I Kobayashi

Summary

Affiliation: University of Tokyo
Country: Japan

Publications

  1. pmc Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases
    Eri Fukuda
    Laboratory of Social Genome Sciences, Department of Medical Genome Sciences, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Genome Biol 9:R163. 2008
  2. pmc Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site
    Katarzyna H Kaminska
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02 109 Warsaw, Poland
    BMC Struct Biol 8:48. 2008
  3. pmc Accumulation of large non-circular forms of the chromosome in recombination-defective mutants of Escherichia coli
    Naofumi Handa
    Division of Molecular Biology, Institute of Medical Science, University of Tokyo, Shirokanedai, Tokyo 108 8639 Japan
    BMC Mol Biol 4:5. 2003
  4. pmc Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes
    Mikihiko Kawai
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato ku, Tokyo, 108 8639, Japan
    BMC Microbiol 11:104. 2011
  5. pmc CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes
    Ikuo Uchiyama
    National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444 8585, Japan
    BMC Bioinformatics 7:472. 2006
  6. pmc Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution
    I Kobayashi
    Department of Molecular Biology, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 29:3742-56. 2001
  7. ncbi request reprint Shaping the genome--restriction-modification systems as mobile genetic elements
    I Kobayashi
    Institute of Medical Science, University of Tokyo, Shirokanedai, 108 8639, Japan
    Curr Opin Genet Dev 9:649-56. 1999
  8. ncbi request reprint Selfishness and death: raison d'être of restriction, recombination and mitochondria
    I Kobayashi
    Department of Molecular Biology, University of Tokyo, Japan
    Trends Genet 14:368-74. 1998
  9. pmc DNA double-strand break repair: genetic determinants of flanking crossing-over
    K Kusano
    Department of Molecular Biology, University of Tokyo, Japan
    Proc Natl Acad Sci U S A 91:1173-7. 1994
  10. ncbi request reprint Involvement of RecE exonuclease and RecT annealing protein in DNA double-strand break repair by homologous recombination
    K Kusano
    Department of Molecular Biology, University of Tokyo, Japan
    Gene 138:17-25. 1994

