Research Topics

Genomes and Genes

Species

bacterial dna

Summary

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

Top Publications

  1. ncbi Acetobacter fabarum sp. nov., an acetic acid bacterium from a Ghanaian cocoa bean heap fermentation
    Ilse Cleenwerck
    BCCM LMG Bacteria Collection, Faculty of Sciences, Ghent University, K L Ledeganckstraat 35, B 9000 Ghent, Belgium
    Int J Syst Evol Microbiol 58:2180-5. 2008
  2. ncbi 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
  3. 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
  4. 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
  5. ncbi 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
  6. ncbi ISfinder: the reference centre for bacterial insertion sequences
    P Siguier
    , C.N.R.S. 118, route de Narbonne, F-31062 Toulouse Cedex, France
    Nucleic Acids Res 34:D32-6. 2006
  7. 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
  8. 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
  9. ncbi 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
  10. ncbi 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

Research Grants

  1. Viral and Bacterial DNA Ligases
    STEWART H SHUMAN; Fiscal Year: 2010
  2. Viral and Bacterial DNA Ligases
    Stewart Shuman; Fiscal Year: 2009
  3. Processing and consequences of DNA-protein crosslinks in E. coli
    Kenneth N Kreuzer; Fiscal Year: 2010
  4. Processing and consequences of DNA-protein crosslinks in E. coli
    Kenneth N Kreuzer; Fiscal Year: 2010
  5. HMGB1 and neutrophil efferocytosis.
    Edward Abraham; Fiscal Year: 2010
  6. HMGB1 and neutrophil efferocytosis.
    Edward Abraham; Fiscal Year: 2009
  7. PATHOBIOCHEMISTRY OF CHLAMYDIA TRACHOMONAS HUMAN SEXUALLY TRANSMITTED DISEASES
    BIBHUTI SINGH; Fiscal Year: 2001
  8. DNA REPLICATION AND GENE EXPRESSION OF CHLORELLA VIRUSES
    James Van Etten; Fiscal Year: 1993
  9. Innate Immune Receptors in Host Responses to Neisseria
    ROBIN INGALLS; Fiscal Year: 2009
  10. BIOPHYSICS AND GENETICS OF VIRAL DNA PACKAGING
    Philip Serwer; Fiscal Year: 1980

Detail Information

Publications260 found, 100 shown here

  1. ncbi Acetobacter fabarum sp. nov., an acetic acid bacterium from a Ghanaian cocoa bean heap fermentation
    Ilse Cleenwerck
    BCCM LMG Bacteria Collection, Faculty of Sciences, Ghent University, K L Ledeganckstraat 35, B 9000 Ghent, Belgium
    Int J Syst Evol Microbiol 58:2180-5. 2008
    ..nov. is proposed. The type strain is strain 985(T) (=R-36330(T) =LMG 24244(T) =DSM 19596(T))...
  2. ncbi 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...
  3. 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...
  4. 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...
  5. ncbi 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...
  6. ncbi ISfinder: the reference centre for bacterial insertion sequences
    P Siguier
    , 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...
  7. 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; ..
  8. 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
  9. ncbi 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...
  10. ncbi 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...
  11. 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...
  12. ncbi 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...
  13. 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...
  14. 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...
  15. 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
    ..Fecal samples were obtained at 3 months intervals. Total bacterial DNA was analyzed by 20 quantitative real-time PCR assays covering approximately 300 bacterial species...
  16. 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...
  17. 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, , , 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...
  18. ncbi 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.)...
  19. 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...
  20. ncbi Mauve: multiple alignment of conserved genomic sequence with rearrangements
    Aaron C E Darling
    Department of Computer Science, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
    Genome Res 14:1394-403. 2004
    ..We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution...
  21. ncbi Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)
    Scot E Dowd
    USDA ARS Livestock Issues Research Unit, Lubbock, TX 79403, USA
    BMC Microbiol 8:125. 2008
    ..We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows...
  22. 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...
  23. ncbi Biofilm formation by Streptococcus pneumoniae: role of choline, extracellular DNA, and capsular polysaccharide in microbial accretion
    Miriam Moscoso
    , , CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
    J Bacteriol 188:7785-95. 2006
    ..Those results, in turn, may provide insight into strategies to prevent pneumococcal colonization of its human host...
  24. ncbi The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions
    Tomohiro Shimada
    Department of Frontier Bioscience and Micro Nano Technology Research Centre, Hosei University, Koganei, Tokyo 184 8584, Nippon Institute for Biological Science, Ome, Tokyo 198 0024, Japan
    Nucleic Acids Res 36:3950-5. 2008
    ..We suggest that either RutR has yet undiscovered function or that evolution has been slow to eliminate non-functional DNA sites for RutR because they do not have an adverse effect on cell fitness...
  25. ncbi 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
    ....
  26. 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
    ....
