bacterial dna

Summary

Summary: Deoxyribonucleic acid that makes up the genetic material of bacteria.

Top Publications

  1. 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
  2. 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
  3. ncbi A Toll-like receptor recognizes bacterial DNA
    H Hemmi
    Department of Host Defense, Research Institute for Microbial Diseases, Osaka University and Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Suita
    Nature 408:740-5. 2000
  4. pmc WebLogo: a sequence logo generator
    Gavin E Crooks
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Genome Res 14:1188-90. 2004
  5. pmc Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis
    Philip Supply
    INSERM U629, Institut Pasteur de Lille, 1, Rue du Prof Calmette, F 59019 Lille cedex, France
    J Clin Microbiol 44:4498-510. 2006
  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. 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
  8. 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
  9. ncbi Review and re-analysis of domain-specific 16S primers
    G C Baker
    Department of Biotechnology, University of the Western Cape, Bellville 7335, Cape Town, South Africa
    J Microbiol Methods 55:541-55. 2003
  10. ncbi Genome-wide insertional mutagenesis of Arabidopsis thaliana
    Jose M Alonso
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Science 301:653-7. 2003

Detail Information

Publications334 found, 100 shown here

  1. 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...
  2. 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...
  3. ncbi A Toll-like receptor recognizes bacterial DNA
    H Hemmi
    Department of Host Defense, Research Institute for Microbial Diseases, Osaka University and Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Suita
    Nature 408:740-5. 2000
    ..effects on mammalian immune cells, which depend on the presence of unmethylated CpG dinucleotides in the bacterial DNA. In contrast, mammalian DNA has a low frequency of CpG dinucleotides, and these are mostly methylated; ..
  4. pmc WebLogo: a sequence logo generator
    Gavin E Crooks
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Genome Res 14:1188-90. 2004
    ..A command line interface and the complete, open WebLogo source code are available for local installation and customization...
  5. pmc Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis
    Philip Supply
    INSERM U629, Institut Pasteur de Lille, 1, Rue du Prof Calmette, F 59019 Lille cedex, France
    J Clin Microbiol 44:4498-510. 2006
    ..This 15-locus system is therefore proposed as the new standard for routine epidemiological discrimination of M. tuberculosis isolates and the 24-locus system as a high-resolution tool for phylogenetic studies...
  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. 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...
  8. 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...
  9. ncbi Review and re-analysis of domain-specific 16S primers
    G C Baker
    Department of Biotechnology, University of the Western Cape, Bellville 7335, Cape Town, South Africa
    J Microbiol Methods 55:541-55. 2003
    ..These primers are found to amplify sequences from Crenarchaeote and Euryarchaeote type strains and environmental DNA...
  10. ncbi Genome-wide insertional mutagenesis of Arabidopsis thaliana
    Jose M Alonso
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Science 301:653-7. 2003
    ..Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene...
  11. ncbi CpG motifs in bacterial DNA and their immune effects
    Arthur M Krieg
    Department of Veterans Affairs Medical Center, Iowa City, Iowa 52246, USA
    Annu Rev Immunol 20:709-60. 2002
    ..CpG ODN also enhance the development of acquired immune responses for prophylactic and therapeutic vaccination...
  12. ncbi GATEWAY vectors for Agrobacterium-mediated plant transformation
    Mansour Karimi
    Dept of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Ghent University, K L Ledeganckstraat 35, B 9000, Gent, Belgium
    Trends Plant Sci 7:193-5. 2002
    ..Because these vectors are generally large, cloning can be time-consuming and laborious. Recently, the GATEWAY conversion technology has provided a fast and reliable alternative to the cloning of sequences into large acceptor plasmids...
  13. 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
    ..We propose that the size and complexity of the P. aeruginosa genome reflect an evolutionary adaptation permitting it to thrive in diverse environments and resist the effects of a variety of antimicrobial substances...
  14. pmc A gateway cloning vector set for high-throughput functional analysis of genes in planta
    Mark D Curtis
    Institute of Plant Biology and Zurich Basel Plant Science Centre, University of Zurich, Zollikerstrasse 107, Ch 8008 Zurich, Switzerland
    Plant Physiol 133:462-9. 2003
    ..All vectors were derived from pCambia T-DNA cloning vectors, with the exception of a chemically inducible vector, for Agrobacterium sp.-mediated transformation of a wide range of plant species...
  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 Pyrosequencing analysis of the oral microflora of healthy adults
    B J F Keijser
    TNO Quality of Life, Business Unit Food and Biotechnology Innovations, Microbial Genomics Group, Zeist, The Netherlands
    J Dent Res 87:1016-20. 2008
    ..This work gives a radically new insight into the diversity of human oral microflora, which, with an estimated number of 19,000 phylotypes, is considerably higher than previously reported...
  17. ncbi Opinion: Re-evaluating prokaryotic species
    Dirk Gevers
    Laboratory of Microbiology and the Bioinformatics and Evolutionary Genomics Research Group, Ghent University VIB, Ghent, Belgium
    Nat Rev Microbiol 3:733-9. 2005
    ..We also consider the potential, and difficulties, of assigning species status to biologically or ecologically meaningful sequence clusters...
  18. ncbi Molecular identification of bacteria associated with bacterial vaginosis
    David N Fredricks
    Program in Infectious Diseases, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    N Engl J Med 353:1899-911. 2005
    ..The cause of bacterial vaginosis remains poorly understood despite numerous studies based on cultures. Bacteria in microbial communities can be identified without cultivation by characterizing their ribosomal DNA (rDNA) sequences...
  19. ncbi A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms
    Marie Allesen-Holm
    Centre for Biomedical Microbiology, BioCentrum DTU, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Mol Microbiol 59:1114-28. 2006
    ....
  20. 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
    ....
  21. pmc RecBCD enzyme and the repair of double-stranded DNA breaks
    Mark S Dillingham
    DNA Protein Interactions Unit, Department of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
    Microbiol Mol Biol Rev 72:642-71, Table of Contents. 2008
    ..In this review, we discuss the biochemical mechanism of the RecBCD enzyme with particular emphasis on new developments relating to the enzyme's structure and DNA translocation mechanism...
