System analysis of stability and plasticity of signal transduction

• Project/Area Number: 17017005
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: The University of Tokyo
• Principal Investigator: KURODA Shinya The University of Tokyo, 大学院・理学系研究科, 教授 (50273850)
• Co-Investigator(Kenkyū-buntansha): KAWATO Mitsuo 株式会社国際電気通信基礎技術研究所, 脳情報通信総合研究所, 所長 (10144445) ; 前田 彰男 東京大学, 大学院・情報理工学系研究科, 科学技術振興特任教員 (30361538) ; 笹川 覚 東京大学, 大学院・情報理工学系研究科, 科学技術振興特任研究員 (80345115) ; 尾碕 裕一 東京大学, 大学院・情報理工学系研究科, 科学技術振興特任研究員 (70345114)
• Project Period (FY): 2005 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥78,500,000 (Direct Cost: ¥78,500,000); Fiscal Year 2009: ¥15,900,000 (Direct Cost: ¥15,900,000); Fiscal Year 2008: ¥15,800,000 (Direct Cost: ¥15,800,000); Fiscal Year 2007: ¥15,600,000 (Direct Cost: ¥15,600,000); Fiscal Year 2006: ¥15,400,000 (Direct Cost: ¥15,400,000); Fiscal Year 2005: ¥15,800,000 (Direct Cost: ¥15,800,000)
• Keywords: システム生物学 / シグナル伝達 / シナプス可塑性 / システム生物 / NMDA受容体 / シグナル伝逹 / 血管収縮 / 安定性 / 生体生命情報 / バイオインフォマティク

Research Abstract

We analyzed the stability and plasticity of signaling transduction cascades. We have especially targeted synaptic plasticity. We developed a computational model of spike-timing dependent plasticity (STDP) in the cerebral cortex, and we found that a novel allosteic kinetics of NMDA receptors is required for STDP. The tectal neurons in the Xenopus tadpole can respond to moving visual stimuli in one preferred direction than in any other direction. Acquirement of direction selectivity has been shown to be mediated through the modification of synaptic connectivity by STDP. We proposed a mechanism for the acquirement of direction selectivity with computational models of STDP and a retino-tectal circuit.

