codon

Summary

Summary: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).

Top Publications

  1. doi Coding-sequence determinants of gene expression in Escherichia coli
    Grzegorz Kudla
    Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
    Science 324:255-8. 2009
  2. pmc Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    Nicholas T Ingolia
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA
    Science 324:218-23. 2009
  3. pmc Synonymous but not the same: the causes and consequences of codon bias
    Joshua B Plotkin
    Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, 433 South University Avenue, Philadelphia, Pennsylvania 19104, USA
    Nat Rev Genet 12:32-42. 2011
  4. ncbi Not so different after all: a comparison of methods for detecting amino acid sites under selection
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego, USA
    Mol Biol Evol 22:1208-22. 2005
  5. doi An evolutionarily conserved mechanism for controlling the efficiency of protein translation
    Tamir Tuller
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Cell 141:344-54. 2010
  6. doi Selection on codon bias
    Ruth Hershberg
    Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
    Annu Rev Genet 42:287-99. 2008
  7. pmc The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
    Gene Wei Li
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA
    Nature 484:538-41. 2012
  8. ncbi Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
    Mol Biol Evol 22:2472-9. 2005
  9. ncbi Synonymous codon usage in Escherichia coli: selection for translational accuracy
    Nina Stoletzki
    Ludwig Maximilan Universität, Biocenter, Planegg Martinsried, Germany
    Mol Biol Evol 24:374-81. 2007
  10. ncbi A "silent" polymorphism in the MDR1 gene changes substrate specificity
    Chava Kimchi-Sarfaty
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
    Science 315:525-8. 2007

Research Grants

  1. Role of troponin T isoforms in nemaline myopathy
    Jian Ping Jin; Fiscal Year: 2009
  2. Role of troponin T isoforms in nemaline myopathy
    Jian Ping Jin; Fiscal Year: 2010
  3. BIOCHEMISTRY OF PRE-MRNA SPLICING
    ADRIAN KRAINER; Fiscal Year: 2009
  4. BIOCHEMISTRY OF PRE-MRNA SPLICING
    ADRIAN KRAINER; Fiscal Year: 2007
  5. A SARS-CoV Spike Protein Vaccine
    B Sim; Fiscal Year: 2005
  6. APOLIPOPROTEIN B48 AND LIPOPROTEIN METABOLISM
    Lawrence Chan; Fiscal Year: 2004
  7. Resolution of Epithelial Cell Hyperplasia
    Yohannes Tesfaigzi; Fiscal Year: 2009
  8. Resolution of Epithelial Cell Hyperplasia
    Yohannes Tesfaigzi; Fiscal Year: 2010
  9. Ribosomal scanning and initiation codon selection
    Tatyana V Pestova; Fiscal Year: 2010
  10. STRUCTURE OF VIRAL RNA IN RIBOSOMAL FRAMESHIFTING
    Alexander Rich; Fiscal Year: 2004

Detail Information

Publications338 found, 100 shown here

  1. doi Coding-sequence determinants of gene expression in Escherichia coli
    Grzegorz Kudla
    Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
    Science 324:255-8. 2009
    ..GFP messenger RNA (mRNA) levels, mRNA degradation patterns, and bacterial growth rates also varied, but codon bias did not correlate with gene expression...
  2. pmc Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    Nicholas T Ingolia
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA
    Science 324:218-23. 2009
    ..Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible...
  3. pmc Synonymous but not the same: the causes and consequences of codon bias
    Joshua B Plotkin
    Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, 433 South University Avenue, Philadelphia, Pennsylvania 19104, USA
    Nat Rev Genet 12:32-42. 2011
    ..As a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology...
  4. ncbi Not so different after all: a comparison of methods for detecting amino acid sites under selection
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego, USA
    Mol Biol Evol 22:1208-22. 2005
    ..We demonstrate our methods on sequence data from the human immunodeficiency virus type 1 env and pol genes and simulated alignments...
  5. doi An evolutionarily conserved mechanism for controlling the efficiency of protein translation
    Tamir Tuller
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Cell 141:344-54. 2010
    ..We suggest that the slow "ramp" at the beginning of mRNAs serves as a late stage of translation initiation, forming an optimal and robust means to reduce ribosomal traffic jams, thus minimizing the cost of protein expression...
  6. doi Selection on codon bias
    Ruth Hershberg
    Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
    Annu Rev Genet 42:287-99. 2008
    In a wide variety of organisms, synonymous codons are used with different frequencies, a phenomenon known as codon bias...
  7. pmc The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
    Gene Wei Li
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA
    Nature 484:538-41. 2012
    ..protein-coding sequences, internal SD sequences are disfavoured, which leads to biased usage, avoiding codons and codon pairs that resemble canonical SD sites...
  8. ncbi Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
    Mol Biol Evol 22:2472-9. 2005
    ..Recently, Yang, Z., and R. Nielsen (2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol...
  9. ncbi Synonymous codon usage in Escherichia coli: selection for translational accuracy
    Nina Stoletzki
    Ludwig Maximilan Universität, Biocenter, Planegg Martinsried, Germany
    Mol Biol Evol 24:374-81. 2007
    ..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...
  10. ncbi A "silent" polymorphism in the MDR1 gene changes substrate specificity
    Chava Kimchi-Sarfaty
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
    Science 315:525-8. 2007
    ..We hypothesize that the presence of a rare codon, marked by the synonymous polymorphism, affects the timing of cotranslational folding and insertion of P-gp into ..
  11. pmc Balanced codon usage optimizes eukaryotic translational efficiency
    Wenfeng Qian
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Genet 8:e1002603. 2012
    ..We hypothesize that this phenomenon is a result of codon usage in proportion to cognate tRNA concentrations, the optimal strategy in enhancing translational efficiency ..
