4th Annual Meeting

From Japanese society for quantitative biology

Q-BioJP 4th Annual Meeting

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  • Tutorial: Jan 7th (sat), 2012.
  • Annual Meeting: Jan 8th (sun) and 9th (mon), 2012.


  • Noyori Conference Hall, Nagoya University [1]
    • Access to Higashiyama Campus of Nagoya University [2]
    • Campus Map [3]
      • Noyori Conference Hall is the building no. 69 in the map.

Scientific Programme


All tutorials are admission free. registration page [4]

Tutorial 1

on 7th Jan. 2012 sat. 11:00 - 12:30
chair: Gen Kurosawa (RIKEN ASI)

  • Hiroshi Kori and Hiroshi Ito (Ochanomizu University)

title: "Reduction" approach to biology.
1. Kori H, Kawamura Y, Nakao H, Arai K, Kuramoto Y. Collective-phase description of coupled oscillators with general network structure. Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Sep;80(3 Pt 2):036207. Epub 2009 Sep 21. [5]

Tutorial 2

on 7th Jan. 2012 sat. 13:30 - 15:30
chair: Noriko Hiroi (Keio University)

  • Akira Funahashi (Keio University)

title: Numerical Calculation and Quantitative Biology.
References(in Japanese only)
1. [6]
2. [7]

Tutorial 3-1

on 7th Jan. 2012 sat. 15:45 - 18:00
chair: Yuki Tsukada (Nagoya University)

  • Katsuyuki Kunida (Department of Pathology and Biology of Disease, Graduate School of Medicine, Kyoto University)

title: Advanced image analysis: Visualization, quantification and classification of cell migration.
1. Welch CM, Elliott H, Danuser G, Hahn KM. Imaging the coordination of multiple signalling activities in living cells. Nat Rev Mol Cell Biol. 2011 Oct 21;12(11):749-56. doi: 10.1038/nrm3212.[8]
2. Tsukada Y, Aoki K, Nakamura T, Sakumura Y, Matsuda M, Ishii S. Quantification of local morphodynamics and local GTPase activity by edge evolution tracking. PLoS Comput Biol. 2008 Nov;4(11):e1000223. Epub 2008 Nov 14.[9]
3. Machacek M, Danuser G. Morphodynamic profiling of protrusion phenotypes. Biophys J. 2006 Feb 15;90(4):1439-52. Epub 2005 Dec 2. [10]

Tutorial 3-2

on 7th Jan. 2012 sat. 17:00 18:00
chair: Kaoru Sugimura (Kyoto University)

  • Shuji Ishihara (The University of Tokyo)

title: Introduction of directional statistics.
1. Statistical Analysis of Circular Data [11]
2. Directional statistics [12]
3. Circular statistics in biology [13]


Session 1

on 8th Jan. 2012 sun. 10:30 - 12:25
chair: Takayuki Suzuki (Nagoya University)

  • Hirofumi Yamada (Graduate School of Engineering, Kyoto University)

title: Overview of Frequency Modulation Atomic Force Microscopy Visualization of Biological Molecules and its Prospect.
1. Published Papers of Graduate School of Engineering Literature Database for Matsushige lab[14]

  • Tasuku UENO (The University of Tokyo)

title: Perturbation system for signal transduction.
1. Inoue T, Heo WD, Grimley JS, Wandless TJ, Meyer T. An inducible translocation strategy to rapidly activate and inhibit small GTPase signaling pathways. Nat Methods. 2005 Jun;2(6):415-8. [15]
2. Komatsu T, Kukelyansky I, McCaffery JM, Ueno T, Varela LC, Inoue T. Organelle-specific, rapid induction of molecular activities and membrane tethering. Nat Methods. 2010 Mar;7(3):206-8. Epub 2010 Feb 14. [16]
3. Umeda N, Ueno T, Pohlmeyer C, Nagano T, Inoue T. A photocleavable rapamycin conjugate for spatiotemporal control of small GTPase activity. J Am Chem Soc. 2011 Jan 12;133(1):12-4. Epub 2010 Dec 13. [17]

