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Designing Colloidal Molecules with Microfluidics
Laboratoire Biophysique et Evolution - B Shen, J Ricouvier, F Malloggi, P Tabeling
Advanced Science - 3 (6) - - 2016
Transient compartmentalization of RNA replicators prevents extinction due to parasites
Laboratoire Biophysique et Evolution - 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
Osmotic pressures of lysozyme solutions from gas-like to crystal states
Laboratoire Colloïdes et Matériaux Divisés - Coralie Pasquier,ab Sylvie Beaufils,b Antoine Bouchoux, Sophie Rigault, Bernard Cabane, Mikael Lund, Valérie Lechevalier, Cécile Le Floch-Fouéré, Maryvonne Pasco, Gilles Pabœuf, Javier Pérezf and Stéphane Pezennec
Phys. Chem. - 18 28458-28465 - DOI: 10.1039/C6CP03867K - 2016
We obtained osmotic pressure data of lysozyme solutions, describing their physical states over a wide concentration range, using osmotic stress for pressures between 0.05 bar and about 40 bar and volume fractions between 0.01 and 0.61. The osmotic pressure vs. volume fraction data consist of a dilute, gas-phase regime, a transition regime with a high-compressibility plateau, and a concentrated regime where the system is nearly incompressible. The first two regimes are shifted towards a higher protein volume fraction upon decreasing the strength or the range of electrostatic interactions. We describe this shift and the overall shape of the experimental data in these two regimes through a model accounting for a steric repulsion, a short-range van der Waals attraction and a screened electrostatic repulsion. The transition is caused by crystallization, as shown by small-angle X-ray scattering. We verified that our data points correspond to thermodynamic equilibria, and thus that they consist of the reference experimental counterpart of a thermodynamic equation of state.
Dyneon THV, a fluorinated thermoplastic as a novel material for microchip capillary electrophoresis
Laboratoire Macromolécules et Microsystèmes en Biologie et Médecine - Aboud, N., Ferraro, D., Taverna, M., Descroix, S., Smadja, C., & Tran, N. T.
Analyst - 141(20) 5776-5783 - - 2016
Transient microfluidic compartmentalization using actionable microfilaments for biochemical assays, cell culture and organs-on-chip.
Laboratoire Macromolécules et Microsystèmes en Biologie et Médecine - Yamada A, Renault R, Chikina A, Venzac B, Pereiro I, Coscoy S, Verhulsel M, Parrini MC, Villard C, Viovy JL, Descroix S.
Lab. Chip - 16(24) 16(24) - DOI: 10.1039/c6lc01143h - 2016
We report here a simple yet robust transient compartmentalization system for microfluidic platforms. Cylindrical microfilaments made of commercially available fishing lines are embedded in a microfluidic chamber and employed as removable walls, dividing the chamber into several compartments. These partitions allow tight sealing for hours, and can be removed at any time by longitudinal sliding with minimal hydrodynamic perturbation. This allows the easy implementation of various functions, previously impossible or requiring more complex instrumentation. In this study, we demonstrate the applications of our strategy, firstly to trigger chemical diffusion, then to make surface co-coating or cell co-culture on a two-dimensional substrate, and finally to form multiple cell-laden hydrogel compartments for three-dimensional cell co-culture in a microfluidic device. This technology provides easy and low-cost solutions, without the use of pneumatic valves or external equipment, for constructing well-controlled microenvironments for biochemical and cellular assays.
Asymmetric axonal edge guidance: a new paradigm for building oriented neuronal networks.
Laboratoire Macromolécules et Microsystèmes en Biologie et Médecine - Renault R, Durand JB, Viovy JL, Villard C.
Lab. Chip - 16(12) 2188-91 - doi: 10.1039/c6lc00479b - 2016
We present a novel kind of directional axon guides for brain-on-a-chip applications. Contrarily to previous works, the directionality in our design is created by rerouting axons growing in the unwanted direction back to their original compartment while leaving the other growth direction unaffected. This design yields state-of-the-art levels of directionality without the disadvantages of previously reported technologies.
In-mold patterning and actionable axo-somatic compartmentalization for on-chip neuron culture.
Laboratoire Macromolécules et Microsystèmes en Biologie et Médecine - Yamada A, Vignes M, Bureau C1, Mamane A, Venzac B, Descroix S, Viovy JL, Villard C, Peyrin JM, Malaquin L.
