Paris Biological Physics Community Day 2014

The Paris Biological Physics Community Day (PBPCD 2014) is a conference organized by young researchers of biological physics in the Paris area. We aim to bring together researchers in biophysics in the Paris area in order to create an opportunity for meeting and sharing knowledge. The meeting is intended for physicists working in diverse areas of biology. You are welcome to join us! It’s going to be a day of conviviality and scientific enthusiasm, we envision to have a dynamic and informal atmosphere. In the program the talks of the invited speakers are interleaved with short presentations by young investigators; the schedule includes pizza for lunch, coffee and a closing cocktail. The event is organized on behalf of GDRI (Groupement de recherche international "Evolution, Regulation and Signaling") which also provides the funding. There is no registration fee and no prior registration is mandatory!

Download the poster

For any questions, please contact:
paris-young-biophysics-community-meeting-organizers@googlegroups.com

Invited speakers:

Organizers:

A. Coucke^{1, 2}, E. De Leonardis^{1, 2}, Y. Elhanati¹ , M. Figliuzzi², S. Grigolon³ , H. Jacquin¹ , G. Malaguti⁴ , Vittore Scolari^{2, 5
1}Ecole Normale Superieure, Paris, ²Biologie Computationnelle et Quantitative, Paris, ³LPTMS, Université Paris-Sud XI, ⁴Institut Curie, ⁵NCBS, Bangalore

Program:

9h25 - 9h30 Welcome

9h30 - 11h00 1st session

• Ergodic protein dynamics and universal fluctuations in cell populations
  Abstract ->
  
  Naama Brenner, Technion - Israel Institute of Technology, Israel
  The copy number of any protein fluctuates among cells in a population; characterizing and understanding these fluctuations is a fundamental problem in biophysics. Much work has been devoted to relating this variation to specific known microscopic processes inside the cell. Despite significant advancement in the field, how the many cellular processes integrate to shape the population-level variation remains unclear.
  We have developed a complementary approach that aims at a phenomenological characterization of protein variation directly at the population level. This approach highlights the integrated effect of all processes rather than the details of any specific one. Using snapshots of large populations of bacteria and yeast cells, we show that protein distributions measured under a broad range of biological realizations collapse to a single non-Gaussian curve under scaling by the first two moments. Moreover in all experiments the variance is found to depend quadratically on the mean, showing that a single degree of freedom determines the entire distribution. Using continuous measurements from individual bacteria over tens of generations, we show that single-cell protein trajectories sample the available states with the same universal distribution shape as the population, i.e. protein fluctuations are contain an ergodic component; they do, also, contain a component with long-term memory. Analysis of temporal trajectories reveals that a single effective random variable, sampled once each cell cycle, is sufficient to reconstruct the distribution from the trajectory. This in turn implies that cellular microscopic processes are strongly buffered and population protein distributions are insensitive to details of the intracellular dynamics, providing a mesoscopic-scale understanding of the observed universality.
• Dynamics of transcription during early Drosophila patterning
  Abstract ->
  
  Teresa Ferraro, ENS & Institut Curie, Paris
  The early Drosophila embryo is an ideal model to understand the transcriptional regulation of well-defined patterns of gene expression in a developing organism. The first step in the spatial organization of an organism consists of the establishment of the Anterior-Posterior polarity axis. In the fruit fly, the maternal morphogen Bicoid (Bcd) forms a spatial gradient with high concentration at the anterior pole that exponentially decreases toward the posterior. Bcd activates the target gene hunchback (hb) which shows an homogeneous and sharp a domain of expression in the anterior half of the embryo.
  Recently my biology collaborators developed a technique to observe live transcription in transgenic flies, by genetically modifying the hb gene with an MS2-MCP fluorescent tag, opening the possibility of studying the dynamics of gene pattern formation. We used the MS2-MCP system to visualize nascent transcripts expressed from the typical hb promoter under the control of the morphogen Bcd. We developed a segmentation and tracking algorithm to analyze the data.
  We find that the transgene used shows an hb expression as homogeneous as the non-modified hb gene in the anterior half of the embryo, but unlike non-modified hb it is also shows activity in the posterior, though more heterogeneously and more transiently than in the anterior. We propose that the establishment of the hb pattern relies on Bcd-dependent lengthening of transcriptional activity periods in the anterior and may require two distinct repression mechanisms in the posterior.
• Combined collapse by bridging and self-adhesion in a prototypical polymer model inspired by the bacterial nucleoid.
  Abstract ->
  
  Vittore Scolari, LCQB & UPMC & NCBS, Paris
  Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework combining solely these two ingredients, in order to characterize their joint effects. Specifically, we study a simple polymer physics computational model with weak ubiquitous short-ranged self attraction and stronger sparse bridging interactions. Combining theoretical arguments and simulations, we study the general phenomenology of polymer collapse induced by these dual contributions, in the case of regularly-spaced bridging. Our results distinguish a regime of classical Flory-like coil-globule collapse dictated by the interplay of excluded volume and attractive energy and a switch-like collapse where bridging interaction compete with entropy loss terms from the looped arms of a star-like rosette. Additionally, we show that bridging can induce stable compartmentalized domains. In these configurations, different “cores” of bridging proteins are kept separated by star-like polymer loops in an entropically favorable multi-domain configuration, with a mechanism that parallels micellar polysoaps. Such compartmentalized domains are stable, and do not need any intra-specific interactions driving their segregation. Domains can be stable also in presence of uniform attraction, as long as the uniform collapse is above its theta point.

