base composition

Summary

Summary: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.

Top Publications

  1. pmc Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    Juliane C Dohm
    Max Planck Institute for Molecular Genetics, Ihnestr 63 73, 14195 Berlin, Germany
    Nucleic Acids Res 36:e105. 2008
  2. ncbi Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
  3. pmc Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
    Daniel Aird
    Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Genome Biol 12:R18. 2011
  4. ncbi The complete genome sequence of Escherichia coli K-12
    F R Blattner
    Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
    Science 277:1453-62. 1997
  5. ncbi Biased gene conversion and the evolution of mammalian genomic landscapes
    Laurent Duret
    Universite de Lyon 1, CNRS, UMR5558, Laboratoire de Biometrie et Biologie Evolutive, F 69622, Villeurbanne, France
    Annu Rev Genomics Hum Genet 10:285-311. 2009
  6. ncbi CpG islands in vertebrate genomes
    M Gardiner-Garden
    Kanematsu Laboratories, Royal Prince Alfred Hospital, Camperdown N S W, Australia
    J Mol Biol 196:261-82. 1987
  7. pmc Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
    Iwanka Kozarewa
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Methods 6:291-5. 2009
  8. 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
  9. pmc G+C content dominates intrinsic nucleosome occupancy
    Desiree Tillo
    Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
    BMC Bioinformatics 10:442. 2009
  10. ncbi Community structure and metabolism through reconstruction of microbial genomes from the environment
    Gene W Tyson
    Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA
    Nature 428:37-43. 2004

Research Grants

  1. Ibis T-6,000 Biosensor System
    CYNTHIA SEARS; Fiscal Year: 2010
  2. Klotho regulation and aging
    Gwendalyn D King; Fiscal Year: 2010
  3. Klotho regulation and aging
    GWENDALYN DIANN KING; Fiscal Year: 2013
  4. FMR 1-SLS: Improving Fragile X diagnosis using amplification-free single locus ta
    STEPHEN WHITFIELD TURNER; Fiscal Year: 2013
  5. The Rate and Molecular Spectrum of Spontaneous Mutations
    Michael Lynch; Fiscal Year: 2009
  6. Gene Prediction by Markov Models and Complementary Methods
    Mark Borodovsky; Fiscal Year: 2012
  7. Forward genetic screens for identifying antimalarial resistance genes
    Manoj T Duraisingh; Fiscal Year: 2010
  8. Statistical Analysis of Epigenomics Data
    Kimberly D Siegmund; Fiscal Year: 2013
  9. COOPERATIVE INTERACTIONS IN DNA REPAIR
    Michael G Fried; Fiscal Year: 2010
  10. CODING & NONCODING REGIONS IN DNA SEQUENCES
    THOMAS JUKES; Fiscal Year: 1991

Detail Information

Publications369 found, 100 shown here

  1. pmc Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    Juliane C Dohm
    Max Planck Institute for Molecular Genetics, Ihnestr 63 73, 14195 Berlin, Germany
    Nucleic Acids Res 36:e105. 2008
    ..Such biases have implications on the use and interpretation of Solexa data, for de novo sequencing, re-sequencing, the identification of single nucleotide polymorphisms and DNA methylation sites, as well as for transcriptome analysis...
  2. ncbi Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  3. pmc Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
    Daniel Aird
    Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Genome Biol 12:R18. 2011
    ..Our improved protocol significantly reduces amplification bias and minimizes the previously severe effects of PCR instrument and temperature ramp rate...
  4. ncbi The complete genome sequence of Escherichia coli K-12
    F R Blattner
    Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
    Science 277:1453-62. 1997
    ..The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer...
  5. ncbi Biased gene conversion and the evolution of mammalian genomic landscapes
    Laurent Duret
    Universite de Lyon 1, CNRS, UMR5558, Laboratoire de Biometrie et Biologie Evolutive, F 69622, Villeurbanne, France
    Annu Rev Genomics Hum Genet 10:285-311. 2009
    ..Here we review the recent evidence for a GC-biased gene conversion process in mammals, and its consequences for genomic landscapes, molecular evolution, and human functional genomics...
  6. ncbi CpG islands in vertebrate genomes
    M Gardiner-Garden
    Kanematsu Laboratories, Royal Prince Alfred Hospital, Camperdown N S W, Australia
    J Mol Biol 196:261-82. 1987
    ..Possible functions of CpG islands in transcriptional and post-transcriptional regulation of gene expression were discussed, and were related to theories for the maintenance of CpG islands as "methylation-free zones" in germline DNA...
  7. pmc Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
    Iwanka Kozarewa
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Methods 6:291-5. 2009
    ..We illustrate this by generating and analyzing DNA sequences from extremely (G+C)-poor (Plasmodium falciparum), (G+C)-neutral (Escherichia coli) and (G+C)-rich (Bordetella pertussis) genomes...
  8. 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...
  9. pmc G+C content dominates intrinsic nucleosome occupancy
    Desiree Tillo
    Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
    BMC Bioinformatics 10:442. 2009
    ..However, the model is complicated, and it is not clear which specific DNA sequence properties are most important for intrinsic nucleosome-forming preferences...
  10. ncbi Community structure and metabolism through reconstruction of microbial genomes from the environment
    Gene W Tyson
    Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA
    Nature 428:37-43. 2004
    ..Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment...
  11. pmc The impact of recombination on nucleotide substitutions in the human genome
    Laurent Duret
    Laboratoire de Biometrie et Biologie Evolutive, Universite de Lyon, Universite Lyon 1, CNRS, UMR 5558, Villeurbanne, France
    PLoS Genet 4:e1000071. 2008
    ..in population size or density in recombination hotspots can have a very strong impact on the evolution of base composition. Furthermore, recombination hotspots can create strong substitution hotspots...
  12. pmc Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes
    Edward Yang
    Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10021 6399, USA
    Genome Res 13:1863-72. 2003
    ....
