Paris Biological Physics Community Day 2013

The Paris Biological Physics Community Day (PBPCD 2013) 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! We recommend registration in order to allow us to estimate the size of the coffee order.

Download the poster

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

Invited speakers:

Organizers:

Alice Coucke^{1, 2}, Yuval Elhanati¹ , Ulisse Ferrari¹, Sophie Rosay¹ , Marc Santolini¹ , Vittore Scolari^{2, 3
1}Ecole Normale Superieure, Paris, ²Laboratorie Genomique des Microorganismes, Paris, ³NCBS, Bangalore

Program:

9h30 - 10h35 1st session

• Superfluid transfer of information in starling flocks
  Abstract ->
  
  Asja Jelic, ISC-Sapienza, Rome
  Turning flocks of starlings are a paradigm for a synchronized, rapid change of direction in moving animal groups. During this collective change of state fast transfer of information is the key factor to prevent cohesion loss and preserve robustness. However, the mechanism by which natural groups achieve such efficiency is currently not fully understood. In this talk I will present an experimental and theoretical study of starling flocks performing collective turns. We find that information to change direction propagates across the flock with a linear dispersion law and negligible attenuation, hence minimizing group decoherence. These results contrast starkly with current models of collective motion. Building on spontaneous symmetry breaking and conservation laws arguments, we formulate a new theory that is mathematically identical to that of superfluid flow in liquid helium. This theory not only explains the data, but also predicts that information transfer must be faster the stronger the group's orientational order, a prediction accurately verified by the data. Our results suggest that swift decision-making is among the adaptive drives for the strong behavioural polarization observed in many living groups.
• Causal network inference from local information-theoretic measures
  Severine Affeldt, Curie Institute, Paris

10h35 - 11h00 Coffee Break

11h00 - 12h25 2nd session

• Stepping and crowding of molecular motors: from theory to mRNA translation
  Abstract ->
  
  Luca Ciandrini, Universite Montpellier II
  Molecular motors are remarkable molecular machines capable to convert energy (e.g., from ATP or GTP) into mechanical movement. By considering particles with an internal degree of freedom that mimics their enzymatic (stepping) cycle, we extend standard driven lattice gas models describing the movement of motors on a linear substrate. We show that the kinetic states induce non trivial collective behaviours of processive motors, and strongly influence the randomness of the system.
  
  We used our model to investigate the translation of mRNAs by ribosomes, one of the last stages of genes expression. Understanding the impact of ribosomal traffic on mRNAs and its regulation is key to unravel the determinants of translation efficiency and protein synthesis. This analysis reveals that codon arrangement, rather than simply codon usage, has a key role in determining translational efficiency. Moreover, the analysis predicted physiological parameters of the translation process that can be related to physical properties of the system (as the three-dimensional conformation of the mRNA) or the balance between supply and demand of resources (as ribosome abundances).
• Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly
  Abstract ->
  
  Jonas Ranft, Ecole Normale Superieure, Paris
  Epithelial spreading is a common and fundamental aspect of various developmental and disease-related processes such as epithelial closure and wound healing. A key challenge for epithelial tissues undergoing spreading is to increase their surface area without disrupting epithelial integrity. In earlier work, we highlighted the importance of tissue mechanical properties in growth phenomena and how these are in turn influenced by cell division and apoptosis. Combining experimental and theoretical approaches, we show here that orienting cell divisions by tension constitutes an efficient mechanism by which the enveloping cell layer (EVL) releases anisotropic tension while undergoing spreading during zebrafish epiboly. We also found that in the absence of tension-oriented cell divisions and in the presence of increased tissue tension, EVL cells undergo ectopic fusions, suggesting that the reduction of tension anisotropy by oriented cell divisions is required to prevent EVL cells from fusing. We conclude that cell-division orientation by tension constitutes a key mechanism for limiting tension anisotropy and thus promoting tissue spreading during EVL epiboly.
• Network function shapes network structure: the case of the Arabidopsis flower Organ specification genetic network
  Abstract ->
  
  Adrien Henry, UMR du Moulon INRA, Gif-sur-Yvette
  The reconstruction of many biological networks has allowed detailed studies of their structural properties. Several features exhibited by these networks have been interpreted to be the result of evolutionary dynamics. For instance the degree distributions may follow from a preferential attachment of new genes to older ones during evolution. Here we argue that even in the absence of any evolutionary dynamics, the presence of atypical features may follow from the fact that the network implements certain functions. To examine this network function shapes network structure scenario, we focus on the Arabidopsis genetic network controlling early flower organogenesis in which gene expression dynamics has been modelled using a Boolean framework. Specifically, for a system with 15 master genes, the phenotype consists of 10 experimentally determined steady-state expression patterns, considered here as the functional constraints on the network. The space of genetic networks satisfying these constraints is sometimes referred to as the neutral or genotype network. We sample this space using Markov Chain Monte Carlo which allows us to demonstrate how the functional (phenotypic) constraints shape the gene network structure. We find that this shaping is strongest for the edge (interaction) usage, with effects that are functionally interpretable. In contrast, higher order features such as degree assortativity and network motifs are hardly shaped by the phenotypic constraints.

