This weekly seminar aims at gathering researcher form different thematics (physicists, biologists and chemists) and from different institutes in the center of Paris. The objective is to cover an interface between physics, chemistry and biology as broad as possible, with experimental, numerical and/or theoretical approaches. To describe life sciences all scales are needed, from single molecules, cell biology, organisms, population dynamics. That's why the range of our seminar is quite broad form embryonic development, genetic regulation, evolution, mechanics and cell migration, immunology, microbiology, synthetic biology, etc.
We study the origin and function of signaling oscillations in embryonic development. Oscillatory activities (period ~2 hours) of the Notch, Wnt and Fgf signaling pathway have been identified in mouse embryos and are linked to periodic mesoderm segmentation and the formation of pre-vertebrae, somites. Most strikingly, Notch signaling oscillations occur highly synchronized, yet phase-shifted, in cell ensembles, leading to spatio-temporal wave patterns sweeping through the embryo. I will discuss how we use general synchronisation principles based on entrainment/Arnold tongues to reveal general properties and function of collective oscillations during the mesoderm patterning process.
Active fluids consist of self-propelled particles (as bacteria or artificial microswimmers) and display properties that differ strongly from their passive counterparts. Unique physical phenomena, as enhanced Brownian diffusivity, viscosity reduction, active transport and mixing or the extraction of work from chaotic motion, result from the activity of the particles, locally injecting energy into the system. The presence of living and cooperative species may also induce collective motion and organization at the mesoscopic or macroscopic level impacting the constitutive relationships in the semi-dilute or dense regimes. Individual bacteria transported in viscous flows, show complex interactions with flows and bounding surfaces resulting from their complex shape as well as their activity. Understanding these transport dynamics is crucial, as they impact soil contamination, transport in biological conducts or catheters, and constitute thus a serious health thread. Here we investigate the trajectories of individual E-coli bacteria in confined geometries under flow, using microfluidic model systems in bulk flows as well as close to surfaces using a novel Langrangian 3D tracking method. Combining experimental observations and modelling we elucidate the origin of upstream swimming, lateral drift or persistent transport along corners. The understanding gained can be used to design channel geometries to guide bacteria towards specific locations or to prevent upstream contamination.
Spatial navigation constitutes an essential behavior that requires internal representations of environments and online memory processing to guide decisions. The precise integration of orientation and directions along trajectories critically determines the ability of animals to explore their surroundings efficiently. First, I will present recent results obtained in the fruit fly, Drosophila melanogaster. These results show how insects use an internal neural compass to store and compute the direction of cues present in their environments. Then, I will present the structure of the involved neural networks and the mechanisms at play during the processing of the information of direction. The results obtained in the fly mainly involve navigation in 2 dimensions, and thus the processing of a unique angular variable. However, a recent study in bats uncovered the existence of cells representing the orientation of bats in 3D. I will show possible mechanisms to extend the neural computation of directions to 3D rotations, a problem that presents much stronger theoretical challenges. I will propose a neural network model that displays activity patterns that continuously maps to the set of all the 3D rotations. Moreover, the general theory can account for psychophysics observations of "mental rotations.”
Coordinating collective behaviors across groups of cells is critical for a wide range of biological processes ranging from development to wound healing. How these basic group phenomena are regulated at the level of single cells, potentially by modulating factors like the frequency of synchronized signaling or the speed of group migration, is still an open question. Identifying what single cells tune in their own signaling programs to produce these phenotypic changes in multicellular population behaviors would yield parameters we can control when reprogramming these systems for our benefit. To address this challenge, we are pursuing complimentary efforts in multiple model systems where single-cell level and collective signaling can be simultaneously visualized with group behaviors. This talk will focus on these efforts in two systems: the social amoeba, Dictyostelium discoideum, and synthetic stromal tissues. We are interrogating signaling behaviors in these systems using a combination of techniques to visualize and control cellular signaling, and developing quantitative models to understand how the signaling behaviors we observe drive multicellular behaviors. Through directly controlling signaling, we can causally link our observations of single-cell signaling dynamics to the population-wide behaviors they control. Together, these efforts will allow us to identify how population-wide multicellular behaviors are regulated by single cells.
