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. 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
  2. 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
  3. 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
  4. pmc Codon-substitution models for heterogeneous selection pressure at amino acid sites
    Z Yang
    Department of Biology, University College London, London NW1 2HE, United Kingdom
    Genetics 155:431-49. 2000
  5. 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
  6. pmc 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
  7. 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
  8. 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
  9. 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
  10. pmc Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    R Nielsen
    Department of Integrative Biology, University of California, Berkeley 94720 3140, USA
    Genetics 148:929-36. 1998

Detail Information

Publications368 found, 100 shown here

  1. 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...
  2. 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...
  3. 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...
  4. pmc Codon-substitution models for heterogeneous selection pressure at amino acid sites
    Z Yang
    Department of Biology, University College London, London NW1 2HE, United Kingdom
    Genetics 155:431-49. 2000
    ..However, we encountered difficulties in estimating the precise distribution of omega among sites from real data sets...
  5. 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...
  6. pmc 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...
  7. 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...
  8. 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 ..
  9. 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...
  10. pmc Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    R Nielsen
    Department of Integrative Biology, University of California, Berkeley 94720 3140, USA
    Genetics 148:929-36. 1998
    Several codon-based models for the evolution of protein-coding DNA sequences are developed that account for varying selection intensity among amino acid sites...
  11. 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...
  12. ncbi 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...
  13. pmc Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
    Wendy S W Wong
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
    Genetics 168:1041-51. 2004
    ..The parsimony method has a very low rate of false positives but very little power for detecting positive selection or identifying positively selected sites...
  14. 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 ..
  15. 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...
  16. ncbi 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...
  17. 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...
  18. 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 ..
  19. 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 ..
  20. 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...
  21. ncbi Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  22. 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...
  23. ncbi 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...
  24. ncbi 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 ..
  25. pmc Exonic transcription factor binding directs codon choice and affects protein evolution
    Andrew B Stergachis
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Science 342:1367-72. 2013
    ..are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons...
  26. ncbi Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study
    Omar Rota-Stabelli
    Department of Biology, The National University of Ireland, Maynooth, Co Kildare, Ireland
    Syst Biol 62:121-33. 2013
    ..between the nucleotide-based and the amino acids-based trees is caused by substitutions within synonymous codon families (especially those of serine-TCN and AGY)...
  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. 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
    ....
  29. ncbi A role for tRNA modifications in genome structure and codon usage
    Eva Maria Novoa
    Institute for Research in Biomedicine, c Baldiri Reixac 15 21, 08028 Barcelona, Catalonia, Spain
    Cell 149:202-13. 2012
    ..contributes to the efficiency of the translational apparatus, but the principles shaping tRNA gene copy number and codon composition are poorly understood...
  30. pmc Wobble base-pairing slows in vivo translation elongation in metazoans
    Michael Stadler
    Department of Genetics, Stanford University, Stanford, California 94305 5324, USA
    RNA 17:2063-73. 2011
    ..ribosome profiling, we obtained transcriptome-wide profiles of in vivo ribosome occupancy as a function of codon identity in Caenorhabditis elegans and human cells...
  31. 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...
  32. 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...
  33. ncbi 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...
  34. ncbi Transient ribosomal attenuation coordinates protein synthesis and co-translational folding
    Gong Zhang
    Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Nat Struct Mol Biol 16:274-80. 2009
    ..We propose that local discontinuous translation temporally separates the translation of segments of the peptide chain and actively coordinates their co-translational folding...
  35. 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...
  36. 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...
  37. pmc Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding
    Sebastian Pechmann
    Department of Biology, Stanford University, Stanford, California, USA
    Nat Struct Mol Biol 20:237-43. 2013
    The choice of codons can influence local translation kinetics during protein synthesis. Whether codon preference is linked to cotranslational regulation of polypeptide folding remains unclear...
  38. pmc CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models
    Manuel Gil
    Department of Computer Science, Swiss Federal Institute of Technology, Zurich, Switzerland
    Mol Biol Evol 30:1270-80. 2013
    Markov models of codon substitution naturally incorporate the structure of the genetic code and the selection intensity at the protein level, providing a more realistic representation of protein-coding sequences compared with nucleotide ..
