bacterial genes

Summary

Summary: The functional hereditary units of BACTERIA.

Top Publications

  1. pmc Improved microbial gene identification with GLIMMER
    A L Delcher
    Department of Computer Science, Loyola College in Maryland, Baltimore, MD 21210, USA
    Nucleic Acids Res 27:4636-41. 1999
  2. 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
  3. ncbi Genes required for mycobacterial growth defined by high density mutagenesis
    Christopher M Sassetti
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard Medical School, Boston, MA 02115, USA
    Mol Microbiol 48:77-84. 2003
  4. ncbi Small CRISPR RNAs guide antiviral defense in prokaryotes
    Stan J J Brouns
    Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, Netherlands
    Science 321:960-4. 2008
  5. 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
  6. 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
  7. pmc Sex and virulence in Escherichia coli: an evolutionary perspective
    Thierry Wirth
    Department of Molecular Biology, Schumannstrasse 21 22, Max Planck Institut für Infektionsbiologie, 10117 Berlin, Germany
    Mol Microbiol 60:1136-51. 2006
  8. ncbi The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae
    Derrick H Lenz
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Cell 118:69-82. 2004
  9. 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
  10. 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

Detail Information

Publications300 found, 100 shown here

  1. pmc Improved microbial gene identification with GLIMMER
    A L Delcher
    Department of Computer Science, Loyola College in Maryland, Baltimore, MD 21210, USA
    Nucleic Acids Res 27:4636-41. 1999
    ..When the analysis is restricted to genes that have significant homology to genes in other organisms, GLIMMER misses <1% of known genes...
  2. 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...
  3. ncbi Genes required for mycobacterial growth defined by high density mutagenesis
    Christopher M Sassetti
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard Medical School, Boston, MA 02115, USA
    Mol Microbiol 48:77-84. 2003
    ....
  4. ncbi Small CRISPR RNAs guide antiviral defense in prokaryotes
    Stan J J Brouns
    Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, Netherlands
    Science 321:960-4. 2008
    ..Our results demonstrate that the formation of mature guide RNAs by the CRISPR RNA endonuclease subunit of Cascade is a mechanistic requirement for antiviral defense...
  5. 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...
  6. 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...
  7. pmc Sex and virulence in Escherichia coli: an evolutionary perspective
    Thierry Wirth
    Department of Molecular Biology, Schumannstrasse 21 22, Max Planck Institut für Infektionsbiologie, 10117 Berlin, Germany
    Mol Microbiol 60:1136-51. 2006
    ..This long-term pattern of evolution was observed in genes distributed throughout the genome, and thereby is the likely result of episodic selection for strains that can escape the host immune response...
  8. ncbi The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae
    Derrick H Lenz
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Cell 118:69-82. 2004
    ..We propose that Hfq, together with these sRNAs, creates an ultrasensitive regulatory switch that controls the critical transition into the high cell density, quorum-sensing mode...
  9. 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...
  10. 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...
  11. 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...
  12. 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...
  13. pmc Comprehensive transposon mutant library of Pseudomonas aeruginosa
    Michael A Jacobs
    Department of Medicine, University of Washington Genome Center, Box 352145, Seattle, WA 98195 2145, USA
    Proc Natl Acad Sci U S A 100:14339-44. 2003
    ..The transposons used to generate the mutant collection have added features that should facilitate downstream studies of gene expression, protein localization, epistasis, and chromosome engineering...
  14. pmc Diversity of the human intestinal microbial flora
    Paul B Eckburg
    Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Room S 169, 300 Pasteur Drive, Stanford CA 94305 5107, USA
    Science 308:1635-8. 2005
    ..We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease...
  15. 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...
  16. 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...
  17. pmc An efficient recombination system for chromosome engineering in Escherichia coli
    D Yu
    Gene Regulation and Chromosome Biology Laboratory and Mouse Cancer Genetics Program, National Cancer Institute, Division of Basic Science, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 97:5978-83. 2000
    ..This system will be especially useful for the engineering of large bacterial plasmids such as those from bacterial artificial chromosome libraries...
  18. pmc PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin
    Bertolt Gust
    Department of Molecular Microbiology, John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom
    Proc Natl Acad Sci U S A 100:1541-6. 2003
    ....
  19. 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...
  20. pmc Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system
    Stefan Pukatzki
    Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 103:1528-33. 2006
    ..Thus, the genes encoding the VAS-related, type VI secretion system likely play an important conserved function in microbial pathogenesis and represent an additional class of targets for vaccine and antimicrobial drug-based therapies...
  21. 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...
  22. pmc Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
    Jonathan A Bernstein
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:9697-702. 2002
    ..Our results identify previously unsuspected features of mRNA decay at a global level and also indicate that generalizations about decay derived from the study of individual gene transcripts may have limited applicability...
  23. pmc Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes
    Deo Prakash Pandey
    Department of Biochemistry and Molecular Biology, University of Southern Denmark DK 5230 Odense M, Denmark
    Nucleic Acids Res 33:966-76. 2005
    ....
  24. pmc Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms
    M C Maiden
    Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
    Proc Natl Acad Sci U S A 95:3140-5. 1998
    ....
  25. 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...
  26. ncbi Identification of genes that are associated with DNA repeats in prokaryotes
    Ruud Jansen
    Department of Infectious Diseases and Immunology, Bacteriology Division, Veterinary Faculty, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
    Mol Microbiol 43:1565-75. 2002
    ..The spatial coherence of CRISPR and cas genes may stimulate new research on the genesis and biological role of these repeats and genes...
  27. 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...
  28. 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...
  29. pmc Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus
    M C Enright
    Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, Oxford University, Oxford OX1 3FY
    J Clin Microbiol 38:1008-15. 2000
    ..MLST provides an unambiguous method for assigning MRSA and MSSA isolates to known clones or assigning them as novel clones via the Internet...
