Oscillator network modeling of the circadian rhythms and its application to their control

2013 Fiscal Year Final Research Report

• Project/Area Number: 23560446
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Communication/Network engineering
• Research Institution: Ritsumeikan University
• Principal Investigator: TOKUDA Isao 立命館大学, 理工学部, 教授 (00261389)
• Co-Investigator(Kenkyū-buntansha): HONMA Sato 北海道大学, 医学研究科, 特任教授 (20142713) ; FUKUDA Hirokazu 大阪府立大学, 工学研究科, 准教授 (90405358)
• Project Period (FY): 2011 – 2013
• Keywords: 概日リズム / 非線形動力学 / 同期 / 制御 / 視交叉上核

Research Abstract

Towards understanding the role of Cry genes in the mammalian circadian clock, this project attempted to construct a mathematical model of a neuronal network in the suprachiasmatic nucleus (SCN). Single cell analysis was applied to the SCN data recorded from Cry1 and Cry2 double deficient mice. Compared to the wild-type SCN, the mutant SCN neurons showed larger level of noise and more variation of the periods. The SCN slice was further analyzed. The neonate showed a clear rhythmicity with synchronized neuronal activities, whereas this rhythmicity was instantly destroyed in the adult. Our mathematical model implies that the network structure (coupling strength and phase) may change during the development, which may drastically change the network dynamics.
Next, multiple light pulses were injected to Arabidopsis thaliana to desynchronize and resynchronize the plant circadian system. Our experiment demonstrates the efficiency of using the phase response property for controlling the plant.