Collaborators

Detail Information

Publications19

  1. pmc Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases
    Eri Fukuda
    Laboratory of Social Genome Sciences, Department of Medical Genome Sciences, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Genome Biol 9:R163. 2008
    ..A methyl-specific deoxyribonuclease, McrBC, of Escherichia coli cuts invading methylated DNAs. Here we examined whether McrBC competes with genome methylation systems through host killing by chromosome cleavage...
  2. pmc Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site
    Katarzyna H Kaminska
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02 109 Warsaw, Poland
    BMC Struct Biol 8:48. 2008
    ....
  3. pmc Accumulation of large non-circular forms of the chromosome in recombination-defective mutants of Escherichia coli
    Naofumi Handa
    Division of Molecular Biology, Institute of Medical Science, University of Tokyo, Shirokanedai, Tokyo 108 8639 Japan
    BMC Mol Biol 4:5. 2003
    ....
  4. pmc Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes
    Mikihiko Kawai
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato ku, Tokyo, 108 8639, Japan
    BMC Microbiol 11:104. 2011
    ..We used newly developed comparative methods to follow the evolution of East Asian H. pylori genomes using 20 complete genome sequences from Japanese, Korean, Amerind, European, and West African strains...
  5. pmc CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes
    Ikuo Uchiyama
    National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444 8585, Japan
    BMC Bioinformatics 7:472. 2006
    ....
  6. pmc Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution
    I Kobayashi
    Department of Molecular Biology, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 29:3742-56. 2001
    ..The capacity of RM systems to act as selfish, mobile genetic elements may underlie the structure and function of RM enzymes...
  7. ncbi request reprint Shaping the genome--restriction-modification systems as mobile genetic elements
    I Kobayashi
    Institute of Medical Science, University of Tokyo, Shirokanedai, 108 8639, Japan
    Curr Opin Genet Dev 9:649-56. 1999
    ..A comparison of bacterial genomes supports the hypothesis that restriction-modification gene complexes are mobile elements involved in various genome rearrangements and evolution...
  8. ncbi request reprint Selfishness and death: raison d'être of restriction, recombination and mitochondria
    I Kobayashi
    Department of Molecular Biology, University of Tokyo, Japan
    Trends Genet 14:368-74. 1998
    ..By extrapolation, the capacity of mitochondria to kill their host eukaryotic cell might have stabilized their initial symbiosis...
  9. pmc DNA double-strand break repair: genetic determinants of flanking crossing-over
    K Kusano
    Department of Molecular Biology, University of Tokyo, Japan
    Proc Natl Acad Sci U S A 91:1173-7. 1994
    ..We discuss how cooperation of the recQ gene product and the recJ gene product brings about double-strand break repair accompanied by flanking crossing-over. We also discuss how this reaction is related to repair of chromosome damages...
  10. ncbi request reprint Involvement of RecE exonuclease and RecT annealing protein in DNA double-strand break repair by homologous recombination
    K Kusano
    Department of Molecular Biology, University of Tokyo, Japan
    Gene 138:17-25. 1994
    ..From these observations, we conclude that both ExoVIII and RecT are essential for ds gap repair. We discuss their possible roles in the ds break repair reaction...
  11. pmc Orientation dependence in homologous recombination
    K Yamamoto
    Laboratory of Clinical Microbiology and Immunology, Bun in Hospital, Faculty of Medicine, University of Tokyo, Japan
    Genetics 143:27-36. 1996
    ..These results are consistent with our previous findings that the major route of recombination in recBC sbcBC strains generates only one recombinant DNA from two DNAs and in recBC sbcA strains generates two recombinant DNAs from two DNAs...
  12. ncbi request reprint Experimental genome evolution: large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction-modification gene complex
    N Handa
    Department of Molecular Biology, Institute of Medical Science, University of Tokyo, Shirokanedai, Tokyo 108-8639 Japan
    Mol Microbiol 40:932-40. 2001
    ..It was strongly suggested that multiple rounds of unequal IS3-IS3 recombination caused large-scale duplication and inversion of the chromosome, and that only one of the duplicated copies of the recipient PaeR7I was replaced...
  13. ncbi request reprint Type V phosphodiesterase inhibition modulates endogenous immunoreactivities of endothelin-1 and endothelial nitric oxide synthase in pulmonary arteries in rats with monocrotaline-induced pulmonary hypertension
    T Takahashi
    Department of Infectious Diseases and Applied Immunology, University of Tokyo, Japan
    Res Exp Med (Berl) 197:319-28. 1998
    ..Oral administration of E4021 modulates endogenous immunoreactivities of endothelin-1 and endothelial nitric oxide synthase with the improvement or right ventricular overload and medial thickening...
  14. ncbi request reprint Endothelin converting enzyme inhibitor protects development of right ventricular overload and medial thickening of pulmonary arteries in rats with monocrotaline-induced pulmonary hypertension
    T Takahashi
    Department of Infectious Diseases, Institute of Medical Science, University of Tokyo, Japan
    Life Sci 63:PL137-43. 1998
    ..FR901533 (100 mg/kg/day), protected the development of right ventricular overload and medial thickening of pulmonary arteries in a rat model of pulmonary hypertension...
  15. ncbi request reprint Gene conversion in the Escherichia coli RecF pathway: a successive half crossing-over model
    K Yamamoto
    Department of Bacteriology, Medical School, University of Tokyo, Japan
    Mol Gen Genet 234:1-13. 1992
    ....
  16. ncbi request reprint A novel, 11 nucleotide variant of chi, chi*: one of a class of sequences defining the Escherichia coli recombination hotspot chi
    D A Arnold
    Sections of Microbiology and of Molecular and Cellular Biology, University of California at Davis, CA 95616, USA
    J Mol Biol 300:469-79. 2000
    ....
  17. ncbi request reprint [Study of diarrhea-inducing strains of Escherichia coli mainly isolated in Kanto area between June and September 1996]
    I Kobayashi
    Department of Clinical Microbiology, Mitsubishi Kagaku Bio Clinical Laboratory, Inc
    Kansenshogaku Zasshi 71:495-500. 1997
    ..coli O157 tested were susceptible to all antibiotics such as ampicillin, doxycylin, levofloxacin, fosfomycin, chloramphenicol and polymyxin B, and no strains resistant to levofloxacin, polymyxin B and fosfomycin were found...
  18. ncbi request reprint A defect in harmonin, a PDZ domain-containing protein expressed in the inner ear sensory hair cells, underlies Usher syndrome type 1C
    E Verpy
    Unité de Génétique des Déficits Sensoriels, CNRS URA 1968, Institut Pasteur, Paris Cedex 15, France
    Nat Genet 26:51-5. 2000
    ..As several of these transcripts were absent from the eye, we propose that USH1C also underlies the DFNB18 form of isolated deafness...
  19. ncbi request reprint Ser298 of MITF, a mutation site in Waardenburg syndrome type 2, is a phosphorylation site with functional significance
    K Takeda
    Department of Molecular Biology and Applied Physiology, Tohoku University School of Medicine, Sendai 980 8575, Japan
    Hum Mol Genet 9:125-32. 2000
    ..These findings suggest that the Ser298 is important for MITF function and is phosphorylated probably by GSK3beta...