  13. ncbi Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
    Olivier Jaillon
    UMR 8030 Genoscope, CNRS and Université d Evry, 2 rue Gaston Cremieux, 91057 Evry Cedex, France
    Nature 431:946-57. 2004
    ....
  14. pmc A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes
    Wanjun Gu
    Key Laboratory of Child Development and Learning Science of Ministry of Education of China, Southeast University, Nanjing, Jiangsu, China
    PLoS Comput Biol 6:e1000664. 2010
    ..We suggest that the origin of this reduction is selection for efficient recognition of the start codon by initiator-tRNA...
  15. pmc Comprehensive analysis of CpG islands in human chromosomes 21 and 22
    Daiya Takai
    Department of Biochemistry and Molecular Biology, University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
    Proc Natl Acad Sci U S A 99:3740-5. 2002
    ..This finding is compatible with the recent detection of 5-methylcytosine in Drosophila, and might suggest that S. cerevisiae has, or once had, CpG methylation...
  16. pmc High nucleosome occupancy is encoded at human regulatory sequences
    Desiree Tillo
    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    PLoS ONE 5:e9129. 2010
    ..We propose that high nucleosome preference is directly encoded at regulatory sequences in the human genome to restrict access to regulatory information that will ultimately be utilized in only a subset of differentiated cells...
  17. 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
    ..Based on these results, we describe a putative scenario for how evolutionary shifts in the identity of selectively favored codons can occur without even temporary weakening of natural selection for codon bias...
  18. pmc Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization
    Valentina Boeva
    Institut Curie, INSERM, U900, Paris, France
    Bioinformatics 27:268-9. 2011
    ..We demonstrate that for Illumina single-end, mate-pair or paired-end sequencing, GC-contentr normalization provides smooth profiles that can be further segmented and analyzed in order to predict CNAs...
  19. 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
    ..This suggests that translational selection may also have some influence in shaping codon usage bias...
  20. ncbi Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of metazoa, and consequences for phylogenetic inferences
    Alexandre Hassanin
    Museum national d histoire naturelle, Départment Systématique et Evolution, Case Postale, Paris, France
    Syst Biol 54:277-98. 2005
    ....
  21. 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...
  22. 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 bias is present in some plant species and warm-blooded vertebrates but not in all plants, or in invertebrates or cold-blooded vertebrates...
  23. 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
    ..Finally, PCGs sequences were used to perform a phylogenetic study. Both maximum likelihood and Bayesian inference analyses highly support Nabidae as the sister group to Anthocoridae and Miridae...
  24. 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
    ..Our data also provide evidence that the negative correlation between codon bias and recombination rates in G. gallus is determined mostly by recombination-dependent mutational patterns...
  25. ncbi Recombination drives the evolution of GC-content in the human genome
    Julien Meunier
    UMR 5558 CNRS, Université Lyon I, Villeurbanne, France
    Mol Biol Evol 21:984-90. 2004
    ..This demonstrates that recombination drives the evolution of base composition in human (probably via the process of biased gene conversion)...
  26. ncbi Linear amplification for deep sequencing
    Wieteke A M Hoeijmakers
    Department of Molecular Biology, Faculty of Science, Nijmegen Center for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
    Nat Protoc 6:1026-36. 2011
    ..Moreover, in contrast to amplification-free methods, LADS can generate sequencing libraries from a few nanograms of DNA, which is essential for all applications in which the starting material is limited...
  27. pmc Comparative mitogenomics of Braconidae (Insecta: Hymenoptera) and the phylogenetic utility of mitochondrial genomes with special reference to Holometabolous insects
    Shu jun Wei
    State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, China
    BMC Genomics 11:371. 2010
    ..e., Braconidae, Hymenoptera, and Holometabola...
  28. pmc Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts
    Matthew B Sullivan
    Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    PLoS Biol 4:e234. 2006
    ..This generates genetic diversity among the phage, which serves as a reservoir for their hosts, and in turn influences photosystem evolution...
  29. pmc Evidence of selection upon genomic GC-content in bacteria
    Falk Hildebrand
    Centre for the Study of Evolution and School of Life Sciences, University of Sussex, Brighton, United Kingdom
    PLoS Genet 6:e1001107. 2010
    ..Since synonymous GC-content is highly correlated to genomic GC-content, we further conclude that there is selection on genomic base composition in many bacteria.
  30. pmc Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
    J V Chamary
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    Genome Biol 6:R75. 2005
    ..Here we test whether synonymous mutations might be under selection owing to their effects on the thermodynamic stability of mRNA, mediated by changes in secondary structure...
  31. pmc Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes
    Jonathan Romiguier
    Universite Montpellier 2, CNRS UMR 5554 Institut des Sciences de l Evolution, 34095 Montpellier, France
    Genome Res 20:1001-9. 2010
    ..We correlated GC-content evolution with species life-history traits and cytology. Significant effects of body mass and genome size were detected, with each being consistent with the GC-biased gene conversion model...
  32. pmc Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments
    Matthew B Sullivan
    Massachusetts Institute of Technology, Cambridge, MA, USA
    Environ Microbiol 12:3035-56. 2010
    ..Finally, genome-wide comparisons of both diverse and closely related, co-isolated genomes provide a locus-to-locus variability metric that will prove valuable for interpreting metagenomic data sets...
  33. ncbi Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics
    Nathan C Sheffield
    Department of Biology, Brigham Young University, Provo, UT 84602, USA
    Syst Biol 58:381-94. 2009
    ..The software packages p4, PHASE, and nhPhyML were able to overcome the systematic bias in our data set, but parsimony, MrBayes, NJ, LogDet, and PhyloBayes were not...
  34. ncbi Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA
    William Wiley Navarre
    Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
    Genes Dev 21:1456-71. 2007
    ..The possibility that microorganisms maintain and exploit their characteristic genomic GC ratios for the purpose of self/non-self-discrimination is discussed...