  30. pmc DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes
    Ren Zhang
    Department of Epidemiology and Biostatistics, Tianjin Cancer Institute and Hospital, Tianjin 300060, China
    Nucleic Acids Res 37:D455-8. 2009
    ..These updates not only represent significant advances of DEG, but also represent the rapid progress of the essential-gene field. DEG is freely available at the website http://tubic.tju.edu.cn/deg or http://www.essentialgene.org...
  31. pmc Deletion of RD1 from Mycobacterium tuberculosis mimics bacille Calmette-Guérin attenuation
    Kaeryn N Lewis
    Department of Pediatrics, University of Washington, Seattle 98195, USA
    J Infect Dis 187:117-23. 2003
    ..Therefore, it was concluded that genes within or controlled by RD1 are essential for MTB virulence and that loss of RD1 was important in BCG attenuation...
  32. pmc Identification of a pathogenicity island required for Salmonella survival in host cells
    H Ochman
    Department of Biology, University of Rochester, NY 14627, USA
    Proc Natl Acad Sci U S A 93:7800-4. 1996
    ..The "pathogenicity island" harboring the spi genes may encode the virulence determinants that set Salmonella apart from other enteric pathogens...
  33. ncbi Pseudomonas biofilm formation and antibiotic resistance are linked to phenotypic variation
    Eliana Drenkard
    Department of Genetics, Harvard Medical School, Massahusetts General Hospital, Boston, MA 02114, USA
    Nature 416:740-3. 2002
    ..Compounds that affect PvrR function could have an important role in the treatment of CF infections...
  34. 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...
  35. ncbi The population genetics of ecological specialization in evolving Escherichia coli populations
    V S Cooper
    Center for Microbial Ecology, Michigan State University, East Lansing 48824, USA
    Nature 407:736-9. 2000
    ..Thus, antagonistic pleiotropy appears more important than mutation accumulation for the decay of unused catabolic functions in these populations...
  36. pmc Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria
    P W Postma
    E C Slater Institute, University of Amsterdam, The Netherlands
    Microbiol Rev 57:543-94. 1993
    ..In gram-positive bacteria, it has been demonstrated that HPr can be phosphorylated by ATP on a serine residue and this modification may perform a regulatory function...
  37. pmc Analysis of a complete library of putative drug transporter genes in Escherichia coli
    K Nishino
    Department of Cell Membrane Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
    J Bacteriol 183:5803-12. 2001
    ..Of these 20 ORFs, cusA, yegMNO, ydgFE, yceE, yceL, yidY, and ybjYZ are novel drug resistance genes. The fsr, bcr, yjiO, ydhE, acrD, and yhiUV genes gave broader resistance spectra than previously reported...
  38. ncbi Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients
    Zackary I Johnson
    Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar Street 48 419, Cambridge, MA 02139, USA
    Science 311:1737-40. 2006
    ..Light, nutrients, and competitor abundances also appeared to play a role in shaping different distributions...
  39. pmc Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Res 12:962-8. 2002
    ..knockout data to compare the rates of evolution and the levels of selection for essential versus nonessential bacterial genes. In contrast to the results obtained for eukaryotic genes, essential bacterial genes appear to be more ..
  40. ncbi The bacterial species challenge: making sense of genetic and ecological diversity
    Christophe Fraser
    Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
    Science 323:741-6. 2009
    ..The resulting data may help to discriminate among the many theories of prokaryotic species that have been produced to date...
  41. pmc Multilocus sequence typing system for Campylobacter jejuni
    K E Dingle
    Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, Oxford OX1 3FY, United Kingdom
    J Clin Microbiol 39:14-23. 2001
    ..Application of this approach to further isolate collections will enable an integrated global picture of C. jejuni epidemiology to be established and will permit more detailed studies of the population genetics of this organism...
  42. pmc Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"
    Herve Tettelin
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 102:13950-5. 2005
    ..Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes...
  43. ncbi SOS response promotes horizontal dissemination of antibiotic resistance genes
    John W Beaber
    Department of Microbiology, Tufts University School of Medicine and Howard Hughes Medical Institute, 136 Harrison Avenue, Boston, Massachusetts 02111, USA
    Nature 427:72-4. 2004
    ..Thus, we present a mechanism by which therapeutic agents can promote the spread of antibiotic resistance genes...
  44. pmc The genome of Rhizobium leguminosarum has recognizable core and accessory components
    J Peter W Young
    Department of Biology, University of York, York, UK
    Genome Biol 7:R34. 2006
    ..We have sequenced the genome of R. leguminosarum biovar viciae strain 3841...
  45. ncbi Entry of L. monocytogenes into cells is mediated by internalin, a repeat protein reminiscent of surface antigens from gram-positive cocci
    J L Gaillard
    Laboratoire de Microbiologie, Faculte de Medecine Necker Enfants Malades, Paris, France
    Cell 65:1127-41. 1991
    ..As evidenced by Southern blot analysis, inlA is part of a gene family. One of them is the gene situated directly downstream of inlA, called inlB, which also encodes a leucine-rich repeat protein...
  46. pmc Yersinia pestis--etiologic agent of plague
    R D Perry
    Department of Microbiology and Immunology, University of Kentucky, Lexington 40536, USA
    Clin Microbiol Rev 10:35-66. 1997
    ..These areas of research have provide new insights into the host-parasite relationship. This review will update our present understanding of the history, etiology, epidemiology, clinical aspects, and public health issues of plague...
  47. ncbi The Listeria transcriptional landscape from saprophytism to virulence
    Alejandro Toledo-Arana
    Institut Pasteur, Unité des Interactions Bactéries Cellules, F 75015 Paris, France
    Nature 459:950-6. 2009
    ..Together, our data unravel successive and coordinated global transcriptional changes during infection and point to previously unknown regulatory mechanisms in bacteria...
