Dynamic simulation and system analysis for gene regulatory networks

• Project/Area Number: 18300098
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: Kyushu Institute of Technology
• Principal Investigator: KURATA Hiroyuki Kyushu Institute of Technology, 大学院・情報工学研究院, 教授 (90251371)
• Co-Investigator(Kenkyū-buntansha): SHIMIZU Kazuyuki 九州工業大学, 大学院・情報工学研究院, 教授 (00150318)
• Project Period (FY): 2006 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥17,910,000 (Direct Cost: ¥15,000,000、Indirect Cost: ¥2,910,000); Fiscal Year 2008: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000); Fiscal Year 2007: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000); Fiscal Year 2006: ¥5,300,000 (Direct Cost: ¥5,300,000)
• Keywords: シミュレーション工学 / 生体生命情報学 / ゲノム / 微生物 / ロバストネス / バイオインフォマティク / アンモニア同化 / シミュレーション / システムバイオロジ / ネットワーク / 大腸菌 / バイオインフォマティクス

Research Abstract

大腸菌アンモニア同化システムの動的モデルをシステム解析することにより環境中のアンモニア濃度の変化に対してシステムがヒステリシスを示すことを予測して, 生物実験を用いて証明した。ヒステリシスがポジティブフィードバック制御に起因することを、理論解析により明らかにした。また、システムのロバストネス解析によって, 窒素同化システムは、ロバストな部分とファインチューンの部分明確に分かれていることわかった.