  39. pmc KRAS codon 61, 146 and BRAF mutations predict resistance to cetuximab plus irinotecan in KRAS codon 12 and 13 wild-type metastatic colorectal cancer
    F Loupakis
    Unit of Medical Oncology 2, Azienda Ospedaliero Universitaria Pisana, Istituto Toscano Tumori and Department of Oncology, Transplantes and New Technologies in Medicine, University of Pisa, Via Roma 67 56126 Pisa, Italy
    Br J Cancer 101:715-21. 2009
    ..KRAS codons 12 and 13 mutations predict resistance to anti-EGFR monoclonal antibodies (moAbs) in metastatic colorectal cancer. Also, BRAF V600E mutation has been associated with resistance. Additional KRAS mutations are described in CRC...
  40. 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...
  41. ncbi Recognition of cognate transfer RNA by the 30S ribosomal subunit
    J M Ogle
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 292:897-902. 2001
    ..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...
  42. pmc Non-optimal codon usage affects expression, structure and function of clock protein FRQ
    Mian Zhou
    Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
    Nature 495:111-5. 2013
    b>Codon-usage bias has been observed in almost all genomes and is thought to result from selection for efficient and accurate translation of highly expressed genes...
  43. ncbi 172G>T variant in the 5' untranslated region of DNA repair gene RAD51 reduces risk of squamous cell carcinoma of the head and neck and interacts with a P53 codon 72 variant
    Jiachun Lu
    Department of Epidemiology, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Carcinogenesis 28:988-94. 2007
    ..The finding that the functional RAD51 172G>T SNP, particularly in the presence of the P53 Arg72Arg genotype, may be a marker of susceptibility to SCCHN needs to be validated by larger studies of different ethnic populations...
  44. ncbi Structure of the 70S ribosome complexed with mRNA and tRNA
    Maria Selmer
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 313:1935-42. 2006
    ..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...
  45. 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...
  46. pmc Reduction of the rate of poliovirus protein synthesis through large-scale codon deoptimization causes attenuation of viral virulence by lowering specific infectivity
    Steffen Mueller
    Department of Molecular Genetics and Microbiology, Life Sciences Building, Stony Brook University, Stony Brook, NY 11794 5222, USA
    J Virol 80:9687-96. 2006
    ..PV variants containing synthetic replacements of the capsid coding sequences either by deoptimizing synonymous codon usage (PV-AB) or by maximizing synonymous codon position changes of the existing wild-type (wt) poliovirus codons (..
  47. pmc High resistance of Plasmodium falciparum to sulphadoxine/pyrimethamine in northern Tanzania and the emergence of dhps resistance mutation at Codon 581
    Samwel Gesase
    National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
    PLoS ONE 4:e4569. 2009
    ..This study compared the in vivo efficacy of SP in symptomatic 6-59 month children with uncomplicated malaria and in asymptomatic 2-10 month old infants...
  48. pmc Cooperation between translating ribosomes and RNA polymerase in transcription elongation
    Sergey Proshkin
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Science 328:504-8. 2010
    ..Such a cooperative mechanism ensures that the transcriptional yield is always adjusted to translational needs at different genes and under various growth conditions...
  49. 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...
  50. 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 ..
  51. 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-..
  52. ncbi Speeding with control: codon usage, tRNAs, and ribosomes
    Eva Maria Novoa
    Institute for Research in Biomedicine IRB, c Baldiri Reixac 15 21 08028, Barcelona, Catalonia, Spain
    Trends Genet 28:574-81. 2012
    b>Codon usage and tRNA abundance are critical parameters for gene synthesis...
  53. pmc Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels
    Milana Frenkel-Morgenstern
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 8:572. 2012
    The cell cycle is a temporal program that regulates DNA synthesis and cell division. When we compared the codon usage of cell cycle-regulated genes with that of other genes, we discovered that there is a significant preference for non-..