  • Tomoaki Matsuura (Osaka University)

title: Analysis of the properties of biochemical reactions in a cell-size compartment.
1. Sunami T, Hosoda K, Suzuki H, Matsuura T, Yomo T. Cellular compartment model for exploring the effect of the lipidic membrane on the kinetics of encapsulated biochemical reactions. Langmuir. 2010 Jun 1;26(11):8544-51. [18]
2. Urabe H, Ichihashi N, Matsuura T, Hosoda K, Kazuta Y, Kita H, Yomo T. Compartmentalization in a water-in-oil emulsion repressed the spontaneous amplification of RNA by Q beta replicase. Biochemistry. 2010 Mar 9;49(9):1809-13.[19]

  • Koichi Takahashi (RIKEN QBiC)

title: Simulating reaction networks in intracellular environments.
1. Takahashi K, Arjunan SN, Tomita M. Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico. FEBS Lett. 2005 Mar 21;579(8):1783-8.[20]
2. Takahashi K, Tanase-Nicola S, ten Wolde PR. Spatio-temporal correlations can drastically change the response of a MAPK pathway. Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2473-8. Epub 2010 Jan 25. [21]

Session 2

on 8th Jan. 2012 sun. 15:45 - 17:15
chair Hiroaki Takagi (Nara Medical University)

  • Motoshi Kaya (University of Tokyo)

title: Molecular mechanics of muscle contraction based on reconstruction of hierarchical structure.
1. Kaya M, Higuchi H. Nonlinear elasticity and an 8-nm working stroke of single myosin molecules in myofilaments. Science. 2010 Aug 6;329(5992):686-9. [22]

  • Daisuke Taniguchi (Graduate school of arts and sciences, the university of Tokyo)

title: Self-organizing phospholipid waves in spontaneously moving amoeboid cells.
1. Arai Y, Shibata T, Matsuoka S, Sato MJ, Yanagida T, Ueda M. Self-organization of the phosphatidylinositol lipids signaling system for random cell migration.
Proc Natl Acad Sci U S A. 2010;107(27):12399-404. [23]
2. Asano Y, Nagasaki A, Uyeda TQ.
Correlated waves of actin filaments and PIP3 in Dictyostelium cells. Cell Motil Cytoskeleton. 2008;65(12):923-34.[24]
3. Gerisch G, Ecke M, Schroth-Diez B, Gerwig S, Engel U, Maddera L, Clarke M.
Self-organizing actin waves as planar phagocytic cup structures. Cell Adh Migr. 2009;3(4):373-82. [25]

  • Reo Maeda (Department of Biological Science and Technology, Toko University of Science)

title: Chirality in planar cell shape contributes to left-right asymmetric epithelial morphogenesis.
1. Taniguchi K, Maeda R, Ando T, Okumura T, Nakazawa N, Hatori R, Nakamura M, Hozumi S, Fujiwara H, Matsuno K. Chirality in planar cell shape contributes to left-right asymmetric epithelial morphogenesis. Science. 2011 Jul 15;333(6040):339-41. [26]

Short Talk Session

on 8th Jan. 2012 sun. 17:20 - 17:45
chair Hiroaki Takagi (Nara Medical University)

  • Yuki Hamamura (Nagoya University)
  • Yusuke Mii (University of Tokyo)

Session 3

on 9th Jan. 2012 mon. 10:00 - 11:30
chair: Tetsuya Kobayashi (University of Tokyo)

  • Kazuo Yamagata (Research Institute for Microbial Diseases, Osaka University)

title: Quantification of embryo quality
1. Yamagata K, Suetsugu R, Wakayama T. Long-term, six-dimensional live-cell imaging for the mouse preimplantation embryo that does not affect full-term development. J Reprod Dev. 2009 Jun;55(3):343-50. Epub 2009 Mar 19.[27]
2. Yamagata K, Suetsugu R, Wakayama T. Assessment of chromosomal integrity using a novel live-cell imaging technique in mouse embryos produced by intracytoplasmic sperm injection. Hum Reprod. 2009 Oct;24(10):2490-9. Epub 2009 Jul 2.[28]

