Data-driven Multiscale Modeling of Signal Processing in Bacterial Chemotaxis

2016 Fiscal Year Annual Research Report

• Project/Area Number: 16H04771
• Research Institution: Hokkaido University
• Principal Investigator: 李 振風 北海道大学, 電子科学研究所, 准教授 (90397795)
• Project Period (FY): 2016-04-01 – 2017-03-31
• Keywords: 細胞情報・動態 / time series analysis

Outline of Annual Research Achievements

Change point analysis that does not require the knowledge of noise model has been developed to detect the time instants at which the observable value and the linear trend change in a time series. The model free change point detection has been applied to various single molecule time series, such as from single protein motor rotary measurements, gating current fluctuation in single ion channel patch clamp measurements, etc., to capture event switching that cannot be resolved using conventional thresholding and binning methods. The outcome from the change point analysis is the dwell time statistics of the system residing in various states, such as the pause and rotation states in rotary protein motor, sub-conductance states in ion channel gating, clockwise and counter-clockwise rotation modes in flagellar motor, different diffusive modes in bacterial chemotaxis, etc. As a next step of the project, the resulting dwell time statistics will then serve as the input to infer the underlying kinetic scheme of the system to reveal hidden kinetic states and transitions among the states.
On the other hand, the mathematical formalism of "transfer entropy" to quantify and detect information flow between multivariate time series has been generalized to detect "time dependent" flows. Before applying the new mathematical formalism to real bacterial chemotaxis time series, the theory is currently tested using time series generated from simple simulation models to benchmark its performance and validity.

Research Progress Status

28年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

28年度が最終年度であるため、記入しない。

Research Products

• [Journal Article] Extracting subcellular fibrillar alignment with error estimation: Application to microtubules (2016)
  • Author(s): S. Tsugawa, N. Hervieux, O. Hamant, A. Boudaoud, R.S. Smith, C.B. Li, T. Komatsuzaki
  • Journal Title: Biophys. J. Volume: 110 Pages: 1836-1844
  • DOI: 10.1016/j.bpj.2016.03.011
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Single molecule data analysis: An introduction (2016)
  • Author(s): M. Tavakoli, J.N. Taylor, C.B. Li, T. Komatsuzaki, S. Presse
  • Journal Title: Adv. Chem. Phys. Volume: - Pages: -
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Variable cell growth yields reproducible organ development through spatiotemporal averaging (2016)
  • Author(s): L. Hong, M. Dumond, S. Tsugawa, A. Sapala, A.L. Routier-Kierzkowska, Y. Zhou, C. Chen, R.S. Smith, T. Komatsuzaki, C.B. Li, A. Boudaoud, A.H.K. Roeder
  • Journal Title: Dev. Cell Volume: 38 Pages: 15-32
  • DOI: 10.1016/j.devcel.2016.06.016
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Presentation] Single Molecule Time Series Analyses of F1-ATPase to Unveil the Roles of ATP Hydrolysis (2016)
  • Author(s): C.B. Li
  • Organizer: Workshop on Super-functional Molecules
  • Place of Presentation: Institute for Molecular Science, Okazaki, Japan
  • Year and Date: 2016-06-27 – 2016-06-28
  • Invited
• [Presentation] A Nano-scale Key-and-Unlock Mechanism in the F1-ATPase revealed by Single Molecule Time Series Analysis (2016)
  • Author(s): C.B. Li
  • Organizer: Beijing Computational Science Research Center
  • Place of Presentation: Beijing Computational Science Research Center, China
  • Year and Date: 2016-05-24 – 2016-05-24
  • Invited