  48. ncbi CRISPR provides acquired resistance against viruses in prokaryotes
    Rodolphe Barrangou
    Danisco USA Inc, 3329 Agriculture Drive, Madison, WI 53716, USA
    Science 315:1709-12. 2007
    ..Thus, CRISPR, together with associated cas genes, provided resistance against phages, and resistance specificity is determined by spacer-phage sequence similarity...
  49. 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...
  50. pmc Widespread selection for local RNA secondary structure in coding regions of bacterial genes
    Luba Katz
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genome Res 13:2042-51. 2003
    ..These results are interpreted in terms of possible roles of RNA structures in RNA processing, regulation of mRNA stability, and translational control...
  51. pmc Genome-wide screen for Salmonella genes required for long-term systemic infection of the mouse
    Trevor D Lawley
    Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
    PLoS Pathog 2:e11. 2006
    ....
  52. 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...
  53. ncbi Inactivation of the dlt operon in Staphylococcus aureus confers sensitivity to defensins, protegrins, and other antimicrobial peptides
    A Peschel
    Mikrobielle Genetik, Universitat Tubingen, Waldhäuser Strasse 70 8, 72076 Tubingen, Germany
    J Biol Chem 274:8405-10. 1999
    ..We propose a role of the D-alanine-esterified teichoic acids which occur in many pathogenic bacteria in the protection against human and animal defense systems...
  54. ncbi Efflux-mediated heavy metal resistance in prokaryotes
    Dietrich H Nies
    Institute of Microbiology, Molecular Microbiology, Martin Luther University Halle Wittenberg, Kurt Mothes Strasse 3, 06099 Halle Saale, Germany
    FEMS Microbiol Rev 27:313-39. 2003
    ..Possession of the latter systems makes a bacterium heavy metal resistant...
  55. ncbi Riboswitches in eubacteria sense the second messenger cyclic di-GMP
    N Sudarsan
    Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
    Science 321:411-3. 2008
    ..In addition, sequences matching the consensus for cyclic di-GMP riboswitches are present in the genome of a bacteriophage...
  56. ncbi Sampling the antibiotic resistome
    Vanessa M D'Costa
    Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario, Canada, L8N 3Z5
    Science 311:374-7. 2006
    ..They are a reservoir of resistance determinants that can be mobilized into the microbial community. Study of this reservoir could provide an early warning system for future clinically relevant antibiotic resistance mechanisms...
  57. ncbi Community genomics among stratified microbial assemblages in the ocean's interior
    Edward F DeLong
    Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 311:496-503. 2006
    ..Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics...
  58. ncbi Chitin induces natural competence in Vibrio cholerae
    Karin L Meibom
    Division of Infectious Diseases and Geographic Medicine, Department of Microbiology and Immunology, and Stanford Institute for the Environment, Stanford University, Stanford, CA 94305, USA
    Science 310:1824-7. 2005
    ....
  59. 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...
  60. pmc Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response
    Jennifer M Auchtung
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Proc Natl Acad Sci U S A 102:12554-9. 2005
    ..The dual regulation of ICEBs1 allows for passive propagation in the host cell until either the potential mating partners lacking ICEBs1 are present or the host cell is in distress...
  61. 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...
  62. ncbi Negative autoregulation speeds the response times of transcription networks
    Nitzan Rosenfeld
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    J Mol Biol 323:785-93. 2002
    ..This agrees with an analytical solution of a mathematical model for negative autoregulation. This may help in understanding the function of negative autoregulation, which appears in over 40% of known transcription factors in E.coli...
  63. pmc Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters
    Dongying Wu
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 4:e188. 2006
    ..coagulata and other sharpshooters serve as vectors of transmission...
  64. pmc The role of RelMtb-mediated adaptation to stationary phase in long-term persistence of Mycobacterium tuberculosis in mice
    John L Dahl
    Tuberculosis Research Section, National Institute of Allergy and Infectious Disease, 12441 Parklawn Drive, Rockville, MD 20852, USA
    Proc Natl Acad Sci U S A 100:10026-31. 2003
    ..Thus, RelMtb is critical for the successful establishment of persistent infection in mice by altering the expression of antigenic and enzymatic factors that may contribute to successful latent infection...
  65. pmc Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence
    Ozan Gundogdu
    Pathogen Molecular Department, London School of Hygiene and Tropical Medicine, UK
    BMC Genomics 8:162. 2007
    ..We now describe the complete re-annotation and re-analysis of the C. jejuni NCTC11168 genome using current database information, novel tools and annotation techniques not used during the original annotation...
  66. pmc Global transcriptomic analysis of Cyanothece 51142 reveals robust diurnal oscillation of central metabolic processes
    Jana Stöckel
    Department of Biology, Washington University, St Louis, MO 63130, USA
    Proc Natl Acad Sci U S A 105:6156-61. 2008
    ..These studies provide a comprehensive picture of how a physiologically relevant diurnal light-dark cycle influences the metabolism in a photosynthetic bacterium...
  67. ncbi The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes
    James S Godde
    Department of Biology, Monmouth College, Monmouth, IL 61462, USA
    J Mol Evol 62:718-29. 2006
    ..We suggest a mechanism by which this HGT has occurred, namely, that the CRISPR loci can be carried between cells on megaplasmids > or = 40 kb in length...
  68. ncbi Molecular mechanisms of antibacterial multidrug resistance
    Michael N Alekshun
    Schering Plough Research Institute, Kenilworth, NJ 07033, USA
    Cell 128:1037-50. 2007
    ..Once established, multidrug-resistant organisms persist and spread worldwide, causing clinical failures in the treatment of infections and public health crises...
  69. ncbi The genome of the natural genetic engineer Agrobacterium tumefaciens C58
    D W Wood
    Department of Microbiology, University of Washington, 1959 NE Pacific Street, Box 357242, Seattle, WA 98195, USA
    Science 294:2317-23. 2001
    ..Availability of the A. tumefaciens sequence will facilitate investigations into the molecular basis of pathogenesis and the evolutionary divergence of pathogenic and symbiotic lifestyles...
