bacterial genome

Summary

Summary: The genetic complement of a BACTERIA as represented in its DNA.

Top Publications

  1. pmc Genome sequencing in microfabricated high-density picolitre reactors
    Marcel Margulies
    454 Life Sciences Corp, 20 Commercial Street, Branford, Connecticut 06405, USA
    Nature 437:376-80. 2005
  2. pmc RNAmmer: consistent and rapid annotation of ribosomal RNA genes
    Karin Lagesen
    Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, University of Oslo, NO 0027 Oslo, Norway
    Nucleic Acids Res 35:3100-8. 2007
  3. pmc Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    Daniel R Zerbino
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 18:821-9. 2008
  4. pmc Identifying bacterial genes and endosymbiont DNA with Glimmer
    Arthur L Delcher
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 23:673-9. 2007
  5. pmc Mauve: multiple alignment of conserved genomic sequence with rearrangements
    Aaron C E Darling
    Department of Computer Science, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Genome Res 14:1394-403. 2004
  6. pmc The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    Ross Overbeek
    Fellowship for Interpretation of Genomes, 15W155 81st Street, Burr Ridge, IL 60527, USA
    Nucleic Acids Res 33:5691-702. 2005
  7. 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
  8. ncbi Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
    S T Cole
    Sanger Centre, Wellcome Trust Genome Campus, Hinxton, UK
    Nature 393:537-44. 1998
  9. pmc Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
    Marie Touchon
    Atelier de BioInformatique, Universite Pierre et Marie Curie Paris 6, Paris, France
    PLoS Genet 5:e1000344. 2009
  10. pmc Metagenomic analysis of the human distal gut microbiome
    Steven R Gill
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 312:1355-9. 2006

Detail Information

Publications337 found, 100 shown here

  1. pmc Genome sequencing in microfabricated high-density picolitre reactors
    Marcel Margulies
    454 Life Sciences Corp, 20 Commercial Street, Branford, Connecticut 06405, USA
    Nature 437:376-80. 2005
    ..Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine...
  2. pmc RNAmmer: consistent and rapid annotation of ribosomal RNA genes
    Karin Lagesen
    Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, University of Oslo, NO 0027 Oslo, Norway
    Nucleic Acids Res 35:3100-8. 2007
    ..pre-screening step makes the method fast with little loss of sensitivity, enabling the analysis of a complete bacterial genome in less than a minute...
  3. pmc Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    Daniel R Zerbino
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 18:821-9. 2008
    ..Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies...
  4. pmc Identifying bacterial genes and endosymbiont DNA with Glimmer
    Arthur L Delcher
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 23:673-9. 2007
    ..This module was developed in response to the discovery that eukaryotic genome sequencing projects sometimes inadvertently capture the DNA of intracellular bacteria living in the host...
  5. pmc Mauve: multiple alignment of conserved genomic sequence with rearrangements
    Aaron C E Darling
    Department of Computer Science, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Genome Res 14:1394-403. 2004
    ..We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution...
  6. pmc The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    Ross Overbeek
    Fellowship for Interpretation of Genomes, 15W155 81st Street, Burr Ridge, IL 60527, USA
    Nucleic Acids Res 33:5691-702. 2005
    ..The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms...
  7. 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...
  8. ncbi Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
    S T Cole
    Sanger Centre, Wellcome Trust Genome Campus, Hinxton, UK
    Nature 393:537-44. 1998
    ....
  9. pmc Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
    Marie Touchon
    Atelier de BioInformatique, Universite Pierre et Marie Curie Paris 6, Paris, France
    PLoS Genet 5:e1000344. 2009
    ..Overall, despite a very high gene flow, genes co-exist in an organised genome...
  10. pmc Metagenomic analysis of the human distal gut microbiome
    Steven R Gill
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 312:1355-9. 2006
    ..Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes...
  11. pmc The human microbiome project
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 449:804-10. 2007
    ..A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease...
  12. pmc CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
    Ibtissem Grissa
    Univ Paris Sud, Institut de Genetique et Microbiologie, UMR 8621, Orsay, F 91405, France
    Nucleic Acids Res 35:W52-7. 2007
    ..CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php...
  13. ncbi Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
    S D Bentley
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 417:141-7. 2002
    ..The genome sequence will greatly increase our understanding of microbial life in the soil as well as aiding the generation of new drug candidates by genetic engineering...
  14. pmc Mapping short DNA sequencing reads and calling variants using mapping quality scores
    Heng Li
    The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
    Genome Res 18:1851-8. 2008
    ..Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile, and user-friendly. It is freely available at http://maq.sourceforge.net...
  15. pmc ISfinder: the reference centre for bacterial insertion sequences
    P Siguier
    Laboratoire de Microbiologie et Genetique Moleculaires, C N R S 118, route de Narbonne, F 31062 Toulouse Cedex, France
    Nucleic Acids Res 34:D32-6. 2006
    ..Finally, this database is currently recommended by several microbiology journals for registration of new IS elements before their publication...
  16. ncbi Complete genome sequence of Salmonella enterica serovar Typhimurium LT2
    M McClelland
    Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, California 92121, USA
    Nature 413:852-6. 2001
    ..Most of these homologues were previously unknown, and 50 may be exported to the periplasm or outer membrane, rendering them accessible as therapeutic or vaccine targets...
  17. pmc Metagenomics: application of genomics to uncultured microorganisms
    Jo Handelsman
    Department of Plant Pathology, University of Wisconsin Madison, Madison, WI 53706, USA
    Microbiol Mol Biol Rev 68:669-85. 2004
    ..The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies...
  18. 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...
  19. pmc The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates
    David A Rasko
    Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201, USA
    J Bacteriol 190:6881-93. 2008
    ..This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens...
