Laboratory For Physical Biology

Advances in measurement technologies have afforded us glimpses into dynamic functional processes, such as morphogenesis and information processing, in cells and tissues involved in development and regeneration. The truly organic dynamism of the biological phenomena exhibited by living cells, individually or in groups, emerges from the coordinated interaction of numerous molecular and genetic factors, and the need for integrated, systems-based approaches to the study of design and operating principles in such "living" phenomena is becoming increasingly clear. This will require not only technologies for the measurement of such elements but the development of applicable mathematical methods as well. In Laboratory for Physical Biology, we will seek to use concepts and methodology from mathematical sciences such as physics in the study and elucidation of these emerging questions in biology.

Research Subjects

• Dynamics of information processes of chemotaxis
• Dynamics of polarization
• Dynamics of gene regulatory networks
• Stochastic behaviors of living systems

Publications

1. Tatsuo Shibata, Masatoshi Nishikawa, Satomi Matsuoka, and Masahiro Ueda:
   "Modeling the self-organized phosphatidylinositol lipid signaling system in chemotactic cells using quantitative image analysis"
   Journal of Cell Science, in press doi:10.1242/jcs.108373 (2012)
2. Akinori Baba, Tetsuya Hiraiwa, and Tatsuo Shibata:
   "Directional sensing of deformed cells under faint gradients"
   Physical Review E, 86, 060901(R), DOI,(2012)
3. Toshinori Namba, Masatoshi Nishikawa, Tatsuo Shibata:
   "The Relation of Signal Transduction to The Sensitivity and Dynamic Range of Bacterial Chemotaxis"
   Biophysical Journal, 103: 1390-1399,(2012)
4. Ooyama S, Shibata T.:
   "Hierarchical organization of noise generates spontaneous signal in Paramecium cell"
   J Theor Biol 283:1–9. (2011)
5. Nishikawa M, Shibata T.:
   "Nonadaptive Fluctuation in an Adaptive Sensory System: Bacterial Chemoreceptor"
   PLoS ONE 5(6): e11224 (2010)
6. Yoshiyuki Arai*, Tatsuo Shibata*, Satomi Matsuoka, Masayuki Sato, Toshio Yanagida and Masahiro Ueda:
   "Self-organization of the phosphatidylinositol lipids signaling system for random cell migration"
   Proc. Natl. Acad. Sci. U.S.A. 107 12399-12404(2010)
7. Matsuoka, S., T. Shibata, and M. Ueda:
   "Statistical analysis of lateral diffusion and multistate kinetics in single-molecule imaging"
   Biophys Journal, 97 1115-24 (2009)
8. Ishihara, S. and Shibata, T.:
   "Mutual interaction in network motifs robustly sharpens gene expression in developmental processes"
   Journal of Theoretical Biology, 252, 131-144 (2008)
9. Shibata, T. and Ueda, M.:
   "Noise generation, amplification and propagation in chemotactic signaling systems of living cells"
   BioSystems, 93, 126-132 (2008)
10. M. Ueda and T. Shibata:
    "Stochastic signal processing and transduction in chemotactic response of eukaryotic cells"
    Biophysical Journal 93:11-20 (2007)