  70. ncbi Mycobacterium tuberculosis invasion of macrophages: linking bacterial gene expression to environmental cues
    Kyle H Rohde
    Cornell University, College of Veterinary Medicine, Department of Microbiology and Immunology, Ithaca, NY 14853, USA
    Cell Host Microbe 2:352-64. 2007
    ..Finally, there are marked species-specific differences in the response of Mtb and M. bovis BCG to intraphagosomal cues...
  71. pmc GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses
    John Besemer
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    Nucleic Acids Res 33:W451-4. 2005
    ..A database of reannotations of >1000 viral genomes by the GeneMarkS program is also available from the web site. The GeneMark website is frequently updated to provide the latest versions of the software and gene models...
  72. pmc Quorum-sensing regulators control virulence gene expression in Vibrio cholerae
    Jun Zhu
    Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 99:3129-34. 2002
    ..Together these data suggest a role for quorum sensing in modulating expression of blocks of virulence genes in a reciprocal fashion in vivo...
  73. ncbi Stochastic gene expression in a single cell
    Michael B Elowitz
    Laboratory of Cancer Biology, Center for Studies in Physics and Biology, Rockefeller University, New York, NY 10021, USA
    Science 297:1183-6. 2002
    ..These results establish a quantitative foundation for modeling noise in genetic networks and reveal how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation...
  74. pmc Individual RD1-region genes are required for export of ESAT-6/CFP-10 and for virulence of Mycobacterium tuberculosis
    Kristi M Guinn
    Department of Pathobiology, University of Washington, Seattle, WA 98195, USA
    Mol Microbiol 51:359-70. 2004
    ..Our results indicate that RD1 genes work together to form a single virulence determinant, and argue that RD1 encodes a novel specialized secretion system that is required for pathogenesis of MTB...
  75. pmc Host cell killing and bacterial conjugation require overlapping sets of genes within a 22-kb region of the Legionella pneumophila genome
    G Segal
    Department of Microbiology, College of Physicians and Surgeons of Columbia University, 701 West 168th Street, New York, NY 10032, USA
    Proc Natl Acad Sci U S A 95:1669-74. 1998
    ..It is possible either that small plasmids can take advantage of an existing secretion system to be mobilized or that DNA transfer is required for human macrophage killing by L. pneumophila...
  76. pmc Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis
    Christoph Schoen
    Institute for Hygiene and Microbiology, University of Wurzburg, Josef Schneider Strasse 2, 97080 Wurzburg, Germany
    Proc Natl Acad Sci U S A 105:3473-8. 2008
    ..meningitidis has emerged as an unencapsulated human commensal from a common ancestor with Neisseria gonorrhoeae and Neisseria lactamica and consecutively acquired the genes responsible for capsule synthesis via horizontal gene transfer...
  77. pmc Attenuation of Pseudomonas aeruginosa virulence by quorum sensing inhibitors
    Morten Hentzer
    BioCentrum DTU, Technical University of Denmark, DK 2800 Lyngby, Denmark
    EMBO J 22:3803-15. 2003
    ..aeruginosa biofilms increased bacterial susceptibility to tobramycin and SDS. In a mouse pulmonary infection model, the drug inhibited quorum sensing of the infecting bacteria and promoted their clearance by the mouse immune response...
  78. ncbi A bacterial guanine nucleotide exchange factor activates ARF on Legionella phagosomes
    Hiroki Nagai
    Section of Microbial Pathogenesis, Yale University School of Medicine, Boyer Center for Molecular Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
    Science 295:679-82. 2002
    ..pneumophila. Translocation of RalF protein through the phagosomal membrane is a dot/icm-dependent process. Thus, RalF is a substrate of the Dot/Icm secretion apparatus...
  79. ncbi Control of cell shape in bacteria: helical, actin-like filaments in Bacillus subtilis
    L J Jones
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
    Cell 104:913-22. 2001
    ..The distribution of the proteins in different species of bacteria, and the similarity of their sequence to eukaryotic actins, suggest that the MreB-like proteins have a cytoskeletal, actin-like role in bacterial cell morphogenesis...
  80. ncbi A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease
    M C Enright
    Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, UK
    Microbiology 144:3049-60. 1998
    ..A Web site for the molecular characterization of pneumococci by MLST is available (http ://mlst.zoo.ox.ac.uk)...
  81. ncbi A novel regulatory system required for pathogenicity of Xanthomonas campestris is mediated by a small diffusible signal molecule
    C E Barber
    Sainsbury Laboratory, John Innes Centre, Norwich Research Park, UK
    Mol Microbiol 24:555-66. 1997
    ..DSF production is confined to certain xanthomonads. We propose a model for the DSF system, which represents a novel mechanism for regulating virulence factor synthesis in response to physiological or environmental changes...
  82. ncbi Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis
    Natalia Ivanova
    Integrated Genomics, Chicago, Illinois 60612, USA
    Nature 423:87-91. 2003
    ..cereus and B. anthracis, and the genes that are unique for each species. We use the former to clarify the phylogeny of the cereus group, and the latter to determine plasmid-independent species-specific markers...
  83. pmc A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae
    Brian J Akerley
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 99:966-71. 2002
    ..This genome-scale phenotypic analysis identifies potential roles for a large set of genes of unknown function...
  84. pmc Two genetic loci produce distinct carbohydrate-rich structural components of the Pseudomonas aeruginosa biofilm matrix
    Lisa Friedman
    Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
    J Bacteriol 186:4457-65. 2004
    ..Either carbohydrate-rich matrix component appears to be sufficient for mature biofilm formation, and at least one of them is required for mature biofilm formation in P. aeruginosa strains PA14 and ZK2870...
  85. pmc NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
    T Z DeSantis
    Lawrence Berkeley National Laboratory, Center for Environmental Biotechnology, Berkeley, CA, USA
    Nucleic Acids Res 34:W394-9. 2006
    ..The ability to align and categorize large sequence sets using a simple interface has enabled researchers with various experience levels to obtain bacterial and archaeal community profiles...