  20. pmc Phage response to CRISPR-encoded resistance in Streptococcus thermophilus
    Hélène Deveau
    Departement de Biochimie et de Microbiologie, Faculte des sciences et de genie, Groupe de Recherche en Ecologie Buccale, Felix d Herelle Reference Center for Bacterial Viruses, Universite Laval, Quebec City, Quebec G1V 0A6, Canada
    J Bacteriol 190:1390-400. 2008
    ..Finally, we show through the analyses of 20 mutant phages that virulent phages are rapidly evolving through single nucleotide mutations as well as deletions, in response to CRISPR1...
  21. pmc An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants
    Nicole T Liberati
    Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
    Proc Natl Acad Sci U S A 103:2833-8. 2006
    ..Comparison of the genes disrupted in the PA14 transposon insertion library with an independently constructed insertion library in P. aeruginosa strain PAO1 provides an estimate of the number of P. aeruginosa essential genes...
  22. pmc GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
    J Besemer
    School of Biology and School of Mathematics, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
    Nucleic Acids Res 29:2607-18. 2001
    ..These motifs were shown to possess a significant variability, the functional and evolutionary connections of which are discussed...
  23. ncbi Environmental genome shotgun sequencing of the Sargasso Sea
    J Craig Venter
    Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
    Science 304:66-74. 2004
    ..2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity...
  24. pmc A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes
    Daniel H Haft
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Comput Biol 1:e60. 2005
    ..It is evident from this analysis that CRISPR/cas loci are larger, more complex, and more heterogeneous than previously appreciated...
  25. pmc The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
    Ibtissem Grissa
    Univ Paris Sud, Institut de Genetique et Microbiologie, UMR 8621, Orsay, France
    BMC Bioinformatics 8:172. 2007
    ..As new genome sequences become available it appears necessary to develop automated scanning tools to make available CRISPRs related information and to facilitate additional investigations...
  26. pmc Essential genes of a minimal bacterium
    John I Glass
    Synthetic Biology Group, J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 103:425-30. 2006
    ..Genes encoding proteins of unknown function constitute 28% of the essential protein-coding genes set. Disruption of some genes accelerated M. genitalium growth...
  27. pmc Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients
    Eric E Smith
    Genome Center, Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 103:8487-92. 2006
    ..aeruginosa strains present in advanced CF infections differ systematically from those of "wild-type" P. aeruginosa and that these differences may offer new opportunities for treatment of this chronic disease...
  28. ncbi DNA-DNA hybridization values and their relationship to whole-genome sequence similarities
    Johan Goris
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Int J Syst Evol Microbiol 57:81-91. 2007
    ..It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available...
  29. pmc Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion
    Harald Brussow
    Nestle, Research Center, Vers chez les Blanc, CH 1000 Lausanne, Switzerland
    Microbiol Mol Biol Rev 68:560-602, table of contents. 2004
    ..Prophages also contribute to the diversification of the bacterial genome architecture. In many cases, they actually represent a large fraction of the strain-specific DNA sequences...
  30. pmc Comparative genomics of the lactic acid bacteria
    K Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Proc Natl Acad Sci U S A 103:15611-6. 2006
    ....
  31. ncbi Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus
    Binh An Diep
    Department of Medicine, University of California, San Francisco General Hospital, San Francisco, CA 94143, USA
    Lancet 367:731-9. 2006
    ..Our aim was to sequence its genome and compare it with those of other strains of S aureus to try to identify genes responsible for its distinctive epidemiological and virulence properties...
  32. ncbi The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome
    Mohammed Sebaihia
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Nat Genet 38:779-86. 2006
    ..The extreme genome variability was confirmed by whole-genome microarray analysis; it may reflect the organism's niche in the gut and should provide information on the evolution of virulence in this organism...
  33. ncbi The uncultured microbial majority
    Michael S Rappé
    Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
    Annu Rev Microbiol 57:369-94. 2003
    ..Genome sequence information that would allow ribosomal RNA gene trees to be related to broader patterns in microbial genome evolution is scant, and therefore microbial diversity remains largely unexplored territory...
  34. pmc A new evolutionary scenario for the Mycobacterium tuberculosis complex
    R Brosch
    Unite de Genetique Moleculaire Bacterienne, Laboratoire de Génomique des Microorganismes Pathogènes, and Centre National de Référence des Mycobactéries, Institut Pasteur, 25 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
    Proc Natl Acad Sci U S A 99:3684-9. 2002
    ..bovis lineage separated from the M. tuberculosis lineage. This observation suggests that the common ancestor of the tubercle bacilli resembled M. tuberculosis or M. canettii and could well have been a human pathogen already...
  35. pmc Genomic insights that advance the species definition for prokaryotes
    Konstantinos T Konstantinidis
    Center for Microbial Ecology, and Department of Crop and Soil Sciences, Michigan State University, East Lansing, MI 48824, USA
    Proc Natl Acad Sci U S A 102:2567-72. 2005
    ....
  36. pmc Complete genome sequence of Lactobacillus plantarum WCFS1
    Michiel Kleerebezem
    Wageningen Centre for Food Sciences, P O Box 557, 6700 AN Wageningen, The Netherlands
    Proc Natl Acad Sci U S A 100:1990-5. 2003
    ..These findings suggest that these genes, which provide an important part of the interaction of L. plantarum with its environment, form a lifestyle adaptation region in the chromosome...
  37. ncbi Host-bacterial mutualism in the human intestine
    Fredrik Backhed
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Science 307:1915-20. 2005
    ..We are also starting to understand how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ...
  38. ncbi A molecular view of microbial diversity and the biosphere
    N R Pace
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Science 276:734-40. 1997
    ....
