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2009 Fiscal Year Final Research Report

Analysis of developmental mechanisms based on functional genomic information of the nematode C. elegans

Research Project

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Project/Area Number 17017038
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionThe Institute of Physical and Chemical Research

Principal Investigator

SUGIMOTO Asako  The Institute of Physical and Chemical Research, 発生ゲノミクス研究チーム, チームリーダー (80281715)

Co-Investigator(Kenkyū-buntansha) ONAMI Shuichi  独立行政法人理化学研究所, 発生システムモデル化研究チーム, チームリーダー (50348843)
KIMURA Akatsuki  慶應義塾大学, 大学院・理工学研究科, 助手 (10365447)
KYODA Koji  独立行政法人理化学研究所, 合成ゲノミクス研究チーム, 研究員 (30415145)
Project Period (FY) 2005 – 2009
Keywordsゲノム / 遺伝子 / 発生・分化 / モデル化 / ライブイメージング / 画像処理 / バイオイメージインフォマティクス
Research Abstract

To understand the genetic networks that control animal development, the following were performed using the early embryogenesis of the nematode C.elegans
as a model system. 1) Development of tools (such as GFP/RFP-tagged protein markers and monoclonal antibodies) and imaging techniques, and imaging data collection, 2) Computational analysis of the phenotype image data, and 3) Development of research strategy that integrate quantitative phenotype analysis and simulation.

  • Research Products

    (48 results)

All 2010 2009 2008 2007 2006 2005 Other

All Journal Article (17 results) (of which Peer Reviewed: 16 results) Presentation (20 results) Book (9 results) Remarks (2 results)

  • [Journal Article] The Role of Protein Phosphatase 4 (PP4) in Regulating Microtubule Severing in the Caenorhabditis elegans Embryo.2009

    • Author(s)
      Sugimoto A. (6名中5番目)
    • Journal Title

      Genetics 181

      Pages: 933-943

    • Peer Reviewed
  • [Journal Article] A new mechanism controlling kinetochore-microtubule interactions revealed by comparison of two dynein-targeting components: SPDL-1 and the Rod/Zwilch/Zw10 complex.2008

    • Author(s)
      Sugimoto A. (13名中6番目)
    • Journal Title

      Genes Dev 22

      Pages: 2385-2399

    • Peer Reviewed
  • [Journal Article] Efficient production of monoclonal antibodies recognizing specific structures in Caenorhabditis elegans embryos using an antigen subtraction method2008

    • Author(s)
      Sugimoto A. (5名中5番目)
    • Journal Title

      Genes Cells 13

      Pages: 653-665

    • Peer Reviewed
  • [Journal Article] The Caenorhabditis elegans DDX-23, a homolog of yeast splicing factor PRP28, is required for the sperm-oocyte switch and differentiation of various cell types2008

    • Author(s)
      Konishi, T., Uodome, N., Sugimoto A.
    • Journal Title

      Dev Dyn 237

      Pages: 2367-2377

    • Peer Reviewed
  • [Journal Article] EGG-3 regulates cell-surface and cortex rearrangements during egg activation in Caenorhabditis elegans.2007

    • Author(s)
      Sugimoto A. (14名中13番目)
    • Journal Title

      Curr Biol 17

      Pages: 1555-1560

    • Peer Reviewed
  • [Journal Article] A system for measuring cell division patterns of early Caenorhabditis elegans embryos by using image processing and object tracking2007

    • Author(s)
      Hamahashi, S., Kitano, H., Onami, S.
    • Journal Title

      Systems and Computers in Japan 38(11)

      Pages: 12-24

    • Peer Reviewed
  • [Journal Article] 線虫Caenorhabditis elegans初期胚の細胞分裂パターン計測システムのリコンフィギャラブルシステムによる高速化2007