  22. pmc Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication
    Patrick H Viollier
    Department of Developmental Biology, Beckman Center, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 101:9257-62. 2004
    ....
  23. pmc Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota
    Sabine Bartosch
    MRC Microbiology and Gut Biology Group, University of Dundee, Dundee, United Kingdom
    Appl Environ Microbiol 70:3575-81. 2004
    ....
  24. pmc DNA gyrase, topoisomerase IV, and the 4-quinolones
    K Drlica
    Public Health Research Institute, New York, New York 10016, USA
    Microbiol Mol Biol Rev 61:377-92. 1997
    ..both for unlinking replicated daughter chromosomes and for controlling negative superhelical tension in bacterial DNA. However, in 1990 a homolog of gyrase, topoisomerase IV, that had a potent decatenating activity was ..
  25. pmc Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases
    Jill E Clarridge
    Department of Laboratory Medicine, University of Washington, Seattle, USA
    Clin Microbiol Rev 17:840-62, table of contents. 2004
    ....
  26. pmc Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates
    Caroline Allix-Béguec
    Genoscreen, 1, rue du Professeur Calmette, Lille 59019 Cedex, France
    J Clin Microbiol 46:2692-9. 2008
    ..The MIRU-VNTRplus database is a powerful tool for high-resolution clonal identification and has little equivalent in terms of functionalities among the bacterial genotyping databases available so far...
  27. 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...
  28. pmc Plasma levels of bacterial DNA correlate with immune activation and the magnitude of immune restoration in persons with antiretroviral-treated HIV infection
    Wei Jiang
    Case Western Reserve University, Cleveland, Ohio 44106, USA
    J Infect Dis 199:1177-85. 2009
    ..These findings are consistent with the importance of microbial translocation in immunodeficiency and T cell homeostasis in chronic HIV infection...
  29. pmc Human TLR9 confers responsiveness to bacterial DNA via species-specific CpG motif recognition
    S Bauer
    Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, 81675 Munich, Germany
    Proc Natl Acad Sci U S A 98:9237-42. 2001
    ..The optimal CpG motif for hTLR9 was GTCGTT, whereas the optimal murine sequence was GACGTT. Overall, these data suggest that hTLR9 conveys CpG-DNA responsiveness to human cells by directly engaging immunostimulating CpG-DNA...
  30. pmc Methicillin-resistant Staphylococcus aureus (MRSA) strain ST398 is present in midwestern U.S. swine and swine workers
    Tara C Smith
    Department of Epidemiology, University of Iowa College of Public Health, Iowa City, IA, USA
    PLoS ONE 4:e4258. 2009
    ..However, no studies to date have investigated carriage of MRSA among swine and swine farmers in the United States (U.S.)...
  31. 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...
  32. pmc Harmonization of pulsed-field gel electrophoresis protocols for epidemiological typing of strains of methicillin-resistant Staphylococcus aureus: a single approach developed by consensus in 10 European laboratories and its application for tracing the spre
    Stephen Murchan
    Laboratory of Hospital Infection, Central Public Health Laboratory, London NW9 5HT, United Kingdom
    J Clin Microbiol 41:1574-85. 2003
    ..This highlights the need for closer international collaboration to monitor the spread of current epidemic strains as well as the emergence of new ones...
  33. ncbi Crystal structure of the lactose operon repressor and its complexes with DNA and inducer
    M Lewis
    Johnson Research Foundation, University of Pennsylvania, Philadelphia 19104, USA
    Science 271:1247-54. 1996
    ....
  34. 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...
  35. pmc CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA
    Luciano A Marraffini
    Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
    Science 322:1843-5. 2008
    ..We conclude that CRISPR loci counteract multiple routes of HGT and can limit the spread of antibiotic resistance in pathogenic bacteria...
  36. ncbi Extracellular DNA required for bacterial biofilm formation
    Cynthia B Whitchurch
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, QLD, Australia
    Science 295:1487. 2002
  37. ncbi Natural genetic transformation: prevalence, mechanisms and function
    Ola Johnsborg
    Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, As, Norway
    Res Microbiol 158:767-78. 2007
    ..Here we will review the most recent advances in our understanding of the phenomenon and discuss its possible biological functions...
  38. 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
    ....
  39. ncbi The complete genome sequence of the gram-positive bacterium Bacillus subtilis
    F Kunst
    Institut Pasteur, Unité de Biochimie Microbienne, Paris, France
    Nature 390:249-56. 1997
    ....
  40. ncbi Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis
    Haruo Ikeda
    Kitasato Institute for Life Sciences, Kitasato University, Kanagawa 228 8555, Japan
    Nat Biotechnol 21:526-31. 2003
    ..In contrast, the terminal regions were not conserved and preferentially contained nonessential genes...
  41. ncbi Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology
    Erko Stackebrandt
    DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
    Int J Syst Evol Microbiol 52:1043-7. 2002
    ..The committee made various recommendations regarding the species definition in the light of developments in methodologies available to systematists...
  42. ncbi Sequence typing reveals extensive strain diversity of the Lyme borreliosis agents Borrelia burgdorferi in North America and Borrelia afzelii in Europe
    Jonas Bunikis
    Department of Microbiology, B240 Medical Sciences I, University of California Irvine, Irvine, CA 92697 4025, USA
    Microbiology 150:1741-55. 2004
    ..burgdorferi. It is concluded that B. burgdorferi and B. afzelii have greater genetic diversity than had previously been estimated, and that the IGS locus alone is sufficient for strain typing and phylogenetic studies...
  43. pmc spa typing method for discriminating among Staphylococcus aureus isolates: implications for use of a single marker to detect genetic micro- and macrovariation
    Larry Koreen
    Public Health Research Institute, International Center for Public Health, Graduate School of Biomedical Sciences and New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, USA
    J Clin Microbiol 42:792-9. 2004
    ..This study showed that genetic analysis of the repeat region of protein A comprehensively characterizes both micro- and macrovariation in the primarily clonal population structure of S. aureus...
  44. ncbi Spatial and temporal organization of replicating Escherichia coli chromosomes
    Ivy F Lau
    Division of Molecular Genetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Mol Microbiol 49:731-43. 2003
    ..This asymmetry could provide a mechanism by which the chromosome segregation protein FtsK, located at the division septum, can act directionally to ensure that the septal region is free of DNA before the completion of cell division...