  39. ncbi The microbial pan-genome
    Duccio Medini
    Immunobiological Research Institute of Siena IRIS, Chiron Vaccines, Via Fiorentina 1, 53100 Siena, Italy
    Curr Opin Genet Dev 15:589-94. 2005
    ..Given that the number of unique genes is vast, the pan-genome of a bacterial species might be orders of magnitude larger than any single genome...
  40. pmc A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
    Adam M Feist
    Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
    Mol Syst Biol 3:121. 2007
    ..The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism...
  41. pmc Genomic islands: tools of bacterial horizontal gene transfer and evolution
    Mario Juhas
    Clinical Microbiology and Infectious Diseases, Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford, UK
    FEMS Microbiol Rev 33:376-93. 2009
    ..Depending on the composition of gene modules, the same type of GEIs can promote survival of pathogenic as well as environmental bacteria...
  42. ncbi Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
    Falk Warnecke
    DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nature 450:560-5. 2007
    ..Our results underscore how complex even a 1-microl environment can be...
  43. pmc New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis
    Michael G Smith
    Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    Genes Dev 21:601-14. 2007
    ..The DNA sequencing approach described in this study allows the rapid elucidation of the DNA sequence of any microbe and, when combined with genetic screens, can identify many novel genes important for microbial pathogenesis...
  44. ncbi Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen
    C K Stover
    PathoGenesis Corporation, Seattle, Washington 98119, USA
    Nature 406:959-64. 2000
    ..aeruginosa strain PAO1. At 6.3 million base pairs, this is the largest bacterial genome sequenced, and the sequence provides insights into the basis of the versatility and intrinsic drug resistance ..
  45. 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...
  46. pmc Evolutionary conservation of sequence and secondary structures in CRISPR repeats
    Victor Kunin
    DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Genome Biol 8:R61. 2007
    ..It has been recently shown that CRISPR provides acquired resistance against viruses in prokaryotes...
  47. pmc The RAST Server: rapid annotations using subsystems technology
    Ramy K Aziz
    Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA
    BMC Genomics 9:75. 2008
    ..The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them...
  48. pmc The complete genome sequence of Mycobacterium bovis
    Thierry Garnier
    Unité de Génétique Moléculaire Bactérienne and PT4 Annotation, Genopole, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    Proc Natl Acad Sci U S A 100:7877-82. 2003
    ..bovis, implying that differential gene expression may be the key to the host tropisms of human and bovine bacilli. The genome sequence therefore offers major insight on the evolution, host preference, and pathobiology of M. bovis...
  49. ncbi Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin
    Alexander Bolotin
    Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas, France
    Microbiology 151:2551-61. 2005
    ..The presence of gene fragments in CRISPR structures and the nuclease motifs in cas genes of both cluster types suggests that CRISPR formation involves a DNA degradation step...
  50. ncbi Comparisons of dN/dS are time dependent for closely related bacterial genomes
    Eduardo P C Rocha
    Atelier de BioInformatique, Universite Paris VI, 75005 Paris, France
    J Theor Biol 239:226-35. 2006
    ..We conclude that, because of the critical effect of time since divergence, inter-taxa comparisons are only possible by comparing trajectories of dN/dS over time and it is not valid to compare taxa on the basis of single time points...
  51. pmc Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus
    Philippe Horvath
    Danisco France SAS, BP10, F 86220 Dangé Saint Romain, France
    J Bacteriol 190:1401-12. 2008
    ..Also, CRISPRs provide critical insights into the relationships between prokaryotes and their environments, notably the coevolution of host and viral genomes...
  52. pmc Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition
    Tristan Lefebure
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    Genome Biol 8:R71. 2007
    ..This study employs comparative evolutionary analyses of 26 Streptococcus genomes to yield an improved understanding of the relative roles of recombination and positive selection in pathogen adaptation to their hosts...
  53. pmc TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
    Jeremy D Selengut
    TIGR, Bioinformatics Department, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 35:D260-4. 2007
    ..The TIGRFAMs and Genome Properties systems can be accessed at http://www.tigr.org/TIGRFAMs and http://www.tigr.org/Genome_Properties...
  54. pmc Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus
    William Martin
    Institut fur Botanik, Heinrich Heine Universitat, Universitatsstrasse 1, 40225 Dusseldorf, Germany
    Proc Natl Acad Sci U S A 99:12246-51. 2002
    ....
  55. pmc Genome of the bacterium Streptococcus pneumoniae strain R6
    J Hoskins
    Infectious Diseases Research and Clinical Investigation, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
    J Bacteriol 183:5709-17. 2001
    ..Among those proteins there may be new targets for vaccine and antibiotic development...
  56. pmc Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis
    Timothy P Stinear
    Department of Microbiology, Monash University, Clayton 3800, Australia
    Genome Res 18:729-41. 2008
    ..tuberculosis. The work described herein provides a foundation for using M. marinum to better understand the determinants of pathogenesis of tuberculosis...
  57. pmc Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways
    Nicholas R Thomson
    The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 18:1624-37. 2008
    ..Enteritidis-harboring mutations in functional homologs of the pseudogenes present in S. Gallinarum could provide an experimentally tractable route toward unraveling the genetic basis of host adaptation in S. enterica...
  58. ncbi The multifarious, multireplicon Burkholderia cepacia complex
    Eshwar Mahenthiralingam
    Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3TL, UK
    Nat Rev Microbiol 3:144-56. 2005
    ..Here we highlight the unique characteristics of the Bcc, focusing on the factors that determine virulence...
  59. ncbi Emergent properties of reduced-genome Escherichia coli
    György Pósfai
    Institute of Biochemistry, Biological Research Center, H 6726 Szeged, Hungary
    Science 312:1044-6. 2006
    ..Eradication of stress-induced transposition evidently stabilized the MDS genomes and provided some of the new properties...