12h25 - 14h00 Lunch Break (ENS, 24 rue Lhomond, salle Conf IV)

14h00 - 15h05 3rd session

• Heredity in evolution and evolution of heredity
  Abstract ->
  
  Olivier Rivoire, Universite Grenoble I
  I will motivate and present an analytically solvable model for studying the generation and transmission of new variations in populations of organisms subject to changing selective pressures.
• Phenotypic diversity during adaptation measured with digital millifluidic
  Abstract ->
  
  Denis Cottinet, Ecole Superieure de Physique et de Chimie Industrielles, Paris
  In this talk, I will present the millifluidic system we developed in order to measure the phenotypic composition in a population of microorganisms. It enable us to measure the growth curves from 1000 isolated individuals with highly homogeneous conditions. We applied this phenotypic analysis to populations facing an environmental transition and we follow the population dynamics.

15h05 - 15h30 Coffee Break

15h30 - 16h35 4th session

• Statistical mechanics of unknown unknowns
  Abstract ->
  
  Yasser Roudi, NTNU Trondheim
  Our understanding of complex systems is typically limited by the fact that we only see a fraction of the variables describing these systems: we only see parts of a financial market, we typically only see and analyze subparts of a protein protein interaction network, and we can only record from the activity of few cells in the brain; a potentially large number of variables in these systems are not directly observed and measured. In addition to the existence of unknown (hidden) variables, we face the problem that we cannot even monitor the known (observed) variables for a very long time, that is, we may have under-sampled data. In many cases we may not even know that other variables beyond what we see exist and influence our system, that is we may be dealing with "unknown unknowns". What is the effect of this incomplete data? This question can be posed as a problem of inference in the presence of latent variable, something that people in machine learning are very interested in. In this talk, I will describe some results on how not knowing the relevant variables influences our effort in modeling complex systems. I will describe recent advances in statistical modeling of data in which by using techniques from non-equilibrium statistical physics we can build efficient approaches to take into account the influence of hidden variable.
  
  References.
  
  B. Dunn, Y. Roudi (2013) Physical Review E
  M. Marsili, I. Mastromatteo, Y. Roudi (2013) Jour. Stat. Mech
  J. Tyrcha, J. Hertz (2013) arXiv:1301.7274v1
• Inferred model of the prefrontal cortex activity unveils task-related coupling potentiations and cell assemblies
  Abstract ->
  
  Gaia Tavoni, Ecole Normale Superieure, Paris
  Memories are thought to be formed through modifications of synaptic couplings, allowing specific groups of neurons to co-activate, the so-called cell assemblies. In this talk, I will present a procedure to identify both structural (synaptic coupling potentiation) and functional (cell assembly activation) signatures of the learning of a task from the spiking activity of cell populations. Our approach is based on the inference of statistical couplings reproducing the pairwise correlations between cells. Comparing the statistical couplings in the prefrontal cortex of a behaving rat between different epochs (Sleep phase before the Task, Task, Sleep after Task) we unveil specific coupling potentiations and relate them to the creation of a new cell assembly, evoked in the Slow-Wave-Sleep (SWS) periods of the Sleep Post epoch (replay phenomenon), and absent in the Sleep Pre epoch. A large-scale analysis across more than one hundred sessions allows us to quantify the dependence of the observed replay on the number of recorded cells. Besides the application to the specific set of data considered here, we think that our approach could be of general interest to identify the presence of co-activated groups of neurons and to understand their relation with learning, one central topic in Neurosciences.

16h35 - 16h45 Break

16h45 - 17h50 5th session

• Thermodynamic limits on noisy cellular sensing
  Abstract ->
  
  Sorin Tanase-Nicola, BMC Uppsala
  Living systems gather and transmit information about the internal and external environments through biochemical networks of interacting molecules. The robustness and fidelity of information processing in biochemical networks can be limited by noise, the structure of biochemical interactions or numbers of participating molecules. Living cells, as a whole, are highly dissipative and it has been long recognized that information processing too require consumption of energy. Less is known about the limits and energetic cost of the capacity of information processing through biologically relevant biochemical reaction networks. Combining non-equilibrium statistical physics and learning theory perspectives we derive fundamental constraints relating the amount of dissipated energy and the fidelity and speed of information processing in individual cell signaling modules. We also derive the limits on equilibrium modules imposed by the available complexity and cooperativity but also by the range of input signals. Finally we analyze the information processing requirements to the energy budget of the cell.
• Nuclear compartmentalization into distinct genomic domains Algebra of (symmetric) positive matrices
  Abstract ->
  
  Julien Riposo, Universite Pierre et Marie Curie
  The spatial organization of chromosomes in the cell nucleus has become a great challenge.
  Hi-C mapping is a complex procedure allowing to obtain a matrix representation of the contacts between the chromosomes.
  Statistical analysis of these contacts allows to split the nucleus into several compartements where the interactions between the chromosomes are different. We showed that there are five distinct nuclear compartments in human Embryonic Stem Cells, with a distinctive role of each of these domains.
  The technique is based on Principal Component Analysis. With this type of matrix, we proved that the first eigenvector is the sum of the lines of the matrix, so that it must be ignored in the analysis. We will finally focus on the preliminaries of the ideas of the proof of this important new theorem, with also some applications to financial markets.

18h25 Cocktail (ENS, 45 rue d’Ulm, salle Normal'Cafe)

Click here to download the program in pdf

Important: The talks will be held at the Centre Culturel Irlandais, the lunch in Salle Conf IV at ENS-Physique and the cocktail in Salle Normal'Cafe at the main ENS building.

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"
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 - for her support, without her it would not have been possible to organize this meeting

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