Biology Inspired Physics at Mesoscales

Team Publications

Year of publication 2012

Maxime Deforet, Maria Carla Parrini, Laurence Petitjean, Marco Biondini, Axel Buguin, Jacques Camonis, Pascal Silberzan (2012 Jan 20)

Automated velocity mapping of migrating cell populations (AVeMap).

Nature methods : 1081-3 : DOI : 10.1038/nmeth.2209 Learn more
Summary

Characterizing the migration of a population of cells remains laborious and somewhat subjective. Advances in genetics and robotics allow researchers to perform many experiments in parallel, but analyzing the large sets of data remains a bottleneck. Here we describe a rapid, fully automated correlation-based method for cell migration analysis, compatible with standard video microscopy. This method allows for the computation of quantitative migration parameters via an extensive dynamic mapping of cell displacements.

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Year of publication 2011

J Saragosti, V Calvez, N Bournaveas, B Perthame, A Buguin, P Silberzan (2011 Sep 14)

Directional persistence of chemotactic bacteria in a traveling concentration wave.

Proceedings of the National Academy of Sciences of the United States of America : 16235-40 : DOI : 10.1073/pnas.1101996108 Learn more
Summary

Chemotactic bacteria are known to collectively migrate towards sources of attractants. In confined convectionless geometries, concentration “waves” of swimming Escherichia coli can form and propagate through a self-organized process involving hundreds of thousands of these microorganisms. These waves are observed in particular in microcapillaries or microchannels; they result from the interaction between individual chemotactic bacteria and the macroscopic chemical gradients dynamically generated by the migrating population. By studying individual trajectories within the propagating wave, we show that, not only the mean run length is longer in the direction of propagation, but also that the directional persistence is larger compared to the opposite direction. This modulation of the reorientations significantly improves the efficiency of the collective migration. Moreover, these two quantities are spatially modulated along the concentration profile. We recover quantitatively these microscopic and macroscopic observations with a dedicated kinetic model.

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Yusuke T Maeda, Axel Buguin, Albert Libchaber (2011 Aug 16)

Thermal separation: interplay between the Soret effect and entropic force gradient.

Physical review letters : 038301 : DOI : 10.1103/PhysRevLett.107.038301 Learn more
Summary

Thermophoresis, the Soret effect, depletes a high concentration of a polyethylene glycol polymer solution from the hot region and builds a concentration gradient. In such a solution, solutes of small concentration experience thermophoresis and polyethylene glycol concentration-dependent restoring forces. We report that by using focused laser heating and varying the polyethylene glycol concentration one observes geometrical localizations of solutes like DNA and RNA into patterns such as a ring. For DNA up to 5.6 kbp, the ring size decreases following a behavior analogous to a gel electrophoresis separation. Above 5.6 kbp, the ring diameter increases with the DNA length. Mixtures of DNA and RNA can be separated as well as different RNA lengths. Separation of colloids is also observed. The experiments might be relevant for the separation of small RNA ribozymes in an early stage of life.

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Fanny Wu-Bavouzet, Juliette Cayer-Barrioz, Alain Le Bot, Françoise Brochard-Wyart, Axel Buguin (2011 Jan 15)

Effect of surface pattern on the adhesive friction of elastomers.

Physical review. E, Statistical, nonlinear, and soft matter physics : 031806 : DOI : 10.1103/PhysRevE.82.031806 Learn more
Summary

We present experimental results for the friction of a flat surface against a hexagonally patterned surface, both being made of PolyDiMethylSiloxane. We simultaneously measure forces of range 10 mN and observe the contact under sliding velocities of about 100 μm/s. We observe adhesive friction on three different pattern heights (80, 310, and 2100 nm). Two kinds of contacts have been observed: the flat surface is in close contact with the patterned one (called intimate contact, observed for 80 nm) or only suspended on the tops on the asperities (called laid contact, observed for 2100 nm). In the range of velocities used, the contact during friction is similar to the static one. Furthermore, our experimental system presents a contact transition during friction for h=310 nm.

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Year of publication 2010

M Reffay, L Petitjean, S Coscoy, E Grasland-Mongrain, F Amblard, A Buguin, P Silberzan (2010 Nov 24)

Orientation and polarity in collectively migrating cell structures: statics and dynamics.

