanModularRegulatoryPrinciples2012, title = {Modular Regulatory Principles of Large Non-Coding {{RNAs}}}, author = {Guttman, Mitchell and Rinn, John L.}, year = 2012, month = feb, journal = {Nature}, volume = {482}, number = {7385}, pages = {339–346}, issn = {0028-0836}, doi = {10.1038/nature10887}, url = {http://www.nature.com/doifinder/10.1038/nature10887}, keywords = {nosource} }

@article{dethoffFunctionalComplexityRegulation2012, title = {Functional Complexity and Regulation through {{RNA}} Dynamics}, author = {{}a Dethoff, Elizabeth and Chugh, Jeetender and Mustoe, Anthony M. and {Al-Hashimi}, Hashim M.}, year = 2012, month = feb, journal = {Nature}, volume = {482}, number = {7385}, pages = {322–330}, issn = {0028-0836}, doi = {10.1038/nature10885}, url = {http://www.nature.com/doifinder/10.1038/nature10885}, keywords = {nosource} }

@article{brufordHGNCDatabase20082008, title = {The {{HGNC Database}} in 2008: A Resource for the Human Genome.}, author = {Bruford, Elspeth and Lush, Michael J. and Wright, Mathew W. and Sneddon, Tam P. and Povey, Sue and Birney, Ewan}, year = 2008, month = jan, journal = {Nucleic Acids Research}, volume = {36}, number = {Database issue}, pages = {D445–8}, issn = {1362-4962}, doi = {10.1093/nar/gkm881}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2238870&tool=pmcentrez&rendertype=abstract}, abstract = {The HUGO Gene Nomenclature Committee (HGNC) aims to assign a unique and ideally meaningful name and symbol to every human gene. The HGNC database currently comprises over 24 000 public records containing approved human gene nomenclature and associated gene information. Following our recent relocation to the European Bioinformatics Institute our homepage can now be found at http://www.genenames.org, with direct links to the searchable HGNC database and other related database resources, such as the HCOP orthology search tool and manually curated gene family webpages.}, pmid = {17984084}, keywords = {Animals,Databases,Genes,Genetic,Genetic Variation,Genome,Genomics,Human,Humans,Internet,Mice,nosource,Systems Integration,Terminology as Topic,User-Computer Interface} }

@phdthesis{glenJVizRNATool2007, title = {{{jViz RNA}}: {{A Tool}} for {{Visual Comparison}} and {{Analysis}} of {{RNA Secondary Structures}}}, author = {Glen, Edward and Simon, B. Sc}, year = 2007, journal = {Structure}, keywords = {nosource} } % == BibTeX quality report for glenJVizRNATool2007: % Missing required field ‘school’ % ? Title looks like it was stored in title-case in Zotero

@article{byunPseudoViewer3GeneratingPlanar2009, title = {{{PseudoViewer3}}: Generating Planar Drawings of Large-Scale {{RNA}} Structures with Pseudoknots.}, author = {Byun, Yanga and Han, Kyungsook}, year = 2009, month = jun, journal = {Bioinformatics}, volume = {25}, number = {11}, eprint = {19369500}, eprinttype = {pubmed}, pages = {1435–1437}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp252}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19369500}, abstract = {Pseudoknots in RNA structures make visualization of RNA structures difficult. Even if a pseudoknot itself is represented without a crossing, visualization of the entire RNA structure with a pseudoknot often results in a drawing with crossings between the pseudoknot and other structural elements, and requires additional intervention by the user to ensure that the structure graph is overlap-free. Many programs such as web services prefer to obtain an overlap-free graph in one-shot rather than get a graph with overlaps to be edited. There are few programs for visualizing RNA pseudoknots, and PseudoViewer has been the almost only program that automatically draws RNA secondary structures with pseudoknots. The previous version of PseudoViewer visualizes all the known types of RNA pseudoknots as planar drawings, but visualizes some hypothetical pseudoknots as non-planar drawings.}, pmid = {19369500}, keywords = {Computational Biology,Computational Biology: methods,Computer Graphics,Models,Molecular,nosource,Nucleic Acid Conformation,RNA,RNA: chemistry,Software} }

@inproceedings{wieseJVizRnaAnInteractive2006, title = {{{jViz}}. {{Rna-An}} Interactive Graphical Tool for Visualizing {{RNA}} Secondary Structure Including Pseudoknots}, booktitle = {Computer-{{Based Medical Systems}}, 2006. {{CBMS}} 2006. 19th {{IEEE International Symposium}}}, author = {Wiese, K. C. and Glen, E.}, year = 2006, pages = {659–664}, publisher = {IEEE}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1647646}, keywords = {nosource} } % == BibTeX quality report for wieseJVizRnaAnInteractive2006: % ? Unsure about the formatting of the booktitle

@article{bonnetEvidenceThatMicroRNA2004, title = {Evidence That {{microRNA}} Precursors, Unlike Other Non-Coding {{RNAs}}, Have Lower Folding Free Energies than Random Sequences.}, author = {Bonnet, Eric and Wuyts, Jan and Rouz{'e}, Pierre and {}de Peer, Yves Van}, year = 2004, month = nov, journal = {Bioinformatics}, volume = {20}, number = {17}, eprint = {15217813}, eprinttype = {pubmed}, pages = {2911–2917}, issn = {1367-4803}, doi = {10.1093/bioinformatics/bth374}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15217813}, abstract = {MOTIVATION: Most non-coding RNAs are characterized by a specific secondary and tertiary structure that determines their function. Here, we investigate the folding energy of the secondary structure of non-coding RNA sequences, such as microRNA precursors, transfer RNAs and ribosomal RNAs in several eukaryotic taxa. Statistical biases are assessed by a randomization test, in which the predicted minimum free energy of folding is compared with values obtained for structures inferred from randomly shuffling the original sequences. RESULTS: In contrast with transfer RNAs and ribosomal RNAs, the majority of the microRNA sequences clearly exhibit a folding free energy that is considerably lower than that for shuffled sequences, indicating a high tendency in the sequence towards a stable secondary structure. A possible usage of this statistical test in the framework of the detection of genuine miRNA sequences is discussed.}, pmid = {15217813}, keywords = {Animals,Caenorhabditis elegans,Caenorhabditis elegans: genetics,Chemical,Computer Simulation,Drosophila melanogaster,Drosophila melanogaster: genetics,Energy Transfer,Humans,MicroRNAs,MicroRNAs: chemistry,Models,nosource,Nucleic Acid Conformation,Nucleic Acid Denaturation,RNA,RNA: methods,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis,Statistical,Structure-Activity Relationship,Thermodynamics} }

@article{freierImprovedFreeenergyParameters1986, title = {Improved Free-Energy Parameters for Predictions of {{RNA}} Duplex Stability.}, author = {Freier, S. M. and Kierzek, R. and {}a Jaeger, J. and Sugimoto, N. and Caruthers, M. H. and Neilson, T. and Turner, D. H.}, year = 1986, month = dec, journal = {Proceedings of the National Academy of Sciences}, volume = {83}, number = {24}, pages = {9373–7}, issn = {0027-8424}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=387140&tool=pmcentrez&rendertype=abstract}, abstract = {Thermodynamic parameters for prediction of RNA duplex stability are reported. One parameter for duplex initiation and 10 parameters for helix propagation are derived from enthalpy and free-energy changes for helix formation by 45 RNA oligonucleotide duplexes. The oligomer sequences were chosen to maximize reliability of secondary structure predictions. Each of the 10 nearest-neighbor sequences is well-represented among the 45 oligonucleotides, and the sequences were chosen to minimize experimental errors in delta GO at 37 degrees C. These parameters predict melting temperatures of most oligonucleotide duplexes within 5 degrees C. This is about as good as can be expected from the nearest-neighbor model. Free-energy changes for helix propagation at dangling ends, terminal mismatches, and internal G X U mismatches, and free-energy changes for helix initiation at hairpin loops, internal loops, or internal bulges are also tabulated.}, pmid = {2432595}, keywords = {Double-Stranded,Hydrogen Bonding,nosource,Nucleic Acid Conformation,Oligoribonucleotides,Oligoribonucleotides: chemical synthesis,RNA,Thermodynamics} }

@article{lyngsoPseudoknotsRNASecondary2000, title = {Pseudoknots in {{RNA}} Secondary Structures}, author = {Lyngs{}, Rune B. and Pedersen, Christian N. S.}, year = 2000, journal = {Proceedings of the Fourth Annual International Conference on Computational Molecular Biology}, pages = {201–209}, publisher = {ACM Press}, doi = {10.1145/332306.332551}, url = {http://portal.acm.org/citation.cfm?doid=332306.332551}, isbn = {1581131860}, keywords = {nosource} }

@article{bonTT2NENovelAlgorithm2011, title = {{{TT2NE}}: A Novel Algorithm to Predict {{RNA}} Secondary Structures with Pseudoknots.}, author = {Bon, Micha{"e}l and Orland, Henri}, year = 2011, month = may, journal = {Nucleic Acids Research}, volume = {39}, number = {14}, eprint = {21593129}, eprinttype = {pubmed}, issn = {1362-4962}, doi = {10.1093/nar/gkr240}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21593129}, abstract = {We present TT2NE, a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. TT2NE is guaranteed to find the minimum free energy structure regardless of pseudoknot topology. This unique proficiency is obtained at the expense of the maximum length of sequences that can be treated, but comparison with state-of-the-art algorithms shows that TT2NE significantly improves the quality of predictions. Analysis of TT2NE’s incorrect predictions sheds light on the need to study how sterical constraints limit the range of pseudoknotted structures that can be formed from a given sequence. An implementation of TT2NE on a public server can be found at http://ipht.cea.fr/rna/tt2ne.php.}, isbn = {3316908757}, pmid = {21593129}, keywords = {nosource} }

@article{yaoCMfinderCovarianceModel2006, title = {{{CMfinder}}–a Covariance Model Based {{RNA}} Motif Finding Algorithm.}, author = {Yao, Zizhen and Weinberg, Zasha and Ruzzo, Walter L.}, year = 2006, month = feb, journal = {Bioinformatics}, volume = {22}, number = {4}, eprint = {16357030}, eprinttype = {pubmed}, pages = {445–52}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btk008}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16357030}, abstract = {MOTIVATION: The recent discoveries of large numbers of non-coding RNAs and computational advances in genome-scale RNA search create a need for tools for automatic, high quality identification and characterization of conserved RNA motifs that can be readily used for database search. Previous tools fall short of this goal. RESULTS: CMfinder is a new tool to predict RNA motifs in unaligned sequences. It is an expectation maximization algorithm using covariance models for motif description, featuring novel integration of multiple techniques for effective search of motif space, and a Bayesian framework that blends mutual information-based and folding energy-based approaches to predict structure in a principled way. Extensive tests show that our method works well on datasets with either low or high sequence similarity, is robust to inclusion of lengthy extraneous flanking sequence and/or completely unrelated sequences, and is reasonably fast and scalable. In testing on 19 known ncRNA families, including some difficult cases with poor sequence conservation and large indels, our method demonstrates excellent average per-base-pair accuracy–79% compared with at most 60% for alternative methods. More importantly, the resulting probabilistic model can be directly used for homology search, allowing iterative refinement of structural models based on additional homologs. We have used this approach to obtain highly accurate covariance models of known RNA motifs based on small numbers of related sequences, which identified homologs in deeply-diverged species.}, pmid = {16357030}, keywords = {Algorithms,Base Sequence,Computer Simulation,Conserved Sequence,Genetic,Models,Molecular Sequence Data,nosource,Nucleic Acid,RNA,RNA: methods,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis,Sequence Homology,Software,Statistics as Topic} }

@article{eddyRNASequenceAnalysis1994, title = {{{RNA}} Sequence Analysis Using Covariance Models}, author = {Eddy, SR R.}, year = 1994, journal = {Nucleic Acids Research}, volume = {22}, number = {11}, url = {http://nar.oxfordjournals.org/content/22/11/2079.short}, keywords = {nosource} }

@article{knudsenPfoldRNASecondary2003, title = {Pfold: {{RNA}} Secondary Structure Prediction Using Stochastic Context-Free Grammars}, author = {Knudsen, B.}, year = 2003, month = jul, journal = {Nucleic Acids Research}, volume = {31}, number = {13}, pages = {3423–3428}, issn = {1362-4962}, doi = {10.1093/nar/gkg614}, url = {http://www.nar.oupjournals.org/cgi/doi/10.1093/nar/gkg614}, isbn = {3523927552}, keywords = {nosource} }

@article{chenFlexStemImprovingPredictions2008, title = {{{FlexStem}}: Improving Predictions of {{RNA}} Secondary Structures with Pseudoknots by Reducing the Search Space.}, author = {Chen, Xiang and He, Si-Min and Bu, Dongbo and Zhang, Fa and Wang, Zhiyong and Chen, Runsheng and Gao, Wen}, year = 2008, month = sep, journal = {Bioinformatics}, volume = {24}, number = {18}, eprint = {18586700}, eprinttype = {pubmed}, pages = {1994–2001}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btn327}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18586700}, abstract = {RNA secondary structures with pseudoknots are often predicted by minimizing free energy, which is proved to be NP-hard. Due to kinetic reasons the real RNA secondary structure often has local instead of global minimum free energy. This implies that we may improve the performance of RNA secondary structure prediction by taking kinetics into account and minimize free energy in a local area.}, pmid = {18586700}, keywords = {Algorithms,Computational Biology,Computational Biology: methods,nosource,Nucleic Acid,Nucleic Acid Conformation,RNA,RNA: chemistry,Sequence Analysis,Sequence Homology} }

@article{rivasRangeComplexProbabilistic2012, title = {A Range of Complex Probabilistic Models for {{RNA}} Secondary Structure Prediction That Includes the Nearest-Neighbor Model and More.}, author = {Rivas, Elena and Lang, Raymond and Eddy, SR Sean R.}, year = 2012, month = feb, journal = {RNA}, volume = {18}, number = {2}, pages = {193–212}, issn = {1469-9001}, doi = {10.1261/rna.030049.111}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3264907&tool=pmcentrez&rendertype=abstract http://www.ncbi.nlm.nih.gov/pubmed/22194308 http://rnajournal.cshlp.org/content/18/2/193.short}, abstract = {The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using complex nearest-neighbor models, including CONTRAfold, Simfold, and ContextFold. Little work has been reported on generative probabilistic models (stochastic context-free grammars [SCFGs]) of comparable complexity, although probabilistic models are generally easier to train and to use. To explore a range of probabilistic models of increasing complexity, and to directly compare probabilistic, thermodynamic, and discriminative approaches, we created TORNADO, a computational tool that can parse a wide spectrum of RNA grammar architectures (including the standard nearest-neighbor model and more) using a generalized super-grammar that can be parameterized with probabilities, energies, or arbitrary scores. By using TORNADO, we find that probabilistic nearest-neighbor models perform comparably to (but not significantly better than) discriminative methods. We find that complex statistical models are prone to overfitting RNA structure and that evaluations should use structurally nonhomologous training and test data sets. Overfitting has affected at least one published method (ContextFold). The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases.}, pmid = {22194308}, keywords = {Algorithms,Computational Biology,Computational Biology: methods,free grammars,language for rna grammar,maximum likelihood training,Models,nosource,Nucleic Acid Conformation,parsing,probabilistic models,RNA,RNA Folding,rna secondary structure prediction,RNA: chemistry,Software,Statistical,stochastic context-,Theoretical,Thermodynamics} }

@article{nawrockiInfernal10Inference2009, title = {Infernal 1.0: Inference of {{RNA}} Alignments.}, author = {Nawrocki, Eric P. and Kolbe, Diana L. and Eddy, Sean R.}, year = 2009, month = may, journal = {Bioinformatics}, volume = {25}, number = {10}, pages = {1335–1337}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp157}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2732312&tool=pmcentrez&rendertype=abstract}, abstract = {SUMMARY: INFERNAL builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence- and structure-based multiple sequence alignments. AVAILABILITY: Source code, documentation and benchmark downloadable from http://infernal.janelia.org. INFERNAL is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X.}, pmid = {19307242}, keywords = {Databases,nosource,Nucleic Acid,Nucleic Acid Conformation,RNA,RNA: chemistry,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis,Software} }

@article{zukerMfoldWebServer2003, title = {Mfold Web Server for Nucleic Acid Folding and Hybridization Prediction}, author = {Zuker, M.}, year = 2003, month = jul, journal = {Nucleic Acids Research}, volume = {31}, number = {13}, pages = {3406–3415}, issn = {1362-4962}, doi = {10.1093/nar/gkg595}, url = {http://www.nar.oupjournals.org/cgi/doi/10.1093/nar/gkg595 http://nar.oxfordjournals.org/content/31/13/3406.short}, keywords = {nosource} }

@article{hamiltonBioinformaticsSearchPipeline2009, title = {A Bioinformatics Search Pipeline, {{RNA2DSearch}}, Identifies {{RNA}} Localization Elements in {{Drosophila}} Retrotransposons.}, author = {Hamilton, RS Russell S. and Hartswood, Eve V. E. and Vendra, Georgia and Jones, Cheryl and Bor, Veronique V. A. N. D. E. and Finnegan, David and Davis, Ilan and Bor, Veronique Van De}, year = 2009, month = feb, journal = {RNA}, volume = {15}, number = {2}, pages = {200–7}, issn = {1469-9001}, doi = {10.1261/rna.1264109}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2648715&tool=pmcentrez&rendertype=abstract http://rnajournal.cshlp.org/content/15/2/200.short}, abstract = {mRNA localization is a widespread mode of delivering proteins to their site of function. The embryonic axes in Drosophila are determined in the oocyte, through Dynein-dependent transport of gurken/TGF-alpha mRNA, containing a small localization signal that assigns its destination. A signal with a similar secondary structure, but lacking significant sequence similarity, is present in the I factor retrotransposon mRNA, also transported by Dynein. It is currently unclear whether other mRNAs exist that are localized to the same site using similar signals. Moreover, searches for other genes containing similar elements have not been possible due to a lack of suitable bioinformatics methods for searches of secondary structure elements and the difficulty of experimentally testing all the possible candidates. We have developed a bioinformatics approach for searching across the genome for small RNA elements that are similar to the secondary structures of particular localization signals. We have uncovered 48 candidates, of which we were able to test 22 for their localization potential using injection assays for Dynein mediated RNA localization. We found that G2 and Jockey transposons each contain a gurken/I factor-like RNA stem-loop required for Dynein-dependent localization to the anterior and dorso-anterior corner of the oocyte. We conclude that I factor, G2, and Jockey are members of a “family” of transposable elements sharing a gurken-like mRNA localization signal and Dynein-dependent mechanism of transport. The bioinformatics pipeline we have developed will have broader utility in fields where small RNA signals play important roles.}, pmid = {19144907}, keywords = {Animals,Base Sequence,bioinformatics,drosophila,Drosophila melanogaster,Drosophila melanogaster: embryology,Drosophila melanogaster: genetics,Drosophila Proteins,Drosophila Proteins: genetics,Genome,Insect,intracellular rna localization,Messenger,Messenger: genetics,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Oocytes,Oocytes: metabolism,Retroelements,Retroelements: genetics,RNA,rna secondary,RNA: methods,Sequence Alignment,Sequence Analysis,Terminal Repeat Sequences,Transforming Growth Factor alpha,Transforming Growth Factor alpha: genetics,transposable elements} }

@article{hammannSearchingGenomesRibozymes2007, title = {Searching Genomes for Ribozymes and Riboswitches.}, author = {Hammann, Christian and Westhof, Eric}, year = 2007, month = jan, journal = {Genome Biology}, volume = {8}, number = {4}, pages = {210}, issn = {1465-6914}, doi = {10.1186/gb-2007-8-4-210}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1895996&tool=pmcentrez&rendertype=abstract}, abstract = {New regulatory RNAs with complex structures have recently been discovered, among them the first catalytic riboswitch, a gene-regulatory RNA sequence with catalytic activity. Here we discuss some of the experimental approaches and theoretical difficulties attached to the identification of new ribozymes in genomes.}, pmid = {17472738}, keywords = {Base Sequence,Catalytic,Catalytic: chemistry,Catalytic: physiology,Computational Biology,Conserved Sequence,Genetic Variation,Genome,Genomics,Genomics: methods,nosource,Nucleic Acid Conformation,Regulatory Sequences,Ribonucleic Acid,Ribonucleic Acid: physiology,RNA,RNA Splicing} }

@article{riccitelliComputationalDiscoveryFolded2010, title = {Computational Discovery of Folded {{RNA}} Domains in Genomes and in Vitro Selected Libraries.}, author = {Riccitelli, Nathan J. and Lupt{'a}k, Andrej}, year = 2010, month = oct, journal = {Methods}, volume = {52}, number = {2}, pages = {133–140}, publisher = {Elsevier Inc.}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2010.06.005}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3137801&tool=pmcentrez&rendertype=abstract}, abstract = {Structured functional RNAs are conserved on the level of secondary and tertiary structure, rather than at sequence level, and so traditional sequence-based searches often fail to identify them. Structure-based searches are increasingly used to discover known RNA motifs in sequence databases. We describe the application of the program RNABOB, which performs such searches by allowing the user to define a desired motif’s sequence, paired and spacer elements and then scans a sequence file for regions capable of assuming the prescribed fold. Structure descriptors of stem-loops, internal loops, three-way junctions, kissing loops, and the hammerhead and hepatitis delta virus ribozymes are shown as examples of implementation of structure-based searches.}, pmid = {20554049}, keywords = {Aptamers,Base Sequence,Catalytic,Catalytic: chemistry,Computational Biology,Computational Biology: methods,Gene Library,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Nucleotide,Nucleotide: chemistry,RNA,Software,Untranslated,Untranslated: chemistry} }

@article{webbWidespreadOccurrenceSelfcleaving2009, title = {Widespread Occurrence of Self-Cleaving Ribozymes}, author = {Webb, CHT C. H. T. and Riccitelli, N. J. NJ and Ruminski, DJ D. J. and Lupt{'a}k, Andrej}, year = 2009, journal = {Science}, volume = {326}, number = {5955}, pages = {5}, publisher = {American Association for the Advancement of Science}, url = {http://www.sciencemag.org/content/326/5955/953.short}, keywords = {nosource} }

@article{eddyAcceleratedProfileHMM2011, title = {Accelerated {{Profile HMM Searches}}}, author = {Eddy, Sean R.}, editor = {Pearson, William R.}, year = 2011, month = oct, journal = {PLoS Computational Biology}, volume = {7}, number = {10}, pages = {e1002195}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002195}, url = {http://dx.plos.org/10.1371/journal.pcbi.1002195}, keywords = {nosource} } % == BibTeX quality report for eddyAcceleratedProfileHMM2011: % ? Title looks like it was stored in title-case in Zotero

@article{altschulGappedBLASTPSIBLAST1997, title = {Gapped {{BLAST}} and {{PSI-BLAST}}: A New Generation of Protein Database Search Programs}, author = {Altschul, SF F. and Madden, TL L.}, year = 1997, journal = {Nucleic Acids Research}, volume = {25}, number = {17}, pages = {3389–3402}, url = {http://nar.oxfordjournals.org/content/25/17/3389.short}, keywords = {nosource} }

@article{fabianRegulationMRNATranslation2010, title = {Regulation of {{mRNA}} Translation and Stability by {{microRNAs}}.}, author = {Fabian, Marc Robert and Sonenberg, Nahum and Filipowicz, Witold}, year = 2010, month = jan, journal = {Annual Review of Biochemistry}, volume = {79}, eprint = {20533884}, eprinttype = {pubmed}, pages = {351–79}, issn = {1545-4509}, doi = {10.1146/annurev-biochem-060308-103103}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20533884}, abstract = {MicroRNAs (miRNAs) are small noncoding RNAs that extensively regulate gene expression in animals, plants, and protozoa. miRNAs function posttranscriptionally by usually base-pairing to the mRNA 3’-untranslated regions to repress protein synthesis by mechanisms that are not fully understood. In this review, we describe principles of miRNA-mRNA interactions and proteins that interact with miRNAs and function in miRNA-mediated repression. We discuss the multiple, often contradictory, mechanisms that miRNAs have been reported to use, which cause translational repression and mRNA decay. We also address the issue of cellular localization of miRNA-mediated events and a role for RNA-binding proteins in activation or relief of miRNA repression.}, pmid = {20533884}, keywords = {Animals,Gene Expression Regulation,Humans,Messenger,Messenger: metabolism,MicroRNAs,MicroRNAs: chemistry,MicroRNAs: metabolism,nosource,Protein Biosynthesis,RNA,RNA Stability,RNA-Binding Proteins,RNA-Binding Proteins: metabolism} }

@article{muhlradTurnoverMechanismsStable1995, title = {Turnover Mechanisms of the Stable Yeast {{PGK1 mRNA}}}, author = {Muhlrad, Denise and Decker, C. J.}, year = 1995, journal = {Molecular and Cellular Biology}, volume = {15}, number = {4}, pages = {2145}, url = {http://mcb.highwire.org/cgi/content/abstract/15/4/2145}, keywords = {nosource} }

@article{kozomaraMiRBaseIntegratingMicroRNA2011, title = {{{miRBase}}: Integrating {{microRNA}} Annotation and Deep-Sequencing Data.}, author = {Kozomara, Ana and {Griffiths-Jones}, Sam}, year = 2011, month = jan, journal = {Nucleic Acids Research}, volume = {39}, number = {Database issue}, pages = {D152–7}, issn = {1362-4962}, doi = {10.1093/nar/gkq1027}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3013655&tool=pmcentrez&rendertype=abstract}, abstract = {miRBase is the primary online repository for all microRNA sequences and annotation. The current release (miRBase 16) contains over 15,000 microRNA gene loci in over 140 species, and over 17,000 distinct mature microRNA sequences. Deep-sequencing technologies have delivered a sharp rise in the rate of novel microRNA discovery. We have mapped reads from short RNA deep-sequencing experiments to microRNAs in miRBase and developed web interfaces to view these mappings. The user can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression. These data can be used as a proxy for relative expression levels of microRNA sequences, provide detailed evidence for microRNA annotations and alternative isoforms of mature microRNAs, and allow us to revisit previous annotations. miRBase is available online at: http://www.mirbase.org/.}, pmid = {21037258}, keywords = {Databases,MicroRNAs,MicroRNAs: chemistry,MicroRNAs: genetics,MicroRNAs: metabolism,nosource,Nucleic Acid,RNA,Sequence Analysis,Systems Integration} }

@article{krugerRNAhybridMicroRNATarget2006, title = {{{RNAhybrid}}: {{microRNA}} Target Prediction Easy, Fast and Flexible.}, author = {Kr{"u}ger, Jan and Rehmsmeier, Marc}, year = 2006, month = jul, journal = {Nucleic Acids Research}, volume = {34}, number = {Web Server issue}, pages = {W451-4}, issn = {1362-4962}, doi = {10.1093/nar/gkl243}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1538877&tool=pmcentrez&rendertype=abstract}, abstract = {In the elucidation of the microRNA regulatory network, knowledge of potential targets is of highest importance. Among existing target prediction methods, RNAhybrid [M. Rehmsmeier, P. Steffen, M. H"ochsmann and R. Giegerich (2004) RNA, 10, 1507-1517] is unique in offering a flexible online prediction. Recently, some useful features have been added, among these the possibility to disallow G:U base pairs in the seed region, and a seed-match speed-up, which accelerates the program by a factor of 8. In addition, the program can now be used as a webservice for remote calls from user-implemented programs. We demonstrate RNAhybrid’s flexibility with the prediction of a non-canonical target site for Caenorhabditis elegans miR-241 in the 3’-untranslated region of lin-39. RNAhybrid is available at http://bibiserv.techfak.uni-bielefeld.de/rnahybrid.}, pmid = {16845047}, keywords = {3’ Untranslated Regions,3’ Untranslated Regions: chemistry,Animals,Binding Sites,Caenorhabditis elegans,Caenorhabditis elegans Proteins,Caenorhabditis elegans Proteins: genetics,Caenorhabditis elegans: genetics,Homeodomain Proteins,Homeodomain Proteins: genetics,Internet,MicroRNAs,MicroRNAs: chemistry,nosource,RNA Interference,Software} }

@article{friendConservedPUFAgoeEF1AComplex2012, title = {A Conserved {{PUF-Ago-eEF1A}} Complex Attenuates Translation Elongation.}, author = {Friend, Kyle and Campbell, Zachary T. and Cooke, Amy and {Kroll-Conner}, Peggy and Wickens, Marvin P. and Kimble, Judith}, year = 2012, month = feb, journal = {Nature structural & molecular biology}, volume = {19}, number = {2}, eprint = {22231398}, eprinttype = {pubmed}, pages = {176–83}, issn = {1545-9985}, doi = {10.1038/nsmb.2214}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22231398 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3293257&tool=pmcentrez&rendertype=abstract}, abstract = {PUF (Pumilio/FBF) RNA-binding proteins and Argonaute (Ago) miRNA-binding proteins regulate mRNAs post-transcriptionally, each acting through similar, yet distinct, mechanisms. Here, we report that PUF and Ago proteins can also function together in a complex with a core translation elongation factor, eEF1A, to repress translation elongation. Both nematode (Caenorhabditis elegans) and mammalian PUF-Ago-eEF1A complexes were identified, using coimmunoprecipitation and recombinant protein assays. Nematode CSR-1 (Ago) promoted repression of FBF (PUF) target mRNAs in in vivo assays, and the FBF-1-CSR-1 heterodimer inhibited EFT-3 (eEF1A) GTPase activity in vitro. Mammalian PUM2-Ago-eEF1A inhibited translation of nonadenylated and polyadenylated reporter mRNAs in vitro. This repression occurred after translation initiation and led to ribosome accumulation within the open reading frame, roughly at the site where the nascent polypeptide emerged from the ribosomal exit tunnel. Together, these data suggest that a conserved PUF-Ago-eEF1A complex attenuates translation elongation.}, pmid = {22231398}, keywords = {Animals,Argonaute Proteins,Argonaute Proteins: metabolism,Caenorhabditis elegans,Caenorhabditis elegans Proteins,Caenorhabditis elegans Proteins: metabolism,Caenorhabditis elegans: physiology,Cell Line,Eukaryotic Initiation Factors,Eukaryotic Initiation Factors: metabolism,Humans,nosource,Peptide Elongation Factor 1,Peptide Elongation Factor 1: metabolism,Protein Biosynthesis,RNA-Binding Proteins,RNA-Binding Proteins: metabolism} }

@article{liDiagnosticPrognosticImplications2008, title = {Diagnostic and Prognostic Implications of {{microRNAs}} in Human Hepatocellular Carcinoma.}, author = {Li, Wenxi and Xie, Lu and He, Xianghuo and Li, Jinjun and Tu, Kang and Wei, Lin and Wu, Jun and Guo, Yong and Ma, Xi and Zhang, Pingping and Pan, Zhimei and Hu, Xin and Zhao, Yingjun and Xie, Haiyang and Jiang, Guoping and Chen, Taoyang and Wang, Jianneng and Zheng, Shusen and Cheng, Jing and Wan, Dafang and Yang, Shengli and Li, Yixue and Gu, Jianren}, year = 2008, month = oct, journal = {International Journal of Cancer}, volume = {123}, number = {7}, eprint = {18649363}, eprinttype = {pubmed}, pages = {1616–1622}, issn = {1097-0215}, doi = {10.1002/ijc.23693}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18649363}, abstract = {MicroRNAs (miRNAs) are important gene regulators, which are often deregulated in cancers. In this study, the authors analyzed the microRNAs profiles of 78 matched cancer/noncanerous liver tissues from HCC patients and 10 normal liver tissues and found that 69 miRNAs were differentially expressed between hepatocellular carcinoma (HCC) and corresponding noncancerous liver tissues (N). Then the expressions of 8 differentially expressed miRNAs were validated by real time RT PCR. The set of differentially expressed miRNAs could distinctly classify HCC, N and normal liver tissues (NL). Moreover, some of these differentially expressed miRNAs were related to the clinical factors of HCC patients. Most importantly, Kaplan-Meier estimates and the log-rank test showed that high expression of hsa-miR-125b was correlated with good survival of HCC patients (hazard ratio, 1.787, 95% confidence interval, 1.020-3.133, p = 0.043). The transfection assay showed that overexpression of miR-125b in HCC cell line could obviously suppress the cell growth and phosporylation of Akt. In conclusion, the authors have demonstrated the diagnostic miRNA profile for HCC, and for the first time, identified the miR-125b with predictive significance for HCC prognosis.}, pmid = {18649363}, keywords = {Blotting,Carcinoma,Cell Line,Cell Proliferation,Chromosome Mapping,Hepatocellular,Hepatocellular: diagnosis,Hepatocellular: genetics,Hepatocellular: pathology,Humans,Liver,Liver Neoplasms,Liver Neoplasms: diagnosis,Liver Neoplasms: genetics,Liver Neoplasms: pathology,Liver: enzymology,Liver: metabolism,MicroRNAs,MicroRNAs: genetics,nosource,Oligonucleotide Array Sequence Analysis,Phosphorylation,Prognosis,Proto-Oncogene Proteins c-akt,Proto-Oncogene Proteins c-akt: metabolism,Reverse Transcriptase Polymerase Chain Reaction,Tumor,Western} }

@article{aliDifferentiallyExpressedMiRNAs2010, title = {Differentially Expressed {{miRNAs}} in the Plasma May Provide a Molecular Signature for Aggressive Pancreatic Cancer.}, author = {Ali, Shadan and Almhanna, Khaldoun and Chen, Wei and Philip, Philip A. and Sarkar, Fazlul H.}, year = 2010, month = jan, journal = {American Journal of Translational Research}, volume = {3}, number = {1}, pages = {28–47}, issn = {1943-8141}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981424/ http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2981424&tool=pmcentrez&rendertype=abstract}, abstract = {Pancreatic cancer (PC) has the poorest overall survival rate among all human cancers because of late diagnosis and absence of screening tools. We compared the expression profile of microRNAs (miRNAs) in the plasma of patients diagnosed with PC (n=50) with healthy volunteers (n=10). Data was further validated by quantitative realtime PCR and cell-based assays. Thirty-seven miRNAs were down-regulated and 54 were up-regulated in plasma from patients with PC. The expression of miR-21 was significantly higher, and the expression of let-7 family (especially let-7d) and miR-146a was significantly lower in PC. Most interestingly, the expression of miR-21 was correlated with worse survival, and the expression of let-7 was inversely correlated with survival in this pilot study with mixed patient population. Moreover, we found that miR-21 family was markedly over-expressed in chemo-resistant PC cell lines, which was consistent with the plasma data from PC patients. Our previous studies have shown increased expression of miR-21 with concomitant loss of PTEN expression in PC cells, which is consistent with our current findings showing the loss of three additional targets of miR-21 (PDCD4, Maspin and TPM1). These results suggest that identifying and validating the expression of miRNAs in newly diagnosed patients could serve as potential biomarker for tumor aggressiveness, and such miRNAs could be useful for the screening of high-risk patients, and may also serve as targets for future drug development.}, pmid = {21139804}, keywords = {drug resistance,let-7d,mir-21,mir-221,nosource,pancreatic cancer,pten} }

@article{jinMiR1226TargetsExpression2010, title = {{{miR-1226}} Targets Expression of the Mucin 1 Oncoprotein and Induces Cell Death}, author = {Jin, Caining and Rajabi, Hasan and Kufe, Donald}, year = 2010, journal = {International journal of oncology}, volume = {37}, number = {1}, pages = {61–69}, doi = {10.3892/ijo}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3027208/}, keywords = {apoptosis,microrna,mitochondria,muc1,necrosis,nosource,reactive oxygen species} }

@article{wolkIL22IncreasesInnate2004, title = {{{IL-22}} Increases the Innate Immunity of Tissues.}, author = {Wolk, Kerstin and Kunz, Stefanie and Witte, Ellen and Friedrich, Markus and Asadullah, Khusru and Sabat, Robert}, year = 2004, month = aug, journal = {Immunity}, volume = {21}, number = {2}, eprint = {15308104}, eprinttype = {pubmed}, pages = {241–254}, issn = {1074-7613}, doi = {10.1016/j.immuni.2004.07.007}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15308104}, abstract = {Interleukin 22 (IL-22) is mainly produced by activated Th1 cells. The data presented here indicate that neither resting nor activated immune cells express IL-22 receptor, and IL-22 did not have any effects on these cells in vitro and in vivo. In contrast, cells of the skin and the digestive and respiratory systems represent putative targets of this cytokine. The expression of IL-22 receptor in keratinocytes was upregulated by Interferon-gamma. In these cells, IL-22 activated STAT3 and directly and transcriptionally increased the expression of beta-Defensin 2 and beta-Defensin 3. High levels of IL-22 were associated with strongly upregulated beta-Defensin expression in skin from patients with T cell-mediated dermatoses. Taken together, IL-22 does not serve the communication between immune cells but is a T cell mediator that directly promotes the innate, nonspecific immunity of tissues.}, pmid = {15308104}, keywords = {Animals,beta-Defensins,beta-Defensins: immunology,beta-Defensins: metabolism,DNA-Binding Proteins,DNA-Binding Proteins: immunology,DNA-Binding Proteins: metabolism,Humans,Immune System,Immune System: immunology,Immune System: metabolism,Immunity,Innate,Innate: immunology,Innate: physiology,Interleukin,Interleukin: immunology,Interleukin: metabolism,Interleukins,Interleukins: immunology,Interleukins: metabolism,Keratinocytes,Keratinocytes: immunology,Keratinocytes: metabolism,Male,Mice,nosource,Receptors,Skin,Skin: immunology,Skin: metabolism,STAT3 Transcription Factor,Trans-Activators,Trans-Activators: immunology,Trans-Activators: metabolism} }

@article{wolkIL22RegulatesExpression2006, title = {{{IL-22}} Regulates the Expression of Genes Responsible for Antimicrobial Defense, Cellular Differentiation, and Mobility in Keratinocytes: A Potential Role in Psoriasis.}, author = {Wolk, Kerstin and Witte, Ellen and Wallace, Elizabeth and D{"o}cke, Wolf-Dietrich and Kunz, Stefanie and Asadullah, Khusru and Volk, Hans-Dieter and Sterry, Wolfram and Sabat, Robert}, year = 2006, month = may, journal = {European Journal of Immunology}, volume = {36}, number = {5}, eprint = {16619290}, eprinttype = {pubmed}, pages = {1309–1323}, issn = {0014-2980}, doi = {10.1002/eji.200535503}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16619290}, abstract = {IL-22 is an IFN-IL-10 cytokine family member, which is produced by activated Th1 and NK cells and acts primarily on epithelial cells. Here we demonstrate that IL-22, in contrast to its relative IFN-gamma, regulates the expression of only a few genes in keratinocytes. This is due to varied signal transduction. Gene expressions regulated by IL-22 should enhance antimicrobial defense [psoriasin (S100A7), calgranulin A (S100A8), calgranulin B (S100A9)], inhibit cellular differentiation (e.g., profilaggrin, keratins 1 and 10, kallikrein 7), and increase cellular mobility [e.g., matrix metalloproteinease 1 (MMP1, collagenase 1), MMP3 (stromelysin 1), desmocollin 1]. In contrast, IFN-gamma favored the expression of MHC pathway molecules, adhesion molecules, cytokines, chemokines, and their receptors. The IL-22 effects were transcriptional and either independent of protein synthesis and secretion, or mediated by a secreted protein. Inflammatory conditions, but not keratinocyte differentiation, amplified the IL-22 effects. IL-22 application in mice enhanced cutaneous S100A9 and MMP1 expression. High IL-22 levels in psoriatic skin were associated with strongly up-regulated cutaneous S100A7, S100A8, S100A9, and MMP1 expression. Psoriatic patients showed strongly elevated IL-22 plasma levels, which correlated with the disease severity. Expression of IL-22 and IL-22-regulated genes was reduced by anti-psoriatic therapy. In summary, despite similarities, IFN-gamma primarily amplifies inflammation, while IL-22 may be important in the innate immunity and reorganization of epithelia.}, pmid = {16619290}, keywords = {Animals,Calgranulin A,Calgranulin A: genetics,Calgranulin B,Calgranulin B: genetics,Cell Differentiation,Cell Movement,Cells,Cultured,Gene Expression Regulation,Humans,Inbred BALB C,Interferon-gamma,Interferon-gamma: physiology,Interleukins,Interleukins: physiology,Keratinocytes,Keratinocytes: cytology,Keratinocytes: metabolism,Male,Matrix Metalloproteinase 1,Matrix Metalloproteinase 1: genetics,Mice,nosource,Psoriasis,Psoriasis: etiology} }

@article{kotenkoIdentificationFunctionalInterleukin222001, title = {Identification of the Functional Interleukin-22 ({{IL-22}}) Receptor Complex: The {{IL-10R2}} Chain ({{IL-10Rbeta}} ) Is a Common Chain of Both the {{IL-10}} and {{IL-22}} ({{IL-10-related T}} Cell-Derived Inducible Factor, {{IL-TIF}}) Receptor Complexes.}, author = {Kotenko, S. V. and Izotova, L. S. and Mirochnitchenko, O. V. and Esterova, E. and Dickensheets, H. and Donnelly, R. P. and Pestka, S.}, year = 2001, month = jan, journal = {The Journal of biological chemistry}, volume = {276}, number = {4}, eprint = {11035029}, eprinttype = {pubmed}, pages = {2725–32}, issn = {0021-9258}, doi = {10.1074/jbc.M007837200}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11035029}, abstract = {Interleukin-10 (IL-10)-related T cell-derived inducible factor (IL-TIF; provisionally designated IL-22) is a cytokine with limited homology to IL-10. We report here the identification of a functional IL-TIF receptor complex that consists of two receptor chains, the orphan CRF2-9 and IL-10R2, the second chain of the IL-10 receptor complex. Expression of the CRF2-9 chain in monkey COS cells renders them sensitive to IL-TIF. However, in hamster cells both chains, CRF2-9 and IL-10R2, must be expressed to assemble the functional IL-TIF receptor complex. The CRF2-9 chain (or the IL-TIF-R1 chain) is responsible for Stat recruitment. Substitution of the CRF2-9 intracellular domain with the IFN-gammaR1 intracellular domain changes the pattern of IL-TIF-induced Stat activation. The CRF2-9 gene is expressed in normal liver and kidney, suggesting a possible role for IL-TIF in regulating gene expression in these tissues. Each chain, CRF2-9 and IL-10R2, is capable of binding IL-TIF independently and can be cross-linked to the radiolabeled IL-TIF. However, binding of IL-TIF to the receptor complex is greater than binding to either receptor chain alone. Sharing of the common IL-10R2 chain between the IL-10 and IL-TIF receptor complexes is the first such case for receptor complexes with chains belonging to the class II cytokine receptor family, establishing a novel paradigm for IL-10-related ligands similar to the shared use of the gamma common chain (gamma(c)) by several cytokines, including IL-2, IL-4, IL-7, IL-9, and IL-15.}, isbn = {7322354567}, pmid = {11035029}, keywords = {Amino Acid Sequence,Biological,Cross-Linking Reagents,Cytokines,Cytokines: metabolism,Humans,Interleukin,Interleukin-10,Interleukin: isolation & purification,Interleukins,Interleukins: metabolism,Ligands,Models,Molecular Sequence Data,nosource,Protein Binding,Receptors,Signal Transduction} }

@article{dumoutierHumanInterleukin10relatedCellderived2000, title = {Human Interleukin-10-Related {{T}} Cell-Derived Inducible Factor: Molecular Cloning and Functional Characterization as an Hepatocyte-Stimulating Factor.}, author = {Dumoutier, L. and Roost, E. Van and Colau, D. and Renauld, J. C.}, year = 2000, month = aug, journal = {Proceedings of the National Academy of Sciences}, volume = {97}, number = {18}, pages = {10144–10149}, issn = {0027-8424}, doi = {10.1073/pnas.170291697}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=27764&tool=pmcentrez&rendertype=abstract}, abstract = {IL-10-related T cell-derived inducible factor (IL-TIF or IL-21) is a new cytokine structurally related to IL-10 and originally identified in the mouse as a gene induced by IL-9 in T cells and mast cells. Here, we report the cloning of the human IL-TIF cDNA, which shares 79% amino acid identity with mouse IL-TIF and 25% identity with human IL-10. Recombinant human IL-TIF was found to activate signal transducer and activator of transcription factors-1 and -3 in several hepatoma cell lines. IL-TIF stimulation of HepG2 human hepatoma cells up-regulated the production of acute phase reactants such as serum amyloid A, alpha1-antichymotrypsin, and haptoglobin. Although IL-10 and IL-TIF have distinct activities, antibodies directed against the beta chain of the IL-10 receptor blocked the induction of acute phase reactants by IL-TIF, indicating that this chain is a common component of the IL-10 and IL-TIF receptors. Similar acute phase reactant induction was observed in mouse liver upon IL-TIF injection, and IL-TIF expression was found to be rapidly increased after lipopolysaccharide (LPS) injection, suggesting that this cytokine contributes to the inflammatory response in vivo.}, pmid = {10954742}, keywords = {Acute-Phase Proteins,Acute-Phase Proteins: genetics,Amino Acid,Amino Acid Sequence,Animals,Carcinoma,Cell Line,Cells,Cloning,Complementary,Cultured,Cytokines,Cytokines: chemistry,Cytokines: genetics,Cytokines: pharmacology,Cytokines: physiology,DNA,Escherichia coli,Female,Gene Expression Regulation,Hepatocellular,Humans,Inbred C3H,Interleukin-10,Interleukin-10: immunology,Liver Neoplasms,Mice,Molecular,Molecular Sequence Data,Neoplastic,Neoplastic: drug effec,nosource,Recombinant Proteins,Recombinant Proteins: chemistry,Recombinant Proteins: pharmacology,Sequence Alignment,Sequence Homology,Signal Transduction,T-Lymphocytes,T-Lymphocytes: immunology,Trans-Activators,Trans-Activators: metabolism,Tumor Cells} }

@article{battenInterleukin27Limits2006, title = {Interleukin 27 Limits Autoimmune Encephalomyelitis by Suppressing the Development of Interleukin 17-Producing {{T}} Cells.}, author = {Batten, Marcel and Li, Ji and Yi, Sothy and Kljavin, Noelyn M. and Danilenko, Dimitry M. and Lucas, Sophie and Lee, James and {}de Sauvage, Frederic J. and Ghilardi, Nico}, year = 2006, month = sep, journal = {Nature Immunology}, volume = {7}, number = {9}, eprint = {16906167}, eprinttype = {pubmed}, pages = {929–936}, issn = {1529-2908}, doi = {10.1038/ni1375}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16906167}, abstract = {Interleukin 27 (IL-27) was first characterized as a proinflammatory cytokine with T helper type 1-inducing activity. However, subsequent work has demonstrated that mice deficient in IL-27 receptor (IL-27R alpha) show exacerbated inflammatory responses to a variety of challenges, suggesting that IL-27 has important immunoregulatory functions in vivo. Here we demonstrate that IL-27R alpha-deficient mice were hypersusceptible to experimental autoimmune encephalomyelitis and generated more IL-17-producing T helper cells. IL-27 acted directly on effector T cells to suppress the development of IL-17-producing T helper cells mediated by IL-6 and transforming growth factor-beta. This suppressive activity was dependent on the transcription factor STAT1 and was independent of interferon-gamma. Finally, IL-27 suppressed IL-6-mediated T cell proliferation. These data provide a mechanistic explanation for the IL-27-mediated immune suppression noted in several in vivo models of inflammation.}, pmid = {16906167}, keywords = {Animals,Autoimmune,Central Nervous System,Central Nervous System: immunology,Central Nervous System: pathology,Cytokine,Cytokine: genetics,Encephalomyelitis,Experimental,Experimental: genet,Experimental: immun,Experimental: patho,Helper-Inducer,Helper-Inducer: drug effects,Helper-Inducer: immunology,Immune Tolerance,Immune Tolerance: genetics,Immune Tolerance: immunology,Interferon-gamma,Interferon-gamma: metabolism,Interleukin-17,Interleukin-17: biosynthesis,Interleukin-17: genetics,Interleukin-6,Interleukin-6: pharmacology,Interleukins,Interleukins: pharmacology,Interleukins: physiology,Knockout,Lymph Nodes,Lymph Nodes: immunology,Lymphocyte Activation,Mice,nosource,Receptors,STAT1 Transcription Factor,STAT1 Transcription Factor: genetics,STAT1 Transcription Factor: metabolism,T-Lymphocytes,Transforming Growth Factor beta,Transforming Growth Factor beta: pharmacology} }

@article{chenDevelopmentTh1typeImmune2000, title = {Development of {{Th1-type}} Immune Responses Requires the Type {{I}} Cytokine Receptor {{TCCR}}.}, author = {Chen, Q. and Ghilardi, N. and Wang, H. and Baker, T. and Xie, M. H. and Gurney, a and Grewal, I. S. and {}de Sauvage, F. J.}, year = 2000, month = oct, journal = {Nature}, volume = {407}, number = {6806}, eprint = {11057672}, eprinttype = {pubmed}, pages = {916–920}, issn = {0028-0836}, doi = {10.1038/35038103}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11057672}, abstract = {On antigen challenge, T-helper cells differentiate into two functionally distinct subsets, Th1 and Th2, characterized by the different effector cytokines that they secrete. Th1 cells produce interleukin (IL)-2, interferon-gamma (IFN-gamma) and lymphotoxin-beta, which mediate pro-inflammatory functions critical for the development of cell-mediated immune responses, whereas Th2 cells secrete cytokines such as IL-4, IL-5 and IL-10 that enhance humoral immunity. This process of T-helper cell differentiation is tightly regulated by cytokines. Here we report a new member of the type I cytokine receptor family, designated T-cell cytokine receptor (TCCR). When challenged in vivo with protein antigen, TCCR-deficient mice had impaired Th1 response as measured by IFN-gamma production. TCCR-deficient mice also had increased susceptibility to infection with an intracellular pathogen, Listeria monocytogenes. In addition, levels of antigen-specific immunoglobulin-gamma2a, which are dependent on Th1 cells, were markedly reduced in these mice. Our results demonstrate the existence of a new cytokine receptor involved in regulating the adaptive immune response and critical to the generation of a Th1 response.}, pmid = {11057672}, keywords = {Amino Acid,Amino Acid Sequence,Animals,CD4-Positive T-Lymphocytes,CD4-Positive T-Lymphocytes: immunology,Cells,Cultured,Cytokine,Cytokine: genetics,Cytokine: immunology,Cytokine: isolation & purification,Cytokine: metabolism,Female,Gene Targeting,Hemocyanin,Hemocyanin: immunology,Humans,Immunoglobulin Isotypes,Immunoglobulin Isotypes: immunology,Inbred C57BL,Interferon-gamma,Interferon-gamma: biosynthesis,Leukopoiesis,Leukopoiesis: physiology,Listeria monocytogenes,Listeria monocytogenes: immunology,Male,Mice,Molecular Sequence Data,nosource,Receptors,Sequence Homology,Th1 Cells,Th1 Cells: cytology,Th1 Cells: immunology,Tissue Distribution} }

@article{yoshidaWSX1RequiredInitiation2001, title = {{{WSX-1}} Is Required for the Initiation of {{Th1}} Responses and Resistance to {{L}}. Major Infection.}, author = {Yoshida, H. and Hamano, S. and Senaldi, G. and Covey, T. and Faggioni, R. and Mu, S. and Xia, M. and Wakeham, a C. and Nishina, H. and Potter, J. and Saris, C. J. and Mak, T. W.}, year = 2001, month = oct, journal = {Immunity}, volume = {15}, number = {4}, eprint = {11672539}, eprinttype = {pubmed}, pages = {569–578}, issn = {1074-7613}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11672539}, abstract = {WSX-1 is a class I cytokine receptor with homology to the IL-12 receptors. The physiological role of WSX-1, which is expressed mainly in T cells, was investigated in gene-targeted WSX-1-deficient mice. IFN-gamma production was reduced in isolated WSX-1(-/-) T cells subjected to primary stimulation in vitro to induce Th1 differentiation but was normal in fully differentiated and activated WSX-1(-/-) Th1 cells that had received secondary stimulation. WSX-1(-/-) mice were remarkably susceptible to Leishmania major infection, showing impaired IFN-gamma production early in the infection. However, IFN-gamma production during the later phases of the infection was not impaired in the knockout. WSX-1(-/-) mice also showed poorly differentiated granulomas with dispersed accumulations of mononuclear cells when infected with bacillus Calmette-Guerin (BCG). Thus, WSX-1 is essential for the initial mounting of Th1 responses but dispensable for their maintenance.}, pmid = {11672539}, keywords = {Animals,Cell Differentiation,Cell Division,Cells,Cultured,Cutaneous,Cutaneous: genetics,Cutaneous: immunology,Cutaneous: pathology,Cytokine,Cytokine: genetics,Cytokine: physiology,Granuloma,Granuloma: pathology,Hematopoietic System,Hematopoietic System: physiology,Interferon-gamma,Interferon-gamma: biosynthesis,Interferon-gamma: genetics,Interleukin-4,Interleukin-4: biosynthesis,Interleukin-4: genetics,Knockout,Leishmania major,Leishmaniasis,Lymphatic System,Lymphatic System: immunology,Messenger,Messenger: biosynthesis,Mice,Mycobacterium bovis,nosource,Receptors,RNA,Th1 Cells,Th1 Cells: immunology,Tuberculosis,Tuberculosis: pathology} }

@article{hamanoWSX1RequiredResistance2003, title = {{{WSX-1}} Is Required for Resistance to {{Trypanosoma}} Cruzi Infection by Regulation of Proinflammatory Cytokine Production.}, author = {Hamano, Shinjiro and Himeno, Kunisuke and Miyazaki, Yoshiyuki and Ishii, Kazunari and Yamanaka, Atsushi and Takeda, Atsunobu and Zhang, Manxin and Hisaeda, Hajime and Mak, Tak W. and Yoshimura, Akihiko and Yoshida, Hiroki}, year = 2003, month = nov, journal = {Immunity}, volume = {19}, number = {5}, eprint = {14614853}, eprinttype = {pubmed}, pages = {657–667}, issn = {1074-7613}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14614853}, abstract = {WSX-1 is a class I cytokine receptor with homology to the IL-12 receptors and is essential for resistance to Leishmania major infection. In the present study, we demonstrated that WSX-1 was also required for resistance to Trypanosoma cruzi. WSX-1-/- mice exhibited prolonged parasitemia, severe liver injury, and increased mortality over wild-type mice. WSX-1-/- splenocytes produced enhanced levels of Th2 cytokines, which were responsible for the prolonged parasitemia. Massive necroinflammatory lesions were observed in the liver of infected WSX-1-/- mice, and IFN-gamma that was overproduced in WSX-1-/- mice compared with wild-type mice was responsible for the lesions. In addition, vast amounts of various proinflammatory cytokines, including IL-6 and TNF-alpha, were produced by liver mononuclear cells in WSX-1-/- mice. Thus, during T. cruzi infection, WSX-1 suppresses liver injury by regulating production of proinflammatory cytokines, while controlling parasitemia by suppression of Th2 responses, demonstrating its novel role as an inhibitory regulator of cytokine production.}, pmid = {14614853}, keywords = {Animals,Blood,Blood: microbiology,Chagas Disease,Chagas Disease: immunology,Chagas Disease: metabolism,Chagas Disease: mortality,Cytokine,Cytokine: metabolism,Cytokines,Cytokines: immunology,Cytokines: metabolism,Knockout,Liver,Liver: pathology,Mice,nosource,Receptors,Spleen,Spleen: metabolism,Th2 Cells,Th2 Cells: metabolism,Trypanosoma cruzi} }

@article{cacalanoNeutrophilCellExpansion1994, title = {Neutrophil and {{B}} Cell Expansion in Mice That Lack the Murine {{IL-8}} Receptor Homolog.}, author = {Cacalano, G. and Lee, J. and Kikly, K. and Ryan, A. M. and {Pitts-Meek}, S. and Hultgren, B. and Wood, W. I. and Moore, M. W.}, year = 1994, month = jul, journal = {Science}, volume = {265}, number = {5172}, pages = {682–684}, publisher = {American Association for the Advancement of Science}, issn = {0036-8075}, doi = {10.1126/science.8036519}, url = {http://www.sciencemag.org/content/265/5172/682.abstract http://www.ncbi.nlm.nih.gov/pubmed/8036519}, abstract = {Interleukin-8 (IL-8) is a proinflammatory cytokine that specifically attracts and activates human neutrophils. A murine gene with a high degree of homology to the two known human IL-8 receptors was cloned and then deleted from the mouse genome by homologous recombination in embryonic stem (ES) cells. These mice, although outwardly healthy, had lymphadenopathy, resulting from an increase in B cells, and splenomegaly, resulting from an increase in metamyelocytes, band, and mature neutrophils. Thus, this receptor may participate in the expansion and development of neutrophils and B cells. This receptor was the major mediator of neutrophil migration to sites of inflammation and may provide a potential therapeutic target in inflammatory disease.}, pmid = {8036519}, keywords = {Animals,B-Lymphocytes,B-Lymphocytes: pathology,Bone Marrow,Bone Marrow: pathology,Cell Movement,Cell Movement: physiology,Chimera,Extramedullary,Extramedullary: physiology,Genetic,Hematopoiesis,Inbred C57BL,Inflammation,Inflammation: immunology,Interleukin,Interleukin-8B,Interleukin: deficiency,Interleukin: genetics,Interleukin: physiology,Leukocyte Count,Lymph Nodes,Lymph Nodes: pathology,Mice,Neutrophils,Neutrophils: pathology,nosource,Receptors,Recombination,Spleen,Spleen: pathology,Stem Cells} }

@article{murphyCloningComplementaryDNA1991, title = {Cloning of Complementary {{DNA}} Encoding a Functional Human Interleukin-8 Receptor.}, author = {Murphy, P. M. and Tiffany, H. L.}, year = 1991, month = sep, journal = {Science (New York, N.Y.)}, volume = {253}, number = {5025}, pages = {1280–3}, publisher = {American Association for the Advancement of Science}, issn = {0036-8075}, doi = {10.1126/science.1891716}, url = {http://www.sciencemag.org/content/253/5025/1280.abstract http://www.ncbi.nlm.nih.gov/pubmed/19696429}, abstract = {Interleukin-8 (IL-8) is an inflammatory cytokine that activates neutrophil chemotaxis, degranulation, and the respiratory burst. Neutrophils express receptors for IL-8 that are coupled to guanine nucleotide-binding proteins (G proteins); binding of IL-8 to its receptor induces the mobilization of intracellular calcium stores. A cDNA clone from HL-60 neutrophils, designated p2, has now been isolated that encodes a human IL-8 receptor. When p2 is expressed in oocytes from Xenopus laevis, the oocytes bind 125I-labeled IL-8 specifically and respond to IL-8 by mobilizing calcium stores with an EC50 of 20 nM. This IL-8 receptor has 77% amino acid identity with a second human neutrophil receptor isotype that binds IL-8 with higher affinity. It also exhibits 69% amino acid identity with a protein reported to be an N-formyl peptide receptor from rabbit neutrophils, but less than 30% identity with all other known G protein-coupled receptors, including the human N-formyl peptide receptor.}, pmid = {1891716}, keywords = {Amino Acid Sequence,Animals,Binding,Cloning,Competitive,DNA,DNA: genetics,Gene Library,Genetic,Humans,Immunologic,Immunologic: drug effects,Immunologic: genetics,Immunologic: physiology,Interleukin-8,Interleukin-8: metabolism,Interleukin-8: pharmacology,Interleukin-8A,Kinetics,Molecular,Molecular Sequence Data,Molecular: methods,Neutrophils,Neutrophils: immunology,nosource,Nucleic Acid,Oocytes,Oocytes: drug effects,Oocytes: physiology,Protein Biosynthesis,Rabbits,Receptors,Recombinant Proteins,Recombinant Proteins: metabolism,Sequence Homology,Signal Transduction,Transcription,Xenopus} } % == BibTeX quality report for murphyCloningComplementaryDNA1991: % ? Possibly abbreviated journal title Science (New York, N.Y.)

@article{vasilescuHaplotypeHumanCXCR12007, title = {A Haplotype of the Human {{CXCR1}} Gene Protective against Rapid Disease Progression in {{HIV-1}}+ Patients.}, author = {Vasilescu, a and Terashima, Y. and Enomoto, M. and Heath, S. and Poonpiriya, V. and Gatanaga, H. and Do, H. and Diop, G. and Hirtzig, T. and Auewarakul, P. and Lauhakirti, D. and Sura, T. and Charneau, P. and Marullo, S. and Therwath, A. and Oka, S. and Kanegasaki, S. and Lathrop, M. and Matsushima, K. and Zagury, J.-F. and Matsuda, F.}, year = 2007, month = feb, journal = {Proceedings of the National Academy of Sciences}, volume = {104}, number = {9}, pages = {3354–3359}, issn = {0027-8424}, doi = {10.1073/pnas.0611670104}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1805621&tool=pmcentrez&rendertype=abstract}, abstract = {Chemokines and their receptors are key factors in the onset and progression of AIDS. Among them, accumulating evidence strongly indicates the involvement of IL-8 and its receptors, CXCR1 and CXCR2, in AIDS-related conditions. Through extensive investigation of genetic variations of the human CXCR1-CXCR2 locus, we identified a haplotype of the CXCR1 gene (CXCR1-Ha) carrying two nonsynonymous single nucleotide polymorphisms, CXCR1_300 (Met to Arg) in the N terminus extracellular domain and CXCR1_142 (Arg to Cys) in the C terminus intracellular domain. Transfection experiments with CXCR1 cDNAs corresponding to the CXCR1-Ha and the alternative CXCR1-HA haplotype showed reduced expression of CD4 and CXCR4 in CXCR1-Ha cells in human osteosarcoma cells as well as in Jurkat and CEM human T lymphocytes. Furthermore, the efficiency of X4-tropic HIV-1(NL4-3) infection was significantly lower in CXCR1-Ha cells than in CXCR1-HA cells. The results were further confirmed by a series of experiments using six HIV-1 clinical isolates from AIDS patients. A genetic association study was performed by using an HIV-1(+) patient cohort consisting of two subpopulations of AIDS with extreme phenotypes of rapid and slow progression of the disease. The frequency of the CXCR1-Ha allele is markedly less frequent in patients with rapid disease onset than those with slow progression (P = 0.0003). These results provide strong evidence of a protective role of the CXCR1-Ha allele on disease progression in AIDS, probably acting through modulation of CD4 and CXCR4 expression.}, pmid = {17360650}, keywords = {Acquired Immunodeficiency Syndrome,Acquired Immunodeficiency Syndrome: genetics,Antigens,Blotting,CD4,CD4: metabolism,Cell Line,CXCR4,CXCR4: metabolism,Disease Progression,Flow Cytometry,Gene Components,Gene Expression Regulation,Gene Expression Regulation: genetics,Gene Frequency,Genetic Variation,Haplotypes,Haplotypes: genetics,HIV-1,Humans,Immunohistochemistry,Interleukin-8A,Interleukin-8A: genetics,nosource,Polymorphism,Receptors,Single Nucleotide,Single Nucleotide: genetics,Tumor,Western} }

@article{holmesStructureFunctionalExpression1991, title = {Structure and Functional Expression of a Human Interleukin-8 Receptor.}, author = {Holmes, W. E. and Lee, J. and Kuang, W. J. and Rice, G. C. and Wood, W. I.}, year = 1991, month = sep, journal = {Science (New York, N.Y.)}, volume = {253}, number = {5025}, pages = {1278–80}, publisher = {American Association for the Advancement of Science}, issn = {0036-8075}, doi = {10.1126/science.1840701}, url = {http://www.sciencemag.org/content/253/5025/1278.abstract http://www.ncbi.nlm.nih.gov/pubmed/19696428}, abstract = {Interleukin-8 (IL-8) is a member of a family of pro-inflammatory cytokines. Although the best characterized activities of IL-8 include the chemoattraction and activation of neutrophils, other members of this family have a wide range of specific actions including the chemotaxis and activation of monocytes, the selective chemotaxis of memory T cells, the inhibition of hematopoietic stem cell proliferation, and the induction of neutrophil infiltration in vivo. A complementary DNA encoding the IL-8 receptor from human neutrophils has now been isolated. The amino acid sequence shows that the receptor is a member of the superfamily of receptors that couple to guanine nucleotide binding proteins (G proteins). The sequence is 29% identical to that of receptors for the other neutrophil chemoattractants, fMet-Leu-Phe and C5a. Mammalian cells transfected with the IL-8 receptor cDNA clone bind IL-8 with high affinity and respond specifically to IL-8 by transiently mobilizing calcium. The IL-8 receptor may be part of a subfamily of related G protein-coupled receptors that transduce signals for the IL-8 family of pro-inflammatory cytokines.}, pmid = {1840701}, keywords = {Amino Acid Sequence,Animals,Cell Line,Cloning,DNA Probes,Humans,Immunologic,Immunologic: genetics,Immunologic: metabolism,Interleukin-8,Interleukin-8: metabolism,Interleukin-8A,Kinetics,Messenger,Messenger: genetics,Molecular,Molecular Sequence Data,nosource,Nucleic Acid,Nucleic Acid Hybridization,Plasmids,Receptors,Recombinant Proteins,Recombinant Proteins: metabolism,RNA,Sequence Homology,Transfection} } % == BibTeX quality report for holmesStructureFunctionalExpression1991: % ? Possibly abbreviated journal title Science (New York, N.Y.)

@article{hartlCleavageCXCR1Neutrophils2007, title = {Cleavage of {{CXCR1}} on Neutrophils Disables Bacterial Killing in Cystic Fibrosis Lung Disease.}, author = {Hartl, Dominik and Latzin, Philipp and Hordijk, Peter and Marcos, Veronica and Rudolph, Carsten and Woischnik, Markus and {Krauss-Etschmann}, Susanne and Koller, Barbara and Reinhardt, Dietrich and {}a Roscher, Adelbert and Roos, Dirk and Griese, Matthias}, year = 2007, month = dec, journal = {Nature Medicine}, volume = {13}, number = {12}, eprint = {18059279}, eprinttype = {pubmed}, pages = {1423–1430}, issn = {1546-170X}, doi = {10.1038/nm1690}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18059279}, abstract = {Interleukin-8 (IL-8) activates neutrophils via the chemokine receptors CXCR1 and CXCR2. However, the airways of individuals with cystic fibrosis are frequently colonized by bacterial pathogens, despite the presence of large numbers of neutrophils and IL-8. Here we show that IL-8 promotes bacterial killing by neutrophils through CXCR1 but not CXCR2. Unopposed proteolytic activity in the airways of individuals with cystic fibrosis cleaved CXCR1 on neutrophils and disabled their bacterial-killing capacity. These effects were protease concentration-dependent and also occurred to a lesser extent in individuals with chronic obstructive pulmonary disease. Receptor cleavage induced the release of glycosylated CXCR1 fragments that were capable of stimulating IL-8 production in bronchial epithelial cells via Toll-like receptor 2. In vivo inhibition of proteases by inhalation of alpha1-antitrypsin restored CXCR1 expression and improved bacterial killing in individuals with cystic fibrosis. The cleavage of CXCR1, the functional consequences of its cleavage, and the identification of soluble CXCR1 fragments that behave as bioactive components represent a new pathophysiologic mechanism in cystic fibrosis and other chronic lung diseases.}, pmid = {18059279}, keywords = {alpha 1-Antitrypsin,alpha 1-Antitrypsin: pharmacology,Animals,Biological,Cystic Fibrosis,Cystic Fibrosis: immunology,Cystic Fibrosis: microbiology,Glycosylation,Humans,Interleukin-8,Interleukin-8: metabolism,Interleukin-8A,Interleukin-8A: metabolism,Interleukin-8A: physiology,Lung,Lung: microbiology,Mice,Models,Neutrophils,Neutrophils: metabolism,Neutrophils: microbiology,nosource,Receptors,Toll-Like Receptor 2,Toll-Like Receptor 2: metabolism} }

@article{plantAchievingGoldenMean2010, title = {Achieving a Golden Mean: Mechanisms by Which Coronaviruses Ensure Synthesis of the Correct Stoichiometric Ratios of Viral Proteins.}, author = {Plant, Ewan P. EP and Rakauskaite, Rasa and Taylor, Deborah R. and Dinman, Jonathan D. and Rakauskait{.e}, R.}, year = 2010, month = may, journal = {Journal of virology}, volume = {84}, number = {9}, pages = {4330–40}, issn = {1098-5514}, doi = {10.1128/JVI.02480-09}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2863758&tool=pmcentrez&rendertype=abstract http://jvi.asm.org/content/84/9/4330.short}, abstract = {In retroviruses and the double-stranded RNA totiviruses, the efficiency of programmed -1 ribosomal frameshifting is critical for ensuring the proper ratios of upstream-encoded capsid proteins to downstream-encoded replicase enzymes. The genomic organizations of many other frameshifting viruses, including the coronaviruses, are very different, in that their upstream open reading frames encode nonstructural proteins, the frameshift-dependent downstream open reading frames encode enzymes involved in transcription and replication, and their structural proteins are encoded by subgenomic mRNAs. The biological significance of frameshifting efficiency and how the relative ratios of proteins encoded by the upstream and downstream open reading frames affect virus propagation has not been explored before. Here, three different strategies were employed to test the hypothesis that the -1 PRF signals of coronaviruses have evolved to produce the correct ratios of upstream- to downstream-encoded proteins. Specifically, infectious clones of the severe acute respiratory syndrome (SARS)-associated coronavirus harboring mutations that lower frameshift efficiency decreased infectivity by {\(>\)}4 orders of magnitude. Second, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the frameshift signals of the SARS-associated coronavirus and mouse hepatitis virus have evolved to promote optimal frameshift efficiencies. Finally, we show that a previously described frameshift attenuator element does not actually affect frameshifting per se but rather serves to limit the fraction of ribosomes available for frameshifting. The findings of these analyses all support a “golden mean” model in which viruses use both programmed ribosomal frameshifting and translational attenuation to control the relative ratios of their encoded proteins.}, pmid = {20164235}, keywords = {Animals,Frameshifting,Gene Expression Regulation,Models,Molecular,Murine hepatitis virus,Murine hepatitis virus: genetics,Murine hepatitis virus: growth & development,Murine hepatitis virus: pathogenicity,Murine hepatitis virus: physiology,Mutation,nosource,Nucleic Acid Conformation,Open Reading Frames,Protein Biosynthesis,Ribosomal,RNA,SARS Virus,SARS Virus: genetics,SARS Virus: growth & development,SARS Virus: pathogenicity,SARS Virus: physiology,Viral,Viral Proteins,Viral Proteins: biosynthesis,Viral: genetics} }

@article{houck-loomisEquilibriumdependentRetroviralMRNA2011, title = {An Equilibrium-Dependent Retroviral {{mRNA}} Switch Regulates Translational Recoding.}, author = {{Houck-Loomis}, Brian and {}a Durney, Michael and Salguero, Carolina and Shankar, Neelaabh and Nagle, Julia M. and Goff, Stephen P. and D’Souza, Victoria M. and D’Souza, Victoria M. and Souza, Victoria M. D.}, year = 2011, month = dec, journal = {Nature}, volume = {480}, number = {7378}, eprint = {22121021}, eprinttype = {pubmed}, pages = {561–4}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature10657}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22121021 http://www.nature.com/doifinder/10.1038/nature10657 http://dx.doi.org/10.1038/nature10657}, abstract = {Most retroviruses require translational recoding of a viral messenger RNA stop codon to maintain a precise ratio of structural (Gag) and enzymatic (Pol) proteins during virus assembly. Pol is expressed exclusively as a Gag-Pol fusion either by ribosomal frameshifting or by read-through of the gag stop codon. Both of these mechanisms occur infrequently and only affect 5-10% of translating ribosomes, allowing the virus to maintain the critical Gag to Gag-Pol ratio. Although it is understood that the frequency of the recoding event is regulated by cis RNA motifs, no mechanistic explanation is currently available for how the critical protein ratio is maintained. Here we present the NMR structure of the murine leukaemia virus recoding signal and show that a protonation-dependent switch occurs to induce the active conformation. The equilibrium is such that at physiological pH the active, read-through permissive conformation is populated at approximately 6%: a level that correlates with in vivo protein quantities. The RNA functions by a highly sensitive, chemo-mechanical coupling tuned to ensure an optimal read-through frequency. Similar observations for a frameshifting signal indicate that this novel equilibrium-based mechanism may have a general role in translational recoding.}, pmid = {22121021}, keywords = {Gene Expression Regulation,Genes,Leukemia Virus,Magnetic Resonance Spectroscopy,Models,Molecular,Murine,Murine: genetics,Murine: physiology,nosource,Nucleic Acid Conformation,Protein Structure,RNA,Switch,Tertiary,Viral,Viral: metabolism} }

@article{snowdonMicroRNA200FamilyUpregulated2011, title = {The {{microRNA-200}} Family Is Upregulated in Endometrial Carcinoma.}, author = {Snowdon, Jaime and Zhang, Xiao and Childs, Tim and {}a Tron, Victor and Feilotter, Harriet}, year = 2011, month = jan, journal = {PloS One}, volume = {6}, number = {8}, pages = {e22828}, issn = {1932-6203}, doi = {10.1371/journal.pone.0022828}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3163579&tool=pmcentrez&rendertype=abstract}, abstract = {MicroRNAs (miRNAs, miRs) are small non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. MicroRNAs are dysregulated in cancer and may play essential roles in tumorigenesis. Additionally, miRNAs have been shown to have prognostic and diagnostic value in certain types of cancer. The objective of this study was to identify dysregulated miRNAs in endometrioid endometrial adenocarcinoma (EEC) and the precursor lesion, complex atypical hyperplasia (CAH).}, pmid = {21897839}, keywords = {Adenocarcinoma,Adenocarcinoma: diagnosis,Adenocarcinoma: genetics,Adult,Aged,Cluster Analysis,Endometrial Neoplasms,Endometrial Neoplasms: diagnosis,Endometrial Neoplasms: genetics,Female,Gene Expression Profiling,Humans,MicroRNAs,MicroRNAs: genetics,Middle Aged,Multigene Family,Multigene Family: genetics,nosource,Oligonucleotide Array Sequence Analysis,Real-Time Polymerase Chain Reaction,Reverse Transcriptase Polymerase Chain Reaction,Up-Regulation,Up-Regulation: genetics} }

@article{liuHighExpressionSerum2011, title = {High Expression of Serum {{miR-21}} and Tumor {{miR-200c}} Associated with Poor Prognosis in Patients with Lung Cancer.}, author = {Liu, Xiao-Guang and Zhu, Wang-Yu and Huang, Yan-Yan and Ma, Li-Na and Zhou, Shi-Quan and Wang, Ye-Kai and Zeng, Fang and Zhou, Ji-Hang and Zhang, Yong-Kui}, year = 2011, month = apr, journal = {Medical Oncology}, eprint = {21516486}, eprinttype = {pubmed}, issn = {1559-131X}, doi = {10.1007/s12032-011-9923-y}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21516486}, abstract = {Serum microRNAs have been identified as potential cancer biomarkers. However, the detailed mechanism by which expression of microRNAs contributes to the development and diagnosis of NSCLC remains unknown. This study was to identify specific miRNAs for diagnosing or predicting the prognosis of NSCLC patients and their correlation between miRNA expression in tissues and serums. Six matched cancer and noncancerous tissues from NSCLC patients were analyzed by miRNA microarray. Among these, three miRNAs (miR-21, miR-141, and miR-200c) were examined in 70 NSCLC paired samples (cancer, normal tissue, and serum) and 44 serum samples of normal volunteers by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Consisting with the microarray results, the expression levels of miR-21, miR-141, and miR-200c in NSCLC were higher than those in normal tissues. While the level of serum miR-21 was increased in cancer patients as compared with that in normal counterpart, expression of miR-141 and miR-200c showed lower levels in serums from cancer patients. Overexpression of serum miR-21 was strongly associated with lymph node metastasis and advanced clinical stage of NSCLC. Finally, log-rank and Cox regression tests demonstrated that high expressions of tumor miR 21 and miR-200c or serum miR-21 were associated with a poor survival in NSCLC patients. Our results suggest that tumor miR-21, miR-141, miR-200c, and serum miR-21 may be potential novel biomarkers for the diagnosis of NSCLC. In addition, this study, for the first time, identifies a significant role of the tumor miR-200c played in predicting prognosis in patients with NSCLC.}, pmid = {21516486}, keywords = {cell lung cancer,mirnas a prognosis a,nosource,quatitative rt-pcr a non-small,serum a survival a} }

@article{dudziecHypermethylationCpGIslands2011, title = {Hypermethylation of {{CpG}} Islands and Shores around Specific {{microRNAs}} and Mirtrons Is Associated with the Phenotype and Presence of Bladder Cancer.}, author = {Dudziec, Ewa and Miah, Saiful and Choudhry, Hani M. Z. and Owen, Helen C. and Blizard, Sheila and Glover, Maggie and Hamdy, Freddie C. and Catto, James W. F.}, year = 2011, month = mar, journal = {Clinical Cancer Research}, volume = {17}, number = {6}, pages = {1287–96}, issn = {1078-0432}, doi = {10.1158/1078-0432.CCR-10-2017}, url = {http://clincancerres.aacrjournals.org/cgi/content/abstract/17/6/1287}, abstract = {To analyze the role and translational potential for hypermethylation of CpG islands and shores in the regulation of small RNAs within urothelial cell carcinoma (UCC). To examine microRNAs (miR) and mirtrons, a new class of RNA located within gene introns and processed in a Drosha-independent manner. Experimental design: The methylation status of 865 small RNAs was evaluated in normal and malignant cell lines by using 5-azacytidine and microarrays. Bisulfite sequencing was used for CpG regions around selected RNAs. Prognostic and diagnostic associations for epigenetically regulated RNAs were examined by using material from 359 patients, including 216 tumors and 121 urinary samples (68 cases and 53 controls). Functional analyses examined the effect of silencing susceptible RNAs in normal urothelial cells.}, pmid = {21138856}, keywords = {Azacitidine,Azacitidine: pharmacology,Cohort Studies,CpG Islands,DNA Methylation,Epigenesis,Exons,Gene Silencing,Genetic,Humans,nosource,Odds Ratio,Oligonucleotide Array Sequence Analysis,Phenotype,Prognosis,Urinary Bladder Neoplasms,Urinary Bladder Neoplasms: genetics,Urothelium,Urothelium: pathology} }

@article{chengCirculatingPlasmaMiR1412011, title = {Circulating Plasma {{MiR-141}} Is a Novel Biomarker for Metastatic Colon Cancer and Predicts Poor Prognosis.}, author = {Cheng, Hanyin and Zhang, Lina and Cogdell, David E. and Zheng, Hong and Schetter, Aaron J. and Nykter, Matti and Harris, Curtis C. and Chen, Kexin and Hamilton, Stanley R. and Zhang, Wei}, year = 2011, month = jan, journal = {PloS One}, volume = {6}, number = {3}, pages = {e17745}, issn = {1932-6203}, doi = {10.1371/journal.pone.0017745}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3060165&tool=pmcentrez&rendertype=abstract}, abstract = {Colorectal cancer (CRC) remains one of the major cancer types and cancer related death worldwide. Sensitive, non-invasive biomarkers that can facilitate disease detection, staging and prediction of therapeutic outcome are highly desirable to improve survival rate and help to determine optimized treatment for CRC. The small non-coding RNAs, microRNAs (miRNAs), have recently been identified as critical regulators for various diseases including cancer and may represent a novel class of cancer biomarkers. The purpose of this study was to identify and validate circulating microRNAs in human plasma for use as such biomarkers in colon cancer.}, pmid = {21445232}, keywords = {Biological,Biological: blood,Colonic Neoplasms,Colonic Neoplasms: blood,Colonic Neoplasms: diagnosis,Colonic Neoplasms: pathology,Female,Humans,Male,MicroRNAs,MicroRNAs: blood,Neoplasm Metastasis,nosource,Prognosis,Reverse Transcriptase Polymerase Chain Reaction,Tumor Markers} }

@article{teIdentificationUniqueMicroRNA2010, title = {Identification of Unique {{microRNA}} Signature Associated with Lupus Nephritis.}, author = {Te, Jeannie L. and Dozmorov, Igor M. and Guthridge, Joel M. and Nguyen, Kim L. and Cavett, Joshua W. and {}a Kelly, Jennifer and Bruner, Gail R. and Harley, John B. and Ojwang, Joshua O.}, year = 2010, month = jan, journal = {PloS One}, volume = {5}, number = {5}, pages = {e10344}, issn = {1932-6203}, doi = {10.1371/journal.pone.0010344}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2867940&tool=pmcentrez&rendertype=abstract}, abstract = {MicroRNAs (miRNA) have emerged as an important new class of modulators of gene expression. In this study we investigated miRNA that are differentially expressed in lupus nephritis. Microarray technology was used to investigate differentially expressed miRNA in peripheral blood mononuclear cells (PBMCs) and Epstein-Barr Virus (EBV)-transformed cell lines obtained from lupus nephritis affected patients and unaffected controls. TaqMan-based stem-loop real-time polymerase chain reaction was used for validation. Microarray analysis of miRNA expressed in both African American (AA) and European American (EA) derived lupus nephritis samples revealed 29 and 50 differentially expressed miRNA, respectively, of 850 tested. There were 18 miRNA that were differentially expressed in both racial groups. When samples from both racial groups and different specimen types were considered, there were 5 primary miRNA that were differentially expressed. We have identified 5 miRNA; hsa-miR-371-5P, hsa-miR-423-5P, hsa-miR-638, hsa-miR-1224-3P and hsa-miR-663 that were differentially expressed in lupus nephritis across different racial groups and all specimen types tested. Hsa-miR-371-5P, hsa-miR-1224-3P and hsa-miR-423-5P, are reported here for the first time to be associated with lupus nephritis. Our work establishes EBV-transformed B cell lines as a useful model for the discovery of miRNA as biomarkers for SLE. Based on these findings, we postulate that these differentially expressed miRNA may be potential novel biomarkers for SLE as well as help elucidate pathogenic mechanisms of lupus nephritis. The investigation of miRNA profiles in SLE may lead to the discovery and development of novel methods to diagnosis, treat and prevent SLE.}, pmid = {20485490}, keywords = {African Americans,African Americans: genetics,B-Lymphocytes,B-Lymphocytes: metabolism,Cell Line,Europe,Gene Expression Profiling,Gene Expression Regulation,Herpesvirus 4,Human,Human: genetics,Humans,Lupus Nephritis,Lupus Nephritis: ethnology,Lupus Nephritis: genetics,MicroRNAs,MicroRNAs: genetics,MicroRNAs: metabolism,Monozygotic,Monozygotic: genetics,nosource,Reproducibility of Results,Transformed,Twins} }

@article{formanSearchConservedSequences2008, title = {A Search for Conserved Sequences in Coding Regions Reveals That the Let-7 {{microRNA}} Targets {{Dicer}} within Its Coding Sequence.}, author = {Forman, Joshua J. and {Legesse-Miller}, Aster and {}a Coller, Hilary}, year = 2008, month = sep, journal = {Proceedings of the National Academy of Sciences}, volume = {105}, number = {39}, pages = {14879–14884}, issn = {1091-6490}, doi = {10.1073/pnas.0803230105}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2567461&tool=pmcentrez&rendertype=abstract}, abstract = {Recognition sites for microRNAs (miRNAs) have been reported to be located in the 3’ untranslated regions of transcripts. In a computational screen for highly conserved motifs within coding regions, we found an excess of sequences conserved at the nucleotide level within coding regions in the human genome, the highest scoring of which are enriched for miRNA target sequences. To validate our results, we experimentally demonstrated that the let-7 miRNA directly targets the miRNA-processing enzyme Dicer within its coding sequence, thus establishing a mechanism for a miRNA/Dicer autoregulatory negative feedback loop. We also found computational evidence to suggest that miRNA target sites in coding regions and 3’ UTRs may differ in mechanism. This work demonstrates that miRNAs can directly target transcripts within their coding region in animals, and it suggests that a complete search for the regulatory targets of miRNAs should be expanded to include genes with recognition sites within their coding regions. As more genomes are sequenced, the methodological approach that we used for identifying motifs with high sequence conservation will be increasingly valuable for detecting functional sequence motifs within coding regions.}, pmid = {18812516}, keywords = {Algorithms,Animals,Base Sequence,Cattle,Computational Biology,Conserved Sequence,DNA,Dogs,Feedback,Humans,Mice,MicroRNAs,MicroRNAs: metabolism,nosource,Physiological,Physiological: genetics,Rabbits,Rats,Ribonuclease III,Ribonuclease III: genetics,Sequence Analysis,Software} }

@article{morettiMechanismTranslationalRegulation2010, title = {Mechanism of Translational Regulation by {{miR-2}} from Sites in the 5{\(\prime\)} Untranslated Region or the Open Reading Frame}, author = {Moretti, Francesca and Thermann, Rolf and Hentze, MW Matthias W.}, year = 2010, month = dec, journal = {Rna}, volume = {16}, number = {12}, pages = {2493–2502}, issn = {1469-9001}, doi = {10.1261/rna.2384610}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2995410&tool=pmcentrez&rendertype=abstract http://rnajournal.cshlp.org/content/16/12/2493.short}, abstract = {MicroRNAs (miRs) commonly regulate translation from target mRNA 3’ untranslated regions (UTRs). While effective miR-binding sites have also been identified in 5’ untranslated regions (UTRs) or open reading frames (ORFs), the mechanism(s) of miR-mediated regulation from these sites has not been defined. Here, we systematically investigate how the position of miR-binding sites influences translational regulation and characterize their mechanistic basis. We show that specific translational regulation is elicited in vitro and in vivo not only from the 3’UTR, but equally effectively from six Drosophila miR-2-binding sites in the 5’UTR or the ORF. In all cases, miR-2 triggers mRNA deadenylation and inhibits translation initiation in a cap-dependent fashion. In contrast, single or dual miR-2-binding sites in the 5’UTR or the ORF yield rather inefficient or no regulation. This work represents the first demonstration that 5’UTR and ORF miR-binding sites can function mechanistically similarly to the intensively investigated 3’UTR sites. Using single or dual binding sites, it also reveals a biological rationale for the high prevalence of miR regulatory sites in the 3’UTR.}, pmid = {20966199}, keywords = {39utr,5’ Untranslated Regions,5’ Untranslated Regions: genetics,59utr,Animals,Cells,Cultured,Drosophila,Drosophila: genetics,Drosophila: metabolism,Embryo,Gene Expression Regulation,microrna,MicroRNAs,MicroRNAs: physiology,Nonmammalian,nosource,Nucleic Acid,Nucleic Acid: genetics,Nucleic Acid: physiology,open reading frame,Open Reading Frames,Open Reading Frames: genetics,Polyadenylation,Protein Biosynthesis,Protein Biosynthesis: genetics,Regulatory Sequences,RNA Interference,Transfection,translational control} }

@article{duursmaMiR148TargetsHuman2008, title = {{{miR-148}} Targets Human {{DNMT3b}} Protein Coding Region.}, author = {Duursma, AM Anja M. and Kedde, Martijn and Schrier, Mariette and {}le Sage, Carlos and Agami, Reuven and Sage, Carlos L. E.}, year = 2008, month = may, journal = {RNA (New York, N.Y.)}, volume = {14}, number = {5}, pages = {872–7}, issn = {1469-9001}, doi = {10.1261/rna.972008}, url = {http://rnajournal.cshlp.org/content/14/5/872.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2327368&tool=pmcentrez&rendertype=abstract}, abstract = {MicroRNAs (miRNAs) are small noncoding RNA molecules of 20-24 nucleotides that regulate gene expression. In animals, miRNAs form imperfect interactions with sequences in the 3’ Untranslated region (3’UTR) of mRNAs, causing translational inhibition and mRNA decay. In contrast, plant miRNAs mostly associate with protein coding regions. Here we show that human miR-148 represses DNA methyltransferase 3b (Dnmt3b) gene expression through a region in its coding sequence. This region is evolutionary conserved and present in the Dnmt3b splice variants Dnmt3b1, Dnmt3b2, and Dnmt3b4, but not in the abundantly expressed Dnmt3b3. Whereas overexpression of miR-148 results in decreased DNMT3b1 expression, short-hairpin RNA-mediated miR-148 repression leads to an increase in DNMT3b1 expression. Interestingly, mutating the putative miR-148 target site in Dnmt3b1 abolishes regulation by miR-148. Moreover, endogenous Dnmt3b3 mRNA, which lacks the putative miR-148 target site, is resistant to miR-148-mediated regulation. Thus, our results demonstrate that the coding sequence of Dnmt3b mediates regulation by the miR-148 family. More generally, we provide evidence that coding regions of human genes can be targeted by miRNAs, and that such a mechanism might play a role in determining the relative abundance of different splice variants.}, pmid = {18367714}, keywords = {Alternative Splicing,Base Sequence,Cell Line,coding region,Complementary,Complementary: genetics,DNA,DNA (Cytosine-5-)-Methyltransferase,DNA (Cytosine-5-)-Methyltransferase: genetics,DNA Primers,DNA Primers: genetics,dnmt3b,Enzymologic,Gene Expression Regulation,Hela Cells,HeLa Cells,Humans,Messenger,Messenger: genetics,Messenger: metabolism,MicroRNAs,MicroRNAs: genetics,mirna,Mutagenesis,nosource,Nucleic Acid,RNA,Sequence Homology,Site-Directed,splice variants,Transfection} } % == BibTeX quality report for duursmaMiR148TargetsHuman2008: % ? Possibly abbreviated journal title RNA (New York, N.Y.)

@article{ahnInterferenceRibosomalFrameshifting2011, title = {Interference of Ribosomal Frameshifting by Antisense Peptide Nucleic Acids Suppresses {{SARS}} Coronavirus Replication.}, author = {Ahn, Dae-Gyun and Lee, Wooseong and Choi, Jin-Kyu and Kim, Seong-Jun and Plant, Ewan P. and Almaz{'a}n, Fernando and Taylor, Deborah R. and Enjuanes, Luis and Oh, Jong-Won}, year = 2011, month = jul, journal = {Antiviral Research}, volume = {91}, number = {1}, eprint = {21549154}, eprinttype = {pubmed}, pages = {1–10}, publisher = {Elsevier B.V.}, issn = {1872-9096}, doi = {10.1016/j.antiviral.2011.04.009}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21549154}, abstract = {The programmed -1 ribosomal frameshifting (-1 PRF) utilized by eukaryotic RNA viruses plays a crucial role for the controlled, limited synthesis of viral RNA replicase polyproteins required for genome replication. The viral RNA replicase polyproteins of severe acute respiratory syndrome coronavirus (SARS-CoV) are encoded by the two overlapping open reading frames 1a and 1b, which are connected by a -1 PRF signal. We evaluated the antiviral effects of antisense peptide nucleic acids (PNAs) targeting a highly conserved RNA sequence on the - PRF signal. The ribosomal frameshifting was inhibited by the PNA, which bound sequence-specifically a pseudoknot structure in the -1 PRF signal, in cell lines as assessed using a dual luciferase-based reporter plasmid containing the -1 PRF signal. Treatment of cells, which were transfected with a SARS-CoV-replicon expressing firefly luciferase, with the PNA fused to a cell-penetrating peptide (CPP) resulted in suppression of the replication of the SARS-CoV replicon, with a 50% inhibitory concentration of 4.4{\(\mu\)}M. There was no induction of type I interferon responses by PNA treatment, suggesting that the effect of PNA is not due to innate immune responses. Our results demonstrate that -1 PRF, critical for SARS-CoV viral replication, can be inhibited by CPP-PNA, providing an effective antisense strategy for blocking -1 PRF signals.}, pmid = {21549154}, keywords = {nosource} }

@article{jackRRNAPseudouridylationDefects2011, title = {{{rRNA}} Pseudouridylation Defects Affect Ribosomal Ligand Binding and Translational Fidelity from Yeast to Human Cells}, author = {Jack, Karen and Bellodi, Cristian and Landry, D. M. Dori M. DM and Niederer, R. O. Rachel O. and Meskauskas, Arturas A. M. and Musalgaonkar, Sharmishtha and Kopmar, Noam and Krasnykh, Olya and Dean, Alison M. and Thompson, Sunnie R. and Ruggero, Davide and Dinman, J. D. Jonathan D.}, year = 2011, month = nov, journal = {Molecular cell}, volume = {44}, number = {4}, pages = {660–666}, publisher = {Elsevier Inc.}, issn = {1097-2765}, doi = {10.1016/j.molcel.2011.09.017}, url = {http://dx.doi.org/10.1016/j.molcel.2011.09.017 http://www.sciencedirect.com/science/article/pii/S1097276511008161 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3222873&tool=pmcentrez&rendertype=abstract http://linkinghub.elsevier.com/retrieve/}, abstract = {How pseudouridylation ({\(\Psi\)}), the most common and evolutionarily conserved modification of rRNA, regulates ribosome activity is poorly understood. Medically, {\(\Psi\)} is important because the rRNA {\(\Psi\)} synthase, DKC1, is mutated in X-linked dyskeratosis congenita (X-DC) and Hoyeraal-Hreidarsson (HH) syndrome. Here, we characterize ribosomes isolated from a yeast strain in which Cbf5p, the yeast homolog of DKC1, is catalytically impaired through a D95A mutation (cbf5-D95A). Ribosomes from cbf5-D95A cells display decreased affinities for tRNA binding to the A and P sites as well as the cricket paralysis virus internal ribosome entry site (IRES), which interacts with both the P and the E sites of the ribosome. This biochemical impairment in ribosome activity manifests as decreased translational fidelity and IRES-dependent translational initiation, which are also evident in mouse and human cells deficient for DKC1 activity. These findings uncover specific roles for {\(\Psi\)} modification in ribosome-ligand interactions that are conserved in yeast, mouse, and humans.}, pmid = {22099312}, keywords = {Amino Acid,Animals,Binding Sites,Cell Cycle Proteins,Cell Cycle Proteins: deficiency,Cell Cycle Proteins: genetics,Dyskeratosis Congenita,Dyskeratosis Congenita: enzymology,Dyskeratosis Congenita: genetics,Fetal Growth Retardation,Fetal Growth Retardation: enzymology,Fetal Growth Retardation: genetics,Genes,Genetic,Humans,Hydro-Lyases,Hydro-Lyases: deficiency,Hydro-Lyases: genetics,Hydro-Lyases: metabolism,Intellectual Disability,Intellectual Disability: enzymology,Intellectual Disability: genetics,Luciferases,Luciferases: analysis,Mice,Microcephaly,Microcephaly: enzymology,Microcephaly: genetics,Microtubule-Associated Proteins,Microtubule-Associated Proteins: deficiency,Microtubule-Associated Proteins: genetics,Mutation,nosource,Nuclear Proteins,Nuclear Proteins: deficiency,Nuclear Proteins: genetics,Plasmids,Protein Biosynthesis,Reporter,Ribonucleoproteins,Ribosomal,Ribosomal: chemistry,Ribosomal: genetics,Ribosomal: metabolism,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae: enzymology,Saccharomyces cerevisiae: genetics,Sequence Homology,Small Nuclear,Small Nuclear: deficiency,Small Nuclear: genetics,Transduction,Transfer,Transfer: chemistry,Transfer: genetics,Transfer: metabolism} }

@article{kobayashiIdentificationCellularFactor2010, title = {Identification of a Cellular Factor That Modulates {{HIV-1}} Programmed Ribosomal Frameshifting}, author = {Kobayashi, Y. and Zhuang, J. and Peltz, S. and Dougherty, J.}, year = 2010, journal = {Journal of Biological Chemistry}, volume = {285}, number = {26}, pages = {19776}, publisher = {ASBMB}, url = {http://www.jbc.org/content/285/26/19776.short}, keywords = {nosource} }

@article{khabarPosttranscriptionalControlInterferon2007, title = {Post-Transcriptional Control of the Interferon System.}, author = {{}a Khabar, Khalid S. and {}a Young, Howard}, year = 2007, journal = {Biochimie}, volume = {89}, number = {6-7}, pages = {761–9}, issn = {0300-9084}, doi = {10.1016/j.biochi.2007.02.008}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1994070&tool=pmcentrez&rendertype=abstract}, abstract = {The interferon (IFN) system is a well-controlled network of signaling, transcriptional, and post-transcriptional processes that orchestrate host defense against microbes. The IFN response comprises a multi-array of IFN-stimulated gene products that mediate a variety of biological processes designed to control infection and regulate specific immune responses. In this review, we focus on post-transcriptional mechanisms of gene regulation that occur during the course of IFN induction and during the response of cells to IFN. Post-transcriptional mechanisms involve different levels of regulation such as mRNA stability, alternative splicing, and translation. Such controls offer a fine tuning mechanism for efficient and rapid response and as a negative feedback control in IFN biosynthesis and response.}, pmid = {17408842}, keywords = {3’ Untranslated Regions,Animals,Base Sequence,Biological,eIF-2 Kinase,eIF-2 Kinase: metabolism,Endoribonucleases,Endoribonucleases: metabolism,Feedback,Genetic,Humans,Interferon-beta,Interferon-beta: metabolism,Interferon-gamma,Interferon-gamma: metabolism,Interferons,Interferons: biosynthesis,Interferons: chemistry,Interferons: metabolism,Models,Molecular Sequence Data,nosource,Physiological,Post-Transcriptional,RNA Processing,Signal Transduction,Transcription} }

@article{cenikArgonauteProteins2011, title = {Argonaute Proteins}, author = {Cenik, Elif Sarinay and Zamore, Phillip D.}, year = 2011, month = jun, journal = {Current Biology}, volume = {21}, number = {12}, pages = {R446-R449}, publisher = {Elsevier}, issn = {0960-9822}, doi = {10.1016/j.cub.2011.05.020}, url = {http://dx.doi.org/10.1016/j.cub.2011.05.020 http://www.ncbi.nlm.nih.gov/pubmed/21683893}, pmid = {21683893}, keywords = {nosource} }

@article{yangReviewAlternativeMiRNA2011, title = {Review {{Alternative miRNA Biogenesis Pathways}} and the {{Interpretation}} of {{Core miRNA Pathway Mutants}}}, author = {Yang, Jr-shiuan and Lai, Eric C.}, year = 2011, journal = {Molecular Cell}, volume = {43}, number = {6}, pages = {892–903}, publisher = {Elsevier Inc.}, issn = {1097-2765}, doi = {10.1016/j.molcel.2011.07.024}, url = {http://dx.doi.org/10.1016/j.molcel.2011.07.024}, keywords = {nosource} } % == BibTeX quality report for yangReviewAlternativeMiRNA2011: % ? Title looks like it was stored in title-case in Zotero

@article{diederichsDualRoleArgonautes2007, title = {Dual {{Role}} for {{Argonautes}} in {{MicroRNA Processing}} and {{Posttranscriptional Regulation}} of {{MicroRNA Expression}}}, author = {Diederichs, Sven and Haber, Daniel A.}, year = 2007, journal = {Cell}, pages = {1097–1108}, doi = {10.1016/j.cell.2007.10.032}, keywords = {nosource} } % == BibTeX quality report for diederichsDualRoleArgonautes2007: % ? Title looks like it was stored in title-case in Zotero

@article{vickersEnhancementRibosomalFrameshifting1992, title = {Enhancement of Ribosomal Frameshifting by Oligonucleotides Targeted to the {{HIV}} Gag-Polregion}, author = {Vickers, T. A. and Ecker, DJ J.}, year = 1992, journal = {Nucleic acids research}, volume = {20}, number = {15}, pages = {3945–3953}, url = {http://nar.oxfordjournals.org/content/20/15/3945.short}, keywords = {nosource} }

@article{chomczynskiSinglestepMethodRNA2006, title = {The Single-Step Method of {{RNA}} Isolation by Acid Guanidinium Thiocyanate-Phenol-Chloroform Extraction: Twenty-Something Years On.}, author = {Chomczynski, Piotr and Sacchi, Nicoletta}, year = 2006, month = jan, journal = {Nature Protocols}, volume = {1}, number = {2}, eprint = {17406285}, eprinttype = {pubmed}, pages = {581–585}, issn = {1750-2799}, doi = {10.1038/nprot.2006.83}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17406285}, abstract = {Since its introduction, the ‘single-step’ method has become widely used for isolating total RNA from biological samples of different sources. The principle at the basis of the method is that RNA is separated from DNA after extraction with an acidic solution containing guanidinium thiocyanate, sodium acetate, phenol and chloroform, followed by centrifugation. Under acidic conditions, total RNA remains in the upper aqueous phase, while most of DNA and proteins remain either in the interphase or in the lower organic phase. Total RNA is then recovered by precipitation with isopropanol and can be used for several applications. The original protocol, enabling the isolation of RNA from cells and tissues in less than 4 hours, greatly advanced the analysis of gene expression in plant and animal models as well as in pathological samples, as demonstrated by the overwhelming number of citations the paper gained over 20 years.}, pmid = {17406285}, keywords = {Chloroform,Chloroform: chemistry,Guanidines,Guanidines: chemistry,Hydrogen-Ion Concentration,nosource,Phenol,Phenol: chemistry,RNA,RNA: chemistry,RNA: isolation & purification,Thiocyanates,Thiocyanates: chemistry} }

@article{hendersonAntisenseinducedRibosomalFrameshifting2006, title = {Antisense-Induced Ribosomal Frameshifting.}, author = {Henderson, Clark M. and Anderson, Christine B. and Howard, Michael T.}, year = 2006, month = jan, journal = {Nucleic Acids Res.}, volume = {34}, number = {15}, pages = {4302–4310}, issn = {1362-4962}, doi = {10.1093/nar/gkl531}, abstract = {Programmed ribosomal frameshifting provides a mechanism to decode information located in two overlapping reading frames by diverting a proportion of translating ribosomes into a second open reading frame (ORF). The result is the production of two proteins: the product of standard translation from ORF1 and an ORF1-ORF2 fusion protein. Such programmed frameshifting is commonly utilized as a gene expression mechanism in viruses that infect eukaryotic cells and in a subset of cellular genes. RNA secondary structures, consisting of pseudoknots or stem-loops, located downstream of the shift site often act as cis-stimulators of frameshifting. Here, we demonstrate for the first time that antisense oligonucleotides can functionally mimic these RNA structures to induce +1 ribosomal frameshifting when annealed downstream of the frameshift site, UCC UGA. Antisense-induced shifting of the ribosome into the +1 reading frame is highly efficient in both rabbit reticulocyte lysate translation reactions and in cultured mammalian cells. The efficiency of antisense-induced frameshifting at this site is responsive to the sequence context 5’ of the shift site and to polyamine levels.}, pmid = {16920740}, keywords = {Animals,Antisense,Antisense: pharmacology,Frameshift Mutation,Frameshift Mutation: drug effects,Frameshifting,Molecular Mimicry,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Oligonucleotides,Open Reading Frames,Polyamines,Polyamines: metabolism,Rabbits,Reticulocytes,Ribosomal,Ribosomal: drug effects,Ribosomal: genetics} } % == BibTeX quality report for hendersonAntisenseinducedRibosomalFrameshifting2006: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{crickGeneralNatureGenetic1961, title = {General Nature of the Genetic Code for Proteins}, author = {Crick, F. H. C. and Barnett, L. and Brenner, S. and {Watts-Tobin}, R. J. and others}, year = 1961, journal = {Nature}, volume = {192}, number = {4809}, pages = {1227–1232}, url = {http://www2.hawaii.edu/~scallaha/SMCsite/MIcro671Links/3-GenCode/GenCodeCrick.pdf}, keywords = {nosource} }

@article{yepiskoposyanAutoregulationNonsensemediatedMRNA2011, title = {Autoregulation of the Nonsense-Mediated {{mRNA}} Decay Pathway in Human Cells}, author = {Yepiskoposyan, Hasmik and Aeschimann, Florian and Nilsson, Daniel and Okoniewski, Michal and Muhlemann, O. and M{"u}hlemann, Oliver}, year = 2011, month = oct, journal = {RNA}, volume = {17}, number = {12}, pages = {2108–18}, issn = {1355-8382}, doi = {10.1261/rna.030247.111}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3222124&tool=pmcentrez&rendertype=abstract http://rnajournal.cshlp.org/cgi/doi/10.1261/rna.030247.111}, abstract = {Nonsense-mediated mRNA decay (NMD) is traditionally portrayed as a quality-control mechanism that degrades mRNAs with truncated open reading frames (ORFs). However, it is meanwhile clear that NMD also contributes to the post-transcriptional gene regulation of numerous physiological mRNAs. To identify endogenous NMD substrate mRNAs and analyze the features that render them sensitive to NMD, we performed transcriptome profiling of human cells depleted of the NMD factors UPF1, SMG6, or SMG7. It revealed that mRNAs up-regulated by NMD abrogation had a greater median 3’-UTR length compared with that of the human mRNAome and were also enriched for 3’-UTR introns and uORFs. Intriguingly, most mRNAs coding for NMD factors were among the NMD-sensitive transcripts, implying that the NMD process is autoregulated. These mRNAs all possess long 3’ UTRs, and some of them harbor uORFs. Using reporter gene assays, we demonstrated that the long 3’ UTRs of UPF1, SMG5, and SMG7 mRNAs are the main NMD-inducing features of these mRNAs, suggesting that long 3’ UTRs might be a frequent trigger of NMD.}, pmid = {22028362}, keywords = {3’ Untranslated Regions,39-utr length,autoregulation,Gene Expression Profiling,Gene Expression Regulation,HeLa Cells,Homeostasis,Homeostasis: genetics,Humans,Introns,Messenger,Messenger: metabolism,microarray,mrna,nmd,Nonsense Mediated mRNA Decay,nosource,Open Reading Frames,RNA} }

@article{maderazoUpf1pControlNonsense2000a, title = {Upf1p {{Control}} of {{Nonsense mRNA Translation Is Regulated}} by {{Nmd2p}} and {{Upf1p Control}} of {{Nonsense mRNA Translation Is Regulated}} by {{Nmd2p}} and {{Upf3p}}}, author = {Maderazo, Alan B. and He, Feng and Mangus, David A. and Jacobson, Allan}, year = 2000, journal = {Molecular and Cellular Biology}, volume = {20}, number = {13}, pages = {4591–4603}, doi = {10.1128/MCB.20.13.4591-4603.2000.Updated}, keywords = {nosource} } % == BibTeX quality report for maderazoUpf1pControlNonsense2000a: % ? Title looks like it was stored in title-case in Zotero

@article{parkerTranslation42nucleotideSegment1990, title = {Translation and a 42-Nucleotide Segment within the Coding Region of the {{mRNA}} Encoded by the {{MAT}} Alpha 1 Gene Are Involved in Promoting Rapid {{mRNA}} Decay in Yeast.}, author = {Parker, R. and Jacobson, A.}, year = 1990, month = apr, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {87}, number = {7}, pages = {2780–4}, issn = {0027-8424}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=53774&tool=pmcentrez&rendertype=abstract}, abstract = {In yeast, the mRNA encoded by the MAT alpha 1 gene is unstable (t1/2 = 5 min) and the mRNAs encoded by the ACT1 gene (t1/2 = 30 min) and the PGK1 gene (t1/2 = 45 min) are stable. To understand the RNA structural features that dictate mRNA decay rates in yeast, we have constructed PGK1/MAT alpha 1 and ACT1/MAT alpha 1 gene fusions and analyzed the decay rates of the resultant chimeric transcripts. Fusion of a MAT alpha 1 segment containing 73% of the coding region and the 3’ untranslated region to either of the stable genes is sufficient to cause rapid decay of the chimeric mRNAs (t1/2 = 6-7.5 min). Sequences required for this rapid decay are not found in the MAT alpha 1 3’ untranslated region but are located within a 42-nucleotide segment of the coding region that has a high content (8 out of 14) of rare codons. Introduction of a translational stop codon upstream of this region stabilizes the hybrid mRNAs, indicating that the rapid decay promoted by these sequences is dependent on ribosomal translocation.}, pmid = {2181450}, keywords = {Base Sequence,Chimera,Fungal,Fungal: genetics,Fungal: metabolism,Genes,Genetic,Kinetics,Messenger,Messenger: genetics,Messenger: metabolism,Molecular Sequence Data,nosource,Plasmids,Protein Biosynthesis,Restriction Mapping,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Time Factors,Transcription} }

@article{dicksonStrategiesViralRNA2011, title = {Strategies for Viral {{RNA}} Stability: Live Long and Prosper.}, author = {Dickson, Alexa M. and Wilusz, Jeffrey}, year = 2011, month = jun, journal = {Trends in Genetics}, volume = {27}, number = {7}, eprint = {21640425}, eprinttype = {pubmed}, pages = {286–293}, publisher = {Elsevier Ltd}, issn = {0168-9525}, doi = {10.1016/j.tig.2011.04.003}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21640425}, abstract = {Eukaryotic cells have a powerful RNA decay machinery that plays an important and diverse role in regulating both the quantity and the quality of gene expression. Viral RNAs need to successfully navigate around this cellular machinery to initiate and maintain a highly productive infection. Recent work has shown that viruses have developed a variety of strategies to accomplish this, including inherent RNA shields, hijacking host RNA stability factors, incapacitating the host decay machinery and changing the entire landscape of RNA stability in cells using virally encoded nucleases. In addition to maintaining the stability of viral transcripts, these strategies can also contribute to the regulation and complexity of viral gene expression as well as to viral RNA evolution.}, pmid = {21640425}, keywords = {nosource} }

@article{renAlternativeReadingFrame2012, title = {Alternative Reading Frame Selection Mediated by a {{tRNA-like}} Domain of an Internal Ribosome Entry Site}, author = {Ren, Qian and Wang, QS Qing S. and Firth, Andrew E. and Chan, Mandy M. Y. and Gouw, Joost W. and Guarna, M. Marta and Foster, Leonard J. and Atkins, John F. and Jan, Eric}, year = 2012, month = jan, journal = {Proceedings of the }, volume = {109}, number = {11}, pages = {1–10}, issn = {1091-6490}, doi = {10.1073/pnas.1111303109}, url = {http://www.pnas.org/content/109/11/E630.short http://www.ncbi.nlm.nih.gov/pubmed/22247292}, abstract = {The dicistrovirus intergenic region internal ribosome entry site (IRES) utilizes a unique mechanism, involving P-site tRNA mimicry, to directly assemble 80S ribosomes and initiate translation at a specific non-AUG codon in the ribosomal A site. A subgroup of dicistrovirus genomes contains an additional stem-loop 5’-adjacent to the IRES and a short open reading frame (ORFx) that overlaps the viral structural polyprotein ORF (ORF2) in the +1 reading frame. Using mass spectrometry and extensive mutagenesis, we show that, besides directing ORF2 translation, the Israeli acute paralysis dicistrovirus IRES also directs ORFx translation. The latter is mediated by a UG base pair adjacent to the P-site tRNA-mimicking domain. An ORFx peptide was detected in virus-infected honey bees by multiple reaction monitoring mass spectrometry. Finally, the 5’ stem-loop increases IRES activity and may couple translation of the two major ORFs of the virus. This study reveals a novel viral strategy in which a tRNA-like IRES directs precise, initiator Met-tRNA-independent translation of two overlapping ORFs.}, pmid = {22247292}, keywords = {nosource} }

@article{hondorpCharacterizationGroupStreptococcus2012, title = {Characterization of the {{Group A Streptococcus Mga}} Virulence Regulator Reveals a Role for the {{C-terminal}} Region in Oligomerization and Transcriptional Activation}, author = {Hondorp, Elise R. and Hou, Sherry C. and Hempstead, Andrew D. and Hause, Lara L. and Beckett, Dorothy M. and McIver, Kevin S.}, year = 2012, month = feb, journal = {Molecular Microbiology}, pages = {no-no}, issn = {0950382X}, doi = {10.1111/j.1365-2958.2012.07980.x}, url = {http://doi.wiley.com/10.1111/j.1365-2958.2012.07980.x}, keywords = {nosource} }

@article{ribardoRoleStreptococcusPyogenes2004, title = {Role of {{Streptococcus}} Pyogenes {{Two-Component Response Regulators}} in the {{Temporal Control}} of {{Mga}} and the {{Mga-Regulated Virulence Gene}} Emm {{Role}} of {{Streptococcus}} Pyogenes {{Two-Component Response Regulators}} in the {{Temporal Control}} of {{Mga}} and the {{Mga-Regulated}}}, author = {Ribardo, Deborah A. and Lambert, Thomas J. and Kevin, S. and Mciver, Kevin S.}, year = 2004, journal = {Infection and Immunity}, volume = {72}, number = {6}, pages = {3668–3673}, doi = {10.1128/IAI.72.6.3668}, keywords = {nosource} }

@article{plattEvidenceThatEcotropic2009, title = {Evidence That Ecotropic Murine Leukemia Virus Contamination in {{TZM-bl}} Cells Does Not Affect the Outcome of Neutralizing Antibody Assays with Human Immunodeficiency Virus Type 1.}, author = {Platt, Emily J. and Bilska, Miroslawa and Kozak, Susan L. and Kabat, David and Montefiori, David C.}, year = 2009, month = aug, journal = {Journal of Virology}, volume = {83}, number = {16}, pages = {8289–92}, issn = {1098-5514}, doi = {10.1128/JVI.00709-09}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2715758&tool=pmcentrez&rendertype=abstract}, abstract = {The TZM-bl cell line that is commonly used to assess neutralizing antibodies against human immunodeficiency virus type 1 (HIV-1) was recently reported to be contaminated with an ecotropic murine leukemia virus (MLV) (Y. Takeuchi, M. O. McClure, and M. Pizzato, J. Virol. 82:12585-12588, 2008), raising questions about the validity of results obtained with this cell line. Here we confirm this observation and show that HIV-1 neutralization assays performed with a variety of serologic reagents in a similar cell line that does not harbor MLV yield results that are equivalent to those obtained in TZM-bl cells. We conclude that MLV contamination has no measurable effect on HIV-1 neutralization when TZM-bl cells are used as targets for infection.}, pmid = {19474095}, keywords = {Cell Line,Cell Line: immunology,Cell Line: virology,HIV Infections,HIV Infections: immunology,HIV Infections: virology,HIV-1,HIV-1: chemistry,HIV-1: immunology,Humans,Leukemia Virus,Murine,Neutralization Tests,nosource,Specimen Handling} }

@article{messieresMeasuringFoldingLandscape2011, title = {Measuring the Folding Landscape of a Harmonically Constrained Biopolymer.}, author = {Messieres, Michel De and {Brawn-cinani}, Barbara and Porta, Arthur La and {}de Messieres, Michel and Porta, Arthur La}, year = 2011, month = jun, journal = {Biophysical Journal}, volume = {100}, number = {11}, pages = {2736–44}, publisher = {Biophysical Society}, issn = {1542-0086}, doi = {10.1016/j.bpj.2011.03.067}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3117164&tool=pmcentrez&rendertype=abstract http://dx.doi.org/10.1016/j.bpj.2011.03.067}, abstract = {Pioneering studies have shown that the probability distribution of opening length for a DNA hairpin, recorded under constant force using an optical trap, can be used to reconstruct the energy landscape of the transition. However, measurements made under constant force are subject to some limitations. Under constant force a system with a sufficiently high energy barrier spends most of its time in the closed or open conformation, with relatively few statistics collected in the transition state region. We describe a measurement scheme in which the system is driven progressively through the transition by an optical trap and an algorithm is used to extract the energy landscape of the transition from the fluctuations recorded during this process. We illustrate this technique in simulations and demonstrate its effectiveness in experiments on a DNA hairpin. We find that the combination of this technique with the use of short DNA handles facilitates a high-resolution measurement of the hairpin’s folding landscape with a very short measurement time.}, pmid = {21641319}, keywords = {Algorithms,DNA,DNA: chemistry,DNA: genetics,Inverted Repeat Sequences,nosource,Nucleic Acid Conformation,Optical Tweezers,Thermodynamics} }

@article{marshallTranslationSinglemoleculeLevel2008, title = {Translation at the Single-Molecule Level}, author = {Marshall, R. A. and Aitken, C. E. and Dorywalska, Magdalena and Puglisi, J. D.}, year = 2008, month = jan, journal = {Annual Review of Biochemistry}, volume = {77}, pages = {177–203}, publisher = {Annual Reviews}, doi = {10.1146/annurev.biochem.77.070606.101431}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.biochem.77.070606.101431}, abstract = {Decades of studies have established translation as a multistep, multicomponent process that requires intricate communication to achieve high levels of speed, accuracy, and regulation. A crucial next step in understanding translation is to reveal the functional significance of the large-scale motions implied by static ribosome structures. This requires determining the trajectories, timescales, forces, and biochemical signals that underlie these dynamic conformational changes. Single-molecule methods have emerged as important tools for the characterization of motion in complex systems, including translation. In this review, we chronicle the key discoveries in this nascent field, which have demonstrated the power and promise of single-molecule techniques in the study of translation.}, keywords = {nosource} }

@article{sternbergTranslationFactorsDirect2009, title = {Translation Factors Direct Intrinsic Ribosome Dynamics during Translation Termination and Ribosome Recycling.}, author = {Sternberg, Samuel H. and Fei, Jingyi and Prywes, Noam and {}a McGrath, Kelly and Gonzalez, Ruben L.}, year = 2009, month = aug, journal = {Nature Structural & Molecular Biology}, volume = {16}, number = {8}, eprint = {19597483}, eprinttype = {pubmed}, pages = {861–8}, publisher = {Nature Publishing Group}, issn = {1545-9985}, doi = {10.1038/nsmb.1622}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19597483}, abstract = {Characterizing the structural dynamics of the translating ribosome remains a major goal in the study of protein synthesis. Deacylation of peptidyl-tRNA during translation elongation triggers fluctuations of the pretranslocation ribosomal complex between two global conformational states. Elongation factor G-mediated control of the resulting dynamic conformational equilibrium helps to coordinate ribosome and tRNA movements during elongation and is thus a crucial mechanistic feature of translation. Beyond elongation, deacylation of peptidyl-tRNA also occurs during translation termination, and this deacylated tRNA persists during ribosome recycling. Here we report that specific regulation of the analogous conformational equilibrium by translation release and ribosome recycling factors has a critical role in the termination and recycling mechanisms. Our results support the view that specific regulation of the global state of the ribosome is a fundamental characteristic of all translation factors and a unifying theme throughout protein synthesis.}, pmid = {19597483}, keywords = {Biological,Carbocyanines,Carbocyanines: chemistry,Electrophoresis,Fluorescence,Kinetics,Messenger,Messenger: genetics,Messenger: metabolism,Models,nosource,Peptide Chain Termination,Peptide Termination Factors,Peptide Termination Factors: chemistry,Peptide Termination Factors: genetics,Peptide Termination Factors: metabolism,Polyacrylamide Gel,Protein Binding,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: genetics,Ribosomal Proteins: metabolism,Ribosomes,Ribosomes: chemistry,Ribosomes: genetics,Ribosomes: metabolism,RNA,Translational} }

@article{zaherPrimaryRoleRelease2011, title = {A {{Primary Role}} for {{Release Factor}} 3 in {{Quality Control}} during {{Translation Elongation}} in {{Escherichia}} Coli.}, author = {Zaher, Hani S. and Green, Rachel}, year = 2011, month = oct, journal = {Cell}, volume = {147}, number = {2}, eprint = {22000017}, eprinttype = {pubmed}, pages = {396–408}, publisher = {Elsevier Inc.}, issn = {1097-4172}, doi = {10.1016/j.cell.2011.08.045}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22000017}, abstract = {Release factor 3 (RF3) is a GTPase found in a broad range of bacteria where it is thought to play a critical “recycling” role in translation by facilitating the removal of class 1 release factors (RF1 and RF2) from the ribosome following peptide release. More recently, RF3 was shown in vitro to stimulate a retrospective editing reaction on the bacterial ribosome wherein peptides carrying mistakes are prematurely terminated during protein synthesis. Here, we examine the role of RF3 in the bacterial cell and show that the deletion of this gene sensitizes cells to other perturbations that reduce the overall fidelity of protein synthesis. We further document substantial effects on mRNA stability and protein expression using reporter systems, native mRNAs and proteins. We conclude that RF3 plays a primary role in vivo in specifying the fidelity of protein synthesis thus impacting overall protein quantity and quality.}, pmid = {22000017}, keywords = {nosource} }

@article{giacamanPorphyromonasGingivalisSelectively2007, title = {Porphyromonas Gingivalis Selectively Up-Regulates the {{HIV-1}} Coreceptor {{CCR5}} in Oral Keratinocytes}, author = {Giacaman, Rodrigo a RA and Nobbs, AH Angela H. and Ross, Karen F. and Herzberg, Mark C.}, year = 2007, month = aug, journal = {The Journal of }, volume = {179}, number = {4}, eprint = {17675516}, eprinttype = {pubmed}, pages = {2542–50}, issn = {0022-1767}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17675516 http://www.jimmunol.org/content/179/4/2542.short}, abstract = {Primary infection of oral epithelial cells by HIV-1, if it occurs, could promote systemic infection. Most primary systemic infections are associated with R5-type HIV-1 targeting the R5-specific coreceptor CCR5, which is not usually expressed on oral keratinocytes. Because coinfection with other microbes has been suggested to modulate cellular infection by HIV-1, we hypothesized that oral keratinocytes may up-regulate CCR5 in response to the oral endogenous pathogen Porphyromonas gingivalis by cysteine-protease (gingipains) activation of the protease-activated receptors (PARs) or LPS signaling through the TLRs. The OKF6/TERT-2-immortalized normal human oral keratinocyte line expressed CXCR4, whereas CCR5 was not detectable. When exposed to P. gingivalis ATCC 33277, TERT-2 cells induced greater time-dependent expression of CCR5-specific mRNA and surface coreceptors than CXCR4. By comparing arg- (Rgp) and lys-gingipain (Kgp) mutants, a mutant deficient in both proteases, and the action of trypsin, P. gingivalis Rgp was strongly suggested to cleave PAR-1 and PAR-2 to up-regulate CCR5. CCR5 was also slightly up-regulated by an isogenic gingipain-deficient mutant, suggesting the presence of a nongingipain-mediated mechanism. Purified P. gingivalis LPS also up-regulated CCR5. Blocking TLR2 and TLR4 receptors with Abs attenuated induction of CCR5, suggesting LPS signaling through TLRs. P. gingivalis, therefore, selectively up-regulated CCR5 by two independent signaling pathways, Rgp acting on PAR-1 and PAR-2, and LPS on TLR2 and TLR4. By inducing CCR5 expression, P. gingivalis coinfection could promote selective R5-type HIV-1 infection of oral keratinocytes.}, pmid = {17675516}, keywords = {Adhesins,Antibodies,Antibodies: immunology,Antibodies: pharmacology,Bacterial,Bacterial: immunology,Bacterial: metabolism,Bacteroidaceae Infections,Bacteroidaceae Infections: genetics,Bacteroidaceae Infections: immunology,Bacteroidaceae Infections: pathology,CCR5,CCR5: biosynthesis,CCR5: immunology,Cell Line,CXCR4,CXCR4: biosynthesis,CXCR4: genetics,CXCR4: immunology,Cysteine Endopeptidases,Cysteine Endopeptidases: deficiency,Cysteine Endopeptidases: immunology,Cysteine Endopeptidases: metabolism,HIV Infections,HIV Infections: genetics,HIV Infections: immunology,HIV Infections: metabolism,HIV Infections: pathology,HIV-1,HIV-1: immunology,HIV-1: metabolism,Humans,Keratinocytes,Keratinocytes: immunology,Keratinocytes: metabolism,Keratinocytes: pathology,Lipopolysaccharides,Lipopolysaccharides: pharmacology,Messenger,Messenger: biosynthesis,Messenger: genetics,Messenger: metabolism,Mouth,Mouth: immunology,Mouth: metabolism,Mouth: pathology,Mutation,Mutation: immunology,nosource,PAR-1,PAR-1: immunology,PAR-1: metabolism,PAR-2,PAR-2: immunology,PAR-2: metabolism,Porphyromonas gingivalis,Porphyromonas gingivalis: genetics,Porphyromonas gingivalis: immunology,Porphyromonas gingivalis: metabolism,Receptor,Receptors,RNA,Signal Transduction,Signal Transduction: drug effects,Signal Transduction: genetics,Signal Transduction: immunology,Toll-Like Receptor 2,Toll-Like Receptor 2: antagonists & inhibitors,Toll-Like Receptor 2: genetics,Toll-Like Receptor 2: immunology,Toll-Like Receptor 2: metabolism,Toll-Like Receptor 4,Toll-Like Receptor 4: antagonists & inhibitors,Toll-Like Receptor 4: genetics,Toll-Like Receptor 4: immunology,Toll-Like Receptor 4: metabolism,Transformed,Up-Regulation,Up-Regulation: drug effects,Up-Regulation: immunology} }

@article{kerteszGenomewideMeasurementRNA2010, title = {Genome-Wide Measurement of {{RNA}} Secondary Structure in Yeast.}, author = {Kertesz, Michael and Wan, Yue and Mazor, Elad and Rinn, John L. and Nutter, Robert C. and Chang, Howard Y. and Segal, Eran}, year = 2010, month = sep, journal = {Nature}, volume = {467}, number = {7311}, eprint = {20811459}, eprinttype = {pubmed}, pages = {103–7}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature09322}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20811459 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3847670&tool=pmcentrez&rendertype=abstract}, abstract = {The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here we describe a novel strategy termed parallel analysis of RNA structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the messenger RNAs (mRNAs) of the budding yeast Saccharomyces cerevisiae and obtain structural profiles for over 3,000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared with untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions and an anti-correlation between the efficiency with which an mRNA is translated and the structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale.}, pmid = {20811459}, keywords = {Base Sequence,Fungal,Fungal: chemistry,Genetic,Genetic Techniques,Genome-Wide Association Study,Messenger,Messenger: chemistry,Molecular Sequence Data,nosource,Nucleic Acid Conformation,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae: chemistry,Saccharomyces cerevisiae: genetics,Transcription} }

@article{chursovSequencestructureRelationshipsYeast2011, title = {Sequence-Structure Relationships in Yeast {{mRNAs}}.}, author = {Chursov, Andrey and Walter, Mathias C. and Schmidt, Thorsten and Mironov, Andrei and Shneider, Alexander and Frishman, Dmitrij}, year = 2011, month = sep, journal = {Nucleic Acids Research}, number = {12}, eprint = {21954438}, eprinttype = {pubmed}, pages = {1–7}, issn = {1362-4962}, doi = {10.1093/nar/gkr790}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21954438}, abstract = {It is generally accepted that functionally important RNA structure is more conserved than sequence due to compensatory mutations that may alter the sequence without disrupting the structure. For small RNA molecules sequence-structure relationships are relatively well understood. However, structural bioinformatics of mRNAs is still in its infancy due to a virtual absence of experimental data. This report presents the first quantitative assessment of sequence-structure divergence in the coding regions of mRNA molecules based on recently published transcriptome-wide experimental determination of their base paring patterns. Structural resemblance in paralogous mRNA pairs quickly drops as sequence identity decreases from 100% to 85-90%. Structures of mRNAs sharing sequence identity below roughly 85% are essentially uncorrelated. This outcome is in dramatic contrast to small functional non-coding RNAs where sequence and structure divergence are correlated at very low levels of sequence similarity. The fact that very similar mRNA sequences can have vastly different secondary structures may imply that the particular global shape of base paired elements in coding regions does not play a major role in modulating gene expression and translation efficiency. Apparently, the need to maintain stable three-dimensional structures of encoded proteins places a much higher evolutionary pressure on mRNA sequences than on their RNA structures.}, pmid = {21954438}, keywords = {nosource} }

@article{atchisonMultipleExtracellularElements1996, title = {Multiple Extracellular Elements of {{CCR5}} and {{HIV-1}} Entry: Dissociation from Response to Chemokines.}, author = {Atchison, R. E. and Gosling, J. and Monteclaro, F. S. and Franci, C. and Digilio, L. and Charo, I. F. and {}a Goldsmith, M.}, year = 1996, month = dec, journal = {Science}, volume = {274}, number = {5294}, eprint = {8943208}, eprinttype = {pubmed}, pages = {1924–1926}, issn = {0036-8075}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8943208}, abstract = {The human beta-chemokine receptor CCR5 is an important cofactor for entry of human immunodeficiency virus-type 1 (HIV-1). The murine form of CCR5, despite its 82 percent identity to the human form, was not functional as an HIV-1 coreceptor. HIV-1 entry function could be reconstituted by fusion of various individual elements derived from the extracellular region of human CCR5 onto murine CCR5. Analysis of chimeras containing elements from human CCR5 and human CCR2B suggested that a complex structure rather than single contact sites is responsible for facilitation of viral entry. Further, certain chimeras lacking the domains necessary to signal in response to their natural chemokine ligands retained vigorous HIV-1 coreceptor activity.}, pmid = {8943208}, keywords = {Animals,Antigens,CCR2,CCR5,CD4,CD4: metabolism,Chemokine,COS Cells,Cytokine,Cytokine: chemistry,Cytokine: genetics,Cytokine: metabolism,HIV,HIV-1,HIV-1: metabolism,HIV: chemistry,HIV: genetics,HIV: metabolism,Humans,Inositol Phosphates,Inositol Phosphates: metabolism,Ligands,Mice,nosource,Receptors,Recombinant Fusion Proteins,Recombinant Fusion Proteins: metabolism,Signal Transduction,Transfection} }