  35. ncbi The fine-scale structure of recombination rate variation in the human genome
    Gilean A T McVean
    Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
    Science 304:581-4. 2004
    ..We demonstrate that recombination hotspots are a ubiquitous feature of the human genome, occurring on average every 200 kilobases or less, but recombination occurs preferentially outside genes...
  36. pmc Comparative mitogenomic analysis of damsel bugs representing three tribes in the family Nabidae (Insecta: Hemiptera)
    Hu Li
    Department of Entomology, China Agricultural University, Beijing, China
    PLoS ONE 7:e45925. 2012
    ....
  37. ncbi Microbial minimalism: genome reduction in bacterial pathogens
    Nancy A Moran
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
    Cell 108:583-6. 2002
    ..Complete genome sequences are providing an understanding of how extreme genome reduction affects evolutionary directions and metabolic capabilities of obligate pathogens and symbionts...
  38. pmc The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae)
    Paola Salvato
    Department of Public Health, Comparative Pathology and Veterinary Hygiene, University of Padova, Agripolis, Viale dell Universita 16, 35020 Legnaro, Italy
    BMC Genomics 9:331. 2008
    ..Thus advance of lepidopteran mitogenomics deeply requires new genomes derived from a broad taxon sampling. In present work we describe the mitochondrial genome of the moth Ochrogaster lunifer...
  39. ncbi The genome of a motile marine Synechococcus
    B Palenik
    Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093 0202, USA
    Nature 424:1037-42. 2003
    ..On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria...
  40. pmc Microsatellites in different eukaryotic genomes: survey and analysis
    G Toth
    Department of Genetics, Eotvos Lorand University, Budapest, Hungary
    Genome Res 10:967-81. 2000
    ..Our results suggest that strand-slippage theories alone are insufficient to explain microsatellite distribution in the genome as a whole. Other possible factors contributing to the observed divergence are discussed...
  41. pmc Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method
    Melissa B Duhaime
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
    Environ Microbiol 14:2526-37. 2012
    ....
  42. pmc Sensitivity of noninvasive prenatal detection of fetal aneuploidy from maternal plasma using shotgun sequencing is limited only by counting statistics
    H Christina Fan
    Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford, California, United States of America
    PLoS ONE 5:e10439. 2010
    ..High throughput shotgun sequencing of maternal plasma DNA should therefore enable noninvasive diagnosis of any type of fetal aneuploidy...
  43. 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
    ..regions in eukaryotes, and this is believed to have major effects on their genome organization in terms of base composition, DNA repeat density, intron size, evolutionary rates and gene order...
  44. pmc The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum
    R Okimoto
    Department of Biology, University of Utah, Salt Lake City 84112
    Genetics 130:471-98. 1992
    ..elegans and A. suum ancestral lines diverged close to the time of divergence of the cow and human ancestral lines, about 80 million years ago...
  45. pmc The multipartite mitochondrial genome of Liposcelis bostrychophila: insights into the evolution of mitochondrial genomes in bilateral animals
    Dan Dan Wei
    Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
    PLoS ONE 7:e33973. 2012
    ..Within parasitic lice, however, the suborder Ischnocera is paraphyletic; this differs from the traditional view that each suborder of parasitic lice is monophyletic...
  46. pmc The architecture and complete sequence of mitochondrial genome of an assassin bug Agriosphodrus dohrni (Hemiptera: Reduviidae)
    Hu Li
    Department of Entomology, China Agricultural University, Beijing 100193, China
    Int J Biol Sci 7:792-804. 2011
    ..The phylogenetic analyses indicated that within Reduviidae, Harpactorinae is a sister group to the Salyavatinae + Triatominae clade...
  47. pmc The mitochondrial genome of the ascalaphid owlfly Libelloides macaronius and comparative evolutionary mitochondriomics of neuropterid insects
    Enrico Negrisolo
    Department of Public Health, Comparative Pathology and Veterinary Hygiene, University of Padova, Agripolis, Viale dell Universita 16, 35020 Legnaro, Italy
    BMC Genomics 12:221. 2011
    ..These analyses are further extended to other endopterygotan orders...
  48. pmc Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content
    Penelope R Haddrill
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
    Genome Biol 6:R67. 2005
    ..No consistent patterns have emerged from studies that have investigated general levels of evolutionary constraint in introns...
  49. pmc Across bacterial phyla, distantly-related genomes with similar genomic GC content have similar patterns of amino acid usage
    John Lightfield
    Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
    PLoS ONE 6:e17677. 2011
    ..These results also indicate that selection for translational efficiency of highly expressed genes is constrained by the genomic parameters associated with the GC content of the host genome...
  50. pmc Dynamic evolution of base composition: causes and consequences in avian phylogenomics
    Benoit Nabholz
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    Mol Biol Evol 28:2197-210. 2011
    ..77 Mb of exonic sequence. First, we find an unexpected heterogeneity in the evolution of base composition among avian lineages...
  51. ncbi Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 447:167-77. 2007
    ..A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation...
  52. ncbi The genome of the model beetle and pest Tribolium castaneum
    Stephen Richards
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 452:949-55. 2008
    ..Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control...
  53. pmc Evidence that mutation is universally biased towards AT in bacteria
    Ruth Hershberg
    Department of Biology, Stanford University, Stanford, California, United States of America
    PLoS Genet 6:e1001115. 2010
    ....
  54. pmc Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont
    John P McCutcheon
    Center for Insect Science, University of Arizona, Tucson, AZ, USA
    PLoS Genet 5:e1000565. 2009
    ..Small genomes typically exhibit low guanine plus cytosine (GC) content, and this bias in base composition has been proposed to drive UGA Stop to Tryptophan (Stop-->Trp) recoding...
  55. ncbi Genome sequence of a polydnavirus: insights into symbiotic virus evolution
    Eric Espagne
    Institut de Recherche sur la Biologie de l Insecte, CNRS UMR 6035, UFR Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
    Science 306:286-9. 2004
    ....
