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Simulation study of organ/tissue dynamics model based on complex shapes of single cells

Research Project

Project/Area Number 17K00410
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionAkita Prefectural University

Principal Investigator

Ishimoto Yukitaka  秋田県立大学, システム科学技術学部, 教授 (30391858)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2019: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2018: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2017: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywordsコンピュータシミュレーション / 細胞・組織・器官 / 発生・分化 / 粘弾性 / データ解析
Outline of Final Research Achievements

On the cell vertex model and the bubbly vertex model, various computer viscoelasticity experiments were performed to show differences. Since this is mainly due to the shape change of each cell, it was clarified numerically that the cellular shape changes are reflected in the physical properties at the tissue level. The wing formation mechanics model was expressed by the cell vertex model, and the results showed that the organs significantly changed depending on the wing margin modulus. We experimentally and analytically revealed that the three-dimensional morphological changes of wing organs and the spatiotemporal dynamics of signaling molecules in the fly pupal stage are closely related.
As additional results, we measured and analyzed dynamical information of cell elasticity by AFM. By quantifying 4D microscopic data of epithelial tissue, we developed a program that recognizes the cell nucleus position by deep learning.

Academic Significance and Societal Importance of the Research Achievements

数理モデルを用いた計算機粘弾性実験により、一細胞形状が組織レベルの物性に反映されることを数値計算上で明らかにした点で、学術的に重要な知見を与えた。また、我々の翅外形力学モデルを一細胞の形状変化をもつものに刷新した。外形力学情報が重要な情報であることを示し、意義深い。シグナル分子の時空間動態と器官形成の研究では、これらが密接に関連することを初めて示した。AFMによって細胞間力学情報に複数種類の距離相関が現れることを示した。深層学習による細胞移動定量化への道を示した。
上記学術的意義に加え、これらの結果は器官・組織の再生技術などへの応用に向けて大きな前進といえ、社会的意義のある成果となった。

Report

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

    (35 results)

All 2020 2019 2018 2017 Other

All Int'l Joint Research (4 results) Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 6 results,  Open Access: 4 results) Presentation (21 results) (of which Int'l Joint Research: 9 results) Remarks (3 results)

  • [Int'l Joint Research] ヘルシンキ大学バイオテクノロ ジーセンター(フィンランド)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] ソルボンヌ大学不均質物質研究所(フランス)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] ヘルシンキ大学バイオテクノロジーセンター(フィンランド)

    • Related Report
      2018 Research-status Report
  • [Int'l Joint Research] ヘルシンキ大学バイオテクノロジーセンター(フィンランド)

    • Related Report
      2017 Research-status Report
  • [Journal Article] Towards Particle Tracking Velocimetry of Cell Flow in Developing Tissue Using Deep Neural Network.2020

    • Author(s)
      Ishimoto Y., Watanabe T.
    • Journal Title

      Lecture Notes in Computational Vision and Biomechanics

      Volume: 36 Pages: 495-504

    • DOI

      10.1007/978-3-030-43195-2_40

    • ISBN
      9783030431945, 9783030431952
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamical Rheological Properties of In-Silico Epithelial Tissue by Vertex Models.2020

    • Author(s)
      Toyoshima T., Ishimoto Y.
    • Journal Title

      Lecture Notes in Computational Vision and Biomechanics

      Volume: 36 Pages: 632-638

    • DOI

      10.1007/978-3-030-43195-2_53

    • ISBN
      9783030431945, 9783030431952
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Coupling between dynamic 3D tissue architecture and BMP morphogen signaling during Drosophila wing morphogenesis2019

    • Author(s)
      J. Gui, Y. Huang, M. Montanari, D. Toddie-Moore, K. Kikushima, S. Nix, Y. Ishimoto, and O. Shimmi
    • Journal Title

      Proceedings of the National Academy of Sciences of the United States of America

      Volume: 116 Issue: 10 Pages: 4352-4361

    • DOI

      10.1073/pnas.1815427116

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Spontaneous Spatial Correlation of Elastic Modulus in Jammed Epithelial Monolayers Observed by AFM2019

    • Author(s)
      Y. Fujii, Y. Ochi, M. Tuchiya, M. Kajita, Y. Fujita, Y. Ishimoto, T. Okajima
    • Journal Title

      Biophysical Journal

      Volume: 116 Issue: 6 Pages: 1152-1158

    • DOI

      10.1016/j.bpj.2019.01.037

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Mechanical models for diversified insect wing margin shapes2018

    • Author(s)
      石本 志高,杉村 薫
    • Journal Title

      The Proceedings of the Bioengineering Conference Annual Meeting of BED/JSME

      Volume: 2018.30 Issue: 0 Pages: 2B04

    • DOI

      10.1299/jsmebio.2018.30.2B04

    • NAID

      130007410951

    • ISSN
      2424-2829
    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] 186 Viscoelasticity of epithelial tissue: Rheological characteristic by in silico experiment2018

    • Author(s)
      豊嶋 拓哉, 石本 志高
    • Journal Title

      The Proceedings of Conference of Tohoku Branch

      Volume: 2018.53 Issue: 0 Pages: 169-170

    • DOI

      10.1299/jsmeth.2018.53.169

    • NAID

      130007486743

    • ISSN
      2424-2713
    • Related Report
      2018 Research-status Report
    • Open Access
  • [Journal Article] A mechanical model for diversified insect wing margin shapes2017

    • Author(s)
      Ishimoto Yukitaka、Sugimura Kaoru
    • Journal Title

      Journal of Theoretical Biology

      Volume: 427 Pages: 17-27

    • DOI

      10.1016/j.jtbi.2017.05.026

    • NAID

      130007410951

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Presentation] Bubbly Cell Tracking Velocimetry-細胞頂点・形状トラッキングの試み2020