@article{melarPhysiologicalLevelsVirionassociated2007, title = {Physiological Levels of Virion-Associated Human Immunodeficiency Virus Type 1 Envelope Induce Coreceptor-Dependent Calcium Flux.}, author = {Melar, Marta and Ott, David E. and Hope, Thomas J.}, year = 2007, month = feb, journal = {Journal of Virology}, volume = {81}, number = {4}, pages = {1773–1785}, issn = {0022-538X}, doi = {10.1128/JVI.01316-06}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1797554&tool=pmcentrez&rendertype=abstract}, abstract = {Human immunodeficiency virus (HIV) entry into target cells requires the engagement of receptor and coreceptor by envelope glycoprotein (Env). Coreceptors CCR5 and CXCR4 are chemokine receptors that generate signals manifested as calcium fluxes in response to binding of the appropriate ligand. It has previously been shown that engagement of the coreceptors by HIV Env can also generate Ca(2+) fluxing. Since the sensitivity and therefore the physiological consequence of signaling activation in target cells is not well understood, we addressed it by using a microscopy-based approach to measure Ca(2+) levels in individual CD4(+) T cells in response to low Env concentrations. Monomeric Env subunit gp120 and virion-bound Env were able to activate a signaling cascade that is qualitatively different from the one induced by chemokines. Env-mediated Ca(2+) fluxing was coreceptor mediated, coreceptor specific, and CD4 dependent. Comparison of the observed virion-mediated Ca(2+) fluxing with the exact number of viral particles revealed that the viral threshold necessary for coreceptor activation of signaling in CD4(+) T cells was quite low, as few as two virions. These results indicate that the physiological levels of virion binding can activate signaling in CD4(+) T cells in vivo and therefore might contribute to HIV-induced pathogenesis.}, pmid = {17121788}, keywords = {Animals,Calcium,Calcium: metabolism,CCR5,CCR5: metabolism,CD4-Positive T-Lymphocytes,CD4-Positive T-Lymphocytes: metabolism,CD4-Positive T-Lymphocytes: virology,CHO Cells,Cricetinae,Cricetulus,CXCR4,CXCR4: metabolism,G-Protein-Coupled,G-Protein-Coupled: metabolism,HIV Envelope Protein gp120,HIV Envelope Protein gp120: physiology,HIV Infections,HIV Infections: virology,HIV-1,HIV-1: physiology,Humans,nosource,Receptors,Signal Transduction,Viral Envelope Proteins,Viral Envelope Proteins: physiology,Virus,Virus Replication,Virus: metabolism} }

@article{chenAllostericVsSpontaneous2011, title = {Allosteric vs. Spontaneous Exit-Site ({{E-site}}) {{tRNA}} Dissociation Early in Protein Synthesis}, author = {Chen, Chunlai and Stevens, Benjamin and Kaur, Jaskiran and Smilansky, Zeev and Cooperman, Barry S. and Goldman, Yale E.}, year = 2011, journal = {Proceedings of the National Academy of Sciences}, volume = {108}, number = {41}, doi = {10.1073/pnas.1106999108/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1106999108}, url = {http://www.pnas.org/content/108/41/16980.short}, keywords = {nosource} }

@article{sharmaPilotStudyBacterial2011, title = {A Pilot Study of Bacterial Genes with Disrupted {{ORFs}} Reveals a Surprising Profusion of Protein Sequence Recoding Mediated by Ribosomal Frameshifting and Transcriptional Realignment.}, author = {Sharma, Virag and Firth, Andrew E. and Antonov, Ivan and Fayet, Olivier and Atkins, John F. and Borodovsky, Mark and Baranov, Pavel V.}, year = 2011, month = jun, journal = {Molecular Biology and Evolution}, volume = {28}, number = {2004}, eprint = {21673094}, eprinttype = {pubmed}, pages = {3195–3211}, issn = {1537-1719}, doi = {10.1093/molbev/msr155}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21673094}, abstract = {Bacterial genome annotations contain a number of coding sequences (CDSs) that, in spite of reading frame disruptions, encode a single continuous polypeptide. Such disruptions have different origins: sequencing errors, frameshift or stop codon mutations, as well as instances of utilization of non-triplet decoding utilization. We have extracted over one thousand CDSs with annotated disruptions and found that about 75% of them can be clustered into 64 groups based on sequence similarity. Analysis of the clusters revealed deep phylogenetic conservation of ORF organization as well as the presence of conserved sequence patterns that indicate likely utilization of the non-standard decoding mechanisms: programmed ribosomal frameshifting (PRF) and programmed transcriptional realignment (PTR). Further enrichment of these clusters with additional homologous nucleotide sequences revealed over six thousand candidate genes utilizing PRF or PTR. Analysis of the patterns of conservation apparently associated with non-triplet decoding revealed the presence of both previously characterized frameshift-prone sequences and a few novel ones. Since the starting point of our analysis was a set of genes with already annotated disruptions, it is highly plausible that in this study we have identified only a fraction of all bacterial genes that utilize PRF or PTR. In addition to the identification of a large number of recoded genes, a surprising observation is that nearly half of them are expressed via PTR - a mechanism that, in contrast to PRF, has not yet received substantial attention.}, pmid = {21673094}, keywords = {frameshift mutation,is element,nonstandard decoding,nosource,programmed ribosomal frameshifting,pseudogene,realignment,recoding,rna editing,transcriptional,transcriptional slippage} }

@article{yuehTranslationRibosomeShunting2000, title = {Translation by Ribosome Shunting on Adenovirus and Hsp70 {{mRNAs}} Facilitated by Complementarity to {{18S rRNA}}}, author = {Yueh, Andrew}, year = 2000, journal = {Genes & Development}, pages = {414–421}, doi = {10.1101/gad.14.4.414}, url = {http://genesdev.cshlp.org/content/14/4/414.short}, keywords = {1999,23,adenovirus,hsp70,in which,initiate translation by a,it is thought that,mrnas,nosource,received october 20,revised version accepted december,ribosome shunting,rrna,scanning mechanism,the majority of eukaryotic,translation} }

@article{mirStorageCellular52008, title = {Storage of Cellular 5’ {{mRNA}} Caps in {{P}} Bodies for Viral Cap-Snatching.}, author = {{}a Mir, M. and {}a Duran, W. and Hjelle, B. L. and Ye, C. and Panganiban, a T.}, year = 2008, month = dec, journal = {Proceedings of the National Academy of Sciences}, volume = {105}, number = {49}, pages = {19294–19299}, issn = {1091-6490}, doi = {10.1073/pnas.0807211105}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2614755&tool=pmcentrez&rendertype=abstract}, abstract = {The minus strand and ambisense segmented RNA viruses include multiple important human pathogens and are divided into three families, the Orthomyxoviridae, the Bunyaviridae, and the Arenaviridae. These viruses all initiate viral transcription through the process of “cap-snatching,” which involves the acquisition of capped 5’ oligonucleotides from cellular mRNA. Hantaviruses are emerging pathogenic viruses of the Bunyaviridae family that replicate in the cytoplasm of infected cells. Cellular mRNAs can be actively translated in polysomes or physically sequestered in cytoplasmic processing bodies (P bodies) where they are degraded or stored for subsequent translation. Here we show that the hantavirus nucleocapsid protein binds with high affinity to the 5’ cap of cellular mRNAs, protecting the 5’ cap from degradation. We also show that the hantavirus nucleocapsid protein accumulates in P bodies, where it sequesters protected 5’ caps. P bodies then serve as a pool of primers during the initiation of viral mRNA synthesis by the viral polymerase. We propose that minus strand segmented viruses replicating in the cytoplasm have co-opted the normal degradation machinery of P bodies for storage of cellular caps. Our data also indicate that modification of the cap-snatching model is warranted to include a role for the nucleocapsid protein in cap acquisition and storage.}, pmid = {19047634}, keywords = {Codon,Cytoplasm,Cytoplasm: virology,Cytoplasmic Granules,Cytoplasmic Granules: virology,Gene Expression Regulation,Genetic,Green Fluorescent Proteins,Green Fluorescent Proteins: genetics,Hantavirus,Hantavirus Infections,Hantavirus Infections: virology,Hantavirus: genetics,Hantavirus: growth & development,HeLa Cells,Humans,Messenger,Messenger: genetics,Nonsense,Nonsense: genetics,nosource,Nucleocapsid Proteins,Nucleocapsid Proteins: genetics,Protein Biosynthesis,RNA,RNA Stability,RNA Stability: physiology,Transcription,Viral} }

@article{krutzfeldtSilencingMicroRNAsVivo2005, title = {Silencing of {{microRNAs}} in Vivo with ‘Antagomirs’.}, author = {Kr{"u}tzfeldt, Jan and Rajewsky, Nikolaus and Braich, Ravi and Rajeev, Kallanthottathil G. and Tuschl, Thomas and Manoharan, Muthiah and Stoffel, Markus}, year = 2005, month = dec, journal = {Nature}, volume = {438}, number = {7068}, eprint = {16258535}, eprinttype = {pubmed}, pages = {685–9}, issn = {1476-4687}, doi = {10.1038/nature04303}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16258535}, abstract = {MicroRNAs (miRNAs) are an abundant class of non-coding RNAs that are believed to be important in many biological processes through regulation of gene expression. The precise molecular function of miRNAs in mammals is largely unknown and a better understanding will require loss-of-function studies in vivo. Here we show that a novel class of chemically engineered oligonucleotides, termed ‘antagomirs’, are efficient and specific silencers of endogenous miRNAs in mice. Intravenous administration of antagomirs against miR-16, miR-122, miR-192 and miR-194 resulted in a marked reduction of corresponding miRNA levels in liver, lung, kidney, heart, intestine, fat, skin, bone marrow, muscle, ovaries and adrenals. The silencing of endogenous miRNAs by this novel method is specific, efficient and long-lasting. The biological significance of silencing miRNAs with the use of antagomirs was studied for miR-122, an abundant liver-specific miRNA. Gene expression and bioinformatic analysis of messenger RNA from antagomir-treated animals revealed that the 3’ untranslated regions of upregulated genes are strongly enriched in miR-122 recognition motifs, whereas downregulated genes are depleted in these motifs. Analysis of the functional annotation of downregulated genes specifically predicted that cholesterol biosynthesis genes would be affected by miR-122, and plasma cholesterol measurements showed reduced levels in antagomir-122-treated mice. Our findings show that antagomirs are powerful tools to silence specific miRNAs in vivo and may represent a therapeutic strategy for silencing miRNAs in disease.}, pmid = {16258535}, keywords = {3’ Untranslated Regions,3’ Untranslated Regions: genetics,3’ Untranslated Regions: metabolism,Animals,Cholesterol,Cholesterol: biosynthesis,Cholesterol: metabolism,Complementary,Complementary: administration & dosage,Complementary: genetics,Complementary: metabolism,Complementary: pharmacology,Computational Biology,Down-Regulation,Down-Regulation: drug effects,Gene Silencing,Gene Silencing: drug effects,Mice,MicroRNAs,MicroRNAs: antagonists & inhibitors,MicroRNAs: genetics,MicroRNAs: metabolism,nosource,Oligonucleotides,Oligonucleotides: metabolism,RNA,Sensitivity and Specificity,Substrate Specificity,Time Factors,Up-Regulation,Up-Regulation: drug effects} }

@article{endresCD4independentInfectionHIV21996, title = {{{CD4-independent}} Infection by {{HIV-2}} Is Mediated by Fusin/{{CXCR4}}.}, author = {Endres, M. J. and Clapham, P. R. and Marsh, M. and Ahuja, M. and Turner, J. D. and McKnight, A. and Thomas, J. F. and {Stoebenau-Haggarty}, B. and Choe, S. and Vance, P. J. and Wells, T. N. and {}a Power, C. and Sutterwala, S. S. and Doms, R. W. and Landau, N. R. and {}a Hoxie, J.}, year = 1996, month = nov, journal = {Cell}, volume = {87}, number = {4}, eprint = {8929542}, eprinttype = {pubmed}, pages = {745–56}, issn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8929542}, abstract = {Several members of the chemokine receptor family have been shown to function in association with CD4 to permit HIV-1 entry and infection. However, the mechanism by which these molecules serve as CD4-associated cofactors is unclear. In the present report, we show that one member of this family, termed Fusin/ CXCR4, is able to function as an alternative receptor for some isolates of HIV-2 in the absence of CD4. This conclusion is supported by the finding that (1) CD4-independent infection by these viruses is inhibited by an anti-Fusin monoclonal antibody, (2) Fusin expression renders human and nonhuman CD4-negative cell lines sensitive to HIV-2-induced syncytium induction and/or infection, and (3) Fusin is selectively down-regulated from the cell surface following HIV-2 infection. The finding that one chemokine receptor can function as a primary viral receptor strongly suggests that the HIV envelope glycoprotein contains a binding site for these proteins and that differences in the affinity and/or the availability of this site can extend the host range of these viruses to include a number of CD4-negative cell types.}, pmid = {8929542}, keywords = {Animals,Antibodies,Antigens,B-Lymphocytes,B-Lymphocytes: virology,Base Sequence,CD4,CD4: metabolism,Cell Fusion,Cell Fusion: drug effects,CHO Cells,Cricetinae,CXCR4,Down-Regulation,Genetic Variation,HIV,HIV-2,HIV-2: genetics,HIV-2: growth & development,HIV: genetics,HIV: immunology,HIV: metabolism,Humans,Lymphocytes,Lymphocytes: virology,Membrane Proteins,Membrane Proteins: genetics,Membrane Proteins: immunology,Membrane Proteins: metabolism,Molecular Sequence Data,Monoclonal,Monoclonal: pharmacology,nosource,Quail,Receptors,Recombinant Proteins,Recombinant Proteins: metabolism,T-Lymphocytes,T-Lymphocytes: virology} }

@article{lewisConservedSeedPairing2005, title = {Conserved Seed Pairing, Often Flanked by Adenosines, Indicates That Thousands of Human Genes Are {{microRNA}} Targets}, author = {Lewis, BP Benjamin P. and Burge, Christopher B. CB and Bartel, David P. DP and Pairing, Conserved Seed}, year = 2005, month = jan, journal = {cell}, volume = {120}, number = {1}, eprint = {15652477}, eprinttype = {pubmed}, pages = {15–20}, issn = {0092-8674}, doi = {10.1016/j.cell.2004.12.035}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15652477 http://www.sciencedirect.com/science/article/pii/S0092867404012607}, abstract = {We predict regulatory targets of vertebrate microRNAs (miRNAs) by identifying mRNAs with conserved complementarity to the seed (nucleotides 2-7) of the miRNA. An overrepresentation of conserved adenosines flanking the seed complementary sites in mRNAs indicates that primary sequence determinants can supplement base pairing to specify miRNA target recognition. In a four-genome analysis of 3’ UTRs, approximately 13,000 regulatory relationships were detected above the estimate of false-positive predictions, thereby implicating as miRNA targets more than 5300 human genes, which represented 30% of our gene set. Targeting was also detected in open reading frames. In sum, well over one third of human genes appear to be conserved miRNA targets.}, pmid = {15652477}, keywords = {3’ Untranslated Regions,3’ Untranslated Regions: genetics,Adenosine,Adenosine: genetics,Adenosine: metabolism,Amino Acid Sequence,Animals,Chickens,Dogs,Gene Expression Regulation,Gene Expression Regulation: genetics,Gene Targeting,Gene Targeting: methods,Humans,Messenger,Messenger: genetics,Mice,MicroRNAs,MicroRNAs: genetics,Molecular Sequence Data,nosource,Nucleic Acid Hybridization,Nucleic Acid Hybridization: physiology,Nucleotides,Nucleotides: metabolism,Rats,RNA} }

@article{petersenShortRNAsRepress2006, title = {Short {{RNAs}} Repress Translation after Initiation in Mammalian Cells.}, author = {Petersen, Christian P. and Bordeleau, Marie-Eve and Pelletier, Jerry and Sharp, Phillip}, year = 2006, month = feb, journal = {Molecular Cell}, volume = {21}, number = {4}, eprint = {16483934}, eprinttype = {pubmed}, pages = {533–542}, issn = {1097-2765}, doi = {10.1016/j.molcel.2006.01.031}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16483934}, abstract = {MicroRNAs (miRNAs) are predicted to regulate 30% of mammalian protein-encoding genes by interactions with their 3’ untranslated regions (UTRs). We use partially complementary siRNAs to investigate the mechanism by which miRNAs mediate translational repression in human cells. Repressed mRNAs are associated with polyribosomes that are engaged in translation elongation, as shown by puromycin sensitivity. The inhibition appears to be postinitiation because translation driven by the cap-independent processes of HCV IRES and CrPV IRES is repressed by short RNAs. Further, metabolic labeling suggests that silencing occurs before completion of the nascent polypeptide chain. In addition, silencing by short RNAs causes a decrease in translational readthrough at a stop codon, and ribosomes on repressed mRNAs dissociate more rapidly after a block of initiation of translation than those on control mRNAs. These results suggest that repression by short RNAs, and thus probably miRNAs, is primarily due to ribosome drop off during elongation of translation.}, pmid = {16483934}, keywords = {Animals,Cell Line,Codon,Gene Expression Regulation,Gene Silencing,Humans,MicroRNAs,MicroRNAs: metabolism,nosource,Peptide Chain Termination,Peptides,Peptides: metabolism,Peptidyl Transferases,Peptidyl Transferases: metabolism,Protein Biosynthesis,Ribosomes,Ribosomes: metabolism,RNA,Small Interfering,Small Interfering: genetics,Small Interfering: metabolism,Terminator,Translational} }

@article{yektaMicroRNAdirectedCleavageHOXB82004, title = {{{MicroRNA-directed}} Cleavage of {{HOXB8 mRNA}}.}, author = {Yekta, Soraya and Shih, I.-hung and Bartel, David P.}, year = 2004, month = apr, journal = {Science}, volume = {304}, number = {5670}, eprint = {15105502}, eprinttype = {pubmed}, pages = {594–6}, issn = {1095-9203}, doi = {10.1126/science.1097434}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15105502}, abstract = {MicroRNAs (miRNAs) are endogenous approximately 22-nucleotide RNAs, some of which are known to play important regulatory roles in animals by targeting the messages of protein-coding genes for translational repression. We find that miR-196, a miRNA encoded at three paralogous locations in the A, B, and C mammalian HOX clusters, has extensive, evolutionarily conserved complementarity to messages of HOXB8, HOXC8, and HOXD8. RNA fragments diagnostic of miR-196-directed cleavage of HOXB8 were detected in mouse embryos. Cell culture experiments demonstrated down-regulation of HOXB8, HOXC8, HOXD8, and HOXA7 and supported the cleavage mechanism for miR-196-directed repression of HOXB8. These results point to a miRNA-mediated mechanism for the posttranscriptional restriction of HOX gene expression during vertebrate development and demonstrate that metazoan miRNAs can repress expression of their natural targets through mRNA cleavage in addition to inhibiting productive translation.}, pmid = {15105502}, keywords = {3’ Untranslated Regions,Animals,Base Sequence,Down-Regulation,Genes,Hela Cells,Homeobox,Homeodomain Proteins,Homeodomain Proteins: genetics,Humans,Messenger,Messenger: chemistry,Messenger: genetics,Messenger: metabolism,Mice,MicroRNAs,MicroRNAs: chemistry,MicroRNAs: genetics,MicroRNAs: metabolism,Molecular Sequence Data,Neoplasm Proteins,Neoplasm Proteins: genetics,nosource,Reporter,RNA,Sequence Alignment,Transcription Factors,Transcription Factors: genetics,Transfection} }

@article{plattEffectsCCR5CD41998a, title = {Effects of {{CCR5}} and {{CD4 Cell Surface Concentrations}} on {{Infections}} by {{Macrophagetropic Isolates}} of {{Human Immunodeficiency Virus Type}} 1 {{Effects}} of {{CCR5}} and {{CD4 Cell Surface Concentrations}} on {{Infections}} by {{Macrophagetropic Isolates}} of {{Human Immunodeficiency}}}, author = {Platt, Emily J. and Wehrly, Kathy and Kuhmann, Shawn E. and Kabat, David and Chesebro, Bruce}, year = 1998, journal = {Microbiology}, keywords = {nosource} } % == BibTeX quality report for plattEffectsCCR5CD41998a: % ? Title looks like it was stored in title-case in Zotero

@article{caiHumanMicroRNAsAre2004, title = {Human {{microRNAs}} Are Processed from Capped, Polyadenylated Transcripts That Can Also Function as {{mRNAs}}}, author = {Cai, Xuezhong and Hagedorn, CH Curt H. and Cullen, Bryan R.}, year = 2004, month = dec, journal = {Rna}, volume = {10}, number = {12}, pages = {1957–1966}, issn = {1355-8382}, doi = {10.1261/rna.7135204}, url = {http://rnajournal.cshlp.org/content/10/12/1957.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1370684&tool=pmcentrez&rendertype=abstract}, abstract = {The factors regulating the expression of microRNAs (miRNAs), a ubiquitous family of approximately 22-nt noncoding regulatory RNAs, remain undefined. However, it is known that miRNAs are first transcribed as a largely unstructured precursor, termed a primary miRNA (pri-miRNA), which is sequentially processed in the nucleus, to give the approximately 65-nt pre-miRNA hairpin intermediate, and then in the cytoplasm, to give the mature miRNA. Here we have sought to identify the RNA polymerase responsible for miRNA transcription and to define the structure of a full-length human miRNA. We show that the pri-miRNA precursors for nine human miRNAs are both capped and polyadenylated and report the sequence of the full-length, approximately 3433-nt pri-miR-21 RNA. This pri-miR-21 gene sequence is flanked 5’ by a promoter element able to transcribe heterologous mRNAs and 3’ by a consensus polyadenylation sequence. Nuclear processing of pri-miRNAs was found to be efficient, thus largely preventing the nuclear export of full-length pri-miRNAs. Nevertheless, an intact miRNA stem-loop precursor located in the 3’ UTR of a protein coding gene only moderately inhibited expression of the linked open reading frame, probably because the 3’ truncated mRNA could still be exported and expressed. Together, these data show that human pri-miRNAs are not only structurally similar to mRNAs but can, in fact, function both as pri-miRNAs and mRNAs.}, pmid = {15525708}, keywords = {Base Sequence,Cloning,Cytoplasm,Cytoplasm: metabolism,Hela Cells,Humans,Messenger,Messenger: genetics,Messenger: metabolism,micrornas,MicroRNAs: genetics,MicroRNAs: metabolism,Molecular,nosource,Post-Transcriptional,RNA,RNA Caps,RNA Caps: genetics,RNA Caps: metabolism,rna interference,RNA Precursors,RNA Precursors: genetics,RNA Precursors: metabolism,rna processing} }

@article{bennasserHIV1EncodedCandidate2004, title = {{{HIV-1}} Encoded Candidate Micro-{{RNAs}} and Their Cellular Targets.}, author = {Bennasser, Yamina and Le, Shu-Yun and Yeung, Man Lung and Jeang, Kuan-Teh}, year = 2004, month = jan, journal = {Retrovirology}, volume = {1}, pages = {43}, issn = {1742-4690}, doi = {10.1186/1742-4690-1-43}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=544590&tool=pmcentrez&rendertype=abstract}, abstract = {MicroRNAs (miRNAs) are small RNAs of 21-25 nucleotides that specifically regulate cellular gene expression at the post-transcriptional level. miRNAs are derived from the maturation by cellular RNases III of imperfect stem loop structures of 70 nucleotides. Evidence for hundreds of miRNAs and their corresponding targets has been reported in the literature for plants, insects, invertebrate animals, and mammals. While not all of these miRNA/target pairs have been functionally verified, some clearly serve roles in regulating normal development and physiology. Recently, it has been queried whether the genome of human viruses like their cellular counterpart also encode miRNA. To date, there has been only one report pertaining to this question. The Epstein-Barr virus (EBV) has been shown to encode five miRNAs. Here, we extend the analysis of miRNA-encoding potential to the human immunodeficiency virus (HIV). Using computer-directed analyses, we found that HIV putatively encodes five candidate pre-miRNAs. We then matched deduced mature miRNA sequences from these 5 pre-miRNAs against a database of 3’ untranslated sequences (UTR) from the human genome. These searches revealed a large number of cellular transcripts that could potentially be targeted by these viral miRNA (vmiRNA) sequences. We propose that HIV has evolved to use vmiRNAs as a means to regulate cellular milieu for its benefit.}, pmid = {15601472}, keywords = {3’ Untranslated Regions,3’ Untranslated Regions: genetics,Base Sequence,Genome,HIV-1,HIV-1: genetics,Human,Humans,MicroRNAs,MicroRNAs: genetics,nosource,Post-Transcriptional,RNA,RNA Processing,Viral,Viral: genetics} }

@article{nairVirusencodedMicroRNAsNovel2006, title = {Virus-Encoded {{microRNAs}}: Novel Regulators of Gene Expression.}, author = {Nair, Venugopal and Zavolan, Mihaela}, year = 2006, month = apr, journal = {Trends in Microbiology}, volume = {14}, number = {4}, eprint = {16531046}, eprinttype = {pubmed}, pages = {169–175}, issn = {0966-842X}, doi = {10.1016/j.tim.2006.02.007}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16531046}, abstract = {MicroRNAs (miRNAs) are a class of small RNAs that have recently been recognized as major regulators of gene expression. They influence diverse cellular processes ranging from cellular differentiation, proliferation, apoptosis and metabolism to cancer. Bioinformatic approaches and direct cloning methods have identified {\(>\)}3500 miRNAs, including orthologues from various species. Experiments to identify the targets and potential functions of miRNAs in various species are continuing but the recent discovery of virus-encoded miRNAs indicates that viruses also use this fundamental mode of gene regulation. Virus-encoded miRNAs seem to evolve rapidly and regulate both the viral life cycle and the interaction between viruses and their hosts.}, pmid = {16531046}, keywords = {Animals,Gene Expression Regulation,Herpesviridae,Herpesviridae: genetics,Herpesviridae: physiology,Humans,MicroRNAs,MicroRNAs: genetics,MicroRNAs: physiology,nosource,Polyomavirus,Polyomavirus: genetics,Polyomavirus: physiology,RNA,Viral,Viral: genetics,Viral: physiology} }

@article{nathansCellularMicroRNABodies2009, title = {Cellular {{microRNA}} and {{P}} Bodies Modulate Host-{{HIV-1}} Interactions.}, author = {Nathans, Robin and Chu, Chia-ying and Serquina, Anna Kristina and Lu, Chih-Chung and Cao, Hong and Rana, Tariq M.}, year = 2009, month = jun, journal = {Molecular Cell}, volume = {34}, number = {6}, pages = {696–709}, publisher = {Elsevier Ltd}, issn = {1097-4164}, doi = {10.1016/j.molcel.2009.06.003}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2763548&tool=pmcentrez&rendertype=abstract http://dx.doi.org/10.1016/j.molcel.2009.06.003}, abstract = {MicroRNAs (miRNAs), approximately 22 nt noncoding RNAs, assemble into RNA-induced silencing complexes (RISCs) and localize to cytoplasmic substructures called P bodies. Dictated by base-pair complementarity between miRNA and a target mRNA, miRNAs specifically repress posttranscriptional expression of several mRNAs. Here we report that HIV-1 mRNA interacts with RISC proteins and that disrupting P body structures enhances viral production and infectivity. In HIV-1-infected human T lymphocytes, we identified a highly abundant miRNA, miR-29a, which specifically targets the HIV-1 3’UTR region. Inhibiting miR-29a enhanced HIV-1 viral production and infectivity, whereas expressing a miR-29 mimic suppressed viral replication. We also found that specific miR-29a-HIV-1 mRNA interactions enhance viral mRNA association with RISC and P body proteins. Thus we provide an example of a single host miRNA regulating HIV-1 production and infectivity. These studies highlight the significance of miRNAs and P bodies in modulating host cell interactions with HIV-1 and possibly other viruses.}, pmid = {19560422}, keywords = {Base Sequence,Binding Sites,Cytoplasmic Structures,Cytoplasmic Structures: physiology,DEAD-box RNA Helicases,DEAD-box RNA Helicases: genetics,DEAD-box RNA Helicases: metabolism,HIV-1,HIV-1: genetics,HIV-1: metabolism,HIV-1: pathogenicity,Humans,Messenger,Messenger: chemistry,Messenger: physiology,MicroRNAs,MicroRNAs: genetics,MicroRNAs: metabolism,MicroRNAs: physiology,Molecular Sequence Data,nosource,Proto-Oncogene Proteins,Proto-Oncogene Proteins: genetics,Proto-Oncogene Proteins: metabolism,Ribonuclease III,Ribonuclease III: antagonists & inhibitors,RNA,RNA-Induced Silencing Complex,RNA-Induced Silencing Complex: metabolism,T-Lymphocytes,T-Lymphocytes: virology,Viral,Viral: chemistry,Viral: physiology,Virus Replication} }

@article{henkeMicroRNA122StimulatesTranslation2008, title = {{{microRNA-122}} Stimulates Translation of Hepatitis {{C}} Virus {{RNA}}.}, author = {Henke, Jura Inga and Goergen, Dagmar and Zheng, Junfeng and Song, Yutong and Sch{"u}ttler, Christian G. and Fehr, Carmen and J{"u}nemann, Christiane and Niepmann, Michael}, year = 2008, month = dec, journal = {The EMBO Journal}, volume = {27}, number = {24}, pages = {3300–3310}, issn = {1460-2075}, doi = {10.1038/emboj.2008.244}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2586803&tool=pmcentrez&rendertype=abstract}, abstract = {Hepatitis C virus (HCV) is a positive strand RNA virus that propagates primarily in the liver. We show here that the liver-specific microRNA-122 (miR-122), a member of a class of small cellular RNAs that mediate post-transcriptional gene regulation usually by repressing the translation of mRNAs through interaction with their 3’-untranslated regions (UTRs), stimulates the translation of HCV. Sequestration of miR-122 in liver cell lines strongly reduces HCV translation, whereas addition of miR-122 stimulates HCV translation in liver cell lines as well as in the non-liver HeLa cells and in rabbit reticulocyte lysate. The stimulation is conferred by direct interaction of miR-122 with two target sites in the 5’-UTR of the HCV genome. With a replication-defective NS5B polymerase mutant genome, we show that the translation stimulation is independent of viral RNA synthesis. miR-122 stimulates HCV translation by enhancing the association of ribosomes with the viral RNA at an early initiation stage. In conclusion, the liver-specific miR-122 may contribute to HCV liver tropism at the level of translation.}, pmid = {19020517}, keywords = {Cell Line,Hepacivirus,Hepacivirus: physiology,Humans,Messenger,Messenger: metabolism,MicroRNAs,MicroRNAs: metabolism,nosource,Protein Biosynthesis,Ribosomes,Ribosomes: metabolism,RNA,Viral,Viral Proteins,Viral Proteins: biosynthesis,Viral: metabolism} }

@article{baoMicroRNABindingSites2004, title = {{{MicroRNA}} Binding Sites in {{Arabidopsis}} Class {{III HD-ZIP mRNAs}} Are Required for Methylation of the Template Chromosome.}, author = {Bao, Ning and Lye, Khar-Wai and Barton, M. Kathryn}, year = 2004, month = nov, journal = {Developmental Cell}, volume = {7}, number = {5}, eprint = {15525527}, eprinttype = {pubmed}, pages = {653–662}, issn = {1534-5807}, doi = {10.1016/j.devcel.2004.10.003}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15525527}, abstract = {Dominant mutations in the Arabidopsis PHABULOSA (PHB) and PHAVOLUTA (PHV) transcription factor genes cause transformation of abaxial to adaxial leaf fates by altering a microRNA complementary site present in processed PHB and PHV mRNAs but not in the corresponding genomic DNA. phb-1d mutants accumulate excess PHB transcript throughout the leaf primordium, indicating defective regulation of PHB transcript synthesis and/or stability. We show that PHB and PHV coding sequences are heavily methylated downstream of the microRNA complementary site in most wild-type plant cells and that methylation is reduced in phb-1d and phv-1d mutants. Decreased methylation is limited to the chromosome bearing the dominant mutant allele in phb-1d heterozygotes. Low levels of methylation are detected in wt PHB DNA isolated from undifferentiated tissues. These results suggest a model in which the microRNA interacts with nascent, newly processed PHB mRNA to alter chromatin of the corresponding PHB template DNA predominantly in differentiated cells.}, pmid = {15525527}, keywords = {Alleles,Arabidopsis,Arabidopsis Proteins,Arabidopsis Proteins: chemistry,Arabidopsis Proteins: genetics,Arabidopsis Proteins: metabolism,Arabidopsis: genetics,Arabidopsis: growth & development,Arabidopsis: metabolism,Base Sequence,Binding Sites,Biological,Chromosome Mapping,Chromosomes,CpG Islands,DNA,DNA Methylation,Dominant,Exons,Genes,Genetic,Heterozygote,Messenger,Messenger: classification,Messenger: metabolism,MicroRNAs,MicroRNAs: chemistry,MicroRNAs: metabolism,Models,Molecular Sequence Data,Mutation,nosource,Nucleic Acid,Plant,Plant: chemistry,Plant: drug effects,Plant: isolation & purification,Plant: metabolism,RNA,Sequence Homology,Sulfites,Sulfites: toxicity,Templates,Transcription Factors,Transcription Factors: genetics} }

@article{kloostermanDiverseFunctionsMicroRNAs2006, title = {The Diverse Functions of {{microRNAs}} in Animal Development and Disease.}, author = {Kloosterman, Wigard P. and Plasterk, Ronald H.}, year = 2006, month = oct, journal = {Developmental Cell}, volume = {11}, number = {4}, eprint = {17011485}, eprinttype = {pubmed}, pages = {441–450}, issn = {1534-5807}, doi = {10.1016/j.devcel.2006.09.009}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17011485}, abstract = {MicroRNAs (miRNAs) control gene expression by translational inhibition and destabilization of mRNAs. While hundreds of miRNAs have been found, only a few have been studied in detail. miRNAs have been implicated in tissue morphogenesis, cellular processes like apoptosis, and major signaling pathways. Emerging evidence suggests a direct link between miRNAs and disease, and miRNA expression signatures are associated with various types of cancer. In addition, the gain and loss of miRNA target sites appears to be causal to some genetic disorders. Here, we discuss the current literature on the role of miRNAs in animal development and disease.}, pmid = {17011485}, keywords = {Animal Diseases,Animal Diseases: physiopathology,Animals,Biological,Embryology,MicroRNAs,MicroRNAs: genetics,MicroRNAs: physiology,Models,nosource} }

@article{bushatiMicroRNAFunctions2007, title = {{{microRNA}} Functions.}, author = {Bushati, Natascha and Cohen, Stephen M.}, year = 2007, month = jan, journal = {Annual Review of Cell and Developmental Biology}, volume = {23}, eprint = {17506695}, eprinttype = {pubmed}, pages = {175–205}, issn = {1081-0706}, doi = {10.1146/annurev.cellbio.23.090506.123406}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17506695}, abstract = {microRNAs (miRNAs) are small noncoding RNAs that play important roles in posttranscriptional gene regulation. In animal cells, miRNAs regulate their targets by translational inhibition and mRNA destabilization. Here, we review recent work in animal models that provide insight into the diverse roles of miRNAs in vivo.}, pmid = {17506695}, keywords = {Animals,Gene Expression Regulation,Genetic Diseases,Humans,Inborn,Inborn: genetics,MicroRNAs,MicroRNAs: chemistry,MicroRNAs: metabolism,MicroRNAs: physiology,nosource} }

@article{lundNuclearExportMicroRNA2004, title = {Nuclear Export of {{microRNA}} Precursors}, author = {Lund, Elsebet and G{"u}ttinger, Stephan and Calado, Angelo and Dahlberg, JE James E. and Kutay, Ulrike}, year = 2004, month = jan, journal = {Science}, volume = {95}, number = {2004}, pages = {95–8}, issn = {1095-9203}, doi = {10.1126/science.1090599}, url = {http://www.sciencemag.org/content/303/5654/95.short http://www.ncbi.nlm.nih.gov/pubmed/14631048}, abstract = {MicroRNAs (miRNAs), which function as regulators of gene expression in eukaryotes, are processed from larger transcripts by sequential action of nuclear and cytoplasmic ribonuclease III-like endonucleases. We show that Exportin-5 (Exp5) mediates efficient nuclear export of short miRNA precursors (pre-miRNAs) and that its depletion by RNA interference results in reduced miRNA levels. Exp5 binds correctly processed pre-miRNAs directly and specifically, in a Ran guanosine triphosphate-dependent manner, but interacts only weakly with extended pre-miRNAs that yield incorrect miRNAs when processed by Dicer in vitro. Thus, Exp5 is key to miRNA biogenesis and may help coordinate nuclear and cytoplasmic processing steps.}, pmid = {14631048}, keywords = {Active Transport,Animals,Carrier Proteins,Carrier Proteins: metabolism,Cell Nucleus,Cell Nucleus: metabolism,Cytoplasm,Cytoplasm: metabolism,Cytoplasmic and Nuclear,Guanosine Triphosphate,Guanosine Triphosphate: metabolism,Hela Cells,Humans,Karyopherins,Karyopherins: metabolism,MicroRNAs,MicroRNAs: chemistry,MicroRNAs: metabolism,nosource,Nucleocytoplasmic Transport Proteins,Oocytes,ran GTP-Binding Protein,ran GTP-Binding Protein: metabolism,Receptors,Recombinant Proteins,Recombinant Proteins: metabolism,Ribonuclease III,Ribonuclease III: metabolism,RNA,RNA Interference,RNA Precursors,RNA Precursors: metabolism,Small Interfering,Small Interfering: metabolism,Xenopus} }

@article{yamazakiProteinSynthesisInhibitors2008, title = {Protein Synthesis Inhibitors Enhance the Expression of {{mRNAs}} for Early Inducible Inflammatory Genes via {{mRNA}} Stabilization.}, author = {Yamazaki, Soh and Takeshige, Koichiro}, year = 2008, month = feb, journal = {Biochimica et Biophysica Acta}, volume = {1779}, number = {2}, eprint = {18068134}, eprinttype = {pubmed}, pages = {108–114}, issn = {0006-3002}, doi = {10.1016/j.bbagrm.2007.11.001}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18068134}, abstract = {Expression of inflammatory genes is regulated at multiple steps, including transcriptional activation and mRNA stabilization. During an investigation into the requirement of de novo protein synthesis for the induction of inflammatory genes, it was revealed that protein synthesis inhibitors unexpectedly potentiated the induction of mRNAs for primary response genes, while the inhibitors suppressed the induction of secondary inducible genes as previously described. Stimulus-induced nuclear translocation and promoter recruitment of NF-kappaB, which is responsible for the transcriptional activation of many inflammatory genes, were largely unaffected by the inhibitors. Instead, these inhibitors prolonged the half-lives of all of the primary inducible mRNAs tested. Thus, these findings emphasize the important contribution of regulated mRNA longevity to gene expression induced by pro-inflammatory stimulation.}, pmid = {18068134}, keywords = {Active Transport,Animals,Anisomycin,Anisomycin: pharmacology,Cell Line,Cell Nucleus,Cell Nucleus: drug effects,Cycloheximide,Cycloheximide: pharmacology,Cytokines,Cytokines: genetics,Gene Expression Regulation,Gene Expression Regulation: drug effects,Genetic,Half-Life,Inflammation,Inflammation: genetics,Lipopolysaccharides,Lipopolysaccharides: pharmacology,Messenger,Messenger: metabolism,Mice,NF-kappa B,NF-kappa B: metabolism,nosource,Promoter Regions,Protein Synthesis Inhibitors,Protein Synthesis Inhibitors: pharmacology,RNA,RNA Stability,RNA Stability: drug effects} }

@article{keRapidEfficientSitedirected1997, title = {Rapid and Efficient Site-Directed Mutagenesis by Single-Tube ‘megaprimer’ {{PCR}} Method.}, author = {Ke, S. H. and Madison, E. L.}, year = 1997, month = aug, journal = {Nucleic acids research}, volume = {25}, number = {16}, pages = {3371–2}, issn = {0305-1048}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=146891&tool=pmcentrez&rendertype=abstract}, abstract = {We describe a rapid and efficient megaprimer PCR procedure for site-directed mutagenesis that does not require any intermediate purification of DNA between the two rounds of PCR. This protocol is based on the design of forward and reverse flanking primers with significantly different melting temperatures ( T m). A megaprimer is synthesized in the first PCR reaction using a mutagenic primer, the low T m flanking primer and a low annealing temperature. The second PCR reaction is performed in the same tube as the first PCR and utilizes the high T m flanking primer, the megaprimer product of the first PCR and a high annealing temperature, which prevents priming by the low T m primer from the first PCR reaction. We have used this protocol with two different plasmids to produce cDNAs encoding seven distinct mutated proteins. We have observed an average mutagenesis efficiency of 82% in these experiments.}, pmid = {9241254}, keywords = {Genetic Engineering,Genetic Engineering: methods,Mutagenesis,nosource,Polymerase Chain Reaction,Polymerase Chain Reaction: methods,Site-Directed,Tissue Plasminogen Activator,Tissue Plasminogen Activator: genetics} }

@article{sheetsHistoryCharacterizationVero2000, title = {History and Characterization of the {{Vero Cell Line}}}, author = {Sheets, Rebecca}, year = 2000, journal = {the Vaccine and Related Biological Product Advisory }, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:History+and+Characterization+of+the+Vero+Cell+Line#0}, keywords = {nosource} }

@article{gossenTightControlGene1992, title = {Tight Control of Gene Expression in Mammalian Cells by Tetracycline-Responsive Promoters.}, author = {Gossen, M. and Bujard, H.}, year = 1992, month = jun, journal = {Proceedings of the National Academy of Sciences}, volume = {89}, number = {12}, pages = {5547–5551}, issn = {0027-8424}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=49329&tool=pmcentrez&rendertype=abstract}, abstract = {Control elements of the tetracycline-resistance operon encoded in Tn10 of Escherichia coli have been utilized to establish a highly efficient regulatory system in mammalian cells. By fusing the tet repressor with the activating domain of virion protein 16 of herpes simplex virus, a tetracycline-controlled transactivator (tTA) was generated that is constitutively expressed in HeLa cells. This transactivator stimulates transcription from a minimal promoter sequence derived from the human cytomegalovirus promoter IE combined with tet operator sequences. Upon integration of a luciferase gene controlled by a tTA-dependent promoter into a tTA-producing HeLa cell line, high levels of luciferase expression were monitored. These activities are sensitive to tetracycline. Depending on the concentration of the antibiotic in the culture medium (0-1 microgram/ml), the luciferase activity can be regulated over up to five orders of magnitude. Thus, the system not only allows differential control of the activity of an individual gene in mammalian cells but also is suitable for creation of “on/off” situations for such genes in a reversible way.}, pmid = {1319065}, keywords = {Bacterial Proteins,Bacterial Proteins: metabolism,Base Sequence,Escherichia coli,Escherichia coli: genetics,Gene Expression,Gene Expression: drug effects,Genetic,Genetic: drug effects,HeLa Cells,Humans,Kinetics,Luciferases,Luciferases: genetics,Luciferases: metabolism,Molecular Sequence Data,nosource,Operon,Promoter Regions,Recombinant Fusion Proteins,Recombinant Fusion Proteins: metabolism,Repressor Proteins,Repressor Proteins: genetics,Repressor Proteins: metabolism,Restriction Mapping,Simplexvirus,Simplexvirus: genetics,Tet-Off,Tetracycline,Tetracycline Resistance,Tetracycline Resistance: genetics,Tetracycline: pharmacology,Trans-Activators,Trans-Activators: metabolism,Transcription,Transcriptional Activation,Transfection} }

@article{plattEffectsCCR5CD41998, title = {Effects of {{CCR5}} and {{CD4}} Cell Surface Concentrations on Infections by Macrophagetropic Isolates of Human Immunodeficiency Virus Type 1}, author = {Platt, E. J. and Wehrly, Kathy and Kuhmann, S. E.}, year = 1998, journal = {Journal of Virology}, volume = {72}, number = {4}, pages = {2855}, publisher = {Am Soc Microbiol}, url = {http://jvi.asm.org/cgi/content/abstract/72/4/2855}, keywords = {nosource} }

@article{kallalFunctionalAnalysisSporulationspecific1990, title = {Functional Analysis of the Sporulation-Specific {{SPR6}} Gene of {{Saccharomyces}} Cerevisiae.}, author = {{}a Kallal, L. and Bhattacharyya, M. and Grove, S. N. and Iannacone, R. F. and {}a Pugh, T. and {}a Primerano, D. and Clancy, M. J.}, year = 1990, month = nov, journal = {Current Genetics}, volume = {18}, number = {4}, eprint = {2253272}, eprinttype = {pubmed}, pages = {293–301}, issn = {0172-8083}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2253272}, abstract = {The SPR6 gene of Saccharomyces cerevisiae encodes a moderately abundant RNA that is present at high levels only during sporulation. The gene contains a long open reading frame that could encode a hydrophilic protein approximately 21 kDa in size. This protein is probably produced by the yeast, because the lacZ gene of Escherichia coli is expressed during sporulation when fused to SPR6 in the expected reading frame. SPR6 is inessential for sporulation; mutants that lack SPR6 activity sporulate normally and produce viable ascospores. Nonetheless, the SPR6 gene encodes a function that is relevant to sporulating cells; the wild-type allele can enhance sporulation in strains that are defective for several SPR functions. SPR6 is located on chromosome V, 14.4 centimorgans centromere-distal to MET6.}, pmid = {2253272}, keywords = {Base Sequence,Chromosome Mapping,DNA,Fungal,Fungal: analysis,Fungal: physiology,Genes,Genetic,Genetic Complementation Test,Molecular Sequence Data,nosource,Open Reading Frames,Protein Biosynthesis,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Spores,Transcription} }

@article{watanabeComprehensiveQuantitativeAnalysis2009, title = {Comprehensive and Quantitative Analysis of Yeast Deletion Mutants Defective in Apical and Isotropic Bud Growth.}, author = {Watanabe, Machika and Watanabe, Daisuke and Nogami, Satoru and Morishita, Shinichi and Ohya, Yoshikazu}, year = 2009, month = aug, journal = {Current Genetics}, volume = {55}, number = {4}, eprint = {19466415}, eprinttype = {pubmed}, pages = {365–380}, issn = {1432-0983}, doi = {10.1007/s00294-009-0251-0}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19466415}, abstract = {To obtain a comprehensive understanding of the budding phase transition, 4,711 Saccharomyces cerevisiae haploid nonessential gene deletion mutants were screened with the image processing program CalMorph, and 35 mutants with a round bud and 173 mutants with an elongated bud were statistically identified. We classified round and elongated bud mutants based on factors thought to affect the duration of the apical bud growth phase. Two round bud mutants (arc18 and sac6) were found to be defective in apical actin patch localization. Several elongated bud mutants demonstrated a delay of cell cycle progression at the apical growth phase, suggesting that these mutants have a defect in the control of cell cycle progression.}, isbn = {0029400902}, pmid = {19466415}, keywords = {Actins,Actins: metabolism,Calcium-Binding Proteins,Calcium-Binding Proteins: genetics,Calcium-Binding Proteins: metabolism,Cell Polarity,Cell Polarity: genetics,Fungal,Gene Deletion,Gene Expression,Genes,Haploidy,Membrane Glycoproteins,Membrane Glycoproteins: genetics,Membrane Glycoproteins: metabolism,Microfilament Proteins,Microfilament Proteins: genetics,Microfilament Proteins: metabolism,nosource,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: cytology,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: growth & development} }

@book{atkinsRecodingExpansionDecoding2010, title = {Recoding: Expansion of Decoding Rules Enriches Gene Expression}, author = {Atkins, J. F. and Gesteland, R. F. and Dinman, Jonathan D. and Connor, Michael O. and Farabaugh, Philip J.}, editor = {Atkins, John F. and Gesteland, Raymond F.}, year = 2010, journal = {Nucleic Acids and Molecular Biology}, volume = {24}, publisher = {Springer New York}, doi = {10.1007/978-0-387-89382-2}, url = {http://link.springer.com/10.1007/978-0-387-89382-2 http://www.springerlink.com/index/10.1007/978-0-387-89382-2}, isbn = {978-0-387-89382-2}, keywords = {nosource} } % == BibTeX quality report for atkinsRecodingExpansionDecoding2010: % ? unused Number of pages (“221-247”)

@article{grandinCdc13CooperatesYeast2000, title = {Cdc13 Cooperates with the Yeast {{Ku}} Proteins and {{Stn1}} to Regulate Telomerase Recruitment}, author = {Grandin, Nathalie and Damon, Christelle and Charbonneau, Michel}, year = 2000, journal = {Molecular and Cellular Biology}, volume = {20}, number = {22}, pages = {8397}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.20.22.8397-8408.2000.Updated}, url = {http://mcb.asm.org/cgi/content/abstract/20/22/8397 http://mcb.asm.org/content/20/22/8397.short}, keywords = {nosource} }

@article{koeringIdentificationHighAffinity2000, title = {Identification of High Affinity {{Tbf1p-binding}} Sites within the Budding Yeast Genome}, author = {Koering, C. E. and Fourel, G. and {Binet-Brasselet} and Laroche, T. and Klein, F. and Gilson, E.}, year = 2000, month = jul, journal = {Nucleic Acids Research}, volume = {28}, number = {13}, pages = {2519–2526}, publisher = {Oxford Univ Press}, issn = {1362-4962}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=102697&tool=pmcentrez&rendertype=abstract http://nar.oxfordjournals.org/content/28/13/2519.short}, abstract = {The yeast TBF1 gene is essential for mitotic growth and encodes a protein that binds the human telomere repeats in vitro, although its cellular function is unknown. The sequence of the DNA-binding domain of Tbf1p is more closely related to that of the human telomeric proteins TRF1 and TRF2 than to any yeast protein sequence, yet the functional homologue of TRF1 and TRF2 is thought to be Rap1p. In this study we show that the Tbf1p DNA-binding domain can target the Gal4 transactivation domain to a (TTAGGG)(n) sequence inserted in the yeast genome, supporting the model that Tbf1p binds this sub-telomeric repeat motif in vivo. Immunofluorescence of Tbf1p shows a spotty pattern throughout the interphase nucleus and along synapsed chromosomes in meiosis, suggesting that Tbf1p binds internal chromosomal sites in addition to sub-telomeric regions. PCR-assisted binding site selection was used to define a consensus for high affinity Tbf1p-binding sites. Compilation of 50 selected oligonucleotides identified the consensus TAGGGTTGG. Five potential Tbf1p-binding sites resulting from a search of the total yeast genome were tested directly in gel shift assays and shown to bind Tbf1p efficiently in vitro, thus confirming this as a valid consensus for Tbf1p recognition.}, pmid = {10871401}, keywords = {Base Sequence,Binding Sites,Cell Nucleus,Cell Nucleus: genetics,Cell Nucleus: metabolism,Chromosomes,Consensus Sequence,Consensus Sequence: genetics,DNA,DNA-Binding Proteins,DNA-Binding Proteins: genetics,DNA-Binding Proteins: metabolism,Fluorescent Antibody Technique,Fungal,Fungal Proteins,Fungal Proteins: genetics,Fungal Proteins: metabolism,Fungal: genetics,Fungal: metabolism,Genome,Interphase,Interphase: genetics,Meiosis,Meiosis: genetics,nosource,Polymerase Chain Reaction,Protein Binding,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae: cytology,Saccharomyces cerevisiae: genetics,Substrate Specificity,Telomere,Telomere: genetics,Transcription Factors,Two-Hybrid System Techniques} }

@article{olsthoornFunctionalAnalysisSRV2010, title = {Functional Analysis of the {{SRV}} -1 {{RNA}} Frameshifting Pseudoknot}, author = {Olsthoorn, RCL C. L. and Reumerman, Richard}, year = 2010, month = nov, journal = {Nucleic Acids Research}, volume = {38}, number = {21}, pages = {7665–72}, issn = {1362-4962}, doi = {10.1093/nar/gkq629}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2995055&tool=pmcentrez&rendertype=abstract http://nar.oxfordjournals.org/content/38/21/7665.short}, abstract = {Simian retrovirus type-1 uses programmed ribosomal frameshifting to control expression of the Gag-Pol polyprotein from overlapping gag and pol open-reading frames. The frameshifting signal consists of a heptanucleotide slippery sequence and a downstream-located 12-base pair pseudoknot. The solution structure of this pseudoknot, previously solved by NMR [Michiels,P.J., Versleijen,A.A., Verlaan,P.W., Pleij,C.W., Hilbers,C.W. and Heus,H.A. (2001) Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting. J. Mol. Biol., 310, 1109-1123] has a classical H-type fold and forms an extended triple helix by interactions between loop 2 and the minor groove of stem 1 involving base-base and base-sugar contacts. A mutational analysis was performed to test the functional importance of the triple helix for -1 frameshifting in vitro. Changing bases in L2 or base pairs in S1 involved in a base triple resulted in a 2- to 5-fold decrease in frameshifting efficiency. Alterations in the length of L2 had adverse effects on frameshifting. The in vitro effects were well reproduced in vivo, although the effect of enlarging L2 was more dramatic in vivo. The putative role of refolding kinetics of frameshifter pseudoknots is discussed. Overall, the data emphasize the role of the triple helix in -1 frameshifting.}, pmid = {20639537}, keywords = {Frameshifting,Gene Expression Regulation,Mason-Pfizer monkey virus,Mason-Pfizer monkey virus: genetics,Mutation,nosource,Nucleic Acid Conformation,Regulatory Sequences,Ribonucleic Acid,Ribosomal,RNA,Viral,Viral: chemistry} }

@article{chouStimulation1Programmed2010, title = {Stimulation of -1 Programmed Ribosomal Frameshifting by a Metabolite-Responsive {{RNA}} Pseudoknot}, author = {Chou, MY Y. and Lin, SC C.}, year = 2010, month = jun, journal = {RNA}, volume = {16}, number = {6}, pages = {1236–1244}, issn = {1469-9001}, doi = {10.1261/rna.1922410}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2874175&tool=pmcentrez&rendertype=abstract http://rnajournal.cshlp.org/content/16/6/1236.short}, abstract = {Specific recognition of metabolites by functional RNA motifs within mRNAs has emerged as a crucial regulatory strategy for feedback control of biochemical reactions. Such riboswitches have been demonstrated to regulate different gene expression processes, including transcriptional termination and translational initiation in prokaryotic cells, as well as splicing in eukaryotic cells. The regulatory process is usually mediated by modulating the accessibility of specific sequence information of the expression platforms via metabolite-induced RNA conformational rearrangement. In eukaryotic systems, viral and the more limited number of cellular decoding -1 programmed ribosomal frameshifting (PRF) are commonly promoted by a 3’ mRNA pseudoknot. In addition, such -1 PRF is generally constitutive rather than being regulatory, and usually results in a fixed ratio of products. We report here an RNA pseudoknot capable of stimulating -1 PRF whose efficiency can be tuned in response to the concentration of S-adenosylhomocysteine (SAH), and the improvement of its frameshifting efficiency by RNA engineering. In addition to providing an alternative approach for small-molecule regulation of gene expression in eukaryotic cells, such a metabolite-responsive pseudoknot suggests a plausible mechanism for metabolite-driven translational regulation of gene expression in eukaryotic systems.}, pmid = {20435898}, keywords = {Adenosylhomocysteinase,Adenosylhomocysteinase: metabolism,Base Sequence,Catalytic,Catalytic: genetics,Cell Culture Techniques,Cell Line,Frameshifting,Gene Expression,Genetic,HIV-1,HIV-1: genetics,Humans,Kidney,Kidney: embryology,Luciferases,Luciferases: metabolism,Messenger,Messenger: chemistry,Messenger: genetics,Messenger: metabolism,Models,Molecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Protein Biosynthesis,Ribosomal,RNA,RNA: chemistry,RNA: genetics,RNA: metabolism,Transcription} }

@article{iskenQualityControlEukaryotic2007, title = {Quality Control of Eukaryotic {{mRNA}}: Safeguarding Cells from Abnormal {{mRNA}} Function}, author = {Isken, Olaf and Maquat, Lynne E. LE}, year = 2007, month = aug, journal = {Genes & development}, volume = {21}, number = {15}, eprint = {17671086}, eprinttype = {pubmed}, pages = {1833–56}, issn = {0890-9369}, doi = {10.1101/gad.1566807}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17671086 http://genesdev.cshlp.org/content/21/15/1833.short}, abstract = {Cells routinely make mistakes. Some mistakes are encoded by the genome and may manifest as inherited or acquired diseases. Other mistakes occur because metabolic processes can be intrinsically inefficient or inaccurate. Consequently, cells have developed mechanisms to minimize the damage that would result if mistakes went unchecked. Here, we provide an overview of three quality control mechanisms–nonsense-mediated mRNA decay, nonstop mRNA decay, and no-go mRNA decay. Each surveys mRNAs during translation and degrades those mRNAs that direct aberrant protein synthesis. Along with other types of quality control that occur during the complex processes of mRNA biogenesis, these mRNA surveillance mechanisms help to ensure the integrity of protein-encoding gene expression.}, pmid = {17671086}, keywords = {Alternative Splicing,Animals,Codon,Eukaryotic Cells,Evolution,Gene Expression,Gene Silencing,Genetic,Humans,Mammals,Mammals: genetics,Mammals: metabolism,Messenger,Messenger: genetics,Messenger: metabolism,Models,Molecular,Mutation,Nonsense,nosource,Peptide Chain Elongation,Protein Biosynthesis,RNA,RNA Stability,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Terminator,Translational} }

@article{gruberViennaRNAWebsuite2008, title = {The {{Vienna RNA}} Websuite.}, author = {Gruber, Andreas R. and Lorenz, Ronny and Bernhart, Stephan H. and Neub{"o}ck, Richard and Hofacker, Ivo L.}, year = 2008, month = jul, journal = {Nucleic Acids Research}, volume = {36}, number = {Web Server issue}, pages = {W70-4}, issn = {1362-4962}, doi = {10.1093/nar/gkn188}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2447809&tool=pmcentrez&rendertype=abstract}, abstract = {The Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. It provides a web interface to the most commonly used programs of the Vienna RNA package. Among them, we find folding of single and aligned sequences, prediction of RNA-RNA interactions, and design of sequences with a given structure. Additionally, we provide analysis of folding landscapes using the barriers program and structural RNA alignments using LocARNA. The web server together with software packages for download is freely accessible at http://rna.tbi.univie.ac.at/.}, pmid = {18424795}, keywords = {Internet,nosource,Nucleic Acid Conformation,RNA,RNA: chemistry,Sequence Alignment,Sequence Analysis,Software} }

@article{clelandPartitionAnalysisConcept1975, title = {Partition Analysis and Concept of Net Rate Constants as Tools in Enzyme Kinetics}, author = {Cleland, W. W.}, year = 1975, month = jul, journal = {Biochemistry}, volume = {14}, number = {14}, eprint = {1148201}, eprinttype = {pubmed}, pages = {3220–3224}, publisher = {ACS Publications}, issn = {0006-2960}, doi = {10.1021/bi00685a029}, url = {http://www.ncbi.nlm.nih.gov/pubmed/1148201 http://pubs.acs.org/doi/abs/10.1021/bi00685a029}, pmid = {1148201}, keywords = {Enzymes,Enzymes: metabolism,Isotope Labeling,Kinetics,Mathematics,Methods,nosource,Time Factors} }

@article{brunellePeptideReleaseRibosome2008, title = {Peptide Release on the Ribosome Depends Critically on the 2’ {{OH}} of the Peptidyl-{{tRNA}} Substrate.}, author = {Brunelle, JL Julie L. and Shaw, JJ Jeffrey J. and Youngman, Elaine M. EM and Green, Rachel}, year = 2008, month = aug, journal = {RNA}, volume = {14}, number = {8}, pages = {1526–1531}, issn = {1469-9001}, doi = {10.1261/rna.1057908}, url = {http://rnajournal.cshlp.org/content/14/8/1526.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2491474&tool=pmcentrez&rendertype=abstract}, abstract = {Peptide release on the ribosome is catalyzed by protein release factors (RFs) on recognition of stop codons positioned in the A site of the small ribosomal subunit. Here we show that the 2’ OH of the peptidyl-tRNA substrate plays an essential role in catalysis of the peptide release reaction. These observations parallel earlier studies of the mechanism of the peptidyl transfer reaction and argue that related mechanisms are at the heart of catalysis for these reactions.}, pmid = {18567817}, keywords = {Amino Acyl,Amino Acyl: chemistry,Amino Acyl: metabolism,Escherichia coli,Escherichia coli: genetics,Escherichia coli: metabolism,nosource,Peptide Chain Termination,Peptide Termination Factors,Peptide Termination Factors: metabolism,Peptides,Peptides: metabolism,Protein Biosynthesis,release factor,ribosome,Ribosomes,Ribosomes: metabolism,RNA,Transfer,translation termination,Translational} }

@article{cimminoMicroRNASignatureAssociated2005, title = {A {{MicroRNA}} Signature Associated with Prognosis and Progression in Chronic Lymphocytic Leukemia.}, author = {Cimmino, Amelia and Ph, D. and Leva, Gianpiero Di and Shimizu, Masayoshi and Wojcik, Sylwia E. and Sc, M. and Iorio, Marilena V. and Liu, Chang-gong and Kipps, Thomas J. and Calin, George Adrian and Ferracin, Manuela and Leva, Gianpiero Di and Visone, Rosa and Sever, Nurettin Ilfer and Fabbri, Muller and Iuliano, Rodolfo and Palumbo, Tiziana and Pichiorri, Flavia and Roldo, Claudia and Garzon, Ramiro and Sevignani, Cinzia and Rassenti, Laura and Alder, Hansjuerg and Volinia, Stefano and Negrini, Massimo and Croce, Carlo M.}, year = 2005, month = oct, journal = {The New England Journal of Medicine}, volume = {353}, number = {17}, eprint = {16251535}, eprinttype = {pubmed}, pages = {1793–1801}, issn = {1533-4406}, doi = {10.1056/NEJMoa050995}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16251535}, abstract = {MicroRNA expression profiles can be used to distinguish normal B cells from malignant B cells in patients with chronic lymphocytic leukemia (CLL). We investigated whether microRNA profiles are associated with known prognostic factors in CLL.}, pmid = {16251535}, keywords = {B-Cell,B-Cell: genetics,B-Cell: metabolism,Chronic,Disease Progression,DNA,Female,Gene Expression,Gene Expression Profiling,Gene Rearrangement,Genes,Germ-Line Mutation,Humans,Immunoglobulin,Immunoglobulin Heavy Chains,Immunoglobulin Heavy Chains: genetics,Immunoglobulin Heavy Chains: metabolism,Immunoglobulin Variable Region,Immunoglobulin Variable Region: genetics,Leukemia,Lymphocytic,Male,MicroRNAs,MicroRNAs: analysis,MicroRNAs: metabolism,Mutation,nosource,Oligonucleotide Array Sequence Analysis,Point Mutation,Prognosis,Protein-Tyrosine Kinases,Protein-Tyrosine Kinases: metabolism,Sequence Analysis,Tumor Suppressor,ZAP-70 Protein-Tyrosine Kinase} }

@article{enrightMicroRNATargetsDrosophila2003, title = {{{MicroRNA}} Targets in {{Drosophila}}.}, author = {Enright, Anton J. and John, Bino and Gaul, Ulrike and Tuschl, Thomas and Sander, Chris and Marks, Debora S.}, year = 2003, month = jan, journal = {Genome Biology}, volume = {5}, number = {1}, pages = {R1}, issn = {1465-6914}, doi = {10.1186/gb-2003-5-1-r1}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=395733&tool=pmcentrez&rendertype=abstract}, abstract = {The recent discoveries of microRNA (miRNA) genes and characterization of the first few target genes regulated by miRNAs in Caenorhabditis elegans and Drosophila melanogaster have set the stage for elucidation of a novel network of regulatory control. We present a computational method for whole-genome prediction of miRNA target genes. The method is validated using known examples. For each miRNA, target genes are selected on the basis of three properties: sequence complementarity using a position-weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Application to the D. melanogaster, Drosophila pseudoobscura and Anopheles gambiae genomes identifies several hundred target genes potentially regulated by one or more known miRNAs.}, pmid = {14709173}, keywords = {3’ Untranslated Regions,3’ Untranslated Regions: genetics,Animals,Computational Biology,Computational Biology: methods,Developmental,Developmental: genetic,Drosophila melanogaster,Drosophila melanogaster: embryology,Drosophila melanogaster: genetics,Ecdysone,Ecdysone: genetics,Gene Expression Regulation,Genes,Homeobox,Homeobox: genetics,Homeodomain Proteins,Homeodomain Proteins: genetics,Insect,Insect: genetics,MicroRNAs,MicroRNAs: genetics,Nervous System,Nervous System: chemistry,Nervous System: embryology,Nervous System: metabolism,nosource,Predictive Value of Tests,Signal Transduction,Signal Transduction: genetics} }

@article{tholstrupMRNAPseudoknotStructures2011, title = {{{mRNA}} Pseudoknot Structures Can Act as Ribosomal Roadblocks}, author = {Tholstrup, J. and Oddershede, L. B. and {}a Sorensen, M.}, year = 2011, month = sep, journal = {Nucleic Acids Research}, number = {2}, pages = {1–11}, issn = {0305-1048}, doi = {10.1093/nar/gkr686}, url = {http://www.nar.oxfordjournals.org/cgi/doi/10.1093/nar/gkr686}, keywords = {nosource} }

@article{feiTransferRNAMediated2011, title = {Transfer {{RNA}}–Mediated Regulation of Ribosome Dynamics during Protein Synthesis}, author = {Fei, Jingyi and Richard, Arianne C. and Bronson, Jonathan E. and Gonzalez, Ruben L.}, year = 2011, month = aug, journal = {Nature Structural & Molecular Biology}, volume = {18}, number = {9}, pages = {1043–1051}, publisher = {Nature Publishing Group}, issn = {1545-9993}, doi = {10.1038/nsmb.2098}, url = {http://www.nature.com/doifinder/10.1038/nsmb.2098}, keywords = {nosource} }

@article{brianiS1RibosomalProtein2011, title = {S1 Ribosomal Protein and the Interplay between Translation and {{mRNA}} Decay.}, author = {Briani, Federica and Delvillani, Francesco and Papiani, Giulia and Deho, Gianni and Deh{`o}, Gianni}, year = 2011, month = jun, journal = {Nucleic Acids Research}, eprint = {21685451}, eprinttype = {pubmed}, pages = {1–14}, issn = {1362-4962}, doi = {10.1093/nar/gkr417}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21685451}, abstract = {S1 is an ‘atypical’ ribosomal protein weakly associated with the 30S subunit that has been implicated in translation, transcription and control of RNA stability. S1 is thought to participate in translation initiation complex formation by assisting 30S positioning in the translation initiation region, but little is known about its role in other RNA transactions. In this work, we have analysed in vivo the effects of different intracellular S1 concentrations, from depletion to overexpression, on translation, decay and intracellular distribution of leadered and leaderless messenger RNAs (mRNAs). We show that the cspE mRNA, like the rpsO transcript, may be cleaved by RNase E at multiple sites, whereas the leaderless cspE transcript may also be degraded via an alternative pathway by an unknown endonuclease. Upon S1 overexpression, RNase E-dependent decay of both cspE and rpsO mRNAs is suppressed and these transcripts are stabilized, whereas cleavage of leaderless cspE mRNA by the unidentified endonuclease is not affected. Overall, our data suggest that ribosome-unbound S1 may inhibit translation and that part of the Escherichia coli ribosomes may actually lack S1.}, pmid = {21685451}, keywords = {nosource} }

@article{yuStimulationRibosomalFrameshifting2010, title = {Stimulation of Ribosomal Frameshifting by Antisense {{LNA}}.}, author = {Yu, Chien-hung and Noteborn, MHM Mathieu H. M. and Olsthoorn, RCL Ren{'e} C. L.}, year = 2010, month = dec, journal = {Nucleic acids research}, volume = {38}, number = {22}, pages = {8277–83}, issn = {1362-4962}, doi = {10.1093/nar/gkq650}, url = {http://nar.oxfordjournals.org/content/38/22/8277.short http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3001050&tool=pmcentrez&rendertype=abstract}, abstract = {Programmed ribosomal frameshifting is a translational recoding mechanism commonly used by RNA viruses to express two or more proteins from a single mRNA at a fixed ratio. An essential element in this process is the presence of an RNA secondary structure, such as a pseudoknot or a hairpin, located downstream of the slippery sequence. Here, we have tested the efficiency of RNA oligonucleotides annealing downstream of the slippery sequence to induce frameshifting in vitro. Maximal frameshifting was observed with oligonucleotides of 12-18 nt. Antisense oligonucleotides bearing locked nucleic acid (LNA) modifications also proved to be efficient frameshift-stimulators in contrast to DNA oligonucleotides. The number, sequence and location of LNA bases in an otherwise DNA oligonucleotide have to be carefully manipulated to obtain optimal levels of frameshifting. Our data favor a model in which RNA stability at the entrance of the ribosomal tunnel is the major determinant of stimulating slippage rather than a specific three-dimensional structure of the stimulating RNA element.}, pmid = {20693527}, keywords = {Antisense,Antisense: chemistry,Frameshifting,nosource,Oligodeoxyribonucleotides,Oligodeoxyribonucleotides: chemistry,Oligonucleotides,Oligonucleotides: chemistry,Ribosomal,Thermodynamics} }

@article{yuStemloopStructuresCan2011, title = {Stem-Loop Structures Can Effectively Substitute for an {{RNA}} Pseudoknot in -1 Ribosomal Frameshifting.}, author = {Yu, Chien-Hung and Noteborn, Mathieu H. and Pleij, Cornelis W. and Olsthoorn, Ren{'e} C. L.}, year = 2011, month = jul, journal = {Nucleic Acids Research}, eprint = {21803791}, eprinttype = {pubmed}, pages = {1–8}, issn = {1362-4962}, doi = {10.1093/nar/gkr579}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21803791}, abstract = {-1 Programmed ribosomal frameshifting (PRF) in synthesizing the gag-pro precursor polyprotein of Simian retrovirus type-1 (SRV-1) is stimulated by a classical H-type pseudoknot which forms an extended triple helix involving base-base and base-sugar interactions between loop and stem nucleotides. Recently, we showed that mutation of bases involved in triple helix formation affected frameshifting, again emphasizing the role of the triple helix in -1 PRF. Here, we investigated the efficiency of hairpins of similar base pair composition as the SRV-1 gag-pro pseudoknot. Although not capable of triple helix formation they proved worthy stimulators of frameshifting. Subsequent investigation of {\(\sim\)}30 different hairpin constructs revealed that next to thermodynamic stability, loop size and composition and stem irregularities can influence frameshifting. Interestingly, hairpins carrying the stable GAAA tetraloop were significantly less shifty than other hairpins, including those with a UUCG motif. The data are discussed in relation to natural shifty hairpins.}, pmid = {21803791}, keywords = {nosource} }

@article{hillerTwostepChemicalMechanism2011, title = {A Two-Step Chemical Mechanism for Ribosome-Catalysed Peptide Bond Formation.}, author = {{}a Hiller, David and Singh, Vipender and Zhong, Minghong and {}a Strobel, Scott}, year = 2011, month = jul, journal = {Nature}, eprint = {21765427}, eprinttype = {pubmed}, pages = {2–6}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/nature10248}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21765427}, abstract = {The chemical step of natural protein synthesis, peptide bond formation, is catalysed by the large subunit of the ribosome. Crystal structures have shown that the active site for peptide bond formation is composed entirely of RNA. Recent work has focused on how an RNA active site is able to catalyse this fundamental biological reaction at a suitable rate for protein synthesis. On the basis of the absence of important ribosomal functional groups , lack of a dependence on pH, and the dominant contribution of entropy to catalysis, it has been suggested that the role of the ribosome is limited to bringing the substrates into close proximity. Alternatively, the importance of the 2’-hydroxyl of the peptidyl-transfer RNA and a Brnsted coefficient near zero have been taken as evidence that the ribosome coordinates a proton-transfer network. Here we report the transition state of peptide bond formation, based on analysis of the kinetic isotope effect at five positions within the reaction centre of a peptidyl-transfer RNA mimic. Our results indicate that in contrast to the uncatalysed reaction, formation of the tetrahedral intermediate and proton transfer from the nucleophilic nitrogen both occur in the rate-limiting step. Unlike in previous proposals, the reaction is not fully concerted; instead, breakdown of the tetrahedral intermediate occurs in a separate fast step. This suggests that in addition to substrate positioning, the ribosome is contributing to chemical catalysis by changing the rate-limiting transition state.}, pmid = {21765427}, keywords = {nosource} }

@article{lauStructureY14MagohCore2003, title = {Structure of the {{Y14-Magoh Core}} of the {{Exon Junction Complex}}}, author = {Lau, Chi-kong and Diem, Michael D. and Dreyfuss, Gideon and Duyne, Gregory D. Van}, year = 2003, journal = {Current Biology}, volume = {13}, pages = {933–941}, doi = {10.1016/S}, keywords = {nosource} } % == BibTeX quality report for lauStructureY14MagohCore2003: % ? Title looks like it was stored in title-case in Zotero

@article{kimY14ProteinCommunicates2001, title = {The {{Y14}} Protein Communicates to the Cytoplasm the Position of Exon-Exon Junctions.}, author = {Kim, V. N. and Yong, J. and Kataoka, N. and Abel, L. and Diem, M. D. and Dreyfuss, G.}, year = 2001, month = apr, journal = {The EMBO Journal}, volume = {20}, number = {8}, pages = {2062–2068}, issn = {0261-4189}, doi = {10.1093/emboj/20.8.2062}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=125236&tool=pmcentrez&rendertype=abstract}, abstract = {We recently described an RNA-binding protein, Y14, that binds preferentially to spliced mRNAs and persists in the cytoplasm. Y14 is part of a multi-protein complex that also contains the mRNA export factor TAP. This suggests that splicing imprints the mRNA with a unique set of proteins that communicate the history of the transcript to the cytoplasm. Here, using microinjection of pre-mRNAs into Xenopus oocyte nuclei followed by immunoprecipitation of RNase-fragmented mRNAs from the cytoplasm, we show that Y14 is stably bound to sequences immediately upstream of exon-exon junctions. This feature appears to be unique to Y14. Using monoclonal antibodies that we produced against Aly/REF, another component recently reported to be an mRNA export factor, we show that Aly/REF is associated with spliced mRNAs in the nucleus but is not detectable on mRNAs in the cytoplasm. Thus, we propose that the splicing- dependent binding of Y14 provides a position-specific molecular memory that communicates to the cytoplasm the location of exon and intron boundaries. This novel mechanism may play an important role in post-splicing events.}, pmid = {11296238}, keywords = {Active Transport,Binding Sites,Biological,Cell Nucleus,Cell Nucleus: metabolism,Cytoplasm,Cytoplasm: metabolism,Exons,Models,nosource,RNA Splicing,RNA-Binding Proteins,RNA-Binding Proteins: metabolism,Transcription Factors,Transcription Factors: metabolism} }

@article{quRibosomeUsesTwo2011, title = {The Ribosome Uses Two Active Mechanisms to Unwind Messenger {{RNA}} during Translation}, author = {Qu, Xiaohui and Wen, Jin-Der and Lancaster, Laura and Noller, Harry F. and Bustamante, Carlos and Tinoco, Ignacio}, year = 2011, month = jul, journal = {Nature}, volume = {475}, number = {7354}, pages = {118–121}, publisher = {Nature Publishing Group}, issn = {0028-0836}, doi = {10.1038/nature10126}, url = {http://www.nature.com/doifinder/10.1038/nature10126}, keywords = {nosource} }

@article{hirUPF3mediatedRegulatorySwitch2009, title = {A {{UPF3-mediated}} Regulatory Switch That Maintains {{RNA}} Surveillance.}, author = {Hir, Le and Nguyen, Lam Son and Huang, Lulu and Ge, Jozef and Chan, Wai-Kin and Bhalla, Angela D. and Wilkinson, Miles F. and Hir, Herv{'e} Le and G{'e}cz, Jozef}, year = 2009, month = jul, journal = {Nature Structural & Molecular Biology}, volume = {16}, number = {7}, eprint = {19503078}, eprinttype = {pubmed}, pages = {747–53}, issn = {1545-9985}, doi = {10.1038/nsmb.1612}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19503078}, abstract = {Nonsense-mediated decay (NMD) is an RNA decay pathway that downregulates aberrant mRNAs and a subset of normal mRNAs. The regulation of NMD is poorly understood. Here we identify a regulatory mechanism acting on two related UPF (up-frameshift) factors crucial for NMD: UPF3A and UPF3B. This regulatory mechanism, which reduces the level of UPF3A in response to the presence of UPF3B, is relieved in individuals harboring UPF3B mutations, leading to strongly increased steady-state levels of UPF3A. UPF3A compensates for the loss of UPF3B by regulating several NMD target transcripts, but it can also impair NMD, as it competes with the stronger NMD activator UPF3B for binding to the essential NMD factor UPF2. This deleterious effect of UPF3A protein is prevented by its destabilization using a conserved UPF3B-dependent mechanism. Together, our results suggest that UPF3A levels are tightly regulated by a post-transcriptional switch to maintain appropriate levels of NMD substrates in cells containing different levels of UPF3B.}, pmid = {19503078}, keywords = {Animals,Hela Cells,Humans,Messenger,Messenger: genetics,Messenger: metabolism,Mice,nosource,Protein Isoforms,Protein Isoforms: genetics,Protein Isoforms: metabolism,RNA,RNA Interference,RNA Stability,RNA-Binding Proteins,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism} }

@article{clericiUnusualBipartiteMode2009, title = {Unusual Bipartite Mode of Interaction between the Nonsense-Mediated Decay Factors, {{UPF1}} and {{UPF2}}.}, author = {Clerici, Marcello and Mour{~a}o, Andr{'e} and Gutsche, Irina and Gehring, Niels H. and Hentze, Matthias W. and Kulozik, Andreas and Kadlec, Jan and Sattler, Michael and Cusack, Stephen}, year = 2009, month = aug, journal = {The EMBO Journal}, volume = {28}, number = {15}, pages = {2293–306}, issn = {1460-2075}, doi = {10.1038/emboj.2009.175}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2726699&tool=pmcentrez&rendertype=abstract}, abstract = {Nonsense-mediated decay (NMD) is a eukaryotic quality control mechanism that degrades mRNAs carrying premature stop codons. In mammalian cells, NMD is triggered when UPF2 bound to UPF3 on a downstream exon junction complex interacts with UPF1 bound to a stalled ribosome. We report structural studies on the interaction between the C-terminal region of UPF2 and intact UPF1. Crystal structures, confirmed by EM and SAXS, show that the UPF1 CH-domain is docked onto its helicase domain in a fixed configuration. The C-terminal region of UPF2 is natively unfolded but binds through separated alpha-helical and beta-hairpin elements to the UPF1 CH-domain. The alpha-helical region binds sixfold more weakly than the beta-hairpin, whereas the combined elements bind 80-fold more tightly. Cellular assays show that NMD is severely affected by mutations disrupting the beta-hairpin binding, but not by those only affecting alpha-helix binding. We propose that the bipartite mode of UPF2 binding to UPF1 brings the ribosome and the EJC in close proximity by forming a tight complex after an initial weak encounter with either element.}, pmid = {19556969}, keywords = {Amino Acid Sequence,Biomolecular,Crystallography,DNA Mutational Analysis,Electron,Messenger,Messenger: metabolism,Microscopy,Missense,Molecular Sequence Data,Mutation,nosource,Nuclear Magnetic Resonance,Protein Binding,Protein Interaction Domains and Motifs,Protein Interaction Mapping,Protein Structure,Quaternary,RNA,RNA Stability,Scattering,Secondary,Sequence Alignment,Small Angle,Tertiary,Trans-Activators,Trans-Activators: chemistry,Trans-Activators: metabolism,Transcription Factors,Transcription Factors: chemistry,Transcription Factors: metabolism,X-Ray} }

@article{chengStructuralFunctionalInsights2007, title = {Structural and Functional Insights into the Human {{Upf1}} Helicase Core}, author = {Cheng, Zhihong and Muhlrad, Denise and Lim, MK Meng Kiat and Parker, Roy and Song, Haiwei}, year = 2007, month = jan, journal = {The EMBO }, volume = {26}, number = {1}, pages = {253–264}, issn = {0261-4189}, doi = {10.1038/sj.emboj.7601464}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1782376&tool=pmcentrez&rendertype=abstract http://onlinelibrary.wiley.com/doi/10.1038/sj.emboj.7601464/full}, abstract = {Nonsense-mediated mRNA decay (NMD) is an mRNA surveillance pathway that recognizes and degrades aberrant mRNAs containing premature stop codons. A critical protein in NMD is Upf1p, which belongs to the helicase super family 1 (SF1), and is thought to utilize the energy of ATP hydrolysis to promote transitions in the structure of RNA or RNA-protein complexes. The crystal structure of the catalytic core of human Upf1p determined in three states (phosphate-, AMPPNP- and ADP-bound forms) reveals an overall structure containing two RecA-like domains with two additional domains protruding from the N-terminal RecA-like domain. Structural comparison combined with mutational analysis identifies a likely single-stranded RNA (ssRNA)-binding channel, and a cycle of conformational change coupled to ATP binding and hydrolysis. These conformational changes alter the likely ssRNA-binding channel in a manner that can explain how ATP binding destabilizes ssRNA binding to Upf1p.}, pmid = {17159905}, keywords = {Adenosine Diphosphate,Adenosine Diphosphate: chemistry,Adenosine Triphosphate,Adenosine Triphosphate: chemistry,Allosteric Site,Binding Sites,Codon,Crystallography,Humans,Hydrolysis,Models,Molecular,Molecular Conformation,mrna decay,nonsense-mediated mrna decay,nosource,Nucleotides,Nucleotides: chemistry,Protein Binding,Protein Conformation,Protein Structure,rna helicase,Tertiary,Trans-Activators,Trans-Activators: chemistry,Trans-Activators: physiology,upf1,X-Ray,x-ray crystallography} }

@article{chamiehNMDFactorsUPF22008, title = {{{NMD}} Factors {{UPF2}} and {{UPF3}} Bridge {{UPF1}} to the Exon Junction Complex and Stimulate Its {{RNA}} Helicase Activity.}, author = {Chamieh, Hala and Ballut, Lionel and Bonneau, Fabien and Hir, Herv{'e} Le and Hir, Le}, year = 2008, month = jan, journal = {Nature Structural & Molecular Biology}, volume = {15}, number = {1}, eprint = {18066079}, eprinttype = {pubmed}, pages = {85–93}, issn = {1545-9985}, doi = {10.1038/nsmb1330}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18066079}, abstract = {Nonsense-mediated mRNA decay (NMD) eliminates mRNAs containing a premature translation termination codon through the recruitment of the conserved NMD factors UPF1, UPF2 and UPF3. In humans, a dynamic assembly pathway allows UPF1 to join UPF2 and UPF3 recruited to the mRNA by the exon-junction complex (EJC). Here we show that the recombinant EJC core is sufficient to reconstitute, with the three UPF proteins, a stable heptameric complex on RNA. The EJC proteins MAGOH, Y14 and eIF4AIII provide a composite binding site for UPF3b that serves as a bridge to UPF2 and UPF1. In the UPF trimeric complex, UPF2 and UPF3b cooperatively stimulate both ATPase and RNA helicase activities of UPF1. This work demonstrates that the EJC core is sufficient to stably anchor the UPF proteins to mRNA and provides insights into the regulation of its central effector, UPF1.}, pmid = {18066079}, keywords = {Binding Sites,Dimerization,Exons,Humans,Macromolecular Substances,Macromolecular Substances: chemistry,Macromolecular Substances: metabolism,nosource,Recombinant Proteins,Recombinant Proteins: chemistry,Recombinant Proteins: metabolism,RNA,RNA Helicases,RNA Helicases: chemistry,RNA Helicases: metabolism,RNA-Binding Proteins,RNA-Binding Proteins: chemistry,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism,RNA: chemistry,RNA: metabolism,Sequence Deletion,Trans-Activators,Trans-Activators: chemistry,Trans-Activators: genetics,Trans-Activators: metabolism,Transcription Factors,Transcription Factors: chemistry,Transcription Factors: genetics,Transcription Factors: metabolism} }

@article{silarHeatShockTranscription1991, title = {Heat Shock Transcription Factor Activates Transcription of the Yeast Metallothionein Gene.}, author = {Silar, P. and Butler, G. and Thiele, D. J.}, year = 1991, month = mar, journal = {Molecular and cellular biology}, volume = {11}, number = {3}, pages = {1232–1238}, issn = {0270-7306}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=369394&tool=pmcentrez&rendertype=abstract}, abstract = {In the yeast Saccharomyces cerevisiae, transcription of the metallothionein gene CUP1 is induced by copper and silver. Strains with a complete deletion of the ACE1 gene, the copper-dependent activator of CUP1 transcription, are hypersensitive to copper. These strains have a low but significant basal level of CUP1 transcription. To identify genes which mediate basal transcription of CUP1 or which activate CUP1 in response to other stimuli, we isolated an extragenic suppressor of an ace1 deletion. We demonstrate that a single amino acid substitution in the heat shock transcription factor (HSF) DNA-binding domain dramatically enhances CUP1 transcription while reducing transcription of the SSA3 gene, a member of the yeast hsp70 gene family. These results indicate that yeast metallothionein transcription is under HSF control and that metallothionein biosynthesis is important in response to heat shock stress. Furthermore, our results suggest that HSF may modulate the magnitude of individual heat shock gene transcription by subtle differences in its interaction with heat shock elements and that a single-amino-acid change can dramatically alter the activity of the factor for different target genes.}, pmid = {1996089}, keywords = {Amino Acid Sequence,Base Sequence,Cloning,DNA-Binding Proteins,DNA-Binding Proteins: genetics,Fungal,Gene Expression Regulation,Genetic,Heat-Shock Proteins,Heat-Shock Proteins: genetics,Metallothionein,Metallothionein: genetics,Molecular,Molecular Sequence Data,Mutation,nosource,Nucleic Acid,Regulatory Sequences,Restriction Mapping,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae: genetics,Transcription,Transcription Factors,Transcription Factors: genetics} }

@book{maquatRNATurnoverEukaryotes2008, title = {{{RNA}} Turnover in Eukaryotes: Analysis of Specialized and Quality Control {{RNA}} Decay Pathways}, author = {Maquat, L. E. and Kiledjian, M.}, year = 2008, volume = {449}, publisher = {Elsevier/Academic Press}, doi = {10.1016/S0076-6879(08)02403-8}, url = {http://books.google.com/books?hl=en&lr=&id=ha4IT5KB5GQC&oi=fnd&pg=PP1&dq=RNA+Turnover+in+Eukaryotes:+Analysis+of+Specialized+and+Quality+Control+RNA+Decay+Pathways&ots=pMfL0VBWaB&sig=honYhFOVqEdwcKyxufKeo71X7GM http://www.lavoisier.fr/livre/notice.asp?id=OR3W2LAKASKOWI}, keywords = {nosource} }

@book{maquatNonsenseMediatedMRNADecay2006, title = {Nonsense-{{Mediated mRNA Decay}}}, author = {Maquat, Lynne E.}, year = 2006, month = may, journal = {Molecular Biology Intelligence Unit}, issn = {1879-0380}, doi = {10.1016/j.gde.2011.03.008}, pmid = {21550797}, keywords = {nosource} } % == BibTeX quality report for maquatNonsenseMediatedMRNADecay2006: % Missing required field ‘publisher’ % ? Title looks like it was stored in title-case in Zotero

@article{spingolaGenomewideBioinformaticMolecular1999, title = {Genome-Wide Bioinformatic and Molecular Analysis of Introns in {{Saccharomyces}} Cerevisiae.}, author = {Spingola, M. and Grate, L. and Haussler, D. and Ares, M. and Jr, M. Ares}, year = 1999, month = feb, journal = {RNA}, volume = {5}, number = {2}, pages = {221–34}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1369754&tool=pmcentrez&rendertype=abstract http://rnajournal.cshlp.org/content/5/2/221.short}, abstract = {Introns have typically been discovered in an ad hoc fashion: introns are found as a gene is characterized for other reasons. As complete eukaryotic genome sequences become available, better methods for predicting RNA processing signals in raw sequence will be necessary in order to discover genes and predict their expression. Here we present a catalog of 228 yeast introns, arrived at through a combination of bioinformatic and molecular analysis. Introns annotated in the Saccharomyces Genome Database (SGD) were evaluated, questionable introns were removed after failing a test for splicing in vivo, and known introns absent from the SGD annotation were added. A novel branchpoint sequence, AAUUAAC, was identified within an annotated intron that lacks a six-of-seven match to the highly conserved branchpoint consensus UACUAAC. Analysis of the database corroborates many conclusions about pre-mRNA substrate requirements for splicing derived from experimental studies, but indicates that splicing in yeast may not be as rigidly determined by splice-site conservation as had previously been thought. Using this database and a molecular technique that directly displays the lariat intron products of spliced transcripts (intron display), we suggest that the current set of 228 introns is still not complete, and that additional intron-containing genes remain to be discovered in yeast. The database can be accessed at http://www.cse.ucsc.edu/research/compbi o/yeast_introns.html.}, pmid = {10024174}, keywords = {Computational Biology,Databases as Topic,Fungal,Genome,Introns,Introns: genetics,Markov Chains,nosource,Ribosomal Proteins,Ribosomal Proteins: genetics,RNA,RNA Precursors,RNA Precursors: genetics,RNA Splicing,RNA Splicing: genetics,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Small Nuclear,Small Nuclear: genetics,Spliceosomes,Spliceosomes: genetics} }

@article{alberghinaYeastGenomeDirectory1997, title = {The Yeast Genome Directory.}, author = {Alberghina, L. and Albermann, K. and Albers, M. and Aldea, M. and Alexandraki, D. and Aljinovic, G. and Allen, E. and Andr{'e}, B. and Andrews, S. and Ansorge, W. and Antoine, G. and Anwar, R. and Aparicio, A. and Araujo, R. and Arino, J. and Arnold, F. and Arroyo, J. and Aviles, E. and Backes, U. and Baclet, M. C. and Badcock, K. and Bahr, A. and Goffeau, A. E. A. and Aert, R. and {Agostini-Carbone}, M. L. and Ahmed, A. and Aigle, M. and others}, year = 1997, month = may, journal = {Nature}, volume = {387}, number = {6632 Suppl}, eprint = {9169864}, eprinttype = {pubmed}, pages = {5}, publisher = {[London: Macmillan Journals], 1869-}, issn = {0028-0836}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9169864 http://crust.stanford.edu/community/nature_genome_dir_pdf/genome_dir.pdf}, pmid = {9169864}, keywords = {Fungal,Genetics,Genome,nosource,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics} }

@article{unterholznerSMG7ActsMolecular2004, title = {{{SMG7}} Acts as a Molecular Link between {{mRNA}} Surveillance and {{mRNA}} Decay.}, author = {Unterholzner, Leonie and Izaurralde, Elisa}, year = 2004, month = nov, journal = {Molecular Cell}, volume = {16}, number = {4}, eprint = {15546618}, eprinttype = {pubmed}, pages = {587–596}, issn = {1097-2765}, doi = {10.1016/j.molcel.2004.10.013}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15546618}, abstract = {Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism that eliminates mRNAs containing premature termination codons (PTCs). The proteins UPF1, SMG5, SMG6, and SMG7 are essential NMD factors in metazoa. SMG5 and SMG7 form a complex with UPF1 and interact with each other via their N-terminal domains. Here we show that SMG5 and SMG7 colocalize in cytoplasmic mRNA decay bodies, while SMG6 forms separate cytoplasmic foci. When SMG7 is tethered to a reporter transcript, it elicits its degradation, bypassing the requirement for a PTC, UPF1, SMG5, or SMG6. This activity is mediated by the C-terminal domain of SMG7. In contrast, SMG5 requires SMG7 to trigger mRNA decay and to localize to decay bodies. Our findings indicate that SMG7 provides a link between the NMD and the mRNA degradation machinery by interacting with SMG5 and UPF1 via its N-terminal domain and targeting bound transcripts for decay via its C-terminal domain.}, pmid = {15546618}, keywords = {Blotting,Carbocyanines,Carrier Proteins,Carrier Proteins: physiology,Cytoplasm,Cytoplasm: metabolism,Dactinomycin,Dactinomycin: pharmacology,Fluorescence,Frameshift Mutation,Genes,Genetic,Hela Cells,Humans,Luciferases,Luciferases: metabolism,Messenger,Messenger: genetics,Messenger: metabolism,Microscopy,Mutation,nosource,Nucleic Acid Synthesis Inhibitors,Nucleic Acid Synthesis Inhibitors: pharmacology,Plasmids,Protein Structure,Recombinant Fusion Proteins,Recombinant Fusion Proteins: metabolism,Reporter,Ribonucleoproteins,RNA,RNA Interference,Small Interfering,Small Interfering: metabolism,Small Nuclear,Small Nuclear: metabolism,Templates,Tertiary,Time Factors,Trans-Activators,Trans-Activators: metabolism,Transfection,Western} }

@article{rebbapragadaExecutionNonsensemediatedMRNA2009, title = {Execution of Nonsense-Mediated {{mRNA}} Decay: What Defines a Substrate?}, author = {Rebbapragada, Indrani and {Lykke-Andersen}, Jens}, year = 2009, month = jun, journal = {Current Opinion in Cell Biology}, volume = {21}, number = {3}, eprint = {19359157}, eprinttype = {pubmed}, pages = {394–402}, issn = {1879-0410}, doi = {10.1016/j.ceb.2009.02.007}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19359157}, abstract = {The nonsense-mediated mRNA decay (NMD) pathway targets mRNAs with premature termination codons as well as a subset of normal mRNAs for rapid decay. Emerging evidence suggests that mRNAs become NMD substrates based on the composition of the mRNP downstream of the translation termination event, which either stimulates or antagonizes recruitment of the NMD machinery. The NMD mRNP subsequently undergoes several remodeling events, which involve hydrolysis of ATP by the NMD factor Upf1 and in metazoans, a phosphorylation/dephosphorylation cycle of Upf1 mediated by Smg proteins. This leads to mRNA decay following translational repression. Recent evidence suggests that in Drosophila and human cells, decay is initiated by the endonuclease Smg6.}, pmid = {19359157}, keywords = {Animals,Codon,Humans,Messenger,Messenger: genetics,Messenger: metabolism,Nonsense,Nonsense: metabolism,nosource,Protein Biosynthesis,Ribonucleoproteins,Ribonucleoproteins: metabolism,RNA,RNA Stability,RNA Stability: genetics} }

@article{longmanMechanisticInsightsIdentification2007, title = {Mechanistic Insights and Identification of Two Novel Factors in the {{C}}. Elegans {{NMD}} Pathway.}, author = {Longman, Dasa and {}a Plasterk, Ronald H. and Johnstone, Iain L. and C{'a}ceres, Javier F.}, year = 2007, month = may, journal = {Genes & Development}, volume = {21}, number = {9}, pages = {1075–85}, issn = {0890-9369}, doi = {10.1101/gad.417707}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1855233&tool=pmcentrez&rendertype=abstract}, abstract = {The nonsense-mediated mRNA decay (NMD) pathway selectively degrades mRNAs harboring premature termination codons (PTCs). Seven genes (smg-1-7, for suppressor with morphological effect on genitalia) that are essential for NMD were originally identified in the nematode Caenorhabditis elegans, and orthologs of these genes have been found in several species. Whereas in humans NMD is linked to splicing, PTC definition occurs independently of exon boundaries in Drosophila. Here, we have conducted an analysis of the cis-acting sequences and trans-acting factors that are required for NMD in C. elegans. We show that a PTC codon is defined independently of introns in C. elegans and, consequently, components of the exon junction complex (EJC) are dispensable for NMD. We also show a distance-dependent effect, whereby PTCs that are closer to the 3’ end of the mRNA are less sensitive to NMD. We also provide evidence for the existence of previously unidentified components of the NMD pathway that, unlike known smg genes, are essential for viability in C. elegans. A genome-wide RNA interference (RNAi) screen resulted in the identification of two such novel NMD genes, which are essential for proper embryonic development, and as such represent a new class of essential NMD genes in C. elegans that we have termed smgl (for smg lethal). We show that the encoded proteins are conserved throughout evolution and are required for NMD in C. elegans and also in human cells.}, pmid = {17437990}, keywords = {Animals,Base Sequence,Caenorhabditis elegans,Caenorhabditis elegans Proteins,Caenorhabditis elegans Proteins: genetics,Caenorhabditis elegans Proteins: metabolism,Caenorhabditis elegans: embryology,Caenorhabditis elegans: genetics,Caenorhabditis elegans: metabolism,Codon,Conserved Sequence,Exons,Genes,Genetically Modified,Hela Cells,Helminth,Helminth: genetics,Helminth: metabolism,Humans,Introns,Messenger,Messenger: genetics,Messenger: metabolism,Nonsense,nosource,Protein Kinases,Protein Kinases: genetics,Protein Kinases: metabolism,Reporter,RNA,RNA Interference,RNA Splicing} }

@article{russellExploringFoldingLandscape2002, title = {Exploring the Folding Landscape of a Structured {{RNA}}.}, author = {Russell, Rick and Zhuang, Xiaowei and Babcock, Hazen P. and Millett, Ian S. and Doniach, Sebastian and Chu, Steven and Herschlag, Daniel}, year = 2002, month = jan, journal = {Proceedings of the National Academy of Sciences}, volume = {99}, number = {1}, pages = {155–160}, issn = {0027-8424}, doi = {10.1073/pnas.221593598}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=117531&tool=pmcentrez&rendertype=abstract}, abstract = {Structured RNAs achieve their active states by traversing complex, multidimensional energetic landscapes. Here we probe the folding landscape of the Tetrahymena ribozyme by using a powerful approach: the folding of single ribozyme molecules is followed beginning from distinct regions of the folding landscape. The experiments, combined with small-angle x-ray scattering results, show that the landscape contains discrete folding pathways. These pathways are separated by large free-energy barriers that prevent interconversion between them, indicating that the pathways lie in deep channels in the folding landscape. Chemical protection and mutagenesis experiments are then used to elucidate the structural features that determine which folding pathway is followed. Strikingly, a specific long-range tertiary contact can either help folding or hinder folding, depending on when it is formed during the process. Together these results provide an unprecedented view of the topology of an RNA folding landscape and the RNA structural features that underlie this multidimensional landscape.}, pmid = {11756689}, keywords = {Animals,Biological,Catalytic,Catalytic: chemistry,Dose-Response Relationship,Drug,Kinetics,Magnesium,Magnesium: pharmacology,Models,nosource,Nucleic Acid Conformation,Protein Folding,Radiation,RNA,RNA: chemistry,Scattering,Sodium,Sodium: pharmacology,Sulfuric Acid Esters,Sulfuric Acid Esters: pharmacology,Tetrahymena,Tetrahymena: chemistry,Thermodynamics,Time Factors,X-Rays} }

@article{arnoldMRNAStabilizationOmpA1998, title = {{{mRNA}} Stabilization by the {{ompA}} 5’ Untranslated Region: Two Protective Elements Hinder Distinct Pathways for {{mRNA}} Degradation}, author = {Arnold, T. E. and Yu, J. and Belasco, J. G.}, year = 1998, journal = {RNA}, volume = {4}, number = {3}, pages = {319–330}, publisher = {Cambridge Univ Press}, url = {http://rnajournal.cshlp.org/content/4/3/319.short}, keywords = {coli,e,mrna degradation,nosource,ompa,ribosome binding,rna stem-loop,rnase e} }

@article{belascoAllThingsMust2010, title = {All Things Must Pass: Contrasts and Commonalities in Eukaryotic and Bacterial {{mRNA}} Decay.}, author = {Belasco, Joel G.}, year = 2010, month = jun, journal = {Nature Reviews Molecular Cell Biology}, volume = {11}, number = {july}, eprint = {20520623}, eprinttype = {pubmed}, publisher = {Nature Publishing Group}, issn = {1471-0080}, doi = {10.1038/nrm2917}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20520623}, abstract = {Despite its universal importance for controlling gene expression, mRNA degradation was initially thought to occur by disparate mechanisms in eukaryotes and bacteria. This conclusion was based on differences in the structures used by these organisms to protect mRNA termini and in the RNases and modifying enzymes originally implicated in mRNA decay. Subsequent discoveries have identified several striking parallels between the cellular factors and molecular events that govern mRNA degradation in these two kingdoms of life. Nevertheless, some key distinctions remain, the most fundamental of which may be related to the different mechanisms by which eukaryotes and bacteria control translation initiation.}, pmid = {20520623}, keywords = {nosource} }

@article{brognaNonsensemediatedMRNADecay2009, title = {Nonsense-Mediated {{mRNA}} Decay ({{NMD}}) Mechanisms}, author = {Brogna, Saverio and Wen, Jikai}, year = 2009, month = feb, journal = {Nature structural & molecular biology}, volume = {16}, number = {2}, eprint = {19190664}, eprinttype = {pubmed}, pages = {107–113}, issn = {1545-9985}, doi = {10.1038/nsmb.1550}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19190664 http://www.nature.com/nsmb/journal/v16/n2/abs/nsmb.1550.html}, abstract = {Nonsense-mediated mRNA decay (NMD) is a translation-coupled mechanism that eliminates mRNAs containing premature translation-termination codons (PTCs). In mammalian cells, NMD is also linked to pre-mRNA splicing, as in many instances strong mRNA reduction occurs only when the PTC is located upstream of an intron. It is proposed that in these systems, the exon junction complex (EJC) mediates the link between splicing and NMD. Recent studies have questioned the role of splicing and the EJC in initiating NMD. Instead, they put forward a general and evolutionarily conserved mechanism in which the main regulator of NMD is the distance between a PTC and the poly(A) tail of an mRNA. Here we discuss the limitations of the new NMD model and the EJC concept; we argue that neither satisfactorily accounts for all of the available data and offer a new model to test in future studies.}, pmid = {19190664}, keywords = {3’ Untranslated Regions,3’ Untranslated Regions: metabolism,Animals,Codon,Humans,Messenger,Messenger: genetics,Messenger: metabolism,nosource,Poly A,Poly A: metabolism,Protein Biosynthesis,RNA,RNA Splicing,RNA Stability,Terminator,Terminator: metabolism} }

@article{condonShutdownDecayMRNA2006, title = {Shutdown Decay of {{mRNA}}}, author = {Condon, Ciar{'a}n and Upr, Cnrs and Diderot, Denis and {Physico-chimique}, Biologie and Curie, Marie}, year = 2006, month = aug, journal = {Molecular microbiology}, volume = {61}, number = {June}, pages = {573–583}, issn = {0950-382X}, doi = {10.1111/j.1365-2958.2006.05270.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2006.05270.x/full http://www.ncbi.nlm.nih.gov/pubmed/16803593}, abstract = {Although plasmid-borne and chromosomal toxin-antitoxin (TA) operons have been known for some time, the recent identification of mRNA as the target of at least two different classes of toxins has led to a dramatic renewal of interest in these systems as mediators of stress responses. Members of the MazF/PemK family, the so-called mRNA interferases, are ribonucleases that inhibit translation by destroying cellular mRNAs under stress conditions, while the founder member of the RelE family promotes cleavage of mRNAs through the ribosome. Detailed structures of these enzymes, often in complex with their inhibitors, have provided vital clues to their mechanisms of action. The primary role and regulation of these systems has been the subject of some controversy. One model suggests they play a beneficial role by wiping the slate clean and preventing wasteful energy consumption by the translational apparatus during adaptation to stress conditions, while another favours the idea that their main function is programmed cell death. The two models might not be mutually exclusive if a side-effect of prolonged exposure to toxic RNase activity without de novo synthesis of the inhibitor were a state of dormancy for which we do not yet understand the key to recovery. In this review, I discuss the recent developments in the rapidly expanding field of what I refer to as bacterial shutdown decay.}, pmid = {16803593}, keywords = {Adaptation,Bacterial,Bacterial: genetics,Bacterial: metabolism,Biological,DNA-Binding Proteins,DNA-Binding Proteins: chemistry,DNA-Binding Proteins: genetics,DNA-Binding Proteins: metabolism,Endoribonucleases,Endoribonucleases: chemistry,Endoribonucleases: genetics,Endoribonucleases: metabolism,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: genetics,Escherichia coli Proteins: metabolism,Gene Expression Regulation,Models,Molecular,nosource,Phylogeny,Protein Conformation,RNA,RNA Stability} }

@article{gowrishankarWhyTranscriptionCoupled2004, title = {Why Is Transcription Coupled to Translation in Bacteria?}, author = {Gowrishankar, J. and Harinarayanan, R.}, year = 2004, month = nov, journal = {Molecular Microbiology}, volume = {54}, number = {3}, pages = {598–603}, issn = {0950-382X}, doi = {10.1111/j.1365-2958.2004.04289.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2004.04289.x/full http://www.ncbi.nlm.nih.gov/pubmed/15491353}, abstract = {Active mechanisms exist to prevent transcription that is uncoupled from translation in the protein-coding genes of bacteria, as exemplified by the phenomenon of nonsense polarity. Bacterial transcription-translation coupling may be viewed as one among several co-transcriptional processes, including those for mRNA processing and export in the eukaryotes, that operate in the various life forms to render the nascent transcript unavailable for formation of otherwise deleterious R-loops in the genome.}, pmid = {15491353}, keywords = {Bacteria,Bacteria: genetics,Bacteria: metabolism,Bacterial,Bacterial: chemistry,Cold Temperature,DNA,Gene Expression Regulation,Genetic,nosource,Nucleic Acid Conformation,Protein Biosynthesis,Transcription} }

@article{edwardsGeneratingPeptideCandidates2002, title = {Generating Peptide Candidates from Amino-Acid Sequence Databases for Protein Identification via Mass Spectrometry}, author = {Edwards, Nathan and Lippert, Ross}, year = 2002, journal = {Algorithms in Bioinformatics}, pages = {68–81}, publisher = {Springer}, url = {http://www.springerlink.com/index/WPK5D35232JNP5XX.pdf}, keywords = {nosource} }

@article{maquatCBP80promotedMRNPRearrangements2010, title = {{{CBP80-promoted mRNP}} Rearrangements during the Pioneer Round of Translation, Nonsense-Mediated {{mRNA}} Decay, and Thereafter}, author = {Maquat, LE L. E. E. and Hwang, J. and Sato, H. and Tang, Y.}, year = 2010, month = jan, journal = {Cold Spring Harbor }, volume = {75}, pages = {127–34}, issn = {1943-4456}, doi = {10.1101/sqb.2010.75.028}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711708/ http://www.ncbi.nlm.nih.gov/pubmed/21447822}, abstract = {In mammalian cells, two different messenger ribonucleoproteins (mRNPs) serve as templates for protein synthesis. Newly synthesized mRNPs bound by the cap-binding protein heterodimer CBP80-CBP20 (CBC) initially undergo a pioneer round of translation. One purpose of this round of translation is to ensure the quality of gene expression, as exemplified by nonsense-mediated messenger RNA (mRNA) decay (NMD). NMD largely functions to eliminate mRNAs that prematurely terminate translation, although NMD also contributes to proper gene control, and it targets CBC-bound mRNPs. CBC-bound mRNPs are remodeled to eukaryotic translation initiation factor (eIF)4E-bound mRNPs in steps that (1) are a consequence of the pioneer round of translation and (2) occur independently of translation. Rather than supporting NMD, eIF4E-bound mRNPs provide for the bulk of cellular protein synthesis and are the primary targets of mRNA decay mechanisms that conditionally regulate gene expression. Here, we overview cellular processes by which CBC-bound mRNPs are remodeled to eIF4E-bound mRNPs. We also describe the molecular movements of certain factors during NMD in view of the influential role of CBP80.}, isbn = {9781936113071}, pmid = {21447822}, keywords = {Animals,Codon,Humans,Nonsense,Nonsense: genetics,nosource,Nuclear Cap-Binding Protein Complex,Nuclear Cap-Binding Protein Complex: metabolism,Protein Binding,Protein Binding: genetics,Protein Biosynthesis,Protein Biosynthesis: genetics,Ribonucleoproteins,Ribonucleoproteins: metabolism,RNA Stability,RNA Stability: genetics} }

@article{holcikTranslationalControlStress2005, title = {Translational Control in Stress and Apoptosis.}, author = {Holcik, Martin and Sonenberg, Nahum}, year = 2005, month = apr, journal = {Nature Reviews Molecular Cell Biology}, volume = {6}, number = {4}, eprint = {15803138}, eprinttype = {pubmed}, pages = {318–327}, issn = {1471-0072}, doi = {10.1038/nrm1618}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15803138}, abstract = {Cells respond to stress stimuli through coordinated changes in gene expression. The regulation of translation is often used under these circumstances because it allows immediate and selective changes in protein levels. There are many examples of translational control in response to stress. Here we examine two representative models, the regulation of eukaryotic initiation factor-2alpha by phosphorylation and internal ribosome initiation through the internal ribosome-entry site, which illustrate the importance of translational control in the cellular stress response and apoptosis.}, pmid = {15803138}, keywords = {Animals,Apoptosis,Apoptosis: genetics,Apoptotic Protease-Activating Factor 1,DNA-Binding Proteins,DNA-Binding Proteins: metabolism,Eukaryotic Initiation Factor-2,Eukaryotic Initiation Factor-2: metabolism,Humans,Messenger,Messenger: metabolism,nosource,Phosphorylation,Physiological,Physiological: genetics,Protein Biosynthesis,Protein Kinases,Protein Kinases: metabolism,Proteins,Proteins: genetics,Proteins: metabolism,Ribosomes,Ribosomes: genetics,RNA,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: metabolism,Stress,X-Linked Inhibitor of Apoptosis Protein} }

@article{rileyDistinct5UTRs2010, title = {Distinct 5’ {{UTRs}} Regulate {{XIAP}} Expression under Normal Growth Conditions and during Cellular Stress.}, author = {Riley, Alura and Jordan, Lindsay E. and Holcik, Martin}, year = 2010, month = apr, journal = {Nucleic Acids Research}, volume = {38}, number = {14}, eprint = {20385593}, eprinttype = {pubmed}, pages = {4665–4674}, issn = {1362-4962}, doi = {10.1093/nar/gkq241}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20385593}, abstract = {X-chromosome linked inhibitor of apoptosis, XIAP, is cellular caspase inhibitor and a key regulator of apoptosis. We and others have previously shown that XIAP expression is regulated primarily at the level of protein synthesis; the 5’ untranslated region (UTR) of XIAP mRNA contains an Internal Ribosome Entry Site (IRES) that supports cap-independent expression of XIAP protein during conditions of pathophysiological stress, such as serum deprivation or gamma irradiation. Here, we show that XIAP is encoded by two distinct mRNAs that differ in their 5’ UTRs. We further show that the dominant, shorter, 5’ UTR promotes a basal level of XIAP expression under normal growth conditions. In contrast, the less abundant longer 5’ UTR contains an IRES and supports cap-independent translation during stress. Our data suggest that the combination of alternate regulatory regions and distinct translational initiation modes is critical in maintaining XIAP levels in response to cellular stress and may represent a general mechanism of cellular adaptation.}, pmid = {20385593}, keywords = {nosource} }

@article{lossonInterferenceNonsenseMutations1979, title = {Interference of Nonsense Mutations with Eukaryotic Messenger {{RNA}} Stability}, author = {Losson, R. and Lacroute, F.}, year = 1979, month = oct, journal = { of the National Academy of Sciences}, volume = {76}, number = {10}, pages = {5134–7}, issn = {0027-8424}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=413094&tool=pmcentrez&rendertype=abstract http://www.pnas.org/content/76/10/5134.short}, abstract = {The fine structure map of the yeast URA 3 gene was established by meiotic recombination, and amber nonsense mutations were located at different points on the map. The effect of the length of the labeling time on the specific radioactivity of ura 3 messenger RNA and on its repartition between poly(A)-RNA and RNA not containing poly(A) has been followed in nonsense mutants. Nonsense mutations reduce the messenger level without lowering its instantaneous rate of synthesis. The strength of the reduction depends on the position of the nonsense codon within the locus and concerns essentially the accumulation of polyadenylylated ura 3 mRNA.}, pmid = {388431}, keywords = {Drug Stability,Genetic,Kinetics,Meiosis,Messenger,Messenger: metabolism,Mitosis,Mutation,nosource,Recombination,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae: physiology,Species Specificity} }

@article{vattemReinitiationInvolvingUpstream2004, title = {Reinitiation Involving Upstream {{ORFs}} Regulates {{ATF4 mRNA}} Translation in Mammalian Cells.}, author = {Vattem, Krishna M. and Wek, Ronald C.}, year = 2004, month = aug, journal = {Proceedings of the National Academy of Sciences}, volume = {101}, number = {31}, pages = {11269–74}, issn = {0027-8424}, doi = {10.1073/pnas.0400541101}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=509193&tool=pmcentrez&rendertype=abstract}, abstract = {During cellular stresses, phosphorylation of eukaryotic initiation factor-2 (eIF2) elicits gene expression designed to ameliorate the underlying cellular disturbance. Central to this stress response is the transcriptional regulator activating transcription factor, ATF4. Here we describe the mechanism regulating ATF4 expression involving the differential contribution of two upstream ORFs (uORFs) in the 5’ leader of the mouse ATF4 mRNA. The 5’ proximal uORF1 is a positive-acting element that facilitates ribosome scanning and reinitiation at downstream coding regions in the ATF4 mRNA. When eIF2-GTP is abundant in nonstressed cells, ribosomes scanning downstream of uORF1 reinitiate at the next coding region, uORF2, an inhibitory element that blocks ATF4 expression. During stress conditions, phosphorylation of eIF2 and the accompanying reduction in the levels of eIF2-GTP increase the time required for the scanning ribosomes to become competent to reinitiate translation. This delayed reinitiation allows for ribosomes to scan through the inhibitory uORF2 and instead reinitiate at the ATF4-coding region. Increased expression of ATF4 would contribute to the expression of genes involved in remediation of cellular stress damage. These results suggest that the mechanism of translation reinitiation involving uORFs is conserved from yeast to mammals.}, pmid = {15277680}, keywords = {Activating Transcription Factor 4,Animals,Base Sequence,Cells,Cultured,DNA-Binding Proteins,DNA-Binding Proteins: genetics,Eukaryotic Initiation Factor-2,Eukaryotic Initiation Factor-2: metabolism,Fibroblasts,Fibroblasts: cytology,Fibroblasts: physiology,Messenger,Messenger: chemistry,Messenger: genetics,Mice,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Open Reading Frames,Open Reading Frames: genetics,Phosphorylation,Protein Biosynthesis,Protein Biosynthesis: genetics,Protein Kinases,Protein Kinases: genetics,Ribosomes,Ribosomes: physiology,RNA,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: genetics,Trans-Activators,Trans-Activators: genetics,Yeasts,Yeasts: genetics} }

@article{hinnebuschTranslationalRegulationGCN42005, title = {Translational Regulation of {{GCN4}} and the General Amino Acid Control of Yeast.}, author = {Hinnebusch, Alan G.}, year = 2005, month = jan, journal = {Annual Review of Microbiology}, volume = {59}, eprint = {16153175}, eprinttype = {pubmed}, pages = {407–50}, issn = {0066-4227}, doi = {10.1146/annurev.micro.59.031805.133833}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16153175}, abstract = {Cells reprogram gene expression in response to environmental changes by mobilizing transcriptional activators. The activator protein Gcn4 of the yeast Saccharomyces cerevisiae is regulated by an intricate translational control mechanism, which is the primary focus of this review, and also by the modulation of its stability in response to nutrient availability. Translation of GCN4 mRNA is derepressed in amino acid-deprived cells, leading to transcriptional induction of nearly all genes encoding amino acid biosynthetic enzymes. The trans-acting proteins that control GCN4 translation have general functions in the initiation of protein synthesis, or regulate the activities of initiation factors, so that the molecular events that induce GCN4 translation also reduce the rate of general protein synthesis. This dual regulatory response enables cells to limit their consumption of amino acids while diverting resources into amino acid biosynthesis in nutrient-poor environments. Remarkably, mammalian cells use the same strategy to downregulate protein synthesis while inducing transcriptional activators of stress-response genes under various stressful conditions, including amino acid starvation.}, pmid = {16153175}, keywords = {Amino Acids,Amino Acids: metabolism,Basic-Leucine Zipper Transcription Factors,Culture Media,DNA-Binding Proteins,DNA-Binding Proteins: genetics,DNA-Binding Proteins: metabolism,Fungal,Gene Expression Regulation,Models,Molecular,nosource,Protein Biosynthesis,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Transcription Factors,Transcription Factors: genetics,Transcription Factors: metabolism} }

@article{johnsonPropertiesOverlappingGenes2004, title = {Properties of Overlapping Genes Are Conserved across Microbial Genomes.}, author = {Johnson, Zackary I. and Chisholm, Sallie W.}, year = 2004, month = nov, journal = {Genome Research}, volume = {14}, number = {11}, pages = {2268–72}, issn = {1088-9051}, doi = {10.1101/gr.2433104}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=525685&tool=pmcentrez&rendertype=abstract}, abstract = {There are numerous examples from the genomes of viruses, mitochondria, and chromosomes that adjacent genes can overlap, sharing at least one nucleotide. Overlaps have been hypothesized to be involved in genome size minimization and as a regulatory mechanism of gene expression. Here we show that overlapping genes are a consistent feature (approximately one-third of all genes) across all microbial genomes sequenced to date, have homologs in more microbes than do non-overlapping genes, and are therefore likely more conserved. In addition, the size, phase (reading frame offset), and distribution, among other characteristics, of overlapping genes are most consistent with the hypothesis that overlaps function in the regulation of gene expression. The upstream sequences and conservation of overlapping orthologs of two model organisms from the genus Prochlorococcus that have significantly different GC-content, and therefore different nucleotide sequences for orthologs, are also consistent with small overlapping sequence regions and programmed shifts in reading frame as a common mechanism in the regulation of microbial gene expression.}, pmid = {15520290}, keywords = {Bacterial,Bacterial: genetics,Computational Biology,Databases,Evolution,Gene Order,Gene Order: genetics,Genes,Genome,Molecular,nosource,Nucleic Acid,Open Reading Frames,Open Reading Frames: genetics,Overlapping,Overlapping: genetics} }

@article{hundsdoerferEukaryoticTranslationInitiation2005, title = {Eukaryotic Translation Initiation Factor {{4GI}} and P97 Promote Cellular Internal Ribosome Entry Sequence-Driven Translation.}, author = {Hundsdoerfer, Patrick and Thoma, Christian and Hentze, Matthias W.}, year = 2005, month = sep, journal = {Proceedings of the National Academy of Sciences}, volume = {102}, number = {38}, pages = {13421–6}, issn = {0027-8424}, doi = {10.1073/pnas.0506536102}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1224658&tool=pmcentrez&rendertype=abstract}, abstract = {Numerous cellular mRNAs encoding proteins critical during cell stress, apoptosis, and the cell cycle seem to be translated by means of internal ribosome entry sequences (IRES) when cap-dependent translation is compromised. The underlying molecular mechanisms are largely unknown. Using a HeLa-based cell-free translation system that mirrors the function of cellular IRESs in vitro, we recently demonstrated that translation from the c-myc IRES continues after proteolytic cleavage of eukaryotic translation initiation factor (eIF) 4G. To address the role of eIF4G in cellular IRES-driven translation directly, we immunodepleted eIF4GI from the HeLa cell translation extracts. After efficient depletion of eIF4GI ({\(>\)}90%), both cap-dependent and c-myc IRES-dependent translations are diminished to residual levels ({\(<\)}5%). In striking contrast to cap-dependent translation, c-myc IRES-dependent translation is fully restored by addition of the conserved middle fragment of eIF4GI, harboring the eIF3- and eIF4A-binding sites. p97, an eIF4G-related protein that has been described both as an inhibitor of translation and as a modulator of apoptosis, not only suffices to also rescue c-myc IRES-driven (but not cap-dependent) translation, but it even superinduces IRES-mediated translation 3-fold compared with nondepleted extracts. Interestingly, both p97 and the middle fragment of eIF4GI also rescue translation driven by proapoptotic (p97) and antiapoptotic [X-linked inhibitor of apoptosis (XIAP) and cellular inhibitor of apoptosis 1 (c-IAP1)] IRESs, reflecting a broader role of these polypeptides in cellular IRES-mediated translation and indicating their importance in apoptosis.}, pmid = {16174738}, keywords = {5’ Untranslated Regions,5’ Untranslated Regions: genetics,5’ Untranslated Regions: metabolism,Apoptosis,Apoptosis: physiology,Cell Cycle,Cell Cycle: physiology,Cell-Free System,Cell-Free System: metabolism,Eukaryotic Initiation Factor-4F,Eukaryotic Initiation Factor-4F: metabolism,Hela Cells,Humans,Inhibitor of Apoptosis Proteins,nosource,Protein Biosynthesis,Protein Biosynthesis: physiology,Proteins,Proteins: metabolism,Proto-Oncogene Proteins c-myc,Proto-Oncogene Proteins c-myc: genetics,Proto-Oncogene Proteins c-myc: metabolism,Regulatory Sequences,Ribonucleic Acid,Ribonucleic Acid: physiology,RNA Caps,RNA Caps: genetics,RNA Caps: metabolism,X-Linked Inhibitor of Apoptosis Protein} }

@article{vagnerIrresistibleIRES2001, title = {Irresistible {{IRES}}}, author = {Vagner, St{'e}phan and Galy, Bruno and Pyronnet, St{'e}phane}, year = 2001, journal = {EMBO Reports}, volume = {2}, number = {10}, pages = {893–898}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/embor/journal/v2/n10/abs/embor313.html}, keywords = {nosource} } % == BibTeX quality report for vagnerIrresistibleIRES2001: % ? Title looks like it was stored in title-case in Zotero

@article{brunoIdentificationMicroRNAThat2011, title = {Identification of a {{MicroRNA}} That {{Activates Gene Expression}} by {{Repressing Nonsense-Mediated RNA Decay}}.}, author = {Bruno, Ivone G. and Karam, Rachid and Huang, Lulu and Bhardwaj, Anjana and Lou, Chih H. and Shum, Eleen Y. and Song, Hye-Won and {}a Corbett, Mark and Gifford, Wesley D. and Gecz, Jozef and Pfaff, Samuel L. and Wilkinson, Miles F.}, year = 2011, month = may, journal = {Molecular Cell}, volume = {42}, number = {4}, eprint = {21596314}, eprinttype = {pubmed}, pages = {500–510}, publisher = {Elsevier Inc.}, issn = {1097-4164}, doi = {10.1016/j.molcel.2011.04.018}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21596314}, abstract = {Nonsense-mediated decay (NMD) degrades both normal and aberrant transcripts harboring stop codons in particular contexts. Mutations that perturb NMD cause neurological disorders in humans, suggesting that NMD has roles in the brain. Here, we identify a brain-specific microRNA-miR-128-that represses NMD and thereby controls batteries of transcripts in neural cells. miR-128 represses NMD by targeting the RNA helicase UPF1 and the exon-junction complex core component MLN51. The ability of miR-128 to regulate NMD is a conserved response occurring in frogs, chickens, and mammals. miR-128 levels are dramatically increased in differentiating neuronal cells and during brain development, leading to repressed NMD and upregulation of mRNAs normally targeted for decay by NMD; overrepresented are those encoding proteins controlling neuron development and function. Together, these results suggest the existence of a conserved RNA circuit linking the microRNA and NMD pathways that induces cell type-specific transcripts during development.}, pmid = {21596314}, keywords = {nosource} }

@article{durandInhibitionNonsensemediatedMRNA2007, title = {Inhibition of Nonsense-Mediated {{mRNA}} Decay ({{NMD}}) by a New Chemical Molecule Reveals the Dynamic of {{NMD}} Factors in {{P-bodies}}.}, author = {Durand, S{'e}bastien and Cougot, Nicolas and {Mahuteau-Betzer}, Florence and Nguyen, Chi-Hung and Grierson, David S. and Bertrand, Edouard and Tazi, Jamal and Lejeune, Fabrice}, year = 2007, month = sep, journal = {The Journal of Cell Biology}, volume = {178}, number = {7}, pages = {1145–60}, issn = {0021-9525}, doi = {10.1083/jcb.200611086}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2064650&tool=pmcentrez&rendertype=abstract http://jcb.rupress.org/content/178/7/1145.short}, abstract = {In mammals, nonsense-mediated mRNA decay (NMD) is a quality-control mechanism that degrades mRNA harboring a premature termination codon to prevent the synthesis of truncated proteins. To gain insight into the NMD mechanism, we identified NMD inhibitor 1 (NMDI 1) as a small molecule inhibitor of the NMD pathway. We characterized the mode of action of this compound and demonstrated that it acts upstream of hUPF1. NMDI 1 induced the loss of interactions between hSMG5 and hUPF1 and the stabilization of hyperphosphorylated isoforms of hUPF1. Incubation of cells with NMDI 1 allowed us to demonstrate that NMD factors and mRNAs subject to NMD transit through processing bodies (P-bodies), as is the case in yeast. The results suggest a model in which mRNA and NMD factors are sequentially recruited to P-bodies.}, pmid = {17893241}, keywords = {Biological,Carrier Proteins,Carrier Proteins: metabolism,Codon,Cytoplasmic Structures,Cytoplasmic Structures: drug effects,Cytoplasmic Structures: metabolism,Down-Regulation,Down-Regulation: drug effects,Exoribonucleases,Exoribonucleases: genetics,Hela Cells,HeLa Cells,Humans,Indoles,Indoles: pharmacology,Messenger,Messenger: metabolism,Microtubule-Associated Proteins,Microtubule-Associated Proteins: genetics,Models,Mutant Proteins,Mutant Proteins: metabolism,Nonsense,Nonsense: metabolism,nosource,Phosphorylation,Phosphorylation: drug effects,Protein Binding,Protein Binding: drug effects,Protein Isoforms,Protein Isoforms: metabolism,Protein Transport,Protein Transport: drug effects,RNA,RNA Stability,RNA Stability: drug effects,RNA-Binding Proteins,RNA-Binding Proteins: metabolism,Thermodynamics,Trans-Activators,Trans-Activators: metabolism,Transcription Factors,Transcription Factors: genetics} }

@article{filipowiczMechanismsPosttranscriptionalRegulation2008, title = {Mechanisms of Post-Transcriptional Regulation by {{microRNAs}}: Are the Answers in Sight?}, author = {Filipowicz, Witold and Bhattacharyya, Suvendra N. and Sonenberg, Nahum}, year = 2008, month = mar, journal = {Nature Reviews Genetics}, volume = {9}, number = {2}, eprint = {18197166}, eprinttype = {pubmed}, pages = {102–14}, issn = {1471-0064}, doi = {10.1038/nrg2290}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18197166}, abstract = {MicroRNAs constitute a large family of small, approximately 21-nucleotide-long, non-coding RNAs that have emerged as key post-transcriptional regulators of gene expression in metazoans and plants. In mammals, microRNAs are predicted to control the activity of approximately 30% of all protein-coding genes, and have been shown to participate in the regulation of almost every cellular process investigated so far. By base pairing to mRNAs, microRNAs mediate translational repression or mRNA degradation. This Review summarizes the current understanding of the mechanistic aspects of microRNA-induced repression of translation and discusses some of the controversies regarding different modes of microRNA function.}, pmid = {18197166}, keywords = {Animals,Base Pairing,Base Pairing: physiology,Biological,Cell Compartmentation,Cell Compartmentation: physiology,Humans,Inclusion Bodies,Inclusion Bodies: metabolism,Inclusion Bodies: physiology,MicroRNAs,MicroRNAs: biosynthesis,MicroRNAs: physiology,Models,nosource,Protein Biosynthesis,Protein Biosynthesis: physiology,Ribonucleoproteins,Ribonucleoproteins: biosynthesis,RNA Interference,RNA Interference: physiology,RNA Stability,RNA Stability: physiology} }

@article{iskenMultipleLivesNMD2008, title = {The Multiple Lives of {{NMD}} Factors: Balancing Roles in Gene and Genome Regulation.}, author = {Isken, Olaf and Maquat, Lynne E.}, year = 2008, month = aug, journal = {Nature Reviews Genetics}, volume = {9}, number = {September}, eprint = {18679436}, eprinttype = {pubmed}, issn = {1471-0064}, doi = {10.1038/nrg2402}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18679436}, abstract = {Nonsense-mediated mRNA decay (NMD) largely functions to ensure the quality of gene expression. However, NMD is also crucial to regulating appropriate expression levels for certain genes and for maintaining genome stability. Furthermore, just as NMD serves cells in multiple ways, so do its constituent proteins. Recent studies have clarified that UPF and SMG proteins, which were originally discovered to function in NMD, also have roles in other pathways, including specialized pathways of mRNA decay, DNA synthesis and cell-cycle progression, and the maintenance of telomeres. These findings suggest a delicate balance of metabolic events - some not obviously related to NMD - that can be influenced by the cellular abundance, location and activity of NMD factors and their binding partners.}, pmid = {18679436}, keywords = {nosource} }

