SpeakersandAbstracts

Speakers and Abstracts

We have brought together researchers who have the potential to take the lead in quantitative biology as next-generation leaders.
次世代のリーダーとして定量生物学を牽引していくポテンシャルを有する研究者が揃っています。大御所を並べただけではない、定量生物学の会ならではの講演者のラインナップになっております。

Session: Quantity - FORCE -

Date and Time: Jan. 9th 13:10-15:25

Otger Campàs ( University of California, Santa Barbara, USA )

油滴を利用して、生体組織の力学を"その場で"測る。

Quantifying tissue mechanics in vivo and in situ

Mechanical cues play a critical role during tissue morphogenesis and organ formation in the embryo. Despite their relevance in sculpting functional embryonic structures, very little is known about the mechanisms by which tissue mechanics affects/controls developmental processes, mainly because it has not been possible to quantify tissue mechanics within developing tissues in vivo. In this talk, I will present two new techniques that permit direct quantification of (1) cell-generated mechanical forces and (2) the mechanical properties of the cellular microenvironment, in situ within living tissues and developing organs. Using these novel techniques, we quantify the cell-generated mechanical stresses and the local mechanical properties within cell aggregates, living mouse mandibles and live zebrafish embryos.

Selected refs: Campàs et al. Nat. Methods (2014); Campàs et al. BPJ (2012); Campàs et al. PNAS (2010)

Kaoru Sugimura ( Kyoto University, Japan )

ベイズ統計学をつかって、見えない力を見る。アクチン結合タンパク質の力生成能と力感知能に注目して、形態形成の力学制御の分子メカニズムに迫る。

Dissecting the mechanical control of Drosophila wing shape determination

Tissues acquire their unique shape and size through a series of deformations. Tissue deformation consists of changes in cell shape, number, and position, which are triggered by forces acting between cells and by biochemical signaling. Reciprocal feedback is present at and among the molecular, cellular, and tissue scales. We sought to clarify the emergence of the Drosophila wing shape from these multi-scale feedback regulations. In the symposium, I shall discuss our ongoing research on the unified quantification of epithelial tissue development and molecular dissection of force sensing/generation by F-actin during directional cell rearrangement.
1. Quantifying tissue mechanics and kinematics in an integrated way We have developed and validated key techniques to quantify the multi-scale dynamics underlying wing shape determination, including Bayesian force inference, whole-wing imaging, and texture tensor formalism (Ishihara and Sugimura, 2012; Ishihara et al., 2013; Sugimura et al., 2013; Guirao et al., 2015). By analyzing space-time maps of tissue deformation, tissue stress, and cell dynamics in control and mutant tissues, we evidenced unexpected interplays between patterns of tissue elongation, cell division and stress. Our methods provide a basis for comprehensive analyses of mechanical control of epithelial tissue development.
This work is done in collaboration with F. Graner, Y. Bellaïche, B. Guirao, S. Rigaud, P. Marcq, and S. Ishihara.
2. Dissecting molecular mechanism of extrinsic force-driven cell rearrangement During tissue morphogenesis, cells change their relative positions along the tissue axis by remodeling cell contact surfaces. This process, called directional cell rearrangement, shapes a tissue and develops its multi-cellular pattern. In the Drosophila pupal wing, anterior-posterior cell contact surfaces shrink and are remodeled to form new proximal-distal cell contact surfaces from 21 hr APF onwards. We previously reported that the extrinsic stretching force provides directional information for assignment of the orientation of cell rearrangement, leading to tissue elongation and hexagonal cell packing (Sugimura and Ishihara, 2013). However, the mechanisms by which cells sense the extrinsic forces and transmit the information to the molecular machinery for cell rearrangement remain unknown. To answer these questions, we performed screening of actin-binding proteins. Our results suggest that AIP1, cofilin, and coronin-1 regulate F-actin to trigger the extrinsic force-driven cell rearrangement.
This work is done in collaboration with K. Ikawa.

Selected refs: Guirao et al. eLife, in press; Sugimura and Ishihara. Development (2013); Ishihara and Sugimura. J. Theor. Biol. (2012)

Emmanuel Farge ( Institut Curie, France )

原腸形成過程は進化的に広くみられるが、コアとなる誘導シグナルははっきりしていなかった。それがなんと機械的応力である可能性が示された。

From mesoderm mechanotransductive evolutionary origins to tumourogenic mechanical induction

