Paris Biological Physics
Community Day 2019

Flowing Active Suspensions: Plankton as a model active particle.

Suspensions of motile living organisms represent a non-equilibrium system of condensed matter of great interest from a fundamental point of view as well as for industrial applications. These are suspensions composed of autonomous units - active particles - capable of converting stored energy into motion. The interactions between the active particles and the liquid in which they swim give rise to mechanical constraints and a large-scale collective movement that have recently attracted a great deal of interest in the physical and mechanical communities. From the industrial point of view, microalgae are used in many applications ranging from the food industry to the development of new generations of biofuels. The biggest challenges in all these applications are the processes of separation, filtration and concentration of microalgae. There is therefore a real need for a better understanding of the flow of active material in order to ensure optimal control of these systems. Our recent work on microalgae suspensions will be presented. The micro alga Chlamydomonas Reinhardtii uses its two anterior flagella to propel itself into aqueous media. It then produces a random walk with persistence that can be characterised quantitatively by analysing the trajectories produced. Moreover, in the presence of a light stimulus, it biases its trajectory to direct it towards the light: this phenomenon is called phototaxis. By coupling experiments and modelling, we propose to extract from the hydrodynamic characteristics of this microalga the generic properties of microswimmer suspensions.

Effect of density on endothelial cell clustering

The endothelium is a thin monolayer of cells lining the inner surfaces of our blood vessels. Due to this strategic position, endothelial cells are constantly exposed to the hemodynamic forces from blood flow and are known to be highly responsive to mechanical stimuli. Numerous studies have shown that endothelial cells change their morphology and align along the flow direction in response to laminar shear stress which is consistent with in vivo observations. Surprisingly, in our experiments, endothelial cells are found to align either in the direction of flow or perpendicular to flow depending on their density. I will describe the emergence of elongation and orientation clusters in dense cellular monolayers and explore how these clusters may be linked to our intriguing experimental observations on cellular morphological changes and alignment.

Hydraulic fracturing and active coarsening position the lumen of the mouse blastocyst

We investigate the role of cell contractility and molecular adhesion in the formation of the blastocoel during early mouse embryo development, a fluid-filled lumen that positions the first axis of symmetry of the embryo. We show that hundreds of micron-sized fluid filled cavities appear throughout the entire embryo on basolateral (adhesive) sides of cells, fracking cell-cell contacts. Via a process akin to Ostwald ripening, these microlumens exchange fluid, such that a single dominant lumen emerges. We build a model to study the coarsening of the network of microlumens, reproducing the features of the dynamics and positioning of the blastocoel.Our results suggest that the lumen forms at the Trophectoderm-ICM interface, corresponding to the lowest contractile cell-cell interface.

Active cellular nematics: collective behaviours under multiscales geometrical cues

Cells are active objects that are able to present various behaviours like migration or division by extracting energy from their surroundings. In vivo, they adhere to extracellular matrix, a complex physico-chemical environnement with cues such as geometric constraints of various lengthscales. How cells respond to these constraints is still unclear. While most of the studies focus on one particular lengthscale, we propose in vitro experiments with C2C12 cells presenting a nematic orientation that oppose two geometric constraints of different directions: a microscale cue made of microabrasions and a mesoscale cue made of cell-adhesive stripes. On these surfaces, we observe a transition in orientation of the cells depending on the width of the stripes. This orientation transition is associated with shear and convergent flows that help form 3D structure we named cell cords starting from a simple planar surface. Ultimately, we were able to differentiate these cells into myotubes.

Gene transfer between bacteria: from single molecules to genome dynamics

Horizontal gene transfer (HGT) plays an important role in bacterial genome evolution. Gene transfer between bacteria of different species but also between bacteria and eukaryotes has been reported. A particularly widespread mechanism of gene transfer is transformation which enables bacteria to import and inheritably integrate external DNA. The first part of the presentation will focus on the import of DNA through the cell envelope, a key step to transformation. The proteins forming the DNA uptake machine have been identified. Yet, the biophysical mechanism of the motor pulling DNA from the environment into the bacterial cell remains poorly understood. We used single molecule approaches for studying the molecular mechanism of DNA uptake. Our results are in remarkable agreement with a translocation ratchet model, whereby a periplasmic chaperone rectifies DNA diffusion through the membrane by reversible binding. In the second part, the I will address the question how gene transfer between different bacterial subspecies affects genome dynamics and bacterial fitness. Using laboratory evolution, we show that despite considerable sequence divergence, large portions of the genome are rapidly transferred.