  54. ncbi Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation
    A A Komar
    Centre de Genetique Moleculaire, CNRS, Gif sur Yvette, France
    FEBS Lett 462:387-91. 1999
    ..coli S30 extract system was shown to possess 20% lower specific activity. The data suggest that kinetics of protein translation can affect the in vivo protein-folding pathway, leading to increased levels of protein misfolding...
  55. ncbi Accounting for background nucleotide composition when measuring codon usage bias
    John A Novembre
    Mol Biol Evol 19:1390-4. 2002
  56. 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 ..
  57. 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...
  58. ncbi The extent of codon usage bias in human RNA viruses and its evolutionary origin
    Gareth M Jenkins
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Virus Res 92:1-7. 2003
    Revealing the determinants of codon usage bias is central to the understanding of factors governing viral evolution...
  59. ncbi 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.
  60. ncbi A pause for thought along the co-translational folding pathway
    Anton A Komar
    Department of Biological, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA
    Trends Biochem Sci 34:16-24. 2009
    ....
  61. pmc OPTIMIZER: a web server for optimizing the codon usage of DNA sequences
    Pere Puigbò
    Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Faculty of Chemistry, Rovira i Virgili University URV, Tarragona, Spain
    Nucleic Acids Res 35:W126-31. 2007
    OPTIMIZER is an on-line application that optimizes the codon usage of a gene to increase its expression level...
  62. 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...
  63. ncbi 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
    ....
  64. 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 ..
  65. 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...
  66. 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...
  67. pmc Mutation bias is the driving force of codon usage in the Gallus gallus genome
    Yousheng Rao
    Department of Biological Technology, Jiangxi Educational Institute, Nanchang, China
    DNA Res 18:499-512. 2011
    ..Up to now, a systematic examination of the codon usage for the chicken genome has not been performed...
  68. pmc The complete mitochondrial genome of the damsel bug Alloeorhynchus bakeri (Hemiptera: Nabidae)
    Hu Li
    Department of Entomology, China Agricultural University, Beijing 100193, China
    Int J Biol Sci 8:93-107. 2012
    ..Nucleotide composition and codon usage are similar to other known heteropteran mitochondrial genomes...
  69. 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...
  70. pmc Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation
    Luca Ciandrini
    SUPA, Institute for Complex Systems and Mathematical Biology, King s College, University of Aberdeen, Aberdeen, United Kingdom
    PLoS Comput Biol 9:e1002866. 2013
    ..This analysis reveals that codon arrangement, rather than simply codon bias, has a key role in determining translational efficiency...
  71. pmc Uncertainty in the tail of the variant Creutzfeldt-Jakob disease epidemic in the UK
    Tini Garske
    Department of Infectious Disease Epidemiology, Medical Research Council Centre of Outbreak Analysis and Modelling, Imperial College London, London, United Kingdom
    PLoS ONE 5:e15626. 2010
    ..Regardless of the numbers of future cases, even in the absence of any further control measures, we do not find any self-sustaining epidemics...
  72. pmc Decoding system for the AUA codon by tRNAIle with the UAU anticodon in Mycoplasma mobile
    Takaaki Taniguchi
    Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 8656, Japan
    Nucleic Acids Res 41:2621-31. 2013
    ..Mycoplasma mobile tRNA(Ile2) cannot distinguish between AUA and AUG codon on E. coli ribosome. However, on M. mobile ribosome, M...
  73. pmc GC3 biology in corn, rice, sorghum and other grasses
    Tatiana V Tatarinova
    Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
    BMC Genomics 11:308. 2010
    The third, or wobble, position in a codon provides a high degree of possible degeneracy and is an elegant fault-tolerance mechanism...
  74. ncbi Fatal familial insomnia, a prion disease with a mutation at codon 178 of the prion protein gene
    R Medori
    Division of Neuropathology, Case Western Reserve University, Cleveland, OH 44106
    N Engl J Med 326:444-9. 1992
    ..Five other family members who died of this disease, which we termed "fatal familial insomnia," had broader neuropathologic changes suggesting that fatal familial insomnia could be a prion disease...
  75. 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...
  76. ncbi 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 ..
  77. 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...
  78. 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...
  79. ncbi 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...
