Paris Biological Physics Community Day 2014
Friday 7th November 2014, 9h30
Centre Culturel Irlandais - Salle Michel Guillaume
5 rue des Irlandais, 75005 Paris
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!
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For any questions, please
contact:
paris-young-biophysics-community-meeting-organizers@googlegroups.com
Invited speakers:
Naama Brenner
Technion - Israel Institute of Technology, Israel
Guillaume Salbreux
Max Planck Institut, Dresden, Germany
Samir Suweis
University of Padova, Italy
Pieter Rein ten Wolde
AMOLF, Netherlands
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The following speakers will give a short talk:
Stéphane Deny
Institut de la vision & UPMC
Christoph Feinauer
Politecnico di Torino & UPMC
Teresa Ferraro
LPT-ENS & Institut Curie
Giulia Foffano
LPTMS Université Paris XI
Sarah Klein
LPT Université Paris XI
Sophie Rosay
École normale supérieure
Vittore Scolari
LCQB & UPMC & NCBS
Alexandre Solon
Université Paris VII
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Organizers:
A. Coucke1,
2,
E. De
Leonardis1, 2,
Y. Elhanati1
,
M.
Figliuzzi2,
S. Grigolon3
,
H. Jacquin1
,
G. Malaguti4
,
Vittore Scolari2,
5
1Ecole Normale Superieure, Paris,
2Biologie Computationnelle et Quantitative,
Paris,
3LPTMS, Université Paris-Sud XI,
4Institut Curie,
5NCBS, Bangalore
Program:
Show all abstracts
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:
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Groupement de recherche international "GDRI Evolution,
Regulation and Signaling"
Regulating Flies, European Research Council
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Marco Cosentino Lagomarsino, Vincent Hakim, Herve
Isambert, Olivier Martin, Thierry Mora and
Aleksandra Walczak
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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