  86. pmc DNA as a nutrient: novel role for bacterial competence gene homologs
    S E Finkel
    Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 1340, USA
    J Bacteriol 183:6288-93. 2001
    ..Homologs of these E. coli genes are present in many members of the gamma subclass of Proteobacteria, suggesting that the mechanisms for consumption of DNA may have been widely conserved during evolution...
  87. ncbi Bacterial heavy metal resistance: new surprises
    S Silver
    Department of Microbiology and Immunology, University of Illinois, College of Medicine, Chicago 60612, USA
    Annu Rev Microbiol 50:753-89. 1996
    ..Finally, the first bacterial metallothionein (which by definition is a small protein that binds metal cations by means of numerous cysteine thiolates) has been characterized in cyanobacteria...
  88. pmc Comparative genomics of multidrug resistance in Acinetobacter baumannii
    Pierre Edouard Fournier
    Information Genomique et Structurale, Institute for Structural Biology and Microbiology, IBSM, Marseille, France
    PLoS Genet 2:e7. 2006
    ..Whole-genome sequencing appears to be a fast and efficient approach to the exhaustive identification of resistance genes in epidemic infectious agents of clinical significance...
  89. ncbi A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes
    Christian Esser
    Institute of Botany III, University of Dusseldorf, Dusseldorf, Germany
    Mol Biol Evol 21:1643-60. 2004
    ..Among eubacteria and archaebacteria, proteobacterial and methanogen genomes, respectively, shared more similarity with the yeast genome than other prokaryotic genomes surveyed...
  90. ncbi Conjugative transfer by the virulence system of Legionella pneumophila
    J P Vogel
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
    Science 279:873-6. 1998
    ..The dot virulence genes encoded a large putative membrane complex that functioned as a secretion system that was able to transfer plasmid DNA from one cell to another...
  91. pmc Type III protein secretion systems in bacterial pathogens of animals and plants
    C J Hueck
    Lehrstuhl fur Mikrobiologie, Biozentrum der Universität Würzburg, 97074 Wurzburg, Germany
    Microbiol Mol Biol Rev 62:379-433. 1998
    ..and the plant pathogens Pseudomonas syringae, Erwinia spp., Ralstonia solanacearum, Xanthomonas campestris, and Rhizobium spp...
  92. ncbi GeneChip expression analysis of the iron starvation response in Pseudomonas aeruginosa: identification of novel pyoverdine biosynthesis genes
    Urs A Ochsner
    Department of Microbiology, Campus Box B 175, University of Colorado Health Sciences Center, 4200 East Ninth Avenue, Denver, CO 80262, USA
    Mol Microbiol 45:1277-87. 2002
    ..The GeneChip proved to be a very useful tool for rapid gene expression analysis and identification of novel genes controlled by Fur or PvdS...
  93. ncbi Quorum sensing and swarming migration in bacteria
    Ruth Daniels
    Centre of Microbial and Plant Genetics, K U Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
    FEMS Microbiol Rev 28:261-89. 2004
    ..Here we also describe how quorum sensing may disperse existing biofilms and control the interaction between bacteria and higher organisms (such as the Rhizobium-bean symbiosis)...
  94. pmc The cyanobacterial genome core and the origin of photosynthesis
    Armen Y Mulkidjanian
    School of Physics, University of Osnabruck, D 49069 Osnabruck, Germany
    Proc Natl Acad Sci U S A 103:13126-31. 2006
    ..From procyanobacteria, photosynthesis spread to other phyla by way of lateral gene transfer...
  95. pmc MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
    Hideki Noguchi
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277 8562, Japan
    Nucleic Acids Res 34:5623-30. 2006
    ..Applied to the Sargasso Sea dataset, MetaGene predicted almost all of the annotated genes and a notable number of novel genes. MetaGene can be applied to wide variety of metagenomic projects and expands the utility of metagenomics...
  96. 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...
  97. pmc Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion
    Michael Callanan
    Moorepark Food Research Centre, Moorepark, Fermoy, Co Cork, Ireland
    J Bacteriol 190:727-35. 2008
    ..helveticus genome. These data suggest a special unobtrusive relationship between the DPC 4571 genome and its mobile DNA complement...
  98. ncbi A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA
    E C Lee
    Mouse Cancer Genetics Program, National Cancer Institute Frederick, Frederick, Maryland 21702, USA
    Genomics 73:56-65. 2001
    ....
  99. ncbi Quorum sensing controls biofilm formation in Vibrio cholerae
    Brian K Hammer
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544 1014, USA
    Mol Microbiol 50:101-4. 2003
    ..Bacterial biofilms could represent a complex habitat where such differentiation occurs...
  100. pmc Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time
    Ramunas Stepanauskas
    Bigelow Laboratory for Ocean Sciences, P O Box 475, West Boothbay Harbor, ME 04575 0475, USA
    Proc Natl Acad Sci U S A 104:9052-7. 2007
    ..Compared with metagenomics, the power of our approach lies in the ability to detect metabolic genes in uncultured microorganisms directly, even when the metabolic and phylogenetic markers are located far apart on the chromosome...
  101. pmc Patterns and implications of gene gain and loss in the evolution of Prochlorococcus
    Gregory C Kettler
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    PLoS Genet 3:e231. 2007
    ....

Research Grants68

  1. Adherent Escherichia coli and associated virulence genes in children with IBD
    Sandra C Kim; Fiscal Year: 2010
    ..the induction of Crohn's disease requires both host genetic susceptible and expression of specific bacterial genes. These hypotheses are addressed by the following Specific Aims: Specific aim 1: Characterize the frequency of ..
  2. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..In these studies, we expect to provide fundamental insights into the mechanisms and targets of diversifying immune selection in M. tuberculosis. ..