  27. ncbi Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses
    Haichun Gao
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
    BMC Genomics 9:42. 2008
    ..Shewanella oneidensis MR-1 contains a gene encoding a putative ArcA homolog with ~81% amino acid sequence identity to the E. coli ArcA protein but not a full-length arcB gene...
  28. ncbi Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus
    Philippe Horvath
    Danisco France SAS, BP10, F 86220 Dangé Saint Romain, France
    J Bacteriol 190:1401-12. 2008
    ..Also, CRISPRs provide critical insights into the relationships between prokaryotes and their environments, notably the coevolution of host and viral genomes...
  29. 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...
  30. ncbi 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...
  31. ncbi Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis
    Claire Lurin
    , , 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...
  32. 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...
  33. ncbi Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM
    Yan Qi
    Graduate Program in Biophysics, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Biol Chem 285:1468-78. 2010
    MutM, a bacterial DNA glycosylase, protects genome integrity by catalyzing glycosidic bond cleavage of 8-oxoguanine (oxoG) lesions, thereby initiating base excision DNA repair...
  34. 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...
  35. ncbi Long PCR improves Wolbachia DNA amplification: wsp sequences found in 76% of sixty-three arthropod species
    A Jeyaprakash
    Department of Entomology and Nematology, University of Florida, Gainesville, Florida 32611, USA
    Insect Mol Biol 9:393-405. 2000
    ..Hence, superinfection also may be more widespread than the 1.2% incidence previously estimated...
  36. ncbi Biofilms formed by nontypeable Haemophilus influenzae in vivo contain both double-stranded DNA and type IV pilin protein
    Joseph A Jurcisek
    Columbus Children s Research Institute, Center for Microbial Pathogenesis, The Ohio State University College of Medicine, 700 Children s Drive, Columbus, OH 43205 2696, USA
    J Bacteriol 189:3868-75. 2007
    ....
  37. ncbi High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease
    Roman Kotlowski
    Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada
    Gut 56:669-75. 2007
    ..One way of determining which bacteria might be likely candidates is to use culture-independent methods to identify microorganisms that are present in diseased tissues but not in controls...
  38. ncbi Attachment to and biofilm formation on abiotic surfaces by Acinetobacter baumannii: involvement of a novel chaperone-usher pili assembly system
    Andrew P Tomaras
    Department of Microbiology, Miami University, 40 Pearson Hall, Oxford, OH 45056, USA
    Microbiology 149:3473-84. 2003
    ..baumannii cells...
  39. ncbi Evaluation of a two-step approach for large-scale, prospective genotyping of Mycobacterium tuberculosis isolates in the United States
    Lauren S Cowan
    Division of TB Elimination, National Center for HIV, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
    J Clin Microbiol 43:688-95. 2005
    ..IS6110 fingerprinting can then be used as a secondary typing method to type the clustered isolates when additional discrimination is needed...
  40. ncbi Composition and temporal stability of gastrointestinal microbiota in irritable bowel syndrome--a longitudinal study in IBS and control subjects
    Jaana Mättö
    VTT Biotechnology, Finland
    FEMS Immunol Med Microbiol 43:213-22. 2005
    ..The present study suggests that instability of intestinal microbiota may be involved in IBS. However, further studies are needed to associate the instability with specific IBS symptoms or with specific bacterial groups and species...
  41. ncbi Polymerase chain reaction primers miss half of rRNA microbial diversity
    Sunhee Hong
    Department of Biology, Northeastern University, Boston, MA, USA
    ISME J 3:1365-73. 2009
    ....
  42. ncbi Novel genes of the dsr gene cluster and evidence for close interaction of Dsr proteins during sulfur oxidation in the phototrophic sulfur bacterium Allochromatium vinosum
    Christiane Dahl
    Institut für Mikrobiologie and Biotechnologie, Rheinische Friedrich Wilhelms Universitat Bonn, Meckenheimer Allee 168, D 53115 Bonn, Germany
    J Bacteriol 187:1392-404. 2005
    ....
  43. ncbi Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing
    Seong Woon Roh
    Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
    ISME J 4:1-16. 2010
    ....
  44. ncbi Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes
    Julie C Dunning Hotopp
    Institute for Genomic Research, J Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 317:1753-6. 2007
    ..Therefore, heritable lateral gene transfer occurs into eukaryotic hosts from their prokaryote symbionts, potentially providing a mechanism for acquisition of new genes and functions...
  45. ncbi Cutting edge: Cytosolic bacterial DNA activates the inflammasome via Aim2
    Sarah E Warren
    Institute for Systems Biology, Seattle, WA 98103, USA
    J Immunol 185:818-21. 2010
    ..We now use biochemical and genetic approaches to demonstrate that the third detector senses bacterial DNA and identify it as Aim2, a receptor that has previously been shown to detect viral DNA.