  45. pmc Molecular evidence for a uniform microbial community in sponges from different oceans
    Ute Hentschel
    Institut für Molekulare Infektionsbiologie, Universitat Wurzburg, D 97070 Wurzburg, Germany
    Appl Environ Microbiol 68:4431-40. 2002
    ..A picture emerges where sponges can be viewed as highly concentrated reservoirs of so far uncultured and elusive marine microorganisms...
  46. pmc Development and application of two multiplex real-time PCR assays for the detection of Mycobacterium ulcerans in clinical and environmental samples
    Janet A M Fyfe
    Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia
    Appl Environ Microbiol 73:4733-40. 2007
    ..This suite of new methods is enabling rapid progress in the understanding of the ecology of this important human pathogen...
  47. pmc Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts
    Xiaodong Bai
    Department of Entomology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, 44691, USA
    J Bacteriol 188:3682-96. 2006
    ..The AY-WB genome is approximately 154 kb smaller than the OY-M genome, primarily as a result of fewer multicopy sequences, including PMUs. Furthermore, AY-WB lacks genes that are truncated and are part of incomplete pathways in OY-M...
  48. pmc Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis
    Claire Lurin
    Unite de Recherche en Genomique Vegetale, Institut National de la Recherche Agronomique Centre National de la Recherche Scientifique Université d Evry Val d Essone, CP 5708, 91057 Evry Cedex, France
    Plant Cell 16:2089-103. 2004
    ..These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms...
  49. 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...
  50. pmc Vaginal lactobacillus flora of healthy Swedish women
    Alejandra Vásquez
    Laboratory of Food Hygiene, Division of Food Technology, Lund University, Sweden
    J Clin Microbiol 40:2746-9. 2002
    ..L. iners has not previously been reported as one of the predominant Lactobacillus species in the vagina...
  51. pmc Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing
    Scot E Dowd
    United States Department of Agriculture ARS Livestock Issues Research Unit, Lubbock, TX, USA
    BMC Microbiol 8:43. 2008
    ....
  52. 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...
  53. pmc Conjugative plasmid transfer in gram-positive bacteria
    Elisabeth Grohmann
    Microbial Ecology Group, University of Technology Berlin, D 10587 Berlin, Germany
    Microbiol Mol Biol Rev 67:277-301, table of contents. 2003
    ....
  54. ncbi Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance
    M J Daly
    Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
    Science 306:1025-8. 2004
    ..In contrast, Shewanella oneidensis and Pseudomonas putida have high iron but low intracellular manganese concentrations and are very sensitive. We propose that Mn(II) accumulation facilitates recovery from radiation injury...
  55. pmc High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology
    E Mazars
    , , U447, Institut Pasteur de Lille, rue du Prof. Calmette, F-59019 Lille Cedex, France
    Proc Natl Acad Sci U S A 98:1901-6. 2001
    ..This typing method opens the way to the construction of digital global databases for molecular epidemiology studies of M. tuberculosis...
  56. ncbi Evaluation of Brucella MLVA typing for human brucellosis
    Sascha Al Dahouk
    Bundeswehr Institute of Microbiology, Department of Bacteriology, Neuherbergstr 11, D 80937 Munich, Germany
    J Microbiol Methods 69:137-45. 2007
    ..MLVA can significantly contribute to epidemiological trace-back analysis of Brucella infections and may advance surveillance and control of human brucellosis...
  57. pmc Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'
    Janelle R Thompson
    Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
    Nucleic Acids Res 30:2083-8. 2002
    ..This simple modification to the protocol may ensure that sequence richness encountered in clone libraries more closely reflects genetic diversity in the original sample...
  58. pmc Dynamic organization of chromosomal DNA in Escherichia coli
    H Niki
    Unit Process and Combined Circuit, PRESTO, Japan Science and Technology Corporation JST, Kumamoto, 862 0976, Japan
    Genes Dev 14:212-23. 2000
    ..These studies thus suggest that the E. coli chromosome is organized to form a compacted ring structure with the Ori and Ter domains; these domains participate in the cell cycle-dependent localization of the chromosome...
  59. ncbi The complete genome sequence of the gastric pathogen Helicobacter pylori
    J F Tomb
    Institute for Genomic Research, Rockville, Maryland 20850, USA
    Nature 388:539-47. 1997
    ..pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH...
  60. 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...
  61. pmc Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group
    Michele Iacono
    National Research Council, Segrate, Milan 20090, Italy
    Antimicrob Agents Chemother 52:2616-25. 2008
    ..These findings provide novel insight into the genetic basis of A. baumannii resistance...
  62. pmc Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited
    Thomas D Leser
    Department of Microbiology, Danish Veterinary Laboratory, Bulowsvej 27, DK 1790 Copenhagen V, Denmark
    Appl Environ Microbiol 68:673-90. 2002
    ..The results document that the intestinal microbial community is very complex and that the majority of the bacterial species colonizing the gastrointestinal tract in pigs have not been characterized...
  63. ncbi Bacterial DNA repair by non-homologous end joining
    Stewart Shuman
    Sloan Kettering Institute, 1275 York Avenue, New York, New York 10021, USA
    Nat Rev Microbiol 5:852-61. 2007
    ..Although still a young field, bacterial NHEJ promises to teach us a great deal about the nexus of DNA repair and bacterial pathogenesis...
  64. pmc Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome
    David C Grainger
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Nucleic Acids Res 34:4642-52. 2006
    ..Hence some targets are associated with combinations of bound FIS, H-NS and IHF. In addition, many regions associated with FIS and H-NS are also associated with RNA polymerase...
  65. ncbi Microbial population structures in the deep marine biosphere
    Julie A Huber
    Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
    Science 318:97-100. 2007
    ....
  66. pmc spa Typing of Staphylococcus aureus as a frontline tool in epidemiological typing
    B Strommenger
    Robert Koch Institute, Wernigerode Branch, Burgstr 37, D 38855 Wernigerode, Germany
    J Clin Microbiol 46:574-81. 2008
    ..They should be selected by dependence on the clonal lineage indicated by spa typing and subsequent BURP analysis as well as on the basis of the particular question to be addressed...