Lab. Chip - 16(11) 2059-68 - doi: 10.1039/c6lc00414h. - 2016
Oriented neuronal networks with controlled connectivity are required for many applications ranging from studies of neurodegeneration to neuronal computation. To build such networks in vitro, an efficient, directed and long lasting guidance of axons toward their target is a pre-requisite. The best guidance achieved so far, however, relies on confining axons in enclosed microchannels, making them poorly accessible for further investigation. Here we describe a method providing accessible and highly regular arrays of axons, emanating from somas positioned in distinct compartments. This method combines the use of a novel removable partition, allowing soma positioning outside of the axon guidance patterns, and in-mold patterning (iMP), a hybrid method combining chemical and mechanical cell positioning clues applied here for the first time to neurons. The axon guidance efficiency of iMP is compared to that of conventional patterning methods, e.g. micro-contact printing (chemical constraints by a poly-l-lysine motif) and micro-grooves (physical constraints by homogeneously coated microstructures), using guiding tracks of different widths and spacing. We show that iMP provides a gain of 10 to 100 in axon confinement efficiency on the tracks, yielding mm-long, highly regular, and fully accessible on-chip axon arrays. iMP also allows well-defined axon guidance from small populations of several neurons confined at predefined positions in μm-sized wells. iMP will thus open new routes for the construction of complex and accurately controlled neuronal networks.
Micro-Nano-Bio Diagnostic System for Food Pathogen Detection Revolutionizes Food Safety Management & Protects Consumers Health.
Laboratoire Macromolécules et Microsystèmes en Biologie et Médecine - Gogolides E1, Tserepi A, Jobst G, Friedt JM, Rabus D, Dupuy B, Bilkova Z, Descroix S, Viovy JL, Papadakis G, Gizeli E.
Lab. Chip - 224 67-72 - - 2016
The development of integrated, fast and affordable platforms for pathogen detection is an emerging area where a multidisciplinary approach is necessary for designing microsystems employing miniaturized devices; these new technologies promise a significant advancement of the current state of analytical testing leading to improved healthcare. In this work, the development of a lab-on-chip microsystem platform for the genetic analysis of Salmonella in milk samples is presented. The heart of the platform is an acoustic detection biochip, integrated with a microfluidic module. This detection platform is combined with a micro-processor, which, alongside with magnetic beads technology and a DNA micro-amplification module, are responsible for performing sample pre-treatment, bacteria lysis, nucleic acid purification and amplification. Automated, multiscale manipulation of fluids in complex microchannel networks is combined with novel sensing principles developed by some of the partners. This system is expected to have a significant impact in food-pathogen detection by providing for the first time an integrated detection test for Salmonella screening in a very short time. Finally, thanks to the low cost and compact technologies involved, the proposed set-up is expected to provide a competitive analytical platform for direct application in field settings.
Microfluidic platform combining droplets and magnetic tweezers: application to HER2 expression in cancer diagnosis
Laboratoire Macromolécules et Microsystèmes en Biologie et Médecine - Davide Ferraro, Jérôme Champ, Bruno Teste, Marco Serra, Laurent Malaquin, Jean-Louis Viovy, Patricia de Cremoux & Stephanie Descroix
Scientific Reports - 25540 67-72 - DOI : 10.1038/srep25540 - 2016
The development of precision medicine, together with the multiplication of targeted therapies and associated molecular biomarkers, call for major progress in genetic analysis methods, allowing increased multiplexing and the implementation of more complex decision trees, without cost increase or loss of robustness. We present a platform combining droplet microfluidics and magnetic tweezers, performing RNA purification, reverse transcription and amplification in a fully automated and programmable way, in droplets of 250nL directly sampled from a microtiter-plate. This platform decreases sample consumption about 100 fold as compared to current robotized platforms and it reduces human manipulations and contamination risk. The platform’s performance was first evaluated on cell lines, showing robust operation on RNA quantities corresponding to less than one cell and then clinically validated with a cohort of 21 breast cancer samples, for the determination of their HER2 expression status, in a blind comparison with an established routine clinical analysis.