In vitro physiological membrane-on-chip and its application in biology

Experimental setups to produce and to monitor model membranes have been successfully used for decades and brought invaluable insights into many areas of biology. However, they all have limitations that prevent the full in vitro mimicking and monitoring of most biological processes. Here, a horizontal free-standing membrane having a physiological lipid composition is reconstituted in a 3D printing-based microfluidic chip. Simultaneous monitoring of the membrane processes with a microscope and patch-clamp amplifier reveals that the membrane is free-standing, horizontal, fully fluid, stable, flat, and large enough. Dual open-channels adjacent to the bilayer are freely used to alter each lipid monolayer composition (e.g. to form an asymmetric membrane) and oriented protein insertion. Currently, this in vitro membrane setup is integrated to investigate various molecular mechanisms in neurons and cell biology. This talk introduces this model membrane setup and its applications.

Evolutionary rescue of bacterial populations: the role of beneficial mutations on multicopy plasmids

Many bacteria carry extra-chromosomal DNA elements, so-called plasmids, in addition to their chromosome. While the essential genes are located on the chromosome, plasmids can contain genes that are advantageous in certain environments such as genes coding for antibiotic resistance. Many of these plasmids have a copy number greater than one, i.e. they are present in the bacterial cell in several copies. The plasmid copy number has consequences for the dynamics of mutations in plasmid-carried genes, which has recently started to gain increased attention, mainly driven by experimental work. We set up a mathematical model to disentangle the various, partially antagonistic effects of the plasmid copy number on bacterial adaptation if adaptation relies on mutations on multi-copy plasmids. Using multitype branching process theory, we determine how the plasmid copy number affects the probability of evolutionary rescue, i.e. the probability that a bacterial population survives exposure to harsh environmental conditions through adaptive evolution, under these circumstances.

Unveiling the structure of neural interactions underlying visual coding

Our perception of the world around us emerges from rich interactions within networks of neurons at the microscopic scale. As such, the firing of each neuron may exhibit complex responses to features in the environment, resulting from inputs from synaptically connected neurons. To unveil the structure of such intricate neural interactions, one is interested in finding the simplest model able to explain the most of the experimentally observed statistics. This can be achieved by maximising entropy in the model with constraints imposed by empirical statistics. In spontaneous activity recorded from the mouse primary visual cortex, applying maximum entropy models with different empirical constraints reveals that dominant interactions between neurons forming synapses to the same neuron are high-order and organised into dynamically distinct clusters. Our results suggest the emergent cluster structure shapes collective dynamics into providing a neural code balancing high dimensionality and robustness to noise for the postsynaptic neuron to read out.

Mechanics of cells and tissues

Cell and tissue mechanics play a crucial role in a number of key biological processes, such as embryo development or cancer progression. Understanding the way cells control their own material properties and mechanically interact with their environment is key. At a more fundamental level, we need to better describe, quantify and monitor cell and tissue mechanics before we can formulate testable hypotheses. In this talk, I will report experimental studies on the mechanical response of two different multicellular structures: epithelial monolayers and early embryonic tissues.In both cases, the material exhibits a strong time-dependant response over a broad distribution of time-scales. The combination of mechanical characterisation with biological perturbations offers new insight into the mechanisms exploited by cells and tissue to control their mechanical properties.

Mechanosensation and coordination of collective cell migration

Collective cell migration is a key phenomenon for morphogenesis, wound healing or cancer metastasis, yet, its cellular bases are just starting to be unravelled. In particular, how cells communicate and coordinate their movement over the large scale of a whole group remains poorly understood. During gastrulation, the Zebrafish prechordal plate undergoes a directed migration. We previously established that, the directional information is, at least partly, transmitted from cell to cell through contact, but the nature of this information is yet unknown. In vitro experiments revealed that Xenopus prechordal plate cells can sense mechanical forces and use this information to orient their migration. I am investing whether such a mechanosensation is actually used in vivo to orient Zebrafish prechordal plate. I first blocked cell mechanotransduction by removing the mechanosensitive domain of α-Catenin, a part of the adherens junction, and observed that this disrupted cell orientation, suggesting that cell migration requires sensing forces. In Xenopus a model has been proposed where the orienting cue comes from a gradient of tension building up across the prechordal plate coming from the interaction with the notochord, an adjacent, elongating tissue. To test that hypothesis, I performed laser ablation to sever the two tissues from each other. Isolating the plate from notochord disrupts directional motion while keeping some notochord is sufficient to restore it, suggesting that contact with the notochord is required for the prechordal plate to migrate directionally. Interestingly, affecting notochord extension by disrupting PCP pathway affects prechordal plate migration, suggestion that it is the extension that is required. By introducing some immotile cells in front of an extending notochord, I observed that the latter is able to push the cells, suggesting that the notochord could exert forces on the prechordal plate that could be used as an orienting cue. In order to challenge this hypothesis, I am developing techniques to directly apply forces inside the tissue, and to measure mechanical constraints exerted on the cells.