  67. ncbi Bacterial contingency loci: the role of simple sequence DNA repeats in bacterial adaptation
    Richard Moxon
    Oxford University Department of Paediatrics, Molecular Infectious Diseases Group, Weatherall Institute of Molecular Medicine Oxford, United Kingdom
    Annu Rev Genet 40:307-33. 2006
    ..These SSRs are located within the reading frame or in the promoter of a subset of genes, often termed contingency loci, whose functions are usually involved in direct interactions with host structures...
  68. 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...
  69. pmc Instability of repetitive DNA sequences: the role of replication in multiple mechanisms
    M Bzymek
    Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
    Proc Natl Acad Sci U S A 98:8319-25. 2001
    ..Replication plays a critical role in the two slipped misalignment mechanisms, and difficulties in replication appear to trigger rearrangements via all these mechanisms...
  70. pmc Phylogeny of Wolbachia in filarial nematodes
    C Bandi
    Istituto di Patologia Generale Veterinaria, Universita di Milano, Italy
    Proc Biol Sci 265:2407-13. 1998
    ..Thus, there is no evidence for recent Wolbachia transmission between arthropods and nematodes. Endosymbiont 16S ribosomal DNA sequences from a subset of filarial species support these findings...
  71. pmc Distribution of Mycobacterium ulcerans in buruli ulcer endemic and non-endemic aquatic sites in Ghana
    Heather R Williamson
    Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
    PLoS Negl Trop Dis 2:e205. 2008
    ..These findings imply that focal demography, along with patterns of human water contact, may play a major role in transmission of Buruli ulcer...
  72. pmc Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function
    Yisheng Kang
    Department of Genetics, 425 Henry Mall, University of Wisconsin, Madison, WI 53706, USA
    J Bacteriol 187:1135-60. 2005
    ..We suggest that E. coli MG1655 has a larger metabolic potential under anaerobic conditions than has been previously recognized...
  73. ncbi Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18
    J Parkhill
    The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Nature 413:848-52. 2001
    ..typhi. CT18 harbours a 218,150-bp multiple-drug-resistance incH1 plasmid (pHCM1), and a 106,516-bp cryptic plasmid (pHCM2), which shows recent common ancestry with a virulence plasmid of Yersinia pestis...
  74. ncbi Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments
    G Muyzer
    Molecular Ecology Unit, Max Planck Institute for Marine Microbiology, Fahrenheitstrasse 1, D 28359 Bremen, Germany
    Arch Microbiol 164:165-72. 1995
    ..The third 'phylotype' was identified as a Desulfovibrio, indicating that sulfate-reducing bacteria, as sources of sulfide, may complement sulfur- and sulfide-oxidizing bacteria ecologically in these sulfide-producing hydrothermal vents...
  75. pmc Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach
    C Manichanh
    Unité d Ecologie et de Physiologie du Système Digestif, INRA UEPSD, 78350 Jouy en Josas, France
    Gut 55:205-11. 2006
    ..However, investigation of such a complex ecosystem is difficult, even with culture independent molecular approaches...
  76. pmc The evolution of class 1 integrons and the rise of antibiotic resistance
    Michael Gillings
    Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
    J Bacteriol 190:5095-100. 2008
    ..The strong selection pressure imposed by the human use of antimicrobial compounds then ensured their fixation and global spread into new species...
  77. ncbi Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands
    Georgios S Vernikos
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SA, UK
    Bioinformatics 22:2196-203. 2006
    ..g. in short sliding windows. Most of the current HGT prediction methods require pre-existing annotation, which may restrict their application on newly sequenced genomes...
  78. ncbi Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase
    Taku Oshima
    Graduate School of Information Science, Nara Institute of Science and Technology, 8916 5 Takayama, Ikoma, Nara, Japan
    DNA Res 13:141-53. 2006
    ..coli genome, sheds light on the mechanism underlying the transcriptional regulation by H-NS, and provides new insight into bacterial genome evolution...
  79. ncbi Population snapshot of emergent Streptococcus pneumoniae serotype 19A in the United States, 2005
    Matthew R Moore
    Respiratory Diseases Branch, Centers for Disease Control and Prevention, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
    J Infect Dis 197:1016-27. 2008
    ..To understand this increase, we characterized serotype 19A isolates recovered during 2005...
  80. pmc Nomenclature of major antimicrobial-resistant clones of Streptococcus pneumoniae defined by the pneumococcal molecular epidemiology network
    L McGee
    MRC SAIMR Wits Pneumococcal Diseases Research Unit, Johannesburg, South Africa
    J Clin Microbiol 39:2565-71. 2001
    ..This network can serve as a prototype for the collaboration of scientists in identifying clones of important human pathogens and as a model for the development of other networks...
  81. pmc Gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease
    M P Conte
    Paediatric Gastroenterology Unit, University of Rome La Sapienza, Viale Regina Elena 324, Rome 00161, Italy
    Gut 55:1760-7. 2006
    ..No paediatric reports are available on intestinal endogenous microflora in IBD...
  82. pmc Microbial gene identification using interpolated Markov models
    S L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 26:544-8. 1998
    ..As a result, GLIMMER is more flexible and more powerful than fixed-order Markov methods, which have previously been the primary content-based technique for finding genes in microbial DNA...
  83. ncbi FramePlot: a new implementation of the frame analysis for predicting protein-coding regions in bacterial DNA with a high G + C content
    J Ishikawa
    Department of Bioactive Molecules, National Institute of Infectious Diseases, Tokyo, Japan
    FEMS Microbiol Lett 174:251-3. 1999
    FramePlot is a web-based tool for predicting protein-coding regions in bacterial DNA with a high G + C content, such as Streptomyces. The graphical output provides for easy distinction of protein-coding regions from non-coding regions...
  84. pmc Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA
    L Ovreas
    Department of Microbiology, University of Bergen, Norway
    Appl Environ Microbiol 63:3367-73. 1997
    ..Several dominant fragments in the DGGE profiles were excised and sequenced. Among the dominant populations were representatives related to Chlorobium phaeovibrioides, chloroplasts from eukaryotic algae, and unidentified Archaea...