Massive radius-dependent flow slippage in carbon nanotubes
Laboratoire Micromégas - Eleonora Secchi, Sophie Marbach, Antoine Niguès, Derek Stein, Alessandro Siria & Lydéric Bocquet
Nature - 537 210–213 - DOI: 10.1038/nature19315 - 2016
Measurements and simulations have found that water moves through carbon nanotubes at exceptionally high rates owing to nearly frictionless interfaces1, 2, 3, 4. These observations have stimulated interest in nanotube-based membranes for applications including desalination, nano-filtration and energy harvesting5, 6, 7, 8, 9, 10, yet the exact mechanisms of water transport inside the nanotubes and at the water–carbon interface continue to be debated11, 12 because existing theories do not provide a satisfactory explanation for the limited number of experimental results available so far13. This lack of experimental results arises because, even though controlled and systematic studies have explored transport through individual nanotubes7, 8, 9, 14, 15, 16, 17, none has met the considerable technical challenge of unambiguously measuring the permeability of a single nanotube11. Here we show that the pressure-driven flow rate through individual nanotubes can be determined with unprecedented sensitivity and without dyes from the hydrodynamics of water jets as they emerge from single nanotubes into a surrounding fluid. Our measurements reveal unexpectedly large and radius-dependent surface slippage in carbon nanotubes, and no slippage in boron nitride nanotubes that are crystallographically similar to carbon nanotubes, but electronically different. This pronounced contrast between the two systems must originate from subtle differences in the atomic-scale details of their solid–liquid interfaces, illustrating that nanofluidics is the frontier at which the continuum picture of fluid mechanics meets the atomic nature of matter.
Randomness and cell fate
Laboratoire Biochimie - Nghe P
Med Sci (Paris). - 31(10): 889-94 - doi: 10.1051/medsci/20153110015 - 2015
Thermal fluctuations at the molecular scale cause random fluctuations of gene expression, which, in association with differentiation circuits, can lead to phenotypic diversification in cell populations. In this synthesis article, we detail the mechanisms that generate this diversification and illustrate their consequences in various organisms. In bacteria, random phenotypic diversification allows to anticipate environmental changes that are otherwise unpredictable, in particular during metabolic transitions and stress responses, for example inducing a transient form of antibiotic resistance. In multi-cellular organisms, similar mechanisms allow the maintenance of healthy tissues, such as intestinal crypts, epidermis and retina, but also seem to play a role in establishment and renewal of tumoral heterogeneity.
Prebiotic network evolution: six key parameters
Laboratoire Biochimie - Philippe Nghe,a Wim Hordijk,b Stuart A. Kauffman,c Sara I. Walker,d Francis J. Schmidt,e Harry Kemble,a Jessica A. M. Yeatesf and Niles Lehman
Molecular Systems Biology - 11 3206-3217 - DOI: 10.1039/C5MB00593K - 2015
The origins of life likely required the cooperation among a set of molecular species interacting in a network. If so, then the earliest modes of evolutionary change would have been governed by the manners and mechanisms by which networks change their compositions over time. For molecular events, especially those in a pre-biological setting, these mechanisms have rarely been considered. We are only recently learning to apply the results of mathematical analyses of network dynamics to prebiotic events. Here, we attempt to forge connections between such analyses and the current state of knowledge in prebiotic chemistry. Of the many possible influences that could direct primordial network, six parameters emerge as the most influential when one considers the molecular characteristics of the best candidates for the emergence of biological information: polypeptides, RNA-like polymers, and lipids. These parameters are viable cores, connectivity kinetics, information control, scalability, resource availability, and compartmentalization. These parameters, both individually and jointly, guide the aggregate evolution of collectively autocatalytic sets. We are now in a position to translate these conclusions into a laboratory setting and test empirically the dynamics of prebiotic network evolution.