  46. ncbi Molecular epidemiology of tuberculosis and other mycobacterial infections: main methodologies and achievements
    D van Soolingen
    Mycobacteria Reference Department, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
    J Intern Med 249:1-26. 2001
    ..tuberculosis complex (atypical) mycobacteria. Important new insights that have been gained through molecular techniques into epidemiological aspects and diagnosis of mycobacterial diseases are highlighted...
  47. ncbi Purification and characterization of PCR-inhibitory components in blood cells
    W A Al-Soud
    Applied Microbiology, Center for Chemistry and Chemical Engineering, Lund Institute of Technology, Lund University, SE-221 00 Lund, Sweden
    J Clin Microbiol 39:485-93. 2001
    ..Including 0.02% (wt/vol) gp32, a single-stranded-DNA binding protein, in the reaction mixture of AmpliTaq Gold was also found to reduce the inhibitory effects of hemoglobin and lactoferrin...
  48. ncbi Wolbachia infection frequencies in insects: evidence of a global equilibrium?
    J H Werren
    Department of Biology, University of Rochester, NY 14627, USA
    Proc Biol Sci 267:1277-85. 2000
    ..Within each of the three geographic regions surveyed, Hymenoptera are more frequently infected with A group Wolbachia and Lepidoptera more frequently infected with B group Wolbachia...
  49. ncbi Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs
    Scot E Dowd
    USDA ARS Livestock Issues Research Unit, Lubbock, Texas 79403, USA
    Foodborne Pathog Dis 5:459-72. 2008
    ..Using bTEFAP, we can expect to gain a better understanding of how the microbiome of an animal contributes to its health and well-being...
  50. ncbi Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes
    J A Carriço
    Grupo de Biomatemática, Istituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande 6 2780 156 Oeiras, Portugal
    J Clin Microbiol 44:2524-32. 2006
    ..803 and 0.655, respectively). This was confirmed by the analysis of the larger data set available from http://spyogenes.mlst.net and underscores the necessity of performing PFGE or MLST to unambiguously define clones in S. pyogenes...
  51. ncbi The Arabidopsis HOMOLOGY-DEPENDENT GENE SILENCING1 gene codes for an S-adenosyl-L-homocysteine hydrolase required for DNA methylation-dependent gene silencing
    Pedro S C F Rocha
    Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
    Plant Cell 17:404-17. 2005
    ..The same T-DNA also complemented the zygotic embryo lethal phenotype of the hog1-4 tagged mutant. A model relating the HOG1 gene, DNA methylation, and methylation-dependent HDG silencing is presented...
  52. ncbi Identification of serotype in culture negative pneumococcal meningitis using sequential multiplex PCR: implication for surveillance and vaccine design
    Samir K Saha
    Department of Microbiology, Bangladesh Institute of Child Health, Dhaka Shishu Children Hospital, Dhaka, Bangladesh
    PLoS ONE 3:e3576. 2008
    ..Furthermore, PCR has not been used to determine serotype distribution in culture-negative meningitis cases...
  53. ncbi Polymerase chain reaction detection of 8 putative periodontal pathogens in subgingival plaque of gingivitis and advanced periodontitis lesions
    A Ashimoto
    Department of Periodontology, School of Dentistry, University of Southern California, Los Angeles 90089 0641, USA
    Oral Microbiol Immunol 11:266-73. 1996
    ..The results indicated a strong association between the study species and periodontitis. Several previously unreported symbiotic relationships were found between the 8 species tested...
  54. ncbi A renaissance for the pioneering 16S rRNA gene
    Susannah G Tringe
    DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
    Curr Opin Microbiol 11:442-6. 2008
    ..The standard conclusion that microbial ecosystems are remarkably complex and diverse is now being replaced by detailed insights into microbial ecology and evolution based only on this one historically important marker gene...
  55. ncbi Phospholipase C5 (NPC5) is involved in galactolipid accumulation during phosphate limitation in leaves of Arabidopsis
    Nicole Gaude
    Max Planck Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476 Potsdam, Germany
    Plant J 56:28-39. 2008
    ....
  56. ncbi A plasmid of phytoplasma encodes a unique replication protein having both plasmid- and virus-like domains: clue to viral ancestry or result of virus/plasmid recombination?
    K Oshima
    Laboratory of Bioresource Technology, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo ku, Tokyo, 113 8657, Japan
    Virology 285:270-7. 2001
    ..Alternatively, a pOYW ancestor could have obtained the helicase domain by recombination with a virus: this would be the first example of recombination between plasmids and viruses...
  57. 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...
  58. ncbi Rapid sequence-based identification of gonococcal transmission clusters in a large metropolitan area
    Iona M C Martin
    Department of Infectious Diseases and Microbiology, Imperial College London, St Mary s Campus, London, United
    J Infect Dis 189:1497-505. 2004
    ....
  59. ncbi Mucosal flora in inflammatory bowel disease
    Alexander Swidsinski
    Innere Klinik, Gastroenterologie, Charité Humboldt Universität, Berlin, Germany
    Gastroenterology 122:44-54. 2002
    ..Microorganisms that directly interact with the intestinal mucosa are obscured by fecal flora and poorly characterized...