  12. pmc Composite effects of gene determinants on the translation speed and density of ribosomes
    Tamir Tuller
    Department of Biomedical Engineering, Tel Aviv University, Israel
    Genome Biol 12:R110. 2011
    ....
  13. pmc General rules for optimal codon choice
    Ruth Hershberg
    Department of Biology, Stanford University, Stanford, California, United States of America
    PLoS Genet 5:e1000556. 2009
    ..Once the effect of the genomic GC content on selectively favored codon choice is taken into account, additional universal amino acid specific rules governing the identity of favored ..
  14. pmc Determinants of translation efficiency and accuracy
    Hila Gingold
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 7:481. 2011
    ..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...
  15. pmc Translation efficiency is determined by both codon bias and folding energy
    Tamir Tuller
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 107:3645-50. 2010
    ..mechanisms by which this effect is achieved are controversial; although some previous studies have suggested that codon bias is the most important determinant of translation efficiency, a recent study suggested that mRNA folding at ..
  16. pmc Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradation
    Fangliang Zhang
    Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Science 329:1534-7. 2010
    ..This degradation mechanism, coupled to nucleotide coding sequence, may regulate protein arginylation in vivo...
  17. ncbi Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
    Beth Shapiro
    Mol Biol Evol 23:7-9. 2006
    ..This problem is exacerbated by the exclusion of codon-based models from commonly employed model selection techniques, presumably due to the computational cost ..
  18. pmc Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis
    L Duret
    Laboratoire de Biometrie, Génétique et Biologie des Populations, Unité Mixte de Recherche Centre National de la Recherche Scientifique 5558, Villeurbanne Cedex, France
    Proc Natl Acad Sci U S A 96:4482-7. 1999
    We measured the expression pattern and analyzed codon usage in 8,133, 1,550, and 2,917 genes, respectively, from Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana...
  19. pmc Solving the riddle of codon usage preferences: a test for translational selection
    Mario dos Reis
    School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
    Nucleic Acids Res 32:5036-44. 2004
    ..Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible...
  20. pmc PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
    Mikita Suyama
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nucleic Acids Res 34:W609-12. 2006
    PAL2NAL is a web server that constructs a multiple codon alignment from the corresponding aligned protein sequences...
  21. ncbi tRNA's wobble decoding of the genome: 40 years of modification
    Paul F Agris
    Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695 7622, USA
    J Mol Biol 366:1-13. 2007
    ..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...
  22. doi Genome sequence of the recombinant protein production host Pichia pastoris
    Kristof De Schutter
    Unit for Molecular Glycobiology, Department for Molecular Biomedical Research, VIB, Ghent Zwijnaarde, Belgium
    Nat Biotechnol 27:561-6. 2009
    ..pastoris. To facilitate progress in these areas, we present the 9.43 Mbp genomic sequence of the GS115 strain of P. pastoris. We also provide manually curated annotation for its 5,313 protein-coding genes...
  23. pmc Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift
    Premal Shah
    Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
    Proc Natl Acad Sci U S A 108:10231-6. 2011
    The genetic code is redundant with most amino acids using multiple codons. In many organisms, codon usage is biased toward particular codons...
  24. pmc Design parameters to control synthetic gene expression in Escherichia coli
    Mark Welch
    DNA2 0, Menlo Park, CA, USA
    PLoS ONE 4:e7002. 2009
    ..Protein-coding sequences are commonly re-designed to enhance expression, but there are no experimentally supported design principles...
  25. doi A role for codon order in translation dynamics
    Gina Cannarozzi
    Institute of Computational Science, ETH Zurich, 8092 Zurich, Switzerland
    Cell 141:355-67. 2010
    ..Here, we show that in coding sequences, once a particular codon has been used, subsequent occurrences of the same amino acid do not use codons randomly, but favor codons that use ..
  26. ncbi Predicting the evolution of human influenza A
    R M Bush
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Science 286:1921-5. 1999
    ..However, not all codons in these sites had predictive value. Monitoring new H3 isolates for additional changes in positively selected codons might help identify the most fit extant viral strains that arise during antigenic drift...
  27. pmc The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae)
    Hu Li
    Department of Entomology, China Agricultural University, Beijing, China
    PLoS ONE 7:e29419. 2012
    ..A microsatellite was identified in the putative control region. Finally, phylogenetic reconstruction suggests that Enicocephalomorpha is the sister group to all the remaining Heteroptera...
  28. ncbi Accounting for background nucleotide composition when measuring codon usage bias
    John A Novembre
    Mol Biol Evol 19:1390-4. 2002
  29. pmc Mitochondrial genome sequence and expression profiling for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae)
    Venu M Margam
    Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
    PLoS ONE 6:e16444. 2011
    ..and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion ..
  30. doi Isocitrate dehydrogenase 1 codon 132 mutation is an important prognostic biomarker in gliomas
    Marc Sanson
    L Institut National de la Santé et de la Recherche Médicale U711, Fédération de Neurologie Mazarin, Groupe Hospitalier Pitie Salpetriere, 75651, Paris Cedex 13, France
    J Clin Oncol 27:4150-4. 2009
    Unexpected mutations affecting the isocitrate dehydrogenase (IDH1) gene at codon 132 have been found in 12% of glioblastomas.
  31. pmc Translationally optimal codons associate with structurally sensitive sites in proteins
    Tong Zhou
    Center for Computational Biology and Bioinformatics, The University of Texas at Austin, TX, USA
    Mol Biol Evol 26:1571-80. 2009
    ..To test this hypothesis, we analyzed the relationship between codon usage bias and protein structure in the genomes of four model organisms, Escherichia coli, yeast, fly, and mouse...
