Université PSL

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Mechanically activated ionic transport across single-digit carbon nanotubes
Laboratoire Micromégas - Alice Marcotte, Timothée Mouterde, Antoine Niguès, Alessandro Siria & Lydéric Bocquet
Nature Materials - 19 1057–1061 - https://doi.org/10.1146/annurev-fluid-071320-095958 - 2020
Fluid and ionic transport at the nanoscale has recently demonstrated a wealth of exotic behaviours1,2,3,4,5,6,7,8,9,10,11,12,13,14. However, artificial nanofluidic devices15,16,17,18 are still far from demonstrating the advanced functionalities existing in biological systems, such as electrically and mechanically activated transport19,20. Here, we focus on ionic transport through 2-nm-radius individual multiwalled carbon nanotubes under the combination of mechanical and electrical forcings. Our findings evidence mechanically activated ionic transport in the form of an ionic conductance that depends quadratically on the applied pressure. Our theoretical study relates this behaviour to the complex interplay between electrical and mechanical drivings, and shows that the superlubricity of the carbon nanotubes4,5,6,7,8,21 is a prerequisite to attaining mechanically activated transport. The pressure sensitivity shares similarities with the response of biological mechanosensitive ion channels19,20, but observed here in an artificial system. This paves the way to build new active nanofluidic functionalities inspired by complex biological machinery
Studying polymer diffusiophoresis with non-equilibrium molecular dynamics
Laboratoire Micromégas - S. Ramírez-Hinestrosa, H. Yoshida, L. Bocquet, and D. Frenkel
Chem. Phys - 152 164901 - https://doi.org/10.1063/5.0007235 - 2020
We report a numerical study of the diffusiophoresis of short polymers using non-equilibrium molecular dynamics simulations. More precisely, we consider polymer chains in a fluid containing a solute that has a concentration gradient and examine the variation of the induced diffusiophoretic velocity of the polymer chains as the interaction between the monomer and the solute is varied. We find that there is a non-monotonic relation between the diffusiophoretic mobility and the strength of the monomer–solute interaction. In addition, we find a weak dependence of the mobility on the length of the polymer chain, which shows clear difference from the diffusiophoresis of a solid particle. Interestingly, the hydrodynamic flow through the polymer is much less screened than for pressure driven flows.
Nanofluidics coming of age
Laboratoire Micromégas - Lydéric Bocquet
Nature Materials - 19 254–256 - https://doi.org/10.1038/s41563-020-0625-8 - 2020
This is a turning point for nanofluidics. Recent progress allows envisioning both fundamental discoveries for the transport of fluids at the ultimate scales, and disruptive technologies for the water–energy nexus
Local and global force balance for diffusiophoretic transport
Laboratoire Micromégas - S. Marbach , H. Yoshida and L. Bocquet
J. Fluid Mech - 892 - doi:10.1017/jfm.2020.137 - 2020
Electro- and diffusio-phoresis of particles correspond respectively to the transport of particles under electric field and solute concentration gradients. Such interfacial transport phenomena take their origin in a diffuse layer close to the particle surface, and the motion of the particle is force free. In the case of electrophoresis, it is further expected that the stress acting on the moving particle vanishes locally as a consequence of local electroneutrality. But the argument does not apply to diffusiophoresis, which takes its origin in solute concentration gradients. In this paper we investigate further the local and global force balance on a particle undergoing diffusiophoresis. We calculate the local tension applied on the particle surface and show that, counter-intuitively, the local force on the particle does not vanish for diffusiophoresis, in spite of the global force being zero, as expected. Incidentally, our description allows us to clarify the osmotic balance in diffusiophoresis, which has been a source of debate in recent years. We explore various cases, including hard and soft interactions, as well as porous particles, and provide analytic predictions for the local force balance in these various systems. The existence of local stresses may induce deformation of soft particles undergoing diffusiophoresis, hence suggesting applications in terms of particle separation based on capillary diffusiophoresis.
