Publications

RECHERCHER

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The Landau-Squire plume
Laboratoire Micromégas - Eleonora Secchi, Sophie Marbach, Antoine Niguès, Alessandro Siria
J Phys Chem C - - doi.org/10.1017/jfm.2017.441 - 2017
In this paper, we analyse the dispersion of a dye by a Landau–Squire plume, generated by a jet flow emerging from a nanocapillary into a reservoir. We demonstrate analytically that the dye concentration profile exhibits a long-range profile decaying as the inverse of the distance to the origin, whereas the plume shape is only a function of a Péclet number defined in terms of the flow characteristics inside the nanocapillary. These predictions are successfully compared with experiments on fluorescent dye dispersion from nanocapillaries under pressure-driven flow. The plume shape allows extraction of the nanojet force characterizing the Landau–Squire velocity profile for a given pressure drop, with results in full agreement with direct velocimetry measurements and finite-element calculations. The peculiarities of the Landau–Squire plume make it a sensitive probe of the flow properties inside the seeding nanocapillary.
Patterned parylene C for cell adhesion, spreading and alignment studies
Laboratoire Nanobioscience et Microsystèmes - Xiaolong Tu, JinWei, BinWang, Yadong Tanga, Jian Shi, Yong Chen
ELSEVIER - 175 56–60 - - 2017
Parylene C iswidely used for insulating coating of implantablemedical devices due to its unique properties of biocompatibility
and biostability.However, the interaction between cells and parylene C is limited with as-deposited
samples. A plasma treatment of the sample can significantly improve the cell adhesion on parylene C. To further
improve the cell adhesion as well as other cell functions, we patterned parylene C into pillars and stripes by soft
lithography and chemical vapor deposition. Such amethod is flexible to produce parylene C patterns on different
surfaces. The fabricated substrates have been tested to culture Hela cells, showing much improved adhesion on
pillar arrays of parylene C. Our results also showed a strong effect of contact guidance for cells on stripes of
parylene C, thereby proving the relevance of the method for cell adhesion, spreading and alignment studies
A plasma/liquid microreactor for radical reaction chemistry: An experimental and numerical investigation by EPR spin trapping
Laboratoire Procédés - Plasmas - Microsystèmes - Mengxue Zhang Stéphanie Ognier Nadia Touati Ines Hauner Cedric Guyon Laurent Binet Michael Tatoulian
Plasma Process - 15 - https://doi.org/10.1002/ppap.201700188 - 2017
In this paper, a novel plasma/liquid microreactor has been developed to generate and inject radical species with the aim to perform chemical synthesis reactions in liquid phase. Plasma has always been considered as a source of reactive species, such as radicals, atoms, electrons, etc., with applications mostly dedicated to surface modifications of materials. By injecting reactive species created by the plasma to the liquid phase, it is possible to initiate liquid phase synthesis reactions. In addition, gas/liquid interactions can be enhanced with a high surface‐area‐to‐volume ratio by confining the plasma and the liquid in diphasic micro‐structured systems. Herein is reported a novel plasma/liquid microreactor for liquid phase radical reactions. Radicals are generated in the gas phase in a steady flow microreactor and then transported to the liquid phase. The spin trapping reaction and the electron paramagnetic resonance (EPR) spectroscopy have been used to identify and quantify the radical species generated in the microreactor. Hydroxyl radicals and hydrogen atoms have been detected and measured in the liquid phase, indicating the huge potential of the microreactor as a handful tool for chemical synthesis.
Efficient laboratory evolution of computationally designed enzymes with low starting activities using fluorescence-activated droplet sorting
Laboratoire Biochimie - Obexer R, Pott M, Zeymer C, Griffiths A, Hilvert D.
Protein Eng Des Sel - 29(9) 355-66 - doi: 10.1093/protein/gzw032 - 2016
De novo biocatalysts with non-natural functionality are accessible by computational enzyme design. The catalytic activities obtained for the initial designs are usually low, but can be optimized significantly by directed evolution. Nevertheless, rate accelerations approaching the level of natural enzymes can only be achieved over many rounds of tedious and time-consuming laboratory evolution. In this work, we show that microfluidic-based screening using fluorescence-activated droplet sorting (FADS) is ideally suited for efficient optimization of designed enzymes with low starting activity, essentially straight out of the computer. We chose the designed retro-aldolase RA95.0, which had been previously evolved by conventional microtiter plate screening, as an example and reoptimized it using the microfluidic-based assay. Our results show that FADS is sufficiently sensitive to detect enzyme activities as low as kcat/Km = 0.5 M(-1)s(-1) The ultra-high throughput of this system makes screening of large mutant libraries possible in which clusters of up to five residues are randomized simultaneously. Thus, combinations of beneficial mutations can be identified directly, leading to large jumps in catalytic activity of up to 80-fold within a single round of evolution. By exploring several evolutionary trajectories in parallel, we identify alternative active site arrangements that exhibit comparably enhanced efficiency but opposite enantioselectivity
High-throughput screening of filamentous fungi using nanoliter-range droplet-based microfluidics
Laboratoire Biochimie - Beneyton T, Wijaya IP,Postros P, Najah M, Leblond P, Couvent A, Mayot E, Griffiths AD, Drevelle A.