  85. pmc Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites
    S Omura
    The Kitasato Institute for Life Sciences, Kitasato University, Tokyo 108 8642, Japan
    Proc Natl Acad Sci U S A 98:12215-20. 2001
    ..These secondary metabolite clusters are widely located in the genome but half of them are near both ends of the genome. The total length of these clusters occupies about 6.4% of the genome...
  86. pmc ISCR elements: novel gene-capturing systems of the 21st century?
    Mark A Toleman
    Department of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
    Microbiol Mol Biol Rev 70:296-316. 2006
    ..It appears that ISCR elements have now firmly established themselves within that regimen...
  87. 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...
  88. ncbi Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR
    Erja Malinen
    Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Section of Microbiology, P O Box 66, FIN 00014 University of Helsinki, Finland
    Am J Gastroenterol 100:373-82. 2005
    ..The gut microbiota may contribute to the onset and maintenance of irritable bowel syndrome (IBS). In this study, the microbiotas of patients suffering from IBS were compared with a control group devoid of gastrointestinal (GI) symptoms...
  89. pmc Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon
    P Seksik
    INRA, CR de Jouy en Josas, 78352 Jouy en Josas, France
    Gut 52:237-42. 2003
    ..We investigated potential differences in the faecal microflora between patients with colonic CD in remission (n=9), patients with active colonic CD (n=8), and healthy volunteers (n=16) using culture independent techniques...
  90. ncbi The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects
    Anna Kassinen
    Department of Basic Veterinary Sciences, Division of Microbiology and Epidemiology, University of Helsinki, Helsinki, Finland
    Gastroenterology 133:24-33. 2007
    ..Our objective was to characterize putative differences in gastrointestinal microbiota between patients with IBS and control subjects. These differences could potentially have a causal relationship with the syndrome...
  91. pmc Unique features of a highly pathogenic Campylobacter jejuni strain
    Dirk Hofreuter
    Section of Microbial Pathogenesis, School of Medicine, Yale University, New Haven, Connecticut 06536, USA
    Infect Immun 74:4694-707. 2006
    ..This information should help the understanding of the pathogenesis of C. jejuni and, in particular, the unique features of this highly pathogenic strain...
  92. ncbi Bacterial conjugation: a two-step mechanism for DNA transport
    Matxalen Llosa
    Dipartmento de Biología Molecular, Unidad Asociada al CIB CSIC, Universidad de Cantabria, Santander, Spain
    Mol Microbiol 45:1-8. 2002
    ..It is proposed that this second step is catalysed by the coupling proteins. Our 'shoot and pump' model solves the protein-DNA transport paradox of T4SS...
  93. pmc The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters
    Audra J Pompeani
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Mol Microbiol 70:76-88. 2008
    ..Together, the in silico and biochemical results enabled us to scan the genome and identify novel targets of LuxR in V. harveyi and thus expand the understanding of the quorum-sensing regulon...
  94. pmc Inhibition of mutation and combating the evolution of antibiotic resistance
    Ryan T Cirz
    Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
    PLoS Biol 3:e176. 2005
    ..Our findings indicate that the inhibition of mutation could serve as a novel therapeutic strategy to combat the evolution of antibiotic resistance...
  95. pmc Bacterial DNA activates cell mediated immune response and nitric oxide overproduction in peritoneal macrophages from patients with cirrhosis and ascites
    R Frances
    Department of Immunology, Hospital General Universitario, Pintor Baeza s n, Alicante, Spain
    Gut 53:860-4. 2004
    ..We have recently reported the detection of bacterial DNA in blood and ascitic fluid from patients with advanced cirrhosis, what we consider as molecular evidence of ..
  96. ncbi Efficient electrotransformation of corynebacterium diphtheriae with a mini-replicon derived from the Corynebacterium glutamicum plasmid pGA1
    Andreas Tauch
    Zentrum für Genomforschung, Universitat Bielefeld, Universitatsstrasse 25, D 33615 Bielefeld, Germany
    Curr Microbiol 45:362-7. 2002
    ..diphtheriae. Thus, the ability to apply the standard methods of C. glutamicum recombinant DNA technology will greatly facilitate the functional analysis of the recently completed C. diphtheriae genome sequence...
  97. ncbi An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics
    Mario G Rosso
    GABI Kat, Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, 50829 Köln, Germany
    Plant Mol Biol 53:247-59. 2003
    ..Finally, the functionality of the GABI-Kat population was demonstrated by exemplary confirmation of several new transparent testa alleles, as well as a number of other mutants, which were identified on the basis of the FST data...
  98. ncbi A comparison of homologous recombination rates in bacteria and archaea
    Michiel Vos
    Department of Zoology, University of Oxford, Oxford, UK
    ISME J 3:199-208. 2009
    ..This enables a direct comparison between species and allows for a first exploration of the question whether phylogeny or ecology is the primary determinant of homologous recombination rate...
  99. ncbi Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12
    T Hayashi
    Department of Microbiology, Miyazaki Medical College, Kiyotake, Japan
    DNA Res 8:11-22. 2001
    ..A complete set of the genes specific to O157:H7 presented here sheds new insight into the pathogenicity and the physiology of O157:H7, and will open a way to fully understand the molecular mechanisms underlying the O157:H7 infection...
  100. pmc Resistance-nodulation-cell division-type efflux pump involved in aminoglycoside resistance in Acinetobacter baumannii strain BM4454
    S Magnet
    , Institut Pasteur, 75724 Paris Cedex 15, France
    Antimicrob Agents Chemother 45:3375-80. 2001
    ..The products of two upstream open reading frames encoding a putative two-component regulatory system might be involved in the regulation of expression of the adeABC gene cluster...
  101. pmc Detection of Streptococcus pneumoniae strain cocolonization in the nasopharynx
    Silvio D Brugger
    Institute for Infectious Diseases, University of Bern, Friedbuhlstrasse 51, CH 3010 Bern, Switzerland
    J Clin Microbiol 47:1750-6. 2009
    ..025). This new technique allows for the rapid and economical study of pneumococcal cocolonization in nasopharyngeal swabs. It will be valuable for the surveillance of S. pneumoniae epidemiology under vaccine selection pressure...

