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Mathematical analyses for oscillatory behaviors in plants by integrating molecular dynamics and cellular mechanics

Planned Research

Project AreaIntrinsic periodicity of cellular systems and its modulation as the driving force behind plant development
Project/Area Number 19H05678
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionKyoto University

Principal Investigator

Mochizuki Atsushi  京都大学, 医生物学研究所, 教授 (10304726)

Project Period (FY) 2019-06-28 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥99,060,000 (Direct Cost: ¥76,200,000、Indirect Cost: ¥22,860,000)
Fiscal Year 2023: ¥19,630,000 (Direct Cost: ¥15,100,000、Indirect Cost: ¥4,530,000)
Fiscal Year 2022: ¥19,630,000 (Direct Cost: ¥15,100,000、Indirect Cost: ¥4,530,000)
Fiscal Year 2021: ¥19,630,000 (Direct Cost: ¥15,100,000、Indirect Cost: ¥4,530,000)
Fiscal Year 2020: ¥19,630,000 (Direct Cost: ¥15,100,000、Indirect Cost: ¥4,530,000)
Fiscal Year 2019: ¥20,540,000 (Direct Cost: ¥15,800,000、Indirect Cost: ¥4,740,000)
Keywords数理モデル / ダイナミクス / 形態形成 / 構造感度解析 / 構造分岐解析 / 細胞周期 / ネットワーク / 植物 / 花弁 / 萼 / 構造理論 / バイオメカニクス / 数理解析 / 数理生物学 / 周期性
Outline of Research at the Start

本計画研究では数理的手法を用い、植物形態形成に対して、(1) 生体分子ダイナミクスと、(2) 細胞メカニクスの2つの階層から、周期性を創出するメカニズムとその変調がもたらす効果の解明に迫る。これまでに開発した構造理論を発展させ、(i) 周期的振る舞いが現れるための生体分子相互作用の条件および、周期性やその変調が器官形態にもたらす効果を数理的に決定する。さらに、これらを用いて、(ii) 領域内の実験グループとの共同研究を推進し、植物形態形成でみられる様々な振動現象のメカニズムを予測検証的に解明する。

Outline of Final Research Achievements

In this study, we used mathematical methods to investigate the mechanisms that create characteristic plant morphogenesis from two levels: (1) biomolecular dynamics and (2) cellular mechanics. We have extended our structural theory to mathematically determine (i) the conditions of biomolecular interactions under which periodic behaviors emerge and (ii) the effects of modulation of cellular properties on organ morphology. Using these, we (ii) collaborated with experimental groups to elucidate the mechanisms of various morphogenetic phenomena observed in plant morphogenesis through a combination of theoretical predictions and experimental validation.

Academic Significance and Societal Importance of the Research Achievements

植物個体の形態形成は、細胞内生体分子のダイナミクスによって細胞分裂や細胞伸長などの細胞の振る舞いが規定され、細胞間相互作用が変調することで形態の調節がなされるのだ、と考えられる。これらを実現する分子メカニズムや、細胞の性質がもたらす形態形成への効果について、理論と実験の組み合わせにより解明をすすめた。研究全体を通じて、生命の時空間ダイナミクスに対して、理論と実験の組み合わせから解明に迫るための方法を構築した。

Report

(6 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • Research Products

    (38 results)

All 2023 2022 2021 2020 2019 Other

All Journal Article (10 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 10 results,  Open Access: 9 results) Presentation (20 results) (of which Int'l Joint Research: 5 results,  Invited: 20 results) Book (1 results) Remarks (5 results) Patent(Industrial Property Rights) (2 results)

  • [Journal Article] Controlling complex dynamical systems based on the structure of the networks2023

    • Author(s)
      Mochizuki A.
    • Journal Title

      Biophysics and Physicobiology

      Volume: 20 Issue: 2 Pages: n/a

    • DOI

      10.2142/biophysico.bppb-v20.0019

    • ISSN
      2189-4779
    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations2023

    • Author(s)
      Ishikawa Masato、Sugino Seiichi、Masuda Yoshie、Tarumoto Yusuke、Seto Yusuke、Taniyama Nobuko、Wagai Fumi、Yamauchi Yuhei、Kojima Yasuhiro、Kiryu Hisanori、Yusa Kosuke、Eiraku Mototsugu、Mochizuki Atsushi
    • Journal Title

      Communications Biology

      Volume: 6 Issue: 1 Pages: 1290-1290

    • DOI

      10.1038/s42003-023-05594-4

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Patterns of change in regulatory modules of chemical reaction systems induced by network modification2023