  3. Colitis Induced by immune responses to luminal bacteria-mouse
    Ryan B Sartor; Fiscal Year: 2012
    ..A. In vivo studies. Do bacterial genes that regulate: 1) mucosal invasion and translocation 2) intracellular survival or 3) secretion of oxygen ..
  4. Mechanisms of Haemophilus influenzae pathogenesis in the lung
    Hao Shen; Fiscal Year: 2013
    ..Relevance: The proposed work will generate insight into the roles of bacterial genes of immune evasion and physiological adaptation required to survive anti-bacterial defenses modeled in vitro, ..
  5. Dysregulation of the inflammatory response by Francisella tularensis
    Lee Ann H Allen; Fiscal Year: 2013
    ..tularensis with a focus on the BAX, XIAP and calpastatin. 2. To identify bacterial genes required for PMN apoptosis inhibition. 3...
  6. Otitis media-associated pneumococcal genes
    Honggao Yan; Fiscal Year: 2013
    ..This study led to the discovery of 169 ear-infection-associated bacterial genes including the gene encoding the major surface protein CbpA of S. pneumoniae...
  7. Regulation of Host Nitrogen Balance by the Gut Microbiome
    Gary D Wu; Fiscal Year: 2012
    ....
  8. Mechanisms of Haemophilus influenzae pathogenesis in the lung
    Hao Shen; Fiscal Year: 2011
    ..Relevance: The proposed work will generate insight into the roles of bacterial genes of immune evasion and physiological adaptation required to survive anti-bacterial defenses modeled in vitro, ..
  9. Novel gene-silencing therapeutics for multidrug-resistant gram-negative pathogens
    DAVID ELIHU GREENBERG; Fiscal Year: 2013
    ..DNA mimics that bind to RNA in a sequence-specific, antisense manner and inhibit expression of essential bacterial genes. PPMOs have already been used successfully to kill a variety of bacterial pathogens including the Gram-..
  10. Symbiotic Rickettsia Species as a Model System for the Study of Folate Biosynthes
    Jianmin Zhong; Fiscal Year: 2012
    ..B9 vitamin pathway of the Rickettsia species are actively transcribed in Ixodes pacificus ticks, and if these bacterial genes encode proteins that synthesize vitamin B9...
  11. New composite material design based on studies of tooth-composite and microbial i
    J Paul Santerre; Fiscal Year: 2013
    ..This approach to material design is novel to the dental health care community and has the potential to change the way composite resin materials and adhesives are formulated, tested, and applied ..
  12. Characterization of a novel role for DEAD-box RNA helicases in bacteria.
    CHRISTOPHER ANTHONY VAKULSKAS; Fiscal Year: 2013
    ..CsrA is an RNA-binding protein that post-transcriptionally regulates numerous important bacterial genes and systems by binding to the 5'untranslated region (5'UTR) of mRNAs, thus altering protein ..
  13. Short-term responses to temperature changes in Escherichia coli
    Christine A White Ziegler; Fiscal Year: 2010
    ..Identification of the bacterial genes more highly expressed at human body temperature (37[unreadable]C) could yield valuable anti-infective targets ..
  14. Group II Intron Mobility and Gene Targeting
    Alan M Lambowitz; Fiscal Year: 2012
    ....
  15. Discovery of Vibrio cholerae factors contributing to virulence in Drosophila.
    ALEXANDRA ELIZABETH PURDY; Fiscal Year: 2010
    ..cholerae mutants in a simple Drosophila survival assay in order to identify bacterial genes that contribute to virulence...
  16. Decoding the roles of critical genes of unknown function in M. tuberculosis
    Dirk Schnappinger; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): An enormous number of bacterial genes either have no annotated function or are only assigned to broad functional categories...
  17. Understanding transcriptional silencing &anti-silencing mechanisms in Shigella
    Helen J Wing; Fiscal Year: 2013
    ..Summary The nucleoid structuring protein H-NS plays important roles in the transcriptional silencing of many bacterial genes. Proteins that alleviate this silencing are central to bacterial physiology and control many processes ..
  18. Functional analysis of the Francisella capBCA gene locus
    Jing Ren Zhang; Fiscal Year: 2010
    ..However, the mechanisms for this extreme versatility are unknown. This project will study three bacterial genes that are potentially responsible for synthesis of an unconventional amino acid polymer called poly-glutamic ..
  19. Identification of bacterial genes required for transmission of tick-borne pathoge
    Susan M Noh; Fiscal Year: 2012
    ..The objective of this research is to identify how bacterial pathogens colonize the tick, with the long-term goal of developing new means of preventing tick colonization, and thus preventing tick-borne disease. ..
  20. Gut L-Histidine Metabolism and Histamine Signaling in Colonic Neoplasia
    James Versalovic; Fiscal Year: 2013
    ..b>Bacterial genes in the microbiome encode for enzymes that perform biochemical conversion of dietary amino acids into various ..
  21. Non-invasive Fluorescent Imaging Mycobacterium tuberculosis Extrapulmonary Infect
    Ying Kong; Fiscal Year: 2013
    ..to study the temporal kinetics of EPTB and specific organ- involvement in live animals and to investigate bacterial genes and host factors involved...
  22. Porphyromonas gingivalis Horizontal DNA Transfer and Genetic Variation
    Gena D Tribble; Fiscal Year: 2013
    ..The identification of bacterial genes that are transferred and favorably selected in response to environmental pressure will provide a novel ..
  23. Impact of Diet on Intestinal Microbiota-Host Dynamics
    Justin Sonnenburg; Fiscal Year: 2013
    ..Host responses will be monitored to determine if epithelial gene expression and systemic and/or mucosal cytokine responses may be modulated via diet-induced changes in the microbiota. ..
  24. Structural Biology of Multifunctional Bacterial Phosphatases
    Matthew B Neiditch; Fiscal Year: 2012
    ..Revealing the molecular mechanisms of Rap-Phr function will enable us to accomplish our long-term goal of designing antibacterial drugs that modulate bacterial signal transduction. ..