Bilaterians are complex organisms, characterized by the existence of a mesoderm tissue from which most of animal complex organs develop. Mesoderm emerged 570 millions years ago from cnidarians that are characterized by and ectoderm and an endoderm only. The lack of conservation of biochemical signalling proteins upstream of early embryonic mesoderm differentiation across bilaterians prevents to answer the question of the signal having been at the origin evolutionary origin of mesoderm emergence and complex animals. Here we found the mechano-transductive phosphorylation of the Y654 site of β-catenin by the first morphogenetic movements of embryogenesis, leading to its release into the cytoplasm and nucleus, as involved and conserved in earliest mesoderm differentiation in the vertebrate zebrafish and un-vertebrate Drosophila, two species having directly diverged from the last common ancestor of bilaterians. We proposed mechanical activation of β-catenin signalling as having initiated the evolutionary transition to mesoderm differentiation and complex animals evolutionary emergence[1].
We additionally find mechanical activation of β-catenin as involved in the mechanical activation of tumorogenic biochemical pathways, in the healthy epithelium compressed by the neighbouring tumour, in response to tumour growth pressure in vivo [2-4].

1 Brunet, T. et al. Evolutionary conservation of early mesoderm specification by mechanotransduction in Bilateria. Nature communications 4, doi:10.1038/ncomms3821 (2013).
2 Whitehead, J. et al. Mechanical factors activate beta-catenin-dependent oncogene expression in APC mouse colon. HFSP journal 2, 286-294, doi:10.2976/1.2955566 (2008).
3 Fernandez-Sanchez, M. E., Barbier, S. & al., e. Mechanical induction of the tumorogenic β-catenin pathway by tumour growth pressure. Nature, 10.1038/nature14329 (2015).
4 Fernandez-Sanchez, M. E., Brunet, T., Roper, J. C. & Farge, E. Mechanotransduction's Impact in Animal Development, Evolution, and Tumorigenesis. Annu Rev Cell Dev Biol, doi:10.1146/annurev-cellbio-102314-112441 (2015).

Background : soft matter biophysics, developmental biology Websites : http://cvscience.aviesan.fr/cv/818/emmanuel-farge, http://umr168.curie.fr/en/Farge-group

Selected refs: Fernández-Sánchez et al. Nature (2015); Brunet et al. Nat. Commun. (2013); Farge. Curr. Biol. (2003)

Session: Quantity - SYMMETRY I -

Date and Time: Jan. 10th 9:00-12:00

Noriko Hiroi ( Keio University, Japan )

Anisotropy shaped by and for the dynamic distribution of heat
abstract:
Selected refs: Sumiyoshi et al. Front Physiol. (2015); Hiroi et al. Front Physiol. (2014)

Nicolas D Plachta ( IMCB, Singapore )

マウス初期胚の対称性の破れに定量イメージングで迫る

Seeing how mammalian life starts: Quantitative imaging in live mouse embryos
abstract:
Selected refs: Samarage et al. Dev. Cell (2015); Fierro-González et al. Nat. Cell Biol. (2013); Plachta et al. Nat. Cell Biol. (2011)

Yusuke Maeda ( Kyushu University, Japan )

構成的手法から探る生命システムの構築原理：生命の起源と人工細胞のダイナミクス

title: tba
abstract:
Selected refs: Fukuyama et al. Langmuir (2015); Maeda et al. PNAS (2012); Maeda et al. PRL (2011)

Zoher Gueroui ( École Normale Supérieure, France )

マグネトジェネティクス：情報流れの時空間制御が明らかにする自己組織化の原理

Studying cytoskeleton symmetry breakings using cellular reconstitution of cytoplasmic extracts and biophysical tools

Studying cytoskeleton symmetry breakings using cellular reconstitution of cytoplasmic extracts and biophysical tools
The cytoskeleton is essential for the function of cellular processes such as cell division and cell migration. Cytoskeleton fibers participate in the maintenance of cell internal organization and play essential roles in breaking symmetry and establishing cell polarity. We have developed an in vitro system capturing the spatial organization of cytoskeleton filaments within a geometry that mimic the cellular environment. This system, based on the cellular reconstitution by confinement of Xenopus cytoplasmic extracts, is used to examine simple aspects of symmetry breaking.
(1) We will first discuss how geometrical confinement and mechanical properties influence the self-organization of microtubules and molecular motors.,br> (2) In most physiological situations, the asymmetric fate of a system follow from certain “cues” that pre-exist before symmetry is broken. These cues are either localized signals often encoded in protein concentration gradients, or “landmarks” inherited from the system’s history. For instance, gradients of signaling proteins and protein localization can be key for cell-fate decision and asymmetric cell division. In order to control the spatiotemporal localizations of these cues, we are using magnetic nanoparticles to spatially localize signaling proteins within confined extracts. This system is used to examine how the spatial localization and clustering of RCC1/RanGTP proteins feedbacks on microtubule spatial organization.

Selected refs: Hoffmann et al. Nat. Nanotech. (2013); Pinot et al. PNAS (2012).