One of the most striking features of embryonic development is that differentiation is happening in a spatially ordered fashion: tissues self-organize to form well-defined patterns that pre-figure the body plan. During gastrulation, the cells of the embryo are allocated into three germ layers: ectoderm, mesoderm and endoderm. During the last decades, signaling pathways responsible for the initiation of gastrulation in mammalian embryos have been identified. However, the physical rules governing the tissue spatial patterning and the extensive morphogenetic movements occurring during that process are still elusive. Studying the spatio-temporal dynamics of pattern formation is difficult in live embryos, because of their inherent lack of observability but also because it is not possible in an embryo to control in a quantitative manner what is relevant for the establishment of the multi-cellular pattern, i.e. the cells' physical and chemical environment. I will discuss how culture and differentiation of mouse ESC on micro-patterned substrates allowed us to recapitulate some aspects of Antero/Posterior axis formation occurring at gastrulation and how microfluidic devices can help us dissect the emergence of A/P polarity.
How cells control their shape is a long-standing question in cell biology. In most rod-shaped bacteria, the external cell wall and actin-like MreB proteins are major determinants of cell shape. In our laboratory, we are interested in the mechanistic details underlying MreB self-organization and morphogenetic function. We have been using total internal reflection fluorescence microscopy (TIRFM) combined with single particle tracking (SPT) analysis to visualize the dynamics of MreB isoforms and cell wall synthases in the Gram-positive model bacterium Bacillus subtilis. We have shown that B. subtilis elongates its sidewalls by the action of peripheral MreB-associated cell wall synthesizing machineries that exhibit processive circumferential motion around the rod width. Motility is powered by cell wall synthesis, and MreB polymers act as platforms that restrict the diffusion of cell wall synthesizing enzymes in the membrane and orient their motion. More recently, we used both stimulated emission depletion (STED) microscopy and TIRFM coupled to structural illumination microscopy (SIM) to investigate the nanostructure and orientation of MreB filaments in the membrane. In parallel, and after years of efforts (functional MreB is notoriously difficult to purify in a state suitable for in vitro studies), we have succeed in observing for the first time filaments of MreB from Gram-positive bacteria by electron microscopy (EM). We are currently characterizing the ultrastructure and biochemical properties of MreB to fill in the gap between structure and function. Taken together, our in vivo and in vitro studies are consistent with a model in which MreB requires ATP or GTP to polymerize into ~150-200 nm long double filaments that have the intrinsic property of binding to the membrane and aligning along the rod width. Such local self-alignment of the nanofilaments orients the motion of cell wall synthases to insert cell wall polymers in circumferential bands around the cell cylinder allowing the establishment and maintenance of rod shape.
The actin cytoskeleton assembles into very dynamic structures that generate various forces. In this active process, filament disassembly must be tightly regulated, either to maintain active units, or to discard excess filaments and replenish the pool of monomeric (G) actin. At the centre of all actin filaments disassembly machineries is the family of proteins ADF/cofilin. ADF/cofilin binds along filaments into domains, induces severing and regulates depolymerisation from filament ends. We performed in vitro experiments, in microfluidic chambers, with purified proteins, to directly observe and quantify interactions between single actin filaments and ADF/cofilin. We recently developed new methods to apply tension, curvature and torsion to filaments, and thus understand how mechanical constraints regulate ADF/cofilin activity. First, we discovered that filament curvature and torsion boost ADF/cofilin-mediated severing. Moreover, ADF/cofilin, by increasing the helicity of actin filaments, generates a torque on twist-constrained filaments that accelerates severing up to 100-fold. These findings highlight the deep connections between mechanical forces and biochemical reactions, and their importance for cell behaviour regulation.
Single-molecule techniques continue to transform imaging, biophysics and, more recently, optical sensing. I will introduce a new class of label-free micro and nanosensors that are starting to emerge and that allow us to observe dynamic processes at the single molecule level directly with light, with unprecedented spatial- and temporal resolution, and without significantly affecting the natural and functional movements of the molecules. Initial demonstration include single ion sensing, and visualisation of functional movements of enzymes directly with light.