    • Author(s)
      大浪修一(6名中5番目)
    • Journal Title

      電子情報通信学会論文誌D J90-D

      Pages: 2970-2980

    • Peer Reviewed
  • [Journal Article] Local cortical pulling-force repression switches centrosomal centration and posterior displacement in C. elegans2007

    • Author(s)
      Kimura, A., Onami, S.
    • Journal Title

      J. Cell Biol. 179

      Pages: 1347-1354

    • Peer Reviewed
  • [Journal Article] Two phases of astral microtubule activity during cytokinesis in C. elegans embryos2006

    • Author(s)
      Motegi, F., Velarde, N.V., Piano, F., Sugimoto A.
    • Journal Title

      Dev. Cell 10

      Pages: 509-20

    • Peer Reviewed
  • [Journal Article] Sequential functioning of ECT-2/RhoGEF, RHO-1 and CDC-42 establishes cell polarity in C. elegans embryos2006

    • Author(s)
      Motegi, F., Sugimoto A.
    • Journal Title

      Nat Cell Biol 8

      Pages: 978-985

    • Peer Reviewed
  • [Journal Article] 画像処理とオブジェクトトラッキングを用いた線虫の初期胚の細胞分裂パターン計測システム2006

    • Author(s)
      濱橋秀互, 北野宏明, 大浪修一
    • Journal Title

      電子情報通信学会論文誌D J89-D

      Pages: 1248-1259

  • [Journal Article] Genome-wide prediction of genetic interactions in a metazoan.2006

    • Author(s)
      Onami, S., Kitano, H.
    • Journal Title

      Bioessays 28

      Pages: 1087-1090

    • Peer Reviewed
  • [Journal Article] The C. elegans eyes absent ortholog EYA-1 is required for tissue differentiation and plays partially redundant roles with PAX-6.2005

    • Author(s)
      Furuya, M., Qadota, H., Chisholm, A.D., Sugimoto A.
    • Journal Title

      Dev Biol 286

      Pages: 452-463

    • Peer Reviewed
  • [Journal Article] Objective measurement of spindle orientation in early Caenorhabditis elegans embryos.2005

    • Author(s)
      Hamahashi, S., Onami, S.
    • Journal Title

      Genome Inform 16

      Pages: 86-93

    • Peer Reviewed
  • [Journal Article] Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking.2005

    • Author(s)
      Hamahashi, S., Onami, S., Kitano, H.
    • Journal Title

      BMC Bioinformatics 6

      Pages: 125

    • Peer Reviewed
  • [Journal Article] Computer simulations and image processing reveal length-dependent pulling force as the primary mechanism for C. elegans male pronuclear migration.2005

    • Author(s)
      Kimura, A., Onami, S.
    • Journal Title

      Dev Cell 8

      Pages: 765-75

    • Peer Reviewed
  • [Journal Article] Caenorhabditis elegans geminin homologue participates in cell cycle regulation and germ line development.2005

    • Author(s)
      Sugimoto A. (9名中6番目)
    • Journal Title

      J Biol Chem 280

      Pages: 19689-94

    • Peer Reviewed
  • [Presentation] Genome-wide collection of quantitative information about cell division dynamics in RNAi-treated C. elegans embryo.2010

    • Author(s)
      Onami, S.
    • Organizer
      Sino-Japan Workshop, Systems Biology and Complex Diseases
    • Place of Presentation
      Shanghai, China.
    • Year and Date
      20100313-20010315
  • [Presentation] Live cell imaging and image-processing enable quantitative and computational analysis of the development.2009

    • Author(s)
      Onami, S.
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      神戸
    • Year and Date
      20091209-20091212
  • [Presentation] 定量・計算解析による発生ダイナミクスの理解2009

    • Author(s)
      大浪修一
    • Organizer
      日本機械学会計算力学講演会
    • Place of Presentation
      金沢大学角間キャンパス, 金沢.
    • Year and Date
      20091010-20091012
  • [Presentation] 線虫C. elegans初期胚の細胞分裂ダイナミクスの定量解析2009