  60. ncbi Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses
    Gene W Tyson
    Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, USA
    Environ Microbiol 10:200-7. 2008
    ..Results reinforce the importance of phage-host interactions in shaping microbial ecology and evolution over very short time scales...
  61. ncbi Leptospirosis
    Alan J A McBride
    Gonçalo Moniz Research Centre, Oswaldo Cruz Foundation, Ministry of Health, Rua Waldemar Falcao 121, 40295 001 Salvador, Bahia, Brazil
    Curr Opin Infect Dis 18:376-86. 2005
    ..This review addresses the issues in the epidemiology, diagnosis and clinical management which confront public health responses, and highlights the progress made towards understanding the Leptospira genome, biology and pathogenesis...
  62. pmc Genome sequence of Avery's virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6
    Joel A Lanie
    Department of Biology, Indiana University Bloomington, Jordan Hall 142, Bloomington, IN 47405, USA
    J Bacteriol 189:38-51. 2007
    ....
  63. pmc Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements
    Martin Wu
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:E69. 2004
    ..With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections...
  64. pmc The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode
    Jeremy Foster
    Molecular Parasitology Division, New England Biolabs, Beverly, Massachusetts, USA
    PLoS Biol 3:e121. 2005
    ..Analysis of this first sequenced endosymbiont genome from a filarial nematode provides insight into endosymbiont evolution and additionally provides new potential targets for elimination of cutaneous and lymphatic human filarial disease...
  65. ncbi Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440
    K E Nelson
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Environ Microbiol 4:799-808. 2002
    ..Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production...
  66. ncbi The composite genome of the legume symbiont Sinorhizobium meliloti
    F Galibert
    UMR6061-CNRS, , , , F-35043 Rennes Cedex, France
    Science 293:668-72. 2001
    ..The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments...
  67. pmc Evolution of sensory complexity recorded in a myxobacterial genome
    B S Goldman
    Monsanto Company, St Louis, MO 63167, USA
    Proc Natl Acad Sci U S A 103:15200-5. 2006
    ..Families of genes encoding the production of secondary metabolites are overrepresented in the genome but may have been received by horizontal gene transfer and are likely to be important for predation...
  68. pmc Dynamics of Pseudomonas aeruginosa genome evolution
    Kalai Mathee
    Department of Molecular Microbiology and Immunology, College of Medicine, School of Computing and Information Sciences, College of Engineering, Florida International University, Miami, FL 33199, USA
    Proc Natl Acad Sci U S A 105:3100-5. 2008
    ..Consequently, this organism can survive in a wide range of environmental reservoirs that can serve as sources of the infecting organisms...
  69. pmc Enzyme-specific profiles for genome annotation: PRIAM
    Clotilde Claudel-Renard
    Laboratoire de Genetique Cellulaire, INRA, INRA CNRS, BP27, 31326 Castanet Tolosan Cedex, France
    Nucleic Acids Res 31:6633-9. 2003
    ..The results of this automated method were compared with the original genome annotation and visualised on KEGG graphs in order to facilitate the interpretation of metabolic pathways and to highlight potentially missing enzymes...
  70. ncbi A genomic view of the human-Bacteroides thetaiotaomicron symbiosis
    Jian Xu
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
    Science 299:2074-6. 2003
    ..These and other expanded paralogous groups shed light on the molecular mechanisms underlying symbiotic host-bacterial relationships in our intestine...
  71. ncbi Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
    N T Perna
    Genome Center of Wisconsin, and Department of Animal Health and Biomedical Sciences, University of Wisconsin, Madison 53706, USA
    Nature 409:529-33. 2001
    ..These include candidate virulence factors, alternative metabolic capacities, several prophages and other new functions--all of which could be targets for surveillance...
  72. pmc Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
    Mark W Silby
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Centre for Adaptation Genetics and Drug Resistance, Boston, MA 02111, USA
    Genome Biol 10:R51. 2009
    ..A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species...
  73. ncbi The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins
    Jorn Kalinowski
    Institut für Genomforschung, Universitat Bielefeld, Universitatsstrasse 25, D 33615 Bielefeld, Germany
    J Biotechnol 104:5-25. 2003
    ..As an example for biotechnological application the complete genome sequence was used to reconstruct the metabolic flow of carbon into a number of industrially important products derived from the amino acid L-aspartate...
  74. pmc Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen
    Dragana Ajdic
    Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
    Proc Natl Acad Sci U S A 99:14434-9. 2002
    ....
  75. 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...
  76. pmc Prodigal: prokaryotic gene recognition and translation initiation site identification
    Doug Hyatt
    Computational Biology and Bioinformatics Group, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    BMC Bioinformatics 11:119. 2010
    ..Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals...
  77. pmc Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000
    Helene Feil
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 102:11064-9. 2005
    ..The genomic comparison suggests that several unique genes for Pss B728a such as ectoine synthase, DNA repair, and antibiotic production may contribute to the epiphytic fitness and stress tolerance of this organism...
  78. pmc Massive comparative genomic analysis reveals convergent evolution of specialized bacteria
    Vicky Merhej
    Faculty of Medicine, Unit for Research on Emergent and Tropical Infectious Diseases, CNRS IRD UMR 6236 IFR48, University of the Mediterranean, Marseilles, France
    Biol Direct 4:13. 2009
    ..The growing number of available sequenced genomes makes it possible to perform a statistical comparative analysis of 317 genomes from bacteria with different lifestyles...
  79. pmc Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution
    Tal Dagan
    Institut für Botanik III, Heinrich Heine Universitat Dusseldorf, Universitatsstrasse 1, 40225 Dusseldorf, Germany
    Proc Natl Acad Sci U S A 105:10039-44. 2008
    ....