Multi-drug resistant bacterial pathogens constitute a critical public health threat. This threat has spurred a multidisciplinary response to develop antibiotic alternatives, including the use of bacteriophage (phage), i.e., viruses that exclusively infect and lyse bacteria. Phage-induced lysis eliminates bacterial cells. However, the death of individuals cells need not translate into the elimination of a target population. Instead, lysis can lead to the depletion of bacterial hosts which, in turn, leads to decreased effectiveness of phage therapy and the evolution of phage-resistant hosts. As a consequence, phage are unlikely to eliminate a target population on their own and may even be eliminated altogether. However, a central difference between in vitro dynamics and in vivo therapy is the influence of the mammalian immune system. In this talk, I present collaborative efforts to address this gap via a dynamical systems approach to phage therapy in an immune system context. In doing so, I highlight how the combined use of mathematical models, in vitro manipulation, and in vivo experiments may shed light on principles underlying curative treatment of acute infections.
Mechanics are ubiquitous in the environments of bacteria, but we are only starting to appreciate how they may affect their physiology. Here, I will discuss how the human pathogen Pseudomonas aeruginosa uses a mechano-chemical sensory system to induce virulence upon mechanical stimulation during surface contact. I will show that successive type IV pili extension, attachment and retraction represents a mechanical input readout by a chemotaxis-like system (Chp). Using iSCAT, a microscopy method based on interference and scattering enabling label-free visualization of small extracellular structures in live cells, we were able to measure type IV pili dynamics during surface exploration, thereby providing a direct measurement of mechanical input. I will discuss how we are using these measurements to understand how type IV pili interacts with the Chp system to activate cellular response. This expands the range of known inputs that bacteria sense, providing a new class of signals that can be processed by two component systems. It furthermore argues that mechanics may play a role in the physiology of many other species.
One of the most critical aspects of cell functioning is the ability of protein molecules to quickly find and recognize specific target sequences on DNA. Kinetic measurements indicate that in many cases the corresponding association rates are surprisingly large. For some proteins they might be even larger than maximal allowed 3D diffusion rates, and these observations stimulated strong debates about possible mechanisms. Current experimental and theoretical studies suggest that the search process is a complex combination of 3D and 1D motions. Although significant progress in understanding protein search and recognition of targets on DNA has been achieved, detailed mechanisms of these processes are still not well understood. The most surprising observation is that proteins spend most of the search time being non-specifically bound on DNA where they supposedly move very slowly, but still the overall search is very fast. Another intriguing result is known as a speed-selectivity paradox. It suggests that experimentally observed fast findings of targets require smooth protein-DNA binding potentials, while the stability of the specific protein-DNA complex imposes a large energy gap which should significantly slow down the protein molecule. Here we discuss a theoretical picture that might explain fast protein search for targets on DNA. We developed a discrete-state stochastic framework that allowed us to investigate explicitly target search phenomena. Using exact calculations by analyzing first passage distributions, it is shown that strong coupling between 3D and 1D motion might accelerate the search. It is argued that the speed-selectivity paradox does not exist since it is an artifact of the continuum approximation. We also show how our method can be utilized for taking into account the inter-segment processes. This is important to explain large deviations from the diffusion limit. Our theoretical analysis is supported by Monte Carlo computer simulations, and it agrees with all available experimental observations. Physical-chemical aspects of the mechanism are also discussed.
The two hands of most humans almost superimpose. Similarly, flowers of an individual plant have almost identical shapes and sizes. This robustness is in striking contrast with growth and deformation of cells during organ morphogenesis, which feature considerable variations in space and in time, raising the question of how organs and organisms reach well-defined size and shape. Because heterogeneous growth induces mechanical stress in tissues, we are exploring the biophysical basis of morphogenesis. By combining approaches from developmental biology (molecular genetics, live imaging), and mechanics/physics (mechanical measurements, models), we are unravelling unexpected cellular patterns and behaviours. During this talk, I will discuss some of our recent results and the resulting perspectives, aiming at a general audience.
Range expansions coupled with fluid flows are of great importance in understanding the organization and competition of microorganism populations in liquid environments. However, combining growth dynamics of an expanding assembly of cells with hydrodynamics leads to challenging problems, involving the coupling of nonlinear dynamics, stochasticity and transport. We have created an extremely viscous medium that allows us to grow cells on a controlled liquid interface over macroscopic scales. In this talk, I will present laboratory experiments, combined with numerical modelling, focused on the collective dynamics of genetically labelled microorganisms undergoing division and competition in the presence of a flow. I will show that an expanding population of microbes can itself generate a flow, leading to an accelerated propagation and fragmentation of the initial colony. Finally, I will show the mechanism at the origin of this metabolically generated flow and how it affects the growth and morphology of these microbial populations.