@article{choeMicroRNAArgonaute22010, title = {{{microRNA}}/{{Argonaute}} 2 Regulates Nonsense-mediated Messenger {{RNA}} Decay}, author = {Choe, Junho and Cho, Hana and Lee, Hyung Chul HC and Kim, YK Yoon Ki}, year = 2010, month = apr, journal = {EMBO reports}, volume = {11}, number = {5}, eprint = {20395958}, eprinttype = {pubmed}, pages = {380–386}, publisher = {Nature Publishing Group}, issn = {1469-221X}, doi = {10.1038/embor.2010.44}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20395958 http://dx.doi.org/10.1038/embor.2010.44 http://onlinelibrary.wiley.com/doi/10.1038/embor.2010.44/full}, abstract = {Imperfect base-pairing between microRNA (miRNA) and the 3’-untranslated region of target messenger RNA (mRNA) triggers translational repression of the target mRNA. Here, we provide evidence that human Argonaute 2 targets cap-binding protein (CBP)80/20-bound mRNAs and exon junction complex-bound mRNAs and inhibits nonsense-mediated mRNA decay (NMD), which is restricted tightly to CBP80/20-bound mRNAs. Furthermore, microarray analyses reveal that a subset of cellular transcripts, which are expected to be targeted for NMD, is stabilized by miRNA-mediated gene silencing. The regulation of NMD by miRNAs will shed light on a new post-transcriptional regulation mechanism of gene expression in mammalian cells.}, pmid = {20395958}, keywords = {10,1038,11,20,2010,380,386,44,ago2,cbp80,doi,eif4e,embo reports,embor,microrna,nmd,nosource} }

@article{liaoManyPathsFrameshifting2010, title = {The Many Paths to Frameshifting: Kinetic Modelling and Analysis of the Effects of Different Elongation Steps on Programmed -1 Ribosomal Frameshifting.}, author = {Liao, PY P. Y. and Choi, Yong Seok YS and Dinman, JD J. D. and Lee, KH Kelvin H.}, year = 2010, month = sep, journal = {Nucleic Acids Res.}, volume = {39}, number = {1}, pages = {300–312}, issn = {1362-4962}, doi = {10.1093/nar/gkq761}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3017607&tool=pmcentrez&rendertype=abstract http://www.ncbi.nlm.nih.gov/pubmed/20823091 http://nar.oxfordjournals.org/content/39/1/300.short}, abstract = {Several important viruses including the human immunodeficiency virus type 1 (HIV-1) and the SARS-associated Coronavirus (SARS-CoV) employ programmed -1 ribosomal frameshifting (PRF) for their protein expression. Here, a kinetic framework is developed to describe -1 PRF. The model reveals three kinetic pathways to -1 PRF that yield two possible frameshift products: those incorporating zero frame encoded A-site tRNAs in the recoding site, and products incorporating -1 frame encoded A-site tRNAs. Using known kinetic rate constants, the individual contributions of different steps of the translation elongation cycle to -1 PRF and the ratio between two types of frameshift products were evaluated. A dual fluorescence reporter was employed in Escherichia coli to empirically test the model. Additionally, the study applied a novel mass spectrometry approach to quantify the ratios of the two frameshift products. A more detailed understanding of the mechanisms underlying -1 PRF may provide insight into developing antiviral therapeutics.}, pmid = {20823091}, keywords = {Frameshifting,Genetic,HIV-1,HIV-1: genetics,Human T-lymphotropic virus 1,Human T-lymphotropic virus 1: genetics,Kinetics,Mass Spectrometry,Models,nosource,Peptide Chain Elongation,Ribosomal,Ribosomes,Ribosomes: metabolism,RNA,Transfer,Transfer: metabolism,Translational} } % == BibTeX quality report for liaoManyPathsFrameshifting2010: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{rakauskaiteRapidInexpensiveYeastbased2011, title = {A Rapid, Inexpensive Yeast-Based Dual-Fluorescence Assay of Programmed–1 Ribosomal Frameshifting for High-Throughput Screening.}, author = {Rakauskaite, Rasa and Liao, P. Y. and Rhodin, Michael H. J. and Lee, Kelvin and Dinman, J. D.}, year = 2011, month = may, journal = {Nucleic Acids Research}, eprint = {21602263}, eprinttype = {pubmed}, pages = {1–7}, issn = {1362-4962}, doi = {10.1093/nar/gkr382}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21602263}, abstract = {Programmed -1 ribosomal frameshifting (-1 PRF) is a mechanism that directs elongating ribosomes to shift-reading frame by 1 base in the 5’ direction that is utilized by many RNA viruses. Importantly, rates of -1 PRF are fine-tuned by viruses, including Retroviruses, Coronaviruses, Flavivriuses and in two endogenous viruses of the yeast Saccharomyces cerevisiae, to deliver the correct ratios of different viral proteins for efficient replication. Thus, -1 PRF presents a novel target for antiviral therapeutics. The underlying molecular mechanism of -1 PRF is conserved from yeast to mammals, enabling yeast to be used as a logical platform for high-throughput screens. Our understanding of the strengths and pitfalls of assays to monitor -1 PRF have evolved since the initial discovery of -1 PRF. These include controlling for the effects of drugs on protein expression and mRNA stability, as well as minimizing costs and the requirement for multiple processing steps. Here we describe the development of an automated yeast-based dual fluorescence assay of -1 PRF that provides a rapid, inexpensive automated pipeline to screen for compounds that alter rates of -1 PRF which will help to pave the way toward the discovery and development of novel antiviral therapeutics.}, pmid = {21602263}, keywords = {nosource} }

@article{rhodinCentralCoreRegion2011, title = {The Central Core Region of Yeast Ribosomal Protein {{L11}} Is Important for Subunit Joining and Translational Fidelity.}, author = {Rhodin, Michael H. J. and Rakauskait{.e}, Rasa and Dinman, Jonathan D.}, year = 2011, month = apr, journal = {Molecular genetics and genomics}, eprint = {21519857}, eprinttype = {pubmed}, pages = {505–516}, issn = {1617-4623}, doi = {10.1007/s00438-011-0623-2}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21519857}, abstract = {Yeast ribosomal protein L11 is positioned at the intersubunit cleft of the large subunit central protuberance, forming an intersubunit bridge with the small subunit protein S18. Mutants were engineered in the central core region of L11 which interacts with Helix 84 of the 25S rRNA. Numerous mutants in this region conferred 60S subunit biogenesis defects. Specifically, many mutations of F96 and the A66D mutant promoted formation of halfmers as assayed by sucrose density ultracentrifugation. Halfmer formation was not due to deficiency in 60S subunit production, suggesting that the mutants affected subunit-joining. Chemical modification analyses indicated that the A66D mutant, but not the F96 mutants, promoted changes in 25S rRNA structure, suggesting at least two modalities for subunit joining defects. 25S rRNA structural changes were located both adjacent to A66D (in H84), and more distant (in H96-7). While none of the mutants significantly affected ribosome/tRNA binding constants, they did have strong effects on cellular growth at both high and low temperatures, in the presence of translational inhibitors, and promoted changes in translational fidelity. Two distinct mechanisms are proposed by which L11 mutants may affect subunit joining, and identification of the amino acids associated with each of these processes are presented. These findings may have implications for our understanding of multifaceted diseases such as Diamond-Blackfan anemia which have been linked in part with mutations in L11.}, pmid = {21519857}, keywords = {nosource} }

@article{rhodinExtensiveNetworkInformation2011, title = {An {{Extensive Network}} of {{Information Flow}} through the {{B1b}}/c {{Intersubunit Bridge}} of the {{Yeast Ribosome}}}, author = {Rhodin, Michael H. J. and Dinman, J. D.}, editor = {Bryk, Mary}, year = 2011, month = may, journal = {PLoS ONE}, volume = {6}, number = {5}, pages = {e20048}, issn = {1932-6203}, doi = {10.1371/journal.pone.0020048}, keywords = {nosource} } % == BibTeX quality report for rhodinExtensiveNetworkInformation2011: % ? Title looks like it was stored in title-case in Zotero

@article{rhodinFlexibleLoopYeast2010, title = {A Flexible Loop in Yeast Ribosomal Protein {{L11}} Coordinates {{P-site tRNA}} Binding.}, author = {Rhodin, Michael H. J. and Dinman, Jonathan D.}, year = 2010, month = dec, journal = {Nucleic Acids Res.}, volume = {38}, number = {22}, pages = {8377–8389}, issn = {1362-4962}, doi = {10.1093/nar/gkq711}, abstract = {High-resolution structures reveal that yeast ribosomal protein L11 and its bacterial/archael homologs called L5 contain a highly conserved, basically charged internal loop that interacts with the peptidyl-transfer RNA (tRNA) T-loop. We call this the L11 ‘P-site loop’. Chemical protection of wild-type ribosome shows that that the P-site loop is inherently flexible, i.e. it is extended into the ribosomal P-site when this is unoccupied by tRNA, while it is retracted into the terminal loop of 25S rRNA Helix 84 when the P-site is occupied. To further analyze the function of this structure, a series of mutants within the P-site loop were created and analyzed. A mutant that favors interaction of the P-site loop with the terminal loop of Helix 84 promoted increased affinity for peptidyl-tRNA, while another that favors its extension into the ribosomal P-site had the opposite effect. The two mutants also had opposing effects on binding of aa-tRNA to the ribosomal A-site, and downstream functional effects were observed on translational fidelity, drug resistance/hypersensitivity, virus maintenance and overall cell growth. These analyses suggest that the L11 P-site loop normally helps to optimize ribosome function by monitoring the occupancy status of the ribosomal P-site.}, pmid = {20705654}, keywords = {Alleles,Drug Resistance,Fungal,Models,Molecular,Mutation,nosource,Phenotype,Protein Binding,Protein Biosynthesis,Protein Conformation,Ribosomal Proteins,Ribosomal Proteins: chemistry,Ribosomal Proteins: genetics,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: chemistry,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae: drug effects,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: growth & development,Temperature,Transfer,Transfer: metabolism} } % == BibTeX quality report for rhodinFlexibleLoopYeast2010: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{suGenomicOrganizationSequence1996, title = {Genomic {{Organization}} and {{Sequence Conservation}} in {{Type I Trichomonas}} Vaginalis {{Viruses}} 1}, author = {Su, Huei-min HM and Tai, Jung-hsiang JH}, year = 1996, journal = {Virology}, volume = {473}, pages = {470–473}, url = {http://www.sciencedirect.com/science/article/pii/S0042682296904468}, keywords = {nosource} }

@article{hugTelomereLengthHomeostasis2006, title = {Telomere Length Homeostasis}, author = {Hug, Nele}, year = 2006, month = dec, journal = {Chromosoma}, volume = {115}, number = {6}, eprint = {16741708}, eprinttype = {pubmed}, pages = {413–425}, publisher = {Springer}, issn = {0009-5915}, doi = {10.1007/s00412-006-0067-3}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16741708 http://www.springerlink.com/index/J733648224002878.pdf}, abstract = {The physical ends of chromosomes, known as telomeres, protect chromosome ends from nucleolytic degradation and DNA repair activities. Conventional DNA replication enzymes lack the ability to fully replicate telomere ends. In addition, nucleolytic activities contribute to telomere erosion. Short telomeres trigger DNA damage checkpoints, which mediate cellular senescence. Telomere length homeostasis requires telomerase, a cellular reverse transcriptase, which uses an internal RNA moiety as a template for the synthesis of telomere repeats. Telomerase elongates the 3’ ends of chromosomes, whereas the complementary strand is filled in by conventional DNA polymerases. In humans, telomerase is ubiquitously expressed only during the first weeks of embryogenesis, and is subsequently downregulated in most cell types. Correct telomere length setting is crucial for long-term survival. The telomere length reserve must be sufficient to avoid premature cellular senescence and the acceleration of age-related disease. On the other side, telomere shortening suppresses tumor formation through limiting the replicative potential of cells. In recent years, novel insight into the regulation of telomerase at chromosome ends has increased our understanding on how telomere length homeostasis in telomerase-positive cells is achieved. Factors that recruit telomerase to telomeres in a cell cycle-dependent manner have been identified in Saccharomyces cerevisiae. In humans, telomerase assembles with telomeres during S phase of the cell cycle. Presumably through mediating formation of alternative telomere structures, telomere-binding proteins regulate telomerase activity in cis to favor preferential elongation of the shortest telomeres. Phosphoinositide 3-kinase related kinases are also required for telomerase activation at chromosome ends, at least in budding and fission yeast. In vivo analysis of telomere elongation kinetics shows that telomerase does not act on every telomere in each cell cycle but that it exhibits an increasing preference for telomeres as their lengths decline. This suggests a model in which telomeres switch between extendible and nonextendible states in a length-dependent manner. In this review we expand this model to incorporate the finding that telomerase levels also limit telomere length and we propose a second switch between a non-telomerase-associated “extendible” and a telomerase-associated “extending” state.}, pmid = {16741708}, keywords = {Animals,Biological,Cell Cycle,Cell Cycle: physiology,Homeostasis,Homeostasis: genetics,Humans,Models,nosource,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Telomerase,Telomerase: metabolism,Telomere,Telomere-Binding Proteins,Telomere-Binding Proteins: metabolism,Telomere-Binding Proteins: physiology,Telomere: metabolism} }

@article{beckerStructureNogoMRNA2011, title = {Structure of the No-Go {{mRNA}} Decay Complex {{Dom34-Hbs1}} Bound to a Stalled {{80S}} Ribosome.}, author = {Becker, Thomas and Armache, Jean-Paul and Jarasch, Alexander and Anger, Andreas M. and Villa, Elizabeth and Sieber, Heidemarie and Motaal, Basma Abdel and Mielke, Thorsten and Berninghausen, Otto and Beckmann, Roland}, year = 2011, month = may, journal = {Nature Structural & Molecular Biology}, volume = {18}, number = {6}, eprint = {21623367}, eprinttype = {pubmed}, pages = {715–720}, publisher = {Nature Publishing Group}, issn = {1545-9985}, doi = {10.1038/nsmb.2057}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21623367}, abstract = {No-go decay (NGD) is a mRNA quality-control mechanism in eukaryotic cells that leads to degradation of mRNAs stalled during translational elongation. The key factors triggering NGD are Dom34 and Hbs1. We used cryo-EM to visualize NGD intermediates resulting from binding of the Dom34-Hbs1 complex to stalled ribosomes. At subnanometer resolution, all domains of Dom34 and Hbs1 were identified, allowing the docking of crystal structures and homology models. Moreover, the close structural similarity of Dom34 and Hbs1 to eukaryotic release factors (eRFs) enabled us to propose a model for the ribosome-bound eRF1-eRF3 complex. Collectively, our data provide structural insights into how stalled mRNA is recognized on the ribosome and how the eRF complex can simultaneously recognize stop codons and catalyze peptide release.}, pmid = {21623367}, keywords = {nosource} }

@article{fischerRibosomeDynamicsTRNA2010, title = {Ribosome Dynamics and {{tRNA}} Movement by Time-Resolved Electron Cryomicroscopy}, author = {Fischer, Niels and Konevega, Andrey L. and Wintermeyer, Wolfgang and Rodnina, M. V. and Stark, Holger}, year = 2010, month = jul, journal = {Nature}, volume = {466}, number = {7304}, pages = {329–333}, publisher = {Nature Publishing Group}, issn = {0028-0836}, doi = {10.1038/nature09206}, url = {http://www.nature.com/doifinder/10.1038/nature09206}, keywords = {nosource} }

@article{banerjee5TerminalCapStructure1980, title = {5’-{{Terminal Cap Structure}} in {{Eucaryotic Messenger Ribonucleic Acids}}.}, author = {Banerjee, a K.}, year = 1980, month = jun, journal = {Microbiological reviews}, volume = {44}, number = {2}, pages = {175–205}, issn = {0146-0749}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=373176&tool=pmcentrez&rendertype=abstract}, pmid = {6247631}, keywords = {Chemical Phenomena,Chemistry,Genetic,Guanine,Guanine: metabolism,Insect Viruses,Insect Viruses: metabolism,Messenger,Messenger: analysis,Messenger: biosynthesis,Messenger: metabolism,Methylation,Methyltransferases,Methyltransferases: metabolism,nosource,Nucleotidyltransferases,Orthomyxoviridae,Orthomyxoviridae: metabolism,Phosphates,Phosphates: analysis,Protein Biosynthesis,Reoviridae,Reoviridae: metabolism,Ribosomes,Ribosomes: metabolism,RNA,RNA Cap Analogs,RNA Cap Analogs: metabolism,RNA Caps,RNA Caps: isolation & purification,RNA Caps: metabolism,RNA Nucleotidyltransferases,RNA Nucleotidyltransferases: metabolism,Templates,Vaccinia virus,Vaccinia virus: metabolism,Vesicular stomatitis Indiana virus,Vesicular stomatitis Indiana virus: metabolism,Viral,Viral: analysis} } % == BibTeX quality report for banerjee5TerminalCapStructure1980: % ? Title looks like it was stored in title-case in Zotero

@article{takaiRoles5substituentsTRNA2003, title = {Roles of 5-Substituents of {{tRNA}} Wobble Uridines in the Recognition of Purine-Ending Codons}, author = {Takai, K.}, year = 2003, month = nov, journal = {Nucleic Acids Research}, volume = {31}, number = {22}, pages = {6383–6391}, issn = {1362-4962}, doi = {10.1093/nar/gkg839}, url = {http://www.nar.oupjournals.org/cgi/doi/10.1093/nar/gkg839}, keywords = {nosource} }

@article{seemanDNANanotechnologyNovel1998, title = {{{DNA}} Nanotechnology: Novel {{DNA}} Constructions.}, author = {Seeman, N. C.}, year = 1998, month = jan, journal = {Annual Review of Biophysics and Biomolecular Structure}, volume = {27}, eprint = {9646868}, eprinttype = {pubmed}, pages = {225–248}, issn = {1056-8700}, doi = {10.1146/annurev.biophys.27.1.225}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9646868}, abstract = {DNA nanotechnology entails the construction of specific geometrical and topological targets from DNA. The goals include the use of DNA molecules to scaffold the assembly of other molecules, particularly in periodic arrays, with the objects of both crystal facilitation and memory-device construction. Many of these products are based on branched DNA motifs. DNA molecules with the connectivities of a cube and a truncated octahedron have been prepared. A solid-support methodology has been developed to construct DNA targets. DNA trefoil and figure-8 knots have been made, predicated on the relationship between a topological crossing and a half-turn of B-DNA or Z-DNA. The same basis has been used to construct Borromean rings from DNA. An RNA knot has been used to demonstrate an RNA topoisomerase activity. The desire to construct periodic matter held together by DNA sticky ends has resulted in a search for stiff components; DNA double crossover molecules appear to be the best candidates. It appears that novel DNA motifs may be of use in the new field of DNA-based computing.}, pmid = {9646868}, keywords = {Biophysics,Biophysics: methods,DNA,DNA: chemistry,Models,Molecular,nosource,Nucleic Acid Conformation} }

@article{omahonyGlycineTRNAMutants1989, title = {Glycine {{tRNA}} Mutants with Normal Anticodon Loop Size Cause -1 Frameshifting.}, author = {O’Mahony, D. J. and Mims, B. H. and Thompson, S. and Murgola, E. J. and Atkins, J. F.}, year = 1989, month = oct, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {86}, number = {20}, pages = {7979–83}, issn = {0027-8424}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=298196&tool=pmcentrez&rendertype=abstract}, abstract = {Mutations in the acceptor stem, the 5-methyluridine-pseudouridine-cytidine (TFC) arm, and the anticodon of Salmonella tRNA2Gly can cause -1 frameshifting. The potential for standard base pairing between acceptor stem positions 1 and 72 is disrupted in the mutant sufS627. This disruption may interfere with the interaction of the tRNA with elongation factor-Tu.GTP or an as-yet-unspecified domain of the ribosome. The potential for standard base pairing in part of the TFC stem is disrupted in mutant sufS625. The nearly universal C-61 base of the TFC stem is altered in mutant sufS617, and the TFC loop is extended in mutant sufS605. These changes are expected to interfere with the stability of the TFC loop and its interaction with the D arm. The mutation in mutant sufS605, and possibly other mutants, alters nucleoside modification in the D arm. Three mutants, sufS601, sufS607, and sufS609, have a cytidine substituted for the modified uridine at position 34, the first anticodon position. None of the alterations grossly disrupts in-frame triplet decoding by the mutant tRNAs. The results show that -1 frameshifting in vivo can be caused by tRNAs with normal anticodon loop size and suggest that alternative conformational states of the mutant tRNAs may allow them to read a codon in frame or to shift reading frame.}, pmid = {2813373}, keywords = {Amino Acid-Specific,Amino Acid-Specific: genetics,Anticodon,Anticodon: genetics,Bacterial,Bacterial: genetics,Base Sequence,Cloning,DNA,Gly,Gly: genetics,Molecular,Molecular Sequence Data,Mutation,nosource,Nucleic Acid Conformation,RNA,Salmonella,Salmonella: genetics,Transfer,Transfer: genetics} }

@article{xuConservedRRNAMethyltransferase2008, title = {A Conserved {{rRNA}} Methyltransferase Regulates Ribosome Biogenesis.}, author = {Xu, Zhili and O’Farrell, Heather C. and Rife, Jason P. and Culver, Gloria M.}, year = 2008, month = may, journal = {Nature Structural & Molecular Biology}, volume = {15}, number = {5}, eprint = {18391965}, eprinttype = {pubmed}, pages = {534–536}, issn = {1545-9985}, doi = {10.1038/nsmb.1408}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18391965}, abstract = {In contrast to the diversity of most ribosomal RNA modification patterns and systems, the KsgA methyltransferase family seems to be nearly universally conserved along with the modifications it catalyzes. Our data reveal that KsgA interacts with small ribosomal subunits near functional sites, including Initiation factor 3 and 50S subunit binding sites. These findings suggest a checkpoint role for this modification system and offer a functional rationale for the unprecedented level of conservation.}, pmid = {18391965}, keywords = {16S,16S: chemistry,16S: metabolism,Animals,Bacteria,Bacteria: cytology,Bacteria: enzymology,Bacteria: metabolism,Binding Sites,Euglena gracilis,Euglena gracilis: cytology,Euglena gracilis: enzymology,Euglena gracilis: metabolism,Methyltransferases,Methyltransferases: chemistry,Methyltransferases: metabolism,Models,Molecular,nosource,Nucleic Acid Conformation,Ribosomal,Ribosomes,Ribosomes: metabolism,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae: cytology,Saccharomyces cerevisiae: enzymology,Saccharomyces cerevisiae: metabolism} }

@article{alonsoNonsensemediatedRNADecay2005, title = {Nonsense-Mediated {{RNA}} Decay: A Molecular System Micromanaging Individual Gene Activities and Suppressing Genomic Noise.}, author = {Alonso, Claudio R.}, year = 2005, month = may, journal = {BioEssays}, volume = {27}, number = {5}, eprint = {15832387}, eprinttype = {pubmed}, pages = {463–466}, issn = {0265-9247}, doi = {10.1002/bies.20227}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15832387}, abstract = {Nonsense-mediated RNA decay (NMD) is an evolutionary conserved system of RNA surveillance that detects and degrades RNA transcripts containing nonsense mutations. Given that these mutations arise at a relatively low frequency, are there any as yet unknown substrates of NMD in a wild-type cell? With this question in mind, Mendell et al. have used a microarray assay to identify those human genes under NMD regulation. Their results show that, in human cells, NMD regulates hundreds of physiologic transcripts and not just those containing nonsense mutations. Among the NMD targets are a number of non-functional RNAs expressed from vestigial sequences derived from retroviral and transposable elements. These findings support the notion that NMD is a high profile post-transcriptional mechanism micromanaging the activity of multiple gene batteries and suppressing the expression of genetic remnants.}, pmid = {15832387}, keywords = {Animals,Evolution,Gene Expression Regulation,Genomics,Humans,Molecular,nosource,RNA,RNA Stability,RNA Stability: genetics,RNA: genetics,RNA: metabolism} }

@article{molnarCompleteNucleotideSequence1997, title = {Complete Nucleotide Sequence of Tobacco Necrosis Virus Strain {{DH}} and Genes Required for {{RNA}} Replication and Virus Movement.}, author = {Moln{'a}r, a and Havelda, Z. and Dalmay, T. and Szutorisz, H. and Burgy{'a}n, J.}, year = 1997, month = jun, journal = {The Journal of General Virology}, volume = {78 ( Pt 6)}, eprint = {9191913}, eprinttype = {pubmed}, pages = {1235–1239}, issn = {0022-1317}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9191913}, abstract = {The complete genome sequence of tobacco necrosis virus strain D (Hungarian isolate, TNV-DH) was determined. The genome (3762 nt) has an organization identical to that reported for TNV-D. Highly infectious synthetic transcripts from a full-length TNV-DH cDNA clone were prepared, the first infectious necrovirus transcript reported. This clone was used for reverse genetic studies to map the viral genes required for replication and movement. Protoplast inoculation with delta 22 and delta 82 mutants revealed that both the 22 kDa and 82 kDa gene products are required for RNA replication. Although the products of three small central genes (p7(1), p7a and p7b) were not essential for RNA replication in protoplasts, mutations in these ORFs prevented infection of plants. In contrast, viral RNA accumulation and cell-to-cell movement were observed in the inoculated, but not the systemically infected, leaves of Nicotiana benthamiana challenged with RNA lacking the intact coat protein (CP) gene. These results strongly suggest that p7(1), p7a, p7b and CP are involved in TNV-DH cell-to-cell and long-distance movement, respectively.}, pmid = {9191913}, keywords = {Base Sequence,Genes,Molecular Sequence Data,Movement,nosource,Plant Viruses,Plant Viruses: genetics,Plant Viruses: physiology,Plants,RNA,Tobacco,Tobacco: virology,Toxic,Viral,Viral: genetics} }

@article{vazquez-laslopMolecularMechanismDrugdependent2008, title = {Molecular Mechanism of Drug-Dependent Ribosome Stalling.}, author = {{Vazquez-Laslop}, Nora and Thum, Celine and Mankin, Alexander S.}, year = 2008, month = apr, journal = {Mol. Cell}, volume = {30}, number = {2}, eprint = {18439898}, eprinttype = {pubmed}, pages = {190–202}, issn = {1097-4164}, doi = {10.1016/j.molcel.2008.02.026}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18439898}, abstract = {Inducible expression of the erm erythromycin resistance genes relies on drug-dependent ribosome stalling. The molecular mechanisms underlying stalling are unknown. We used a cell-free translation system to elucidate the contribution of the nascent peptide, the drug, and the ribosome toward formation of the stalled complex during translation of the ermC leader cistron. Toe-printing mapping, selective amino acid labeling, and mutational analyses revealed the peptidyl transferase center (PTC) as the focal point of the stalling mechanism. In the ribosome exit tunnel, the C-terminal sequence of the nascent peptide, critical for stalling, is in the immediate vicinity of the universally conserved A2062 of 23S rRNA. Mutations of this nucleotide eliminate stalling. Because A2062 is located in the tunnel, it may trigger a conformational change in the PTC, responding to the presence of a specific nascent peptide. The cladinose-containing macrolide antibiotic in the tunnel positions the nascent peptide for interaction with the tunnel sensory elements.}, pmid = {18439898}, keywords = {5’ Untranslated Regions,5’ Untranslated Regions: metabolism,Amino Acid Sequence,Amino Acyl,Amino Acyl: metabolism,Anti-Bacterial Agents,Anti-Bacterial Agents: metabolism,Bacterial,Bacterial: genetics,Base Sequence,Cell-Free System,DNA Footprinting,Drug Resistance,Erythromycin,Erythromycin: metabolism,Escherichia coli,Escherichia coli: genetics,Escherichia coli: metabolism,Methyltransferases,Methyltransferases: genetics,Methyltransferases: metabolism,Models,Molecular,Molecular Sequence Data,Mutation,nosource,Peptidyl Transferases,Peptidyl Transferases: genetics,Peptidyl Transferases: metabolism,Protein Biosynthesis,Protein Biosynthesis: genetics,Ribosomes,Ribosomes: chemistry,Ribosomes: genetics,Ribosomes: metabolism,RNA,Transfer} } % == BibTeX quality report for vazquez-laslopMolecularMechanismDrugdependent2008: % ? Possibly abbreviated journal title Mol. Cell

@article{johnsonXrn1Ski2Sep11995, title = {(Xrn1) Ski2 and Sep1 (Xrn1) Ski3 Mutants of {{Saccharomyces}} Cerevisiae Is Independent of Killer Virus and Suggests a General Role for These Genes in Translation Control.}, author = {Johnson, AW A. W. W. and Kolodner, R. D. D. RD}, year = 1995, journal = {Molecular and cellular biology}, volume = {15}, number = {5}, pages = {2719–2727}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/15/5/2719 http://mcb.asm.org/content/15/5/2719.short}, keywords = {nosource} }

@article{hirSpliceosomeDepositsMultiple2000, title = {The Spliceosome Deposits Multiple Proteins 20-24 Nucleotides Upstream of {{mRNA}} Exon-Exon Junctions.}, author = {Hir, H. Le and Izaurralde, E. and Maquat, L. E. E. and Moore, M. J.}, year = 2000, month = dec, journal = {The EMBO journal}, volume = {19}, number = {24}, pages = {6860–9}, issn = {0261-4189}, doi = {10.1093/emboj/19.24.6860}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=305905&tool=pmcentrez&rendertype=abstract}, abstract = {Eukaryotic mRNAs exist in vivo as ribonucleoprotein particles (mRNPs). The protein components of mRNPs have important functions in mRNA metabolism, including effects on subcellular localization, translational efficiency and mRNA half-life. There is accumulating evidence that pre-mRNA splicing can alter mRNP structure and thereby affect downstream mRNA metabolism. Here, we report that the spliceosome stably deposits several proteins on mRNAs, probably as a single complex of approximately 335 kDa. This complex protects 8 nucleotides of mRNA from complete RNase digestion at a conserved position 20-24 nucleotides upstream of exon-exon junctions. Splicing-dependent RNase protection of this region was observed in both HeLa cell nuclear extracts and Xenopus laevis oocyte nuclei. Immunoprecipitations revealed that five components of the complex are the splicing-associated factors SRm160, DEK and RNPS1, the mRNA-associated shuttling protein Y14 and the mRNA export factor REF. Possible functions for this complex in nucleocytoplasmic transport of spliced mRNA, as well as the nonsense-mediated mRNA decay pathway, are discussed.}, pmid = {11118221}, keywords = {Animals,Antigens,Cell Nucleus,Cell Nucleus: physiology,Cytoplasm,Cytoplasm: physiology,DNA-Binding Proteins,DNA-Binding Proteins: metabolism,Exons,Female,Half-Life,Hela Cells,Humans,Messenger,Messenger: genetics,Messenger: metabolism,nosource,Nuclear,Nuclear Matrix-Associated Proteins,Nuclear Proteins,Nuclear Proteins: metabolism,Oocytes,Oocytes: physiology,Protein Biosynthesis,Ribonuclease H,Ribonucleoproteins,RNA,RNA Splicing,RNA-Binding Proteins,RNA-Binding Proteins: metabolism,Spliceosomes,Spliceosomes: metabolism,Xenopus laevis} }

@article{hirPremRNASplicingAlters2000, title = {Pre-{{mRNA}} Splicing Alters {{mRNP}} Composition: Evidence for Stable Association of Proteins at Exon-Exon Junctions.}, author = {Hir, H. Le and Moore, M. J. and Maquat, L. E. E.}, year = 2000, month = may, journal = {Genes & development}, volume = {14}, number = {9}, pages = {1098–108}, issn = {0890-9369}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=316578&tool=pmcentrez&rendertype=abstract}, abstract = {We provide direct evidence that pre-mRNA splicing alters mRNP protein composition. Using a novel in vitro cross-linking approach, we detected several proteins that associate with mRNA exon-exon junctions only as a consequence of splicing. Immunoprecipitation experiments suggested that these proteins are part of a tight complex around the junction. Two were identified as SRm160, a nuclear matrix-associated splicing coactivator, and hPrp8p, a core component of U5 snRNP and spliceosomes. Glycerol gradient fractionation showed that a subset of these proteins remain associated with mRNA after its release from the spliceosome. These results demonstrate that the spliceosome can leave behind signature proteins at exon-exon junctions. Such proteins could influence downstream metabolic events in vivo such as mRNA transport, translation, and nonsense-mediated decay.}, pmid = {10809668}, keywords = {Antigens,Base Sequence,Cell Nucleus,Cell Nucleus: metabolism,Exons,Hela Cells,Humans,Introns,Messenger,Messenger: genetics,Molecular Sequence Data,nosource,Nuclear,Nuclear Matrix-Associated Proteins,Nuclear Proteins,Nuclear Proteins: isolation & purification,Nuclear Proteins: metabolism,Ribonucleoprotein,Ribonucleoproteins,Ribonucleoproteins: genetics,Ribonucleoproteins: metabolism,RNA,RNA Precursors,RNA Precursors: chemical synthesis,RNA Precursors: chemistry,RNA Precursors: metabolism,RNA Splicing,RNA-Binding Proteins,RNA-Binding Proteins: isolation & purification,RNA-Binding Proteins: metabolism,Spliceosomes,Spliceosomes: metabolism,U5 Small Nuclear,U5 Small Nuclear: isolation & p,U5 Small Nuclear: metabolism} }

@article{hanPredictionRNAbindingProteins2004, title = {Prediction of {{RNA-binding}} Proteins from Primary Sequence by a Support Vector Machine Approach}, author = {Han, L. Y. I. Y. I. and Cai, C. Z. Z. and Lo, S. L. I. N. and Chung, M. and Chen, Y. U. Z. U. Z.}, year = 2004, journal = {RNA}, volume = {10}, number = {3}, pages = {355}, publisher = {Cold Spring Harbor Lab}, doi = {10.1261/rna.5890304.al.}, url = {http://rnajournal.cshlp.org/content/10/3/355.short}, keywords = {mrna,nosource,protein interactions,rna,rna-binding proteins,rrna,snrna,support vector machine,trna} }

@article{alekhinaTranslationNoncappedMRNAs2007, title = {Translation of Non-Capped {{mRNAs}} in a Eukaryotic Cell-Free System: Acceleration of Initiation Rate in the Course of Polysome Formation.}, author = {Alekhina, Olga M. and Vassilenko, Konstantin S. and Spirin, Alexander S.}, year = 2007, month = jan, journal = {Nucleic Acids Research}, volume = {35}, number = {19}, pages = {6547–6559}, issn = {1362-4962}, doi = {10.1093/nar/gkm725}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2095793&tool=pmcentrez&rendertype=abstract}, abstract = {Real-time monitoring of the translation of non-capped luciferase mRNA in a wheat germ cell-free system has been performed by continuous in situ measurement of the luminescence increase in the translation mixture. The phenomenon of acceleration of translation has been revealed. It has been shown that the acceleration is accompanied by the loading of translating polysomes with additional ribosomes, and thus is caused mainly by a rise in the initiation rate, rather than the stimulation of elongation or the involvement of additional mRNA molecules in translation. The acceleration requires a sufficient concentration of mRNA and depends on the sequence of the 5’ untranslated region (UTR). It can be abolished by the addition of excess cap analog (m(7)GpppGm). As the acceleration does not depend on the preliminary translation of other mRNAs in the same extract, the conclusion has been made that the effect is not due to activation of the ribosome population or other components of the system during translation, but rather it is the consequence of intra-polysomal events. The acceleration observed is discussed in terms of the model of two overlapping initiation pathways in eukaryotic polysomes: translation of non-capped mRNAs starts with eIF4F-independent initiation at 5’ UTR, and after the formation of sufficiently loaded polysomes, they rearrange in such a way that a mechanism of re-initiation of terminating ribosomes switches on. The eIF4F-mediated circularization of polysomes may be considered as a possible event that leads to the re-initiation switch and the resultant acceleration effect.}, pmid = {17897963}, keywords = {5’ Untranslated Regions,5’ Untranslated Regions: chemistry,Cell-Free System,Firefly,Firefly: biosynthesis,Firefly: genetics,Kinetics,Luciferases,Luminescent Agents,Luminescent Agents: analysis,nosource,Peptide Chain Elongation,Peptide Chain Initiation,Plant Extracts,Plant Extracts: metabolism,Polyribosomes,Polyribosomes: metabolism,Ribosome Subunits,Ribosome Subunits: metabolism,RNA Cap Analogs,RNA Cap Analogs: chemistry,Translational,Triticum,Triticum: metabolism} }

@article{malyginHumanRibosomalProtein2007, title = {Human Ribosomal Protein {{S13}} Regulates Expression of Its Own Gene at the Splicing Step by a Feedback Mechanism.}, author = {{}a Malygin, Alexey and Parakhnevitch, Natalia M. and Ivanov, Anton V. and Eperon, Ian C. and Karpova, Galina G.}, year = 2007, month = jan, journal = {Nucleic Acids Research}, volume = {35}, number = {19}, pages = {6414–6423}, issn = {1362-4962}, doi = {10.1093/nar/gkm701}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2095825&tool=pmcentrez&rendertype=abstract}, abstract = {The expression of ribosomal protein (rp) genes is regulated at multiple levels. In yeast, two genes are autoregulated by feedback effects of the protein on pre-mRNA splicing. Here, we have investigated whether similar mechanisms occur in eukaryotes with more complicated and highly regulated splicing patterns. Comparisons of the sequences of ribosomal protein S13 gene (RPS13) among mammals and birds revealed that intron 1 is more conserved than the other introns. Transfection of HEK 293 cells with a minigene-expressing ribosomal protein S13 showed that the presence of intron 1 reduced expression by a factor of four. Ribosomal protein S13 was found to inhibit excision of intron 1 from rpS13 pre-mRNA fragment in vitro. This protein was shown to be able to specifically bind the fragment and to confer protection against ribonuclease cleavage at sequences near the 5’ and 3’ splice sites. The results suggest that overproduction of rpS13 in mammalian cells interferes with splicing of its own pre-mRNA by a feedback mechanism.}, pmid = {17881366}, keywords = {Animals,Base Sequence,Binding Sites,Cell Line,Chickens,Chickens: genetics,Conserved Sequence,Down-Regulation,Homeostasis,Humans,Introns,Messenger,Messenger: metabolism,Mice,nosource,Rats,Ribosomal Proteins,Ribosomal Proteins: genetics,Ribosomal Proteins: metabolism,RNA,RNA Precursors,RNA Precursors: metabolism,RNA Splice Sites,RNA Splicing} }

@article{ulyanovPseudoknotStructuresConserved2007, title = {Pseudoknot Structures with Conserved Base Triples in Telomerase {{RNAs}} of Ciliates.}, author = {Ulyanov, Nikolai B. and Shefer, Kinneret and James, Thomas L. and Tzfati, Yehuda}, year = 2007, month = jan, journal = {Nucleic Acids Research}, volume = {35}, number = {18}, eprint = {17827211}, eprinttype = {pubmed}, pages = {6150–6160}, issn = {1362-4962}, doi = {10.1093/nar/gkm660}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17827211}, abstract = {Telomerase maintains the integrity of telomeres, the ends of linear chromosomes, by adding G-rich repeats to their 3’-ends. Telomerase RNA is an integral component of telomerase. It contains a template for the synthesis of the telomeric repeats by the telomerase reverse transcriptase. Although telomerase RNAs of different organisms are very diverse in their sequences, a functional non-template element, a pseudoknot, was predicted in all of them. Pseudoknot elements in human and the budding yeast Kluyveromyces lactis telomerase RNAs contain unusual triple-helical segments with AUU base triples, which are critical for telomerase function. Such base triples in ciliates have not been previously reported. We analyzed the pseudoknot sequences in 28 ciliate species and classified them in six different groups based on the lengths of the stems and loops composing the pseudoknot. Using miniCarlo, a helical parameter-based modeling program, we calculated 3D models for a representative of each morphological group. In all cases, the predicted structure contains at least one AUU base triple in stem 2, except for that of Colpidium colpoda, which contains unconventional GCG and AUA triples. These results suggest that base triples in a pseudoknot element are a conserved feature of all telomerases.}, pmid = {17827211}, keywords = {Animals,Base Sequence,Ciliophora,Ciliophora: genetics,Conserved Sequence,Models,Molecular,nosource,Nucleic Acid Conformation,Protozoan,Protozoan: chemistry,Protozoan: classification,RNA,RNA: chemistry,RNA: classification,Telomerase,Telomerase: chemistry,Telomerase: classification,Tetrahymenina,Tetrahymenina: genetics} }

@article{pavithraStabilizationSMAR1MRNA2007, title = {Stabilization of {{SMAR1 mRNA}} by {{PGA2}} Involves a Stem Loop Structure in the 5’ {{UTR}}.}, author = {Pavithra, Lakshminarasimhan and Rampalli, Shravanti and Sinha, Surajit and Sreenath, Kadreppa and Pestell, Richard G. and Chattopadhyay, Samit}, year = 2007, month = jan, journal = {Nucleic Acids Research}, volume = {35}, number = {18}, pages = {6004–6016}, issn = {1362-4962}, doi = {10.1093/nar/gkm649}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2094063&tool=pmcentrez&rendertype=abstract}, abstract = {Prostaglandins are anticancer agents known to inhibit tumor cell proliferation both in vitro and in vivo by affecting the mRNA stability. Here we report that a MAR-binding protein SMAR1 is a target of Prostaglandin A2 (PGA2) induced growth arrest. We identify a regulatory mechanism leading to stabilization of SMAR1 transcript. Our results show that a minor stem and loop structure present in the 5’ UTR of SMAR1 (1-UTR) is critical for nucleoprotein complex formation that leads to SMAR1 stabilization in response to PGA2. This results in an increased SMAR1 transcript and altered protein levels, that in turn causes downregulation of Cyclin D1 gene, essential for G1/S phase transition. We also provide evidence for the presence of a variant 5’ UTR SMAR1 (17-UTR) in breast cancer-derived cell lines. This form lacks the minor stem and loop structure required for mRNA stabilization in response to PGA2. As a consequence of this, there is a low level of endogenous tumor suppressor protein SMAR1 in breast cancer-derived cell lines. Our studies provide a mechanistic insight into the regulation of tumor suppressor protein SMAR1 by a cancer therapeutic PGA2, that leads to repression of Cyclin D1 gene.}, pmid = {17726044}, keywords = {5’ Untranslated Regions,5’ Untranslated Regions: chemistry,Antineoplastic Agents,Antineoplastic Agents: pharmacology,Base Sequence,Breast Neoplasms,Breast Neoplasms: genetics,Breast Neoplasms: metabolism,Cell Cycle,Cell Cycle Proteins,Cell Cycle Proteins: biosynthesis,Cell Cycle Proteins: genetics,Cell Line,Cyclin D,Cyclins,Cyclins: metabolism,DNA-Binding Proteins,DNA-Binding Proteins: biosynthesis,DNA-Binding Proteins: genetics,Humans,Messenger,Messenger: metabolism,Molecular Sequence Data,nosource,Nuclear Proteins,Nuclear Proteins: biosynthesis,Nuclear Proteins: genetics,Nucleic Acid Conformation,Prostaglandins A,Prostaglandins A: pharmacology,RNA,RNA Stability,RNA Stability: drug effects,Tumor} }

@article{frankProcessMRNAtRNATranslocation2007, title = {The Process of {{mRNA-tRNA}} Translocation.}, author = {Frank, Joachim and Gao, Haixiao and Sengupta, Jayati and Gao, Ning and Taylor, Derek J.}, year = 2007, month = dec, journal = {PNAS}, volume = {104}, number = {50}, pages = {19671–19678}, issn = {1091-6490}, doi = {10.1073/pnas.0708517104}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2148355&tool=pmcentrez&rendertype=abstract}, abstract = {In the elongation cycle of translation, translocation is the process that advances the mRNA-tRNA moiety on the ribosome, to allow the next codon to move into the decoding center. New results obtained by cryoelectron microscopy, interpreted in the light of x-ray structures and kinetic data, allow us to develop a model of the molecular events during translocation.}, pmid = {18003906}, keywords = {Animals,Biological Transport,Catalysis,Genetic,Guanosine Triphosphate,Guanosine Triphosphate: metabolism,Humans,Hydrolysis,Messenger,Messenger: chemistry,Messenger: genetics,Messenger: metabolism,Messenger: ultrastructure,Models,nosource,Peptide Elongation Factor G,Peptide Elongation Factor G: chemistry,Peptide Elongation Factor G: metabolism,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,RNA,Transfer,Transfer: chemistry,Transfer: genetics,Transfer: metabolism,Transfer: ultrastructure} }

@article{saguezFormationExportcompetentMRNP2005, title = {Formation of Export-Competent {{mRNP}}: Escaping Nuclear Destruction.}, author = {Saguez, Cyril and Olesen, Jens Raabjerg and Jensen, Torben Heick}, year = 2005, month = jun, journal = {Current Opinion in Cell Biology}, volume = {17}, number = {3}, eprint = {15901499}, eprinttype = {pubmed}, pages = {287–293}, issn = {0955-0674}, doi = {10.1016/j.ceb.2005.04.009}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15901499}, abstract = {In eukaryotic cells, primary transcripts are processed and bound by proteins before export to the cytoplasm. Nuclear production of export-competent messenger ribonucleoprotein particles (mRNPs) is a complicated process, and mRNP biogenic events that function sub-optimally are rapidly attacked by surveillance leading to degradation of the mRNA. Export of nuclear mRNAs is therefore constantly challenged by the opposing force of mRNA retention and decay. This balance ensures that only ‘perfect’ transcripts persist, and that non-functional and potentially deleterious transcripts are removed early in their biogenesis. Thus, eukaryotic systems of mRNP quality control can be viewed as simple Darwinian principles operating at the molecular level.}, pmid = {15901499}, keywords = {Active Transport,Biological,Cell Nucleus,Cell Nucleus: metabolism,Cell Nucleus: physiology,Fungal,Gene Expression Regulation,Genetic,Messenger,Messenger: genetics,Messenger: metabolism,Models,nosource,Polyadenylation,Polyadenylation: physiology,Post-Transcriptional,Post-Transcriptional: physiology,Ribonucleoproteins,Ribonucleoproteins: genetics,Ribonucleoproteins: metabolism,RNA,RNA Caps,RNA Caps: genetics,RNA Caps: metabolism,RNA Processing,RNA Splicing,RNA Splicing: physiology,RNA Transport,RNA Transport: physiology,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Transcription} }

@article{satoEfficiencyPioneerTranslation2008, title = {Efficiency of the Pioneer Round of Translation Affects the Cellular Site of Nonsense-Mediated {{mRNA}} Decay}, author = {Sato, Hanae and Hosoda, Nao and Maquat, Lynne E. LE}, year = 2008, month = feb, journal = {Molecular cell}, volume = {29}, number = {2}, eprint = {18243119}, eprinttype = {pubmed}, pages = {255–262}, issn = {1097-2765}, doi = {10.1016/j.molcel.2007.12.009}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18243119 http://www.sciencedirect.com/science/article/pii/S109727650700860X}, abstract = {In mammalian cells, nonsense-mediated mRNA decay (NMD) is a consequence of nonsense codon recognition during a pioneer round of translation. This round can occur largely before or largely after the release of newly synthesized mRNA from nuclei, depending on the mRNA, and likely utilizes cytoplasmic ribosomes. We show that increasing the cellular concentration of the splicing factor SF2/ASF augments the efficiency of NMD and ultimately shifts NMD that takes place after mRNA export to the cytoplasm to NMD that occurs before mRNA release from nuclei. These changes are accompanied by an increased association of pioneer translation initiation complexes with SF2/ASF, translationally active ribosomes, and the translational activator TAP. Increased TAP binding correlates with increased SF2/ASF binding, but not increased REF/Aly or Y14 binding. Our results uncover an additional role for SF2/ASF and indicate that the efficiency of the pioneer round of translation influences the efficiency of subsequent rounds of translation.}, pmid = {18243119}, keywords = {Active Transport,Animals,Cell Nucleus,Cell Nucleus: genetics,Cell Nucleus: metabolism,Cell Nucleus: physiology,Cercopithecus aethiops,Codon,COS Cells,Cytoplasm,Cytoplasm: genetics,Cytoplasm: metabolism,Hela Cells,Humans,Messenger,Messenger: genetics,Messenger: metabolism,Nonsense,Nonsense: genetics,Nonsense: metabolism,nosource,Nuclear Proteins,Nuclear Proteins: genetics,Nuclear Proteins: metabolism,Protein Biosynthesis,Protein Biosynthesis: physiology,Ribosomes,Ribosomes: genetics,Ribosomes: metabolism,RNA,RNA Stability,RNA Stability: physiology,RNA-Binding Proteins,RNA-Binding Proteins: genetics,RNA-Binding Proteins: metabolism,Transcription Factors,Transcription Factors: genetics,Transcription Factors: metabolism} }

@article{mannRNASurveillanceWatching1999, title = {{{RNA}} Surveillance: Watching the Defectives}, author = {Mann, K.}, year = 1999, journal = {NCBI Coffee Break}, publisher = {Sage Publications}, url = {http://csp.sagepub.com/content/14/41/79.short}, keywords = {nosource} }

@article{chenEmergingConsensusTelomerase2004, title = {An Emerging Consensus for Telomerase {{RNA}} Structure.}, author = {Chen, Jiunn-Liang and Greider, Carol W.}, year = 2004, month = oct, journal = {Proceedings of the National Academy of Sciences}, volume = {101}, number = {41}, pages = {14683–14684}, issn = {0027-8424}, doi = {10.1073/pnas.0406204101}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=522039&tool=pmcentrez&rendertype=abstract}, pmid = {15466703}, keywords = {Animals,Base Sequence,Biological Evolution,Conserved Sequence,DNA-Binding Proteins,Fungal,Fungal: chemistry,Fungal: genetics,nosource,Nucleic Acid,RNA,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Sequence Alignment,Sequence Homology,Telomerase,Telomerase: chemistry,Telomerase: genetics,Telomerase: metabolism} }

@article{benensonDNAMoleculeProvides2003, title = {{{DNA}} Molecule Provides a Computing Machine with Both Data and Fuel}, author = {Benenson, Yaakov and Adar, Rivka and {Paz-Elizur}, Tamar and Livneh, Zvi and Shapiro, Ehud}, year = 2003, journal = {Proceedings of the }, volume = {100}, number = {5}, pages = {2191}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/100/5/2191.short}, keywords = {nosource} }

@article{changNonsensemediatedDecayRNA2007, title = {The Nonsense-Mediated Decay {{RNA}} Surveillance Pathway.}, author = {Chang, Yao-Fu and Imam, J. Saadi and Wilkinson, Miles F.}, year = 2007, month = jan, journal = {Annual Review of Biochemistry}, volume = {76}, eprint = {17352659}, eprinttype = {pubmed}, pages = {51–74}, issn = {0066-4154}, doi = {10.1146/annurev.biochem.76.050106.093909}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17352659}, abstract = {Nonsense-mediated mRNA decay (NMD) is a quality-control mechanism that selectively degrades mRNAs harboring premature termination (nonsense) codons. If translated, these mRNAs can produce truncated proteins with dominant-negative or deleterious gain-of-function activities. In this review, we describe the molecular mechanism of NMD. We first cover conserved factors known to be involved in NMD in all eukaryotes. We then describe a unique protein complex that is deposited on mammalian mRNAs during splicing, which defines a stop codon as premature. Interaction between this exon-junction complex (EJC) and NMD factors assembled at the upstream stop codon triggers a series of steps that ultimately lead to mRNA decay. We discuss whether these proofreading events preferentially occur during a “pioneer” round of translation in higher and lower eukaryotes, their cellular location, and whether they can use alternative EJC factors or act independent of the EJC.}, pmid = {17352659}, keywords = {Animals,Codon,Exons,Humans,Messenger,Messenger: genetics,Messenger: metabolism,Missense,Multiprotein Complexes,Mutation,nosource,Protein Biosynthesis,RNA,RNA Splicing,RNA Stability,RNA-Binding Proteins,RNA-Binding Proteins: metabolism,Trans-Activators,Trans-Activators: metabolism,Transcription Factors,Transcription Factors: metabolism} }

@article{meskauskasMolecularClampEnsures2010, title = {A Molecular Clamp Ensures Allosteric Coordination of Peptidyltransfer and Ligand Binding to the Ribosomal {{A-site}}}, author = {Meskauskas, A. and Dinman, J. D.}, year = 2010, journal = {Nucleic Acids Res.}, volume = {38}, number = {21}, pages = {7800–13}, publisher = {Oxford Univ Press}, keywords = {nosource,nucleic acids research} } % == BibTeX quality report for meskauskasMolecularClampEnsures2010: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{mokrejsIRESiteDatabaseExperimentally2006, title = {{{IRESite}}: The Database of Experimentally Verified {{IRES}} Structures (Www. Iresite. Org)}, author = {Mokrej{}, M. and Vop{'a}lensk{'y}, V{'a}clav and Mokrejs, Martin and Kolenaty, Ondrej and Masek, Tom{'a}s and Feketov{'a}, Zuzana and Sekyrov{'a}, Petra and Skaloudov{'a}, Barbora and Kr{'i}z, V{'i}tezslav and Posp{'i}sek, Martin}, year = 2006, month = jan, journal = {Nucleic acids }, volume = {34}, number = {Database issue}, pages = {125–130}, issn = {1362-4962}, doi = {10.1093/nar/gkj081}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1347444&tool=pmcentrez&rendertype=abstract http://nar.oxfordjournals.org/content/34/suppl_1/D125.short}, abstract = {IRESite is an exhaustive, manually annotated non-redundant relational database focused on the IRES elements (Internal Ribosome Entry Site) and containing information not available in the primary public databases. IRES elements were originally found in eukaryotic viruses hijacking initiation of translation of their host. Later on, they were also discovered in 5’-untranslated regions of some eukaryotic mRNA molecules. Currently, IRESite presents up to 92 biologically relevant aspects of every experiment, e.g. the nature of an IRES element, its functionality/defectivity, origin, size, sequence, structure, its relative position with respect to surrounding protein coding regions, positive/negative controls used in the experiment, the reporter genes used to monitor IRES activity, the measured reporter protein yields/activities, and references to original publications as well as cross-references to other databases, and also comments from submitters and our curators. Furthermore, the site presents the known similarities to rRNA sequences as well as RNA-protein interactions. Special care is given to the annotation of promoter-like regions. The annotated data in IRESite are bound to mostly complete, full-length mRNA, and whenever possible, accompanied by original plasmid vector sequences. New data can be submitted through the publicly available web-based interface at http://www.iresite.org and are curated by a team of lab-experienced biologists.}, pmid = {16381829}, keywords = {5’ Untranslated Regions,5’ Untranslated Regions: chemistry,Databases,Genetic,Internet,Messenger,Messenger: chemistry,nosource,Nucleic Acid,Peptide Chain Initiation,Peptide Initiation Factors,Peptide Initiation Factors: metabolism,Plasmids,Plasmids: chemistry,Promoter Regions,Regulatory Sequences,Ribonucleic Acid,RNA,Translational,User-Computer Interface,Viral,Viral: chemistry} }

@article{shyuMessengerRNARegulation2008, title = {Messenger {{RNA}} Regulation: To Translate or to Degrade.}, author = {Shyu, Ann-Bin and Wilkinson, Miles F. and {}van Hoof, Ambro}, year = 2008, month = feb, journal = {The EMBO Journal}, volume = {27}, number = {3}, pages = {471–481}, issn = {1460-2075}, doi = {10.1038/sj.emboj.7601977}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2241649&tool=pmcentrez&rendertype=abstract}, abstract = {Quality control of gene expression operates post-transcriptionally at various levels in eukaryotes. Once transcribed, mRNAs associate with a host of proteins throughout their lifetime. These mRNA-protein complexes (mRNPs) undergo a series of remodeling events that are influenced by and/or influence the translation and mRNA decay machinery. In this review we discuss how a decision to translate or to degrade a cytoplasmic mRNA is reached. Nonsense-mediated mRNA decay (NMD) and microRNA (miRNA)-mediated mRNA silencing are provided as examples. NMD is a surveillance mechanism that detects and eliminates aberrant mRNAs whose expression would result in truncated proteins that are often deleterious to the organism. miRNA-mediated mRNA silencing is a mechanism that ensures a given protein is expressed at a proper level to permit normal cellular function. While NMD and miRNA-mediated mRNA silencing use different decision-making processes to determine the fate of their targets, both are greatly influenced by mRNP dynamics. In addition, both are linked to RNA processing bodies. Possible modes involving 3’ untranslated region and its associated factors, which appear to play key roles in both processes, are discussed.}, pmid = {18256698}, keywords = {Animals,Gene Expression Regulation,Gene Expression Regulation: physiology,Humans,Messenger,Messenger: metabolism,Messenger: physiology,MicroRNAs,MicroRNAs: metabolism,MicroRNAs: physiology,nosource,Protein Biosynthesis,Protein Biosynthesis: physiology,RNA,RNA Stability,RNA Stability: physiology} }

@article{jamesRNASecondaryStructure2008, title = {{{RNA}} Secondary Structure of the Feline Immunodeficiency Virus 5’{{UTR}} and {{Gag}} Coding Region.}, author = {James, Laurie and Sargueil, Bruno}, year = 2008, month = aug, journal = {Nucleic Acids Research}, volume = {36}, number = {14}, pages = {4653–4666}, issn = {1362-4962}, doi = {10.1093/nar/gkn447}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2504303&tool=pmcentrez&rendertype=abstract}, abstract = {The 5’ untranslated region (5’UTR) of lentiviral genomic RNA is highly structured, and is the site of multiple RNA-RNA and RNA-protein interactions throughout the viral life cycle. The 5’UTR plays a critical role during transcription, translational regulation, genome dimerization, reverse transcription priming and encapsidation. The 5’UTR structures of human lentiviruses have been extensively studied, yet the respective role and conformation of each domain is still controversial. To gain insight into the structure-function relationship of lentiviral 5’UTRs, we modelled the RNA structure of the feline immunodeficiency virus (FIV), a virus that is evolutionarily distant from the primate viruses. Through combined chemical and enzymatic structure probing and a thorough phylogenetic study, we establish a model for the secondary structure of the 5’UTR and Gag coding region. This work highlights properties common to all lentiviruses, like the primer binding site structure and the presence of a stable stem-loop at the 5’ extremity. We find that FIV has also evolved specific features, including a long stem loop overlapping the end of the 5’UTR and the beginning of the coding region. In addition, we observed footprints of Gag protein on each side of the initiation codon, this sheds light on the role of the sequences required for encapsidation.}, pmid = {18625613}, keywords = {5’ Untranslated Regions,5’ Untranslated Regions: chemistry,5’ Untranslated Regions: metabolism,Base Sequence,Binding Sites,Dimerization,Feline,Feline: genetics,gag,gag Gene Products,gag: genetics,Gene Products,HIV-1,HIV-1: genetics,HIV-2,HIV-2: genetics,Human Immunodeficiency Virus,Human Immunodeficiency Virus: m,Immunodeficiency Virus,Magnesium,Magnesium: chemistry,Models,Molecular,Molecular Sequence Data,nosource,Nucleic Acid Conformation,Protein Footprinting,RNA,Viral,Viral: chemistry,Viral: metabolism} }

@article{rodninaLongrangeSignallingActivation2009, title = {Long-Range Signalling in Activation of the Translational {{GTPase EF-Tu}}.}, author = {Rodnina, M. V.}, year = 2009, month = mar, journal = {EMBO J.}, volume = {28}, number = {6}, pages = {619–620}, issn = {1460-2075}, doi = {10.1038/emboj.2009.50}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2666028&tool=pmcentrez&rendertype=abstract}, pmid = {19295500}, keywords = {Amino Acyl,Amino Acyl: metabolism,Animals,Biological,Enzyme Activation,Humans,Models,nosource,Peptide Elongation Factor Tu,Peptide Elongation Factor Tu: metabolism,Protein Biosynthesis,RNA,Signal Transduction,Transfer} } % == BibTeX quality report for rodninaLongrangeSignallingActivation2009: % ? Possibly abbreviated journal title EMBO J.

@article{schuetteGTPaseActivationElongation2009, title = {{{GTPase}} Activation of Elongation Factor {{EF-Tu}} by the Ribosome during Decoding.}, author = {Schuette, Jan-Christian and Murphy, Frank V. and Kelley, Ann C. and Weir, John R. and Giesebrecht, Jan and Connell, Sean R. and Loerke, Justus and Mielke, Thorsten and Zhang, Wei and {}a Penczek, Pawel and Ramakrishnan, V. and Spahn, Christian M. T.}, year = 2009, month = mar, journal = {EMBO J.}, volume = {28}, number = {6}, pages = {755–65}, issn = {1460-2075}, doi = {10.1038/emboj.2009.26}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2666022&tool=pmcentrez&rendertype=abstract}, abstract = {We have used single-particle reconstruction in cryo-electron microscopy to determine a structure of the Thermus thermophilus ribosome in which the ternary complex of elongation factor Tu (EF-Tu), tRNA and guanine nucleotide has been trapped on the ribosome using the antibiotic kirromycin. This represents the state in the decoding process just after codon recognition by tRNA and the resulting GTP hydrolysis by EF-Tu, but before the release of EF-Tu from the ribosome. Progress in sample purification and image processing made it possible to reach a resolution of 6.4 A. Secondary structure elements in tRNA, EF-Tu and the ribosome, and even GDP and kirromycin, could all be visualized directly. The structure reveals a complex conformational rearrangement of the tRNA in the A/T state and the interactions with the functionally important switch regions of EF-Tu crucial to GTP hydrolysis. Thus, the structure provides insights into the molecular mechanism of signalling codon recognition from the decoding centre of the 30S subunit to the GTPase centre of EF-Tu.}, pmid = {19229291}, keywords = {Cryoelectron Microscopy,Enzyme Activation,Guanosine Diphosphate,Guanosine Diphosphate: chemistry,Models,Molecular,nosource,Peptide Elongation Factor Tu,Peptide Elongation Factor Tu: chemistry,Peptide Elongation Factor Tu: metabolism,Peptide Elongation Factor Tu: ultrastructure,Protein Structure,Pyridones,Pyridones: chemistry,Ribosomes,Ribosomes: chemistry,Ribosomes: enzymology,Ribosomes: ultrastructure,RNA,Secondary,Static Electricity,Thermus thermophilus,Thermus thermophilus: enzymology,Transfer,Transfer: chemistry,Transfer: ultrastructure} } % == BibTeX quality report for schuetteGTPaseActivationElongation2009: % ? Possibly abbreviated journal title EMBO J.

@article{vincentiPositionYeastSnoRNAcoding2007, title = {The Position of Yeast {{snoRNA-coding}} Regions within Host Introns Is Essential for Their Biosynthesis and for Efficient Splicing of the Host Pre-{{mRNA}}}, author = {Vincenti, Sara and Chiara, Valentina De E. and Bozzoni, Irene and Presutti, Carlo and Chiara, Valentina De}, year = 2007, month = jan, journal = {Rna}, volume = {13}, number = {1}, pages = {138–150}, issn = {1355-8382}, doi = {10.1261/rna.251907}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1705755&tool=pmcentrez&rendertype=abstract http://rnajournal.cshlp.org/content/13/1/138.short}, abstract = {Genomic location of sequences encoding small nucleolar RNAs (snoRNAs) is peculiar in all eukaryotes from yeast to mammals: most of them are encoded within the introns of host genes. In Saccharomyces cerevisiae, seven snoRNAs show this location. In this work we demonstrate that the position of snoRNA-coding regions with respect to splicing consensus sequences is critical: yeast strains expressing mutant constructs containing shorter or longer spacers (the regions between snoRNA ends and intron splice sites) show a drop in accumulation of U24 and U18 snoRNAs. Further mutational analysis demonstrates that altering the distance between the 3’ end of the snoRNA and the branch point is the most important constraint for snoRNA biosynthesis, and that stable external stems, which are sometimes present in introns containing snoRNAs, can overcome the positional effect. Surprisingly enough, splicing of the host introns is clearly affected in most of these constructs indicating that, at least in S. cerevisiae, an incorrect location of snoRNA-coding sequences within the host intron is detrimental to the splicing process. This is different with respect to what was demonstrated in mammals, where the activity of the splicing machinery seems to be dominant with respect to the assembly of snoRNPs, and it is not affected by the location of snoRNA sequences. We also show that intronic box C/D snoRNA recognition and assembly of snoRNPs occur during transcription when splicing sequences are recognized.}, pmid = {17135484}, keywords = {Fungal,Fungal: genetics,Fungal: metabolism,Genetic,Introns,Introns: genetics,Mutation,nosource,Nuclear Proteins,Nuclear Proteins: metabolism,Ribonucleoproteins,RNA,RNA Precursors,RNA Precursors: genetics,RNA Precursors: metabolism,rna processing,RNA Splicing,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: genetics,Small Nucleolar,Small Nucleolar: biosynthesis,Small Nucleolar: genetics,Small Nucleolar: metabolism,snorna,splicing,Transcription,yeast} }

@article{mccloryMissenseSuppressorMutations2010, title = {Missense Suppressor Mutations in {{16S rRNA}} Reveal the Importance of Helices H8 and H14 in Aminoacyl-{{tRNA}} Selection.}, author = {McClory, Sean P. and Leisring, Joshua M. and Qin, Daoming and Fredrick, Kurt}, year = 2010, month = oct, journal = {RNA}, volume = {16}, number = {10}, eprint = {20699303}, eprinttype = {pubmed}, pages = {1925–1934}, issn = {1469-9001}, doi = {10.1261/rna.2228510}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20699303}, abstract = {The molecular basis of the induced-fit mechanism that determines the fidelity of protein synthesis remains unclear. Here, we isolated mutations in 16S rRNA that increase the rate of miscoding and stop codon read-through. Many of the mutations clustered along interfaces between the 30S shoulder domain and other parts of the ribosome, strongly implicating shoulder movement in the induced-fit mechanism of decoding. The largest subset of mutations mapped to helices h8 and h14. These helices interact with each other and with the 50S subunit to form bridge B8. Previous cryo-EM studies revealed a contact between h14 and the switch 1 motif of EF-Tu, raising the possibility that h14 plays a direct role in GTPase activation. To investigate this possibility, we constructed both deletions and insertions in h14. While ribosomes harboring a 2-base-pair (bp) insertion in h14 were completely inactive in vivo, those containing a 2-bp deletion retained activity but were error prone. In vitro, the truncation of h14 accelerated GTP hydrolysis for EF-Tu bearing near-cognate aminoacyl-tRNA, an effect that can largely account for the observed miscoding in vivo. These data show that h14 does not help activate EF-Tu but instead negatively controls GTP hydrolysis by the factor. We propose that bridge B8 normally acts to counter inward rotation of the shoulder domain; hence, mutations in h8 and h14 that compromise this bridge decrease the stringency of aminoacyl-tRNA selection.}, pmid = {20699303}, keywords = {decoding,ef-tu,gtpase,nosource,ribosome,translation} }

@article{ramakrishnanRibosomeStructureMechanism2002, title = {Ribosome Structure and the Mechanism of Translation}, author = {Ramakrishnan, V.}, year = 2002, journal = {Cell}, volume = {108}, number = {4}, pages = {557–572}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0092867402006190 http://www.sciencedirect.com/science/article/pii/S0092867402006190}, keywords = {nosource} }

@article{choAssemblyMechanismsRNA2009, title = {Assembly Mechanisms of {{RNA}} Pseudoknots Are Determined by the Stabilities of Constituent Secondary Structures.}, author = {Cho, Samuel S. and Pincus, David L. and Thirumalai, D.}, year = 2009, month = oct, journal = {Proceedings of the National Academy of Sciences}, volume = {106}, number = {41}, pages = {17349–54}, issn = {1091-6490}, doi = {10.1073/pnas.0906625106}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2765080&tool=pmcentrez&rendertype=abstract}, abstract = {Understanding how RNA molecules navigate their rugged folding landscapes holds the key to describing their roles in a variety of cellular functions. To dissect RNA folding at the molecular level, we performed simulations of three pseudoknots (MMTV and SRV-1 from viral genomes and the hTR pseudoknot from human telomerase) using coarse-grained models. The melting temperatures from the specific heat profiles are in good agreement with the available experimental data for MMTV and hTR. The equilibrium free energy profiles, which predict the structural transitions that occur at each melting temperature, are used to propose that the relative stabilities of the isolated helices control their folding mechanisms. Kinetic simulations, which corroborate the inferences drawn from the free energy profiles, show that MMTV folds by a hierarchical mechanism with parallel paths, i.e., formation of one of the helices nucleates the assembly of the rest of the structure. The SRV-1 pseudoknot, which folds in a highly cooperative manner, assembles in a single step in which the preformed helices coalesce nearly simultaneously to form the tertiary structure. Folding occurs by multiple pathways in the hTR pseudoknot, the isolated structural elements of which have similar stabilities. In one of the paths, tertiary interactions are established before the formation of the secondary structures. Our work shows that there are significant sequence-dependent variations in the folding landscapes of RNA molecules with similar fold. We also establish that assembly mechanisms can be predicted using the stabilities of the isolated secondary structures.}, pmid = {19805055}, keywords = {Cell Line,Computer Simulation,Genome,Hot Temperature,Humans,Kinetics,Mammary Tumor Virus,Mason-Pfizer monkey virus,Mason-Pfizer monkey virus: chemistry,Mason-Pfizer monkey virus: enzymology,Mason-Pfizer monkey virus: genetics,Models,Molecular,Molecular Conformation,Mouse,Mouse: chemistry,Mouse: enzymology,Mouse: genetics,nosource,Nucleic Acid Conformation,Nucleic Acid Denaturation,RNA,RNA: chemistry,Telomerase,Telomerase: metabolism,Thermodynamics,Tumor,Viral,Viral: chemistry,Viral: metabolism} }

@article{ivanovInteractionsUPF1ERFs2008, title = {Interactions between {{UPF1}}, {{eRFs}}, {{PABP}} and the Exon Junction Complex Suggest an Integrated Model for Mammalian {{NMD}} Pathways}, author = {Ivanov, Pavel V. PV and Gehring, NH Niels H. and Kunz, JB Joachim B. and Hentze, Matthias W. and Kulozik, Andreas E.}, year = 2008, month = mar, journal = {The EMBO }, volume = {27}, number = {5}, pages = {736–747}, issn = {1460-2075}, doi = {10.1038/emboj.2008.17}, url = {http://onlinelibrary.wiley.com/doi/10.1038/emboj.2008.17/full http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2265754&tool=pmcentrez&rendertype=abstract http://www.ncbi.nlm.nih.gov/pubmed/18256688}, abstract = {Nonsense-mediated mRNA decay (NMD) represents a key mechanism to control the expression of wild-type and aberrant mRNAs. Phosphorylation of the protein UPF1 in the context of translation termination contributes to committing mRNAs to NMD. We report that translation termination is inhibited by UPF1 and stimulated by cytoplasmic poly(A)-binding protein (PABPC1). UPF1 binds to eRF1 and to the GTPase domain of eRF3 both in its GTP- and GDP-bound states. Importantly, mutation studies show that UPF1 can interact with the exon junction complex (EJC) alternatively through either UPF2 or UPF3b to become phosphorylated and to activate NMD. On this basis, we discuss an integrated model where UPF1 halts translation termination and is phosphorylated by SMG1 if the termination-promoting interaction of PABPC1 with eRF3 cannot readily occur. The EJC, with UPF2 or UPF3b as a cofactor, interferes with physiological termination through UPF1. This model integrates previously competing models of NMD and suggests a mechanistic basis for alternative NMD pathways.}, pmid = {18256688}, keywords = {Biological,exon junction complex,Exons,Hela Cells,Humans,Messenger,Messenger: metabolism,Models,nmd,nosource,Peptide Termination Factors,Peptide Termination Factors: metabolism,Poly(A)-Binding Protein I,Poly(A)-Binding Protein I: metabolism,release factors,RNA,RNA-Binding Proteins,RNA-Binding Proteins: metabolism,Trans-Activators,Trans-Activators: metabolism,Transcription Factors,Transcription Factors: metabolism,translation termination,upf1} }

@article{gingrasEIF4InitiationFactors1999, title = {{{eIF4}} Initiation Factors: Effectors of {{mRNA}} Recruitment to Ribosomes and Regulators of Translation}, author = {Gingras, AC C. and Raught, B. and Sonenberg, N.}, year = 1999, month = jan, journal = {Annual review of }, volume = {68}, pages = {913–963}, issn = {0066-4154}, doi = {10.1146/annurev.biochem.68.1.913}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.biochem.68.1.913 http://www.ncbi.nlm.nih.gov/pubmed/10872469}, abstract = {Eukaryotic translation initiation factor 4F (eIF4F) is a protein complex that mediates recruitment of ribosomes to mRNA. This event is the rate-limiting step for translation under most circumstances and a primary target for translational control. Functions of the constituent proteins of eIF4F include recognition of the mRNA 5’ cap structure (eIF4E), delivery of an RNA helicase to the 5’ region (eIF4A), bridging of the mRNA and the ribosome (eIF4G), and circularization of the mRNA via interaction with poly(A)-binding protein (eIF4G). eIF4 activity is regulated by transcription, phosphorylation, inhibitory proteins, and proteolytic cleavage. Extracellular stimuli evoke changes in phosphorylation that influence eIF4F activity, especially through the phosphoinositide 3-kinase (PI3K) and Ras signaling pathways. Viral infection and cellular stresses also affect eIF4F function. The recent determination of the structure of eIF4E at atomic resolution has provided insight about how translation is initiated and regulated. Evidence suggests that eIF4F is also implicated in malignancy and apoptosis.}, pmid = {10872469}, keywords = {-binding protein,a,Amino Acid,Amino Acid Sequence,Cell Division,eif4f,Eukaryotic Initiation Factor-4F,Messenger,Messenger: genetics,Messenger: metabolism,Molecular Sequence Data,nosource,Peptide Initiation Factors,Peptide Initiation Factors: chemistry,Peptide Initiation Factors: metabolism,poly,Poly A,Poly A: metabolism,Protein Biosynthesis,Ribosomes,Ribosomes: metabolism,RNA,Sequence Homology,signal transduction,translation initiation,viral infection} }

@article{wuHomoSapiensDullard2011, title = {Homo Sapiens Dullard Protein Phosphatase Shows a Preference for the Insulin-Dependent Phosphorylation Site of Lipin1}, author = {Wu, Rui and Garland, Megan and {Dunaway-Mariano}, Debra and Allen, KN Karen N.}, year = 2011, month = apr, journal = {Biochemistry}, volume = {50}, number = {15}, pages = {1–3}, issn = {1520-4995}, doi = {10.1021/bi200336b}, url = {http://pubs.acs.org/doi/abs/10.1021/bi200336b http://www.ncbi.nlm.nih.gov/pubmed/21604856}, abstract = {Human lipin1 catalyzes the highly regulated conversion of phosphatidic acids to diacylglycerides. Lipin’s cellular location, protein partners, and biological function are directed by phosphorylation-dephosphorylation events catalyzed by the phosphoserine phosphatase dullard. To define the determinants of dullard substrate recognition and catalysis, and hence, lipin regulation, steady-state kinetic analysis was performed on phosphoserine-bearing nonapeptides based on the phosphorylation sites of lipin. The results demonstrate that dullard shows specificity for the peptide corresponding to the insulin-dependent phosphorylation site (Ser106) of lipin with a k(cat)/K(m) of 2.9 10(4) M(-1) s(-1). These results are consistent with a coil-loop structure for the insulin-dependent phosphorylation site on human lipin1 and make unlikely the requirement for an adaptor protein to confer activity such as that proposed for the yeast homologue.}, pmid = {21413788}, keywords = {nosource} }

@article{sherlinChemicalEnzymaticSynthesis2001, title = {Chemical and Enzymatic Synthesis of {{tRNAs}} for High-Throughput Crystallization}, author = {Sherlin, L. D. D. and BULLOCK, T. L. L. and Nissan, T. A. and Perona, J. J. J. and Lariviere, F. J. J. and Uhlenbeck, O. C. C. and Scaringe, S. A. A.}, year = 2001, journal = {RNA}, volume = {7}, number = {11}, pages = {1671–1678}, publisher = {Cambridge Univ Press}, url = {http://journals.cambridge.org/abstract_S1355838201019975}, isbn = {1355838201013}, keywords = {aminoacyl-trna synthetase,nosource,rna ligase,t7 rna polymerase,x-ray crystallography} }

@article{byrneYeastGeneOrder2005, title = {The {{Yeast Gene Order Browser}}: Combining Curated Homology and Syntenic Context Reveals Gene Fate in Polyploid Species}, author = {Byrne, K. P. P. and Wolfe, K. H. H.}, year = 2005, journal = {Genome Research}, volume = {15}, number = {10}, pages = {1456}, publisher = {Cold Spring Harbor Lab}, doi = {10.1101/gr.3672305.}, url = {http://genome.cshlp.org/content/15/10/1456.short}, keywords = {nosource} }

@article{doudnaChemicalRepertoireNatural2002, title = {The Chemical Repertoire of Natural Ribozymes.}, author = {{}a Doudna, Jennifer and Cech, Thomas R.}, year = 2002, month = jul, journal = {Nature}, volume = {418}, number = {6894}, eprint = {12110898}, eprinttype = {pubmed}, pages = {222–228}, issn = {0028-0836}, doi = {10.1038/418222a}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12110898}, abstract = {Although RNA is generally thought to be a passive genetic blueprint, some RNA molecules, called ribozymes, have intrinsic enzyme-like activity–they can catalyse chemical reactions in the complete absence of protein cofactors. In addition to the well-known small ribozymes that cleave phosphodiester bonds, we now know that RNA catalysts probably effect a number of key cellular reactions. This versatility has lent credence to the idea that RNA molecules may have been central to the early stages of life on Earth.}, pmid = {12110898}, keywords = {Animals,Biogenesis,Catalysis,Catalytic,Catalytic: chemistry,Catalytic: genetics,Catalytic: metabolism,Endoribonucleases,Endoribonucleases: chemistry,Endoribonucleases: genetics,Endoribonucleases: metabolism,Humans,Introns,Introns: genetics,Models,Molecular,nosource,Nucleic Acid Conformation,Ribonuclease P,Ribonucleoproteins,Ribonucleoproteins: chemistry,Ribonucleoproteins: genetics,Ribonucleoproteins: metabolism,RNA,RNA Splicing,RNA Splicing: genetics,Substrate Specificity} }

@article{simonettiStructure30STranslation2008, title = {Structure of the {{30S}} Translation Initiation Complex.}, author = {Simonetti, Angelita and Marzi, Stefano and Myasnikov, Alexander G. and Fabbretti, Attilio and Yusupov, Marat and Gualerzi, Claudio O. and Klaholz, Bruno P.}, year = 2008, month = sep, journal = {Nature}, volume = {455}, number = {7211}, eprint = {18758445}, eprinttype = {pubmed}, pages = {416–420}, issn = {1476-4687}, doi = {10.1038/nature07192}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18758445}, abstract = {Translation initiation, the rate-limiting step of the universal process of protein synthesis, proceeds through sequential, tightly regulated steps. In bacteria, the correct messenger RNA start site and the reading frame are selected when, with the help of initiation factors IF1, IF2 and IF3, the initiation codon is decoded in the peptidyl site of the 30S ribosomal subunit by the fMet-tRNA(fMet) anticodon. This yields a 30S initiation complex (30SIC) that is an intermediate in the formation of the 70S initiation complex (70SIC) that occurs on joining of the 50S ribosomal subunit to the 30SIC and release of the initiation factors. The localization of IF2 in the 30SIC has proved to be difficult so far using biochemical approaches, but could now be addressed using cryo-electron microscopy and advanced particle separation techniques on the basis of three-dimensional statistical analysis. Here we report the direct visualization of a 30SIC containing mRNA, fMet-tRNA(fMet) and initiation factors IF1 and GTP-bound IF2. We demonstrate that the fMet-tRNA(fMet) is held in a characteristic and precise position and conformation by two interactions that contribute to the formation of a stable complex: one involves the transfer RNA decoding stem which is buried in the 30S peptidyl site, and the other occurs between the carboxy-terminal domain of IF2 and the tRNA acceptor end. The structure provides insights into the mechanism of 70SIC assembly and rationalizes the rapid activation of GTP hydrolysis triggered on 30SIC-50S joining by showing that the GTP-binding domain of IF2 would directly face the GTPase-activated centre of the 50S subunit.}, pmid = {18758445}, keywords = {Cryoelectron Microscopy,Crystallography,Guanosine Triphosphate,Guanosine Triphosphate: chemistry,Guanosine Triphosphate: metabolism,Messenger,Messenger: chemistry,Messenger: genetics,Messenger: metabolism,Met,Met: chemistry,Met: genetics,Met: metabolism,Met: ultrastructure,Models,Molecular,Multiprotein Complexes,Multiprotein Complexes: chemistry,Multiprotein Complexes: genetics,Multiprotein Complexes: metabolism,Multiprotein Complexes: ultrastructure,nosource,Peptide Chain Initiation,Prokaryotic Initiation Factor-1,Prokaryotic Initiation Factor-1: chemistry,Prokaryotic Initiation Factor-1: genetics,Prokaryotic Initiation Factor-1: metabolism,Prokaryotic Initiation Factor-1: ultrastructure,Prokaryotic Initiation Factor-2,Prokaryotic Initiation Factor-2: chemistry,Prokaryotic Initiation Factor-2: genetics,Prokaryotic Initiation Factor-2: metabolism,Prokaryotic Initiation Factor-2: ultrastructure,Protein Conformation,Ribosome Subunits,Ribosome Subunits: chemistry,Ribosome Subunits: metabolism,Ribosome Subunits: ultrastructure,Ribosomes,Ribosomes: chemistry,Ribosomes: metabolism,Ribosomes: ultrastructure,RNA,Thermus thermophilus,Thermus thermophilus: enzymology,Thermus thermophilus: genetics,Thermus thermophilus: ultrastructure,Transfer,Translational,X-Ray} }

@article{munroCorrelatedConformationalEvents2010, title = {Correlated Conformational Events in {{EF-G}} and the Ribosome Regulate Translocation.}, author = {Munro, James B. and Wasserman, Michael R. and Altman, Roger B. and Wang, Leyi and Blanchard, Scott C.}, year = 2010, month = dec, journal = {Nature Structural & Molecular Biology}, volume = {17}, number = {12}, pages = {1470–1477}, publisher = {Nature Publishing Group}, issn = {1545-9985}, doi = {10.1038/nsmb.1925}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2997181&tool=pmcentrez&rendertype=abstract}, abstract = {In bacteria, the translocation of tRNA and mRNA with respect to the ribosome is catalyzed by the conserved GTPase elongation factor-G (EF-G). To probe the rate-determining features in this process, we imaged EF-G-catalyzed translocation from two unique structural perspectives using single-molecule fluorescence resonance energy transfer. The data reveal that the rate at which the ribosome spontaneously achieves a transient, ‘unlocked’ state is closely correlated with the rate at which the tRNA-like domain IV-V element of EF-G engages the A site. After these structural transitions, translocation occurs comparatively fast, suggesting that conformational processes intrinsic to the ribosome determine the rate of translocation. Experiments conducted in the presence of non-hydrolyzable GTP analogs and specific antibiotics further reveal that allosterically linked conformational events in EF-G and the ribosome mediate rapid, directional substrate movement and EF-G release.}, pmid = {21057527}, keywords = {Escherichia coli,Escherichia coli: genetics,Fluorescence Resonance Energy Transfer,Genetic,Kinetics,Models,nosource,Peptide Elongation Factor G,Peptide Elongation Factor G: chemistry,Peptide Elongation Factor G: physiology,Protein Biosynthesis,Protein Structure,Ribosomes,Ribosomes: chemistry,Ribosomes: physiology,RNA,Tertiary,Transfer,Transfer: metabolism} }

@article{elzenDissectionDom34Hbs1Reveals2010, title = {Dissection of {{Dom34}}–{{Hbs1}} Reveals Independent Functions in Two {{RNA}} Quality Control Pathways}, author = {Elzen, AMG van den Antonia M. G. Van Den and Henri, Julien and Lazar, Noureddine and {}van den Elzen, Antonia M. G. and Gas, Mar{'i}a Eugenia and Durand, Dominique and Lacroute, Fran{}ois and Nicaise, Magali and {}van Tilbeurgh, Herman and S{'e}raphin, Bertrand and Graille, Marc and Tilbeurgh, Herman Van}, year = 2010, month = dec, journal = {Nature structural & }, volume = {17}, number = {12}, pages = {1446–1452}, publisher = {Nature Publishing Group}, issn = {1545-9993}, doi = {10.1038/nsmb.1963}, url = {http://dx.doi.org/10.1038/nsmb.1963 http://www.ncbi.nlm.nih.gov/pubmed/21102444 http://www.nature.com/nsmb/journal/v17/n12/abs/nsmb.1963.html}, abstract = {Eukaryotic cells have several quality control pathways that rely on translation to detect and degrade defective RNAs. Dom34 and Hbs1 are two proteins that are related to translation termination factors and are involved in no-go decay (NGD) and nonfunctional 18S ribosomal RNA (rRNA) decay (18S NRD) pathways that eliminate RNAs that cause strong ribosomal stalls. Here we present the structure of Hbs1 with and without GDP and a low-resolution model of the Dom34-Hbs1 complex. This complex mimics complexes of the elongation factor and transfer RNA or of the translation termination factors eRF1 and eRF3, supporting the idea that it binds to the ribosomal A-site. We show that nucleotide binding by Hbs1 is essential for NGD and 18S NRD. Mutations in Hbs1 that disrupted the interaction between Dom34 and Hbs1 strongly impaired NGD but had almost no effect on 18S NRD. Hence, NGD and 18S NRD could be genetically uncoupled, suggesting that mRNA and rRNA in a stalled translation complex may not always be degraded simultaneously.}, pmid = {21102444}, keywords = {nosource} }

@article{chanQuantitativeSystemsApproach2010, title = {A {{Quantitative Systems Approach Reveals Dynamic Control}} of {{tRNA Modifications}} during {{Cellular Stress}}.}, author = {Chan, Clement T. Y. and Dyavaiah, Madhu and Demott, Michael S. and Taghizadeh, Koli and Dedon, Peter C. and Begley, Thomas J.}, year = 2010, month = jan, journal = {PLoS Genetics}, volume = {6}, number = {12}, pages = {e1001247}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1001247}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3002981&tool=pmcentrez&rendertype=abstract}, abstract = {Decades of study have revealed more than 100 ribonucleoside structures incorporated as post-transcriptional modifications mainly in tRNA and rRNA, yet the larger functional dynamics of this conserved system are unclear. To this end, we developed a highly precise mass spectrometric method to quantify tRNA modifications in Saccharomyces cerevisiae. Our approach revealed several novel biosynthetic pathways for RNA modifications and led to the discovery of signature changes in the spectrum of tRNA modifications in the damage response to mechanistically different toxicants. This is illustrated with the RNA modifications Cm, m(5)C, and m(2) (2)G, which increase following hydrogen peroxide exposure but decrease or are unaffected by exposure to methylmethane sulfonate, arsenite, and hypochlorite. Cytotoxic hypersensitivity to hydrogen peroxide is conferred by loss of enzymes catalyzing the formation of Cm, m(5)C, and m(2) (2)G, which demonstrates that tRNA modifications are critical features of the cellular stress response. The results of our study support a general model of dynamic control of tRNA modifications in cellular response pathways and add to the growing repertoire of mechanisms controlling translational responses in cells.}, pmid = {21187895}, keywords = {nosource} } % == BibTeX quality report for chanQuantitativeSystemsApproach2010: % ? Title looks like it was stored in title-case in Zotero

@article{erdmannCollectionPublished5S1983, title = {Collection of Published {{5S}} and 5.8 {{S}} Ribosomal {{RNA}} Sequences}, author = {Erdmann, V. A. and Huysmans, E. and Vandenberghe, A. and Wachter, R. De}, year = 1983, journal = {Nucleic Acids Research}, volume = {11}, number = {1}, pages = {r105}, publisher = {Oxford University Press}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC325704/}, keywords = {nosource} }

@article{cechConservedSequencesStructures1988, title = {Conserved Sequences and Structures of Group {{I}} Introns: Building an Active Site for {{RNA}} Catalysis–a Review}, author = {Cech, T. R.}, year = 1988, journal = {Gene}, volume = {73}, number = {2}, pages = {259–271}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0378111988904921}, keywords = {nosource} }

@article{michelComparativeFunctionalAnatomy1989, title = {Comparative and Functional Anatomy of Group {{II}} Catalytic Introns–a Review}, author = {Michel, F. and Kazuhiko, U. and Haruo, O.}, year = 1989, journal = {Gene}, volume = {82}, number = {1}, pages = {5–30}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0378111989900267}, keywords = {nosource} }

@article{gutellPredictingUturnsRibosomal2000, title = {Predicting {{U-turns}} in {{Ribosomal RNA}} with {{Comparative Sequence Analysis}}{\(\bullet\)} 1}, author = {Gutell, R. R. and Cannone, J. J. and Konings, D. and Gautheret, D.}, year = 2000, journal = {Journal of molecular biology}, volume = {300}, number = {4}, pages = {791–803}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283600939007}, keywords = {nosource} }

@article{gutellComparativeSequenceAnalysis1995, title = {Comparative Sequence Analysis and the Structure of {{16S}} and {{23S rRNA}}}, author = {Gutell, R. R.}, year = 1995, journal = {Ribosomal RNA: structure, evolution,}, pages = {111–128}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Comparative+sequence+analysis+and+the+structure+of+16+S+and+23+S+rRNA.#3}, keywords = {nosource} }

@article{sahTranslationInhibitorsSensitize2003, title = {Translation Inhibitors Sensitize Prostate Cancer Cells to Apoptosis Induced by Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand ({{TRAIL}}) by Activating c-{{Jun N-}}}, author = {Sah, N. K. and Munshi, A. and Kurland, J. F.}, year = 2003, journal = {Journal of Biological}, volume = {250}, pages = {546–551}, url = {http://www.jbc.org/content/278/23/20593.short}, keywords = {nosource} }

@article{rajbhandarySTUDIESPOLYNUCLEOTIDESLXVIII1967, title = {{{STUDIES ON POLYNUCLEOTIDES}}, {{LXVIII}}* {{THE PRIMARY STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA}}}, author = {RajBhandary, U. L. and Chang, S. H.}, year = 1967, journal = {Proceedings of the }, volume = {31}, pages = {409–416}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC335572/}, keywords = {nosource} } % == BibTeX quality report for rajbhandarySTUDIESPOLYNUCLEOTIDESLXVIII1967: % ? Title looks like it was stored in title-case in Zotero

@article{maidakRibosomalDatabaseProject1994, title = {The Ribosomal Database Project}, author = {Maidak, B. L. BL and Larsen, N. and McCaughey, M. J. MJ and Overbeek, R. and Olsen, G. J. and Fogel, K. and Blandy, J. and Woese, C. R.}, year = 1994, journal = {Nucleic Acids Research}, volume = {22}, number = {17}, pages = {3485}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/22/17/3485.short}, keywords = {nosource} }

@article{leontisAnalysisRNAMotifs2003, title = {Analysis of {{RNA}} Motifs}, author = {Leontis, N. B. B. and Westhof, E.}, year = 2003, journal = {Current opinion in structural biology}, volume = {13}, number = {3}, pages = {300–308}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0959440x03000769}, keywords = {nosource} }

@article{rossiIdentificationCharacterisationRPD31998, title = {Identification and Characterisation of an {{RPD3}} Homologue from Maize ({{Zea}} Mays {{L}}.) That Is Able to Complement an Rpd3 Null Mutant of {{Saccharomycescerevisiae}}}, author = {Rossi, V. and Hartings, H.}, year = 1998, month = may, journal = {Molecular and General Genetics}, volume = {258}, number = {3}, pages = {288–296}, publisher = {Springer}, url = {http://www.springerlink.com/index/7XPW3EC290LRH6NU.pdf}, abstract = {In mammals, yeast and Drosophila, the histone deacetylase RPD3 proteins can alter the expression of genes involved in fundamental biological processes by affecting the degree of acetylation of histones and changing chromatin structure. Here we report the isolation of a cDNA sequence encoding an RPD3 homologue from maize, which is able to complement the phenotype of an rpd3 null mutant of the yeast Saccharomyces cerevisiae. The expression of the corresponding gene(s) was assessed in different maize tissues. The number of homologous loci was estimated by Southern hybridisation to be in the range of two to three, and the chromosomal location of one of these loci was determined. Phylogenetic analysis and tests for relative divergence rates, using related RPD3 sequences from different species, were performed, and suggest that different polymorphic forms of RPD3-like proteins that evolve at distinct rates are present in the species considered}, keywords = {nosource} }

@article{liProgrammed11Frameshifting2001, title = {Programmed 11 Frameshifting Stimulated by Complementarity between a Downstream {{mRNA}} Sequence and an Error-Correcting Region of {{rRNA}}}, author = {LI, Z. and STAHL, G.}, year = 2001, month = feb, journal = {RNA}, volume = {7}, number = {2}, pages = {275–284}, url = {http://www.research.umbc.edu/~farabaug/lab/papers/rna2001.pdf}, abstract = {Like most retroviruses and retrotransposons, the retrotransposon Ty3 expresses its pol gene analog (POL3) as a translational fusion to the upstream gag analog (GAG3). The Gag3-Pol3 fusion occurs by frameshifting during translation of the mRNA that encodes the two separate but overlapping ORFs. We showed previously that the shift occurs by out-of-frame binding of a normal aminoacyl-tRNA in the ribosomal A site caused by an aberrant codonoanticodon interaction in the P site. This event is unlike all previously described programmed translational frameshifts because it does not require tRNA slippage between cognate or near-cognate codons in the mRNA. A sequence of 15 nt distal to the frameshift site stimulates frameshifting 7.5-fold. Here we show that the Ty3 stimulator acts as an unstructured region to stimulate frameshifting. Its function depends on strict spacing from the site of frameshifting. Finally, the stimulator increases frameshifting dependent on sense codon-induced pausing, but has no effect on frameshifting dependent on pauses induced by nonsense codons. Complementarity between the stimulator and a portion of the accuracy center of the ribosome, Helix 18, implies that the stimulator may directly disrupt error correction by the ribosome}, keywords = {nosource} }

@article{merrickProteinBiosynthesisElongation2000, title = {The Protein Biosynthesis Elongation Cycle}, author = {Merrick, W. C. and Nyborg, J.}, year = 2000, journal = {Translational control of gene expression}, pages = {89–125}, publisher = {Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY}, url = {http://books.google.com/books?hl=en&lr=&id=InXRuBRGkLYC&oi=fnd&pg=PA89&dq=The+protein+biosynthesis+elongation+cycle&ots=GMCSOi3f_q&sig=AsIa95CZP8bYnbopBUfe71Ez30o}, isbn = {0-87969-568-568-4}, keywords = {nosource} }

@article{nagaiRNAProteinComplexes1996, title = {{{RNA}}–Protein Complexes}, author = {Nagai, K.}, year = 1996, month = feb, journal = {Current Opinion in Structural Biology}, volume = {6}, number = {1}, pages = {53–61}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0959440X96800959}, keywords = {nosource} }

@article{thrashIdentificationSaccharomycesCerevisiae1984, title = {Identification of {{Saccharomyces}} Cerevisiae Mutants Deficient in {{DNA}} Topoisomerase {{I}} Activity.}, author = {Thrash, C. and Voelkel, K. and DiNardo, S. and Sternglanz, R.}, year = 1984, journal = {Journal of Biological Chemistry}, volume = {259}, number = {3}, pages = {1375}, publisher = {ASBMB}, url = {http://www.jbc.org/content/259/3/1375.short}, keywords = {nosource} }

@article{tyersComparisonSaccharomycesCerevisiae1993, title = {Comparison of the {{Saccharomyces}} Cerevisiae {{G1}} Cyclins: {{Cln3}} May Be an Upstream Activator of {{Cln1}}, {{Cln2}} and Other Cyclins.}, author = {Tyers, M. and Tokiwa, G. and Futcher, B.}, year = 1993, journal = {The EMBO journal}, volume = {12}, number = {5}, pages = {1955}, publisher = {Nature Publishing Group}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC413417/}, keywords = {nosource} }

@article{millerSequencesThatSurround1989, title = {Sequences That Surround the Stop Codons of Upstream Open Reading Frames in {{GCN4 mRNA}} Determine Their Distinct Functions in Translational Control.}, author = {Miller, P. F. and Hinnebusch, A. G.}, year = 1989, journal = {Genes & Development}, volume = {3}, number = {8}, pages = {1217}, publisher = {Cold Spring Harbor Lab}, url = {http://genesdev.cshlp.org/content/3/8/1217.short}, keywords = {nosource} }

@article{karinPrimaryStructureTranscription1984, title = {Primary Structure and Transcription of an Amplified Genetic Locus: The {{CUP1}} Locus of Yeast}, author = {Karin, M. and Najarian, R. and Haslinger, A. and Valenzuela, P. and Welch, J. and Fogel, S.}, year = 1984, journal = {Proceedings of the National Academy of Sciences}, volume = {81}, number = {2}, pages = {337}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/81/2/337.short}, keywords = {nosource} }

@article{wicknerDoublestrandedSinglestrandedRNA1992, title = {Double-Stranded and Single-Stranded {{RNA}} Viruses of {{Saccharomyces}} Cerevisiae}, author = {Wickner, R. B.}, year = 1992, journal = {Annual Reviews in Microbiology}, volume = {46}, number = {1}, pages = {347–375}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.mi.46.100192.002023}, keywords = {nosource} }

@article{riceGagPolGenes1985, title = {The Gag and Pol Genes of Bovine Leukemia Virus: {{Nucleotide}} Sequence and Analysis{\(\bullet\)} 1}, author = {Rice, N. R. and Stephens, R. M. and Burny, A. and Gilden, R. V.}, year = 1985, journal = {Virology}, volume = {142}, number = {2}, pages = {357–377}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0042682285903447}, keywords = {nosource} }

@article{pohjanpeltoPolyamineDeprivationCauses1982, title = {Polyamine Deprivation Causes Major Chromosome Aberrations in a Polyamine-Dependent {{Chinese}} Hamster Ovary Cell Line{\(\bullet\)} 1}, author = {Pohjanpelto, P. and Knuutila, S.}, year = 1982, month = oct, journal = {Experimental Cell Research}, volume = {141}, number = {2}, pages = {333–339}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/001448278290221X}, keywords = {nosource} }

@article{terceroYeastMAK3Nacetyltransferase1993, title = {Yeast {{MAK3 N-acetyltransferase}} Recognizes the {{N-terminal}} Four Amino Acids of the Major Coat Protein (Gag) of the {{LA}} Double-Stranded {{RNA}} Virus.}, author = {Tercero, J. C. and Dinman, J. D. and Wickner, R. B.}, year = 1993, journal = {Journal of bacteriology}, volume = {175}, number = {10}, pages = {3192}, publisher = {Am Soc Microbiol}, url = {http://jb.asm.org/cgi/content/abstract/175/10/3192}, keywords = {nosource} }

@article{osswaldRibosomalNeighbourhoodCentral1995, title = {The Ribosomal Neighbourhood of the Central Fold of {{tRNA}}: Cross-Links from Position 47 of {{tRNA}} Located at the {{A}}, {{P}} or Site}, author = {Osswald, M. and D{"o}ring, T. and Brimacombe, R.}, year = 1995, month = nov, journal = {Nucleic acids research}, volume = {23}, number = {22}, pages = {4635}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/23/22/4635.short}, abstract = {The naturally occurring nucleotide 3-(3-amino-3-carboxy-propyl)uridine (acp3U) at position 47 of tRNA(Phe) from Escherichia coli was modified with a diazirine derivative and bound to ribosomes in the presence of suitable mRNA analogues under conditions specific for the ribosomal A, P or E sites. After photo-activation at 350 nm the cross-links to ribosomal proteins and RNA were identified by our standard procedures. In the 30S subunit protein S19 (and weakly S9 and S13) was the target of cross-linking from tRNA at the A site, S7, S9 and S13 from the P site and S7 from the E site. Similarly, in the 50S subunit L16 and L27 were cross-linked from the A site, L1, L5, L16, L27 and L33 from the P site and L1 and L33 from the E site. Corresponding cross-links to rRNA were localized by RNase H digestion to the following areas: in 16S rRNA between positions 687 and 727 from the P and E sites, positions 1318 and 1350 (P site) and 1350 and 1387 (E site); in the 23S rRNA between positions 865 and 910 from the A site, 1845 and 1892 (P site), 1892 and 1945 (A site), 2282 and 2358 (P site), 2242 and 2461 (P and E sites), 2461 and 2488 (A site), 2488 and 2539 (all three sites) and 2572 and 2603 (A and P sites). In most (but not all) cases, more precise localizations of the cross-link sites could be made by primer extension analysis}, keywords = {nosource} }

@article{macbethPhenotypeMutationsG26551999, title = {The {{Phenotype}} of {{Mutations}} of {{G2655}} in the {{Sarcin}}/{{Ricin Domain}} of 23 {{S Ribosomal RNA}}* 1,* 2}, author = {Macbeth, M. R.}, year = 1999, month = jan, journal = {Journal of Molecular Biology}, volume = {285}, number = {3}, pages = {965–975}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(98)92388-9}, abstract = {The sarcin/ricin domain (SRD) in Escherichia coli 23 S rRNA forms a part of the site for the association of the elongation factors with the ribosome and hence is critical for the binding of aminoacyl-tRNA and for translocation. The domain is also the site of action of the eponymous toxins which catalyze covalent modification of single nucleotides that inactivate the ribosome. The conformation of the conserved guanosine at position 2655 is an especially prominent feature of the structure of the SRD: the nucleotide is bulged out of a helix and forms a base-triple with A2665 and U2656. G2655 in 23 S rRNA is protected from chemical modification when the elongation factors, EF-Tu and EF-G, are bound to ribosomes and the analog of G2655 in oligoribonucleotides is critical for recognition by the toxin sarcin and by EF-G. The contribution of G2655 to the function of the ribosome has been evaluated by constructing mutations in the nucleotide and determining the phenotype. Constitutive expression of a plasmid-encoded rrnB operon with a deletion of, or transversions in, G2655 is lethal to E. coli cells, whereas a defect in the growth of cells with a G2655A transition is observed only in competition with wild-type cells. The sedimentation profiles of ribosomes with mutations in G2655 are altered; most markedly by deletion or transversion of the nucleotide, less severely by transition to adenosine. Mutations of G2655 confer resistance to sarcin on ribosomes. Ribosomes with G2655Delta, G2655C, or G2655U mutations in 23 S rRNA are not active in protein synthesis, whereas those with the G2655A transition mutation suffer decreased activity}, keywords = {nosource} } % == BibTeX quality report for macbethPhenotypeMutationsG26551999: % ? Title looks like it was stored in title-case in Zotero

@article{rodriguez-fonsecaFineStructurePeptidyl1995, title = {Fine {{Structure}} of the {{Peptidyl Transferase Centre}} on 23 {{S-like rRNAs Deduced}} from {{Chemical Probing}} of {{Antibiotic-Ribosome Complexes}}{\(\bullet\)} 1}, author = {{Rodriguez-Fonseca}, C. and Amils, R. and Garrett, R. A.}, year = 1995, month = mar, journal = {Journal of molecular biology}, volume = {247}, number = {2}, pages = {224–235}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(84)70135-5}, abstract = {Ribosomal binding sites were investigated for the diverse group of antibiotics: anisomycin, anthelmycin, blasticidin S, bruceantin, carbomycin, chloramphenicol, griseoviridin, narciclasine, T2 toxin, tylosin and virginiamycin M1 all of which are considered to inhibit the peptidyl transferase reaction by different mechanisms. The drugs also exhibit differing degrees of specificity for bacterial, archaeal and eukaryotic ribosomes despite a high level of conservation of sequence and secondary structure at the peptidyl transferase centre of the 23 S-like rRNAs. The drug binding sites were characterized by incubating each antibiotic with ribosomes from a bacterium, an archaeon and a eukaryote and chemically probing the 23 S-like rRNA. The complexity of the changes in reactivity ranged from one or two nucleotides (anthelmycin, narciclasine) to eight or nine (virginiamycin M1) and it was inferred, at least for those drugs producing complex changes, that they induce, and stabilize, a particular functional conformer in the peptidyl transferase centre. The results were correlated with literature data on both ribosomal ligand binding and the putative inhibitory mechanisms of the drugs, and the following inferences are made concerning the fine structure of the peptidyl transferase centre. (1) An irregular secondary structural motif, which includes unpaired A2439 (Escherichia coli numbering), lies close to the catalytic centre; (2) nucleotides A2451 and C2452 contribute to a site for the binding of the side chains of aromatic amino acids; (3) the P-substrate site encompasses U2585, U2506 and, possibly, a site in domain IV (A1787), and (4) the sequence A2058 to A2062 and nucleotide U2609 contribute to, or modulate, the start of the peptide channel. No drug effects were found that could be directly attributed to an A-site and the possibility is raised that, if it exists, it consists mainly of ribosomal proteins. However, two drugs T2 toxin and virginiamycin M1 protected the only nucleotide in the peptidyl transferase loop region (C2394) associated with the E-site. Finally, it is proposed that the putative sub-sites are physically separated, that some drugs bind to more than one of them, and that they are conformationally interdependent}, keywords = {nosource} } % == BibTeX quality report for rodriguez-fonsecaFineStructurePeptidyl1995: % ? Title looks like it was stored in title-case in Zotero

@article{fujimuraThermolabileViruslikeParticles1986, title = {Thermolabile {{LA}} Virus-like Particles from Pet18 Mutants of {{Saccharomyces}} Cerevisiae.}, author = {Fujimura, T. and Wickner, R. B.}, year = 1986, month = feb, journal = {Molecular and cellular biology}, volume = {6}, number = {2}, pages = {404}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/6/2/404}, abstract = {pet18 mutations in Saccharomyces cerevisiae confer on the cell the inability to maintain either L-A or M double-stranded RNAs (dsRNAs) at the nonpermissive temperature. In in vitro experiments, we examined the effects of pet18 mutations on the RNA-dependent RNA polymerase activity associated with virus-like particles (VLPs). pet18 mutations caused thermolabile RNA polymerase activity of L-A VLPs, and this thermolability was found to be due to the instability of the L-A VLP structure. The pet18 mutations did not affect RNA polymerase activity of M VLPs. Furthermore, the temperature sensitivity of wild-type L-A RNA polymerase differed substantially from that of M RNA polymerase. From these results, and from other genetic and biochemical lines of evidence which suggest that replication of M dsRNA requires the presence of L-A dsRNA, we propose that the primary effect of the pet18 mutation is on the L-A VLP structure and that the inability of pet18 mutants to maintain M dsRNA comes from the loss of L-A dsRNA}, keywords = {nosource} }

@article{tangUnusualMRNAPseudoknot1989, title = {Unusual {{mRNA}} Pseudoknot Structure Is Recognized by a Protein Translational Repressor}, author = {Tang, C. K. and Draper, D. E.}, year = 1989, month = may, journal = {Cell}, volume = {57}, number = {4}, pages = {531–536}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867489901232}, keywords = {nosource} }

@article{guarenteYeastPromotersLacZ1983, title = {Yeast Promoters and {{lacZ}} Fusions Designed to Study Expression of Cloned Genes in Yeast.}, author = {Guarente, L.}, year = 1983, journal = {Methods in enzymology}, volume = {101}, eprint = {6310321}, eprinttype = {pubmed}, pages = {181}, url = {http://www.ncbi.nlm.nih.gov/pubmed/6310321/}, keywords = {nosource} }

@article{kambourisCloningGeneticCharacterization1993, title = {Cloning and Genetic Characterization of a Calcium-and Phospholipid-Binding Protein from {{Saccharomyces}} Cerevisiae That Is Homologous to Translation Elongation Factor-1{\(\gamma\)}}, author = {Kambouris, N. G. and Burke, D. J. and Creutz, C. E.}, year = 1993, month = feb, journal = {Yeast}, volume = {9}, number = {2}, pages = {151–163}, publisher = {Wiley Online Library}, url = {http://onlinelibrary.wiley.com/doi/10.1002/yea.320090206/abstract}, abstract = {We have isolated a gene (CAM1) from the yeast Saccharomyces cerevisiae that encodes a protein homologous to the translational cofactor elongation factor-1 gamma (EF-1 gamma) first identified in the brine shrimp Artemia salina. The predicted Cam1 amino acid sequence consists of 415 residues that share 32% identity with the Artemia protein, increasing to 72% when conservative substitutions are included. The calculated M(r) of Cam1p (47,092 Da) is in close agreement with that of EF-1 gamma (M(r) = 49,200 Da), and hydropathy plots of each protein exhibit strikingly similar profiles. Disruption of the CAM1 locus yields four viable meiotic progeny, indicating that under normal growth conditions the Cam1 protein is non-essential. Attempts to elicit a translational phenotype have been unsuccessful. Since EF-1 gamma participates in the regulation of a GTP-binding protein (EF-1 alpha), double mutants with cam1 disruptions and various mutant alleles of known GTP-binding proteins were constructed and examined. No evidence was found for an interaction of CAM1 with TEF1, TEF2, SEC4, YPT1, RAS1, RAS2, CDC6, ARF1, ARF2 or CIN4. The possibility that Cam1p may play a redundant role in the regulation of protein synthesis or another GTP-dependent process is discussed}, keywords = {nosource} }

@article{leeIdentificationRibosomalFrameshift1996, title = {Identification of a Ribosomal Frameshift in {{Leishmania RNA}} Virus 1–4}, author = {Lee, S. E. and Suh, J. M. and Scheffter, S. and Patterson, J. L. and Chung, I. K.}, year = 1996, month = jul, journal = {Journal of biochemistry}, volume = {120}, number = {1}, pages = {22}, publisher = {Jpn Biochemical Soc}, url = {http://jb.oxfordjournals.org/content/120/1/22.short}, abstract = {Double-stranded Leishmania RNA virus 1-4 (LRV 1-4) has at least four open reading frames (ORFs), The two small ORFs located near its 5’ terminus, ORF1 and ORFx, could encode 34- and 60-amino acid polypeptides, respectively, ORF2 encodes an 82-kDa major capsid protein, and ORF3 encodes a 98-kDa polypeptide which contains the consensus sequence for RNA-dependent RNA polymerases of plus-strand and double-stranded RNA viruses, The complete sequence of LRV 1-4 shows that ORF2 and ORF3 overlap by 71 nucleotides, and that ORF3 lacks a potential translation initiation site, suggesting that the viral polymerase may be synthesized as a 180-kDa fusion protein with the virus capsid, In this report, we present evidence for the synthesis of a fusion protein through a ribosomal frameshift. In vitro-translation experimentation and immunostudies involving antiserum against the viral capsid protein demonstrated that the overlapping 71 nucleotides of ORF2 and ORF3 are contained in a region which promotes translational frameshifting. Computer analysis of the putative frameshift region revealed a potential pseudoknot structure! located within the overlapping 71 nucleotide sequence}, keywords = {nosource} }

@article{livakAnalysisRelativeGene2001, title = {Analysis of Relative Gene Expression Data Using Real-Time Quantitative {{PCR}} and the 2-[{{Delta}}][{{Delta}}] {{CT}} Method}, author = {Livak, K. J. and Schmittgen, T. D.}, year = 2001, month = dec, journal = {Methods}, volume = {25}, number = {4}, pages = {402–408}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1046202301912629}, abstract = {The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data}, keywords = {nosource} }

@article{estebanInternalTerminalCisacting1989, title = {Internal and Terminal Cis-Acting Sites Are Necessary for in Vitro Replication of the {{LA}} Double-Stranded {{RNA}} Virus of Yeast.}, author = {Esteban, R. and Fujimura, T. and Wickner, R. B.}, year = 1989, month = mar, journal = {The EMBO Journal}, volume = {8}, number = {3}, pages = {947}, publisher = {Nature Publishing Group}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC400895/}, keywords = {nosource} }

@article{spahnStructure80SRibosome2001, title = {Structure of the {{80S}} Ribosome from {{Saccharomyces}} Cerevisiae–{{tRNA-ribosome}} and Subunit-Subunit Interactions}, author = {Spahn, C. M. T. and Beckmann, R. and Eswar, N. and Penczek, P. A. and Sali, A. and Blobel, G. and Frank, J.}, year = 2001, month = nov, journal = {Cell}, volume = {107}, number = {3}, pages = {373–386}, publisher = {Elsevier}, issn = {0092-8674}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867401005396}, abstract = {A cryo-EM reconstruction of the translating yeast 80S ribosome was analyzed. Computationally separated rRNA and protein densities were used for docking of appropriately modified rRNA models and homology models of yeast ribosomal proteins. The core of the ribosome shows a remarkable degree of conservation. However, some significant differences in functionally important regions and dramatic changes in the periphery due to expansion segments and additional ribosomal proteins are evident. As in the bacterial ribosome, bridges between the subunits are mainly formed by RNA contacts. Four new bridges are present at the periphery. The position of the P site tRNA coincides precisely with its prokaryotic counterpart, with mainly rRNA contributing to its molecular environment. This analysis presents an exhaustive inventory of an eukaryotic ribosome at the molecular level.}, keywords = {nosource} }

@article{macuraElucidationCrossRelaxation1980, title = {Elucidation of Cross Relaxation in Liquids by Two-Dimensional {{NMR}} Spectroscopy}, author = {Macura, S. and Ernst, R. R.}, year = 1980, journal = {Molecular Physics}, volume = {41}, number = {1}, pages = {95–117}, publisher = {Taylor & Francis}, url = {http://www.informaworld.com/index/V19N3G21674PL081.pdf}, keywords = {nosource} }

@article{stofflerImmunoElectronMicroscopy1986, title = {Immuno Electron Microscopy on {{Escherichia}} Coli Ribosomes}, author = {St{"o}ffler, G. and {St{"o}ffler-Meilicke}, M.}, year = 1986, journal = {Structure, Function, and Genetics of Ribosomes}, pages = {28–46}, publisher = {Springer Verlag}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Immuno+electron+microscopy+on+?Escherchia+coli?+ribosomes.#0}, keywords = {nosource} }

@article{kolodziejEpitopeTaggingProtein1991, title = {Epitope Tagging and Protein Surveillance.}, author = {Kolodziej, P. A. and Young, R. A.}, year = 1991, journal = {Methods in enzymology}, volume = {194}, eprint = {1706460}, eprinttype = {pubmed}, pages = {508}, publisher = {Academic Press}, url = {http://www.ncbi.nlm.nih.gov/pubmed/1706460}, keywords = {nosource} }

@article{thompsonProofreadingCodonanticodonInteraction1977a, title = {Proofreading of the Codon-Anticodon Interaction on Ribosomes}, author = {Thompson, R. C. and Stone, P. J.}, year = 1977, journal = {Proceedings of the National Academy of Sciences}, volume = {74}, number = {1}, pages = {198}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/74/1/198.short}, keywords = {nosource} }

@article{schulerGMCSFOncogeneMRNA1988, title = {{{GM-CSF}} and Oncogene {{mRNA}} Stabilities Are Independently Regulated in Trans in a Mouse Monocytic Tumor}, author = {Schuler, G. D. and Cole, M. D.}, year = 1988, journal = {Cell}, volume = {55}, number = {6}, pages = {1115–1122}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867488902565}, keywords = {nosource} }

@article{leedsGeneProductsThat1992, title = {Gene Products That Promote {{mRNA}} Turnover in {{Saccharomyces}} Cerevisiae.}, author = {Leeds, P. and Wood, J. M. and Lee, B.-S. and Culbertson, M. R.}, year = 1992, journal = {Molecular and cellular biology}, volume = {12}, number = {5}, pages = {2165}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/12/5/2165}, keywords = {nosource} }

@article{maicasTranslationSaccharomycesCerevisiae1990, title = {Translation of the {{Saccharomyces}} Cerevisiae Tcm1 Gene in the Absence of a 5{\(\prime\)}-Untranslated Leader}, author = {Maicas, E. and Shago, M. and Friesen, J. D.}, year = 1990, month = oct, journal = {Nucleic acids research}, volume = {18}, number = {19}, pages = {5823}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/18/19/5823.short}, keywords = {nosource} }

@article{kurlandTranslationalAccuracyFitness1992, title = {Translational {{Accuracy}} and the {{Fitness}} of {{Bacteria}}{\(\bullet\)}}, author = {Kurland, C. G.}, year = 1992, journal = {Annual review of genetics}, volume = {26}, number = {1}, pages = {29–50}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.ge.26.120192.000333}, keywords = {nosource} } % == BibTeX quality report for kurlandTranslationalAccuracyFitness1992: % ? Title looks like it was stored in title-case in Zotero

@article{westhofComputerModelingSolution1989, title = {Computer Modeling from Solution Data of Spinach Chloroplast and of {{Xenopus}} Laevis Somatic and Oocyte 5 {{S rRNAs}}{\(\bullet\)} 1}, author = {Westhof, E. and Romby, P. and Romaniuk, P. J. and Ebel, J. P. and Ehresmann, C. and Ehresmann, B.}, year = 1989, month = may, journal = {Journal of molecular biology}, volume = {207}, number = {2}, pages = {417–431}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0022283689902647}, abstract = {Detailed atomic models of a eubacterial 5 S rRNA (spinach chloroplast 5 S rRNA) and of a eukaryotic 5 S rRNA (somatic and oocyte 5 S rRNA from Xenopus laevis) were built using computer graphic. Both models integrate stereochemical constraints and experimental data on the accessibility of bases and phosphates towards several structure- specific probes. The base sequence was first inserted on to three- dimensional structural fragments picked up in a specially devised databank. The fragments were modified and assembled interactively on an Evans & Sutherland PS330. Modeling was finalized by stereochemical and energy refinement. In spite of some uncertainty in the relative spatial orientation of the substructures, the broad features of the models can be generalized and several conclusions can be reached: (1) both models adopt a distorted Y-shape structure, with helices B and D not far from colinearity; (2) no tertiary interactions exist between loop c and region d or loop e; (3) the internal loops, in particular region d, contain several non-canonical base-pairs of A.A, U.U and A.G types; (4) invariant residues appear to be more important for protein or RNA binding than for maintaining the tertiary structure. The models are corroborated by footprinting experiments with ribosomal proteins and by the analysis of various mutants. Such models help to clarify the structure-function relationship of 5 S rRNA and are useful for designing site-directed mutagenesis experiments}, keywords = {nosource} }

@article{culottiGeneticControlCell1971, title = {Genetic Control of the Cell Division Cycle in Yeast{\(\bullet\)} 1:: {{III}}. {{Seven}} Genes Controlling Nuclear Division}, author = {Culotti, J. and Hartwell, L. H.}, year = 1971, journal = {Experimental cell research}, volume = {67}, number = {2}, pages = {389–401}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0014482771904241}, keywords = {nosource} }

@article{curcioSinglestepSelectionTy11991, title = {Single-Step Selection for {{Ty1}} Element Retrotransposition}, author = {Curcio, M. J. and Garfinkel, D. J.}, year = 1991, journal = {Proceedings of the National Academy of Sciences}, volume = {88}, number = {3}, pages = {936}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/88/3/936.short}, keywords = {nosource} }

@article{schindlerTrichoderminResistanceMutation1974, title = {Trichodermin Resistance—Mutation Affecting Eukaryotic Ribosomes}, author = {Schindler, D. and Grant, P. and Davies, J.}, year = 1974, journal = {Nature}, volume = {248}, pages = {535–536}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/nature/journal/v248/n5448/abs/248535a0.html}, keywords = {nosource} }

@article{pazinWhat39Histone1997, title = {What&#39;s {{Up}} and {{Down}} with {{Histone Deacetylation}} and {{Transcription}}?’’ Cell, Vol. 89}, author = {Pazin, M. J.}, year = 1997, month = may, journal = {May}, volume = {89}, number = {3}, pages = {325–328}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:What's+up+and+down+with+histone+deacetylation+and+transcription?#2}, keywords = {nosource} }

@article{tumerPokeweedAntiviralProtein1998, title = {The Pokeweed Antiviral Protein Specifically Inhibits {{Ty1-directed}}+ 1 Ribosomal Frameshifting and Retrotransposition in {{Saccharomyces}} Cerevisiae}, author = {Tumer, N. E. and Parikh, B. A. and Li, P. and Dinman, J. D.}, year = 1998, journal = {Journal of virology}, volume = {72}, number = {2}, pages = {1036}, publisher = {Am Soc Microbiol}, url = {http://jvi.asm.org/cgi/content/abstract/72/2/1036}, keywords = {nosource} }

@article{pervushinNMRScalarCouplings1998, title = {{{NMR}} Scalar Couplings across {{Watson}}–{{Crick}} Base Pair Hydrogen Bonds in {{DNA}} Observed by Transverse Relaxation-Optimized Spectroscopy}, author = {Pervushin, K. and Ono, A. and Fern{'a}ndez, C. and Szyperski, T. and Kainosho, M. and W{}{"u}thrich, K.}, year = 1998, month = nov, journal = {Proceedings of the National Academy of Sciences}, volume = {95}, number = {24}, pages = {14147}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/95/24/14147.short}, abstract = {This paper describes the NMR observation of 15N—15N and 1H—15N scalar couplings across the hydrogen bonds in Watson-Crick base pairs in a DNA duplex, hJNN and hJHN. These couplings represent new parameters of interest for both structural studies of DNA and theoretical investigations into the nature of the hydrogen bonds. Two dimensional [15N,1H]-transverse relaxation-optimized spectroscopy (TROSY) with a 15N-labeled 14-mer DNA duplex was used to measure hJNN, which is in the range 6-7 Hz, and the two-dimensional hJNN-correlation-[15N,1H]-TROSY experiment was used to correlate the chemical shifts of pairs of hydrogen bond-related 15N spins and to observe, for the first time, hJHN scalar couplings, with values in the range 2-3.6 Hz. TROSY-based studies of scalar couplings across hydrogen bonds should be applicable for large molecular sizes, including protein-bound nucleic acids}, keywords = {nosource} }

@article{wicknerMutantsSaccharomycesCerevisiae1974, title = {Mutants of {{Saccharomyces}} Cerevisiae That Incorporate Deoxythymidine-5’-Monophosphate into Deoxyribonucleic Acid in Vivo}, author = {Wickner, R. B.}, year = 1974, journal = {Journal of Bacteriology}, volume = {117}, number = {1}, pages = {252}, publisher = {Am Soc Microbiol}, url = {http://jb.asm.org/cgi/content/abstract/117/1/252}, keywords = {nosource} }

@article{gallantLeftwardRibosomeFrameshifting1992, title = {Leftward Ribosome Frameshifting at a Hungry Codon{\(\bullet\)} 1}, author = {Gallant, J. A. and Lindsley, D.}, year = 1992, month = jan, journal = {Journal of molecular biology}, volume = {223}, number = {1}, pages = {31–40}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/002228369290713T}, keywords = {nosource} }

@article{weinerRapidPCRSitedirected1994, title = {Rapid {{PCR}} Site-Directed Mutagenesis.}, author = {Weiner, M. P. and Costa, G. L.}, year = 1994, journal = {Genome Research}, volume = {4}, number = {3}, pages = {S131}, publisher = {Cold Spring Harbor Lab}, url = {http://genome.cshlp.org/content/4/3/S131.full.pdf?ck=nck}, keywords = {nosource} }

@article{wowerPhotochemicalCrosslinkingYeast1988, title = {Photochemical Cross-Linking of Yeast {{tRNAPhe}} Containing 8-Azidoadenosine at Positions 73 and 76 to the {{Escherichia}} Coli Ribosome}, author = {Wower, J. and Hixson, S. S. and Zimmermann, R. A.}, year = 1988, month = oct, journal = {Biochemistry}, volume = {27}, number = {21}, pages = {8114–8121}, publisher = {ACS Publications}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00421a021}, abstract = {The 3’-terminal -A-C-C-A sequence of yeast tRNA(Phe) has been modified by replacing either adenosine-73 or adenosine-76 with the photoreactive analogue 8-azidoadenosine (8N3A). The incorporation of 8N3A into tRNA(Phe) was accomplished by ligation of 8-azidoadenosine 3’,5’-bisphosphate to the 3’ end of tRNA molecules which were shortened by either one or four nucleotides. Replacement of the 3’-terminal A76 with 8N3A completely blocked aminoacylation of the tRNA. In contrast, the replacement of A73 with 8N3A has virtually no effect on the aminoacylation of tRNA(Phe). Neither substitution hindered binding of the modified tRNAs to Escherichia coli ribosomes in the presence of poly(U). Photoreactive tRNA derivatives bound noncovalently to the ribosomal P site were cross-linked to the 50S subunit upon irradiation at 300 nm. Nonaminoacylated tRNA(Phe) containing 8N3A at either position 73 or position 76 cross-linked exclusively to protein L27. When N-acetylphenylalanyl-tRNA(Phe) containing 8N3A at position 73 was bound to the P site and irradiated, 23S rRNA was the main ribosomal component labeled, while smaller amounts of the tRNA were cross-linked to proteins L27 and L2. Differences in the labeling pattern of nonaminoacylated and aminoacylated tRNA(Phe) containing 8N3A in position 73 suggest that the aminoacyl moiety may play an important role in the proper positioning of the 3’ end of tRNA in the ribosomal P site. More generally, the results demonstrate the utility of 8N3A-substituted tRNA probes for the specific labeling of ribosomal components at the peptidyltransferase center}, keywords = {nosource} }

@article{mitchellNMDPathwayYeast2003, title = {An {{NMD}} Pathway in Yeast Involving Accelerated Deadenylation and Exosome-Mediated 3’–{\(>\)} 5’degradation}, author = {Mitchell, P. and Tollervey, D.}, year = 2003, month = may, journal = {Molecular cell}, volume = {11}, number = {5}, pages = {1405–1413}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276503001904}, abstract = {Eukaryotic mRNAs containing premature termination codons are subjected to accelerated turnover, known as nonsense-mediated decay (NMD). Recognition of translation termination events as premature requires a surveillance complex, which includes the RNA helicase Upf1p. In Saccharomyces cerevisiae, NMD provokes rapid decapping followed by 5’–{\(>\)}3’exonucleolytic decay. Here we report an alternative, decapping-independent NMD pathway involving deadenylation and subsequent 3’–{\(>\)}5’ exonucleolytic decay. Accelerated turnover via this pathway required Upf1p and was blocked by the translation inhibitor cycloheximide. Degradation of the deadenylated mRNA required the Rrp4p and Ski7p components of the cytoplasmic exosome complex, as well as the putative RNA helicase Ski2p. We conclude that recognition of NMD substrates by the Upf surveillance complex can target mRNAs to rapid deadenylation and exosome-mediated degradation}, keywords = {nosource} }

@article{willsReportedTranslationalBypass1997, title = {Reported Translational Bypass in a {{trpR}}’-{{lacZ}}’fusion Is Accounted for by Unusual Initiation And+ 1 Frameshifting1}, author = {Wills, N. M. and Ingram, J. A. and Gesteland, R. F. and Atkins, J. F.}, year = 1997, month = aug, journal = {Journal of molecular biology}, volume = {271}, number = {4}, pages = {491–498}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283697911876}, keywords = {nosource} }

@article{weissColiRibosomesRephase1989, title = {E. Coli Ribosomes Re-Phase on Retroviral Frameshift Signals at Rates Ranging from 2 to 50 Percent.}, author = {Weiss, R. B. and Dunn, D. M. and Shuh, M. and Atkins, J. F. and Gesteland, R. F.}, year = 1989, journal = {The New Biologist}, volume = {1}, number = {2}, eprint = {2562219}, eprinttype = {pubmed}, pages = {159}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2562219}, keywords = {nosource} }

@article{rivlinContributionZincFinger1999, title = {The Contribution of a Zinc Finger Motif to the Function of Yeast Ribosomal Protein {{YL37a1}}}, author = {Rivlin, A. A. and Chan, Y. L. and Wool, I. G.}, year = 1999, month = dec, journal = {Journal of Molecular Biology}, volume = {294}, number = {4}, pages = {909–919}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283699933090}, abstract = {Eukaryotic ribosomes have a large number of proteins but the exact nature of their contribution to the structure and to the function of the particle is not known. Of the 78 proteins in yeast ribosomes, six have zinc finger motifs of the C-2-C-2 variety. Both genes encoding the essential yeast ribosomal protein YL37a, which has such a zinc finger motif, were disrupteXXPd. The double deletion, which is lethal, can be rescued with a plasmid-encoded copy of a YL37a gene. Mutations were constructed in a plasmid-encoded copy of YL37a; the mutations caused the cysteine residues in the motif (at positions 39, 42, 57 and 60) to be replaced, one at a time, with serine. The cysteine residue at position 39, the first of the four in the motif, is essential for the function of YL37a, since a C39S mutation did not complement the null phenotype. However, plasmids encoding variants with C42S, C57S, or C60S mutations in the zinc finger motif were able to rescue the null mutant. YL37a binds zinc, but none of the mutant proteins, C39S, C42S, C57S, or C60S, was able to bind the metal. Thus, all four cysteine residues are essential for the binding of zinc; only one, C39, is essential for the function of the ribosomal protein. (C) 1999 Academic Press}, keywords = {nosource} }