  80. ncbi Prophages and bacterial genomics: what have we learned so far?
    Sherwood Casjens
    Department of Pathology, University of Utah Medical School, Salt Lake City, UT 84132 2501, USA
    Mol Microbiol 49:277-300. 2003
    b>Bacterial genome nucleotide sequences are being completed at a rapid and increasing rate. Integrated virus genomes (prophages) are common in such genomes...
  81. pmc The consequences of genetic drift for bacterial genome complexity
    Chih Horng Kuo
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    Genome Res 19:1450-4. 2009
    ..This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria...
  82. pmc Comparative analysis of Acinetobacters: three genomes for three lifestyles
    David Vallenet
    Génomique Métabolique, CNRS UMR8030, CEA Institut de Génomique Genoscope, Evry, France
    PLoS ONE 3:e1805. 2008
    ..Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil...
  83. pmc The CGView Server: a comparative genomics tool for circular genomes
    Jason R Grant
    Department of Agricultural, Food and Nutritional Science, University of Alberta, Canada
    Nucleic Acids Res 36:W181-4. 2008
    ..The CGView Server can be accessed at http://stothard.afns.ualberta.ca/cgview_server/..
  84. pmc Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts
    Byung Kwan Cho
    Department of Bioengineering, University of California San Diego, La Jolla, California 92093 0412, USA
    Genome Res 18:900-10. 2008
    ..These novel results provide new insight into how Fis modulates DNA topology at a genome scale and thus advance our understanding of the architectural bases of the E. coli nucleoid...
  85. pmc Trends between gene content and genome size in prokaryotic species with larger genomes
    Konstantinos T Konstantinidis
    Center for Microbial Ecology and Departments of Crop and Soil Sciences, Michigan State University, East Lansing, MI 48824 1325, USA
    Proc Natl Acad Sci U S A 101:3160-5. 2004
    ..These trends suggest that larger genome-sized species may dominate in environments where resources are scarce but diverse and where there is little penalty for slow growth, such as soil...
  86. pmc Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions
    Nicolaas C Gey van Pittius
    DST NRF Centre of Excellence in Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
    BMC Evol Biol 6:95. 2006
    ....
  87. pmc Evolution of symbiotic bacteria in the distal human intestine
    Jian Xu
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Biol 5:e156. 2007
    ....
  88. ncbi Explaining microbial population genomics through phage predation
    Francisco Rodriguez-Valera
    Departmento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, Spain
    Nat Rev Microbiol 7:828-36. 2009
    ..Periodic selection and phage predation dynamics are not mutually exclusive; we compare their predictions to shed light on the ecological circumstances under which each type of dynamics could predominate...
  89. pmc Determination of the core of a minimal bacterial gene set
    Rosario Gil
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartat Oficial 2085, 46071 Valencia, Spain
    Microbiol Mol Biol Rev 68:518-37, table of contents. 2004
    ..The main features of such a minimal gene set, as well as the metabolic functions that must be present in the hypothetical minimal cell, are discussed...
  90. ncbi Genome-wide experimental determination of barriers to horizontal gene transfer
    Rotem Sorek
    Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
    Science 318:1449-52. 2007
    ..coli, a computational analysis of gene-transfer rates across available bacterial and archaeal genomes supports that the barriers observed in our study are general across the tree of life...
  91. pmc VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics
    Jian Yang
    State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100176, China
    Nucleic Acids Res 36:D539-42. 2008
    ..VFDB 2008 release offers more user-friendly tools for comparative pathogenomics and it is publicly accessible at http://www.mgc.ac.cn/VFs/...
  92. pmc Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition
    Vinita Joardar
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    J Bacteriol 187:6488-98. 2005
    ..With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific...
  93. ncbi Insertion sequences in prokaryotic genomes
    Patricia Siguier
    Laboratoire de Microbiologie et Génétique Moléculaires UMR5100 CNRS Campus Université Paul Sabatier 118, route de Narbonne, F 31062 Toulouse Cedex, France
    Curr Opin Microbiol 9:526-31. 2006
    ..They can have large and spectacular effects in shaping and reshuffling the bacterial genome. Recent studies have provided dramatic examples of such IS activity, including massive IS expansion during ..
  94. pmc De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
    Josephine A Reinhardt
    Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
    Genome Res 19:294-305. 2009
    ..syringae pan-genome, a corresponding contraction of the core genome, and a further diversification of the type III effector complement for this important plant pathogen species...
  95. pmc DOOR: a database for prokaryotic operons
    Fenglou Mao
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 37:D459-63. 2009
    ..We believe that DOOR provides a useful resource to many biologists working on bacteria and archaea, which can be accessed at http://csbl1.bmb.uga.edu/OperonDB...
  96. ncbi An obesity-associated gut microbiome with increased capacity for energy harvest
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University, St Louis, Missouri 63108, USA
    Nature 444:1027-31. 2006
    ..These results identify the gut microbiota as an additional contributing factor to the pathophysiology of obesity...
  97. pmc Molecular correlates of host specialization in Staphylococcus aureus
    Lisa Herron-Olson
    Department of Microbiology, Veterinary Pathobiology and Biomedical Genomics Center, University of Minnesota, Saint Paul, Minnesota, United States of America
    PLoS ONE 2:e1120. 2007
    ..aureus clonal groups associated with human and ruminant infection. However, the molecular basis of host specialization in S. aureus is not understood...
  98. pmc Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum
    Marco Ventura
    Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parco Area delle Scienze 11A, 43100 Parma, Italy
    Microbiol Mol Biol Rev 71:495-548. 2007
    ..This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context...