  • Naoki Irie (RIKEN CDB)

title: Tackling problems in idealistic morphology by molecular-level quantification.
1. Naoki Irie and Shigeru Kuratani. Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis. Nat Commun. 2011 March 22; 2: 248. doi: 10.1038/ncomms1248, PMCID: PMC3109953 [29]
2. Naoki Irie and Atsuko Sehara-Fujisawa. The vertebrate phylotypic stage and an early bilaterian-related stage in mouse embryogenesis defined by genomic information. BMC Biol. 2007; 5: 1. Published online 2007 January 12. doi: 10.1186/1741-7007-5-1 PMCID: PMC1797197[30]

  • Yuichi Taniguchi (Quantitative Biology Center, RIKEN)

title: Quantitative analysis of stochastic gene expression in single cells
1. Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, Emili A, Xie XS. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science. 2010 Jul 30;329(5991):533-8. [31]

Session 4

on 9th Jan. 2012 mon. 14:00 - 16:00
chair: Akatsuki Kimura (National Institute of Genetics)

  • Jun-nosuke Teramae (RIKEN Brain Science Institute (BSI))

title: Origin and computational role of ongoing noise in cortical circuits.
1. Song S, Sjöström PJ, Reigl M, Nelson S, Chklovskii DB. Highly nonrandom features of synaptic connectivity in local cortical circuits. PLoS Biol. 2005 Mar;3(3):e68. Epub 2005 Mar 1. [32]

  • Kazuhiro Aoki (Graduate School of Biostudies, Kyoto University)

title: Development of reaction kinetics under the condition of molecular crowding.
1. Aoki K, Yamada M, Kunida K, Yasuda S, Matsuda M. Processive phosphorylation of ERK MAP kinase in mammalian cells. Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12675-80. Epub 2011 Jul 18. [33]
2. Minton AP. How can biochemical reactions within cells differ from those in test tubes? J Cell Sci. 2006 Jul 15;119(Pt 14):2863-9. [34]

  • Namiko Mitarai (Niels Bohr Institute)

title: Control the ribosome traffic: Benefit of having slow codons
1. N. Mitarai, K. Sneppen, and S. Pedersen. Ribosome Collisions and Translation Efficiency: Optimization by Codon Usage and mRNA Destabilization. J. Mol. Biol. (2008) 382, 236.[35]
2. M. Pedersen, S. Nissen, N. Mitarai, S. L. Svenningsen, K.Sneppen. The Functional Half-Life of an mRNA Depends on the Ribosome Spacing in an Early Coding Region. J. Mol. Biol. (2011) 407, 35.[36]

  • Yuta Shimamoto (The Rockefeller University)

title: Micromechanics of the metaphase spindle
1. Shimamoto Y, Maeda YT, Ishiwata S, Libchaber AJ, Kapoor TM. Insights into the micromechanical properties of the metaphase spindle. Cell. 2011 Jun 24;145(7):1062-74.[37]

Poster Sessions

Registration Fee

  • Tutorial: free
  • Annual Meeting: 1,500 JPY
    • Coffee Break: 700 JPY
    • Lunch: 600 JPY (prn)

Seating Capacity

  • Tutorial:~ 190
  • Annual Meeting: ~ 155

The Organizing Committee

  • Akatsuki Kimura(Cell Architecture Laboratory, National Institute of Genetics)
  • Gen Kurosawa (RIKEN Advanced Science Institute)
  • Tetsuya J. Kobayashi (Institute of Industrial Science, the University of Tokyo)
  • Kaoru Sugimura (iCeMS, Kyoto University)
  • Takayuki Suzuki (Nagoya University)
  • Hiroaki Takagi (Department of Physics, School of Medicine, Nara Medical University)
  • Yuki Tsukada (Division of Biological Science, Graduate School of Science, Nagoya University)
  • Noriko Hiroi (Department of Biosciences and Informatics, Keio University)
  • Akira Funahashi (Department of Biosciences and Informatics, Keio University)