@article{zhouPurificationFunctionalRNAaEUProtein2003, title = {Purification of {{Functional RNA^a}}{{Protein Complexes}} Using {{MS2^a}}{{MBP}}}, author = {Zhou, Z. and Reed, R.}, year = 2003, journal = {Current Protocols in Molecular Biology}, volume = {Chapter 27}, pages = {Unit}, publisher = {Wiley Online Library}, url = {http://onlinelibrary.wiley.com/doi/10.1002/0471142727.mb2703s63/pdf http://onlinelibrary.wiley.com/doi/10.1002/0471142727.mb2703s63/full}, abstract = {Biological machines composed of RNAs and proteins play essential roles in many biological processes. To better understand the mechanism and function of these machines, it is critical to isolate them in a highly purified and functional form. A method for isolating functional RNA-protein complexes assembled in vitro is described. The approach combines gel filtration and an affinity-chromatography strategy using the bacteriophage MS2 coat protein, which binds to a specific RNA-hairpin structure. Using this method, highly purified and functional human spliceosomes have been isolated. The purified spliceosome preparation is used to determine the protein components of the spliceosome by mass spectrometry and to examine the structure of the spliceosome by electron microscopy}, keywords = {nosource} }

@book{welchTranslationTerminationIt2000, title = {Translation Termination: It’s Not the End of the Story}, author = {Welch, E. M. and Wang, W. and Peltz, S. W.}, year = 2000, publisher = {Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY}, url = {http://books.google.com/books?hl=en&lr=&id=InXRuBRGkLYC&oi=fnd&pg=PA467&dq=Translation+termination:+It's+not+the+end+of+the+story.&ots=GMCSOm4eZo&sig=bpdQE5r94zuE5bWXFkXeedR3fOo}, keywords = {nosource} }

@article{blevinsNMRViewComputerProgram1994, title = {{{NMRView}}: A Computer Program for the Visualization and Analysis of {{NMR}} Data}, author = {Blevins, B.}, year = 1994, journal = {J Biomol NMR}, volume = {4⬚ ⬚}, pages = {630–614}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:NMRView:+A+computer+program+for+the+visualization+and+analysis+of+NMR+data.#1}, keywords = {nosource} }

@article{liMolecularGeneticAnalysis1996, title = {Molecular Genetic Analysis of Plastocyanin Biosynthesis in {{Chlamydomonas}} Reinhardtii}, author = {Li, H. H. and Quinn, J. and Culler, D. and {Girard-Bascou}, J. and Merchant, S.}, year = 1996, journal = {Journal of Biological Chemistry}, volume = {271}, number = {49}, pages = {31283}, publisher = {ASBMB}, url = {http://www.jbc.org/content/271/49/31283.short}, keywords = {nosource} }

@article{marmorsteinStructureHistoneAcetyltransferases12001, title = {Structure of Histone Acetyltransferases1}, author = {Marmorstein, R.}, year = 2001, journal = {Journal of Molecular Biology}, volume = {311}, number = {3}, pages = {433–444}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283601948594}, abstract = {Histone acetyltranferase (HAT) enzymes are the catalytic subunits of multisubunit protein complexes that acetylate specific lysine residues on the N-terminal regions of the histone components of chromatin to promote gene activation. These enzymes, which now include more than 20 members, fall into distinct families that generally have high sequence similarity and related substrate specificity within families, but have divergent sequence and substrate specificity between families. Significant insights into the mode of catalysis and histone substrate binding have been provided by the structure determination of the divergent HAT enzymes Hat1, Gcn5/PCAF and Esa1. A comparison of these structures reveals a structurally conserved central core domain that mediates extensive interactions with the acetyl-coenzyme A cofactor, and structurally divergent N and C-terminal domains. A correlation of these structures with other studies reveals that the core domain plays a particularly important role in histone substrate catalysis and that the N and C-terminal domains play important roles in histone substrate binding. These correlations imply a related mode of catalysis and histone substrate binding by a diverse group of HAT enzymes. (C) 2001 Academic Press}, keywords = {nosource} }

@article{xiongSynthesisPutativeRed1993, title = {Synthesis of the Putative Red Clover Necrotic Mosaic Virus {{RNA}} Polymerase by Ribosomal Frameshifting in Vitro}, author = {Xiong, Z. and Kim, K. H. and Kendall, T. L. and Lommel, S. A.}, year = 1993, month = mar, journal = {Virology}, volume = {193}, number = {1}, pages = {213–221}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0042682283711177}, keywords = {nosource} }

@article{lessardStudiesFormationTransfer1972, title = {Studies on the Formation of Transfer Ribonucleic Acid-Ribosome Complex. {{XXII}}. {{Binding}} of Aminoacyl-Oligonucleotides to Ribosomes}, author = {Lessard, J. S.}, year = 1972, month = nov, journal = {J. Biol. Chem}, volume = {247}, number = {21}, pages = {6901–6908}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Studies+on+the+formation+of+transfer+ribonucleic+acid-ribosome+complexes.+XXII.+Binding+of+aminoacyl-oligonucleotides+to+ribosomes#2}, keywords = {nosource} } % == BibTeX quality report for lessardStudiesFormationTransfer1972: % ? Possibly abbreviated journal title J. Biol. Chem

@article{nazarHigherOrderStructure1991, title = {Higher Order Structure of the Ribosomal 5 {{S RNA}}.}, author = {Nazar, R. N.}, year = 1991, journal = {Journal of Biological Chemistry}, volume = {226}, pages = {4562–4567}, url = {http://www.jbc.org/content/266/7/4562.short}, keywords = {nosource} }

@article{macbethCharacterizationVitroVivo1999, title = {Characterization of in Vitro and in Vivo Mutations in Non-Conserved Nucleotides in the Ribosomal {{RNA}} Recognition Domain for the Ribotoxins Ricin and Sarcin and the Translation Elongation Factors1}, author = {Macbeth, M. R. and Wool, I. G.}, year = 1999, month = jan, journal = {Journal of molecular biology}, volume = {285}, number = {2}, pages = {567–580}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283698923373}, abstract = {The sarcin/ricin domain in 23 S/28 S rRNA is crucial for ribosome function, since it constitutes at least part of the binding site for the elongation factors and hence is essential for binding aminoacyl- tRNA and for translocation. The domain is also the site of action of ricin and sarcin and analysis of the effect of mutations in the RNA on recognition by the cytotoxins has helped to define the structure and to understand the function of the region. We have constructed deletions, separately, of pairs of non-conserved, juxtaposed but non-hydrogen- bonded nucleotides that correspond to C4317 and C4331, and to U4316 and C4332, in an oligoribonucleotide that mimics the sarcin/ricin domain in rat 28 S rRNA. The deletions had no effect on the depurination of A4324 by ricin nor on the cleavage of the phosphodiester bond on the 3’ side of G4325 by sarcin. However, simultaneous deletion of the four nucleotides decreased cleavage by sarcin but did not affect depurination by ricin. Removal of the non-canonical A4318.A4330 pair abolished recognition by both toxins. Deletion from oligoribonucleotides, that reproduce the sarcin/ricin domain of Escherichia coli 23 S rRNA, of U2653 and C2667 (equivalent to U4316, C4317 and C4331, C4332 in 28 S rRNA), or substitution of guanosine for U2653 (designed to form a Watson-Crick G2653.C2667 pair), reduced cleavage by sarcin whereas depurination by ricin was slightly increased. An increase in the stability of the mutant oligoribonucleotides may be the basis of the impairment in sarcin action. The tm for the wild-type RNA is 60 degreesC; for the double- deletion mutant U2653Delta/C2667Delta it is 65 degreesC; and for the U2653G transversion it is 69 degreesC. Expression of a mutant 23 S rRNA gene lacking U2653 and C2667 is lethal and a U2653G transversion mutation impairs growth. The mutant ribosomes are less active in protein synthesis than the wild-type and ribosomes with the U2653G mutation are resistant to sarcin. The binding of EF-G to oligoribonucleotides with a U2653/C2667 double deletion is reduced and an effect on the affinity of the factor for the sarcin/ricin domain may account in part for the decrease in ribosome efficiency. The results stress the potential importance in rRNA structure and function of non- conserved nucleotides, and suggest that the sarcin/ricin domain in ribosomes requires a region of structural flexibility for optimal efficiency}, keywords = {nosource} }

@article{leerPrimaryStructureGene1984, title = {The Primary Structure of the Gene Encoding Yeast Ribosomal Protein {{L}} 16}, author = {Leer, R. J. and {}van {Raamsdonk-Duin}, M. and Mager, W. H. and Planta, R. J.}, year = 1984, month = oct, journal = {FEBS letters}, volume = {175}, number = {2}, pages = {371–376}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0014579384807711}, abstract = {As part of our studies on the molecular basis for the coordinate expression of ribosomal protein genes in yeast we analyzed the primary structure of the gene encoding protein L16 of the large ribosomal subunit including the flanking sequences. L16 turned out to be a ribosomal protein with a molecular mass of 22662 Da and a net charge of +12. Both the 5’- and the 3’-end of the L16 mRNA were mapped by primer extension and S1 nuclease analysis. In the DNA regions flanking the coding sequence several conserved elements are present that may be involved in transcription initiation or termination}, keywords = {nosource} }

@article{oenPeptidylTransferaseInhibitors1974, title = {Peptidyl Transferase Inhibitors Alter the Covalent Reaction of {{BrAcPhe-tRNA}} with the {{E}}. Coli Ribosome.}, author = {Oen, H. and Pellegrini, M. and Cantor, C. R.}, year = 1974, journal = {FEBS letters}, volume = {45}, number = {1}, eprint = {4606896}, eprinttype = {pubmed}, pages = {218}, url = {http://www.ncbi.nlm.nih.gov/pubmed/4606896}, keywords = {nosource} }

@article{kinzyNontranslationalFunctionsComponents2000, title = {Nontranslational Functions of Components of the Translational Apparatus}, author = {Kinzy, T. G. and Goldman, E.}, year = 2000, journal = {COLD SPRING HARBOR MONOGRAPH SERIES}, volume = {39}, pages = {973–998}, publisher = {CSH COLD SPRING HARBOR LABORATORY PRESS}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Nontranslational+functions+of+components+of+the+translational+apparatus.#0}, keywords = {nosource} }

@article{pestovaTranslationElongationAssembly2003, title = {Translation Elongation after Assembly of Ribosomes on the {{Cricket}} Paralysis Virus Internal Ribosomal Entry Site without Initiation Factors or Initiator {{tRNA}}}, author = {Pestova, T. V. and Hellen, C. U. T.}, year = 2003, month = jan, journal = {Genes & development}, volume = {17}, number = {2}, pages = {181}, publisher = {Cold Spring Harbor Lab}, url = {http://genesdev.cshlp.org/content/17/2/181.short}, abstract = {Reconstitution of translation elongation from purified components confirmed that ribosomes that assembled on the Cricket paralysis virus intercistronic internal ribosomal entry site (IRES) without the involvement of initiation factors or initiator tRNA were active in elongation and are, therefore, true initiation complexes. The first elongation cycle occurred without peptide bond formation on 80S ribosomes that did not contain tRNA in the P site. It required elongation factors 1A and 2 and A site-cognate aminoacylated tRNA. Cycloheximide arrested ribosomes on the IRES only after two cycles of elongation, when the first deacylated tRNA reached the E-site after translocation from the A-site}, keywords = {nosource} }

@article{toh-eSuperkillerMutationsSuppress1980, title = {” {{Superkiller}}” Mutations Suppress Chromosomal Mutations Affecting Double-Stranded {{RNA}} Killer Plasmid Replication in {{Saccharomyces}} Cerevisiae}, author = {{Toh-e}, A. and Wickner, R. B.}, year = 1980, journal = {Proceedings of the National Academy of Sciences}, volume = {77}, number = {1}, pages = {527}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/77/1/527.short}, keywords = {nosource} }

@article{vaismanRoleOfSaccharomycesCerevisiae1995, title = {The Role {{ofSaccharomyces}} Cerevisiae {{Cdc40p}} in {{DNA}} Replication and Mitotic Spindle Formation and/or Maintenance}, author = {Vaisman, N. and Tsouladze, A. and Robzyk, K. and {Ben-Yehuda}, S. and Kupiec, M. and Kassir, Y.}, year = 1995, journal = {Molecular and General Genetics MGG}, volume = {247}, number = {2}, pages = {123–136}, publisher = {Springer}, url = {http://www.springerlink.com/index/t31x14u1010pk30q.pdf}, keywords = {nosource} }

@article{narandaSUI1P16Required1996, title = {{{SUI1}}/P16 Is Required for the Activity of Eukaryotic Translation Initiation Factor 3 in {{Saccharomyces}} Cerevisiae}, author = {Naranda, T. and MacMillan, S. E. and Donahue, T. F. and Hershey, J. W. B.}, year = 1996, journal = {Molecular and cellular biology}, volume = {16}, number = {5}, pages = {2307}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/16/5/2307}, keywords = {nosource} }

@article{limAnalysisInteractionsCodonAnticodon1997, title = {Analysis of Interactions between the {{Codon-Anticodon}} Duplexes within the Ribosome: Their Role in Translation1}, author = {Lim, V. I.}, year = 1997, month = mar, journal = {Journal of Molecular Biology}, volume = {266}, number = {5}, pages = {877–890}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283696908025}, keywords = {nosource} }

@article{vijayraghavanIsolationCharacterizationPremRNA1989, title = {Isolation and Characterization of Pre-{{mRNA}} Splicing Mutants of {{Saccharomyces}} Cerevisiae.}, author = {Vijayraghavan, U. and others}, year = 1989, journal = {Genes & development}, volume = {3}, number = {8}, pages = {1206}, publisher = {Cold Spring Harbor Lab}, url = {http://genesdev.cshlp.org/content/3/8/1206.short}, keywords = {nosource} }

@article{wicknerHostFunctionMAK161988, title = {Host Function of {{MAK16}}: {{G1}} Arrest by a Mak16 Mutant of {{Saccharomyces}} Cerevisiae}, author = {Wickner, R. B.}, year = 1988, journal = {Proceedings of the National Academy of Sciences}, volume = {85}, number = {16}, pages = {6007}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/85/16/6007.short}, keywords = {nosource} }

@article{jeonIntegrationHumanPapillomavirus1995, title = {Integration of Human Papillomavirus Type 16 {{DNA}} into the Human Genome Leads to Increased Stability of {{E6}} and {{E7 mRNAs}}: Implications for Cervical Carcinogenesis}, author = {Jeon, S. and Lambert, P. F.}, year = 1995, journal = {Proceedings of the National Academy of Sciences}, volume = {92}, number = {5}, pages = {1654}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/92/5/1654.short}, keywords = {nosource} }

@article{xuHostGenesThat1990, title = {Host Genes That Influence Transposition in Yeast: The Abundance of a Rare {{tRNA}} Regulates {{Ty1}} Transposition Frequency}, author = {Xu, H. and Boeke, J. D.}, year = 1990, journal = {Proceedings of the National Academy of Sciences}, volume = {87}, number = {21}, pages = {8360}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/87/21/8360.short}, keywords = {nosource} }

@article{ribasGagDomainGagPol1998, title = {The {{Gag Domain}} of the {{Gag-Pol Fusion Protein Directs Incorporation}} into the {{LA Double-stranded RNA Viral Particles inSaccharomyces}} Cerevisiae}, author = {Ribas, J. C. and Wickner, R. B.}, year = 1998, month = apr, journal = {Journal of Biological Chemistry}, volume = {273}, number = {15}, pages = {9306}, publisher = {ASBMB}, url = {http://www.jbc.org/content/273/15/9306.short}, abstract = {The L-A double-stranded RNA virus of yeast encodes its major coat protein, Gag, and a Gag-Pol fusion protein made by a -1 ribosomal frameshift, a coding strategy used by many retroviruses. We find that cells expressing only Gag from one plasmid and only Gag-Pol (in frame) from a separate plasmid can support the propagation of M-1 double-stranded RNA, encoding the killer toxin. We use this system to separately investigate the functions of Gag and the Gag part of Gag-Pol. L-A contains two fusion protein molecules per particle, and although N-terminal acetylation of Gag is essential for viral assembly, it is completely dispensable for function of Gag-Pol. In general, the requirements on Gag for viral assembly and propagation are more stringent than on the Gag part of Gag-Pol. Finally, we directly show that it is Gag that instructs the incorporation of Gag-Pol into the viral particles}, keywords = {nosource} }

@article{pfundMolecularChaperoneSsb1998, title = {The Molecular Chaperone {{Ssb}} from {{Saccharomyces}} Cerevisiae Is a Component of the Ribosome–Nascent Chain Complex}, author = {Pfund, C. and {Lopez-Hoyo}, N. and Ziegelhoffer, T. and Schilke, B. A. and {Lopez-Buesa}, P. and Walter, W. A. and Wiedmann, M. and Craig, E. A.}, year = 1998, month = jul, journal = {The EMBO journal}, volume = {17}, number = {14}, pages = {3981–3989}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/emboj/journal/v17/n14/abs/7591099a.html}, abstract = {The 70 kDa heat shock proteins (Hsp70s) are a ubiquitous class of molecular chaperones. The Ssbs of Saccharomyces cerevisiae are an abundant type of Hsp70 found associated with translating ribosomes, To understand better the function of Ssb in association with ribosomes, the Ssb-ribosome interaction was characterized. Incorporation of the aminoacyl-tRNA analog puromycin by translating ribosomes caused the release of Ssb concomitant with the release of nascent chains. In addition, Ssb could be cross-linked to nascent chains containing a modified lysine residue with a photoactivatable cross-linker. Together, these results suggest an interaction of Ssb with the nascent chain. The interaction of Ssb with the ribosome-nascent chain complex was stable, as demonstrated by resistance to treatment with high salt; however, Ssb interaction with the ribosome in the absence of nascent chain was salt sensitive. We propose that Ssb is a core component of the translating ribosome which interacts with both the nascent polypeptide chain and the ribosome, These interactions allow Ssb to function as a chaperone on the ribosome, preventing the misfolding of newly synthesized proteins}, keywords = {nosource} }

@article{sanbonmatsuEnergyLandscapeOfathearibosomal2006, title = {Energy Landscape Of'athe'aribosomal Decoding Center}, author = {Sanbonmatsu, K. Y.}, year = 2006, journal = {Biochimie}, volume = {88}, number = {8}, pages = {1053–1059}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0300908406001246}, abstract = {The ribosome decodes the genetic information that resides in nucleic acids. A key component of the decoding mechanism is a conformational switch in the decoding center of the small ribosomal subunit discovered in high-resolution X-ray crystallography studies. It is known that small subunit nucleotides A1492 and A1493 flip out of helix 44 upon transfer RNA (tRNA) binding; however, the operation principles of this switch remain unknown. Replica molecular dynamics simulations reveal a low free energy barrier between flipped-out and flipped-in states, consistent with a switch that can be controlled by shifting the equilibrium between states. The barrier determined by the simulations is sufficiently small for the binding of ligands, such as tRNAs or aminoglycoside antibiotics, to shift the equilibrium}, keywords = {nosource} }

@article{ridleySuperkillerMutationsSaccharomyces1984, title = {Superkiller Mutations in {{Saccharomyces}} Cerevisiae Suppress Exclusion of {{M2}} Double-Stranded {{RNA}} by {{LA-HN}} and Confer Cold Sensitivity in the Presence of {{M}} and {{LA-HN}}.}, author = {Ridley, S. P. and Sommer, S. S. and Wickner, R. B.}, year = 1984, month = apr, journal = {Molecular and Cellular Biology}, volume = {4}, number = {4}, pages = {761}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/4/4/761}, keywords = {nosource} }

@article{sandbakenMutationsElongationFactor1988, title = {Mutations in Elongation Factor {{EF-1}} $$alpha$$ Affect the Frequency of Frameshifting and Amino Acid Misincorporation in {{Saccharomyces}} Cerevisiae}, author = {Sandbaken, M. G. and Culbertson, M. R.}, year = 1988, journal = {Genetics}, volume = {120}, number = {4}, pages = {923}, publisher = {Genetics Soc America}, url = {http://www.genetics.org/content/120/4/923.short}, keywords = {nosource} }

@article{xueKelchEncodesComponent1993, title = {Kelch Encodes a Component of Intercellular Bridges in {{Drosophila}} Egg Chambers}, author = {Xue, F. and Cooley, L.}, year = 1993, month = mar, journal = {Cell}, volume = {72}, number = {5}, pages = {681–693}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867493903979}, keywords = {nosource} }

@article{jimenezSimultaneousRibosomalResistance1975, title = {Simultaneous Ribosomal Resistance to Trichodermin and Anisomycin in {{Saccharomyces}} Cerevisiae Mutants}, author = {Jimenez, A. and Sanchez, L. and Vazquez, D.}, year = 1975, journal = {Biochimica et Biophysica Acta (BBA)-Nucleic Acids and Protein Synthesis}, volume = {383}, number = {4}, pages = {427–434}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0005278775903123}, abstract = {A spontaneous mutant of Saccharomyces cerevisiae resistant to trichodermin has been isolated. It displays cross resistance both in vivo and in vitro to a number of sesquiterpene antibiotics (fusarenon X, trichothecin and verrucarin A) and to the chemically unrelated antibiotic anisomycin. The mutation conferring resistance to anisomycin and trichodermin is expressed in the 60-S subunit of the yeast 80-S ribosome. Mutant ribosomes bind [-14C]trichodermin much less efficiently than wild type ribosomes, suggesting that resistance may be due, at least in part, to this property. However, both types of ribosomes bind [-3H] anisomycin equally. These results suggest that anisomycin and trichodermin have different binding sites on the 60-S subunit of eukaryotic ribosomes, even though previous results have shown that both antibiotics bind to mutually exclusive sites.}, keywords = {nosource} }

@article{gaoEvidenceThatUncharged1995, title = {Evidence That {{Uncharged tRNA Can Inhibit}} a {{Programmed Translational Frameshift inEscherichia}} Coli}, author = {Gao, W. and Jakubowski, H. and Goldman, E.}, year = 1995, journal = {Journal of molecular biology}, volume = {251}, number = {2}, pages = {210–216}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283685704287}, abstract = {In the modified release factor 2 (RF2) programmed translational frameshift (with a sense codon replacing the wild-type in-frame UGA codon at the shift site), ribosomes shift +1 into the reading frame for an out-of-frame reporter fused to the frameshift sequence. Partitioning of ribosomes between the out-of-frame shift and in-frame reading depends on the codon at the shift site and on the levels of tRNA decoding the in-frame codon. Overexpression of a tRNA species cognate to the in-frame codon at the shift site significantly reduces the frequency of frame-shifting, presumably by facilitating in-frame reading, which would reduce production of the out-of-frame reporter. However, since overexpression of a tRNA increases levels of both charged and uncharged tRNA, it is possible that uncharged cognate tRNA might be able to reduce the frequency of the frameshift, by entering the A site on the ribosome. To test this, we manipulated charged and uncharged tRNA levels in vivo, using the tryptophan analog tryptophan hydroxamate, which increases the proportion of uncharged tRNA(Trp) by competing with cognate amino acid tryptophan for tryptophanyl-tRNA synthetase, thereby reducing protein synthesis. We report here that a slight but reproducible reduction in the relative frequency of the frameshift is observed when tryptophan hydroxamate is added to cells containing the modified RF2 shift with UGG (Trp codon) at the shift site. When tRNA(Trp) is overexpressed from another plasmid, the shift frequency drops three- to fourfold, as expected, however, this reduction is still seen in the presence of the analog. Thus, under conditions when most of the tRNA(Trp) is apparently uncharged, excess tRNA(Trp) still causes a significant reduction in the frameshift when UGG is at the shift site, providing evidence that uncharged cognate tRNA also can inhibit this frameshift}, keywords = {nosource} }

@article{leonovAffinityPurificationRibosomes2003, title = {Affinity Purification of Ribosomes with a Lethal {{G2655C}} Mutation in 23 {{S rRNA}} That Affects the Translocation}, author = {Leonov, A. A. and Sergiev, P. V. and Bogdanov, A. A. and Brimacombe, R. and Dontsova, O. A.}, year = 2003, month = may, journal = {Journal of Biological Chemistry}, volume = {278}, number = {28}, pages = {25664}, publisher = {ASBMB}, url = {http://www.jbc.org/content/278/28/25664.short}, abstract = {A method for preparation of E. coli ribosomes carrying lethal mutations in 23S rRNA was developed. The method is based on the site-directed incorporation of a streptavidin-binding tag into functionally neutral sites of the 23S rRNA and subsequent affinity chromatography. It was tested with ribosomes mutated at 23S rRNA position 2655 (the EF-G binding site). Ribosomes carrying the lethal G2655C mutation were purified and studied in vitro. It was found in particular that this mutation confers strong inhibition of the translocation process, but only moderately affects GTPase activity and binding of EF-G}, keywords = {nosource} }

@article{zhangPeptideBondFormation1997, title = {Peptide Bond Formation by in Vitro Selected Ribozymes}, author = {Zhang, B. and Cech, T. R.}, year = 1997, journal = {Nature}, volume = {390}, number = {6655}, pages = {96–100}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/nature/journal/v390/n6655/abs/390096a0.html}, keywords = {nosource} }

@article{roseMethodsYeastGenetics1990, title = {Methods in Yeast Genetics: A Laboratory Course Manual}, author = {Rose, M. D. and Winston, F. M. and Heiter, P.}, year = 1990, publisher = {Cold Spring Harbor Laboratory Press}, url = {http://agris.fao.org/agris-search/search/display.do?f=1992/US/US92038.xml;US9140801}, keywords = {nosource} } % == BibTeX quality report for roseMethodsYeastGenetics1990: % Missing required field ‘journal’

@article{martinInhibitorsProteinSynthesis1988, title = {Inhibitors of Protein Synthesis and {{RNA}} Synthesis Prevent Neuronal Death Caused by Nerve Growth Factor Deprivation}, author = {Martin, D. P. and Schmidt, R. E. and DiStefano, P. S. and Lowry, O. H. and Carter, J. G. and Johnson, E. M.}, year = 1988, journal = {The Journal of cell biology}, volume = {106}, number = {3}, eprint = {1612831}, eprinttype = {jstor}, pages = {829–844}, publisher = {JSTOR}, url = {http://www.jstor.org/stable/1612831}, keywords = {nosource} }

@article{weissSeleniumRegulationClassical1997, title = {Selenium Regulation of Classical Glutathione Peroxidase Expression Requires the 3{\(\prime\)} Untranslated Region in {{Chinese}} Hamster Ovary Cells}, author = {Weiss, S. L. and Sunde, R. A.}, year = 1997, month = jul, journal = {The Journal of nutrition}, volume = {127}, number = {7}, pages = {1304}, publisher = {Am Soc Nutrition}, url = {http://jn.nutrition.org/content/127/7/1304.short}, abstract = {Classical glutathione peroxidase (GPX) mRNA levels fall dramatically in selenium (Se)-deficient animals, but it is not known whether this mechanism is related to the mRNA 3’ untranslated region (3’UTR) sequences that have been shown to direct Se incorporation. In this study, we used recombinant GPX constructs to investigate the role of the GPX 3’UTR in Se regulation of GPX mRNA levels in Chinese hamster ovary (CHO) cells. The CHO cells were transfected with GPX (pRc/GPX), GPX lacking the 3’UTR (pRc/Delta3’UTR) or the pRc/CMV vector alone, and GPX activity and GPX mRNA levels were determined in stable transfectants grown in low Se basal medium with a range of added Se concentrations. We identified two pRc/GPX transfectants with significantly elevated GPX activity levels compared with pRc/CMV transfectants. The elevated GPX expression did not dramatically shift the amount of Se that was sufficient for GPX activity to reach the Se- adequate plateau level (100 nmol/L added Se). As expected, GPX activity was not significantly different when pRc/Delta3’UTR transfectants were compared with pRc/CMV control transfectants. Among the wild type and transfected CHO cells, Se-deficient GPX activity levels averaged 35 +/- 5% of Se-adequate levels. Selenium-deficient levels of endogenous GPX mRNA as well as recombinant pRc/GPX mRNA averaged 54-58% of Se-adequate levels; 3-4 nmol/L added Se was sufficient for maximal GPX mRNA levels. In contrast, pRc/Delta3’UTR mRNA levels in the unsupplemented cells remained at Se-adequate levels and showed no distinct Se regulation. These studies demonstrate that the GPX 3’UTR is necessary for Se regulation of GPX mRNA levels in addition to its role in Se incorporation}, keywords = {nosource} }

@article{lawrenceClassicalMutagenesisTechniques1991, title = {Classical Mutagenesis Techniques.}, author = {Lawrence, C. W.}, year = 1991, journal = {Methods in enzymology}, volume = {194}, pages = {273}, publisher = {Academic Press}, url = {http://ukpmc.ac.uk/abstract/MED/2005792}, keywords = {nosource} }

@article{stadlerSARSBeginningUnderstand2003, title = {{{SARS}}—Beginning to Understand a New Virus}, author = {Stadler, K. and Masignani, V. and Eickmann, M. and Becker, S. and Abrignani, S. and Klenk, H. D. and Rappuoli, R.}, year = 2003, month = dec, journal = {Nature Reviews Microbiology}, volume = {1}, number = {3}, pages = {209–218}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/nrmicro/journal/v1/n3/abs/nrmicro775.html}, abstract = {The 114-day epidemic of the severe acute respiratory syndrome (SARS) swept 29 countries, affected a reported 8,098 people, left 774 patients dead and almost paralyzed the Asian economy. Aggressive quarantine measures, possibly aided by rising summer temperatures, successfully terminated the first eruption of SARS and provided at least a temporal break, which allows us to consolidate what we have learned so far and plan for the future. Here, we review the genomics of the SARS coronavirus (SARS-CoV), its phylogeny, antigenic structure, immune response and potential therapeutic interventions should the SARS epidemic flare up again}, keywords = {nosource} }

@article{ofengandMappingNucleotideResolution1997, title = {Mapping to Nucleotide Resolution of Pseudouridine Residues in Large Subunit Ribosomal {{RNAs}} from Representative Eukaryotes, Prokaryotes, Archaebacteria, Mitochondria and Chloroplasts1}, author = {Ofengand, J. and Bakin, A.}, year = 1997, month = feb, journal = {Journal of molecular biology}, volume = {266}, number = {2}, pages = {246–268}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(96)90737-8}, abstract = {The pseudouridine (psi) residues present in the high molecular mass RNA from the large ribosomal subunit (LSU) have been sequenced from representative species of the eukaryotes, prokaryotes and archaebacteria, and from mitochondrial and chloroplast organelles. Ribosomes from Bacillus subtilis, Halobacter halobium, Drosphilia melanogaster, Mus musculus, Homo sapiens, mitochondria of M. musculus, H. sapiens and Trypanosoma brucei, and Zea mays chloroplasts were examined, resulting in the exact localization of 190 psi residues. The number of psi residues per RNA varied from one in the mitochondrial RNAs to 57 in the cytoplasmic LSU RNA of D. melanogaster and M. musculus. Despite this, all of the psi residues were found in three domains, II, IV and V. All three are at or have been linked to the peptidyl transferase center according to the literature. Comparison of the sites for psi among the species examined revealed four conserved or semi-conserved segments. One is the region 1911 to 1917, which contains three psi or modified psi in almost all species examined. This site is also juxtaposed to the decoding site of the 30 S subunit in the 70 S ribosome and has been implicated in the fidelity of codon recognition. Three additional sites were at the peptidyl transferase center itself. The juxtaposition of the conserved sites for psi with the two important functions of the ribosome, codon recognition and peptide bond formation, implies an important role for psi in ribosome function. We report some new putative modified nucleosides in LSU RNAs as detected by reverse transcription, correct a segment of the sequence of Z. mays chloroplasts and D. melanogaster LSU RNA, correlate the secondary structural context for all known psi residues in ribosomal RNA, and compare the sites for psi with those known for methylated nucleosides in H. sapiens}, keywords = {nosource} }

@article{wittmann-lieboldSequenceComparisonEvolution1990, title = {Sequence Comparison and Evolution of Ribosomal Proteins and Their Genes}, author = {{Wittmann-Liebold}, B. and Kopke, A. K. E. and Arndt, E. and Kromer, W.}, year = 1990, journal = {The Ribosome, Structure,}, volume = {1}, pages = {598–616}, publisher = {A.S.M.}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Sequence+comparison+and+evolution+of+ribosomal+proteins+and+their+genes.#1}, keywords = {nosource} }

@article{stupina3ProximalTranslational2008, title = {The 3{\(\prime\)} Proximal Translational Enhancer of {{Turnip}} Crinkle Virus Binds to {{60S}} Ribosomal Subunits}, author = {Stupina, V. A. and Meskauskas, A. and McCormack, J. C. and Yingling, Y. G. and Shapiro, B. A. and Dinman, J. D. and Simon, A. E.}, year = 2008, journal = {RNA}, volume = {14}, number = {11}, pages = {2379}, publisher = {Cold Spring Harbor Lab}, url = {http://rnajournal.cshlp.org/content/14/11/2379.short}, abstract = {During cap-dependent translation of eukaryotic mRNAs, initiation factors interact with the 5’ cap to attract ribosomes. When animal viruses translate in a cap-independent fashion, ribosomes assemble upstream of initiation codons at internal ribosome entry sites (IRES). In contrast, many plant viral genomes do not contain 5’ ends with substantial IRES activity but instead have 3’ translational enhancers that function by an unknown mechanism. A 393-nucleotide (nt) region that includes the entire 3’ UTR of the Turnip crinkle virus (TCV) synergistically enhances translation of a reporter gene when associated with the TCV 5’ UTR. The major enhancer activity was mapped to an internal region of approximately 140 nt that partially overlaps with a 100-nt structural domain previously predicted to adopt a form with some resemblance to a tRNA, according to a recent study by J.C. McCormack and colleagues. The T-shaped structure binds to 80S ribosomes and 60S ribosomal subunits, and binding is more efficient in the absence of surrounding sequences and in the presence of a pseudoknot that mimics the tRNA-acceptor stem. Untranslated TCV satellite RNA satC, which contains the TCV 3’ end and 6-nt differences in the region corresponding to the T-shaped element, does not detectably bind to 80S ribosomes and is not predicted to form a comparable structure. Binding of the TCV T-shaped element by 80S ribosomes was unaffected by salt-washing, reduced in the presence of AcPhe-tRNA, which binds to the P-site, and enhanced binding of Phe-tRNA to the ribosome A site. Mutations that reduced translation in vivo had similar effects on ribosome binding in vitro. This strong correlation suggests that ribosome entry in the 3’ UTR is a key function of the 3’ translational enhancer of TCV and that the T-shaped element contains some tRNA-like properties}, keywords = {nosource} }

@article{kirn-safranCloningExpressionChromosome2000, title = {Cloning, {{Expression}}, and {{Chromosome Mapping}} of the {{Murine Hip}}/{{Rpl29 Gene}}{\(\bullet\)} 1,{\(\bullet\)} 2}, author = {{Kirn-Safran}, C. B. and Dayal, S. and {Martin-DeLeon}, P. A. and Carson, D. D.}, year = 2000, journal = {Genomics}, volume = {68}, number = {2}, pages = {210–219}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0888754300962839}, abstract = {We previously have identified murine heparin/heparan sulfate-interacting protein (HIP) identical to mouse ribosomal protein L29 that is, like its human orthologue, distinctively expressed both on the cell surface and intracellularly in different adult tissues and cell types. In the present study, we show that mouse HIP/RPL29 is encoded by a single mRNA and that it is expressed to different extents in most of the tissues of the developing embryo without restriction to a specific cell type. We isolated the single-copy gene coding for murine Hip/Rpl29 among a large number of pseudogenes, established its structure, and assigned its location to distal chromosome 9. Similar to other ribosomal protein promoters, the promoter of Hip/Rpl29 is rich in polypyrimidine tracts, contains binding motifs for ubiquitously expressed transcription factors, and lacks a TATA box. Progressive 5’ deletion analyses identified a strong enhancer region that includes CT-rich sequences and a potential consensus binding site for NF-kappaB. These data will provide valuable tools to progress the understanding of HIP/RPL29 function as a ribosomal protein and/or as a regulator of growth and cell adhesion through interaction with heparan sulfate proteoglycans}, keywords = {nosource} } % == BibTeX quality report for kirn-safranCloningExpressionChromosome2000: % ? Title looks like it was stored in title-case in Zotero

@article{kobernaRibosomalGenesFocus2002, title = {Ribosomal Genes in Focus: New Transcripts Label the Dense Fibrillar Components and Form Clusters Indicative of `{{Christmas}} Trees'' in Situ}, author = {Koberna, K. and Mal{\textbackslash}'{\i}nsk{\y}, J. and Pliss, A. and Ma{}ata, M. and Ve{}e{}vrov{'a}, J. and Fialov{'a}, M. and Bedn{'a}r, J. and Ra{}ka, I.}, year = 2002, month = may, journal = {The Journal of cell biology}, volume = {157}, number = {5}, pages = {743}, publisher = {The Rockefeller University Press}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/pmc2173423/}, abstract = {T he organization of transcriptionally active ribosomal genes in animal cell nucleoli is investigated in this study in order to address the long-standing controversy with regard to the intranucleolar localization of these genes. Detailed analyses of HeLa cell nucleoli include direct localization of ribosomal genes by in situ hybridization and their indirect localization via nascent ribosomal transcript mappings. On the light microscopy (LM) level, ribosomal genes map in 10-40 fluorescence foci per nucleus, and transcription activity is associated with most foci. We demonstrate that each nucleolar focus observed by LM corresponds, on the EM level, to an individual fibrillar center (FC) and surrounding dense fibrillar components (DFCs). The EM data identify the DFC as the nucleolar subcompartment in which rRNA synthesis takes place, consistent with detection of rDNA within the DFC. The highly sensitive method for mapping nascent transcripts in permeabilized cells on ultrastructural level provides intense and unambiguous clustered immunogold signal over the DFC, whereas very little to no label is detected over the FC. This signal is strongly indicative of nascent “Christmas trees” of rRNA associated with individual rDNA genes, sampled on the surface of thin sections. Stereological analysis of the clustered transcription signal further suggests that these Christmas trees may be contorted in space and exhibit a DNA compaction ratio on the order of 4-5.5}, keywords = {nosource} }

@article{stansfieldMissenseTranslationErrors1998, title = {Missense Translation Errors in {{Saccharomyces}} Cerevisiae1}, author = {Stansfield, I. and Jones, K. M. and Herbert, P. and Lewendon, A. and Shaw, W. V. and Tuite, M. F.}, year = 1998, journal = {Journal of molecular biology}, volume = {282}, number = {1}, pages = {13–24}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283698919763}, abstract = {We describe the development of a novel plasmid-based assay for measuring the in vivo frequency of misincorporation of amino acids into polypeptide chains in the yeast Saccharomyces cerevisiae. The assay is based upon the measurement of the catalytic activity of an active site mutant of type III chloramphenicol acetyl transferase (CAT(III)) expressed in S. cerevisiae. A His195(CAC) –{\(>\)} Tyr195(UAC) mutant of CAT(III) is completely inactive, but catalytic activity can be restored by misincorporation of histidine at the mutant UAC codon. The average error frequency of misincorporation of histidine at this tyrosine UAC codon in wild-type yeast strains was measured as 0.5 x 10(-5) and this frequency was increased some 50-fold by growth in the presence of paromomycin, a known translational-error-inducing antibiotic. A detectable frequency of misincorporation of histidine at a mutant Ala195 GCU codon was also measured as 2 x 10(-5), but in contrast to the Tyr195 –{\(>\)} His195 misincorporation event, the frequency of histidine misincorporation at Ala195 GCU was not increased by paromomycin, inferring that this error did not result from miscognate codon-anticodon interaction. The His195 to Tyr195 missense error assay was used to demonstrate increased frequencies of missense error at codon 195 in SUP44 and SUP46 mutants. These two mutants have previously been shown to exhibit a translation termination error phenotype and the sup44(+) and sup46(+) genes encode the yeast ribosomal proteins S4 and S9, respectively. These data represent the first accurate in vivo measurement of a specific mistranslation event in a eukaryotic cell and directly confirm that the eukaryotic ribosome plays an important role in controlling missense errors arising from non-cognate codon-anticodon interactions. (C) 1998 Academic Press}, keywords = {nosource} }

@article{qinSiteSpecificLabelingRNA1999a, title = {Site-{{Specific Labeling}} of {{RNA}} with {{Fluorophores}} and {{Other Structural Probes}}{\(\bullet\)} 1}, author = {Qin, P. Z. and Pyle, A. M.}, year = 1999, month = may, journal = {Methods}, volume = {18}, number = {1}, pages = {60–70}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1046202399907570}, abstract = {Site-specific probes provide a powerful tool for structure and function studies of nucleic acids, especially in elucidating tertiary structures of large ribozymes and other folded RNA molecules. Among many types of extrinsic labels, fluorophores are most attractive because they can provide structural information at millisecond time resolution, thus allowing real-time observation of structural transition during biological function. Methods for introducing fluorophores in RNA molecules are summarized here. These methods are robust and readily applicable to the labeling of other types of probes. However, as each case of RNA modification is unique, fine tuning of the general methodology is beneficial}, keywords = {nosource} } % == BibTeX quality report for qinSiteSpecificLabelingRNA1999a: % ? Title looks like it was stored in title-case in Zotero

@article{xuHighfrequencyDeletionHomologous1987, title = {High-Frequency Deletion between Homologous Sequences during Retrotransposition of {{Ty}} Elements in {{Saccharomyces}} Cerevisiae}, author = {Xu, H. and Boeke, J. D.}, year = 1987, journal = {Proceedings of the National Academy of Sciences}, volume = {84}, number = {23}, pages = {8553}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/84/23/8553.short}, keywords = {nosource} }

@article{lhoestColdSensitiveRibosomeAssembly1981a, title = {Cold-{{Sensitive Ribosome Assembly}} in an {{Esclzerichia}} Coli {{Mutant Lacking}} a {{Single Methyl Group}} in {{Ribosomal Protein L3}}}, author = {LHOEST, J. and COLSON, C.}, year = 1981, month = dec, journal = {European Journal of Biochemistry}, volume = {121}, number = {1}, pages = {33–37}, publisher = {Wiley Online Library}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1981.tb06425.x/abstract}, abstract = {Ribosomal protein methylation has been well documented but its function remains unclear. We have examined this phenomenon using an Escherichia coli mutant (prmB2), which fails to methylate glutamine residue number 150 of ribosomal protein L3. This mutant exhibits a cold-sensitive phenotype: its growth rate at 22 degrees C is abnormally low in complete medium. In addition, strains with this mutation accumulate abnormal and unstable ribosomal particles; 50-S and 30-S subunits are formed, but at a lower rate. Once assembled, ribosomes with unmethylated L3 are fully active by several criteria. (a) Protein synthesis in vitro with purified 70-S prmB2 ribosomes is as active as wild-type using either a natural (R17) or an artificial [poly(U)] messenger. (b) The induction of beta-galactosidase in vivo exhibits normal kinetics and the enzyme has a normal rate of thermal denaturation. (c) These ribosomes are standard when exposed in vitro to a low magnesium concentration or increasing molarities of LiCl. Efficient methylation of L3 in vitro requires either unfolded ribosomes or a mixture of ribosomal protein and RNA. We suggest that the L3-specific methyltransferase may qualify as one of the postulated ‘assembly factors’ of the E. coli ribosome}, keywords = {nosource} }

@article{wengCharacterizationNonsensemediatedMRNA1997, title = {Characterization of the Nonsense-Mediated {{mRNA}} Decay Pathway and Its Effect on Modulating Translation Termination and Programmed Frameshifting}, author = {Weng, Y. and {Ruiz-Echevarria}, M. J. and Zhang, S. and Cui, Y. and Czaplinksi, K. and Dinman, J. D. and Peltz, S. W.}, year = 1997, journal = {Modern Cell Biology}, volume = {17}, pages = {241–280}, publisher = {JOHN WILEY & SONS LTD}, url = {http://books.google.com/books?hl=en&lr=&id=uMvcQK_QZXUC&oi=fnd&pg=PA241&dq=Characterization+of+the+nonsense-mediated+mRNA+decay+pathway+and+its+effect+on+modulating+translation+termination+and+programmed+frameshifting.&ots=MrJ4BBpeAu&sig=Fs3qbINkg6X3L7mST-NA3rYqqsw}, keywords = {nosource} }

@article{vila-sanjurjoMutationalAnalysisConserved2001, title = {Mutational Analysis of the Conserved Bases {{C1402}} and {{A1500}} in the Center of the Decoding Domain of {{Escherichia}} Coli 16 {{S rRNA}} Reveals an Important Tertiary Interaction1}, author = {{Vila-Sanjurjo}, A. and Dahlberg, A. E.}, year = 2001, month = may, journal = {Journal of Molecular Biology}, volume = {308}, number = {3}, pages = {457–463}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283601945760}, abstract = {Interactions within the decoding center of the 30 S ribosomal subunit have been investigated by constructing all 15 possible mutations at nucleotides C1402 and A1500 in helix 44 of 16 S rRNA. As expected, most of the mutations resulted in highly deleterious phenotypes, consistent with the high degree of conservation of this region and its functional importance. A total of seven mutants were viable under conditions where the mutant ribosomes comprised 100 % of the ribosomal pool. A suppressor mutation specific for the C1402U-A1500G mutant was isolated at position 1520 in helix 45 of 16 S rRNA. In addition, lack of dimethylation of A1518/A1519 caused by mutation of the ksgA methylase enhanced the deleterious effect of many of the 1402/1500 mutations. These data suggest that a higher-order interaction between helices 44 and 45 in 16 S rRNA is important for the proper functioning of the ribosome. This is consistent with the recent high-resolution crystal structures of the 30 S subunit, which show a tertiary interaction between the 1402/1500 region of helix 44 and the dimethyl A stem loop. (C) 2001 Academic Press}, keywords = {nosource} }

@article{jonesEffectSpecificMutations1989, title = {The Effect of Specific Mutations at and around the Gag-Pol Gene Junction of {{Moloney}} Murine Leukaemia Virus}, author = {Jones, D. S. and Nemoto, F. and Kuchino, Y. and Masuda, M. and Yoshikura, H. and Nishimura, S.}, year = 1989, journal = {Nucleic acids research}, volume = {17}, number = {15}, pages = {5933}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/17/15/5933.short}, keywords = {nosource} }

@article{raymondRemovalMRNADestabilizing1989, title = {Removal of an {{mRNA}} Destabilizing Element Correlates with the Increased Oncogenicity of Proto-Oncogene Fos.}, author = {Raymond, V. and Atwater, J. A. and Verma, I. M.}, year = 1989, journal = {Oncogene research}, volume = {5}, number = {1}, eprint = {2506502}, eprinttype = {pubmed}, pages = {1}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2506502}, keywords = {nosource} }

@article{krokowskiElevatedCopyNumber2007, title = {Elevated Copy Number of {{LA}} Virus in Yeast Mutant Strains Defective in Ribosomal Stalk}, author = {Krokowski, D. and Tchorzewski, M. and Boguszewska, A. and Mckay, A. R. and Maslen, S. L. and Robinson, C. V. and Grankowski, N.}, year = 2007, month = apr, journal = {Biochemical and biophysical research communications}, volume = {355}, number = {2}, pages = {575–580}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006291X07002872}, abstract = {The eukaryotic ribosomal stalk, composed of the P-proteins, is a part of the GTPase-associated-center which is directly responsible for stimulation of translation-factor-dependent GTP hydrolysis. Here we report that yeast mutant strains lacking P1/P2-proteins show high propagation of the yeast L-A virus. Affinity-capture-MS analysis of a protein complex isolated from a yeast mutant strain lacking the P1A/P2B proteins using anti-P0 antibodies showed that the Gag protein, the major coat protein of the L-A capsid, is associated with the ribosomal stalk. Proteomic analysis revealed that the elongation factor eEF1A was also present in the isolated complex. Additionally, yeast strains lacking the P1/P2-proteins are hypersensitive to paromomycin and hygromycin B, underscoring the fact that structural perturbations in the stalk strongly influence the ribosome function, especially at the level of elongation}, keywords = {nosource} }

@article{pintoCisandTransactingSuppressors1992, title = {Cis-and Trans-Acting Suppressors of a Translation Initiation Defect at the Cyc1 Locus of {{Saccharomyces}} Cerevisiae}, author = {Pinto, I. and Na, J. G. and Sherman, F. and Hampsey, M.}, year = 1992, journal = {Genetics}, volume = {132}, number = {1}, pages = {97}, publisher = {Genetics Soc America}, url = {http://www.genetics.org/content/132/1/97.short}, keywords = {nosource} }

@article{vogelPossibleInvolvementPeptidyl1969, title = {Possible Involvement of Peptidyl Transferase in the Termination Step of Protein Biosynthesis}, author = {Vogel, Z. and Zamir, A. and Elson, D.}, year = 1969, journal = {Biochemistry}, volume = {8}, number = {12}, pages = {5161–5168}, publisher = {ACS Publications}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00840a070}, keywords = {nosource} }

@article{farabaughProgrammedAlternativeReading1997, title = {Programmed Alternative Reading of the Genetic Code}, author = {Farabaugh, P. J.}, year = 1997, journal = {RG Landes, Austin, TX}, publisher = {R.G. Landes Company}, url = {http://www.getcited.org/pub/100131305}, isbn = {0-412-13751-8}, keywords = {nosource} }

@article{mooreCompleteNucleotideSequence1987, title = {Complete Nucleotide Sequence of a Milk-Transmitted Mouse Mammary Tumor Virus: Two Frameshift Suppression Events Are Required for Translation of Gag and Pol.}, author = {Moore, R. and Dixon, M. and Smith, R. and Peters, G.}, year = 1987, month = feb, journal = {Journal of}, volume = {61}, number = {2}, pages = {480–490}, url = {http://jvi.asm.org/cgi/content/abstract/61/2/480}, keywords = {nosource} }

@article{nakamuraMakingSenseMimic2003, title = {Making Sense of Mimic in Translation Termination* 1}, author = {Nakamura, Y.}, year = 2003, month = feb, journal = {Trends in Biochemical Sciences}, volume = {28}, number = {2}, pages = {99–105}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000403000069}, abstract = {The mechanism of translation termination has long been a puzzle. Recent crystallographic evidence suggests that the eukaryotic release factor (eRF1), the bacterial release factor (RF2) and the ribosome recycling factor (RRF) all mimic a tRNA structure, whereas biochemical and genetic evidence supports the idea of a tripeptide ‘anticodon’ in bacterial release factors RF1 and RF2. However, the suggested structural mimicry of RF2 is not in agreement with the tripeptide ‘anticodon’ hypothesis and, furthermore, recently determined structures using cryo-electron microscopy show that, when bound to the ribosome, RF2 has a conformation that is distinct from the RF2 crystal structure. In addition, hydroxyl-radical probings of RRF on the ribosome are not in agreement with the simple idea that RRF mimics tRNA in the ribosome A-site. All of this evidence seriously questions the simple concept of structural mimicry between proteins and RNA and, thus, leaves only functional mimicry of protein factors of translation to be investigated}, keywords = {nosource} }

@article{merrymanNucleotides23SRRNA1999, title = {Nucleotides in {{23S rRNA}} Protected by the Association of {{30S}} and {{50S}} Ribosomal Subunits1}, author = {Merryman, C. and Moazed, D. and Daubresse, G. and Noller, H. F.}, year = 1999, month = jan, journal = {Journal of molecular biology}, volume = {285}, number = {1}, pages = {107–113}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283698922434}, abstract = {We have studied the effect of subunit association on the accessibility of nucleotides in 23 S and 5 S rRNA. Escherichia coli 50 S subunits and 70 S ribosomes were subjected to a combination of chemical probes and the sites of attack identified by primer extension. Since the ribose groups and all of the bases were probed, the present study provides a comprehensive map of the nucleotides that are likely to be involved in subunit-subunit interactions. Upon subunit association, the bases of 22 nucleotides and the ribose groups of more than 60 nucleotides are protected in 23 S rRNA; no changes are seen in 5S rRNA. interestingly, the bases of nucleotides A1866, A1891 and A1896, and G2505 become more reactive to chemical probes, indicating localized rearrangement of the structure of the 50 S subunit upon association with the 30 S subunit. Most of the protected nucleotides are located in four stem-loop structures around positions 715, 890, 1700, and 1920. In free 50 S subunits, virtually all of the ribose groups in these four regions are strongly cleaved by hydroxyl radicals, suggesting that these stems protrude from the 50 S subunit. When the 30 S subunit is bound, most of the ribose groups in the 715, 890, 1700 and 1920 stemloops are protected, as are many bases in and around the corresponding apical loops. Intriguingly, three of the protected regions of 23 S rRNA are known to be linked via tertiary interactions to features of the peptidyl transferase center. Together with the juxtaposition of the subunit-protected regions of 16 S rRNA with the small subunit tRNA binding sites, our findings suggest the existence of a communication pathway between the codon-anticodon binding sites of the 30 S subunit with the peptidyl transferase center of the 50 S subunit via rRNA-rRNA interactions. (C) 1999 Academic Press}, keywords = {nosource} }

@article{weiss-brummerParomomycinResistanceMutation1989, title = {The Paromomycin Resistance Mutation (Par r-454) in the 15 {{S rRNA}} Gene of the {{yeastSaccharomyces}} Cerevisiae Is Involved in Ribosomal Frameshifting}, author = {{Weiss-Brummer}, B. and H{}{"u}ttenhofer, A.}, year = 1989, month = jun, journal = {Molecular and General Genetics MGG}, volume = {217}, number = {2}, pages = {362–369}, publisher = {Springer}, url = {http://www.springerlink.com/index/N5281UQ1R3693645.pdf}, keywords = {nosource} }

@article{schmittCloningExpressionCDNA1995, title = {Cloning and Expression of a {{cDNA}} Copy of the Viral {{K}} 28 Killer Toxin Gene in Yeast}, author = {Schmitt, M. J.}, year = 1995, month = jan, journal = {Molecular and General Genetics MGG}, volume = {246}, number = {2}, pages = {236–246}, publisher = {Springer}, url = {http://www.springerlink.com/index/R01827417Q004N4X.pdf}, abstract = {The killer toxin K28, secreted by certain killer strains of the yeast Saccharomyces cerevisiae is genetically encoded by a 1.9 kb double- stranded RNA, M-dsRNA (M28), that is present within the cell as a cytoplasmically inherited virus-like particle (VLP). For stable maintenance and replication, M28-VLPs depend on a second dsRNA virus (LA), which has been shown to encode the major capsid protein (cap) and a capsid-polymerase fusion protein (cap-pol) that provides the toxin- coding M-satellites with their transcription and replicase functions. K28 toxin-coding M28-VLPs were isolated, purified and used in vitro for the synthesis of the single-stranded M28 transcript, which was shown to be of plus strand polarity and to bind to oligo(dT)-cellulose, indicating that M28(+)ssRNA contains an internal A-rich tract. Strand separation of the 1.9 kb M28-dsRNA and direct RNA sequencing of its 3’ ends was performed in order to obtain specific DNA oligonucleotides that could be used as primers for cDNA synthesis. The nucleotide sequence of the toxin-coding M28-cDNA identified a single open reading frame (ORF) coding for a polypeptide of 345 amino acids, which contained two potential Kex2p/Kex1p processing sites and three potential sites for protein N-glycosylation. The toxin-coding cDNA was cloned and expressed in sensitive non-killer strains under the control of the yeast PGK promoter. Upon transformation, this construct conferred the complete K28 phenotype, demonstrating that both toxin and immunity determinants are contained within the cloned cDNA. In vitro translational analysis of the M28(+)ssRNA in vitro transcript identified the primary gene product of M28 as a K28 preprotoxin of 38 kDa (M-p38)}, keywords = {nosource} }

@article{schultzNucleotideSequenceTcml1983, title = {Nucleotide Sequence of the Tcml Gene (Ribosomal Protein {{L3}}) of {{Saccharomyces}} Cerevisiae.}, author = {Schultz, L. D. and Friesen, J. D.}, year = 1983, journal = {Journal of Bacteriology}, volume = {155}, number = {1}, pages = {8}, publisher = {Am Soc Microbiol}, url = {http://jb.asm.org/cgi/content/abstract/155/1/8}, abstract = {The yeast tcml gene, which codes for ribosomal protein L3, has been isolated by using recombinant DNA and genetic complementation. The DNA fragment carrying this gene has been subcloned and we have determined its DNA sequence. The 20 amino acid residues at the amino terminus as inferred from the nucleotide sequence agreed exactly with the amino acid sequence data. The amino acid composition of the encoded protein agreed with that determined for purified ribosomal protein L3. Codon usage in the tcml gene was strongly biased in the direction found for several other abundant Saccharomyces cerevisiae proteins. The tcml gene has no introns, which appears to be atypical of ribosomal protein structural genes.}, keywords = {nosource} }

@article{fujimuraInteractionTwoCis1992, title = {Interaction of Two Cis Sites with the {{RNA}} Replicase of the Yeast {{LA}} Virus.}, author = {Fujimura, T. and Wickner, R. B.}, year = 1992, journal = {Journal of Biological Chemistry}, volume = {267}, number = {4}, pages = {2708}, publisher = {ASBMB}, url = {http://www.jbc.org/content/267/4/2708.short}, keywords = {nosource} }

@article{kunkelRapidEfficientSitespecific1985, title = {Rapid and Efficient Site-Specific Mutagenesis without Phenotypic Selection}, author = {Kunkel, T. A.}, year = 1985, journal = {Proceedings of the National Academy of Sciences}, volume = {82}, number = {2}, pages = {488}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/82/2/488.short}, keywords = {nosource} }

@article{moriartyAbundanceMRNASedependent1998, title = {Abundance of {{mRNA}} for {{Se-dependent}} Glutathione Peroxidase 1 by a {{UGA-dependent}} Mechanism Likely to Be Nonsense Codon-Mediated Decay of Cytoplasmic {{mRNA}}}, author = {Moriarty, P. M. and Reddy, C. C.}, year = 1998, month = may, journal = {Molecular and cellular}, volume = {18}, number = {5}, pages = {2932–2939}, url = {http://mcb.asm.org/cgi/content/abstract/18/5/2932}, abstract = {The mammalian mRNA for selenium-dependent glutathione peroxidase 1 (Se- GPx1) contains a UGA codon that is recognized as a codon for the nonstandard amino acid selenocysteine (Sec). Inadequate concentrations of selenium (Se) result in a decrease in Se-GPx1 mRNA abundance by an uncharacterized mechanism that may be dependent on translation, independent of translation, or both. In this study, we have begun to elucidate this mechanism. We demonstrate using hepatocytes from rats fed either a Se-supplemented or Se-deficient diet for 9 to 13 weeks that Se deprivation results in an approximately 50-fold reduction in Se- GPx1 activity and an approximately 20-fold reduction in Se-GPx1 mRNA abundance. Reverse transcription-PCR analyses of nuclear and cytoplasmic fractions revealed that Se deprivation has no effect on the levels of either nuclear pre-mRNA or nuclear mRNA but reduces the level of cytoplasmic mRNA. The regulation of Se-GPx1 gene expression by Se was recapitulated in transient transfections of NIH 3T3 cells, and experiments were extended to examine the consequences of converting the Sec codon (TGA) to either a termination codon (TAA) or a cysteine codon (TGC). Regardless of the type of codon, an alteration in the Se concentration was of no consequence to the ratio of nuclear Se-GPx1 mRNA to nuclear Se-GPx1 pre-mRNA. The ratio of cytoplasmic Se-GPx1 mRNA to nuclear Se-GPx1 mRNA from the wild-type (TGA-containing) allele was reduced twofold when cells were deprived of Se for 48 h after transfection, which has been shown to be the extent of the reduction for the endogenous Se-GPx1 mRNA of cultured cells incubated as long as 20 days in Se-deficient medium. In contrast to the TGA allele, Se had no effect on expression of either the TAA allele or the TGC allele. Under Se-deficient conditions, the TAA and TGC alleles generated, respectively, 1.7-fold-less and 3-fold-more cytoplasmic Se-GPx1 mRNA relative to the amount of nuclear Se-GPx1 mRNA than the TGA allele. These results indicate that (i) under conditions of Se deprivation, the Sec codon reduces the abundance of cytoplasmic Se-GPx1 mRNA by a translation-dependent mechanism and (ii) there is no additional mechanism by which Se regulates Se-GPx1 mRNA production. These data suggest that the inefficient incorporation of Sec at the UGA codon during mRNA translation augments the nonsense-codon-mediated decay of cytoplasmic Se-GPx1 mRNA}, keywords = {nosource} }

@article{yoonSuilSuppressorLocus1992, title = {The Suil Suppressor Locus in {{Saccharomyces}} Cerevisiae Encodes a Translation Factor That Functions during {{tRNA}} ({{iMet}}) Recognition of the Start Codon.}, author = {Yoon, H. J. and Donahue, T. F.}, year = 1992, journal = {Molecular and cellular biology}, volume = {12}, number = {1}, pages = {248}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/12/1/248}, keywords = {nosource} }

@article{farabaughPosttranscriptionalRegulationTransposition1995, title = {Post-Transcriptional Regulation of Transposition by {{Ty}} Retrotransposons of {{Saccharomyces}} Cerevisiae}, author = {Farabaugh, P. J.}, year = 1995, journal = {Journal of Biological Chemistry}, volume = {270}, number = {18}, pages = {10361}, publisher = {ASBMB}, url = {http://www.jbc.org/content/270/18/10361.short}, keywords = {nosource} }

@article{wicknerDoublestrandedRNAReplication1986, title = {Double-Stranded {{RNA}} Replication in Yeast: The Killer System}, author = {Wickner, R. B.}, year = 1986, journal = {Annual review of biochemistry}, volume = {55}, number = {1}, pages = {373–395}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.bi.55.070186.002105}, keywords = {nosource} }

@article{unaidsReportGlobalAIDS1990, title = {Report on the Global {{AIDS}} Epidemic}, author = {UNAIDS, {WHO}}, year = 1990, journal = {Adult (15–9) HIV Prevalence percent by country}, volume = {10}, publisher = {UNAIDS}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Report+on+the+global+AIDS+epidemic#1}, isbn = {92 9 173511 6}, keywords = {nosource} }

@article{sharpREGULATIONADENOVIRUSMRNA1980a, title = {{{REGULATION OF ADENOVIRUS mRNA SYNTHESIS}}{\(\bullet\)}}, author = {Sharp, P. A. and Manley, J. and Fire, A. and Gefter, M.}, year = 1980, journal = {Annals of the New York Academy of Sciences}, volume = {354}, number = {1}, pages = {1–15}, publisher = {Wiley Online Library}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1980.tb27954.x/abstract}, abstract = {The lytic cycle of adenovirus is a tightly regulated sequence of stages. When this regulation is studied at the level of mRNA production, the most significant step in controlling gene expression is initiation of transcription. Thus in preceding from one stage of expression to another, viral factors seem to turn on transcription of new sets of genes. At the moment, it is thought that viral mRNA synthesis involves initiation of transcription at ten different promoter sites. It is likely that in some manner the frequency of an initiation of transcription at nine of these sites is affected by one or more viral gene products. With the recent development of soluble in vitro transcription systems that respond to exogenously added DNA, it should be possible to begin to study regulation of gene expression at this stage of transcription. At present, these systems yield the paradoxical observation that extracts prepared from uninfected human cells more efficiently recognize the late promoter as compared to the early promoter of adenovirus. As more is learned about regulation of synthesis of viral mRNAs, examples will surely be found where RNA processing and RNA turnover play a critical role in determining the level of mRNAs. Such cases are more likely to appear in the balancing of synthesis of different mRNAs derived from one transcriptional unit. Few experiments have been directed to this possibility and the study of adenovirus molecular biology is only now entering the age of maturity where these experiments are feasible}, keywords = {nosource} } % == BibTeX quality report for sharpREGULATIONADENOVIRUSMRNA1980a: % ? Title looks like it was stored in title-case in Zotero

@article{valleEliminationDoublestrandedRNA1993, title = {Elimination of {{LA}} Double-Stranded {{RNA}} Virus of {{Saccharomyces}} Cerevisiae by Expression of Gag and Gag-Pol from an {{LA cDNA}} Clone.}, author = {Valle, R. P. C. and Wickner, R. B.}, year = 1993, journal = {Journal of virology}, volume = {67}, number = {5}, pages = {2764}, publisher = {Am Soc Microbiol}, url = {http://jvi.asm.org/cgi/content/abstract/67/5/2764}, keywords = {nosource} }

@article{schneiderTranslationInitiationViral2003, title = {Translation Initiation and Viral Tricks{\(\bullet\)} 1}, author = {Schneider, R. J. and Mohr, I.}, year = 2003, month = mar, journal = {Trends in Biochemical Sciences}, volume = {28}, number = {3}, pages = {130–136}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S096800040300029X}, abstract = {A variety of viral strategies are utilized for dominance of the host-cell protein synthetic machinery, optimization of viral mRNA translation and evasion of host-cell antiviral responses that act at the translational level. Many viruses exploit regulated steps in the initiation of cellular protein synthesis to their own advantage. They have developed some rather unconventional means for mRNA translation, which were probably adapted from specialized cellular mRNA translation systems. Regardless of the type of translational tricks exploited, viruses typically ensure efficient viral translation, often at the expense of host-cell protein synthesis}, keywords = {nosource} }

@article{hirExonExonJunction2001, title = {The Exon–Exon Junction Complex Provides a Binding Platform for Factors Involved in {{mRNA}} Export and Nonsense-Mediated {{mRNA}} Decay}, author = {Hir, H. Le and Gatfield, D. and Izaurralde, E. and Moore, M. J.}, year = 2001, journal = {The EMBO Journal}, volume = {20}, number = {17}, pages = {4987–4997}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/emboj/journal/v20/n17/abs/7593994a.html}, abstract = {We recently reported that spliceosomes alter messenger ribonucleoprotein particle (mRNP) composition by depositing several proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. When assembled in vitro, this so-called ‘exon-exon junction complex’ (EJC) contains at least five proteins: SRm160, DEK, RNPS1, Y14 and REF. To better investigate its functional attributes, we now describe a method for generating spliced mRNAs both in vitro and in vivo that either do or do not carry the EJC. Analysis of these mRNAs in Xenopus laevis oocytes revealed that this complex is the species responsible for enhancing nucleocytoplasmic export of spliced mRNAs. It does so by providing a strong binding site for the mRNA export factors REF and TAP/p15. Moreover, by serving as an anchoring point for the factors Upf2 and Upf3, the EJC provides a direct link between splicing and nonsense-mediated mRNA decay. Finally, we show that the composition of the EJC is dynamic in vivo and is subject to significant evolution upon mRNA export to the cytoplasm}, keywords = {nosource} }

@article{rykEffectSequenceMutations1992, title = {Effect of Sequence Mutations on the Higher Order Structure of the Yeast 5 {{S rRNA}}}, author = {Ryk, D. I. Van and Nazar, R. N.}, year = 1992, journal = {Journal of molecular biology}, volume = {226}, number = {4}, pages = {1027–1035}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/002228369291050Y}, keywords = {nosource} }

@book{peltzMRNATurnoverSaccharomyces1993, title = {{{mRNA}} Turnover in {{Saccharomyces}} Cerevisiae}, author = {Peltz, S. W.}, year = 1993, journal = {Control of Messenger RNA Stability. Academic Press}, publisher = {Academic Press}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:mRNA+turnover+in+?Saccharomyces+cerevisiae?.#7}, keywords = {nosource} } % == BibTeX quality report for peltzMRNATurnoverSaccharomyces1993: % ? Possibly abbreviated journal title Control of Messenger RNA Stability. Academic Press % ? unused Number of pages (“291-328”)

@article{moxhamJunNterminalKinase1996, title = {Jun {{N-terminal}} Kinase Mediates Activation of Skeletal Muscle Glycogen Synthase by Insulin in Vivo}, author = {Moxham, C. M. and Tabrizchi, A. and Davis, R. J. and Malbon, C. C.}, year = 1996, journal = {Journal of Biological Chemistry}, volume = {271}, number = {48}, pages = {30765}, publisher = {ASBMB}, url = {http://www.jbc.org/content/271/48/30765.short}, keywords = {nosource} }

@article{lempereurConformationYeast18S1985, title = {Conformation of Yeast {{18S rRNA}}. {{Direct}} Chemical Probing of the 5{\(\prime\)} Domain in Ribosomal Subunits and in Deproteinized {{RNA}} by Reverse Transcriptase Mapping of Dimethyl Sulfate-Accessible Sites}, author = {Lempereur, L. and Nicoloso, M. and Riehl, N. and Ehresmann, C. and Ehresmann, B. and Bachellerie, J. P.}, year = 1985, month = dec, journal = {Nucleic acids research}, volume = {13}, number = {23}, pages = {8339}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/13/23/8339.short}, abstract = {The structure of the 5’ domain of yeast 18S rRNA has been probed by dimethyl sulfate (DMS), either in “native” deproteinized molecules or in the 40S ribosomal subunits. DMS-reacted RNA has been used as a template for reverse transcription and a large number of reactive sites, corresponding to all types of bases have been mapped by a primer extension procedure, taking advantage of blocks in cDNA elongation immediately upstream from bases methylated at atom positions involved in the base-pair recognition of the template. Since the same atom positions are protected from DMS in base-paired nucleotides, the secondary structure status of each nucleotide can be directly assessed in this procedure, thus allowing to evaluate the potential contribution of proteins in modulating subunit rRNA conformation. While the DMS probing of deproteinized rRNA confirms a number of helical stems predicted by phylogenetic comparisons, it is remarkable that a few additional base-pairings, while proven by the comparative analysis, appear to require the presence of the bound ribosomal subunit proteins to be stabilized}, keywords = {nosource} }

@article{riddleFrameshiftSuppressionNucleotide1973, title = {Frameshift Suppression: A Nucleotide Addition in the Anticodon of a Glycine Transfer {{RNA}}}, author = {RIDDLE, D. L. and CARBON, J.}, year = 1973, month = jun, journal = {Nature}, volume = {242}, number = {121}, pages = {230–234}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/nature-newbio/journal/v242/n121/abs/newbio242230a0.html}, keywords = {nosource} }

@article{lyamichevUnusualDMAStructure1989, title = {An Unusual {{DMA}} Structure Detected in a Telomeric Sequence under Superhelical Stress and at Low {{pH}}}, author = {Lyamichev, V. I. and Mirkin, S. M. and Danilevskaya, O. N. and Voloshin, O. N. and Balatskaya, S. V. and Dobrynin, V. N. and Filippov, S. A. and {Frank-Kamenetskii}, M. D.}, year = 1989, month = jun, journal = {Nature}, volume = {339}, number = {6226}, pages = {634–637}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/nature/journal/v339/n6226/abs/339634a0.html}, abstract = {Telomeric sequences of DNA, which are found at the ends of linear chromosomes, have been attracting attention as potential sites for the formation of unusual DNA structures. They consist of (GnTm) or (GnATm) motifs (n greater than or equal to m) and, in the single-stranded state, form hairpins stabilized by non-canonical G.G pairs. In the duplex state and under superhelical stress they exhibit hypersensitivity to SI nuclease which by analogy with homopurine- homopyrimidine sequences may reflect the formation of an unusual structure. To determine whether this is the case we have inserted into a plasmid the Tetrahymena telomeric motif (G4T2).(A2C4) and probed it by two-dimensional gel electrophoresis, chemical modification and oligonucleotide binding. Our data demonstrate that, under superhelical stress and at low pH, the insert does indeed adopt a novel DNA conformation. We have concluded that in this structure the C-rich strand forms a hairpin stabilized by non-Watson-Crick base pairs C.C+ and A.A+, whereas the G-rich strand remains unstructured. We term this new DNA structure the (C,A)-hairpin}, keywords = {nosource} }

@article{loftfieldFrequencyErrorsProtein1972, title = {The Frequency of Errors in Protein Biosynthesis.}, author = {Loftfield, R. B. and Vanderjagt, D.}, year = 1972, journal = {Biochemical Journal}, volume = {128}, number = {5}, pages = {1353}, publisher = {Portland Press Ltd}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1174024/}, keywords = {nosource} }

@article{parkPhosphorylationRibosomalProtein1999, title = {Phosphorylation of {{Ribosomal Protein L5}} by {{Protein Kinase CKII Decreases Its 5S rRNA Binding Activity}}{\(\bullet\)} 1}, author = {Park, J. W. and Bae, Y. S.}, year = 1999, journal = {Biochemical and biophysical research communications}, volume = {263}, number = {2}, pages = {475–481}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006291X99913451}, abstract = {We have recently reported that ribosomal protein L5 associates with the beta subunit of protein kinase CKII (CKII) (Kim, J.-M., Cha, J. -Y., Marshak, D. R., and Bae, Y.-S. (1996) Biochem. Biophys. Res. Commun. 226, 180-186). In this study, we demonstrate that CKII is able to catalyze the phosphorylation of the human L5 protein in vitro, which results in a decrease in 5S rRNA binding activity. Phosphoamino acid analysis indicated that the phosphorylation occurs on serine residues. Sequence analysis of cyanogen bromide-digested phosphopeptides and analysis of L5 deletion mutants indicates that the main phosphorylated residues are located within two fragments corresponding of residues 142- 200 and residues 272-297 of the human L5. Based on our present results, we suggest that the phosphorylation of L5 by CKII is one of the mechanisms that regulates nucleolar targeting of 5S rRNA and/or ribosome assembly in the cell. Copyright 1999 Academic Press}, keywords = {nosource} } % == BibTeX quality report for parkPhosphorylationRibosomalProtein1999: % ? Title looks like it was stored in title-case in Zotero

@article{sergievMutationsPositionA9602000, title = {Mutations at Position {{A960}} of {{E}}. Coli 23 {{S}} Ribosomal {{RNA}} Influence the Structure of 5 {{S}} Ribosomal {{RNA}} and the Peptidyltransferase Region of 23 {{S}} Ribosomal {{RNA1}}}, author = {Sergiev, P. V. and Bogdanov, A. A. and Dahlberg, A. E. and Dontsova, O.}, year = 2000, month = jun, journal = {Journal of molecular biology}, volume = {299}, number = {2}, pages = {379–389}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(00)93739-2}, abstract = {The proximity of loop D of 5 S rRNA to two regions of 23 S rRNA, domain II involved in translocation and domain V involved in peptide bond formation, is known from previous cross-linking experiments. Here, we have used site-directed mutagenesis and chemical probing to further define these contacts and possible sites of communication between 5 S and 23 S rRNA. Three different mutants were constructed at position A960, a highly conserved nucleotide in domain II previously crosslinked to 5 S rRNA, and the mutant rRNAs were expressed from plasmids as homogeneous populations of ribosomes in Escherichia coli deficient in all seven chromosomal copies of the rRNA operon. Mutations A960U, A960G and, particularly, A960C caused structural rearrangements in the loop D of 5 S rRNA and in the peptidyltransferase region of domain V, as well as in the 960 loop itself. These observations support the proposal that loop D of 5 S rRNA participates in signal transmission between the ribosome centers responsible for peptide bond formation and translocation}, keywords = {nosource} }

@article{parentVectorSystemsExpression1985, title = {Vector Systems for the Expression, Analysis and Cloning of {{DNA}} Sequence in {{S}}. Cerevisiae}, author = {Parent, S. A. and Fenimore, C. M. and Bostian, K. A.}, year = 1985, month = dec, journal = {Yeast}, volume = {1}, number = {2}, pages = {83–138}, publisher = {Wiley Online Library}, url = {http://onlinelibrary.wiley.com/doi/10.1002/yea.320010202/abstract}, keywords = {nosource} }

@article{tuRibosomalMovementImpeded1992, title = {Ribosomal Movement Impeded at a Pseudoknot Required for Frameshifting}, author = {Tu, C. and Tzeng, T.-H. and Bruenn, J. A.}, year = 1992, journal = {Proceedings of the National Academy of Sciences}, volume = {89}, number = {18}, pages = {8636}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/89/18/8636.short}, keywords = {nosource} }

@article{parkOverexpressionGagpolPrecursor1991, title = {Overexpression of the Gag-Pol Precursor from Human Immunodeficiency Virus Type 1 Proviral Genomes Results in Efficient Proteolytic Processing in the Absence of Virion Production.}, author = {Park, J. and Morrow, C. D.}, year = 1991, journal = {Journal of virology}, volume = {65}, number = {9}, pages = {5111}, publisher = {Am Soc Microbiol}, url = {http://jvi.asm.org/cgi/content/abstract/65/9/5111}, keywords = {nosource} }

@article{ribasRNAdependentRNAPolymerase1992, title = {{{RNA-dependent RNA}} Polymerase Consensus Sequence of the {{LA}} Double-Stranded {{RNA}} Virus: Definition of Essential Domains}, author = {Ribas, J. C. and Wickner, R. B.}, year = 1992, journal = {Proceedings of the National Academy of Sciences}, volume = {89}, number = {6}, pages = {2185}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/89/6/2185.short}, keywords = {nosource} }

@article{sommerCocuringPlasmidsAffecting1982, title = {Co-Curing of Plasmids Affecting Killer Double-Stranded {{RNAs}} of {{Saccharomyces}} Cerevisiae:[{{HOK}}],[{{NEX}}], and the Abundance of {{L}} Are Related and Further Evidence That {{M1}} Requires {{L}}.}, author = {Sommer, S. S. and Wickner, R. B.}, year = 1982, journal = {Journal of Bacteriology}, volume = {150}, number = {2}, pages = {545}, publisher = {Am Soc Microbiol}, url = {http://jb.asm.org/cgi/content/abstract/150/2/545}, keywords = {nosource} }

@article{singhPhenotypicSuppressionMisreading1979, title = {Phenotypic Suppression and Misreading in {{Saccharomyces}} Cerevisiae}, author = {Singh, A. and Ursic, D. and Davies, J.}, year = 1979, journal = {Nature}, volume = {277}, pages = {146–148}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/nature/journal/v277/n5692/abs/277146a0.html}, keywords = {nosource} }

@article{nixonEnergeticsStronglyPH2000, title = {Energetics of a Strongly {{pH}} Dependent {{RNA}} Tertiary Structure in a Frameshifting Pseudoknot1}, author = {Nixon, P. L. and Giedroc, D. P.}, year = 2000, month = feb, journal = {Journal of Molecular Biology}, volume = {296}, number = {2}, pages = {659–671}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283699934642}, abstract = {Retroviruses employ -1 translational frameshifting to regulate the relative concentrations of structural and non-structural proteins critical to the viral life cycle. The 1.6 Angstrom crystal structure of the -1 frameshifting pseudoknot from beet western yellows virus reveals, in addition to Watson-Crick base-pairing, many loop-stem RNA tertiary structural interactions and a bound Na+. Investigation of the thermodynamics of unfolding of the beet western yellows virus pseudoknot reveals strongly pH-dependent loop-stem tertiary structural interactions which stabilize the molecule, contributing a net of Delta H approximate to - 30 kcal mol(-1) and Delta G(37)degrees, of -3.3 kcal mol(-1) to a total Delta H and aG(37)degrees, of -121 and -16 kcal mol(-1), respectively, at pH 6.0, 0.5 M K+ by DSC. Characterization of mutant RNAs supports the presence of a C8(+).G12-C26 loop 1-stem 2 base-triple (pK(a) = 6.8), protonation of which contributes nearly -3.5 kcal mol(-1.) in net stability in the presence of a wild-type loop 2. Substitution of the nucleotides in loop 2 with uridine bases, which would eliminate the minor groove triplex, destroys pseudoknot formation. An examination of the dependence of the monovalent ion and type on melting profiles suggests that tertiary structure unfolding occurs in a manner quantitatively consistent with previous studies on the stabilizing effects of K+, NH4+ and Na+ on other simple duplex and pseudoknotted RNAs. (C) 2000 Academic Press}, keywords = {nosource} }

@article{gardonyiStreptomycesRubiginosusXylose2003, title = {The {{Streptomyces}} Rubiginosus Xylose Isomerase Is Misfolded When Expressed in {{Saccharomyces}} Cerevisiae}, author = {G{'a}rdonyi, M. and {Hahn-H{}{"a}gerdal}, B.}, year = 2003, journal = {Enzyme and microbial technology}, volume = {32}, number = {2}, pages = {252–259}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0141022902002855}, keywords = {nosource} }

@article{johnstonCoordinationGrowthCell1977, title = {Coordination of Growth with Cell Division in the Yeast {{Saccharomyces}} Cerevisiae{\(\bullet\)} 1}, author = {Johnston, G. C. and Pringle, J. R. and Hartwell, L. H.}, year = 1977, journal = {Experimental Cell Research}, volume = {105}, number = {1}, pages = {79–98}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0014482777901549}, keywords = {nosource} }

@article{ribasSaccharomycesCerevisiaeLBC1996, title = {Saccharomyces Cerevisiae {{L-BC}} Double-Stranded {{RNA}} Virus Replicase Recognizes the {{LA}} Positive-Strand {{RNA}} 3’end}, author = {Ribas, J. C. and Wickner, R. B.}, year = 1996, month = jan, journal = {Journal of virology}, volume = {70}, number = {1}, pages = {292}, publisher = {Am Soc Microbiol}, url = {http://jvi.asm.org/cgi/content/abstract/70/1/292}, abstract = {L-A and L-BC are two double-stranded RNA viruses present in almost all strains of Saccharomyces cervisiae. L-A, the major species, has been extensively characterized with in vitro systems established, but little is known about L-BC, Here we report in vitro template-dependent transcription, replication, and RNA recognition activities of L-BC. The L-BC replicase activity converts positive, single stranded RNA to double-stranded RNA by synthesis of the complementary RNA strand, Although L-A and L-BC do not interact in vivo, in vitro L-BC virions can replicate the positive, single-stranded RNA of L-A and its satellite, M(1), with the same 3’ end sequence and stem-loop requirements shown by L-A virions for its own template, However, the L-BC virions do not recognize the internal replication enhancer of the L-A positive strand. In a direct comparison of L-A and L-BC virions, each preferentially recognizes its own RNA for binding, replication, and transcription, These results suggest a close evolutionary relation of these two viruses, consistent with their RNA-dependent RNA polymerase sequence similarities}, keywords = {nosource} }

@article{mcmahonTandemlyArrangedVariant1984, title = {Tandemly Arranged Variant {{5S}} Ribosomal {{RNA}} Genes in the Yeast {{Saccharomyces}} Cerevisiae}, author = {McMahon, M. E. and Stamenkovich, D. and Petes, T. D.}, year = 1984, journal = {Nucleic Acids Research}, volume = {12}, number = {21}, pages = {8001}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/12/21/8001.short}, keywords = {nosource} }

@article{razgaRibosomalRNAKinkturn2004, title = {Ribosomal {{RNA}} Kink-Turn Motif–a Flexible Molecular Hinge.}, author = {Razga, F. and Spackova, N. and R{'e}blova, K. and Koca, J. and Leontis, N. B. and Sponer, J.}, year = 2004, month = oct, journal = {Journal of biomolecular structure & dynamics}, volume = {22}, number = {2}, eprint = {15317479}, eprinttype = {pubmed}, pages = {183}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15317479}, abstract = {Ribosomal RNA K-turn motifs are asymmetric internal loops characterized by a sharp bend in the phosphodiester backbone resulting in “V” shaped structures, recurrently observed in ribosomes and showing a high degree of sequence conservation. We have carried out extended explicit solvent molecular dynamics simulations of selected K-turns, in order to investigate their intrinsic structural and dynamical properties. The simulations reveal an unprecedented dynamical flexibility of the K-turns around their X-ray geometries. The K-turns sample, on the nanosecond timescale, different conformational substates. The overall behavior of the simulations suggests that the sampled geometries are essentially isoenergetic and separated by minimal energy barriers. The nanosecond dynamics of isolated K-turns can be qualitatively considered as motion of two rigid helix stems controlled by a very flexible internal loop which then leads to substantial hinge-like motions between the two stems. This internal dynamics of K-turns is strikingly different for example from the bacterial 5S rRNA Loop E motif or BWYV frameshifting pseudoknot which appear to be rigid in the same type of simulations. Bistability and flexibility of K-turns was also suggested by several recent biochemical studies. Although the results of MD simulations should be considered as a qualitative picture of the K-turn dynamics due to force field and sampling limitations, the main advantage of the MD technique is its ability to investigate the region close to K-turn ribosomal-like geometries. This part of the conformational space is not well characterized by the solution experiments due to large-scale conformational changes seen in the experiments. We suggest that K-turns are well suited to act as flexible structural elements of ribosomal RNA. They can for example be involved in mediation of large-scale motions or they can allow a smooth assembling of the other parts of the ribosome}, keywords = {nosource} }

@article{yanagiharaAssociationElongationFactor1997, title = {Association of {{Elongation Factor}} 1 [Alpha] and {{Ribosomal Protein L3}} with the {{Proline-Rich Region}} of {{Yeast Adenylyl Cyclase-Associated Protein CAP}}{\(\bullet\)} 1,{\(\bullet\)} 2}, author = {Yanagihara, C. and Shinkai, M. and Kariya, K. and {Yamawaki-Kataoka}, Y. and Hu, C. D. and Masuda, T. and Kataoka, T.}, year = 1997, month = mar, journal = {Biochemical and Biophysical Research Communications}, volume = {232}, number = {2}, pages = {503–507}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006291X97963269}, abstract = {CAP is a multifunctional protein; the N-terminal region binds adenylyl cyclase and controls its response to Ras while the C-terminal region is involved in cytoskeletal regulation. In between the two regions, CAP possesses two proline-rich segments, P-1 and P-2, resembling a consensus sequence for binding SH3 domains, We have identified two yeast proteins with molecular sizes of 48 and 46 kDa associated specifically with P-2. Determination of partial protein sequences demonstrated that the 48-kDa and 46-kDa proteins correspond to EF1 alpha and rL3, respectively, neither of which contains any SH3-domain-like sequence. Deletion of P-2 from CAP resulted in loss of the activity to bind the two proteins either in vivo or in vitro. Yeast cells whose chromosomal CAP was replaced by the P-2-deletion mutant displayed an abnormal phenotype represented by dissociated localizations of CAP and F-actin, which were colocalized in wild-type cells. These results suggest that these associations may have functional significance. (C) 1997 Academic Press}, keywords = {nosource} }

@article{wicknerRibosomalProteinL31982, title = {Ribosomal Protein {{L3}} Is Involved in Replication or Maintenance of the Killer Double-Stranded {{RNA}} Genome of {{Saccharomyces}} Cerevisiae}, author = {Wickner, R. B. and Ridley, S. P. and Fried, H. M. and Ball, S. G.}, year = 1982, journal = {Proceedings of the National Academy of Sciences}, volume = {79}, number = {15}, pages = {4706}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/79/15/4706.short}, keywords = {nosource} }

@article{theimerEquilibriumUnfoldingPathway1999, title = {Equilibrium Unfolding Pathway of an {{H-type RNA}} Pseudoknot Which Promotes Programmed-1 Ribosomal Frameshifting1}, author = {Theimer, C. A. and Giedroc, D. P.}, year = 1999, month = jun, journal = {Journal of Molecular Biology}, volume = {289}, number = {5}, pages = {1283–1299}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(99)92850-4}, abstract = {The equilibrium unfolding pathway of a 41-nucleotide frameshifting RNA pseudoknot from the gag-pro junction of mouse intracisternal A-type particles (mIAP), an endogenous retrovirus, has been determined through analysis of dual optical wavelength, equilibrium thermal melting profiles and differential scanning calorimetry. The mIAP pseudoknot is an H-type pseudoknot proposed to have structural features in common with the gag-pro frameshifting pseudoknots from simian retrovirus-l (SRV-1) and mouse mammary tumor virus (MMTV). Ln particular, the mIAP pseudoknot is proposed to contain an unpaired adenosine base at the junction of the two helical stems (A15), as well as one in the middle of stem 2 (A35). A mutational analysis of stem 1 hairpins and compensatory base-pair substitutions incorporated into helical stem 2 was used to assign optical melting transitions to molecular unfolding events. The optical melting profile of the wild-type RNA is most simply described by four sequential two-state unfolding transitions. Stem 2 melts first in two closely coupled low-enthalpy transitions at low t(m) in which the stem 3’ to A35, unfolds first, followed by unfolding of the remainder of the helical stem. The third unfolding transition is associated with some type of stacking interactions in the stem 1 hairpin loop not present in the pseudoknot. The fourth transition is assigned to unfolding of stem 1. in all RNAs investigated, Delta H-vH approximate to Delta H-cal, suggesting that Delta C-p for unfolding is small. A35 has the thermodynamic properties expected for an extrahelical, unpaired nucleotide. Deletion of A15 destabilizes the stem 2 unfolding transition in the context of both the wild-type and Delta A35 mutant RNAs only slightly, by Delta Delta G degrees approximate to 1 kcal mol(-1) (at 37 degrees C). The Delta A15 RNA is considerably more susceptible to thermal denaturation in the presence of moderate urea concentrations than is the wild-type RNA, further evidence of a detectable global destabilization of the molecule. interestingly, substitution of the nine loop 2 nucleotides with uridine residues induces a more pronounced destabilization of the molecule (Delta Delta G degrees approximate to 2.0 kcal mol(-1)), a long-range, non-nearest neighbor effect. These findings provide the thermodynamic basis with which to further refine the relationship between efficient ribosomal frameshifting and pseudoknot structure and stability. (C) 1998 Academic Press}, keywords = {nosource} }

@article{sakaguchiDNADamageActivates1998, title = {{{DNA}} Damage Activates P53 through a Phosphorylation–Acetylation Cascade}, author = {Sakaguchi, K. and Herrera, J. E. and Saito, S. and Miki, T. and Bustin, M. and Vassilev, A. and Anderson, C. W. and Appella, E.}, year = 1998, journal = {Genes & development}, volume = {12}, number = {18}, pages = {2831}, publisher = {Cold Spring Harbor Lab}, url = {http://genesdev.cshlp.org/content/12/18/2831.short}, abstract = {Activation of p53-mediated transcription is a critical cellular response to DNA damage. p53 stability and site-specific DNA-binding activity and, therefore, transcriptional activity, are modulated by post-translational modifications including phosphorylation and acetylation. Here we show that p53 is acetylated in vitro at separate sites by two different histone acetyltransferases (HATs), the coactivators p300 and PCAF. p300 acetylates Lys-382 in the carboxy- terminal region of p53, whereas PCAF acetylates Lys-320 in the nuclear localization signal. Acetylations at either site enhance sequence- specific DNA binding. Using a polyclonal antisera specific for p53 that is phosphorylated or acetylated at specific residues, we show that Lys- 382 of human p53 becomes acetylated and Ser-33 and Ser-37 become phosphorylated in vivo after exposing cells to UV light or ionizing radiation. In vitro, amino-terminal p53 peptides phosphorylated at Ser- 33 and/or at Ser-37 differentially inhibited p53 acetylation by each HAT. These results suggest that DNA damage enhances p53 activity as a transcription factor in part through carboxy-terminal acetylation that, in turn, is directed by amino-terminal phosphorylation}, keywords = {nosource} }

@article{wicknerMutantsKillerPlasmid1976, title = {Mutants of the Killer Plasmid of {{Saccharomyces}} Cerevisiae Dependent on Chromosomal Diploidy for Expression and Maintenance}, author = {Wickner, R. B.}, year = 1976, journal = {Genetics}, volume = {82}, number = {2}, pages = {273}, publisher = {Genetics Soc America}, url = {http://www.genetics.org/content/82/2/273.short}, keywords = {nosource} }

@article{watanabeEncapsidationSequencesSpleen1982, title = {Encapsidation Sequences for Spleen Necrosis Virus, an Avian Retrovirus, Are between the 5’long Terminal Repeat and the Start of the Gag Gene}, author = {Watanabe, S. and Temin, H. M.}, year = 1982, journal = {Proceedings of the National Academy of Sciences}, volume = {79}, number = {19}, pages = {5986}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/79/19/5986.short}, keywords = {nosource} }

@article{tateTranslationalTerminationStop1992, title = {Translational Termination:” Stop” for Protein Synthesis or” Pause” for Regulation of Gene Expression}, author = {Tate, W. P. and Brown, C. M.}, year = 1992, journal = {Biochemistry}, volume = {31}, number = {9}, pages = {2443–2450}, publisher = {ACS Publications}, url = {http://pubs.acs.org/doi/abs/10.1021/bi00124a001}, keywords = {nosource} }

@article{dabrowskiInteractionTRNAsRibosome1995, title = {Interaction of {{tRNAs}} with the Ribosome at the {{A}} and {{P}} Sites.}, author = {Dabrowski, M. and Spahn, C. M. T. and Nierhaus, K. H.}, year = 1995, month = oct, journal = {The EMBO Journal}, volume = {14}, number = {19}, pages = {4872}, publisher = {Nature Publishing Group}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC394585/}, abstract = {In vitro transcribed tRNA(Phe) analogues from Escherichia coli containing up to four randomly distributed A, G, U or C phosphorothioated nucleotides were used to investigate contact patterns with the ribosome in the A and P sites. The tRNAs were biologically active. Molecular iodine (I-2) can trigger a break in the sugar-phosphate backbone at phosphorothioated positions of the ribosomal bound tRNAs if contacts with ribosomal components do not prevent access of the iodine, Highly differentiated protection patterns were found which were strikingly different in the A and P sites, respectively. Strong protections accumulated in the T Psi C loop and no protection was seen in the extra-arm region in both sites, whereas the phosphates in the anticodon loop are more strongly protected in the A site. Strong common protections in both the A and P sites were found neighbouring universally or semiuniversally conserved bases in prominent regions of the tertiary structure of tRNAs: Y11, Y32, U33, Psi 55, C56, A58 and Y60, These bases are therefore candidates for ‘identity elements’ in ribosomal tRNA recognition, The data further indicate that tRNAs change their conformations upon binding to either ribosomal site}, keywords = {nosource} }

@article{lovkvist-wallstromEtal1995Regulation1995, title = {Etal.(1995) {{Regulation}} of Mammalian Ornithine Decarboxylase—{{Studies}} on the Induction of the Enzyme by Hypotonic Stress}, author = {{Lovkvist-Wallstrom}, E. and {Stjernborg-Ulvsback}, L.}, year = 1995, month = jul, journal = {European Journal of Biochemistry}, volume = {231}, number = {1}, pages = {40–44}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Regulation+of+mammalian+ornithine+decarboxylase.+Studies+on+the+induction+of+the+enzyme+by+hypotonic+stress#3}, abstract = {One of the cellular responses to hypotonic stress is a marked induction of a key regulatory enzyme in the polyamine biosynthetic pathway, i.e. ornithine decarboxylase (ODC). This increase in ODC activity appears to be a physiological response since the elevated putrescine production seen after the hypotonic shock renders the cells less sensitive to the decrease in osmolarity. In the present study, we have investigated the mechanisms by which the hypotonicity may induce ODC activity. We provide support for a translational mechanism, closely related to the polyamine-mediated feedback regulation of ODC synthesis. In addition, we have examined whether the long G+C-rich 5’ untranslated region of the ODC mRNA, which has been demonstrated to negatively affect the translatability of the message, is of any importance for the induction of ODC by hypotonic stress. Chinese hamster ovary (CHO) cells expressing ODC mRNA, with or without the 5’ untranslated region, were isolated after transfecting ODC-deficient CHO cells with the appropriate constructs. Hypotonic treatment of the stable transfectants, however, revealed no major difference in ODC induction between the cells expressing a full-length ODC mRNA and those expressing an ODC mRNA deleted of its 5’ untranslated region, demonstrating that this part of the message was not essential for the osmotic effects on ODC expression}, keywords = {nosource} }

@article{rheinbergerHistoryProteinBiosynthesis2004, title = {A History of Protein Biosynthesis and Ribosome Research}, author = {Rheinberger, H. J.}, year = 2004, pages = {1–51}, publisher = {Wiley Online Library}, url = {http://onlinelibrary.wiley.com/doi/10.1002/3527603433.ch1/summary}, keywords = {nosource} } % == BibTeX quality report for rheinbergerHistoryProteinBiosynthesis2004: % Missing required field ‘journal’

@article{websterVitroProteinSynthesis1966, title = {In Vitro Protein Synthesis: Chain Initiation.}, author = {Webster, R. E. and Engelhardt, D. L. and Zinder, N. D.}, year = 1966, journal = {Proceedings of the National Academy of Sciences}, volume = {55}, number = {1}, pages = {155}, publisher = {National Academy of Sciences}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC285769/}, keywords = {nosource} }

@article{rosoriusHumanRibosomalProtein2000, title = {Human Ribosomal Protein {{L5}} Contains Defined Nuclear Localization and Export Signals}, author = {Rosorius, O. and Fries, B. and Stauber, R. H. and Hirschmann, N. and Bevec, D. and Hauber, J.}, year = 2000, month = apr, journal = {Journal of Biological Chemistry}, volume = {275}, number = {16}, pages = {12061}, publisher = {ASBMB}, url = {http://www.jbc.org/content/275/16/12061.short}, abstract = {Ribosomal protein L5 is part of the 60 S ribosomal subunit and localizes in both the cytoplasm and the nucleus of eukaryotic cells, accumulating particularly in the nucleoli. L5 is known to bind specifically to 5 S rRNA and is involved in nucleocytoplasmic transport of this rRNA. Here, we report a detailed analysis of the domain organization of the human ribosomal protein L5. We show that a signal that mediates nuclear import and nucleolar localization maps to amino acids 21-37 within the 297-amino acid L5 protein. Furthermore, carboxyl-terminal residues at positions 255-297 serve as an additional nuclear/nucleolar targeting signal. Domains involved in 5 S rRNA binding are located at both the amino terminus and the carboxyl terminus of L5. Microinjection studies in somatic cells demonstrate that a nuclear export signal (NES) that maps to amino acids 101-111 resides in the central region of L5. This NES is characterized by a pronounced clustering of critical leucine residues, which creates a peptide motif not previously observed in other leucine-rich NESs. Finally, we present a refined model of the multidomain structure of human ribosomal protein L5}, keywords = {nosource} }

@article{muellerArrangement23RRNA2000, title = {The 3 {{D Arrangement}} of the 23 {{S}} and 5 {{S rRNA}} in the {{Escherichia}} Coli 50 {{S Ribosomal Subunit Based}} on a {{Cryo-electron Microscopic Reconstruction}} at 7. 5 {{Aa Resolution}}}, author = {Mueller, F. and Sommer, I. and Baranov, P. and Matadeen, R. and Stoldt, M. and Wo{`E}hnert, J. and Goerlach, M. and {}van Heel, M. and Brimacombe, R.}, year = 2000, month = apr, journal = {Journal of Molecular Biology}, volume = {298}, number = {1}, pages = {35–59}, url = {http://lapti.ucc.ie/pubs/JMB2000.pdf}, abstract = {The Escherichia coli 23 S and 5 S rRNA molecules have been fitted helix by helix to a cryo-electron microscopic (EM) reconstruction of the 50 S ribosomal subunit, using an unfiltered version of the recently published 50 S reconstruction at 7.5 A resolution. At this resolution, the EM density shows a well-defined network of fine structural elements, in which the major and minor grooves of the rRNA helices can be discerned at many locations. The 3D folding of the rRNA molecules within this EM density is constrained by their well-established secondary structures, and further constraints are provided by intra and inter-rRNA crosslinking data, as well as by tertiary interactions and pseudoknots. RNA-protein cross-link and foot-print sites on the 23 S and 5 S rRNA were used to position the rRNA elements concerned in relation to the known arrangement of the ribosomal proteins as determined by immuno-electron microscopy. The published X-ray or NMR structures of seven 50 S ribosomal proteins or RNA-protein complexes were incorporated into the EM density. The 3D locations of cross-link and foot-print sites to the 23 S rRNA from tRNA bound to the ribosomal A, P or E sites were correlated with the positions of the tRNA molecules directly observed in earlier reconstructions of the 70 S ribosome at 13 A or 20 A. Similarly, the positions of cross-link sites within the peptidyl transferase ring of the 23 S rRNA from the aminoacyl residue of tRNA were correlated with the locations of the CCA ends of the A and P site tRNA. Sites on the 23 S rRNA that are cross- linked to the N termini of peptides of different lengths were all found to lie within or close to the internal tunnel connecting the peptidyl transferase region with the presumed peptide exit site on the solvent side of the 50 S subunit. The post-transcriptionally modified bases in the 23 S rRNA form a cluster close to the peptidyl transferase area. The minimum conserved core elements of the secondary structure of the 23 S rRNA form a compact block within the 3D structure and, conversely, the points corresponding to the locations of expansion segments in 28 S rRNA all lie on the outside of the structure}, keywords = {nosource} }

@article{tyersInhibitionG1Cyclin1994, title = {Inhibition of {{G1}} Cyclin Activity by {{Ras}}/{{cAMP}} Pathway in Yeast}, author = {Tyers, M.}, year = 1994, journal = {Nature}, volume = {371}, pages = {342–345}, url = {http://dialnet.unirioja.es/servlet/articulo?codigo=391136}, keywords = {nosource} }

@article{kollmusSequencesDistanceTwo1994, title = {The Sequences of and Distance between Two Cis-Acting Signals Determine the Efficiency of Ribosomal Frameshifting in Human Immunodeficiency Virus Type 1 and Human {{T-cell}} Leukemia Virus Type {{II}} in Vivo.}, author = {Kollmus, H. and Honigman, A. and Panet, A. and Hauser, H.}, year = 1994, journal = {Journal of virology}, volume = {68}, number = {9}, pages = {6087}, publisher = {Am Soc Microbiol}, url = {http://jvi.asm.org/cgi/content/abstract/68/9/6087}, keywords = {nosource} }

@article{sarkhelWaternucleobaseStackingHp2003, title = {Water-Nucleobase ``Stacking’’: {{H-\(\pi\)}} and Lone Pair-{\(\pi\)} Interactions in the Atomic Resolution Crystal Structure of an {{RNA}} Pseudoknot}, author = {Sarkhel, S. and Rich, A. and Egli, M.}, year = 2003, month = jul, journal = {Journal of the American Chemical Society}, volume = {125}, number = {30}, pages = {8998–8999}, publisher = {ACS Publications}, url = {http://pubs.acs.org/doi/abs/10.1021/ja0357801}, keywords = {nosource} }

@article{namEffectsProgressiveDepletion1986, title = {Effects of Progressive Depletion of {{TCM1}} or {{CYH2 mRNA}} on {{Saccharomyces}} Cerevisiae Ribosomal Protein Accumulation.}, author = {Nam, H. G. and Fried, H. M.}, year = 1986, journal = {Molecular and cellular biology}, volume = {6}, number = {5}, pages = {1535}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/6/5/1535}, keywords = {nosource} }

@article{reijoDeletionSinglecopyTRNA1993, title = {Deletion of a Single-Copy {{tRNA}} Affects Microtubule Function in {{Saccharomyces}} Cerevisiae}, author = {Reijo, R. A. and Cho, D. S. and Huffaker, T. C.}, year = 1993, month = dec, journal = {Genetics}, volume = {135}, number = {4}, pages = {955}, publisher = {Genetics Soc America}, url = {http://www.genetics.org/content/135/4/955.short}, abstract = {rts1-1 was identified as an extragenic suppressor of tub2-104, a cold-sensitive allele of the sole gene encoding P-tubulin in the yeast, Saccharomyces cerevisiae. In addition, rts1-1 cells are heat sensitive and resistant to the microtubule-destabilizing drug, benomyl. The rts1-1 mutation is a deletion of approximately 5 kb of genomic DNA on chromosome X that includes one open reading frame and three tRNA genes. Dissection of this region shows that heat sensitivity is due to deletion of the open reading frame (HIT1). Suppression and benomyl resistance are caused by deletion of the gene encoding a tRNA(AGG)(Arg) (HSX1). Northern analysis of rts1-1 cells indicates that HSX1 is the only gene encoding this tRNA. Deletion of HSX1 does not suppress the tub2-104 mutation by misreading at the AGG codons in TUB2. It also does not suppress by interfering with the protein arginylation that targets certain proteins for degradation. These results leave open the prospect that this tRNA(AGG)(Arg) plays a novel role in the cell}, keywords = {nosource} }

@article{josephEFGcatalyzedTranslocationAnticodon1998, title = {{{EF-G-catalyzed}} Translocation of Anticodon Stem–Loop Analogs of Transfer {{RNA}} in the Ribosome}, author = {Joseph, S. and Noller, H. F.}, year = 1998, month = jun, journal = {The EMBO journal}, volume = {17}, number = {12}, pages = {3478–3483}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/emboj/journal/v17/n12/abs/7591051a.html}, abstract = {Translocation, catalyzed by elongation factor EF-G, is the precise movement of the tRNA-mRNA complex within the ribosome following peptide bond formation. Here we examine the structural requirement for A- and P-site tRNAs in EF-G-catalyzed translocation by substituting anticodon stem-loop (ASL) analogs for the respective tRNAs. Translocation of mRNA and tRNA was monitored independently; mRNA movement was assayed by toeprinting, while tRNA and ASL movement was monitored by hydroxyl radical probing by Fe(II) tethered to the ASLs and by chemical footprinting. Translocation depends on occupancy of both A and P sites by tRNA bound in a mRNA-dependent fashion. The requirement for an A-site tRNA can be satisfied by a 15 nucleotide ASL analog comprising only a 4 base pair (bp) stem and a 7 nucleotide anticodon loop. Translocation of the ASL is both EF-G- and GTP-dependent, and is inhibited by the translocational inhibitor thiostrepton. These findings show that the D, T and acceptor stem regions of A-site tRNA are not essential for EF-G-dependent translocation. In contrast, no translocation occurs if the P-site tRNA is substituted with an ASL, indicating that other elements of P-site tRNA structure are required for translocation. We also tested the effect of increasing the A-site ASL stem length from 4 to 33 bp on translocation from A to P site. Translocation efficiency decreases as the ASL stem extends beyond 22 bp, corresponding approximately to the maximum dimension of tRNA along the anticodon-D arm axis. This result suggests that a structural feature of the ribosome between the A and P sites, interferes with movement of tRNA analogs that exceed the normal dimensions of the coaxial tRNA anticodon-D arm}, keywords = {nosource} }

@article{terceroMAK3EncodesNacetyltransferase1992, title = {{{MAK3}} Encodes an {{N-acetyltransferase}} Whose Modification of the {{LA}} Gag {{NH2}} Terminus Is Necessary for Virus Particle Assembly.}, author = {Tercero, J. C. and Wickner, R. B.}, year = 1992, journal = {Journal of Biological Chemistry}, volume = {267}, number = {28}, pages = {20277}, publisher = {ASBMB}, url = {http://www.jbc.org/content/267/28/20277.short}, keywords = {nosource} }

@article{ichoMAK11ProteinEssential1988, title = {The {{MAK11}} Protein Is Essential for Cell Growth and Replication of {{M}} Double-Stranded {{RNA}} and Is Apparently a Membrane-Associated Protein.}, author = {Icho, T. and Wickner, R. B.}, year = 1988, journal = {Journal of Biological Chemistry}, volume = {263}, number = {3}, pages = {1467}, publisher = {ASBMB}, url = {http://www.jbc.org/content/263/3/1467.short}, keywords = {nosource} }

@article{petesCharacterizationTwoTypes1978, title = {Characterization of Two Types of Yeast Ribosomal {{DNA}} Genes.}, author = {Petes, T. D. and Hereford, L. M. and Skryabin, K. G.}, year = 1978, journal = {Journal of bacteriology}, volume = {134}, number = {1}, pages = {295}, publisher = {Am Soc Microbiol}, url = {http://jb.asm.org/cgi/content/abstract/134/1/295}, keywords = {nosource} }

@article{iizukaCapdependentCapindependentTranslation1994a, title = {Cap-Dependent and Cap-Independent Translation by Internal Initiation of {{mRNAs}} in Cell Extracts Prepared from {{Saccharomyces}} Cerevisiae.}, author = {Iizuka, N. and Najita, L. and Franzusoff, A. and Sarnow, P.}, year = 1994, journal = {Molecular and cellular biology}, volume = {14}, number = {11}, pages = {7322}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/14/11/7322}, keywords = {nosource} }

@article{leeVivoAnalysesUpstream1997, title = {In Vivo Analyses of Upstream Promoter Sequence Elements in the 5 {{S rRNA}} Gene from Saccharomyces Cerevisiae1}, author = {Lee, Y. and Wong, W. M. and Guyer, D. and Erkine, A. M.}, year = 1997, month = jun, journal = {Journal of molecular}, volume = {269}, number = {5}, pages = {676–683}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283697910718}, abstract = {Upstream promoter elements of the Saccharomyces cerevisiae 5S rRNA gene have been characterized by genomic DNase I ‘’footprinting’’ and by in vivo mutational analyses using base substitutions and deletions. A high copy shuttle-vectar was used to efficiently express the mutant 5S rRNA genes in vivo and a structural mutation in the 5S rRNA, which was previously shown to be functionally neutral but easily detected by gel electrophoresis, allowed for an accurate measure of gene expression. The results provide direct evidence for upstream regulatory elements which confirms a start site element (sse) from -1 to -8 and identifies a new independent upstream promoter element (upe) centered from about -17 to -20. In contrast to previous reports with reconstituted systems, both elements dramatically affect the efficiency of gene expression and suggest that the saturated conditions which are used in reconstituted studies mask sequence dependence; a dependency that could be physiologically significant and play a role in the regulation of 5S rRNA expression. The footprint analyses support an extended region of protein interaction as recently observed in reconstituted systems but again provide evidence of significant structural rearrangements when the upstream sequence is changed. (C) 1997 Academic Press Limited}, keywords = {nosource} }

@article{khaitovichEffectAntibioticsLarge1999, title = {Effect of Antibiotics on Large Ribosomal Subunit Assembly Reveals Possible Function of 5 {{S rRNA1}}}, author = {Khaitovich, P. and Mankin, A. S.}, year = 1999, journal = {Journal of molecular biology}, volume = {291}, number = {5}, pages = {1025–1034}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(99)93030-9}, abstract = {Functional large ribosomal subunits of Thermus aquaticus can be reconstituted from ribosomal proteins and either natural or in vitro transcribed 23 S and 5 S rRNA. Omission of 5 S rRNA during subunit reconstitution results in dramatic decrease of the peptidyl transferase activity of the assembled subunits. However, the presence of some ribosome-targeted antibiotics of the macrolide, ketolide or streptogramin B groups during 50 S subunit reconstitution can partly restore the activity of ribosomal subunits assembled without 5 S rRNA. Among tested antibiotics, macrolide RU69874 was the most active: activity of the subunits assembled in the absence of 5 S rRNA was increased more than 30-fold if antibiotic was present during reconstitution procedure. Activity of the subunits assembled with 5 S rRNA was also slightly stimulated by RU69874, but to a much lesser extent, approximately 1.5-fold. Activity of the native T. aquaticus 50 S subunits incubated in the reconstitution conditions in the presence of RU69874 was, in contrast, slightly decreased. The presence of antibiotics was essential during the last incubation step of the in vitro assembly, indicating that drugs affect one of the last assembly steps. The 5 S rRNA was previously shown to form contacts with segments of domains II and V of 23 S rRNA. All the antibiotics which can functionally compensate for the lack of 5 S rRNA during subunit reconstitution interact simultaneously with the central loop in domain V (which is known to be a component of peptidyl transferase center) and a loop of the helix 35 in domain II of 23 S rRNA. It is proposed that simultaneous interaction of 5 S rRNA or of antibiotics with the two domains of 23 S rRNA is essential for the successful assembly of ribosomal peptidyl transferase center. Consequently, one of the functions of 5 S rRNA in the ribosome can be that of assisting the assembly of ribosomal peptidyl transferase by correctly positioning functionally important segments of domains II and V of 23 S rRNA}, keywords = {nosource} }

@article{napthineRoleRNAPseudoknot1999, title = {The Role of {{RNA}} Pseudoknot Stem 1 Length in the Promotion of Efficient-1 Ribosomal Frameshifting 1}, author = {Napthine, S. and Liphardt, J. and Bloys, A. and Routledge, S. and Brierley, I.}, year = 1999, month = may, journal = {Journal of molecular biology}, volume = {288}, number = {3}, pages = {305–320}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(99)92688-8}, abstract = {The ribosomal frameshifting signal present in the genomic RNA of the coronavirus infectious bronchitis virus (IBV) contains a classic hairpin-type RNA pseudoknot that is believed to possess coaxially stacked stems of 11 bp (stem 1) and 6 bp (stem 2). We investigated the influence of stem 1 length on the frameshift process by measuring the frameshift efficiency in vitro of a series of IBV-based pseudoknots whose stem 1 length was varied from 4 to 13 bp in single base-pair increments. Efficient frameshifting depended upon the presence of a minimum of 11 bp; pseudoknots with a shorter stem 1 were either non- functional or had reduced frameshift efficiency, despite the fact that a number of them had a stem 1 with a predicted stability equal to or greater than that of the wild-type IBV pseudoknot. An upper limit for stem 1 length was not determined, but pseudoknots containing a 12 or 13 bp stem 1 were fully functional. Structure probing analysis was carried out on RNAs containing either a ten or 11 bp stem 1; these experiments confirmed that both RNAs formed pseudoknots and appeared to be indistinguishable in conformation. Thus the difference in frameshifting efficiency seen with the two structures was not simply due to an inability of the 10 bp stem 1 construct to fold into a pseudoknot. In an attempt to identify other parameters which could account for the poor functionality of the shorter stem 1-containing pseudoknots, we investigated, in the context of the 10 bp stem 1 construct, the influence on frameshifting of altering the slippery sequence-pseudoknot spacing distance, loop 2 length, and the number of G residues at the bottom of the 5’-arm of stem 1. For each parameter, it was possible to find a condition where a modest stimulation of frameshifting was observable (about twofold, from seven to a maximal 17 %), but we were unable to find a situation where frameshifting approached the levels seen with 11 bp stem 1 constructs (48-57 %). Furthermore, in the next smaller construct (9 bp stem 1), changing the bottom four base-pairs to G.C (the optimal base composition) only stimulated frameshifting from 3 to 6 %, an efficiency about tenfold lower than seen with the 11 bp construct. Thus stem 1 length is a major factor in determining the functionality of this class of pseudoknot and this has implications for models of the frameshift process. Copyright 1999 Academic Press}, keywords = {nosource} }

@article{tsuchihashiSequenceRequirementsEfficient1992, title = {Sequence Requirements for Efficient Translational Frameshifting in the {{Escherichia}} Coli {{dnaX}} Gene and the Role of an Unstable Interaction between {{tRNA}} ({{Lys}}) and an {{AAG}} Lysine Codon.}, author = {Tsuchihashi, Z. and Brown, P. O.}, year = 1992, month = mar, journal = {Genes & development}, volume = {6}, number = {3}, pages = {511}, publisher = {Cold Spring Harbor Lab}, url = {http://genesdev.cshlp.org/content/6/3/511.short}, abstract = {Synthesis of the gamma-subunit of DNA polymerase III holoenzyme depends on precise and efficient translational frameshifting to the -1 frame at a specific site in the dnaX gene of Escherichia coli. In vitro mutagenesis of this frameshift site demonstrated the importance of an A AAA AAG heptanucleotide sequence, which allows two adjacent tRNAs to retain a stable interaction with mRNA after they slip to the -1 position. The AAG lysine codon present in the 3’ half of this heptanucleotide was a key element for highly efficient frameshifting. A tRNA(Lys) with a CUU anticodon, which has a strong affinity for AAG lysine codons, is present in eukaryotic cells but absent in E. coli. Expression in E. coli of a mutant tRNA(Lys) with a CUU anticodon specifically inhibited the frameshifting at the AAG codon, suggesting that the absence of this tRNA in E. coli contributes to the efficiency of the dnaX frameshift}, keywords = {nosource} }

@article{johnstonRegulationCellSize1979, title = {Regulation of Cell Size in the Yeast {{Saccharomyces}} Cerevisiae.}, author = {Johnston, G. C. and Ehrhardt, C. W. and Lorincz, A. and Carter, B. L. A.}, year = 1979, journal = {Journal of bacteriology}, volume = {137}, number = {1}, pages = {1}, publisher = {Am Soc Microbiol}, url = {http://jb.asm.org/cgi/content/abstract/137/1/1}, keywords = {nosource} }

@article{ozakiIsolationThreeTestisSpecific1996a, title = {Isolation of {{Three Testis-Specific Genes}} ({{TSA303}}, {{TSA806}}, {{TSA903}}) by a {{Differential mRNA Display Method}}{\(\bullet\)} 1}, author = {Ozaki, K. and Kuroki, T. and Hayashi, S. and Nakamura, Y.}, year = 1996, month = sep, journal = {Genomics}, volume = {36}, number = {2}, pages = {316–319}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S088875439690467X}, keywords = {nosource} } % == BibTeX quality report for ozakiIsolationThreeTestisSpecific1996a: % ? Title looks like it was stored in title-case in Zotero

@article{wicknerYeastRNAVirology1991, title = {Yeast {{RNA}} Virology: The Killer Systems}, author = {Wickner, R. B.}, year = 1991, journal = {The molecular and cellular biology of the yeast Saccharomyces: genome dynamics, proteins synthesis, and energetics}, volume = {1}, pages = {263–296}, publisher = {Cold Spring Harbor Press}, url = {http://books.google.com/books?hl=en&lr=&id=FRyWfsr4DNQC&oi=fnd&pg=PA263&dq=Yeast+RNA+virology:+the+killer+systems&ots=ye_uEY-Ifq&sig=soAy_rIAhF6hE_eRPqDDatfQv-8}, keywords = {nosource} }

@article{wicknerKillerSaccharomycesCerevisiae1976, title = {Killer of {{Saccharomyces}} Cerevisiae: A Double-Stranded Ribonucleic Acid Plasmid.}, author = {Wickner, R. B.}, year = 1976, journal = {Microbiology and Molecular Biology Reviews}, volume = {40}, number = {3}, pages = {757}, publisher = {Am Soc Microbiol}, url = {http://mmbr.asm.org/cgi/reprint/40/3/757.pdf}, keywords = {nosource} }

@article{leeInactivationCapbindingProteins1982, title = {Inactivation of Cap-Binding Proteins Accompanies the Shut-off of Host Protein Synthesis by Poliovirus}, author = {Lee, K. A. and Sonenberg, N.}, year = 1982, journal = {Proceedings of the National Academy of Sciences}, volume = {79}, number = {11}, pages = {3447}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/79/11/3447.short}, keywords = {nosource} }

@article{morasRNAProteinInteractionsDiverse1995, title = {{{RNA-Protein Interactions}}: {{Diverse}} Modes of Recognition}, author = {Moras, D.}, year = 1995, month = mar, journal = {Current Biology}, volume = {5}, number = {3}, pages = {249–251}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0960-9822(95)00051-0}, keywords = {nosource} }

@article{varela-echavarriaComparisonMoloneyMurine1992, title = {Comparison of {{Moloney}} Murine Leukemia Virus Mutation Rate with the Fidelity of Its Reverse Transcriptase in Vitro.}, author = {{Varela-Echavarria}, A. and Garvey, N. and Preston, B. D. and Dougherty, J. P.}, year = 1992, journal = {Journal of Biological Chemistry}, volume = {267}, number = {34}, pages = {24681}, publisher = {ASBMB}, url = {http://www.jbc.org/content/267/34/24681.short}, keywords = {nosource} }

@article{wicknerChromosomalNonchromosomalMutations1974, title = {Chromosomal and Nonchromosomal Mutations Affecting the” Killer Character” of {{Saccharomyces}} Cerevisiae}, author = {Wickner, R. B.}, year = 1974, month = mar, journal = {Genetics}, volume = {88}, number = {3}, pages = {423}, publisher = {Genetics Soc America}, url = {http://www.genetics.org/content/76/3/423.short http://www.genetics.org/content/88/3/419.short}, keywords = {nosource} }

@article{estebanSitespecificBindingViral1986, title = {Site-Specific Binding of Viral plus Single-Stranded {{RNA}} to Replicase-Containing Open Virus-like Particles of Yeast}, author = {Esteban, R. and Fujimura, T. and Wickner, R. B.}, year = 1986, month = jun, journal = {Proceedings of the National Academy of Sciences}, volume = {83}, number = {12}, pages = {4433}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/83/12/4433.short http://www.pnas.org/content/85/12/4411.short}, keywords = {nosource} }

@book{sambrookMolecularCloningLaboratory2001, title = {Molecular Cloning: A Laboratory Manual}, author = {Sambrook, J. and Russell, D. W.}, year = 2001, volume = {3}, publisher = {Cold spring harbor laboratory press}, url = {http://books.google.com/books?hl=en&lr=&id=Bosc5JVxNpkC&oi=fnd&pg=PR21&dq=Molecular+cloning,+a+laboratory+manual.&ots=eecSmIASgP&sig=zOqDQpXk_NE49WSdjvd6Y2wwgtE}, keywords = {nosource} }

@article{moonPredictingGenesExpressed2004, title = {Predicting Genes Expressed via -1 and +1 Frameshifts}, author = {Moon, S. and Byun, Y. and Kim, H. J. and Jeong, S.}, year = 2004, journal = {Nucleic Acids Research}, volume = {32}, number = {16}, pages = {4884–4892}, url = {http://nar.oxfordjournals.org/content/32/16/4884.short}, abstract = {Computational identification of ribosomal frameshift sites in genomic sequences is difficult due to their diverse nature, yet it provides useful information for understanding the underlying mechanisms and discovering new genes. We have developed an algorithm that searches entire genomic or mRNA sequences for frameshifting sites, and implements the algorithm as a web-based program called FSFinder (Frameshift Signal Finder). The current version of FSFinder is capable of finding -1 frameshift sites on heptamer sequences X XXY YYZ, and +1 frameshift sites for two genes: protein chain release factor B (prfB) and ornithine decarboxylase antizyme (oaz). We tested FSFinder on approximately 190 genomic and partial DNA sequences from a number of organisms and found that it predicted frameshift sites efficiently and with greater sensitivity and specificity than existing approaches. It has improved sensitivity because it considers many known components of a frameshifting cassette and searches these components on both + and - strands, and its specificity is increased because it focuses on overlapping regions of open reading frames and prioritizes candidate frameshift sites. FSFinder is useful for discovering unknown genes that utilize alternative decoding, as well as for analyzing frameshift sites. It is freely accessible at http://wilab.inha.ac.kr/FSFinder/}, keywords = {nosource} }

@article{plantDifferentiatingNearandNoncognate2007, title = {Differentiating between Near-and Non-Cognate Codons in {{Saccharomyces}} Cerevisiae}, author = {Plant, E. P. and Nguyen, P. and Russ, J. R. and Pittman, Y. R. and Nguyen, T. and Quesinberry, J. T. and Kinzy, T. G. and Dinman, J. D.}, year = 2007, journal = {PloS ONE}, volume = {2}, number = {6}, pages = {e517}, abstract = {BACKGROUND: Decoding of mRNAs is performed by aminoacyl tRNAs (aa-tRNAs). This process is highly accurate, however, at low frequencies (10(-3) - 10(-4)) the wrong aa-tRNA can be selected, leading to incorporation of aberrant amino acids. Although our understanding of what constitutes the correct or cognate aa-tRNA:mRNA interaction is well defined, a functional distinction between near-cognate or single mismatched, and unpaired or non-cognate interactions is lacking. METHODOLOGY/PRINCIPAL FINDINGS: Misreading of several synonymous codon substitutions at the catalytic site of firefly luciferase was assayed in Saccharomyces cerevisiae. Analysis of the results in the context of current kinetic and biophysical models of aa-tRNA selection suggests that the defining feature of near-cognate aa-tRNAs is their potential to form mini-helical structures with A-site codons, enabling stimulation of GTPase activity of eukaryotic Elongation Factor 1A (eEF1A). Paromomycin specifically stimulated misreading of near-cognate but not of non-cognate aa-tRNAs, providing a functional probe to distinguish between these two classes. Deletion of the accessory elongation factor eEF1Bgamma promoted increased misreading of near-cognate, but hyperaccurate reading of non-cognate codons, suggesting that this factor also has a role in tRNA discrimination. A mutant of eEF1Balpha, the nucleotide exchange factor for eEF1A, promoted a general increase in fidelity, suggesting that the decreased rates of elongation may provide more time for discrimination between aa-tRNAs. A mutant form of ribosomal protein L5 promoted hyperaccurate decoding of both types of codons, even though it is topologically distant from the decoding center. CONCLUSIONS/SIGNFICANCE: It is important to distinguish between near-cognate and non-cognate mRNA:tRNA interactions, because such a definition may be important for informing therapeutic strategies for suppressing these two different categories of mutations underlying many human diseases. This study suggests that the defining feature of near-cognate aa-tRNAs is their potential to form mini-helical structures with A-site codons in the ribosomal decoding center. An aminoglycoside and a ribosomal factor can be used to distinguish between near-cognate and non-cognate interactions}, keywords = {A SITE,A-SITE,ACID,ACIDS,Amino Acids,AMINO-ACID,AMINO-ACIDS,analysis,BIOLOGY,CEREVISIAE,Codon,CODONS,decoding,disease,elongation,eukaryotic elongation factor,Fidelity,FIREFLY LUCIFERASE,FORM,Genetic,genetics,GTPase,GTPASE ACTIVITY,human,L5,La,luciferase,MODEL,models,MOLECULAR-GENETICS,mRNA,Mutation,MUTATIONS,nosource,NUCLEOTIDE EXCHANGE,Paromomycin,protein,RIBOSOMAL-PROTEIN,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SELECTION,SITE,structure,tRNA,United States} }

@article{philippeRibosomalProteinS151993, title = {Ribosomal Protein {{S15}} from {{Escherichia}} Coli Modulates Its Own Translation by Trapping the Ribosome on the {{mRNA}} Initiation Loading Site}, author = {Philippe, C. and Eyermann, F. and B{'e}nard, L. and Portier, C. and Ehresmann, B. and Ehresmann, C.}, year = 1993, month = may, journal = {Proceedings of the National Academy of Sciences}, volume = {90}, number = {10}, pages = {4394}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/90/10/4394.short}, abstract = {From genetic and biochemical evidence, we previously proposed that S15 inhibits its own translation by binding to its mRNA in a region overlapping the ribosome loading site. This binding was postulated to stabilize a pseudoknot structure that exists in equilibrium with two stem-loops. Here, we use ‘’toeprint’’ experiments with Moloney murine leukemia virus reverse transcriptase to analyze the effect of S15 on the formation of the ternary mRNA-30S-tRNA(f)Met complex. We show that the binding of the 30S subunit on the mRNA stops reverse transcriptase near position +10, corresponding to the 3’ terminus of the pseudoknot, most likely by stabilizing the pseudoknot conformation. Furthermore, S15 is found to stabilize the binary 30S-mRNA complex. When the ternary 30S-mRNA-tRNA(f)Met complex is formed, a toeprint is observed at position +17. This toeprint progressively disappears when the ternary complex is formed in the presence of increasing concentrations of S15, while a shift from position +17 to position +10 is observed. Beside, RNase T1 footprinting experiments reveal the simultaneous binding of S15 and 30S subunit on the mRNA. Otherwise, we show by filter binding assays that initiator tRNA remains bound to the 30S subunit even in the presence of S15. Our results indicate that S15 prevents the formation of a functional ternary 30S-mRNA-tRNA(f)Met complex, the ribosome being trapped in a preternary 30S-mRNA-tRNA(f)Met complex}, keywords = {assays,BINDING,COMPLEX,COMPLEXES,CONFORMATION,Escherichia coli,ESCHERICHIA-COLI,Genetic,initiation,MESSENGER-RNA,mRNA,nosource,pseudoknot,REPRESSOR,ribosome,RNAse,structure,SUBUNIT,translation,tRNA,virus} }

@article{wicknerExpressionYeastDoublestranded1991, title = {Expression of Yeast {{LA}} Double-Stranded {{RNA}} Virus Proteins Produces Derepressed Replication: A Ski-Phenocopy.}, author = {Wickner, R. B. B. and Icho, T. and Fujimura, T. and Widner, W. R. R.}, year = 1991, month = jan, journal = {Journal of Virology}, volume = {65}, number = {1}, pages = {155}, publisher = {Am Soc Microbiol}, url = {http://jvi.asm.org/cgi/content/abstract/65/1/155}, abstract = {The plus strand of the L-A double-stranded RNA virus of Saccharomyces cerevisiae has two large open reading frames, ORF1, which encodes the major coat protein, and ORF2, which encodes a single-stranded RNA-binding protein having a sequence diagnostic of viral RNA-dependent RNA polymerases. ORF2 is expressed only as a Gag-Pol-type fusion protein with ORF1. We have constructed a plasmid which expresses these proteins from the yeast PGK1 promoter. We show that this plasmid can support the replication of the killer toxin-encoding M1 satellite virus in the absence of an L-A double-stranded RNA helper virus itself. This requires ORF2 expression, providing a potential in vivo assay for the RNA polymerase and single-stranded RNA-binding activities of the fusion protein determined by ORF2. ORF1 expression, like a host ski- mutation, can suppress the usual requirement of M1 for the MAK11, MAK18, and MAK27 genes and allow a defective L-A (L-A-E) to support M1 replication. These results suggest that expression of ORF1 from the vector makes the cell a ski- phenocopy. Indeed, expression of ORF1 in a wild-type killer makes it a superkiller, suggesting that a target of the SKI antiviral system may be the major coat protein}, keywords = {0,antiviral,ANTIVIRAL SYSTEM,Capsid,CEREVISIAE,COAT PROTEIN,disease,DNA-Directed RNA Polymerase,DNA-Directed RNA Polymerases,DOUBLE-STRANDED-RNA,ENCODES,enzymology,Escherichia coli,expression,FRAME,FUSION PROTEIN,gene,Genes,Genes-Viral,Genetic,Genetic Vectors,genetics,Genotype,IN-VIVO,Kidney,killer,L-A,La,M1,Mutagenesis,Mutation,nosource,OPEN READING FRAME,Open Reading Frames,PLASMID,Plasmids,polymerase,PROMOTER,protein,Proteins,READING FRAME,Reading Frames,REPLICATION,REQUIRES,Restriction Mapping,Rna,RNA Viruses,RNA-BINDING-PROTEIN,RNA-DEPENDENT RNA POLYMERASE,RNA-dependent RNA polymerases,RNA-Double-Stranded,RNA-POLYMERASE,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,sequence,SKI,Support,Suppression-Genetic,SYSTEM,TARGET,vector,vectors,virus,WILD-TYPE,yeast} }

@article{mitchellExosomeConservedEukaryotic1997, title = {The Exosome: A Conserved Eukaryotic {{RNA}} Processing Complex Containing Multiple 3’–{\(>\)}5’ Exoribonucleases}, author = {Mitchell, P. and Petfalski, E. and Shevchenko, A. and Mann, M. and Tollervey, D.}, year = 1997, month = nov, journal = {Cell}, volume = {91}, number = {4}, eprint = {9390555}, eprinttype = {pubmed}, pages = {457–466}, issn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9390555}, abstract = {We identified a complex in S. cerevisiae, the “exosome,” consisting of the five essential proteins Rrp4p, Rrp41p, Rrp42p, Rrp43p, and Rrp44p (Dis3p). Remarkably, four of these proteins are homologous to characterized bacterial 3’–{\(>\)}5’ exoribonucleases; Rrp44p is homologous to RNase II, while Rrp41p, Rrp42p, and Rrp43p are related to RNase PH. Recombinant Rrp4p, Rrp44p, and Rrp41p are 3’–{\(>\)}5’ exoribonucleases in vitro that have distributive, processive, and phosphorolytic activities, respectively. All components of the exosome are required for 3’ processing of the 5.8S rRNA. Human Rrp4p is found in a comparably sized complex, and expression of the hRRP4 gene in yeast complements the rrp4-1 mutation. We conclude that the exosome constitutes a highly conserved eukaryotic RNA processing complex.}, keywords = {Amino Acid Sequence,Exoribonucleases,Fungal Proteins,Genetic Complementation Test,Hela Cells,Humans,Molecular Sequence Data,Molecular Weight,Multienzyme Complexes,Mutation,nosource,Recombinant Fusion Proteins,RNA Processing- Post-Transcriptional,RNA- Ribosomal- 5.8S,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins} }

@article{shigemotoIdentificationCharacterisationDevelopmentally2001, title = {Identification and Characterisation of a Developmentally Regulated Mammalian Gene That Utilises 21 Programmed Ribosomal Frameshifting}, author = {Shigemoto, K. and Brennan, K. and Walls, E. and Watson, C. J. J. and Stott, DW W. and Rigby, P. W. J. W. J. and Reith, A. D. D.}, year = 2001, journal = {Nucleic Acids Research}, volume = {29}, number = {19}, pages = {4079–4088}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Identification+and+characterisation+of+a+developmentally+regulated+mammalian+gene+that+utilises+-1+programmed+ribosomal+frameshifting#0}, abstract = {Translational recoding of mRNA through a -1 ribosomal slippage mechanism has been observed in RNA viruses and retrotransposons of both eukaryotes and prokaryotes. Whilst this provides a potentially powerful mechanism of gene regulation, the utilization of -1 translational frameshifting in regulating mammalian gene expression has remained obscure. Here we report a mammalian gene, Edr, which provides the first example of -1 translational recoding in a eukaryotic cellular gene. In addition to bearing functional frameshift elements that mediate expression of distinct polypeptides, Edr bears both CCHC zinc-finger and putative aspartyl protease catalytic site retroviral-like motifs, indicative of a relic retroviral-like origin for Edr. These features, coupled with conservation of Edr as a single copy gene in mouse and man and striking spatio-temporal regulation of expression during embryogenesis, suggest that Edr plays a functionally important role in mammalian development.}, keywords = {development,ELEMENTS,expression,frameshift,Frameshifting,gene,Gene Expression,GENE-EXPRESSION,IDENTIFICATION,MECHANISM,mRNA,nosource,recoding,regulation,retrotransposon,ribosomal frameshifting,Rna,RNA Viruses,SLIPPAGE} }

@article{mathewsExpandedSequenceDependence1999, title = {Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of {{RNA}} Secondary Structure1}, author = {Mathews, D. H. and Sabina, J. and Zuker, M. and Turner, D. H.}, year = 1999, month = may, journal = {Journal of Molecular Biology}, volume = {288}, number = {5}, pages = {911–940}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283699927006}, abstract = {An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization. Thermodynamic parameters for the stabilities of secondary structure motifs are revised to include expanded sequence dependence as revealed by recent experiments. Additional algorithmic improvements include reduced search time and storage for multibranch loop free energies and improved imposition of folding constraints. An extended database of 151,503 nt in 955 structures? determined by comparative sequence analysis was assembled to allow optimization of parameters not based on experiments and to test the accuracy of the algorithm. On average, the predicted lowest free energy structure contains 73 % of known base-pairs when domains of fewer than 700 nt are folded; this compares with 64 % accuracy for previous versions of the algorithm and parameters. For a given sequence, a set of 750 generated structures contains one structure that, on average, has 86 % of known base-pairs. Experimental constraints, derived from enzymatic and flavin mononucleotide cleavage, improve the accuracy of structure predictions}, keywords = {0,accuracy,Algorithms,Amino Acid Sequence,analysis,Bacteriophage T4,BASE-PAIR,chemistry,CLEAVAGE,DATABASE,Databases-Factual,DOMAIN,DOMAINS,dynamic programming,Escherichia coli,Flavin Mononucleotide,Kinetics,La,LOOP,MFOLD,Models-Genetic,Models-Statistical,Molecular Sequence Data,MOTIFS,nosource,Nucleic Acid Conformation,pharmacology,PREDICTION,Protein Structure-Secondary,Rna,RNA SECONDARY STRUCTURE,RNA-Ribosomal-5S,search,SECONDARY STRUCTURE,secondary structure prediction,sequence,Sequence Analysis,SEQUENCE-ANALYSIS,stability,structure,support-u.s.gov’t-p.h.s.,Thermodynamics,Time Factors} }

@article{cobucci-ponzanoGeneArchaealAlfucosidase2006, title = {The Gene of an Archaeal {\(\alpha\)}-l-Fucosidase Is Expressed by Translational Frameshifting}, author = {{Cobucci-Ponzano}, B. and Conte, F. and Benelli, D.}, year = 2006, journal = {Nucleic Acids Research}, volume = {34}, number = {15}, pages = {4258}, publisher = {Oxford Univ Press}, doi = {doi:10.1093/nar/gkl574}, url = {http://nar.oxfordjournals.org/content/34/15/4258.short}, abstract = {The standard rules of genetic translational decoding are altered in specific genes by different events that are globally termed recoding. In Archaea recoding has been unequivocally determined so far only for termination codon readthrough events. We study here the mechanism of expression of a gene encoding for a alpha-l-fucosidase from the archaeon Sulfolobus solfataricus (fucA1), which is split in two open reading frames separated by a -1 frameshifting. The expression in Escherichia coli of the wild-type split gene led to the production by frameshifting of full-length polypeptides with an efficiency of 5%. Mutations in the regulatory site where the shift takes place demonstrate that the expression in vivo occurs in a programmed way. Further, we identify a full-length product of fucA1 in S.solfataricus extracts, which translate this gene in vitro by following programmed -1 frameshifting. This is the first experimental demonstration that this kind of recoding is present in Archaea}, keywords = {alpha-L-Fucosidase,Archaea,Codon,decoding,efficiency,Escherichia coli,ESCHERICHIA-COLI,expression,EXTRACTS,FRAME,Frameshift Mutation,Frameshifting,Frameshifting-Ribosomal,gene,Gene Expression Regulation-Archaeal,Genes,Genetic,genetics,IDENTIFY,In Vitro,IN-VITRO,IN-VIVO,La,MECHANISM,Mutation,MUTATIONS,nosource,OPEN READING FRAME,Open Reading Frames,physiology,POLYPEPTIDE,POLYPEPTIDES,PRODUCT,protein,READING FRAME,Reading Frames,readthrough,recoding,REGULATORY SITE,Research Support-Non-U.S.Gov’t,RULES,SITE,Sulfolobus,Sulfolobus solfataricus,termination,TERMINATION CODON,TERMINATION-CODON,TRANSLATIONAL FRAMESHIFTING,WILD-TYPE} }

@article{meskauskasRibosomalProteinL32008, title = {Ribosomal Protein {{L3}} Functions as a `Rocker Switch’ to Aid in Coordinating of Large Subunit-Associated Functions in Eukaryotes and {{Archaea}}}, author = {Meskauskas, A. and Dinman, J. D.}, year = 2008, month = oct, journal = {Nucleic Acids Res.}, volume = {36}, number = {19}, pages = {6175–86}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/36/19/6175.short}, abstract = {Although ribosomal RNAs (rRNAs) comprise the bulk of the ribosome and carry out its main functions, ribosomal proteins also appear to play important structural and functional roles. Many ribosomal proteins contain long, nonglobular domains that extend deep into the rRNA cores. In eukaryotes and Archaea, ribosomal protein L3 contains two such extended domains tethered to a common globular hub, thus providing an excellent model to address basic questions relating to ribosomal protein structure/function relationships. Previous work in our laboratory identified the central ‘W-finger’ extension of yeast L3 in helping to coordinate ribosomal functions. New studies on the ‘N-terminal’ extension in yeast suggest that it works with the W-finger to coordinate opening and closing of the corridor through which the 3’ end of aa-tRNA moves during the process of accommodation. Additionally, the effect of one of the L3 N-terminal extension mutants on the interaction between C75 of the aa-tRNA and G2921 (Escherichia coli G2553) of 25S rRNA provides the first evidence of the effect of a ribosomal protein on aa-tRNA positioning and peptidyltransfer, possibly through the induced fit model. A model is presented describing how all three domains of L3 may function together as a ‘rocker switch’ to coordinate the stepwise processes of translation elongation}, keywords = {3,Archaea,BIOLOGY,DOMAIN,DOMAINS,elongation,Escherichia coli,ESCHERICHIA-COLI,Genetic,genetics,L3,La,microbiology,MODEL,MOF,MOLECULAR-GENETICS,MUTANTS,nosource,protein,Proteins,Ribosomal Proteins,ribosomal RNA,RIBOSOMAL-PROTEIN,RIBOSOMAL-RNA,ribosome,Rna,rRNA,Structural,structure/function,translation,yeast} } % == BibTeX quality report for meskauskasRibosomalProteinL32008: % ? Possibly abbreviated journal title Nucleic Acids Res.