Research Grants63

  1. Protein composition and interactions of telemeric chromatin
    Michael P Killoran; Fiscal Year: 2010
    ..Second, they will expand on my background in bacterial DNA metabolism to address fundamental biological questions in a different research organism, S. cerevisiae...
  2. DEVELOPMENT OF SPLIT DAMID AS AN ALTERNATIVE METHODOLOGY TO CHROMATIN IMMUNOPRECI
    Raphael Kopan; Fiscal Year: 2010
    ..Our solution (Split-DamID) relies on our ability to successfully split the bacterial DNA adenine methyltransferase (Dam) into N-terminal (D) and C-terminal (AM) halves...
  3. Modulation of TLR4 and TLR9 Signaling in NEC
    David J Hackam; Fiscal Year: 2013
    ..We also showed that the homologous receptor for TLR4, namely TLR9 - which recognizes bacterial DNA ("CpG-DNA") - attenuated NEC through the inhibition of TLR4 signaling and a reduction in enterocyte apoptosis...
  4. DNA recombinational repair in Helicobacter pylori
    Ge Wang; Fiscal Year: 2010
    ..maintain persistence in the human gastric mucosa, a niche full of oxidative and acid stress agents that cause bacterial DNA damage. H...
  5. Synergistic actions by multiple Toll-like receptors in alcoholic liver disease
    Ekihiro Seki; Fiscal Year: 2013
    ..Not only LPS, but also bacterial DNA levels in blood and ascites are elevated in patients with alcoholic-induced liver cirrhosis...
  6. Processing and consequences of DNA-protein crosslinks in E. coli
    Kenneth N Kreuzer; Fiscal Year: 2012
    ..The quinolone antibiotics, which target bacterial DNA gyrase, stabilize a reaction intermediate in which the enzyme is covalently attached to a broken DNA molecule ..
  7. Genetic analysis of DNA methylation in Neurospora crassa
    ANDREW DAVID KLOCKO; Fiscal Year: 2013
    ..DamID experiments using translational fusions to the bacterial DNA Adenine Methylase (dam) gene will analyze the genomic localization of this protein...
  8. Ciprofloxacin enhances DNA repair capacity after radiation combined injury
    JULIANN GONG KIANG; Fiscal Year: 2012
    ..CIP works by inhibiting bacterial DNA gyrase (bacterial topo II or topo IV), but has a slight inhibitory effects on eukaryotic topo II...
  9. HMGB1 and neutrophil efferocytosis.
    JAROSLAW WALDEMAR ZMIJEWSKI; Fiscal Year: 2012
    ..not associated with HMGB1;2) To examine the role of HMGB1 binding co-factors, including IL-12, LPS, TNF-1, and bacterial DNA, in modulating the ability of HMGB1 to affect phagocytosis of apoptotic neutrophils and activation of ..
  10. Genetic and Biochemical Analysis of DNA Exchange in Helicobacter pylori
    MARION SHONN DORER; Fiscal Year: 2010
    ..Genetic diversity is influenced by environmental factors, since the chronic host inflammatory response damages bacterial DNA [8]. My studies show that DNA damage alters transcription of at least 25% of the H...
  11. Mechanism of H. pylori-induced risk reduction for inflammatory bowel disease
    Jay Luther; Fiscal Year: 2009
    ..genomic DNA and TLR9 knockout mice and small interfering RNA to knockdown TLR-9, we will examine the role of bacterial DNA-TLR-9 interaction in shaping the phenotype of murine bone marrow- derived and tissue isolated gastric mucosal ..
  12. Viral and Bacterial DNA Ligases
    STEWART H SHUMAN; Fiscal Year: 2012
    ..We have extended our interests in bacterial DNA ligases to two subfamilies of ATP-dependent strand joining enzymes (named LigD and LigC) that participate in a ..
  13. Modifications of host RNA polymerase during bacteriophage development
    KONSTANTIN V SEVERINOV; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Our long-term goal is to understand the function and regulation of bacterial DNA-dependent RNA polymerase (RNAP) in molecular detail...
  14. Novel Antibacterial Drugs Targeting DNA Repair Enzymes
    Gerald R Smith; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): Upon bacterial infection, host cells release chemicals that damage the bacterial DNA. Such damage, if left unrepaired, leads to bacterial death...
  15. Restoring Immune Function Following Radiation Injuries by TLR9 Agonist Treatment
    James A Lederer; Fiscal Year: 2013
    ..During the course of this project, we discovered that a CpG-containing oligodeoxynucleotide (ODN) that mimics bacterial DNA could signal a highly protective immune response in mice when given at 1 day after radiation injury or RCI...
  16. DNA helicase and primase inhibitors for biodefense
    Donald T Moir; Fiscal Year: 2010
    ..The goal of this project is to discover new inhibitors of the helicase or primase activities in bacterial DNA replication and develop them into antibiotics for biodefense and clinical applications...
  17. TLR Ligand and Pesticide Exposure in Farms: Role in Atopic Immune Responses
    Atin Adhikari; Fiscal Year: 2011
    ..first specific aim we will characterize exposures of environmental TLR ligands (endotoxin, peptidoglycan, and bacterial DNA) and two conventional pesticides relevant to atopic asthma in 10 farms of Ohio before and after pesticide ..
  18. Genetics of MRSA Infection
    George M Weinstock; Fiscal Year: 2010
    ..b. Phenotyping of the clinical presentation of each infection;c. Sampling: isolation of human and bacterial DNA from these subjects. 3...
  19. Cell Cycle and sporulation in Bacillis subtillis
    Alan D Grossman; Fiscal Year: 2013
    Project summary The long term goals of this proposal are to understand the control of bacterial DNA replication and the connections between replication and gene expression...
  20. Disposable Microfluidic Devices for Point of Care Diagnostics
    Catherine M Klapperich; Fiscal Year: 2010
    ..difficile bacterial DNA. The proposed work is to adapt a microfluidic technique for isolation of nucleic acids from mammalian cells ..
  21. Systemic Delivery of CpG Oligonucleotides
    Moo J Cho; Fiscal Year: 2012
    ..It was only recently discovered that the active component in the ill-defined cancer treatment is bacterial DNA, not protein, carbohydrate, or lipid...