Liquid-liquid coffee-ring effect.
Laboratoire Nanobioscience et Microsystèmes group - Vincent Poulichet,Mathieu Morel,Sergii Rudiuk,Damien Baigl
Journal of Colloid and Interface Science - - DOI: 10.1016/j.jcis.2020.03.094 - 2020
The so-called coffee-ring effect (CRE) is extraordinarily common, problematic in industry and attractively puzzling for researchers, with the accepted rule that it requires two key-ingredients: solvent evaporation and contact line pinning. Here, we demonstrate that the CRE also occurs when the solvent of a pinned sessile drop transfers into another liquid, without involving any evaporation. We show that it shares all characteristic features of the evaporative CRE: solvent transfer-driven transport of solutes to the contact line, ring-shaped deposit, closely-packed particle organization at the contact line, and size-dependent particle sorting. We thus suggest expanding the definition of the coffee-ring effect to any pinned drop having its solvent transferring to an outer medium where the drop compounds cannot be dissolved.
Liquid-liquid coffee-ring effect
Laboratoire Nanobioscience et Microsystèmes group - Vincent Poulichet,Mathieu Morel,Sergii Rudiuk,Damien Baigl
X-MOL - - DOI: 10.1016/j.jcis.2020.03.094 - 2020
The so-called coffee-ring effect (CRE) is extraordinarily common, problematic in industry and attractively puzzling for researchers, with the accepted rule that it requires two key-ingredients: solvent evaporation and contact line pinning. Here, we demonstrate that the CRE also occurs when the solvent of a pinned sessile drop transfers into another liquid, without involving any evaporation. We show that it shares all characteristic features of the evaporative CRE: solvent transfer-driven transport of solutes to the contact line, ring-shaped deposit, closely-packed particle organization at the contact line, and size-dependent particle sorting. We thus suggest expanding the definition of the coffee-ring effect to any pinned drop having its solvent transferring to an outer medium where the drop compounds cannot be dissolved.
Self-Propelled Water Drops on Bare Glass Substrates in Air: Fast, Controllable, and Easy Transport Powered by Surfactants
Laboratoire Nanobioscience et Microsystèmes group - Pauline E. Galy, Sergii Rudiuk, Mathieu Morel, and Damien Baigl
Langmuir - 36, 25 6916–6923 - doi : 10.1021/acs.langmuir.9b03727 - 2020
Self-propelled drops are capable of motion without external intervention. As such, they constitute attractive entities for fundamental investigations in active soft matter, hydrodynamics, and surface sciences, as well as promising systems for autonomous microfluidic operations. In contrast with most of the examples relying on organic drops or specifically treated substrates, here we describe the first system of nonreactive water drops in air that can propel themselves on a commercially available ordinary glass substrate that was used as received. This is achieved by exploiting the dynamic adsorption behavior of common n-alkyltrimethylammonium bromide (CnTAB) surfactants added to the drop. We precisely analyze the drop motion for a broad series of surfactants carrying n = 6 to 18 carbon atoms in their tail and establish how the motion characteristics (speed, probability of motion) are tuned by both the hydrophobicity and the concentration of the surfactant. We show that motion occurs regardless of the n value but only in a specific concentration range with a maximum speed at around one tenth of the critical micelle concentration (CMC/10) for most of the tested surfactants. Surfactants of intermediate hydrophobicity are shown to be the best candidates to power drops that can move at a high speed (1–10 cm s–1), the optimal performance being reached with [C12TAB] = 800 μM. We propose a mechanism where the motion originates from the anisotropic wettability of the substrate created by the electrostatic adsorption of surfactants beneath the moving drop. Simply drawing lines with a marker pen allows us to create guiding paths for drop motion and to achieve operations such as complex trajectory control, programmed drop fusion, drop refilling, as well as drop moving vertically against gravity. This work revisits the role of surfactants in dynamic wetting and self-propelled motion as well as brings an original strategy to build the future of microfluidics with lower-cost, simpler, and more autonomous portable devices that could be made available to everyone and everywhere.