  56. pmc High guanine and cytosine content increases mRNA levels in mammalian cells
    Grzegorz Kudla
    International Institute of Molecular and Cell Biology, Warsaw, Poland
    PLoS Biol 4:e180. 2006
    ..We conclude that silent-site GC content correlates with gene expression efficiency in mammalian cells...
  57. ncbi Drosophila mitochondrial DNA: conserved sequences in the A + T-rich region and supporting evidence for a secondary structure model of the small ribosomal RNA
    D O Clary
    Department of Biology, University of Utah, Salt Lake City 84112
    J Mol Evol 25:116-25. 1987
    ..virilis and D. yakuba strongly support the secondary structure model for the Drosophila small mt-rRNA that we previously proposed...
  58. pmc Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination "hot spots"
    Jan Drouaud
    Station de Genetique et d Amelioration des plantes, Institut Jean Pierre Bourgin, Institut National de la Recherche Agronomique, 78026, Versailles Cedex, France
    Genome Res 16:106-14. 2006
    ..Both the intensity and the density of these hot spots explain the variation of CO rates along the chromosome...
  59. ncbi Genome streamlining in a cosmopolitan oceanic bacterium
    Stephen J Giovannoni
    Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
    Science 309:1242-5. 2005
    ..P. ubique has no pseudogenes, introns, transposons, extrachromosomal elements, or inteins; few paralogs; and the shortest intergenic spacers yet observed for any cell...
  60. pmc A selective force favoring increased G+C content in bacterial genes
    Rahul Raghavan
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 109:14504-7. 2012
    ..Because bacterial genomes have high gene content, forces that operate on the base composition of individual genes could help shape the overall genomic base composition...
  61. ncbi Chromatin organization marks exon-intron structure
    Schraga Schwartz
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
    Nat Struct Mol Biol 16:990-5. 2009
    ..Our results suggest an RNA polymerase II-mediated cross-talk between chromatin structure and exon-intron architecture, implying that exon selection may be modulated by chromatin structure...
  62. 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
    ....
  63. 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
    ..It also provides new evidence that a selective force for the optimization of the translation machinery is the maximization of growth...
  64. ncbi An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure
    Jerome Waldispühl
    School of Computer Science and McGill Center for Bioinformatics, McGill University, Montreal, Canada
    J Comput Biol 18:1465-79. 2011
    ..On the other hand, high G+C-contents significantly reduce the size of the evolutionary accessible mutational landscapes...
  65. pmc Phylogenetic analysis of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha): evidence from mitochondrial genomes
    Jimeng Hua
    Department of Zoology and Developmental Biology, Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
    BMC Evol Biol 9:134. 2009
    ..In this study we analyzed the unresolved problems in Nepomorpha using evidence from mitochondrial genomes...
  66. ncbi The mitochondrial genome of the mosquito Anopheles gambiae: DNA sequence, genome organization, and comparisons with mitochondrial sequences of other insects
    C B Beard
    Centers for Disease Control and Prevention, Public Health Service, US Department of Health and Human Services, Atlanta, GA 30314 3724, USA
    Insect Mol Biol 2:103-24. 1993
    ..Comparisons were made with the mitochondrial genomes of other insects on the basis genome size and organization, DNA and putative amino acid sequence data, nucleotide substitutions, codon usage and bias, and patterns of AT enrichment...
  67. pmc GC content and recombination: reassessing the causal effects for the Saccharomyces cerevisiae genome
    Marie Claude Marsolier-Kergoat
    Institut de Biologie et de Technologies de Saclay, Commissariat àl Energie Atomique Saclay, 91191 Gif sur Yvette, France
    Genetics 183:31-8. 2009
    ..These results pave the way for further analyses aimed at the detailed untangling of drives involved in the evolutionary shaping of the yeast genome...
  68. ncbi 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
    ..We also find that, contrary to expectation, codon usage bias is highest in areas of intermediate levels of recombination for GC-ending optimal codons. Possible reasons for this are discussed...
  69. ncbi GC3 of genes can be used as a proxy for isochore base composition: a reply to Elhaik et al
    Oliver K Clay
    Mol Biol Evol 28:21-3. 2011
    ..The answer reasserts that in human and other vertebrates, genes have a strong tendency to reside in compositionally corresponding isochores, which has far-reaching implications for genome structure and evolution...
  70. ncbi The complete mitogenome sequence of the Japanese oak silkmoth, Antheraea yamamai (Lepidoptera: Saturniidae)
    Seong Ryeol Kim
    Department of Agricultural Biology, National Institute of Agricultural Science and Technology, Suwon, Republic of Korea
    Mol Biol Rep 36:1871-80. 2009
    ..As has been previously suggested, Bombycidae (Bombyx mori and B. mandarina) and Saturniidae (A. yamamai and Caligula boisduvalii) formed a reciprocal monophyletic group...
  71. ncbi 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
    ..In contrast, numbers of substitutions between preferred and unpreferred codons are similar in both directions in the Y-linked genes, contrary to the expectation of genetic degeneration...
  72. ncbi GC composition of the human genome: in search of isochores
    Netta Cohen
    School of Computing, University of Leeds, Leeds, United Kingdom
    Mol Biol Evol 22:1260-72. 2005
    ..These findings undermine the utility of the isochore theory and seem to indicate that the theory may have reached the limits of its usefulness as a description of genomic compositional structures...
  73. pmc The complete mitochondrial genome of the citrus red mite Panonychus citri (Acari: Tetranychidae): high genome rearrangement and extremely truncated tRNAs
    Ming Long Yuan
    Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
    BMC Genomics 11:597. 2010
    ..In this study, we sequenced the complete mitochondrial genome of Panonychus citri (Family Tetranychidae), a worldwide citrus pest, and provide a comparison to other Acari...
  74. 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
    ..Arginine and leucine, amino acids that allow GC-changing synonymous substitutions in the first and third codon positions, have codons which may be expected to show different usage patterns...