  60. ncbi Silencing of episomal transgene expression by plasmid bacterial DNA elements in vivo
    Z Y Chen
    Departments of Pediatrics and Genetics, Stanford University School of Medicine, 200 Pasteur Drive, Room G305, Stanford, CA 94305-5208, USA
    Gene Ther 11:856-64. 2004
    We previously demonstrated that sustainable enhanced levels of transgene products could be expressed from a bacterial DNA-free expression cassette either formed from a fragmented plasmid in mouse liver or delivered as a minicircle vector...
  61. ncbi Development of a new PCR-ribotyping method for Clostridium difficile based on ribosomal RNA gene sequencing
    P Bidet
    Laboratoire de Bacteriologie, Centre Hospitalo Universitaire Saint Antoine, Assistance Publique Hopitaux de Paris, France
    FEMS Microbiol Lett 175:261-6. 1999
    ..This typing method has evidenced major qualities such as easiness, rapidity and reproducibility. However, its discriminatory power has to be evaluated to validate its importance as a typing tool for C. difficile...
  62. ncbi Comparison of seven techniques for typing international epidemic strains of Clostridium difficile: restriction endonuclease analysis, pulsed-field gel electrophoresis, PCR-ribotyping, multilocus sequence typing, multilocus variable-number tandem-repeat an
    George Killgore
    Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
    J Clin Microbiol 46:431-7. 2008
    ..All techniques appear to be capable of detecting outbreak strains, but only REA and MLVA showed sufficient discrimination to distinguish strains from different outbreaks...
  63. ncbi Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed
    K Smalla
    Federal Biological Research Centre for Agriculture and Forestry, D 38104 Braunschweig, D 18051 Rostock, Germany
    Appl Environ Microbiol 67:4742-51. 2001
    ..Sequencing of dominant bands excised from the rhizosphere patterns revealed that 6 out of 10 bands resembled gram-positive bacteria. Nocardia populations were identified as strawberry-specific bands...
  64. ncbi 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...
  65. ncbi Phylogenetic analysis and description of Eperythrozoon coccoides, proposal to transfer to the genus Mycoplasma as Mycoplasma coccoides comb. nov. and Request for an Opinion
    Harold Neimark
    Department of Microbiology and Immunology, Morse Institute of Molecular Genetics, College of Medicine, State University of New York, Brooklyn, 11203, USA
    Int J Syst Evol Microbiol 55:1385-91. 2005
    ..nov. A Request for an Opinion is submitted to the Judicial Commission of the International Committee on Systematics of Prokaryotes regarding this reclassification...
  66. ncbi Natural association of Gluconacetobacter diazotrophicus and diazotrophic Acetobacter peroxydans with wetland rice
    Ramachandran Muthukumarasamy
    Main Bio control Research Laboratory Unit of Tamilnadu Co operative Sugar Federation, Good Will Avenue, Venpakkam, Chengalpattu 603 111, Tamilnadu, India
    Syst Appl Microbiol 28:277-86. 2005
    ..This is the first report of diazotrophic nature of A. peroxydans...
  67. ncbi Nitrate-dependent [Fe(II)EDTA]2- oxidation by Paracoccus ferrooxidans sp. nov., isolated from a denitrifying bioreactor
    Rajkumari Kumaraswamy
    Environmental Biotechnology Group, Department of Biotechnology, Delft University of Technology, Julianalaan 67, NL-2628 BC Delft, The Netherlands
    Syst Appl Microbiol 29:276-86. 2006
    ..Fe(II)EDTA]2- oxidation dependent denitrification was also performed by other Paracoccus species, that were closely affiliated to P. ferrooxidans...
  68. ncbi Phylogenetic assignment and mechanism of action of a crop growth promoting Rhizobium radiobacter strain used as a biofertiliser on graminaceous crops in Russia
    David R Humphry
    Department of Biology, University of York, P O Box 373, University Road, Heslington, York, UK
    Antonie Van Leeuwenhoek 91:105-13. 2007
    ..radiobacter type strain and that the mechanism of its effect on growth of cereals is via the production of plant growth promoting substances. GA is likely to play an important role in the strain 204 stimulation of early growth of barley...
  69. ncbi Clostridium asparagiforme sp. nov., isolated from a human faecal sample
    Ruchika Mohan
    Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
    Syst Appl Microbiol 29:292-9. 2006
    ..Based on these findings, we propose the novel bacterium from human faeces to be classified as a new species, Clostridium asparagiforme. The type strain of C. asparagiforme is N6 (DSM 15981 and CCUG 48471)...
  70. ncbi Isolation of a psychrotrophic Exiguobacterium sp. SKPB5 (MTCC 7803) and characterization of its alkaline protease
    Ramesh C Kasana
    Hill Area Tea Science Division, Institute of Himalayan Bioresource Technology CSIR, Palampur 176061, India
    Curr Microbiol 54:224-9. 2007
    ..SKPB5 belongs to the cysteine family. The results highlight the relevance of unexplored microbes from cold environments of Western Himalayas for the isolation of protease enzymes active at wide range of temperature and pH...
