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RCCSB Seminar

James A. Glazier
(Biocomplexity Institute, Indiana University)

Somites without a clock

Date:
2014.3.19 (Wed) 10:40-12:10
Place:
16-827
Abstract:
The formation of body segments (somites) in vertebrate embryos is accompanied by molecular oscillations (segmentation clock). Interaction of this oscillator with a wave traveling along the body axis (the clock-and-wavefront model) is generally believed to control somite number, size, and axial identity. Here we show that a clock-and-wavefront mechanism is unnecessary for somite formation. Non-somite mesoderm treated with Noggin generates many somites that form simultaneously, without cyclic expression of Notch-pathway genes, yet have normal size, shape, and fate. These somites have axial identity: The Hox code is fixed independently of somite fate. However, these somites are not subdivided into rostral and caudal halves, which is necessary for neural segmentation. We propose that somites are self-organizing structures whose size and shape is controlled by local cell-cell interactions.

Kumar Selvarajoo
(Keio University)

Regulating proinflammatory cell response using simple physical rules

Date:
2014.3.12 (Wed) 14:00-15:30
Place:
16-827
Abstract:
Living cells are well known to display complex and variable behavior to different environmental perturbations. The innate immune cells, in particular, are specialized cells within mammalian host that eradicate invading pathogens using precise cell signaling mechanisms. In my talk, I will discuss the innate immune response invoked by the Toll-like receptors on recognition with pathogenic microbial components. Our research investigates the dynamic experimental profiles of key proinflammatory molecules using network-based computational models adopting physical laws. Remarkably, I will show evidence for the presence of linear response during the early signaling process. Utilizing the simplicity, we have developed 9 response rules that can be successfully used to predict novel i) signaling mechanisms and ii) targets to regulate proinflammatory responses for disease control.

Philippe Marcq
(Laboratoire Physico-Chimie Curie, Institut Curie)

Epithelial closure dynamics

Date:
2013.12.20 (Fri) 13:30-15:00
Place:
Advanced lab 410
Abstract:
Epithelization is the process whereby a migrating epithelium covers a cell-free surface. We studied the closure dynamics of well-controlled circular apertures within an epithelial monolayer. When the underlying substrate allows cell adhesion, we found that border protrusive activity drove epithelial closure despite the presence of a contractile actomyosin cable at the periphery of the wound. Taking into account border forces and friction with the substrate we proposed a hydrodynamic model of the epithelium, and classified different phenotypes according to the value of a single parameter, the epithelization coefficient. When surface treatment of the aperture prevents cell adhesion, force generation was dominated by the contractile cable. Closure dynamics could be described quantitatively by a simple stochastic force balance equation at the wound margin.

Julyan Cartwright
(Universidad de Granada)

The dynamics of life

Date:
2013.10.18 (Fri) 14:30-15:30
Place:
16-107
Abstract:
The modern theory of dynamical systems studies how phenomena such as chaos, self-organization, synchronization, complexity, and patterns, can emerge from nonlinear interactions within a system. This field comprises a growing set of powerful tools with which nonlinear phenomena in any field of natural science may be analysed, and as it looks for universal behaviour of a system it provides a systematic way of approaching a problem that can unite disparate observations. The procedure is both reductionistic and at the same time holistic; first one must strip a problem down to its essence, and then one can see how interactions between the parts lead to the emergence of complex behaviour of the whole that is not present in any one part. The nonlinear revolution is still taking place; at present nonlinear dynamics has only partially been assimilated into the edifice of science, as the foundations of the field are not yet complete, and there is still much to understand regarding the fundamentals of many aspects of nonlinear systems. But it is from these ideas that I see a new, as yet only incipient, theoretical biology germinating. Biology is the science that, perhaps, has most to gain from this paradigm shift; being the science in which, beginning from inanimate matter, the astounding complexity of the natural world has evolved. In this talk I shall give an overview, through the use of biological examples, of the revolution or paradigm shift these ideas are producing in science.

François Graner
(Matière et Systèmes Complexes, Université Paris Diderot - CNRS)

Dynamics of cellular materials : from cell mechanics to tissue shape

Date:
2013.10.18 (Fri) 13:30-14:30
Place:
16-107
Abstract:
During its metamorphosis, a fly changes from larval to adult shape within a few days. The morphogenesis of its tissues is determined by a coordinated collective cell behavior. In turn, the mechanics at the tissue scale feedbacks on the cell level dynamics. In close interaction between biologists and physicists, we have investigated how genetics can affect these different scales.