Scientific Reports - 0.25 27223 - doi: 10.1038/srep27223 - 2016
Filamentous fungi are an extremely important source of industrial enzymes because of their capacity to secrete large quantities of proteins. Currently, functional screening of fungi is associated with low throughput and high costs, which severely limits the discovery of novel enzymatic activities and better production strains. Here, we describe a nanoliter-range droplet-based microfluidic system specially adapted for the high-throughput sceening (HTS) of large filamentous fungi libraries for secreted enzyme activities. The platform allowed (i) compartmentalization of single spores in ~10 nl droplets, (ii) germination and mycelium growth and (iii) high-throughput sorting of fungi based on enzymatic activity. A 10(4) clone UV-mutated library of Aspergillus niger was screened based on α-amylase activity in just 90 minutes. Active clones were enriched 196-fold after a single round of microfluidic HTS. The platform is a powerful tool for the development of new production strains with low cost,
Hierarchy and extremes in selections from pools of randomized proteins
Laboratoire Biochimie - Boyer S, Biswas D, Kumar Soshee A, Scaramozzino N, Nizak C2, Rivoire O.
Proc. Nat. Acad. Sci. USA - 113(13) 3482-7 - doi: 10.1073/pnas. - 2016
Variation and selection are the core principles of Darwinian evolution, but quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in the context of populations of partially randomized proteins selected for binding to well-defined targets. We built several minimal protein libraries, screened them in vitro by phage display, and analyzed their response to selection by high-throughput sequencing. A statistical analysis of the results reveals two main findings. First, libraries with the same sequence diversity but built around different "frameworks" typically have vastly different responses; second, the distribution of responses of the best binders in a library follows a simple scaling law. We show how an elementary probabilistic model based on extreme value theory rationalizes the latter finding. Our results have implications for designing synthetic protein libraries, estimating the density of functional biomolecules in sequence space, characterizing diversity in natural populations, and experimentally investigating evolvability (i.e., the potential for future evolution).
Lineage Tracking for Probing Heritable Phenotypes at Single-Cell Resolution
Laboratoire Biochimie - Denis Cottinet , Florence Condamine, Nicolas Bremond, Andrew D. Griffiths, Paul B. Rainey, J. Arjan G. M. de Visser, Jean Baudry, Jérôme Bibette
Nature Biotechnology - 11(4) e0152395 - doi.org/10.1371/journal.pone.0152395 - 2016
Determining the phenotype and genotype of single cells is central to understand microbial evolution. DNA sequencing technologies allow the detection of mutants at high resolution, but similar approaches for phenotypic analyses are still lacking. We show that a drop-based millifluidic system enables the detection of heritable phenotypic changes in evolving bacterial populations. At time intervals, cells were sampled and individually compartmentalized in 100 nL drops. Growth through 15 generations was monitored using a fluorescent protein reporter. Amplification of heritable changes–via growth–over multiple generations yields phenotypically distinct clusters reflecting variation relevant for evolution. To demonstrate the utility of this approach, we follow the evolution of Escherichia coli populations during 30 days of starvation. Phenotypic diversity was observed to rapidly increase upon starvation with the emergence of heritable phenotypes. Mutations corresponding to each phenotypic class were identified by DNA sequencing. This scalable lineage-tracking technology opens the door to large-scale phenotyping methods with special utility for microbiology and microbial population biology.
Transient compartmentalization of RNA replicators prevents extinction due to parasites
Laboratoire Biochimie - S. Matsumura, Á. Kun, M. Ryckelynck, F. Coldren, A. Szilágyi, F. Jossinet, C. Rick, P. Nghe, E. Szathmáry, A.D. Griffiths
Science - 354 1293-1296 - - 2016
Arc/Arg3.1 governs inflammatory dendritic cell migration from the skin and thereby controls T cell activation.
Laboratoire Biologie cellulaire systémique de la polarité et de la division - Ufer F, Vargas P, Engler JB, Tintelnot J, Schattling B, Winkler H, Bauer S,Kursawe N, Willing A, Keminer O, Ohana O, Salinas-Riester G, Pless O, Kuhl D, Friese MA.