Session: Quantity - SYMMETRY II -

Date and Time: Jan. 10th 13:30-15:45

Cliff Brangwynne ( Princeton University, USA )

Cliff Brangwynne博士は物理学の視点から細胞生物学に新しいコンセプトを導入し、近年、大きなインパクトを与えて続けている新進気鋭の研究者です。「相転移/phase transition」は、例えば水分子が沸点や融点をまたぐと固体、液体、気体と急激に状態を変化させるような物理学のコンセプトです。Brangwynne博士は、細胞内で核小体や生殖顆粒が形成・消滅する過程を、この相転移現象として理解できることを明らかにしています。

Measuring the Intracellular Dew Point: The Physics and Biology of Membrane-less Organelles

RNP bodies are RNA and Protein-rich, membraneless organelles that play important roles in regulating gene expression. The largest and most well-known nuclear RNP body is the nucleolus, whose primary function in ribosome biogenesis makes it key for cell growth and size homeostasis. The nucleolus and other nuclear bodies behave like liquid-phase droplets. Increasing evidence suggests they condense from the nucleoplasm by concentration-dependent phase separation. However, nucleoli actively consume chemical energy, and it is unclear how such nonequilibrium activity might impact classical liquid–liquid phase separation. We combine in vivo and in vitro experiments with theory and simulation to characterize the assembly and disassembly dynamics of nucleoli in early Caenorhabditis elegans embryos. In addition to classical nucleoli that assemble at the transcriptionally active nucleolar organizing regions, we observe dozens of “extranucleolar droplets” (ENDs) that condense in the nucleoplasm in a transcription-independent manner. We show that growth of nucleoli and ENDs is consistent with a first-order phase transition in which late-stage coarsening dynamics are mediated by Brownian coalescence and, to a lesser degree, Ostwald ripening. By manipulating C.elegans cell size, we change nucleolar component concentration and confirm several key model predictions. Our results show that rRNA transcription and other nonequilibrium biological activity can modulate the effective thermodynamic parameters governing nucleolar and END assembly, but do not appear to fundamentally alter the passive phase separation mechanism.

selected refs: Berry et al. PNAS (2015); Feric and Brangwynne. Nat. Cell Biol. (2013); Brangwynne et al. Science (2009)

Akatsuki Kimura ( National Insititute of Genetics, Japan )

多数の小さな分子たちによってどのように細胞レベルでの空間的な秩序ができるのかを研究しています。本発表では、線虫C. elegansの細胞質流動を例に、流れの方向が定まらない（不安定）流動が、必ず（安定的に）生じるメカニズムについて発表します。

title: How a cell-wide cytoplasmic flow with unstable direction emerges reproducibly?
abstract:
selected refs: Kimura and Kimura. J. Cell Sci. (2012); Niwayama et al. PNAS (2011); Kimura and Kimura. PNAS (2011)

Brian Stramer ( King's College London, UK )

細胞のミクロとマクロを定量的 in vivo イメージングでつなぐ：細胞内アクチン動態・張力から細胞の巨視的挙動へ

Intercellular forces orchestrate contact inhibition of locomotion

Contact Inhibition of locomotion (CIL), a process where migrating cells repel upon collision, was first observed in cultured cells more than 60 years ago. We have recently revealed that Drosophila hemocytes have precise CIL interactions in vivo, which lead to their subsequent developmental patterning. To quantify the dynamics of collisions we have recently developed techniques to analyze the exact velocity and acceleration changes surrounding the contact inhibition process. This analysis has revealed rapid and synchronous kinematic changes (over second timescales) during collisions, which further highlight the precision of the CIL response.
To examine the cause of such intriguing CIL kinematics we have examined the actin network dynamics surrounding collisions. We adapted a pseudo-speckle microscopy technique to track the retrograde flow dynamics of the actin cytoskeleton during hemocyte developmental dispersal. Non-colliding cells show rapid retrograde flow (3-4μm/min), which moves centripetally towards the cell body where actin flow significantly decreases. Analysis of collisions reveals that the actin flow undergoes significant temporal and spatial reorganization across the entire lamella, which occurs simultaneously in colliding partners. A region of low retrograde flow develops perpendicular to the leading edge spanning colliding cells, and upon repulsion, retrograde flow simultaneously spikes in both lamellae. These dynamics suggest that hemocytes are becoming transiently coupled during CIL via a clutch-like mechanism, analogous to the integrin clutch encountered in migrating cells.
Exploiting the precise retrograde flow displacements, we subsequently modelled the cytoskeletal stresses in freely moving and colliding cells using a linear viscoelastic model. Preliminary results show that non-colliding cells have high regions of network stress surrounding the cell body, explaining the convergence of the retrograde flow within this region. Upon collision, forces are redistributed from the cell body to the leading edge along the region of low retrograde flow. This region of stress becomes decorated with myosin II suggesting the development of a transient stress fiber as colliding cells pull on each other during the collision. We speculate that this “haptic feedback” mechanism, and subsequent release of lamellar tension, explains the precise and synchronous nature of the contact inhibition response.