  22. Impact of Bacterial-Animal Lateral Gene Transfer on Human Health
    JULIE HOTOPP; Fiscal Year: 2010
    ..Thus, our mucosal cells are bathed in bacterial DNA. Does this bacterial DNA get incorporated into the chromosomes of our somatic cells? Could such integrations ..
  23. Membranes in the Initiation of Chromsomal Replication
    Elliott Crooke; Fiscal Year: 2010
    b>Bacterial DNA replication is carefully controlled at the initiation stage, largely by regulation of-the essential activity of DnaA protein...
  24. Synergistic effect of HIV virions and bacterial LPS on memory B cell apoptosis
    Wei Jiang; Fiscal Year: 2013
    ..disease, resulting in increased systemic exposure to microbial products such as Lipopolysaccharide (LPS) and bacterial DNA. Perturbations in the gut barrier in HIV disease may stem from deletion of CD4+ T cells, loss of Th17 helper ..
  25. Discovery of Inhibitors of DNA Replication in Gram-Positive Bacteria
    H Garry Dallmann; Fiscal Year: 2010
    ..Presently there are no antibacterials targeting the essential process of DNA replication in bacteria. Bacterial DNA replication is initiated by a specific origin binding protein that recruits helicase assembly proteins and the ..
  26. Impact of Antibiotics and PBP2a on the Immunopathology of MRSA pneumonia
    David M Underhill; Fiscal Year: 2013
    ..strongly enhances inflammatory responses by releasing pro-inflammatory intracellular components such as bacterial DNA. S...
  27. Inflammatory responses initiated by periodontal bacterial DNA
    Sinem Esra Sahingur; Fiscal Year: 2013
    ..This proposal is designed to extend our previous studies to primary human and mouse macrophages determine the role of periodontal bDNA and its receptors with regard to induction of cytokines, tolerance/cross and synergy. ..
  28. Screening for Inhibitors of DNA Replication in Gram-Positive Bacteria
    H Garry Dallmann; Fiscal Year: 2010
    ..Presently there are no antibacterial targeting the essential process of DNA replication in bacteria. Bacterial DNA replication is performed by the cellular replicase, DNA polymerase III holoenzyme that has the processivity to ..
  29. Integrated Dual-Use Systems for Bio-Defense & Sepsis Diagnosis
    David Alland; Fiscal Year: 2010
    ..This system will offer unparalleled sensitivity by extracting bacterial DNA from all three "compartments" in whole blood: bacteria free in the blood, intracellular bacteria (principally ..
  30. Blood genomics and proteomics of CpG-induced neuroprotection in primate stroke.
    REBECCA LYNN WILLIAMS; Fiscal Year: 2013
    ..g. bacterial lipopolysaccharide, bacterial DNA, single stranded RNA)...
  31. Enabling Technology to Prepare Ultrapure Dialysate in Dialysis Clinics
    Mohamed E Labib; Fiscal Year: 2013
    ..We plan to also include testing for bacterial DNA fragments in the dialysate before and after the ultrafilter...
  32. National Epidemiologic Survey on Alcohol and Related Conditions: DNA Repository
    JAY ARNOLD TISCHFIELD; Fiscal Year: 2013
    ..e., bacterial DNA contamination). 2...
  33. Dissecting the structural basis for regulation of bacterial DNA polymerase III
    BRIAN ANTHONY KELCH; Fiscal Year: 2010
    ..Moreover, defects in DNA replication have been associated with cancer and neurodegenerative disorders, further highlighting the importance of this process to health science. ..
  34. Innate Immune Receptors in Host Responses to Neisseria
    ROBIN INGALLS; Fiscal Year: 2009
    ..This includes TLR2 for the recognition of bacterial lipoproteins and TLR9 for the recognition of bacterial DNA. The goal of this proposal is to identify the innate immune receptors in the urogenital tract that are ..
  35. Ciprofloxacin enhances DNA repair capacity after radiation combined injury
    JULIANN KIANG; Fiscal Year: 2009
    ..CIP works by inhibiting bacterial DNA gyrase (bacterial topo II or topo IV), but has a slight inhibitory effects on eukaryotic topo II...
  36. Early Life Exposure to Microbial Products and Asthma
    Joel Kline; Fiscal Year: 2005
    ..CpG-ODN mimics the immunostimulatory effects of native bacterial DNA. Like endotoxin, bacterial DNA is recognized by a toll-like receptor (TLR-9) and potently activates the innate ..
  37. Oral Biofilms and the Immune System
    Kim Janda; Fiscal Year: 2009
    ..bacterially-derived molecules, such as bacterial lipopolysaccharides (LPS), peptidoglycan fragments, and bacterial DNA, into the local environment...
  38. Modulation of the innate immunity by bacterial signaling molecules
    Vladimir Kravchenko; Fiscal Year: 2009
    ..bacterially-derived molecules, such as bacterial lipopolysaccharides (LPS), peptidoglycan fragments, and bacterial DNA, into the local environment...
  39. FROM COLEY'S TOXINS TO CpG IMMUNOSTIMULANTS FOR CANCER *
    Anthony Sandler; Fiscal Year: 2004
    ..Unmethylated CpG oligodeoxynucleotides (ODN) are present in bacterial DNA and display potent immune stimulatory properties. CpG ODN could potentially link the pioneering work of Dr...
  40. MED1 MUTATIONS IN COLORECTAL CANCER
    Alfonso Bellacosa; Fiscal Year: 2002
    ..The MED1 protein functionally interacts with MLH1 in human cells, is homologous to bacterial DNA repair glycosylases/lyases, and binds to CpG-methylated DNA, suggesting that cytosine methylation plays a ..
  41. Extracorporeal Blood Purification For Sepsis Therapy
    Susan Szathmary; Fiscal Year: 2006
    ..on affinity binding of bacterial components from both Gram- and Gram+ sepsis, endotoxin, peptidoglycan and bacterial DNA present in blood or plasma flowing through a cartridge filled with agarose beads modified to bind these ..
  42. PENETRATION OF THE BLOOD BRAIN BARRIER IN GBS MENINGITIS
    Victor Nizet; Fiscal Year: 2000
    ..GBS invasion of BMEC requires active bacterial DNA, RNA, and protein synthesis...