    • Author(s)
      Hishida Atsuki、Okada Takashi、Mochizuki Atsushi
    • Journal Title

      PNAS Nexus

      Volume: 3 Issue: 1

    • DOI

      10.1093/pnasnexus/pgad441

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A structural approach to understanding enzymatic regulation of chemical reaction networks2022

    • Author(s)
      Mochizuki Atsushi
    • Journal Title

      Biochemical Journal

      Volume: 479 Issue: 11 Pages: 1265-1283

    • DOI

      10.1042/bcj20210545

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Position of meristems and the angles of the cell division plane regulate the uniqueness of lateral organ shape2022

    • Author(s)
      Kinoshita Ayaka、Naito Makiko、Wang Zining、Inoue Yasuhiro、Mochizuki Atsushi、Tsukaya Hirokazu
    • Journal Title

      Development

      Volume: 149 Issue: 23

    • DOI

      10.1242/dev.199773

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo2021

    • Author(s)
      Kobayashi Kenji、Maeda Kazuki、Tokuoka Miki、Mochizuki Atsushi、Satou Yutaka
    • Journal Title

      Scientific Reports

      Volume: 11 Issue: 1 Pages: 4001-4001

    • DOI

      10.1038/s41598-021-83045-y

    • NAID

      120006997057

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The gene regulatory system for specifying germ layers in early embryos of the simple chordate2021

    • Author(s)
      Tokuoka Miki、Maeda Kazuki、Kobayashi Kenji、Mochizuki Atsushi、Satou Yutaka
    • Journal Title

      Science Advances

      Volume: 7 Issue: 24

    • DOI

      10.1126/sciadv.abf8210

    • NAID

      120007052732

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Quantitative analyses reveal extracellular dynamics of Wnt ligands in Xenopus embryos2021

    • Author(s)
      Mii Yusuke、Nakazato Kenichi、Pack Chan-Gi、Ikeda Takafumi、Sako Yasushi、Mochizuki Atsushi、Taira Masanori、Takada Shinji
    • Journal Title

      eLife

      Volume: 10 Pages: 55108-55108

    • DOI

      10.7554/elife.55108

    • NAID

      120007041648

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Flux-augmented bifurcation analysis in chemical reaction network systems2021

    • Author(s)
      Okada Takashi、Mochizuki Atsushi、Furuta Mikio、Tsai Je-Chiang
    • Journal Title

      Physical Review E

      Volume: 103 Issue: 6 Pages: 062212-062212

    • DOI

      10.1103/physreve.103.062212

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] IRAK1-dependent Regnase-1-14-3-3 complex formation controls Regnase-1-mediated mRNA decay2021

    • Author(s)
      Akaki Kotaro、Ogata Kosuke、Yamauchi Yuhei、Iwai Noriki、Tse Ka Man、Hia Fabian、Mochizuki Atsushi、Ishihama Yasushi、Mino Takashi、Takeuchi Osamu
    • Journal Title

      eLife

      Volume: 10

    • DOI

      10.7554/elife.71966

    • NAID

      120007166024

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Determining dynamical behaviors of complex biological systems from network topology2023

    • Author(s)
      Mochizuki A.
    • Organizer
      STATPHYS28 Satellite Meeting “Physics of Open Systems and Beyond”
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Controlling cell fate specification system based on network structure.2023

    • Author(s)
      Mochizuki A.
    • Organizer
      ICIAM 2023 10th International Congress on Industrial and Applied Mathematics
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Biological function and functional module originated in structure of network.2023

    • Author(s)
      Mochizuki A.
    • Organizer
      OKO International Symposium 2023 "Mathematical Biology from Genes to Cells to Humans"
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ネットワーク構造に由来する生命機能と機能単位2023

    • Author(s)
      望月敦史
    • Organizer
      2023年度日本数理生物学会年会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 生命システムの振る舞いをネットワークの形だけから決定する2023

    • Author(s)
      望月敦史
    • Organizer
      第96回 日本生化学会大会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Biological function and functional module originated in structure of network.2022

    • Author(s)
      Mochizuki A.
    • Organizer
      Workshop on Non-equilibrium Phenomena in Physics and Biology
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Controlling cell fate specification system based on network structure2022

    • Author(s)
      望月敦史
    • Organizer
      第60回生物物理学会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] ネットワークから生まれる機能と機能単位2022

    • Author(s)
      望月敦史
    • Organizer
      分子生物学会2022年度年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 生命のシステムの振る舞いをネットワーク構造だけから解明する2021