Selected refs: Davis et al. Cell (2015); Davis et al. Development (2012); Stramer et al. J. Cell Biol. (2010)

Session: Quantity - INFORMATION -

Date and Time: Jan. 10th 16:00-19:00

Satoshi Sawai ( the University of Tokyo, Japan )

title: tba
abstract:
Selected refs: Nakajima et al. Nat. Commun. (2014); Taniguchi et al. PNAS (2013); Gregor et al. Science (2010)

Damon Clark ( Yale University, USA )

ショウジョウバエの視覚神経回路：動きを読みだす情報処理に迫る定量生物学

Dissecting neural circuits for motion estimation in Drosophila
abstract:
Selected refs: Fitzgerald and Clark. eLife (2015); Clark et al. Nat. Neurosci. (2014); Clark et al. Neuron (2011);

Yuki Tsukada ( Nagoya University, Japan )

定量と再構築から理解する感覚神経細胞の環境認識

Quantification and reconstruction of thermosensory neuronal processing in C. elegans
abstract:
Selected refs:

David Umulis ( Purdue University, USA )

勾配情報が作り出す発生メカニズム

Quantification and modeling of BMP signaling during zebrafish embryo development

Bone Morphogenetic Proteins (BMPs) act in developmental pattern formation as a paradigm of extracellular information that is passed from an extracellular morphogen to cells that process the information and differentiate into distinct cell types based on the morphogen level. In addition to their role in development, BMPs play an important role in tissue homeostasis and mutations in the BMP family are associated with a number of human cancers. Numerous extracellular modulators and feedback regulators establish and control the BMP signaling distribution along the dorsal-ventral (DV) embryonic axis in vertebrates to induce space and time-dependent patterns of gene expression. To identify how the dynamic pattern is regulated during development, we have developed a seamless data-to-model integration and optimization strategy. First, the nuclear intensities of fluorescent stained Phosphorylated-Smad5 (P-Smad) are acquired for each nuclei in each embryo from staged populations to provide a quantitative time-course for the BMP signaling gradient. Next, the nuclei are segmented to yield quantitative point-clouds of P-Smad level at each nuclei. The individual point clouds are registered to similarly staged embryos using a process called Coherent Point Drift (CPD) and the registered populations provide rigorous quantification and comparison of phenotype. To delineate the mechanism of BMP signal inhibition by the secreted binding proteins Chordin (Chd), Noggin (Nog), and Follistatin (Flst), a mathematical model was developed and optimized against the population data for wild type and combinations of the Chd mutants with and without morpholino knockdown of Noggin and Follistatin. We found a model that reproduced the experimentally observed reliability of the patterning network for Chd LOF, and for Nog/Flst morpholino knockdown that was also consistent with the dramatic increase in signaling observed in Chd LOF, Nog/Flst knockdown. Models consistent with experimental behavior require that Chordin has a greater range than Noggin, that Noggin is not freely diffusible, and that Noggin rapidly binds available BMP ligands in the organizer region. We are continuing to experimentally test the model predictions and isolate the roles of Noggin and Follistatin to determine the extent of dorsal enrichment under different conditions.

Selected refs: Pargett et al. PLoS Comp. Biol. (2014); Peluso et al. Dev. Cell (2011); Umulis et al. Dev. Cell (2010)

Session: Quantities and Beyond -

Date and Time: Jan. 11th 9:00-11:00

Naoki Irie( the University of Tokto, Japan )

胚発生と進化の法則性として近年支持された砂時計モデル。この法則性を生み出すメカニズムの有力候補がみえてきた。

Double bladed aspect of gene recruitment to morphological evolution.
abstract:
Selected refs: Wang et al. Nat. Genetics (2013); Irie and Kuratani. Nat. Commun. (2011)

Yuichi Wakamoto ( the University of Tokyo, Japan )

1細胞ヒストリーの観点から適応度と遺伝子発現を捉え直す

Fitness and gene expression from the viewpoint of single-cell histories
abstract:
Selected refs: Wakamoto et al. Science (2013); Wakamoto et al. Evolution (2012); Tomita et al. Langmuir (2011)

Tetsuya J Kobayashi( the University of Tokyo, Japan )

「量」をつなぐ：情報から適応度まで

Linking quantities from information to fitness
abstract:
Selected refs: Kobayashi and Sughiyama. PRL (2015); Kobayashi. PRL (2011); Kobayashi. PRL (2010)

Tokyo Symposium: Force, Information and Dynamics: X factors shaping living systems
NIG International Symposium 2016 satellite workshop
Toyota Physical & Chemical Research Institute Workshop
Mishima Symposium: Quantitative Biology - force, information and dynamics