  75. ncbi Cytosine methylation and CpG, TpG (CpA) and TpA frequencies
    Kamel Jabbari
    Laboratoire de Genetique Moleculaire, Institut Jacques Monod, 2 place Jussieu, F 75005 Paris, France
    Gene 333:143-9. 2004
    ..The implications of these results are discussed...
  76. ncbi Strand-specific compositional asymmetries in double-stranded DNA viruses
    A Grigoriev
    Max Planck Institute for Molecular Genetics, Berlin, Germany
    Virus Res 60:1-19. 1999
    ..Use of cumulative skew plots for genome comparisons is demonstrated on the example of herpes simplex virus...
  77. pmc Partial mitochondrial genome sequences of Ostrinia nubilalis and Ostrinia furnicalis
    Brad S Coates
    USDA ARS, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, c o Insectary, Iowa State University, Ames, Iowa, 50011
    Int J Biol Sci 1:13-8. 2005
    ..2%) compared to 2-fold degenerate codons (2.6%). These are the 3(rd) and 4(th) lepidopteran mitochondrial genome reference sequences in GenBank and useful for comparative mitochondrial studies...
  78. ncbi Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12
    T Hayashi
    Department of Microbiology, Miyazaki Medical College, Kiyotake, Japan
    DNA Res 8:11-22. 2001
    ..A complete set of the genes specific to O157:H7 presented here sheds new insight into the pathogenicity and the physiology of O157:H7, and will open a way to fully understand the molecular mechanisms underlying the O157:H7 infection...
  79. ncbi Complete genome sequence of a virulent isolate of Streptococcus pneumoniae
    H Tettelin
    The Institute for Genomic Research (TIGR, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 293:498-506. 2001
    ..Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity...
  80. 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
    ....
  81. 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
    ..honmai, an apoditrysian tortricid moth joined basally within the monophyly of Lepidoptera, supporting its relationship with other more derived species including obtectomeran Ostrinia species...
  82. ncbi Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system
    C Saccone
    Centro di Studio sui Mitocondri e Metabolismo Energetico, CNR, Bari, Italy
    Gene 238:195-209. 1999
    ..b>Base composition of mtDNA is extremely variable...
  83. 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
    ..In our analysis, mRNA folding and associated rates of translation initiation play a predominant role in shaping expression levels of individual genes, whereas codon bias influences global translation efficiency and cellular fitness...
  84. pmc Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophiles
    Robert Friedman
    Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
    Genetics 167:1507-12. 2004
    ....
  85. pmc A complete sequence of the T. tengcongensis genome
    Qiyu Bao
    Beijing Genomics Institute Genomics and Bioinformatics Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences CAS, Beijing 100101, China
    Genome Res 12:689-700. 2002
    ..It is concluded that thermophiles are a biologically and phylogenetically divergent group of prokaryotes that have converged to sustain extreme environmental conditions over evolutionary timescale...
  86. pmc Chromosomal G + C content evolution in yeasts: systematic interspecies differences, and GC-poor troughs at centromeres
    Denise B Lynch
    Conway Institute of Biomedical and Biomolecular Sciences, University College Dublin, Belfield, Dublin 4, Ireland
    Genome Biol Evol 2:572-83. 2010
    ....
  87. ncbi Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome
    S Kanaya
    Department of Bio-System Engineering, Faculty of Engineering, Yamagata University, Yonezawa, 992-8510, Yamagata-ken, Japan
    Gene 276:89-99. 2001
    ..We used SOM to examine codon usage heterogeneity in the E. coli O157 genome, which contains 'O157-unique segments' (O-islands), and showed that SOM is a powerful tool for characterization of horizontally transferred genes...
  88. pmc Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    Andreas Gnirke
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Biotechnol 27:182-9. 2009
    ..One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space...
  89. ncbi Increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes
    Megan Woolfit
    Centre for the Study of Evolution, School of Biological Sciences, University of Sussex, United Kingdom
    Mol Biol Evol 20:1545-55. 2003
    ..T content, another indicator of increased genetic drift, and find that there is no significant difference in base composition between endosymbiont and nonendosymbiont 16S genes...
  90. ncbi Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses
    Tong Zhou
    Key Laboratory of Molecular and Biomolecular Electronics of the Ministry of Education, Southeast University, Nanjing, Jiangsu 210096, China
    Biosystems 81:77-86. 2005
    ..However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes...
  91. pmc Human-macaque comparisons illuminate variation in neutral substitution rates
    Svitlana Tyekucheva
    Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA
    Genome Biol 9:R76. 2008
    ..Here we investigate the human-macaque neutral substitution rate as a function of a number of genomic parameters...
  92. pmc Cross-species analysis of genic GC3 content and DNA methylation patterns
    Tatiana Tatarinova
    Laboratory of Applied Pharmacokinetics and Bioinformatics, University of Southern California
    Genome Biol Evol 5:1443-56. 2013
    ..Specifically, we propose that the opposite effects of methylation and compositional gradients along coding regions of GC(3)-poor and GC(3)-rich genes are the products of several competing processes...
  93. ncbi Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology
    Patrick Schwientek
    Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
    J Biotechnol 155:68-77. 2011
    ....
  94. pmc Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases
    Bradley Zamft
    Jason L Choy Laboratory of Single Molecule Biophysics and Department of Physics, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 109:8948-53. 2012
    ..These results reveal that RNA secondary structures provide a cis-acting mechanism by which sequence modulates transcriptional elongation...
  95. ncbi Cloacibacillus evryensis gen. nov., sp. nov., a novel asaccharolytic, mesophilic, amino-acid-degrading bacterium within the phylum 'Synergistetes', isolated from an anaerobic sludge digester
    Akila Ganesan
    CEA Genoscope, 2 rue Gaston Cremieux, 91057 Evry, France
    Int J Syst Evol Microbiol 58:2003-12. 2008
    ..nov., sp. nov., in the phylum 'Synergistetes'. The type strain is 158T (=DSM 19522T=JCM 14828T)...