Proteins are very heterogeneous objects: they are sensitive to perturbations at some sites distant from their active site while being insensitive to perturbations at closer sites. I’ll review the evidence for the ubiquity of these long range effects and discuss our current understanding of their physical nature and evolutionary origin. This will motivate the introduction of a new theoretical model where long-range effects emerge spontaneously. I’ll explain how this model accounts for the evolution of long-range regulation (allostery) and for the different patterns of coevolution that may be inferred from protein sequences.
The emergent active behaviors of systems comprising large numbers of molecular motors and cytoskeletal filaments remain poorly understood, even though individual molecules have been extensively characterized. Here, we show in vitro with a minimal acto-myosin system that flagellar-like beating emerges naturally and robustly in polar bundles of filaments. Using surface micro-patterns of a nucleation-promoting factor, we controlled the geometry of actin polymerization to produce thin networks of parallel actin filaments. With either myosin Va or heavy-mero myosin II motors added in bulk, growing actin filaments self-organized into bundles that displayed periodic wave-like beating resembling those observed in eukaryotic cilia and flagella. We studied how varying the motor type or changing the size of the actin bundles influenced the properties of the actin-bending waves. In addition, using myosin-Va-GFP to visualize the motors within the actin bundle, we identified a novel feedback mechanism between motor activity and filament bending. Overall, structural control over the self-assembly process provides key information to clarify the physical principles underlying flagellar-like beating.
Nuclear Pore Complex (NPC) is a biomolecular “nanomachine” that controls nucleocytoplasmic transport in eukaryotic cells, and is operation is central for a multitude of health and disease processes in the cell. The key component of the functional architecture of the NPC is the assembly of the polymer-like intrinsically disordered proteins that line its passageway and play a central role in the NPC transport mechanism. Due to the unstructured nature of the proteins in the NPC passageway, it does not possess a molecular “gate” that transitions from an open to a closed state during translocation of individual cargoes. Rather, its passageway is crowded with multiple transport proteins carrying different cargoes in both directions. It remains unclear how the NPC maintains selective and efficient bi-directional transport under such crowded conditions. Remarkably, although the molecular conservation of the NPC components is low, its physical transport mechanism appears to be universal across eukaryotes – from yeast to humans. Due to the paucity of experimental methods capable to directly probe the internal morphology and the dynamics of NPCs, much of our knowledge about its properties derives from in vitro experiments interpreted through theoretical and computational modeling. I will present the current understanding of the Nuclear Pore Complex structure and function arising from the analysis of in vitro and in vivo experimental data in light of minimal complexity models relying on the statistical physics of molecular assemblies on the nanoscale.
The actin cytoskeleton is able to exert both pushing and pulling forces on the cell membrane, mediating processes such as cellular motility, endocytosis and cytokinesis. In order to investigate the exclusive role of actin dynamics on membrane deformations, the actin dynamics is reconstituted on the outer surface of a deformable liposome. Depending on the elasticity of the membrane and the forces generated by the actin polymerization, both tubular extrusions (i.e. towards the actin cortex) and localized spike-like protrusions occur along the surface of the liposome. In this talk I present a theoretical model where uniform actin polymerization can drive localized membrane deformations and show how polymerization kinetics and membrane/cortex mechanics impact their size and stability.
The coordinated flight of bird flocks is a striking example of collective behavior in biology. Using 3D positions and velocities of large natural flocks of starlings, I will show how to build an explicit mapping of flock behaviour onto statistical physics models of magnetism. Learning the parameters of these models allows us to infer the local rules of alignment, and to reveal that flocks are poised close to a critical point, where susceptibility to external perturbations is maximal. Extending the approach to alignment dynamics shows that flocks are in a state of local quasi-equilibrium.