11h00 - 11h30 Coffee Break

11h30 - 13h00 2nd session

• Fundamental limits to chemical sensing
  Abstract ->
  
  Pieter Rein ten Wolde, AMOLF, Netherlands
  Cells can measure chemical concentrations with extraordinary precision. This raises the question what is the fundamental limit to the accuracy of chemical concentration measurements. In this talk, I will show that the sensing accuracy of passive signaling systems is limited by the number of receptors; a downstream processing network can never increase the sensing precision. Non-equilibrium systems can beat this limit. However, this requires receptors and their integration time, downstream molecules, and energy. Each resource imposes a fundamental sensing limit, which means that the sensing precision is bounded by the limiting resource and cannot be enhanced by increasing another resource. This result yields a new design principle, namely that of optimal resource allocation in cellular sensing. It states that in an optimally designed system, each resource is equally limiting, so that no resource is wasted. We find that the chemotaxis network of E. coli obeys this principle, indicating a selective pressure for the efficient design of cellular sensing systems.
• Decoding place cell activity: how and what?
  Abstract ->
  
  Sophie Rosay, Ecole Normale Superieure, Paris
  Place cells are neurons in the hippocampus which get their name from the strong correlation between their activity and the animal's position in space. Hence, it is in principle possible to “decode” this position, that is to retrieve it from the lone observation of place cell activity. I will review the ways this problem has been tackled, the difficulties that arise and some attempts to circumvent them in the analysis of single-unit recordings (work done with Remi Monasson, data from the Moser lab in Trondheim).
• A spatially distributed code in the retina
  Abstract ->
  
  Stéphane Deny, Institut de la vision & UPMC
  We are interested in the structure of the code with which the retina sends the visual information to the brain. We show that the output neurons of the retina, the so-called ganglion cells, code for a much larger region of the visual field when there is motion than when the scene is static. The fact that ganglion cells code for visual events happening an order of magnitude away from their static receptive field raises a number of issues concerning the neural code in the retina. A first problem is that such a distributed code can easily lead to ambiguities. How does the brain distinguish an event happening in the receptive field of a cell from an event happening 30° away from it? Another puzzling question is: how will the cell respond when it is solicited at the same time by a scene happening in its receptive field and by another scene in its periphery? Will it simply add the central response to the peripheral one linearly? Or will it do something subtler, such as prioritizing the central response on the peripheral one? Answers are in the talk.

13h00 - 14h30 Lunch Break (ENS, 24 rue Lhomond, Cafétéria, ground floor)

14h30 - 16h00 3rd session

• Active mechanics of epithelia during morphogenesis
  Abstract ->
  
  Guillaume Salbreux, MPI, Dresden, Germany
  Epithelial tissues are dynamically remodeled during development due to forces generated in the cells, cellular rearrangements, and cell division and apoptosis. Such remodeling leads over long timescales to reorganization of the tissue, allowing to establish the shape of the organism. In this work, we introduce a physical description of the slow timescale behavior of an epithelium. We obtain hydrodynamic constitutive equations describing the continuum mechanics of an epithelium in two dimensions on spatial scales larger than a cell. Within this framework, topological rearrangements relax elastic stresses in the tissue and can be actively triggered by internal cell processes. Using segmentations of the Drosophila wing tissue flows at pupal stage, we analyze experimental coarse-grained patterns of cell shape and tissue shear and relate experimental observations to our continuum description.
• The role of the environment in cargo transport by teams of molecular motors
  Abstract ->
  
  Sarah Klein, Université Paris XI
  For various intracellular cargos bidirectional motion is observed. Most times this transport is mediated by teams of molecular motors moving in opposite direction. It remains an open question how the cell can ensure efficient transport by relying on this biased stochastic process. We present a model which takes explicitly into account the elastic coupling of the cargo with each motor. In focus is here the analysis of the influence of the cellular properties. By varying those parameter the cell can control the bias in a counter-intuitive manner. Furthermore, we observe in our one dimensional model sub- and superdiffusion on short and intermediate time scales, respectively, due to a temporal correlation in the cargo displacement.
• Understanding the self-assembly of filamentous actin into higher order structures
  Abstract ->
  