Research Products

• [Journal Article] A gradual update method for simulating the steady-state solution of stiff differential equations in metabolic circuits (2009)
  • Author(s): Emi Shiraishi Kazuhiro Maeda Hiroyuki Kurata
  • Journal Title: Bioprocess Biosyst. Eng 32 Pages: 283-288
  • Peer Reviewed
• [Journal Article] A gradual update method for simulating the steady-state solution of stiff differential equations in metabolic circuits (2009)
  • Author(s): Emi Shiraishi Kazuhiro Maed a Hiroyuki Kurata
  • Journal Title: Bioprocess Biosyst. Eng. 32 Pages: 283-288
  • Peer Reviewed
• [Journal Article] Visualizing Global Properties of Large Complex Networks (2008)
  • Author(s): Li W., Kurata H.
  • Journal Title: PLoS ONE 3
  • Peer Reviewed
• [Journal Article] Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli (2008)
  • Author(s): Yousuke Nishio, Yoshihiro Usuda, Kazuhiko Matsui, Hiroyuki Kurata
  • Journal Title: Molecular Systems Biology 4 Pages: 160-160
  • NAID: 120006366982
  • Peer Reviewed
• [Journal Article] Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli (2008)
  • Author(s): Yousuke Nishio, Yoshihiro U suda, Kazuhiko Matsui, Hiro yuki Kurata
  • Journal Title: Molecular Systems Biology 4 Pages: 140-150
  • NAID: 120006366982
  • Peer Reviewed
• [Journal Article] Extended CADLIVE : a novel graphical notation for designing a biochemical network map that enables computational pathway analysis (2007)
  • Author(s): Hiroyuki Kurata, Kentaro Inoue, Kazuhiro Maeda, Koichi Masaki, Yuki Shimokawa, Quanyu Zhao
  • Journal Title: Nucleic Acids Res 35
  • Peer Reviewed
• [Journal Article] Mathematical identification of critical reactions in the interlocked feedback model (2007)
  • Author(s): H. Kurata, T. Tanaka, F. Ohnishi
  • Journal Title: PLoS One 2
  • Peer Reviewed
• [Journal Article] A simple model of positive feedback of the nitrogen assimilation system in E. coli (2007)
  • Author(s): Kouichi Masaki, Hiroyuki Kurata
  • Journal Title: IPSJ Transactions on Mathematical Modeling and Its Applications 48 Pages: 104-109
  • NAID: 110006242974
  • Peer Reviewed
• [Journal Article] Extended CADLIVE: a novel graphical notation for designing a biochemical network map that enables computational pathway analysis (2007)
  • Author(s): Hiroyuki Kurata, Kentaro Inoue, Kazuhiro Maeda, Koichi Masaki, Yuki Shimokawa, Quanyu Zhao
  • Journal Title: Nucleic Acids Res. 35
  • Peer Reviewed
• [Journal Article] Mathematical identification of critical reactions in the interlocked feedback model (2007)
  • Author(s): H.Kurata, T.Tanaka, F.Ohnishi
  • Journal Title: PLoS One 2
  • Peer Reviewed
• [Journal Article] Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System (2006)
  • Author(s): H. Kurata, H. El Samad, R. Iwasaki, H. Othake, J.C. Doyle, I. Grigorova, C. Gross, and M. Khammash
  • Journal Title: PLoS Computational Biology 2
• [Journal Article] Effective and fast optimization for a dynamic model of the Drosophila circadian oscillator (2006)
  • Author(s): Shin Tanaka, Hiroyuki Kurata, Takeshi Ohashi
  • Journal Title: IEEE International Conference on Systems, Man, and Cybernetics(Taipei, Taiwan) Pages: 3596-3601
• [Journal Article] Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System (2006)
  • Author(s): H.Kurata, H.El Samad, R.Iwasaki, H.Othake, J.C.Doyle, I.Grigorova, C.Gross, M.Khammash
  • Journal Title: PLoS Computational Biology 2
• [Journal Article] Effective and fast optimization for a dynamic model of the Drosophila circadian oscillator (2006)
  • Author(s): Shin Tanaka, Hiroyuki Kurata, akeshi Ohashi
  • Journal Title: IEEE International Conference on Systems, Man, and Cybernetics Pages: 3596-3601
• [Journal Article] 大腸菌窒素同化システムのポジティブフィードバック制御シンプルモデル (2006)
  • Author(s): 真崎浩一, 倉田博之
  • Journal Title: 数理モデル化と問題解決研究報告 MPS-59 Pages: 61-64
• [Journal Article] Sensitivity analysis for the E. coli nitrogen assimilation system (2006)
  • Author(s): Koichi Masaki, Hiroyuki Kurata
  • Journal Title: The 16th International Conference on Genome Informatics 16
• [Presentation] Extended CADLIVE : Computer-aided rational design of living systems(S02-1-2) (2008)
  • Author(s): Kentaro Inoue, Tetsuya Shimabara, Toshikazu Onaka, Erika Fujiura, Hiroyuki Kurata
  • Organizer: The proceedings of the 2th annual conference of the Japanese Society for Bioinformatics
  • Place of Presentation: Osaka
• [Presentation] Searching multiple sets of kinetic parameters values reproducing target experimental data in dynamic biochemical models(S063-1-2) (2008)
  • Author(s): Kazuhiro Maeda, Hiroyuki Kurata
  • Organizer: The proceedings of the 2008th annual conference of the Japanese Society for Bioinformatics
  • Place of Presentation: Osaka
• [Presentation] CADLIVE : Computer aided design of biochemical systems(Oral Presentation) (2008)
  • Author(s): Hiroyuki Kurata
  • Organizer: Supplement of Journal of Biotechnology : 13 th International Biotechnology Symposium and Exhibition (IBS2008)
  • Place of Presentation: Dailen, China
• [Presentation] Prediction of flux distribution of mutants by enzyme control fluxes with maximum entropy principal(Oral Presentation) (2008)
  • Author(s): Quanyu Zhao, Hiroyuki Kurata
  • Organizer: Supplement of Journal of Biotechnology : 13 th International Biotechnology Symposium and Exhibition (IBS2008)
  • Place of Presentation: Dailen, China
• [Presentation] Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli(Oral Presentation) (2008)
  • Author(s): Yousuke Nishio, Yoshihiro Usuda, Kazuhiko Matsui, Hiroyuki Kurata
  • Organizer: Supplement of Journal of Biotechnology : 13 th International Biotechnology Symposium and Exhibition (IBS2008)
  • Place of Presentation: Dailen, China
• [Presentation] CADLIVE : Computer aided design of biochemical systems. Supp lement of Journal of Biotechnology (2008)
  • Author(s): Hiroyuki Kurata
  • Organizer: 13 th International Biotechnology Symposium and Exhibition (IBS2008)
  • Place of Presentation: Dailen, China
• [Presentation] CADLIVE for Construction and Dynamic Simulation of Biochemical Networks (2007)
  • Author(s): Kazuhiro Maeda, Hiroyuki Kurata
  • Organizer: Proceedings of Asia Pacific Biochemical Engineering Conference
  • Place of Presentation: Taipei
• [Presentation] 大腸菌窒素同化システムのポジティブフィードバック制御シンプルモデル (2006)
  • Author(s): 真崎浩一, 倉田博之
  • Organizer: 数理モデル化と問題解決研究報告
  • Place of Presentation: 名古屋大学(MPS-59 : 61-64)
• [Presentation] Sensitivity analysis for the E. coli nitrogen assimilation system(16 : P010-1-2) (2006)
  • Author(s): Koichi Masaki, Hiroyuki Kurata
  • Organizer: The 16th International Conference on Genome Informatics
  • Place of Presentation: Yokohama
• [Remarks]
  • URL: http://www.cadlive.jp
• [Remarks]
  • URL: http://www.cadlive.jp