  71. ncbi Molecular phylogeny based on the 16S rRNA gene of elite rhizobial strains used in Brazilian commercial inoculants
    Pâmela Menna
    Embrapa Soja, Cx Postal 231, 86001 970, Londrina, PR, Brazil
    Syst Appl Microbiol 29:315-32. 2006
    ..Finally, the great diversity observed in this study emphasizes that tropics are an important reservoir of N2-fixation genes...
  72. ncbi Molecular microbial diversity of a soil sample and detection of ammonia oxidizers from Cape Evans, Mcmurdo Dry Valley, Antarctica
    Bhupendra V Shravage
    Molecular Biology Unit, National Centre for Cell Science, Ganeshkhind, Pune 411007, India
    Microbiol Res 162:15-25. 2007
    ..The presence of ammonia oxidizing bacteria in Antarctica soil was confirmed by the presence of the amoA gene. Phylogenetic analysis revealed grouping of clones with their respective groups...
  73. ncbi Shewanella donghaensis sp. nov., a psychrophilic, piezosensitive bacterium producing high levels of polyunsaturated fatty acid, isolated from deep-sea sediments
    Sung Hyun Yang
    Marine Biotechnology Research Centre, Korea Ocean Research and Development Institute, PO Box 29, Ansan 425 600, Republic of Korea
    Int J Syst Evol Microbiol 57:208-12. 2007
    ..On the basis of this polyphasic evidence, strain LT17T represents a novel species of the genus Shewanella, for which the name Shewanella donghaensis sp. nov. is proposed. The type strain is LT17T (=KCTC 10635BPT=JCM 12524T)...
  74. ncbi Vibrio comitans sp. nov., Vibrio rarus sp. nov. and Vibrio inusitatus sp. nov., from the gut of the abalones Haliotis discus discus, H. gigantea, H. madaka and H. rufescens
    Tomoo Sawabe
    Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3 1 1 Minato cho, Hakodate 041, Japan
    Int J Syst Evol Microbiol 57:916-22. 2007
    ..8 mol%) are proposed to encompass these new taxa. Several phenotypic features were revealed that discriminate V. comitans, V. rarus and V. inusitatus from other Vibrio species...
  75. ncbi Rhizobium oryzae sp. nov., isolated from the wild rice Oryza alta
    Guixiang Peng
    College of Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China
    Int J Syst Evol Microbiol 58:2158-63. 2008
    ..Based on these results, we propose to place them in a novel species, as Rhizobium oryzae sp. nov. The type strain is Alt 505(T) (=LMG 24253(T) =CGMCC 1.7048(T))...
  76. ncbi Mariniflexile fucanivorans sp. nov., a marine member of the Flavobacteriaceae that degrades sulphated fucans from brown algae
    Tristan Barbeyron
    Centre National de la Recherche Scientifique, Universite Pierre et Marie Curie Paris 6, Unité Mixte de Recherche 7139 Végétaux Marins et Biomolécules, Station Biologique, F 29682 Roscoff Cedex, Bretagne, France
    Int J Syst Evol Microbiol 58:2107-13. 2008
    ..nov. is proposed. Strain SW5(T) (=CIP 109502(T) =DSM 18792(T)) is the type strain...
  77. ncbi Molecular systematics support the revival of Mycobacterium salmoniphilum (ex Ross 1960) sp. nov., nom. rev., a species closely related to Mycobacterium chelonae
    Christopher M Whipps
    Center for Fish Disease Research, Department of Microbiology, 220 Nash Hall, Oregon State University, Corvallis, OR 97331 3404, USA
    Int J Syst Evol Microbiol 57:2525-31. 2007
    ..salmoniphilum' as Mycobacterium salmoniphilum (ex Ross 1960) sp. nov., nom. rev., with the type strain SCT (=ATCC 13578T =DSM 43276T)...
  78. ncbi Acidaminococcus intestini sp. nov., isolated from human clinical samples
    Estelle Jumas-Bilak
    Universite Montpellier 1, Faculte de Pharmacie, Laboratoire de Bacteriologie virologie, 15 Avenue Charles Flahault, BP 14491, 34060 Montpellier Cedex 5, France
    Int J Syst Evol Microbiol 57:2314-9. 2007
    ..nov. is proposed. The type strain is ADV 255.99(T) (=AIP 283.01(T)=CIP 108586(T)=CCUG 50930(T))...
  79. ncbi Vibrio rhizosphaerae sp. nov., a red-pigmented bacterium that antagonizes phytopathogenic bacteria
    N Ramesh Kumar
    Microbiology Department, M S Swaminathan Research Foundation, 3rd Cross Street, Taramani Institutional Area, Chennai 600 113, India
    Int J Syst Evol Microbiol 57:2241-6. 2007
    ..nov. is proposed...