@article{wicknerDoublestrandedRNAViruses1996, title = {Double-Stranded {{RNA}} Viruses of {{Saccharomyces}} Cerevisiae}, author = {Wickner, R. B. B.}, year = 1996, journal = {Microbiology and Molecular Biology Reviews}, volume = {60}, number = {1}, pages = {109–139}, publisher = {Am Soc Microbiol}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.genet.30.1.109 http://mmbr.asm.org/cgi/reprint/60/1/250.pdf}, keywords = {DOUBLE-STRANDED-RNA,nosource,prion,Prions,Review,review article,Rna,RNA Viruses,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,virus,yeast} }

@article{ingoliaGenomeWideTranslationalProfiling2010, title = {Genome-{{Wide Translational Profiling}} by {{Ribosome Footprinting}}}, author = {Ingolia, N. T. T.}, year = 2010, journal = {Methods in Enzymology}, volume = {470}, pages = {119–142}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0076687910700069}, isbn = {9780123751720}, keywords = {nosource} } % == BibTeX quality report for ingoliaGenomeWideTranslationalProfiling2010: % ? Title looks like it was stored in title-case in Zotero

@article{plantRoleProgrammed12008, title = {The Role of Programmed -1 Ribosomal Frameshifting in Coronavirus Propagation}, author = {Plant, E. P. and Dinman, J. D.}, year = 2008, month = sep, journal = {Frontiers in Bioscience}, volume = {13}, pages = {4873–4881}, publisher = {NIH Public Access}, doi = {10.1007/s11240-008-9374-0}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2435135&tool=pmcentrez&rendertype=abstract http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435135/}, abstract = {Coronaviruses have the potential to cause significant economic, agricultural and health problems. The severe acute respiratory syndrome (SARS) associated coronavirus outbreak in late 2002, early 2003 called attention to the potential damage that coronaviruses could cause in the human population. The ensuing research has enlightened many to the molecular biology of coronaviruses. A programmed -1 ribosomal frameshift is required by coronaviruses for the production of the RNA dependent RNA polymerase which in turn is essential for viral replication. The frameshifting signal encoded in the viral genome has additional features that are not essential for frameshifting. Elucidation of the differences between coronavirus frameshift signals and signals from other viruses may help our understanding of these features. Here we summarize current knowledge and add additional insight regarding the function of the programmed -1 ribosomal frameshift signal in the coronavirus lifecycle.}, keywords = {coronavirus,frameshifting,nosource,review,sars} }

@article{yangClassIIHistone2005, title = {Class {{II}} Histone Deacetylases: From Sequence to Function, Regulation, and Clinical Implication}, author = {Yang, XJ X. J. and Gr{'e}goire, S.}, year = 2005, month = apr, journal = {Molecular and cellular biology}, volume = {25}, number = {8}, pages = {2873}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.25.8.2873}, url = {http://mcbasm.academyofeating.com/cgi/content/full/25/8/2873 http://mcb.asm.org/cgi/content/abstract/25/8/2873}, keywords = {nosource} }

@article{salas-marcoDistinctPathsStop2006, title = {Distinct Paths to Stop Codon Reassignment by the Variant-Code Organisms {{Tetrahymena}} and {{Euplotes}}}, author = {{Salas-Marco}, J. and {Fan-Minogue}, H. and Kallmeyer, A. K. and Klobutcher, L. A. and Farabaugh, P. J. and Bedwell, D. M.}, year = 2006, month = jan, journal = { and cellular biology}, volume = {26}, number = {2}, pages = {438}, publisher = {Am Soc Microbiol}, doi = {10.1128/MCB.26.2.438}, url = {http://mcb.asm.org/cgi/content/abstract/26/2/438 http://mcb.asm.org/content/26/2/438.short}, abstract = {The reassignment of stop codons is common among many ciliate species. For example, Tetrahymena species recognize only UGA as a stop codon, while Euplotes species recognize only UAA and UAG as stop codons. Recent studies have shown that domain 1 of the translation termination factor eRF1 mediates stop codon recognition. While it is commonly assumed that changes in domain 1 of ciliate eRF1s are responsible for altered stop codon recognition, this has never been demonstrated in vivo. To carry out such an analysis, we made hybrid proteins that contained eRF1 domain 1 from either Tetrahymena thermophila or Euplotes octocarinatus fused to eRF1 domains 2 and 3 from Saccharomyces cerevisiae. We found that the Tetrahymena hybrid eRF1 efficiently terminated at all three stop codons when expressed in yeast cells, indicating that domain 1 is not the sole determinant of stop codon recognition in Tetrahymena species. In contrast, the Euplotes hybrid facilitated efficient translation termination at UAA and UAG codons but not at the UGA codon. Together, these results indicate that while domain 1 facilitates stop codon recognition, other factors can influence this process. Our findings also indicate that these two ciliate species used distinct approaches to diverge from the universal genetic code}, keywords = {nosource} }

@article{kimExpressionGenesEncoding2005, title = {Expression of Genes Encoding Innate Host Defense Molecules in Normal Human Monocytes in Response to {{Candida}} Albicans}, author = {Kim, HS H. S. and Choi, EH E. H. and Khan, Javed and Roilides, E. and Francesconi, A. and Kasai, M. and Sein, T. and Schaufele, R. L. and Sakurai, K. and Son, C. G. and others}, year = 2005, month = jun, journal = {Infection and immunity}, volume = {73}, number = {6}, pages = {3714}, publisher = {Am Soc Microbiol}, doi = {10.1128/IAI.73.6.3714}, url = {http://iai.asm.org/cgi/content/abstract/73/6/3714 http://iai.asm.org/content/73/6/3714.short}, abstract = {Little is known about the regulation and coordinated expression of genes involved in the innate host response to Candida albicans. We therefore examined the kinetic profile of gene expression of innate host defense molecules in normal human monocytes infected with C. albicans using microarray technology. Freshly isolated peripheral blood monocytes from five healthy donors were incubated with C. albicans for 0 to 18 h in parallel with time-matched uninfected control cells. RNA from monocytes was extracted and amplified for microarray analysis, using a 42,421-gene cDNA chip. Expression of genes encoding proinflammatory cytokines, including tumor necrosis factor alpha, interleukin 1 (IL-1), IL-6, and leukemia inhibitory factor, was markedly enhanced during the first 6 h and coincided with an increase in phagocytosis. Expression of these genes returned to near baseline by 18 h. Genes encoding chemokines, including IL-8; macrophage inflammatory proteins 1, 3, and 4; and monocyte chemoattractant protein 1, also were strongly up-regulated, with peak expression at 4 to 6 h, as were genes encoding chemokine receptors CCR1, CCR5, CCR7, and CXCR5. Expression of genes whose products may protect monocyte viability, such as BCL2-related protein, metallothioneins, CD71, and SOCS3, was up-regulated at 4 to 6 h and remained elevated throughout the 18-h time course. On the other hand, expression of genes encoding T-cell-regulatory molecules (e.g., IL-12, gamma interferon, and transforming growth factor beta) was not significantly affected during the 18-h incubation. Moreover, genes encoding IL-15, the IL-13 receptor (IL-13Ra1), and CD14 were suppressed during the 18-h exposure to C. albicans. Thus, C. albicans is a potent inducer of a dynamic cascade of expression of genes whose products are related to the recruitment, activation, and protection of neutrophils and monocytes}, keywords = {nosource} }

@article{taylorGeneSetCoregulated2005, title = {Gene Set Coregulated by the {{Saccharomyces}} Cerevisiae Nonsense-Mediated {{mRNA}} Decay Pathway}, author = {Taylor, Rachel and Kebaara, B. W. BW and Nazarenus, Tara and Jones, A. and Yamanaka, R. and Uhrenholdt, R. and Wendler, J. P. and Atkin, A. L.}, year = 2005, month = dec, journal = {Eukaryotic cell}, volume = {4}, number = {12}, pages = {2066}, publisher = {Am Soc Microbiol}, doi = {10.1128/EC.4.12.2066}, url = {http://ec.asm.org/content/4/12/2066.short http://ec.asm.org/cgi/content/abstract/4/12/2066}, abstract = {The nonsense-mediated mRNA decay (NMD) pathway has historically been thought of as an RNA surveillance system that degrades mRNAs with premature translation termination codons, but the NMD pathway of Saccharomyces cerevisiae has a second role regulating the decay of some wild-type mRNAs. In S. cerevisiae, a significant number of wild-type mRNAs are affected when NMD is inactivated. These mRNAs are either wild-type NMD substrates or mRNAs whose abundance increases as an indirect consequence of NMD. A current challenge is to sort the mRNAs that accumulate when NMD is inactivated into direct and indirect targets. We have developed a bioinformatics-based approach to address this challenge. Our approach involves using existing genomic and function databases to identify transcription factors whose mRNAs are elevated in NMD-deficient cells and the genes that they regulate. Using this strategy, we have investigated a coregulated set of genes. We have shown that NMD regulates accumulation of ADR1 and GAL4 mRNAs, which encode transcription activators, and that Adr1 is probably a transcription activator of ATS1. This regulation is physiologically significant because overexpression of ADR1 causes a respiratory defect that mimics the defect seen in strains with an inactive NMD pathway. This strategy is significant because it allows us to classify the genes regulated by NMD into functionally related sets, an important step toward understanding the role NMD plays in the normal functioning of yeast cells}, keywords = {nosource} }

@article{zoubenkoNontoxicPokeweedAntiviral2000, title = {A Non-Toxic Pokeweed Antiviral Protein Mutant Inhibits Pathogen Infection via a Novel Salicylic Acid-Independent Pathway}, author = {Zoubenko, O. and Hudak, K. A. and Tumer, N. E.}, year = 2000, journal = {Plant Molecular Biology}, volume = {44}, number = {2}, pages = {219–229}, publisher = {Springer}, url = {http://www.springerlink.com/index/qrj87q3824w32k86.pdf}, keywords = {nosource} }

@article{youngPartialCorrectionSevere1997, title = {Partial Correction of a Severe Molecular Defect in Hemophilia {{A}}, Because of Errors during Expression of the Factor {{VIII}} Gene.}, author = {Young, M. and Inaba, H. and Hoyer, L. W. and Higuchi, M. and Kazazian, H. H. and Antonarakis, S. E. and Jr, H. H. Kazazian}, year = 1997, month = mar, journal = {American journal of human genetics}, volume = {60}, number = {3}, pages = {565}, publisher = {Elsevier}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1712533/}, keywords = {nosource} }

@article{woolfordRibosomeItsSynthesis1991, title = {The Ribosome and Its Synthesis}, author = {Woolford, J. L. and Warner, J. R. and Broach, J. R. and Pringle, J. R. and Jones, E. W. and Jr, JL Woolford}, year = 1991, journal = {The molecular and cellular biology of the yeast}, pages = {587–626}, publisher = {Cold Spring Harbor Press}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:The+ribosome+and+its+synthesis.#0}, keywords = {nosource} }

@article{williamsMutationsStructuralGenes1989, title = {Mutations in the Structural Genes for Eukaryotic Initiation Factors 2`a and 2'a of {{Saccharomyces}} Cerevisiae Disrupt Translational Control of {{GCN4 mRNA}}.}, author = {Williams, N. P. and Hinnebusch, A. G. and Donahue, T. F.}, year = 1989, journal = {Proceedings of the National Academy of Sciences}, volume = {86}, pages = {7515–7519}, keywords = {nosource} }

@article{wengIdentificationCharacterizationMutations1996, title = {Identification and Characterization of Mutations in the {{UPF1}} Gene That Affect Nonsense Suppression and the Formation of the {{Upf}} Protein Complex but Not {{mRNA}} Turnover}, author = {Weng, Y. and Czaplinski, K. and Peltz, S. W.}, year = 1996, journal = {Molecular and Cellular Biology}, volume = {16}, number = {10}, pages = {5491}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/16/10/5491 http://mcb.asm.org/cgi/content/abstract/16/10/5477}, keywords = {nosource} }

@article{weissbrummerMutationHighlyConserved1995, title = {Mutation of a Highly Conserved Base in the Yeast Mitochondrial {{21S rRNA}} Restricts Ribosomal Frameshifting}, author = {Weissbrummer, B. and Zollner, A. and Haid, A. and Thompson, S. and {Weiss-Brummer}, B. and Thomnson, S.}, year = 1995, month = jul, journal = {Molecular and General Genetics MGG}, volume = {248}, number = {2}, pages = {207–216}, publisher = {Springer}, url = {http://www.springerlink.com/index/P8L62203LRV7L513.pdf ISI:A1995RP47700011}, abstract = {A mutation shown to cause resistance to chloramphenicol in Saccharomyces cerevisiae was mapped to the central loop in domain V of the yeast mitochondrial 21S rRNA. The mutant 21S rRNA has a basepair exchange from U-2677 (corresponding to U-2504 in Escherichia coli) to C-2677, which significantly reduces rightward frameshifting at a UU UUU UCC A site in a + 1 U mutant. There is evidence to suggest that this reduction also applies to leftward frameshifting at the same site in a - 1 U mutant. The mutation did not increase the rate of misreading of a number of mitochondrial missense, nonsense or frameshift (of both signs) mutations, and did not adversely affect the synthesis of wild-type mitochondrial gene products. It is suggested here that ribosomes bearing either the C-2677 mutation or its wild-type allele may behave identically during normal decoding and only differ at sites where a ribosomal stall, by permitting non-standard decoding, differentially affects the normal interaction of tRNAs with the chloramphenicol resistant domain V. Chloramphenicol-resistant mutations mapping at two other sites in domain V are described. These mutations had no effect on frameshifting}, keywords = {nosource} }

@article{weijlandModelInteractionElongation1993, title = {Toward a Model for the Interaction between Elongation Factor {{Tu}} and the Ribosome}, author = {Weijland, A. and Parmeggiani, A.}, year = 1993, journal = {Science}, volume = {259}, number = {5099}, pages = {1311}, publisher = {American Association for the Advancement of Science}, url = {http://www.sciencemag.org/content/259/5099/1311.short}, keywords = {nosource} }

@article{warnerHowCommonAre2009, title = {How Common Are {{Extra-ribosomal}} Functions of Ribosomal Proteins?}, author = {Warner, J. R. JR and McIntosh, K. B. KB}, year = 2009, month = apr, journal = {Molecular cell}, volume = {34}, number = {1}, pages = {3–11}, doi = {10.1016/j.molcel.2009.03.006.How}, url = {http://www.sciencedirect.com/science/article/pii/S1097276509001774 PM:19362532}, abstract = {Ribosomal proteins are ubiquitous, abundant, and RNA binding: prime candidates for recruitment to extraribosomal functions. Indeed, they participate in balancing the synthesis of the RNA and protein components of the ribosome itself. An exciting new story is that ribosomal proteins are sentinels for the self-evaluation of cellular health. Perturbation of ribosome synthesis frees ribosomal proteins to interface with the p53 system, leading to cell-cycle arrest or to apoptosis. Yet in only a few cases can we clearly identify the recruitment of ribosomal proteins for other extraribosomal functions. Is this due to a lack of imaginative evolution by cells and viruses, or to a lack of imaginative experiments by molecular biologists?}, keywords = {nosource} }

@article{wangPokeweedAntiviralProtein1999, title = {Pokeweed Antiviral Protein Cleaves Double-Stranded Supercoiled {{DNA}} Using the Same Active Site Required to Depurinate {{rRNA}}}, author = {Wang, P. and Tumer, N. E.}, year = 1999, month = apr, journal = {Nucleic acids research}, volume = {27}, number = {8}, pages = {1900}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/27/8/1900.short}, abstract = {Ribosome-inactivating proteins (RIPs) are N-glycosyl-ases that remove a specific adenine from the sarcin/ricin loop of the large rRNA in a manner analogous to N-glycosylases that are involved in DNA repair. Some RIPs have been reported to remove adenines from single-stranded DNA and cleave double-stranded supercoiled DNA. The molecular basis for the activity of RIPs on double-stranded DNA is not known. Pokeweed antiviral protein (PAP), a single-chain RIP from Phytolacca americana, cleaves supercoiled DNA into relaxed and linear forms. Double-stranded DNA treated with PAP contains apurinic/apyrimidinic (AP) sites due to the removal of adenine. Using an active-site mutant of PAP (PAPx) which does not depurinate rRNA, we present evidence that double-stranded DNA treated with PAPx does not contain AP sites and is not cleaved. These results demonstrate for the first time that PAP cleaves supercoiled double-stranded DNA using the same active site that is required for depurination of rRNA}, keywords = {nosource} }

@article{wainbergEnhancedFidelity3TCselected1996, title = {Enhanced Fidelity of {{3TC-selected}} Mutant {{HIV-1}} Reverse Transcriptase}, author = {Wainberg, M. A. and Drosopoulos, W. C. and Salomon, H. and Hsu, M. and Borkow, G. and Parniak, M. A. and Gu, Z. and Song, Q. and Manne, J. and Islam, S. and others and Castriota, G. and Prasad, V. R.}, year = 1996, month = mar, journal = {Science}, volume = {271}, number = {5253}, pages = {1282}, publisher = {American Association for the Advancement of Science}, url = {http://www.sciencemag.org/content/271/5253/1282.short}, keywords = {nosource} }

@article{voorn-boruwerSequencePAS8Gene1993, title = {Sequence of the {{PAS8}} Gene, the Product of Which Is Essential for Biogenesis of Peroxisomes in {{Saccharomyces}} Cerevisiae}, author = {{Voorn-Boruwer}, T. and {}van der Leij, I. and Hemrika, W. and Distel, B. and Tabak, H. F. and {Voorn-Brouwer}, T.}, year = 1993, journal = {Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression}, volume = {1216}, number = {2}, pages = {325–328}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/016747819390166B}, keywords = {nosource} }

@article{derAffinityElutionPrinciples1974, title = {Affinity Elution: Principles and Applications to Purification of Aminoacyl-{{tRNA}} Synthetases.}, author = {{}von {der}, Haar F. and {}der Haar, F. Von}, year = 1974, journal = {Methods in enzymology}, volume = {34}, eprint = {4449447}, eprinttype = {pubmed}, pages = {163}, url = {http://www.ncbi.nlm.nih.gov/pubmed/4449447 PM:4449447}, keywords = {nosource} }

@article{vermutXIVYeastSequencing1994, title = {{{XIV}}. {{Yeast}} Sequencing Reports. {{Sequence}} of {{MKT1}}, Needed for Propagation of {{M2}} Satellite {{dsRNA}} of the {{L-A}} Virus of {{Saccharomyces}} Cerevisiae}, author = {Vermut, M. and Widner, W. R. and Dinman, J. D. and Wickner, R. B.}, year = 1994, journal = {Yeast}, volume = {10}, number = {11}, pages = {1477–1479}, publisher = {Wiley Online Library}, url = {http://onlinelibrary.wiley.com/doi/10.1002/yea.320101111/abstract}, keywords = {nosource} }

@article{nessADPribosylationElongationFactor1980, title = {{{ADP-ribosylation}} of Elongation Factor 2 by Diphtheria Toxin. {{Isolation}} and Properties of the Novel Ribosyl-Amino Acid and Its Hydrolysis Products.}, author = {Ness, B. G. Van and Howard, J. B. and Bodley, J. W.}, year = 1980, journal = {Journal of Biological Chemistry}, volume = {255}, number = {22}, pages = {10717}, publisher = {ASBMB}, url = {http://www.jbc.org/content/255/22/10717.short}, keywords = {nosource} }

@article{uemuraSuppressionChromosomalMutations1988, title = {Suppression of Chromosomal Mutations Affecting {{M1}} Virus Replication in {{Saccharomyces}} Cerevisiae by a Variant of a Viral {{RNA}} Segment ({{LA}}) That Encodes Coat Protein.}, author = {Uemura, H. and Wickner, R. B.}, year = 1988, journal = {Molecular and cellular biology}, volume = {8}, number = {2}, pages = {938}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/8/2/938}, keywords = {nosource} }

@article{tothEvidenceUniqueFirst1988, title = {Evidence for a Unique First Position Codon-Anticodon Mismatch in Vivo{\(\bullet\)} 1}, author = {Toth, M. J. and Murgola, E. J. and Schimmel, P.}, year = 1988, month = may, journal = {Journal of molecular biology}, volume = {201}, number = {2}, pages = {451–454}, publisher = {Elsevier}, url = {ISI:A1988N543900018 http://linkinghub.elsevier.com/retrieve/pii/0022283688901520}, keywords = {nosource} }

@article{todaThreeDifferentGenes1987, title = {Three Different Genes in {{S}}. Cerevisiae Encode the Catalytic Subunits of the {{cAMP-dependent}} Protein Kinase}, author = {Toda, T. and Comeron, S. and Sass, P. and Zoller, M. and Wigler, M. and Cameron, S.}, year = 1987, journal = {Cell}, volume = {50}, number = {2}, pages = {277–287}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867487902236}, keywords = {nosource} }

@article{tatchellRAS2SaccharomycesCerevisiae1985, title = {{{RAS2}} of {{Saccharomyces}} Cerevisiae Is Required for Gluconeogenic Growth and Proper Response to Nutrient Limitation}, author = {Tatchell, K. and Robinson, L. C. and Breitenbach, M.}, year = 1985, journal = {Proceedings of the National Academy of Sciences}, volume = {82}, number = {11}, pages = {3785}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/82/11/3785.short}, keywords = {nosource} }

@article{stockleinAlteredRibosomalProtein1980, title = {Altered Ribosomal Protein {{L29}} in a Cycloheximide-Resistant Strain of {{Saccharomyces}} Cerevisiae}, author = {St{"o}cklein, W. and Piepersberg, W. and Stocklein, W.}, year = 1980, journal = {Current Genetics}, volume = {1}, number = {3}, pages = {177–183}, publisher = {Springer}, url = {http://www.springerlink.com/index/H12K22212KL96577.pdf}, keywords = {nosource} }

@article{stenebergTranslationalReadthroughHdc1998, title = {Translational Readthrough in the Hdc {{mRNA}} Generates a Novel Branching Inhibitor in {{theDrosophila}} Trachea}, author = {Steneberg, P. and Englund, C. and Kronhamn, J. and Weaver, T. A. and Samakovlis, C. and Stenberg, P.}, year = 1998, journal = {Genes & development}, volume = {12}, number = {7}, pages = {956}, publisher = {Cold Spring Harbor Lab}, url = {http://genesdev.cshlp.org/content/12/7/956.short}, keywords = {nosource} }

@article{stansfieldProductsSUP45ERF11995, title = {The Products of the {{SUP45}} ({{eRF1}}) and {{SUP35}} Genes Interact to Mediate Translation Termination in {{Saccharomyces}} Cerevisiae.}, author = {Stansfield, I. and Jones, K. M. and Kushnirov, V. V. and Dagkesamanskaya, A. R. and Poznyakovski, A. I. and Paushkin, S. V. and Nierras, C. R. and Cox, B. S. and {Ter-Avanesyan}, M. D. and Tuite, M. F.}, year = 1995, journal = {The EMBO Journal}, volume = {14}, number = {17}, pages = {4365}, publisher = {Nature Publishing Group}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC394521/}, keywords = {nosource} }

@article{snijderCarboxylterminalPartPutative1990a, title = {The Carboxyl-Terminal Part of the Putative {{Berne}} Virus Polymerase Is Expressed by Ribosomal Frameshifting and Contains Sequence Motifs Which Indicate That Toro-and Coronaviruses Are Evolutionary Related}, author = {Snijder, E. J. and Denboon, J. A. and Bredenbeek, P. J. and Horzinek, M. C. and Rijnbrand, R. and Spaan, W. J. M. and Boon, J. A.}, year = 1990, journal = {Nucleic acids research}, volume = {18}, number = {15}, pages = {4535}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/18/15/4535.short ISI:A1990DV48300028}, keywords = {nosource} }

@article{selimogluAminoglycosideinducedOtotoxicity1990, title = {Aminoglycoside-Induced Ototoxicity}, author = {Selimoglu, E. and Govaerts, P. J. and Claes, J. and Heyning, PH Van De and Jorens, P. G. and Marquet, J. and Broe, M. E.}, year = 1990, journal = {Toxicology letters}, volume = {52}, number = {3}, pages = {227–251}, publisher = {Elsevier}, url = {PM:17266591 http://linkinghub.elsevier.com/retrieve/pii/037842749090033I}, abstract = {It has long been known that the major irreversible toxicity of aminoglycosides is ototoxicity. Among them, streptomycin and gentamicin are primarily vestibulotoxic, whereas amikacin, neomycin, dihydrosterptomycin, and kanamicin are primarily cochleotoxic. Cochlear damage can produce permanent hearing loss, and damage to the vestibular apparatus results in dizziness, ataxia, and/or nystagmus. Aminoglycosides appear to generate free radicals within the inner ear, with subsequent permanent damage to sensory cells and neurons, resulting in permanent hearing loss. Two mutations in the mitochondrial 12S ribosomal RNA gene have been previously reported to predispose carriers to aminoglycoside-induced ototoxicity. As aminoglycosides are indispensable agents both in the treatment of infections and Meniere’s disease, a great effort has been made to develop strategies to prevent aminoglycoside ototoxicity. Anti-free radical agents, such as salicylate, have been shown to attenuate the ototoxic effects of aminoglycosides. In this paper, incidence, predisposition, mechanism, and prevention of aminoglycoside-induced ototoxicity is discussed in the light of literature data}, keywords = {nosource} }

@article{sedlakDNAMicroarrayAnalysis2003, title = {{{DNA}} Microarray Analysis of the Expression of the Genes Encoding the Major Enzymes in Ethanol Production during Glucose and Xylose Co-Fermentation by Metabolically Engineered {{Saccharomyces}} Yeast}, author = {Sedlak, M. and Edenberg, H. J. and Ho, N. W. Y. and Sedlack, M.}, year = 2003, journal = {Enzyme and microbial technology}, volume = {33}, number = {1}, pages = {19–28}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S014102290300067X}, keywords = {nosource} }

@article{schenaMammalianGlucocorticoidReceptor1988, title = {Mammalian Glucocorticoid Receptor Derivatives Enhance Transcription in Yeast}, author = {Schena, M. and Yamamoto, K. R.}, year = 1988, journal = {Science}, volume = {241}, number = {4868}, pages = {965}, publisher = {American Association for the Advancement of Science}, url = {http://www.sciencemag.org/content/241/4868/965.short}, keywords = {nosource} }

@article{ruiz-echevarriaRNABindingProtein2000, title = {The {{RNA}} Binding Protein {{Pub1}} Modulates the Stability of Transcripts Containing Upstream Open Reading Frames}, author = {{Ruiz-Echevarria}, M. J. and Peltz, S. W. and {Ruiz-Echevarr{}‘{}a}, M. J.}, year = 2000, month = jun, journal = {Cell}, volume = {101}, number = {7}, pages = {741–751}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0092-8674(00)80886-7}, abstract = {The nonsense-mediated mRNA decay (NMD) pathway functions to degrade transcripts containing nonsense codons. Transcripts containing mutations that insert an upstream open reading frame (uORF) in the 5’-UTR are degraded through NMD. However, several naturally occurring uORF-containing transcripts are resistant to NMD. Here we demonstrate that the GCN4 and YAP1 mRNAs, which contain uORFs, harbor a stabilizer element (STE) that prevents rapid NMD by interacting with the RNA binding protein Pub1. Conversely, a uORF-containing mRNA that lacks an STE, such as CPA1, is degraded by the NMD pathway. These results indicate that uORFs can play a pivotal role regulating both translation and turnover and that the Pub1p is a critical factor that modulates the stability of uORF-containing transcripts}, keywords = {nosource} }

@article{ruiz-echevarriaUpf3ProteinComponent1998, title = {The Upf3 Protein Is a Component of the Surveillance Complex That Monitors Both Translation and {{mRNA}} Turnover and Affects Viral Propagation}, author = {{Ruiz-Echevarr{'i}a}, M. J. and Yasenchak, J. M. M. and Han, X. and Dinman, J. D. D. and Peltz, S. W. W. and {Ruiz-Echevarria}, M. J.}, year = 1998, month = jul, journal = {Proceedings of the National Academy of Sciences}, volume = {95}, number = {15}, pages = {8721}, publisher = {National Acad Sciences}, issn = {0027-8424}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=21143&tool=pmcentrez&rendertype=abstract http://www.pnas.org/content/95/15/8721.short}, abstract = {The nonsense-mediated mRNA decay pathway functions to degrade aberrant mRNAs that contain premature translation termination codons. In Saccharomyces cerevisiae, the Upf1, Upf2, and Upf3 proteins have been identified as trans-acting factors involved in this pathway. Recent results have demonstrated that the Upf proteins may also be involved in maintaining the fidelity of several aspects of the translation process. Certain mutations in the UPF1 gene have been shown to affect the efficiency of translation termination at nonsense codons and/or the process of programmed -1 ribosomal frameshifting used by viruses to control their gene expression. Alteration of programmed frameshift efficiencies can affect virus assembly leading to reduced viral titers or elimination of the virus. Here we present evidence that the Upf3 protein also functions to regulate programmed -1 frameshift efficiency. A upf3-Delta strain demonstrates increased sensitivity to the antibiotic paromomycin and increased programmed -1 ribosomal frameshift efficiency resulting in loss of the M1 virus. Based on these observations, we hypothesize that the Upf proteins are part of a surveillance complex that functions to monitor translational fidelity and mRNA turnover.}, pmid = {9671745}, keywords = {Alleles,Cloning,Frameshifting,Fungal Proteins,Fungal Proteins: genetics,Fungal Proteins: metabolism,Messenger,Messenger: genetics,Messenger: metabolism,Molecular,nosource,Paromomycin,Paromomycin: pharmacology,Phenotype,Protein Biosynthesis,Ribosomal,RNA,RNA-Binding Proteins,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae: genetics,Virus Replication,Virus Replication: genetics} }

@article{rosenwaldTransientInhibitionProtein1995, title = {Transient Inhibition of Protein Synthesis Induces Expression of Proto-Oncogenes and Stimulates Resting Cells to Enter the Cell Cycle}, author = {Rosenwald, I. B. and Setkov, N. A. and Kazakov, V. N. and Chen, J. J. and Ryazanov, A. G. and London, I. M. and Epifanova, O. I.}, year = 1995, journal = {Cell proliferation}, volume = {28}, number = {12}, pages = {631–644}, publisher = {Wiley Online Library}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2184.1995.tb00050.x/abstract}, keywords = {nosource} }

@article{romPolyaminesRegulateExpression1994, title = {Polyamines Regulate the Expression of Ornithine Decarboxylase Antizyme in Vitro by Inducing Ribosomal Frame-Shifting}, author = {Rom, E. and Kahana, C.}, year = 1994, journal = {Proceedings of the National Academy of Sciences}, volume = {91}, number = {9}, pages = {3959}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/91/9/3959.short}, keywords = {nosource} }

@article{rilesPhysicalMapsSix1993, title = {Physical {{Maps}} of the {{Six Smallest Chromosomes}} of {{Saccharomyces}} Cerevisiae at a {{Resolution}} of 2.6 {{Kilobase Pairs}}}, author = {Riles, Linda and Dutchik, J. E. James E. James E. and Baktha, Amara and Mccauley, B. K. Brigid K. Brigid K. and Thayer, Edward C. E. C. C. and Leckiet, Mary P. and Braden, Valerie V. V. V. and Depketv, Julie E. and Olsontvs, Maynard V. and Leckie, M. P. P. and Depke, J. E. E. and Olsen, M. V. V. and Olson, M. V. V.}, year = 1993, journal = {Genetics}, volume = {134}, number = {1}, pages = {81–150}, publisher = {Genetics Soc America}, url = {http://www.genetics.org/content/134/1/81.short}, keywords = {Chromosomes,lambda grids,mapping,nosource,Saccharomyces,yeast} }

@article{dahlforsNovelMutantsElongation1990, title = {Novel Mutants of Elongation Factor {{G}}{\(\bullet\)}}, author = {Dahlfors, A. A. Richter and Kurland, C. G. and Dahlfors, A.}, year = 1990, month = oct, journal = {Journal of molecular biology}, volume = {215}, number = {4}, pages = {549–557}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283605801676}, abstract = {A novel mutant form of elongation factor G (EF-G) in Escherichia coli is described. This variant EF-G restricts reading frame errors by a factor of 2 to 3 in vivo at two different positions in a lacIZ fusion. In addition, a conventional fusidic acid resistant (fusR) mutant of EF-G was compared with the restrictive mutant. Both mutants were characterized in vitro in a steady-state poly(U) translating system. The data indicate that the restrictive EF-G variant has an altered interaction with the ribosome both in vivo and in vitro. In contrast, the conventional fusR variant is altered in its interaction with GTP, which is evident in vitro}, keywords = {nosource} }

@article{perez-canadillasHighlyRefinedSolution2000, title = {The Highly Refined Solution Structure of the Cytotoxic Ribonuclease [Alpha]-Sarcin Reveals the Structural Requirements for Substrate Recognition and Ribonucleolytic Activity1}, author = {{P{'e}rez-Ca{}adillas}, J. M. and Santoro, J. and {Campos-Olivas}, R. and Lacadena, J. and others and {Perez-Canadillas}, J. M. and {}del Pozo, A. M. and Gavilanes, J. G. and Rico, M. and Bruix, M.}, year = 2000, month = jun, journal = {Journal of molecular biology}, volume = {299}, number = {4}, pages = {1061–1073}, publisher = {Elsevier}, url = {ISI:000087680400019 http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(00)93813-0}, abstract = {alpha-Sarcin selectively cleaves a single phosphodiester bond in a universally conserved sequence of the major rRNA, that inactivates the ribosome. The elucidation of the three-dimensional solution structure of this 150 residue enzyme is a crucial step towards understanding alpha-sarcin’s conformational stability, ribonucleolytic activity, and its exceptionally high level of specificity. Here, the solution structure has been determined on the basis of 2658 conformationally relevant distances restraints (including stereoespecific assignments) and 119 torsional angular restraints, by nuclear magnetic resonance spectroscopy methods. A total of 60 converged structures have been computed using the program DYANA. The 47 best DYANA structures, following restrained energy minimization by GROMOS, represent the solution structure of alpha-sarcin. The resulting average pairwise root-mean-square-deviation is 0.86 Angstrom for backbone atoms and 1.47 A for all heavy atoms. When the more variable regions are excluded from the analysis, the pairwise root-mean-square deviation drops to 0.50 Angstrom and 1.00 Angstrom, for backbone and heavy atoms, respectively. The alpha-sarcin structure is similar to that reported for restrictocin, although some differences are clearly evident, especially in the loop regions. The average rmsd between the structurally aligned backbones of the 47 final alpha-sarcin structures and the crystal structure of restrictocin is 1.46 Angstrom. On the basis of a docking model constructed with alpha-sarcin solution structure and the crystal structure of a 29-nt RNA containing the sarcin/ricin domain, the regions in the protein that could interact specifically with the substrate have been identified. The structural elements that account for the specificity of RNA recognition are located in two separate regions of the protein. One is composed by residues 51 to 55 and loop 5, and the other region, located more than 11 A away in the structure, is the positively charged segment formed by residues 110 to 114. (C) 2000 Academic Press}, keywords = {nosource} }

@article{perentesisSaccharomycesCerevisiaeElongation1992, title = {Saccharomyces Cerevisiae Elongation Factor 2. {{Genetic}} Cloning, Characterization of Expression, and {{G-domain}} Modeling.}, author = {Perentesis, J. P. and Phan, L. D. and Gleason, W. B. and LaPorte, D. C. and Livingston, K. M. and Bodley, J. W. and Livingston, D. M.}, year = 1992, journal = {Journal of Biological Chemistry}, volume = {267}, number = {2}, pages = {1190}, publisher = {ASBMB}, url = {http://www.jbc.org/content/267/2/1190.short}, keywords = {nosource} }

@article{pelsyEffectsOchreNonsense1984, title = {Effects of Ochre Nonsense Mutations on Yeast {{URA1}} Stability.}, author = {Pelsy, F. and LaCroute, F.}, year = 1984, journal = {Curr.Genet.}, volume = {8}, pages = {277–282}, keywords = {nosource} } % == BibTeX quality report for pelsyEffectsOchreNonsense1984: % ? Possibly abbreviated journal title Curr.Genet.

@article{pedersenCrystallizationYeastElongation2001, title = {Crystallization of the Yeast Elongation Factor Complex {{eEF1A-eEF1B}}}, author = {Pedersen, L. and Andersen, G. R. and Knudsen, C. R.}, year = 2001, month = jan, journal = {Section D: Biological}, volume = {57}, number = {Pt 1}, pages = {159–161}, url = {PM:11134944 http://scripts.iucr.org/cgi-bin/paper?jn0084}, abstract = {Crystals of the Saccharomyces cerevisiae elongation factor eEF1A (formerly EF-1alpha) in complex with a catalytic C-terminal fragment of the nucleotide-exchange factor eEF1Balpha (formerly EF-1beta) were grown by the sitting-drop vapour-diffusion technique, using polyethylene glycol 2000 monomethyl ether as precipitant. Crystals diffract to better than 1.7 A and belong to the space group P2(1)2(1)2(1). The unit-cell parameters of the crystals are sensitive to the choice of cryoprotectant. The structure of the 61 kDa complex was determined with the multiple anomalous dispersion technique using three selenomethionine residues in a 11 kDa eEF1Balpha fragment generated by limited proteolysis of full-length eEF1Balpha expressed in Escherichia coli}, keywords = {nosource} }

@article{parthasarathiGeneticRearrangementsOccurring1995, title = {Genetic Rearrangements Occurring during a Single Cycle of Murine Leukemia Virus Vector Replication: Characterization and Implications}, author = {Parthasarathi, S. and {Varela-Echavarria}, A. and Ron, Y. and Preston, B. D. and Dougherty, J. P.}, year = 1995, journal = {Journal of virology}, volume = {69}, number = {12}, pages = {7991}, publisher = {Am Soc Microbiol}, url = {http://jvi.asm.org/cgi/content/abstract/69/12/7991}, keywords = {nosource} }

@article{ouCloningCharaterizationHuman1987, title = {Cloning and Charaterization of a Human Ribosomal Protein Gene with Enhanced Expression in Fetal and Neoplastic Cells}, author = {Ou, J. H. and Yen, T. S. and Wang, Y. F. and Kam, W. K. and Rutter, W. J.}, year = 1987, journal = {Nucleic acids research}, volume = {15}, number = {21}, pages = {8919}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/15/21/8919.short}, abstract = {Hepatocellular carcinoma is strongly associated with hepatitis B virus carrier patients who usually have HBV sequences integrated in the chromosomal DNA of liver cells. To assess the possible effects of HBV regulatory sequences (e.g., the enhancer) on expression of neighboring host genes we have screened for cellular genes that are both overexpressed and adjacent to integrated HBV sequences in hepatocellular carcinoma cells. The cloned cDNA for one such gene encodes a protein similar to the E. coli L-3 ribosomal protein which is thought to play a role in mRNA binding to the ribosome. The protein encoded by the cDNA localizes to the nucleolus and is also found in ribosomes; possibly it is the mammalian homologue of L-3 (MRL3). The expression of MRL3 is higher in colon carcinoma and lymphoma cell lines than in normal liver, placenta and diploid fibroblasts, and is also higher in fetal than in adult liver. Therefore, MRL3 overexpression seems to be a property of rapidly dividing cells and is not directly linked to oncogenesis}, keywords = {nosource} }

@article{brimacombeStructureFunctionRibosomal1985, title = {Structure and Function of Ribosomal {{RNA}}.}, author = {Brimacombe, R. and Stiege, W. and Noller, H. F. and Green, R. and Heilek, G. and Hoffarth, V. and Huttenhofer, A. and Joseph, S. and Lee, I. and Lieberman, K. and Mankin, A. and Merryman, C. and {.}}, year = 1985, month = nov, journal = {Biochemical Journal}, volume = {229}, number = {1}, pages = {1}, publisher = {Portland Press Ltd}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1145144/}, abstract = {A refined model has been developed for the folding of 16S rRNA in the 30S subunit, based on additional constraints obtained from new experimental approaches. One set of constraints comes from hydroxyl radical footprinting of each of the individual 30S ribosomal proteins, using free Fe(2+)-EDTA complex. A second approach uses localized hydroxyl radical cleavage from a single Fe2+ tethered to unique positions on the surface of single proteins in the 30S subunit. This has been carried out for one position on the surface of protein S4, two on S17, and three on S5. Nucleotides in 16S rRNA that are essential for P-site tRNA binding were identified by a modification interference strategy. Ribosomal subunits were partially inactivated by chemical modification at a low level. Active, partially modified subunits were separated from inactive ones by binding 3’-biotinderivatized tRNA to the 30S subunits and captured with streptavidin beads. Essential bases are those that are unmodified in the active population but modified in the total population. The four essential bases, G926, 2mG966, G1338, and G1401 are a subset of those that are protected from modification by P-site tRNA. They are all located in the cleft of our 30S subunit model. The rRNA neighborhood of the acceptor end of tRNA was probed by hydroxyl radical probing from Fe2+ tethered to the 5’ end of tRNA via an EDTA linker. Cleavage was detected in domains IV, V, and VI of 23S rRNA, but not in 5S or 16S rRNA. The sites were all found to be near bases that were protected from modification by the CCA end of tRNA in earlier experiments, except for a set of E-site cleavages in domain IV and a set of A-site cleavages in the alpha-sarcin loop of domain VI. In vitro genetics was used to demonstrate a base-pairing interaction between tRNA and 23S rRNA. Mutations were introduced at positions C74 and C75 of tRNA and positions 2252 and 2253 of 23S rRNA. Interaction of the CCA end of tRNA with mutant ribosomes was tested using chemical probing in conjunction with allele-specific primer extension. The interaction occurred only when there was a Watson-Crick pairing relationship between positions 74 of tRNA and 2252 of 23S rRNA. Using a novel chimeric in vitro reconstitution method, it was shown that the peptidyl transferase reaction depends on this same Watson-Crick base pair}, keywords = {nosource} }

@article{nissenCrystalStructureTernary1995, title = {Crystal Structure of the Ternary Complex of {{Phe-tRNAPhe}}, {{EF-Tu}}, and a {{GTP}} Analog}, author = {Nissen, P. and Kjeldgaard, M. and Thirup, S. and Polekhina, G. and Reshetnikova, L. and Clark, B. F. C. and Nyborg, J.}, year = 1995, journal = {Science}, volume = {270}, number = {5241}, pages = {1464}, publisher = {American Association for the Advancement of Science}, url = {http://www.sciencemag.org/content/270/5241/1464.short}, keywords = {nosource} }

@article{naldiniVivoGeneDelivery1996, title = {In Vivo Gene Delivery and Stable Transduction of Nondividing Cells by a Lentiviral Vector}, author = {Naldini, L. and Blomer, U. and Gallay, P. and Ory, D. and Mulligan, R. and Gage, F. H. and Verma, I. M. and Trono, D. and Bl{"o}mer, U.}, year = 1996, month = apr, journal = {Science}, volume = {272}, number = {5259}, pages = {263}, publisher = {American Association for the Advancement of Science}, url = {http://www.sciencemag.org/content/272/5259/263.short}, keywords = {nosource} }

@article{nakamuraEmergingUnderstandingTranslation1996, title = {Emerging Understanding of Translation Termination}, author = {Nakamura, Y. and Ito, K. and Isaksson, L. A.}, year = 1996, journal = {Cell}, volume = {87}, number = {2}, pages = {147–150}, publisher = {Cell Press}, url = {http://cat.inist.fr/?aModele=afficheN&cpsidt=11021919}, keywords = {nosource} }

@article{nagaiRNPDomainSequencespecific1995, title = {The {{RNP}} Domain: A Sequence-Specific {{RNA-binding}} Domain Involved in Processing and Transport of {{RNA}}}, author = {Nagai, K. and Oubridge, C. and Ito, N. and Avis, J. and Evans, P.}, year = 1995, month = jun, journal = {Trends in biochemical sciences}, volume = {20}, number = {6}, pages = {235–240}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000400890246}, keywords = {nosource} }

@article{mollenbeckEvolutionProgrammedRibosomal2004, title = {Evolution of {{Programmed Ribosomal Frameshifting}} in the {{TERT Genesof Euplotes}}}, author = {Mollenbeck, M. and Gavin, M. C. and Klobutcher, L. A. and M{"o}llenbeck, M.}, year = 2004, month = jun, journal = {Journal of molecular evolution}, volume = {58}, number = {6}, pages = {701–711}, url = {http://www.springerlink.com/index/9LL4QCAKQYAQ91EW.pdf PM:15461427}, abstract = {A number of recent studies indicate that programmed + 1 ribosomal frameshifting is frequently required for the expression of genes in species of the genus Euplotes. In E. crassus, three genes encoding the telomerase reverse transcriptase (TERT) subunit have been previously found to possess one or two + 1 frameshift sites. To examine the origin of frameshift sites within the Euplotes group, we have isolated segments of the TERT gene from five Euplotes species. Coupled with phylogenetic analysis, the results indicate that one frameshift site in the TERT gene arose late in the evolution of the group. In addition, a novel frameshift site was identified in the TERT gene of E. minuta, a species where frameshifting has not been previously reported. Coupled with other studies, the results indicate that frameshift sites have arisen during the diversification of the euplotids. The results also are discussed in regard to the mutations necessary to generate frameshift sites, and the specialization of TERT protein function that has apparently occurred in E. crassus}, keywords = {nosource} } % == BibTeX quality report for mollenbeckEvolutionProgrammedRibosomal2004: % ? Title looks like it was stored in title-case in Zotero

@article{mereauVivoVitroStructurefunction1997, title = {An in Vivo and in Vitro Structure-Function Analysis of the {{Saccharomyces}} Cerevisiae {{U3A snoRNP}}: Protein-{{RNA}} Contacts and Base-Pair Interaction with the Pre-Ribosomal {{RNA1}}}, author = {M{'e}reau, A. and Fournier, R. and Gr{'e}goire, A. and Mougin, A. and Fabrizio, P. and L{}{"u}hrmann, R. and Branlant, C. and Mereau, A. and Gregoire, A. and Luhrmann, R.}, year = 1997, month = oct, journal = {Journal of molecular biology}, volume = {273}, number = {3}, pages = {552–571}, publisher = {Elsevier}, url = {PM:9356246 http://linkinghub.elsevier.com/retrieve/pii/S0022283697913206}, abstract = {The structure and accessibility of the S. cerevisiae U3A snoRNA was studied in semi-purified U3A snoRNPs using both chemical and enzymatic probes and in vivo using DMS as the probe. The results obtained show that S. cerevisiae U3A snoRNA is composed of a short 5’ domain with two stem-loop structures containing the phylogenetically conserved boxes A’ and A and a large cruciform 3’ domain containing boxes B, C, C’ and D. A precise identification of RNA-protein contacts is provided. Protection by proteins in the snoRNP and in vivo are nearly identical and were exclusively found in the 3’ domain. There are two distinct protein anchoring sites: (i), box C’ and its surrounding region, this site probably includes box D, (ii) the boxes B and C pair and the bases of stem-loop 2 and 4. Box C’ is wrapped by the proteins. RNA-protein interactions are more loose at the level of boxes C and D and a box C and D interaction is preserved in the snoRNP. In accord with this location of the protein binding sites, an in vivo mutational analysis showed that box C’ is important for U3A snoRNA accumulation, whereas mutations in the 5’ domain have little effect on RNA stability. Our in vivo probing experiments strongly suggest that, in exponentially growing cells, most of the U3A snoRNA molecules are involved in the 10- bp interaction with the 5’-ETS region and in two of the interactions recently proposed with 18S rRNA sequences. Our experimental study leads to a slightly revised version of the model of interaction proposed by J. Hughes. Single-stranded segments linking the heterologous helices are highly sensitive to DMS in vivo and their functional importance was tested by a mutational analysis}, keywords = {nosource} }

@article{menningerPeptidylTransferRNA1976, title = {Peptidyl Transfer {{RNA}} Dissociates during Protein Synthesis from Ribosomes of {{Escherichia}} Coli.}, author = {Menninger, J. R.}, year = 1976, journal = {Journal of Biological Chemistry}, volume = {251}, number = {11}, pages = {3392}, publisher = {ASBMB}, url = {http://www.jbc.org/content/251/11/3392.short}, keywords = {nosource} }

@article{menendezIS1473PutativeInsertion1997, title = {{{IS1473}}, a {{Putative Insertion Sequence Identified}} in the {{Plasmid pAO1 fromArthrobacter}} Nicotinovorans: {{Isolation}}, {{Characterization}}, and {{Distribution amongArthrobacterSpecies}}{\(\bullet\)} 1}, author = {Menendez, C. and Igloi, G. L. and Brandsch, R. and Men{'e}ndez, C.}, year = 1997, journal = {Plasmid}, volume = {37}, number = {1}, pages = {35–41}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0147619X9691272X}, keywords = {nosource} }

@article{sturmanMolecularBiologyCoronaviruses1983, title = {The Molecular Biology of Coronaviruses}, author = {Sturman, L. S. and Holmes, K. V. and others}, year = 1983, journal = {Adv. Virus Res}, volume = {28}, pages = {35–112}, url = {PM:16877062 http://books.google.com/books?hl=en&lr=&id=appGdg4QlXQC&oi=fnd&pg=PA35&dq=The+molecular+biology+of+coronaviruses&ots=Zc3FWOtnvw&sig=SWSSan4rOQNGtK5CblnjV_Y1m2g http://books.google.com/books?hl=en&lr=&id=appGdg4QlXQC&oi=fnd&pg=PA35&dq=The+molecular+biology+of+coronaviruses&ots=Zc5GSPxfwv&sig=jE0sVHJSpXjCsZlUc6I0e9C75Vc}, abstract = {Coronaviruses are large, enveloped RNA viruses of both medical and veterinary importance. Interest in this viral family has intensified in the past few years as a result of the identification of a newly emerged coronavirus as the causative agent of severe acute respiratory syndrome (SARS). At the molecular level, coronaviruses employ a variety of unusual strategies to accomplish a complex program of gene expression. Coronavirus replication entails ribosome frameshifting during genome translation, the synthesis of both genomic and multiple subgenomic RNA species, and the assembly of progeny virions by a pathway that is unique among enveloped RNA viruses. Progress in the investigation of these processes has been enhanced by the development of reverse genetic systems, an advance that was heretofore obstructed by the enormous size of the coronavirus genome. This review summarizes both classical and contemporary discoveries in the study of the molecular biology of these infectious agents, with particular emphasis on the nature and recognition of viral receptors, viral RNA synthesis, and the molecular interactions governing virion assembly}, keywords = {nosource} } % == BibTeX quality report for sturmanMolecularBiologyCoronaviruses1983: % ? Possibly abbreviated journal title Adv. Virus Res

@article{marczinkeQbaseAsparaginyltRNADispensable2000, title = {The {{Q-base}} of Asparaginyl-{{tRNA}} Is Dispensable for Efficient-1 Ribosomal Frameshifting in Eukaryotes1}, author = {Marczinke, B. and Hagervall, T. and Brierley, I.}, year = 2000, month = jan, journal = {Journal of Molecular Biology}, volume = {295}, number = {2}, pages = {179–191}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283699933612 ISI:000084778700005}, abstract = {The frameshift signal of the avian coronavirus infectious bronchitis virus (IBV) contains two cis-acting signals essential for efficient frameshifting, a heptameric slippery sequence (UUUAAAC) and an RNA pseudoknot structure located downstream. The frameshift takes place at the slippery sequence with the two ribosome-bound tRNAs slipping back simultaneously by one nucleotide from the zero phase (U UUA AAC) to the -1 phase (UUU AAA). Asparaginyl-tRNA, which decodes the A-site codon AAC, has the modified base Q at the wobble position of the anticodon (5’ QUU 3’) and it has been speculated that Q may be required for frameshifting. To test this, we measured frameshifting in cos cells that had been passaged in growth medium containing calf serum or horse serum. Growth in horse serum, which contains no free queuine, eliminates Q from the cellular tRNA population upon repeated passage. Over ten cell passages, however, we found no significant difference in frameshift efficiency between the cell types, arguing against a role for Q in frameshifting. We confirmed that the cells cultured in horse serum were devoid of Q by purifying tRNAs and assessing their Q-content by tRNA transglycosylase assays and coupled HPLC-mass spectroscopy. Supplementation of the growth medium of cells grown either on horse serum or calf serum with free queuine had no effect on frameshifting either. These findings were recapitulated in an in vitro system using rabbit reticulocyte lysates that had been largely depleted of endogenous tRNAs and resupplemented with Q-free or Q-containing tRNA populations. Thus Q-base is not required for frameshifting at the IBV signal and some other explanation is required to account for the slipperiness of eukaryotic asparaginyl-tRNA. (C) 2000 Academic Press}, keywords = {nosource} }

@article{liangDistributionCloningEukaryotic1993, title = {Distribution and Cloning of Eukaryotic {{mRNAs}} by Means of Differential Display: Refinements and Optimization}, author = {Liang, P. and Pardee, A. B. and Averboukh, L.}, year = 1993, journal = {Nucleic Acids Research}, volume = {21}, number = {14}, pages = {3269}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/21/14/3269.short}, keywords = {nosource} }

@article{levievRoleHighlyConserved1995, title = {Role for the Highly Conserved Region of Domain {{IV}} of 23 {{S-1}} Ike {{rRNA}} in Subunit-Subunit Interactions at the Peptidyl Transferase Centre}, author = {Leviev, I. and Levieva, S. and Garrett, R. A.}, year = 1995, journal = {Nucleic acids research}, volume = {23}, number = {9}, pages = {1512}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/23/9/1512.short}, keywords = {nosource} }

@article{leibowitzVitroProteinSynthesis1991, title = {In Vitro Protein Synthesis.}, author = {Leibowitz, M. J. and Barbone, F. P. and Georgopoulos, D. E.}, year = 1991, journal = {Meth.Enzymol.}, volume = {194}, pages = {536–545}, keywords = {nosource} } % == BibTeX quality report for leibowitzVitroProteinSynthesis1991: % ? Possibly abbreviated journal title Meth.Enzymol.

@article{kontosRibosomalPausingFrameshifter2001, title = {Ribosomal Pausing at a Frameshifter {{RNA}} Pseudoknot Is Sensitive to Reading Phase but Shows Little Correlation with Frameshift Efficiency}, author = {Kontos, H. and Napthine, S. and Brierley, I.}, year = 2001, month = dec, journal = {Molecular and Cellular Biology}, volume = {21}, number = {24}, pages = {8657}, publisher = {Am Soc Microbiol}, doi = {10.1128/​MCB.21.24.8657-8670.2001}, url = {PM:11713298 http://mcb.asm.org/cgi/content/abstract/21/24/8657}, abstract = {Here we investigated ribosomal pausing at sites of programmed -1 ribosomal frameshifting, using translational elongation and ribosome heelprint assays. The site of pausing at the frameshift signal of infectious bronchitis virus (IBV) was determined and was consistent with an RNA pseudoknot-induced pause that placed the ribosomal P- and A- sites over the slippery sequence. Similarly, pausing at the simian retrovirus 1 gag/pol signal, which contains a different kind of frameshifter pseudoknot, also placed the ribosome over the slippery sequence, supporting a role for pausing in frameshifting. However, a simple correlation between pausing and frameshifting was lacking. Firstly, a stem-loop structure closely related to the IBV pseudoknot, although unable to stimulate efficient frameshifting, paused ribosomes to a similar extent and at the same place on the mRNA as a parental pseudoknot. Secondly, an identical pausing pattern was induced by two pseudoknots differing only by a single loop 2 nucleotide yet with different functionalities in frameshifting. The final observation arose from an assessment of the impact of reading phase on pausing. Given that ribosomes advance in triplet fashion, we tested whether the reading frame in which ribosomes encounter an RNA structure (the reading phase) would influence pausing. We found that the reading phase did influence pausing but unexpectedly, the mRNA with the pseudoknot in the phase which gave the least pausing was found to promote frameshifting more efficiently than the other variants. Overall, these experiments support the view that pausing alone is insufficient to mediate frameshifting and additional events are required. The phase dependence of pausing may be indicative of an activity in the ribosome that requires an optimal contact with mRNA secondary structures for efficient unwinding}, keywords = {0,animal,assays,Base Sequence,chemistry,efficiency,elongation,frameshift,Frameshift Mutation,Frameshifting,Infectious bronchitis virus,La,metabolism,Molecular Sequence Data,mRNA,Mutagenesis-Site-Directed,nosource,Nucleic Acid Conformation,pathology,pausing,physiology,Plasmids,pseudoknot,Rabbits,Reticulocytes,retrovirus,ribosomal frameshifting,ribosome,Ribosomes,Rna,RNA PSEUDOKNOT,RNA-Messenger,sequence,SIGNAL,structure,Support,support-non-u.s.gov’t,Time Factors,Translation-Genetic,virology,virus} }

@article{kiparisovStructuralFunctionalAnalysis2005, title = {Structural and Functional Analysis of {{5S rRNA}} in {{Saccharomyces}} Cerevisiae}, author = {Kiparisov, S. and Petrov, A. and Meskauskas, A. and Sergiev, P. V. and Dontsova, O. A. and Dinman, J. D.}, year = 2005, journal = {Mol. Genet. Gen.}, volume = {274}, number = {3}, pages = {235–247}, publisher = {Springer}, abstract = {5S rRNA extends from the central protuberance of the large ribosomal subunit, through the A-site finger, and down to the GTPase-associated center. Here, we present a structure-function analysis of seven 5S rRNA alleles which are sufficient for viability in the yeast Saccharomyces cerevisiae when expressed in the absence of wild-type 5S rRNAs, and extend this analysis using a large bank of mutant alleles that show semi-dominant phenotypes in the presence of wild-type 5S rRNA. This analysis supports the hypothesis that 5S rRNA serves to link together several different functional centers of the ribosome. Data are also presented which suggest that in eukaryotic genomes selection has favored the maintenance of multiple alleles of 5S rRNA, and that these may provide cells with a mechanism to post-transcriptionally regulate gene expression.}, keywords = {5S rRNA,A SITE,A-SITE,Alleles,analysis,CELLS,CEREVISIAE,expression,functional analysis,gene,Gene Expression,GENE-EXPRESSION,Genome,MECHANISM,nosource,Phenotype,RIBOSOMAL-SUBUNIT,ribosome,rRNA,Saccharomyces,Saccharomyces cerevisiae,SACCHAROMYCES-CEREVISIAE,SELECTION,Structural,SUBUNIT,Support,WILD-TYPE,yeast} } % == BibTeX quality report for kiparisovStructuralFunctionalAnalysis2005: % ? Possibly abbreviated journal title Mol. Genet. Gen.

@article{johnsonCoordinationGrowthCell1977, title = {Coordination of Growth with Cell Division in the Yeast {{Saccharomyces}} Cerevisiae .}, author = {Johnson, G. C. and Pringle, J. R. and Hartwell, L. H.}, year = 1977, journal = {Exp.Cell.Res.}, volume = {105}, pages = {79–89}, keywords = {nosource} } % == BibTeX quality report for johnsonCoordinationGrowthCell1977: % ? Possibly abbreviated journal title Exp.Cell.Res.

@article{jacksCharacterizationRibosomalFrameshifting1988, title = {Characterization of Ribosomal Frameshifting in {{HIV-1}} Gag-Pol Expression}, author = {Jacks, T. and Power, M. D. and Masiarz, F. R. and Luciw, {PA} and Barr, P. J. and Varmus, H. E.}, year = 1988, journal = {Nature}, volume = {331}, pages = {280–283}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/nature/journal/v331/n6153/abs/331280a0.html}, keywords = {nosource} }

@article{ivanovDrosophilaGeneAntizyme1998, title = {The {{Drosophila}} Gene for Antizyme Requires Ribosomal Frameshifting for Expression and Contains an Intronic Gene for {{snRNP Sm D3}} on the Opposite Strand.}, author = {Ivanov, I. P. P. P. and Simin, K. and Letsou, A. and Atkins, J. F. F. F. and Gesteland, R. F. F. F.}, year = 1998, month = mar, journal = {Molecular and Cellular Biology}, volume = {18}, number = {3}, pages = {1553–1561}, publisher = {Am Soc Microbiol}, issn = {0270-7306}, url = {http://mcb.asm.org/cgi/content/abstract/18/3/1553 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=108870&tool=pmcentrez&rendertype=abstract}, abstract = {Previously, a Drosophila melanogaster sequence with high homology to the sequence for mammalian antizyme (ornithine decarboxylase antizyme) was reported. The present study shows that homology of this coding sequence to its mammalian antizyme counterpart also extends to a 5’ open reading frame (ORF) which encodes the amino-terminal part of antizyme and overlaps the +1 frame (ORF2) that encodes the carboxy-terminal three-quarters of the protein. Ribosomes shift frame from the 5’ ORF to ORF2 with an efficiency regulated by polyamines. At least in mammals, this is part of an autoregulatory circuit. The shift site and 23 of 25 of the flanking nucleotides which are likely important for efficient frameshifting are identical to their mammalian homologs. In the reverse orientation, within one of the introns of the Drosophila antizyme gene, the gene for snRNP Sm D3 is located. Previously, it was shown that two closely linked P-element transposon insertions caused the gutfeeling phenotype of embryonic lethality and aberrant neuronal and muscle cell differentiation. The present work shows that defects in either snRNP Sm D3 or antizyme, or both, are likely causes of the phenotype.}, pmid = {9488472}, keywords = {+1 frameshifting,Amino Acid,Amino Acid Sequence,Animals,antizyme,Base Sequence,Chromosome Mapping,Complementary,DNA,Drosophila,Drosophila melanogaster,Drosophila melanogaster: genetics,expression,Frameshifting,gene,Gene Expression,Genes,Humans,Insect,Introns,Messenger,Molecular Sequence Data,nosource,Open Reading Frames,Protein Biosynthesis,Proteins,Proteins: genetics,Ribonucleoproteins,Ribosomal,ribosomal frameshifting,RNA,Sequence Homology,Single-Stranded,Small Nuclear,Small Nuclear: genetics} }

@article{ikemuraCorrelationAbundanceYeast1982, title = {Correlation between the Abundance of Yeast Transfer {{RNAs}} and the Occurrence of the Respective Codons in Protein Genes. {{Differences}} in Synonymous Codon Choice Patterns of Yeast and {{Escherichia}} Coli with Reference to the Abundance of Isoaccepting Transfer {{R}}}, author = {Ikemura, T.}, year = 1982, month = jul, journal = {J.Mol.Biol}, volume = {158}, number = {4}, pages = {573–597}, url = {PM:6750137}, keywords = {nosource} } % == BibTeX quality report for ikemuraCorrelationAbundanceYeast1982: % ? Possibly abbreviated journal title J.Mol.Biol

@article{hurwitzDifferentialActivationYeast1995, title = {Differential Activation of Yeast Adenylyl Cyclase by {{Ras1}} and {{Ras2}} Depends on the Conserved {{N}} Terminus}, author = {Hurwitz, N. and Segal, M. and Marbach, I. and Levitzki, A.}, year = 1995, journal = {Proceedings of the National Academy of Sciences}, volume = {92}, number = {24}, pages = {11009}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/92/24/11009.short}, keywords = {nosource} }

@article{hurIsolationCharacterizationPokeweed1995, title = {Isolation and Characterization of Pokeweed Antiviral Protein Mutations in {{Saccharomyces}} Cerevisiae: Identification of Residues Important for Toxicity}, author = {Hur, Y. and Hwang, D.-J. and Zoubenko, O. and Coetzer, C. and Uckun, F. M. and Tumer, N. E.}, year = 1995, journal = {Proceedings of the National Academy of Sciences}, volume = {92}, number = {18}, pages = {8448}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/92/18/8448.short}, keywords = {nosource} }

@article{hudsonIdentificationNewLocalized1996, title = {Identification of New Localized {{RNAs}} in the {{Xenopus}} Oocyte by Differential Display {{PCR}}}, author = {Hudson, J. W. and Alarcon, V. B. and Elinson, R. P.}, year = 1996, journal = {Developmental genetics}, volume = {19}, number = {3}, pages = {190–198}, publisher = {Wiley Online Library}, url = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1520-6408(1996)19:3<190::AID-DVG2>3.0.CO;2-4/abstract}, keywords = {nosource} }

@article{huberStructureHelixIII2001, title = {The Structure of Helix {{III}} in {{Xenopus}} Oocyte 5 {{S rRNA}}: An {{RNA}} Stem Containing a Two-Nucleotide Bulge1}, author = {Huber, P. W. and Rife, J. P. and Moore, P. B.}, year = 2001, journal = {Journal of Molecular Biology}, volume = {312}, number = {4}, pages = {823–832}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283601949666}, abstract = {The solution structure of an oligonucleotide containing the helix III sequence from Xenopus oocyte 5 S rRNA has been determined by NMR spectroscopy. Helix III includes two unpaired adenosine residues, flanked on either side by G:C base-pairs, that are required for binding of ribosomal protein L5. The consensus conformation of helix III in the context provided by this oligonucleotide has the two adenosine residues located in the minor groove and stacked upon the 3’ flanking guanosine residue, consistent with biochemical studies of free 5 S rRNA in solution. A distinct break in stacking that occurs between the first adenosine residue of the bulge and the flanking 5’ guanosine residue exposes the base of the adenosine residue in the minor groove and the base of the guanosine residue in the major groove. The major groove of the helix is widened at the site of the unpaired nucleotides and the helix is substantially bent; nonetheless, the G:C base-pairs flanking the bulge are intact. The data indicate that there may be conformational heterogeneity centered in the bulge region. The corresponding adenosine residues in the Haloarcula marismortui 50 S ribosomal subunit form a dinucleotide platform, which is quite different from the motif seen in solution. Thus, the conformation of helix III probably changes when 5 S rRNA is incorporated into the ribosome}, keywords = {nosource} }

@article{huangRoleMetallothioneinDetoxification1987, title = {Role of Metallothionein in Detoxification and Tolerance to Transition Metals.}, author = {Huang, P. C. and Morris, S. and Dinman, J. D. and Pine, R. and Smith, B.}, year = 1987, journal = {Experientia. Supplementum}, volume = {52}, eprint = {2959533}, eprinttype = {pubmed}, pages = {439}, publisher = {Birkhauser Verlag}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2959533}, keywords = {nosource} } % == BibTeX quality report for huangRoleMetallothioneinDetoxification1987: % ? Possibly abbreviated journal title Experientia. Supplementum

@article{hsuYeastCellsLacking1993, title = {Yeast Cells Lacking 5’–{\(>\)} 3’exoribonuclease 1 Contain {{mRNA}} Species That Are Poly ({{A}}) Deficient and Partially Lack the 5’cap Structure.}, author = {Hsu, C. L. and Stevens, A.}, year = 1993, month = aug, journal = {Molecular and cellular biology}, volume = {13}, number = {8}, pages = {4826}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/13/8/4826}, keywords = {nosource} }

@article{hopperTranslationLspeciesDsRNA1977, title = {Translation of the {{L-species dsRNA}} Genome of the Killer-Associated Virus-like Particles of {{Saccharomyces}} Cerevisiae.}, author = {Hopper, J. E. and Bostian, K. A. and Rowe, L. B. and Tipper, D. J.}, year = 1977, journal = {Journal of Biological Chemistry}, volume = {252}, number = {24}, pages = {9010}, publisher = {ASBMB}, url = {http://www.jbc.org/content/252/24/9010.short}, keywords = {nosource} }

@article{hopkinsSimultaneousDNABinding2004, title = {Simultaneous {{DNA Binding}}, {{Bending}}, and {{Base Flipping}}}, author = {Hopkins, B. B. and Reich, N. O.}, year = 2004, journal = {Journal of Biological Chemistry}, volume = {279}, number = {35}, pages = {37049}, publisher = {ASBMB}, url = {PM:15210696 http://www.jbc.org/content/279/35/37049.short}, abstract = {We measured the kinetics of DNA bending by M.EcoRI using DNA labeled at both 5’-ends and observed changes in fluorescence resonance energy transfer. Although known to bend its cognate DNA site, energy transfer is decreased upon enzyme binding. This unanticipated effect is shown to be robust because we observe the identical decrease with different dye pairs, when the dye pairs are placed on the respective 3’-ends, the effect is cofactor- and protein-dependent, and the effect is observed with duplexes ranging from 14 through 17 base pairs. The same labeled DNA shows the anticipated increased energy transfer with EcoRV endonuclease, which also bends this sequence, and no change in energy transfer with EcoRI endonuclease, which leaves this sequence unbent. We interpret these results as evidence for an increased end-to-end distance resulting from M.EcoRI binding, mediated by a mechanism novel for DNA methyltransferases, combining DNA bending and an overall expansion of the DNA duplex. The M.EcoRI protein sequence is poorly accommodated into well defined classes of DNA methyltransferases, both at the level of individual motifs and overall alignment. Interestingly, M.EcoRI has an intercalation motif observed in the FPG DNA glycosylase family of repair enzymes. Enzyme-dependent changes in anisotropy and fluorescence resonance energy transfer have similar rate constants, which are similar to the previously determined rate constant for base flipping; thus, the three processes are nearly coincidental. Similar fluorescence resonance energy transfer experiments following AdoMet-dependent catalysis show that the unbending transition determines the steady state product release kinetics}, keywords = {nosource} } % == BibTeX quality report for hopkinsSimultaneousDNABinding2004: % ? Title looks like it was stored in title-case in Zotero

@article{hinnebuschProteinSynthesisTranslational1991, title = {Protein Synthesis and Translational Control in {{Saccharomyces}} Cerevisiae}, author = {Hinnebusch, A. G.}, year = 1991, journal = {The Molecular Biology of the Yeast Saccharomyces.}, volume = {IV}, pages = {627–736}, publisher = {Cold Spring Harbor Laboratory Press.}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Protein+synthesis+and+translational+control+in+?Saccharomyces+cerevisiae?.#1}, keywords = {nosource} } % == BibTeX quality report for hinnebuschProteinSynthesisTranslational1991: % ? Possibly abbreviated journal title The Molecular Biology of the Yeast Saccharomyces.

@article{heldEscherichiaColi30S1975, title = {Escherichia Coli {{30S}} Ribosomal Proteins Uniquely Required for Assembly.}, author = {Held, W. A. and Nomura, M.}, year = 1975, month = apr, journal = {Journal of Biological Chemistry}, volume = {250}, number = {8}, pages = {3179}, publisher = {ASBMB}, url = {http://www.jbc.org/content/250/8/3179.short}, keywords = {nosource} }

@article{heldAssemblyMapping30S1974, title = {Assembly Mapping of {{30S}} Ribosomal Proteins from {{Escherichia}} Coli}, author = {Held, W. A. and Ballou, B. and Mizushima, S. and Nomura, M.}, year = 1974, month = may, journal = {J. Biol. Chem.}, volume = {249}, number = {10}, pages = {3103–11}, publisher = {ASBMB}, url = {http://www.jbc.org/content/249/10/3103.short}, abstract = {Further studies were performed on the sequence of addition of proteins to 16 S RNA during the in vitro reconstitution of 30 S ribosomal subunits from Escherichia coli. Direct binding of protein S17 to 16 S RNA was studied in detail, and the following results were obtained: (a) under reconstitution conditions, a maximum of approximately 1 mole of S17 is bound per mole of 16 S RNA, either alone, or in the presence of all other 30 S proteins; (b) S17 binds only to 16 S RNA and not to 23 S RNA; and (c) radioactive S17-16 S RNA complexes are directly converted (without dissociation) to 30 S subunits by the addition of excess unlabeled total 30 S proteins. From these results, we conclude that the binding of S17 to 16 S RNA is specific. We have also determined the positions of S15, S16, S17, and S12 in the assembly map and have clarified subsequent interactions depending on these proteins. A revised assembly map is presented which incorporates the additional information obtained from these experimental results}, keywords = {nosource} } % == BibTeX quality report for heldAssemblyMapping30S1974: % ? Possibly abbreviated journal title J. Biol. Chem.

@article{heldReconstitutionEscherichiaColi1973, title = {Reconstitution of {{Escherichia}} Coli {{30S}} Ribosomal Subunits from Purified Molecular Components}, author = {Held, W. A. and Mizushima, S. and Nomura, M.}, year = 1973, journal = {J. Biol. Chem.}, volume = {248}, number = {16}, pages = {5720–30}, publisher = {ASBMB}, url = {http://www.jbc.org/content/248/16/5720.short}, abstract = {Reconstitution of 30 S ribosomal subunits from 16 S RNA and a mixture of purified individual 30 S ribosomal proteins has been studied.Proteins from the 30 S ribosomal subunit of Escherichia coli were purified by a combination of phosphocellulose and DEAE-chromatography, and Sephadex gel filtration. The proteins purified correspond to the 21 proteins generally accepted as 30 S proteins, with the exception of two proteins, P3b and P3c, which correspond to the protein S6 studied by other workers. P3b and P3c are closely related, and one is probably a derivative of the other.Using a mixture of these purified proteins, reconstitution of functionally active 30 S subunits has been demonstrated. Reconstituted particles had higher activities in poly(U)-directed polyphenylalanine synthesis than reference 30 S particles in several experiments. The functional activity of reconstituted particles was also examined in several other assays; these included natural messenger RNA-directed polypeptide synthesis, poly(U)-directed Phe-tRNA binding, AUG-directed fMet-puromycin formation, AUG-directed fMet-tRNA binding, and the binding of termination codon UAA in the presence of chain termination factors. In all cases, activities comparable to reference 30 S subunits were observed. The sedimentation properties and the protein composition of reconstituted particles were also similar to 30 S ribosomal subunits. The kinetics of reconstitution using purified protein mixtures was essentially identical with those of reconstitution using unfractionated 30 S proteins. These results strongly suggest that 21 purified 30 S proteins together with 16 S RNA are sufficient to reconstitute 30 S subunits, and that no essential 30 S components were lost during the fractionation and purification of the 30 S proteins.Single component omission experiments indicated that all purified proteins, except P1(S1) and P3b,c(S6), are required for full functional activity. A requirement for P9a(S16) has been shown in some, but not all, experiments. P3b,c(S6) and P9a(S16) have been shown to be involved in the reconstitution reaction in other experiments (Mizushima, S., and Nomura, M. (1970) Nature 226, 1214; Nomura, M. (1973) Science 179, 864) and therefore are 30 S components. It is still not clear whether P1(S1) should be considered a “true” 30 S protein or a ribosomal-associated “factor.”}, keywords = {nosource} } % == BibTeX quality report for heldReconstitutionEscherichiaColi1973: % ? Possibly abbreviated journal title J. Biol. Chem.

@article{hebertPhosphorylationVitroVivo1977, title = {Phosphorylation in Vitro and in Vivo of {{Ribosomal Proteins}} from {{Saccharomyces}} Cerevisiae}, author = {Hebert, J. and Pierre, M. and LOEB, J. E. and H{'E}BERT, J.}, year = 1977, month = jan, journal = {European Journal of Biochemistry}, volume = {72}, number = {1}, pages = {167–174}, publisher = {Wiley Online Library}, url = {PM:318998 http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1977.tb11236.x/full}, abstract = {Crude ribosomes from Saccharomyces cerevisiae cultures were phosphorylated in vitro when incubated in the presence of [gamma-32P]ATP. Analysis of the ribosomal proteins with two-dimensional electrophoresis revealed that of the 29 proteins identified in the small subunit, only protein S6 was phosphorylated. Of the 37 proteins identified in the large subunit, one was highly phosphorylated (L3) and two only slightly phosphorylated (L11 and L14). The protein kinase activity associated with the ribosomes was extracted with 1 M KCl and was not dependent on adenosine 3’:5’-monophosphate; it preferentially phosphorylated casein and phosvitin, but was less active on histones. Structural ribosomal proteins were also phosphorylated in vivo when the yeast cultures were incubated with [32P]orthophosphate; the radioactivity resistant to hydrolysis by hot perchloric acid was incorporated into the proteins of the two subunits. Radioactive phosphoserine was found by subjecting hydrolysates of ribosomal proteins to high-voltage electrophoresis. After two-dimensional electrophoresis, one poorly phosphorylated protein (S10) was identified in the small subunit. In the large subunit, one protein (L3) was highly labelled, and two proteins (L11 and L24) only slightly labelled}, keywords = {nosource} }

@article{hazzalinP38RKEssential1996, title = {P38/{{RK}} Is Essential for Stress-Induced Nuclear Responses: {{JNK}}/{{SAPKs}} and c-{{Jun}}/{{ATF-2}} Phosphorylation Are Insufficient}, author = {Hazzalin, C. A. and Cano, E. and Cuenda, A. and Barratt, M. J. and Cohen, P.}, year = 1996, journal = {Current Biology}, volume = {6}, number = {8}, pages = {1028–1031}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982202006498}, keywords = {nosource} }

@article{hamilConstitutiveTranscriptionYeast1988, title = {Constitutive Transcription of Yeast Ribosomal Protein Gene {{TCM1}} Is Promoted by Uncommon Cis-and Trans-Acting Elements.}, author = {Hamil, K. G. and Nam, H. G. and Fried, H. M.}, year = 1988, journal = {Molecular and cellular biology}, volume = {8}, number = {10}, pages = {4328}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/8/10/4328}, keywords = {nosource} }

@article{ryazanovElongationFactor2Kinase2002, title = {Elongation Factor-2 Kinase and Its Newly Discovered Relatives}, author = {Ryazanov, A. G.}, year = 2002, journal = {FEBS letters}, volume = {397}, pages = {55–60}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579302022998}, keywords = {nosource} }

@article{haenniBehaviourAcetylphenylalanylSoluble1966, title = {The Behaviour of Acetylphenylalanyl Soluble Ribonucleic Acid in Polyphenylalanine Synthesis}, author = {Haenni, A. L. and Chapeville, F.}, year = 1966, month = jan, journal = {Biochimica et Biophysica Acta (BBA)-Nucleic Acids and Protein Synthesis}, volume = {114}, number = {1}, pages = {135–148}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0005278766902619}, keywords = {nosource} }

@article{gregoryMutationalAnalysis16S2005, title = {Mutational Analysis of {{16S}} and {{23S rRNA}} Genes of {{Thermus}} Thermophilus}, author = {Gregory, ST S. T. and Carr, JF J. F. and {Rodriguez-Correa}, D. and Dahlberg, A. E.}, year = 2005, month = jul, journal = {Journal of bacteriology}, volume = {187}, number = {14}, pages = {4804}, publisher = {Am Soc Microbiol}, doi = {10.1128/JB.187.14.4804}, url = {http://jb.asm.org/cgi/content/abstract/187/14/4804 http://jb.asm.org/content/187/14/4804.short}, abstract = {Structural studies of the ribosome have benefited greatly from the use of organisms adapted to extreme environments. However, little is known about the mechanisms by which ribosomes or other ribonucleoprotein complexes have adapted to functioning under extreme conditions, and it is unclear to what degree mutant phenotypes of extremophiles will resemble those of their counterparts adapted to more moderate environments. It is conceivable that phenotypes of mutations affecting thermophilic ribosomes, for instance, will be influenced by structural adaptations specific to a thermophilic existence. This consideration is particularly important when using crystal structures of thermophilic ribosomes to interpret genetic results from nonextremophilic species. To address this issue, we have conducted a survey of spontaneously arising antibiotic-resistant mutants of the extremely thermophilic bacterium Thermus thermophilus, a species which has featured prominently in ribosome structural studies. We have accumulated over 20 single-base substitutions in T. thermophilus 16S and 23S rRNA, in the decoding site and in the peptidyltransferase active site of the ribosome. These mutations produce phenotypes that are largely identical to those of corresponding mutants of mesophilic organisms encompassing a broad phylogenetic range, suggesting that T. thermophilus may be an ideal model system for the study of ribosome structure and function}, keywords = {nosource} }

@article{gregoryMutationsConservedLoop1999, title = {Mutations in the Conserved {{P}} Loop Perturb the Conformation of Two Structural Elements in the Peptidyl Transferase Center of 23 s Ribosomal {{RNA1}}}, author = {Gregory, S. T. and Dahlberg, A. E.}, year = 1999, month = jan, journal = {Journal of molecular biology}, volume = {285}, number = {4}, pages = {1475–1483}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(98)92410-x}, abstract = {Evidence is presented for the participation of the P loop (nucleotides G2250-C2254) of 23 S rRNA in establishing the tertiary structure of the peptidyl transferase center. Single base substitutions were introduced into the P loop, which participates in peptide bond formation through direct interaction with the CCA end of P site-bound tRNA. These mutations altered the pattern of reactivity of RNA to chemical probes in a structural subdomain encompassing the P loop and extending roughly from G2238 to A2433. Most of the effects on chemical modification in the P loop subdomain occurred near sites of tertiary interactions inferred from comparative sequence analysis, indicating that these mutations perturb the tertiary structure of this region of RNA. Changes in chemical modification were also seen in a subdomain composed of the 2530 loop (nucleotides G2529-A2534) and the A loop (nucleotides U2552-C2556), the latter a site of interaction with the CCA end of A site-bound tRNA. Mutations in the P loop induced effects on chemical modification that were commensurate with the severity of their characterized functional defects in peptide bond formation, tRNA binding and translational fidelity. These results indicate that, in addition to its direct role in peptide bond formation, the P loop contributes to the tertiary structure of the peptidyl transferase center and influences the conformation of both the acceptor and peptidyl tRNA binding sites. (C) 1999 Academic Press}, keywords = {nosource} }

@article{gregoryMolecularBasisDiamond2007, title = {Molecular Basis of {{Diamond}}–{{Blackfan}} Anemia: Structure and Function Analysis of {{RPS19}}}, author = {Gregory, L. A. and {Aguissa-Tour{'e}}, A. H. and Pinaud, N. and Legrand, P. and Gleizes, P. E. and Fribourg, S.}, year = 2007, journal = {Nucleic Acids Research}, volume = {35}, number = {17}, pages = {5913}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/35/17/5913.short}, abstract = {Diamond-Blackfan anemia (DBA) is a rare congenital disease linked to mutations in the ribosomal protein genes rps19, rps24 and rps17. It belongs to the emerging class of ribosomal disorders. To understand the impact of DBA mutations on RPS19 function, we have solved the crystal structure of RPS19 from Pyrococcus abyssi. The protein forms a five alpha-helix bundle organized around a central amphipathic alpha-helix, which corresponds to the DBA mutation hot spot. From the structure, we classify DBA mutations relative to their respective impact on protein folding (class I) or on surface properties (class II). Class II mutations cluster into two conserved basic patches. In vivo analysis in yeast demonstrates an essential role for class II residues in the incorporation into pre-40S ribosomal particles. This data indicate that missense mutations in DBA primarily affect the capacity of the protein to be incorporated into pre-ribosomes, thus blocking maturation of the pre-40S particles}, keywords = {nosource} }

@article{greenMutationsNucleotidesG22511997, title = {Mutations at Nucleotides {{G2251}} and {{U2585}} of 23 {{S rRNA}} Perturb the Peptidyl Transferase Center of the Ribosome1}, author = {Green, R. and Samaha, R. R. and Noller, H. F.}, year = 1997, month = feb, journal = {Journal of molecular biology}, volume = {266}, number = {1}, pages = {40–50}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(96)90780-9}, abstract = {Previous experiments have shown that the phylogenetically conserved G2252 of 23 S rRNA forms a Watson-Crick base-pair with C74 of peptidyl-tRNA. In the studies presented here, site-directed mutations were introduced at two other conserved positions in 23 S rRNA, G2251 and U2585, that were previously implicated in interaction of the CCA acceptor end of tRNA with the 50 S subunit P site. The mutant 23 S rRNAs were characterized by determining (1) the in vivo phenotypes, (2) the ability of mutant ribosomes to bind tRNA oligonucleotide fragments in vitro, using footprinting with allele-specific primer extension and (3) the ability of mutant ribosomes to catalyze peptide bond formation using a chimeric reconstitution approach. Mutations at either position confer a dominant lethal phenotype when the mutant 23 S rRNA is coexpressed with the endogenous wild-type 23 S rRNA. Mutations at 2585 disrupt binding of the wild-type (CCA) tRNA oligonucleotide fragment and cause a modest decrease in the peptidyl transferase activity of reconstituted ribosomes. By contrast, mutations at 2251 abolish both binding of the wild-type (CCA) tRNA fragment and peptidyl transferase activity using the wild-type tRNA fragment. In neither case was the loss of binding or peptidyl transferase activity suppressed by mutations in the tRNA oligonucleotide fragment. Chemical modification analysis revealed that mutations at 2251 perturb the reactivity of bases 2584 to 2586, providing further evidence that the 2250 loop of 23 S rRNA interacts, either directly or indirectly, with the 2585 region in the central loop of domain V of 23 S rRNA. (C) 1997 Academic Press Limited}, keywords = {nosource} }

@article{greenIdentificationNovelVertebrate1996, title = {Identification of a Novel Vertebrate Circadian Clock-Regulated Gene Encoding the Protein Nocturnin}, author = {Green, C. B. and Besharse, J. C.}, year = 1996, month = dec, journal = {Proceedings of the National Academy of Sciences}, volume = {93}, number = {25}, pages = {14884}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/93/25/14884.short}, keywords = {nosource} }

@article{grantMappingTrichoderminResistance1976, title = {Mapping of Trichodermin Resistance in {{Saccharomyces}} Cerevisiae: A Genetic Locus for a Component of the {{60S}} Ribsomal Subunit}, author = {Grant, P. G. and Schindler, D. and Davies, J. E.}, year = 1976, journal = {Genetics}, volume = {83}, number = {4}, pages = {667}, publisher = {Genetics Society of America}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1213542/}, abstract = {Resistance to the protein synthesis inhibitor trichodermin in Saccharomyces cerevisiae has been studied. A single recessive nuclear gene was responsible for resistance. The resistance locus, tcm1 was found to be closely linked (1 centi-morgan) to the locus pet 17 on the right arm of chromosome XV. The mutation to trichodermin resistance conferred resistance to other 12,13-epoxytrichothecenes and to the structurally unrelated antibiotic anisomycin.}, keywords = {nosource} }

@article{graberProbabilisticPredictionSaccharomyces2002, title = {Probabilistic Prediction of {{Saccharomyces}} Cerevisiae {{mRNA}} 3{\(\prime\)}-Processing Sites}, author = {Graber, J. H. and McAllister, G. D. and Smith, T. F.}, year = 2002, month = apr, journal = {Nucleic acids research}, volume = {30}, number = {8}, pages = {1851}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/30/8/1851.short}, abstract = {We present a tool for the prediction of mRNA 3’-processing (cleavage and polyadenylation) sites in the yeast Saccharomyces cerevisiae, based on a discrete state-space model or hidden Markov model. Comparison of predicted sites with experimentally verified 3’-processing sites indicates good agreement. All predicted or known yeast genes were analyzed to find probable 3’-processing sites. Known alternative 3’-processing sites, both within the 3’-untranslated region and within the protein coding sequence were successfully identified, leading to the possibility of prediction of previously unknown alternative sites. The lack of an apparent 3’-processing site calls into question the validity of some predicted genes. This is specifically investigated for predicted genes with overlapping coding sequences}, keywords = {nosource} }

@article{gormanHighEfficiencyGene1984, title = {High Efficiency Gene Transfer into Mammalian Cells}, author = {Gorman, C. M. and Lane, D. P. and Rigby, P. W. J.}, year = 1984, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, volume = {307}, number = {1132}, eprint = {2990215}, eprinttype = {jstor}, pages = {343–346}, publisher = {JSTOR}, url = {http://www.jstor.org/stable/2990215}, keywords = {nosource} } % == BibTeX quality report for gormanHighEfficiencyGene1984: % ? Possibly abbreviated journal title Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences

@article{gonzalezSolutionStructureThermodynamics1999, title = {Solution Structure and Thermodynamics of a Divalent Metal Ion Binding Site in an {{RNA}} Pseudokno1}, author = {Gonzalez, R. L. and Tinoco, I. Jr and Jr, R. L. Gonzalez and Jr, I. Tinoco}, year = 1999, month = jun, journal = {Journal of molecular biology}, volume = {289}, number = {5}, pages = {1267–1282}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283699928413}, abstract = {Identification and characterization of a metal ion binding site in an RNA pseudoknot was accomplished using cobalt (III) hexammine, Co(NH3)63+, as a probe for magnesium (II) hexahydrate, Mg(H2O)62+, in nuclear magnetic resonance (NMR) structural studies. The pseudoknot causes efficient -1 ribosomal frameshifting in mouse mammary tumor virus. Divalent metal ions, such as Mg2+, are critical for RNA structure and function; Mg2+preferentially stabilizes the pseudoknot relative to its constituent hairpins. The use of Co(NH3)63+as a substitute for Mg2+was investigated by ultraviolet absorbance melting curves, NMR titrations of the imino protons, and analysis of NMR spectra in the presence of Mg2+or Co (NH3)63+. The structure of the pseudoknot-Co(NH3)63+complex reveals an ion-binding pocket formed by a short, two-nucleotide loop and the major groove of a stem. Co(NH3)63+stabilizes the sharp loop-to-stem turn and reduces the electrostatic repulsion of the phosphates in three proximal strands. Hydrogen bonds are identified between the Co(NH3)63+protons and non- bridging phosphate oxygen atoms, 2’ hydroxyl groups, and nitrogen and oxygen acceptors on the bases. The binding site is significantly different from that previously characterized in the major groove surface of tandem G.U base-pairs, but is similar to those observed in crystal structures of a fragment of the 5 S rRNA and the P5c helix of the Tetrahymena thermophila group I intron. Changes in chemical shifts occurred at the same pseudoknot protons on addition of Mg2+as on addition of Co(NH3)63+, indicating that both ions bind at the same site. Ion binding dissociation constants of approximately 0.6 mM and 5 mM (in 200 mM Na+and a temperature of 15 degrees C) were obtained for Co(NH3)63+and Mg2+, respectively, from the change in chemical shift as a function of metal ion concentration. An extensive array of non- sequence-specific hydrogen bond acceptors coupled with conserved structural elements within the binding pocket suggest a general mode of divalent metal ion stabilization of this type of frameshifter pseudoknot. These results provide new thermodynamic and structural insights into the role divalent metal ions play in stabilizing RNA tertiary structural motifs such as pseudoknots. Copyright 1999 Academic Press}, keywords = {nosource} }

@article{goebel3CisactingGenomic2004, title = {The 3{\(\prime\)} Cis-Acting Genomic Replication Element of the Severe Acute Respiratory Syndrome Coronavirus Can Function in the Murine Coronavirus Genome}, author = {Goebel, S. J. and Taylor, J. and Masters, P. S.}, year = 2004, month = jul, journal = {Journal of virology}, volume = {78}, number = {14}, pages = {7846}, publisher = {American Society for Microbiology (ASM)}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC434098/}, abstract = {The 3’ untranslated region (3’ UTR) of the genome of the severe acute respiratory syndrome coronavirus can functionally replace its counterpart in the prototype group 2 coronavirus mouse hepatitis virus (MHV). By contrast, the 3’ UTRs of representative group 1 or group 3 coronaviruses cannot operate as substitutes for the MHV 3’ UTR}, keywords = {nosource} }

@inproceedings{gluckRibosomalRNAIdentity1993, title = {Ribosomal {{RNA}} Identity Elements for Recognition by Ricin and by Alpha-Sarcin: Mutation in the Putative {{CG}} Pair That Closes a {{GAGA}} Tetraloop.}, booktitle = {Nucleic Acids Symposium Series}, author = {Gluck, A. and Endo, Y. and Wool, I. G.}, year = 1993, month = feb, volume = {22}, eprint = {8247752}, eprinttype = {pubmed}, pages = {165}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8247752}, abstract = {alpha-Sarcin is a ribonuclease that cleaves the phosphodiester bond on the 3’ side of G4325 in 28S rRNA; ricin A-chain is a RNA N-glycosidase that depurinates the 5’ adjacent A4324. These single covalent modifications inactivate the ribosome. An oligoribonucleotide that reproduces the structure of the sarcin/ricin domain in 28S rRNA was synthesized and mutations were constructed in the 5’ C and the 3’ G that surround a GAGA tetrad that has the sites of toxin action. Covalent modification of the RNA by ricin, but not by alpha-sarcin, requires a Watson-Crick pair to shut off a putative GAGA tetraloop. Either the recognition elements for the two toxins are different despite their catalyzing covalent modification of adjacent nucleotides in 28S rRNA or there are transitions in the conformation of the alpha- sarcin/ricin domain in 28S rRNA and one conformer is recognized by alpha-sarcin and the other by ricin A-chain}, keywords = {nosource} } % == BibTeX quality report for gluckRibosomalRNAIdentity1993: % ? Unsure about the formatting of the booktitle % ? unused Issue (“29”)

@article{giedrocStructureStabilityFunction2000, title = {Structure, Stability and Function of {{RNA}} Pseudoknots Involved in Stimulating Ribosomal Frameshifting1}, author = {Giedroc, D. P. and Theimer, C. A. and Nixon, P. L.}, year = 2000, month = apr, journal = {Journal of Molecular Biology}, volume = {298}, number = {2}, pages = {167–185}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283600936684}, abstract = {Programmed -1 ribosomal frameshifting has become the subject of increasing interest over the last several years, due in part to the ubiquitous nature of this translational recoding mechanism in pathogenic animal and plant viruses. All cis-acting frameshift signals encoded in mRNAs are minimally composed of two functional elements: a heptanucleotide “slippery sequence” conforming to the general form X XXY YYZ, followed by an RNA structural element, usually an H-type RNA pseudoknot, positioned an optimal number of nucleotides (5 to 9) downstream. The slippery sequence itself promotes a low level ( approximately 1 %) of frameshifting; however, downstream pseudoknots stimulate this process significantly, in some cases up to 30 to 50 %. Although the precise molecular mechanism of stimulation of frameshifting remains poorly understood, significant advances have been made in our knowledge of the three-dimensional structures, thermodynamics of folding, and functional determinants of stimulatory RNA pseudoknots derived from the study of several well-characterized frameshift signals. These studies are summarized here and provide new insights into the structural requirements and mechanism of programmed - 1 ribosomal frameshifting}, keywords = {nosource} }

@article{gerbiExpansionSegmentsRegions1996, title = {Expansion Segments: {{Regions}} of Variable Size That Interrupt the Universal Core Secondary Structure of Ribosomal {{RNA}}}, author = {Gerbi, S. A.}, year = 1996, journal = {Ribosomal RNA: Structure, evolution, processing, and function in protein biosynthesis}, pages = {71–87}, publisher = {CRC Press, Boca Raton, Florida}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Expansion+segment:+regions+of+variable+size+that+interrupt+the+universal+core+secondary+structure+of+ribosomal+RNA.#0}, keywords = {nosource} }

@article{garcia-barrioGCD10TranslationalRepressor1995, title = {{{GCD10}}, a Translational Repressor of {{GCN4}}, Is the {{RNA-binding}} Subunit of Eukaryotic Translation Initiation Factor-3.}, author = {{Garcia-Barrio}, M. T. and Naranda, T. and {}de Aldana, C. R. Vazquez and Cuesta, R. and Hinnebusch, A. G. and Hershey, J. W. B. and Tamame, M.}, year = 1995, journal = {Genes & Development}, volume = {9}, number = {14}, pages = {1781}, publisher = {Cold Spring Harbor Lab}, url = {http://genesdev.cshlp.org/content/9/14/1781.short}, keywords = {nosource} }

@article{gallantRibosomeFrameshiftingHungry1993, title = {Ribosome Frameshifting at Hungry Codons: Sequence Rules, Directional Specificity and Possible Relationship to Mobile Element Behaviour}, author = {Gallant, J. and Lindsley, D.}, year = 1993, month = nov, journal = {Biochemical Society Transactions}, volume = {21}, number = {4}, pages = {817–821}, url = {ISI:A1993MN41200002 http://cat.inist.fr/?aModele=afficheN&cpsidt=4088304}, keywords = {nosource} }

@article{fujimuraRecognitionRNAEncapsidation2000, title = {Recognition of {{RNA}} Encapsidation Signal by the Yeast {{LA}} Double-Stranded {{RNA}} Virus}, author = {Fujimura, T. and Esteban, R.}, year = 2000, month = nov, journal = {Journal of Biological Chemistry}, volume = {275}, number = {47}, pages = {37118}, publisher = {ASBMB}, url = {http://www.jbc.org/content/275/47/37118.short}, abstract = {The encapsidation signal of the yeast L-A virus contains a 24-nucleotide stem-loop structure with a 5-nucleotide loop and an A bulged at the 5’ side of the stem. The Pol part of the Gag-Pol fusion protein is responsible for encapsidation of viral RNA. Opened empty viral particles containing Gag-Pol specifically bind to this encapsidation signal in vitro. We found that binding to empty particles protected the bulged A and the flanking-two nucleotides from cleavage by Fe(II)-EDTA-generated hydroxyl radicals. The five nucleotides of the loop sequence ((4190)GAUCC(4194)) were not protected. However, T1 RNase protection and in vitro mutagenesis experiments indicated that G(4190) is essential for binding. Although the sequence of the other four nucleotides of the loop is not essential, data from RNase protection and chemical modification experiments suggested that C(4194) was also directly involved in binding to empty particles rather than indirectly through its potential base pairing with G(4190). These results suggest that the Pol domain of Gag-Pol contacts the encapsidation signal at two sites: one, the bulged A, and the other, G and C bases at the opening of the loop. These two sites are conserved in the encapsidation signal of M1, a satellite RNA of the L-A virus}, keywords = {nosource} }

@article{fujimuraPolGagPol1992, title = {Pol of Gag–Pol Fusion Protein Required for Encapsidation of Viral {{RNA}} of Yeast {{LA}} Virus}, author = {Fujimura, T. and Ribas, J. C. and Makhov, A. M. and Wickner, R. B.}, year = 1992, month = oct, journal = {Nature}, volume = {359}, number = {6397}, pages = {746–749}, publisher = {Nature Publishing Group}, url = {http://www.nature.com/nature/journal/v359/n6397/abs/359746a0.html}, abstract = {DOUBLE-STRANDED RNA viruses have an RNA-dependent RNA polymerase activity associated with the viral particles which is indispensable for their replication cycle. Using the yeast L-A double-stranded RNA virus we have investigated the mechanism by which the virus encapsidates its genomic RNA and RNA polymerase. The L-A gag gene encodes the principal viral coat protein and the overlapping pol gene is expressed as a gag-pol fusion protein which is formed by a -1 ribosomal frameshift1-3. Here we show that Gag alone is sufficient for virus particle formation, but that it fails to package the viral single-stranded RNA genome. Encapsidation of the viral RNA requires only a part of the Pol region (the N-terminal quarter), which is presumably distinct from the RNA polymerase domain. Given that the Pol region has single-stranded RNA-binding activity, these results are consistent with our LA virus encapsidation model1: the Pol region of the fusion protein binds specifically to the viral genome (+) strand, and the N-terminal gag-encoded region primes polymerization of Gag to form the capsid, thus ensuring the packaging of both the viral genome and the RNA polymerase}, keywords = {nosource} }

@article{fujimuraPortableEncapsidationSignal1990, title = {Portable Encapsidation Signal of the {{LA}} Double-Stranded {{RNA}} Virus of {{S}}. Cerevisiae}, author = {Fujimura, T. and Esteban, R. and Esteban, L. M. and Wickner, R. B.}, year = 1990, journal = {Cell}, volume = {62}, number = {4}, pages = {819–828}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/009286749090125X}, keywords = {nosource} }

@article{fujimuraDoublestrandedRNAGenome1989, title = {The Double-Stranded {{RNA}} Genome of Yeast Virus {{LA}} Encodes Its Own Putative {{RNA}} Polymerase by Fusing Two Open Reading Frames.}, author = {Fujimura, T. and Wickner, R. B. and Icho, T.}, year = 1989, month = jun, journal = {Journal of Biological Chemistry}, volume = {264}, number = {12}, pages = {10872}, publisher = {ASBMB}, url = {http://www.jbc.org/content/264/12/6716.short http://www.jbc.org/content/264/18/10872.short}, keywords = {nosource} }

@article{fujimuraReplicaseViruslikeParticles1988a, title = {Replicase of {{LA}} Virus-like Particles of {{Saccharomyces}} Cerevisiae. {{In}} Vitro Conversion of Exogenous {{LA}} and {{M1}} Single-Stranded {{RNAs}} to Double-Stranded Form.}, author = {Fujimura, T. and Wickner, R. B.}, year = 1988, month = jan, journal = {Journal of Biological Chemistry}, volume = {263}, number = {1}, pages = {454}, publisher = {ASBMB}, url = {http://www.jbc.org/content/263/1/454.short}, keywords = {nosource} }

@article{fujimuraGeneOverlapResults1988, title = {Gene Overlap Results in a Viral Protein Having an {{RNA}} Binding Domain and a Major Coat Protein Domain}, author = {Fujimura, T. and Wickner, R. B.}, year = 1988, journal = {Cell}, volume = {55}, number = {4}, pages = {663–671}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0092867488902255}, keywords = {nosource} }

@article{fujimuraDoublestrandedRNAViruslike1987, title = {{{LA}} Double-Stranded {{RNA}} Viruslike Particle Replication Cycle in {{Saccharomyces}} Cerevisiae: Particle Maturation in Vitro and Effects of Mak10 and Pet18 Mutations.}, author = {Fujimura, T. and Wickner, R. B.}, year = 1987, month = jan, journal = {Molecular and cellular biology}, volume = {7}, number = {1}, pages = {420}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/7/1/420 ISI:A1987F500500051}, keywords = {nosource} }

@article{frohlichYeastCellCycle1991, title = {Yeast Cell Cycle Protein {{CDC48p}} Shows Full-Length Homology to the Mammalian Protein {{VCP}} and Is a Member of a Protein Family Involved in Secretion, Peroxisome Formation, and Gene Expression.}, author = {Fr{"o}hlich, K. U. and Fries, H. W. and R{}{"u}diger, M. and Erdmann, R. and Botstein, D. and Mecke, D.}, year = 1991, journal = {The Journal of cell biology}, volume = {114}, number = {3}, pages = {443}, publisher = {Rockefeller Univ Press}, url = {http://jcb.rupress.org/content/114/3/443.abstract}, keywords = {nosource} }

@article{frankHumanHomologueYeast1996, title = {The Human Homologue of the Yeast {{CHL1}} Gene Is a Novel Keratinocyte Growth Factor-Regulated Gene}, author = {Frank, S. and Werner, S.}, year = 1996, month = oct, journal = {Journal of Biological Chemistry}, volume = {271}, number = {40}, pages = {24337}, publisher = {ASBMB}, url = {http://www.jbc.org/content/271/40/24337.short}, keywords = {nosource} }

@article{frankSingleparticleReconstructionBiological2009, title = {Single-Particle Reconstruction of Biological Macromolecules in Electron Microscopy–30 Years}, author = {Frank, Joachim}, year = 2009, journal = {Quarterly reviews of biophysics}, volume = {42}, number = {3}, pages = {139–158}, publisher = {Cambridge Univ Press}, doi = {10.1017/S0033583509990059.Single-particle}, url = {http://journals.cambridge.org/abstract_S0033583509990059}, keywords = {nosource} }

@article{fourmyStructureSiteEscherichia1996, title = {Structure of the {{A}} Site of {{Escherichia}} Coli {{16S}} Ribosomal {{RNA}} Complexed with an Aminoglycoside Antibiotic}, author = {Fourmy, D. and Recht, M. I. and Blanchard, S. C. and Puglisi, J. D.}, year = 1996, journal = {Science}, volume = {274}, number = {5291}, pages = {1367}, publisher = {American Association for the Advancement of Science}, url = {http://www.sciencemag.org/content/274/5291/1367.short}, keywords = {nosource} }

@article{flowerTranscriptionalOrganizationEscherichia1991, title = {Transcriptional Organization of the {{Escherichia}} Coli {{dnaX}} Gene{\(\bullet\)} 1}, author = {Flower, A. M. and McHenry, C. S.}, year = 1991, month = aug, journal = {Journal of molecular biology}, volume = {220}, number = {3}, pages = {649–658}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/002228369190107H}, keywords = {nosource} }

@article{fillibenProbabilityPlotCorrelation1975, title = {The Probability Plot Correlation Coefficient Test for Normality}, author = {Filliben, J. J.}, year = 1975, journal = {Technometrics}, volume = {17}, number = {1}, eprint = {1268008}, eprinttype = {jstor}, pages = {111–117}, publisher = {JSTOR}, url = {http://www.jstor.org/stable/1268008}, keywords = {nosource} }

@article{fieldsExpressedSequenceTags1994, title = {Expressed Sequence Tags Identify a Human Isolog of the Suil Translation Initiation Factor}, author = {Fields, C. and Adams, M. D.}, year = 1994, journal = {Biochemical and biophysical research communications}, volume = {198}, number = {1}, pages = {288–291}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006291X84710400}, keywords = {nosource} }

@article{fewellRibosomalProteinS141999, title = {Ribosomal {{Protein S14}} of {{Saccharomyces}} Cerevisiae {{Regulates Its Expression}} by {{Binding toRPS14B Pre-mRNA}} and to {{18S rRNA}}}, author = {Fewell, S. W. SW and Jr, J. L. Woolford and Woolford, J. L.}, year = 1999, month = jan, journal = {Molecular and cellular biology}, volume = {19}, number = {1}, pages = {826}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/content/19/1/826.short http://mcb.asm.org/cgi/content/abstract/19/1/826}, abstract = {Production of ribosomal protein S14 in Saccharomyces cerevisiae is coordinated with the rate of ribosome assembly by a feedback mechanism that represses expression of RPS14B. Three-hybrid assays in vivo and filter binding assays in vitro demonstrate that rpS14 directly binds to an RNA stem-loop structure in RPS14B pre-mRNA that is necessary for RPS14B regulation. Moreover, rpS14 binds to a conserved helix in 18S rRNA with approximately five- to sixfold-greater affinity. These results support the model that RPS14B regulation is mediated by direct binding of rpS14 either to its pre-mRNA or to rRNA. Investigation of these interactions with the three-hybrid system reveals two regions of rpS14 that are involved in RNA recognition. D52G and E55G mutations in rpS14 alter the specificity of rpS14 for RNA, as indicated by increased affinity for RPS14B RNA but reduced affinity for the rRNA target. Deletion of the C terminus of rpS14, where multiple antibiotic resistance mutations map, prevents binding of rpS14 to RNA and production of functional 40S subunits. The emetine-resistant protein, rpS14-EmRR, which contains two mutations near the C terminus of rpS14, does not bind either RNA target in the three-hybrid or in vitro assays. This is the first direct demonstration that an antibiotic resistance mutation alters binding of an r protein to rRNA and is consistent with the hypothesis that antibiotic resistance mutations can result from local alterations in rRNA structure}, keywords = {nosource} }

@article{felsensteinExpressionGagpolFusion1988, title = {Expression of the Gag-Pol Fusion Protein of {{Moloney}} Murine Leukemia Virus without Gag Protein Does Not Induce Virion Formation or Proteolytic Processing.}, author = {Felsenstein, K. M. and Goff, S. P.}, year = 1988, journal = {Journal of virology}, volume = {62}, number = {6}, pages = {2179}, publisher = {Am Soc Microbiol}, url = {http://jvi.asm.org/cgi/content/abstract/62/6/2179}, keywords = {nosource} }

@article{estebanThreeDifferentM11986, title = {Three Different {{M1 RNA-containing}} Viruslike Particle Types in {{Saccharomyces}} Cerevisiae: In Vitro {{M1}} Double-Stranded {{RNA}} Synthesis.}, author = {Esteban, R. and Wickner, R. B.}, year = 1986, journal = {Molecular and cellular biology}, volume = {6}, number = {5}, pages = {1552}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/6/5/1552}, keywords = {nosource} }

@article{egertonVCPMammalianHomolog1992, title = {{{VCP}}, the Mammalian Homolog of Cdc48, Is Tyrosine Phosphorylated in Response to {{T}} Cell Antigen Receptor Activation.}, author = {Egerton, M. and Ashe, O. R. and Chen, D. and Druker, B. J. and Burgess, W. H. and Samelson, L. E.}, year = 1992, journal = {The EMBO journal}, volume = {11}, number = {10}, pages = {3533}, publisher = {Nature Publishing Group}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC556811/}, keywords = {nosource} }

@article{eckerPseudoHalfKnot1992, title = {Pseudo–Half-Knot Formation with {{RNA}}}, author = {Ecker, D. J. and Vickers, T. A. and Bruice, T. W. and Freier, S. M. and Jenison, R. D. and Manoharan, M. and Zounes, M.}, year = 1992, journal = {Science}, volume = {257}, number = {5072}, pages = {958}, publisher = {American Association for the Advancement of Science}, url = {http://www.sciencemag.org/content/257/5072/958.short}, abstract = {A pseudo-half-knot can be formed by binding an oligonucleotide asymmetrically to an RNA hairpin loop. This binding motif was used to target the human immunodeficiency virus TAR element, an important viral RNA structure that is the receptor for Tat, the major viral transactivator protein. Oligonucleotides complementary to different halves of the TAR structure bound with greater affinity than molecules designed to bind symmetrically around the hairpin. The pseudo-half-knot-forming oligonucleotides altered the TAR structure so that specific recognition and binding of a Tat-derived peptide was disrupted. This general binding motif may be used to disrupt the structure of regulatory RNA hairpins}, keywords = {nosource} }

@article{easterwoodOrientationsTransferRNA1994, title = {Orientations of Transfer {{RNA}} in the Ribosomal {{A}} and {{P}} Sites}, author = {Easterwood, T. R. and Major, F. and Malhotra, A. and Harvey, S. C.}, year = 1994, journal = {Nucleic acids research}, volume = {22}, number = {18}, pages = {3779}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/22/18/3779.short}, abstract = {In protein synthesis, peptide bond formation requires that the tRNA carrying the amino acid (A site tRNA) contact the tRNA carrying the growing peptide chain (P site tRNA) at their 3’ termini. Two models have been proposed for the orientations of two tRNAs as they would be bound to the mRNA in the ribosome. Viewing the tRNA as an upside down L, anticodon loop pointing down, acceptor stem pointing right, and calling this the front view, the R (Rich) model would have the back of the P site tRNA facing the front of the A site tRNA. In the S (Sundaralingam) model the front of the P site tRNA faces the back of the A site tRNA. Models of two tRNAs bound to mRNA as they would be positioned in the ribosomal A and P sites have been created using MC-SYM, a constraint satisfaction search program designed to build nucleic acid structures. The models incorporate information from fluorescence energy transfer experiments and chemical crosslinks. The models that best answer the constraints are of the S variety, with no R conformations produced consistent with the constraints}, keywords = {nosource} }

@article{dongGeneticIdentificationYeast2008, title = {Genetic Identification of Yeast {{18S rRNA}} Residues Required for Efficient Recruitment of Initiator {{tRNAMet}} and {{AUG}} Selection}, author = {Dong, J. and Nanda, J. S. and Rahman, H. and Pruitt, M. R. and Shin, B. S. and Wong, C. M. and Lorsch, J. R. and Hinnebusch, A. G.}, year = 2008, journal = {Genes & Development}, volume = {22}, number = {16}, pages = {2242}, publisher = {Cold Spring Harbor Lab}, url = {http://genesdev.cshlp.org/content/22/16/2242.short}, abstract = {High-resolution structures of bacterial 70S ribosomes have provided atomic details about mRNA and tRNA binding to the decoding center during elongation, but such information is lacking for preinitiation complexes (PICs). We identified residues in yeast 18S rRNA critical in vivo for recruiting methionyl tRNA(i)(Met) to 40S subunits during initiation by isolating mutations that derepress GCN4 mRNA translation. Several such Gcd(-) mutations alter the A928:U1389 base pair in helix 28 (h28) and allow PICs to scan through the start codons of upstream ORFs that normally repress GCN4 translation. The A928U substitution also impairs TC binding to PICs in a reconstituted system in vitro. Mutation of the bulge G926 in h28 and certain other residues corresponding to direct contacts with the P-site codon or tRNA in bacterial 70S complexes confer Gcd(-) phenotypes that (like A928 substitutions) are suppressed by overexpressing tRNA(i)(Met). Hence, the nonconserved 928:1389 base pair in h28, plus conserved 18S rRNA residues corresponding to P-site contacts in bacterial ribosomes, are critical for efficient Met-tRNA(i)(Met) binding and AUG selection in eukaryotes}, keywords = {nosource} }

@article{donahueGeneticApproachesTranslation2000, title = {Genetic Approaches to Translation Initiation in {{Saccharomyces}} Cerevisiae}, author = {Donahue, T. F.}, year = 2000, journal = {Translational control of gene expression}, volume = {39}, pages = {487}, publisher = {Cold Spring Harbor Laboratory Pr}, url = {http://books.google.com/books?hl=en&lr=&id=InXRuBRGkLYC&oi=fnd&pg=PA487&dq=Genetic+approaches+to+translation+initiation+in+⬚Saccharomyces+cerevisiae⬚.&ots=GMCSNi6j0q&sig=00Z75G45nTcu_0PBal7MtIwvFSQ}, keywords = {nosource} }

@article{donahueGeneticSelectionMutations1988, title = {Genetic Selection for Mutations That Reduce or Abolish Ribosomal Recognition of the {{HIS4}} Translational Initiator Region.}, author = {Donahue, T. F. and Cigan, A. M.}, year = 1988, journal = {Molecular and cellular biology}, volume = {8}, number = {7}, pages = {2955}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/8/7/2955}, keywords = {nosource} }

@article{dinmanTranslatingOldDrugs1998, title = {Translating Old Drugs into New Treatments: Ribosomal Frameshifting as a Target for Antiviral Agents}, author = {Dinman, J. D. and {Ruiz-Echevarria}, M. J. and Peltz, S. W.}, year = 1998, journal = {Trends in Biotechnology}, volume = {16}, number = {4}, pages = {190–196}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0167779997011670}, keywords = {nosource} }

@article{dinmanTranslationalMisreadingMutations1997, title = {Translational Misreading: Mutations in Translation Elongation Factor 1alpha Differentially Affect Programmed Ribosomal Frameshifting and Drug Sensitivity.}, author = {Dinman, J. D. and Kinzy, T. G.}, year = 1997, journal = {RNA}, volume = {3}, number = {8}, pages = {870}, publisher = {Cold Spring Harbor Lab}, url = {http://rnajournal.cshlp.org/content/3/8/870.short}, keywords = {nosource} }

@article{dinmanTranslationalMaintenanceFrame1994, title = {Translational Maintenance of Frame: Mutants of {{Saccharomyces}} Cerevisiae with Altered -1 Ribosomal Frameshifting Efficiencies.}, author = {Dinman, JD J. D. and Wickner, RB R. B.}, year = 1994, journal = {Genetics}, volume = {136}, pages = {75–86}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Translational+maintenance+of+frame:+mutants+of+?Saccharomyces+cerevisiae?+with+altered+-1+ribosomal+frameshifting+efficiencies.#0 http://www.genetics.org/content/136/1/75.short}, keywords = {nosource} }

@article{dinmanOnchocercaVolvulusMolecular1990, title = {Onchocerca Volvulus: {{Molecular}} Cloning, Primary Structure, and Expression of a Microfilarial Surface-Associated Antigen}, author = {Dinman, J. D. and Scott, A. L.}, year = 1990, journal = {Experimental parasitology}, volume = {71}, number = {2}, pages = {176–188}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/001448949090020D}, keywords = {nosource} }

@article{kaltschmidtRibosomalProteinsVII1970, title = {Ribosomal Proteins. {{VII}}* 1:: {{Two-dimensional}} Polyacrylamide Gel Electrophoresis for Fingerprinting of Ribosomal Proteins}, author = {Kaltschmidt, E.}, year = 1970, journal = {Analytical biochemistry}, volume = {109}, number = {4}, pages = {298–302}, url = {http://linkinghub.elsevier.com/retrieve/pii/0003269770903763}, keywords = {nosource} }

@article{denhardtDenhardtSignaltransducingProtein1996, title = {Denhardt {{Signal-transducing}} Protein Phosphorylation Cascades Mediated by {{Ras}}/{{Rho}} Proteins in the Mammalian Cell: The Potential for Multiplex Signalling. [{{Review}}] [228 Refs]}, author = {Denhardt, D. T.}, year = 1996, month = sep, journal = {Biochemical Journal}, volume = {318}, number = {Pt 3}, pages = {729–747}, keywords = {nosource} }

@article{decaturDifferentMechanismsPseudouridine2008, title = {Different Mechanisms for Pseudouridine Formation in Yeast {{5S}} and 5.8 {{S rRNAs}}}, author = {Decatur, W. A. and Schnare, M. N.}, year = 2008, month = may, journal = {Molecular and Cellular Biology}, volume = {28}, number = {10}, pages = {3089}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/28/10/3089}, abstract = {The selection of sites for pseudouridylation in eukaryotic cytoplasmic rRNA occurs by the base pairing of the rRNA with specific guide sequences within the RNA components of box H/ACA small nucleolar ribonucleoproteins (snoRNPs). Forty-four of the 46 pseudouridines (Psis) in the cytoplasmic rRNA of Saccharomyces cerevisiae have been assigned to guide snoRNAs. Here, we examine the mechanism of Psi formation in 5S and 5.8S rRNA in which the unassigned Psis occur. We show that while the formation of the Psi in 5.8S rRNA is associated with snoRNP activity, the pseudouridylation of 5S rRNA is not. The position of the Psi in 5.8S rRNA is guided by snoRNA snR43 by using conserved sequence elements that also function to guide pseudouridylation elsewhere in the large-subunit rRNA; an internal stem-loop that is not part of typical yeast snoRNAs also is conserved in snR43. The multisubstrate synthase Pus7 catalyzes the formation of the Psi in 5S rRNA at a site that conforms to the 7-nucleotide consensus sequence present in other substrates of Pus7. The different mechanisms involved in 5S and 5.8S rRNA pseudouridylation, as well as the multiple specificities of the individual trans factors concerned, suggest possible roles in linking ribosome production to other processes, such as splicing and tRNA synthesis}, keywords = {nosource} }

@article{daviterRenewedFocusTransfer2005, title = {A Renewed Focus on Transfer {{RNA}}}, author = {Daviter, T. and Murphy, F. V. and Ramakrishnan, V.}, year = 2005, month = may, journal = {Science}, volume = {308}, number = {5725}, pages = {1123–1124}, url = {PM:15905389}, keywords = {nosource} }

@article{daumDiverseEffectsHeparin1997, title = {Diverse {{Effects}} of {{Heparin}} on {{Mitogen-Activated Protein Kinase}}–{{Dependent Signal Transduction}} in {{Vascular Smooth Muscle Cells}}}, author = {Daum, G. and Hedin, U. and Wang, Y. and Wang, T. and Clowes, A. W.}, year = 1997, month = jul, journal = {Circulation research}, volume = {81}, number = {1}, pages = {17}, publisher = {Am Heart Assoc}, url = {http://circres.ahajournals.org/cgi/content/abstract/circresaha;81/1/17}, keywords = {nosource} } % == BibTeX quality report for daumDiverseEffectsHeparin1997: % ? Title looks like it was stored in title-case in Zotero

@article{cuiMutationsMOF2SUI11998, title = {Mutations in the {{MOF2}}/{{SUI1}} Gene Affect Both Translation and Nonsense-Mediated {{mRNA}} Decay.}, author = {Cui, Y. and Gonz{'a}lez, C. I. and Kinzy, T. G. and Dinman, J. D. and Peltz, S. W.}, year = 1998, journal = {RNA}, volume = {5}, number = {3}, pages = {1506}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/18/3/1506 http://rnajournal.cshlp.org/content/5/6/794.short}, keywords = {nosource} }

@article{cuiMof41AlleleUPF11996, title = {Mof4-1 Is an Allele of the {{UPF1}}/{{IFS2}} Gene Which Affects Both {{mRNA}} Turnover and-1 Ribosomal Frameshifting Efficiency.}, author = {Cui, Y. and Dinman, J. D. and Peltz, S. W.}, year = 1996, journal = {The EMBO Journal}, volume = {15}, number = {20}, pages = {5726}, publisher = {Nature Publishing Group}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC452316/}, keywords = {nosource} }

@article{culbertsonFrameshiftSuppressionSaccharomyces1980, title = {Frameshift Suppression in {{Saccharomyces}} Cerevisiae. {{II}}. {{Genetic}} Properties of Group {{II}} Suppressors}, author = {Culbertson, M. R. and Underbrink, K. M. and Fink, G. R.}, year = 1980, journal = {Genetics}, volume = {95}, number = {4}, pages = {833}, publisher = {Genetics Soc America}, url = {http://www.genetics.org/cgi/content/abstract/95/4/833}, keywords = {nosource} }

@article{coxFactorYeastProblem1988, title = {The {\(\psi\)} Factor of Yeast: A Problem in Inheritance}, author = {Cox, B. S. and Tuite, M. F. and McLaughlin, C. S.}, year = 1988, journal = {Yeast}, volume = {4}, number = {3}, pages = {159–178}, publisher = {Wiley Online Library}, url = {http://onlinelibrary.wiley.com/doi/10.1002/yea.320040302/pdf}, keywords = {nosource} }

@article{costantinoTRNAMRNAMimicry2007, title = {{{tRNA}}–{{mRNA}} Mimicry Drives Translation Initiation from a Viral {{IRES}}}, author = {Costantino, D. A. and Pfingsten, J. S. and Rambo, R. P. and Kieft, J. S.}, year = 2007, month = jan, journal = {Nat. Struct. Mol. Biol.}, volume = {15}, number = {1}, pages = {57–64}, publisher = {Nature Publishing Group}, url = {PM:18157151 http://www.nature.com/nsmb/journal/v15/n1/abs/nsmb1351.html}, abstract = {Internal ribosome entry site (IRES) RNAs initiate protein synthesis in eukaryotic cells by a noncanonical cap-independent mechanism. IRESes are critical for many pathogenic viruses, but efforts to understand their function are complicated by the diversity of IRES sequences as well as by limited high-resolution structural information. The intergenic region (IGR) IRESes of the Dicistroviridae viruses are powerful model systems to begin to understand IRES function. Here we present the crystal structure of a Dicistroviridae IGR IRES domain that interacts with the ribosome’s decoding groove. We find that this RNA domain precisely mimics the transfer RNA anticodon-messenger RNA codon interaction, and its modeled orientation on the ribosome helps explain translocation without peptide bond formation. When combined with a previous structure, this work completes the first high-resolution description of an IRES RNA and provides insight into how RNAs can manipulate complex biological machines}, keywords = {nosource} } % == BibTeX quality report for costantinoTRNAMRNAMimicry2007: % ? Possibly abbreviated journal title Nat. Struct. Mol. Biol.