  Giulia Foffano, Université Paris XI
  Filamentous actin is one of the main components of the cytoskeleton. Cells regulate F-actin self-assembly into various structures -- mediated by crosslinkers - to control their own mechanical properties. Reconstituted actin - crosslinkers solutions have been observed to aggregate into structures ranging between homogeneous networks of filaments to highly bundled phases. It has been shown experimentally [1] that equilibrium physics cannot account for these structures, and a comprehensive understanding of the phenomenology of F-actin self-assembly is still lacking. We develop a mean-field model taking into account the competition between the two fundamental mechanisms of bundling and of steric hindrance, that predicts the existence of a bundled phase -- corresponding to thermodynamic equilibrium - and of a kinetically arrested phase, consisting of a homogeneous network of filaments [2].
  More complex phases are observed in experiments (see e.g. [3,4]) and are often characterised by spatial inhomogeneities which are not accounted for in a mean-field description. We hypothesise that their emergence is still to be attributed to the competition between bundling and steric hindrance between actin filaments. In the longer term we hope that our simulation methodology will help understand the influence of different types of cross-links, the actin assembly kinetics as well as actin severing and treadmilling on the microstructure of the cytoskeleton.
  
  [1] Falzone T. T., Lenz M., Kovar D. R., and Gardel M., Nature Communications 3, 861 (2012).
  [2] Levernier, N. “A mean-field model for the microstructure of the cell cytoskeleton”, Rapport de stage de recherche, 2013 - internal communication.
  [3] Lieleg O., Schmoller K. M., Cyron C. J., Luan Y., Wall W., and Bausch A., Soft Matter 5, 1796-1803 (2009).
  [4] Nguyen L. T. and Hirst L., Phys. Rev. E 83, 031910 (2011).

16h00 - 16h30 Coffee Break

16h30 - 18h00 4th session

• From Patterns to Principles: Statistical Physics of Ecological Networks
  Abstract ->
  
  Samir Suweis, Università di Padova, Italy
  In the last decades ecologists have unveiled several macroscopic patterns, emerging from ecosystems self-organization, that show a surprising simplicity reminiscent of many physical systems and that may represent a signature of the “universality” of the processes underlying ecosystem evolution. Nevertheless, understanding an ecosystem is a formidable many-body problem and the study of ecological communities represents a fantastic challenge for statistical physicists. One has an interacting system, made up of individuals of various species with imperfectly known interactions and characterized by a wide range of spatial and temporal scales. The topological properties of the ecological interaction networks have been the subject of sparkling research and they indicate non-random pattern of community organization. Indeed, ecologists have collected extensive data on species interactions showing that, independently of species composition and latitude, mutualistic networks (such as plant-pollinator systems) have nested architectures (specialists interact with proper subsets of the nodes with whom generalists interact), whereas antagonistic communities are preferentially compartmentalized (species are divided in small groups wherein interactions are more accentuated than between different groups). Despite sustained efforts to explain the observed network structures, the elucidation of a fundamental mechanism that drives network architectures has been elusive.
  In my talk I will propose an unifying theoretical framework that can provide a parsimonious and general explanation for the emergent structural and dynamical properties of ecological networks.
• From sequence co-evolution to protein interaction: An inverse statistical-mechanics approach
  
  Abstract ->
  
  Christoph Feinauer, Politecnico di Torino & Université Paris VI
  In recent years, the method of predicting contacts between protein residues by inferring statistical mechanics models on multiple sequence alignments has met with spectacular success. In this talk, I will review the main points of the approach and show how to extent the method to the prediction of protein-protein interactions.
• Liquid-gas transition in polar flocking models
  Abstract ->
  
  Alexandre Solon, Université Paris VII
  To understand the onset of collective motion in large groups of animals (like bird flocks, fish shoals, etc.), one can model these systems as collections of self-propelled particles that interact locally to align their direction of motion. When the noise on the alignment interaction is reduced, one goes from a disordered system to a state of collective motion, with individuals moving globally in the same direction, through the so-called flocking transition.
  We will show that the flocking transition is very similar to an equilibrium liquid-gas transition. In doing so, we shall distinguish between two classes of models when particles are self-propelled along any direction in space or only along one preferred direction. These two different symmetry classes feature qualitatively different fluctuations in the ordered state, and surprisingly these fluctuations control the shape of the system at phase coexistence.

18h00 Cocktail (ENS, 45 rue d’Ulm, salle Normal'Cafe)

The program and website of last year conference can be find at this link.

Important: The talks will be held at the Centre Culturel Irlandais, the lunch the Cafétéria, ground floor at ENS-Physique and the cocktail in Salle Normal'Cafe at the main ENS building. See the map for directions.

Click here to get the map of the ENS main building
The cocktail will be held in Normal'cafe, which is located at the bottom of the restaurant

Funding and acknowledgments:

	Groupement de recherche international "GDRI Evolution, Regulation and Signaling" Regulating Flies, European Research Council
Marco Cosentino Lagomarsino, Vincent Hakim, Herve Isambert, Olivier Martin, Thierry Mora and Aleksandra Walczak

We also thank for helping the organization of the event:

Marco Cosentino Lagomarsino - Genomique des Microorganismes, Genomic Physics Group
Aleksandra Walczak - Laboratoire de Physique Theorique, Ecole Normale Supérieure
Viviane Sebille and Sandrine Patacchini - for their support, without them it would not have been possible to organize this meeting