Research Products

• [Journal Article] Characterization of circadian rhythms through a bioluminescence reporter assay in Lactuca sativa L (2014)
  • Author(s): T. Higashi, A. Kamitamari, N. Okamura, K. Ukai, K. Okamura, T. Tezuka, H. Fukuda
  • Journal Title: Environmental Control in Biology Volume: Vol. 52 Pages: 21-27
  • DOI: 10.2525/ecb.52.21
  • Peer Reviewed
• [Journal Article] Detecting connectivity of small, dense oscillator networks from dynamical measurements based on a phase modeling approach (2013)
  • Author(s): I.T. Tokuda, M. Wickramasinghe, I.Z. Kiss
  • Journal Title: Physics Letters A Volume: Vol. 377 Pages: 1862-1867
  • DOI: 10.1016/j.physleta.2013.05.016
  • Peer Reviewed
• [Journal Article] Oscillator network modeling of circadian rhythm in the suprachiasmatic nucleus (2013)
  • Author(s): I. Tokuda, H. Fukuda, N. Hayasaka
  • Journal Title: In Advances in Cognitive Neurodynamics (III), Y.Yamaguchi ed. Springer, Tokyo Pages: 191-197
  • DOI: 10.1007/978-94-007-4792-0_26
• [Journal Article] Oscillator cell networks in the hypothalamic suprachiasmatic nucleus, the mammalian circadian clock (2013)
  • Author(s): S. Honma, D. Ono, K.-I. Honma
  • Journal Title: In Advances in Cognitive Neurodynamics (III), Y.Yamaguchi ed. Springer, Tokyo Pages: 185-190
  • DOI: 10.1007/978-94-007-4792-0_25
• [Journal Article] Postnatal constant light compensates Cryptochrome 1 and 2 double deficiency for disruption of circadian behavioral rhythms in mice under constant dark (2013)
  • Author(s): D. Ono, S. Honma, K.-I. Honma
  • Journal Title: PLoS One Volume: Vol. 8 Pages: e80615
  • DOI: 10.1371/journal.pone.0080615
  • Peer Reviewed
• [Journal Article] Solution to the inverse problem of estimating gap junctional and inhibitory conductance in inferior olive neurons from the spike trains by network model simulation (2013)
  • Author(s): M. Oniuzka, H.T. Huu, M. Kawato, I. Tokuda, N. Schweighofer, Y. Katori, K. Aihara, E.J. Lang, K. Toyama
  • Journal Title: Neural Networks Volume: Vol. 47 Pages: 51-63
  • DOI: 10.1016/j.neunet.2013.01.006
  • Peer Reviewed
• [Journal Article] Adaptive coupling of inferior olive neurons in cerebellar learning (2013)
  • Author(s): I.T. Tokuda, H. Huu, N. Schweighofer, M. Kawato
  • Journal Title: Neural Networks Volume: Vol. 47 Pages: 42-50
  • DOI: 10.1016/j.neunet.2012.12.006
  • Peer Reviewed
• [Journal Article] Controlling circadian rhythms by dark pulse perturbations in Arabidopsis thaliana (2013)
  • Author(s): H. Fukuda, H. Murase, I.T. Tokuda
  • Journal Title: Scientific Reports Volume: Vol. 3 Pages: 1533
  • DOI: 10.1038/srep01533
  • Peer Reviewed
• [Journal Article] Cryptochromes are critical for the development of coherent circadian rhythms in the mouse suprachiasmatic nucleus (2013)
  • Author(s): D. Ono, S. Honma, and K.-I. Honma
  • Journal Title: Nature Communications Volume: Vol. 4 Pages: 1666
  • DOI: 10.1038/ncomms2670
  • Peer Reviewed
• [Journal Article] Circadian regulation of food anticipatory activity in molecular clock deficient mice (2012)
  • Author(s): N.N. Takasu, G. Kurosawa, I.T. Tokuda, Mochizuki, T. Todo, W. Nakamura
  • Journal Title: PLoS ONE Volume: Vol. 7 Pages: e48892
  • DOI: 10.1371/journal.pone.0048892
  • Peer Reviewed
• [Journal Article] Self-arrangement of cellular circadian rhythms through phase resetting in plant roots (2012)
  • Author(s): H. Fukuda, K. Ukai, and T. Oyama
  • Journal Title: Phys. Rev. E Volume: Vol. 86 Pages: 041917
  • DOI: 10.1103/PhysRevE.86.041917
  • Peer Reviewed
• [Journal Article] Topological specificity and hierarchical network of the circadian calcium rhythm in the suprachiasmatic nucleus (2012)
  • Author(s): R. Enoki, S. Kuroda, D. Ono, M.T. Hasan, T. Ueda, S. Honma, K.-I. Honma
  • Journal Title: Proc Natl Acad Sci USA Volume: Vol. 109 Pages: 21498-21503
  • DOI: 10.1073/pnas.1214415110
  • Peer Reviewed
• [Journal Article] Engineering of synchronization and clustering of a population of chaotic chemical oscillators (2011)
  • Author(s): C.G. Rusin, I. Tokuda, I.Z. Kiss, J.L. Hudson
  • Journal Title: Angewandte Chemie Volume: Vol. 50, Issue 43 Pages: 10212-10215
  • DOI: 10.1002/anie.201008194
  • Peer Reviewed
• [Journal Article] Quantitative analysis of phase wave of gene expression in the mammalian central circadian clock network (2011)
  • Author(s): H. Fukuda, I. Tokuda, S. Hashimoto, N. Hayasaka
  • Journal Title: PLoS ONE Volume: Vol. 6, No. 8
  • DOI: 10.1371/journal.pone.0023568
  • Peer Reviewed
• [Journal Article] Early diagnosis of productivity through a clock gene promoter activity using a Luciferase bioluminescence assay in Arabidopsis thaliana (2011)
  • Author(s): H. Fukuda, T. Ichino, T. Kondo, H. Murase
  • Journal Title: Environment Control in Biology Volume: Vol. 49 Pages: 51-60
  • DOI: 10.2525/ecb.49.51
  • Peer Reviewed
• [Journal Article] Production of biologically active human thioredoxin 1 protein in lettuce chloroplasts (2011)
  • Author(s): S. Lim, H. Ashida, R. Watanabe, K. Inai, Y.-S. Kim, K. Mukougawa, H. Fukuda, K.-I. Tomizawa, K.-I. Ushiyama, H. Asao, M. Tamoi, H. Masutani, S. Shigeoka, J. Yodoi, A. Yokota