  99. ncbi Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity
    Christel Cazalet
    Laboratoire de Génomique des Microorganismes Pathogènes and CNRS URA 2171, Institut Pasteur, 28, rue du Dr Roux, 75724 Paris Cedex 15, France
    Nat Genet 36:1165-73. 2004
    ..The genome thus reflects the history and lifestyle of L. pneumophila, a human pathogen of macrophages that coevolved with fresh-water amoebae...
  100. ncbi Functional metagenomic profiling of nine biomes
    Elizabeth A Dinsdale
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nature 452:629-32. 2008
    ....
  101. pmc Genetic basis of virulence attenuation revealed by comparative genomic analysis of Mycobacterium tuberculosis strain H37Ra versus H37Rv
    HuaJun Zheng
    State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
    PLoS ONE 3:e2375. 2008
    ..These findings have implications not only for improved understanding of pathogenesis of M. tuberculosis but also for development of new vaccines and new therapeutic agents...

Research Grants63

  1. High Throughput Protein Production by Novel E. coli Expression-Secretion System
    WILLIAM MACCONNELL; Fiscal Year: 2006
    ..They will improve protein production and yield high quality protein. These products will be essentially ready for market at the end of Phase II. [unreadable] [unreadable] [unreadable]..
  2. Iron acquisition mechanisms utilized by Neisseria gonorrhoeae
    Cynthia Nau Cornelissen; Fiscal Year: 2010
    ..Finally, the contribution that TdfF provides to growth and survival within cultured cells will be evaluated using intracellular survival assays and state-of-the-art immunofluorescence microscopy techniques. ..
  3. Characterization of new toxins (YmgD and YdfD) from E.coli, targeting cell wall
    Hisako Masuda; Fiscal Year: 2012
    ....
  4. Microbial Diversity in Mechanisms of Disulfide Bond Formation and Reduction
    Dana Boyd; Fiscal Year: 2013
    ..Also, since disulfide-bonded proteins are found in many of the most prominent bacterial virulence factors, these studies may contribute to antibiotic development. ..
  5. Identification of vaccine antigens based on expression in blood
    PETER TRIP BEERNINK; Fiscal Year: 2011
    ....
  6. Structure and mechanism of CRISPR interference.
    Ailong Ke; Fiscal Year: 2013
    ..Our findings will serve to reveal the common theme and mechanistic diversity among different CRISPR-Cas systems. ..
  7. Understanding of a Family of Bacterial Transcription Factors
    Hwan Youn; Fiscal Year: 2012
    ..The proteins can be good therapeutic targets;therefore, the knowledge gained from this study might lead to the development of an alternative therapeutic strategy to control the pathogen. ..
  8. Decoding the roles of critical genes of unknown function in M. tuberculosis
    Dirk Schnappinger; Fiscal Year: 2013
    ..RELEVANCE: A huge number of bacterial genome sequences have become available yet a substantial fraction of their identified genes have no known function, ..
  9. In vivo observations of transcription at single-nucleotide resolution
    MATTHEW HERBERT LARSON; Fiscal Year: 2013
    ..vitro and in vivo transcription measurements in order to assess the prevalence of pausing across the complete bacterial genome, as well as to determine their role in regulating gene expression...
  10. Helper phage mobilization of S. aureus superantigen pathogenicity islands
    Gail E Christie; Fiscal Year: 2010
    ..systemic infections by producing several toxins from genes carried on so-called pathogenicity islands in the bacterial genome. Understanding the mechanism by which these pathogenicity islands are mobilized by staphylococcal ..
  11. Structural basis for pathogenicity island mobilization in S. aureus
    Terje Dokland; Fiscal Year: 2013
    ..systemic infections by producing several toxins from genes carried on so-called pathogenicity islands in the bacterial genome. The bacteriophage/pathogenicity island system under study in this project is of special interest for its ..
  12. CHAPERONE ASSISTED PILI ASSEMBLY IN PATHOGENIC E COLI
    Scott J Hultgren; Fiscal Year: 2013
    ..A single bacterial genome can encode as many as twelve such systems...
  13. Effect of Crohn's Disease Risk Alleles on Enteric Microbiota
    Ellen Li; Fiscal Year: 2010
    ..Genetic probes for pathogenic commensal organisms developed by mining the bacterial genome data and shotgun sequencing data will be used to test the hypothesis that increased numbers of these ..
  14. STAPHYLOCOCCAL METHICILLIN RESISTANCE LOCUS
    Gordon Archer; Fiscal Year: 2009
    ..In addition, we hope to add to the body of data that associates changes in the bacterial genome with exposure to antimicrobials that target the cell wall and cell membrane...
  15. Solution NMR Structure and Function of the Integral Membrane Protein DsbB
    JOHN HACKETT BUSHWELLER; Fiscal Year: 2013
    ..If we can inhibit the function of DsbB, we will have a new approach to treat bacterial infections. To that end, we are proposing to develop inhibitors of DsbB, a new potential approach to treating bacterial infections. ..
  16. ANALYSIS AND ANNOTATION OF THE E. COLI GENOME SEQUENCE
    KENNETH EDWARD RUDD; Fiscal Year: 2012
    ..EcoGene.org demonstrates that a high impact, reliable bacterial genome database can be constructed with open source tools and maintained with low overhead in an academic research ..
  17. STRUCTURE AND FUNCTION OF RESPONSE REGULATOR PROTEINS
    Ann M Stock; Fiscal Year: 2013
    ..Hence, understanding the molecular details of signaling pathways and their protein components provides a foundation for the development of antimicrobial drugs. ..
  18. Phylogenomic epidemiology of Clostridium difficile
    Seth T Walk; Fiscal Year: 2013
    ..will be used to characterize the genomic diversity of a large collection of isolates (n=5,000) and assess the bacterial genome-based correlates of CDI severity...