  32. ncbi A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution
    Joseph P Bielawski
    Department of Biology, University College London, London, WC1E 6BT, UK
    J Mol Evol 59:121-32. 2004
    ..The method is based on a codon model of evolution and uses the nonsynonymous-to-synonymous rate ratio (omega) as a measure of selection on the ..
  33. doi Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes
    Henri Grosjean
    Universite Paris Sud, CNRS, UMR8621, Institut de Génétique et de Microbiologie, Orsay F 91405, France
    FEBS Lett 584:252-64. 2010
    ....
  34. ncbi Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula
    Par K Ingvarsson
    Umea Plant Science Centre, Department of Ecology and Environmental Science, Umea University, Umea, Sweden
    Mol Biol Evol 24:836-44. 2007
    b>Codon bias is generally thought to be determined by a balance between mutation, genetic drift, and natural selection on translational efficiency...
  35. ncbi Germ-line mutations of the RET proto-oncogene in multiple endocrine neoplasia type 2A
    L M Mulligan
    Department of Pathology, University of Cambridge, UK
    Nature 363:458-60. 1993
    ..Further, 19 of these 20 mutations affect the same conserved cysteine residue at the boundary of the RET extracellular and transmembrane domains...
  36. pmc Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models
    Stephan Waack
    Institut fur Informatik, Universitat Gottingen, Lotzestr, 16 18, 37083 Göttingen, Germany
    BMC Bioinformatics 7:142. 2006
    ..Frequently, the transferred pieces of DNA have a considerable length, comprise several genes and are called genomic islands (GIs) or more specifically pathogenicity or symbiotic islands...
  37. pmc A general model of codon bias due to GC mutational bias
    Gareth A Palidwor
    Ottawa Hospital Research Institute, Ottawa, Canada
    PLoS ONE 5:e13431. 2010
    In spite of extensive research on the effect of mutation and selection on codon usage, a general model of codon usage bias due to mutational bias has been lacking...
  38. ncbi Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
    Manolis Kellis
    The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02138, USA
    Nature 428:617-24. 2004
    ..Strikingly, 95% of cases of accelerated evolution involve only one member of a gene pair, providing strong support for a specific model of evolution, and allowing us to distinguish ancestral and derived functions...
  39. ncbi Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California, San Diego, CA 92103, USA
    Bioinformatics 21:2531-3. 2005
    ..The methods range from very fast data exploration to the some of the most complex models available in public domain software, and are implemented to run in parallel on a cluster of computers...
  40. doi Parallel on-chip gene synthesis and application to optimization of protein expression
    Jiayuan Quan
    Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
    Nat Biotechnol 29:449-52. 2011
    ..19 errors per kb. We applied this approach to synthesize pools of thousands of codon-usage variants of lacZα and 74 challenging Drosophila protein antigens, which were then screened for expression ..
  41. pmc Forces that influence the evolution of codon bias
    Paul M Sharp
    Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK
    Philos Trans R Soc Lond B Biol Sci 365:1203-12. 2010
    ..The strength of selection on codon usage can be estimated by two different approaches...
  42. pmc How the sequence of a gene can tune its translation
    Kurt Fredrick
    Department of Microbiology, Ohio State Biochemistry Program, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
    Cell 141:227-9. 2010
    ..Two new studies (Cannarrozzi et al., 2010; Tuller et al., 2010) now foster the idea that patterns of codon usage can control ribosome speed, fine-tuning translation to increase the efficiency of protein synthesis.
  43. pmc Codon usage in twelve species of Drosophila
    Saverio Vicario
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 8105, USA
    BMC Evol Biol 7:226. 2007
    b>Codon usage bias (CUB), the uneven use of synonymous codons, is a ubiquitous observation in virtually all organisms examined...
  44. doi Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in Populus tremula
    Par K Ingvarsson
    Umea Plant Science Centre, Department of Ecology and Environmental Science, Umea University, Umea, Sweden
    Mol Biol Evol 27:650-60. 2010
    ..tremula. The results presented here show that this has resulted in an increase in codon bias in P. tremula, consistent with stronger selection acting on synonymous codon usage...
  45. pmc Frequent somatic mutations of GNAQ in uveal melanoma and blue naevi
    Catherine D Van Raamsdonk
    Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada
    Nature 457:599-602. 2009
    ..The mutations occur exclusively in codon 209 in the Ras-like domain and result in constitutive activation, turning GNAQ into a dominant acting oncogene...
  46. pmc A multicenter blinded study to evaluate KRAS mutation testing methodologies in the clinical setting
    Vicki Whitehall
    Queensland Institute of Medical Research, Bancroft Building, 300 Herston Road, Herston Queensland 4029, Australia
    J Mol Diagn 11:543-52. 2009
    ..These results demonstrate that a variety of detection methodologies are suitable and provide comparable results for KRAS mutation analysis of clinical samples...
  47. doi Real-time tRNA transit on single translating ribosomes at codon resolution
    Sotaro Uemura
    Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305 5126, USA
    Nature 464:1012-7. 2010
    ..Translation at each codon is monitored by stable binding of transfer RNAs (tRNAs)-labelled with distinct fluorophores-to translating ..
  48. pmc Impact of translational error-induced and error-free misfolding on the rate of protein evolution
    Jian Rong Yang
    Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat Sen University, Guangzhou, PR China
    Mol Syst Biol 6:421. 2010
    ..These findings provide unambiguous support to the role of protein-misfolding-avoidance in determining the rate of protein sequence evolution...
  49. ncbi A mutation in the RET proto-oncogene associated with multiple endocrine neoplasia type 2B and sporadic medullary thyroid carcinoma
    R M Hofstra
    Department of Medical Genetics, University of Groningen, The Netherlands
    Nature 367:375-6. 1994
    ..We now show that MEN 2B is also associated with mutation of the RET proto-oncogene. A mutation in codon 664, causing the substitution of a threonine for a methionine in the tyrosine kinase domain of the protein, was ..