    • Author(s)
      望月敦史
    • Organizer
      明治非線形サマーセミナー
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 遺伝子ネットワークの構造に基づく細胞運命の操作2021

    • Author(s)
      望月敦史
    • Organizer
      MathHuB研究会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 生命のシステムの振る舞いをネットワーク構造だけから決定する2021

    • Author(s)
      望月敦史
    • Organizer
      武蔵野大学数理工学シンポジウム
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 化学反応ネットワークの構造に基づく振る舞いの解析 -基礎から生命機能まで-2021

    • Author(s)
      望月敦史
    • Organizer
      開放系トポロジーの探求
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 生命のシステムの振る舞いをネットワーク構造だけから決定する2021

    • Author(s)
      望月敦史
    • Organizer
      第35回分子シミュレーション討論会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Controlling cell fate specification system based on network structure2021

    • Author(s)
      Atsushi Mochizuki
    • Organizer
      DARS-SWARM2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 生命システムの振る舞いをネットワークの形だけから予測する2020

    • Author(s)
      望月敦史
    • Organizer
      生物物理若手の会夏の学校
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] 理論とデータの協働によるネットワークシステムの解明2020

    • Author(s)
      望月敦史
    • Organizer
      日本数理生物学会年会 大会企画シンポジウム
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] 遺伝子ネットワークの構造に基づく細胞運命決定システムの制御2020

    • Author(s)
      望月敦史
    • Organizer
      三重大学病理医学セミナー
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 生命システムの振る舞いをネットワークの形だけから決定する2019

    • Author(s)
      望月敦史
    • Organizer
      応用物理学会・応用電子物性分科会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 遺伝子ネットワークの構造に基づく細胞運命決定システムの制御2019

    • Author(s)
      望月敦史
    • Organizer
      日本蛋白質科学会年会・日本細胞生物学会合同年次大会シンポジウム「染色体のホメオスタティック制御システム」
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 遺伝子ネットワークの構造に基づく細胞運命決定システムの制御2019

    • Author(s)
      望月敦史
    • Organizer
      現象数理学研究集会「ネットワーク構造に基づく化学反応システムの挙動解析」
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Book] 理論生物学概論2021

    • Author(s)
      望月 敦史
    • Total Pages
      328
    • Publisher
      共立出版
    • ISBN
      9784320058309
    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
  • [Remarks] 摂動に基づく遺伝子制御ネットワーク推定―数理モデルによる自動決定―

    • URL

      https://www.kyoto-u.ac.jp/ja/research-news/2024-01-04

    • Related Report
      2023 Annual Research Report
  • [Remarks] 反応ネットワークの構造変化による摂動応答変化を解析する

    • URL

      https://www.kyoto-u.ac.jp/ja/research-news/2024-02-02-1

    • Related Report
      2023 Annual Research Report
  • [Remarks] 花びらの形が葉と違う仕組みを解明

    • URL

      https://www.s.u-tokyo.ac.jp/ja/press/2022/8175/

    • Related Report
      2022 Annual Research Report
  • [Remarks] 数理理論が予測した6つの因子で、92因子を含むホヤの遺伝子ネットワークを完全操作

    • URL

      https://www.infront.kyoto-u.ac.jp/achievements/post-6523/

    • Related Report
      2020 Annual Research Report
  • [Remarks] Complete control of a gene regulatory network

    • URL

      https://www.infront.kyoto-u.ac.jp/achievements/post-6523/?lang=en

    • Related Report
      2020 Annual Research Report
  • [Patent(Industrial Property Rights)] 代謝ネットワーク処理システム、および代謝ネットワーク処理方法2023

    • Inventor(s)
      佐藤 美和、田辺 麻衣子、渡辺 康一、望月 敦史、岡田 崇
    • Industrial Property Rights Holder
      国立大学法人京都大学/株式会社日立製作所
    • Industrial Property Rights Type
      特許
    • Filing Date
      2023
    • Related Report
      2023 Annual Research Report
  • [Patent(Industrial Property Rights)] 物質合成を実施する方法、およびCO2を吸収し、コハク酸を製造するための方法2023

    • Inventor(s)
      田辺 麻衣子、佐藤 美和、渡辺 康一、望月 敦史、岡田 崇
    • Industrial Property Rights Holder
      国立大学法人京都大学/株式会社日立製作所
    • Industrial Property Rights Type
      特許
    • Filing Date
      2023
    • Related Report
      2023 Annual Research Report

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Published: 2019-07-04   Modified: 2025-01-30  

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