in silico reproduction of physicochemical field of genetic activities

2012 Fiscal Year Final Research Report

• Project Area: The physicochemical field for genetic activities
• Project/Area Number: 20114008
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: National Institute of Genetics
• Principal Investigator: KIMURA Akatsuki 国立遺伝学研究所, 構造遺伝学研究センター, 准教授 (10365447)
• Project Period (FY): 2008 – 2012
• Keywords: 遺伝情報場 / コンピュータシミュレーション / 細胞核 / 染色体 / 線虫

Research Abstract

The purpose of this project was to propose theoretical frameworks of how nuclear environment("genofield")affects genetic activities. Using Caenorhabditis elegans as a model organism, I quantified spatial parameters on genofield, and constructed simulation models that reproduce the quantified features of genofield. I focused on the sizes of cells and nucleus as the spatial parameters, and quantified how the changes in these parameters affect storage of genetic information into chromosomes and mitotic spindles. Based on the quantification, I reproduced these quantitative relationships of genofield in silieo.

Research Products

• [Journal Article] An allometric relationship between mitotic spindle width, spindle length, and ploidy in Caenorhabditis elegans embryos (2013)
  • Author(s): Hara Y. and Kimura A
  • Journal Title: Mol. Biol. Cell Volume: 24 Pages: 1411-1419
  • DOI: DOI:10.1091/mbc.E12-07-0528
  • Peer Reviewed
• [Journal Article] 細胞分裂の力学的理解 (2013)
  • Author(s): 木村健二, 木村暁
  • Journal Title: 細胞工学 Volume: 32 Pages: 280-284
  • Peer Reviewed
• [Journal Article] Rab6 is required for the exocytosis of cortical granules and the recruitment of separase to the granules during the oocyte-to-embryo transition in Caenorhabditis elegans (2012)
  • Author(s): Kimura K. and Kimura A
  • Journal Title: J. Cell Sci Volume: 125 Pages: 5897-5905
  • DOI: DOI:10.1242/jcs.116400
  • Peer Reviewed
• [Journal Article] What determines cell size? (2012)
  • Author(s): Marshall M.F., Young K.D., Swaffer M., Wood E., Nurse P., Kimura A., Frankel J., Wallingford J., Walbot V., Qu X. and Roeder A.H.K.
  • Journal Title: BMC Biology Volume: 10 Pages: 101
  • DOI: DOI:10.1186/1741-7007-10-101
• [Journal Article] Lfng regulates the synchronized oscillation of the mouse segmentation clock via trans-repression of Notch signaling (2012)
  • Author(s): Okubo Y., Sugawara T., Abe-Koduka N., Kanno J., Kimura A. and *Saga Y
  • Journal Title: Nat. Comm Volume: 3 Pages: 1141
  • DOI: DOI:10.1038/ncomms2133
  • Peer Reviewed
• [Journal Article] Localized accumulation of tubulin during semi-open mitosis in the Caenorhabditis elegans embryo (2012)
  • Author(s): Hayashi H., Kimura K. and Kimura A
  • Journal Title: Mol. Biol. Cell Volume: 23 Pages: 1688-1699
  • DOI: DOI:10.1091/mbc.E11-09-0815
  • Peer Reviewed
• [Journal Article] A high-resolution shape fitting and simulation demonstrated equatorial cell surface softening during cytokinesis and its promotive role in cytokinesis (2012)
  • Author(s): Koyama H., Umeda T., Nakamura K, Higuchi T. and Kimura A
  • Journal Title: PLoS ONE Volume: 7 Pages: e31607
  • DOI: DOI:10.1371/journal.pone.0031607
  • Peer Reviewed
• [Journal Article] The hydrodynamic property of the cytoplasm is sufficient to mediate cytoplasmic streaming in the Caenorhabditis elegans embryo (2011)
  • Author(s): Niwayama R., Shinohara K. and Kimura A
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 108 Pages: 11900-11905
  • Peer Reviewed
• [Journal Article] Intracellular organelles mediate cytoplasmic pulling force for centrosome centration in the Caenorhabditis elegans early embryo (2011)
  • Author(s): Kimura K. and Kimura A
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 108 Pages: 137-142
  • DOI: DOI:10.1073/pnas.1013275108
  • Peer Reviewed
• [Journal Article] 細胞サイズの定量生物学 (2010)
  • Author(s): 木村暁
  • Journal Title: 生化学 Volume: 82 Pages: 302-305
• [Journal Article] New look inside the spindle: microtubule-dependent microtubule generation within the spindle (2009)
  • Author(s): Goshima G. and Kimura A
  • Journal Title: Curr. Opin. Cell Biol Volume: 22 Pages: 44-49
  • DOI: DOI: 10.1016/j.ceb.2009.11.012
• [Journal Article] Cell-size-dependent spindle elongation in the Caenorhabditis elegans early embryo (2009)
  • Author(s): Hara Y. and Kimura A