  80. 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...
  81. 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.
  82. 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...
  83. 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...
  84. 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...
  85. ncbi 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 ..
  86. 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...
  87. 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 ..
  88. ncbi 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...
  89. ncbi 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.
  90. 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...
  91. 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...
  92. 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...
  93. ncbi 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...
  94. 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
    ....
  95. ncbi 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...
  96. ncbi 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...
  97. 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...
  98. 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...
  99. 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...
  100. 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 ..
  101. 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.

Research Grants78

  1. Regulation of ER stress-induced cell death
    Randal J Kaufman; Fiscal Year: 2013
    ..The impact of eIF2a phosphorylation and CHOP expression on mRNA translational efficiency and AUG initiation codon selection will be measured using a new technique of ribosome profiling...
  2. BIOCHEMISTRY OF PRE-MRNA SPLICING
    Adrian R Krainer; Fiscal Year: 2010
    ..NMD degrades mature mRNAs with a premature termination codon (PTC)...
  3. Monitoring cellular redox signaling and oxidant stress in vivo
    Paul T Schumacker; Fiscal Year: 2010
    ..expression of the RoGFP genes in primary cells cultured from these mice, using Cre recombinase to delete the stop codon. We will confirm correct targeting of the expressed protein, and confirm its function in response to redox stress...
  4. MR Monitoring of PTC124 Treatment in DMD
    KRISTA H VANDENBORNE; Fiscal Year: 2010
    ..PTC124 phase 2a extension study, which involves the long-term administration (96 weeks) of PTC124, a novel stop codon suppression drug...
  5. Novel Collagen II Alternative Transcripts and Mouse Skeletal Development
    Audrey McAlinden; Fiscal Year: 2010
    ..first 34 nucleotides of exon 2 by use of an alternative splice site in exon 2 resulting in a premature termination codon. IID mRNA contains an extra three nucleotides at the end of exon 2 that encodes either tryptophan (in human) or ..
  6. Role of troponin T isoforms in nemaline myopathy
    Jian Ping Jin; Fiscal Year: 2012
    ..In an alternative approach, suppression of the ANM nonsense stop codon will also be explored using emerging reagents...
  7. Role of formyl peptide receptor variants in mucosal innate immune defense
    HEINI MARITA MIETTINEN; Fiscal Year: 2010
    ..The FPR haplotypes to be tested have been selected on the basis of results from SNP-based codon bias and codon pair bias calculations that suggest that certain haplotypes may be either under- or overrepresented...
  8. Host Defense Mechanisms in Polyaromatic Hydrogen Carcinogenesis
    Craig A Elmets; Fiscal Year: 2013
    ..the polyaromatic hydrocarbon 7,12- dimethylbenz(a)anthracene (DMBA) produces a specific point mutation in 61st codon of the H- ras oncogene and that this mutation is necessary for tumors to develop...
  9. Serotonin, Autism, and investigating cell types for CNS disorders.
    Joseph D Dougherty; Fiscal Year: 2010
    ..Preliminary sequencing studies in the first gene have identified a premature stop codon in patient DNA...
  10. Lipid peroxidation product induced DNA damage in the p53 gene and liver cancer
    ERIC MOON SHONG M TANG; Fiscal Year: 2010
    ..p53 gene fragments and genomic DNA we have found that 4-HNE preferentially binds to -GAGGC/A- sequences, including codon 249 of the p53 gene, the sole mutational hotspot in liver cancer...
  11. Transcriptional Regulation by a Deacetylase, CobB, in a Periodontopathogen
    DAVID J KOLODRUBETZ; Fiscal Year: 2013
    ..set of site-specific mutants, which mimic an acetylated lysine or a deacetylated lysine, in the acetylated- lysine codon for each of the genes encoding any of the acetylated transcription factors found...
  12. IRES-mediated translation initiation on viral mRNAs
    CHRISTOPHER ULRICH TRISTRAM HELLEN; Fiscal Year: 2013
    ..to eIF4G/eIF4A: we will investigate how these factors promote recruitment of 43S complexes to the initiation codon, how ITAFs induce conformational changes in these IRESs and why only a subset of type 2 IRESs require their ..