Research Products

• [Journal Article] Analysis of Development of Direction Selectivity in Retinotectum by a Neural Circuit Model with Spike Timing-Dependent Plasticity (2011)
  • Author(s): Honda, M., Urakubo, H., Tanaka, K., Kuroda, S.
  • Journal Title: J.Neurosci. 31(4) Pages: 1516-1527
  • Peer Reviewed
• [Journal Article] Analysis of Development of Direction Selectivity in Retinotectum by a Neural Circuit Model with Spike Timing-Dependent Plasticity. (2011)
  • Author(s): Honda, M., Urakubo, H., Tanaka, K., Kuroda, S.
  • Journal Title: The Journal of Neuroscience Volume: 31(4) Pages: 1516-1527
  • Peer Reviewed
• [Journal Article] Experimental and computational aspects of signaling mechanisms of spike-timing-dependent plasticity (2009)
  • Author(s): Urakubo, H., Honda, M., Tanaka, K., Kuroda, S.
  • Journal Title: HFSP Journal 3 Pages: 240-254
  • Peer Reviewed
• [Journal Article] Experimental and computational aspects of signaling mechanisms of spike-timing-dependent plasticity (2009)
  • Author(s): Hidetoshi Urakubo, Minoru Honda, Keiko Tanaka, Shinya Kuroda
  • Journal Title: HFSP Journal 3 Pages: 240-254
  • Peer Reviewed
• [Journal Article] Requirement of an allosteric kinetics of NMDA receptors for spike-timing-dependent plasticity (2008)
  • Author(s): Urakubo, H., Honda, M., Froemke, R.C., Kuroda, S.
  • Journal Title: J.Neurosci. 28 Pages: 3310-3323
  • Peer Reviewed
• [Journal Article] Requirement of an allosteric kinetics of NMDA receptors for spike-timing-dependent plasticity (2008)
  • Author(s): Urakubo, H., et. al.
  • Journal Title: J. Neurosci. 28 Pages: 3310-3323
  • Peer Reviewed
• [Journal Article] Nitric oxide regulates input specificity of long-term depression and context dependence of cerebellar learning (2007)
  • Author(s): Ogasawara, H., Doi, T., Doya, K., Kawato, M.
  • Journal Title: PLoS. Computat. Biol. 3
  • Peer Reviewed
• [Journal Article] Ca2+ requirements for cerebellar long-term synaptic depression : role for a postsynaptic leaky integrator (2007)
  • Author(s): Tanaka, K., Khiroug, L., Santamaria, F., Doi, T., Ogasawara, H., Ellis-Davies, G.C., Kawato, M., Augustine, G.J.
  • Journal Title: Neuron 54 Pages: 787-800
  • Peer Reviewed
• [Journal Article] A Mass Conserved Reaction--Diffusion System Captures Properties of Cell Polarity (2007)
  • Author(s): Otsuji, M., Ishihara, S., Co C., Kaibuchi, K., Mochizuki, A., Kuroda, S.
  • Journal Title: PLoS. Comput. Biol. 3
  • Peer Reviewed
• [Journal Article] Nitric oxide regulates input specificity of long-term depression and context dependence of cerebellar learning (2007)
  • Author(s): Ogasawara, H., et. al.
  • Journal Title: ploS. Comput. Biol. 3 Pages: 179-179
  • Peer Reviewed
• [Journal Article] Ca2+ requirements for cerebellar long-term synaptic depression: role for a postsynaptic leaky integrator. (2007)
  • Author(s): Tanaka, K., et. al.
  • Journal Title: Neuron 54 Pages: 787-800
  • Peer Reviewed
• [Journal Article] Ca2+-independent phospholipase A2-dependent sustained Rho-kinase activation exhibits all-or-none response (2006)
  • Author(s): Maeda, A., Ozaki, Y., Sivakumaran, S., Akiyama, T., Urakubo, H., Usami, A., Sato, M., Kaibuchi, K., Kuroda, S.
  • Journal Title: Genes Cells 11 Pages: 1071-1083
  • Peer Reviewed
• [Journal Article] Ca^<2+>-independent phospholipase A_2-dependent sustained Rho-kinase activation exhibits all-or-none response (2006)
  • Author(s): Maeda.A., et al.
  • Journal Title: Genes Cells 11 Pages: 1071-1083
• [Journal Article] Inositol 1,4,5-trisphosphate-dependent Ca2+ threshold dynamics detect spike timing in cerebellar Purkinje cells (2005)
  • Author(s): Doi, T., Kuroda, S., Michikawa, T., Kawato, M.
  • Journal Title: J.Neurosci. 25(4) Pages: 950-961