  50. doi RET codon 804 mutations in multiple endocrine neoplasia 2: genotype-phenotype correlations and implications in clinical management
    S Mukherjee
    Beaumont Cancer Genetics Program, Beaumont Cancer Institute, William Beaumont Hospital, Royal Oak, MI 48073, USA
    Clin Genet 79:1-16. 2011
    ..This review summarizes the genotypic and phenotypic characteristics of RET codon 804 mutation, a prototype for the less well-defined non-cysteine RET mutations associated with MEN 2.
  51. ncbi Two germline missense mutations at codons 804 and 806 of the RET proto-oncogene in the same allele in a patient with multiple endocrine neoplasia type 2B without codon 918 mutation
    A Miyauchi
    Kuma Hospital, Kobe
    Jpn J Cancer Res 90:1-5. 1999
    ..Combinations of mutations of the RET proto-oncogene may cause oncogenic activities different from those of single mutations...
  52. ncbi Microsatellites within genes: structure, function, and evolution
    You Chun Li
    Institute of Evolution, University of Haifa, Haifa, Israel
    Mol Biol Evol 21:991-1007. 2004
    ..These SSRs may provide a molecular basis for fast adaptation to environmental changes in both prokaryotes and eukaryotes...
  53. pmc Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11
    Manqing Li
    Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
    Nature 491:125-8. 2012
    ..SLFN11 acts at the late stage of virus production by selectively inhibiting the expression of viral proteins in a codon-usage-dependent manner...
  54. pmc The complete mitochondrial genome sequence of the planthopper, Sivaloka damnosus
    Nan Song
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P R China
    J Insect Sci 10:76. 2010
    ..In the phylogenetic analyses based on protein-coding genes, Cicadomorpha is a sister to Fulgoromorpha+Sternorrhyncha, and Heteroptera is a sister to all other Hemiptera...
  55. doi Evolution in regulatory regions rapidly compensates the cost of nonoptimal codon usage
    Dolors Amorós-Moya
    Genomics and Health, Centre for Public Health Research Centro Superior de Investigación en Salud Pública, CSISP, Valencia, Spain
    Mol Biol Evol 27:2141-51. 2010
    The redundant genetic code contains synonymous codons, whose relative frequencies vary among species. Nonoptimal codon usage lowers gene translation efficiency, potentially leading to a fitness cost...
  56. ncbi Atypical MEN type 2B associated with two germline RET mutations on the same allele not involving codon 918
    Fred H Menko
    Department of Clinical Genetics and Human Genetics, Vrije Universiteit Medical Center, 1007 MB Amsterdam, The Netherlands
    J Clin Endocrinol Metab 87:393-7. 2002
    ..Mutation analysis revealed a double RET germline mutation, Val804Met and Ser904Cys, in affected individuals. The clinical phenotype, the functional effect of the mutations, and the clinical implications of our findings are discussed...
  57. pmc Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana
    G Marais
    Institute of Cell, Animal and Population Biology, University of Edinburgh, EH9 3JT Edinburgh, UK
    Genome Biol 5:R45. 2004
    ....
  58. doi Determinants of synonymous and nonsynonymous variability in three species of Drosophila
    Penelope R Haddrill
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
    Mol Biol Evol 28:1731-43. 2011
    ..We found evidence for stronger selection at X-linked loci, consistent with their higher levels of codon usage bias...
  59. pmc Estimating translational selection in eukaryotic genomes
    Mario dos Reis
    School of Crystallography, Birkbeck College, London, UK
    Mol Biol Evol 26:451-61. 2009
    Natural selection on codon usage is a pervasive force that acts on a large variety of prokaryotic and eukaryotic genomes...
  60. doi Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage
    Mary M Guisinger
    Section of Integrative Biology, University of Texas, Austin, USA
    Mol Biol Evol 28:583-600. 2011
    ..Geraniaceae plastomes were found to be highly variable in size, gene content and order, repetitive DNA, and codon usage...
  61. doi Investigating protein-coding sequence evolution with probabilistic codon substitution models
    Maria Anisimova
    Institute of Computational Science, Swiss Federal Institute of Technology, Zurich, Switzerland
    Mol Biol Evol 26:255-71. 2009
    ..by the true explosion in the number of recent studies both developing and ameliorating probabilistic models of codon evolution...
  62. doi The aflatoxin-induced TP53 mutation at codon 249 (R249S): biomarker of exposure, early detection and target for therapy
    Doriane Gouas
    International Agency for Research on Cancer, 150 cours Albert Thomas, 69372 Lyon Cedex 08, France
    Cancer Lett 286:29-37. 2009
    ..HCC) in high-incidence areas (sub-Saharan Africa, South-Eastern Asia) often contains a somatic mutation at codon 249 in TP53 (R249S). This mutation is rare in low-incidence areas of Europe and the United States...
  63. ncbi An empirical codon model for protein sequence evolution
    Carolin Kosiol
    EMBL European corrected Bioinformatics Institute, Hinxton, United Kingdom
    Mol Biol Evol 24:1464-79. 2007
    In the past, 2 kinds of Markov models have been considered to describe protein sequence evolution. Codon-level models have been mechanistic with a small number of parameters designed to take into account features, such as transition-..
  64. pmc Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15, France
    Genome Res 14:2279-86. 2004
    The selection-mutation-drift theory of codon usage plays a major role in the theory of molecular evolution by explaining the co-evolution of codon usage bias and tRNA content in the framework of translation optimization...
  65. pmc Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag
    Jonathan M Carlson
    eScience Group, Microsoft Research, Redmond, Washington, United States of America
    PLoS Comput Biol 4:e1000225. 2008
    ..I alleles, previous population-based studies have been limited by the inability to simultaneously account for HIV codon covariation, linkage disequilibrium among HLA alleles, and the confounding effects of HIV phylogeny when ..