Sci Immunol - 1(3) 8665 - doi: 10.1126/sciimmunol.aaf8665. - 2016
Skin-migratory dendritic cells (migDCs) are pivotal antigen-presenting cells that continuously transport antigens to draining lymph nodes and regulate immune responses. However, identification of migDCs is complicated by the lack of distinguishing markers, and it remains unclear which molecules determine their migratory capacity during inflammation. We show that, in the skin, the neuronal plasticity molecule activity-regulated cytoskeleton-associated protein/activity-regulated gene 3.1 (Arc/Arg3.1) was strictly confined to migDCs. Mechanistically, Arc/Arg3.1 was required for accelerated DC migration during inflammation because it regulated actin dynamics through nonmuscle myosin II. Accordingly, Arc/Arg3.1-dependent DC migration was critical for mounting T cell responses in experimental autoimmune encephalomyelitis and allergic contact dermatitis. Thus, Arc/Arg3.1 was restricted to migDCs in the skin and drove fast DC migration by exclusively coordinating cytoskeletal changes in response to inflammatory challenges. These findings commend Arc/Arg3.1 as a universal switch in migDCs that may be exploited to selectively modify immune responses.
Deterministic patterns in cell motility
Laboratoire Biologie cellulaire systémique de la polarité et de la division - Ido Lavi, Matthieu Piel, Ana-Maria Lennon-Duménil, Raphaël Voituriez & Nir S. Gov
Nature Physics - 12 1146–1152 - DOI : 10.1038/nphys3836 - 2016
Cell migration paths are generally described as random walks, associated with both intrinsic and extrinsic noise. However, complex cell locomotion is not merely related to such fluctuations, but is often determined by the underlying machinery. Cell motility is driven mechanically by actin and myosin, two molecular components that generate contractile forces. Other cell functions make use of the same components and, therefore, will compete with the migratory apparatus. Here, we propose a physical model of such a competitive system, namely dendritic cells whose antigen capture function and migratory ability are coupled by myosin II. The model predicts that this coupling gives rise to a dynamic instability, whereby cells switch from persistent migration to unidirectional self-oscillation, through a Hopf bifurcation. Cells can then switch to periodic polarity reversals through a homoclinic bifurcation. These predicted dynamic regimes are characterized by robust features that we identify through in vitro trajectories of dendritic cells over long timescales and distances. We expect that competition for limited resources in other migrating cell types can lead to similar deterministic migration modes.
On-Chip Quantitative Measurement of Mechanical Stresses During Cell Migration with Emulsion Droplets.
Laboratoire Biologie cellulaire systémique de la polarité et de la division - D Molino, S Quignard, C Gruget, F Pincet, Y Chen, M Piel, J Fattaccioli
Scientific Reports - 6 29113 - DOI : 10.1038/srep29113 - 2016
The ability of immune cells to migrate within narrow and crowded spaces is a critical feature involved in various physiological processes from immune response to metastasis. Several in-vitro techniques have been developed so far to study the behaviour of migrating cells, the most recent being based on the fabrication of microchannels within which cells move. To address the question of the mechanical stress a cell is able to produce during the encounter of an obstacle while migrating, we developed a hybrid microchip made of parallel PDMS channels in which oil droplets are sparsely distributed and serve as deformable obstacles. We thus show that cells strongly deform droplets while passing them. Then, we show that the microdevice can be used to study the influence of drugs on migration at the population level. Finally, we describe a quantitative analysis method of the droplet deformation that allows measuring in real-time the mechanical stress exerted by a single cell. The method presented herein thus constitutes a powerful analytical tool for cell migration studies under confinement.
FMN2 Makes Perinuclear Actin to Protect Nuclei during Confined Migration and Promote Metastasis
Laboratoire Biologie cellulaire systémique de la polarité et de la division - Skau CT, Fischer RS, Gurel P, Thiam HR, Tubbs A, Baird MA, Davidson MW, Piel M, Alushin GM, Nussenzweig A, Steeg PS, Waterman CM
Cell - 167(6) 1571-1585 - doi: 10.1016/j.cell.2016.10.023 - 2016
ESCRT III repairs nuclear envelope ruptures during cell migration to limit DNA damage and cell death
Laboratoire Biologie cellulaire systémique de la polarité et de la division -  Raab M, Gentili M, de Belly H, Thiam HR, Vargas P, Jimenez AJ, Lautenschlaeger F, Voituriez R, Lennon-Duménil AM, Manel N, Piel M
Science - 352(6283) 359-62 - 359-62 - 2016
Innate control of actin nucleation determines two distinct migration behaviours in dendritic cells
Laboratoire Biologie cellulaire systémique de la polarité et de la division - Vargas P, Maiuri P, Bretou M, Sáez PJ, Pierobon P, Maurin M, Chabaud M, Lankar D, Obino D, Terriac E, Raab M, Thiam HR, Brocker T, Kitchen-Goosen SM, Alberts AS, Sunareni P, Xia S, Li R, Voituriez R, Piel M, Lennon-Duménil AM
Nat. Cell Biol. - 18(1) 43-53 - doi: 10.1038/ncb3284 - 2016
Study of the Stability and Hydrophilicity of Plasma‐Modified Microfluidic Materials
Laboratoire Biophysique et Evolution - Bradley Da Silva Mengxue Zhang Guillaume Schelcher Lea Winter Cédric Guyon Patrick Tabeling Daniel Bonn Michael Tatoulian
Plasma Process - 14 1600034 - https://doi.org/10.1002/ppap.201600034 - 2016
Polymers among new classes of materials such as polydimethylsiloxane (PDMS), cyclic olefin copolymer (COC), Norland optical adhesive (NOA), and THV (fluoropolymer) were evaluated as surface‐modified microfluidic materials, including investigating the incorporation of silica‐like functional groups onto these surfaces. The functionalization of these materials was performed using a hybrid reactor equipped with magnetron sputtering using a silica target and with a PECVD apparatus starting from hexamethyldisiloxane as a chemical precursor. Coated microfluidic materials were then evaluated in terms of wettability, stability, composition, and structure. The deposited coatings were proved to be stable up to 2 month in air and water storage for these materials, with COC providing the most stable substrate.