@article{costaCloningAnalysisPCRgenerated1994, title = {Cloning and Analysis of {{PCR-generated DNA}} Fragments.}, author = {Costa, G. L. and Grafsky, A. and Weiner, M. P.}, year = 1994, journal = {Genome Research}, pages = {555–580}, publisher = {Cold Spring Harbor Press}, url = {http://genome.cshlp.org/content/3/6/338.short}, keywords = {nosource} }

@article{correllTwoFacesEscherichia1999, title = {The Two Faces of the {{Escherichia}} Coli 23 {{S rRNA}} Sarcin/Ricin Domain: {{The}} Structure at 1.11 Angstrom Resolution {{J}}}, author = {Correll, C. C. and Wool, I. G.}, year = 1999, journal = {Mol. Biol}, volume = {292}, number = {2}, pages = {275–287}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:The+two+faces+of+the+Escherichia+coli+23+S+rRNA+sarcin/ricin+domain:+The+structure+at+1.11+angstrom+resolution#1}, abstract = {The sarcin/ricin domain of 23 S - 28 S ribosomal RNA is essential for protein synthesis because it forms a critical part of the binding site for elongation factors. A crystal structure of an RNA of 27 nucleotides that mimics the domain in Escherichia coli 23 S rRNA was determined at 1.11 Angstrom resolution. The domain folds into a hairpin distorted by four noncanonical base-pairs and one base triple. The fold is stabilized by cross-strand and intra-stand stacking; no intramolecular stabilizing metal ions are observed. This is the first structure to reveal in great detail the geometry and the hydration of two common motifs that are conserved in this rRNA domain, a GAGA tetraloop and a G-bulged cross-strand A stack. Differences in the region connecting these motifs to the stem in the E. coli and in the rat sarcin/ricin domains may contribute to the species-specific binding of elongation factors. Correlation of nucleotide protection data with the structure indicates that the domain has two surfaces. One surface is accessible, lies primarily in the major groove, and is likely to bind the elongation factors. The second lies primarily in the minor groove, and is likely to be buried in the ribosome. This minor groove surface includes the Watson-Crick faces of the cytosine bases in the unusual A2654 C2666 and U2653.C2667 water-mediated base-pairs. (C) 1999 Academic Press}, keywords = {nosource} } % == BibTeX quality report for correllTwoFacesEscherichia1999: % ? Possibly abbreviated journal title Mol. Biol

@article{colganMechanismRegulationMRNA1997, title = {Mechanism and Regulation of {{mRNA}} Polyadenylation}, author = {Colgan, D. F. and Manley, J. L.}, year = 1997, month = nov, journal = {Genes & development}, volume = {11}, number = {21}, pages = {2755}, publisher = {Cold Spring Harbor Lab}, url = {http://genesdev.cshlp.org/content/11/21/2755.short}, keywords = {nosource} }

@article{cohlbergReconstitutionBacillusStearothermophilus1976, title = {Reconstitution of {{Bacillus}} Stearothermophilus {{50S}} Ribosomal Subunits from Purified Molecular Components.}, author = {Cohlberg, J. A. and Nomura, M.}, year = 1976, month = jan, journal = {J. Biol. Chem.}, volume = {251}, number = {1}, pages = {209–21}, publisher = {ASBMB}, url = {http://www.jbc.org/content/251/1/209.short}, keywords = {nosource} } % == BibTeX quality report for cohlbergReconstitutionBacillusStearothermophilus1976: % ? Possibly abbreviated journal title J. Biol. Chem.

@article{coffinHIVPopulationDynamics1995, title = {{{HIV}} Population Dynamics in Vivo: Implications for Genetic Variation, Pathogenesis, and Therapy}, author = {Coffin, J. M.}, year = 1995, month = jan, journal = {Science}, volume = {267}, number = {5197}, pages = {483}, publisher = {American Association for the Advancement of Science}, url = {http://www.sciencemag.org/content/267/5197/483.short}, keywords = {nosource} }

@article{ciganYeastTranslationInitiation1989, title = {Yeast Translation Initiation Suppressor Sui2 Encodes the Alpha Subunit of Eukaryotic Initiation Factor 2 and Shares Sequence Identity with the Human Alpha Subunit}, author = {Cigan, A. M. and Pabich, E. K. and Feng, L. and Donahue, T. F.}, year = 1989, journal = {Proceedings of the National Academy of Sciences}, volume = {86}, number = {8}, pages = {2784}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/86/8/2784.short}, keywords = {nosource} }

@article{chienTwohybridSystemMethod1991, title = {The Two-Hybrid System: A Method to Identify and Clone Genes for Proteins That Interact with a Protein of Interest}, author = {Chien, C.-T. and Bartel, P. L. and Sternglanz, R. and Fields, S.}, year = 1991, journal = {Proceedings of the National Academy of Sciences}, volume = {88}, number = {21}, pages = {9578}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/88/21/9578.short}, keywords = {nosource} }

@article{chengFungalVirusCapsids1994, title = {Fungal {{Virus Capsids}} Are {{Cytoplasmic Compartments}} for the {{Replication}} of {{Double-stranded RNA}}, {{Formed}} as {{Icosahedral Shells}} of {{Asymmetric Gag Dimers}}}, author = {Cheng, R. H. and Caston, J. R. and Wang, G. J. and Gu, F. and Smith, T. J. and Baker, T. S. and Bozarth, R. F. and Trus, B. L. and Cheng, N. and Wickner, R. B. and others}, year = 1994, journal = {Journal of molecular biology}, volume = {244}, number = {3}, pages = {255–258}, publisher = {London, New York, Academic Press.}, url = {http://cryoem.ucsd.edu/publication-pdfs/1994-Cheng-etal-JMB.pdf}, keywords = {nosource} }

@article{chardinHumanSos1Guanine1993, title = {Human {{Sos1}}: A Guanine Nucleotide Exchange Factor for {{Ras}} That Binds to {{GRB2}}}, author = {Chardin, P. and Camonis, J. H. and Gale, N. W. and Aelst, L. Van and Schlessinger, J. and Wigler, M. H. and {Bar-Sagi}, D.}, year = 1993, journal = {Science}, volume = {260}, number = {5112}, pages = {1338}, publisher = {American Association for the Advancement of Science}, url = {http://www.sciencemag.org/content/260/5112/1338.short}, keywords = {nosource} }

@article{chanPhenotypeMutationsBasepair2000, title = {The Phenotype of Mutations of the Base-Pair {{C2658}}{\(\cdot\)} {{G2663}} That Closes the Tetraloop in the Sarcin/Ricin Domain of {{Escherichia}} Coli 23 {{S}} Ribosomal {{RNA1}}}, author = {Chan, Y. L. and Sitikov, A. S. and Wool, I. G.}, year = 2000, month = may, journal = {Journal of molecular biology}, volume = {298}, number = {5}, pages = {795–805}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022-2836(00)93720-3}, abstract = {The sarcin/ricin domain (SRD) in Escherichia coli 23 S rRNA is a part of the site for the association of elongation factors with ribosomes and for that reason is critical for the binding of aminoacyl-tRNA and for translocation during the reiterative elongation reactions of protein synthesis. The SRD has a GAGA tetraloop that is shut off by a Watson-Crick C2658.G2663 pair. The contribution of this pair to the function of the ribosome has been evaluated by constructing mutations in the nucleotides and determining their phenotype. Constitutive expression of a plasmid-encoded rrnB operon with a G2663C transversion mutation that disrupts the Watson-Crick pair was lethal. Double transversion mutations, C2658G.G2663C and C2658A.G2663U, that reverse the polarity of the pyrimidine and the purine but restore the potential to form a canonical pair, were also lethal. Induction of transcription of 23 S rRNA with the same mutations, but encoded in a plasmid with a lambda P-L promoter and expressed at a lower level, retarded growth. The sedimentation profiles of ribosomes with transversion mutations in C2658 and/or G2663 are altered; the ratio of 50 S subunits to 30 S particles is changed and polysomes are reduced. Ribosomes with a G2663C, a C2658G.G2663C, or a C2658A.G2663U mutation in 23 S rRNA were not active in protein synthesis, indeed, they appeared to inhibit the activity of ribosomes with wild-type 23 S rRNA. Transversion mutations in the analogs of C2658 and G2663 decreased binding of EF-G to SRD oligoribonucleotides; the same mutations in 23 S rRNA decreased binding of the factor to intact ribosomes. The most severe phenotype, in growth, in protein synthesis, and in the binding of EF-G, was associated with a C2658G.G2663C mutation; it is surprising that this was more severe than an analogous C2658A.G2663U mutation. A double transition mutation, C2658U.G2663A, which is not known to have occurred in nature, had no effect on the growth of cells or on the function of ribosomes. The lethal phenotype of transversion mutations in C2658 and G2663 appears to derive from a loss of the capacity of ribosomes to bind EF-G and by indirection the EF-Tu ternary complex. (C) 2000 Academic Press}, keywords = {nosource} }

@article{chadaPosttranscriptionalRegulationGlutathione1989, title = {Post-Transcriptional Regulation of Glutathione Peroxidase Gene Expression by Selenium in the {{HL-60}} Human Myeloid Cell Line}, author = {Chada, S. and Whitney, C. and Newburger, P. E.}, year = 1989, month = nov, journal = {Blood}, volume = {74}, number = {7}, pages = {2535}, publisher = {American Society of Hematology}, url = {http://bloodjournal.hematologylibrary.org/content/74/7/2535.short}, abstract = {We have used a cloned cDNA for the major human selenoprotein, glutathione peroxidase (GPx), to assess the mode of regulation of human GPx gene (GPX-1) expression by selenium. When the HL-60 human myeloid cell line is grown in a selenium-deficient medium, GPx enzymatic activity decreases 30-fold compared with selenium-replete cells. Upon return to a medium containing selenium in the form of selenite, GPx activity in the cells starts to increase within 48 hours and reaches maximal (selenium-replete) levels at 7 days. Steady-state immunoreactive protein levels correlate with enzymatic activity. Cycloheximide inhibits the rise in GPx activity that accompanies selenium replenishment, indicating that protein synthesis is required for the increase. However, GPx mRNA levels and the rate of transcription of the human GPx gene change very little and thus appear to be independent of the selenium supply. Thus the human GPx gene appears to be regulated post-transcriptionally, probably cotranslationally, in response to selenium availability}, keywords = {nosource} }

@article{cavalliusSitedirectedMutagenesisYeast1998, title = {Site-Directed Mutagenesis of Yeast {{eEF1A}}}, author = {Cavallius, J. and Merrick, W. C.}, year = 1998, month = oct, journal = {Journal of Biological Chemistry}, volume = {273}, number = {44}, pages = {28752}, publisher = {ASBMB}, url = {PM:9786872 http://www.jbc.org/content/273/44/28752.short}, abstract = {Site-directed mutants of eEF1A (formerly eEF-1alpha) were generated using a modification of a highly versatile yeast shuttle vector (Cavallius, J., Popkie, A. P., and Merrick, W. C. (1997) Biochim. Biophys. Acta 1350, 345-358). The nucleotide specificity sequence NKMD (residues number 153-156) was targeted for mutagenesis, and the following mutants were obtained: N153D (DKMD), N153T (TKMD), D156N (NKMN), D156W (NKMW), and the double mutant N153T,D156E (TKNE). All of the yeast strains containing the mutant eEF1As as the sole source of eEF1A were viable except for the N153D mutant. Most of the purified mutant eEF1As had specific activities in the poly(U)-directed synthesis of polyphenylalanine similar to wild type, although with a Km for GTP increased by 1-2 orders of magnitude. The mutants showed a reduced rate of GTP hydrolysis, and most displayed misincorporation rates greater than wild type. The mutant NKMW eEF1A showed unusual properties. The yeast strain was temperature sensitive for growth, although the purified protein was not. Second, this form of eEF1A was 10-fold more accurate in protein synthesis, and its rate of GTP hydrolysis was about 20% of wild type. In total, the wild-type protein contains the most optimal nucleotide specificity sequence, NKMD, and even subtle changes in this sequence have drastic consequences on eEF1A function in vitro or yeast viability}, keywords = {nosource} }

@article{castonStructureVirusSpecialized1997, title = {Structure of {{LA}} Virus: A Specialized Compartment for the Transcription and Replication of Double-Stranded {{RNA}}}, author = {Caston, J. R. and Trus, B. L. and Booy, F. P. and Wickner, R. B. and Wall, J. S. and Steven, A. C. and Cast{'o}n, J. R.}, year = 1997, journal = {The Journal of cell biology}, volume = {138}, number = {5}, pages = {975}, publisher = {Rockefeller Univ Press}, url = {http://jcb.rupress.org/content/138/5/975.abstract}, keywords = {nosource} }

@article{castilho-valviciusGeneticCharacterizationSaccharomyces1990, title = {Genetic Characterization of the {{Saccharomyces}} Cerevisiae Translational Initiation Suppressors Sui1, Sui2 and {{SUI3}} and Their Effects on {{HIS4}} Expression}, author = {{Castilho-Valvicius}, B. and Yoon, H. and Donahue, T. F. and {Castilho-Valavicius}, B.}, year = 1990, journal = {Genetics}, volume = {124}, number = {3}, pages = {483}, publisher = {Genetics Soc America}, url = {http://www.genetics.org/content/124/3/483.short}, keywords = {nosource} }

@article{carrollTranslationM1Doublestranded1995, title = {Translation and {{M1}} Double-Stranded {{RNA}} Propagation: {{MAK18}}= {{RPL41B}} and Cycloheximide Curing}, author = {Carroll, K. and Wickner, R. B.}, year = 1995, journal = {J.Bacteriol.}, volume = {177}, pages = {2887–2891}, keywords = {nosource} } % == BibTeX quality report for carrollTranslationM1Doublestranded1995: % ? Possibly abbreviated journal title J.Bacteriol.

@article{carlsonTransferRNAModification1999, title = {Transfer {{RNA Modification Status Influences Retroviral Ribosomal Frameshifting}}* 1}, author = {Carlson, B. A. and Kwon, S. Y. and Chamorro, M. and Oroszlan, S.}, year = 1999, month = mar, journal = {Virology}, volume = {255}, number = {1}, pages = {2–8}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0042682298995691}, abstract = {The possibility of whether tRNAs with and without a highly modified base in their anticodon loop may influence the level of retroviral ribosomal frameshifting was examined. Rabbit reticulocyte lysates were programmed with mRNA encoding UUU or AAC at the frameshift site and the corresponding Phe tRNA with or without the highly modified wyebutoxine (Y) base on the 3’ side of its anticodon or Asn tRNA with or without the highly modified queuine (Q) base in the wobble position of its anticodon added. Phe and Asn tRNAs without the Y or Q base, respectively, stimulated the level of frameshifting, suggesting that the frameshift event is influenced by tRNA modification status. In addition, when AAU occurred immediately upstream of UUU as the penultimate frameshift site codon, addition of tRNAAsn without the Q base reduced the stimulatory effect of tRNAPhe without the Y base, whereas addition of tRNAAsn with the Q base did not alter the stimulatory effect. The addition of tRNAAsn without the Q base and tRNAPhe with the Y base inhibited frameshifting. The latter studies suggest an interplay between the tRNAs decoded at the penulimate frameshift and frameshift site codons that is also influenced by tRNA modification status. These data may be intrepreted as indicating that a hypomodified isoacceptor modulates frameshifting in an upward manner when utilized at the frameshift site codon, but modulates frameshifting in a downward manner when utilized at the penultimate frameshift site codon}, keywords = {nosource} } % == BibTeX quality report for carlsonTransferRNAModification1999: % ? Title looks like it was stored in title-case in Zotero

@article{cannonCharacterizationSaccharomycesCerevisiae1987, title = {Characterization of {{Saccharomyces}} Cerevisiae Genes Encoding Subunits of Cyclic {{AMP-dependent}} Protein Kinase.}, author = {Cannon, J. F. and Tatchell, K.}, year = 1987, journal = {Molecular and cellular biology}, volume = {7}, number = {8}, pages = {2653}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/7/8/2653}, keywords = {nosource} }

@article{bruennViruslikeParticlesYeast1980, title = {Virus-like Particles of Yeast}, author = {Bruenn, J. A.}, year = 1980, journal = {Annual Reviews in Microbiology}, volume = {34}, number = {1}, pages = {49–68}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}, url = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.mi.34.100180.000405}, keywords = {nosource} }

@article{bruenn5EndsYeast1976, title = {The 5{\(\prime\)} Ends of Yeast Killer Factor {{RNAs}} Are {{pppGp}}}, author = {Bruenn, J. and Keitz, B.}, year = 1976, month = oct, journal = {Nucleic acids research}, volume = {3}, number = {10}, pages = {2427}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/3/10/2427.short}, keywords = {nosource} }

@article{browModulationYeast51987, title = {Modulation of Yeast 5 {{S rRNA}} Synthesis in Vitro by Ribosomal Protein {{YL3}}. {{A}} Possible Regulatory Loop.}, author = {Brow, D. A. and Geiduschek, E. P.}, year = 1987, journal = {Journal of Biological Chemistry}, volume = {262}, number = {29}, pages = {13953}, publisher = {ASBMB}, url = {http://www.jbc.org/content/262/29/13953.short}, keywords = {nosource} }

@article{brognaRibosomeComponentsAre2002, title = {Ribosome Components Are Associated with Sites of Transcription}, author = {Brogna, S. and Sato, T. A. and Rosbash, M.}, year = 2002, month = oct, journal = {Molecular cell}, volume = {10}, number = {1}, pages = {93–104}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276502005658}, abstract = {It is generally believed that eukaryotic ribosomes first associate with mRNA in the cytoplasm. However, we show with chromosomal immunostaining and in situ hybridization that ribosomal subunits are present at transcription sites of Drosophila salivary gland chromosomes. Immunostaining was carried out with antibodies specific for 27 ribosomal proteins, two translation factors and one that specifically recognizes rRNA. In situ hybridization was with several probes specific for both rRNA subunits. The kinetics of recruitment following transcription initiation suggest that the association is with newly transcribed pol II transcripts. These data indicate that ribosome components associate with nascent RNP complexes within the nucleus}, keywords = {nosource} }

@article{broekDifferentialActivationYeast1985, title = {Differential Activation of Yeast Adenylate Cyclase by Wild Type and Mutant {{Ras}} Proteins}, author = {Broek, D. and Samiy, N. and Fasano, O. and Fujiyama, S. and Ysmsnoi, R. and Northup, J. and Wigler, M. and Fujiyama, A. and Tamanoi, F.}, year = 1985, journal = {Cell}, volume = {41}, number = {3}, pages = {763–769}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S009286748580057X}, keywords = {nosource} }

@article{brodersenCrystalStructure302002, title = {Crystal Structure of the 30 s Ribosomal Subunit from {{Thermus}} Thermophilus: Structure of the Proteins and Their Interactions with 16 s {{RNA1}}}, author = {Brodersen, D. E. and Jr, W. M. Clemons and Carter, A. P. and Wimberly, B. T. and Ramakrishnan, V.}, year = 2002, month = feb, journal = {Journal of molecular biology}, volume = {316}, number = {3}, pages = {725–768}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283601953598}, abstract = {We present a detailed analysis of the protein structures in the 30 S ribosomal subunit from Thermus thermophilus, and their interactions with 16 S RNA based on a crystal structure at 3.05 Angstrom resolution. With 20 different polypeptide chains, the 30 S subunit adds significantly to our data base of RNA structure and protein-RNA interactions. In addition to globular domains, many of the proteins have long, extended regions, either in the termini or in internal loops, which make extensive contact to the RNA component and are involved in stabilizing RNA tertiary structure. Many ribosomal proteins share similar alpha + beta sandwich folds, but we show that the topology of this domain varies considerably, as do the ways in which the proteins interact with RNA. Analysis of the protein-RNA interactions in the context of ribosomal assembly shows that the primary binders are globular proteins that bind at RNA multihelix junctions, whereas proteins with long extensions assemble later. We attempt to correlate the structure with a large body of biochemical and genetic data on the 30 S subunit. (C) 2002 Elsevier Science Ltd}, keywords = {nosource} }

@article{broachTransformationYeastDevelopment1979, title = {Transformation in Yeast: Development of a Hybrid Cloning Vector and Isolation of the {{CAN1}} Gene}, author = {Broach, J. R. and Strathern, J. N. and Hicks, J. B.}, year = 1979, journal = {Gene}, volume = {8}, number = {1}, pages = {121–133}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/037811197990012X}, keywords = {nosource} }

@article{brierleyMutationalAnalysisRNA1991, title = {Mutational Analysis of the {{RNA}} Pseudoknot Component of a Coronavirus Ribosomal Frameshifting Signal{\(\bullet\)} 1}, author = {Brierley, I. A. and Rolley, N. J. and Jenner, A. J. and Inglis, S. C.}, year = 1991, journal = {Journal of molecular biology}, volume = {220}, number = {4}, pages = {889–902}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0022283691903619}, keywords = {nosource} }

@article{brierleyExpressionCoronavirusRibosomal1997, title = {Expression of a Coronavirus Ribosomal Frameshift Signal in {{Escherichia}} Coli: Influence of {{tRNA}} Anticodon Modification on Frameshifting1}, author = {Brierley, I. and Meredith, M. R. and Bloys, A. J. and Hagervall, T. G.}, year = 1997, month = jul, journal = {Journal of molecular biology}, volume = {270}, number = {3}, pages = {360–373}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283697911347}, keywords = {nosource} }

@article{brewerCharacterizationCmyc31998, title = {Characterization of C-Myc 3{\(\prime\)} to 5{\(\prime\)} {{mRNA}} Decay Activities in an in Vitro System}, author = {Brewer, G.}, year = 1998, month = dec, journal = {Journal of Biological Chemistry}, volume = {273}, number = {52}, pages = {34770}, publisher = {ASBMB}, url = {http://www.jbc.org/content/273/52/34770.short}, abstract = {The levels of mRNA and protein encoded by the c-myc protooncogene set the balance between proliferation and differentiation of mammalian cells. Thus, it is essential for the cell to tightly control c-myc expression. Indeed, cells utilize many mechanisms to control c-myc expression, including transcription, RNA processing, translation, and protein stability. We have focused on turnover of c-myc mRNA as a key modulator of the timing and level of c-myc expression. c-myc mRNA is labile in cells, and its half-life is controlled by multiple instability elements located within both the coding region and the 3’-untranslated region (3’-UTR). Much work has focused on the protein factors that bind the instability elements, yet little is known about the enzymatic activities that effect the degradation of c-myc mRNA. Here I have utilized a novel cell-free mRNA decay system to characterize the c-myc mRNA decay machinery. This machinery consists of 3’ to 5’ mRNA decay activities that are Mg2+-dependent, require neither exogenous ATP/GTP nor an ATP-regenerating system, and act independently of a 7mG(5’)ppp(5’)G cap structure to deadenylate an exogenous mRNA substrate in a c-myc 3’-UTR-dependent fashion. Following deadenylation, nucleolytic decay of the 3’-UTR occurs generating 3’ decay intermediates via a ribonucleolytic activity that can assemble on the c-myc 3’-UTR in a poly(A)-independent manner}, keywords = {nosource} }

@article{brewerRNASequenceElements2004, title = {{{RNA Sequence Elements Required}} for {{High Affinity Binding}} by the {{Zinc Finger Domain}} of {{Tristetraprolin}}}, author = {Brewer, B. Y. and Malicka, J. and Blackshear, P. J. and Wilson, G. M.}, year = 2004, month = jul, journal = {Journal of Biological Chemistry}, volume = {279}, number = {27}, pages = {27870}, publisher = {ASBMB}, url = {PM:15117938 http://www.jbc.org/content/279/27/27870.short}, abstract = {Tristetraprolin (TTP) binds AU-rich elements (AREs) encoded within selected labile mRNAs and targets these transcripts for rapid cytoplasmic decay. RNA binding by TTP is mediated by an approximately 70-amino acid domain containing two tandemly arrayed CCCH zinc fingers. Here we show that a 73-amino acid peptide spanning the TTP zinc finger domain, denoted TTP73, forms a dynamic, equimolar RNA.peptide complex with a 13-nucleotide fragment of the ARE from tumor necrosis factor alpha mRNA, which includes small but significant contributions from ionic interactions. Association of TTP73 with high affinity RNA substrates is accompanied by a large negative change in heat capacity without substantial modification of RNA structure, consistent with conformational changes in the peptide moiety during RNA binding. Analyses using mutant ARE substrates indicate that two adenylate residues located 3-6 bases apart within a uridylate-rich sequence are sufficient for high affinity recognition by TTP73 (K(d) {\(<\)}20 nm), with optimal affinity observed for RNA substrates containing AUUUA or AUUUUA. Linkage of conformational changes and binding affinity to the presence and spacing of these adenylate residues provides a thermodynamic basis for the RNA substrate specificity of TTP}, keywords = {nosource} } % == BibTeX quality report for brewerRNASequenceElements2004: % ? Title looks like it was stored in title-case in Zotero

@article{borkSpermeggBindingProtein1996, title = {Sperm-Egg Binding Protein or Proto-Oncogene?}, author = {Bork, P.}, year = 1996, month = mar, journal = {Science}, volume = {271}, number = {5254}, pages = {1431-2; discussion 1434-5}, keywords = {nosource} }

@article{bonettiEfficiencyTranslationTermination1995, title = {The Efficiency of Translation Termination Is Determined by a Synergistic Interplay between Upstream and Downstream Sequences Insaccharomyces Cerevisiae}, author = {Bonetti, B. and Fu, L. and Moon, J. and Bedwell, D. M.}, year = 1995, journal = {Journal of molecular biology}, volume = {251}, number = {3}, pages = {334–345}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S002228368570438X}, abstract = {In a recent study we found that the efficiency of translation termination could be decreased several hundred fold by altering the local sequence context surrounding stop codons in the yeast Saccharomyces cerevisiae. Suppression of termination was shown to be mediated by near-cognate tRNA mispairing with the termination codon. We have now examined in greater detail how the local sequence context affects the efficiency of translation termination in this organism. Our results indicate that the sequence immediately upstream of the termination codon plays a significant role in determining the efficiency of translation termination. An extended termination sequence (containing the stop codon and the following three nucleotides) was also found to be a major determinant of termination efficiency, with effects attributable to the fourth nucleotide being largely independent of the termination codon. For the UGA and UAA stop codons, the influence of the fourth position on termination efficiency (from most efficient to least efficient termination) was found to be G {\(>\)} U,A {\(>\)} C, while for the UAG codon it was U,A {\(>\)} C {\(>\)} G. These sequence-specific effects on the efficiency of translation termination suggest that polypeptide chain release factor (or another molecule that may play a role in translation termination, such as rRNA) recognizes an extended termination sequence in yeast. A previous study found a statistically significant bias toward certain tetranucleotide sequences (containing the stop codon and the first distal nucleotide) in several organisms. We found that tetranucleotide sequences most frequently used in yeast are among the most efficient at mediating translation termination, while rare tetranucleotide sequences mediate much less efficient termination. Taken together, our results indicate that upstream and downstream components of an extended sequence context act synergistically to determine the overall efficiency of translation termination in yeast}, keywords = {nosource} }

@article{boekeYeastTransposableElements1991, title = {Yeast Transposable Elements}, author = {Boeke, J. D. and Sandmeyer, S. B.}, year = 1991, journal = {The molecular and cellular biology of the yeast Saccharomyces: genome dynamics, protein synthesis, and energetics}, volume = {1}, pages = {193–261}, publisher = {Cold Spring Harbor Press}, url = {http://books.google.com/books?hl=en&lr=&id=FRyWfsr4DNQC&oi=fnd&pg=PA193&dq=Yeast+transposable+elements.&ots=ye_uC47Jen&sig=WIM9roX_QR-KAnuCQiGqpIoSxsQ}, keywords = {nosource} }

@article{blinkowaWalkerProgrammedRibosomal1990, title = {Walker, {{Programmed}} Ribosomal Frameshifting Generates the {{Escherichia}} Coli {{DNA}} Polymerase {{III}} Gamma Subunit from within the Tau Subunit Reading Frame}, author = {Blinkowa, JR AL}, year = 1990, month = apr, journal = {Nucleic Acids Research}, volume = {18}, number = {7}, pages = {1725–1729}, url = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:Programmed+ribosomal+frameshifting+generates+the+Escherichia+coli+DNA+polymerase+III+gamma+subunit+from+within+the+tau+subunit+reading+frame#4}, keywords = {nosource} }

@article{blancCoatProteinYeast1992, title = {The Coat Protein of the Yeast Double-Stranded {{RNA}} Virus {{LA}} Attaches Covalently to the Cap Structure of Eukaryotic {{mRNA}}.}, author = {Blanc, A. and Goyer, C. and Sonenberg, N.}, year = 1992, journal = {Molecular and cellular biology}, volume = {12}, number = {8}, pages = {3390}, publisher = {Am Soc Microbiol}, url = {http://mcb.asm.org/cgi/content/abstract/12/8/3390}, keywords = {nosource} }

@article{bidouVivoHIV1Frameshifting1997, title = {In Vivo {{HIV-1}} Frameshifting Efficiency Is Directly Related to the Stability of the Stem-Loop Stimulatory Signal.}, author = {Bidou, L. and Stahl, G. and Grima, B. and Liu, H. and Cassan, M. and Rousset, J.-P.}, year = 1997, journal = {Rna}, volume = {3}, number = {10}, pages = {1153}, publisher = {Cold Spring Harbor Laboratory Press}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1369557/}, keywords = {nosource} }

@article{beusYeastNOP2Encodes1994, title = {Yeast {{NOP2}} Encodes an Essential Nucleolar Protein with Homology to a Human Proliferation Marker.}, author = {Beus, e and Brokenbrough, J. S. and Hong, B. and Aris, J. P. and {}de Beus, E. and Brockenbrough, J. S.}, year = 1994, journal = {The Journal of cell biology}, volume = {127}, number = {6}, pages = {1799}, publisher = {Rockefeller Univ Press}, url = {http://jcb.rupress.org/content/127/6/1799.abstract}, keywords = {nosource} }

@article{beadleGeneticControlBiochemical1941, title = {Genetic Control of Biochemical Reactions in {{Neurospora}}}, author = {Beadle, G. W. and Tatum, E. L.}, year = 1941, journal = {Proceedings of the National Academy of Sciences}, volume = {27}, number = {11}, pages = {499}, publisher = {National Academy of Sciences}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1078370/}, keywords = {nosource} }

@article{beckenbachSingleNucleotide12005, title = {Single {{Nucleotide}}+ 1 {{Frameshifts}} in an {{Apparently FunctionalMitochondrial Cytochrome}} b {{Gene}} in {{Ants}} of the {{Genus Polyrhachis}}}, author = {Beckenbach, A. T. and Robson, S. K. A. and Crozier, R. H.}, year = 2005, month = feb, journal = {Journal of molecular evolution}, volume = {60}, number = {2}, pages = {141–152}, publisher = {Springer}, url = {http://www.springerlink.com/index/n540qu413j60487j.pdf}, abstract = {Twelve of 30 species examined in the ant genus Polyrhachis carry single nucleotide insertions at one or two positions within the mitochondrial cytochrome b (cytb) gene. Two of the sites are present in more than one species. Nucleotide substitutions in taxa carrying insertions show the strong codon position bias expected of functional protein coding genes, with substitutions concentrated in the third positions of the original reading frame. This pattern of evolution of the sequences strongly suggests that they are functional cytb sequences. This result is not the first report of +1 frameshift insertions in animal mitochondrial genes. A similar site was discovered in vertebrates, where single nucleotide frameshift insertions in many birds and a turtle were reported by Mindell et al. (Mol Biol Evol 15:1568, 1998). They hypothesized that the genes are correctly decoded by a programmed frameshift during translation. The discovery of four additional sites gives us the opportunity to look for common features that may explain how programmed frameshifts can arise. The common feature appears to be the presence of two consecutive rare codons at the insertion site. We hypothesize that the second of these codons is not efficiently translated, causing a pause in the translation process. During the stall the weak wobble pairing of the tRNA bound in the peptidyl site of the ribosome, together with an exact Watson-Crick codon-anticodon pairing in the +1 position, allows translation to continue in the +1 reading frame. The result of these events is an adequate level of translation of a full-length and fully functional protein. A model is presented for decoding of these mitochondrial genes, consistent with known features of programmed translational frameshifting in the yeast TY1 and TY3 retrotransposons}, keywords = {nosource} } % == BibTeX quality report for beckenbachSingleNucleotide12005: % ? Title looks like it was stored in title-case in Zotero

@article{barrettImmunologicalIdentityProteins1984, title = {Immunological Identity of Proteins That Bind Stored {{5S RNA}} in {{Xenopus}} Oocytes{\(\bullet\)} 1}, author = {Barrett, P. and Johnson, R. M. and Sommerville, J.}, year = 1984, journal = {Experimental Cell Research}, volume = {153}, number = {2}, pages = {299–307}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/0014482784906025}, abstract = {In small oocytes of Xenopus laevis, the three most abundant proteins are isolated as basic polypeptides with molecular weights of 48 kD (P48), 43 kD (P43) and 40 kD (P40, also known as transcription factor IIIA). All three proteins share common properties in being able to bind specifically ribosomal 5S RNA molecules and influence, in different ways, their rates of production and utilization. It has been shown by biochemical analysis and immunological characterization that the three proteins are structurally distinct and are most probably the products of different genes. Immunostaining and radio-immunoassays indicate that both P48 and P43 have diverged considerably in structure between the amphibian genera Xenopus and Triturus. Antibodies raised against the transcription factor for Xenopus laevis 5S RNA genes (P40/TFIIIA) do not cross-react with the transcription factor isolated from oocytes of the closely related species Xenopus borealis. A protein equivalent of TFIIIA is not found in 5S RNA-containing RNP storage particles of Triturus oocytes. The functions of the three Xenopus oocyte proteins in transporting 5S RNA between different cellular compartments are considered in the light of these variations}, keywords = {nosource} }

@article{balasundaramTwoEssentialGenes1994, title = {Two Essential Genes in the Biosynthesis of Polyamines That Modulate +1 Ribosomal Frameshifting in {{Saccharomyces}} Cerevisiae}, author = {Balasundaram, D. and Dinman, J. D. and Tabor, C. W. and Tabor, H.}, year = 1994, journal = {J.Bacteriol.}, volume = {176}, pages = {7126–7128}, keywords = {nosource} } % == BibTeX quality report for balasundaramTwoEssentialGenes1994: % ? Possibly abbreviated journal title J.Bacteriol.

@article{balasundaramSpermidineDeficiencyIncreases1994, title = {Spermidine Deficiency Increases+ 1 Ribosomal Frameshifting Efficiency and Inhibits {{Ty1}} Retrotransposition in {{Saccharomyces}} Cerevisiae}, author = {Balasundaram, D. and Dinman, J. D. and Wickner, R. B. and Tabor, C. W. and Tabor, H.}, year = 1994, journal = {Proceedings of the National Academy of Sciences}, volume = {91}, number = {1}, pages = {172}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/91/1/172.short}, keywords = {nosource} }

@article{aravaGenomewideAnalysisMRNA2003, title = {Genome-Wide Analysis of {{mRNA}} Translation Profiles in {{Saccharomycescerevisiae}}}, author = {Arava, Y. and Wang, Y. L. and Storey, J. D. and Liu, C. L. and Brown, P. O. and Herschlag, D.}, year = 2003, month = apr, journal = {Proceedings of the National Academy of Sciences}, volume = {100}, number = {7}, pages = {3889}, publisher = {National Acad Sciences}, url = {http://www.pnas.org/content/100/7/3889.short}, abstract = {We have analyzed the translational status of each mRNA in rapidly growing Saccharomyces cerevisiae. mRNAs were separated by velocity sedimentation on a sucrose gradient, and 14 fractions across the gradient were analyzed by quantitative microarray analysis, providing a profile of ribosome association with mRNAs for thousands of genes. For most genes, the majority of mRNA molecules were associated with ribosomes and presumably engaged in translation. This systematic approach enabled us to recognize genes with unusual behavior. For 43 genes, most mRNA molecules were not associated with ribosomes, suggesting that they may be translationally controlled. For 53 genes, including GCN4, CPA1, and ICY2, three genes for which translational control is known to play a key role in regulation, most mRNA molecules were associated with a single ribosome. The number of ribosomes associated with mRNAs increased with increasing length of the putative protein-coding sequence, consistent with longer transit times for ribosomes translating longer coding sequences. The density at which ribosomes were distributed on each mRNA (i.e., the number of ribosomes per unit ORF length) was well below the maximum packing density for nearly all mRNAs, consistent with initiation as the rate-limiting step in translation. Global analysis revealed an unexpected correlation: Ribosome density decreases with increasing ORF length: Models to account for this surprising observation are discussed}, keywords = {nosource} }

@article{anderssonRamRibosomesAre1983, title = {Ram Ribosomes Are Defective Proofreaders}, author = {Andersson, D. I. and Kurland, C. G.}, year = 1983, journal = {Molecular and General Genetics MGG}, volume = {191}, number = {3}, pages = {378–381}, publisher = {Springer}, url = {http://www.springerlink.com/index/N6682677577154J3.pdf}, keywords = {nosource} }

@article{andersenStructuralBasisNucleotide2000, title = {Structural Basis for Nucleotide Exchange and Competition with {{tRNA}} in the Yeast Elongation Factor Complex {{eEF1A}}: {{eEF1B}} [Alpha]}, author = {Andersen, G. R. and Pedersen, L. and Valente, L. and Chatterjee, I. and Kinzy, T. G. and Kjeldgaard, M. and Nyborg, J.}, year = 2000, month = nov, journal = {Molecular cell}, volume = {6}, number = {5}, pages = {1261–1266}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276500001222}, abstract = {The crystal structure of a complex between the protein biosynthesis elongation factor eEF1A (formerly EF-1alpha) and the catalytic C terminus of its exchange factor, eEF1Balpha (formerly EF-1beta), was determined to 1.67 A resolution. One end of the nucleotide exchange factor is buried between the switch 1 and 2 regions of eEF1A and destroys the binding site for the Mg(2+) ion associated with the nucleotide. The second end of eEF1Balpha interacts with domain 2 of eEF1A in the region hypothesized to be involved in the binding of the CCA-aminoacyl end of the tRNA. The competition between eEF1Balpha and aminoacylated tRNA may be a central element in channeling the reactants in eukaryotic protein synthesis. The recognition of eEF1A by eEF1Balpha is very different from that observed in the prokaryotic EF-Tu:EF-Ts complex. Recognition of the switch 2 region in nucleotide exchange is, however, common to the elongation factor complexes and those of Ras:Sos and Arf1:Sec7}, keywords = {nosource} }

@article{agrawalLocalizationL11Protein2001, title = {Localization of {{L11}} Protein on the Ribosome and Elucidation of Its Involvement in {{EF-G-dependent}} Translocation1}, author = {Agrawal, R. K. and Linde, J. and Sengupta, J. and Nierhaus, K. H. and Frank, J.}, year = 2001, journal = {Journal of molecular biology}, volume = {311}, number = {4}, pages = {777–787}, publisher = {Elsevier}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283601949071}, abstract = {L11 protein is located at the base of the L7/L12 stalk of the 50 S subunit of the Escherichia coli ribosome. Because of the flexible nature of the region, recent X-ray crystallographic studies of the 50 S subunit failed to locate the N-terminal domain of the protein. We have determined the position of the complete L11 protein by comparing a three-dimensional cryo-EM reconstruction of the 70 S ribosome, isolated from a mutant lacking ribosomal protein L11, with the three-dimensional map of the wild-type ribosome. Fitting of the X-ray coordinates of L11-23 S RNA complex and EF-G into the cryo-EM maps combined with molecular modeling, reveals that, following EF-G-dependent GTP hydrolysis, domain V of EF-G intrudes into the cleft between the 23 S ribosomal RNA and the N-terminal domain of L11 (where the antibiotic thiostrepton binds), causing the N-terminal domain to move and thereby inducing the formation of the arc-like connection with the G’ domain of EF-G. The results provide a new insight into the mechanism of EF-G-dependent translocation}, keywords = {nosource} }

@article{agrawalDirectVisualizationEsite1996, title = {Direct Visualization of {{A-}}, {{P-}}, and {{E-site}} Transfer {{RNAs}} in the {{Escherichia}} Coli Ribosome}, author = {Agrawal, R. K. and Penczek, P. and Grassucci, R. A. and Li, Y. and Leith, A. D. and Nierhaus, K. H. and Frank, J.}, year = 1996, journal = {Science}, volume = {271}, number = {5251}, pages = {1000}, publisher = {American Association for the Advancement of Science}, url = {http://www.sciencemag.org/content/271/5251/1000.short}, keywords = {nosource} }

@article{elelaRole58RRNA1997, title = {Role of the 5.8 {{S rRNA}} in Ribosome Translocation}, author = {Elela, S. A. and Nazar, R. N. and Abou, Elela S.}, year = 1997, month = may, journal = {Nucleic Acids Research}, volume = {25}, number = {9}, pages = {1788}, publisher = {Oxford Univ Press}, url = {http://nar.oxfordjournals.org/content/25/9/1788.short}, abstract = {Studies on the inhibition of protein synthesis by specific anti 5.8S rRNA oligonucleotides have suggested that this RNA plays an important role in eukaryotic ribosome function. Mutations in the 5. 8S rRNA can inhibit cell growth and compromise protein synthesis in vitro . Polyribosomes from cells expressing these mutant 5.8S rRNAs are elevated in size and ribosome-associated tRNA. Cell free extracts from these cells also are more sensitive to antibiotics which act on the 60S ribosomal subunit by inhibiting elongation. The extracts are especially sensitive to cycloheximide and diphtheria toxin which act specifically to inhibit translocation. Studies of ribosomal proteins show no reproducible changes in the core proteins, but reveal reduced levels of elongation factors 1 and 2 only in ribosomes which contain large amounts of mutant 5.8S rRNA. Polyribosomes from cells which are severely inhibited, but contain little mutant 5.8S rRNA, do not show the same reductions in the elongation factors, an observation which underlines the specific nature of the change. Taken together the results demonstrate a defined and critical function for the 5.8S rRNA, suggesting that this RNA plays a role in ribosome translocation}, keywords = {nosource} }

@article{birnboimRapidAlkalineExtraction1983, title = {Rapid Alkaline Extraction Method for the Isolation of Plasmid {{DNA}}}, author = {Birnboim, H. C.}, year = 1983, journal = {Methods Enzymol.;(United States)}, volume = {100}, pages = {243–255}, issn = {0076-6879}, url = {http://www.osti.gov/energycitations/product.biblio.jsp?osti_id=5021853}, keywords = {nosource} } % == BibTeX quality report for birnboimRapidAlkalineExtraction1983: % ? Possibly abbreviated journal title Methods Enzymol.;(United States)

@article{jagannathanAssemblyCentralDomain2003, title = {Assembly of the Central Domain of the 30 {{S}} Ribosomal Subunit: Roles for the Primary Binding Ribosomal Proteins {{S15}} and {{S8}}}, author = {Jagannathan, Indu}, year = 2003, month = jul, journal = {Journal of molecular biology}, volume = {330}, number = {2}, pages = {373–383}, issn = {0022-2836}, url = {http://linkinghub.elsevier.com/retrieve/pii/s0022283603005862}, abstract = {Assembly of the 30S ribosomal subunit occurs in a highly ordered and sequential manner. The ordered addition of ribosomal proteins to the growing ribonucleoprotein particle is initiated by the association of primary binding proteins. These proteins bind specifically and independently to 16S ribosomal RNA (rRNA). Two primary binding proteins, S8 and S15, interact exclusively with the central domain of 16S rRNA. Binding of S15 to the central domain results in a conformational change in the RNA and is followed by the ordered assembly of the S6/S18 dimer, S11 and finally S21 to form the platform of the 30S subunit. In contrast, S8 is not part of this major platform assembly branch. Of the remaining central domain binding proteins, only S21 association is slightly dependent on S8. Thus, although S8 is a primary binding protein that extensively contacts the central domain, its role in assembly of this domain remains unclear. Here, we used directed hydroxyl radical probing from four unique positions on S15 to assess organization of the central domain of 16S rRNA as a consequence of S8 association. Hydroxyl radical probing of Fe(II)-S15/16S rRNA and Fe(II)-S15/S8/16S rRNA ribonucleoprotein particles reveal changes in the 16S rRNA environment of S15 upon addition of S8. These changes occur predominantly in helices 24 and 26 near previously identified S8 binding sites. These S8-dependent conformational changes are consistent with 16S rRNA folding in complete 30S subunits. Thus, while S8 binding is not absolutely required for assembly of the platform, it appears to affect significantly the 16S rRNA environment of S15 by influencing central domain organization.}, keywords = {nosource} }

@article{tanguayIsolationCharacterization102kilodalton1996, title = {Isolation and Characterization of the 102-Kilodalton {{RNA-binding}} Protein That Binds to the 5{\(\prime\)} and 3{\(\prime\)} Translational Enhancers of Tobacco Mosaic Virus {{RNA}}}, author = {Tanguay, R. L. L. and Gallie, D. R. R.}, year = 1996, month = jun, journal = {Journal of Biological Chemistry}, volume = {271}, number = {24}, pages = {14316}, publisher = {ASBMB}, issn = {0021-9258}, url = {http://www.jbc.org/content/271/24/14316.short}, abstract = {Tobacco mosaic virus (TMV) is a positive-sense, single-stranded RNA virus the genome of which acts as a mRNA in the cytoplasm. On infection, TMV mRNA is efficiently and selectively translated by the host translation machinery despite the lack of a poly(A) tail, which is normally required for efficient translation. Both the 68-base 5’ leader (Omega) and the 205-base 3’ untranslated region of TMV promote efficient translation. A 25-base poly(CAA) region within Omega and the upstream pseudoknot domain, a 72-base region composed of three RNA pseudoknots, are responsible for the translational regulation. We have identified, purified, and characterized a 102-kDa RNA-binding protein (p102) from wheat that binds specifically to the poly(CAA) region within Omega and the upstream pseudoknot domain within the TMV 3’ untranslated region. Polyclonal antibodies raised against wheat p102 were used to demonstrate that p102 is widely conserved in plant species. Moreover, specific RNA binding activity was detected in all plant species tested. Addition of anti-p102 antibodies to an in vitro translation lysate derived from wheat germ repressed translation, which was subsequently reversed by supplementing the lysate with p102. These findings suggest that this protein may play an important role in determining translational efficiency in plants.}, keywords = {Antibodies,Base Sequence,Binding Sites,Electrophoresis- Polyacrylamide Gel,Heparin,Molecular Sequence Data,Molecular Weight,nosource,Nucleic Acid Conformation,Protein Biosynthesis,RNA- Messenger,RNA- Viral,RNA-Binding Proteins,Substrate Specificity,Tobacco Mosaic Virus,Triticum} }

@article{byersKillingMessengerNew2002, title = {Killing the Messenger: New Insights into Nonsense-Mediated {{mRNA}} Decay}, author = {Byers, PH Peter H. P. H.}, year = 2002, month = jan, journal = {Journal of Clinical Investigation}, volume = {109}, number = {1}, pages = {3–6}, publisher = {Am Soc Clin Investig}, issn = {0021-9738}, doi = {10.1172/JCI200214841.Nonsense-mediated}, url = {http://www.jci.org/cgi/content/full/jci;109/1/3}, keywords = {nosource} }

@article{pillsburySteepestDescentCalculation2002, title = {A Steepest Descent Calculation of {{RNA}} Pseudoknots}, author = {Pillsbury, M. and Orland, Henri and Zee, A.}, year = 2002, month = jul, journal = {Arxiv preprint physics/0207110}, volume = {72}, number = {1 Pt 1}, eprint = {16090005}, eprinttype = {pubmed}, pages = {11911}, issn = {1539-3755}, doi = {10.1103/PhysRevE.72.011911}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16090005 http://arxiv.org/abs/physics/0207110}, abstract = {We enumerate possible topologies of pseudoknots in single-stranded RNA molecules. We use a steepest-descent approximation in the large N matrix field theory, and a Feynman diagram formalism to describe the resulting pseudoknot structure.}, keywords = {Biophysics,Models- Statistical,Models- Theoretical,Normal Distribution,nosource,Nucleic Acid Conformation,RNA,Statistics as Topic,Thermodynamics} }

@article{geerlingsFinalStepFormation2000, title = {The Final Step in the Formation of {{25S rRNA}} in {{Saccharomyces}} Cerevisiae Is Performed by 5’–{\(>\)} 3’exonucleases.}, author = {Geerlings, T. H. TH and Vos, J. C. and Rau{'e}, H. A. HA}, year = 2000, month = dec, journal = {Rna}, volume = {6}, number = {12}, pages = {1698–1703}, publisher = {Cold Spring Harbor Lab}, issn = {1355-8382}, url = {http://rnajournal.cshlp.org/content/6/12/1698.short}, abstract = {The final stage in the formation of the two large subunit rRNA species in Saccharomyces cerevisiae is the removal of internal transcribed spacer 2 (ITS2) from the 27SB precursors. This removal is initiated by endonucleolytic cleavage approximately midway in ITS2. The resulting 7S pre-rRNA, which is easily detectable, is then converted into 5.8S rRNA by the concerted action of a number of 3’–{\(>\)}5’ exonucleases, many of which are part of the exosome. So far the complementary precursor to 25S rRNA resulting from the initial cleavage in ITS2 has not been detected and the manner of its conversion into the mature species is unknown. Using various yeast strains that carry different combinations of wild-type and mutant alleles of the major 5’–{\(>\)}3’ exonucleases Rat1p and Xrn1p, we now demonstrate the existence of a short-lived 25.5S pre-rRNA whose 5’ end is located closely downstream of the previously mapped 3’ end of 7S pre-rRNA. The 25.5S pre-rRNA is converted into mature 25S rRNA by rapid exonucleolytic trimming, predominantly carried out by Rat1p. In the absence of Rat1p, however, the removal of the ITS2 sequences from 25.5S pre-rRNA can also be performed by Xrn1p, albeit somewhat less efficiently.}, keywords = {its2,nosource,processing,rat1p,ribosomal rna,ribosome,xrn1p} }

@article{arfvidssonTimeminimizedDeterminationRibosome2003, title = {Time-Minimized Determination of Ribosome and {{tRNA}} Levels in Bacterial Cells Using Flow Field-Flow Fractionation{\(\bullet\)} 1}, author = {Arfvidsson, Cecilia and Wahlund, K. G.}, year = 2003, month = feb, journal = {Analytical Biochemistry}, volume = {313}, number = {1}, pages = {76–85}, publisher = {Elsevier}, issn = {0003-2697}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0003269702005419}, abstract = {The evaluation of the translation capacity of cells that produce recombinant proteins can be made by monitoring their ribosomal composition. In a previous use of asymmetrical flow field-flow fractionation (AsFlFFF) for this purpose the overall analysis time was more than 1 h and 40 min, based on a standard protocol for cell harvest, washing, cell disruption, and the final 8-min AsFlFFF determination of ribosome and subunits. In the present work the overall analysis time was reduced to 16 min. The washing step was deleted and a time-consuming freeze-thaw cycle. Cell disruption was obtained by a time-minimized lysozyme and detergent treatment for 1.5 min, respectively. The ribosomal material was finally fractionated and quantified in only 6 min, without previous centrifugation, using AsFlFFF. The great time reduction will enable the future use of AsFlFFF at-line to a growing cell cultivation, continuously monitoring the change in ribosomal composition or in other applications requiring high sample throughput. To demonstrate the high efficiency of the method the ribosome and tRNA composition in an Escherichia coli cultivation was monitored every half an hour, giving 18 measurements across the complete growth curve, a frequency of data enough to make decisions about induction or termination of the cultivation.}, keywords = {nosource} }

@article{kimGraphbasedGenomeAlignment2019, title = {Graph-Based Genome Alignment and Genotyping with {{HISAT2}} and {{HISAT-genotype}}}, author = {Kim, Daehwan and Paggi, Joseph M. and Park, Chanhee and Bennett, Christopher and Salzberg, Steven L.}, year = 2019, month = aug, journal = {Nature Biotechnology}, volume = {37}, number = {8}, pages = {907–915}, issn = {1546-1696}, doi = {10.1038/s41587-019-0201-4}, url = {https://doi.org/10.1038/s41587-019-0201-4}, abstract = {The human reference genome represents only a small number of individuals, which limits its usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for spliced alignment of transcripts 2) that can align both DNA and RNA sequences using a graph Ferragina Manzini index. We use HISAT2 to represent and search an expanded model of the human reference genome in which over 14.5 million genomic variants in combination with haplotypes are incorporated into the data structure used for searching and alignment. We benchmark HISAT2 using simulated and real datasets to demonstrate that our strategy of representing a population of genomes, together with a fast, memory-efficient search algorithm, provides more detailed and accurate variant analyses than other methods. We apply HISAT2 for HLA typing and DNA fingerprinting; both applications form part of the HISAT-genotype software that enables analysis of haplotype-resolved genes or genomic regions. HISAT-genotype outperforms other computational methods and matches or exceeds the performance of laboratory-based assays.}, keywords = {nosource} }

@article{putriAnalysingHighthroughputSequencing2022, title = {Analysing High-Throughput Sequencing Data in {{Python}} with {{HTSeq}} 2.0}, author = {Putri, Givanna H and Anders, Simon and Pyl, Paul Theodor and Pimanda, John E and Zanini, Fabio}, year = 2022, month = may, journal = {Bioinformatics}, volume = {38}, number = {10}, pages = {2943–2945}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btac166}, url = {https://doi.org/10.1093/bioinformatics/btac166}, urldate = {2022-09-29}, abstract = {HTSeq 2.0 provides a more extensive application programming interface including a new representation for sparse genomic data, enhancements for htseq-count to suit single-cell omics, a new script for data using cell and molecular barcodes, improved documentation, testing and deployment, bug fixes and Python 3 support.HTSeq 2.0 is released as an open-source software under the GNU General Public License and is available from the Python Package Index at https://pypi.python.org/pypi/HTSeq. The source code is available on Github at https://github.com/htseq/htseq.Supplementary data are available at Bioinformatics online.}, file = {/home/trey/Zotero/storage/28CUKUTE/Putri et al. - 2022 - Analysing high-throughput sequencing data in Pytho.pdf;/home/trey/Zotero/storage/Q5YV86KZ/6551247.html} } % == BibTeX quality report for putriAnalysingHighthroughputSequencing2022: % ? unused Library catalog (“Silverchair”)

@article{kolbergGprofiler2PackageGene2020, title = {Gprofiler2 – an {{R}} Package for Gene List Functional Enrichment Analysis and Namespace Conversion Toolset g:{{Profiler}}.}, author = {Kolberg, Liis and Raudvere, Uku and Kuzmin, Ivan and Vilo, Jaak and Peterson, Hedi}, year = 2020, journal = {F1000Research}, volume = {9}, pages = {ELIXIR-709}, issn = {2046-1402}, doi = {10.12688/f1000research.24956.2}, abstract = {g:Profiler ( https://biit.cs.ut.ee/gprofiler) is a widely used gene list functional profiling and namespace conversion toolset that has been contributing to reproducible biological data analysis already since 2007. Here we introduce the accompanying R package, gprofiler2, developed to facilitate programmatic access to g:Profiler computations and databases via REST API. The gprofiler2 package provides an easy-to-use functionality that enables researchers to incorporate functional enrichment analysis into automated analysis pipelines written in R. The package also implements interactive visualisation methods to help to interpret the enrichment results and to illustrate them for publications. In addition, gprofiler2 gives access to the versatile gene/protein identifier conversion functionality in g:Profiler enabling to map between hundreds of different identifier types or orthologous species. The gprofiler2 package is freely available at the CRAN repository.}, copyright = {Copyright: 2020 Kolberg L et al.}, langid = {english}, pmcid = {PMC7859841}, pmid = {33564394}, keywords = {Computational Biology,Gene Expression Profiling,*Software,functional enrichment analysis,g:Profiler,Gene Ontology,identifier mapping,nosource,pathways,R package} } % == BibTeX quality report for kolbergGprofiler2PackageGene2020: % ? unused Journal abbr (“F1000Res”)

@article{hanzelmannGSVAGeneSet2013, title = {{{GSVA}}: Gene Set Variation Analysis for Microarray and {{RNA-Seq}} Data}, author = {H{"a}nzelmann, Sonja and Castelo, Robert and Guinney, Justin}, year = 2013, month = jan, journal = {BMC Bioinformatics}, volume = {14}, number = {1}, pages = {7}, issn = {1471-2105}, doi = {10.1186/1471-2105-14-7}, url = {https://doi.org/10.1186/1471-2105-14-7}, abstract = {Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as well as greater biological interpretability. As molecular profiling experiments move beyond simple case-control studies, robust and flexible GSE methodologies are needed that can model pathway activity within highly heterogeneous data sets.}, keywords = {nosource} }

@misc{andrewsFastQCQualityControl, title = {{{FastQC}}: {{A Quality Control Tool}} for {{High Throughput Sequence Data}}}, author = {Andrews, Simon}, url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}, keywords = {nosource} } % == BibTeX quality report for andrewsFastQCQualityControl: % ? Title looks like it was stored in title-case in Zotero % ? unused Version (“0.39”)

@article{patroSalmonProvidesFast2017, title = {Salmon Provides Fast and Bias-Aware Quantification of Transcript Expression}, author = {Patro, Rob and Duggal, Geet and Love, Michael I. and Irizarry, Rafael A. and Kingsford, Carl}, year = 2017, month = apr, journal = {Nature Methods}, volume = {14}, number = {4}, pages = {417–419}, publisher = {Nature Publishing Group}, issn = {1548-7105}, doi = {10.1038/nmeth.4197}, url = {https://www.nature.com/articles/nmeth.4197}, urldate = {2022-12-09}, abstract = {Salmon is a computational tool that uses sample-specific models and a dual-phase inference procedure to correct biases in RNA-seq data and rapidly quantify transcript abundances.}, copyright = {2017 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.}, langid = {english}, keywords = {Software,Statistical methods,Transcriptomics}, file = {/home/trey/Zotero/storage/N4JZ3SPU/Patro et al. - 2017 - Salmon provides fast and bias-aware quantification.pdf} } % == BibTeX quality report for patroSalmonProvidesFast2017: % ? unused Journal abbr (“Nat Methods”) % ? unused Library catalog (“www.nature.com”)

@article{subramanianGeneSetEnrichment2005a, title = {Gene Set Enrichment Analysis: {{A}} Knowledge-Based Approach for Interpreting Genome-Wide Expression Profiles}, shorttitle = {Gene Set Enrichment Analysis}, author = {Subramanian, Aravind and Tamayo, Pablo and Mootha, Vamsi K. and Mukherjee, Sayan and Ebert, Benjamin L. and Gillette, Michael A. and Paulovich, Amanda and Pomeroy, Scott L. and Golub, Todd R. and Lander, Eric S. and Mesirov, Jill P.}, year = 2005, month = oct, journal = {Proceedings of the National Academy of Sciences}, volume = {102}, number = {43}, pages = {15545–15550}, publisher = {Proceedings of the National Academy of Sciences}, doi = {10.1073/pnas.0506580102}, url = {https://www.pnas.org/doi/abs/10.1073/pnas.0506580102}, urldate = {2022-12-09}, abstract = {Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information r…}, copyright = {Copyright 2005, The National Academy of Sciences}, langid = {english}, file = {/home/trey/Zotero/storage/LZQ2DEJ4/Subramanian et al. - 2005 - Gene set enrichment analysis A knowledge-based ap.pdf} } % == BibTeX quality report for subramanianGeneSetEnrichment2005a: % ? unused Archive location (“world”) % ? unused Library catalog (“www.pnas.org”)

@article{woodImprovedMetagenomicAnalysis2019, title = {Improved Metagenomic Analysis with {{Kraken}} 2}, author = {Wood, Derrick E. and Lu, Jennifer and Langmead, Ben}, year = 2019, month = dec, journal = {Genome Biology}, volume = {20}, number = {1}, pages = {1–13}, publisher = {BioMed Central}, issn = {1474-760X}, doi = {10.1186/s13059-019-1891-0}, url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1891-0}, urldate = {2022-12-09}, abstract = {Although Kraken’s k-mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 by reducing memory usage by 85%, allowing greater amounts of reference genomic data to be used, while maintaining high accuracy and increasing speed fivefold. Kraken 2 also introduces a translated search mode, providing increased sensitivity in viral metagenomics analysis.}, copyright = {2019 The Author(s).}, langid = {english}, file = {/home/trey/Zotero/storage/2X2JDJQB/Wood et al. - 2019 - Improved metagenomic analysis with Kraken 2.pdf} } % == BibTeX quality report for woodImprovedMetagenomicAnalysis2019: % ? unused Journal abbr (“Genome Biol”) % ? unused Library catalog (“genomebiology.biomedcentral.com”)

@misc{garrisonHaplotypebasedVariantDetection2012, title = {Haplotype-Based Variant Detection from Short-Read Sequencing}, author = {Garrison, Erik and Marth, Gabor}, year = 2012, month = jul, number = {arXiv:1207.3907}, eprint = {1207.3907}, primaryclass = {q-bio}, publisher = {arXiv}, doi = {10.48550/arXiv.1207.3907}, url = {http://arxiv.org/abs/1207.3907}, urldate = {2022-12-09}, abstract = {The direct detection of haplotypes from short-read DNA sequencing data requires changes to existing small-variant detection methods. Here, we develop a Bayesian statistical framework which is capable of modeling multiallelic loci in sets of individuals with non-uniform copy number. We then describe our implementation of this framework in a haplotype-based variant detector, FreeBayes.}, archiveprefix = {arXiv}, keywords = {Quantitative Biology - Genomics,Quantitative Biology - Quantitative Methods}, file = {/home/trey/Zotero/storage/BFQWSGVK/Garrison and Marth - 2012 - Haplotype-based variant detection from short-read .pdf;/home/trey/Zotero/storage/UHCWCUB2/1207.html} }

@article{ritchieLimmaPowersDifferential2015a, title = {Limma Powers Differential Expression Analyses for {{RNA-sequencing}} and Microarray Studies}, author = {Ritchie, Matthew E. and Phipson, Belinda and Wu, Di and Hu, Yifang and Law, Charity W. and Shi, Wei and Smyth, Gordon K.}, year = 2015, month = apr, journal = {Nucleic Acids Research}, volume = {43}, number = {7}, pages = {e47-e47}, publisher = {Oxford Academic}, issn = {0305-1048}, doi = {10.1093/nar/gkv007}, url = {https://academic.oup.com/nar/article/43/7/e47/2414268}, urldate = {2023-01-02}, abstract = {Abstract. limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich}, langid = {english}, file = {/home/trey/Zotero/storage/5UAQZHIV/Ritchie et al. - 2015 - limma powers differential expression analyses for .pdf} } % == BibTeX quality report for ritchieLimmaPowersDifferential2015a: % ? unused Journal abbr (“Nucleic Acids Res”) % ? unused Library catalog (“academic.oup.com”)

@article{edgarDiscoveryGlycerolPhosphate2019, title = {Discovery of Glycerol Phosphate Modification on Streptococcal Rhamnose Polysaccharides}, author = {Edgar, Rebecca J. and {}{van Hensbergen}, Vincent P. and Ruda, Alessandro and Turner, Andrew G. and Deng, Pan and Le Breton, Yoann and {El-Sayed}, Najib M. and Belew, Ashton T. and McIver, Kevin S. and McEwan, Alastair G. and Morris, Andrew J. and Lambeau, G{'e}rard and Walker, Mark J. and Rush, Jeffrey S. and Korotkov, Konstantin V. and Widmalm, G{"o}ran and {}{van Sorge}, Nina M. and Korotkova, Natalia}, year = 2019, month = may, journal = {Nature Chemical Biology}, volume = {15}, number = {5}, pages = {463–471}, issn = {1552-4450, 1552-4469}, doi = {10.1038/s41589-019-0251-4}, url = {http://www.nature.com/articles/s41589-019-0251-4}, urldate = {2023-02-22}, langid = {english}, file = {/home/trey/Zotero/storage/Z6K5TQP6/Edgar et al. - 2019 - Discovery of glycerol phosphate modification on st.pdf} } % == BibTeX quality report for edgarDiscoveryGlycerolPhosphate2019: % ? unused Journal abbr (“Nat Chem Biol”) % ? unused Library catalog (“DOI.org (Crossref)”)

@article{burchamIdentificationZincDependentMechanisms2020, title = {Identification of {{Zinc-Dependent Mechanisms Used}} by {{Group B}} {{{}}} {{To Overcome Calprotectin-Mediated Stress}}}, author = {Burcham, Lindsey R. and Le Breton, Yoann and Radin, Jana N. and Spencer, Brady L. and Deng, Liwen and Hiron, Aur{'e}lia and Ransom, Monica R. and Mendon{}a, J{'e}ssica da C. and Belew, Ashton T. and {El-Sayed}, Najib M. and McIver, Kevin S. and {Kehl-Fie}, Thomas E. and Doran, Kelly S.}, editor = {Cook, Laura and McDaniel, Larry S.}, year = 2020, month = dec, journal = {mBio}, volume = {11}, number = {6}, pages = {e02302-20}, issn = {2161-2129, 2150-7511}, doi = {10.1128/mBio.02302-20}, url = {https://journals.asm.org/doi/10.1128/mBio.02302-20}, urldate = {2023-02-22}, abstract = {Group B Streptococcus (GBS) asymptomatically colonizes the female reproductive tract but is a common causative agent of meningitis. GBS meningitis is characterized by extensive infiltration of neutrophils carrying high concentrations of calprotectin, a metal chelator. To persist within inflammatory sites and cause invasive disease, GBS must circumvent host starvation attempts. Here, we identified global requirements for GBS survival during calprotectin challenge, including known and putative systems involved in metal ion transport. We characterized the role of zinc import in tolerating calprotectin stress in vitro and in a mouse model of infection. We observed that a global zinc uptake mutant was less virulent than the parental GBS strain and found calprotectin knockout mice to be equally susceptible to infection by wild-type (WT) and mutant strains. These findings suggest that calprotectin production at the site of infection results in a zinc-limited environment and reveals the importance of GBS metal homeostasis to invasive disease. , ABSTRACT Nutritional immunity is an elegant host mechanism used to starve invading pathogens of necessary nutrient metals. Calprotectin, a metal-binding protein, is produced abundantly by neutrophils and is found in high concentrations within inflammatory sites during infection. Group B Streptococcus (GBS) colonizes the gastrointestinal and female reproductive tracts and is commonly associated with severe invasive infections in newborns such as pneumonia, sepsis, and meningitis. Although GBS infections induce robust neutrophil recruitment and inflammation, the dynamics of GBS and calprotectin interactions remain unknown. Here, we demonstrate that disease and colonizing isolate strains exhibit susceptibility to metal starvation by calprotectin. We constructed a mariner transposon ( Krmit ) mutant library in GBS and identified 258 genes that contribute to surviving calprotectin stress. Nearly 20% of all underrepresented mutants following treatment with calprotectin are predicted metal transporters, including known zinc systems. As calprotectin binds zinc with picomolar affinity, we investigated the contribution of GBS zinc uptake to overcoming calprotectin-imposed starvation. Quantitative reverse transcriptase PCR (qRT-PCR) revealed a significant upregulation of genes encoding zinc-binding proteins, adcA , adcAII , and lmb , following calprotectin exposure, while growth in calprotectin revealed a significant defect for a global zinc acquisition mutant ({\(\Delta\)} adcA {\(\Delta\)} adcAII {\(\Delta\)} lmb ) compared to growth of the GBS wild-type (WT) strain. Furthermore, mice challenged with the {\(\Delta\)} adcA {\(\Delta\)} adcAII {\(\Delta\)} lmb mutant exhibited decreased mortality and significantly reduced bacterial burden in the brain compared to mice infected with WT GBS; this difference was abrogated in calprotectin knockout mice. Collectively, these data suggest that GBS zinc transport machinery is important for combatting zinc chelation by calprotectin and establishing invasive disease. IMPORTANCE Group B Streptococcus (GBS) asymptomatically colonizes the female reproductive tract but is a common causative agent of meningitis. GBS meningitis is characterized by extensive infiltration of neutrophils carrying high concentrations of calprotectin, a metal chelator. To persist within inflammatory sites and cause invasive disease, GBS must circumvent host starvation attempts. Here, we identified global requirements for GBS survival during calprotectin challenge, including known and putative systems involved in metal ion transport. We characterized the role of zinc import in tolerating calprotectin stress in vitro and in a mouse model of infection. We observed that a global zinc uptake mutant was less virulent than the parental GBS strain and found calprotectin knockout mice to be equally susceptible to infection by wild-type (WT) and mutant strains. These findings suggest that calprotectin production at the site of infection results in a zinc-limited environment and reveals the importance of GBS metal homeostasis to invasive disease.}, langid = {english}, file = {/home/trey/Zotero/storage/ZD3CXFGX/Burcham et al. - 2020 - Identification of Zinc-Dependent Mechanisms Used b.pdf} } % == BibTeX quality report for burchamIdentificationZincDependentMechanisms2020: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“DOI.org (Crossref)”)

@article{oliveiraGeneExpressionNetwork2020, title = {Gene Expression Network Analyses during Infection with Virulent and Avirulent {{Trypanosoma}} Cruzi Strains Unveil a Role for Fibroblasts in Neutrophil Recruitment and Activation}, author = {Oliveira, Antonio Edson R. and Pereira, Milton C. A. and Belew, Ashton T. and Ferreira, Ludmila R. P. and Pereira, Larissa M. N. and Neves, Eula G. A. and Nunes, Maria do Carmo P. and Burleigh, Barbara A. and Dutra, Walderez O. and {El-Sayed}, Najib M. and Gazzinelli, Ricardo T. and Teixeira, Santuza M. R.}, editor = {Hill, Kent L.}, year = 2020, month = aug, journal = {PLOS Pathogens}, volume = {16}, number = {8}, pages = {e1008781}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1008781}, url = {https://dx.plos.org/10.1371/journal.ppat.1008781}, urldate = {2023-02-22}, langid = {english}, file = {/home/trey/Zotero/storage/QVNLXA5Z/Oliveira et al. - 2020 - Gene expression network analyses during infection .pdf} } % == BibTeX quality report for oliveiraGeneExpressionNetwork2020: % ? unused Journal abbr (“PLoS Pathog”) % ? unused Library catalog (“DOI.org (Crossref)”)

@article{hamidzadehTransitionMCSFDerived2020, title = {The Transition of {{M-CSF}}–Derived Human Macrophages to a Growth-Promoting Phenotype}, author = {Hamidzadeh, Kajal and Belew, Ashton T. and {El-Sayed}, Najib M. and Mosser, David M.}, year = 2020, month = nov, journal = {Blood Advances}, volume = {4}, number = {21}, pages = {5460–5472}, issn = {2473-9529, 2473-9537}, doi = {10.1182/bloodadvances.2020002683}, url = {https://ashpublications.org/bloodadvances/article/4/21/5460/474108/The-transition-of-MCSFderived-human-macrophages-to}, urldate = {2023-02-22}, abstract = {Abstract Stimulated macrophages are potent producers of inflammatory mediators. This activity is highly regulated, in part, by resolving molecules to prevent tissue damage. In this study, we demonstrate that inflammation induced by Toll-like receptor stimulation is followed by the upregulation of receptors for adenosine (Ado) and prostaglandin E2 (PGE2), which help terminate macrophage activation and initiate tissue remodeling and angiogenesis. Macrophages can be hematopoietically derived from monocytes in response to 2 growth factors: macrophage colony-stimulating factor (M-CSF) and granulocyte-macrophage colony-stimulating factor (GM-CSF). We examine how exposure to either of these differentiation factors shapes the macrophage response to resolving molecules. We analyzed the transcriptomes of human monocyte-derived macrophages stimulated in the presence of Ado or PGE2 and demonstrated that, in macrophages differentiated in M-CSF, Ado and PGE2 induce a shared transcriptional program involving the downregulation of inflammatory mediators and the upregulation of growth factors. In contrast, macrophages generated in GM-CSF fail to convert to a growth-promoting phenotype, which we attribute to the suppression of receptors for Ado and PGE2 and lower production of these endogenous regulators. These observations indicate that M-CSF macrophages are better prepared to transition to a program of tissue repair, whereas GM-CSF macrophages undergo more profound activation. We implicate the differential sensitivity to pro-resolving mediators as a contributor to these divergent phenotypes. This research highlights a number of molecular targets that can be exploited to regulate the strength and duration of macrophage activation.}, langid = {english}, file = {/home/trey/Zotero/storage/EA85DBBX/Hamidzadeh et al. - 2020 - The transition of M-CSF–derived human macrophages .pdf} } % == BibTeX quality report for hamidzadehTransitionMCSFDerived2020: % ? unused Library catalog (“DOI.org (Crossref)”)

@techreport{wangPhysiologicalMagnesiumConcentrations2021, type = {Preprint}, title = {Physiological {{Magnesium Concentrations Increase Fidelity}} of {{Diverse Reverse Transcriptases}} from {{HIV-1}}, {{HIV-2}}, and {{Foamy Virus}}, but Not {{MuLV}} or {{AMV}}}, author = {Wang, Ruofan and Belew, Ashton T. and Achuthan, Vasudevan and Sayed, Najib El and DeStefano, Jeffrey J.}, year = 2021, month = aug, institution = {Biochemistry}, doi = {10.1101/2021.08.05.455312}, url = {http://biorxiv.org/lookup/doi/10.1101/2021.08.05.455312}, urldate = {2023-02-22}, abstract = {Abstract Reverse transcriptases (RTs) are typically assayed in vitro using optimized Mg 2+ concentrations ({\(\sim\)}5-10 mM) several-fold higher than physiological cellular free Mg 2+ ({\(\sim\)}0.5 mM). Analysis of fidelity using lacZ{\(\alpha\)} -based {\(\alpha\)}-complementation assays showed that tested HIV RTs, including HIV-1 from subtype B (HXB2-derived), HIV-2, subtype A/E, and several drug-resistant HXB2 derivatives all showed significantly higher fidelity using physiological Mg 2+ . This also occurred with prototype foamy virus (PFV) RT. In contrast, Moloney murine leukemia virus (MuLV) and avian myeloblastosis virus (AMV) RTs demonstrated equivalent fidelity in both low and high Mg 2+ . In 0.5 mM Mg 2+ , all RTs demonstrated {\(\approx\)} equal fidelity, except for PFV RT which showed higher fidelity. A Next Generation Sequencing (NGS) approach that used barcoding to accurately determine mutation rates and profiles was used to examine the types of mutations made by HIV-1 (subtype B, wild type) in low (0.5 mM) and high (6 mM) Mg 2+ with DNA or RNA that coded for lacZ{\(\alpha\)} . Unlike the {\(\alpha\)}-complementation assay, which is dependent on LacZ {\(\alpha\)} activity, the NGS assay scores mutations at all positions and of every type. Consistent with {\(\alpha\)}-complementation assays, a {\(\sim\)}4-fold increase in mutations was observed in high Mg 2+ . These findings help explain why HIV RT displays lower fidelity in vitro (with high Mg 2+ concentrations) than other RTs (e.g., MuLV and AMV), yet cellular fidelity for these viruses is comparable. Establishing in vitro conditions that accurately represent RT’s activity in cells is pivotal to determining the contribution of RT and other factors to the mutation profile observed with HIV.}, langid = {english}, file = {/home/trey/Zotero/storage/67625KCP/Wang et al. - 2021 - Physiological Magnesium Concentrations Increase Fi.pdf} } % == BibTeX quality report for wangPhysiologicalMagnesiumConcentrations2021: % ? unused Library catalog (“DOI.org (Crossref)”)

@article{tavaresTrypanosomaCruziZinc2021, title = {A {{{}}}{} Zinc Finger Protein That Is Implicated in the Control of Epimastigote-Specific Gene Expression and Metacyclogenesis}, author = {Tavares, Thais S. and M{"u}gge, Fernanda L. B. and {Grazielle-Silva}, Viviane and Valente, Bruna M. and Goes, Wanessa M. and Oliveira, Antonio E. R. and Belew, Ashton T. and Guarneri, Alessandra A. and Pais, Fabiano S. and {El-Sayed}, Najib M. and Teixeira, Santuza M. R.}, year = 2021, month = sep, journal = {Parasitology}, volume = {148}, number = {10}, pages = {1171–1185}, issn = {0031-1820, 1469-8161}, doi = {10.1017/S0031182020002176}, url = {https://www.cambridge.org/core/product/identifier/S0031182020002176/type/journal_article}, urldate = {2023-02-22}, abstract = {Abstract Trypanosoma cruzi has three biochemically and morphologically distinct developmental stages that are programmed to rapidly respond to environmental changes the parasite faces during its life cycle. Unlike other eukaryotes, Trypanosomatid genomes contain protein coding genes that are transcribed into polycistronic pre-mRNAs and have their expression controlled by post-transcriptional mechanisms. Transcriptome analyses comparing three stages of the T. cruzi life cycle revealed changes in gene expression that reflect the parasite adaptation to distinct environments. Several genes encoding RNA binding proteins (RBPs), known to act as key post-transcriptional regulatory factors, were also differentially expressed. We characterized one T. cruzi RBP, named TcZH3H12, which contains a zinc finger domain and is up-regulated in epimastigotes compared to trypomastigotes and amastigotes. TcZC3H12 knockout (KO) epimastigotes showed decreased growth rates and increased capacity to differentiate into metacyclic trypomastigotes. Transcriptome analyses comparing wild type and TcZC3H12 KOs revealed a TcZC3H12-dependent expression of epimastigote-specific genes such as genes encoding amino acid transporters and proteins associated with differentiation (PADs). RNA immunoprecipitation assays showed that transcripts from the PAD family interact with TcZC3H12. Taken together, these findings suggest that TcZC3H12 positively regulates the expression of genes involved in epimastigote proliferation and also acts as a negative regulator of metacyclogenesis.}, langid = {english}, file = {/home/trey/Zotero/storage/ELCSFWJ9/Tavares et al. - 2021 - A Trypanosoma cruzi zinc finger protein tha.pdf} } % == BibTeX quality report for tavaresTrypanosomaCruziZinc2021: % ? unused Library catalog (“DOI.org (Crossref)”)

@article{gomezEarlyLeukocyteResponses2021, title = {Early {{Leukocyte Responses}} in {{Ex-Vivo Models}} of {{Healing}} and {{Non-Healing Human Leishmania}} ({{Viannia}}) Panamensis {{Infections}}}, author = {Gomez, Maria Adelaida and Belew, Ashton Trey and Navas, Adriana and {Rosales-Chilama}, Mariana and Murillo, Julieth and Dillon, Laura A. L. and Alexander, Theresa A. and {Martinez-Valencia}, Alvaro and {El-Sayed}, Najib M.}, year = 2021, month = sep, journal = {Frontiers in Cellular and Infection Microbiology}, volume = {11}, pages = {687607}, issn = {2235-2988}, doi = {10.3389/fcimb.2021.687607}, url = {https://www.frontiersin.org/articles/10.3389/fcimb.2021.687607/full}, urldate = {2023-02-22}, abstract = {Early host-pathogen interactions drive the host response and shape the outcome of natural infections caused by intracellular microorganisms. These interactions involve a number of immune and non-immune cells and tissues, along with an assortment of host and pathogen-derived molecules. Our current knowledge has been predominantly derived from research on the relationships between the pathogens and the invaded host cell(s), limiting our understanding of how microbes elicit and modulate immunological responses at the organismal level. In this study, we explored the early host determinants of healing and non-healing responses in human cutaneous leishmaniasis (CL) caused by Leishmania (Viannia) panamensis . We performed a comparative transcriptomic profiling of peripheral blood mononuclear cells from healthy donors (PBMCs, n=3) exposed to promastigotes isolated from patients with chronic (CHR, n=3) or self-healing (SH, n=3) CL, and compared these to human macrophage responses. Transcriptomes of L. V. panamensis- infected PBMCs showed enrichment of functional gene categories derived from innate as well as adaptive immune cells signatures, demonstrating that Leishmania modulates adaptive immune cell functions as early as after 24h post interaction with PBMCs from previously unexposed healthy individuals. Among differentially expressed PBMC genes, four broad categories were commonly modulated by SH and CHR strains: cell cycle/proliferation/differentiation, metabolism of macromolecules, immune signaling and vesicle trafficking/transport; the first two were predominantly downregulated, and the latter upregulated in SH and CHR as compared to uninfected samples. Type I IFN signaling genes were uniquely up-regulated in PBMCs infected with CHR strains, while genes involved in the immunological synapse were uniquely downregulated in SH infections. Similarly, pro-inflammatory response genes were upregulated in isolated macrophages infected with CHR strains. Our data demonstrate that early responses during Leishmania infection extend beyond innate cell and/or phagocytic host cell functions, opening new frontiers in our understanding of the triggers and drivers of human CL.}, file = {/home/trey/Zotero/storage/4F6KL9ZN/Gomez et al. - 2021 - Early Leukocyte Responses in Ex-Vivo Models of Hea.pdf} } % == BibTeX quality report for gomezEarlyLeukocyteResponses2021: % ? unused Journal abbr (“Front. Cell. Infect. Microbiol.”) % ? unused Library catalog (“DOI.org (Crossref)”)

@article{garciademouraPD1BlockadeModulates2021, title = {{{PD-1 Blockade Modulates Functional Activities}} of {{Exhausted-Like T Cell}} in {{Patients With Cutaneous Leishmaniasis}}}, author = {{Garcia de Moura}, Renan and Covre, Luciana Polaco and Fantecelle, Carlos Henrique and Gajardo, Vitor Alejandro Torres and Cunha, Carla Baroni and Stringari, Lorenzzo Lyrio and Belew, Ashton Trey and Daniel, Camila Batista and Zeidler, Sandra Ventorin Von and Tadokoro, Carlos Eduardo and {}{de Matos Guedes}, Herbert Leonel and Zanotti, Raphael Lubiana and Mosser, David and Falqueto, Aloisio and Akbar, Arne N. and Gomes, Daniel Claudio Oliveira}, year = 2021, month = mar, journal = {Frontiers in Immunology}, volume = {12}, pages = {632667}, issn = {1664-3224}, doi = {10.3389/fimmu.2021.632667}, url = {https://www.frontiersin.org/articles/10.3389/fimmu.2021.632667/full}, urldate = {2023-02-22}, abstract = {Patients infected by Leishmania braziliensis develop debilitating skin lesions. The role of inhibitory checkpoint receptors (ICRs) that induce T cell exhaustion during this disease is not known. Transcriptional profiling identified increased expression of ICRs including PD-1, PDL-1, PDL-2, TIM-3, and CTLA-4 in skin lesions of patients that was confirmed by immunohistology where there was increased expression of PD-1, TIM-3, and CTLA-4 in both CD4 + and CD8 + T cell subsets. Moreover, PDL-1/PDL-2 ligands were increased on skin macrophages compared to healthy controls. The proportions PD1 + , but not TIM-3 or CTLA-4 expressing T cells in the circulation were positively correlated with those in the lesions of the same patients, suggesting that PD-1 may regulate T cell function equally in both compartments. Blocking PD-1 signaling in circulating T cells enhanced their proliferative capacity and IFN-{\(\gamma\)} production, but not TNF-{\(\alpha\)} secretion in response to L. braziliensis recall antigen challenge in vitro . While we previously showed a significant correlation between the accumulation of senescent CD8 + CD45RA + CD27 - T cells in the circulation and skin lesion size in the patients, there was no such correlation between the extent of PD-1 expression by circulating on T cells and the magnitude of skin lesions suggesting that exhausted-like T cells may not contribute to the cutaneous immunopathology. Nevertheless, we identified exhausted-like T cells in both skin lesions and in the blood. Targeting this population by PD-1 blockade may improve T cell function and thus accelerate parasite clearance that would reduce the cutaneous pathology in cutaneous leishmaniasis.}, file = {/home/trey/Zotero/storage/LVJ28H5G/Garcia de Moura et al. - 2021 - PD-1 Blockade Modulates Functional Activities of E.pdf} } % == BibTeX quality report for garciademouraPD1BlockadeModulates2021: % ? Title looks like it was stored in title-case in Zotero % ? unused Journal abbr (“Front. Immunol.”) % ? unused Library catalog (“DOI.org (Crossref)”)

@article{romLossRpoEEncoding2022, title = {Loss of {{rpoE Encoding}} the {\(\delta\)}-{{Factor}} of {{RNA Polymerase Impacts Pathophysiology}} of the {{Streptococcus}} Pyogenes {{M1T1 Strain}} 5448}, author = {Rom, Joseph S. and Le Breton, Yoann and Islam, Emrul and Belew, Ashton T. and {El-Sayed}, Najib M. and McIver, Kevin S.}, year = 2022, month = aug, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {1686}, issn = {2076-2607}, doi = {10.3390/microorganisms10081686}, url = {https://www.mdpi.com/2076-2607/10/8/1686}, urldate = {2023-02-22}, abstract = {Streptococcus pyogenes, also known as the Group A Streptococcus (GAS), is a Gram-positive bacterial pathogen of major clinical significance. Despite remaining relatively susceptible to conventional antimicrobial therapeutics, GAS still causes millions of infections and hundreds of thousands of deaths each year worldwide. Thus, a need for prophylactic and therapeutic interventions for GAS is in great demand. In this study, we investigated the importance of the gene encoding the delta ({\(\delta\)}) subunit of the GAS RNA polymerase, rpoE, for its impact on virulence during skin and soft-tissue infection. A defined 5448 mutant with an insertionally-inactivated rpoE gene was defective for survival in whole human blood and was attenuated for both disseminated lethality and lesion size upon mono-culture infection in mouse soft tissue. Furthermore, the mutant had reduced competitive fitness when co-infected with wild type (WT) 5448 in the mouse model. We were unable to attribute this attenuation to any observable growth defect, although colony size and the ability to grow at higher temperatures were both affected when grown with nutrient-rich THY media. RNA-seq of GAS grown in THY to late log phase found that mutation of rpoE significantly impacted ({\(>\)}2-fold) the expression of 429 total genes (205 upregulated, 224 downregulated), including multiple virulence and ``housekeeping’’ genes. The arc operon encoding the arginine deiminase (ADI) pathway was the most upregulated in the rpoE mutant and this could be confirmed phenotypically. Taken together, these findings demonstrate that the delta ({\(\delta\)}) subunit of RNA polymerase is vital in GAS gene expression and virulence.}, langid = {english}, file = {/home/trey/Zotero/storage/SPWZ4K6Z/Rom et al. - 2022 - Loss of rpoE Encoding the δ-Factor of RNA Polymera.pdf} } % == BibTeX quality report for romLossRpoEEncoding2022: % ? unused Library catalog (“DOI.org (Crossref)”)

@article{mekonnenCatheterassociatedUrinaryTract2022, title = {Catheter-Associated Urinary Tract Infection by {{{}}}{} Progresses through Acute and Chronic Phases of Infection}, author = {Mekonnen, Solomon A. and El Husseini, Nour and Turdiev, Asan and Carter, Jared A. and Belew, Ashton Trey and {El-Sayed}, Najib M. and Lee, Vincent T.}, year = 2022, month = dec, journal = {Proceedings of the National Academy of Sciences}, volume = {119}, number = {50}, pages = {e2209383119}, issn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.2209383119}, url = {https://pnas.org/doi/10.1073/pnas.2209383119}, urldate = {2023-02-22}, abstract = {Healthcare-associated infections are major causes of complications that lead to extended hospital stays and significant medical costs. The use of medical devices, including catheters, increases the risk of bacterial colonization and infection through the presence of a foreign surface. Two outcomes are observed for catheterized patients: catheter-associated asymptomatic bacteriuria and catheter-associated urinary tract infection (CAUTI). However, the relationship between these two events remains unclear. To understand this relationship, we studied a murine model of Pseudomonas aeruginosa CAUTI. In this model, we also observe two outcomes in infected animals: acute symptoms that is associated with CAUTI and chronic colonization that is associated with asymptomatic bacteriuria. The timing of the acute outcome takes place in the first week of infection, whereas chronic colonization occurs in the second week of infection. We further showed that mutants lacking genes encoding type III secretion system (T3SS), T3SS effector proteins, T3SS injection pore, or T3SS transcriptional activation all fail to cause acute symptoms of CAUTI. Nonetheless, all mutants defective for T3SS colonized the catheter and bladders at levels similar to the parental strain. In contrast, through induction of the T3SS master regulator ExsA, all infected animals showed acute phenotypes with bacteremia. Our results demonstrated that the acute symptoms, which are analogous to CAUTI, and chronic colonization, which is analogous to asymptomatic bacteriuria, are independent events that require distinct bacterial virulence factors. Experimental delineation of asymptomatic bacteriuria and CAUTI informs different strategies for the treatment and intervention of device-associated infections.}, langid = {english}, keywords = {nosource} } % == BibTeX quality report for mekonnenCatheterassociatedUrinaryTract2022: % ? unused Journal abbr (“Proc. Natl. Acad. Sci. U.S.A.”) % ? unused Library catalog (“DOI.org (Crossref)”)

@article{menckeIdentificationCharacterizationVB2022, title = {Identification and {{Characterization}} of {{vB}}_{{PreP}}_{{EPr2}}, a {{Lytic Bacteriophage}} of {{Pan-Drug Resistant Providencia}} Rettgeri}, author = {Mencke, Jaime L. and He, Yunxiu and Filippov, Andrey A. and Nikolich, Mikeljon P. and Belew, Ashton T. and Fouts, Derrick E. and McGann, Patrick T. and Swierczewski, Brett E. and Getnet, Derese and Ellison, Damon W. and Margulieux, Katie R.}, year = 2022, month = mar, journal = {Viruses}, volume = {14}, number = {4}, pages = {708}, issn = {1999-4915}, doi = {10.3390/v14040708}, url = {https://www.mdpi.com/1999-4915/14/4/708}, urldate = {2023-02-22}, abstract = {Providencia rettgeri is an emerging opportunistic Gram-negative pathogen with reports of increasing antibiotic resistance. Pan-drug resistant (PDR) P. rettgeri infections are a growing concern, demonstrating a need for the development of alternative treatment options which is fueling a renewed interest in bacteriophage (phage) therapy. Here, we identify and characterize phage vB_PreP_EPr2 (EPr2) with lytic activity against PDR P. rettgeri MRSN 845308, a clinical isolate that carries multiple antibiotic resistance genes. EPr2 was isolated from an environmental water sample and belongs to the family Autographiviridae, subfamily Studiervirinae and genus Kayfunavirus, with a genome size of 41,261 base pairs. Additional phenotypic characterization showed an optimal MOI of 1 and a burst size of 12.3 3.4 PFU per bacterium. EPr2 was determined to have a narrow host range against a panel of clinical P. rettgeri strains. Despite this fact, EPr2 is a promising lytic phage with potential for use as an alternative therapeutic for treatment of PDR P. rettgeri infections.}, langid = {english}, file = {/home/trey/Zotero/storage/Y2DJVSYH/Mencke et al. - 2022 - Identification and Characterization of vB_PreP_EPr.pdf} } % == BibTeX quality report for menckeIdentificationCharacterizationVB2022: % ? unused Library catalog (“DOI.org (Crossref)”)

@article{burchamGenomicAnalysesIdentify2022, title = {Genomic {{Analyses Identify Manganese Homeostasis}} as a {{Driver}} of {{Group B Streptococcal Vaginal Colonization}}}, author = {Burcham, Lindsey R. and Akbari, Madeline S. and Alhajjar, Norhan and Keogh, Rebecca A. and Radin, Jana N. and {Kehl-Fie}, Thomas E. and Belew, Ashton T. and {El-Sayed}, Najib M. and McIver, Kevin S. and Doran, Kelly S.}, editor = {Freitag, Nancy E.}, year = 2022, month = jun, journal = {mBio}, volume = {13}, number = {3}, pages = {e00985-22}, issn = {2150-7511}, doi = {10.1128/mbio.00985-22}, url = {https://journals.asm.org/doi/10.1128/mbio.00985-22}, urldate = {2023-02-22}, abstract = {Morbidity and mortality associated with GBS begin with colonization of the female reproductive tract (FRT). To date, our understanding of the factors required for GBS persistence in this environment remain limited. , ABSTRACT Group B Streptococcus (GBS) is associated with severe infections in utero and in newborn populations, including pneumonia, sepsis, and meningitis. GBS vaginal colonization of the pregnant mother is an important prerequisite for transmission to the newborn and the development of neonatal invasive disease; however, our understanding of the factors required for GBS persistence and ascension in the female reproductive tract (FRT) remains limited. Here, we utilized a GBS mariner transposon ( Krmit ) mutant library previously developed by our group and identified underrepresented mutations in 535 genes that contribute to survival within the vaginal lumen and colonization of vaginal, cervical, and uterine tissues. From these mutants, we identified 47 genes that were underrepresented in all samples collected, including mtsA , a component of the mtsABC locus, encoding a putative manganese (Mn 2+ )-dependent ATP-binding cassette transporter. RNA sequencing analysis of GBS recovered from the vaginal tract also revealed a robust increase of mtsA expression during vaginal colonization. We engineered an {\(\Delta\)} mtsA mutant strain and found by using inductively coupled plasma mass spectrometry that it exhibited decreased concentrations of intracellular Mn 2+ , confirming its involvement in Mn 2+ acquisition. The {\(\Delta\)} mtsA mutant was significantly more susceptible to the metal chelator calprotectin and to oxidative stressors, including both H 2 O 2 and paraquat, than wild-type (WT) GBS. We further observed that the {\(\Delta\)} mtsA mutant strain exhibited a significant fitness defect in comparison to WT GBS in vivo by using a murine model of vaginal colonization. Taken together, these data suggest that Mn 2+ homeostasis is an important process contributing to GBS survival in the FRT. IMPORTANCE Morbidity and mortality associated with GBS begin with colonization of the female reproductive tract (FRT). To date, our understanding of the factors required for GBS persistence in this environment remain limited. We identified several necessary systems for initial colonization of the vaginal lumen and penetration into the reproductive tissues via transposon mutagenesis sequencing. We determined that mutations in mtsA , the gene encoding a protein putatively involved in manganese (Mn 2+ ) transport, were significantly underrepresented in all in vivo samples collected. We also show that mtsA contributes to Mn 2+ acquisition and GBS survival during metal limitation by calprotectin, a metal-chelating protein complex. We further demonstrate that a mutant lacking mtsA is hypersusceptible to oxidative stress induced by both H 2 O 2 and paraquat and has a severe fitness defect compared to WT GBS in the murine vaginal tract. This work reveals the importance of Mn 2+ homeostasis at the host-pathogen interface in the FRT.}, langid = {english}, file = {/home/trey/Zotero/storage/W2WPNQZU/Burcham et al. - 2022 - Genomic Analyses Identify Manganese Homeostasis as.pdf} } % == BibTeX quality report for burchamGenomicAnalysesIdentify2022: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“DOI.org (Crossref)”)

@article{pilcherCrossCenterSinglecell2023, title = {Cross Center Single-Cell {{RNA}} Sequencing Study of the Immune Microenvironment in Rapid Progressing Multiple Myeloma}, author = {Pilcher, William and Thomas, Beena E. and Bhasin, Swati S. and Jayasinghe, Reyka G. and Yao, Lijun and {Gonzalez-Kozlova}, Edgar and Dasari, Surendra and {Kim-Schulze}, Seunghee and Rahman, Adeeb and Patton, Jonathan and Fiala, Mark and Cheloni, Giulia and Kourelis, Taxiarchis and Dhodapkar, Madhav V. and Vij, Ravi and Mehr, Shaadi and Hamilton, Mark and Cho, Hearn Jay and Auclair, Daniel and Avigan, David E. and Kumar, Shaji K. and Gnjatic, Sacha and Ding, Li and Bhasin, Manoj}, year = 2023, month = jan, journal = {npj Genomic Medicine}, volume = {8}, number = {1}, pages = {3}, issn = {2056-7944}, doi = {10.1038/s41525-022-00340-x}, url = {https://www.nature.com/articles/s41525-022-00340-x}, urldate = {2023-02-24}, abstract = {Abstract Despite advancements in understanding the pathophysiology of Multiple Myeloma (MM), the cause of rapid progressing disease in a subset of patients is still unclear. MM’s progression is facilitated by complex interactions with the surrounding bone marrow (BM) cells, forming a microenvironment that supports tumor growth and drug resistance. Understanding the immune microenvironment is key to identifying factors that promote rapid progression of MM. To accomplish this, we performed a multi-center single-cell RNA sequencing (scRNA-seq) study on 102,207 cells from 48 CD138 - BM samples collected at the time of disease diagnosis from 18 patients with either rapid progressing (progression-free survival (PFS),{\(<\)},18 months) or non-progressing (PFS,{\(>\)},4 years) disease. Comparative analysis of data from three centers demonstrated similar transcriptome profiles and cell type distributions, indicating subtle technical variation in scRNA-seq, opening avenues for an expanded multicenter trial. Rapid progressors depicted significantly higher enrichment of GZMK + and TIGIT + exhausted CD8 + T-cells ( P ,=,0.022) along with decreased expression of cytolytic markers ( PRF1, GZMB, GNLY ). We also observed a significantly higher enrichment of M2 tolerogenic macrophages in rapid progressors and activation of pro-proliferative signaling pathways, such as BAFF, CCL, and IL16. On the other hand, non-progressive patients depicted higher enrichment for immature B Cells (i.e., Pre/Pro B cells), with elevated expression for markers of B cell development ( IGLL1 , SOX4 , DNTT ). This multi-center study identifies the enrichment of various pro-tumorigenic cell populations and pathways in those with rapid progressing disease and further validates the robustness of scRNA-seq data generated at different study centers.}, langid = {english}, file = {/home/trey/Zotero/storage/ZBJ6EW99/Pilcher et al. - 2023 - Cross center single-cell RNA sequencing study of t.pdf} } % == BibTeX quality report for pilcherCrossCenterSinglecell2023: % ? unused Journal abbr (“npj Genom. Med.”) % ? unused Library catalog (“DOI.org (Crossref)”)

@article{kuhnBuildingPredictiveModels2008, title = {Building {{Predictive Models}} in {{R Using}} the Caret {{Package}}}, author = {Kuhn, Max}, year = 2008, month = nov, journal = {Journal of Statistical Software}, volume = {28}, number = {5}, pages = {1–26}, issn = {1548-7660}, doi = {10.18637/jss.v028.i05}, url = {https://www.jstatsoft.org/index.php/jss/article/view/v028i05}, urldate = {2023-08-09}, abstract = {The caret package, short for classification and regression training, contains numerous tools for developing predictive models using the rich set of models available in R. The package focuses on simplifying model training and tuning across a wide variety of modeling techniques. It also includes methods for pre-processing training data, calculating variable importance, and model visualizations. An example from computational chemistry is used to illustrate the functionality on a real data set and to benchmark the benefits of parallel processing with several types of models.}, chapter = {Articles}, copyright = {Copyright (c) 2008 Max Kuhn}, langid = {english}, file = {/home/trey/Zotero/storage/EM9DDMNZ/Kuhn - 2008 - Building Predictive Models in R Using the caret Package.pdf} } % == BibTeX quality report for kuhnBuildingPredictiveModels2008: % ? unused Journal abbr (“J. Stat. Soft.”) % ? unused Library catalog (“www.jstatsoft.org”)

@article{mcconvilleMetabolicPathwaysRequired2011, title = {Metabolic {{Pathways Required}} for the {{Intracellular Survival}} of {{Leishmania}}}, author = {McConville, Malcolm J. and Naderer, Thomas}, year = 2011, journal = {Annual Review of Microbiology}, volume = {65}, number = {1}, pages = {543–561}, doi = {10.1146/annurev-micro-090110-102913}, url = {https://doi.org/10.1146/annurev-micro-090110-102913}, urldate = {2023-10-20}, abstract = {Leishmania spp. are sandfly-transmitted parasitic protozoa that cause a spectrum of important diseases and lifelong chronic infections in humans. In the mammalian host, these parasites proliferate within acidified vacuoles in several phagocytic host cells, including macrophages, dendritic cells, and neutrophils. In this review, we discuss recent progress that has been made in defining the nutrient composition of the Leishmania parasitophorous vacuole, as well as metabolic pathways required by these parasites for virulence. Analysis of the virulence phenotype of Leishmania mutants has been particularly useful in defining carbon sources and nutrient salvage pathways that are essential for parasite persistence and/or induction of pathology. We also review data suggesting that intracellular parasite stages modulate metabolic processes in their host cells in order to generate a more permissive niche.}, pmid = {21721937}, keywords = {intracellular pathogens,leishmaniasis,macrophage,phagolysosome,protozoan parasites,virulence}, file = {/home/trey/Zotero/storage/CRKDGRNT/McConville and Naderer - 2011 - Metabolic Pathways Required for the Intracellular .pdf} } % == BibTeX quality report for mcconvilleMetabolicPathwaysRequired2011: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“Annual Reviews”)

@article{el-sayedCrystallizationPreliminaryXray1995, title = {Crystallization and Preliminary {{X-ray}} Investigation of the Recombinant {{Trypanosoma}} Brucei Rhodesiense Calmodulin}, author = {{El-Sayed}, Najib M. A. and Patton, Curtis L. and Harkins, Paul C. and Fox, Robert O. and Anderson, Karen}, year = 1995, journal = {Proteins: Structure, Function, and Bioinformatics}, volume = {21}, number = {4}, pages = {354–357}, issn = {1097-0134}, doi = {10.1002/prot.340210409}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.340210409}, urldate = {2023-10-20}, abstract = {Bipyramidal crystals of the recombinant calmodulin from Trypanosoma brucei rhodesiense were obtained by vapor diffusion against 55% (v/v) 2-methyl-2,4-pentanediol in 0.05 M cacodylate buffer, pH 5.6. When few nucleation events occurred, crystals grew to 0.25 0.25 1.20 mm. The space group of the crystal is I4122, with unit cell dimensions a = b = 56.88 , c = 230.11 , {\(\alpha\)} = {\(\beta\)} = {\(\gamma\)} = 90{\(^\circ\)}, z = 16. The molecular mass and volume of the unit cell suggest that there is one molecule in the asymmetric unit. The I/{\(\sigma\)}(I) ratio for data at 3.0 resolution was 3.67, indicating that the final structure can be refined at higher resolution. Molecular replacement methods and the PC-refinement technique have not yet yielded the structure under a variety of search conditions. We are currently investigating the multiple isomorphous replacement approach to determine this crystal structure. 1995 Wiley-Liss, Inc.}, copyright = {Copyright 1995 Wiley-Liss, Inc.}, langid = {english}, keywords = {calcium-binding protein,crystallography,nosource}, file = {/home/trey/Zotero/storage/TGYUUCDI/prot.html} } % == BibTeX quality report for el-sayedCrystallizationPreliminaryXray1995: % ? unused extra: _eprint (“https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.340210409”) % ? unused Library catalog (“Wiley Online Library”)

@article{bujaRemarksParallelAnalysis1992, title = {Remarks on {{Parallel Analysis}}}, author = {Buja, Andreas and Eyuboglu, Nermin}, year = 1992, month = oct, journal = {Multivariate Behavioral Research}, volume = {27}, number = {4}, pages = {509–540}, publisher = {Routledge}, issn = {0027-3171}, doi = {10.1207/s15327906mbr2704_2}, url = {https://doi.org/10.1207/s15327906mbr2704_2}, urldate = {2023-10-20}, abstract = {We investigate parallel analysis (PA), a selection rule for the number-of-factors problem, from the point of view of permutation assessment. The idea of applying permutation test ideas to PA leads to a quasi-inferential, non-parametric version of PA which accounts not only for finite-sample bias but sampling variability as well. We give evidence, however, that quasi-inferential PA based on normal random variates (as opposed to data permutations) is surprisingly independent of distributional assumptions, and enjoys therefore certain non- parametric properties as well. This is a justification for providing tables for quasi-inferential PA. Based on permutation theory, we compare PA of principal components with PA of principal factor analysis and show that PA of principal factors may tend to select too many factors. We also apply parallel analysis to so-called resistant correlations and give evidence that this yields a slightly more conservative factor selection method. Finally, we apply PA to loadings and show how this provides benchmark values for loadings which are sensitive to the number of variables, number of subjects, and order of factors. These values therefore improve on conventional fixed thresholds such as 0.5 or 0.8 which are used irrespective of the size of the data}, pmid = {26811132}, keywords = {nosource} } % == BibTeX quality report for bujaRemarksParallelAnalysis1992: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“Taylor and Francis+NEJM”)

@article{hoffmanDreamPowerfulDifferential2020, title = {Dream: Powerful Differential Expression Analysis for Repeated Measures Designs}, shorttitle = {Dream}, author = {Hoffman, Gabriel E and Roussos, Panos}, year = 2020, month = jul, journal = {Bioinformatics}, volume = {37}, number = {2}, pages = {192–201}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btaa687}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8055218/}, urldate = {2023-10-20}, abstract = {Summary Large-scale transcriptome studies with multiple samples per individual are widely used to study disease biology. Yet, current methods for differential expression are inadequate for cross-individual testing for these repeated measures designs. Most problematic, we observe across multiple datasets that current methods can give reproducible false-positive findings that are driven by genetic regulation of gene expression, yet are unrelated to the trait of interest. Here, we introduce a statistical software package, dream, that increases power, controls the false positive rate, enables multiple types of hypothesis tests, and integrates with standard workflows. In 12 analyses in 6 independent datasets, dream yields biological insight not found with existing software while addressing the issue of reproducible false-positive findings. Availability and implementation Dream is available within the variancePartition Bioconductor package at http://bioconductor.org/packages/variancePartition. Contact gabriel.hoffman@mssm.edu Supplementary information are available at Bioinformatics online.}, pmcid = {PMC8055218}, pmid = {32730587}, keywords = {nonfile}, file = {/home/trey/Zotero/storage/X744TCFW/Hoffman and Roussos - 2020 - Dream powerful differential expression analysis f.pdf} } % == BibTeX quality report for hoffmanDreamPowerfulDifferential2020: % ? unused Library catalog (“PubMed Central”)

@article{cuypersFourLayerMultiomics2022, title = {Four Layer Multi-Omics Reveals Molecular Responses to Aneuploidy in {{Leishmania}}}, author = {Cuypers, Bart and Meysman, Pieter and Erb, Ionas and Bittremieux, Wout and Valkenborg, Dirk and Baggerman, Geert and Mertens, Inge and Sundar, Shyam and Khanal, Basudha and Notredame, Cedric and Dujardin, Jean-Claude and Domagalska, Malgorzata A. and Laukens, Kris}, year = 2022, month = sep, journal = {PLOS Pathogens}, volume = {18}, number = {9}, pages = {e1010848}, publisher = {Public Library of Science}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1010848}, url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010848}, urldate = {2023-11-16}, abstract = {Aneuploidy causes system-wide disruptions in the stochiometric balances of transcripts, proteins, and metabolites, often resulting in detrimental effects for the organism. The protozoan parasite Leishmania has an unusually high tolerance for aneuploidy, but the molecular and functional consequences for the pathogen remain poorly understood. Here, we addressed this question in vitro and present the first integrated analysis of the genome, transcriptome, proteome, and metabolome of highly aneuploid Leishmania donovani strains. Our analyses unambiguously establish that aneuploidy in Leishmania proportionally impacts the average transcript- and protein abundance levels of affected chromosomes, ultimately correlating with the degree of metabolic differences between closely related aneuploid strains. This proportionality was present in both proliferative and non-proliferative in vitro promastigotes. However, as in other Eukaryotes, we observed attenuation of dosage effects for protein complex subunits and in addition, non-cytoplasmic proteins. Differentially expressed transcripts and proteins between aneuploid Leishmania strains also originated from non-aneuploid chromosomes. At protein level, these were enriched for proteins involved in protein metabolism, such as chaperones and chaperonins, peptidases, and heat-shock proteins. In conclusion, our results further support the view that aneuploidy in Leishmania can be adaptive. Additionally, we believe that the high karyotype diversity in vitro and absence of classical transcriptional regulation make Leishmania an attractive model to study processes of protein homeostasis in the context of aneuploidy and beyond.}, langid = {english}, keywords = {Aneuploidy,Genomics,Leishmania,Leishmania donovani,Protein abundance,Protein metabolism,Proteomes,Transcriptome analysis}, file = {/home/trey/Zotero/storage/P288DFTV/Cuypers et al. - 2022 - Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania.pdf} } % == BibTeX quality report for cuypersFourLayerMultiomics2022: % ? unused Library catalog (“PLoS Journals”)

@article{tarazonaDataQualityAware2015, title = {Data Quality Aware Analysis of Differential Expression in {{RNA-seq}} with {{NOISeq R}}/{{Bioc}} Package}, author = {Tarazona, Sonia and {Furi{'o}-Tar{'i}}, Pedro and Turr{`a}, David and Pietro, Antonio Di and Nueda, Mar{'i}a Jos{'e} and Ferrer, Alberto and Conesa, Ana}, year = 2015, month = dec, journal = {Nucleic Acids Research}, volume = {43}, number = {21}, pages = {e140}, issn = {0305-1048}, doi = {10.1093/nar/gkv711}, url = {https://doi.org/10.1093/nar/gkv711}, urldate = {2023-11-16}, abstract = {As the use of RNA-seq has popularized, there is an increasing consciousness of the importance of experimental design, bias removal, accurate quantification and control of false positives for proper data analysis. We introduce the NOISeq R-package for quality control and analysis of count data. We show how the available diagnostic tools can be used to monitor quality issues, make pre-processing decisions and improve analysis. We demonstrate that the non-parametric NOISeqBIO efficiently controls false discoveries in experiments with biological replication and outperforms state-of-the-art methods. NOISeq is a comprehensive resource that meets current needs for robust data-aware analysis of RNA-seq differential expression.}, file = {/home/trey/Zotero/storage/967333V7/Tarazona et al. - 2015 - Data quality aware analysis of differential expression in RNA-seq with NOISeq RBioc package.pdf;/home/trey/Zotero/storage/UIW46GE7/2468096.html} } % == BibTeX quality report for tarazonaDataQualityAware2015: % ? unused Library catalog (“Silverchair”)

@book{ripleyPatternRecognitionNeural1996, title = {Pattern {{Recognition}} and {{Neural Networks}}}, author = {Ripley, Brian D.}, year = 1996, publisher = {Cambridge University Press}, address = {Cambridge}, doi = {10.1017/CBO9780511812651}, url = {https://www.cambridge.org/core/books/pattern-recognition-and-neural-networks/4E038249C9BAA06C8F4EE6F044D09C5C}, urldate = {2024-01-30}, abstract = {This 1996 book is a reliable account of the statistical framework for pattern recognition and machine learning. With unparalleled coverage and a wealth of case-studies this book gives valuable insight into both the theory and the enormously diverse applications (which can be found in remote sensing, astrophysics, engineering and medicine, for example). So that readers can develop their skills and understanding, many of the real data sets used in the book are available from the author’s website: www.stats.ox.ac.uk/ripley/PRbook/. For the same reason, many examples are included to illustrate real problems in pattern recognition. Unifying principles are highlighted, and the author gives an overview of the state of the subject, making the book valuable to experienced researchers in statistics, machine learning/artificial intelligence and engineering. The clear writing style means that the book is also a superb introduction for non-specialists.}, isbn = {978-0-521-71770-0}, file = {/home/trey/Zotero/storage/GFIKWE9E/Ripley - 1996 - Pattern Recognition and Neural Networks.pdf;/home/trey/Zotero/storage/R8T8YAUP/4E038249C9BAA06C8F4EE6F044D09C5C.html} } % == BibTeX quality report for ripleyPatternRecognitionNeural1996: % ? Title looks like it was stored in title-case in Zotero

@article{wrightRangerFastImplementation2017, title = {Ranger: {{A Fast Implementation}} of {{Random Forests}} for {{High Dimensional Data}} in {{C}}++ and {{R}}}, shorttitle = {Ranger}, author = {Wright, Marvin N. and Ziegler, Andreas}, year = 2017, month = mar, journal = {Journal of Statistical Software}, volume = {77}, pages = {1–17}, issn = {1548-7660}, doi = {10.18637/jss.v077.i01}, url = {https://doi.org/10.18637/jss.v077.i01}, urldate = {2024-01-30}, abstract = {We introduce the C++ application and R package ranger. The software is a fast implementation of random forests for high dimensional data. Ensembles of classification, regression and survival trees are supported. We describe the implementation, provide examples, validate the package with a reference implementation, and compare runtime and memory usage with other implementations. The new software proves to scale best with the number of features, samples, trees, and features tried for splitting. Finally, we show that ranger is the fastest and most memory efficient implementation of random forests to analyze data on the scale of a genome-wide association study.}, copyright = {Copyright (c) 2017 Marvin N. Wright, Andreas Ziegler}, langid = {english}, keywords = {C,classification,machine learning,R,random forests,Rcpp,recursive partitioning,survival analysis}, file = {/home/trey/Zotero/storage/U4QR47PQ/Wright and Ziegler - 2017 - ranger A Fast Implementation of Random Forests for High Dimensional Data in C++ and R.pdf} } % == BibTeX quality report for wrightRangerFastImplementation2017: % ? unused Library catalog (“www.jstatsoft.org”)

@article{friedmanRegularizationPathsGeneralized2010, title = {Regularization {{Paths}} for {{Generalized Linear Models}} via {{Coordinate Descent}}}, author = {Friedman, Jerome H. and Hastie, Trevor and Tibshirani, Rob}, year = 2010, month = feb, journal = {Journal of Statistical Software}, volume = {33}, pages = {1–22}, issn = {1548-7660}, doi = {10.18637/jss.v033.i01}, url = {https://doi.org/10.18637/jss.v033.i01}, urldate = {2024-01-30}, abstract = {We develop fast algorithms for estimation of generalized linear models with convex penalties. The models include linear regression, two-class logistic regression, and multi- nomial regression problems while the penalties include {\(\ell\)}1 (the lasso), {\(\ell\)}2 (ridge regression) and mixtures of the two (the elastic net). The algorithms use cyclical coordinate descent, computed along a regularization path. The methods can handle large problems and can also deal efficiently with sparse features. In comparative timings we find that the new algorithms are considerably faster than competing methods.}, copyright = {Copyright (c) 2009 Jerome H. Friedman, Trevor Hastie, Rob Tibshirani}, langid = {english}, file = {/home/trey/Zotero/storage/5J38IZ26/Friedman et al. - 2010 - Regularization Paths for Generalized Linear Models via Coordinate Descent.pdf} } % == BibTeX quality report for friedmanRegularizationPathsGeneralized2010: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“www.jstatsoft.org”)

@inproceedings{chenXGBoostScalableTree2016, title = {{{XGBoost}}: {{A Scalable Tree Boosting System}}}, shorttitle = {{{XGBoost}}}, booktitle = {Proceedings of the 22nd {{ACM SIGKDD International Conference}} on {{Knowledge Discovery}} and {{Data Mining}}}, author = {Chen, Tianqi and Guestrin, Carlos}, year = 2016, month = aug, eprint = {1603.02754}, primaryclass = {cs}, pages = {785–794}, doi = {10.1145/2939672.2939785}, url = {http://arxiv.org/abs/1603.02754}, urldate = {2024-01-30}, abstract = {Tree boosting is a highly effective and widely used machine learning method. In this paper, we describe a scalable end-to-end tree boosting system called XGBoost, which is used widely by data scientists to achieve state-of-the-art results on many machine learning challenges. We propose a novel sparsity-aware algorithm for sparse data and weighted quantile sketch for approximate tree learning. More importantly, we provide insights on cache access patterns, data compression and sharding to build a scalable tree boosting system. By combining these insights, XGBoost scales beyond billions of examples using far fewer resources than existing systems.}, archiveprefix = {arXiv}, keywords = {Computer Science - Machine Learning}, file = {/home/trey/Zotero/storage/3B9QE9B4/Chen and Guestrin - 2016 - XGBoost A Scalable Tree Boosting System.pdf;/home/trey/Zotero/storage/5BPF6LMJ/1603.html} } % == BibTeX quality report for chenXGBoostScalableTree2016: % ? Title looks like it was stored in title-case in Zotero

@article{trincadoSUPPA2FastAccurate2018, title = {{{SUPPA2}}: Fast, Accurate, and Uncertainty-Aware Differential Splicing Analysis across Multiple Conditions}, shorttitle = {{{SUPPA2}}}, author = {Trincado, Juan L. and Entizne, Juan C. and Hysenaj, Gerald and Singh, Babita and Skalic, Miha and Elliott, David J. and Eyras, Eduardo}, year = 2018, month = mar, journal = {Genome Biology}, volume = {19}, number = {1}, pages = {40}, issn = {1474-760X}, doi = {10.1186/s13059-018-1417-1}, url = {https://doi.org/10.1186/s13059-018-1417-1}, urldate = {2024-02-09}, abstract = {Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method that addresses these challenges, and enables streamlined analysis across multiple conditions taking into account biological variability. Using experimental and simulated data, we show that SUPPA2 achieves higher accuracy compared to other methods, especially at low sequencing depth and short read length. We use SUPPA2 to identify novel Transformer2-regulated exons, novel microexons induced during differentiation of bipolar neurons, and novel intron retention events during erythroblast differentiation.}, langid = {english}, keywords = {Alternative splicing,Biological variability,Differential splicing,Differentiation,RNA-seq,Uncertainty}, file = {/home/trey/Zotero/storage/26R2YMS4/Trincado et al. - 2018 - SUPPA2 fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditi.pdf} } % == BibTeX quality report for trincadoSUPPA2FastAccurate2018: % ? unused Journal abbr (“Genome Biol”) % ? unused Library catalog (“Springer Link”)

@article{brouardGATKJointGenotyping2019, title = {The {{GATK}} Joint Genotyping Workflow Is Appropriate for Calling Variants in {{RNA-seq}} Experiments}, author = {Brouard, Jean-Simon and Schenkel, Flavio and Marete, Andrew and Bissonnette, Nathalie}, year = 2019, month = jun, journal = {Journal of Animal Science and Biotechnology}, volume = {10}, number = {1}, pages = {44}, issn = {2049-1891}, doi = {10.1186/s40104-019-0359-0}, url = {https://doi.org/10.1186/s40104-019-0359-0}, urldate = {2024-02-16}, abstract = {The Genome Analysis Toolkit (GATK) is a popular set of programs for discovering and genotyping variants from next-generation sequencing data. The current GATK recommendation for RNA sequencing (RNA-seq) is to perform variant calling from individual samples, with the drawback that only variable positions are reported. Versions 3.0 and above of GATK offer the possibility of calling DNA variants on cohorts of samples using the HaplotypeCaller algorithm in Genomic Variant Call Format (GVCF) mode. Using this approach, variants are called individually on each sample, generating one GVCF file per sample that lists genotype likelihoods and their genome annotations. In a second step, variants are called from the GVCF files through a joint genotyping analysis. This strategy is more flexible and reduces computational challenges in comparison to the traditional joint discovery workflow. Using a GVCF workflow for mining SNP in RNA-seq data provides substantial advantages, including reporting homozygous genotypes for the reference allele as well as missing data. Taking advantage of RNA-seq data derived from primary macrophages isolated from 50 cows, the GATK joint genotyping method for calling variants on RNA-seq data was validated by comparing this approach to a so-called ``per-sample’’ method. In addition, pair-wise comparisons of the two methods were performed to evaluate their respective sensitivity, precision and accuracy using DNA genotypes from a companion study including the same 50 cows genotyped using either genotyping-by-sequencing or with the Bovine SNP50 Beadchip (imputed to the Bovine high density). Results indicate that both approaches are very close in their capacity of detecting reference variants and that the joint genotyping method is more sensitive than the per-sample method. Given that the joint genotyping method is more flexible and technically easier, we recommend this approach for variant calling in RNA-seq experiments.}, keywords = {GATK,GVCF,Joint genotyping,RNA-seq,SNP}, file = {/home/trey/Zotero/storage/5R98YF7K/Brouard et al. - 2019 - The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments.pdf;/home/trey/Zotero/storage/PEYK97QG/s40104-019-0359-0.html} } % == BibTeX quality report for brouardGATKJointGenotyping2019: % ? unused Library catalog (“BioMed Central”)

@article{quinlanBEDToolsSwissArmyTool2014, title = {{{BEDTools}}: {{The Swiss-Army Tool}} for {{Genome Feature Analysis}}}, shorttitle = {{{BEDTools}}}, author = {Quinlan, Aaron R.}, year = 2014, journal = {Current Protocols in Bioinformatics}, volume = {47}, number = {1}, pages = {11.12.1-11.12.34}, issn = {1934-340X}, doi = {10.1002/0471250953.bi1112s47}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/0471250953.bi1112s47}, urldate = {2024-02-16}, abstract = {Technological advances have enabled the use of DNA sequencing as a flexible tool to characterize genetic variation and to measure the activity of diverse cellular phenomena such as gene isoform expression and transcription factor binding. Extracting biological insight from the experiments enabled by these advances demands the analysis of large, multi-dimensional datasets. This unit describes the use of the BEDTools toolkit for the exploration of high-throughput genomics datasets. Several protocols are presented for common genomic analyses, demonstrating how simple BEDTools operations may be combined to create bespoke pipelines addressing complex questions. Curr. Protoc. Bioinform. 47:11.12.1-11.12.34. 2014 by John Wiley & Sons, Inc.}, copyright = { 2014 John Wiley & Sons, Inc.}, langid = {english}, keywords = {bioinformatics,genome analysis,genome features,genome intervals,genomics}, file = {/home/trey/Zotero/storage/HGNTEFNQ/Quinlan - 2014 - BEDTools The Swiss-Army Tool for Genome Feature Analysis.pdf;/home/trey/Zotero/storage/53H3JABI/0471250953.html} } % == BibTeX quality report for quinlanBEDToolsSwissArmyTool2014: % ? Title looks like it was stored in title-case in Zotero % ? unused extra: _eprint (“https://onlinelibrary.wiley.com/doi/pdf/10.1002/0471250953.bi1112s47”) % ? unused Library catalog (“Wiley Online Library”)

@techreport{bushnellBBMapFastAccurate2014, title = {{{BBMap}}: {{A Fast}}, {{Accurate}}, {{Splice-Aware Aligner}}}, shorttitle = {{{BBMap}}}, author = {Bushnell, Brian}, year = 2014, month = mar, number = {LBNL-7065E}, institution = {Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)}, url = {https://www.osti.gov/biblio/1241166}, urldate = {2024-02-16}, abstract = {Alignment of reads is one of the primary computational tasks in bioinformatics. Of paramount importance to resequencing, alignment is also crucial to other areas - quality control, scaffolding, string-graph assembly, homology detection, assembly evaluation, error-correction, expression quantification, and even as a tool to evaluate other tools. An optimal aligner would greatly improve virtually any sequencing process, but optimal alignment is prohibitively expensive for gigabases of data. Here, we will present BBMap [1], a fast splice-aware aligner for short and long reads. We will demonstrate that BBMap has superior speed, sensitivity, and specificity to alternative high-throughput aligners bowtie2 [2], bwa [3], smalt, [4] GSNAP [5], and BLASR [6].}, langid = {english}, file = {/home/trey/Zotero/storage/I5GKXH58/Bushnell - 2014 - BBMap A Fast, Accurate, Splice-Aware Aligner.pdf} } % == BibTeX quality report for bushnellBBMapFastAccurate2014: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“www.osti.gov”)

@misc{ElsayedlabHpgltools2023, title = {Elsayed-Lab/Hpgltools}, year = 2023, month = oct, url = {https://github.com/elsayed-lab/hpgltools}, urldate = {2024-02-16}, abstract = {A collection of R functions to aid in host-pathogen genomic research}, howpublished = {elsayed-lab}, keywords = {annotations,bioconductor,nosource,ontology-search,pathogen-genomics,plotting-in-r,rna-seq-analysis,visualization} } % == BibTeX quality report for ElsayedlabHpgltools2023: % ? Title looks like it was stored in lower-case in Zotero % ? unused Library catalog (“GitHub”) % ? unused Original date (“2015-01-26T19:44:36Z”) % ? unused Programming language (“R”)

@article{giraldo-parraConsolidationMolecularSignature2024, title = {Consolidation of a {{Molecular Signature}} of {{Healing}} in {{Cutaneous Leishmaniasis Is Achieved}} during the {{First}} 10 {{Days}} of {{Treatment}}}, author = {{Giraldo-Parra}, Lina and {Rebell{'o}n-S{'a}nchez}, David E. and Navas, Adriana and Belew, Ashton Trey and {El-Sayed}, Najib M. and G{'o}mez, Mar{'i}a Adelaida}, year = 2024, month = jan, journal = {The Journal of Immunology}, volume = {212}, number = {5}, pages = {894–903}, issn = {0022-1767}, doi = {10.4049/jimmunol.2300576}, url = {https://doi.org/10.4049/jimmunol.2300576}, urldate = {2024-03-11}, abstract = {The immune response is central to the pathogenesis of cutaneous leishmaniasis (CL). However, most of our current understanding of the immune response in human CL derives from the analysis of systemic responses, which only partially reflect what occurs in the skin. In this study, we characterized the transcriptional dynamics of skin lesions during the course of treatment of CL patients and identified gene signatures and pathways associated with healing and nonhealing responses. We performed a comparative transcriptome profiling of serial skin lesion biopsies obtained before, in the middle, and at the end of treatment of CL patients (eight who were cured and eight with treatment failure). Lesion transcriptomes from patients who healed revealed recovery of the stratum corneum, suppression of the T cell–mediated inflammatory response, and damping of neutrophil activation, as early as 10 d after initiation of treatment. These transcriptional programs of healing were consolidated before lesion re-epithelization. In stark contrast, downregulation of genes involved in keratinization was observed throughout treatment in patients who did not heal, indicating that in addition to uncontrolled inflammation, treatment failure of CL is mediated by impaired mechanisms of wound healing. This work provides insights into the factors that contribute to the effective resolution of skin lesions caused by Leishmania (Viannia) species, sheds light on the consolidation of transcriptional programs of healing and nonhealing responses before the clinically apparent resolution of skin lesions, and identifies inflammatory and wound healing targets for host-directed therapies for CL.}, file = {/home/trey/Zotero/storage/5RABM57Y/Giraldo-Parra et al. - 2024 - Consolidation of a Molecular Signature of Healing in Cutaneous Leishmaniasis Is Achieved during the.pdf;/home/trey/Zotero/storage/43RX9V4Z/266619.html} } % == BibTeX quality report for giraldo-parraConsolidationMolecularSignature2024: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“Silverchair”)