Movies of the developing animal resolve cell contour details. The tissue as a whole behaves as a continuous material; its mechanical properties, although complex, can be surprisingly well modelled by a physical approach. A general set of quantitative tools has been developed and tested on a simple model system: soap froth. The tools link the sub-cell scale, the cell dynamics, the level of the group of cells, and the whole tissue. They enable to establish how changes at the individual cell level (displacements, deformations, divisions) determine the development of the tissue shape.

Ryo Miyazaki
(National Institute of Advanced Industrial Science and Technology)

Evolutionary implication of phenotypic heterogeneity in a clonal population

Date:
2013.9.26 (Thu) 11:00-12:00
Place:
16-107
Abstract:
The main interest of my research is to globally analyze and understand phenotypic heterogeneity in a clonal cell population. We may be tempted to think of clonal populations of bacterial cells growing in liquid cultures or as colonies on plates as millions (or billions) of largely uniform cells, exhibiting little or no phenotypic diversity. However, with the development of enhanced approaches for single-cell based analyses, such an idea is increasingly revealed as an oversimplification. Rather, a pool of genetically identical bacterial cells can readily contain phenotypically distinct subpopulations, which may arise either from stochastic variation or deterministic processes. In this seminar, I will show how horizontal gene transfer, a unique way of heredity allowing to exchange DNA among bacterial cells, depends on variation of a particular gene (i.e. RpoS, a stress response factor) expression at individual cell levels. Furthermore, I will discuss a novel programmed cell death phenotype we found in such subpopulations where horizontal gene transfer is launched.

Greg Stephens
(Biological Physics Theory Unit, Okinawa Institute of Science and Technology)

Towards a biophysics of organisms: Stochastic dynamics in the reversal motions of C. elegans

Date:
2013.9.13 (Fri) 11:00-12:30
Place:
Advanced Research Laboratories, Room 410
Abstract:
While there has been an explosion in our ability to characterize the molecules, cells, and circuits that generate natural behavior, our understanding of behavior itself is less advanced. Here we use high-resolution video microscopy to record the motions of the nematode C. elegans, freely-wiggling on a flat agar plate. We show that the space of shapes is low-dimensional, with just four dimensions accounting for 95% of the shape variance. Projections of worm shape along these four “eigenworms” provide a precise yet substantially complete description of locomotory behavior, capturing both classical motion such as forward crawling, reversals, and Ω-turns and novel behaviors such as “pause” states at particular postures. We use the eigenworms to construct a stochastic model of the body wave dynamics that predicts transitions between attractors corresponding to abrupt reversals in crawling direction and we show that the noise amplitude decreases systematically with increasing time away from food, resulting in longer bouts of forward crawling and suggesting that worms use noise to adaptive benefit.
Note:
複雑生命システム動態研究教育拠点との共催です(link

Namiko Mitarai
(Niels Bohr Institute)

Conditional Cooperativity in Toxin-Antitoxin Battle in Bacteria

Date:
2013.7.15 (Thu) 11:00-12:30
Place:
Room 107, Building 16
Abstract:
Many toxin-antitoxin operons are regulated by the toxin/antitoxin ratio by mechanisms collectively coined ”conditional cooperativity”. Toxin and antitoxin form heteromers with different stoichiometric ratios, and the complex with the intermediate ratio works best as a transcription repressor. This allows transcription at low toxin level, strong repression at intermediate toxin level, and then again transcription at high toxin level. Such regulation has two interesting features; firstly, it provides a non-monotonous response to the concentration of one of the proteins, and secondly, it opens for ultra-sensitivity mediated by the sequestration of the functioning heteromers. We explore possible functions of conditional regulation in simple feedback motifs, and show that it can provide bistability for wide a range of parameters. We demonstrate that the conditional cooperativity in toxin-antitoxin systems combined with the growth-inhibition activity of free toxin can mediate bistability between a growing state and a dormant state. Conditional cooperativity also secures that the antitoxin dominated state has a substantial amount of toxins present, which helps the transition to the toxin dominated state under stress. These features may be relevant for understanding persister formation in E. coli.