The development and numerical simulation of a plasma microreactor dedicated to chemical synthesis
Laboratoire Biophysique et Evolution - Mengxue Zhang, Stéphanie Ognier, Nadia Touati, Laurent Binet
Green Processing and Synthesis - 6(1) 61 - DOI: 10.1515/gps-2016-0086 - 2016
A plasma microreactor dedicated to chemical synthesis has been conceived and developed using soft-lithography techniques. In this study, we propose to use highly reactive species created by the plasma discharge to replace traditionally used chemical initiators. A dielectric barrier discharge plasma was generated under atmospheric pressure and then dispersed into a continuous liquid phase with a T-junction geometry. Injected metal electrodes made it possible for in situ optical observations with an intensified charge-coupled device camera. No signal was detected when analyzing the exhaust liquid by electron spin resonance (ESR) spectroscopy. Numerical simulations confirmed that only low quantities of hydroxyl radicals could diffuse into the liquid phase, giving a concentration of DMPO-OH of 10
Large deformation effect in Mode I crack opening displacement of an Agar gel: A comparison of experiment and theory
Laboratoire Biophysique et Evolution - Rong Long, Maxime Lefranc, Elisabeth Bouchaud, Chung-Yuen Hui
 Extreme Mechanics Letters - 9 66-73 - DOI: 10.1016/j.eml.2016.05.005 - 2016
In a recent work, Lefranc and Bouchaud (LB) showed that the Mode I crack opening displacement in a thin sheet of Agar gel deviates significantly from the square root profile predicted by linear elastic fracture mechanics. In this letter we re-examine this problem and show that the experimentally measured crack opening displacement is consistent with the prediction based on finite elastostatics and a hyperelastic strain hardening model.
Absolute 3D reconstruction of thin films topography in microfluidic channels by interference reflection microscopy
Laboratoire Biophysique et Evolution - O. Theodoly, M.-P. Valignat A. Huerre, M.-C. Jullien
Lab. Chip - 16 911 - DOI: 10.1039/C5LC01417D - 2016
The travel of droplets, bubbles, vesicles, capsules, living cells or small organisms in microchannels is a hallmark in microfluidics applications. A full description of the dynamics of such objects requires a quantitative understanding of the complex hydrodynamic and interfacial interactions between objects and channel walls. In this paper, we present an interferometric method that allows absolute topographic reconstruction of the interspace between an object and channel walls for objects confined in microfluidic channels. Wide field microscopic imaging in reflection interference contrast mode (RICM) is directly performed at the bottom wall of microfluidic chips. Importantly, we show that the reflections at both the lower and upper surface of the microchannel have to be considered in the quantitative analysis of the optical signal. More precisely, the contribution of the reflection at the upper surface is weighted depending on the light coherence length and channel height. Using several wavelengths and illumination apertures, our method allows reconstructing the topography of thin films on channel walls in a range of 0–500 nm, with a precision as accurate as 2 nm for the thinnest films. A complete description of the protocol is exemplified for oil in water droplets travelling in channels of height 10–400 μm at a speed up to 5 mm s−1.
Multiscale surface-attached hydrogel thin films with tailored architecture
Laboratoire Biophysique et Evolution - B Chollet, M Li, E Martwong, B Bresson, C Fretigny, P Tabeling, Y Tran
ACS Appl. Mater. Interfaces - 8 (18) 11729-11738 - - 2016
Tailoring Patterns of Surface-Attached Multiresponsive Polymer Networks
Laboratoire Biophysique et Evolution - B Chollet, L D’eramo, E Martwong, M Li, J Macron, TQ Mai, P Tabeling
ACS Appl. Mater. Interfaces - 8 (37) 24870-24879 - - 2016

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579 publications.