@article{elhusseiniCharacterizationEntnerDoudoroffPathway2023, title = {Characterization of the {{Entner-Doudoroff}} Pathway in {{Pseudomonas}} Aeruginosa Catheter-Associated Urinary Tract Infections}, author = {El Husseini, Nour and Mekonnen, Solomon A. and Hall, Cherisse L. and Cole, Stephanie J. and Carter, Jared A. and Belew, Ashton T. and {El-Sayed}, Najib M. and Lee, Vincent T.}, year = 2023, month = dec, journal = {Journal of Bacteriology}, volume = {206}, number = {1}, pages = {e00361-23}, publisher = {American Society for Microbiology}, doi = {10.1128/jb.00361-23}, url = {https://journals.asm.org/doi/full/10.1128/jb.00361-23}, urldate = {2024-03-11}, file = {/home/trey/Zotero/storage/AFBMW9D9/El Husseini et al. - 2023 - Characterization of the Entner-Doudoroff pathway in Pseudomonas aeruginosa catheter-associated urina.pdf} } % == BibTeX quality report for elhusseiniCharacterizationEntnerDoudoroffPathway2023: % ? unused Library catalog (“journals.asm.org (Atypon)”)

@article{vargasMacrophageMetallothioneinsParticipate2023, title = {Macrophage Metallothioneins Participate in the Antileishmanial Activity of Antimonials}, author = {Vargas, Deninson Alejandro and Gregory, David J. and Koren, Roni Nitzan and Zilberstein, Dan and Belew, Ashton Trey and {El-Sayed}, Najib M. and G{'o}mez, Mar{'i}a Adelaida}, year = 2023, journal = {Frontiers in parasitology}, volume = {2}, pages = {1242727}, issn = {2813-2424}, doi = {10.3389/fpara.2023.1242727}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10795579/}, urldate = {2024-03-11}, abstract = {Host cell functions that participate in the pharmacokinetics and pharmacodynamics (PK/PD) of drugs against intracellular pathogen infections are critical for drug efficacy. In this study, we investigated whether macrophage mechanisms of xenobiotic detoxification contribute to the elimination of intracellular Leishmania upon exposure to pentavalent antimonials (SbV). Primary macrophages from patients with cutaneous leishmaniasis (CL) (n=6) were exposed ex vivo to L. V. panamensis infection and SbV, and transcriptomes were generated. Seven metallothionein (MT) genes, potent scavengers of heavy metals and central elements of the mammalian cell machinery for xenobiotic detoxification, were within the top 20 up-regulated genes. To functionally validate the participation of MTs in drug-mediated killing of intracellular Leishmania, tandem knockdown (KD) of MT2-A and MT1-E, MT1-F, and MT1-X was performed using a pan-MT shRNA approach in THP-1 cells. Parasite survival was unaffected in tandem-KD cells, as a consequence of strong transcriptional upregulation of MTs by infection and SbV, overcoming the KD effect. Gene silencing of the metal transcription factor-1 (MTF-1) abrogated expression of MT1 and MT2-A genes, but not ZnT-1. Upon exposure to SbV, intracellular survival of Leishmania in MTF-1KD cells was significantly enhanced. Results from this study highlight the participation of macrophage MTs in Sb-dependent parasite killing.}, pmcid = {PMC10795579}, pmid = {38239429}, keywords = {nonfile}, file = {/home/trey/Zotero/storage/NGTHRDFX/Vargas et al. - 2023 - Macrophage metallothioneins participate in the antileishmanial activity of antimonials.pdf} } % == BibTeX quality report for vargasMacrophageMetallothioneinsParticipate2023: % ? unused Journal abbr (“Front Parasitol”) % ? unused Library catalog (“PubMed Central”)

@article{akbariImpactNutritionalImmunity2023, title = {The Impact of Nutritional Immunity on {{Group B}} Streptococcal Pathogenesis during Wound Infection}, author = {Akbari, Madeline S. and Keogh, Rebecca A. and Radin, Jana N. and {Sanchez-Rosario}, Yamil and Johnson, Michael D. L. and Horswill, Alexander R. and {Kehl-Fie}, Thomas E. and Burcham, Lindsey R. and Doran, Kelly S.}, year = 2023, month = jun, journal = {mBio}, volume = {14}, number = {4}, pages = {e00304-23}, publisher = {American Society for Microbiology}, doi = {10.1128/mbio.00304-23}, url = {https://journals.asm.org/doi/full/10.1128/mbio.00304-23}, urldate = {2024-03-11}, file = {/home/trey/Zotero/storage/XQ9ZGJPQ/Akbari et al. - 2023 - The impact of nutritional immunity on Group B streptococcal pathogenesis during wound infection.pdf} } % == BibTeX quality report for akbariImpactNutritionalImmunity2023: % ? unused Library catalog (“journals.asm.org (Atypon)”)

@article{lengEBSeqEmpiricalBayes2013, title = {{{EBSeq}}: An Empirical {{Bayes}} Hierarchical Model for Inference in {{RNA-seq}} Experiments}, shorttitle = {{{EBSeq}}}, author = {Leng, Ning and Dawson, John A. and Thomson, James A. and Ruotti, Victor and Rissman, Anna I. and Smits, Bart M. G. and Haag, Jill D. and Gould, Michael N. and Stewart, Ron M. and Kendziorski, Christina}, year = 2013, month = apr, journal = {Bioinformatics}, volume = {29}, number = {8}, pages = {1035–1043}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btt087}, url = {https://doi.org/10.1093/bioinformatics/btt087}, urldate = {2024-06-21}, abstract = {Motivation: Messenger RNA expression is important in normal development and differentiation, as well as in manifestation of disease. RNA-seq experiments allow for the identification of differentially expressed (DE) genes and their corresponding isoforms on a genome-wide scale. However, statistical methods are required to ensure that accurate identifications are made. A number of methods exist for identifying DE genes, but far fewer are available for identifying DE isoforms. When isoform DE is of interest, investigators often apply gene-level (count-based) methods directly to estimates of isoform counts. Doing so is not recommended. In short, estimating isoform expression is relatively straightforward for some groups of isoforms, but more challenging for others. This results in estimation uncertainty that varies across isoform groups. Count-based methods were not designed to accommodate this varying uncertainty, and consequently, application of them for isoform inference results in reduced power for some classes of isoforms and increased false discoveries for others.Results: Taking advantage of the merits of empirical Bayesian methods, we have developed EBSeq for identifying DE isoforms in an RNA-seq experiment comparing two or more biological conditions. Results demonstrate substantially improved power and performance of EBSeq for identifying DE isoforms. EBSeq also proves to be a robust approach for identifying DE genes.Availability and implementation: An R package containing examples and sample datasets is available at http://www.biostat.wisc.edu/{$\sim$}kendzior/EBSEQ/.Contact: ~kendzior@biostat.wisc.eduSupplementary information: ~Supplementary data are available at Bioinformatics online.}, file = {/home/trey/Zotero/storage/6E778RQE/Leng et al. - 2013 - EBSeq an empirical Bayes hierarchical model for i.pdf;/home/trey/Zotero/storage/3AFVZCLH/228913.html} } % == BibTeX quality report for lengEBSeqEmpiricalBayes2013: % ? unused Library catalog (“Silverchair”)

@article{rissoNormalizationRNAseqData2014, title = {Normalization of {{RNA-seq}} Data Using Factor Analysis of Control Genes or Samples}, author = {Risso, Davide and Ngai, John and Speed, Terence P. and Dudoit, Sandrine}, year = 2014, month = sep, journal = {Nature Biotechnology}, volume = {32}, number = {9}, pages = {896–902}, publisher = {Nature Publishing Group}, issn = {1546-1696}, doi = {10.1038/nbt.2931}, url = {https://www.nature.com/articles/nbt.2931}, urldate = {2024-06-21}, abstract = {Remove unwanted variation (RUV) is a new statistical method for RNA-seq data normalization that uses control genes or samples to improve differential expression analysis.}, copyright = {2014 Springer Nature America, Inc.}, langid = {english}, keywords = {Gene expression,Next-generation sequencing,RNA sequencing,Statistical methods}, file = {/home/trey/Zotero/storage/E24E4G7Q/Risso et al. - 2014 - Normalization of RNA-seq data using factor analysi.pdf} } % == BibTeX quality report for rissoNormalizationRNAseqData2014: % ? unused Journal abbr (“Nat Biotechnol”) % ? unused Library catalog (“www.nature.com”)

@article{molaniaRemovingUnwantedVariation2023, title = {Removing Unwanted Variation from Large-Scale {{RNA}} Sequencing Data with {{PRPS}}}, author = {Molania, Ramyar and Foroutan, Momeneh and {Gagnon-Bartsch}, Johann A. and Gandolfo, Luke C. and Jain, Aryan and Sinha, Abhishek and Olshansky, Gavriel and Dobrovic, Alexander and Papenfuss, Anthony T. and Speed, Terence P.}, year = 2023, month = jan, journal = {Nature Biotechnology}, volume = {41}, number = {1}, pages = {82–95}, publisher = {Nature Publishing Group}, issn = {1546-1696}, doi = {10.1038/s41587-022-01440-w}, url = {https://www.nature.com/articles/s41587-022-01440-w}, urldate = {2024-06-21}, abstract = {Accurate identification and effective removal of unwanted variation is essential to derive meaningful biological results from RNA sequencing (RNA-seq) data, especially when the data come from large and complex studies. Using RNA-seq data from The Cancer Genome Atlas (TCGA), we examined several sources of unwanted variation and demonstrate here how these can significantly compromise various downstream analyses, including cancer subtype identification, association between gene expression and survival outcomes and gene co-expression analysis. We propose a strategy, called pseudo-replicates of pseudo-samples (PRPS), for deploying our recently developed normalization method, called removing unwanted variation III (RUV-III), to remove the variation caused by library size, tumor purity and batch effects in TCGA RNA-seq data. We illustrate the value of our approach by comparing it to the standard TCGA normalizations on several TCGA RNA-seq datasets. RUV-III with PRPS can be used to integrate and normalize other large transcriptomic datasets coming from multiple laboratories or platforms.}, copyright = {2022 The Author(s)}, langid = {english}, keywords = {Cancer genomics,Statistical methods}, file = {/home/trey/Zotero/storage/42DFS9NJ/Molania et al. - 2023 - Removing unwanted variation from large-scale RNA s.pdf} } % == BibTeX quality report for molaniaRemovingUnwantedVariation2023: % ? unused Journal abbr (“Nat Biotechnol”) % ? unused Library catalog (“www.nature.com”)

@misc{TopGO, title = {{{topGO}}}, journal = {Bioconductor}, url = {http://bioconductor.org/packages/topGO/}, urldate = {2024-06-21}, abstract = {topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.}, langid = {american}, keywords = {nosource}, file = {/home/trey/Zotero/storage/2EWGPTK2/topGO.html} }

@article{chungBestPracticesDifferential2021, title = {Best Practices on the Differential Expression Analysis of Multi-Species {{RNA-seq}}}, author = {Chung, Matthew and Bruno, Vincent M. and Rasko, David A. and Cuomo, Christina A. and Mu{~n}oz, Jos{'e} F. and Livny, Jonathan and Shetty, Amol C. and Mahurkar, Anup and Dunning Hotopp, Julie C.}, year = 2021, month = apr, journal = {Genome Biology}, volume = {22}, pages = {121}, issn = {1474-7596}, doi = {10.1186/s13059-021-02337-8}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082843/}, urldate = {2024-06-21}, abstract = {Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.}, pmcid = {PMC8082843}, pmid = {33926528}, keywords = {nonfile}, file = {/home/trey/Zotero/storage/ENPDN56A/Chung et al. - 2021 - Best practices on the differential expression anal.pdf} } % == BibTeX quality report for chungBestPracticesDifferential2021: % ? unused Journal abbr (“Genome Biol”) % ? unused Library catalog (“PubMed Central”)

@book{yuIntroductionBiomedicalKnowledge, title = {📖 {{Introduction}} {{Biomedical Knowledge Mining}} Using {{GOSemSim}} and {{clusterProfiler}}}, author = {Yu, Guangchuang}, url = {https://yulab-smu.top/biomedical-knowledge-mining-book/}, urldate = {2024-06-21}, abstract = {Biomedical knowledge mining using GOSemSim and clusterProfiler.}, langid = {english}, keywords = {nosource}, file = {/home/trey/Zotero/storage/XICLASLK/biomedical-knowledge-mining-book.html} } % == BibTeX quality report for yuIntroductionBiomedicalKnowledge: % Missing required field ‘publisher’ % Missing required field ‘year’ % ? unused Library catalog (“yulab-smu.top”)

@article{ashburnerGeneOntologyTool2000a, title = {Gene {{Ontology}}: Tool for the Unification of Biology}, shorttitle = {Gene {{Ontology}}}, author = {Ashburner, Michael and Ball, Catherine A. and Blake, Judith A. and Botstein, David and Butler, Heather and Cherry, J. Michael and Davis, Allan P. and Dolinski, Kara and Dwight, Selina S. and Eppig, Janan T. and Harris, Midori A. and Hill, David P. and {Issel-Tarver}, Laurie and Kasarskis, Andrew and Lewis, Suzanna and Matese, John C. and Richardson, Joel E. and Ringwald, Martin and Rubin, Gerald M. and Sherlock, Gavin}, year = 2000, month = may, journal = {Nature Genetics}, volume = {25}, number = {1}, pages = {25–29}, publisher = {Nature Publishing Group}, issn = {1546-1718}, doi = {10.1038/75556}, url = {https://www.nature.com/articles/ng0500_25}, urldate = {2024-06-21}, abstract = {Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.}, copyright = {2000 Nature America Inc.}, langid = {english}, keywords = {Agriculture,Animal Genetics and Genomics,Biomedicine,Cancer Research,Gene Function,general,Human Genetics}, file = {/home/trey/Zotero/storage/6BDQLCXT/Ashburner et al. - 2000 - Gene Ontology tool for the unification of biology.pdf} } % == BibTeX quality report for ashburnerGeneOntologyTool2000a: % ? unused Journal abbr (“Nat Genet”) % ? unused Library catalog (“www.nature.com”)

@article{kanehisaKEGGKyotoEncyclopedia2000, title = {{{KEGG}}: {{Kyoto Encyclopedia}} of {{Genes}} and {{Genomes}}}, shorttitle = {{{KEGG}}}, author = {Kanehisa, Minoru and Goto, Susumu}, year = 2000, month = jan, journal = {Nucleic Acids Research}, volume = {28}, number = {1}, pages = {27–30}, issn = {0305-1048}, doi = {10.1093/nar/28.1.27}, url = {https://doi.org/10.1093/nar/28.1.27}, urldate = {2024-06-21}, abstract = {KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www.genome.ad.jp/kegg/ ).}, file = {/home/trey/Zotero/storage/NEHR8MIG/Kanehisa and Goto - 2000 - KEGG Kyoto Encyclopedia of Genes and Genomes.pdf;/home/trey/Zotero/storage/2HMZ9ND2/2384332.html} } % == BibTeX quality report for kanehisaKEGGKyotoEncyclopedia2000: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“Silverchair”)

@article{croftReactomeDatabaseReactions2011, title = {Reactome: A Database of Reactions, Pathways and Biological Processes}, shorttitle = {Reactome}, author = {Croft, David and O’Kelly, Gavin and Wu, Guanming and Haw, Robin and Gillespie, Marc and Matthews, Lisa and Caudy, Michael and Garapati, Phani and Gopinath, Gopal and Jassal, Bijay and Jupe, Steven and Kalatskaya, Irina and Mahajan, Shahana and May, Bruce and Ndegwa, Nelson and Schmidt, Esther and Shamovsky, Veronica and Yung, Christina and Birney, Ewan and Hermjakob, Henning and D’Eustachio, Peter and Stein, Lincoln}, year = 2011, month = jan, journal = {Nucleic Acids Research}, volume = {39}, number = {suppl_1}, pages = {D691-D697}, issn = {0305-1048}, doi = {10.1093/nar/gkq1018}, url = {https://doi.org/10.1093/nar/gkq1018}, urldate = {2024-06-21}, abstract = {Reactome ( http://www.reactome.org ) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice.}, file = {/home/trey/Zotero/storage/6QK7SEGU/Croft et al. - 2011 - Reactome a database of reactions, pathways and bi.pdf;/home/trey/Zotero/storage/3NJ6UXHX/2505841.html} } % == BibTeX quality report for croftReactomeDatabaseReactions2011: % ? unused Library catalog (“Silverchair”)

@article{kutmonWikiPathwaysCapturingFull2016, title = {{{WikiPathways}}: Capturing the Full Diversity of Pathway Knowledge}, shorttitle = {{{WikiPathways}}}, author = {Kutmon, Martina and Riutta, Anders and Nunes, Nuno and Hanspers, Kristina and Willighagen, Egon~L. and Bohler, Anwesha and M{'e}lius, Jonathan and Waagmeester, Andra and Sinha, Sravanthi~R. and Miller, Ryan and Coort, Susan L. and Cirillo, Elisa and Smeets, Bart and Evelo, Chris~T. and Pico, Alexander R.}, year = 2016, month = jan, journal = {Nucleic Acids Research}, volume = {44}, number = {D1}, pages = {D488-D494}, issn = {0305-1048}, doi = {10.1093/nar/gkv1024}, url = {https://doi.org/10.1093/nar/gkv1024}, urldate = {2024-06-21}, abstract = {WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis. Since our last NAR update, 4 years ago, WikiPathways has experienced massive growth in content, which continues to be contributed by hundreds of individuals each year. New aspects of the diversity and depth of the collected pathways are described from the perspective of researchers interested in using pathway information in their studies. We provide updates on extensions and services to support pathway analysis and visualization via popular standalone tools, i.e. PathVisio and Cytoscape, web applications and common programming environments. We introduce the Quick Edit feature for pathway authors and curators, in addition to new means of publishing pathways and maintaining custom pathway collections to serve specific research topics and communities. In addition to the latest milestones in our pathway collection and curation effort, we also highlight the latest means to access the content as publishable figures, as standard data files, and as linked data, including bulk and programmatic access.}, file = {/home/trey/Zotero/storage/59YVWAL4/Kutmon et al. - 2016 - WikiPathways capturing the full diversity of path.pdf} } % == BibTeX quality report for kutmonWikiPathwaysCapturingFull2016: % ? unused Library catalog (“Silverchair”)

@article{wingenderTRANSFACDatabaseTranscription1996, title = {{{TRANSFAC}}: {{A Database}} on {{Transcription Factors}} and {{Their DNA Binding Sites}}}, shorttitle = {{{TRANSFAC}}}, author = {Wingender, E. and Dietze, P. and Karas, H. and Kn{"u}ppel, R.}, year = 1996, month = jan, journal = {Nucleic Acids Research}, volume = {24}, number = {1}, pages = {238–241}, issn = {0305-1048}, doi = {10.1093/nar/24.1.238}, url = {https://doi.org/10.1093/nar/24.1.238}, urldate = {2024-06-21}, abstract = {TRANSFAC is a database about eukaryotic transcription regulating DNA sequence elements and the transcription factors binding to and acting through them. This report summarizes the present status of this database and accompanying retrieval tools.}, file = {/home/trey/Zotero/storage/FLKP6QXU/Wingender et al. - 1996 - TRANSFAC A Database on Transcription Factors and .pdf;/home/trey/Zotero/storage/UP2I2CPV/2360291.html} } % == BibTeX quality report for wingenderTRANSFACDatabaseTranscription1996: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“Silverchair”)

@article{hsuMiRTarBaseDatabaseCurates2011, title = {{{miRTarBase}}: A Database Curates Experimentally Validated {{microRNA}}–Target Interactions}, shorttitle = {{{miRTarBase}}}, author = {Hsu, Sheng-Da and Lin, Feng-Mao and Wu, Wei-Yun and Liang, Chao and Huang, Wei-Chih and Chan, Wen-Ling and Tsai, Wen-Ting and Chen, Goun-Zhou and Lee, Chia-Jung and Chiu, Chih-Min and Chien, Chia-Hung and Wu, Ming-Chia and Huang, Chi-Ying and Tsou, Ann-Ping and Huang, Hsien-Da}, year = 2011, month = jan, journal = {Nucleic Acids Research}, volume = {39}, number = {suppl_1}, pages = {D163-D169}, issn = {0305-1048}, doi = {10.1093/nar/gkq1107}, url = {https://doi.org/10.1093/nar/gkq1107}, urldate = {2024-06-21}, abstract = {MicroRNAs (miRNAs), i.e. small non-coding RNA molecules ({\(\sim\)}22,nt), can bind to one or more target sites on a gene transcript to negatively regulate protein expression, subsequently controlling many cellular mechanisms. A current and curated collection of miRNA–target interactions (MTIs) with experimental support is essential to thoroughly elucidating miRNA functions under different conditions and in different species. As a database, miRTarBase has accumulated more than 3500 MTIs by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs. miRTarBase curates 3576 experimentally verified MTIs between 657 miRNAs and 2297 target genes among 17 species. miRTarBase contains the largest amount of validated MTIs by comparing with other similar, previously developed databases. The MTIs collected in the miRTarBase can also provide a large amount of positive samples to develop computational methods capable of identifying miRNA–target interactions. miRTarBase is now available on http://miRTarBase.mbc.nctu.edu.tw/ , and is updated frequently by continuously surveying research articles.}, file = {/home/trey/Zotero/storage/3LVPCWI4/Hsu et al. - 2011 - miRTarBase a database curates experimentally vali.pdf;/home/trey/Zotero/storage/QQV6CDFP/2506831.html} } % == BibTeX quality report for hsuMiRTarBaseDatabaseCurates2011: % ? unused Library catalog (“Silverchair”)

@article{pontenHumanProteinAtlas2011, title = {The {{Human Protein Atlas}} as a Proteomic Resource for Biomarker Discovery}, author = {Pont{'e}n, F. and Schwenk, J. M. and Asplund, A. and Edqvist, P.-H. D.}, year = 2011, journal = {Journal of Internal Medicine}, volume = {270}, number = {5}, pages = {428–446}, issn = {1365-2796}, doi = {10.1111/j.1365-2796.2011.02427.x}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2796.2011.02427.x}, urldate = {2024-06-21}, abstract = {Abstract. Pont'en F, Schwenk JM, Asplund A, Edqvist P-HD (Uppsala University, Uppsala; and KTH – Royal Institute of Technology, Stockholm; Sweden). The Human Protein Atlas as a proteomic resource for biomarker discovery (Review). J Intern Med 2011; 270: 428–446. The analysis of tissue-specific expression at both the gene and protein levels is vital for understanding human biology and disease. Antibody-based proteomics provides a strategy for the systematic generation of antibodies against all human proteins to combine with protein profiling in tissues and cells using tissue microarrays, immunohistochemistry and immunofluorescence. The Human Protein Atlas project was launched in 2003 with the aim of creating a map of protein expression patterns in normal cells, tissues and cancer. At present, 11 200 unique proteins corresponding to over 50% of all human protein-encoding genes have been analysed. All protein expression data, including underlying high-resolution images, are published on the free and publically available Human Protein Atlas portal (http://www.proteinatlas.org). This database provides an important source of information for numerous biomedical research projects, including biomarker discovery efforts. Moreover, the global analysis of how our genome is expressed at the protein level has provided basic knowledge on the ubiquitous expression of a large proportion of our proteins and revealed the paucity of cell- and tissue-type-specific proteins.}, copyright = { 2011 The Association for the Publication of the Journal of Internal Medicine}, langid = {english}, keywords = {antibody,biomarker,cancer,plasma profiling,proteomics,tissue microarray}, file = {/home/trey/Zotero/storage/2NJ7UJAC/Pontén et al. - 2011 - The Human Protein Atlas as a proteomic resource fo.pdf;/home/trey/Zotero/storage/KJV6QDWY/j.1365-2796.2011.02427.html} } % == BibTeX quality report for pontenHumanProteinAtlas2011: % ? unused extra: _eprint (“https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2796.2011.02427.x”) % ? unused Library catalog (“Wiley Online Library”)

@article{giurgiuCORUMComprehensiveResource2019, title = {{{CORUM}}: The Comprehensive Resource of Mammalian Protein Complexes—2019}, shorttitle = {{{CORUM}}}, author = {Giurgiu, Madalina and Reinhard, Julian and Brauner, Barbara and {Dunger-Kaltenbach}, Irmtraud and Fobo, Gisela and Frishman, Goar and Montrone, Corinna and Ruepp, Andreas}, year = 2019, month = jan, journal = {Nucleic Acids Research}, volume = {47}, number = {D1}, pages = {D559-D563}, issn = {0305-1048}, doi = {10.1093/nar/gky973}, url = {https://doi.org/10.1093/nar/gky973}, urldate = {2024-06-21}, abstract = {CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (67%), mouse (15%) and rat (10%). Given the vital functions of these macromolecular machines, their identification and functional characterization is foundational to our understanding of normal and disease biology. The new CORUM 3.0 release encompasses 4274 protein complexes offering the largest and most comprehensive publicly available dataset of mammalian protein complexes. The CORUM dataset is built from 4473 different genes, representing 22% of the protein coding genes in humans. Protein complexes are described by a protein complex name, subunit composition, cellular functions as well as the literature references. Information about stoichiometry of subunits depends on availability of experimental data. Recent developments include a graphical tool displaying known interactions between subunits. This allows the prediction of structural interconnections within protein complexes of unknown structure. In addition, we present a set of 58 protein complexes with alternatively spliced subunits. Those were found to affect cellular functions such as regulation of apoptotic activity, protein complex assembly or define cellular localization. CORUM is freely accessible at http://mips.helmholtz-muenchen.de/corum/.}, file = {/home/trey/Zotero/storage/RY5NLT98/Giurgiu et al. - 2019 - CORUM the comprehensive resource of mammalian pro.pdf;/home/trey/Zotero/storage/SVADLNS9/5144160.html} } % == BibTeX quality report for giurgiuCORUMComprehensiveResource2019: % ? unused Library catalog (“Silverchair”)

@article{kohlerHumanPhenotypeOntology2017, title = {The {{Human Phenotype Ontology}} in 2017}, author = {K{"o}hler, Sebastian and Vasilevsky, Nicole A. and Engelstad, Mark and Foster, Erin and McMurry, Julie and Aym{'e}, S{'e}gol{`e}ne and Baynam, Gareth and Bello, Susan M. and Boerkoel, Cornelius F. and Boycott, Kym M. and Brudno, Michael and Buske, Orion J. and Chinnery, Patrick F. and Cipriani, Valentina and Connell, Laureen E. and Dawkins, Hugh J.S. and DeMare, Laura E. and Devereau, Andrew D. and {de~Vries}, Bert~B.A. and Firth, Helen V. and Freson, Kathleen and Greene, Daniel and Hamosh, Ada and Helbig, Ingo and Hum, Courtney and J{"a}hn, Johanna A. and James, Roger and Krause, Roland and F.~Laulederkind, Stanley J. and Lochm{"u}ller, Hanns and Lyon, Gholson J. and Ogishima, Soichi and Olry, Annie and Ouwehand, Willem H. and Pontikos, Nikolas and Rath, Ana and Schaefer, Franz and Scott, Richard H. and Segal, Michael and Sergouniotis, Panagiotis I. and Sever, Richard and Smith, Cynthia L. and Straub, Volker and Thompson, Rachel and Turner, Catherine and Turro, Ernest and Veltman, Marijcke W.M. and Vulliamy, Tom and Yu, Jing and {von~Ziegenweidt}, Julie and Zankl, Andreas and Z{"u}chner, Stephan and Zemojtel, Tomasz and Jacobsen, Julius O.B. and Groza, Tudor and Smedley, Damian and Mungall, Christopher J. and Haendel, Melissa and Robinson, Peter N.}, year = 2017, month = jan, journal = {Nucleic Acids Research}, volume = {45}, number = {D1}, pages = {D865-D876}, issn = {0305-1048}, doi = {10.1093/nar/gkw1039}, url = {https://doi.org/10.1093/nar/gkw1039}, urldate = {2024-06-21}, abstract = {Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.}, file = {/home/trey/Zotero/storage/KUI2UV48/Köhler et al. - 2017 - The Human Phenotype Ontology in 2017.pdf;/home/trey/Zotero/storage/WFFLHVES/2574174.html} } % == BibTeX quality report for kohlerHumanPhenotypeOntology2017: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“Silverchair”)

@article{amorimVariableGeneExpression2019a, title = {Variable Gene Expression and Parasite Load Predict Treatment Outcome in Cutaneous Leishmaniasis}, author = {Amorim, C. and Novais, F. and Nguyen, B. T. and Misic, A. and Carvalho, L. and Carvalho, E. and Beiting, D. and Scott, P.}, year = 2019, journal = {Science Translational Medicine}, volume = {11}, doi = {10.1126/scitranslmed.aax4204}, url = {https://www.science.org/doi/10.1126/scitranslmed.aax4204}, urldate = {2024-06-24}, langid = {english}, file = {/home/trey/Zotero/storage/WBW75DWN/Variable gene expression and parasite load predict.pdf;/home/trey/Zotero/storage/8IU5KRE6/scitranslmed.html} }

@misc{ElsayedlabCYOA, title = {Elsayed-Lab/{{CYOA}}}, url = {https://github.com/elsayed-lab/CYOA}, urldate = {2024-06-24}, keywords = {nosource}, file = {/home/trey/Zotero/storage/Q4NDSYE7/CYOA.html} } % == BibTeX quality report for ElsayedlabCYOA: % ? Title looks like it was stored in lower-case in Zotero

@article{luMetagenomeAnalysisUsing2022, title = {Metagenome Analysis Using the {{Kraken}} Software Suite}, author = {Lu, Jennifer and Rincon, Natalia and Wood, Derrick E. and Breitwieser, Florian P. and Pockrandt, Christopher and Langmead, Ben and Salzberg, Steven L. and Steinegger, Martin}, year = 2022, month = dec, journal = {Nature Protocols}, volume = {17}, number = {12}, pages = {2815–2839}, publisher = {Nature Publishing Group}, issn = {1750-2799}, doi = {10.1038/s41596-022-00738-y}, url = {https://www.nature.com/articles/s41596-022-00738-y}, urldate = {2024-06-24}, abstract = {Metagenomic experiments expose the wide range of microscopic organisms in any microbial environment through high-throughput DNA sequencing. The computational analysis of the sequencing data is critical for the accurate and complete characterization of the microbial community. To facilitate efficient and reproducible metagenomic analysis, we introduce a step-by-step protocol for the Kraken suite, an end-to-end pipeline for the classification, quantification and visualization of metagenomic datasets. Our protocol describes the execution of the Kraken programs, via a sequence of easy-to-use scripts, in two scenarios: (1) quantification of the species in a given metagenomics sample; and (2) detection of a pathogenic agent from a clinical sample taken from a human patient. The protocol, which is executed within 1–2 h, is targeted to biologists and clinicians working in microbiome or metagenomics analysis who are familiar with the Unix command-line environment.}, copyright = {2022 Springer Nature Limited}, langid = {english}, keywords = {Bioinformatics,Metagenomics,Software}, file = {/home/trey/Zotero/storage/4KI7C45I/Lu et al. - 2022 - Metagenome analysis using the Kraken software suit.pdf} } % == BibTeX quality report for luMetagenomeAnalysisUsing2022: % ? unused Journal abbr (“Nat Protoc”) % ? unused Library catalog (“www.nature.com”)

@misc{HomoSapiensEnsembl, title = {Homo Sapiens - {{Ensembl}} Genome Browser 100}, url = {http://apr2020.archive.ensembl.org/Homo_sapiens/Info/Index}, urldate = {2024-06-24}, keywords = {nosource}, file = {/home/trey/Zotero/storage/AU8RFKQY/Index.html} }

@article{shanmugasundramTriTrypDBIntegratedFunctional2023, title = {{{TriTrypDB}}: {{An}} Integrated Functional Genomics Resource for Kinetoplastida}, shorttitle = {{{TriTrypDB}}}, author = {Shanmugasundram, Achchuthan and Starns, David and B{"o}hme, Ulrike and Amos, Beatrice and Wilkinson, Paul A. and Harb, Omar S. and Warrenfeltz, Susanne and Kissinger, Jessica C. and McDowell, Mary Ann and Roos, David S. and Crouch, Kathryn and Jones, Andrew R.}, year = 2023, month = jan, journal = {PLOS Neglected Tropical Diseases}, volume = {17}, number = {1}, pages = {e0011058}, publisher = {Public Library of Science}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0011058}, url = {https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0011058}, urldate = {2024-06-24}, abstract = {Parasitic diseases caused by kinetoplastid parasites are a burden to public health throughout tropical and subtropical regions of the world. TriTrypDB (https://tritrypdb.org) is a free online resource for data mining of genomic and functional data from these kinetoplastid parasites and is part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org). As of release 59, TriTrypDB hosts 83 kinetoplastid genomes, nine of which, including Trypanosoma brucei brucei TREU927, Trypanosoma cruzi CL Brener and Leishmania major Friedlin, undergo manual curation by integrating information from scientific publications, high-throughput assays and user submitted comments. TriTrypDB also integrates transcriptomic, proteomic, epigenomic, population-level and isolate data, functional information from genome-wide RNAi knock-down and fluorescent tagging, and results from automated bioinformatics analysis pipelines. TriTrypDB offers a user-friendly web interface embedded with a genome browser, search strategy system and bioinformatics tools to support custom in silico experiments that leverage integrated data. A Galaxy workspace enables users to analyze their private data (e.g., RNA-sequencing, variant calling, etc.) and explore their results privately in the context of publicly available information in the database. The recent addition of an annotation platform based on Apollo enables users to provide both functional and structural changes that will appear as `community annotations’ immediately and, pending curatorial review, will be integrated into the official genome annotation.}, langid = {english}, keywords = {Data visualization,Database searching,Gene ontologies,Genome analysis,Genome annotation,Genomics,Kinetoplastids,Trypanosoma}, file = {/home/trey/Zotero/storage/AGYU6F3B/Shanmugasundram et al. - 2023 - TriTrypDB An integrated functional genomics resou.pdf} } % == BibTeX quality report for shanmugasundramTriTrypDBIntegratedFunctional2023: % ? unused Library catalog (“PLoS Journals”)

@article{bonfieldHTSlibLibraryReading2021, title = {{{HTSlib}}: {{C}} Library for Reading/Writing High-Throughput Sequencing Data}, shorttitle = {{{HTSlib}}}, author = {Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies, Robert M}, year = 2021, month = feb, journal = {GigaScience}, volume = {10}, number = {2}, pages = {giab007}, issn = {2047-217X}, doi = {10.1093/gigascience/giab007}, url = {https://doi.org/10.1093/gigascience/giab007}, urldate = {2024-06-24}, abstract = {Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health.We present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and iterators, and better use of threading.Since the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen HTSlib downloaded &gt;1 million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust, and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT/BSD license.}, file = {/home/trey/Zotero/storage/AVQDZ4BE/Bonfield et al. - 2021 - HTSlib C library for readingwriting high-through.pdf;/home/trey/Zotero/storage/ZYIKPL3I/6139334.html} } % == BibTeX quality report for bonfieldHTSlibLibraryReading2021: % ? unused Library catalog (“Silverchair”)

@article{chenFastpUltrafastAllinone2018, title = {Fastp: An Ultra-Fast All-in-One {{FASTQ}} Preprocessor}, shorttitle = {Fastp}, author = {Chen, Shifu and Zhou, Yanqing and Chen, Yaru and Gu, Jia}, year = 2018, month = sep, journal = {Bioinformatics}, volume = {34}, number = {17}, pages = {i884-i890}, issn = {1367-4803}, doi = {10.1093/bioinformatics/bty560}, url = {https://doi.org/10.1093/bioinformatics/bty560}, urldate = {2024-06-24}, abstract = {Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient.We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools.The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.}, file = {/home/trey/Zotero/storage/4GKSFQ77/Chen et al. - 2018 - fastp an ultra-fast all-in-one FASTQ preprocessor.pdf;/home/trey/Zotero/storage/EJUKFKLT/5093234.html} } % == BibTeX quality report for chenFastpUltrafastAllinone2018: % ? unused Library catalog (“Silverchair”)

@article{amorimVariableGeneExpression2019, title = {Variable Gene Expression and Parasite Load Predict Treatment Outcome in Cutaneous Leishmaniasis}, author = {Amorim, Camila Farias and Novais, Fernanda O. and Nguyen, Ba T. and Misic, Ana M. and Carvalho, Lucas P. and Carvalho, Edgar M. and Beiting, Daniel P. and Scott, Phillip}, year = 2019, month = nov, journal = {Science Translational Medicine}, volume = {11}, number = {519}, pages = {eaax4204}, issn = {1946-6242}, doi = {10.1126/scitranslmed.aax4204}, abstract = {Patients infected with Leishmania braziliensis develop chronic lesions that often fail to respond to treatment with antiparasite drugs. To determine whether genes whose expression is highly variable in lesions between patients might influence disease outcome, we obtained biopsies of lesions from patients before treatment with pentavalent antimony and performed transcriptomic profiling on these clinical samples. We identified genes that were highly variably expressed between patients, and the variable expression of these genes correlated with treatment outcome. Among the most variable genes in all the patients were components of the cytolytic pathway, and the expression of these genes correlated with parasite load in the skin. We demonstrated that treatment failure was linked to the cytolytic pathway activated during infection. Using a host-pathogen marker profile of as few as three genes, we showed that eventual treatment outcome could be predicted before the start of treatment in two separate cohorts of patients with cutaneous leishmaniasis (n = 21 and n = 25). These findings raise the possibility of point-of-care diagnostic screening to identify patients at high risk of treatment failure and provide a rationale for a precision medicine approach to drug selection in cutaneous leishmaniasis. This work more broadly demonstrates the value of identifying genes of high variability in other diseases to better understand and predict diverse clinical outcomes.}, langid = {english}, pmcid = {PMC7068779}, pmid = {31748229}, keywords = {CD8-Positive T-Lymphocytes,Cell Death,Gene Expression Profiling,Gene Expression Regulation,Humans,Killer Cells Natural,Leishmania braziliensis,Leishmaniasis Cutaneous,Parasite Load,Skin,Treatment Outcome}, file = {/home/trey/Zotero/storage/XDBEHRKB/Amorim et al. - 2019 - Variable gene expression and parasite load predict.pdf} } % == BibTeX quality report for amorimVariableGeneExpression2019: % ? unused Journal abbr (“Sci Transl Med”) % ? unused Library catalog (“PubMed”)

@article{fariasamorimMultiomicProfilingCutaneous2023, title = {Multiomic Profiling of Cutaneous Leishmaniasis Infections Reveals Microbiota-Driven Mechanisms Underlying Disease Severity}, author = {Farias Amorim, Camila and Lovins, Victoria M. and Singh, Tej Pratap and Novais, Fernanda O. and Harris, Jordan C. and Lago, Alexsandro S. and Carvalho, Lucas P. and Carvalho, Edgar M. and Beiting, Daniel P. and Scott, Phillip and Grice, Elizabeth A.}, year = 2023, month = oct, journal = {Science Translational Medicine}, volume = {15}, number = {718}, pages = {eadh1469}, issn = {1946-6242}, doi = {10.1126/scitranslmed.adh1469}, abstract = {Leishmania braziliensis is a parasitic infection that can result in inflammation and skin injury with highly variable and unpredictable clinical outcomes. Here, we investigated the potential impact of microbiota on infection-induced inflammatory responses and disease resolution by conducting an integrated analysis of the skin microbiome and host transcriptome on a cohort of 62 patients infected with L. braziliensis. We found that overall bacterial burden and microbiome configurations dominated with Staphylococcus spp. were associated with delayed healing and enhanced inflammatory responses, especially by IL-1 family members. Quantification of host and bacterial transcripts on human lesions revealed that high lesional S. aureus transcript abundance was associated with delayed healing and increased expression of IL-1{\(\beta\)}. This cytokine was critical for modulating disease outcomes in L. braziliensis-infected mice colonized with S. aureus, given that its neutralization reduced pathology and inflammation. These results highlight how the human microbiome can shape disease outcomes in cutaneous leishmaniasis and suggest pathways toward host-directed therapies to mitigate the inflammatory consequences.}, langid = {english}, pmcid = {PMC10627035}, pmid = {37851822}, keywords = {Animals,Bacteria,Humans,Inflammation,Leishmaniasis Cutaneous,Mice,Microbiota,Multiomics,Patient Acuity,Staphylococcus aureus}, file = {/home/trey/Zotero/storage/MD948DEP/Farias Amorim et al. - 2023 - Multiomic profiling of cutaneous leishmaniasis inf.pdf} } % == BibTeX quality report for fariasamorimMultiomicProfilingCutaneous2023: % ? unused Journal abbr (“Sci Transl Med”) % ? unused Library catalog (“PubMed”)

@article{sacramentoCCR5PromotesMigration2024, title = {{{CCR5}} Promotes the Migration of Pathological {{CD8}}+ {{T}} Cells to the Leishmanial Lesions}, author = {Sacramento, La{'i}s Amorim and Amorim, Camila Farias and Lombana, Claudia G. and Beiting, Daniel and Novais, Fernanda and Carvalho, Lucas P. and Carvalho, Edgar M. and Scott, Phillip}, year = 2024, month = may, journal = {PLOS Pathogens}, volume = {20}, number = {5}, pages = {e1012211}, publisher = {Public Library of Science}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1012211}, url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1012211}, urldate = {2024-06-24}, abstract = {Cytolytic CD8+ T cells mediate immunopathology in cutaneous leishmaniasis without controlling parasites. Here, we identify factors involved in CD8+ T cell migration to the lesion that could be targeted to ameliorate disease severity. CCR5 was the most highly expressed chemokine receptor in patient lesions, and the high expression of CCL3 and CCL4, CCR5 ligands, was associated with delayed healing of lesions. To test the requirement for CCR5, Leishmania-infected Rag1-/- mice were reconstituted with CCR5-/- CD8+ T cells. We found that these mice developed smaller lesions accompanied by a reduction in CD8+ T cell numbers compared to controls. We confirmed these findings by showing that the inhibition of CCR5 with maraviroc, a selective inhibitor of CCR5, reduced lesion development without affecting the parasite burden. Together, these results reveal that CD8+ T cells migrate to leishmanial lesions in a CCR5-dependent manner and that blocking CCR5 prevents CD8+ T cell-mediated pathology.}, langid = {english}, keywords = {Cytopathology,Cytotoxic T cells,Ear infections,Gene expression,Leishmaniasis,Lesions,Mouse models,Parasitic diseases}, file = {/home/trey/Zotero/storage/9585SWFW/Sacramento et al. - 2024 - CCR5 promotes the migration of pathological CD8+ T.pdf} } % == BibTeX quality report for sacramentoCCR5PromotesMigration2024: % ? unused Library catalog (“PLoS Journals”)

@article{hoffmanVariancePartitionInterpretingDrivers2016, title = {{{variancePartition}}: Interpreting Drivers of Variation in Complex Gene Expression Studies}, shorttitle = {{{variancePartition}}}, author = {Hoffman, Gabriel E. and Schadt, Eric E.}, year = 2016, month = nov, journal = {BMC Bioinformatics}, volume = {17}, number = {1}, pages = {483}, issn = {1471-2105}, doi = {10.1186/s12859-016-1323-z}, url = {https://doi.org/10.1186/s12859-016-1323-z}, urldate = {2024-06-25}, abstract = {As large-scale studies of gene expression with multiple sources of biological and technical variation become widely adopted, characterizing these drivers of variation becomes essential to understanding disease biology and regulatory genetics.}, langid = {english}, keywords = {Linear mixed model,RNA-seq,Transcriptome profiling}, file = {/home/trey/Zotero/storage/MTZRKSPY/Hoffman and Schadt - 2016 - variancePartition interpreting drivers of variati.pdf} } % == BibTeX quality report for hoffmanVariancePartitionInterpretingDrivers2016: % ? unused Library catalog (“Springer Link”)

@article{garneauPhageTermToolFast2017, title = {{{PhageTerm}}: A Tool for Fast and Accurate Determination of Phage Termini and Packaging Mechanism Using next-Generation Sequencing Data}, shorttitle = {{{PhageTerm}}}, author = {Garneau, Julian R. and Depardieu, Florence and Fortier, Louis-Charles and Bikard, David and Monot, Marc}, year = 2017, month = aug, journal = {Scientific Reports}, volume = {7}, number = {1}, pages = {8292}, publisher = {Nature Publishing Group}, issn = {2045-2322}, doi = {10.1038/s41598-017-07910-5}, url = {https://www.nature.com/articles/s41598-017-07910-5}, urldate = {2024-06-25}, abstract = {The worrying rise of antibiotic resistance in pathogenic bacteria is leading to a renewed interest in bacteriophages as a treatment option. Novel sequencing technologies enable description of an increasing number of phage genomes, a critical piece of information to understand their life cycle, phage-host interactions, and evolution. In this work, we demonstrate how it is possible to recover more information from sequencing data than just the phage genome. We developed a theoretical and statistical framework to determine DNA termini and phage packaging mechanisms using NGS data. Our method relies on the detection of biases in the number of reads, which are observable at natural DNA termini compared with the rest of the phage genome. We implemented our method with the creation of the software PhageTerm and validated it using a set of phages with well-established packaging mechanisms representative of the termini diversity, i.e. 5{\(\prime\)}cos (Lambda), 3{\(\prime\)}cos (HK97), pac (P1), headful without a pac site (T4), DTR (T7) and host fragment (Mu). In addition, we determined the termini of nine Clostridium difficile phages and six phages whose sequences were retrieved from the Sequence Read Archive. PhageTerm is freely available (https://sourceforge.net/projects/phageterm), as a Galaxy ToolShed and on a Galaxy-based server (https://galaxy.pasteur.fr).}, copyright = {2017 The Author(s)}, langid = {english}, keywords = {Bacteriophages,Software}, file = {/home/trey/Zotero/storage/HXUXDB86/Garneau et al. - 2017 - PhageTerm a tool for fast and accurate determinat.pdf} } % == BibTeX quality report for garneauPhageTermToolFast2017: % ? unused Journal abbr (“Sci Rep”) % ? unused Library catalog (“www.nature.com”)

@article{emmsOrthoFinderPhylogeneticOrthology2019, title = {{{OrthoFinder}}: Phylogenetic Orthology Inference for Comparative Genomics}, shorttitle = {{{OrthoFinder}}}, author = {Emms, David M. and Kelly, Steven}, year = 2019, month = nov, journal = {Genome Biology}, volume = {20}, number = {1}, pages = {238}, issn = {1474-760X}, doi = {10.1186/s13059-019-1832-y}, url = {https://doi.org/10.1186/s13059-019-1832-y}, urldate = {2024-06-25}, abstract = {Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics. Each output is benchmarked on appropriate real or simulated datasets, and where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinder’s comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder.}, langid = {english}, keywords = {Comparative genomics,Gene duplication,Gene tree inference,Ortholog inference}, file = {/home/trey/Zotero/storage/FSXUPNLP/Emms and Kelly - 2019 - OrthoFinder phylogenetic orthology inference for .pdf} } % == BibTeX quality report for emmsOrthoFinderPhylogeneticOrthology2019: % ? unused Journal abbr (“Genome Biol”) % ? unused Library catalog (“Springer Link”)

@article{jonesInterProScanGenomescaleProtein2014, title = {{{InterProScan}} 5: Genome-Scale Protein Function Classification}, shorttitle = {{{InterProScan}} 5}, author = {Jones, Philip and Binns, David and Chang, Hsin-Yu and Fraser, Matthew and Li, Weizhong and McAnulla, Craig and McWilliam, Hamish and Maslen, John and Mitchell, Alex and Nuka, Gift and Pesseat, Sebastien and Quinn, Antony F. and {Sangrador-Vegas}, Amaia and Scheremetjew, Maxim and Yong, Siew-Yit and Lopez, Rodrigo and Hunter, Sarah}, year = 2014, month = may, journal = {Bioinformatics}, volume = {30}, number = {9}, pages = {1236–1240}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btu031}, url = {https://doi.org/10.1093/bioinformatics/btu031}, urldate = {2024-06-25}, abstract = {Motivation: Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan. Developments include improvements and additions to the outputs of the software and the complete reimplementation of the software framework, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis. InterProScan is freely available for download from the EMBl-EBI FTP site and the open source code is hosted at Google Code.Availability and implementation: InterProScan is distributed via FTP at ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/ and the source code is available from http://code.google.com/p/interproscan/.Contact: ~http://www.ebi.ac.uk/support or interhelp@ebi.ac.uk or mitchell@ebi.ac.uk}, file = {/home/trey/Zotero/storage/VRAV734Q/Jones et al. - 2014 - InterProScan 5 genome-scale protein function clas.pdf} } % == BibTeX quality report for jonesInterProScanGenomescaleProtein2014: % ? unused Library catalog (“Silverchair”)

@article{seemannProkkaRapidProkaryotic2014a, title = {Prokka: Rapid Prokaryotic Genome Annotation}, shorttitle = {Prokka}, author = {Seemann, Torsten}, year = 2014, month = jul, journal = {Bioinformatics}, volume = {30}, number = {14}, pages = {2068–2069}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btu153}, url = {https://doi.org/10.1093/bioinformatics/btu153}, urldate = {2024-06-25}, abstract = {Summary: The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Availability and implementation: Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/ . Contact: ~torsten.seemann@monash.edu}, file = {/home/trey/Zotero/storage/XQHHIHYZ/Seemann - 2014 - Prokka rapid prokaryotic genome annotation.pdf} } % == BibTeX quality report for seemannProkkaRapidProkaryotic2014a: % ? unused Library catalog (“Silverchair”)

@article{ilieRACERRapidAccurate2013, title = {{{RACER}}: {{Rapid}} and Accurate Correction of Errors in Reads}, shorttitle = {{{RACER}}}, author = {Ilie, Lucian and Molnar, Michael}, year = 2013, month = oct, journal = {Bioinformatics}, volume = {29}, number = {19}, pages = {2490–2493}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btt407}, url = {https://doi.org/10.1093/bioinformatics/btt407}, urldate = {2024-06-25}, abstract = {Motivation: High-throughput next-generation sequencing technologies enable increasingly fast and affordable sequencing of genomes and transcriptomes, with a broad range of applications. The quality of the sequencing data is crucial for all applications. A significant portion of the data produced contains errors, and ever more efficient error correction programs are needed.Results: We propose RACER (Rapid and Accurate Correction of Errors in Reads), a new software program for correcting errors in sequencing data. RACER has better error-correcting performance than existing programs, is faster and requires less memory. To support our claims, we performed extensive comparison with the existing leading programs on a variety of real datasets.Availability: RACER is freely available for non-commercial use at www.csd.uwo.ca/{\(\sim\)}ilie/RACER/.Contact: ~ilie@csd.uwo.caSupplementary information: ~Supplementary data are available at Bioinformatics online.}, file = {/home/trey/Zotero/storage/6DSBL777/Ilie and Molnar - 2013 - RACER Rapid and accurate correction of errors in .pdf;/home/trey/Zotero/storage/T3SUMGBL/187046.html} } % == BibTeX quality report for ilieRACERRapidAccurate2013: % ? unused Library catalog (“Silverchair”)

@article{coverNearestNeighborPattern1967, title = {Nearest Neighbor Pattern Classification}, author = {Cover, T. and Hart, P.}, year = 1967, month = jan, journal = {IEEE Transactions on Information Theory}, volume = {13}, number = {1}, pages = {21–27}, issn = {0018-9448, 1557-9654}, doi = {10.1109/TIT.1967.1053964}, url = {http://ieeexplore.ieee.org/document/1053964/}, urldate = {2024-06-26}, copyright = {https://ieeexplore.ieee.org/Xplorehelp/downloads/license-information/IEEE.html}, langid = {english}, file = {/home/trey/Zotero/storage/I3IIJVG6/Cover and Hart - 1967 - Nearest neighbor pattern classification.pdf} } % == BibTeX quality report for coverNearestNeighborPattern1967: % ? unused Journal abbr (“IEEE Trans. Inform. Theory”) % ? unused Library catalog (“DOI.org (Crossref)”)

@book{breimanClassificationRegressionTrees2017, title = {Classification and {{Regression Trees}}}, author = {Breiman, Leo and Friedman, Jerome and Olshen, R. A. and Stone, Charles J.}, year = 2017, month = oct, publisher = {{Chapman and Hall/CRC}}, address = {New York}, doi = {10.1201/9781315139470}, abstract = {The methodology used to construct tree structured rules is the focus of this monograph. Unlike many other statistical procedures, which moved from pencil and paper to calculators, this text’s use of trees was unthinkable before computers. Both the practical and theoretical sides have been developed in the authors’ study of tree methods. Classification and Regression Trees reflects these two sides, covering the use of trees as a data analysis method, and in a more mathematical framework, proving some of their fundamental properties.}, isbn = {978-1-315-13947-0}, keywords = {nosource} } % == BibTeX quality report for breimanClassificationRegressionTrees2017: % ? Title looks like it was stored in title-case in Zotero % ? unused Number of pages (“368”)

@article{cerianiOriginsGiniIndex2012, title = {The Origins of the {{Gini}} Index: Extracts from {{Variabilit`a}} e {{Mutabilit`a}} (1912) by {{Corrado Gini}}}, shorttitle = {The Origins of the {{Gini}} Index}, author = {Ceriani, Lidia and Verme, Paolo}, year = 2012, month = sep, journal = {The Journal of Economic Inequality}, volume = {10}, number = {3}, pages = {421–443}, issn = {1573-8701}, doi = {10.1007/s10888-011-9188-x}, url = {https://doi.org/10.1007/s10888-011-9188-x}, urldate = {2024-06-26}, abstract = {The scope of this paper is to celebrate the 100th anniversary of the Gini index by providing the original formulae. Corrado Gini introduced his index for the first time in a 1912 book published in Italian under the name of `Variabilit\a e Mutabilit`a’’ (Variability and Mutability). This article provides selected extracts of Part I of the book dedicated to measures of variability. We find that Gini proposed no less than 13 formulations of his index, none of which is known today to the large public. We also find that Gini anticipated some of the developments that derived from the study of his index.}, langid = {english}, keywords = {Corrado Gini,Gini index,Income distribution,Inequality}, file = {/home/trey/Zotero/storage/GNM83SNW/Ceriani and Verme - 2012 - The origins of the Gini index extracts from Varia.pdf} } % == BibTeX quality report for cerianiOriginsGiniIndex2012: % ? unused Journal abbr (“J Econ Inequal”) % ? unused Library catalog (“Springer Link”)

@misc{HomoSapiensEnsembla, title = {Homo Sapiens - {{Ensembl}} Genome Browser 100}, url = {http://apr2020.archive.ensembl.org/Homo_sapiens/Info/Index}, urldate = {2024-06-27}, keywords = {nosource}, file = {/home/trey/Zotero/storage/2QE5RAYX/Index.html} }

@misc{TriTrypDBLeishmaniaPanamensis, title = {{{TriTrypDB Leishmania}} Panamensis, Version 46}, url = {https://tritrypdb.org/common/downloads/release-46/LpanamensisMHOMCOL81L13/}, urldate = {2024-06-27}, keywords = {nosource}, file = {/home/trey/Zotero/storage/TR8GT5DK/LpanamensisMHOMCOL81L13.html} }

@article{smedleyBioMartBiologicalQueries2009, title = {{{BioMart}} – Biological Queries Made Easy}, author = {Smedley, Damian and Haider, Syed and Ballester, Benoit and Holland, Richard and London, Darin and Thorisson, Gudmundur and Kasprzyk, Arek}, year = 2009, month = jan, journal = {BMC Genomics}, volume = {10}, number = {1}, pages = {22}, issn = {1471-2164}, doi = {10.1186/1471-2164-10-22}, url = {https://doi.org/10.1186/1471-2164-10-22}, urldate = {2024-06-27}, abstract = {Biologists need to perform complex queries, often across a variety of databases. Typically, each data resource provides an advanced query interface, each of which must be learnt by the biologist before they can begin to query them. Frequently, more than one data source is required and for high-throughput analysis, cutting and pasting results between websites is certainly very time consuming. Therefore, many groups rely on local bioinformatics support to process queries by accessing the resource’s programmatic interfaces if they exist. This is not an efficient solution in terms of cost and time. Instead, it would be better if the biologist only had to learn one generic interface. BioMart provides such a solution.}, langid = {english}, keywords = {Arrhythmogenic Right Ventricular Dysplasia,Central Portal,Complex Query,Distribute Annotation System,Ensembl Genome Browser}, file = {/home/trey/Zotero/storage/FUV47Q3P/Smedley et al. - 2009 - BioMart – biological queries made easy.pdf} } % == BibTeX quality report for smedleyBioMartBiologicalQueries2009: % ? unused Library catalog (“Springer Link”)

@article{huberOrchestratingHighthroughputGenomic2015, title = {Orchestrating High-Throughput Genomic Analysis with {{Bioconductor}}}, author = {Huber, Wolfgang and Carey, Vincent J. and Gentleman, Robert and Anders, Simon and Carlson, Marc and Carvalho, Benilton S. and Bravo, Hector Corrada and Davis, Sean and Gatto, Laurent and Girke, Thomas and Gottardo, Raphael and Hahne, Florian and Hansen, Kasper D. and Irizarry, Rafael A. and Lawrence, Michael and Love, Michael I. and MacDonald, James and Obenchain, Valerie and Ole{'s}, Andrzej K. and Pag{`e}s, Herv{'e} and Reyes, Alejandro and Shannon, Paul and Smyth, Gordon K. and Tenenbaum, Dan and Waldron, Levi and Morgan, Martin}, year = 2015, month = feb, journal = {Nature Methods}, volume = {12}, number = {2}, pages = {115–121}, publisher = {Nature Publishing Group}, issn = {1548-7105}, doi = {10.1038/nmeth.3252}, url = {https://www.nature.com/articles/nmeth.3252}, urldate = {2024-06-27}, abstract = {A Perspective on the open-source and open-development software project Bioconductor provides an overview for prospective users and developers dealing with high-throughput data in genomics and molecular biology.}, copyright = {2015 Springer Nature America, Inc.}, langid = {english}, keywords = {Computational platforms and environments}, file = {/home/trey/Zotero/storage/CZT24CYX/Huber et al. - 2015 - Orchestrating high-throughput genomic analysis wit.pdf} } % == BibTeX quality report for huberOrchestratingHighthroughputGenomic2015: % ? unused Journal abbr (“Nat Methods”) % ? unused Library catalog (“www.nature.com”)

@misc{SlurmWorkloadManager, title = {Slurm {{Workload Manager}} - {{Documentation}}}, url = {https://slurm.schedmd.com/}, urldate = {2024-06-28}, keywords = {nosource}, file = {/home/trey/Zotero/storage/94PE2ZQG/slurm.schedmd.com.html} } % == BibTeX quality report for SlurmWorkloadManager: % ? Title looks like it was stored in title-case in Zotero

@article{xuUseGgbreakEffectively2021, title = {Use Ggbreak to {{Effectively Utilize Plotting Space}} to {{Deal With Large Datasets}} and {{Outliers}}}, author = {Xu, Shuangbin and Chen, Meijun and Feng, Tingze and Zhan, Li and Zhou, Lang and Yu, Guangchuang}, year = 2021, month = nov, journal = {Frontiers in Genetics}, volume = {12}, publisher = {Frontiers}, issn = {1664-8021}, doi = {10.3389/fgene.2021.774846}, url = {https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.774846/full}, urldate = {2024-08-02}, abstract = {{\(<\)}p{\(>\)}With the rapid increase of large-scale datasets, biomedical data visualization is facing challenges. The data may be large, have different orders of magnitude, contain extreme values, and the data distribution is not clear. Here we present an R package {\(<\)}italic{\(>\)}ggbreak{\(<\)}/italic{\(>\)} that allows users to create broken axes using {\(<\)}italic{\(>\)}ggplot2{\(<\)}/italic{\(>\)} syntax. It can effectively use the plotting area to deal with large datasets (especially for long sequential data), data with different magnitudes, and contain outliers. The {\(<\)}italic{\(>\)}ggbreak{\(<\)}/italic{\(>\)} package increases the available visual space for a better presentation of the data and detailed annotation, thus improves our ability to interpret the data. The {\(<\)}italic{\(>\)}ggbreak{\(<\)}/italic{\(>\)} package is fully compatible with {\(<\)}italic{\(>\)}ggplot2{\(<\)}/italic{\(>\)} and it is easy to superpose additional layers and applies scale and theme to adjust the plot using the {\(<\)}italic{\(>\)}ggplot2{\(<\)}/italic{\(>\)} syntax. The {\(<\)}italic{\(>\)}ggbreak{\(<\)}/italic{\(>\)} package is open-source software released under the Artistic-2.0 license, and it is freely available on CRAN ({\(<\)}ext-link ext-link-type=“uri” xlink:href=“https://CRAN.R-project.org/package=ggbreak” xmlns:xlink=“http://www.w3.org/1999/xlink”{\(>\)}https://CRAN.R-project.org/package=ggbreak{$<\(}/ext-link{\)>\(}) and Github ({\)<\(}ext-link ext-link-type="uri" xlink:href="https://github.com/YuLab-SMU/ggbreak" xmlns:xlink="http://www.w3.org/1999/xlink"{\)>\(}https://github.com/YuLab-SMU/ggbreak{\)<\(}/ext-link{\)>\(}).{\)<\(}/p{\)>$}}, langid = {english}, keywords = {Axis break,gap plot,Ggplot2,long sequential data,nosource,outlier} } % == BibTeX quality report for xuUseGgbreakEffectively2021: % ? unused Journal abbr (“Front. Genet.”)

@article{martinCutadaptRemovesAdapter2011a, title = {Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads}, author = {Martin, Marcel}, year = 2011, month = may, journal = {EMBnet.journal}, volume = {17}, number = {1}, pages = {10–12}, issn = {2226-6089}, doi = {10.14806/ej.17.1.200}, url = {https://journal.embnet.org/index.php/embnetjournal/article/view/200}, urldate = {2024-08-08}, abstract = {When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3’ adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features. Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/}, copyright = {Copyright (c)}, langid = {english}, keywords = {adapter removal,microRNA,next generation sequencing,small RNA}, file = {/home/trey/Zotero/storage/T3MKP58N/Martin - 2011 - Cutadapt removes adapter sequences from high-throu.pdf} } % == BibTeX quality report for martinCutadaptRemovesAdapter2011a: % ? Possibly abbreviated journal title EMBnet.journal % ? unused Library catalog (“journal.embnet.org”)

@misc{SandrewsFastQCQuality, title = {S-Andrews/{{FastQC}}: {{A}} Quality Control Analysis Tool for High Throughput Sequencing Data}, url = {https://github.com/s-andrews/FastQC}, urldate = {2024-08-08}, keywords = {nosource}, file = {/home/trey/Zotero/storage/VXAJ9FES/FastQC.html} }

@article{smithUMItoolsModelingSequencing2017, title = {{{UMI-tools}}: Modeling Sequencing Errors in {{Unique Molecular Identifiers}} to Improve Quantification Accuracy}, shorttitle = {{{UMI-tools}}}, author = {Smith, Tom and Heger, Andreas and Sudbery, Ian}, year = 2017, month = jan, journal = {Genome Research}, volume = {27}, number = {3}, pages = {491–499}, publisher = {Cold Spring Harbor Lab}, issn = {1088-9051, 1549-5469}, doi = {10.1101/gr.209601.116}, url = {https://genome.cshlp.org/content/27/3/491}, urldate = {2024-08-08}, abstract = {Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughput sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalized. In particular, sequencing errors in the UMI sequence are often ignored or else resolved in an ad hoc manner. We show that errors in the UMI sequence are common and introduce network-based methods to account for these errors when identifying PCR duplicates. Using these methods, we demonstrate improved quantification accuracy both under simulated conditions and real iCLIP and single-cell RNA-seq data sets. Reproducibility between iCLIP replicates and single-cell RNA-seq clustering are both improved using our proposed network-based method, demonstrating the value of properly accounting for errors in UMIs. These methods are implemented in the open source UMI-tools software package.}, langid = {english}, pmid = {28100584}, file = {/home/trey/Zotero/storage/AJHKHLP7/Smith et al. - 2017 - UMI-tools modeling sequencing errors in Unique Mo.pdf} } % == BibTeX quality report for smithUMItoolsModelingSequencing2017: % ? unused Journal abbr (“Genome Res.”) % ? unused Library catalog (“genome.cshlp.org”)

@misc{Mus_musculusEnsemblGenome, title = {Mus_musculus - {{Ensembl}} Genome Browser 112}, url = {http://May2024.archive.ensembl.org/Mus_musculus/Info/Index}, urldate = {2024-08-08}, keywords = {nosource}, file = {/home/trey/Zotero/storage/PFIQ5XDM/Index.html} }

@article{liMaleGermcellspecificRibosome2022, title = {A Male Germ-Cell-Specific Ribosome Controls Male Fertility}, author = {Li, Huiling and Huo, Yangao and He, Xi and Yao, Liping and Zhang, Hao and Cui, Yiqiang and Xiao, Huijuan and Xie, Wenxiu and Zhang, Dejiu and Wang, Yue and Zhang, Shu and Tu, Haixia and Cheng, Yiwei and Guo, Yueshuai and Cao, Xintao and Zhu, Yunfei and Jiang, Tao and Guo, Xuejiang and Qin, Yan and Sha, Jiahao}, year = 2022, month = dec, journal = {Nature}, volume = {612}, number = {7941}, pages = {725–731}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/s41586-022-05508-0}, url = {https://www.nature.com/articles/s41586-022-05508-0}, urldate = {2024-08-08}, abstract = {Ribosomes are highly sophisticated translation machines that have been demonstrated to be heterogeneous in the regulation of protein synthesis1,2. Male germ cell development involves complex translational regulation during sperm formation3. However, it remains unclear whether translation during sperm formation is performed by a specific ribosome. Here we report a ribosome with a specialized nascent polypeptide exit tunnel, RibosomeST, that is assembled with the male germ-cell-specific protein RPL39L, the paralogue of core ribosome (RibosomeCore) protein RPL39. Deletion of RibosomeST in mice causes defective sperm formation, resulting in substantially reduced fertility. Our comparison of single-particle cryo-electron microscopy structures of ribosomes from mouse kidneys and testes indicates that RibosomeST features a ribosomal polypeptide exit tunnel of distinct size and charge states compared with RibosomeCore. RibosomeST predominantly cotranslationally regulates the folding of a subset of male germ-cell-specific proteins that are essential for the formation of sperm. Moreover, we found that specialized functions of RibosomeST were not replaceable by RibosomeCore. Taken together, identification of this sperm-specific ribosome should greatly expand our understanding of ribosome function and tissue-specific regulation of protein expression pattern in mammals.}, copyright = {2022 The Author(s), under exclusive licence to Springer Nature Limited}, langid = {english}, keywords = {Cryoelectron microscopy,Ribosome,Spermatogenesis}, file = {/home/trey/Zotero/storage/2TAIQSJV/Li et al. - 2022 - A male germ-cell-specific ribosome controls male f.pdf} } % == BibTeX quality report for liMaleGermcellspecificRibosome2022: % ? unused Library catalog (“www.nature.com”)

@article{ritchieLimmaPowersDifferential2015, title = {Limma Powers Differential Expression Analyses for {{RNA-sequencing}} and Microarray Studies}, author = {Ritchie, Matthew E. and Phipson, Belinda and Wu, Di and Hu, Yifang and Law, Charity W. and Shi, Wei and Smyth, Gordon K.}, year = 2015, month = apr, journal = {Nucleic Acids Research}, volume = {43}, number = {7}, pages = {e47}, issn = {0305-1048}, doi = {10.1093/nar/gkv007}, url = {https://doi.org/10.1093/nar/gkv007}, urldate = {2024-08-08}, abstract = {limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.}, file = {/home/trey/Zotero/storage/YM98LAWZ/Ritchie et al. - 2015 - limma powers differential expression analyses for .pdf;/home/trey/Zotero/storage/A4KENEPZ/2414268.html} } % == BibTeX quality report for ritchieLimmaPowersDifferential2015: % ? unused Library catalog (“Silverchair”)

@article{robinsonEdgeRBioconductorPackage2010, title = {{{edgeR}}: A {{Bioconductor}} Package for Differential Expression Analysis of Digital Gene Expression Data}, shorttitle = {{{edgeR}}}, author = {Robinson, Mark D. and McCarthy, Davis J. and Smyth, Gordon K.}, year = 2010, month = jan, journal = {Bioinformatics}, volume = {26}, number = {1}, pages = {139–140}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btp616}, url = {https://doi.org/10.1093/bioinformatics/btp616}, urldate = {2024-08-08}, abstract = {Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data.Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org).Contact: ~mrobinson@wehi.edu.au}, file = {/home/trey/Zotero/storage/EI8LBUKC/Robinson et al. - 2010 - edgeR a Bioconductor package for differential exp.pdf;/home/trey/Zotero/storage/47SRVIZV/182458.html} } % == BibTeX quality report for robinsonEdgeRBioconductorPackage2010: % ? unused Library catalog (“Silverchair”)

@article{tarazonaNOIseqRNAseqDifferential2011, title = {{{NOIseq}}: A {{RNA-seq}} Differential Expression Method Robust for Sequencing Depth Biases}, shorttitle = {{{NOIseq}}}, author = {Tarazona, Sonia and Garc{'i}a, Fernando and Ferrer, Alberto and Dopazo, Joaqu{'i}n and Conesa, Ana}, year = 2011, journal = {EMBnet.journal}, volume = {17}, number = {B}, pages = {18–19}, issn = {2226-6089}, doi = {10.14806/ej.17.B.265}, url = {https://journal.embnet.org/index.php/embnetjournal/article/view/265}, urldate = {2024-08-08}, abstract = {http://bioinfo.cipf.es/aconesaIntroductionNext Generation Sequencing (NGS) technologies have brought a revolution to research in genome and genome regulation. One of the most breaking applications of NGS is in transcriptome analysis. RNA-seq has revealed exciting new data on gene models, alternative splicing and extra-genic expression. Also RNA-seq permits the quantification of gene expression across a large dynamic range and with more reproducibility than microarrays. Several methods for the assessment of differential expression from count data have been proposed but biases associated to transcript length and transcript frequency distributions have been reported. It is still not clear how much sequencing reads should be generated in a RNA-seq experiment to obtain reliable results and what’s exactly being detected. In general we observed that many RNA-seq datasets have not reached saturation for detection of expressed genes and that the relative proportion of different transcript biotypes changes with increasing sequencing depth. In this work we investigate the effect that library size has on the assessment of differential expression on different aspects of the selected genes. We show that current statistical methods suffer from a strong dependency of their significant calls on the number of mapped reads considered and proposed a novel differential expression methodology – NOISeq1- that is robust to the amount of reads.ResultsNOISeq is a non-parametric approach for the differential expression analysis of RNseq-data. NOISeq creates a null or noise distribution of count changes by comparing the number of reads of each gene in samples within the same condition. This reference distribution is then used to assess whether the change in count number between two conditions for a given gene is likely to be part of the noise or represents a true differential expression. Two variants of the method are implemented: NOISeq-real uses replicates, when available, to compute the noise distribution and, NOISeq-sim simulates them in absence of replication. We compared our method with edgeR2, DESeq3, baySeq4 and Fisher Exact Test (FET) using three different experimental datasets. Results are presented for MAQC experiment where the transcriptome of brain and Universal Human Reference (HUR) samples were sequenced at about 45 million Solexa reads each.We first determined that although protein-coding gene is the most abundant transcript type within differential expression calls for all methodologies, other RNA types, such as processed-transcript, pseudogenes and lincRNAs are readily detected. NOISeq dected comparatively more protein-coding genes than other methods that called significant a considerable number of non-coding and small RNA transcripts. Additionally, all comparing methods except FET greatly increased the number of detected (non-coding) genes as sequencing depth raised while NOISeq showed a constant pattern. Also these other methods tend to select shorter genes and smaller fold change differences with the increasing amounts of reads. In general, parametric approaches selected much more genes than NOISeq, specially at high sequencing depth rates. When analyzing the functional content of these genes by functional enrichment analysis, we observed that the pool of genes detected both by NOISeq and the parametric methods where highly enriched in functional categories, while genes selected only by parametric methods did not. To check whether this differences were indicative of different false calls between methods, we used the RT-PCR data available at the MAQC project that contains 330 true positive and 83 true negative differentially expressed genes. Performance plots indicate that edgeR, DESeq, baySeq strongly increased the number of false calls with sequencing depth, while NOISeq was constant and low. On the contrary true discoveries were slightly better for these methods, presumably consequence of their large number of selected genes. FET showed in low false and true discovery rates, due to its general lower detection power.ConclusionsWe showed that most current RNA-seq statistical analysis methods fail to control the number of false discoveries as the size of the sequenced library increases. These false positive are mainly short, non- coding genes and/or genes with small fold changes. NOISeq, but adopting an empirical approach to model the null distribution of differential expression captures better the shape of noise in RNA-seq data, resulting in a sequencing-depth robust method for differential expression analysis.References1. Tarazona S., Garcia-Alcalde F., Ferrer A., Dopazo J., Conesa, A. Differential expression in RNA-seq:a matter of depth. Genome Research, Sep 2011, doi:10.1101/gr.124321.11.2. Robinson, MD, McCarthy, DJ, and Smyth, GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1):139,140.3. Anders, S and Huber, W. 2010. Differential expression analysis for sequence count data. Genome Biology 11(10):R106.4. Hardcastle, T and Kelly, K. 2010. baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11(1):422+.Relevant Web sites5. http://bioinfo.cipf.es/noiseq}, copyright = {Copyright (c)}, langid = {american}, keywords = {COST,differential expression,next generation sequencing,non-parametric approach,RNA-seq}, file = {/home/trey/Zotero/storage/5UH8VBV2/Tarazona et al. - 2011 - NOIseq a RNA-seq differential expression method r.pdf} } % == BibTeX quality report for tarazonaNOIseqRNAseqDifferential2011: % ? Possibly abbreviated journal title EMBnet.journal % ? unused Library catalog (“journal.embnet.org”)

@article{raudvereProfilerWebServer2019, title = {G:{{Profiler}}: A Web Server for Functional Enrichment Analysis and Conversions of Gene Lists (2019 Update)}, shorttitle = {G}, author = {Raudvere, Uku and Kolberg, Liis and Kuzmin, Ivan and Arak, Tambet and Adler, Priit and Peterson, Hedi and Vilo, Jaak}, year = 2019, month = jul, journal = {Nucleic Acids Research}, volume = {47}, number = {W1}, pages = {W191-W198}, issn = {0305-1048}, doi = {10.1093/nar/gkz369}, url = {https://doi.org/10.1093/nar/gkz369}, urldate = {2024-08-08}, abstract = {Biological data analysis often deals with lists of genes arising from various studies. The g:Profiler toolset is widely used for finding biological categories enriched in gene lists, conversions between gene identifiers and mappings to their orthologs. The mission of g:Profiler is to provide a reliable service based on up-to-date high quality data in a convenient manner across many evidence types, identifier spaces and organisms. g:Profiler relies on Ensembl as a primary data source and follows their quarterly release cycle while updating the other data sources simultaneously. The current update provides a better user experience due to a modern responsive web interface, standardised API and libraries. The results are delivered through an interactive and configurable web design. Results can be downloaded as publication ready visualisations or delimited text files. In the current update we have extended the support to 467 species and strains, including vertebrates, plants, fungi, insects and parasites. By supporting user uploaded custom GMT files, g:Profiler is now capable of analysing data from any organism. All past releases are maintained for reproducibility and transparency. The 2019 update introduces an extensive technical rewrite making the services faster and more flexible. g:Profiler is freely available at https://biit.cs.ut.ee/gprofiler.}, file = {/home/trey/Zotero/storage/2HUTSHI2/Raudvere et al. - 2019 - gProfiler a web server for functional enrichment.pdf;/home/trey/Zotero/storage/TUFX8P8X/5486750.html} } % == BibTeX quality report for raudvereProfilerWebServer2019: % ? unused Library catalog (“Silverchair”)

@article{hanzelmannGSVAGeneSet2013a, title = {{{GSVA}}: Gene Set Variation Analysis for Microarray and {{RNA-Seq}} Data}, shorttitle = {{{GSVA}}}, author = {H{"a}nzelmann, Sonja and Castelo, Robert and Guinney, Justin}, year = 2013, month = jan, journal = {BMC Bioinformatics}, volume = {14}, number = {1}, pages = {7}, issn = {1471-2105}, doi = {10.1186/1471-2105-14-7}, url = {https://doi.org/10.1186/1471-2105-14-7}, urldate = {2024-08-08}, abstract = {Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as well as greater biological interpretability. As molecular profiling experiments move beyond simple case-control studies, robust and flexible GSE methodologies are needed that can model pathway activity within highly heterogeneous data sets.}, langid = {english}, keywords = {Adjusted Rand Index,Differentially Express,Differentially Express Gene,Enrichment Score,Linear Additive Model}, file = {/home/trey/Zotero/storage/MMV4PEE5/Hänzelmann et al. - 2013 - GSVA gene set variation analysis for microarray a.pdf} } % == BibTeX quality report for hanzelmannGSVAGeneSet2013a: % ? unused Library catalog (“Springer Link”)

@article{wrightRangerFastImplementation2017a, title = {Ranger: {{A Fast Implementation}} of {{Random Forests}} for {{High Dimensional Data}} in {{C}}++ and {{R}}}, shorttitle = {Ranger}, author = {Wright, Marvin N. and Ziegler, Andreas}, year = 2017, month = mar, journal = {Journal of Statistical Software}, volume = {77}, pages = {1–17}, issn = {1548-7660}, doi = {10.18637/jss.v077.i01}, url = {https://doi.org/10.18637/jss.v077.i01}, urldate = {2024-08-22}, abstract = {We introduce the C++ application and R package ranger. The software is a fast implementation of random forests for high dimensional data. Ensembles of classification, regression and survival trees are supported. We describe the implementation, provide examples, validate the package with a reference implementation, and compare runtime and memory usage with other implementations. The new software proves to scale best with the number of features, samples, trees, and features tried for splitting. Finally, we show that ranger is the fastest and most memory efficient implementation of random forests to analyze data on the scale of a genome-wide association study.}, copyright = {Copyright (c) 2017 Marvin N. Wright, Andreas Ziegler}, langid = {english}, keywords = {C,classification,machine learning,R,random forests,Rcpp,recursive partitioning,survival analysis}, file = {/home/trey/Zotero/storage/Q8TM9F5Q/Wright and Ziegler - 2017 - ranger A Fast Implementation of Random Forests fo.pdf} } % == BibTeX quality report for wrightRangerFastImplementation2017a: % ? unused Library catalog (“www.jstatsoft.org”)

@inproceedings{chenXGBoostScalableTree2016a, title = {{{XGBoost}}: {{A Scalable Tree Boosting System}}}, shorttitle = {{{XGBoost}}}, booktitle = {Proceedings of the 22nd {{ACM SIGKDD International Conference}} on {{Knowledge Discovery}} and {{Data Mining}}}, author = {Chen, Tianqi and Guestrin, Carlos}, year = 2016, month = aug, series = {{{KDD}} ’16}, pages = {785–794}, publisher = {Association for Computing Machinery}, address = {New York, NY, USA}, doi = {10.1145/2939672.2939785}, url = {https://dl.acm.org/doi/10.1145/2939672.2939785}, urldate = {2024-08-27}, abstract = {Tree boosting is a highly effective and widely used machine learning method. In this paper, we describe a scalable end-to-end tree boosting system called XGBoost, which is used widely by data scientists to achieve state-of-the-art results on many machine learning challenges. We propose a novel sparsity-aware algorithm for sparse data and weighted quantile sketch for approximate tree learning. More importantly, we provide insights on cache access patterns, data compression and sharding to build a scalable tree boosting system. By combining these insights, XGBoost scales beyond billions of examples using far fewer resources than existing systems.}, isbn = {978-1-4503-4232-2}, file = {/home/trey/Zotero/storage/3DAVVAR5/Chen and Guestrin - 2016 - XGBoost A Scalable Tree Boosting System.pdf} } % == BibTeX quality report for chenXGBoostScalableTree2016a: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“ACM Digital Library”)

@article{liberzonMolecularSignaturesDatabase2011, title = {Molecular Signatures Database ({{MSigDB}}) 3.0}, author = {Liberzon, Arthur and Subramanian, Aravind and Pinchback, Reid and Thorvaldsd{'o}ttir, Helga and Tamayo, Pablo and Mesirov, Jill P.}, year = 2011, month = jun, journal = {Bioinformatics}, volume = {27}, number = {12}, pages = {1739–1740}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btr260}, url = {https://doi.org/10.1093/bioinformatics/btr260}, urldate = {2024-09-16}, abstract = {Motivation: Well-annotated gene sets representing the universe of the biological processes are critical for meaningful and insightful interpretation of large-scale genomic data. The Molecular Signatures Database (MSigDB) is one of the most widely used repositories of such sets.Results: We report the availability of a new version of the database, MSigDB 3.0, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site.Availability and Implementation: MSigDB is freely available for non-commercial use at http://www.broadinstitute.org/msigdb.Contact: ~gsea@broadinstitute.org}, file = {/home/trey/Zotero/storage/5Y7D8NPX/Liberzon et al. - 2011 - Molecular signatures database (MSigDB) 3.0.pdf;/home/trey/Zotero/storage/IRLNT6WC/257711.html} } % == BibTeX quality report for liberzonMolecularSignaturesDatabase2011: % ? unused Library catalog (“Silverchair”)

@misc{GSVAdata, title = {{{GSVAdata}}}, journal = {Bioconductor}, url = {http://bioconductor.org/packages/GSVAdata/}, urldate = {2024-09-16}, abstract = {This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010}, langid = {american}, keywords = {nosource}, file = {/home/trey/Zotero/storage/PGJBXYV5/GSVAdata.html} }

@article{langfelderWGCNAPackageWeighted2008, title = {{{WGCNA}}: An {{R}} Package for Weighted Correlation Network Analysis}, shorttitle = {{{WGCNA}}}, author = {Langfelder, Peter and Horvath, Steve}, year = 2008, month = dec, journal = {BMC Bioinformatics}, volume = {9}, number = {1}, pages = {559}, issn = {1471-2105}, doi = {10.1186/1471-2105-9-559}, url = {https://doi.org/10.1186/1471-2105-9-559}, urldate = {2024-09-16}, abstract = {Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial.}, langid = {english}, keywords = {Brown Module,Correlation Network,Hierarchical Cluster Dendrogram,Module Eigengene,Module Membership}, file = {/home/trey/Zotero/storage/JN33LEJN/Langfelder and Horvath - 2008 - WGCNA an R package for weighted correlation netwo.pdf} } % == BibTeX quality report for langfelderWGCNAPackageWeighted2008: % ? unused Library catalog (“Springer Link”)

@article{szklarczykSTRINGDatabase20112011, title = {The {{STRING}} Database in 2011: Functional Interaction Networks of Proteins, Globally Integrated and Scored}, shorttitle = {The {{STRING}} Database in 2011}, author = {Szklarczyk, Damian and Franceschini, Andrea and Kuhn, Michael and Simonovic, Milan and Roth, Alexander and Minguez, Pablo and Doerks, Tobias and Stark, Manuel and Muller, Jean and Bork, Peer and Jensen, Lars J. and {}von Mering, Christian}, year = 2011, month = jan, journal = {Nucleic Acids Research}, volume = {39}, number = {suppl_1}, pages = {D561-D568}, issn = {0305-1048}, doi = {10.1093/nar/gkq973}, url = {https://doi.org/10.1093/nar/gkq973}, urldate = {2024-09-16}, abstract = {An essential prerequisite for any systems-level understanding of cellular functions is to correctly uncover and annotate all functional interactions among proteins in the cell. Toward this goal, remarkable progress has been made in recent years, both in terms of experimental measurements and computational prediction techniques. However, public efforts to collect and present protein interaction information have struggled to keep up with the pace of interaction discovery, partly because protein–protein interaction information can be error-prone and require considerable effort to annotate. Here, we present an update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING); it provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information. Interactions in STRING are provided with a confidence score, and accessory information such as protein domains and 3D structures is made available, all within a stable and consistent identifier space. New features in STRING include an interactive network viewer that can cluster networks on demand, updated on-screen previews of structural information including homology models, extensive data updates and strongly improved connectivity and integration with third-party resources. Version 9.0 of STRING covers more than 1100 completely sequenced organisms; the resource can be reached at http://string-db.org .}, file = {/home/trey/Zotero/storage/AK3ZLRCR/Szklarczyk et al. - 2011 - The STRING database in 2011 functional interactio.pdf;/home/trey/Zotero/storage/L2JJUE3Z/2509054.html} } % == BibTeX quality report for szklarczykSTRINGDatabase20112011: % ? unused Library catalog (“Silverchair”)

@article{cuypersMultiplexedSplicedLeaderSequencing2017, title = {Multiplexed {{Spliced-Leader Sequencing}}: {{A}} High-Throughput, Selective Method for {{RNA-seq}} in {{Trypanosomatids}}}, shorttitle = {Multiplexed {{Spliced-Leader Sequencing}}}, author = {Cuypers, Bart and Domagalska, Malgorzata A. and Meysman, Pieter and {}de Muylder, G{'e}raldine and Vanaerschot, Manu and Imamura, Hideo and Dumetz, Franck and Verdonckt, Thomas Wolf and Myler, Peter J. and Ramasamy, Gowthaman and Laukens, Kris and Dujardin, Jean-Claude}, year = 2017, month = jun, journal = {Scientific Reports}, volume = {7}, number = {1}, pages = {3725}, publisher = {Nature Publishing Group}, issn = {2045-2322}, doi = {10.1038/s41598-017-03987-0}, url = {https://www.nature.com/articles/s41598-017-03987-0}, urldate = {2024-09-25}, abstract = {High throughput sequencing techniques are poorly adapted for in vivo studies of parasites, which require prior in vitro culturing and purification. Trypanosomatids, a group of kinetoplastid protozoans, possess a distinctive feature in their transcriptional mechanism whereby a specific Spliced Leader (SL) sequence is added to the 5{\(\prime\)}end of each mRNA by trans-splicing. This allows to discriminate Trypansomatid RNA from mammalian RNA and forms the basis of our new multiplexed protocol for high-throughput, selective RNA-sequencing called SL-seq. We provided a proof-of-concept of SL-seq in Leishmania donovani, the main causative agent of visceral leishmaniasis in humans, and successfully applied the method to sequence Leishmania mRNA directly from infected macrophages and from highly diluted mixes with human RNA. mRNA profiles obtained with SL-seq corresponded largely to those obtained from conventional poly-A tail purification methods, indicating both enumerate the same mRNA pool. However, SL-seq offers additional advantages, including lower sequencing depth requirements, fast and simple library prep and high resolution splice site detection. SL-seq is therefore ideal for fast and massive parallel sequencing of parasite transcriptomes directly from host tissues. Since SLs are also present in Nematodes, Cnidaria and primitive chordates, this method could also have high potential for transcriptomics studies in other organisms.}, copyright = {2017 The Author(s)}, langid = {english}, keywords = {Pathogens,RNA sequencing}, file = {/home/trey/Zotero/storage/FV8GNEAM/Cuypers et al. - 2017 - Multiplexed Spliced-Leader Sequencing A high-thro.pdf} } % == BibTeX quality report for cuypersMultiplexedSplicedLeaderSequencing2017: % ? unused Journal abbr (“Sci Rep”) % ? unused Library catalog (“www.nature.com”)

@article{gibsonStructureSequenceVariation2000, title = {Structure and Sequence Variation of the Trypanosome Spliced Leader Transcript}, author = {Gibson, Wendy and Bingle, Lewis and Blendeman, Wim and Brown, Julia and Wood, James and Stevens, Jamie}, year = 2000, month = apr, journal = {Molecular and Biochemical Parasitology}, volume = {107}, number = {2}, pages = {269–277}, issn = {0166-6851}, doi = {10.1016/S0166-6851(00)00193-6}, url = {https://www.sciencedirect.com/science/article/pii/S0166685100001936}, urldate = {2024-09-25}, abstract = {We have assessed the potential of using the spliced leader (SL) or mini-exon gene as a marker for molecular phylogenetic analysis of genus Trypanosoma. A total of 27 trypanosome sequences were compared, 18 of these being newly reported. In contrast to genus Leishmania, we found the non-transcribed spacer region of the SL locus in trypanosomes to be far too variable for informative comparison of all but the most closely related species. At the other extreme, the short (39 nt) SL exon was usually completely conserved and hence uninformative. The SL RNA showed variation in both length (97–152 nt) and sequence among different trypanosome species, with most variation occurring in stem-loop II. Consequently, this region could not be aligned with confidence in multiple sequence alignment, severely reducing the number of phylogenetically informative nucleotide positions. In computer simulation, most of the SL RNAs readily folded into the 3 stem–loop secondary structure predicted previously, but again stem-loop II was highly variable. No obvious correlation could be seen between the length of this stem-loop and trypanosome biology. We conclude that the SL repeat is not an informative phylogenetic marker for long range evolutionary studies of genus Trypanosoma.}, keywords = {Mini-exon,nosource,Phylogeny,Spliced leader,Trypanosome}, file = {/home/trey/Zotero/storage/MDSMJARQ/S0166685100001936.html} } % == BibTeX quality report for gibsonStructureSequenceVariation2000: % ? unused Library catalog (“ScienceDirect”)

@article{thorvaldsdottirIntegrativeGenomicsViewer2013, title = {Integrative {{Genomics Viewer}} ({{IGV}}): High-Performance Genomics Data Visualization and Exploration}, shorttitle = {Integrative {{Genomics Viewer}} ({{IGV}})}, author = {Thorvaldsd{'o}ttir, Helga and Robinson, James T. and Mesirov, Jill P.}, year = 2013, month = mar, journal = {Briefings in Bioinformatics}, volume = {14}, number = {2}, pages = {178–192}, issn = {1467-5463}, doi = {10.1093/bib/bbs017}, url = {https://doi.org/10.1093/bib/bbs017}, urldate = {2024-10-08}, abstract = {Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today’s sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license.}, file = {/home/trey/Zotero/storage/XKCJUSKU/Thorvaldsdóttir et al. - 2013 - Integrative Genomics Viewer (IGV) high-performanc.pdf;/home/trey/Zotero/storage/SQ9G2VHJ/208453.html} } % == BibTeX quality report for thorvaldsdottirIntegrativeGenomicsViewer2013: % ? unused Library catalog (“Silverchair”)

@article{loveModeratedEstimationFold2014a, title = {Moderated Estimation of Fold Change and Dispersion for {{RNA-seq}} Data with {{DESeq2}}}, author = {Love, Michael I. and Huber, Wolfgang and Anders, Simon}, year = 2014, month = dec, journal = {Genome Biology}, volume = {15}, number = {12}, pages = {550}, issn = {1474-760X}, doi = {10.1186/s13059-014-0550-8}, url = {https://doi.org/10.1186/s13059-014-0550-8}, urldate = {2024-10-08}, abstract = {In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html.}, keywords = {DESeq2 Package,Differential Expression Analysis,Negative Binomial Generalize Linear Model,Observe Fisher Information,Read Count}, file = {/home/trey/Zotero/storage/AQ5IK8NR/Love et al. - 2014 - Moderated estimation of fold change and dispersion.pdf;/home/trey/Zotero/storage/JZ2CQF2N/s13059-014-0550-8.html} } % == BibTeX quality report for loveModeratedEstimationFold2014a: % ? unused Library catalog (“BioMed Central”)

@article{leekSvaPackageRemoving2012a, title = {The Sva Package for Removing Batch Effects and Other Unwanted Variation in High-Throughput Experiments}, author = {Leek, Jeffrey T. and Johnson, W. Evan and Parker, Hilary S. and Jaffe, Andrew E. and Storey, John D.}, year = 2012, month = mar, journal = {Bioinformatics}, volume = {28}, number = {6}, pages = {882–883}, issn = {1367-4803}, doi = {10.1093/bioinformatics/bts034}, url = {https://doi.org/10.1093/bioinformatics/bts034}, urldate = {2024-10-08}, abstract = {Summary: Heterogeneity and latent variables are now widely recognized as major sources of bias and variability in high-throughput experiments. The most well-known source of latent variation in genomic experiments are batch effects—when samples are processed on different days, in different groups or by different people. However, there are also a large number of other variables that may have a major impact on high-throughput measurements. Here we describe the sva package for identifying, estimating and removing unwanted sources of variation in high-throughput experiments. The sva package supports surrogate variable estimation with the sva function, direct adjustment for known batch effects with the ComBat function and adjustment for batch and latent variables in prediction problems with the fsva function.Availability: The R package sva is freely available from http://www.bioconductor.org.Contact: ~jleek@jhsph.eduSupplementary information: ~Supplementary data are available at Bioinformatics online.}, file = {/home/trey/Zotero/storage/SSJKQDSP/Leek et al. - 2012 - The sva package for removing batch effects and oth.pdf;/home/trey/Zotero/storage/QZVU7TI6/311263.html} } % == BibTeX quality report for leekSvaPackageRemoving2012a: % ? unused Library catalog (“Silverchair”)

@article{liFastAccurateShort2009a, title = {Fast and Accurate Short Read Alignment with {{Burrows}}–{{Wheeler}} Transform}, author = {Li, Heng and Durbin, Richard}, year = 2009, month = jul, journal = {Bioinformatics}, volume = {25}, number = {14}, pages = {1754–1760}, issn = {1367-4811, 1367-4803}, doi = {10.1093/bioinformatics/btp324}, url = {https://academic.oup.com/bioinformatics/article/25/14/1754/225615}, urldate = {2024-10-11}, abstract = {Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals.}, copyright = {http://creativecommons.org/licenses/by-nc/2.0/uk/}, langid = {english}, file = {/home/trey/Zotero/storage/GFC2LFQA/Li and Durbin - 2009 - Fast and accurate short read alignment with Burrow.pdf} } % == BibTeX quality report for liFastAccurateShort2009a: % ? unused Library catalog (“DOI.org (Crossref)”)

@article{dejesusTRANSITSoftwareTool2015, title = {{{TRANSIT}} - {{A Software Tool}} for {{Himar1 TnSeq Analysis}}}, author = {DeJesus, Michael A. and Ambadipudi, Chaitra and Baker, Richard and Sassetti, Christopher and Ioerger, Thomas R.}, editor = {Gardner, Paul P}, year = 2015, month = oct, journal = {PLOS Computational Biology}, volume = {11}, number = {10}, pages = {e1004401}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1004401}, url = {https://dx.plos.org/10.1371/journal.pcbi.1004401}, urldate = {2024-10-11}, langid = {english}, file = {/home/trey/Zotero/storage/IDJ82AJH/DeJesus et al. - 2015 - TRANSIT - A Software Tool for Himar1 TnSeq Analysi.pdf} } % == BibTeX quality report for dejesusTRANSITSoftwareTool2015: % ? Title looks like it was stored in title-case in Zotero % ? unused Journal abbr (“PLoS Comput Biol”) % ? unused Library catalog (“DOI.org (Crossref)”)

@incollection{longIdentifyingEssentialGenes2015, title = {Identifying {{Essential Genes}} in {{Mycobacterium}} Tuberculosis by {{Global Phenotypic Profiling}}}, booktitle = {Gene {{Essentiality}}: {{Methods}} and {{Protocols}}}, author = {Long, Jarukit E. and DeJesus, Michael and Ward, Doyle and Baker, Richard E. and Ioerger, Thomas and Sassetti, Christopher M.}, editor = {Lu, Long Jason}, year = 2015, pages = {79–95}, publisher = {Springer}, address = {New York, NY}, doi = {10.1007/978-1-4939-2398-4_6}, url = {https://doi.org/10.1007/978-1-4939-2398-4_6}, urldate = {2024-10-11}, abstract = {Transposon sequencing (TnSeq) is a next-generation deep sequencing-based method to quantitatively assess the composition of complex mutant transposon libraries after pressure from selection. Although this method can be used for any organism in which transposon mutagenesis is possible, this chapter describes its use in Mycobacterium tuberculosis. More specifically, the methods for generating complex libraries through transposon mutagenesis, design of selective pressure, extraction of genomic DNA, amplification and quantification of transposon insertions through next-generation deep sequencing are covered. Determining gene essentiality and statistical analysis on data collected are also discussed.}, isbn = {978-1-4939-2398-4}, langid = {english}, keywords = {Essentiality,Himar1 mutagenesis,Illumina next-generation sequencing,Mycobacterium tuberculosis,Transposon sequencing (TnSeq)}, file = {/home/trey/Zotero/storage/B4U7UB4Z/Long et al. - 2015 - Identifying Essential Genes in Mycobacterium tuber.pdf} } % == BibTeX quality report for longIdentifyingEssentialGenes2015: % ? unused Library catalog (“Springer Link”)

@book{luGeneEssentialityMethods2015, title = {Gene {{Essentiality}}: {{Methods}} and {{Protocols}}}, shorttitle = {Gene {{Essentiality}}}, editor = {Lu, Long Jason}, year = 2015, series = {Methods in {{Molecular Biology}}}, volume = {1279}, publisher = {Springer}, address = {New York, NY}, doi = {10.1007/978-1-4939-2398-4}, url = {https://link.springer.com/10.1007/978-1-4939-2398-4}, urldate = {2024-10-11}, copyright = {https://www.springernature.com/gp/researchers/text-and-data-mining}, isbn = {978-1-4939-2397-7 978-1-4939-2398-4}, langid = {english}, keywords = {Candida albicans,Computational predictions,Microbial essential genes,Prokaryotes,Single-gene knockouts,Transposon mutagenesis}, file = {/home/trey/Zotero/storage/DWVQ4U9E/Lu - 2015 - Gene Essentiality Methods and Protocols.pdf} } % == BibTeX quality report for luGeneEssentialityMethods2015: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“DOI.org (Crossref)”)

@article{perryTrypanosomeMRNAsHave1987, title = {Trypanosome {{mRNAs}} Have Unusual “Cap 4” Structures Acquired by Addition of a Spliced Leader}, author = {Perry, K. L. and Watkins, K. P. and Agabian, N.}, year = 1987, month = dec, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {84}, number = {23}, pages = {8190}, doi = {10.1073/pnas.84.23.8190}, url = {https://pmc.ncbi.nlm.nih.gov/articles/PMC299507/}, urldate = {2024-10-24}, abstract = {A single capped oligonucleotide is released from Trypanosoma brucei poly(A)+ RNA upon digestion with RNase T2. This observation supports the hypothesis that all T. brucei mRNAs share a common leader sequence. Digestion of the T2-resistant species …}, langid = {english}, pmid = {3120186}, file = {/home/trey/Zotero/storage/U5J2SYQM/Perry et al. - 1987 - Trypanosome mRNAs have unusual cap 4 structures acquired by addition of a spliced leader.pdf} } % == BibTeX quality report for perryTrypanosomeMRNAsHave1987: % ? unused Library catalog (“pmc.ncbi.nlm.nih.gov”)

@article{assisBaseRolesJBP12023, title = {Behind {{Base J}}: {{The Roles}} of {{JBP1}} and {{JBP2}} on {{Trypanosomatids}}}, shorttitle = {Behind {{Base J}}}, author = {Assis, Luiz Henrique de Castro and {}de Paiva, Stephany Cacete and Cano, Maria Isabel Nogueira}, year = 2023, month = mar, journal = {Pathogens}, volume = {12}, number = {3}, pages = {467}, doi = {10.3390/pathogens12030467}, url = {https://pmc.ncbi.nlm.nih.gov/articles/PMC10057400/}, urldate = {2024-10-24}, abstract = {{\(\beta\)}-D-glucopyranosyloxymethiluracil (Base J) is a modified thymidine base found in kinetoplastids and some related organisms. Interestingly, Base J distribution into the genome can vary depending on the organism and its life stage. Base J is reported …}, langid = {english}, pmid = {36986389}, file = {/home/trey/Zotero/storage/66ZGIQ73/Assis et al. - 2023 - Behind Base J The Roles of JBP1 and JBP2 on Trypanosomatids.pdf} } % == BibTeX quality report for assisBaseRolesJBP12023: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“pmc.ncbi.nlm.nih.gov”)

@article{hamidzadehTransitionMCSFderivedHuman2020, title = {The Transition of {{M-CSF-derived}} Human Macrophages to a Growth-Promoting Phenotype}, author = {Hamidzadeh, Kajal and Belew, Ashton T. and {El-Sayed}, Najib M. and Mosser, David M.}, year = 2020, month = nov, journal = {Blood Advances}, volume = {4}, number = {21}, pages = {5460–5472}, issn = {2473-9537}, doi = {10.1182/bloodadvances.2020002683}, abstract = {Stimulated macrophages are potent producers of inflammatory mediators. This activity is highly regulated, in part, by resolving molecules to prevent tissue damage. In this study, we demonstrate that inflammation induced by Toll-like receptor stimulation is followed by the upregulation of receptors for adenosine (Ado) and prostaglandin E2 (PGE2), which help terminate macrophage activation and initiate tissue remodeling and angiogenesis. Macrophages can be hematopoietically derived from monocytes in response to 2 growth factors: macrophage colony-stimulating factor (M-CSF) and granulocyte-macrophage colony-stimulating factor (GM-CSF). We examine how exposure to either of these differentiation factors shapes the macrophage response to resolving molecules. We analyzed the transcriptomes of human monocyte-derived macrophages stimulated in the presence of Ado or PGE2 and demonstrated that, in macrophages differentiated in M-CSF, Ado and PGE2 induce a shared transcriptional program involving the downregulation of inflammatory mediators and the upregulation of growth factors. In contrast, macrophages generated in GM-CSF fail to convert to a growth-promoting phenotype, which we attribute to the suppression of receptors for Ado and PGE2 and lower production of these endogenous regulators. These observations indicate that M-CSF macrophages are better prepared to transition to a program of tissue repair, whereas GM-CSF macrophages undergo more profound activation. We implicate the differential sensitivity to pro-resolving mediators as a contributor to these divergent phenotypes. This research highlights a number of molecular targets that can be exploited to regulate the strength and duration of macrophage activation.}, langid = {english}, pmcid = {PMC7656919}, pmid = {33166408}, keywords = {Humans,Macrophage Activation,Macrophage Colony-Stimulating Factor,Macrophages,Monocytes,Phenotype}, file = {/home/trey/Zotero/storage/MXRXQT3F/Hamidzadeh et al. - 2020 - The transition of M-CSF-derived human macrophages to a growth-promoting phenotype.pdf} } % == BibTeX quality report for hamidzadehTransitionMCSFderivedHuman2020: % ? unused Journal abbr (“Blood Adv”) % ? unused Library catalog (“PubMed”)

@article{squairConfrontingFalseDiscoveries2021, title = {Confronting False Discoveries in Single-Cell Differential Expression}, author = {Squair, Jordan W. and Gautier, Matthieu and Kathe, Claudia and Anderson, Mark A. and James, Nicholas D. and Hutson, Thomas H. and Hudelle, R{'e}mi and Qaiser, Taha and Matson, Kaya J. E. and Barraud, Quentin and Levine, Ariel J. and La Manno, Gioele and Skinnider, Michael A. and Courtine, Gr{'e}goire}, year = 2021, month = sep, journal = {Nature Communications}, volume = {12}, number = {1}, pages = {5692}, publisher = {Nature Publishing Group}, issn = {2041-1723}, doi = {10.1038/s41467-021-25960-2}, url = {https://www.nature.com/articles/s41467-021-25960-2}, urldate = {2024-11-25}, abstract = {Differential expression analysis in single-cell transcriptomics enables the dissection of cell-type-specific responses to perturbations such as disease, trauma, or experimental manipulations. While many statistical methods are available to identify differentially expressed genes, the principles that distinguish these methods and their performance remain unclear. Here, we show that the relative performance of these methods is contingent on their ability to account for variation between biological replicates. Methods that ignore this inevitable variation are biased and prone to false discoveries. Indeed, the most widely used methods can discover hundreds of differentially expressed genes in the absence of biological differences. To exemplify these principles, we exposed true and false discoveries of differentially expressed genes in the injured mouse spinal cord.}, copyright = {2021 The Author(s)}, langid = {english}, keywords = {Computational biology and bioinformatics,Functional genomics,Gene expression analysis,Spinal cord injury,Statistics}, file = {/home/trey/Zotero/storage/49YMNB73/Squair et al. - 2021 - Confronting false discoveries in single-cell differential expression.pdf} } % == BibTeX quality report for squairConfrontingFalseDiscoveries2021: % ? unused Journal abbr (“Nat Commun”) % ? unused Library catalog (“www.nature.com”)

@article{hoffmanEfficientDifferentialExpression, title = {Efficient Differential Expression Analysis of Large-Scale Single Cell Transcriptomics Data Using Dreamlet}, author = {Hoffman, Gabriel E and Lee, Donghoon and Bendl, Jaroslav and Casey, Clara and Alvia, Marcela and Shao, Zhiping and Argyriou, Stathis and Venkatesh, Sanan and Voloudakis, Georgios and Haroutunian, Vahram and Fullard, F and Roussos, Panos}, abstract = {Advances in single-cell and -nucleus transcriptomics have enabled generation of increasingly large-scale datasets from hundreds of subjects and millions of cells. These studies promise to give unprecedented insight into the cell type specific biology of human disease. Yet performing differential expression analyses across subjects remains difficult due to challenges in statistical modeling of these complex studies and scaling analyses to large datasets. Our open-source R package dreamlet (DiseaseNeurogenomics.github.io/dreamlet) uses a pseudobulk approach based on precision-weighted linear mixed models to identify genes differentially expressed with traits across subjects for each cell cluster. Designed for data from large cohorts, dreamlet is substantially faster and uses less memory than existing workflows, while supporting complex statistical models and controlling the false positive rate. We demonstrate computational and statistical performance on published datasets, and a novel dataset of 1.4M single nuclei from postmortem brains of 150 Alzheimer’s disease cases and 149 controls.}, langid = {english}, keywords = {Multiple DOI,nonfile}, file = {/home/trey/Zotero/storage/H28ZHDC6/Hoffman et al. - Efficient differential expression analysis of large-scale single cell transcriptomics data using dre.pdf} } % == BibTeX quality report for hoffmanEfficientDifferentialExpression: % Missing required field ‘journal’ % Missing required field ‘year’ % ? unused Library catalog (“Zotero”)

@misc{hoffmanEfficientDifferentialExpression2024, title = {Efficient Differential Expression Analysis of Large-Scale Single Cell Transcriptomics Data Using Dreamlet}, author = {Hoffman, Gabriel E. and Lee, Donghoon and Bendl, Jaroslav and Prashant, N. M. and Hong, Aram and Casey, Clara and Alvia, Marcela and Shao, Zhiping and Argyriou, Stathis and Therrien, Karen and Venkatesh, Sanan and Voloudakis, Georgios and Haroutunian, Vahram and Fullard, John F. and Roussos, Panos}, year = 2024, month = nov, primaryclass = {New Results}, pages = {2023.03.17.533005}, publisher = {bioRxiv}, doi = {10.1101/2023.03.17.533005}, url = {https://www.biorxiv.org/content/10.1101/2023.03.17.533005v2}, urldate = {2024-12-02}, abstract = {Advances in single-cell and -nucleus transcriptomics have enabled generation of increasingly large-scale datasets from hundreds of subjects and millions of cells. These studies promise to give unprecedented insight into the cell type specific biology of human disease. Yet performing differential expression analyses across subjects remains difficult due to challenges in statistical modeling of these complex studies and scaling analyses to large datasets. Our open-source R package dreamlet (DiseaseNeurogenomics.github.io/dreamlet) uses a pseudobulk approach based on precision-weighted linear mixed models to identify genes differentially expressed with traits across subjects for each cell cluster. Designed for data from large cohorts, dreamlet is substantially faster and uses less memory than existing workflows, while supporting complex statistical models and controlling the false positive rate. We demonstrate computational and statistical performance on published datasets, and a novel dataset of 1.4M single nuclei from postmortem brains of 150 Alzheimer’s disease cases and 149 controls.}, archiveprefix = {bioRxiv}, chapter = {New Results}, copyright = { 2024, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}, langid = {english}, keywords = {differential expression,scRNA}, file = {/home/trey/Zotero/storage/6SAFAMHL/Hoffman et al. - 2024 - Efficient differential expression analysis of large-scale single cell transcriptomics data using dre.pdf} }

@article{ayalaAdvancesLeishmaniaVaccines2024, title = {Advances in {{Leishmania Vaccines}}: {{Current Development}} and {{Future Prospects}}}, shorttitle = {Advances in {{Leishmania Vaccines}}}, author = {Ayala, Andreina and Llanes, Alejandro and Lleonart, Ricardo and Restrepo, Carlos M.}, year = 2024, month = sep, journal = {Pathogens}, volume = {13}, number = {9}, pages = {812}, publisher = {Multidisciplinary Digital Publishing Institute}, issn = {2076-0817}, doi = {10.3390/pathogens13090812}, url = {https://www.mdpi.com/2076-0817/13/9/812}, urldate = {2024-12-03}, abstract = {Leishmaniasis is a neglected tropical disease caused by parasites of the genus Leishmania. As approved human vaccines are not available, treatment and prevention rely heavily on toxic chemotherapeutic agents, which face increasing resistance problems. The development of effective vaccines against human leishmaniasis is of utmost importance for the control of the disease. Strategies that have been considered for this purpose range from whole-killed and attenuated parasites to recombinant proteins and DNA vaccines. The ideal vaccine must be safe and effective, ensuring lasting immunity through a robust IL-12-driven Th1 adaptive immune response. Despite some success and years of effort, human vaccine trials have encountered difficulties in conferring durable protection against Leishmania, a problem that may be attributed to the parasite’s antigenic diversity and the intricate nature of the host’s immune response. The aim of this review is to provide a thorough overview of recent advances in Leishmania vaccine development, ranging from initial trials to recent achievements, such as the ChAd63-KH DNA vaccine, which underscores the potential for effective control of leishmaniasis through continued research in this field.}, copyright = {http://creativecommons.org/licenses/by/3.0/}, langid = {english}, keywords = {Leishmania,immunity,leishmaniasis,treatment,vaccine,vaccine development}, file = {/home/trey/Zotero/storage/9ILB3DL2/Ayala et al. - 2024 - Advances in Leishmania Vaccines Current Development and Future Prospects.pdf} } % == BibTeX quality report for ayalaAdvancesLeishmaniaVaccines2024: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“www.mdpi.com”)

@book{midwayChapter9Random, title = {Chapter 9 {{Random Effects}} {{Data Analysis}} in {{R}}}, author = {Midway, Steve}, url = {https://bookdown.org/steve_midway/DAR/random-effects.html}, urldate = {2024-12-05}, abstract = {This is a text that covers the principles and practices of handling and analyzing data.}, keywords = {nosource}, file = {/home/trey/Zotero/storage/7XP6FAB5/random-effects.html} } % == BibTeX quality report for midwayChapter9Random: % Missing required field ‘publisher’ % Missing required field ‘year’ % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“bookdown.org”)

@article{hoffmanDreamPowerfulDifferential2021, title = {Dream: Powerful Differential Expression Analysis for Repeated Measures Designs}, shorttitle = {Dream}, author = {Hoffman, Gabriel E and Roussos, Panos}, year = 2021, month = apr, journal = {Bioinformatics}, volume = {37}, number = {2}, pages = {192–201}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btaa687}, url = {https://doi.org/10.1093/bioinformatics/btaa687}, urldate = {2024-12-05}, abstract = {Large-scale transcriptome studies with multiple samples per individual are widely used to study disease biology. Yet, current methods for differential expression are inadequate for cross-individual testing for these repeated measures designs. Most problematic, we observe across multiple datasets that current methods can give reproducible false-positive findings that are driven by genetic regulation of gene expression, yet are unrelated to the trait of interest. Here, we introduce a statistical software package, dream, that increases power, controls the false positive rate, enables multiple types of hypothesis tests, and integrates with standard workflows. In 12 analyses in 6 independent datasets, dream yields biological insight not found with existing software while addressing the issue of reproducible false-positive findings.Dream is available within the variancePartition Bioconductor package at http://bioconductor.org/packages/variancePartition.gabriel.hoffman@mssm.eduSupplementary data are available at Bioinformatics online.}, file = {/home/trey/Zotero/storage/U9Q437JX/Hoffman and Roussos - 2021 - Dream powerful differential expression analysis for repeated measures designs.pdf} } % == BibTeX quality report for hoffmanDreamPowerfulDifferential2021: % ? unused Library catalog (“Silverchair”)

@book{edwardsPlantBioinformaticsMethods2022, title = {Plant {{Bioinformatics}}: {{Methods}} and {{Protocols}}}, shorttitle = {Plant {{Bioinformatics}}}, editor = {Edwards, David}, year = 2022, series = {Methods in {{Molecular Biology}}}, volume = {2443}, publisher = {Springer US}, address = {New York, NY}, doi = {10.1007/978-1-0716-2067-0}, url = {https://link.springer.com/10.1007/978-1-0716-2067-0}, urldate = {2025-01-12}, copyright = {https://creativecommons.org/licenses/by/4.0}, isbn = {978-1-0716-2066-3 978-1-0716-2067-0}, langid = {english}, keywords = {Applied bioinformatics,Crop breeding,Database systems and repositories,High throughput data,Machine learning,Plant research}, file = {/home/trey/Zotero/storage/W6NWNN8R/Edwards - 2022 - Plant Bioinformatics Methods and Protocols.pdf} } % == BibTeX quality report for edwardsPlantBioinformaticsMethods2022: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“DOI.org (Crossref)”)

@misc{DataScience, title = {R for {{Data Science}}}, url = {https://r4ds.hadley.nz/}, urldate = {2025-01-26}, keywords = {nosource}, file = {/home/trey/Zotero/storage/VLVM2PFB/r4ds.hadley.nz.html} } % == BibTeX quality report for DataScience: % ? Title looks like it was stored in title-case in Zotero

@misc{WelcomeAdvanced, title = {Welcome {{Advanced R}}}, url = {https://adv-r.hadley.nz/}, urldate = {2025-01-26}, keywords = {nosource}, file = {/home/trey/Zotero/storage/6UHAHXUW/adv-r.hadley.nz.html} } % == BibTeX quality report for WelcomeAdvanced: % ? Title looks like it was stored in title-case in Zotero

@article{goffeauLife6000Genes1996, title = {Life with 6000 Genes}, author = {Goffeau, A. and Barrell, B. G. and Bussey, H. and Davis, R. W. and Dujon, B. and Feldmann, H. and Galibert, F. and Hoheisel, J. D. and Jacq, C. and Johnston, M. and Louis, E. J. and Mewes, H. W. and Murakami, Y. and Philippsen, P. and Tettelin, H. and Oliver, S. G.}, year = 1996, month = oct, journal = {Science (New York, N.Y.)}, volume = {274}, number = {5287}, pages = {546, 563–567}, issn = {0036-8075}, doi = {10.1126/science.274.5287.546}, abstract = {The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast’s 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate the biological functions of all of these genes.}, langid = {english}, pmid = {8849441}, keywords = {Amino Acid Sequence,Base Sequence,Chromosome Mapping,Chromosomes Fungal,Computer Communication Networks,DNA Fungal,Evolution Molecular,Fungal Proteins,Gene Library,Genes Fungal,Genome Fungal,International Cooperation,Multigene Family,Open Reading Frames,RNA Fungal,Saccharomyces cerevisiae,Sequence Analysis DNA}, file = {/home/trey/Zotero/storage/SDCQJISP/Goffeau et al. - 1996 - Life with 6000 genes.pdf} } % == BibTeX quality report for goffeauLife6000Genes1996: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”) % ? unused Library catalog (“PubMed”)

@article{chungBestPracticesDifferential2021a, title = {Best Practices on the Differential Expression Analysis of Multi-Species {{RNA-seq}}}, author = {Chung, Matthew and Bruno, Vincent M. and Rasko, David A. and Cuomo, Christina A. and Mu{~n}oz, Jos{'e} F. and Livny, Jonathan and Shetty, Amol C. and Mahurkar, Anup and Dunning Hotopp, Julie C.}, year = 2021, month = apr, journal = {Genome Biology}, volume = {22}, number = {1}, pages = {121}, issn = {1474-760X}, doi = {10.1186/s13059-021-02337-8}, url = {https://doi.org/10.1186/s13059-021-02337-8}, urldate = {2025-01-29}, abstract = {Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.}, langid = {english}, keywords = {Best practices,Differential gene expression,RNA-Seq,Transcriptomics}, file = {/home/trey/Zotero/storage/DFAIWZVN/Chung et al. - 2021 - Best practices on the differential expression analysis of multi-species RNA-seq.pdf} } % == BibTeX quality report for chungBestPracticesDifferential2021a: % ? unused Journal abbr (“Genome Biol”) % ? unused Library catalog (“Springer Link”)

@article{altschulGappedBLASTPSIBLAST1997a, title = {Gapped {{BLAST}} and {{PSI-BLAST}}: A New Generation of Protein Database Search Programs}, shorttitle = {Gapped {{BLAST}} and {{PSI-BLAST}}}, author = {Altschul, Stephen F. and Madden, Thomas L. and Sch{"a}ffer, Alejandro A. and Zhang, Jinghui and Zhang, Zheng and Miller, Webb and Lipman, David J.}, year = 1997, month = sep, journal = {Nucleic Acids Research}, volume = {25}, number = {17}, pages = {3389–3402}, issn = {0305-1048}, doi = {10.1093/nar/25.17.3389}, url = {https://doi.org/10.1093/nar/25.17.3389}, urldate = {2025-01-30}, abstract = {The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.}, file = {/home/trey/Zotero/storage/DL2DUCKY/Altschul et al. - 1997 - Gapped BLAST and PSI-BLAST a new generation of protein database search programs.pdf;/home/trey/Zotero/storage/3XGWX7J2/1061651.html} } % == BibTeX quality report for altschulGappedBLASTPSIBLAST1997a: % ? unused Library catalog (“Silverchair”)

@article{mackayDrosophilaMelanogasterGenetic2012, title = {The {{Drosophila}} Melanogaster {{Genetic Reference Panel}}}, author = {Mackay, Trudy F. C. and Richards, Stephen and Stone, Eric A. and Barbadilla, Antonio and Ayroles, Julien F. and Zhu, Dianhui and Casillas, S{`o}nia and Han, Yi and Magwire, Michael M. and Cridland, Julie M. and Richardson, Mark F. and Anholt, Robert R. H. and Barr{'o}n, Maite and Bess, Crystal and Blankenburg, Kerstin Petra and Carbone, Mary Anna and Castellano, David and Chaboub, Lesley and Duncan, Laura and Harris, Zeke and Javaid, Mehwish and Jayaseelan, Joy Christina and Jhangiani, Shalini N. and Jordan, Katherine W. and Lara, Fremiet and Lawrence, Faye and Lee, Sandra L. and Librado, Pablo and Linheiro, Raquel S. and Lyman, Richard F. and Mackey, Aaron J. and Munidasa, Mala and Muzny, Donna Marie and Nazareth, Lynne and Newsham, Irene and Perales, Lora and Pu, Ling-Ling and Qu, Carson and R{`a}mia, Miquel and Reid, Jeffrey G. and Rollmann, Stephanie M. and Rozas, Julio and Saada, Nehad and Turlapati, Lavanya and Worley, Kim C. and Wu, Yuan-Qing and Yamamoto, Akihiko and Zhu, Yiming and Bergman, Casey M. and Thornton, Kevin R. and Mittelman, David and Gibbs, Richard A.}, year = 2012, month = feb, journal = {Nature}, volume = {482}, number = {7384}, pages = {173–178}, issn = {1476-4687}, doi = {10.1038/nature10811}, abstract = {A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.}, langid = {english}, pmcid = {PMC3683990}, pmid = {22318601}, keywords = {Alleles,Animals,broken,Centromere,Chromosomes Insect,Drosophila melanogaster,Genome-Wide Association Study,Genomics,Genotype,Phenotype,Polymorphism Single Nucleotide,Quantitative Trait Loci,Selection Genetic,Starvation,Telomere,X Chromosome}, file = {/home/trey/Zotero/storage/7ASQU3CL/Mackay et al. - 2012 - The Drosophila melanogaster Genetic Reference Panel.pdf} } % == BibTeX quality report for mackayDrosophilaMelanogasterGenetic2012: % ? unused Library catalog (“PubMed”)

@article{huangMultiomicsCharacterizationMonkeypox2024, title = {Multi-Omics Characterization of the Monkeypox Virus Infection}, author = {Huang, Yiqi and Bergant, Valter and Grass, Vincent and Emslander, Quirin and Hamad, M. Sabri and Hubel, Philipp and Mergner, Julia and Piras, Antonio and Krey, Karsten and Henrici, Alexander and {"O}llinger, Rupert and Tesfamariam, Yonas M. and Dalla Rosa, Ilaria and Bunse, Till and Sutter, Gerd and Ebert, Gregor and Schmidt, Florian I. and Way, Michael and Rad, Roland and Bowie, Andrew G. and Protzer, Ulrike and Pichlmair, Andreas}, year = 2024, month = aug, journal = {Nature Communications}, volume = {15}, number = {1}, pages = {6778}, publisher = {Nature Publishing Group}, issn = {2041-1723}, doi = {10.1038/s41467-024-51074-6}, url = {https://www.nature.com/articles/s41467-024-51074-6}, urldate = {2025-02-08}, abstract = {Multiple omics analyzes of Vaccinia virus (VACV) infection have defined molecular characteristics of poxvirus biology. However, little is known about the monkeypox (mpox) virus (MPXV) in humans, which has a different disease manifestation despite its high sequence similarity to VACV. Here, we perform an in-depth multi-omics analysis of the transcriptome, proteome, and phosphoproteome signatures of MPXV-infected primary human fibroblasts to gain insights into the virus-host interplay. In addition to expected perturbations of immune-related pathways, we uncover regulation of the HIPPO and TGF-{\(\beta\)} pathways. We identify dynamic phosphorylation of both host and viral proteins, which suggests that MAPKs are key regulators of differential phosphorylation in MPXV-infected cells. Among the viral proteins, we find dynamic phosphorylation of H5 that influenced the binding of H5 to dsDNA. Our extensive dataset highlights signaling events and hotspots perturbed by MPXV, extending the current knowledge on poxviruses. We use integrated pathway analysis and drug-target prediction approaches to identify potential drug targets that affect virus growth. Functionally, we exemplify the utility of this approach by identifying inhibitors of MTOR, CHUK/IKBKB, and splicing factor kinases with potent antiviral efficacy against MPXV and VACV.}, copyright = {2024 The Author(s)}, langid = {english}, keywords = {Cell signalling,Phosphorylation,Pox virus,Proteomics}, file = {/home/trey/Zotero/storage/9JSTSL82/Huang et al. - 2024 - Multi-omics characterization of the monkeypox virus infection.pdf} } % == BibTeX quality report for huangMultiomicsCharacterizationMonkeypox2024: % ? unused Journal abbr (“Nat Commun”) % ? unused Library catalog (“www.nature.com”)

@article{ignatiadisDatadrivenHypothesisWeighting2016, title = {Data-Driven Hypothesis Weighting Increases Detection Power in Genome-Scale Multiple Testing}, author = {Ignatiadis, Nikolaos and Klaus, Bernd and Zaugg, Judith B. and Huber, Wolfgang}, year = 2016, month = jul, journal = {Nature Methods}, volume = {13}, number = {7}, pages = {577–580}, publisher = {Nature Publishing Group}, issn = {1548-7105}, doi = {10.1038/nmeth.3885}, url = {https://www.nature.com/articles/nmeth.3885}, urldate = {2025-02-12}, abstract = {For multiple hypothesis testing in genomics and other large-scale data analyses, the independent hypothesis weighting (IHW) approach uses data-driven P-value weight assignment to improve power while controlling the false discovery rate.}, copyright = {2016 Springer Nature America, Inc.}, langid = {english}, keywords = {Software,Statistical methods}, file = {/home/trey/Zotero/storage/3CGU2ERI/Ignatiadis et al. - 2016 - Data-driven hypothesis weighting increases detection power in genome-scale multiple testing.pdf} } % == BibTeX quality report for ignatiadisDatadrivenHypothesisWeighting2016: % ? unused Journal abbr (“Nat Methods”) % ? unused Library catalog (“www.nature.com”)

@article{cuypersFourLayerMultiomics2022a, title = {Four Layer Multi-Omics Reveals Molecular Responses to Aneuploidy in {{Leishmania}}}, author = {Cuypers, Bart and Meysman, Pieter and Erb, Ionas and Bittremieux, Wout and Valkenborg, Dirk and Baggerman, Geert and Mertens, Inge and Sundar, Shyam and Khanal, Basudha and Notredame, Cedric and Dujardin, Jean-Claude and Domagalska, Malgorzata A. and Laukens, Kris}, year = 2022, month = sep, journal = {PLOS Pathogens}, volume = {18}, number = {9}, pages = {e1010848}, publisher = {Public Library of Science}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1010848}, url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010848}, urldate = {2025-04-01}, abstract = {Aneuploidy causes system-wide disruptions in the stochiometric balances of transcripts, proteins, and metabolites, often resulting in detrimental effects for the organism. The protozoan parasite Leishmania has an unusually high tolerance for aneuploidy, but the molecular and functional consequences for the pathogen remain poorly understood. Here, we addressed this question in vitro and present the first integrated analysis of the genome, transcriptome, proteome, and metabolome of highly aneuploid Leishmania donovani strains. Our analyses unambiguously establish that aneuploidy in Leishmania proportionally impacts the average transcript- and protein abundance levels of affected chromosomes, ultimately correlating with the degree of metabolic differences between closely related aneuploid strains. This proportionality was present in both proliferative and non-proliferative in vitro promastigotes. However, as in other Eukaryotes, we observed attenuation of dosage effects for protein complex subunits and in addition, non-cytoplasmic proteins. Differentially expressed transcripts and proteins between aneuploid Leishmania strains also originated from non-aneuploid chromosomes. At protein level, these were enriched for proteins involved in protein metabolism, such as chaperones and chaperonins, peptidases, and heat-shock proteins. In conclusion, our results further support the view that aneuploidy in Leishmania can be adaptive. Additionally, we believe that the high karyotype diversity in vitro and absence of classical transcriptional regulation make Leishmania an attractive model to study processes of protein homeostasis in the context of aneuploidy and beyond.}, langid = {english}, keywords = {Aneuploidy,Genomics,Leishmania,Leishmania donovani,Protein abundance,Protein metabolism,Proteomes,Transcriptome analysis}, file = {/home/trey/Zotero/storage/BJM4UK98/Cuypers et al. - 2022 - Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania.pdf} } % == BibTeX quality report for cuypersFourLayerMultiomics2022a: % ? unused Library catalog (“PLoS Journals”)

@article{silvapereiraVariantAntigenDiversity2020, title = {Variant Antigen Diversity in {{Trypanosoma}} Vivax Is Not Driven by Recombination}, author = {Silva Pereira, Sara and {}{de Almeida Castilho Neto}, Kayo J. G. and Duffy, Craig W. and Richards, Peter and Noyes, Harry and Ogugo, Moses and Rog{'e}rio Andr{'e}, Marcos and Bengaly, Zakaria and Kemp, Steve and Teixeira, Marta M. G. and Machado, Rosangela Z. and Jackson, Andrew P.}, year = 2020, month = feb, journal = {Nature Communications}, volume = {11}, number = {1}, pages = {844}, publisher = {Nature Publishing Group}, issn = {2041-1723}, doi = {10.1038/s41467-020-14575-8}, url = {https://www.nature.com/articles/s41467-020-14575-8}, urldate = {2025-04-01}, abstract = {African trypanosomes (Trypanosoma) are vector-borne haemoparasites that survive in the vertebrate bloodstream through antigenic variation of their Variant Surface Glycoprotein (VSG). Recombination, or rather segmented gene conversion, is fundamental in Trypanosoma brucei for both VSG gene switching and for generating antigenic diversity during infections. Trypanosoma vivax is a related, livestock pathogen whose VSG lack structures that facilitate gene conversion in T. brucei and mechanisms underlying its antigenic diversity are poorly understood. Here we show that species-wide VSG repertoire is broadly conserved across diverse T. vivax clinical strains and has limited antigenic repertoire. We use variant antigen profiling, coalescent approaches and experimental infections to show that recombination plays little role in diversifying T. vivax VSG sequences. These results have immediate consequences for both the current mechanistic model of antigenic variation in African trypanosomes and species differences in virulence and transmission, requiring reconsideration of the wider epidemiology of animal African trypanosomiasis.}, copyright = {2020 The Author(s)}, langid = {english}, keywords = {Molecular evolution,Parasite genomics,Parasite immune evasion}, file = {/home/trey/Zotero/storage/53Q4XACB/Silva Pereira et al. - 2020 - Variant antigen diversity in Trypanosoma vivax is not driven by recombination.pdf} } % == BibTeX quality report for silvapereiraVariantAntigenDiversity2020: % ? unused Journal abbr (“Nat Commun”) % ? unused Library catalog (“www.nature.com”)

