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Virtual Metabolism: Development of a standard dynamic model of metabolic systems

Research Project

Project/Area Number 25280107
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionKyushu Institute of Technology

Principal Investigator

Kurata Hiroyuki  九州工業大学, 大学院情報工学研究院, 教授 (90251371)

Co-Investigator(Renkei-kenkyūsha) MORI Hirotada  奈良先端科学技術大学院大学, バイオサイエンス研究科, 教授 (90182203)
Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥18,330,000 (Direct Cost: ¥14,100,000、Indirect Cost: ¥4,230,000)
Fiscal Year 2015: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Fiscal Year 2014: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Fiscal Year 2013: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Keywordsシステム生物学 / 情報科学 / シミュレーション / 代謝 / 合成生物学 / 生物プロセス / ネットワーク / 物質生産 / ダイナミクス / 数学モデル / 生体生命情報学 / 代謝ネットワーク / システム / 遺伝子
Outline of Final Research Achievements

We have developed a dynamic model of the central metabolism (including glycolysis, TCA cycle, pentose phosphate pathways, and anaplerotic reactions) which is responsible for material conversion and energy metabolism. This is the largest-scale kinetic model for a batch culture and is a base for synthetic biology to aim at a design of cell functions. We integrated gene regulation networks that perform glucose uptake and intracellular metabolic changes into the central carbon metabolism and predicted the dynamic behaviors under different environmental and genetic conditions. It is employed to rationally design a microbial system for enhanced production of useful compounds and to understand how complex metabolisms are regulated at the molecular interaction level.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (41 results)

All 2016 2015 2014 2013 Other

All Journal Article (13 results) (of which Peer Reviewed: 9 results,  Acknowledgement Compliant: 2 results,  Open Access: 2 results) Presentation (21 results) (of which Int'l Joint Research: 6 results,  Invited: 3 results) Book (2 results) Remarks (5 results)

  • [Journal Article] Metabolic analysis of antibody producing CHO cell culture under different stresses conditions2016

    • Author(s)
      Md. Bahadur Badsha, Hiroyuki Kurata, Masayoshi Onitsuka, Takushi Oga, Takeshi Omasa
    • Journal Title

      J. Biosci. Bioeng.

      Volume: - Issue: 1 Pages: 117-124

    • DOI

      10.1016/j.jbiosc.2015.12.013

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] S-system-based Analysis of the Robust Properties Common to Many Biochemical Network Models2016

    • Author(s)
      Yu Matsuoka, Nusrat Jahan, Hiroyuki Kurata
    • Journal Title

      Bioprocess Biosyst Eng

      Volume: 39 Issue: 5 Pages: 735-746

    • DOI

      10.1007/s00449-016-1554-4

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Web application for Genetic Modification Flux with database to estimate metabolic fluxes of genetic mutants2016

    • Author(s)
      Noorlin Mohd Ali, Ryo Tsuboi, Yuta Matsumoto, Daisuke Koishi, Kentaro Inoue, Kazuhiro Maeda, and Hiroyuki Kurata
    • Journal Title

      Journal of Bioscience and Bioengineering

      Volume: 印刷中 Issue: 1 Pages: 111-116

    • DOI

      10.1016/j.jbiosc.2015.12.001

    • NAID

      40020886002

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Complementary elementary modes for fast and efficient analysis of metabolic networks2014

    • Author(s)
      Md. Bahadur Badsha, Ryo Tsuboi, Hiroyuki Kurata
    • Journal Title

      Biochem Eng J.

      Volume: 90 Pages: 121130-121130

    • DOI

      10.1016/j.bej.2014.05.022

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis2014

    • Author(s)
      Kentaro Inoue, Kazuhiro Maeda, Takaaki Miyabe, Yu Matsuoka, Hiroyuki Kurata
    • Journal Title

      Bioprocess and Biosystems Engineering

      Volume: Epub Issue: 9 Pages: 19251927-19251927

    • DOI

      10.1007/s00449-014-1167-8

    • Related Report
      2014 Annual Research Report 2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity2014

    • Author(s)
      Kazuhiro Maeda, Hiroyuki Kurata
    • Journal Title

      BMC Syst. Biol.

