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Induced orderliness in biological networks

Research Project

Project/Area Number 16K00399
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionMaebashi Institute of Technology

Principal Investigator

Sakata Katsumi  前橋工科大学, 工学部, 教授 (90545419)

Project Period (FY) 2016-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2018: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2016: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywords環境変動と生命秩序 / 生命系ネットワーク / 生命現象の物理 / 状態空間モデル / システムバイオロジー / 生物ネットワーク
Outline of Final Research Achievements

Meaurement of variation of system-state that the system could maintain from a state-space description of the temporal profiles of the system-states was developed. The method was applied to a soybean during the flooding response and a human myelomonocytic leukaemia cell transcriptional network in response to a phorbol-ester stimulus. A loss of variation of state in response to the environmental stress was observed in both systems.
An information-theoretic model for managing predator-prey ecosystems undergoing climate-related changes was developed. This model estimates the amount of information transferred between the number of predator and prey categories, and the uncertainty of the number of the prey categories in a predator-prey ecosystem as measured by Shannon entropy, which is achieved by predation events and decay in the ecosystem. We examined the model with a numerical experiment using a well-studied bass-crayfish predator-prey ecosystem in a closed lake.

Academic Significance and Societal Importance of the Research Achievements

従来は異なる分野(分子生物学、生態学、神経科学)において研究が進められてきた、生命系ネットワーク(転写ネットワーク、食物網、神経網)の生成機構に対し、情報学的モデルによる統一的解釈を目指した。
ネットワークの統一モデルにより、分子生物学、生態学、神経科学、各分野の知見を相互に活用してネットワークを解析することが可能になり、同分野およびネットワーク科学の大いなる発展が期待できる。本研究による成果は、自然界の開放系システムにおける構成要素間の相互作用構造と振る舞いの法則性の記述に拡張できる可能性がある。

Report

(5 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (13 results)

All 2020 2019 2018 2017 2016 Other

All Int'l Joint Research (2 results) Journal Article (3 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 3 results,  Open Access: 3 results,  Acknowledgement Compliant: 1 results) Presentation (8 results) (of which Int'l Joint Research: 4 results)

  • [Int'l Joint Research] Florida A&M University(米国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] King Abdullah Univ. of Sci. and Tech.(サウジアラビア)

    • Related Report
      2019 Annual Research Report
  • [Journal Article] An Information-Theoretic Model for Managing Predator-Prey Ecosystems Facing Climate Changes2020

    • Author(s)
      Katsumi Sakata, Ramesh Katam, Toshiyuki Saito, Hajime Ohyanagi, Setsuko Komatsu
    • Journal Title

      International Journal on Advances in Life Sciences

      Volume: 12

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] An Integrated Approach of Proteomics and Computational Genetic Modification Effectiveness Analysis to Uncover the Mechanisms of Flood Tolerance in Soybeans2018

    • Author(s)
      Wang Xin、Sakata Katsumi、Komatsu Setsuko
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 19 Issue: 5 Pages: 1301-1301

    • DOI

      10.3390/ijms19051301

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Loss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimuli2016

    • Author(s)
      坂田 他
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 35946-35946

    • DOI

      10.1038/srep35946

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] Mathematical Formulation of Environmental Responses of Life Systems2020

    • Author(s)
      Katsumi Sakata, Ramesh Katam
    • Organizer
      International Conferences on STEM/STEAM and Education
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A mathematical model for predator-prey ecosystems facing climate changes2019

    • Author(s)
      Katsumi Sakata, Toshiyuki Saito, Hajime Ohyanagi, Setsuko Komatsu
    • Organizer
      11th International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 気候変動下の捕食者-被食者生態系の数理モデル構築とシミュレーション2019

    • Author(s)
      坂田 克己
    • Organizer
      日本応用数理学会 2019年 研究部会連合発表会
    • Related Report
      2018 Research-status Report
  • [Presentation] Information flow analysis of genetic regulatory systems2018

    • Author(s)
      Sakata K, Saito T, Ohyanagi H, Asahi S, Sato D, Morikawa Y, Komatsu S
    • Organizer
      2018 SIAM Annual Meeting
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] ヒト転写とダイズ代謝反応の外部刺激に対する応答-デジタル物理学的モデルによる一般化2018

    • Author(s)
      坂田 克己、大柳 一、齋藤 俊行、小松 節子
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] 生物相互作用ネットワークの動特性解析2017

    • Author(s)
      坂田 克己, 新堀 航大, 大柳 一, 朝日 頌, 佐藤 大輝, 森川 雄太, 齋藤 俊行
    • Organizer
      日本応用数理学会 2017年度 年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Information Transfer-Model Interprets Loss of Control Capability in Biological Systems under External Stimuli2017

    • Author(s)
      K. Sakata, H. Ohyanagi, T. Saito
    • Organizer
      The IV International AMMCS Interdisciplinary Conference
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] A stability analysis of the biological networks, transcriptional network, neural circuit and ecosystem2016

    • Author(s)
      坂田 克己
    • Organizer
      SIAM Conferences on the Life Sciences
    • Place of Presentation
      ボストン(米国)
    • Year and Date
      2016-07-11
    • Related Report
      2016 Research-status Report

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Published: 2016-04-21   Modified: 2021-02-19  

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