  25. Methods to enable cholesterol catabolism in human monocyte derived macrophages
    Richard E Honkanen; Fiscal Year: 2013
    ..The main objectives are to: 1) humanize bacterial genes encoding key ring opening enzymes, 2) develop an innovative expressions systems to regulate the expression of ..
  26. PATHOGENESIS OF HAEMOPHILUS DUCREYI INFECTIONS
    Stanley M Spinola; Fiscal Year: 2013
    ..In the last funding period, we found that several hundred bacterial genes were differentially regulated in vivo relative to in vitro growth, suggesting that H...
  27. Identifying mechanisms of translocation of epithelial cells by P. aeruginosa.
    DANIELLE KRISTY AUGUSTIN; Fiscal Year: 2010
    ..Established in vitro and in vivo models will then be used to determine the role(s) of differentially expressed genes in modulating P. aeruginosa translocation of corneal epithelia. ..
  28. Bacterial gene regulation in response to oxidative stress
    Anne Grove; Fiscal Year: 2013
    ....
  29. Microbial Regulation of Host Nutrient Metabolism
    John F Rawls; Fiscal Year: 2012
    ..In Specific Aim 1, we will use a bacterial genetic approach to identify bacterial genes required for suppression of Fiaf...
  30. National Gnotobiotic Rodent Resource Center
    Ryan B Sartor; Fiscal Year: 2013
    ..rodents of different genetic backgrounds, and to define the physiologic and pathophysiologic relevance of bacterial genes. The microbiota can be precisely manipulated by colonizing germ-free rodents with single or multiple ..
  31. Decoding methylation mediated epigenetic control using single molecule sequencing
    Michael Chao; Fiscal Year: 2013
    ..This work will likely be extrapolateable to other species, and thus will provide us with a deeper understanding of how DNA methylation functions as a universal mechanism for regulating cellular processes across the bacterial kingdom. ..
  32. How glycans shape gut microbiota function and assembly
    Eric C Martens; Fiscal Year: 2013
    ..In Aim 1, transcription of bacterial genes that are known to respond to specific glycans will be used as biosensors to measure variation in bacterial ..
  33. The role of Plasminogen activator Inhibitor-1 in Helicobacter pylori infection.
    Sarah E Keates; Fiscal Year: 2010
    ..pylori and isogenic mutants, and overexpression of bacterial genes will be carried out...
  34. Genetics of Salmonella Resistance to the Inflammatory Response in the Gut
    Helene L Andrews Polymenis; Fiscal Year: 2010
    ..This project is a first step toward a comprehensive determination of the molecular mechanism of the bacterial genes involved in the response to inflammation in the gut...
  35. Bacterial gene regulation by the NTP substrates of transcription initiation
    Charles L Turnbough; Fiscal Year: 2013
    ..Defining these mechanisms in molecular detail enhances our understanding of the inner workings of bacteria and increases our ability to control bacterial pathogens and to create new tools for biotechnology. ..
  36. Borrelia burdorferi Ebfc regulon
    Brian Stevenson; Fiscal Year: 2013
    ..Thus, our continued studies will focus efforts toward production of improved preventative and curative therapies for not only Lyme disease, but also many other significant human infectious diseases. ..
  37. 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. ..
  38. The Rochester Conference on Oral Biology Post Genomics for the Oral Microbiome
    Robert G Quivey; Fiscal Year: 2011
    ..approaches to evaluating microbial community metabolic networks;and genome-wide screens for bacterial genes involved with health or disease...
  39. Development of IMPDH-Targeted Drugs against Crytosporidium
    LIZBETH K HEDSTROM; Fiscal Year: 2010
    ..The enzymes encoded by these bacterial genes provide highly divergent targets for the design of parasite-specific drugs...
  40. Survival of Neisseria gonorrhoeae after primary human neutrophil challenge
    Alison K Criss; Fiscal Year: 2013
    ..Taken together, the results from this application will reveal the diverse approaches used by Gc to survive in the presence of antimicrobial PMNs, which ensures the continued persistence of gonorrhea within the human population. ..
  41. Modulation of NF-kB Signaling by Immunoprobiotics
    James Versalovic; Fiscal Year: 2011
    ..1. Generate insertional mutants of immunoprobiotic Lactobacillus reuteri and identify key bacterial genes that regulate factors affecting NF-?B and MAP kinase signaling pathways. 2...
  42. Polymyxin-resistant Pseudomonas in CF Lung Infection
    Samuel M Moskowitz; Fiscal Year: 2010
    ..An interdisciplinary study of polymyxin resistant Pseudomonas from patients with cystic fibrosis is proposed to pinpoint the bacterial genes responsible for this resistance, so that management strategies may be devised to overcome it.
  43. Role of bacteria in development and lifespan of Drosophila melanogaster
    William W Ja; Fiscal Year: 2012
    ..To fully characterize host-microbe interactions, a genetic screen will be performed to identify bacterial genes that are critical for colonization of the fly host (Aim 3).
  44. Single-Molecule and Single-Cell Analysis of Transcription Factor-DNA Complexes
    Rob Phillips; Fiscal Year: 2013
    ..synthetic networks and as the basis of discovering the regulatory architectures for a number of important bacterial genes for which essentially nothing is known...
  45. Single-molecule study of cooperation between bacterial gene expression machines
    Shixin Liu; Fiscal Year: 2013
    ..These skills will facilitate his successful transitionto independence. ..
  46. The cervical microbiome mediates hormonal increases in HIV1 susceptibility
    Daniel Frank; Fiscal Year: 2012
    ..microscopy, to comprehensively determine whether menopause results in 1) different kinds of bacteria inhabiting the female reproductive tract;2) expression of different bacterial genes;and/or 3) modification of cervical gene expression.