      Volume: 8 Issue: S5 Pages: 112-112

    • DOI

      10.1186/1752-0509-8-s5-s1

    • NAID

      120005698506

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Dynamic Modeling of Metabolic and Gene Regulatory Systems toward Developing Virtual Microbes2014

    • Author(s)
      Hiroyuki Kurata, Kazuhiro Maeda, Yu Matsuoka
    • Journal Title

      JOURNAL OF CHEMICAL ENGINEERING OF JAPAN

      Volume: 47 Issue: 1 Pages: 1-9

    • DOI

      10.1252/jcej.13we152

    • NAID

      130003361309

    • ISSN
      0021-9592, 1881-1299
    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] S-systemを用いた代謝反応モデルの感度解析2014

    • Author(s)
      松岡結, Nusrat Jahan, 倉田博之
    • Journal Title

      IPSJ SIG technical reports

      Volume: BIO-37(1) Pages: 1-2

    • NAID

      110009675848

    • Related Report
      2013 Annual Research Report
  • [Journal Article] Effect of cra gene mutation on the metabolism of Escherichia coli for a mixture of multiple carbon sources2013

    • Author(s)
      Ruilian Yao, Hiroyuki Kurata, Kazuyuki Shimizu
    • Journal Title

      Advances in Bioscience and Biotechnology

      Volume: 4 Issue: 03 Pages: 477-486

    • DOI

      10.4236/abb.2013.43a063

    • NAID

      120005698503

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] BioFNet: Biological functional network database for analysis and synthesis of biological systems2013

    • Author(s)
      Hiroyuki Kurata, Kazuhiro Maeda, Toshikazu Onaka, Takenori Takata
    • Journal Title

      Briefings in Bioinformatics

      Volume: Epub Issue: 5 Pages: 699-709

    • DOI

      10.1093/bib/bbt048

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 大腸菌アンモニア同化制御機構のダイナミックモデルの構築2013

    • Author(s)
      前田和勲, Fred C. Boogerd, Frank J. Bruggeman, Hans V. Westerhoff, 倉田博之
    • Journal Title

      IPSJ SIG technical reports

      Volume: BIO-35(7) Pages: 1-6

    • NAID

      110009605329

    • Related Report
      2013 Annual Research Report
  • [Journal Article] Database for predicting a metabolic flux distribution within a cell2013

    • Author(s)
      Noorlin MohdAli , Kentaro Inoue , Hiroyuki Kurata
    • Journal Title

      IPSJ SIG technical reports

      Volume: BIO-35(6) Pages: 1-2

    • Related Report
      2013 Annual Research Report
  • [Journal Article] Complementary elementary mode analysis for large-scale metabolic networks,2013

    • Author(s)
      Md. BahadurBadsha , Ryo Tsuboi , Hiroyuki Kurata
    • Journal Title

      IPSJ SIG technical reports

      Volume: BIO-35(5) Pages: 1-2

    • Related Report
      2013 Annual Research Report
  • [Presentation] 増永拓之、倉田博之、動的感度を用いたErbBシグナル伝達ネットワークのロバストネス解析2016

    • Author(s)
      増永拓之、倉田博之
    • Organizer
      化学工学会第81回年会
    • Place of Presentation
      関西大学
    • Year and Date
      2016-03-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] Developing a kinetic model of the E. coli ammonium assimilation network2015

    • Author(s)
      Kazuhiro Maeda, Fred C. Boogerd, Hans V. Westerhoff, Hiroyuki Kurata
    • Organizer
      Proceedings of the 16th International Conference on Systems Biology
    • Place of Presentation
      Singapore
    • Year and Date
      2015-11-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A detailed kinetic model of E. coli central metabolism in a batch culture2015