Biophysical journal : 2566-75 : DOI : 10.1016/j.bpj.2011.04.047 Learn more
Summary

Collective cell migration is often characterized by the spontaneous onset of multicellular protrusions (known as fingers) led by a single leader cell. Working with epithelial Madin-Darby canine kidney monolayers we show that cells within the fingers, as compared with the epithelium, are well oriented and polarized along the main finger direction, which suggests that these cells actively migrate. The cell orientation and polarity decrease continuously from the tip toward the epithelium over a penetration distance of typically two finger lengths. Furthermore, laser photoablation experiments at various locations along these fingers demonstrate that the cells in the fingers are submitted to a tensile stress whose value is larger close to the tip. From a dynamical point of view, cells entering a finger gradually polarize on timescales that depend upon their particular initial position. Selective laser nanosurgery of the leader lamellipodium shows not only that these structures need a leader to progress, but that this leader itself is the consequence of a prior self-organization of the cells forming the finger. These results highlight the complex interplay between the collective orientation within the fingers and the mechanical action of the leader.

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A Saez, E Anon, M Ghibaudo, O du Roure, J-M Di Meglio, P Hersen, P Silberzan, A Buguin, B Ladoux (2010 Apr 26)

Traction forces exerted by epithelial cell sheets.

Journal of physics. Condensed matter : an Institute of Physics journal : 194119 : DOI : 10.1088/0953-8984/22/19/194119 Learn more
Summary

Whereas the adhesion and migration of individual cells have been well described in terms of physical forces, the mechanics of multicellular assemblies is still poorly understood. Here, we study the behavior of epithelial cells cultured on microfabricated substrates designed to measure cell-to-substrate interactions. These substrates are covered by a dense array of flexible micropillars whose deflection enables us to measure traction forces. They are obtained by lithography and soft replica molding. The pillar deflection is measured by video microscopy and images are analyzed with home-made multiple particle tracking software. First, we have characterized the temporal and spatial distributions of traction forces of cellular assemblies of various sizes. The mechanical force balance within epithelial cell sheets shows that the forces exerted by neighboring cells strongly depend on their relative position in the monolayer: the largest deformations are always localized at the edge of the islands of cells in the active areas of cell protrusions. The average traction stress rapidly decreases from its maximum value at the edge but remains much larger than the inherent noise due to the force resolution of our pillar tracking software, indicating an important mechanical activity inside epithelial cell islands. Moreover, these traction forces vary linearly with the rigidity of the substrate over about two decades, suggesting that cells exert a given amount of deformation rather than a force. Finally, we engineer micropatterned substrates supporting pillars with anisotropic stiffness. On such substrates cellular growth is aligned with respect to the stiffest direction in correlation with the magnitude of the applied traction forces.

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Jonathan Saragosti, Vincent Calvez, Nikolaos Bournaveas, Axel Buguin, Pascal Silberzan, Benoît Perthame (2010 Jan 10)

Mathematical description of bacterial traveling pulses.

PLoS computational biology : DOI : 10.1371/journal.pcbi.1000890 Learn more
Summary

The Keller-Segel system has been widely proposed as a model for bacterial waves driven by chemotactic processes. Current experiments on Escherichia coli have shown the precise structure of traveling pulses. We present here an alternative mathematical description of traveling pulses at the macroscopic scale. This modeling task is complemented with numerical simulations in accordance with the experimental observations. Our model is derived from an accurate kinetic description of the mesoscopic run-and-tumble process performed by bacteria. This can account for recent experimental observations with E. coli. Qualitative agreements include the asymmetry of the pulse and transition in the collective behaviour (clustered motion versus dispersion). In addition, we can capture quantitatively the traveling speed of the pulse as well as its characteristic length. This work opens several experimental and theoretical perspectives since coefficients at the macroscopic level are derived from considerations at the cellular scale. For instance, the particular response of a single cell to chemical cues turns out to have a strong effect on collective motion. Furthermore, the bottom-up scaling allows us to perform preliminary mathematical analysis and write efficient numerical schemes. This model is intended as a predictive tool for the investigation of bacterial collective motion.

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Year of publication 2009

Bastien Cayrol, Claude Nogues, Alexandre Dawid, Irit Sagi, Pascal Silberzan, Hervé Isambert (2009 Oct 14)

A nanostructure made of a bacterial noncoding RNA.