  19. Genome Variability and Population Processes of Lyme Disease Pathogens
    Weigang Qiu; Fiscal Year: 2013
    ..customized genome database, a suite of Perl/BioPerl based software tools ("DNATweezers"), and a simulator of bacterial genome evolution ("SimBac"). The latter two tools have been released into public repository SourceForge...
  20. Genetics of MRSA Infection
    George M Weinstock; Fiscal Year: 2010
    ..for variants using the Genome Center at Washington University variant detection pipeline as modified for bacterial genome analysis. 8...
  21. Identifying novel Pseudomonas Aeruginosa pathogenesis-associated genomic islands
    EGON ANDERSON OZER; Fiscal Year: 2011
    ..Genomic islands, regions of DNA contained within the bacterial genome that vary between strains, comprise up to 10% of the P. aeruginosa genome, but remain relatively unexplored...
  22. Diversity-Generating Retroelements in Phage and Bacterial Genomes
    Jeffery F Miller; Fiscal Year: 2010
    ..2. Probe the receptor repertoire and the structural basis of ligand recognition by a DGR-encoded receptor protein. 3. Investigate DGR function in the human gastrointestinal commensal Bacteroides thetaiotaomicron. ..
  23. Comprehensive transcriptome analysis for Porphyromonas gingivalis
    Tsute Chen; Fiscal Year: 2009
    ..array platform allows the design of tiling arrays that contains probes covering every nucleotide of a typical bacterial genome. The use of genomic tiling arrays permits true genome-wide monitoring of all the RNA molecules in parallel ..
  24. Pervasive transcription in bacterial genomes
    JOSEPH THOMAS WADE; Fiscal Year: 2010
    ..We have identified over 1,000 novel RNAs in the model bacterium, Escherichia coli. We will determine the impact of these RNAs on gene expression. ..
  25. How bacteria corrupt the host vesicular trafficking:Role of SNARE-like Proteins
    FABIENNE MICHELLE PAUMET; Fiscal Year: 2012
    ..Additionally, the proposed studies have practical applications for the development of new therapeutic approaches to induce the clearance of intracellular bacteria by the host cell. ..
  26. A new genetic approach for studying prions and other pathogenic protein aggregate
    Ann Hochschild; Fiscal Year: 2011
    ..abstract_text> ..
  27. A new genetic approach for studying prions and other pathogenic protein aggregate
    Ann Hochschild; Fiscal Year: 2012
    ..abstract_text> ..
  28. CSHL Course on Advanced Sequencing Technologies &Applications
    David J Stewart; Fiscal Year: 2013
    ....
  29. Mechanisms and Population Genomics of Pneumococcal Antigenic Diversity
    Marc Lipsitch; Fiscal Year: 2013
    ....
  30. Evolution of a bacterial genome encoding increased virulence: the genomics of Hel
    Mark H Forsyth; Fiscal Year: 2012
    ..To examine the evolution of virulence in this significant human pathogen, more research is needed on the genomes of H. pylori strains that produce disease less frequently ..
  31. Illumina Genome Analyzer IIx
    Norma J Nowak; Fiscal Year: 2010
    ..abstract_text> ..
  32. Repair of Damaged Chromosomes Mediated by the Bacterial RecN Protein
    Shelley Lusetti; Fiscal Year: 2013
    ..Although extensive genetic evidence underscores the importance of RecN proteins to bacterial genome maintenance, there has been little substantive biochemical investigation into their function and, ..
  33. The Evolutionary Dynamics of Plasmid Uptake in Pathogenic Bacteria
    ARIEL WEINBERGER; Fiscal Year: 2013
    ....
  34. DNA PATTERN IDENTIFICATION AND ANALYSIS
    Gary D Stormo; Fiscal Year: 2013
    ....
  35. Discovery of inhibitors of the lipopolysaccharide synthesis pathway enzymes LpxA
    Vicki Nienaber; Fiscal Year: 2010
    ..Chemical properties of successful antibiotics have been identified and will be adhered to through the course of this study. ..
  36. Genomic Interactions between Psyllids and Their Obligately Intracellular Bacteria
    DANIEL SLOAN; Fiscal Year: 2012
    ..Hemiptera) and their nutritional symbiont Carsonella, which exhibits one of the most extreme cases of bacterial genome reduction and degradation ever identified...
  37. Development of novel field-appropriate differential diagnostics of multiple patho
    Irina Smolina; Fiscal Year: 2013
    ..Once developed for pathogens under study, the combined workflow would be readily adaptable for rapid sensitive detection of other clinically relevant organisms. ..
  38. Molecular prostheses for mitochondrial disorders
    VAMSI KRISHNA MOOTHA; Fiscal Year: 2013
    ..If successful, this project will yield an entire pipeline of small molecules and proteins that may represent the starting point for a new class of therapeutics for these disorders. ..
  39. Measuring whole genome expression, cell by cell: bistability in Vibrio cholerae
    Richard N Zare; Fiscal Year: 2010
    ..will develop a robust and broadly applicable method to characterize the expression behavior of each gene in a bacterial genome, by individual cells, in response to a suite of biologically relevant conditions...
  40. Evolutionary Analysis of Bacterial Genomes: High-Throughput Computational Tools
    Luay Nakhleh; Fiscal Year: 2012
    ..3) Algorithmic techniques for phylogenetic (macro-level) analyses of genomes for detecting HGT. (4) Software tools that implement the protocols and methodologies and make them available to the research community. ..
  41. SciBay: A New Methodology for Scientific Collaboration and Gene Function Determi
    MARTIN A contact STEFFEN; Fiscal Year: 2010
    ..A key factor in deciding priorities will be the health implications of successful predictions. ..