Activity-Fed Translation (AFT) Assay: A New High-Throughput Screening Strategy for Enzymes in Droplets
Laboratoire Biochimie - Woronoff G, Ryckelynck M, Wessel J, Schicke O, Griffiths A, Soumillion P
Chembiochem - 16(9) 1343-9 - doi: 10.1002/cbic.201500087 - 2015
There is an increasing demand for the development of sensitive enzymatic assays compatible with droplet-based microfluidics. Here we describe an original strategy, activity-fed translation (AFT), based on the coupling of enzymatic activity to in vitro translation of a fluorescent protein. We show that methionine release upon the hydrolysis of phenylacetylmethionine by penicillin acylase enabled in vitro expression of green fluorescent protein. An autocatalytic setup where both proteins are expressed makes the assay highly sensitive, as fluorescence was detected in droplets containing single PAC genes. Adding a PCR step in the droplets prior to the assay increased the sensitivity further. The strategy is potentially applicable for any activity that can be coupled to the production of an amino acid, and as the microdroplet volume is small the use of costly reagents such as in vitro expression mixtures is not limiting for high-throughput screening projects.
Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions
Laboratoire Biochimie - Michael Ryckelynck, Stéphanie Baudrey, Christian Rick, Annick Marin, Faith Coldren, Eric Westhof, and Andrew D. Griffiths
RNA. - 21(3) 458–469 - doi: 10.1261/rna.048033.114 - 2015
In vitro evolution methodologies are powerful approaches to identify RNA with new functionalities. While Systematic Evolution of Ligands by Exponential enrichment (SELEX) is an efficient approach to generate new RNA aptamers, it is less suited for the isolation of efficient ribozymes as it does not select directly for the catalysis. In vitro compartmentalization (IVC) in aqueous droplets in emulsions allows catalytic RNAs to be selected under multiple-turnover conditions but suffers severe limitations that can be overcome using the droplet-based microfluidics workflow described in this paper. Using microfluidics, millions of genes in a library can be individually compartmentalized in highly monodisperse aqueous droplets and serial operations performed on them. This allows the different steps of the evolution process (gene amplification, transcription, and phenotypic assay) to be uncoupled, making the method highly flexible, applicable to the selection and evolution of a variety of RNAs, and easily adaptable for evolution of DNA or proteins. To demonstrate the method, we performed cycles of random mutagenesis and selection to evolve the X-motif, a ribozyme which, like many ribozymes selected using SELEX, has limited multiple-turnover activity. This led to the selection of variants, likely to be the optimal ribozymes that can be generated using point mutagenesis alone, with a turnover number under multiple-turnover conditions, ksscat, ∼28-fold higher than the original X-motif, primarily due to an increase in the rate of product release, the rate-limiting step in the multiple-turnover reaction.
Random fluctuations, metabolism and growth at the single-cell level
Laboratoire Biochimie - Nghe, P., Boulineau, S., & Tans, S. J.
Med Sci (Paris). - 1(3) 233 - - 2015
Optical volume and mass measurements show that mammalian cells swell during mitosis.
Laboratoire Biologie cellulaire systémique de la polarité et de la division - Zlotek-Zlotkiewicz E, Monnier S, Cappello G, Le Berre M, Piel M
J. Cell Biol. - 211( 4): 765-74 - DOI: 10.1016/j.jim.2015.12.005 - 2015
The extent, mechanism, and function of cell volume changes during specific cellular events, such as cell migration and cell division, have been poorly studied, mostly because of a lack of adequate techniques. Here we unambiguously report that a large range of mammalian cell types display a significant increase in volume during mitosis (up to 30%). We further show that this increase in volume is tightly linked to the mitotic state of the cell and not to its spread or rounded shape and is independent of the presence of an intact actomyosin cortex. Importantly, this volume increase is not accompanied by an increase in dry mass and thus corresponds to a decrease in cell density. This mitotic swelling might have important consequences for mitotic progression: it might contribute to produce strong pushing forces, allowing mitotic cells to round up; it might also, by lowering cytoplasmic density, contribute to the large change of physicochemical properties observed in mitotic cells.
Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.
Laboratoire Biologie cellulaire systémique de la polarité et de la division - Maiuri P, Rupprecht J-F, Wieser S, Ruprecht V, Bénichou O, Carpi N, Coppey M, De Beco S, Gov N, Heisenberg C-P, Lage Crespo C, Lautenschlaeger F, Le Berre M, Lennon-Dumenil A-M, Raab M, Thiam H-R, Piel M, Sixt M, Voituriez R
Cell - 161(2) 374-86 - DOI: 10.1016/j.cell.2015.01.056 - 2015
Cell movement has essential functions in development, immunity, and cancer. Various cell migration patterns have been reported, but no general rule has emerged so far. Here, we show on the basis of experimental data in vitro and in vivo that cell persistence, which quantifies the straightness of trajectories, is robustly coupled to cell migration speed. We suggest that this universal coupling constitutes a generic law of cell migration, which originates in the advection of polarity cues by an actin cytoskeleton undergoing flows at the cellular scale. Our analysis relies on a theoretical model that we validate by measuring the persistence of cells upon modulation of actin flow speeds and upon optogenetic manipulation of the binding of an actin regulator to actin filaments. Beyond the quantitative prediction of the coupling, the model yields a generic phase diagram of cellular trajectories, which recapitulates the full range of observed migration patterns.