  13. HCV Strain Variation and HCC
    Andrea D Branch; Fiscal Year: 2012
    ..e., the quasispecies) has a codon 70 mutation...
  14. Understanding the Role of COMT Variants in Sensorimotor Gating
    XIANJIN ZHOU; Fiscal Year: 2010
    A single nucleotide polymorphism (SNP), causing a missense mutation of codon 158 Valine to Methionine in the coding region (termed val158met), exists in the human catechol-o-methyltransferase (COMT) gene...
  15. Oral immune modulatory therapy using antigens bioencapsulated in plant cells
    Roland W Herzog; Fiscal Year: 2013
    ..For example, patients with hemophilia B due to deletion or early stop codon in the factor IX (F.IX) gene are at increased risk for inhibitor formation. Not only are most F...
  16. The mechanism of mRNA recruitment to the human ribosome.
    Christopher S Fraser; Fiscal Year: 2013
    ..III. Determine how human ribosomes scan along the 5" untranslated region (5"UTR) to locate the AUG codon. We will establish a fluorescent kinetic RNA unwinding assay to determine how initiation factors contribute to the ..
  17. Regulation of an Iron Import Facilitator by Transcriptional Interference
    CAMILLE REYES NERY; Fiscal Year: 2010
    ..3kb upstream of the FIT3 translation initiation codon. Clearly, the regulation of FIT3 involves mechanisms other than induction by the transcriptional activators Aft1/..
  18. The Roles of Trm9 and tRNA Methylation in the DNA Damage Response
    Thomas J Begley; Fiscal Year: 2010
    ..We have computationally identified a novel environmental stress code (ESC) that (1) is a gene-specific codon usage pattern and (2) is predicted to help regulate cellular responses to DNA alkylation damage...
  19. Phase 2a Study of Ataluren in Hemophilia A and B (IND 104,321)
    JAY A BARTH; Fiscal Year: 2010
    ..is a novel, oral drug that promotes ribosomal read through of mRNA containing a nonsense mutation (premature stop codon)...
  20. Novel Adeno-Associated Viral Therapy for Wet Age-Related Macular Degeneration
    James M Wilson; Fiscal Year: 2012
    ..Expression of ranibizumab will be optimized by replacement of the leader sequence and tailoring codon usage for expression in human tissues...
  21. Role of Intronic Variants Affecting Splicing in Juvenile Myoclonic Epilepsy
    Debra J Wolgemuth; Fiscal Year: 2010
    ..intron 2 of BRD2 contains a highly conserved, alternatively spliced exon, which introduces a premature termination codon and we have identified polymorphisms in the lengths of CA-repeats in intron 2 that are associated with JME...
  22. RNA Modifications as Biomarkers of Environmental Stress and Inflammation
    Thomas J Begley; Fiscal Year: 2013
    ..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 ..
  23. Single Molecule Dynamics of mRNA Translation
    Yale E Goldman; Fiscal Year: 2013
    ..We have 3 Specific Aims that focus on determining how the rhythm of protein synthesis is modulated by: 1. Codon usage and codon pair usage;2...
  24. Functional Analysis of p53 Polymorphic Variants
    Maureen E Murphy; Fiscal Year: 2013
    ..There are three polymorphic variants of p53. A common polymorphism exists at codon 72, encoding either arginine (R72) or proline (P72)...
  25. A fully integrated assay and platform for detecting Clostridium difficile
    BRUCE D IRVINE; Fiscal Year: 2010
    ..difficile, BI/NAP1, has a single point mutation in this gene that results in a premature stop codon. The lack of a functional TcdC protein in these strains results in an over expression of the TcdA and TcdB toxins...
  26. TNIP1 risk haplotypes and immune endophenotypes
    Peter K Gregersen; Fiscal Year: 2013
    ..91;p =3.2x10-10) that implicates an amino acid change of Pro to Ala at codon 151 as a possible causative variant...