Developing tissues have the capacity to cope with perturbations, including the modification of cell growth rate and the elimination of a large number of cells through wounding. This plasticity is well illustrated by cell competition, a process that drives the elimination of suboptimal cells (so called “losers”) by fitter cells (so called “winners”) through apoptosis without morphological defects. In the past years, the number of genetic and tissular contexts leading to cell competition has been constantly increasing. Yet, the mechanisms allowing recognition and elimination of suboptimal cells is still actively debated. I will present here our attempt to characterize quantitatively the process of cell competition which led to the characterization of two independent modes of elimination: first a contact dependent elimination which can be modulated by the shape of the interfaces between the two populations, secondly a compaction-driven competition where cell elimination is triggered by mechanical stress and differential sensitivity to compaction. I will then present recent results regarding the characterization of the pathway sensing cell compaction and triggering cell elimination in the Drosophila pupal notum (a single layer epithelium). Eventually I will present our ongoing characterization of the process of cell extrusion (the concerted removal of one cell from the epithelial layer) and its regulation by caspases.
In a similar way to bacteria that have to navigate in their environment, soaring birds try to minimize their effort by finding and exploiting ascending currents. However the environment is highly turbulent and unpredictable with thermals constantly forming, disintegrating and being transported within minutes timescales. How the birds navigate these environments remains unknown. It is a notoriously difficult/impossible task to assess what cues are used by the soaring birds and what strategies they developed to explore and exploit such turbulent environments. For this investigation, we chose to emulate how an agent could learn to see what strategies would emerge. I then set up an experimental reinforcement learning framework that I implemented in a two-meter wingspan glider. Here, the soaring agent measured its state (height and a set of cues), took actions (change the left/right direction it is heading to) and recorded what resulted from these actions given the previous state. After an initial learning period, the glider chose the actions according to their state that would maximize the gain in altitude. In short, the glider learned to soar through its past experience. The learned strategy was based on accurate estimates of local wind accelerations and roll-wise torque. In the field, the glider could typically gain hundreds of meters in height in a few minutes when facing environments with thermals. Our results not only highlight the vertical wind accelerations and roll-wise torques as effective mechanosensory cues for soaring birds but also provide navigational strategy that is directly applicable to the development of autonomous soaring vehicles to increase their time aloft with minimal energy cost.
Fertilization is one of the fundamental processes of living systems. Here I will address marine external fertilization and comment on recent work on mammals. I will show experiments that substantiate that sea urchin sperms exhibit chemotaxis as they swim towards the ovum. They are guided by flagellum internal [Ca2+] concentration fluctuations triggered by the binding of chemicals from the oocyte surroundings. Based on experiment, I present a family of logical regulatory networks for the [Ca2+] fluctuation signaling-pathway that reproduce previously observed electrophysiological behaviors and provide predictions, which have been confirmed with new experiments. These studies give insight on the operation of drugs that control sperm navigation. In this systems biology approach, global properties of the [Ca2+] discrete regulatory network dynamics such as: stability, redundancy, degeneracy, chaoticity and criticality can be determined. Our models operate near a critical dynamical regime, where robustness and evolvablity coexist. This regime is preserved under a class of strong perturbations. Based on global dynamics considerations, we have implemented a network node-reduction method. The coincidence of this reduced network with our bottom-up step-by-step, continuous differential equation modeling is reassuring. For the case of mammals our research has centered on the understanding of capacitation and acrosomal reaction. The first is a process by means of which roughly one third of the spermatozoa acquire the “capacity” to fertilize; the second enables the spermatozoa to penetrate the egg´s surrounding zona pellucida. Overall, our studies might contribute to fertility issues such as the development of male contraception treatments, which is an area of intense research.
The development of most metazoans can be divided in an early phase of embryogenesis and a subsequent phase of post-embryonic development. Developmental dynamics during the post-embryonic phase are generally much slower and often controlled by very different molecular mechanisms that, e.g., ensure tissue synchrony and integrate metabolic queues. However, obtaining long-term in-vivo quantitative imaging data post-embryonically with good statistical and cellular resolution has been highly challenging because animals must be allowed to grow, feed, and move in order to properly develop after embryogenesis. In this talk, I will discuss our recent progress in overcoming these challenges in the model organism C. elegans, using microfluidics technology. I will then outline two of our studies, in which quantitative in-vivo imaging data of post-embryonic development allows novel insights into mechanisms of cell-fate acquisition and the regulation of oscillator