  80. ncbi Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes
    Jennifer C Ast
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
    Int J Syst Evol Microbiol 57:2073-8. 2007
    ..nov. is proposed. The type strain, pjapo.1.1(T) (=ATCC BAA-1194(T)=LMG 23890(T)), is a luminous symbiont isolated from the light organ of the deep-water fish Physiculus japonicus...
  81. ncbi Francisella philomiragia subsp. noatunensis subsp. nov., isolated from farmed Atlantic cod (Gadus morhua L.)
    J Mikalsen
    National Veterinary Institute, Oslo, Norway
    Int J Syst Evol Microbiol 57:1960-5. 2007
    ..noatunensis subsp. nov. with the type strain 2005/50/F292-6C(T) (=NCIMB 14265(T)=LMG 23800(T)). Francisella philomiragia ATCC 25015(T) (=DSM 735(T)) is reclassified as Francisella philomiragia subsp. philomiragia subsp. nov...
  82. ncbi Different Mesorhizobium species sharing the same symbiotic genes nodulate the shrub legume Anagyris latifolia
    Javier Donate Correa
    Departamento de Microbiologia y Biologia Celular, Universidad de La Laguna, 38071 La Laguna, Tenerife, Spain
    Syst Appl Microbiol 30:615-23. 2007
    ....
  83. ncbi Acetobacter ghanensis sp. nov., a novel acetic acid bacterium isolated from traditional heap fermentations of Ghanaian cocoa beans
    Ilse Cleenwerck
    BCCM LMG Bacteria Collection, Faculty of Sciences, Ghent University, K L Ledeganckstraat 35, B 9000 Ghent, Belgium
    Int J Syst Evol Microbiol 57:1647-52. 2007
    ..nov. is proposed. The type strain is R-29337(T) (=430A(T)=LMG 23848(T)=DSM 18895(T))...
  84. ncbi Amycolatopsis saalfeldensis sp. nov., a novel actinomycete isolated from a medieval alum slate mine
    Marc René Carlsohn
    Leibniz Institut für Naturstoff Forschung und Infektionsbiologie eV, Hans Knöll Institut, Beutenbergstrasse 11a, 07745 Jena, Germany
    Int J Syst Evol Microbiol 57:1640-6. 2007
    ..On the basis of these results, a novel species, Amycolatopsis saalfeldensis sp. nov., is proposed. The type strain is HKI 0457(T) (=DSM 44993(T)=NRRL B-24474(T))...
  85. ncbi Lactobacillus crustorum sp. nov., isolated from two traditional Belgian wheat sourdoughs
    Ilse Scheirlinck
    Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K L Ledeganckstraat 35, B 9000 Ghent, Belgium
    Int J Syst Evol Microbiol 57:1461-7. 2007
    ..nov. is proposed. The type strain of the new species is LMG 23699(T) (=CCUG 53174(T))...
  86. ncbi Alloscardovia omnicolens gen. nov., sp. nov., from human clinical samples
    Geert Huys
    Laboratory of Microbiology, Ghent University, K L Ledeganckstraat 35, B 9000 Ghent, Belgium
    Int J Syst Evol Microbiol 57:1442-6. 2007
    ..nov., sp. nov. is proposed. The type strain of Alloscardovia omnicolens is CCUG 31649(T) (=LMG 23792(T))...
  87. ncbi Alcanivorax balearicus sp. nov., isolated from Lake Martel
    Raul Rivas
    Departamento de Microbiologia y Genetica, Universidad de Salamanca, Spain
    Int J Syst Evol Microbiol 57:1331-5. 2007
    ..nov. is proposed. The type strain is MACL04(T) (=LMG 22508(T)=CECT 5683(T))...
  88. ncbi Proposal of six species of moderately thermophilic, acidophilic, endospore-forming bacteria: Alicyclobacillus contaminans sp. nov., Alicyclobacillus fastidiosus sp. nov., Alicyclobacillus kakegawensis sp. nov., Alicyclobacillus macrosporangiidus sp. nov.,
    Keiichi Goto
    Microbiological and Analytical Group, Food Research Laboratories, Mitsui Norin Co Ltd, 223 1, Miyahara, Fujieda, Shizuoka 426 0133, Japan
    Int J Syst Evol Microbiol 57:1276-85. 2007
    ..type strain 5-A239-2O-A(T)=DSM 17980(T)=IAM 15370(T)), Alicyclobacillus sacchari sp. nov. (type strain RB718(T)=DSM 17974(T)=IAM 15230(T)) and Alicyclobacillus shizuokensis sp. nov. (type strain 4-A336(T)=DSM 17981(T)=IAM 15226(T))...