  42. Extending Bayesian Phylogenetic Analysis
    John P Huelsenbeck; Fiscal Year: 2013
    ..For example, by comparing the DNA sequences of deferent genes, we can learn about how natural selection has acted. This proposal develops improved methods for the analysis of DNA sequences. 1 ..
  43. DNA SEQUENCE OF STAPHYLOCOCCUS AUREUS 8325 GENOME
    JOHN LANDOLO; Fiscal Year: 1999
    ..Therefore, as a single specific aim, we will sequence and annotate the 2.8 Mb genome of this important pathogen. ..
  44. Polony Sequencing and the $1000 Genome
    Jeremy S Edwards; Fiscal Year: 2012
    ..We firmly believe that polony sequencing technology, as proposed, can achieve the $1,000 genome goal and undoubtedly revolutionize medicine. ..
  45. Biosynthesis and Physiology of Vitamin B12 in Prokaryotes
    MICHIKO TAGA; Fiscal Year: 2009
    ..Together, these studies will contribute to the overall understanding of B12 biosynthesis and the function of B12 in bacteria-host interactions. ..
  46. Modification of Helicobacter pylori Lipid A
    MICHAEL TRENT; Fiscal Year: 2004
    ..pylori and H. heihnannii but also lay the foundation for new molecular insights into the pathogenesis of these unique organisms. ..
  47. Gene Expression Levels Across Diverse Genomes
    Samuel Karlin; Fiscal Year: 2006
    ..We can predict highly expressed genes in each bacterial genome, which correlate very well with 2D-gel protein abundances...
  48. RECOMBINANT LISTERIA--BIOLOGIC VACCINE VECTOR FOR FIV
    Gregg Dean; Fiscal Year: 2001
    ..antigens into the cytoplasm of macrophages either through stable integration of viral sequences into the bacterial genome or by transfecting the bacteria with a plasmid containing viral genes that are driven by a eukaryotic ..
  49. CELL-SURFACE PROTEINS IN CAMPYLOBACTER FETUS VIRULENCE
    Martin Blaser; Fiscal Year: 2004
    ..The homologs share multiple areas of homology with each other, are clustered on the bacterial genome, and together with an invertible region (IR) of 6kb form the sap locus...
  50. Oral Immunotherapy for C. difficile Disease via Bacteria
    Thomas Parks; Fiscal Year: 2005
    ..These strains will contain the expression cassettes stably integrated into the bacterial genome, lack antibiotic resistance, and will not be able to survive outside the body...
  51. Analyses of sodium bioenergetics in Vibrio cholerae
    CLAUDIA C HASE; Fiscal Year: 2010
    ..The recent completion of many bacterial genome sequences revealed the presence of genes encoding a variety of sodium-dependent systems in many organisms, ..
  52. Comparative Genomics of the Chlamydiaceae
    Garry Myers; Fiscal Year: 2007
    ..With broad and international support from the scientific community, we consider this a groundbreaking proposal and anticipate it will be a benchmark study in comparative microbial genomics. ..
  53. 454 Life Sciences Massively Parallel System for DNA Sequencing Technology
    Marcel Margulies; Fiscal Year: 2007
    ..Michael Egholm. This facility will cover less than 3,000 sq. ft and be staffed by less than 10 personnel. We will be ready to deploy such a facility commercially at other sites at the end of year 3. [unreadable] [unreadable]..
  54. Large Scale Chemical Screen Against Pathogenic Bacteria
    Sanford Simon; Fiscal Year: 2003
    ..They are encoded on the pathogenicity islands and are not part of the host bacterial genome. This is an application for a large-scale chemical screen for agents that affect the gating of these channels ..
  55. Identifying Periodontal Antigens By Protein Microarray
    Douglas Darling; Fiscal Year: 2006
    ..This approach takes advantage of the extremely high gene density of the bacterial genome, which lacks introns, and of the technological advances for construction of microarrays...
  56. The alpha subunits of Francisella tularensis RNA polymerase
    SIMON DOVE; Fiscal Year: 2007
    ..tularensis. [unreadable] [unreadable] [unreadable]..
  57. Regulation of restriction-modification genes expression
    Konstantin Severinov; Fiscal Year: 2007
    ..These systems are widespread; they contribute significantly to bacterial genome evolution and are practically significant as a source of tools for genetic engineering...
  58. A Microbial Genome Reference Platform for Metagenomics
    JOSEPH FRANK PETROSINO; Fiscal Year: 2010
    ..When all technical advances are combined, the cost of sequencing an individual bacterial genome will be less than $1,000.
  59. FUNCTIONAL GENOMICS OF E FACEIUM AND F NUCLEATUM
    Michael Fonstein; Fiscal Year: 2000
    ..proposed commercial application: not available ..
  60. GENETIC ORGANIZATION OF TREPONEMA DENTICOLA
    George Weinstock; Fiscal Year: 2000
    ....
  61. MOLECULAR DIAGNOSIS OF ORTHOPAEDIC BACTERIAL INFECTIONS
    Rocky Tuan; Fiscal Year: 2000
    ....
  62. A GENOME-DERIVED, EPITOPE-DRIVEN TULAREMIA VACCINE
    Anne De Groot; Fiscal Year: 2005
    ..secreted proteins will be screened for immunodominant epitopes by computer-driven (EpiMatrix) analysis of the bacterial genome. Limited in vitro assays will be performed to confirm MHC binding and immunogenicity of representative ..
  63. RECOMBINATION DIRECTED CONSTRUCTION OF PORTABLE LIBRARY
    Rodney Rothstein; Fiscal Year: 1999
    ..Therefore, a library can be designed for sequenced bacterial genomes or even human cDNAs. In addition, this technology will serve as a testing ground for these other organisms. ..