    • Author(s)
      Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto, Hiroyuki Kurata
    • Organizer
      Proceedings of Asian Congress on Biotechnology 2015 (ACB2015)
    • Place of Presentation
      Kuala Lumpur, Malaysia
    • Year and Date
      2015-11-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Effect of NaCl and Trehalose Condition on Antibody Producing CHO Cell Culture.2015

    • Author(s)
      Md. Bahadur Badsha, Hiroyuki Kurata, Masayoshi Onitsuka, Takushi Oga, Takeshi Omasa
    • Organizer
      Proceedings of Asian Congress on Biotechnology 2015 (ACB2015)
    • Place of Presentation
      Kuala Lumpur, Malaysia
    • Year and Date
      2015-11-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 抗体生産強化のためのCHO細胞メタボロームの統計解析2015

    • Author(s)
      倉田博之
    • Organizer
      化学工学会第47回秋季大会
    • Place of Presentation
      北海道大学
    • Year and Date
      2015-09-19
    • Related Report
      2015 Annual Research Report
  • [Presentation] For mutual repression: Noise induced bimodality, even multimodality in deterministically monostable description without cooperative binding2015

    • Author(s)
      A.B.M. Shamim Ul Hasan, Hiroyuki Kurata
    • Organizer
      Proceedings of GIW/InCoB, Odaiba
    • Place of Presentation
      Tokyo
    • Year and Date
      2015-09-09
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Construction of a dynamic model for the central metabolism of Escherichia coli2015

    • Author(s)
      Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto, Hiroyuki Kurata
    • Organizer
      Proceedings of GIW/InCoB
    • Place of Presentation
      Tokyo
    • Year and Date
      2015-09-09
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Metabolome analysis of CHO cell culture under different stresses2015

    • Author(s)
      Md. Bahadur Badsha, Hiroyuki Kurata, Masayuki Onitsuka, Takushi Oga, Takeshi Omasa
    • Organizer
      Proceedings of GIW/InCoB
    • Place of Presentation
      Tokyo
    • Year and Date
      2015-09-09
    • Related Report
      2015 Annual Research Report
  • [Presentation] Dynamic sensitivity analysis of ErbB signaling network2015

    • Author(s)
      Hiroyuki Masunaga, Ryunosuke Itasaki, Kentaro Inoue, Mariko Okada, Hiroyuki Kurata
    • Organizer
      Proceedings of GIW/InCoB
    • Place of Presentation
      Tokyo
    • Year and Date
      2015-09-09
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Dynamic modeling of the E. coli ammonium assimilation network2015

    • Author(s)
      Kazuhiro Maeda, Fred Boogerd, Hans Westerhoff, Hiroyuki Kurata
    • Organizer
      Proceedings of GIW/InCoB
    • Place of Presentation
      Tokyo
    • Year and Date
      2015-09-09
    • Related Report
      2015 Annual Research Report
  • [Presentation] アンモニア同化システムの詳細なダイナミックモデル2015

    • Author(s)
      倉田博之
    • Organizer
      化学工学第80回年会
    • Place of Presentation
      芝浦工業大学
    • Year and Date
      2015-03-19 – 2015-03-21
    • Related Report
      2014 Annual Research Report
  • [Presentation] 情報工学を基盤としたバイオメディカルインフォマティクスおよびコンピュータ支援による診断予防治療介護医薬品開発システム2015

    • Author(s)
      倉田博之
    • Organizer
      第2回シンポジウムYUBECS2 「次世代治療・診断技術の開発のための医工学」
    • Place of Presentation
      東京田町
    • Year and Date
      2015-03-10
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Synthesis and decomposition approach for rational design of a biochemical network2015

    • Author(s)
      Hiroyuki Kurata
    • Organizer
      Third BMIRC International Symposium for Virtual Physiological Human
    • Place of Presentation
      Fukuoka
    • Year and Date
      2015-03-05 – 2015-03-06
    • Related Report
      2014 Annual Research Report
  • [Presentation] Toward a quantitative in silico model for the E. coli ammonium assimilation system2015