  89. ncbi Marichromatium bheemlicum sp. nov., a non-diazotrophic, photosynthetic gammaproteobacterium from a marine aquaculture pond
    P Anil Kumar
    Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, JNT University, Kukatpally, Hyderabad 500 085, India
    Int J Syst Evol Microbiol 57:1261-5. 2007
    ..nov...
  90. ncbi Corynebacterium hansenii sp. nov., an alpha-glucosidase-negative bacterium related to Corynebacterium xerosis
    François N R Renaud
    Universite de Lyon, Nosoco tech, ISPB, EA 3090, Universite Claude Bernard Lyon 1, Laboratoire de Microbiologie, 8 av Rockefeller, 69373 Lyon Cedex 08, France
    Int J Syst Evol Microbiol 57:1113-6. 2007
    ..The name Corynebacterium hansenii sp. nov. is proposed for this novel species; the type strain is C-138(T) (=CIP 108444(T)=CCUG 53252(T))...
  91. ncbi Lentibacillus salarius sp. nov., isolated from saline sediment in China, and emended description of the genus Lentibacillus
    Che Ok Jeon
    Environmental Biotechnology National Core Research Center, Division of Environmental Biotechnology, Gyeongsang National University, Korea
    Int J Syst Evol Microbiol 55:1339-43. 2005
    ..nov. is proposed. The type strain is BH139(T) (= KCTC 3911(T) = DSM 16459(T))...
  92. ncbi Citrate synthase gene comparison, a new tool for phylogenetic analysis, and its application for the rickettsiae
    V Roux
    Unite des Rickettsies, Centre National de la Recherche Scientifique, EPJ 0054, Faculte de Medecine, Marseille, France
    Int J Syst Bacteriol 47:252-61. 1997
    ....
  93. ncbi Desulfovibrio alaskensis sp. nov., a sulphate-reducing bacterium from a soured oil reservoir
    Maria J Feio
    School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michael's Building, White Swan Rd, Portsmouth PO1 2DT, UK
    Int J Syst Evol Microbiol 54:1747-52. 2004
    ..Based on the results obtained, the name Desulfovibrio alaskensis sp. nov. is therefore proposed, with Al1T (= NCIMB 13491T = DSM 16109T) as the type strain...
  94. ncbi Streptomyces glauciniger sp. nov., a novel mesophilic streptomycete isolated from soil in south China
    Ying Huang
    State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
    Int J Syst Evol Microbiol 54:2085-9. 2004
    ..1858(T)=JCM 12278(T)=LMG 22082(T)) should be classified as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces glauciniger sp. nov. is proposed...
  95. ncbi Methylobacterium nodulans sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria
    Philippe Jourand
    Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 1063, IRD CIRAD INRA Agro M UMII, TA 10 J, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
    Int J Syst Evol Microbiol 54:2269-73. 2004
    ..The name Methylobacterium nodulans sp. nov. (type strain, ORS 2060(T)=CNCM I 2342(T)=LMG 21967(T)) is proposed for this group of root-nodule-forming bacteria...
  96. ncbi Classification of isolates from locations in Austria and Yellowstone National Park as Geobacillus tepidamans sp. nov
    Christina Schäffer
    Center for NanoBiotechnology, University of Applied Life Sciences and Natural Resources, A 1180 Wien, Austria
    Int J Syst Evol Microbiol 54:2361-8. 2004
    ..nov., with GS5-97(T) (=ATCC BAA-942(T)=DSM 16325(T)) as the type strain. Strain YNP10 has been deposited in the American Type Culture Collection as ATCC BAA-943...
  97. ncbi Mycobacterium cosmeticum sp. nov., a novel rapidly growing species isolated from a cosmetic infection and from a nail salon
    Robert C Cooksey
    Division of AIDS, STD, and TB Laboratory Research, National Center for HIV, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
    Int J Syst Evol Microbiol 54:2385-91. 2004
    ....
  98. ncbi Phylogenetic analysis and PCR-restriction fragment length polymorphism identification of Campylobacter species based on partial groEL gene sequences
    R I Kärenlampi
    Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, P O Box 66, University of Helsinki, FI 00014 Helsinki, Finland
    J Clin Microbiol 42:5731-8. 2004
    ..jejuni strains. In conclusion, groEL gene sequencing and PCR-RFLP analysis are recommended as valuable tools for the identification of Campylobacter species...
  99. ncbi A novel enterohepatic Helicobacter species 'Helicobacter mastomyrinus' isolated from the liver and intestine of rodents
    Zeli Shen
    Division of Comparative Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Helicobacter 10:59-70. 2005
    ..A number of novel Helicobacter species have been isolated from both animals and humans. Many of these helicobacters colonize the lower gastrointestinal tract and hepatobiliary tract and are associated with diseases...
  100. ncbi Mycobacterium parascrofulaceum sp. nov., novel slowly growing, scotochromogenic clinical isolates related to Mycobacterium simiae
    C Y Turenne
    National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Health Canada, Winnipeg, Manitoba, Canada
    Int J Syst Evol Microbiol 54:1543-51. 2004
    ..nov. is proposed, follows the present trend of a large number of novel Mycobacterium species identified due in great part to sequence-based methods. The type strain is HSC68T (= ATCC BAA-614T = DSM 44648T)...