  66. pmc Assays to detect beta-tubulin codon 200 polymorphism in Trichuris trichiura and Ascaris lumbricoides
    Aissatou Diawara
    Institute of Parasitology, McGill University, Quebec, Canada
    PLoS Negl Trop Dis 3:e397. 2009
    ..We have developed pyrosequencer assays for codon 200 (TTC or TAC) in A. lumbricoides and T. trichiura to screen for this single nucleotide polymorphism (SNP).
  67. ncbi Codon bias and heterologous protein expression
    Claes Gustafsson
    DNA 2 0, 1455 Adams Drive, Menlo Park, CA 94025, USA
    Trends Biotechnol 22:346-53. 2004
    ..Redesign strategies are discussed here, including modification of translation initiation regions, alteration of mRNA structural elements and use of different codon biases.
  68. pmc Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
    Michael F Lin
    Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genome Res 21:1916-28. 2011
    ..alignment provides statistical power to locate more than 10,000 such regions with resolution down to nine-codon windows, which are found within more than a quarter of all human protein-coding genes and contain ∼2% of their ..
  69. pmc Comparison of Sanger sequencing, pyrosequencing, and melting curve analysis for the detection of KRAS mutations: diagnostic and clinical implications
    Athanasios C Tsiatis
    The Johns Hopkins Medical Institutions, Department of Pathology, 600 N Wolfe Street, Park SB202, Baltimore, MD 21287, USA
    J Mol Diagn 12:425-32. 2010
    ..Therefore, we assessed Sanger sequencing, pyrosequencing, and melting curve analysis for the detection of KRAS codon 12/13 mutations in formalin-fixed paraffin-embedded samples, including 58 primary and 42 metastatic colorectal ..
  70. pmc Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species
    Peter Andolfatto
    Department of Ecology and Evolutionary Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, USA
    Genome Biol Evol 3:114-28. 2011
    ..We observe significantly higher levels of polymorphism and evidence for stronger selection on codon usage bias in D...
  71. pmc Estimating selection intensity on synonymous codon usage in a nonequilibrium population
    Kai Zeng
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
    Genetics 183:651-62, 1SI-23SI. 2009
    b>Codon usage bias is the nonrandom use of synonymous codons for the same amino acid. Most population genetic models of codon usage evolution assume that the population is at mutation-selection-drift equilibrium...
  72. doi The complete mitochondrial genome of Diadegma semiclausum (hymenoptera: ichneumonidae) indicates extensive independent evolutionary events
    Shu jun Wei
    Institute of Insect Sciences, Zhejiang University, Hangzhou 310029, China
    Genome 52:308-19. 2009
    ....
  73. pmc Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages
    Yedael Y Waldman
    Blavatnik School of Computer Science, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 38:2964-74. 2010
    Various studies in unicellular and multicellular organisms have shown that codon bias plays a significant role in translation efficiency (TE) by co-adaptation to the tRNA pool...
  74. pmc GroEL dependency affects codon usage--support for a critical role of misfolding in gene evolution
    Tobias Warnecke
    Department of Biology and Biochemistry, University of Bath, Bath, UK
    Mol Syst Biol 6:340. 2010
    ..We propose that putative error limitation in cis can be elucidated by examining the interaction between codon usage and chaperoning processes...
  75. ncbi The codon 620 tryptophan allele of the lymphoid tyrosine phosphatase (LYP) gene is a major determinant of Graves' disease
    M R Velaga
    Institute of Human Genetics, University of Newcastle upon Tyne NE1 3BZ, United Kingdom
    J Clin Endocrinol Metab 89:5862-5. 2004
    ..a single nucleotide polymorphism (SNP), encoding a functional arginine to tryptophan residue change at LYP codon 620 has been shown to be associated with type 1 diabetes and other autoimmune disorders...
  76. pmc Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host
    Evelina Angov
    Molecular Parasitology, Division of Malaria Vaccine Development, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
    PLoS ONE 3:e2189. 2008
    Synonymous codon replacement can change protein structure and function, indicating that protein structure depends on DNA sequence...
  77. ncbi Germline dinucleotide mutation in codon 883 of the RET proto-oncogene in multiple endocrine neoplasia type 2B without codon 918 mutation
    O Gimm
    Translational Research Laboratory, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    J Clin Endocrinol Metab 82:3902-4. 1997
    ..More than 95% of all MEN 2B cases are caused by germline mutation at codon 918 (M918T) in exon 16 of the RET proto-oncogene...
  78. pmc Live attenuated influenza virus vaccines by computer-aided rational design
    Steffen Mueller
    Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, USA
    Nat Biotechnol 28:723-6. 2010
    ..A/PR/8/34 to rationally design live attenuated influenza virus vaccine candidates through genome-scale changes in codon-pair bias...
  79. ncbi Characterization of mammalian selenoproteomes
    Gregory V Kryukov
    Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 0664, USA
    Science 300:1439-43. 2003
    In the genetic code, UGA serves as a stop signal and a selenocysteine codon, but no computational methods for identifying its coding function are available. Consequently, most selenoprotein genes are misannotated...
  80. ncbi Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses
    Laura A Shackelton
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    J Mol Evol 62:551-63. 2006
    Understanding the extent and causes of biases in codon usage and nucleotide composition is essential to the study of viral evolution, particularly the interplay between viruses and host cells or immune responses...
  81. ncbi Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes
    Manfred T Reetz
    Max Planck Institut fur Kohlenforschung, Kaiser Wilhelm Platz 1, 45470 Mulheim Ruhr, Germany
    Nat Protoc 2:891-903. 2007
    ..The pronounced increase in thermostability of the lipase from Bacillus subtilis (Lip A) as a result of applying ISM is illustrated here...