  47. Structure/Function of Transcription Complex Regulation
    Robert Landick; Fiscal Year: 2013
    ..Pausing and premature termination by RNA polymerase affect expression of bacterial genes in many ways...
  48. AMYLASE BINDING STREPTOCOCCI, DENTAL PLAQUE AND CARIES
    FRANK ANDREW SCANNAPIECO; Fiscal Year: 2011
    ..abstract_text> ..
  49. The Biological Function of Bacterial Argonaute Proteins
    KRISTIN M KOTULAK; Fiscal Year: 2012
    ....
  50. Molecular basis of bacterial-dependent colony formation in choanoflagellates
    ROSANNA ANOLANI ALEGADO; Fiscal Year: 2010
    ..Third, I will characterize the function of candidate PR1 colony induction bacterial genes and pathways by determining the expression patterns and regulation of candidate gene products...
  51. Prophage contribution to the virulence of Staphylococcus aureus
    Taeok Bae; Fiscal Year: 2013
    ..abstract_text> ..
  52. Feedback regulation and transcirptional coupling in bacterial stress-response
    Oleg A Igoshin; Fiscal Year: 2013
    ..The Specific Aims are (SA1) To understand the relationship between co-expression of bacterial genes from a single operon and stochasticity in information processing of the corresponding networks and (SA2) To ..
  53. Genes Associated with Mycobacterium avium Pathogenesis
    LUIZ EDUARDO BERMUDEZ; Fiscal Year: 2013
    ..M. avium interference with macrophage killing mechanisms: (a) studying bacterial genes that participate in modifying/interfering with the mycobacterial vacuole formation upon uptake into ..
  54. Ecological drivers of virulence evolution in an emerging avian pathogen
    DANA MICHELLE HAWLEY; Fiscal Year: 2013
    ..These data will serve as an independent test of the partial immunity hypothesis by addressing whether bacterial genes responsible for evading host immune systems are systematically changing in vivo and in vitro under selection ..
  55. Drug Targets for Tuberculosis
    ERIC JOSEPH RUBIN; Fiscal Year: 2010
    ..We have previously defined the set of bacterial genes that are required for optimal in vitro growth of Mycobacterium tuberculosis...
  56. Agents of Bioterrorism: Pathogenesis and host defense
    Jorge L Benach; Fiscal Year: 2010
    ..pestis survival in macrophages, we recently identified several bacterial genes important for intracellular survival, have determined that Y...
  57. A Network Biology Approach to Antibiotic Action and Bacterial Defense Mechanisms
    James J Collins; Fiscal Year: 2011
    ..This project may thus enable the development of novel classes of antibiotics that account for and utilize the complex regulatory properties of genetic networks. ..
  58. NOVEL CELLULAR &GENETIC ANALYSES USING A NEW CHLAMYDIA PENETRANT PEPTIDE
    Alison J Quayle; Fiscal Year: 2012
    ..trachomatis;and 2) Providing, for the first time, a robust reverse genetic technique to dissect the role of specific bacterial genes in the developmental cycle and pathogenesis.
  59. Fiber Intake, Gut Bacteria Metabolites and Risk of Colorectal Cancer
    Jiyoung Ahn; Fiscal Year: 2013
    ..Impact: This study will clarify the etiologic basis of the fiber-CRC relationship and provide directly applicable information for tailored dietary guidance for gut microbiome-related CRC prevention. ..
  60. LISTERIA VIRULENCE GENE EXPRESSION WITHIN HOST CELLS
    NANCY ELIZABETH FREITAG; Fiscal Year: 2010
    ..The ultimate goal of the proposed work is to elucidate the regulatory pathways that enable bacterial survival within host cells, and the functional identification of additional bacterial factors that support replication within the host. ..
  61. Human Intestinal Microbial Ecologies of Indigenous Communities
    Cecil M Lewis; Fiscal Year: 2013
    ..AIM2 is to characterize the bacterial species and bacterial genes observed in these samples using next generation genome sequencing and novel gene array technologies...
  62. Mechanism of Regulating Division in Escherichia coli
    Jennifer R Juarez; Fiscal Year: 2012
    ..The study of bacterial cell division is important because it is a basic cellular process that needs to be understood and because it is a highly relevant target for potentially new antimicrobial drugs. ..
  63. Risk factors for gastric disease in pediatric H. pylori
    Benjamin Gold; Fiscal Year: 2006
    ..We propose to further our previous work with critically lacking studies from a multivariate approach leading to a better understanding of the gastroduodenal disease sequelae and overall pathobiology of Hp infection in humans. ..
  64. SALMONELLA ANTIMICROBIAL PEPTIDE RESISTANCE
    John Gunn; Fiscal Year: 2002
    ..It is hoped that these studies will increase our understanding of the molecular basis of Salmonella pathogenesis. ..
  65. REGULATION OF GENE EXPRESSION IN THE SMALL INTESTINE
    Jeffrey Gordon; Fiscal Year: 2005
    ..thetaiotaomicron genome. The investigators will identify ORFs using a variety of computational methods. Bacterial genes that are preferentially expressed in vivo will then be identified using promoter traps, as well as direct ..
  66. ALTERNATIVE SIGMA FACTORS AND ANTIBIOTIC SYNTHESIS
    GEORGE JONES; Fiscal Year: 1999
    ....
  67. GENETICS OF H. AEGYPTIUS BRAZILIAN PURPURIC FEVER CLONE
    Luis Actis; Fiscal Year: 2000
    ..aegyptius. Furthermore, these studies will lead to a better comprehension of the nature of other vascular destructive infectious diseases. ..
  68. Group II Intron-Based Gene Targeting Methods for Xenopus
    Alan Lambowitz; Fiscal Year: 2009
    ..It will also be a major step toward our ultimate goal of generalizable group II intron- based gene targeting systems for eukaryotes, with potentially broad applications in genetic engineering, functional genomics, and gene therapy. ..