  27. Aminoglycoside microbicides restore natural expression of anti-HIV-1 retrocyclins
    ALEXANDER MICHAEL COLE; Fiscal Year: 2013
    ..Multiple human ?-defensin genes exist, but they harbor a premature termination codon that blocks translation...
  28. Aminoglycoside microbicides restore natural expression of anti-HIV-1 retrocyclins
    Alexander M Cole; Fiscal Year: 2010
    ..Multiple human ?-defensin genes exist, but they harbor a premature termination codon that blocks translation...
  29. Diet by Gene Interactions Affecting Calcium and Bone Metabolism
    James C Fleet; Fiscal Year: 2010
    ..SA2: Develop humanized mouse models to test whether the less active "f" allele of the FokI start codon polymorphism in the human (vitamin D receptor) VDR gene make these mice more sensitive to the negative impact of ..
  30. The Biological and Chemical Function of Selenium in Enzymes
    Robert J Hondal; Fiscal Year: 2013
    ..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...
  31. Leber Hereditary Optic Neuropathy: Gene Therapy Trial
    John Guy; Fiscal Year: 2012
    ..Using site directed mutagenesis of the nuclear version of ND4 we replaced the codon for arginine to that for histidine at amino acid 340...
  32. PET Imaging of KRAS2 Activation to Guide EGFR Targeting in Cancer Therapy
    Eric Wickstrom; Fiscal Year: 2013
    ..carry out essential preclinical steps to maximize the sensitivity of imaging multiple mutants of KRAS2 mRNA with a codon 12 redundant chelator-KRAS2 genetic imaging agent in lung cancer xenografts...
  33. MicroRNA-mediated regulation of ATG16L1 expression and autophagy
    John Kwon; Fiscal Year: 2012
    ..While the strongest genetic association results in a threonine to alanine transition at codon 300 (T300A) that may alter function of the resultant protein and initial studies have not yet identified Crohn&..
  34. Modular Chimeric Vaccines tailored for malaria parasites
    Alberto Moreno; Fiscal Year: 2010
    ..The amino acid sequences of these chimeric constructs will be reverse translated, codon optimized and assembled into synthetic genes. The synthetic genes will be cloned, inserted into E...
  35. Identification and Function of nuDMP1 in Odontoblast Differentiation
    Yongbo Lu; Fiscal Year: 2013
    ..We hypothesize that nuDMP1 is translated from alternative downstream in-frame AUG start codon(s) and controls odontoblast differentiation by regulating Dspp expression...
  36. Presenilin 2 and Neuroinflammation
    Suman Jayadev; Fiscal Year: 2013
    ..We have recently described an early onset AD patient who carries a novel PS2 premature termination codon mutation leading to decreased PS2 protein, supporting the hypothesis that loss of PS2 function can contribute to ..
  37. Mechanistic Basis Underlying Protein Repair of CFTR Nonsense Mutations
    STEVEN MARK ROWE; Fiscal Year: 2010
    ..The proposed studies will capitalize on data emerging from an international clinical trial testing the stop codon suppressor PTC124 in CF patients (led by Dr...
  38. Resolution of Epithelial Cell Hyperplasia
    Yohannes Tesfaigzi; Fiscal Year: 2013
    ..A polymorphism in the p53 gene at codon 72 (Arg/Pro) differentially affects Bcl-2 expression;p53Pro increases more efficiently than p53Arg, the pro-..
  39. Mechanism of HigB-mediated ribosome-dependent mRNA degradation
    MARC ANTHONY SCHURECK; Fiscal Year: 2013
    ..evidence strongly suggests that the manner in which HigB recognizes mRNA is novel because there is no strict codon requirement (i.e. recognition of all three bases)...
  40. Epigenetic Changes Link COPD and Lung Cancer
    Yohannes Tesfaigzi; Fiscal Year: 2013
    ..specific genes within this pathway as determinants for gene methylation in sputum and that the proline variant at codon 72 of p53 is protective from mucous cell hyperplasia and decline of pulmonary function in the LSC...
  41. Analysis of metallo-beta-lactamase sequence constraints at high resolution
    Timothy Palzkill; Fiscal Year: 2013
    ..This question will be addressed using a strategy of codon randomization and selection followed by deep sequencing...