  82. pmc Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences
    Iris Bahir
    Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
    Mol Syst Biol 5:311. 2009
    ..We consider their respective amino acid and codon usages and compare them among the viruses and their hosts...
  83. ncbi Instruction of translating ribosome by nascent peptide
    Feng Gong
    Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
    Science 297:1864-7. 2002
    ..Replacing the tnaC stop codon with a tryptophan codon allows tryptophan-charged tryptophan transfer RNA to substitute for tryptophan as inducer...
  84. pmc Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAS and has a gene arrangement relatable to those of coelomate metazoans
    D V Lavrov
    Department of Biology, University of Michigan, Ann Arbor, Michigan 48109 1048, USA
    Genetics 157:621-37. 2001
    ..The sequence also contains a large repeat region that is polymorphic in size at the population and/or individual level...
  85. ncbi Generation and immunogenicity of novel HIV/AIDS vaccine candidates targeting HIV-1 Env/Gag-Pol-Nef antigens of clade C
    Carmen Elena Gómez
    Department of Molecular and Cellular Biology, Centro Nacional de Biotecnologia, CSIC, Ciudad Universitaria Cantoblanco, 28049 Madrid, Spain
    Vaccine 25:1969-92. 2007
    ..in transgenic HHD mice the immunogenicity of two attenuated poxvirus vectors expressing in a single locus (TK) the codon optimized HIV-1 genes encoding gp120 and Gag-Pol-Nef (GPN) polyprotein of clade C (referred as MVA-C and NYVAC-C)...
  86. pmc Mutations at embB codon 306 are an important molecular indicator of ethambutol resistance in Mycobacterium tuberculosis
    Angela M Starks
    Division of Tuberculosis Elimination, National Center for HIV AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
    Antimicrob Agents Chemother 53:1061-6. 2009
    ..However, recent reports have described the presence of embB mutations, especially those at embB codon 306, in isolates susceptible to ethambutol...
  87. doi Patterns of codon usage bias in Silene latifolia
    Suo Qiu
    State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat Sen University, Guangzhou 510275, China
    Mol Biol Evol 28:771-80. 2011
    Patterns of codon usage bias (CUB) convey useful information about the selection on synonymous codons induced by gene expression and contribute to an understanding of substitution patterns observed at synonymous sites...
  88. doi Biased gene conversion affects patterns of codon usage and amino acid usage in the Saccharomyces sensu stricto group of yeasts
    Richard J Harrison
    Institute of Evolutionary Biology, School of Biological Sciences, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, United Kingdom
    Mol Biol Evol 28:117-29. 2011
    Patterns of synonymous codon usage vary between organisms and are controlled by neutral processes (such as drift and mutation) as well as by selection...
  89. doi Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage
    Ziheng Yang
    Department of Biology, Galton Laboratory, University College London, London, United Kingdom
    Mol Biol Evol 25:568-79. 2008
    Current models of codon substitution are formulated at the levels of nucleotide substitution and do not explicitly consider the separate effects of mutation and selection...
  90. pmc Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus
    Emily H M Wong
    Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China
    BMC Evol Biol 10:253. 2010
    ..As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission...
  91. ncbi Gene disruption in Candida albicans using a synthetic, codon-optimised Cre-loxP system
    Paul M J Dennison
    Aberdeen Fungal Group, School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
    Fungal Genet Biol 42:737-48. 2005
    ..These markers were then resolved from the C. albicans genome using a synthetic codon-optimised cre recombinase gene, with near 100% efficiency...
  92. pmc Following translation by single ribosomes one codon at a time
    Jin Der Wen
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Nature 452:598-603. 2008
    ..Each translocation step measures three bases--one codon-and occurs in less than 0.1 s...
  93. ncbi The mitochondrial genome of the smaller tea tortrix Adoxophyes honmai (Lepidoptera: Tortricidae)
    Eun Seung Lee
    Department of Plant Medicine, Chungbuk National University, Cheongju, Republic of Korea
    Gene 373:52-7. 2006
    ..Nucleotide composition, amino acid composition and codon usage are in the range of values estimated from other insect mitogenomes. In AT rich region of A...
  94. pmc Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains
    Justin S Hogg
    Allegheny General Hospital, Allegheny Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania 15212, USA
    Genome Biol 8:R103. 2007
    ..Studies based on random sequencing of multiple strain libraries suggested that free-living bacterial species possess a supragenome that is much larger than the genome of any single bacterium...
  95. ncbi RET codon 634 mutations in multiple endocrine neoplasia type 2: variable clinical features and clinical outcome
    Marcia K Puñales
    Endocrine Division, Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre 90035 003, Rio Grande do Sul, Brazil
    J Clin Endocrinol Metab 88:2644-9. 2003
    ..Sixty-nine individuals from 12 different families presented a codon 634 mutation, the most prevailing missense mutation in our series...
  96. pmc Patterns of molecular evolution in Caenorhabditis preclude ancient origins of selfing
    Asher D Cutter
    Department of Ecology and Evolutionary Biology and the Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3G5, Canada
    Genetics 178:2093-104. 2008
    ..Here we contrast rates of nucleotide substitution and codon usage bias among thousands of orthologous groups of genes in six species of Caenorhabditis, including the classic ..
  97. pmc Trm9-catalyzed tRNA modifications link translation to the DNA damage response
    Ulrike Begley
    Department of Biomedical Sciences, GenNYsis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, Rensselaer, NY 12144, USA
    Mol Cell 28:860-70. 2007
    ..Additionally, we identified 425 genes, which included YEF3, RNR1, and RNR3, with a unique codon usage pattern linked to Trm9...