  101. ncbi Mycobacterium canariasense sp. nov
    M Soledad Jimenez
    Laboratorio de Micobacterias, Servicio de Bacteriologia, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
    Int J Syst Evol Microbiol 54:1729-34. 2004
    ..The name Mycobacterium canariasense sp. nov. is proposed for this novel opportunistic pathogen, which is most closely related to Mycobacterium diernhoferi. The type strain is 502329T (= CIP 107998T = CCUG 47953T)...

Research Grants79

  1. Viral and Bacterial DNA Ligases
    STEWART H SHUMAN; Fiscal Year: 2010
    ..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 ..
  2. Viral and Bacterial DNA Ligases
    Stewart Shuman; Fiscal Year: 2009
    ..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 ..
  3. Processing and consequences of DNA-protein crosslinks in E. coli
    Kenneth N Kreuzer; Fiscal Year: 2010
    ..The quinolone antibiotics, which target bacterial DNA gyrase, stabilize a reaction intermediate in which the enzyme is covalently attached to a broken DNA molecule ..
  4. Processing and consequences of DNA-protein crosslinks in E. coli
    Kenneth N Kreuzer; Fiscal Year: 2010
    ..The quinolone antibiotics, which target bacterial DNA gyrase, stabilize a reaction intermediate in which the enzyme is covalently attached to a broken DNA molecule ..
  5. HMGB1 and neutrophil efferocytosis.
    Edward Abraham; Fiscal Year: 2010
    ..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 ..
  6. HMGB1 and neutrophil efferocytosis.
    Edward Abraham; Fiscal Year: 2009
    ..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 ..
  7. PATHOBIOCHEMISTRY OF CHLAMYDIA TRACHOMONAS HUMAN SEXUALLY TRANSMITTED DISEASES
    BIBHUTI SINGH; Fiscal Year: 2001
    E. coli microcin B17 (MccB17) is a posttranslationally modified peptide antibiotic that inhibits bacterial DNA gyrase...
  8. DNA REPLICATION AND GENE EXPRESSION OF CHLORELLA VIRUSES
    James Van Etten; Fiscal Year: 1993
    ..iii) To determine if the high homology between certain chlorella virus and bacterial DNA methyltransferases indicates natural interkingdom gene exchange between bacteria and the chlorella viruses...
  9. 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 ..
  10. BIOPHYSICS AND GENETICS OF VIRAL DNA PACKAGING
    Philip Serwer; Fiscal Year: 1980
    During the morphogenesis of several animal and bacterial DNA viruses DNA is packaged in a proteinaceous envelope. Our long-range objective is to understand the mechanism of viral DNA packaging at the molecular level...
  11. LONG RANGE INTERACTIONS IN MU AND BACTERIAL DNA
    NORMAN HIGGINS; Fiscal Year: 2009
    ..This work provides a rationale for developing new antibiotics to fight pathogenic microorganisms and to solve old problems about how chromosomes become disentangled during cell growth. ..
  12. LONG RANGE INTERACTIONS IN MU AND BACTERIAL DNA
    NORMAN P HIGGINS; Fiscal Year: 2010
    ..This work provides a rationale for developing new antibiotics to fight pathogenic microorganisms and to solve old problems about how chromosomes become disentangled during cell growth. ..
  13. Synergistic actions by multiple Toll-like receptors in alcoholic liver disease
    Ekihiro Seki; Fiscal Year: 2010
    ..Not only LPS, but also bacterial DNA levels in blood and ascites are elevated in patients with alcoholic-induced liver cirrhosis...
  14. 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 ..
  15. MOLECULAR ANALYSIS OF PATHOGENS IN OTITIS MEDIA BY PCR
    Garth Ehrlich; Fiscal Year: 2002
    ..Ehrlich's group has documented the presence of bacterial DNA and H. influenzae transcripts in culture-negative, otitis media with effusions (OME)...
  16. 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 ..
  17. Mechanism of Activation of Innate Immunity by ISS-DNA
    Wen Ming Chu; Fiscal Year: 2005
    ..b>Bacterial DNA is also a potent inducer of innate immunity...
  18. 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,..
  19. 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...
  20. 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 ..
  21. LONG RANGE INTERACTIONS IN MU AND BACTERIAL DNA
    NORMAN HIGGINS; Fiscal Year: 2001
    ..The third aim involves the theory that knots and tangling of DNA strands pose a major impediment to long range DNA dynamics. Special transposons will be built to find and count knots in different regions of the chromosome. ..
  22. Membranes in the Initiation of Chromsomal Replication
    Elliott Crooke; Fiscal Year: 2006
    b>Bacterial DNA replication is carefully controlled at the initiation stage, including by regulation of the essential activity of DnaA protein...