    • Author(s)
      Kazuhiro Maeda, Fred C. Boogerd, Frank J. Bruggeman, Hans V. Westerhoff, Hiroyuki Kurata
    • Organizer
      Third BMIRC International Symposium for Virtual Physiological Human
    • Place of Presentation
      Fukuoka
    • Year and Date
      2015-03-05 – 2015-03-06
    • Related Report
      2014 Annual Research Report
  • [Presentation] Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity2014

    • Author(s)
      Kazuhiro Maeda, Hiroyuki Kurata
    • Organizer
      GIW/ISCB-Asia 2014
    • Place of Presentation
      Tokyo
    • Year and Date
      2014-12-15 – 2014-12-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] 設計原理に基づく生物システムの合理的合成2014

    • Author(s)
      倉田博之
    • Organizer
      平成26年度JSBi生命システム理論研究会
    • Place of Presentation
      京都大学iPS細胞研究所
    • Year and Date
      2014-11-18
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 代謝とシステムバイオロジー2014

    • Author(s)
      倉田博之
    • Organizer
      第87回日本生化学会大会
    • Place of Presentation
      京都国際会議場
    • Year and Date
      2014-10-17
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 生物システムの合理的設計を支援するBioFNetデータベース2014

    • Author(s)
      倉田博之
    • Organizer
      化学工学会第46回秋季大会
    • Place of Presentation
      九州大学
    • Year and Date
      2014-09-17 – 2014-09-19
    • Related Report
      2014 Annual Research Report
  • [Presentation] Integration of omics into metabolic flux distribution by complementary elementary mode analysis for large-scale metabolic networks2014

    • Author(s)
      Md. Bahadur Badsha
    • Organizer
      3rd International Conference and Exhibition on Metabolomics & Systems Biology
    • Place of Presentation
      San Antonio, USA
    • Related Report
      2013 Annual Research Report
  • [Presentation] 生物学的基本ネットワークの組み立てによるダイナミックモデルの合理的設計2014

    • Author(s)
      倉田博之,前田和勲
    • Organizer
      化学工学会第79年会
    • Place of Presentation
      岐阜大学
    • Related Report
      2013 Annual Research Report
  • [Presentation] ゲノムスケールヒト代謝ネットワークの高速エレメンタリモード解析2013

    • Author(s)
      倉田博之、Badsha Md. Bahadur, 坪井遼
    • Organizer
      化学工学会第45回秋季大会
    • Place of Presentation
      岡山大学
    • Related Report
      2013 Annual Research Report
  • [Book] システム工学的アプローチを用いた細胞モデリング,In 抗体医薬における細胞構築・培養・ダウンストリームのすべて(ファインケミカルシリーズ)2015

    • Author(s)
      倉田博之
    • Total Pages
      200
    • Publisher
      シーエムシー出版
    • Related Report
      2015 Annual Research Report
  • [Book] 抗体医薬における細胞構築・培養・ダウンストリームのすべて2015

    • Author(s)
      倉田博之
    • Total Pages
      273
    • Publisher
      シーエムシー出版
    • Related Report
      2014 Annual Research Report
  • [Remarks] CADLIVE

    • URL

      http://www.cadlive.jp

    • Related Report
      2015 Annual Research Report
  • [Remarks] BMIRC

    • URL

      http://www.bmirc.kyutech.ac.jp/

    • Related Report
      2015 Annual Research Report
  • [Remarks] CADLIVE

    • URL

      http://www.cadlive.jp/

    • Related Report
      2014 Annual Research Report
  • [Remarks] Virtual Physiological Human

    • URL

      http://www.bmirc.jp/2015/

    • Related Report
      2014 Annual Research Report
  • [Remarks] BioFNet

    • URL

      http://kurata22.bio.kyutech.ac.jp/db/pub/pub_main.php?Ver=3.6

    • Related Report
      2013 Annual Research Report

URL: 

Published: 2013-05-21   Modified: 2019-07-29  

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