  96. ncbi DNA G+C content of the third codon position and codon usage biases of human genes
    N Sueoka
    University of Colorado, Department of Molecular, Cellular, and Developmental Biology, Boulder, CO 80309 0347, USA
    Gene 261:53-62. 2000
    The human genome, as in other eukaryotes, has a wide heterogeneity in the DNA base composition. The evolutionary basis for this heterogeneity has been unknown...
  97. ncbi Bacterial genomic G+C composition-eliciting environmental adaptation
    Scott Mann
    Faculty of Science and Technology, Deakin University, Australia
    Genomics 95:7-15. 2010
    ..We conclude the review with an analysis of current bioinformatics tools seeking to elicit compositional variances and highlight the practical implications when using such techniques...
  98. pmc Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes
    Herman Tse
    Carol Yu Centre for Infection, Department of Microbiology, The University of Hong Kong, Hong Kong, China
    BMC Genomics 11:491. 2010
    ..Given such a functional significance, we expect statistically overrepresented OSCs in coding sequences as a result of a widespread selection. Accordingly, we examined available prokaryotic genomes to look for evidence of this selection...
  99. pmc Genomic and proteomic adaptations to growth at high temperature
    Donal A Hickey
    Department of Biology, Concordia University, 7141 Sherbrooke Street, Montreal, Quebec, H4B 1R6, Canada
    Genome Biol 5:117. 2004
    ..We review the evidence for direct temperature-dependent natural selection acting on genomes, transcriptomes and proteomes...
  100. ncbi Correlation between codon usage and thermostability
    Marx Gomes Van der Linden
    Laboratório Nacional de Computação Científica, Petropolis, Rio de Janeiro, Brazil
    Extremophiles 10:479-81. 2006
    ..This bias is not a mere consequence of increased G + C content, as it has been previously suggested, and may represent a new mechanism of adaptation to protein thermostability...
  101. ncbi GC-biased gene conversion and selection affect GC content in the Oryza genus (rice)
    Aline Muyle
    Institut des Sciences de l Evolution, UMR 5554 CNRS, Universite Montpellier II, France
    Mol Biol Evol 28:2695-706. 2011
    b>Base composition varies among and within eukaryote genomes...

Research Grants62

  1. Ibis T-6,000 Biosensor System
    CYNTHIA SEARS; Fiscal Year: 2010
    ..by electrospray ionization time-of-flight (ESI-TOF) mass spectrometric analysis to determine the precise base composition of the PCR amplicons...
  2. Klotho regulation and aging
    Gwendalyn D King; Fiscal Year: 2010
    ..The aging suppressor protein, Klotho is decreased in the brain with age and may be a target for therapeutic development against neurodegenerative disorders. ..
  3. Klotho regulation and aging
    GWENDALYN DIANN KING; Fiscal Year: 2013
    ..The results of this work will add new knowledge on both the anti-aging gene Klotho and elucidate a possible mechanism for how oxidative damage selectively downregulates specific genes. ..
  4. FMR 1-SLS: Improving Fragile X diagnosis using amplification-free single locus ta
    STEPHEN WHITFIELD TURNER; Fiscal Year: 2013
    ....
  5. The Rate and Molecular Spectrum of Spontaneous Mutations
    Michael Lynch; Fiscal Year: 2009
    ..The contextual dependency of these features will be evaluated with respect to neighboring-base composition, transcription and replication activity, and meiotic recombination rate...
  6. Gene Prediction by Markov Models and Complementary Methods
    Mark Borodovsky; Fiscal Year: 2012
    ..This work will be done in close contact with sequencing and annotation groups from leading genome centers both in the US and abroad. ..
  7. Forward genetic screens for identifying antimalarial resistance genes
    Manoj T Duraisingh; Fiscal Year: 2010
    ..knowlesi parasites resistant to specific drugs of interest, which is feasible due to its GC-rich base composition. These cosmid libraries will be transfected into drug-susceptible P. knowlesi and P...
  8. Statistical Analysis of Epigenomics Data
    Kimberly D Siegmund; Fiscal Year: 2013
    ....
  9. COOPERATIVE INTERACTIONS IN DNA REPAIR
    Michael G Fried; Fiscal Year: 2010
    ..It binds DNA with substantial cooperativity but little sequence or base composition dependence. These results argue against mechanisms of target recognition that depend strongly on sequence...
  10. CODING & NONCODING REGIONS IN DNA SEQUENCES
    THOMAS JUKES; Fiscal Year: 1991
    ..As a start, we shall use codon tables in our possession for 1,737 protein genes from eukaryotes and bacteria...
  11. Rapid High-Throughput Mycobacterium Tuberculosis Genotyping
    Christian Massire; Fiscal Year: 2009
    ..multiplexed PCR reactions with electrospray ionization mass spectrometry (PCR/ESI-MS) and high resolution base composition analysis of the amplicons...
  12. Pathogen diagnostic products--Biodefense developments
    Lawrence Blyn; Fiscal Year: 2005
    ..The process uses mass spectrometry, signal processing, and base composition analysis of PCR amplification products from biologically conserved regions of microbial genomes to ..
  13. Sequencing DNA by transverse electrical measurements in Nanochannels
    Robert Riehn; Fiscal Year: 2009
    ..Devices will be evaluated using both single and double stranded DNA. We will assess the resolution and quality of the obtained data by sequencing or GC-content mapping of synthetic block oligomers and genomic DNA samples. ..
  14. MUTATIONAL MECHANISMS OF REPETITIVE DNA IN HUMAN CELLS
    Kristin Eckert; Fiscal Year: 2001
    ..and to ascertain precise in vitro polymerase error rates in STR sequences as a function of repeat size and base composition. The bimodal targets sequences also will be incorporated into ori-rho-tk shuttle vectors which replicate ..
  15. DNA BENDING AND CONFORMATIONAL SWITCHING
    J Schurr; Fiscal Year: 2003
    ..In addition, the effects of binding IHF to the ends of a 277 bp DNA will be studied to determine any effect of the large induced bends on the intervening DNA. ..