Kenneth Showalter
(West Virginia University)

Synchronization in Populations of Chemical Oscillators: Quorum Sensing, Phase Clusters and Chimeras

Date:
2012.11.9 (Fri) 15:00-16:00
Place:
Advanced Research Laboratories, 410
Abstract:
We have studied large, heterogeneous populations of discrete chemical oscillators (~100,000) to characterize two different types of density-dependent transitions to synchronized oscillatory behavior. For different chemical exchange rates between the oscillators and the surrounding solution, we find with increasing oscillator number density (1) the gradual Kuramoto synchronization of oscillatory activity or (2) the sudden quorum sensing "switching on" of synchronized oscillatory activity. We also describe the formation of phase clusters, where each cluster has the same frequency but is phase shifted with respect to other clusters, giving rise to a global signal that is more complex than that of the individual oscillators. Finally, we describe studies of chimera states and their relation to other synchronization states in populations of coupled chemical oscillators.
A. F. Taylor, M. R. Tinsley, F. Wang, Z. Huang, K. Showalter, Science 323, 614 (2009).
A. F. Taylor, M. R. Tinsley, F. Wang, K. Showalter, Angew. Chemie Int. Ed. 50, 10161 (2011).
M. R. Tinsley, S. Nkomo, K. Showalter, Nature Physics 8, 662 (2012).

Benjamin Pfeuty
(CR2, CNRS, Laboratoire de Physique des Lasers, Atomes, Molecules)

Principles of coordination between cell proliferation and differentiation during multicellular development

Date:
2012.10.19 (Fri) 13:00-14:30
Place:
16-107

Pasquale Stano
(Biology Department, University of Roma Tre, Italy)

Semi-synthetic minimal cells: from origin of life to synthetic biology

Date:
2012.10.8 (Mon) 13:30-15:00
Place:
Advanced Research Laboratories, 410

Martin Robert
(Institute for Advanced Biosciences, Keio University)

Metabolomics-based functional discovery in Escherichia coli

Date:
2012.7.20 (Fri) 14:50-16:20
Place:
16-829

Takanari Inoue
(Department of Cell Biology, Johns Hopkins University School of Medicine)

Synthetic cell biology of primary cilia

Date:
2012.6.22 (Fri) 14:50-16:20
Place:
16-829

Tom Shimizu
(AMOLF, Netherlands)

Sensory response rescaling in bacteria

Date:
2012.5.2 (Wed) 15:00-16:30
Place:
Advanced Research Laboratories, Room 410

Kazumasa Takeuchi
(Department of Physics, Univ. of Tokyo)

Active interfaces: speculative bridge from liquid-crystal turbulence to competing biological populations

Date:
2012.4.18 (Wed) 13:00-14:30
Place:
Advanced Research Laboratories, Room 410

Kazufumi Hosoda
(Osaka University)

Experimental evolution of an artificial bacterial mutualism

Date:
2012.3.29 (Thu) 15:30-17:00
Place:
16-107

Kazuhiro Aoki
(Kyoto University, JST PRESTO)

Experimental validation of the effects of macromolecular crowding on enzymatic reaction: Thermodynamic activity, viscosity and processivity

Date:
2012.2.22 (Wed) 15:30-17:00
Place:
16-107

Tamás Vicsek
(Eötvös Loránd University (ELTE), Dept. of Biological Physics)

Hierarchy and/versus Controllability of Complex Networks

Date:
2011.12.5 (Mon) 14:40-16:10
Place:
16-829

Henrik J. Jensen
(Department of Mathematics and Complexity & Networks Group Imperial College London)

Self-similar correlation function in brain resting-state functional magnetic resonance imaging.

Date:
2011.11.17 (Thu) 10:40-12:10
Place:
16-829

Julyan Cartwright
(CSIC [Spanish research council])

Fluid dynamics, Self-organization, and Biology

Date:
2011.10.3 (Mon) 10:40-12:10
Place:
16-107

小宮山 進
(東京大学大学院総合文化研究科)

パッシブテラヘルツ近接場顕微鏡 -新規バイオ計測を目指して-

Date:
2011.9.28 (Wed) 16:30-18:00
Place:
16-107

Yusuke Maeda
(Center for Studies in Physics and Biology, The Rockefeller University)

Selection of RNA by molecular transport: A physics approach to the origins of life