From bulk crystallization of inorganic nanoparticles at the air/water interface: tunable organization and intense structural colors
Laboratoire Nanobioscience et Microsystèmes group - Jacopo Vialetto,Sergii Rudiuk,Mathieu Morel,Damien Baigl
Nanoscale - 36, 25 6916–6923 - DOI: 10.1039/c9nr10965j - 2020
The "flipping method" is a new straightforward way to both adsorb and organize microparticles at a liquid interface, with ultralow amounts of a surfactant and no other external forces than gravity. Here we demonstrate that it allows the adsorption of a variety of inorganic nanoparticles at an air/water interface, in an organized way, which is directly controlled by the surfactant concentration, ranging from amorphous to highly crystalline two-dimensional assemblies. With micromolar amounts of a conventional cationic surfactant (dodecyltrimethylammonium bromide, DTAB), nanoparticles of different compositions (silica, silver, and gold), sizes (down to 100 nm) and shapes (spheres and cubes) adsorb from the bulk and directly organize at the air/water interface, resulting in marked optical properties such as reflectivity or intense structural coloration.

Stereo Darkfield Interferometry : a versatile localization method for subnanometer force spectroscopy of single molecules and 3D-tracking of single cells
Laboratoire Physique des biomolécules - Martin Rieu, Thibault Vieille, Gaël Radou, Raphaël Jeanneret, Nadia Ruiz, Bertrand Ducos, Jean-François Allemand, Vincent Croquette
Biological Physics - - DOI:10.1126/sciadv.abe3902 - 2020
Super-resolutive 3D tracking, such as PSF engineering or evanescent field imaging has long been used to track microparticles and to enhance the throughput of single molecules force spectroscopic measurements. However, current methods present two drawbacks. First, they lack precision compared with optical tweezers or AFM. Second, the dependence of their signal upon the position is complex creating the need for a time-consuming calibration step.
Here, we introduce a new optical technique that circumvents both issues and allows for a simple, versatile and efficient 3D tracking of diluted particles while offering a sub-nanometer frame-to-frame precision in all three spatial directions. The principle is to combine stereoscopy and interferometry, such that the z (axial) position is measured through the distance between two interferometric fringe patterns. The linearity of this stereoscopy technique alleviates the need for lookup tables while the structured interferometric pattern enhances precision. On the other hand, the extended spatial footprint of this PSF maximizes the number of photons detected per frame without the need of fancy cameras, nor the need for complex hardware. Hence, thanks to its simplicity and versatility, we believe that SDI (Stereo Darkfield Interferometry) technology has the potential to significantly enhance the spreading of 3D tracking.
We demonstrate the efficiency of this technique on various single-molecule measurements thanks to magnetic tweezers. In particular we demonstrate the precise quantification of two-state dynamics involving axial steps as short as 1 nm. We then show that SDI can be directly embedded in a commercial objective providing a means to track multiple single cells in 3D .
Visualizing the dynamics of exported bacterial proteins with the chemogenetic fluorescent reporter FAST
Laboratoire Physique des biomolécules - Chekli, Yankel; Peron-Cane, Caroline; Dell'Arciprete, Dario; Allemand, Jean-François; Li, Chenge; Ghigo, Jean-Marc; Gautier, Arnaud; Lebreton, Alice; Desprat, Nicolas; Beloin, Christophe
Scientific Reports - 10(1) 15791 - 10.1038/s41598-020-72498-2 - 2020
Bacterial proteins exported to the cell surface play key cellular functions. However, despite the interest to study the localisation of surface proteins such as adhesins, transporters or hydrolases, monitoring their dynamics in live imaging remains challenging, due to the limited availability of fluorescent probes remaining functional after secretion. In this work, we used the Escherichia coli intimin and the Listeria monocytogenes InlB invasin as surface exposed scaffolds fused with the recently developed chemogenetic fluorescent reporter protein FAST. Using both membrane permeant (HBR-3,5DM) and non-permeant (HBRAA-3E) fluorogens that fluoresce upon binding to FAST, we demonstrated that fully functional FAST can be exposed at the cell surface and used to specifically tag the external side of the bacterial envelop in both diderm and monoderm bacteria. Our work opens new avenues to study the organization and dynamics of the bacterial cell surface proteins.