  98. pmc Effect of codon optimization and subcellular targeting on Toxoplasma gondii antigen SAG1 expression in tobacco leaves to use in subcutaneous and oral immunization in mice
    Melina Laguía-Becher
    IIB INTECH, Camino de Circunvalación Km 6, Provincia de Buenos Aires, Argentina
    BMC Biotechnol 10:52. 2010
    b>Codon optimization and subcellular targeting were studied with the aim to increase the expression levels of the SAG178-322 antigen of Toxoplasma gondii in tobacco leaves...
  99. doi Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks
    Simon Y W Ho
    Research School of Biology, Centre for Macroevolution and Macroecology, Australian National University, Canberra, ACT, 0200, Australia
    Mitochondrial DNA 21:138-46. 2010
    ..However, this is rarely the case for differences in the lineage-specific patterns of rate variation among sites...
  100. pmc Transfer of embB codon 306 mutations into clinical Mycobacterium tuberculosis strains alters susceptibility to ethambutol, isoniazid, and rifampin
    Hassan Safi
    Division of Infectious Disease and Center for Emerging Pathogens, Department of Medicine, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, USA
    Antimicrob Agents Chemother 52:2027-34. 2008
    ..a major mechanism of ethambutol (EMB) resistance in clinical studies of Mycobacterium tuberculosis, mutations in codon 306 of the embB gene (embB306) have also been detected in EMB-susceptible clinical isolates...
  101. ncbi Positive selection at sites of multiple amino acid replacements since rat-mouse divergence
    Georgii A Bazykin
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
    Nature 429:558-62. 2004
    ..This pattern cannot be explained by correlated mutation or episodes of relaxed negative selection, but instead indicates that positive selection acts at many sites of rapid, successive amino acid replacement...

Research Grants104 found, 100 shown here

  1. Role of troponin T isoforms in nemaline myopathy
    Jian Ping Jin; Fiscal Year: 2009
    ..In an alternative approach, suppression of the ANM nonsense stop codon will also be explored using emerging reagents...
  2. Role of troponin T isoforms in nemaline myopathy
    Jian Ping Jin; Fiscal Year: 2010
    ..In an alternative approach, suppression of the ANM nonsense stop codon will also be explored using emerging reagents...
  3. BIOCHEMISTRY OF PRE-MRNA SPLICING
    ADRIAN KRAINER; Fiscal Year: 2009
    ..NMD degrades mature mRNAs with a premature termination codon (PTC)...
  4. BIOCHEMISTRY OF PRE-MRNA SPLICING
    ADRIAN KRAINER; Fiscal Year: 2007
    ..NMD degrades mature mRNAs with a premature termination codon (PTC)...
  5. A SARS-CoV Spike Protein Vaccine
    B Sim; Fiscal Year: 2005
    ..Our experience with expression of proteins in Pichia pastoris indicates that altering codon usage based on our proprietary information leads to enhanced expression of recombinant proteins and in vivo ..
  6. APOLIPOPROTEIN B48 AND LIPOPROTEIN METABOLISM
    Lawrence Chan; Fiscal Year: 2004
    ..ApoB mRNA editing is a process whereby the cytidine (C) in a CAA codon in apoB-100 mRNA, encoding Gln-2153, is deaminated to a uridine (U), producing an in-frame UAA stop codon in apoB-..
  7. Resolution of Epithelial Cell Hyperplasia
    Yohannes Tesfaigzi; Fiscal Year: 2009
    ..A polymorphism in the p53 gene at codon 72 (Arg/Pro) differentially affects Bcl-2 expression; p53Pro increases more efficiently than p53Arg, the pro-..
  8. Resolution of Epithelial Cell Hyperplasia
    Yohannes Tesfaigzi; Fiscal Year: 2010
    ..A polymorphism in the p53 gene at codon 72 (Arg/Pro) differentially affects Bcl-2 expression;p53Pro increases more efficiently than p53Arg, the pro-..
  9. Ribosomal scanning and initiation codon selection
    Tatyana V Pestova; Fiscal Year: 2010
    ..It occurs in two stages: formation of a 48S initiation complex at the initiation codon of mRNA and its joining with a 60S ribosomal subunit...
  10. STRUCTURE OF VIRAL RNA IN RIBOSOMAL FRAMESHIFTING
    Alexander Rich; Fiscal Year: 2004
    ..The - 1 shift in reading frames causes stop codon readthrough, and results in production of a single fusion protein...
  11. RNA Modifications as Biomarkers of Environmental Stress and Inflammation
    Thomas J Begley; Fiscal Year: 2010
    ..have recently demonstrated that enzyme-catalyzed methylation of a modified uridine (mcm5U) in tRNA plays a role in codon- specific translational control after DNA damage, and we have preliminary data demonstrating that the levels of ..
  12. FUNCTIONAL CHARACTERIZATION OF AGT GENETIC POLYMORPHISM
    Jun yan Hong; Fiscal Year: 2001
    ..One missense alteration occurs at the codon 143 (isoleucine to valine)...
  13. Ribosomal scanning and initiation codon selection
    Tatyana V Pestova; Fiscal Year: 2011
    ..It occurs in two stages: formation of a 48S initiation complex at the initiation codon of mRNA and its joining with a 60S ribosomal subunit...
  14. CONTROL OF ARG-2 GENE EXPRESSION IN NEUROSPORA
    MATTHEW SACHS; Fiscal Year: 2007
    ..These data support a regulatory model in which ribosome stalling at the uORF termination codon in response to Arg destabilizes CPA1 mRNA by increasing the extent of nonsense codon recognition by NMD...
  15. CONTROL OF ARG-2 GENE EXPRESSION IN NEUROSPORA
    MATTHEW SACHS; Fiscal Year: 2006
    ..This data supports a regulatory model in which ribosome stalling at the uORF termination codon in response to Arg destabilizes CPA1 mRNA by increasing the extent of nonsense codon recognition by NMD...