Journal of the American Chemical Society : 17270-6 : DOI : 10.1021/ja906076e Learn more
Summary

Natural RNAs, unlike many proteins, have never been reported to form extended nanostructures, despite their wide variety of cellular functions. This is all the more striking, as synthetic DNA and RNA forming large nanostructures have long been successfully designed. Here, we show that DsrA, a 87-nt noncoding RNA of Escherichia coli, self-assembles into a hierarchy of nanostructures through antisense interactions of three contiguous self-complementary regions. Yet, the extended nanostructures, observed using atomic force microscopy (AFM) and fluorescence microscopy, are easily disrupted into >100 nm long helical bundles of DsrA filaments, including hundreds of DsrA monomers, and are surprisingly resistant to heat and urea denaturation. Molecular modeling demonstrates that this structural switch of DsrA nanostructures into filament bundles results from the relaxation of stored torsional constraints and suggests possible implications for DsrA regulatory function.

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Hong Yang, Axel Buguin, Jean-Marie Taulemesse, Kosuke Kaneko, Stéphane Méry, Anne Bergeret, Patrick Keller (2009 Sep 26)

Micron-sized main-chain liquid crystalline elastomer actuators with ultralarge amplitude contractions.

Journal of the American Chemical Society : 15000-4 : DOI : 10.1021/ja905363f Learn more
Summary

Responsive surfaces composed of cylindrical or square micrometer-sized thermoresponsive pillars made of thiol-ene nematic main-chain liquid crystalline elastomers (LCEs) are produced by replica molding. The individual pillars behave as microactuators, showing ultralarge and reversible contractions of around 300-400% at the nematic to isotropic phase transition. The nematic main-chain LCE microactuators described here present contractions as large as the best macroscopic systems reported in the literature. Moreover, the contraction observed for this new system outperforms the best values already reported for other LCE microsystems.

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Shirley Mark, Roie Shlomovitz, Nir S Gov, Mathieu Poujade, Erwan Grasland-Mongrain, Pascal Silberzan (2009 Jul 30)

Physical model of the dynamic instability in an expanding cell culture.

Biophysical journal : 361-70 : DOI : 10.1016/j.bpj.2009.10.022 Learn more
Summary

Collective cell migration is of great significance in many biological processes. The goal of this work is to give a physical model for the dynamics of cell migration during the wound healing response. Experiments demonstrate that an initially uniform cell-culture monolayer expands in a nonuniform manner, developing fingerlike shapes. These fingerlike shapes of the cell culture front are composed of columns of cells that move collectively. We propose a physical model to explain this phenomenon, based on the notion of dynamic instability. In this model, we treat the first layers of cells at the front of the moving cell culture as a continuous one-dimensional membrane (contour), with the usual elasticity of a membrane: curvature and surface-tension. This membrane is active, due to the forces of cellular motility of the cells, and we propose that this motility is related to the local curvature of the culture interface; larger convex curvature correlates with a stronger cellular motility force. This shape-force relation gives rise to a dynamic instability, which we then compare to the patterns observed in the wound healing experiments.

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Benoit Ladoux, Ester Anon, Mireille Lambert, Aleksandr Rabodzey, Pascal Hersen, Axel Buguin, Pascal Silberzan, René-Marc Mège (2009 Jul 14)

Strength dependence of cadherin-mediated adhesions.

Biophysical journal : 534-42 : DOI : 10.1016/j.bpj.2009.10.044 Learn more
Summary

Traction forces between adhesive cells play an important role in a number of collective cell processes. Intercellular contacts, in particular cadherin-based intercellular junctions, are the major means of transmitting force within tissues. We investigated the effect of cellular tension on the formation of cadherin-cadherin contacts by spreading cells on substrates with tunable stiffness coated with N-cadherin homophilic ligands. On the most rigid substrates, cells appear well-spread and present cadherin adhesions and cytoskeletal organization similar to those classically observed on cadherin-coated glass substrates. However, when cells are cultured on softer substrates, a change in morphology is observed: the cells are less spread, with a more disorganized actin network. A quantitative analysis of the cells adhering on the cadherin-coated surfaces shows that forces are correlated with the formation of cadherin adhesions. The stiffer the substrates, the larger are the average traction forces and the more developed are the cadherin adhesions. When cells are treated with blebbistatin to inhibit myosin II, the forces decrease and the cadherin adhesions disappear. Together, these findings are consistent with a mechanosensitive regulation of cadherin-mediated intercellular junctions through the cellular contractile machinery.