  • Peer Reviewed
• [Journal Article] Dynamic characteristics of transient responses (2005)
  • Author(s): Ozaki, Y., Sasagawa, S., Kuroda, S.
  • Journal Title: J.Biochem. 137 Pages: 659-663
  • NAID: 10017345350
  • Peer Reviewed
• [Journal Article] Prediction and validation of the distinct dynamics of transient and sustained ERK activation (2005)
  • Author(s): Sasagawa, S., Ozaki, Y. Fujita, K., Kuroda, S.
  • Journal Title: Nat.Cell Biol. 7 Pages: 365-373
  • Peer Reviewed
• [Journal Article] Dynamic characteristics of transient responses (2005)
  • Author(s): Ozaki, Y., et al.
  • Journal Title: J.Biochem. 137 Pages: 659-663
  • NAID: 10017345350
• [Presentation] Emerging direction sensitivity through STDP in a model of Xenopus visual system (2010)
  • Author(s): Honda, M., Urakubo, H., Kuroda, S.
  • Organizer: Neuro2010
  • Place of Presentation: 神戸(神戸コンベンションセンター)
  • Year and Date: 2010-09-04
• [Presentation] Acquirement of direction selectivity through STDP in retinotectum (2009)
  • Author(s): Honda, M., Urakubo, H., Kuroda, S.
  • Organizer: 第32回日本神経科学大会
  • Place of Presentation: 名古屋
• [Presentation] Systems biology of spike-timing dependent synaptic plasticity (2008)
  • Author(s): 黒田 真也
  • Organizer: 日本生理学会大会
  • Place of Presentation: 新宿、日本
  • Year and Date: 2008-03-26
• [Presentation] Simulation Analysis of Spike-Timing Dependent Synaptic Plasticity from Signal Transduction Pathway to Visual Neuronal Network (2008)
  • Author(s): Honda, M., Urakubo, H., Kuroda, S.
  • Organizer: The 2nd Taiwan-Japan Young Researchers Conference on Computational and System Biology
  • Place of Presentation: Tokyo
• [Presentation] Systems biology of Spike-Timing Dependent synaptic Plasticity (2008)
  • Author(s): 黒田真也、浦久保秀俊、本田稔、Robert C.Froemke
  • Organizer: 第85回日本生理学会大会
  • Place of Presentation: 東京
• [Presentation] Encoding of Visual Information into Neuronal Networks by Spike-Timing Dependent Synaptic plasticity (2008)
  • Author(s): Honda, M., Urakubo, H., Kuroda, S.
  • Organizer: The Japan-Taiwan Young Researchers Conference on Computational and Systems Biology
  • Place of Presentation: Taiwan
• [Presentation] An allosteric kinetics of NMDA receptors required for spike timing-dependent plasticity (2007)
  • Author(s): Urakubo, H., Honda, M., Robert C. Froemke., Kuroda, S.
  • Organizer: The 37th annual meeting of the Society for Neuroscience
  • Place of Presentation: San Diego, USA
• [Presentation] 細胞成長を制御するシグナル伝達機構の定量的解析 (2007)
  • Author(s): 藤田一広、黒田真也
  • Organizer: 第30回日本分子生物学会年会・第80回日本生化学会大会合同大会
  • Place of Presentation: 横浜
• [Presentation] スパイクタイミングシナプス可塑性のタイミング検知メカニズム (2007)
  • Author(s): 浦久保秀俊
  • Organizer: シナプス研究会「シナプスの形成と成熟の分子機序」
  • Place of Presentation: 岡崎
• [Presentation] スパイクタイミング依存シナプス可塑性のタイミング検知メカニズム (2007)
  • Author(s): 浦久保秀俊、本田稔、Robert C.Froemke、黒田真也
  • Organizer: 生命科学研究ネットワークシンポジウム2007
  • Place of Presentation: 東京
• [Presentation] Prediction and validation of a novel allosteric kinetics of NMDARs as a spike-timing detector (2007)
  • Author(s): Kuroda, S., Urakubo, H., Robert C.Froemke
  • Organizer: Cosyne 2007 meeting
  • Place of Presentation: Salt Lake, USA
• [Book] 生命科学の新しい潮流理論生物学 (2010)
  • Author(s): 望月敦史, 石原秀至, 杉村薫, 柴田達夫, 黒澤元, 齋藤大助, 津元国親, 小林徹也, 上田昌宏, 澤井哲, 大浪修一, 本田稔, 黒田真也, 小林亮, 中垣俊之, 三浦岳, 本多久夫, 森下喜弘
  • Publisher: 共立出版
• [Book] 生命科学の新しい潮流 理論生物学 (2010)
  • Author(s): 望月敦史、石原秀至、杉村薫、柴田達夫、黒澤元、齊藤大助、津元国親、小林徹也、上田昌宏、澤井哲、大浪修一、本田稔、黒田真也、小林亮、中垣俊之、三浦岳、本多久夫、森下喜弘
  • Total Pages: 2
  • Publisher: 共立出版
• [Remarks] ホームページ等
• [Remarks] STDPの電気生理・生化学モデル
  • URL: http://www.kurodalab.org/info/STDP/index.html
• [Remarks] 0708071208(データベース)
• [Remarks] ミオシンリン酸化反応の生化学反応モデル
  • URL: http://www.kurodalab.org/info/myosin.g