Date:
2011.8.29 (Mon) 10:40-12:10
Place:
16-107

入江 直樹
(理化学研究所 発生・再生科学総合研究センター)

発生砂時計モデルと脊椎動物が持つ発生学的構造特性への思索

Date:
2011.6.16 (Thu) 14:40-16:10
Place:
16-829

Leroy Lee Cronin
(WestCHEM, Dept. of Chemistry, University of Glasgow)

Linking Non Equilibrium Structured Nanostructures, Reaction Pathways and Materials to Engineer Inorganic Chemical Cells (iChells)

Date:
2011.3.9 (Wed) 15:00-16:30
Place:
Advanced Research Laboratories, Room 410

谷口 雄一
(Department of Chemistry and Chemical Biology, Harvard University)

単一の生細胞におけるプロテオームとトランスクリプトームとを単一分子検出感度で定量化する

Date:
2010.12.2 (Thu) 10:40-12:10
Place:
16-107

Marco Cosentino Lagomarsino
(Genomic Physics Group, Universite Pierre et Marie Curie)

The recipe for a genome. Scaling laws and partitioning in functional categories and evolutionary classes

Date:
2010.11.25 (Wed) 10:40-12:30
Place:
16-107

Roeland M. H. Merks
(Netherlands Institute for Systems Biology (NISB) and Centrum Wiskunde & Informatica (CWI))

Cell-based modeling of lood vessel growth

Date:
2010.11.16 (Tue) 10:40-12:30
Place:
16-107

Michael P.H. Stumpf
(Division of Molecular Biosciences, Centre for Bioinformatics Imperial College London)

Robust Inference for Systems and Synthetic Biology

Date:
2010.10.29 (Fri) 11:00-12:30
Place:
Advanced Research Laboratories, Room 410

Martin Hanczyc
(Univ. Southern Denmark, センター学外連携研究者)

油滴やベシクルを用いた人工細胞構築の最近の話題

Date:
2010.6.25 (Fri) 14:00-16:00
Place:
Advanced Research Laboratories, Room 410

センター研究会「生命のスペクトラム」

日時:
2013年5月18日(土) 10:00 - 17:00
場所:
東京大学駒場Iキャンパス 数理科学研究棟 大講義室
詳細:

Poster

シンポジウム「諸科学の統合と複雑系:哲学と自然科学の対話」

日時:
2012年10月10日(水) 17:00 - 19:00
場所:
理想の教育棟 K402教室
内容:
17:00 - 17:50 講演
クラウス・マインツァー(Klaus Mainzer)
ミュンヘン工科大学(科学哲学、複雑系の科学)
The Cause of Complexity in Nature -- An Analytical, Computational, and Philosophical Approach
Abstract (pdf)

18:00 - 19:00 パネルディスカッション
パネリスト
クラウス・マインツァー
金子邦彦
菅原正
池上高志
司会:澤井哲
詳細:

Poster

複雑系生命システム研究センター若手研究交流会

大学院生、ポスドクを中心としたポスタープレゼンテーションの研究会を行います。途中から軽食と飲み物も用意します。

交流機会の少ない、異分野の若手研究者同士で、研究交流や率直な意見交換を行うことが目的です。 広く生命科学に関する研究をおこなっている、多くの若手研究者の参加を歓迎します。

日時:
2011年10月29日(土) 14:00 - 18:00 (13:30 - 受付)
場所:
東京大学駒場Iキャンパス 生協食堂2階
参加費:
大学院生・学部生 1500円
ポスドク 2000円
その他 3000円
お知らせ:
ポスターサイズは横90cm×縦180cm以内で作成して下さい。
発表なしの当日参加も受け付けます。事前登録なしの発表も可能ですが、ポスターボードの数に限りがあります。
連絡先:
rccsb.wakate @ gmail.com
世話人:野添 嵩(大学院総合文化研究科広域科学専攻修士1年)

RCCSB_Wakate_Poster

第4回学融合ビジュアライゼーションシンポジウム

日時:
2011年1月11日(火) 午前10時〜
場所:
駒場Iキャンパス アドバンストリサーチラボラトリー 大会議室(410)
詳細:
こちらをご参照ください。

RCCSB symposium on cellular biophysics with guests from Niels Bohr Institute and Bangalore

日時:
2010年12月7日-8日
場所:
駒場Iキャンパス アドバンストリサーチラボラトリー 大会議室(410)

Symposium