  • Journal Title: Curr. Biol Volume: 19 Pages: 1549-1554
  • DOI: DOI:10.1016/j.cub.2009.07.050
  • Peer Reviewed
• [Journal Article] 細胞核の大きさと場所はどのように決まるのか (2009)
  • Author(s): 木村暁
  • Journal Title: 実験医学(増刊) Volume: 27 Pages: 2779-2786
• [Journal Article] Intranuclear DNA Density Affects Chromosome Condensation in Metazoans
  • Author(s): Hara Y., Iwabuchi M., Ohsumi K. and Kimura A.
  • Journal Title: Mol. Biol. Cell Volume: (in press)
  • DOI: DOI:10.1091/mbc.E13-01-0043
  • Peer Reviewed
• [Presentation] Quantification of Size Scaling Relationship of the Mitotic Spindle in the Caenorhabditis elegans Embryo (2013)
  • Author(s): Kimura A
  • Organizer: The 10th NIBB-EMBL Symposium 2013 .Quantitative Bioimaging
  • Place of Presentation: Okazaki Conference Center, Okazaki, Japan
  • Year and Date: 2013-03-17
• [Presentation] Allometric Scaling in the Mitotic Spindle (2012)
  • Author(s): Kimura A
  • Organizer: 2012 ASCB Annual Meeting. Special Interest Subgroup E. Building the Cell
  • Place of Presentation: The Moscone Center, San Francisco, USA
  • Year and Date: 2012-12-15
• [Presentation] A cellular funicular: one active force generation drives two directional organelle movements (2012)
  • Author(s): Kimura A
  • Organizer: The 50th Annual Meeting of the BSJ
  • Place of Presentation: Nagoya University, Nagoya, Japan
  • Year and Date: 2012-09-22
• [Presentation] Size-dependency/independency in the spatial organization of the cell: nuclear positioning and chromosome dynamics in C. elegans embryos (2011)
  • Author(s): Kimura A
  • Organizer: International Symposium Physicochemical Field for Genetic Activities
  • Place of Presentation: Awaji Yumebutai International Conference Center, Awaji, Japan
  • Year and Date: 20110124-26
• [Presentation] Spatial Organization of the Cell (2011)
  • Author(s): Constructing Cell Model, to Study the Kimura A
  • Organizer: The 49th Annual Meeting of the Biophysical Society of Japan
  • Place of Presentation: University of Hyogo, Himeji, Japan
  • Year and Date: 2011-09-16
• [Presentation] An equation to calculate mitotic spindle width function of spindle length: astudyinas Caaenorhabditis elegans embryos (2011)
  • Author(s): Kimura A
  • Organizer: RIKEN CDB-QBiC Joint Symposium
  • Place of Presentation: RIKEN Center for Developmental Biology (CDB), Kobe, Japan
  • Year and Date: 2011-07-01
• [Presentation] 線虫 C. elegans初期胚における紡錘体伸長と細胞質分裂のモデル構築 (2010)
  • Author(s): Kimura A
  • Organizer: 日本動物学会第81回大会
  • Place of Presentation: 東京大学駒場キャンパス, 東京
  • Year and Date: 2010-09-24
• [Presentation] Quantitative Measurement and Modeling reveal Cell Size dependent Mechanisms to Elongate Mitotic Spindles in the C. elegans embryo (2010)
  • Author(s): Kimura A
  • Organizer: 2nd Joint Meeting of the French and Japanease Societies for Developmental Biology
  • Place of Presentation: Institut Pasteur, Paris, France
  • Year and Date: 2010-05-26
• [Presentation] Force balance models of centrosome centering and apindle elongation in C. elegans embryos (2010)
  • Author(s): Kimura A
  • Organizer: The 101st Boehringer Ingelheim Fonds International Titisee Conferences
  • Place of Presentation: Schwarzwaldhotel Titisee, Germany
  • Year and Date: 2010-03-19
• [Presentation] Construction of cell architecture models focusing on centrosome positioning in C. elegans (2009)
  • Author(s): Kimura A
  • Organizer: Japanese Molecular Biology Pre-meeting Symposium 2009
  • Place of Presentation: Yokohama, Japan
  • Year and Date: 2009-12-08
• [Presentation] 線虫初期胚における中心体配置のオルガネラ綱引きモデル (2009)
  • Author(s): Kimura A
  • Organizer: 日本遺伝学会第81回大会
  • Place of Presentation: 信州大学(松本)
  • Year and Date: 2009-09-18
• [Presentation] 細胞建築の力学的理解をめざして～線虫 C. elegans初期胚を用いた紡錘体伸長の解析～ (2009)
  • Author(s): Kimura A
  • Organizer: 第19回日本数理生物学会年会
  • Place of Presentation: 東京大学(東京)
  • Year and Date: 2009-09-09
• [Book] Cell-size-dependent control of organelle sizes during development. In "Cell Cycle in Development" (Kubiak JZ Ed.) (2011)
  • Author(s): Hara Y. and Kimura A
  • Total Pages: 93-108
  • Publisher: Springer Series: Results and Problems in Cell Differentiation 53
• [Remarks] プレスリリース 2011年7月5日(科学新聞に掲載)
• [Remarks] プレスリリース 2011年1月4日(科学新聞、山形新聞に掲載)
• [Remarks] プレスリリース 2009年8月14日(科学新聞、静岡新聞に掲載)