Fluorescent secreted bacterial effectors reveal active intravacuolar proliferation of Listeria monocytogenes in epithelial cells
Laboratoire Physique des biomolécules - Peron-Cane, Caroline; Fernandez, José-Carlos; Leblanc, Julien; Wingertsmann, Laure; Gautier, Arnaud; Desprat, Nicolas; Lebreton, Alice
journal article - 16(10) e1009001 - 10.1371/journal.ppat.1009001 - 2020
Real-time imaging of bacterial virulence factor dynamics is hampered by the limited number of fluorescent tools suitable for tagging secreted effectors. Here, we demonstrated that the fluorogenic reporter FAST could be used to tag secreted proteins, and we implemented it to monitor infection dynamics in epithelial cells exposed to the human pathogen Listeria monocytogenes (Lm). By tracking individual FAST-labelled vacuoles after Lm internalisation into cells, we unveiled the heterogeneity of residence time inside entry vacuoles. Although half of the bacterial population escaped within 13 minutes after entry, 12% of bacteria remained entrapped over an hour inside long term vacuoles, and sometimes much longer, regardless of the secretion of the pore-forming toxin listeriolysin O (LLO). We imaged LLO-FAST in these long-term vacuoles, and showed that LLO enabled Lm to proliferate inside these compartments, reminiscent of what had been previously observed for Spacious Listeria-containing phagosomes (SLAPs). Unexpectedly, inside epithelial SLAP-like vacuoles (eSLAPs), Lm proliferated as fast as in the host cytosol. eSLAPs thus constitute an alternative replication niche in epithelial cells that might promote the colonization of host tissues.s.
Fluorescence-free quantification of protein/nucleic-acid binding through single-molecule kinetic locking
Laboratoire Physique des biomolécules - Martin Rieu; Valle-Orero, Jessica; Ducos, Bertrand; Allemand, Jean-François; Croquette, Vincent
bioRxiv - - 10.1101/2020.09.30.321232 - 2020
Fluorescence-free micro-manipulation of nucleic acids (NA) allows the functional characterization of DNA/RNA processing proteins, without the interference of labels, but currently fails to detect and quantify their binding. To overcome this limitation, we developed a new method based on single-molecule force spectroscopy, called kinetic locking, that allows a direct in vitro visualization of protein binding while avoiding any kind of chemical disturbance of the protein’s natural function. We validate kinetic locking by measuring accurately the hybridization energy of ultrashort nucleotides (5,6,7 bases) and use it to measure the dynamical interactions of E. coli RecQ helicase with its DNA substrate.Competing Interest StatementThe authors have declared no competing interest.
Dynamic Contrast for Plant Phenotyping
Laboratoire Pôle de chimie physique et biologique de la matière vivante - Zsolt Kelemen, Ruikang Zhang, Lionel Gissot, Raja Chouket, Yannick Bellec, Vincent Croquette, Ludovic Jullien, Jean-Denis Faure, and Thomas Le Saux
ACS Omega - 5(25) 15105–15114 - https://doi.org/10.1021/acsomega.0c00957 - 2020
Noninvasiveness, minimal handling, and immediate response are favorable features of fluorescence readout for high-throughput phenotyping of labeled plants.Yet, remote fluorescence imaging may suffer from an autofluorescent background and artificial or natural ambient light. In this work, the latter limitations are overcome by adopting reversibly photoswitchable fluorescent proteins (RSFPs) as labels and Speed OPIOM (out-of-phase imaging after optical modulation), a fluorescence imaging protocol exploiting dynamic contrast. Speed OPIOM can efficiently distinguish the RSFP signal from autofluorescence and other spectrally interfering fluorescent reporters like GFP. It can quantitatively assess gene expressions, even when they are weak. It is as quantitative, sensitive, and robust in dark and bright light conditions. Eventually, it can be used to nondestructively record abiotic stress responses like water or iron limitations in real time at the level of individual plants and even of specific organs. Such Speed OPIOM validation could find numerous applications to identify plant lines in selection programs, design plants as environmental sensors, or ecologically monitor transgenic plants in the environment.