    • Author(s)
      京田耕司、足立絵瑠、倉持順子、島田久美子、大浪修一
    • Organizer
      第19回日本数理生物学会大会
    • Place of Presentation
      東京大学駒場キャンパス, 東京
    • Year and Date
      20090909-20090911
  • [Presentation] Computational analysis of quantitative information of cell division dynamics of early embryos.2009

    • Author(s)
      Kyoda, K., Adachi, E., Shimada, K., Kuramochi, J., Onami, S.
    • Organizer
      17th International C. elegans Meeting.
    • Place of Presentation
      LA, USA
    • Year and Date
      20090624-20090628
  • [Presentation] Quantitative cell division dynamics analysis and prediction of the mechanisms of development in C. elegans.2009

    • Author(s)
      Onami, S.
    • Organizer
      The 9th NIBB-EMBL Symposium, Functional Imaging from Atoms to Organisms.
    • Place of Presentation
      Okazaki Conference Center, Okazaki, Japan.
    • Year and Date
      20090420-20090422
  • [Presentation] Quantitative cell division dynamics analysis and prediction of the mechanism of development in C. elegans.2009

    • Author(s)
      Onami, S.
    • Organizer
      International Symposium on System Biology and Proteomics in Biomedical Science
    • Place of Presentation
      Kolkata, India.
    • Year and Date
      20090327-20090329
  • [Presentation] Quantitative cell division dynamics analysis and prediction of the mechanisms of development in C. elegans.2009

    • Author(s)
      Onami, S.
    • Organizer
      The 2nd RIKEN-University of Edinburgh Joint Workshop.
    • Place of Presentation
      British Embassy, Tokyo, Japan.
    • Year and Date
      20090314-20090315
  • [Presentation] 細胞・発生生物学の超ペタフロップス級コンピュータへの展開2009

    • Author(s)
      大浪修一
    • Organizer
      超ペタフロップス級コンピュータと実験生物学の連携による生命現象への挑戦
    • Place of Presentation
      理化学研究所横浜研究所, 横浜
    • Year and Date
      20090205-20090206
  • [Presentation] Self-aggregation of PGL proteins plays a crucial role in P granule assembly.2009

    • Author(s)
      Hanazawa, M., M. Yonetani, A. Sugimoto.
    • Organizer
      17th International C. elegans Meeting.
    • Place of Presentation
      Los Angeles, California, USA.
    • Year and Date
      2009-06-25
  • [Presentation] Assembly and positioning of mitotic spindles in early C. elegans embryos. BMB20082008

    • Author(s)
      Sugimoto, A.
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会合同大会
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2008-12-09
  • [Presentation] Reconstituting C. elegans germ granules in mammalian cells.2008

    • Author(s)
      Sugimoto, A.
    • Organizer
      Cold Spring Harbor Laboratory meeting on Germ Cells.
    • Place of Presentation
      Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
    • Year and Date
      2008-10-03
  • [Presentation] Structure and assembly of germ granules in C. elegans.2008

    • Author(s)
      Sugimoto, A.
    • Organizer
      Frontiers in Developmental Biology.
    • Place of Presentation
      Presqu'ile de Giens, Southern France.
    • Year and Date
      2008-09-14
  • [Presentation] Dissecting the structure and assembly of C. elegans germ granules in heterologous cells.2008

    • Author(s)
      Sugimoto, A.
    • Organizer
      "RNA" Granules Meeting.
    • Place of Presentation
      Chevy Chase, Maryland, USA
    • Year and Date
      2008-04-02
  • [Presentation] Structure and assembly of germ granules in C. elegans.2008

    • Author(s)
      Sugimoto, A.
    • Organizer
      Swiss-Japan Joint Seminar.
    • Place of Presentation
      Arosa, Switzerland.
    • Year and Date
      2008-01-08
  • [Presentation] Cellular dynamics in early C. elegans embryos. Establishment of polarity in C. elegans 1-cell embryos.2007