  43. Cross-Priming Mechanisms Induced by Microbial Products
    Sandip Datta; Fiscal Year: 2007
    ..and immunostimulatory DNA sequences (ISS) containing unmethylated CpG dinucleotide motifs derived from bacterial DNA, are able to induce cross-priming of CD8+ T cells by dendritic cells...
  44. Triggering intestinal inflammation
    Hai Shi; Fiscal Year: 2005
    ..proposed in this application address the hypothesis that luminal bacterial products (bacterial toxin and bacterial DNA) play a role in triggering and/or regulating intestinal inflammatory and immune response to commensal bacteria,..
  45. SEARCHING FOR EVIDENCE OF INFECTION IN CROHN'S DISEASE
    Zhiheng Pei; Fiscal Year: 2001
    ..After deparaffinization of the granuloma, DNA will be extracted and used as a template to amplify bacterial DNA using consensus eubacterial rDNA primers...
  46. NEW HUMAN DNA REPAIR ENDONUCLEASE
    Alfonso Bellacosa; Fiscal Year: 2002
    ..For its interaction with hMLH1 and homology to bacterial DNA repair proteins, MED1 is a putative mismatch repair protein and might be a long sought eukaryotic functional ..
  47. Alcoholism: Modulation & Function of Lymphocyte Subsets
    Robert Cook; Fiscal Year: 2005
    ..cell activation in the alcoholic mice; 3) mimic bacterial translocation by exposure to defined substitutes for bacterial DNA, and determine whether this products alterations of the T cell balance (antigen-specific T cell loss, and Th1/..
  48. IRAK4 Kinase activity's role in immunodeficiency
    Derek Abbott; Fiscal Year: 2009
    ..inability to respond to a variety of pathogen-associated molecules including LPS, peptidoglycan, viral RNA and bacterial DNA. In addition, while showing a normal TNF response, these mice cannot respond to IL-1 (30-33)...
  49. The Relationship of Protein dynamics to Enzyme Catalysis
    Norbert Reich; Fiscal Year: 2002
    ..Mammalian and bacterial DNA methyltransferases are important drug targets for anticancer and antibiotic drugs, respectively. M...
  50. BACTERIAL DNA REPLICATION STUDIES BY FLOW CYTOMETRY
    Erik Boye; Fiscal Year: 1990
    ..In particular, we will study methylation of the adenines in GATC sequences within the origin and its effects on initiation...
  51. Identification of Biological Materials of Unknown Origin
    Khalid Sayood; Fiscal Year: 2010
    ..the attainment of this long term goal, is to develop techniques for elucidating occult structural features in bacterial DNA which can be used for identification and differentiation of microbial organisms, including organisms whose ..
  52. Novel approach to measure DNA adducts in humans
    ROBERT TURESKY; Fiscal Year: 2007
    ..will be compared to isolate buccal cells that maximize the recovery of human DNA and minimize contaminating bacterial DNA. The standardization of the buccal cell DNA isolation method will permit reliable assessment of genotoxin ..
  53. Single Cell DNA Fragment Sizing
    RICHARD KELLER; Fiscal Year: 2005
    We propose to develop a microscope-based imaging system for analysis of bacterial DNA fragments from single bacterial cells...
  54. Based deamination by CEM15 suppresses HIV-1 Infectivity
    Harold Smith; Fiscal Year: 2005
    ..Additionally, a bacterial DNA mismatch detection system wherein DNA repair confers a positive selection for clones containing CEM15 ..
  55. NCRR Shared Instrumentation/1H (13C/15N) 5mm Cold Probe
    Frederick Dahlquist; Fiscal Year: 2005
    ..structure of self assembly of RNA-RNA recognition units, the coupling of protein dynamics and catalysis in the bacterial DNA cytosine methyltransferase, structural studies of the proteins involved in the epigenetic control of the ..
  56. IN VITRO STUDIES OF HUMAN ANAPHYLAXIS
    LAWRENCE LICHTENSTEIN; Fiscal Year: 2004
    ..The second involves immunotherapy involving allergen coupled to oligonucleotide sequences derived from bacterial DNA. This modified allergen has the characteristics which have been sought in the field for decades...
  57. Bacterial DNA Internalization in B Lymphocytes
    Mara Gerloni; Fiscal Year: 2006
    ..this newly discovered phenomenon in general terms and also pertain to current views on the interaction between bacterial DNA and cells of the immune system...
  58. DISCOVERY OF NOVEL FUNGICIDAL AGENTS
    LESTER MITSCHER; Fiscal Year: 1992
    ..Our present lead compounds have arisen from these projects and will be further modified and expanded as test assays become available...
  59. BACTERIAL DNA HELICASES: TARGETS FOR NOVEL ANTIBIOTICS
    Marjorie Barnes; Fiscal Year: 2005
    ..In Phase II, we will characterize the mechanism of action of the validated hits in more detail and optimize the most promising of these structures utilizing a rational drug design approach to develop antibacterial lead compounds. ..
  60. DNA VACCINES--IMMUNE RESPONSES AND ANTIGEN PROCESSING
    Margaret Liu; Fiscal Year: 1999
    ..antigens to various subcellular locations to alter the type of immune response, and adjuvanticity of the bacterial DNA sequences themselves...
  61. Pneumococcal Biofilms in Otitis Media
    James Post; Fiscal Year: 2007
    ..the Center for Genomic Sciences (CGS) has shown that culturally-negative middle-ear effusions actually contain bacterial DNA, mRNA and protein...
  62. SYNTHETIC ANTIBACTERIAL PEPTIDES
    Gennadi Glinsky; Fiscal Year: 2000
    DESCRIPTION (Adapted from the application): Bacterial DNA-dependent, RNA polymerase (RNAP) is a multiprotein complex consisting of two alpha-subunits, one beta, one beta', and one sigma subunit; the ultimate step of assembly being the ..
  63. Reverse Line Blot Daignostic Test for Agents of Sepsis
    Andrew Levin; Fiscal Year: 2007
    ..Extracted bacterial DNA is then incubated with the membrane permitting complementary sequences to hybridize with the corresponding ..