@book{akalinComputationalGenomics, title = {Computational {{Genomics}} with {{R}}}, author = {Akalin, Altuna}, url = {https://compmgenomr.github.io/book/}, urldate = {2025-04-25}, abstract = {A guide to computationa genomics using R. The book covers fundemental topics with practical examples for an interdisciplinery audience}, keywords = {nosource}, file = {/home/trey/Zotero/storage/C2WFJ7CH/book.html} } % == BibTeX quality report for akalinComputationalGenomics: % Missing required field ‘publisher’ % Missing required field ‘year’ % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“compgenomr.github.io”)

@article{zhengBenchmarkLongNoncoding2019, title = {Benchmark of Long Non-Coding {{RNA}} Quantification for {{RNA}} Sequencing of Cancer Samples}, author = {Zheng, Hong and Brennan, Kevin and Hernaez, Mikel and Gevaert, Olivier}, year = 2019, month = dec, journal = {GigaScience}, volume = {8}, number = {12}, pages = {giz145}, issn = {2047-217X}, doi = {10.1093/gigascience/giz145}, url = {https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giz145/5663671}, urldate = {2025-08-05}, abstract = {Background: Long non-coding RNAs (lncRNAs) are emerging as important regulators of various biological processes. While many studies have exploited public resources such as RNA sequencing (RNA-Seq) data in The Cancer Genome Atlas to study lncRNAs in cancer, it is crucial to choose the optimal method for accurate expression quantification. Results: In this study, we compared the performance of pseudoalignment methods Kallisto and Salmon, alignment-based transcript quantification method RSEM, and alignment-based gene quantification methods HTSeq and featureCounts, in combination with read aligners STAR, Subread, and HISAT2, in lncRNA quantification, by applying them to both un-stranded and stranded RNA-Seq datasets. Full transcriptome annotation, including protein-coding and non-coding RNAs, greatly improves the specificity of lncRNA expression quantification. Pseudoalignment methods and RSEM outperform HTSeq and featureCounts for lncRNA quantification at both sample- and gene-level comparison, regardless of RNA-Seq protocol type, choice of aligners, and transcriptome annotation. Pseudoalignment methods and RSEM detect more lncRNAs and correlate highly with simulated ground truth. On the contrary, HTSeq and featureCounts often underestimate lncRNA expression. Antisense lncRNAs are poorly quantified by alignment-based gene quantification methods, which can be improved using stranded protocols and pseudoalignment methods. Conclusions: Considering the consistency with ground truth and computational resources, pseudoalignment methods Kallisto or Salmon in combination with full transcriptome annotation is our recommended strategy for RNA-Seq analysis for lncRNAs.}, copyright = {http://creativecommons.org/licenses/by/4.0/}, langid = {english}, file = {/home/trey/Zotero/storage/MSSXWGIU/Zheng et al. - 2019 - Benchmark of long non-coding RNA quantification for RNA sequencing of cancer samples.pdf} } % == BibTeX quality report for zhengBenchmarkLongNoncoding2019: % ? unused Library catalog (“DOI.org (Crossref)”)

@article{zhangPredictingProteinproteinInteractions2025, title = {Predicting Protein-Protein Interactions in the Human Proteome}, author = {Zhang, Jing and Humphreys, Ian R. and Pei, Jimin and Kim, Jinuk and Choi, Chulwon and Yuan, Rongqing and Durham, Jesse and Liu, Siqi and Choi, Hee-Jung and Baek, Minkyung and Baker, David and Cong, Qian}, year = 2025, month = sep, journal = {Science}, pages = {eadt1630}, issn = {0036-8075, 1095-9203}, doi = {10.1126/science.adt1630}, url = {https://www.science.org/doi/10.1126/science.adt1630}, urldate = {2025-10-17}, abstract = {Protein-protein interactions (PPI) are essential for biological function. Coevolutionary analysis and deep learning (DL) based protein structure prediction have enabled comprehensive PPI identification in bacteria and yeast, but these approaches have had limited success for the more complex human proteome. We overcame this challenge by enhancing the coevolutionary signals with 7-fold deeper multiple sequence alignments harvested from 30 petabytes of unassembled genomic data and developing a new DL network trained on augmented datasets of domain-domain interactions from 200 million predicted protein structures. We systematically screened 200 million human protein pairs and predicted 17,849 interactions with an expected precision of 90%, of which 3,631 interactions were not identified in previous experimental screens. Three-dimensional models of these predicted interactions provide numerous hypotheses about protein function and mechanisms of human diseases.}, langid = {english}, keywords = {duplicate}, file = {/home/trey/Zotero/storage/DGJYQANR/Zhang et al. - 2025 - Predicting protein-protein interactions in the human proteome.pdf;/home/trey/Zotero/storage/U3NPZB9A/Zhang et al. - 2025 - Predicting protein-protein interactions in the human proteome.pdf} } % == BibTeX quality report for zhangPredictingProteinproteinInteractions2025: % ? unused Library catalog (“DOI.org (Crossref)”)

@article{humphreysComputedStructuresCore2021, title = {Computed Structures of Core Eukaryotic Protein Complexes}, author = {Humphreys, Ian R. and Pei, Jimin and Baek, Minkyung and Krishnakumar, Aditya and Anishchenko, Ivan and Ovchinnikov, Sergey and Zhang, Jing and Ness, Travis J. and Banjade, Sudeep and Bagde, Saket R. and Stancheva, Viktoriya G. and Li, Xiao-Han and Liu, Kaixian and Zheng, Zhi and Barrero, Daniel J. and Roy, Upasana and Kuper, Jochen and Fern{'a}ndez, Israel S. and Szakal, Barnabas and Branzei, Dana and Rizo, Josep and Kisker, Caroline and Greene, Eric C. and Biggins, Sue and Keeney, Scott and Miller, Elizabeth A. and Fromme, J. Christopher and Hendrickson, Tamara L. and Cong, Qian and Baker, David}, year = 2021, month = nov, journal = {Science}, volume = {374}, number = {6573}, pages = {eabm4805}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.abm4805}, url = {https://www.science.org/doi/10.1126/science.abm4805}, urldate = {2025-10-16}, abstract = {Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coevolution analysis and deep-learning–based structure modeling to systematically identify and build accurate models of core eukaryotic protein complexes within the Saccharomyces cerevisiae proteome. We use a combination of RoseTTAFold and AlphaFold to screen through paired multiple sequence alignments for 8.3 million pairs of yeast proteins, identify 1505 likely to interact, and build structure models for 106 previously unidentified assemblies and 806 that have not been structurally characterized. These complexes, which have as many as five subunits, play roles in almost all key processes in eukaryotic cells and provide broad insights into biological function.}, file = {/home/trey/Zotero/storage/BCAGWFTD/Humphreys et al. - 2021 - Computed structures of core eukaryotic protein complexes.pdf} } % == BibTeX quality report for humphreysComputedStructuresCore2021: % ? unused Library catalog (“science.org (Atypon)”)

@article{zotero-item-25046, keywords = {nosource} } % == BibTeX quality report for zotero-item-25046: % Missing required field ‘author’ % Missing required field ‘title’ % Missing required field ‘journal’ % Missing required field ‘year’

@article{samNovelFamilyRepeat1996, title = {A Novel Family of Repeat Sequences in the Mouse Genome Responsive to Retinoic Acid}, author = {Sam, M. and Wurst, W. and Forrester, L. and Vauti, F. and Heng, H. and Bernstein, A.}, year = 1996, month = oct, journal = {Mammalian Genome}, volume = {7}, number = {10}, pages = {741–748}, issn = {0938-8990, 1432-1777}, doi = {10.1007/s003359900224}, url = {http://link.springer.com/10.1007/s003359900224}, urldate = {2025-10-17}, abstract = {Repetitive DNA sequences form a substantial portion of eukaryotic genomes and exist as members of families that differ in copy number, length, and sequence. Various functions, including chromosomal integrity, gene regulation, and gene rearrangement have been ascribed to repetitive DNA. Although there is evidence that some repetitive sequences may participate in gene regulation, little is known about how their own expression may be regulated. During the course of gene trapping experiments with embryonic stem (ES) cells, we identified a novel class of expressed repetitive sequences in the mouse, using 5’ rapid amplification of cDNA ends-polymerase chain reaction (5’ RACE-PCR) to clone fusion transcripts from these lines. The expression of these repeats was induced by retinoic acid (RA) in cultured ES cells examined by Northern blot analyses. In vivo, their expression was spatially restricted in embryos and in the adult brain as determined by RNA in situ hybridization. We designated this family of sequences as Dr (developmentally regulated) repeats. The members of the Dr family, identified by cDNA cloning and through database search, are highly similar in sequence and show peculiar structural features. Our results suggest the expression of Dr-containing transcripts may be part of an ES cell differentiation program triggered by RA.}, copyright = {http://www.springer.com/tdm}, langid = {english}, file = {/home/trey/Zotero/storage/9GNDZW43/Sam et al. - 1996 - A novel family of repeat sequences in the mouse genome responsive to retinoic acid.pdf} } % == BibTeX quality report for samNovelFamilyRepeat1996: % ? unused Library catalog (“DOI.org (Crossref)”)

@article{alquraishiMachineLearningProtein2021, title = {Machine Learning in Protein Structure Prediction}, author = {AlQuraishi, Mohammed}, year = 2021, month = dec, journal = {Current Opinion in Chemical Biology}, series = {Mechanistic {{Biology}} * {{Machine Learning}} in {{Chemical Biology}}}, volume = {65}, pages = {1–8}, issn = {1367-5931}, doi = {10.1016/j.cbpa.2021.04.005}, url = {https://www.sciencedirect.com/science/article/pii/S1367593121000508}, urldate = {2025-10-17}, abstract = {Prediction of protein structure from sequence has been intensely studied for many decades, owing to the problem’s importance and its uniquely well-defined physical and computational bases. While progress has historically ebbed and flowed, the past two years saw dramatic advances driven by the increasing ``neuralization’’ of structure prediction pipelines, whereby computations previously based on energy models and sampling procedures are replaced by neural networks. The extraction of physical contacts from the evolutionary record; the distillation of sequence–structure patterns from known structures; the incorporation of templates from homologs in the Protein Databank; and the refinement of coarsely predicted structures into finely resolved ones have all been reformulated using neural networks. Cumulatively, this transformation has resulted in algorithms that can now predict single protein domains with a median accuracy of 2.1~, setting the stage for a foundational reconfiguration of the role of biomolecular modeling within the life sciences.}, keywords = {Alphafold,Biophysics,Deep learning,Machine learning,Protein design,Protein folding,Protein modeling,Protein structure,Protein structure prediction}, file = {/home/trey/Zotero/storage/SHVTT7DG/AlQuraishi - 2021 - Machine learning in protein structure prediction.pdf;/home/trey/Zotero/storage/TBTTIMYZ/S1367593121000508.html} } % == BibTeX quality report for alquraishiMachineLearningProtein2021: % ? unused Library catalog (“ScienceDirect”)

@article{venterSequenceHumanGenome2001, title = {The {{Sequence}} of the {{Human Genome}}}, author = {Venter, J. Craig and Adams, Mark D. and Myers, Eugene W. and Li, Peter W. and Mural, Richard J. and Sutton, Granger G. and Smith, Hamilton O. and Yandell, Mark and Evans, Cheryl A. and Holt, Robert A. and Gocayne, Jeannine D. and Amanatides, Peter and Ballew, Richard M. and Huson, Daniel H. and Wortman, Jennifer Russo and Zhang, Qing and Kodira, Chinnappa D. and Zheng, Xiangqun H. and Chen, Lin and Skupski, Marian and Subramanian, Gangadharan and Thomas, Paul D. and Zhang, Jinghui and Gabor Miklos, George L. and Nelson, Catherine and Broder, Samuel and Clark, Andrew G. and Nadeau, Joe and McKusick, Victor A. and Zinder, Norton and Levine, Arnold J. and Roberts, Richard J. and Simon, Mel and Slayman, Carolyn and Hunkapiller, Michael and Bolanos, Randall and Delcher, Arthur and Dew, Ian and Fasulo, Daniel and Flanigan, Michael and Florea, Liliana and Halpern, Aaron and Hannenhalli, Sridhar and Kravitz, Saul and Levy, Samuel and Mobarry, Clark and Reinert, Knut and Remington, Karin and {Abu-Threideh}, Jane and Beasley, Ellen and Biddick, Kendra and Bonazzi, Vivien and Brandon, Rhonda and Cargill, Michele and Chandramouliswaran, Ishwar and Charlab, Rosane and Chaturvedi, Kabir and Deng, Zuoming and Francesco, Valentina Di and Dunn, Patrick and Eilbeck, Karen and Evangelista, Carlos and Gabrielian, Andrei E. and Gan, Weiniu and Ge, Wangmao and Gong, Fangcheng and Gu, Zhiping and Guan, Ping and Heiman, Thomas J. and Higgins, Maureen E. and Ji, Rui-Ru and Ke, Zhaoxi and Ketchum, Karen A. and Lai, Zhongwu and Lei, Yiding and Li, Zhenya and Li, Jiayin and Liang, Yong and Lin, Xiaoying and Lu, Fu and Merkulov, Gennady V. and Milshina, Natalia and Moore, Helen M. and Naik, Ashwinikumar K and Narayan, Vaibhav A. and Neelam, Beena and Nusskern, Deborah and Rusch, Douglas B. and Salzberg, Steven and Shao, Wei and Shue, Bixiong and Sun, Jingtao and Wang, Zhen Yuan and Wang, Aihui and Wang, Xin and Wang, Jian and Wei, Ming-Hui and Wides, Ron and Xiao, Chunlin and Yan, Chunhua and Yao, Alison and Ye, Jane and Zhan, Ming and Zhang, Weiqing and Zhang, Hongyu and Zhao, Qi and Zheng, Liansheng and Zhong, Fei and Zhong, Wenyan and Zhu, Shiaoping C. and Zhao, Shaying and Gilbert, Dennis and Baumhueter, Suzanna and Spier, Gene and Carter, Christine and Cravchik, Anibal and Woodage, Trevor and Ali, Feroze and An, Huijin and Awe, Aderonke and Baldwin, Danita and Baden, Holly and Barnstead, Mary and Barrow, Ian and Beeson, Karen and Busam, Dana and Carver, Amy and Center, Angela and Cheng, Ming Lai and Curry, Liz and Danaher, Steve and Davenport, Lionel and Desilets, Raymond and Dietz, Susanne and Dodson, Kristina and Doup, Lisa and Ferriera, Steven and Garg, Neha and Gluecksmann, Andres and Hart, Brit and Haynes, Jason and Haynes, Charles and Heiner, Cheryl and Hladun, Suzanne and Hostin, Damon and Houck, Jarrett and Howland, Timothy and Ibegwam, Chinyere and Johnson, Jeffery and Kalush, Francis and Kline, Lesley and Koduru, Shashi and Love, Amy and Mann, Felecia and May, David and McCawley, Steven and McIntosh, Tina and McMullen, Ivy and Moy, Mee and Moy, Linda and Murphy, Brian and Nelson, Keith and Pfannkoch, Cynthia and Pratts, Eric and Puri, Vinita and Qureshi, Hina and Reardon, Matthew and Rodriguez, Robert and Rogers, Yu-Hui and Romblad, Deanna and Ruhfel, Bob and Scott, Richard and Sitter, Cynthia and Smallwood, Michelle and Stewart, Erin and Strong, Renee and Suh, Ellen and Thomas, Reginald and Tint, Ni Ni and Tse, Sukyee and Vech, Claire and Wang, Gary and Wetter, Jeremy and Williams, Sherita and Williams, Monica and Windsor, Sandra and {Winn-Deen}, Emily and Wolfe, Keriellen and Zaveri, Jayshree and Zaveri, Karena and Abril, Josep F. and Guig{'o}, Roderic and Campbell, Michael J. and Sjolander, Kimmen V. and Karlak, Brian and Kejariwal, Anish and Mi, Huaiyu and Lazareva, Betty and Hatton, Thomas and Narechania, Apurva and Diemer, Karen and Muruganujan, Anushya and Guo, Nan and Sato, Shinji and Bafna, Vineet and Istrail, Sorin and Lippert, Ross and Schwartz, Russell and Walenz, Brian and Yooseph, Shibu and Allen, David and Basu, Anand and Baxendale, James and Blick, Louis and Caminha, Marcelo and {Carnes-Stine}, John and Caulk, Parris and Chiang, Yen-Hui and Coyne, My and Dahlke, Carl and Mays, Anne Deslattes and Dombroski, Maria and Donnelly, Michael and Ely, Dale and Esparham, Shiva and Fosler, Carl and Gire, Harold and Glanowski, Stephen and Glasser, Kenneth and Glodek, Anna and Gorokhov, Mark and Graham, Ken and Gropman, Barry and Harris, Michael and Heil, Jeremy and Henderson, Scott and Hoover, Jeffrey and Jennings, Donald and Jordan, Catherine and Jordan, James and Kasha, John and Kagan, Leonid and Kraft, Cheryl and Levitsky, Alexander and Lewis, Mark and Liu, Xiangjun and Lopez, John and Ma, Daniel and Majoros, William and McDaniel, Joe and Murphy, Sean and Newman, Matthew and Nguyen, Trung and Nguyen, Ngoc and Nodell, Marc and Pan, Sue and Peck, Jim and Peterson, Marshall and Rowe, William and Sanders, Robert and Scott, John and Simpson, Michael and Smith, Thomas and Sprague, Arlan and Stockwell, Timothy and Turner, Russell and Venter, Eli and Wang, Mei and Wen, Meiyuan and Wu, David and Wu, Mitchell and Xia, Ashley and Zandieh, Ali and Zhu, Xiaohong}, year = 2001, month = feb, journal = {Science}, volume = {291}, number = {5507}, pages = {1304–1351}, publisher = {American Association for the Advancement of Science}, doi = {10.1126/science.1058040}, url = {https://www.science.org/doi/full/10.1126/science.1058040}, urldate = {2025-10-20}, abstract = {A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies—a whole-genome assembly and a regional chromosome assembly—were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional {\(\sim\)}12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.}, file = {/home/trey/Zotero/storage/R9WY3U5Z/Venter et al. - 2001 - The Sequence of the Human Genome.pdf} } % == BibTeX quality report for venterSequenceHumanGenome2001: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“science.org (Atypon)”)

@misc{TAIRHome, title = {{{TAIR}} - {{Home}}}, url = {https://www.arabidopsis.org/}, urldate = {2025-10-20}, keywords = {nosource}, file = {/home/trey/Zotero/storage/MVQQDE63/www.arabidopsis.org.html} } % == BibTeX quality report for TAIRHome: % ? Title looks like it was stored in title-case in Zotero

@article{bevanSequenceAnalysisArabidopsis2001, title = {Sequence and Analysis of the {{{}}} Genome}, author = {Bevan, Michael and Mayer, Klaus and White, Owen and Eisen, Jonathan A and Preuss, Daphne and Bureau, Thomas and Salzberg, Steven L and Mewes, Hans-Werner}, year = 2001, month = apr, journal = {Current Opinion in Plant Biology}, volume = {4}, number = {2}, pages = {105–110}, issn = {1369-5266}, doi = {10.1016/S1369-5266(00)00144-8}, url = {https://www.sciencedirect.com/science/article/pii/S1369526600001448}, urldate = {2025-10-20}, abstract = {The comprehensive analysis of the genome sequence of the plant Arabidopsis thaliana has been completed recently. The genome sequence and associated analyses provide the foundations for rapid progress in many fields of plant research, such as the exploitation of genetic variation in Arabidopsis ecotypes, the assessment of the transcriptome and proteome, and the association of genome changes at the sequence level with evolutionary processes. Nevertheless, genome sequencing and analysis are only the first steps towards a new plant biology. Much remains to be done to refine the analysis of encoded genes, to define the functions of encoded proteins systematically, and to establish new generations of databases to capture and relate diverse data sets generated in widely distributed laboratories.}, keywords = {Arabidopsis,bioinformatics,chromosome duplications,gene families,genome sequence,plant genes,sequence analysis}, file = {/home/trey/Zotero/storage/2ZRAH6M8/Bevan et al. - 2001 - Sequence and analysis of the Arabidopsis genome.pdf;/home/trey/Zotero/storage/B2WAYRUY/S1369526600001448.html} } % == BibTeX quality report for bevanSequenceAnalysisArabidopsis2001: % ? unused Library catalog (“ScienceDirect”)

@misc{CaenorhabditisElegansWormBase, title = {Caenorhabditis Elegans - {{WormBase ParaSite}}}, url = {https://parasite.wormbase.org/Caenorhabditis_elegans_prjna13758/Info/Index/}, urldate = {2025-10-20}, keywords = {nosource} }

@article{waterstonGenomeCaenorhabditisElegans1995, title = {The Genome of {{Caenorhabditis}} Elegans.}, author = {Waterston, R and Sulston, J}, year = 1995, month = nov, journal = {Proceedings of the National Academy of Sciences}, volume = {92}, number = {24}, pages = {10836–10840}, publisher = {Proceedings of the National Academy of Sciences}, doi = {10.1073/pnas.92.24.10836}, url = {https://www.pnas.org/doi/abs/10.1073/pnas.92.24.10836}, urldate = {2025-10-20}, abstract = {The physical map of the 100-Mb Caenorhabditis elegans genome consists of 17,500 cosmids and 3500 yeast artificial chromosomes (YACs). A total of 22.5 Mb has been sequenced, with the remainder expected by 1998. A further 15.5 Mb of unfinished sequence is freely available online: because the areas sequenced so far are relatively gene rich, about half the 13,000 genes can now be scanned. More than a quarter of the genes are represented by expressed sequence tags (ESTs). All information pertaining to the genome is publicly available in the ACeDB data base.}, file = {/home/trey/Zotero/storage/44D8HILA/Waterston and Sulston - 1995 - The genome of Caenorhabditis elegans..pdf} } % == BibTeX quality report for waterstonGenomeCaenorhabditisElegans1995: % ? unused Library catalog (“pnas.org (Atypon)”)

@misc{ZFINZebrafishInformation, title = {{{ZFIN The Zebrafish Information Network}}}, url = {https://zfin.org/}, urldate = {2025-10-20}, keywords = {nosource}, file = {/home/trey/Zotero/storage/7MJHRXNP/zfin.org.html} } % == BibTeX quality report for ZFINZebrafishInformation: % ? Title looks like it was stored in title-case in Zotero

@incollection{dahmZebrafishDanioRerio2006, title = {Zebrafish ({{Danio}} Rerio) {{Genome}} and {{Genetics}}}, booktitle = {Reviews in {{Cell Biology}} and {{Molecular Medicine}}}, author = {Dahm, Ralf and Geisler, Robert and {N{"u}sslein-Volhard}, Christiane}, year = 2006, publisher = {John Wiley & Sons, Ltd}, doi = {10.1002/3527600906.mcb.200400059}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/3527600906.mcb.200400059}, urldate = {2025-10-20}, abstract = {Owing to its transparent, easily accessible embryos, simple breeding, and short generation time, the zebrafish has become one of the most important model organisms to study the genetic control of embryonic development. Zebrafish research initially focused on forward genetics (mutagenesis screening), but reverse genetic methods, transgenesis, and microarrays are now equally available to characterize known genes. The zebrafish genome consists of 25 chromosome pairs and has an estimated haploid size of 1.5 Gb. Several genome maps exist for the zebrafish. The meiotic MGH map is generally used for placement of mutant loci and, in combination with the T51 radiation hybrid map and BAC fingerprinting, forms the basis of genome sequencing. A genome sequence is being generated by a combination of whole-genome shotgun and BAC-based sequencing, and is expected to be finished in 2005.}, copyright = {Copyright 2006 Wiley-VCH Verlag GmbH & Co. KGaA}, isbn = {978-3-527-60090-8}, langid = {english}, keywords = {Bacterial Artificial Chromosomes (BACs),Expressed Sequence Tags (ESTs),Forward Genetics,Knockdown,Microsatellite Markers,Positional Cloning,Radiation Hybrid Mapping,Restriction Fingerprinting,Reverse Genetics,Single Nucleotide Polymorphisms (SNPs),Targeting Induced Local Lesions In Genomes (TILLING),Teleost Genome Duplication}, file = {/home/trey/Zotero/storage/L9UFYUG3/Dahm et al. - 2006 - Zebrafish (Danio rerio) Genome and Genetics.pdf;/home/trey/Zotero/storage/2Y78ECVJ/3527600906.mcb.html} } % == BibTeX quality report for dahmZebrafishDanioRerio2006: % ? unused extra: _eprint (“https://onlinelibrary.wiley.com/doi/pdf/10.1002/3527600906.mcb.200400059”) % ? unused Library catalog (“Wiley Online Library”)

@misc{FlyBaseHomepage, title = {{{FlyBase Homepage}}}, url = {https://flybase.org/}, urldate = {2025-10-20}, keywords = {nosource}, file = {/home/trey/Zotero/storage/ZDCC764A/flybase.org.html} } % == BibTeX quality report for FlyBaseHomepage: % ? Title looks like it was stored in title-case in Zotero

@article{hoskinsRelease6Reference2015, title = {The {{Release}} 6 Reference Sequence of the {{Drosophila}} Melanogaster Genome}, author = {Hoskins, Roger A. and Carlson, Joseph W. and Wan, Kenneth H. and Park, Soo and Mendez, Ivonne and Galle, Samuel E. and Booth, Benjamin W. and Pfeiffer, Barret D. and George, Reed A. and Svirskas, Robert and Krzywinski, Martin and Schein, Jacqueline and Accardo, Maria Carmela and Damia, Elisabetta and Messina, Giovanni and {M{'e}ndez-Lago}, Mar{'i}a and {}{de Pablos}, Beatriz and Demakova, Olga V. and Andreyeva, Evgeniya N. and Boldyreva, Lidiya V. and Marra, Marco and Carvalho, A. Bernardo and Dimitri, Patrizio and Villasante, Alfredo and Zhimulev, Igor F. and Rubin, Gerald M. and Karpen, Gary H. and Celniker, Susan E.}, year = 2015, month = mar, journal = {Genome Research}, volume = {25}, number = {3}, pages = {445–458}, issn = {1549-5469}, doi = {10.1101/gr.185579.114}, abstract = {Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.}, langid = {english}, pmcid = {PMC4352887}, pmid = {25589440}, keywords = {Animals,Chromosome Mapping,Chromosomes Artificial Bacterial,Computational Biology,Contig Mapping,Drosophila melanogaster,Genome,High-Throughput Nucleotide Sequencing,In Situ Hybridization Fluorescence,Molecular Sequence Data,Polytene Chromosomes,Restriction Mapping}, file = {/home/trey/Zotero/storage/LR9J8LWP/Hoskins et al. - 2015 - The Release 6 reference sequence of the Drosophila melanogaster genome.pdf} } % == BibTeX quality report for hoskinsRelease6Reference2015: % ? unused Journal abbr (“Genome Res”) % ? unused Library catalog (“PubMed”)

@misc{EcoCycEncyclopediaColi, title = {{{EcoCyc}}: {{Encyclopedia}} of {{E}}. Coli {{Genes}} and {{Metabolism}}}, url = {https://ecocyc.org/}, urldate = {2025-10-20}, keywords = {nosource} }

@article{blattnerCompleteGenomeSequence1997, title = {The Complete Genome Sequence of {{Escherichia}} Coli {{K-12}}}, author = {Blattner, F. R. and Plunkett, G. and Bloch, C. A. and Perna, N. T. and Burland, V. and Riley, M. and {Collado-Vides}, J. and Glasner, J. D. and Rode, C. K. and Mayhew, G. F. and Gregor, J. and Davis, N. W. and Kirkpatrick, H. A. and Goeden, M. A. and Rose, D. J. and Mau, B. and Shao, Y.}, year = 1997, month = sep, journal = {Science (New York, N.Y.)}, volume = {277}, number = {5331}, pages = {1453–1462}, issn = {0036-8075}, doi = {10.1126/science.277.5331.1453}, abstract = {The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.}, langid = {english}, pmid = {9278503}, keywords = {Bacterial Proteins,Bacteriophage lambda,Base Composition,Binding Sites,Chromosome Mapping,DNA Bacterial,DNA Replication,DNA Transposable Elements,Escherichia coli,Genes Bacterial,Genome Bacterial,Molecular Sequence Data,Mutation,Operon,Recombination Genetic,Regulatory Sequences Nucleic Acid,Repetitive Sequences Nucleic Acid,RNA Bacterial,RNA Transfer,Sequence Analysis DNA,Sequence Homology Amino Acid}, file = {/home/trey/Zotero/storage/CVRRI6JC/Blattner et al. - 1997 - The complete genome sequence of Escherichia coli K-12.pdf} } % == BibTeX quality report for blattnerCompleteGenomeSequence1997: % ? Possibly abbreviated journal title Science (New York, N.Y.) % ? unused Journal abbr (“Science”) % ? unused Library catalog (“PubMed”)

@misc{NCBIVirus, title = {{{NCBI Virus}}}, url = {https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=taxid:197911&VirusLineage_ss=taxid:197912&VirusLineage_ss=taxid:197913&VirusLineage_ss=taxid:1511083}, urldate = {2025-10-20}, keywords = {nosource} } % == BibTeX quality report for NCBIVirus: % ? Title looks like it was stored in title-case in Zotero

@article{tsaiInfluenzaGenomeDiversity2011, title = {Influenza Genome Diversity and Evolution}, author = {Tsai, Kun-Nan and Chen, Guang-Wu}, year = 2011, month = may, journal = {Microbes and Infection}, series = {Special Issue on Influenza}, volume = {13}, number = {5}, pages = {479–488}, issn = {1286-4579}, doi = {10.1016/j.micinf.2011.01.013}, url = {https://www.sciencedirect.com/science/article/pii/S1286457911000438}, urldate = {2025-10-20}, abstract = {The influenza viruses contain highly variable genomes and are able to infect a wide range of host species. Large-scale sequencing projects have collected abundant influenza sequence data for assessing influenza genome diversity and evolution. This work reviews current influenza sequence databases characteristics and statistics, as well as recent studies utilizing these databases to unravel influenza virus diversity and evolution. Also discussed are the newest deep sequencing methods and their applications to influenza virus research.}, keywords = {Deep sequencing,Evolution,Genome,Influenza A virus,Quasispecies}, file = {/home/trey/Zotero/storage/MBQ2YXRJ/Tsai and Chen - 2011 - Influenza genome diversity and evolution.pdf;/home/trey/Zotero/storage/TV495SLG/S1286457911000438.html} } % == BibTeX quality report for tsaiInfluenzaGenomeDiversity2011: % ? unused Library catalog (“ScienceDirect”)

@misc{MouseGenomesProject, title = {The {{Mouse Genomes Project}} {{Reference}} Genomes and Genetic Variation for Laboratory Mouse Strains}, url = {https://www.mousegenomes.org/}, urldate = {2025-10-20}, langid = {american}, keywords = {nosource}, file = {/home/trey/Zotero/storage/QK8EPUQ9/www.mousegenomes.org.html} }

@article{guenetMouseGenome2005, title = {The Mouse Genome}, author = {Gu{'e}net, Jean Louis}, year = 2005, month = jan, journal = {Genome Research}, volume = {15}, number = {12}, pages = {1729–1740}, publisher = {Cold Spring Harbor Lab}, issn = {1088-9051, 1549-5469}, doi = {10.1101/gr.3728305}, url = {http://genome.cshlp.org/content/15/12/1729}, urldate = {2025-10-20}, abstract = {The house mouse has been used as a privileged model organism since the early days of genetics, and the numerous experiments made with this small mammal have regularly contributed to enrich our knowledge of mammalian biology and pathology, ranging from embryonic development to metabolic disease, histocompatibility, immunology, behavior, and cancer. Over the past two decades, a number of large-scale integrated and concerted projects have been undertaken that will probably open a new era in the genetics of the species. The sequencing of the genome, which will allow researchers to make comparisons with other mammals and identify regions conserved by evolution, is probably the most important project, but many other initiatives, such as the massive production of point or chromosomal mutations associated with comprehensive and standardized phenotyping of the mutant phenotypes, will help annotation of the {\(\sim\)}25,000 genes packed in the mouse genome. In the same way, and as another consequence of the sequencing, the discovery of many single nucleotide polymorphisms and the development of new tools and resources, like the Collaborative Cross, will contribute to the development of modern quantitative genetics. It is clear that mouse genetics has changed dramatically over the last 10-15 years and its future looks promising.}, langid = {english}, pmid = {16339371}, file = {/home/trey/Zotero/storage/GX6HVI78/Guénet - 2005 - The mouse genome.pdf} } % == BibTeX quality report for guenetMouseGenome2005: % ? unused Journal abbr (“Genome Res.”) % ? unused Library catalog (“genome.cshlp.org”)

@article{larsonHaplotyperesolvedReferenceGenome2025, title = {A Haplotype-Resolved Reference Genome of {{Quercus}} Alba Sheds Light on the Evolutionary History of Oaks}, author = {Larson, Drew A. and Staton, Margaret E. and Kapoor, Beant and {Islam-Faridi}, Nurul and Zhebentyayeva, Tetyana and Fan, Shenghua and Stork, Jozsef and Thomas, Austin and Ahmed, Alaa S. and Stanton, Elizabeth C. and Houston, Allan and Schlarbaum, Scott E. and Hahn, Matthew W. and Carlson, John E. and Abbott, Albert G. and DeBolt, Seth and Nelson, C. Dana}, year = 2025, journal = {New Phytologist}, volume = {246}, number = {1}, pages = {331–348}, issn = {1469-8137}, doi = {10.1111/nph.20463}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20463}, urldate = {2025-10-20}, abstract = {White oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. We report the first haplotype-resolved chromosome-scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. We investigate the genetic diversity of this widespread species and the phylogenetic relationships among oaks using whole genome data. Despite strongly conserved chromosome synteny and genome size across Quercus, certain gene families have undergone rapid changes in size, including defense genes. Unbiased annotation of resistance (R) genes across oaks revealed that the overall number of R genes is similar across species – as are the chromosomal locations of R gene clusters – but, gene number within clusters is more labile. We found that Q. alba has high genetic diversity, much of which predates its divergence from other oaks and likely impacts divergence time estimations. Our phylogenetic results highlight widespread phylogenetic discordance across the genus. The white oak genome represents a major new resource for studying genome diversity and evolution in Quercus. Additionally, we show that unbiased gene annotation is key to accurately assessing R gene evolution in Quercus.}, copyright = { 2025 The Author(s). New Phytologist 2025 New Phytologist Foundation.}, langid = {english}, keywords = {comparative genomics,gene family evolution,genome assembly,phylogenetic tree,population structure,Quercus alba (white oak)}, file = {/home/trey/Zotero/storage/7TPB4J4C/Larson et al. - 2025 - A haplotype-resolved reference genome of Quercus alba sheds light on the evolutionary history of oak.pdf;/home/trey/Zotero/storage/H3FCYKHP/nph.html} } % == BibTeX quality report for larsonHaplotyperesolvedReferenceGenome2025: % ? unused extra: _eprint (“https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20463”) % ? unused Library catalog (“Wiley Online Library”)

@article{hamiltonRiceGenomeAnnotation2025, title = {The Rice Genome Annotation Project: An Updated Database for Mining the Rice Genome}, shorttitle = {The Rice Genome Annotation Project}, author = {Hamilton, John~P and Li, Chenxin and Buell, C Robin}, year = 2025, month = jan, journal = {Nucleic Acids Research}, volume = {53}, number = {D1}, pages = {D1614-D1622}, issn = {0305-1048, 1362-4962}, doi = {10.1093/nar/gkae1061}, url = {https://academic.oup.com/nar/article/53/D1/D1614/7903367}, urldate = {2025-10-20}, abstract = {Abstract Rice (Oryza sativa L.) is a major cereal crop that provides calories across the world. With a small genome, rice has been used extensively as a model for genetic and genomic studies in the Poaceae. Since the release of the first rice genome sequence in 2002, an improved reference genome assembly, multiple whole genome assemblies, extensive gene expression profiles, and resequencing data from over 3000 rice accessions have been generated. To facilitate access to the rice genome for plant biologists, we updated the Rice Genome Annotation Project database (RGAP; https://rice.uga.edu) with new datasets including 16 whole genome rice assemblies and sequence variants generated from multiple rice pan-genome projects including the 3000 Rice Genomes Project. We updated gene expression abundance data with 80 RNA-sequencing datasets and to facilitate gene function discovery, performed gene coexpression resulting in 39 coexpression modules that capture highly connected sets of co-regulated genes. To facilitate comparative genome analyses, 32~335 syntelogs were identified between the Nipponbare reference genome and other rice genomes and 19~371 syntelogs were identified between Nipponbare and four other Poaceae genomes. Infrastructure improvements to the RGAP database include an upgraded genome browser and data access portals, enhanced website security~and increased performance of the website.}, copyright = {https://creativecommons.org/licenses/by-nc/4.0/}, langid = {english}, file = {/home/trey/Zotero/storage/VY7I693D/Hamilton et al. - 2025 - The rice genome annotation project an updated database for mining the rice genome.pdf} } % == BibTeX quality report for hamiltonRiceGenomeAnnotation2025: % ? unused Library catalog (“DOI.org (Crossref)”)

@article{sasakiInternationalRiceGenome2000, title = {International {{Rice Genome Sequencing Project}}: The Effort to Completely Sequence the Rice Genome}, shorttitle = {International {{Rice Genome Sequencing Project}}}, author = {Sasaki, Takuji and Burr, Benjamin}, year = 2000, month = apr, journal = {Current Opinion in Plant Biology}, volume = {3}, number = {2}, pages = {138–142}, issn = {1369-5266}, doi = {10.1016/S1369-5266(99)00047-3}, url = {https://www.sciencedirect.com/science/article/pii/S1369526699000473}, urldate = {2025-10-20}, abstract = {The International Rice Genome Sequencing Project (IRGSP) involves researchers from ten countries who are working to completely and accurately sequence the rice genome within a short period. Sequencing uses a map-based clone-by-clone shotgun strategy; shared bacterial artificial chromosome/ P1-derived artificial chromosome libraries have been constructed from Oryza sativa ssp. japonica variety `Nipponbare’. End-sequencing, fingerprinting and marker-aided PCR screening are being used to make sequence-ready contigs. Annotated sequences are immediately released for public use and are made available with supplemental information at each IRGSP member’s website. The IRGSP works to promote the development of rice and cereal genomics in addition to producing genome sequence data.}, keywords = {Annotation,Bacterial artificial chromosome (BAC),Expressed sequence tag (EST),Genome sequencing,P1-derived artificial chromosome (PAC),Rice,Rice genome}, file = {/home/trey/Zotero/storage/GSM3T8H4/Sasaki and Burr - 2000 - International Rice Genome Sequencing Project the effort to completely sequence the rice genome.pdf;/home/trey/Zotero/storage/FAW837CD/S1369526699000473.html} } % == BibTeX quality report for sasakiInternationalRiceGenome2000: % ? unused Library catalog (“ScienceDirect”)

@article{zhangEssentialGenomeCrenarchaeal2018, title = {The Essential Genome of the Crenarchaeal Model {{Sulfolobus}} Islandicus}, author = {Zhang, Changyi and Phillips, Alex P. R. and Wipfler, Rebecca L. and Olsen, Gary J. and Whitaker, Rachel J.}, year = 2018, month = nov, journal = {Nature Communications}, volume = {9}, number = {1}, pages = {4908}, publisher = {Nature Publishing Group}, issn = {2041-1723}, doi = {10.1038/s41467-018-07379-4}, url = {https://www.nature.com/articles/s41467-018-07379-4}, urldate = {2025-10-20}, abstract = {Sulfolobus islandicus is a model microorganism in the TACK superphylum of the Archaea, a key lineage in the evolutionary history of cells. Here we report a genome-wide identification of the repertoire of genes essential to S. islandicus growth in culture. We confirm previous targeted gene knockouts, uncover the non-essentiality of functions assumed to be essential to the Sulfolobus cell, including the proteinaceous S-layer, and highlight essential genes whose functions are yet to be determined. Phyletic distributions illustrate the potential transitions that may have occurred during the evolution of this archaeal microorganism, and highlight sets of genes that may have been associated with each transition. We use this comparative context as a lens to focus future research on archaea-specific uncharacterized essential genes that may provide valuable insights into the evolutionary history of cells.}, copyright = {2018 The Author(s)}, langid = {english}, keywords = {Archaeal biology,Archaeal evolution,Archaeal genomics,Evolutionary genetics}, file = {/home/trey/Zotero/storage/S3ZV9C6Y/Zhang et al. - 2018 - The essential genome of the crenarchaeal model Sulfolobus islandicus.pdf} } % == BibTeX quality report for zhangEssentialGenomeCrenarchaeal2018: % ? unused Journal abbr (“Nat Commun”) % ? unused Library catalog (“www.nature.com”)

@article{comeauModularArchitectureT42007, title = {Modular Architecture of the {{T4}} Phage Superfamily: {{A}} Conserved Core Genome and a Plastic Periphery}, shorttitle = {Modular Architecture of the {{T4}} Phage Superfamily}, author = {Comeau, Andr{'e} M. and Bertrand, Claire and Letarov, Andrei and T{'e}tart, Fran{}oise and Krisch, H. M.}, year = 2007, month = jun, journal = {Virology}, volume = {362}, number = {2}, pages = {384–396}, issn = {0042-6822}, doi = {10.1016/j.virol.2006.12.031}, url = {https://www.sciencedirect.com/science/article/pii/S0042682206009251}, urldate = {2025-10-20}, abstract = {Among the most numerous objects in the biosphere, phages show enormous diversity in morphology and genetic content. We have sequenced 7 T4-like phages and compared their genome architecture. All seven phages share a core genome with T4 that is interrupted by several hyperplastic regions (HPRs) where most of their divergence occurs. The core primarily includes homologues of essential T4 genes, such as the virion structure and DNA replication genes. In contrast, the HPRs contain mostly novel genes of unknown function and origin. A few of the HPR genes that can be assigned putative functions, such as a series of novel Internal Proteins, are implicated in phage adaptation to the host. Thus, the T4-like genome appears to be partitioned into discrete segments that fulfil different functions and behave differently in evolution. Such partitioning may be critical for these large and complex phages to maintain their flexibility, while simultaneously allowing them to conserve their highly successful virion design and mode of replication.}, keywords = {Conserved core genome,Genome evolution,Genome plasticity,Phage,T4 superfamily}, file = {/home/trey/Zotero/storage/ULKWXCFN/Comeau et al. - 2007 - Modular architecture of the T4 phage superfamily A conserved core genome and a plastic periphery.pdf;/home/trey/Zotero/storage/IVE79WCB/S0042682206009251.html} } % == BibTeX quality report for comeauModularArchitectureT42007: % ? unused Library catalog (“ScienceDirect”)

@article{turing1936computable, title = {On Computable Numbers, with an Application to the {{Entscheidungsproblem}}}, author = {Turing, Alan Mathison and others}, year = 1936, journal = {J. of Math}, volume = {58}, number = {345-363}, pages = {5}, publisher = {Wiley Online Library}, langid = {english}, keywords = {No DOI found}, file = {/home/trey/Zotero/storage/L2GYHQ58/Tuking - ON COMPUTABLE NUMBERS, WITH AN APPLICATION TO THE ENTSCHEIDUNGSPROBLEM.pdf} } % == BibTeX quality report for turing1936computable: % ? Possibly abbreviated journal title J. of Math % ? unused Library catalog (“Zotero”)

@book{kleene1956representation, title = {Representation of Events in Nerve Nets and Finite Automata}, author = {Kleene, Stephen Cole}, year = 1956, volume = {34}, publisher = {Princeton University Press Princeton}, file = {/home/trey/Zotero/storage/GRTQYY7K/Kleene - 1956 - Representation of events in nerve nets and finite automata.pdf} }

@inproceedings{burge1964evaluation, title = {The Evaluation, Classification and Interpretation of Expressions}, booktitle = {Proceedings of the 1964 19th {{ACM}} National Conference}, author = {Burge, William H}, year = 1964, pages = {11–401}, keywords = {No DOI found}, file = {/home/trey/Zotero/storage/F3YMD89T/Burge - 1964 - The evaluation, classification and interpretation of expressions.pdf} } % == BibTeX quality report for burge1964evaluation: % ? Unsure about the formatting of the booktitle

@article{glasnerASAPSystematicAnnotation2003, title = {{{ASAP}}, a Systematic Annotation Package for Community Analysis of Genomes}, author = {Glasner, Jeremy D. and Liss, Paul and Plunkett III, Guy and Darling, Aaron and Prasad, Tejasvini and Rusch, Michael and Byrnes, Alexis and Gilson, Michael and Biehl, Bryan and Blattner, Frederick R. and Perna, Nicole T.}, year = 2003, month = jan, journal = {Nucleic Acids Research}, volume = {31}, number = {1}, pages = {147–151}, issn = {0305-1048}, doi = {10.1093/nar/gkg125}, url = {https://doi.org/10.1093/nar/gkg125}, urldate = {2025-10-30}, abstract = {ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and functional characterization ( https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm ). ASAP facilitates ongoing community annotation of genomes and tracking of information as genome projects move from preliminary data collection through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. ASAP supports three levels of users: public viewers, annotators and curators. Public viewers can currently browse updated annotation information for Escherichia coli K-12 strain MG1655, genome-wide transcript profiles from more than 50 microarray experiments and an extensive collection of mutant strains and associated phenotypic data. Annotators worldwide are currently using ASAP to participate in a community annotation project for the Erwinia chrysanthemi strain 3937 genome. Curation of the E. chrysanthemi genome annotation as well as those of additional published enterobacterial genomes is underway and will be publicly accessible in the near future.}, keywords = {duplicate}, file = {/home/trey/Zotero/storage/22R5IRDM/Glasner et al. - 2003 - ASAP, a systematic annotation package for community analysis of genomes.pdf;/home/trey/Zotero/storage/XZAX8LRP/Glasner et al. - 2003 - ASAP, a systematic annotation package for community analysis of genomes.pdf;/home/trey/Zotero/storage/WTMA3TD8/gkg125.html} } % == BibTeX quality report for glasnerASAPSystematicAnnotation2003: % ? unused Journal abbr (“Nucleic Acids Res”) % ? unused Library catalog (“Silverchair”)

@article{eichlerIdentificationCharacterizationCaiF1996, title = {Identification and Characterization of the {{caiF}} Gene Encoding a Potential Transcriptional Activator of Carnitine Metabolism in {{Escherichia}} Coli}, author = {Eichler, K and Buchet, A and Lemke, R and Kleber, H P and {Mandrand-Berthelot}, M A}, year = 1996, month = mar, journal = {Journal of Bacteriology}, volume = {178}, number = {5}, pages = {1248–1257}, publisher = {American Society for Microbiology}, doi = {10.1128/jb.178.5.1248-1257.1996}, url = {https://journals.asm.org/doi/10.1128/jb.178.5.1248-1257.1996}, urldate = {2025-10-30}, abstract = {Expression of the Escherichia coli caiTABCDE and fixABCX operons involved in carnitine metabolism is induced by both carnitine and anaerobiosis. When cloned into a multicopy plasmid, the 3’ region adjacent to the caiTABCDE operon was found to increase levels of carnitine dehydratase activity synthesized from the chromosomal caiB gene. The nucleotide sequence was determined, and it was shown to contain an open reading frame of 393 bp named caiF which is transcribed in the direction opposite that of the cai operon. This open reading frame encodes a protein of 131 amino acids with a predicted molecular mass of 15,438 Da which does not have any significant homology with proteins available in data libraries. In vivo overexpression consistently led to the synthesis of a 16-kDa protein. The caiF gene was transcribed as a monocistronic mRNA under anaerobiosis independently of the presence of carnitine. Primer extension analysis located the start site of transcription to position 82 upstream of the caiF initiation codon. It was preceded by a cyclic AMP receptor protein motif centered at position -41.5. Overproduction of CaiF resulted in the stimulation of transcription of the divergent cai and fix operons in the presence of carnitine. This suggested that CaiF by interacting with carnitine plays the role of an activator, thereby mediating induction of carnitine metabolism. Moreover, CaiF could complement in trans the regulatory defect of laboratory strain MC4100 impaired in the carnitine pathway. Expression of a caiF-lacZ operon fusion was subject to FNR regulator-mediated anaerobic induction and cyclic AMP receptor protein activation. The histone-like protein H-NS and the NarL (plus nitrate) regulator acted as repressors. Because of the multiple controls to which the caiF gene is subjected, it appears to be a key element in the regulation of carnitine metabolism.}, file = {/home/trey/Zotero/storage/XAGHRIM6/Eichler et al. - 1996 - Identification and characterization of the caiF gene encoding a potential transcriptional activator.pdf} } % == BibTeX quality report for eichlerIdentificationCharacterizationCaiF1996: % ? unused Library catalog (“journals.asm.org (Atypon)”)

@book{MyNCBIHelp2005, title = {My {{NCBI Help}}}, year = 2005, publisher = {National Center for Biotechnology Information (US)}, abstract = {This book contains information on how to use My NCBI, a tool developed by the National Center for Biotechnology Information (NCBI).}, file = {/home/trey/Zotero/storage/4QZ5ICKV/Bookshelf_NBK3843.pdf} } % == BibTeX quality report for MyNCBIHelp2005: % Missing required field ‘author/editor’ % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“PubMed”)

@article{ramirezDeepToolsFlexiblePlatform2014, title = {{{deepTools}}: A Flexible Platform for Exploring Deep-Sequencing Data}, shorttitle = {{{deepTools}}}, author = {Ram{'i}rez, Fidel and D{"u}ndar, Friederike and Diehl, Sarah and Gr{"u}ning, Bj{"o}rn A. and Manke, Thomas}, year = 2014, month = jul, journal = {Nucleic Acids Research}, volume = {42}, number = {W1}, pages = {W187-W191}, issn = {0305-1048}, doi = {10.1093/nar/gku365}, url = {https://doi.org/10.1093/nar/gku365}, urldate = {2025-11-03}, abstract = {We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server’s core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg.de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy.}, file = {/home/trey/Zotero/storage/FM3W8TMY/Ramírez et al. - 2014 - deepTools a flexible platform for exploring deep-sequencing data.pdf;/home/trey/Zotero/storage/BW285YVM/gku365.html} } % == BibTeX quality report for ramirezDeepToolsFlexiblePlatform2014: % ? unused Journal abbr (“Nucleic Acids Res”) % ? unused Library catalog (“Silverchair”)

@article{songGgcoveragePackageVisualize2023, title = {Ggcoverage: An {{R}} Package to Visualize and Annotate Genome Coverage for Various {{NGS}} Data}, shorttitle = {Ggcoverage}, author = {Song, Yabing and Wang, Jianbin}, year = 2023, month = aug, journal = {BMC Bioinformatics}, volume = {24}, number = {1}, pages = {309}, issn = {1471-2105}, doi = {10.1186/s12859-023-05438-2}, url = {https://doi.org/10.1186/s12859-023-05438-2}, urldate = {2025-11-03}, abstract = {Visualizing genome coverage is of vital importance to inspect and interpret various next-generation sequencing (NGS) data. Besides genome coverage, genome annotations are also crucial in the visualization. While different NGS data require different annotations, how to visualize genome coverage and add the annotations appropriately and conveniently is challenging. Many tools have been developed to address this issue. However, existing tools are often inflexible, complicated, lack necessary preprocessing steps and annotations, and the figures generated support limited customization.}, langid = {english}, keywords = {Genome annotation,Genome coverage,Multi-omics,Next-generation sequencing,Visualization}, file = {/home/trey/Zotero/storage/6I7DB6TB/Song and Wang - 2023 - ggcoverage an R package to visualize and annotate genome coverage for various NGS data.pdf} } % == BibTeX quality report for songGgcoveragePackageVisualize2023: % ? unused Library catalog (“Springer Link”)

@article{almMicrobesOnlineWebSite2005, title = {The {{MicrobesOnline Web}} Site for Comparative Genomics}, author = {Alm, Eric J. and Huang, Katherine H. and Price, Morgan N. and Koche, Richard P. and Keller, Keith and Dubchak, Inna L. and Arkin, Adam P.}, year = 2005, month = jul, journal = {Genome Research}, volume = {15}, number = {7}, pages = {1015–1022}, issn = {1088-9051}, doi = {10.1101/gr.3844805}, url = {http://genome.cshlp.org/lookup/doi/10.1101/gr.3844805}, urldate = {2025-11-04}, abstract = {At present, hundreds of microbial genomes have been sequenced, and hundreds more are currently in the pipeline. The Virtual Institute for Microbial Stress and Survival has developed a publicly available suite of Web-based comparative genomic tools (http://www.microbesonline.org) designed to facilitate multispecies comparison among prokaryotes. Highlights of the MicrobesOnline Web site include operon and regulon predictions, a multispecies genome browser, a multispecies Gene Ontology browser, a comparative KEGG metabolic pathway viewer, a Bioinformatics Workbench for in-depth sequence analysis, and Gene Carts that allow users to save genes of interest for further study while they browse. In addition, we provide an interface for genome annotation, which like all of the tools reported here, is freely available to the scientific community.}, langid = {english}, file = {/home/trey/Zotero/storage/WGHPT3TP/Alm et al. - 2005 - The MicrobesOnline Web site for comparative genomics.pdf} } % == BibTeX quality report for almMicrobesOnlineWebSite2005: % ? unused Journal abbr (“Genome Res.”) % ? unused Library catalog (“DOI.org (Crossref)”)

@article{schulteMultiLanguageComputingEnvironment2012, title = {A {{Multi-Language Computing Environment}} for {{Literate Programming}} and {{Reproducible Research}}}, author = {Schulte, Eric and Davison, Dan and Dye, Thomas and Dominik, Carsten}, year = 2012, month = jan, journal = {Journal of Statistical Software}, volume = {46}, pages = {1–24}, issn = {1548-7660}, doi = {10.18637/jss.v046.i03}, url = {https://doi.org/10.18637/jss.v046.i03}, urldate = {2025-11-05}, abstract = {We present a new computing environment for authoring mixed natural and computer language documents. In this environment a single hierarchically-organized plain text source file may contain a variety of elements such as code in arbitrary programming languages, raw data, links to external resources, project management data, working notes, and text for publication. Code fragments may be executed in situ with graphical, numerical and textual output captured or linked in the file. Export to LATEX, HTML, LATEX beamer, DocBook and other formats permits working reports, presentations and manuscripts for publication to be generated from the file. In addition, functioning pure code files can be automatically extracted from the file. This environment is implemented as an extension to the Emacs text editor and provides a rich set of features for authoring both prose and code, as well as sophisticated project management capabilities.}, copyright = {Copyright (c) 2010 Eric Schulte, Dan Davison, Thomas Dye, Carsten Dominik}, langid = {english}, file = {/home/trey/Zotero/storage/MT99TBH4/Schulte et al. - 2012 - A Multi-Language Computing Environment for Literate Programming and Reproducible Research.pdf} } % == BibTeX quality report for schulteMultiLanguageComputingEnvironment2012: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“www.jstatsoft.org”)

@inproceedings{furlaniModulesProvidingFlexible1991, title = {Modules: {{Providing}} a Flexible User Environment}, shorttitle = {Modules}, booktitle = {Proceedings of the Fifth Large Installation Systems Administration Conference ({{LISA V}})}, author = {Furlani, John L.}, year = 1991, pages = {141–152}, url = {https://usablesecurity.net/OSCAR/pkgs/downloads/modules-oscar/Modules-Paper.pdf}, urldate = {2025-11-05}, keywords = {No DOI found}, file = {/home/trey/Zotero/storage/J92HJ8VH/Furlani - 1991 - Modules Providing a flexible user environment.pdf} } % == BibTeX quality report for furlaniModulesProvidingFlexible1991: % ? Unsure about the formatting of the booktitle % ? unused Library catalog (“Google Scholar”)

@article{rileyEscherichiaColiK122006, title = {Escherichia Coli {{K-12}}: A Cooperatively Developed Annotation Snapshot—2005}, shorttitle = {Escherichia Coli {{K-12}}}, author = {Riley, Monica and Abe, Takashi and Arnaud, Martha B. and Berlyn, Mary K.B. and Blattner, Frederick R. and Chaudhuri, Roy R. and Glasner, Jeremy D. and Horiuchi, Takashi and Keseler, Ingrid M. and Kosuge, Takehide and Mori, Hirotada and Perna, Nicole T. and Plunkett, III, Guy and Rudd, Kenneth E. and Serres, Margrethe H. and Thomas, Gavin H. and Thomson, Nicholas R. and Wishart, David and Wanner, Barry L.}, year = 2006, month = jan, journal = {Nucleic Acids Research}, volume = {34}, number = {1}, pages = {1–9}, issn = {0305-1048}, doi = {10.1093/nar/gkj405}, url = {https://doi.org/10.1093/nar/gkj405}, urldate = {2025-11-06}, abstract = {The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. Known and predicted functions were assigned to each gene product on the basis of experimental evidence or sequence analysis. Since both kinds of evidence are constantly expanding, no annotation is complete at any moment in time. This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles.}, file = {/home/trey/Zotero/storage/QU65DC6R/Riley et al. - 2006 - Escherichia coli K-12 a cooperatively developed annotation snapshot—2005.pdf;/home/trey/Zotero/storage/UNWB6K8B/gkj405.html} } % == BibTeX quality report for rileyEscherichiaColiK122006: % ? unused Journal abbr (“Nucleic Acids Res”) % ? unused Library catalog (“Silverchair”)

@misc{klimesDklimesDantools2025, title = {Dklimes/Dantools}, author = {Klimes, Daniel}, year = 2025, month = jun, url = {https://github.com/dklimes/dantools}, urldate = {2025-11-07}, abstract = {Utilities to compare disparate genomes}, keywords = {nosource} } % == BibTeX quality report for klimesDklimesDantools2025: % ? Title looks like it was stored in lower-case in Zotero % ? unused Library catalog (“GitHub”) % ? unused Original date (“2024-05-01T20:56:36Z”) % ? unused Programming language (“Perl”)

@article{debakkerCRISPRiseqGenomewideFitness2022, title = {{{CRISPRi-seq}} for Genome-Wide Fitness Quantification in Bacteria}, author = {{}{de Bakker}, Vincent and Liu, Xue and Bravo, Afonso M. and Veening, Jan-Willem}, year = 2022, month = feb, journal = {Nature Protocols}, volume = {17}, number = {2}, pages = {252–281}, issn = {1750-2799}, doi = {10.1038/s41596-021-00639-6}, url = {https://doi.org/10.1038/s41596-021-00639-6}, urldate = {2025-11-11}, abstract = {CRISPR interference (CRISPRi) is a powerful tool to link essential and nonessential genes to specific phenotypes and to explore their functions. Here we describe a protocol for CRISPRi screenings to assess genome-wide gene fitness in a single sequencing step (CRISPRi-seq). We demonstrate the use of the protocol in Streptococcus pneumoniae, an important human pathogen; however, the protocol can easily be adapted for use in other organisms. The protocol includes a pipeline for single-guide RNA library design, workflows for pooled CRISPRi library construction, growth assays and sequencing steps, a read analysis tool (2FAST2Q) and instructions for fitness quantification. We describe how to make an IPTG-inducible system with small libraries that are easy to handle and cost-effective and overcome bottleneck issues, which can be a problem when using similar, transposon mutagenesis-based methods. Ultimately, the procedure yields a fitness score per single-guide RNA target for any given growth condition. A genome-wide screening can be finished in 1 week with a constructed library. Data analysis and follow-up confirmation experiments can be completed in another 2–3 weeks.}, langid = {english}, keywords = {duplicate}, file = {/home/trey/Zotero/storage/8FK7MH2Q/de Bakker et al. - 2022 - CRISPRi-seq for genome-wide fitness quantification in bacteria.pdf;/home/trey/Zotero/storage/ZBJ989P5/de Bakker et al. - 2022 - CRISPRi-seq for genome-wide fitness quantification in bacteria.pdf} } % == BibTeX quality report for debakkerCRISPRiseqGenomewideFitness2022: % ? unused Journal abbr (“Nat Protoc”) % ? unused Library catalog (“Springer Link”)

@article{liuHighthroughputCRISPRiPhenotyping2017, title = {High-throughput {{CRISPRi}} Phenotyping Identifies New Essential Genes in {{Streptococcus}} Pneumoniae}, author = {Liu, Xue and Gallay, Clement and Kjos, Morten and Domenech, Arnau and Slager, Jelle and {}{van Kessel}, Sebastiaan P and Knoops, K{`e}vin and Sorg, Robin A and Zhang, Jing-Ren and Veening, Jan-Willem}, year = 2017, month = may, journal = {Molecular Systems Biology}, volume = {13}, number = {5}, pages = {931}, publisher = {John Wiley & Sons, Ltd}, issn = {1744-4292}, doi = {10.15252/msb.20167449}, url = {https://www.embopress.org/doi/full/10.15252/msb.20167449}, urldate = {2025-11-11}, abstract = {Genome-wide screens have discovered a large set of essential genes in the opportunistic human pathogen Streptococcus pneumoniae. However, the functions of many essential genes are still unknown, hampering vaccine development and drug discovery. Based on results from transposon sequencing (Tn-seq), we refined the list of essential genes in S.~pneumoniae serotype 2 strain D39. Next, we created a knockdown library targeting 348 potentially essential genes by CRISPR interference (CRISPRi) and show a growth phenotype for 254 of them (73%). Using high-content microscopy screening, we searched for essential genes of unknown function with clear phenotypes in cell morphology upon CRISPRi-based depletion. We show that SPD_1416 and SPD_1417 (renamed to MurT and GatD, respectively) are essential for peptidoglycan synthesis, and that SPD_1198 and SPD_1197 (renamed to TarP and TarQ, respectively) are responsible for the polymerization of teichoic acid (TA) precursors. This knowledge enabled us to reconstruct the unique pneumococcal TA biosynthetic pathway. CRISPRi was also employed to unravel the role of the essential Clp-proteolytic system in regulation of competence development, and we show that ClpX is the essential ATPase responsible for ClpP-dependent repression of competence. The CRISPRi library provides a valuable tool for characterization of pneumococcal genes and pathways and revealed several promising antibiotic targets.}, keywords = {bacterial cell wall,competence,DNA replication,gene essentiality,teichoic acid biosynthesis}, file = {/home/trey/Zotero/storage/HBK3Q4ND/Liu et al. - 2017 - High‐throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae.pdf} } % == BibTeX quality report for liuHighthroughputCRISPRiPhenotyping2017: % ? unused Library catalog (“embopress.org (Atypon)”)

@article{vanopijnenTnseqHighthroughputParallel2009, title = {Tn-Seq: High-Throughput Parallel Sequencing for Fitness and Genetic Interaction Studies in Microorganisms}, shorttitle = {Tn-Seq}, author = {{}{van Opijnen}, Tim and Bodi, Kip L. and Camilli, Andrew}, year = 2009, month = oct, journal = {Nature Methods}, volume = {6}, number = {10}, pages = {767–772}, publisher = {Nature Publishing Group}, issn = {1548-7105}, doi = {10.1038/nmeth.1377}, url = {https://www.nature.com/articles/nmeth.1377}, urldate = {2025-11-11}, abstract = {High-throughput sequencing of Mariner transposon insertion libraries is used for quantitative studies of fitness and of genetic interactions in Streptococcus pneumoniae. The approach should allow similar studies in several microorganismal species.}, copyright = {2009 Springer Nature America, Inc.}, langid = {english}, keywords = {Bioinformatics,Biological Microscopy,Biological Techniques,Biomedical Engineering/Biotechnology,general,Life Sciences,Proteomics}, file = {/home/trey/Zotero/storage/ESA9H9BN/van Opijnen et al. - 2009 - Tn-seq high-throughput parallel sequencing for fitness and genetic interaction studies in microorga.pdf} } % == BibTeX quality report for vanopijnenTnseqHighthroughputParallel2009: % ? unused Journal abbr (“Nat Methods”) % ? unused Library catalog (“www.nature.com”)

@article{schulzElucidationSigmaFactorAssociated2015, title = {Elucidation of {{Sigma Factor-Associated Networks}} in {{Pseudomonas}} Aeruginosa {{Reveals}} a {{Modular Architecture}} with {{Limited}} and {{Function-Specific Crosstalk}}}, author = {Schulz, Sebastian and Eckweiler, Denitsa and Bielecka, Agata and Nicolai, Tanja and Franke, Raimo and D{"o}tsch, Andreas and Hornischer, Klaus and Bruchmann, Sebastian and D{"u}vel, Juliane and H{"a}ussler, Susanne}, year = 2015, month = mar, journal = {PLOS Pathogens}, volume = {11}, number = {3}, pages = {e1004744}, publisher = {Public Library of Science}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1004744}, url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004744}, urldate = {2025-11-14}, abstract = {Sigma factors are essential global regulators of transcription initiation in bacteria which confer promoter recognition specificity to the RNA polymerase core enzyme. They provide effective mechanisms for simultaneously regulating expression of large numbers of genes in response to challenging conditions, and their presence has been linked to bacterial virulence and pathogenicity. In this study, we constructed nine his-tagged sigma factor expressing and/or deletion mutant strains in the opportunistic pathogen Pseudomonas aeruginosa. To uncover the direct and indirect sigma factor regulons, we performed mRNA profiling, as well as chromatin immunoprecipitation coupled to high-throughput sequencing. We furthermore elucidated the de novo binding motif of each sigma factor, and validated the RNA- and ChIP-seq results by global motif searches in the proximity of transcriptional start sites (TSS). Our integrated approach revealed a highly modular network architecture which is composed of insulated functional sigma factor modules. Analysis of the interconnectivity of the various sigma factor networks uncovered a limited, but highly function-specific, crosstalk which orchestrates complex cellular processes. Our data indicate that the modular structure of sigma factor networks enables P. aeruginosa to function adequately in its environment and at the same time is exploited to build up higher-level functions by specific interconnections that are dominated by a participation of RpoN.}, langid = {english}, keywords = {DNA transcription,Gene expression,Gene regulation,Genomics,Pseudomonas aeruginosa,Regulons,RNA sequencing,Transcriptional control}, file = {/home/trey/Zotero/storage/RHWT72F3/Schulz et al. - 2015 - Elucidation of Sigma Factor-Associated Networks in Pseudomonas aeruginosa Reveals a Modular Architec.pdf} } % == BibTeX quality report for schulzElucidationSigmaFactorAssociated2015: % ? unused Library catalog (“PLoS Journals”)

@article{wehenkelMycobacterialSerThr2008, title = {Mycobacterial {{Ser}}/{{Thr}} Protein Kinases and Phosphatases: {{Physiological}} Roles and Therapeutic Potential}, shorttitle = {Mycobacterial {{Ser}}/{{Thr}} Protein Kinases and Phosphatases}, author = {Wehenkel, Annemarie and Bellinzoni, Marco and Gra{~n}a, Martin and Duran, Rosario and Villarino, Andrea and Fernandez, Pablo and {Andre-Leroux}, Gw{'e}na{"e}lle and England, Patrick and Takiff, Howard and Cerve{~n}ansky, Carlos and Cole, Stewart T. and Alzari, Pedro M.}, year = 2008, month = jan, journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics}, series = {Inhibitors of {{Protein Kinases}} (5th {{International Conference}}, {{IPK-2007}}) and {{Workshop Session}} on {{Molecular Design}} and {{Simulation Methods}} ({{Warsaw}}, {{Poland}}, {{June}} 23-27, 2007)}, volume = {1784}, number = {1}, pages = {193–202}, issn = {1570-9639}, doi = {10.1016/j.bbapap.2007.08.006}, url = {https://www.sciencedirect.com/science/article/pii/S1570963907001902}, urldate = {2025-11-14}, abstract = {Reversible protein phosphorylation is a major regulation mechanism of fundamental biological processes, not only in eukaryotes but also in bacteria. A growing body of evidence suggests that Ser/Thr phosphorylation play important roles in the physiology and virulence of Mycobacterium tuberculosis, the etiological agent of tuberculosis. This pathogen uses `eukaryotic-like’ Ser/Thr protein kinases and phosphatases not only to regulate many intracellular metabolic processes, but also to interfere with signaling pathways of the infected host cell. Disrupting such processes by means of selective inhibitors may thus provide new pharmaceutical weapons to combat the disease. Here we review the current knowledge on Ser/Thr protein kinases and phosphatases in M. tuberculosis, their regulation mechanisms and putative substrates, and we explore their therapeutic potential as possible targets for the development of new anti-mycobacterial compounds.}, keywords = {Drug design,Protein kinases,Protein phosphatases,Ser/Thr protein phosphorylation}, file = {/home/trey/Zotero/storage/TAIBCAX6/Wehenkel et al. - 2008 - Mycobacterial SerThr protein kinases and phosphatases Physiological roles and therapeutic potentia.pdf;/home/trey/Zotero/storage/GKEWUK6M/S1570963907001902.html} } % == BibTeX quality report for wehenkelMycobacterialSerThr2008: % ? unused Library catalog (“ScienceDirect”)

@incollection{prisicMycobacteriumTuberculosisSerine2014, title = {Mycobacterium Tuberculosis {{Serine}}/{{Threonine Protein Kinases}}}, booktitle = {Molecular {{Genetics}} of {{Mycobacteria}}}, author = {Prisic, Sladjana and Husson, Robert N.}, year = 2014, pages = {681–708}, publisher = {John Wiley & Sons, Ltd}, doi = {10.1128/9781555818845.ch33}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1128/9781555818845.ch33}, urldate = {2025-11-14}, abstract = {Signal transduction is an essential activity of all living cells. Broadly defined, signal transduction is the sensing of a signal or input and its conversion into an output or response that alters cell physiology. The sensor is the molecule or domain of a molecule (typically a protein) that senses the signal. The transducer is the molecule or domain that converts the signal into a response. Most commonly, signal transduction refers to the sensing of an extracellular signal that is transduced across the cytoplasmic membrane and converted into an intracellular response. Thus, signal transduction is critical for cellular adaptation to changes in the extracellular environment. In the case of bacterial pathogens, including Mycobacterium tuberculosis, these adaptive responses allow growth and/or survival in the environments encountered by the pathogen during the course of infection in the human host.}, chapter = {33}, copyright = { 2014 American Society for Microbiology}, isbn = {978-1-68367-100-8}, langid = {english}, keywords = {Mycobacterium tuberculosis,nosource,phosphoproteome,protein phosphatases,serine protein kinases,threonine protein kinases}, file = {/home/trey/Zotero/storage/ZHYIGRNR/9781555818845.html} } % == BibTeX quality report for prisicMycobacteriumTuberculosisSerine2014: % ? unused extra: _eprint (“https://onlinelibrary.wiley.com/doi/pdf/10.1128/9781555818845.ch33”) % ? unused Library catalog (“Wiley Online Library”)

@article{dulbergerMycobacterialCellEnvelope2020, title = {The Mycobacterial Cell Envelope — a Moving Target}, author = {Dulberger, Charles L. and Rubin, Eric J. and Boutte, Cara C.}, year = 2020, month = jan, journal = {Nature Reviews Microbiology}, volume = {18}, number = {1}, pages = {47–59}, publisher = {Nature Publishing Group}, issn = {1740-1534}, doi = {10.1038/s41579-019-0273-7}, url = {https://www.nature.com/articles/s41579-019-0273-7}, urldate = {2025-11-14}, abstract = {Mycobacterium tuberculosis, the leading cause of death due to infection, has a dynamic and immunomodulatory cell envelope. The cell envelope structurally and functionally varies across the length of the cell and during the infection process. This variability allows the bacterium to manipulate the human immune system, tolerate antibiotic treatment and adapt to the variable host environment. Much of what we know about the mycobacterial cell envelope has been gleaned from model actinobacterial species, or model conditions such as growth in vitro, in macrophages and in the mouse. In this Review, we combine data from different experimental systems to build a model of the dynamics of the mycobacterial cell envelope across space and time. We describe the regulatory pathways that control metabolism of the cell wall and surface lipids in M. tuberculosis during growth and stasis, and speculate about how this regulation might affect antibiotic susceptibility and interactions with the immune system.}, copyright = {2019 Springer Nature Limited}, langid = {english}, keywords = {Antibacterial drug resistance,Antibiotics,Bacterial immune evasion,Bacterial pathogenesis,Bacterial physiology,Bacterial structural biology,Tuberculosis}, file = {/home/trey/Zotero/storage/28DBNDZ3/Dulberger et al. - 2020 - The mycobacterial cell envelope — a moving target.pdf} } % == BibTeX quality report for dulbergerMycobacterialCellEnvelope2020: % ? unused Journal abbr (“Nat Rev Microbiol”) % ? unused Library catalog (“www.nature.com”)

@article{guoFoundationModelsBioinformatics2025, title = {Foundation Models in Bioinformatics}, author = {Guo, Fei and Guan, Renchu and Li, Yaohang and Liu, Qi and Wang, Xiaowo and Yang, Can and Wang, Jianxin}, year = 2025, month = apr, journal = {National Science Review}, volume = {12}, number = {4}, pages = {nwaf028}, issn = {2095-5138}, doi = {10.1093/nsr/nwaf028}, url = {https://doi.org/10.1093/nsr/nwaf028}, urldate = {2026-01-08}, abstract = {With the adoption of foundation models (FMs), artificial intelligence (AI) has become increasingly significant in bioinformatics and has successfully addressed many historical challenges, such as pre-training frameworks, model evaluation and interpretability. FMs demonstrate notable proficiency in managing large-scale, unlabeled datasets, because experimental procedures are costly and labor intensive. In various downstream tasks, FMs have consistently achieved noteworthy results, demonstrating high levels of accuracy in representing biological entities. A new era in computational biology has been ushered in by the application of FMs, focusing on both general and specific biological issues. In this review, we introduce recent advancements in bioinformatics FMs employed in a variety of downstream tasks, including genomics, transcriptomics, proteomics, drug discovery and single-cell analysis. Our aim is to assist scientists in selecting appropriate FMs in bioinformatics, according to four model types: language FMs, vision FMs, graph FMs and multimodal FMs. In addition to understanding molecular landscapes, AI technology can establish the theoretical and practical foundation for continued innovation in molecular biology.}, file = {/home/trey/Zotero/storage/JPAT5MJR/Guo et al. - 2025 - Foundation models in bioinformatics.pdf} } % == BibTeX quality report for guoFoundationModelsBioinformatics2025: % ? unused Journal abbr (“Natl Sci Rev”) % ? unused Library catalog (“Silverchair”)

@article{cuiMultimodalFoundationModels2025, title = {Towards Multimodal Foundation Models in Molecular Cell Biology}, author = {Cui, Haotian and {Tejada-Lapuerta}, Alejandro and Brbi{'c}, Maria and {Saez-Rodriguez}, Julio and Cristea, Simona and Goodarzi, Hani and Lotfollahi, Mohammad and Theis, Fabian J. and Wang, Bo}, year = 2025, month = apr, journal = {Nature}, volume = {640}, number = {8059}, pages = {623–633}, publisher = {Nature Publishing Group}, issn = {1476-4687}, doi = {10.1038/s41586-025-08710-y}, url = {https://www.nature.com/articles/s41586-025-08710-y}, urldate = {2026-01-08}, abstract = {The rapid advent of high-throughput omics technologies has created an exponential growth in biological data, often outpacing our ability to derive molecular insights. Large-language models have shown a way out of this data deluge in natural language processing by integrating massive datasets into a joint model with manifold downstream use cases. Here we envision developing multimodal foundation models, pretrained on diverse omics datasets, including genomics, transcriptomics, epigenomics, proteomics, metabolomics and spatial profiling. These models are expected to exhibit unprecedented potential for characterizing the molecular states of cells across a broad continuum, thereby facilitating the creation of holistic maps of cells, genes and tissues. Context-specific transfer learning of the foundation models can empower diverse applications from novel cell-type recognition, biomarker discovery and gene regulation inference, to in silico perturbations. This new paradigm could launch an era of artificial intelligence-empowered analyses, one that promises to unravel the intricate complexities of molecular cell biology, to support experimental design and, more broadly, to profoundly extend our understanding of life sciences.}, copyright = {2025 Springer Nature Limited}, langid = {english}, keywords = {Cell biology,Computational models,Functional genomics,Genomics,Machine learning}, file = {/home/trey/Zotero/storage/65KQMAWR/Cui et al. - 2025 - Towards multimodal foundation models in molecular cell biology.pdf} } % == BibTeX quality report for cuiMultimodalFoundationModels2025: % ? unused Library catalog (“www.nature.com”)

@article{wigginsOpportunitiesRisksFoundation2022, title = {On the {{Opportunities}} and {{Risks}} of {{Foundation Models}} for {{Natural Language Processing}} in {{Radiology}}}, author = {Wiggins, Walter F. and Tejani, Ali S.}, year = 2022, month = jul, journal = {Radiology: Artificial Intelligence}, volume = {4}, number = {4}, pages = {e220119}, publisher = {Radiological Society of North America}, doi = {10.1148/ryai.220119}, url = {https://pubs.rsna.org/doi/full/10.1148/ryai.220119}, urldate = {2026-01-09}, file = {/home/trey/Zotero/storage/PME2FQHR/Wiggins and Tejani - 2022 - On the Opportunities and Risks of Foundation Models for Natural Language Processing in Radiology.pdf} } % == BibTeX quality report for wigginsOpportunitiesRisksFoundation2022: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“pubs.rsna.org (Atypon)”)

@inproceedings{devlinBERTPretrainingDeep2019, title = {{{BERT}}: {{Pre-training}} of {{Deep Bidirectional Transformers}} for {{Language Understanding}}}, shorttitle = {{{BERT}}}, booktitle = {Proceedings of the 2019 {{Conference}} of the {{North American Chapter}} of the {{Association}} for {{Computational Linguistics}}: {{Human Language Technologies}}, {{Volume}} 1 ({{Long}} and {{Short Papers}})}, author = {Devlin, Jacob and Chang, Ming-Wei and Lee, Kenton and Toutanova, Kristina}, editor = {Burstein, Jill and Doran, Christy and Solorio, Thamar}, year = 2019, month = jun, pages = {4171–4186}, publisher = {Association for Computational Linguistics}, address = {Minneapolis, Minnesota}, doi = {10.18653/v1/N19-1423}, url = {https://aclanthology.org/N19-1423/}, urldate = {2026-01-12}, abstract = {We introduce a new language representation model called BERT, which stands for Bidirectional Encoder Representations from Transformers. Unlike recent language representation models (Peters et al., 2018a; Radford et al., 2018), BERT is designed to pre-train deep bidirectional representations from unlabeled text by jointly conditioning on both left and right context in all layers. As a result, the pre-trained BERT model can be fine-tuned with just one additional output layer to create state-of-the-art models for a wide range of tasks, such as question answering and language inference, without substantial task-specific architecture modifications. BERT is conceptually simple and empirically powerful. It obtains new state-of-the-art results on eleven natural language processing tasks, including pushing the GLUE score to 80.5 (7.7 point absolute improvement), MultiNLI accuracy to 86.7% (4.6% absolute improvement), SQuAD v1.1 question answering Test F1 to 93.2 (1.5 point absolute improvement) and SQuAD v2.0 Test F1 to 83.1 (5.1 point absolute improvement).}, file = {/home/trey/Zotero/storage/TS2PU76N/Devlin et al. - 2019 - BERT Pre-training of Deep Bidirectional Transformers for Language Understanding.pdf} } % == BibTeX quality report for devlinBERTPretrainingDeep2019: % ? unused Conference name (“NAACL-HLT 2019”) % ? unused Library catalog (“ACLWeb”)

@misc{bommasaniOpportunitiesRisksFoundation2022, title = {On the {{Opportunities}} and {{Risks}} of {{Foundation Models}}}, author = {Bommasani, Rishi and Hudson, Drew A. and Adeli, Ehsan and Altman, Russ and Arora, Simran and {}von Arx, Sydney and Bernstein, Michael S. and Bohg, Jeannette and Bosselut, Antoine and Brunskill, Emma and Brynjolfsson, Erik and Buch, Shyamal and Card, Dallas and Castellon, Rodrigo and Chatterji, Niladri and Chen, Annie and Creel, Kathleen and Davis, Jared Quincy and Demszky, Dora and Donahue, Chris and Doumbouya, Moussa and Durmus, Esin and Ermon, Stefano and Etchemendy, John and Ethayarajh, Kawin and {Fei-Fei}, Li and Finn, Chelsea and Gale, Trevor and Gillespie, Lauren and Goel, Karan and Goodman, Noah and Grossman, Shelby and Guha, Neel and Hashimoto, Tatsunori and Henderson, Peter and Hewitt, John and Ho, Daniel E. and Hong, Jenny and Hsu, Kyle and Huang, Jing and Icard, Thomas and Jain, Saahil and Jurafsky, Dan and Kalluri, Pratyusha and Karamcheti, Siddharth and Keeling, Geoff and Khani, Fereshte and Khattab, Omar and Koh, Pang Wei and Krass, Mark and Krishna, Ranjay and Kuditipudi, Rohith and Kumar, Ananya and Ladhak, Faisal and Lee, Mina and Lee, Tony and Leskovec, Jure and Levent, Isabelle and Li, Xiang Lisa and Li, Xuechen and Ma, Tengyu and Malik, Ali and Manning, Christopher D. and Mirchandani, Suvir and Mitchell, Eric and Munyikwa, Zanele and Nair, Suraj and Narayan, Avanika and Narayanan, Deepak and Newman, Ben and Nie, Allen and Niebles, Juan Carlos and Nilforoshan, Hamed and Nyarko, Julian and Ogut, Giray and Orr, Laurel and Papadimitriou, Isabel and Park, Joon Sung and Piech, Chris and Portelance, Eva and Potts, Christopher and Raghunathan, Aditi and Reich, Rob and Ren, Hongyu and Rong, Frieda and Roohani, Yusuf and Ruiz, Camilo and Ryan, Jack and R{'e}, Christopher and Sadigh, Dorsa and Sagawa, Shiori and Santhanam, Keshav and Shih, Andy and Srinivasan, Krishnan and Tamkin, Alex and Taori, Rohan and Thomas, Armin W. and Tram{`e}r, Florian and Wang, Rose E. and Wang, William and Wu, Bohan and Wu, Jiajun and Wu, Yuhuai and Xie, Sang Michael and Yasunaga, Michihiro and You, Jiaxuan and Zaharia, Matei and Zhang, Michael and Zhang, Tianyi and Zhang, Xikun and Zhang, Yuhui and Zheng, Lucia and Zhou, Kaitlyn and Liang, Percy}, year = 2022, month = jul, number = {arXiv:2108.07258}, eprint = {2108.07258}, primaryclass = {cs}, publisher = {arXiv}, doi = {10.48550/arXiv.2108.07258}, url = {http://arxiv.org/abs/2108.07258}, urldate = {2026-01-12}, abstract = {AI is undergoing a paradigm shift with the rise of models (e.g., BERT, DALL-E, GPT-3) that are trained on broad data at scale and are adaptable to a wide range of downstream tasks. We call these models foundation models to underscore their critically central yet incomplete character. This report provides a thorough account of the opportunities and risks of foundation models, ranging from their capabilities (e.g., language, vision, robotics, reasoning, human interaction) and technical principles(e.g., model architectures, training procedures, data, systems, security, evaluation, theory) to their applications (e.g., law, healthcare, education) and societal impact (e.g., inequity, misuse, economic and environmental impact, legal and ethical considerations). Though foundation models are based on standard deep learning and transfer learning, their scale results in new emergent capabilities,and their effectiveness across so many tasks incentivizes homogenization. Homogenization provides powerful leverage but demands caution, as the defects of the foundation model are inherited by all the adapted models downstream. Despite the impending widespread deployment of foundation models, we currently lack a clear understanding of how they work, when they fail, and what they are even capable of due to their emergent properties. To tackle these questions, we believe much of the critical research on foundation models will require deep interdisciplinary collaboration commensurate with their fundamentally sociotechnical nature.}, archiveprefix = {arXiv}, keywords = {Computer Science - Artificial Intelligence,Computer Science - Computers and Society,Computer Science - Machine Learning}, file = {/home/trey/Zotero/storage/UQHKQSVY/Bommasani et al. - 2022 - On the Opportunities and Risks of Foundation Models.pdf;/home/trey/Zotero/storage/UKJDXBBU/2108.html} } % == BibTeX quality report for bommasaniOpportunitiesRisksFoundation2022: % ? Title looks like it was stored in title-case in Zotero

@article{rivesBiologicalStructureFunction2021, title = {Biological Structure and Function Emerge from Scaling Unsupervised Learning to 250 Million Protein Sequences}, author = {Rives, Alexander and Meier, Joshua and Sercu, Tom and Goyal, Siddharth and Lin, Zeming and Liu, Jason and Guo, Demi and Ott, Myle and Zitnick, C. Lawrence and Ma, Jerry and Fergus, Rob}, year = 2021, month = apr, journal = {Proceedings of the National Academy of Sciences}, volume = {118}, number = {15}, pages = {e2016239118}, publisher = {Proceedings of the National Academy of Sciences}, doi = {10.1073/pnas.2016239118}, url = {https://www.pnas.org/doi/full/10.1073/pnas.2016239118}, urldate = {2026-01-12}, abstract = {In the field of artificial intelligence, a combination of scale in data and model capacity enabled by unsupervised learning has led to major advances in representation learning and statistical generation. In the life sciences, the anticipated growth of sequencing promises unprecedented data on natural sequence diversity. Protein language modeling at the scale of evolution is a logical step toward predictive and generative artificial intelligence for biology. To this end, we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million protein sequences spanning evolutionary diversity. The resulting model contains information about biological properties in its representations. The representations are learned from sequence data alone. The learned representation space has a multiscale organization reflecting structure from the level of biochemical properties of amino acids to remote homology of proteins. Information about secondary and tertiary structure is encoded in the representations and can be identified by linear projections. Representation learning produces features that generalize across a range of applications, enabling state-of-the-art supervised prediction of mutational effect and secondary structure and improving state-of-the-art features for long-range contact prediction.}, file = {/home/trey/Zotero/storage/R74EY84B/Rives et al. - 2021 - Biological structure and function emerge from scaling unsupervised learning to 250 million protein s.pdf} } % == BibTeX quality report for rivesBiologicalStructureFunction2021: % ? unused Library catalog (“pnas.org (Atypon)”)

@article{sodingProteinSequenceComparison2011, title = {Protein Sequence Comparison and Fold Recognition: Progress and Good-Practice Benchmarking}, shorttitle = {Protein Sequence Comparison and Fold Recognition}, author = {S{"o}ding, Johannes and Remmert, Michael}, year = 2011, month = jun, journal = {Current Opinion in Structural Biology}, volume = {21}, number = {3}, pages = {404–411}, issn = {0959-440X}, doi = {10.1016/j.sbi.2011.03.005}, url = {https://www.sciencedirect.com/science/article/pii/S0959440X11000418}, urldate = {2026-01-16}, abstract = {Protein sequence comparison methods have grown increasingly sensitive during the last decade and can often identify distantly related proteins sharing a common ancestor some 3 billion years ago. Although cellular function is not conserved so long, molecular functions and structures of protein domains often are. In combination with a domain-centered approach to function and structure prediction, modern remote homology detection methods have a great and largely underexploited potential for elucidating protein functions and evolution. Advances during the last few years include nonlinear scoring functions combining various sequence features, the use of sequence context information, and powerful new software packages. Since progress depends on realistically assessing new and existing methods and published benchmarks are often hard to compare, we propose 10 rules of good-practice benchmarking.}, file = {/home/trey/Zotero/storage/N4R8QH2K/Söding and Remmert - 2011 - Protein sequence comparison and fold recognition progress and good-practice benchmarking.pdf;/home/trey/Zotero/storage/DFU6WNZG/S0959440X11000418.html} } % == BibTeX quality report for sodingProteinSequenceComparison2011: % ? unused Library catalog (“ScienceDirect”)

@article{jaffePracticalImpactsGenomic2015, title = {Practical Impacts of Genomic Data Cleaning'' on Biological Discovery Using Surrogate Variable Analysis}, author = {Jaffe, Andrew E. and Hyde, Thomas and Kleinman, Joel and Weinbergern, Daniel R. and Chenoweth, Joshua G. and McKay, Ronald D. and Leek, Jeffrey T. and Colantuoni, Carlo}, year = 2015, month = nov, journal = {BMC Bioinformatics}, volume = {16}, number = {1}, pages = {372}, issn = {1471-2105}, doi = {10.1186/s12859-015-0808-5}, url = {https://doi.org/10.1186/s12859-015-0808-5}, urldate = {2026-01-16}, abstract = {Genomic data production is at its highest level and continues to increase, making available novel primary data and existing public data to researchers for exploration. Here we explore the consequences ofbatch’’ correction for biological discovery in two publicly available expression datasets. We consider this to include the estimation of and adjustment for wide-spread systematic heterogeneity in genomic measurements that is unrelated to the effects under study, whether it be technical or biological in nature.}, langid = {english}, keywords = {Batch correction,Gene expression,Surrogate variable analysis}, file = {/home/trey/Zotero/storage/VKVD633C/Jaffe et al. - 2015 - Practical impacts of genomic data “cleaning” on biological discovery using surrogate variable analys.pdf} } % == BibTeX quality report for jaffePracticalImpactsGenomic2015: % ? unused Library catalog (“Springer Link”)

@article{liaoSubreadAlignerFast2013, title = {The {{Subread}} Aligner: Fast, Accurate and Scalable Read Mapping by Seed-and-Vote}, shorttitle = {The {{Subread}} Aligner}, author = {Liao, Yang and Smyth, Gordon K. and Shi, Wei}, year = 2013, month = may, journal = {Nucleic Acids Research}, volume = {41}, number = {10}, pages = {e108}, issn = {0305-1048}, doi = {10.1093/nar/gkt214}, url = {https://doi.org/10.1093/nar/gkt214}, urldate = {2026-01-21}, abstract = {Read alignment is an ongoing challenge for the analysis of data from sequencing technologies. This article proposes an elegantly simple multi-seed strategy, called seed-and-vote, for mapping reads to a reference genome. The new strategy chooses the mapped genomic location for the read directly from the seeds. It uses a relatively large number of short seeds (called subreads) extracted from each read and allows all the seeds to vote on the optimal location. When the read length is &lt;160 bp, overlapping subreads are used. More conventional alignment algorithms are then used to fill in detailed mismatch and indel information between the subreads that make up the winning voting block. The strategy is fast because the overall genomic location has already been chosen before the detailed alignment is done. It is sensitive because no individual subread is required to map exactly, nor are individual subreads constrained to map close by other subreads. It is accurate because the final location must be supported by several different subreads. The strategy extends easily to find exon junctions, by locating reads that contain sets of subreads mapping to different exons of the same gene. It scales up efficiently for longer reads.}, file = {/home/trey/Zotero/storage/9JCXHU2X/Liao et al. - 2013 - The Subread aligner fast, accurate and scalable read mapping by seed-and-vote.pdf;/home/trey/Zotero/storage/PSQ3R4F8/gkt214.html} } % == BibTeX quality report for liaoSubreadAlignerFast2013: % ? unused Journal abbr (“Nucleic Acids Res”) % ? unused Library catalog (“Silverchair”)

@misc{luRemovingContaminantsMetagenomic2018, title = {Removing {{Contaminants}} from {{Metagenomic Databases}}}, author = {Lu, Jennifer and Salzberg, Steven L.}, year = 2018, month = feb, primaryclass = {New Results}, pages = {261859}, publisher = {bioRxiv}, doi = {10.1101/261859}, url = {https://www.biorxiv.org/content/10.1101/261859v1}, urldate = {2026-01-22}, abstract = {Metagenomic sequencing of patient samples is a very promising method for the diagnosis of human infections. Sequencing has the ability to capture all the DNA or RNA from pathogenic organisms in a human sample. However, complete and accurate characterization of the sequence, including identification of any pathogens, depends on the availability and quality of genomes for comparison. Thousands of genomes are now available, and as these numbers grow, the power of metagenomic sequencing for diagnosis should increase. However, recent studies have exposed the presence of contamination in published genomes, which when used for diagnosis increases the risk of falsely identifying the wrong pathogen. To address this problem, we have developed a bioinformatics system for eliminating contamination as well as low-complexity genomic sequences in the draft genomes of eukaryotic pathogens. We applied this software to identify and remove human, bacterial, archaeal, and viral sequences present in a comprehensive database of all sequenced eukaryotic pathogen genomes. We also removed low-complexity genomic sequences, another source of false positives. Using this pipeline, we have produced a database of ``clean’’ eukaryotic pathogen genomes for use with bioinformatics classification and analysis tools. We demonstrate that when attempting to find eukaryotic pathogens in metagenomic samples, the new database provides better sensitivity than one using the original genomes while offering a dramatic reduction in false positives.}, archiveprefix = {bioRxiv}, chapter = {New Results}, copyright = { 2018, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), CC BY-NC 4.0, as described at http://creativecommons.org/licenses/by-nc/4.0/}, langid = {english}, file = {/home/trey/Zotero/storage/H85UK5LR/Lu and Salzberg - 2018 - Removing Contaminants from Metagenomic Databases.pdf} } % == BibTeX quality report for luRemovingContaminantsMetagenomic2018: % ? Title looks like it was stored in title-case in Zotero

@article{grunebastLifeCycleStageSpecific2021, title = {Life {{Cycle Stage-Specific Accessibility}} of {{Leishmania}} Donovani {{Chromatin}} at {{Transcription Start Regions}}}, author = {Gr{"u}nebast, Janne and Lorenzen, Stephan and Zummack, Julia and Clos, Joachim}, year = 2021, month = jul, journal = {mSystems}, volume = {6}, number = {4}, pages = {10.1128/msystems.00628-21}, publisher = {American Society for Microbiology}, doi = {10.1128/msystems.00628-21}, url = {https://journals.asm.org/doi/full/10.1128/msystems.00628-21}, urldate = {2026-02-03}, abstract = {Leishmania donovani is a parasitic protist that causes the lethal Kala-azar fever in India and East Africa. Gene expression in Leishmania is regulated by gene copy number variation and inducible translation while RNA synthesis initiates at a small number of sites per chromosome and proceeds through polycistronic transcription units, precluding a gene-specific regulation (C. Clayton and M. Shapira, Mol Biochem Parasitol 156:93–101, 2007, https://doi.org/10.1016/j.molbiopara.2007.07.007). Here, we analyze the dynamics of chromatin structure in both life cycle stages of the parasite and find evidence for an additional, epigenetic gene regulation pathway in this early branching eukaryote. The assay for transposase-accessible chromatin using sequencing (ATAC-seq) analysis (J. D. Buenrostro, P. G. Giresi, L. C. Zaba, H. Y. Chang, and W. J. Greenleaf, Nat Methods 10:1213–1218, 2013, https://doi.org/10.1038/nmeth.2688) predominantly shows euchromatin at transcription start regions in fast-growing promastigotes, but mostly heterochromatin in the slowly proliferating amastigotes, the mammalian stage, reflecting a previously shown increase of histone synthesis in the latter stage. IMPORTANCE Leishmania parasites are important pathogens with a global impact and cause poverty-related illness and death. They are devoid of classic cis- and trans-acting transcription regulators but use regulated translation and gene copy number variations to adapt to hosts and environments. In this work, we show that transcription start regions present as open euchromatin in fast-growing insect stages but as less-accessible heterochromatin in the slowly proliferating amastigote stage, indicating an epigenetic control of gene accessibility in this early branching eukaryotic pathogen. This finding should stimulate renewed interest in the control of RNA synthesis in Leishmania and related parasites.}, file = {/home/trey/Zotero/storage/Z7JUE253/Grünebast et al. - 2021 - Life Cycle Stage-Specific Accessibility of Leishmania donovani Chromatin at Transcription Start Regi.pdf} } % == BibTeX quality report for grunebastLifeCycleStageSpecific2021: % ? unused Library catalog (“journals.asm.org (Atypon)”)

@article{yanReadsInsightHitchhikers2020, title = {From Reads to Insight: A Hitchhiker’s Guide to {{ATAC-seq}} Data Analysis}, shorttitle = {From Reads to Insight}, author = {Yan, Feng and Powell, David R. and Curtis, David J. and Wong, Nicholas C.}, year = 2020, month = feb, journal = {Genome Biology}, volume = {21}, number = {1}, pages = {22}, issn = {1474-760X}, doi = {10.1186/s13059-020-1929-3}, url = {https://doi.org/10.1186/s13059-020-1929-3}, urldate = {2026-02-03}, abstract = {Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely used in studying chromatin biology, but a comprehensive review of the analysis tools has not been completed yet. Here, we discuss the major steps in ATAC-seq data analysis, including pre-analysis (quality check and alignment), core analysis (peak calling), and advanced analysis (peak differential analysis and annotation, motif enrichment, footprinting, and nucleosome position analysis). We also review the reconstruction of transcriptional regulatory networks with multiomics data and highlight the current challenges of each step. Finally, we describe the potential of single-cell ATAC-seq and highlight the necessity of developing ATAC-seq specific analysis tools to obtain biologically meaningful insights.}, langid = {english}, file = {/home/trey/Zotero/storage/2TU6SQS2/Yan et al. - 2020 - From reads to insight a hitchhiker’s guide to ATAC-seq data analysis.pdf} } % == BibTeX quality report for yanReadsInsightHitchhikers2020: % ? unused Journal abbr (“Genome Biol”) % ? unused Library catalog (“Springer Link”)

@article{grandiChromatinAccessibilityProfiling2022, title = {Chromatin Accessibility Profiling by {{ATAC-seq}}}, author = {Grandi, Fiorella C. and Modi, Hailey and Kampman, Lucas and Corces, M. Ryan}, year = 2022, month = jun, journal = {Nature Protocols}, volume = {17}, number = {6}, pages = {1518–1552}, publisher = {Nature Publishing Group}, issn = {1750-2799}, doi = {10.1038/s41596-022-00692-9}, url = {https://www.nature.com/articles/s41596-022-00692-9}, urldate = {2026-02-04}, abstract = {The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a simple and scalable way to detect the unique chromatin landscape associated with a cell type and how it may be altered by perturbation or disease. ATAC-seq requires a relatively small number of input cells and does not require a priori knowledge of the epigenetic marks or transcription factors governing the dynamics of the system. Here we describe an updated and optimized protocol for ATAC-seq, called Omni-ATAC, that is applicable across a broad range of cell and tissue types. The ATAC-seq workflow has five main steps: sample preparation, transposition, library preparation, sequencing and data analysis. This protocol details the steps to generate and sequence ATAC-seq libraries, with recommendations for sample preparation and downstream bioinformatic analysis. ATAC-seq libraries for roughly 12 samples can be generated in 10 h by someone familiar with basic molecular biology, and downstream sequencing analysis can be implemented using benchmarked pipelines by someone with basic bioinformatics skills and with access to a high-performance computing environment.}, copyright = {2022 Springer Nature Limited}, langid = {english}, keywords = {Chromatin analysis,Epigenetics}, file = {/home/trey/Zotero/storage/RS3B44GE/Grandi et al. - 2022 - Chromatin accessibility profiling by ATAC-seq.pdf} } % == BibTeX quality report for grandiChromatinAccessibilityProfiling2022: % ? unused Journal abbr (“Nat Protoc”) % ? unused Library catalog (“www.nature.com”)

@article{lalDeepLearningbasedEnhancement2021, title = {Deep Learning-Based Enhancement of Epigenomics Data with {{AtacWorks}}}, author = {Lal, Avantika and Chiang, Zachary D. and Yakovenko, Nikolai and Duarte, Fabiana M. and Israeli, Johnny and Buenrostro, Jason D.}, year = 2021, month = mar, journal = {Nature Communications}, volume = {12}, number = {1}, pages = {1507}, publisher = {Nature Publishing Group}, issn = {2041-1723}, doi = {10.1038/s41467-021-21765-5}, url = {https://www.nature.com/articles/s41467-021-21765-5}, urldate = {2026-02-04}, abstract = {ATAC-seq is a widely-applied assay used to measure genome-wide chromatin accessibility; however, its ability to detect active regulatory regions can depend on the depth of sequencing coverage and the signal-to-noise ratio. Here we introduce AtacWorks, a deep learning toolkit to denoise sequencing coverage and identify regulatory peaks at base-pair resolution from low cell count, low-coverage, or low-quality ATAC-seq data. Models trained by AtacWorks can detect peaks from cell types not seen in the training data, and are generalizable across diverse sample preparations and experimental platforms. We demonstrate that AtacWorks enhances the sensitivity of single-cell experiments by producing results on par with those of conventional methods using 10 times as many cells, and further show that this framework can be adapted to enable cross-modality inference of protein-DNA interactions. Finally, we establish that AtacWorks can enable new biological discoveries by identifying active regulatory regions associated with lineage priming in rare subpopulations of hematopoietic stem cells.}, copyright = {2021 The Author(s)}, langid = {english}, keywords = {Chromatin,Epigenomics,Haematopoietic stem cells,Machine learning}, file = {/home/trey/Zotero/storage/6VFQRAL5/Lal et al. - 2021 - Deep learning-based enhancement of epigenomics data with AtacWorks.pdf} } % == BibTeX quality report for lalDeepLearningbasedEnhancement2021: % ? unused Journal abbr (“Nat Commun”) % ? unused Library catalog (“www.nature.com”)

@article{lareauMitochondrialSinglecellATACseq2023, title = {Mitochondrial Single-Cell {{ATAC-seq}} for High-Throughput Multi-Omic Detection of Mitochondrial Genotypes and Chromatin Accessibility}, author = {Lareau, Caleb A. and Liu, Vincent and Muus, Christoph and Praktiknjo, Samantha D. and Nitsch, Lena and Kautz, Pauline and Sandor, Katalin and Yin, Yajie and Gutierrez, Jacob C. and Pelka, Karin and Satpathy, Ansuman T. and Regev, Aviv and Sankaran, Vijay G. and Ludwig, Leif S.}, year = 2023, month = may, journal = {Nature Protocols}, volume = {18}, number = {5}, pages = {1416–1440}, publisher = {Nature Publishing Group}, issn = {1750-2799}, doi = {10.1038/s41596-022-00795-3}, url = {https://www.nature.com/articles/s41596-022-00795-3}, urldate = {2026-02-04}, abstract = {Natural sequence variation within mitochondrial DNA (mtDNA) contributes to human phenotypes and may serve as natural genetic markers in human cells for clonal and lineage tracing. We recently developed a single-cell multi-omic approach, called `mitochondrial single-cell assay for transposase-accessible chromatin with sequencing’ (mtscATAC-seq), enabling concomitant high-throughput mtDNA genotyping and accessible chromatin profiling. Specifically, our technique allows the mitochondrial genome-wide inference of mtDNA variant heteroplasmy along with information on cell state and accessible chromatin variation in individual cells. Leveraging somatic mtDNA mutations, our method further enables inference of clonal relationships among native ex vivo-derived human cells not amenable to genetic engineering-based clonal tracing approaches. Here, we provide a step-by-step protocol for the use of mtscATAC-seq, including various cell-processing and flow cytometry workflows, by using primary hematopoietic cells, subsequent single-cell genomic library preparation and sequencing that collectively take 3–4 days to complete. We discuss experimental and computational data quality control metrics and considerations for the extension to other mammalian tissues. Overall, mtscATAC-seq provides a broadly applicable platform to map clonal relationships between cells in human tissues, investigate fundamental aspects of mitochondrial genetics and enable additional modes of multi-omic discovery.}, copyright = {2023 Springer Nature Limited}, langid = {english}, keywords = {Epigenomics,Genetics research,Genotype,Sequencing}, file = {/home/trey/Zotero/storage/QC5E28V7/Lareau et al. - 2023 - Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotyp.pdf} } % == BibTeX quality report for lareauMitochondrialSinglecellATACseq2023: % ? unused Journal abbr (“Nat Protoc”) % ? unused Library catalog (“www.nature.com”)

@misc{CreatingCustomReference2026, title = {Creating a {{Custom Reference}} {{Official}} 10x {{Genomics Support}}}, year = 2026, month = feb, journal = {10x Genomics}, url = {https://www.10xgenomics.com/support/software/cell-ranger-arc/latest/tutorials/creating-a-custom-reference}, urldate = {2026-02-04}, abstract = {Cell Ranger ARC is an advanced analytical suite designed for the Chromium Single Cell Multiome ATAC + Gene Expression sequencing. It provides in-depth analysis of gene expression and chromatin accessibility at a single cell level, uniquely linking these aspects for enhanced genomic understanding.}, langid = {english}, keywords = {nosource}, file = {/home/trey/Zotero/storage/C9HL9DSE/creating-a-custom-reference.html} } % == BibTeX quality report for CreatingCustomReference2026: % ? Title looks like it was stored in title-case in Zotero

@misc{CreatingReferencePackage2026, title = {Creating a {{Reference Package}} with Cellranger-Arc Mkref {{Official}} 10x {{Genomics Support}}}, year = 2026, month = feb, journal = {10x Genomics}, url = {https://www.10xgenomics.com/support/software/cell-ranger-arc/latest/analysis/mkref}, urldate = {2026-02-04}, abstract = {Cell Ranger ARC is an advanced analytical suite designed for the Chromium Single Cell Multiome ATAC + Gene Expression sequencing. It provides in-depth analysis of gene expression and chromatin accessibility at a single cell level, uniquely linking these aspects for enhanced genomic understanding.}, langid = {english}, keywords = {nosource} }

@misc{CellRangerARC2026, title = {Cell {{Ranger ARC}} {{Official}} 10x {{Genomics Support}}}, year = 2026, month = feb, journal = {10x Genomics}, url = {https://www.10xgenomics.com/support/software/cell-ranger-arc/latest}, urldate = {2026-02-04}, abstract = {Cell Ranger ARC is an advanced analytical suite designed for the Chromium Single Cell Multiome ATAC + Gene Expression sequencing. It provides in-depth analysis of gene expression and chromatin accessibility at a single cell level, uniquely linking these aspects for enhanced genomic understanding.}, langid = {english}, keywords = {nosource}, file = {/home/trey/Zotero/storage/ECSFQ2U4/latest.html} } % == BibTeX quality report for CellRangerARC2026: % ? Title looks like it was stored in title-case in Zotero

@misc{InterpretingCellRanger2026, title = {Interpreting {{Cell Ranger ATAC Web Summary Files}} for {{Single Cell ATAC Assay}} {{Official}} 10x {{Genomics Support}}}, year = 2026, month = feb, journal = {10x Genomics}, url = {https://www.10xgenomics.com/support/epi-atac/documentation/steps/sequencing/interpreting-cell-ranger-atac-web-summary-files-for-single-cell-atac-assay}, urldate = {2026-02-04}, langid = {english}, keywords = {nosource}, file = {/home/trey/Zotero/storage/EST9W34G/interpreting-cell-ranger-atac-web-summary-files-for-single-cell-atac-assay.html} } % == BibTeX quality report for InterpretingCellRanger2026: % ? Title looks like it was stored in title-case in Zotero

@misc{InterpretingCellRanger2026a, title = {Interpreting {{Cell Ranger ARC Web Summary Files}} for {{Single Cell Multiome ATAC}} + {{Gene Expression Assay}} {{Official}} 10x {{Genomics Support}}}, year = 2026, month = feb, journal = {10x Genomics}, url = {https://www.10xgenomics.com/support/epi-multiome/documentation/steps/sequencing/interpreting-cell-ranger-arc-web-summary-files-for-single-cell-multiome-atac-plus-gene-expression-assay}, urldate = {2026-02-04}, langid = {english}, keywords = {nosource}, file = {/home/trey/Zotero/storage/E3DL7E4B/interpreting-cell-ranger-arc-web-summary-files-for-single-cell-multiome-atac-plus-gene-expressi.html} } % == BibTeX quality report for InterpretingCellRanger2026a: % ? Title looks like it was stored in title-case in Zotero

@article{shiFundamentalPracticalApproaches2022, title = {Fundamental and Practical Approaches for Single-Cell {{ATAC-seq}} Analysis}, author = {Shi, Peiyu and Nie, Yage and Yang, Jiawen and Zhang, Weixing and Tang, Zhongjie and Xu, Jin}, year = 2022, month = sep, journal = {aBIOTECH}, volume = {3}, number = {3}, pages = {212–223}, publisher = {Springer Nature Singapore}, issn = {2662-1738}, doi = {10.1007/s42994-022-00082-5}, url = {https://link.springer.com/article/10.1007/s42994-022-00082-5}, urldate = {2026-02-04}, abstract = {Assays for transposase-accessible chromatin through high-throughput sequencing (ATAC-seq) are effective tools in the study of genome-wide chromatin accessibility landscapes. With the rapid development of single-cell technology, open chromatin regions that play essential roles in epigenetic regulation have been measured at the single-cell level using single-cell ATAC-seq approaches. The application of scATAC-seq has become as popular as that of scRNA-seq. However, owing to the nature of scATAC-seq data, which are sparse and noisy, processing the data requires different methodologies and empirical experience. This review presents a practical guide for processing scATAC-seq data, from quality evaluation to downstream analysis, for various applications. In addition to the epigenomic profiling from scATAC-seq, we also discuss recent studies in which the function of non-coding variants has been investigated based on cell type-specific cis-regulatory elements and how to use the by-product genetic information obtained from scATAC-seq to infer single-cell copy number variants and trace cell lineage. We anticipate that this review will assist researchers in designing and implementing scATAC-seq assays to facilitate research in diverse fields.}, copyright = {2022 The Authors}, langid = {english}, file = {/home/trey/Zotero/storage/2XKNHNCN/Shi et al. - 2022 - Fundamental and practical approaches for single-cell ATAC-seq analysis.pdf} } % == BibTeX quality report for shiFundamentalPracticalApproaches2022: % ? unused Library catalog (“link.springer.com”)

@article{granjaArchRScalableSoftware2021, title = {{{ArchR}} Is a Scalable Software Package for Integrative Single-Cell Chromatin Accessibility Analysis}, author = {Granja, Jeffrey M. and Corces, M. Ryan and Pierce, Sarah E. and Bagdatli, S. Tansu and Choudhry, Hani and Chang, Howard Y. and Greenleaf, William J.}, year = 2021, month = mar, journal = {Nature Genetics}, volume = {53}, number = {3}, pages = {403–411}, publisher = {Nature Publishing Group}, issn = {1546-1718}, doi = {10.1038/s41588-021-00790-6}, url = {https://www.nature.com/articles/s41588-021-00790-6}, urldate = {2026-02-04}, abstract = {The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; https://www.archrproject.com/) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses, including doublet removal, single-cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing (scRNA-seq). Enabling the analysis of over 1.2 million single cells within 8,h on a standard Unix laptop, ArchR is a comprehensive software suite for end-to-end analysis of single-cell chromatin accessibility that will accelerate the understanding of gene regulation at the resolution of individual cells.}, copyright = {2021 The Author(s), under exclusive licence to Springer Nature America, Inc.}, langid = {english}, keywords = {Epigenetics,Epigenomics,Gene regulation}, file = {/home/trey/Zotero/storage/78DAZTSK/Granja et al. - 2021 - ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis.pdf} } % == BibTeX quality report for granjaArchRScalableSoftware2021: % ? unused Journal abbr (“Nat Genet”) % ? unused Library catalog (“www.nature.com”)

@article{fangComprehensiveAnalysisSingle2021, title = {Comprehensive Analysis of Single Cell {{ATAC-seq}} Data with {{SnapATAC}}}, author = {Fang, Rongxin and Preissl, Sebastian and Li, Yang and Hou, Xiaomeng and Lucero, Jacinta and Wang, Xinxin and Motamedi, Amir and Shiau, Andrew K. and Zhou, Xinzhu and Xie, Fangming and Mukamel, Eran A. and Zhang, Kai and Zhang, Yanxiao and Behrens, M. Margarita and Ecker, Joseph R. and Ren, Bing}, year = 2021, month = feb, journal = {Nature Communications}, volume = {12}, number = {1}, pages = {1337}, publisher = {Nature Publishing Group}, issn = {2041-1723}, doi = {10.1038/s41467-021-21583-9}, url = {https://www.nature.com/articles/s41467-021-21583-9}, urldate = {2026-02-04}, abstract = {Identification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volume of data pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nystr"om method, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC is applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis reveals 370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate cell-type specific transcriptional regulators.}, copyright = {2021 The Author(s)}, langid = {english}, keywords = {Bioinformatics,Computational biology and bioinformatics,Epigenomics,Sequencing}, file = {/home/trey/Zotero/storage/A86NWAZM/Fang et al. - 2021 - Comprehensive analysis of single cell ATAC-seq data with SnapATAC.pdf} } % == BibTeX quality report for fangComprehensiveAnalysisSingle2021: % ? unused Journal abbr (“Nat Commun”) % ? unused Library catalog (“www.nature.com”)

@article{stuartSinglecellChromatinState2021, title = {Single-Cell Chromatin State Analysis with {{Signac}}}, author = {Stuart, Tim and Srivastava, Avi and Madad, Shaista and Lareau, Caleb A. and Satija, Rahul}, year = 2021, month = nov, journal = {Nature Methods}, volume = {18}, number = {11}, pages = {1333–1341}, publisher = {Nature Publishing Group}, issn = {1548-7105}, doi = {10.1038/s41592-021-01282-5}, url = {https://www.nature.com/articles/s41592-021-01282-5}, urldate = {2026-02-04}, abstract = {The recent development of experimental methods for measuring chromatin state at single-cell resolution has created a need for computational tools capable of analyzing these datasets. Here we developed Signac, a comprehensive toolkit for the analysis of single-cell chromatin data. Signac enables an end-to-end analysis of single-cell chromatin data, including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis and interactive visualization. Through its seamless compatibility with the Seurat package, Signac facilitates the analysis of diverse multimodal single-cell chromatin data, including datasets that co-assay DNA accessibility with gene expression, protein abundance and mitochondrial genotype. We demonstrate scaling of the Signac framework to analyze datasets containing over 700,000 cells.}, copyright = {2021 The Author(s), under exclusive licence to Springer Nature America, Inc.}, langid = {english}, keywords = {Data integration,Epigenomics,Software,Statistical methods}, file = {/home/trey/Zotero/storage/AAHCIMEF/Stuart et al. - 2021 - Single-cell chromatin state analysis with Signac.pdf} } % == BibTeX quality report for stuartSinglecellChromatinState2021: % ? unused Journal abbr (“Nat Methods”) % ? unused Library catalog (“www.nature.com”)

@article{kwokHierarchicalCountbasedModel2025, title = {A Hierarchical, Count-Based Model Highlights Challenges in {{scATAC-seq}} Data Analysis and Points to Opportunities to Extract Finer-Resolution Information}, author = {Kwok, Aaron Wing Cheung and Shim, Heejung and McCarthy, Davis J.}, year = 2025, month = sep, journal = {Genome Biology}, volume = {26}, number = {1}, pages = {282}, issn = {1474-760X}, doi = {10.1186/s13059-025-03735-y}, url = {https://doi.org/10.1186/s13059-025-03735-y}, urldate = {2026-02-04}, abstract = {Data from Single-cell Assay for Transposase Accessible Chromatin with Sequencing (scATAC-seq) is highly sparse. While current computational methods feature a range of transformation procedures to extract meaningful information, major challenges remain.}, langid = {english}, file = {/home/trey/Zotero/storage/HI4HNSW2/Kwok et al. - 2025 - A hierarchical, count-based model highlights challenges in scATAC-seq data analysis and points to op.pdf} } % == BibTeX quality report for kwokHierarchicalCountbasedModel2025: % ? unused Journal abbr (“Genome Biol”) % ? unused Library catalog (“Springer Link”)

@article{liAPECAccessonbasedMethod2020, title = {{{APEC}}: An Accesson-Based Method for Single-Cell Chromatin Accessibility Analysis}, shorttitle = {{{APEC}}}, author = {Li, Bin and Li, Young and Li, Kun and Zhu, Lianbang and Yu, Qiaoni and Cai, Pengfei and Fang, Jingwen and Zhang, Wen and Du, Pengcheng and Jiang, Chen and Lin, Jun and Qu, Kun}, year = 2020, month = may, journal = {Genome Biology}, volume = {21}, number = {1}, pages = {116}, issn = {1474-760X}, doi = {10.1186/s13059-020-02034-y}, url = {https://doi.org/10.1186/s13059-020-02034-y}, urldate = {2026-02-04}, abstract = {The development of sequencing technologies has promoted the survey of genome-wide chromatin accessibility at single-cell resolution. However, comprehensive analysis of single-cell epigenomic profiles remains a challenge. Here, we introduce an accessibility pattern-based epigenomic clustering (APEC) method, which classifies each cell by groups of accessible regions with synergistic signal patterns termed ``accessons’’. This python-based package greatly improves the accuracy of unsupervised single-cell clustering for many public datasets. It also predicts gene expression, identifies enriched motifs, discovers super-enhancers, and projects pseudotime trajectories. APEC is available at https://github.com/QuKunLab/APEC.}, langid = {english}, keywords = {Accesson,Cell clustering,Pseudotime trajectory,Regulome,scATAC-seq}, file = {/home/trey/Zotero/storage/YLFR7MA5/Li et al. - 2020 - APEC an accesson-based method for single-cell chromatin accessibility analysis.pdf} } % == BibTeX quality report for liAPECAccessonbasedMethod2020: % ? unused Journal abbr (“Genome Biol”) % ? unused Library catalog (“Springer Link”)

@article{wangComputationalAnalysesChallenges2025, title = {Computational {{Analyses}} and {{Challenges}} of {{Single-cell ATAC-seq}}}, author = {Wang, Chenfei and Zhou, Jiaojiao and Zhang, Hong and Zhuang, Zihan and Bai, Gali and Tang, Ming and Liu, Song and Liu, Tao}, year = 2025, month = dec, journal = {Genomics, Proteomics & Bioinformatics}, volume = {23}, number = {6}, pages = {qzaf115}, issn = {1672-0229}, doi = {10.1093/gpbjnl/qzaf115}, url = {https://doi.org/10.1093/gpbjnl/qzaf115}, urldate = {2026-02-04}, abstract = {Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) has emerged as a powerful technique to study cell-specific epigenetic landscapes and to provide a multidimensional portrait of gene regulation. However, low genomic coverage per cell results in intrinsic data sparsity and missing-data issues, presenting unique methodological challenges. Consequently, numerous computational methods and techniques have been developed to address these challenges. This review provides a concise overview of published workflows for scATAC-seq analysis, covering preprocessing through downstream analysis including quality control, alignment, peak calling, dimensionality reduction, clustering, gene regulation score calculation, cell type annotation, and multiomics integration. Additionally, we survey key scATAC-seq databases that offer curated, accessible resources; discuss emerging deep-learning methods and Artificial Intelligence (AI) foundation models tailored to scATAC-seq data; and highlight recent advances in spatial ATAC-seq technologies and associated computational approaches. Our objective is to equip readers with a clear understanding of current scATAC-seq methodologies so they can select appropriate tools and construct customized workflows for exploring gene regulation and cellular diversity.}, file = {/home/trey/Zotero/storage/SGM89465/Wang et al. - 2025 - Computational Analyses and Challenges of Single-cell ATAC-seq.pdf;/home/trey/Zotero/storage/7NHVPTYM/qzaf115.html} } % == BibTeX quality report for wangComputationalAnalysesChallenges2025: % ? unused Journal abbr (“genom. proteom. bioinform.”) % ? unused Library catalog (“Silverchair”)

@misc{BuildNotesReference2026, title = {Build {{Notes}} for {{Reference Packages}} {{Official}} 10x {{Genomics Support}}}, year = 2026, month = feb, journal = {10x Genomics}, url = {https://www.10xgenomics.com/support/software/cell-ranger/downloads/cr-ref-build-steps}, urldate = {2026-02-04}, abstract = {A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3’ and 5’ gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data.}, langid = {english}, keywords = {nosource}, file = {/home/trey/Zotero/storage/JJSPCCN8/cr-ref-build-steps.html} } % == BibTeX quality report for BuildNotesReference2026: % ? Title looks like it was stored in title-case in Zotero

@misc{CellRangerATAC2026, title = {Cell {{Ranger ATAC}} {{Official}} 10x {{Genomics Support}}}, year = 2026, month = feb, journal = {10x Genomics}, url = {https://www.10xgenomics.com/support/software/cell-ranger-atac/latest}, urldate = {2026-02-04}, abstract = {Cell Ranger ATAC and Loupe Browser are software applications for analyzing and visualizing Epi ATAC (formerly Single Cell ATAC) data produced by the 10x Genomics Chromium platform.}, langid = {english}, keywords = {nosource}, file = {/home/trey/Zotero/storage/7PPL8NP7/latest.html} } % == BibTeX quality report for CellRangerATAC2026: % ? Title looks like it was stored in title-case in Zotero

@article{erdoganATACseqEmergingModel2025, title = {{{ATAC-seq}} in {{Emerging Model Organisms}}: {{Challenges}} and {{Strategies}}}, shorttitle = {{{ATAC-seq}} in {{Emerging Model Organisms}}}, author = {Erdo{}an, Du{}{}ar Ebrar and Karimifard, Shadi and Khodadadi, Mozhgan and Ling, Liucong and Linke, Luisa and Catal{'a}n, Ana and Doublet, Vincent and {Glaser-Schmitt}, Amanda and Niehuis, Oliver and Nowick, Katja and Soro, Antonella and Turetzek, Natascha and Feldmeyer, Barbara and Posnien, Nico}, year = 2025, journal = {Journal of Experimental Zoology Part B: Molecular and Developmental Evolution}, volume = {344}, number = {7}, pages = {394–414}, issn = {1552-5015}, doi = {10.1002/jez.b.23305}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jez.b.23305}, urldate = {2026-02-04}, abstract = {The Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) is a versatile and widely utilized method for identifying potential regulatory regions, such as promoters and enhancers, within a genome. ATAC-seq has been successfully applied to a wide range of established and emerging model organisms. However, implementing this method in emerging model systems, such as arthropods, can be challenging due to several factors that influence data quality. These factors include the availability of a sufficient amount and quality of tissue or cells, the need for species- and tissue-specific protocol optimization, the completeness and accuracy of the reference genome, and the quality of the genome annotation. In this article, we emphasize the key steps in the ATAC-seq protocol that, based on our experience, have the greatest impact on data quality when adapting this method for emerging model organisms. Specifically, we discuss the importance of nuclei isolation, the incubation conditions of the Tn5 transposase, and PCR amplification of the library. Furthermore, we outline essential quality checkpoints during the bioinformatic analysis of ATAC-seq data to assist in assessing data integrity and consistency. Given that many emerging model organisms may not be readily available in laboratory cultures, we also emphasize the importance of evaluating how different preservation methods affect ATAC-seq data quality. Based on examples in one spider and one ant species, we demonstrate that replication and thorough quality controls at all steps of the protocol and data analysis are essential to assess the usability of ATAC-seq data. Our data highlights the importance of isolating the right number of intact nuclei, as well as ensuring optimal amplification conditions during library preparation to obtain good-quality sequence data for downstream analyses. We recommend using fresh tissue samples if possible because we show that direct cryopreservation of the tissue may affect chromatin integrity. This effect could be avoided or reduced by preserving the homogenate in cell culture medium. Overall, we explain the ATAC-seq protocol and downstream analyses in detail and give step-by-step advice to researchers who are new to the field and want to implement this method. With careful planning and validation, ATAC-seq can reveal the regulatory landscape of a genome and aid in identifying elements that govern gene expression.}, copyright = { 2025 The Author(s). Journal of Experimental Zoology Part B: Molecular and Developmental Evolution published by Wiley Periodicals LLC.}, langid = {english}, keywords = {ATAC-seq,benchmarking,chromatin accessibility,gene regulation,insects,protocol optimization,quality control,spiders,tissue preservation}, file = {/home/trey/Zotero/storage/FNVFMW2B/Erdoğan et al. - 2025 - ATAC-seq in Emerging Model Organisms Challenges and Strategies.pdf;/home/trey/Zotero/storage/NWI97X2R/jez.b.html} } % == BibTeX quality report for erdoganATACseqEmergingModel2025: % ? unused extra: _eprint (“https://onlinelibrary.wiley.com/doi/pdf/10.1002/jez.b.23305”) % ? unused Library catalog (“Wiley Online Library”)

@misc{ title = {Training {{Compute-Optimal Large Language Models}}}, author = {Hoffmann, Jordan and Borgeaud, Sebastian and Mensch, Arthur and Buchatskaya, Elena and Cai, Trevor and Rutherford, Eliza and Casas, Diego de Las and Hendricks, Lisa Anne and Welbl, Johannes and Clark, Aidan and Hennigan, Tom and Noland, Eric and Millican, Katie and {}van den Driessche, George and Damoc, Bogdan and Guy, Aurelia and Osindero, Simon and Simonyan, Karen and Elsen, Erich and Rae, Jack W. and Vinyals, Oriol and Sifre, Laurent}, year = 2022, month = mar, number = {arXiv:2203.15556}, eprint = {2203.15556}, primaryclass = {cs}, publisher = {arXiv}, doi = {10.48550/arXiv.2203.15556}, url = {http://arxiv.org/abs/2203.15556}, urldate = {2026-02-17}, abstract = {We investigate the optimal model size and number of tokens for training a transformer language model under a given compute budget. We find that current large language models are significantly undertrained, a consequence of the recent focus on scaling language models whilst keeping the amount of training data constant. By training over 400 language models ranging from 70 million to over 16 billion parameters on 5 to 500 billion tokens, we find that for compute-optimal training, the model size and the number of training tokens should be scaled equally: for every doubling of model size the number of training tokens should also be doubled. We test this hypothesis by training a predicted compute-optimal model, Chinchilla, that uses the same compute budget as Gopher but with 70B parameters and 4$times$ more more data. Chinchilla uniformly and significantly outperforms Gopher (280B), GPT-3 (175B), Jurassic-1 (178B), and Megatron-Turing NLG (530B) on a large range of downstream evaluation tasks. This also means that Chinchilla uses substantially less compute for fine-tuning and inference, greatly facilitating downstream usage. As a highlight, Chinchilla reaches a state-of-the-art average accuracy of 67.5% on the MMLU benchmark, greater than a 7% improvement over Gopher.}, archiveprefix = {arXiv}, langid = {english}, keywords = {Computer Science - Computation and Language,Computer Science - Machine Learning}, file = {/home/trey/Zotero/storage/A7XCV79U/Hoffmann et al. - 2022 - Training Compute-Optimal Large Language Models.pdf} } % == BibTeX quality report for undefined: % ? Title looks like it was stored in title-case in Zotero

@incollection{shigeokaAxonTRAPRiboTagAffinityPurification2018, title = {Axon-{{TRAP-RiboTag}}: {{Affinity Purification}} of {{Translated mRNAs}} from {{Neuronal Axons}} in {{Mouse In Vivo}}}, shorttitle = {Axon-{{TRAP-RiboTag}}}, booktitle = {{{RNA Detection}}: {{Methods}} and {{Protocols}}}, author = {Shigeoka, Toshiaki and Jung, Jane and Holt, Christine E. and Jung, Hosung}, editor = {Gaspar, Imre}, year = 2018, pages = {85–94}, publisher = {Springer}, address = {New York, NY}, doi = {10.1007/978-1-4939-7213-5_5}, url = {https://doi.org/10.1007/978-1-4939-7213-5_5}, urldate = {2026-03-06}, abstract = {Translating ribosome affinity purification (TRAP) is a widely used technique to analyze ribosome-bound mRNAs in particular target cells that express a tagged ribosomal protein. We developed axon-TRAP-RiboTag, a TRAP-based method that allows purification and identification of translated mRNAs from distal neuronal axons in mouse, and identified more than 2000 of translated mRNAs in retinal ganglion cell (RGC) axons in vivo. The use of Cre-negative littermate control to filter out false-positive signals allows unbiased detection, and combining TRAP with in vitro ribosome run-off enables identification of actively translated mRNAs. Here, we describe a detailed protocol to identify translated mRNAs in RGC axons in mouse in vivo. This method can be applied to any neurons whose cell bodies and distal axons are anatomically separated.}, isbn = {978-1-4939-7213-5}, langid = {english}, keywords = {Axon,Immunoprecipitation,mRNAs,Neuron,Ribosome,Translation}, file = {/home/trey/Zotero/storage/TYTQEPQ8/Shigeoka et al. - 2018 - Axon-TRAP-RiboTag Affinity Purification of Translated mRNAs from Neuronal Axons in Mouse In Vivo.pdf} } % == BibTeX quality report for shigeokaAxonTRAPRiboTagAffinityPurification2018: % ? Title looks like it was stored in title-case in Zotero % ? unused Library catalog (“Springer Link”)

@preamble{ “

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% The following packages could be loaded to get more precise latex output: % * inputenx % * textalpha % * textcomp % * unicode-math