    • Author(s)
      Sugimoto, A.
    • Organizer
      Gordon Research Conference "Developmental Biology"2007 Taiwan- Japan Bi-lateral Symposium.
    • Place of Presentation
      Andover, NH, USA, Taiwan.
    • Year and Date
      20070627,20070119
  • [Presentation] Structure and assembly of germ granules in C. elegans.2007

    • Author(s)
      Sugimoto, A.
    • Organizer
      Pasteur + CDB Joint Meeting.
    • Place of Presentation
      Paris, France.
    • Year and Date
      2007-11-29
  • [Presentation] 線虫発生過程のフェノーム解析2006

    • Author(s)
      杉本亜砂子
    • Organizer
      日本遺伝学会第78回大会
    • Place of Presentation
      つくば国際会議場
    • Year and Date
      2006-09-25
  • [Presentation] 線虫発生過程のフェノーム解析2005

    • Author(s)
      杉本亜砂子
    • Organizer
      表現型をどう「表現」するか?日本分子生物学会年会
    • Place of Presentation
      福岡
    • Year and Date
      20051200
  • [Presentation] Profiling and cluster analysis of developmental RNAi phenotypes in C. elegans.2005

    • Author(s)
      Sugimoto, A.
    • Organizer
      Gordon Research Conference "Developmental Biology"
    • Place of Presentation
      Andover, NH
    • Year and Date
      2005-06-20
  • [Book] 蛋白質核酸酵素(線虫における生殖顆粒の形成と配分, 54)2009

    • Author(s)
      花澤桃世、米谷匡史, 杉本亜砂子
    • Total Pages
      2147-2152
    • Publisher
      共立出版
  • [Book] 文部科学省科学研究費特定領域研究「ゲノム4領域」(ゲノムに書かれた発生プログラムを読み解く--線虫をモデル系として. ゲノムは何をどのように決めているのか? 生命システムの理解に向けて)2007

    • Author(s)
      杉本亜砂子
    • Total Pages
      101-112
    • Publisher
      クパブロ
  • [Book] 比較ゲノム学から読み解く生命システム(線虫の比較ゲノム)2007

    • Author(s)
      杉本亜砂子
    • Total Pages
      105-110
    • Publisher
      秀潤社
  • [Book] 実験医学(体系的表現型解析で探る線虫の発生機構, 25)2007

    • Author(s)
      杉本亜砂子
    • Total Pages
      151-157
  • [Book] DBRF-MEGN method: An algorithm for inferring gene regulatory networks from large-scale gene expression profiles.2007

    • Author(s)
      Onami, S., Kyoda, K.
    • Total Pages
      435-448
    • Publisher
      Humana Press
  • [Book] 蛋白質核酸酵素(コンピュータシミュレーションを利用した核の配置のダイナミクス解析, 51)2006

    • Author(s)
      木村暁、大浪修一
    • Total Pages
      2172-2179
    • Publisher
      共立出版
  • [Book] 蛋白質核酸酵素(線虫ゲノムの体系的発現・機能解析, 50)2005

    • Author(s)
      杉本亜砂子、小原雄治
    • Total Pages
      2140-2145
    • Publisher
      共立出版
  • [Book] RNA工学の最前線 線虫(C. elegans)におけるRNAiの応用2005

    • Author(s)
      飯田直子、杉本亜砂子
    • Total Pages
      41-51
    • Publisher
      シーエムシー出版
  • [Book] 蛋白質核酸酵素(発生のシステムバイオロジー, 50)2005

    • Author(s)
      大浪修一、北野宏明
    • Total Pages
      798-803
    • Publisher
      共立出版
  • [Remarks]

    • URL

      http://www.cdb.riken.jp/dge/KTmAbDB/KTtop.html

  • [Remarks]

    • URL

      http://so.gsc.riken.jp/cdd/

URL: 

Published: 2011-06-18   Modified: 2016-04-21  

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