  42. Virulence factor identification by comparative transcriptomics in Candida species
    Michael C Lorenz; Fiscal Year: 2013
    ..Overlapping the Candida genus is a group of species referred to as the CTG clade, because they translate the CUG codon non-canonically...
  43. Mechanism of selenoprotein synthesis
    Marla Berry; Fiscal Year: 2009
    ..into proteins as the amino acid, selenocysteine, and is specified by UGA, which typically functions as a stop codon. This occurs via secondary structures in the 3'UTRs of eukaryotic mRNAs, termed SECIS elements, and the ..
  44. Assays for Discovery of Translation Inhibitors
    Gerhard Wagner; Fiscal Year: 2009
    ..involved in assembly of the 80S ribosome-RNA complex enabling interaction of the initiator Met-tRNA with the start codon of the mRNA...
  45. rAAV5-hCNGB3 Gene Therapy for Achromatopsia: Safety and Efficacy in a Dog Model
    Guo jie Ye; Fiscal Year: 2013
    ..coli. To overcome toxicity related to a presumed cryptic promoter, we will also introduce a mutation at codon 340 (from methionine to leucine), and additional silent mutations (i.e...
  46. HSV-1 LAT miRNAs: Neurovirulence, reactivation, mechanism
    Steven L Wechsler; Fiscal Year: 2013
    ..By making use of codon redundancy to not alter the amino acid sequence of an overlapping gene, we changed 21 of the 75 nts in one of the ..
  47. Self-Complementary AAV2 Factor IX for Hemophilia B
    SCOTT WILLIAM JOHN MCPHEE; Fiscal Year: 2010
    ..Using scAAV2 with an optimized FIX codon sequence under a liver-specific promoter (scAAV2-hFIX), we have shown correction of hemophilic mice using 15- to ..
  48. REGULATION OF BACILLUS SUBTILIS TRNA SYNTHETASE GENES
    Tina M Henkin; Fiscal Year: 2012
    ..tRNA recognition requires pairing of the tRNA anticodon with a single codon, the "Specifier Sequence," in the leader RNA, as well as pairing of the acceptor end of the tRNA to an ..
  49. Translational Recoding of UGA as Selenocysteine in Selenoprotein Synthesis
    Donna M Driscoll; Fiscal Year: 2013
    ..of Sec into the growing polypeptide chain requires a translational recoding event in which the UGA stop codon is read as Sec...
  50. EVC2: A novel modulator in tooth development
    Yoshiyuki Mochida; Fiscal Year: 2013
    ..dwarfism/tooth development seen in EVC patients, Evc2 mutant mice were generated by introducing a premature stop codon in exon12, mimicking mutations found in EVC patients and bcd cattle...
  51. Assessment of the Immunogenicity and Protective Efficacy of a Multiagent DNA Vacc
    Connie Schmaljohn; Fiscal Year: 2010
    ..are to: (1) Generate improved DNA vaccine constructs for two species of EBOV and two strains of MARV through codon-optimization of the GP genes of each virus;(2) Compare the immunogenicity of the individual DNA vaccine candidates ..
  52. The Role of Osteoactivin in Osteoblast Development and Function
    Fayez F Safadi; Fiscal Year: 2013
    ..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...
  53. Gene Therapy for Urea Cycle Disorders
    James M Wilson; Fiscal Year: 2013
    ..A Clinical Candidate vector was established: AAVS expressing a codon-optimized cDNA for ornithine transcarbamylase (OTC) from the liver-specific TBG promoter...
  54. The Biology and Biochemistry of ADAR RNA Editing Enzymes
    Brenda L Bass; Fiscal Year: 2013
    ..b>Codon editing is found in many neuronally important mRNAs, and aberrant levels of editing have been linked to ..
  55. STRUCTURE AND FUNCTION OF TRANSFER RIBONUCLEIC ACIDS
    Uttam L RajBhandary; Fiscal Year: 2013
    ..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...