    • Author(s)
      柏正幸,豊嶋拓哉,石本志高
    • Organizer
      機械学会東北支部会第55期支部総会・講演会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Dynamical rheological properties of in-silico epithelial tissue by vertex models.2019

    • Author(s)
      Y. Ishimoto, T. Toyoshima
    • Organizer
      International Soft Matter Conference 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Towards particle tracking velocimetry of cell flow in developing tissue using deep neural network2019

    • Author(s)
      Y. Ishimoto, T. Watanabe
    • Organizer
      16th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering and 4th Conference on Imaging and Visualization
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Dynamical rheological properties of in-silico epithelial tissue by vertex models2019

    • Author(s)
      T. Toyoshima, Y. Ishimoto
    • Organizer
      16th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering and 4th Conference on Imaging and Visualization
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Towards Particle Tracking Velocimetry of Cell Flow Using Deep Learning2019

    • Author(s)
      Y. Ishimoto, T. Watanabe
    • Organizer
      The 10th Asian-Pacific Conference on Biomechanics (AP Biomech 2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 生物学的によく保存されたトンボの翅の構造と流体工学的機能2019

    • Author(s)
      石本志高,大森瑠奈
    • Organizer
      第47回可視化情報シンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] 生物・生命の移動現象:実験とシミュレーションと機械と私2019

    • Author(s)
      石本志高
    • Organizer
      研究会「理論と実験」2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] Dynamical rheological properties of in-silico epithelial tissue by vertex models2019

    • Author(s)
      豊嶋拓哉,石本志高
    • Organizer
      研究会「理論と実験」2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] 生体組織内多細胞構造のレオロジーおよび移動現象に関するシミュレーション研究2019

    • Author(s)
      豊嶋拓哉,石本志高
    • Organizer
      ソフトバイオ研究会2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] In-silico rheological experiments of an epithelial sheet by the cell vertex model and the bubbly vertex model2018

    • Author(s)
      Y. Ishimoto and T. Toyoshima
    • Organizer
      12th European Fluid Mechanics Conference (EFMC12)
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 力学的平衡状態にある上皮組織の動的レオロジー特性2018

    • Author(s)
      豊嶋拓哉,石本志高
    • Organizer
      第31回バイオエンジニアリング講演会
    • Related Report
      2018 Research-status Report
  • [Presentation] 上皮組織の粘弾性:シミュレーション実験によるレオロジー特性2018

    • Author(s)
      豊嶋拓哉,ニックス・ステファニー,石本志高
    • Organizer
      日本機械学会東北支部第53期総会・講演会
    • Related Report
      2017 Research-status Report
  • [Presentation] 細胞vertexモデルおよび bubbly vertex モデルによる細胞組織のレオロジー特性2018

    • Author(s)
      石本志高,豊嶋拓哉
    • Organizer
      日本物理学会年会第73回年次大会
    • Related Report
      2017 Research-status Report
  • [Presentation] Mechanical models for insect wing margin shapes2017

    • Author(s)
      Y. Ishimoto, K. Sugimura
    • Organizer
      XXVI Congress of the International Society of Biomechanics (ISB2017)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Bubbly vertex model for viscoelastic properties of epithelial tissues2017

    • Author(s)
      Y. Ishimoto
    • Organizer
      2nd Edwards Symposium. Challenges and Opportunities in Soft Matter
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Realisation of viscoelastic epithelial tissues in the bubbly vertex dynamics2017

    • Author(s)
      Y. Ishimoto
    • Organizer
      The Ninth JSME-KSME Thermal and Fluids Engineering Conference (TFEC9)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Viscoelastic epithelial tissues by bubbly vertex model2017

    • Author(s)
      Y. Ishimoto
    • Organizer
      International Symposium on Fluctuation and Structure out of Equilibrium 2017 (SFS2017)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] A mechanical model for diversified insect wing margin shapes2017

    • Author(s)
      石本志高,杉村薫
    • Organizer
      日本生物物理学会第55回年会
    • Related Report
      2017 Research-status Report
  • [Presentation] 昆虫の翅外形多様性に関する力学モデル2017

    • Author(s)
      石本志高,杉村薫
    • Organizer
      日本物理学会2017年秋季大会
    • Related Report
      2017 Research-status Report
  • [Presentation] Simulations on Chromosome, Lipid membrane, and Epithelial tissues2017

    • Author(s)
      石本志高
    • Organizer
      研究会「理論と実験2017」
    • Related Report
      2017 Research-status Report
  • [Presentation] 昆虫の翅外形多様性に関する力学モデル2017

    • Author(s)
      石本志高,杉村薫
    • Organizer
      第30回バイオエンジニアリング講演会
    • Related Report
      2017 Research-status Report
  • [Remarks] 秋田県立大学 研究者総覧

    • URL

      http://www.akita-pu.ac.jp/stic/souran/scholar/detail.php?id=308

    • Related Report
      2018 Research-status Report 2017 Research-status Report
  • [Remarks] Research Gate: Yukitaka Ishimoto -- Publications

    • URL

      http://www.researchgate.net/profile/Yukitaka_Ishimoto/publications

    • Related Report
      2018 Research-status Report 2017 Research-status Report
  • [Remarks] Yukitaka Ishimoto, Dr

    • URL

      http://www2.yukawa.kyoto-u.ac.jp/~yukitaka.ishimoto/

    • Related Report
      2018 Research-status Report 2017 Research-status Report

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Published: 2017-04-28   Modified: 2021-02-19  

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