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L Petitjean, M Reffay, E Grasland-Mongrain, M Poujade, B Ladoux, A Buguin, P Silberzan (2009 Jul 9)

Velocity fields in a collectively migrating epithelium.

Biophysical journal : 1790-800 : DOI : 10.1016/j.bpj.2010.01.030 Learn more
Summary

We report quantitative measurements of the velocity field of collectively migrating cells in a motile epithelium. The migration is triggered by presenting free surface to an initially confluent monolayer by using a microstencil technique that does not damage the cells. To avoid the technical difficulties inherent in the tracking of single cells, the field is mapped using the technique of particle image velocimetry. The main relevant parameters, such as the velocity module, the order parameter, and the velocity correlation function, are then extracted from this cartography. These quantities are dynamically measured on two types of cells (collectively migrating Madin-Darby canine kidney (MDCK) cells and fibroblastlike normal rat kidney (NRK) cells), first as they approach confluence, and then when the geometrical constraints are released. In particular, for MDCK cells filling up the patterns, we observe a sharp decrease in the average velocity after the point of confluence, whereas the densification of the monolayer is much more regular. After the peeling off of the stencil, a velocity correlation length of approximately 200 microm is measured for MDCK cells versus only approximately 40 microm for the more independent NRK cells. Our conclusions are supported by parallel single-cell tracking experiments. By using the biorthogonal decomposition of the velocity field, we conclude that the velocity field of MDCK cells is very coherent in contrast with the NRK cells. The displacements in the fingers arising from the border of MDCK epithelia are very oriented along their main direction. They influence the velocity field in the epithelium over a distance of approximately 200 microm.

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Year of publication 2008

C Douarche, A Buguin, H Salman, A Libchaber (2008 Nov 21)

E. Coli and oxygen: a motility transition.

Physical review letters : 198101 Learn more
Summary

The motility of Escherichia coli is correlated with oxygen concentration. We show that oxygen penetrating into an anaerobic sample induces the coexistence of two domains of motile and nonmotile bacteria. This coexistence generates a bacterial accumulation at the border that propagates slowly with a constant velocity. To show that this front propagation follows general scaling arguments, we characterize the sharp and fast motile to nonmotile transition occurring when bacteria exhaust oxygen. Additionally, we develop a novel technique to quantify oxygen in situ without affecting bacteria.

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Mathieu Poujade, Erwan Grasland-Mongrain, Laurence Petitjean, Myriam Reffay, Axel Buguin, Benoît Ladoux, Pascal Silberzan (2008 Sep 16)

[Social life of epithelial cells].

Médecine sciences : M/S : 684-6 : DOI : 10.1051/medsci/20082489684 Learn more
Summary

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Year of publication 2007

M Poujade, E Grasland-Mongrain, A Hertzog, J Jouanneau, P Chavrier, B Ladoux, A Buguin, P Silberzan (2007 Sep 28)

Collective migration of an epithelial monolayer in response to a model wound.

Proceedings of the National Academy of Sciences of the United States of America : 15988-93 Learn more
Summary

Using an original microfabrication-based technique, we experimentally study situations in which a virgin surface is presented to a confluent epithelium with no damage made to the cells. Although inspired by wound-healing experiments, the situation is markedly different from classical scratch wounding because it focuses on the influence of the free surface and uncouples it from the other possible contributions such as cell damage and/or permeabilization. Dealing with Madin-Darby canine kidney cells on various surfaces, we found that a sudden release of the available surface is sufficient to trigger collective motility. This migration is independent of the proliferation of the cells that mainly takes place on the fraction of the surface initially covered. We find that this motility is characterized by a duality between collective and individual behaviors. On the one hand, the velocity fields within the monolayer are very long range and involve many cells in a coordinated way. On the other hand, we have identified very active “leader cells” that precede a small cohort and destabilize the border by a fingering instability. The sides of the fingers reveal a pluricellular actin “belt” that may be at the origin of a mechanical signaling between the leader and the followers. Experiments performed with autocrine cells constitutively expressing hepatocyte growth factor (HGF) or in the presence of exogenous HGF show a higher average velocity of the border and no leader.

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