  16. YEAST CENTROMERE STRUCTURE AND FUNCTION
    Molly Fitzgerald Hayes; Fiscal Year: 1993
    ..Results from functional analyses of our CDE II replacement mutants have begun to delineate the base composition and structural organization required for function of that segment of CEN DNA...
  17. SATURATED GENOME ANALYSIS VIA 2D GELS
    CHARLES SIDMAN; Fiscal Year: 1993
    ..In brief, existing techniques of 2D electrophoresis of DNA fragments (by size and base composition/sequence), probing for highly repetitive DNA sequences, computer-assisted analysis of complex spot patterns ..
  18. PCR MS/MS FINGERPRINTS FOR SEQUENCE POLYMORPHISM
    Alvin Fox; Fiscal Year: 2000
    ..The strength of MS/MS (unlike other fingerprinting techniques) is that nucleotide base composition (not sequence) can be readily obtained for each oligonucleotide fragment of the parent PCR molecule...
  19. SITE SPECIFIC CHEMICAL METHODS FOR CLEAVING GENOMIC DNA
    Peter Dervan; Fiscal Year: 1993
    ..binding by studying the influence of pH, temperature, and organic cosolvent on probes of different base composition, (3) generalize a set of conditions for unique recognition at purine-DNA sites 15-18 base pairs in length, (4)..
  20. TRANSLATIONAL REGULATION AND MALIGNANCY
    STEPHEN ZIMMER; Fiscal Year: 2002
    ..These samples will be taken to monitor the effects of the treatment of the tumors with genes or drugs that affect eIF-4E function. ..
  21. Y CHROMOSOME VARIATION
    Luigi Cavalli Sforza; Fiscal Year: 1999
    ..in length will be scanned for the presence or absence of heteroduplexes, which reflect single-nucleotide base composition differences...
  22. SYNTHESIS OF AROMATIC DIOL EPOXIDE DNA MODEL ADDUCTS
    Nicholas Geacintov; Fiscal Year: 1993
    ..selected mutagenic polycyclic aromatic diol epoxide compounds with deoxyribooligonucleotides of defined base composition and sequence...
  23. Single Well MPCR Donor Screen to ID Blood Pathogens
    Raymond Ranken; Fiscal Year: 2004
    ..The exact mass of each PCR product in a mixture is used to determine the base composition of each product and this composition uniquely identifies all the organisms present in the original sample...
  24. Natural variation in Drosophila female postmating traits
    DAVID BEGUN; Fiscal Year: 2008
    ..abstract_text> ..
  25. Functional Dissection of an F-box Protein in Development
    Michael Weir; Fiscal Year: 2006
    ..abstract_text> ..
  26. Empirical analysis of natural selection on codon usage in eukaryotes
    RICHARD KLIMAN; Fiscal Year: 2007
    ..is to confirm a preliminary finding that the genomes of these viruses are not at equilibrium with respect to base composition and codon usage...
  27. Campylobacter jejuni outer membrane protein vaccine
    Stuart Thompson; Fiscal Year: 2009
    ..Specific Aim 3. We will determine whether immunization of mice with conserved, purified recombinant OMPs protects against subsequent experimental C. jejuni infection. ..
  28. Computational Analysis of Retinal Regulatory Interactions: structure and dynamics
    Jiang Qian; Fiscal Year: 2010
    ..Beyond investigation of retinal disease, the computational programs developed in this proposal should also be generally useful for a broad community. ..
  29. Determinants of X-chromosome transcriptional regulation in C. elegans
    Sevinc Ercan; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  30. Male Mutation Bias and Paternal Age Effect in Mammals
    Kateryna Makova; Fiscal Year: 2010
    ..Additionally, the conclusions of this project will be important for genetic counseling. Namely, our results will indicate whether the age of a father at the time of conception represents a risk factor for pathology in the offspring. ..
  31. Non-coding RNAs involved in HIV-1 Latency
    Kevin V Morris; Fiscal Year: 2010
    ..Results from this project will result in a paradigm shift with regards to controlled expression of HIV-1 that could prove valuable to society with regards to new anti-HIV therapeutics and vaccine design. 1 ..
  32. Rapid Microbial Identification by MALDI-TOF Mass Spectrometry of Ribosomal RNA
    George Jackson; Fiscal Year: 2007
    ..This project focuses on developing a total system for microbial identification using predictive software, novel molecular techniques, and mass spectral analysis of ribosomal RNA fragments. [unreadable] [unreadable] [unreadable]..
  33. Application of Bioinformatics to Retinal Gene Regulation
    Jiang Qian; Fiscal Year: 2006
    ..abstract_text> ..
  34. SEQUENCING THE DICTYOSTELIUM GENOME
    Adam Kuspa; Fiscal Year: 2004
    ..Complete sequence data obtained from experimentally tractable organisms, such as Dictyostelium, will continue to stimulate genomic investigations in many systems, including humans. ..
  35. E. coli Annotation Workshop
    Monica Riley; Fiscal Year: 2005
    ..coli information as it is fragmented into several databases with different objectives and there is contradictions.The output of a workshop and a follow-up smaller meeting will meet and solve this serious problem. ..
  36. DNA LIGASE I AS A POTENTIAL TARGET FOR ANTICANCER DRUGS
    Daekyu Sun; Fiscal Year: 2002
    ..3) Test whether DNA ligase I inhibition produces antitumor activity using antisense strategy in preclinical in vitro and in vivo evaluation systems. 4) Develop a sensitive and reproducible assay for DNA ligase I. ..
  37. Evolution of Duplicate Genes at the Genomic Level
    Wen Hsiung Li; Fiscal Year: 2005
    ..5. To study the mechanisms of evolution of duplicate genes or how duplicate genes evolve following the duplication event. We shall examine various models for the retention and evolution of duplicate genes. ..