A computational mechanics approach to assess the link between cell morphology and forces during confined migration.
Laboratoire Biologie cellulaire systémique de la polarité et de la division - Aubry D, Thiam H, Piel M, Allena R
Biomech Model Mechanobiol - 14(1): 143-57 - DOI: 10.1016/bs.mcb.2014.11.007 - 2015
Confined migration plays a fundamental role during several biological phenomena such as embryogenesis, immunity and tumorogenesis. Here, we propose a two-dimensional mechanical model to simulate the migration of a HeLa cell through a micro-channel. As in our previous works, the cell is modelled as a continuum and a standard Maxwell model is used to describe the mechanical behaviour of both the cytoplasm (including active strains) and the nucleus. The cell cyclically protrudes and contracts and develops viscous forces to adhere to the substrate. The micro-channel is represented by two rigid walls, and it exerts an additional viscous force on the cell boundaries. We test four channels whose dimensions in terms of width are i) larger than the cell diameter, ii) sub-cellular, ii) sub-nuclear and iv) much smaller than the nucleus diameter. The main objective of the work is to assess the necessary conditions for the cell to enter into the channel and migrate through it. Therefore, we evaluate both the evolution of the cell morphology and the cell-channel and cell-substrate surface forces, and we show that there exists a link between the two, which is the essential parameter determining whether the cell is permeative, invasive or penetrating.
Confinement and low adhesion induce fast amoeboid migration of slow mesenchymal cells.
Laboratoire Biologie cellulaire systémique de la polarité et de la division - Liu Y-J, Le Berre M, Lautenschlaeger F, Maiuri P, Callan-Jones A, Heuzé M, Takaki T, Voituriez R, Piel M
Cell - 160( 4): 659-72 - DOI: 10.1016/j.cell.2015.01.007 - 2015
The mesenchymal-amoeboid transition (MAT) was proposed as a mechanism for cancer cells to adapt their migration mode to their environment. While the molecular pathways involved in this transition are well documented, the role of the microenvironment in the MAT is still poorly understood. Here, we investigated how confinement and adhesion affect this transition. We report that, in the absence of focal adhesions and under conditions of confinement, mesenchymal cells can spontaneously switch to a fast amoeboid migration phenotype. We identified two main types of fast migration-one involving a local protrusion and a second involving a myosin-II-dependent mechanical instability of the cell cortex that leads to a global cortical flow. Interestingly, transformed cells are more prone to adopt this fast migration mode. Finally, we propose a generic model that explains migration transitions and predicts a phase diagram of migration phenotypes based on three main control parameters: confinement, adhesion, and contractility.
Laser induced wounding of the plasma membrane and methods to study the repair process.
Laboratoire Biologie cellulaire systémique de la polarité et de la division - Jimenez AJ, Maiuri P, Lafaurie-Janvore J, Perez F, Piel M
Methods Cell Biol. - 5.2083333333 391-408 - DOI: 10.1016/bs.mcb.2014.11.007 - 2015
Cells are constantly exposed to agents that can trigger the perforation of their plasma membrane. This damage occurs naturally, and the frequency and intensity depends on how much cells are exposed to damaging threats. The following protocol is a simple and powerful method to damage the plasma membrane using laser ablation. It allows the induction of a single and localized wound at the plasma membrane of cultured cells, which can be followed with fast time-lapse imaging. The first part of the protocol describes simple cell culture techniques and the material ideal to make the experiments. A second part of the protocol gives advice about the procedures to make effective wounds in cells while ensuring a good survival rate. We also propose different ways to follow the opening and closure of the plasma membrane. Finally, we describe the procedure to efficiently analyze the data acquired after single cell photodamage to characterize the wounding process.


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