  56. Preclinical Assessment of a Multi-Head Electroporation Device for Delivery of Bio
    Connie Schmaljohn; Fiscal Year: 2013
    ..We showed that a codon optimized DNA vaccine for LASV delivered by intradermal electroporation (ID-EP) is completely protective against ..
  57. Longitudinal Imaging of Frontal Cortex Afferents in a Mouse Model of Anxiety
    LINDA E WILBRECHT; Fiscal Year: 2013
    ..20-30% of Caucasians carry a polymorphism in the BDNF gene, where codon 66 is altered from a valine to methionine (Shimizu et al...
  58. KINETIC DISSECTION OF EUKARYOTIC TRANSLATION INITIATION
    Rachel Green; Fiscal Year: 2013
    ..The first aim focuses on the mechanism through which the start codon in an mRNA is recognized by the ribosomal pre-initiation complex...
  59. Rational Design of Live Attenuated Influenza A Vaccine Candidates
    Eckard Wimmer; Fiscal Year: 2013
    ..The custom designed attenuation used in the SAVE technology operates through genome-scale changes in codon pair bias (Mueller et al., 2010. Nature Biotechnology 28:723-727)...
  60. Evaluating the efficiency and specificity of stop codon suppression therapy
    Michael T Howard; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Stop codon suppression therapy is a treatment strategy based on the ability of ribosome binding pharmaceutical agents to reduce the fidelity of translation termination at premature stop codon ..
  61. Modified Bases in tRNA-Mediated Antitermination
    Edward P Nikonowicz; Fiscal Year: 2011
    ..In the mRNA of these genes, a leader region upstream from the translation start site binds tRNA in a codon specific fashion...
  62. NMR STUDIES OF RETROVIRAL NUCLEIC ACID BINDING PROTEINS
    MICHAEL FINLEY SUMMERS; Fiscal Year: 2013
    ..by a novel allosteric "nucleotide displacement" RNA switch mechanism, in which residues near the gag start codon induce a global rearrangement that simultaneously exposes a dimer-promoting stem loop (DIS) and high affinity NC ..
  63. 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 ..
  64. 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-..
  65. HETEROGENEITY OF ESTROGEN RECEPTOR STRUCTURE AND ACTION
    Beth Schachter; Fiscal Year: 1993
    ..Sequence analysis revealed two point mutations; an Ala-to-Val change in codon 86 and a silent base change in codon 87...
  66. TEST OF NEUTRAL MOLECULAR EVOLUTION
    Martin Kreitman; Fiscal Year: 1999
    ..melanogaster is smaller than that of D. simulans, because there is less codon bias in the former than the latter...
  67. 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...
  68. FUNCTIONAL CHARACTERIZATION OF AGT GENETIC POLYMORPHISM
    Jun yan Hong; Fiscal Year: 2001
    ..One missense alteration occurs at the codon 143 (isoleucine to valine)...
  69. 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...
  70. 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...
  71. ENTEROHEPATIC LIPID FLUX AND APOPROTEIN BIOSYNTHESIS.
    NICHOLAS DAVIDSON; Fiscal Year: 2009
    ..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 ..
  72. 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...
  73. NONSENSE RNA SURVEILLANCE IN HEALTH AND DISEASE
    Harry Dietz; Fiscal Year: 2000
    ..from eubacteria to eukaryotes have mechanisms for degrading transcripts that contain a premature termination codon. The process of nonsense-mediated RNA decay (NMRD) has been best studied in the yeast S...
  74. 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)...
  75. 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...
  76. '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 ..
  77. STRUCTURE AND FUNCTION OF TRANSFER RIBONUCLEIC ACIDS
    UTTAM RAJBHANDARY; Fiscal Year: 2009
    ..Another question being addressed is (1) whether the AUG initiation codon is an absolute requirement for translation of leaderless mRNAs in E...
  78. MECHANISM OF APOLIPOPROTEIN B-48 BIOGENESIS
    Lawrence Chan; Fiscal Year: 1993
    ..The protein was shown to be the product of an intestinal mRNA that has an inframe stop codon UAA resulting from a C--->U change in the codon CAA encoding Gln-2153 in apoB-100 mRNA...