  16. CONTROL OF ARG-2 GENE EXPRESSION IN NEUROSPORA
    MATTHEW SACHS; Fiscal Year: 2009
    ..These data support a regulatory model in which ribosome stalling at the uORF termination codon in response to Arg destabilizes CPA1 mRNA by increasing the extent of nonsense codon recognition by NMD...
  17. CONTROL OF ARG-2 GENE EXPRESSION IN NEUROSPORA
    MATTHEW SACHS; Fiscal Year: 2007
    ..These data support a regulatory model in which ribosome stalling at the uORF termination codon in response to Arg destabilizes CPA1 mRNA by increasing the extent of nonsense codon recognition by NMD...
  18. ENTEROHEPATIC LIPID FLUX AND APOPROTEIN BIOSYNTHESIS.
    NICHOLAS DAVIDSON; Fiscal Year: 2007
    ..RNA modification that results in C to U deaminaton of a single cytidine base and creates a translational stop codon. This process occurs in the mammalian small intestine and is mediated by a multicomponent enzyme complex ..
  19. Gene Expression Levels Across Diverse Genomes
    Samuel Karlin; Fiscal Year: 2006
    ..The main focus of our research is to evaluate gene expression levels based on codon usage...
  20. BACTERIAL LIVE VECTOR-BASED VACCINE AGAINST MALARIA
    Myron Levine; Fiscal Year: 2004
    ..the priming potential of Shigella live vectors harboring DNA vaccines, we propose to use DNA vaccines in which codon usage has been optimized for expression by mammalian (human) cells...
  21. STRUCTURE AND FUNCTION OF TRANSFER RIBONUCLEIC ACIDS
    Uttam L RajBhandary; Fiscal Year: 2010
    ..In eubacteria, ochre suppressor tRNAs, which read the UAA stop codon also read the amber stop codon UAG. In eukaryotes, however, ochre suppressors are specific for UAA...
  22. EDITING OF APOLIPOPROTEIN-B MRNA
    DONNA DRISCOLL; Fiscal Year: 2004
    ..The editing of apolipoprotein-B (apo-B) mRNA involves the deamination of C6666 to U which converts a glutamine codon (CAA) to an in-frame stop codon (UAA)...
  23. tRNA editing by deamination: Balancing affinity and specificity
    Juan D Alfonzo; Fiscal Year: 2010
    ..amino acids and, with the exception of methionine and tryptophan, each amino acid is encoded by more than one codon. This discrepancy between codon and amino acid numbers was first explained by Crick's wobble hypothesis, ..
  24. tRNA editing by deamination: Balancing affinity and specificity
    Juan Alfonzo; Fiscal Year: 2009
    ..amino acids and, with the exception of methionine and tryptophan, each amino acid is encoded by more than one codon. This discrepancy between codon and amino acid numbers was first explained by Crick's wobble hypothesis, ..
  25. Listeria Immunotherapy for Pancreatic and Ovarian Cancer
    Thomas Dubensky; Fiscal Year: 2006
    ..is to continue development of our Listeria monocytogenes (Lm)-based immunotherapy to target Mesothelin and codon 12-mutated activated K-ras antigens in patients with pancreatic and ovarian cancers...
  26. Regulation of the Na/K Pump by RNA Editing
    Joshua J C Rosenthal; Fiscal Year: 2010
    ..A central premise to our approach is that naturally occurring codon changes, caused by RNA editing, can lead us to functionally important regions of the Na/K pump...
  27. 'RECODING: DYNAMIC REPROGRAMMING OF GENETIC READOUT'
    John Atkins; Fiscal Year: 2004
    ..cassettes with different defects in the gene 60 bypassing signals: poorly functioning matched take-off and landing codon pairs, extended coding gap, extended stem loop and related studies with mutants of nascent peptide affecting frame ..
  28. The Biological and Chemical Function of Selenium in Enzymes
    ROBERT J contact HONDAL; Fiscal Year: 2010
    ..of selenocysteine (Sec) into a protein is much more complicated than the other 20 amino acids because a UGA stop codon must be recoded as a sense codon for Sec and this process requires complex cellular machinery...
  29. Translational Research in the Dystrophinopathies
    Kevin Flanigan; Fiscal Year: 2002
    ..The remainder consist of point mutations (primarily premature stop codon mutations), small deletions resulting in shift of the reading frame, and (in less than 5%) duplications...
  30. Translation Regulation in Giardia lamblia
    CHING CHUNG WANG; Fiscal Year: 2010
    ..analysis of an internal ribosomal entry site (IRES) in the Giardia-virus transcript, we identified the AUG start codon at the center of an unstructured 31 nucleotide stretch between two stem-loops, suggesting a direct recruitment of ..
  31. The Role of Osteoactivin in Osteoblast Development and Function
    Fayez F Safadi; Fiscal Year: 2010
    ..in mice with the null allele for OA and in mice with a natural mutation in the OA gene caused a premature stop codon that results in the generation of a truncated OA protein...
  32. MOLECULAR ANALYSIS OF SITE-SPECIFIC TRANSLATIONAL FRAMES
    Philip Farabaugh; Fiscal Year: 1993
    ..This sequence includes no obvious secondary structure, but does include an unusual codon, AGG. This codon is recognized by a rare tRNA encoded by a single genetic locus...
  33. APOLIPOPROTEIN B48 AND LIPOPROTEIN METABOLISM
    Lawrence Chan; Fiscal Year: 1999
    ..The apoB-48 mRNA is the product of RNA editing, whereby the first nucleotide (C) for the codon CAA, encoding Gln-2153, in apoB-100 mRNA is converted to U producing an in-frame stop codon...
  34. Ribosomal scanning and initiation codon selection
    Tatyana Pestova; Fiscal Year: 2007
    The ribosomal scanning model postulates a three-step mechanism for initiation codon selection...