  • Journal Title: Plant Mol. Biol. Volume: Vol. 76 Pages: 335-44
  • DOI: 10.1007/s11103-011-9745-5
  • Peer Reviewed
• [Presentation] Analysis of phase response of Arabidopsis to light pulses with different wavelength (2014)
  • Author(s): T. Ohara, I. Tokuda, S. Okamura, H. Fukuda
  • Organizer: 第55回日本植物生理学会年会
  • Place of Presentation: 富山大学(富山県)
  • Year and Date: 2014-03-18
• [Presentation] SCNスライスデータにおける領域分割とその細胞間結合への影響に関する研究 (2013)
  • Author(s): 豊田慎五,徳田功,福田弘和,早坂直人
  • Organizer: 第20回日本時間生物学会学術大会
  • Place of Presentation: 近畿大学(大阪府)
  • Year and Date: 2013-11-09
• [Presentation] 波長の異なる光パルスを用いた植物概日リズムの位相応答曲線の計測と推定に関する研究 (2013)
  • Author(s): 大原隆之,徳田功,岡村信弥,福田弘和
  • Organizer: 第20回日本時間生物学会学術大会
  • Place of Presentation: 近畿大学(大阪府)
  • Year and Date: 2013-11-09
• [Presentation] 根の概日時計におけるストライプパターンを用いた位相応答関数の算出 (2013)
  • Author(s): 鵜飼和也,上山昌三,福田弘和
  • Organizer: 第20回日本時間生物学会学術大会
  • Place of Presentation: 近畿大学(大阪府)
  • Year and Date: 2013-11-09
• [Presentation] A role of salt-inducible kinase 3 in the central circadian pacemaker in mammals : phosphorylation-dependent degradation of the clock protein (2013)
  • Author(s): N. Hayasaka, I. Tokuda, H. Takemori
  • Organizer: XIII Congress of the European Biological Rhythms Society
  • Place of Presentation: Munich(Germany)
  • Year and Date: 2013-08-20
• [Presentation] Single cell analysis and oscillator network modeling of Cry1 and Cry2 double deficient mice (2013)
  • Author(s): I. Tokuda, H. Herzel, D. Ono, S. Honma, K.-I. Honma
  • Organizer: XIII Congress of the European Biological Rhythms Society
  • Place of Presentation: Munich(Germany)
  • Year and Date: 2013-08-19
• [Presentation] A role for Salt-inducible kinase 3 (SIK3) in the circadian rhythm regulation : phosphorylation-dependent degradation of the clock protein (2013)
  • Author(s): N . Hayasaka, I. Tokuda, H. Takemori
  • Organizer: 36th annual meeting of the Japan Neuroscience Society
  • Place of Presentation: 京都国際会館(京都府)
  • Year and Date: 2013-06-22
• [Presentation] 線形予測による給餌予想活動のモデル化:制限給餌データの定量解析 (2013)
  • Author(s): 牛田明里,徳田功,高須奈々,中村渉
  • Organizer: 電子情報通信学会総合大会
  • Place of Presentation: 岐阜大学(岐阜県)
  • Year and Date: 2013-03-21
• [Presentation] Oscillator network modeling of suprachiasmatic nucleus in Cry1/Cry2 double-deficient mice (2012)
  • Author(s): I. Tokuda, D. Ono, S. Honma, K.-I. Honma
  • Organizer: 35th annual meeting of the Japan Neuroscience Society
  • Place of Presentation: 名古屋国際会議場(愛知県)
  • Year and Date: 2012-09-18
• [Presentation] 概日リズムネットワークモデルとその結合推定方法の検証 (2012)
  • Author(s): 豊田慎五,徳田功,福田弘和,早坂直人
  • Organizer: 第19回日本時間生物学会学術大会
  • Place of Presentation: 北海道大学(北海道)
  • Year and Date: 2012-09-15
• [Presentation] データ分析によるCry遺伝子欠損マウスのSCNモデル (2012)
  • Author(s): 徳田功,小野大輔,本間さと,本間研一
  • Organizer: 第19回日本時間生物学会学術大会
  • Place of Presentation: 北海道大学(北海道)
  • Year and Date: 2012-09-15
• [Presentation] Oscillator network modeling of mutant SCN (2012)
  • Author(s): I. Tokuda, D. Ono, S. Honma, K.-I. Honma
  • Organizer: Meeting Society for Research on Biological Rhythms
  • Place of Presentation: Sandestin (米国)
  • Year and Date: 2012-05-22
• [Presentation] Oscillator network modeling of circadian rhythm in the suprachiasmatic nucleus (2011)
  • Author(s): I. Tokuda, H. Herzel
  • Organizer: 26th Symposium on Biological and Physiological Engineering
  • Place of Presentation: 立命館大学(滋賀県)
  • Year and Date: 2011-09-22
• [Presentation] Oscillator network modeling of circadian rhythm in the suprachiasmatic nucleus (2011)
  • Author(s): I. Tokuda, H. Fukuda, N. Hayasaka
  • Organizer: 3rd International Conference on Cognitive Neurodynamics
  • Place of Presentation: ヒルトンニセコビレッジ(北海道)
  • Year and Date: 2011-06-12
• [Book] "Cellular circadian rhythms in the suprachiasmatic nucleus : An oscillatory or a stochastic process?"Dynamics of Circadian Oscillation in the SCN(Honma K. (ed.)) (2014)
  • Author(s): D. Ono, H. Kori, S. Honma, S. Daan, and K. Honma
  • Total Pages: 21-32
  • Publisher: Hokkaido Univ. Press
• [Book] "Imaging Circadian Calcium Rhythm in the Suprachiasmatic Nucleus."Dynamics of Circadian Oscillation in the SCN(Honma K. (ed.)) (2014)
  • Author(s): R. Enoki, S. Honma and K. Honma
  • Total Pages: 33-45
  • Publisher: Hokkaido Univ. Press
• [Book] "Cellular oscillators in the suprachiasmatic nucleus for behavior rhythm expression in the mouse lacking CRYPTOCHROME."Dynamics of Circadian Oscillation in the SCN(Honma K. (ed.)) (2014)
  • Author(s): S. Honma, D. Ono, and K. Honma
  • Total Pages: 79-89
  • Publisher: Hokkaido Univ. Press
• [Book] "Bout Oscillator : hypothetical circadian oscillators for activity bouts."Dynamics of Circadian Oscillation in the SCN(Honma K. (ed.)) (2014)
  • Author(s): K. Honma, D. Ono, S. Honma, and I. Tokuda
  • Total Pages: 91-105
  • Publisher: Hokkaido Univ. Press
• [Book] "Oscillator Network modeling of the suprachiasmatic nucleus in Cry1/Cry2 double deficient mice."Dynamics of Circadian Oscillation in the SCN(Honma K. (ed.)) (2014)
  • Author(s): I. Tokuda, H. Herzel, D. Ono, S. Honma, and K. Honma
  • Total Pages: 139-153
  • Publisher: Hokkaido Univ. Press