  38. HYPOTRICH GENOME IN DEVELOPMENT AND EVOLUTION
    David Prescott; Fiscal Year: 2001
    ..The experiments deal with the general problem of how an organism can manipulate its own DNA. ..
  39. Enzymatic Mechanisms of Two Pyrimidine Decarboxylases
    Jeffrey Smiley; Fiscal Year: 2003
    ....
  40. Transgenic Plant-Derived CMV Glycoprotein B Vaccine
    Mark Schleiss; Fiscal Year: 2007
    ..These studies will advance the fields of plant and CMV vaccines. [unreadable] [unreadable] [unreadable]..
  41. Mutation Rate Variation Among Human Genomic Regions
    Wen Hsiung Li; Fiscal Year: 2004
    ..Sequence each of them in chimpanzee, gorilla, orangutan, siamang, baboon and colobus. 4. To conduct statistical analyses of the new and existing data to address the above issues. ..
  42. Anti-Inflammatory Bioconjugates
    Benjamin Bowen; Fiscal Year: 2008
    ....
  43. FORCES STABILIZING NATIVE PROTEIN STRUCTURES
    PETER PRIVALOV; Fiscal Year: 2003
    ..This project proposes to realize these objectives with combined investigations on several extended groups of DNA-binding proteins and their complexes. ..
  44. HUMAN DNA POLYMORPHISM AND EVOLUTION
    Wen Hsiung Li; Fiscal Year: 2001
    ..The new methods and some existing methods will used to analyze the data to be obtained. The new methods will be accessible on the World Wide Web. ..
  45. Targeting Tumor Angiogenesis with G-Quadruplex Binders
    Daekyu Sun; Fiscal Year: 2010
    ..abstract_text> ..
  46. CAMPYLOBACTER FETUS SURFACE LAYER PROTEIN SECRETION
    Stuart Thompson; Fiscal Year: 2002
    ..coli. They will use deletion and mutational analyses to define the C. fetus SapA C-terminal secretion signal. The ability of the SapA secretion to mediate the transport of normally non-secreted proteins also will be assessed. ..
  47. MOLECULAR COEVOLUTION OF GROWTH HORMONE AND ITS RECEPTOR
    Wen Hsiung Li; Fiscal Year: 2002
    ..For amino acid differences with observed significant effects on binding, determine their collective effect in combinations. 6. Conduct statistical analyses of data to characterize evolution of GH and GHR. ..
  48. FUNCTION AND CONSERVATION IN GLOBIN LOCUS CONTROL REGION
    Ross Hardison; Fiscal Year: 2001
    ..5 and isolate the binding proteins. ..
  49. MECHANISMS AND CONSEQUENCES OF DELETERIOUS EVOLUTION IN BACTERIA
    Jennifer J Wernegreen; Fiscal Year: 2010
    ..By deciphering fundamental mechanisms that influence bacterial genome evolution, this study will contribute to a predictive framework for understanding how microbes evolve. ..
  50. Evolution of codon usage bias in the genus Drosophila
    Jeffrey Powell; Fiscal Year: 2009
    ..willistoni, one of the species being sequenced. ..
  51. High through-put detection of fungal pathogens
    JACK FELL; Fiscal Year: 2004
    ..Resulting data will be disseminated via GenBank, publications in leading scientific journals and as an inexpensive commercial detection system. ..
  52. In vivo Selection of Ribosomal Aptamers for Improved Bioremediation
    George Jackson; Fiscal Year: 2008
    ..Additionally, the developed strains are expected to have considerable commercial value for bioremediation at industrial, government, and military clean-up sites. [unreadable] [unreadable] [unreadable]..
  53. Broad Detection System for Tick-Borne Pathogens
    Mark Eshoo; Fiscal Year: 2008
    ..Results of this work will lead to a commercially available diagnostic to detect and identify tick-borne diseases in humans for improved medical treatment and public health surveillance. [unreadable] [unreadable] [unreadable]..
  54. Temperature Gradient Hybridizer and Real-time Imager for DNA Microarrays
    George Jackson; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  55. Novel Strategy for Animal Model Testing of HCMV Vaccines
    Mark Schleiss; Fiscal Year: 2007
    ..These studies will represent the first efficacy test of a human CMV subunit vaccine in a small animal model of congenital CMV infection. [unreadable] [unreadable]..
  56. Forward Genetics in Tetrahymena: Cloning by Complementation
    ROBERT COYNE; Fiscal Year: 2008
    ..Numerous other basic studies with far-reaching relevance to human health would be facilitated by the availability of the proposed freely available resource. [unreadable] [unreadable] [unreadable] [unreadable]..
  57. Genetic Studies of African Anopheles Vectors of Malaria
    Jeffrey Powell; Fiscal Year: 2009
    ..Replacing natural vector populations with such strains require that the strain have high fitness. ..
  58. Fos, Jun and transcriptional control of synaptic plasticity
    Giovanni Bosco; Fiscal Year: 2007
    ..Finally, results from these experiments may identify and validate new molecules to target for pharmacological therapy. ..
  59. The Mechanism of Interferon Regulatory Factor (IRF) Activation
    Peter L Privalov; Fiscal Year: 2010
    ..Now, during two years of the expected Bridge Grant, we will concentrate on the realization of the (b) and (d) points of our proposal. ..
  60. Evolution of vertebrate sensory genes
    Jianzhi Zhang; Fiscal Year: 2010
    ..These studies will also help understand human smell and taste variations and disorders. ..
  61. Campylobacter jejuni DNA methylation and gene regulation
    Stuart Thompson; Fiscal Year: 2004
    ..Specific Aim 3. Elucidate the upstream factors and signals controlling Cj1461 and Cj0355 expression to reveal the entire regulatory circuit. ..
  62. Disease Ontology: An Open Biomedical Ontology for Disease
    LYNN MARIE SCHRIML; Fiscal Year: 2010
    ..The DO project will also validate mappings to standard terminologies containing disease concepts such as UMLS, SNOMED-CT and ICD-9-CM. ..