Dynamic contrast for overcoming spectral interferences in fluorescence imaging
Laboratoire Pôle de chimie physique et biologique de la matière vivante - R Chouket, A Pellissier-Tanon, A Lemarchand, A Espagne, T Le Saux and L Jullien
Journal of Physics: Photonics - 2(3) - - 2020
Fluorescence has become a ubiquitous observable in biology. Yet it encounters limitations, which may originate from optical interferences such as ambient light, autofluorescence, and spectrally interfering fluorophores. In this review, we first report on dynamic contrast which can overcome these limitations. Then we specifically describe out-of-phase imaging after optical modulation, which proved relevant for multiplexed fluorescence imaging even under adverse optical conditions with several optical setups.
Dynamic contrast with reversibly photoswitchable fluorescent labels for imaging living cells
Laboratoire Pôle de chimie physique et biologique de la matière vivante - Raja Chouket, Agnès Pellissier-Tanon, Annie Lemarchand, Agathe Espagne, Thomas Le Sauxa and Ludovic Jullien
Chem. Sci - 11 2882-2887 - doi.org/10.1039/D0SC00182A - 2020
Interrogating living cells requires sensitive imaging of a large number of components in real time. The state-of-the-art of multiplexed imaging is usually limited to a few components. This review reports on the promise and the challenges of dynamic contrast to overcome this limitation.

Active diffusion in oocytes nonspecifically centers large objects during prophase I and meiosis I
Laboratoire Pôle de chimie physique et biologique de la matière vivante - Alexandra Colin, Gaëlle Letort, Nitzan Razin, Maria Almonacid, Wylie Ahmed, Timo Betz, Marie-Emilie Terret, Nir S Gov, Raphaël Voituriez, Zoher Gueroui, Marie-Hélène Verlhac
J Cell Biol - 219(3) e201908195 - doi: 10.1083/jcb.201908195 - 2020
Nucleus centering in mouse oocytes results from a gradient of actin-positive vesicle activity and is essential for developmental success. Here, we analyze 3D model simulations to demonstrate how a gradient in the persistence of actin-positive vesicles can center objects of different sizes. We test model predictions by tracking the transport of exogenous passive tracers. The gradient of activity induces a centering force, akin to an effective pressure gradient, leading to the centering of oil droplets with velocities comparable to nuclear ones. Simulations and experimental measurements show that passive particles subjected to the gradient exhibit biased diffusion toward the center. Strikingly, we observe that the centering mechanism is maintained in meiosis I despite chromosome movement in the opposite direction; thus, it can counteract a process that specifically off-centers the spindle. In conclusion, our findings reconcile how common molecular players can participate in the two opposing functions of chromosome centering versus off-centering.


Engineering E. coli for Magnetic Control and the Spatial Localization of Functions
Laboratoire Pôle de chimie physique et biologique de la matière vivante - Mary Aubry, Wei-An Wang, Yohan Guyodo, Eugénia Delacou, Jean-Michel Guigner, Olivier Espeli, Alice Lebreton, François Guyot, Zoher Gueroui
ACS Synth Biol - 9(11) 3030-3041 - doi: 10.1021/acssynbio.0c00286 - 2020
The fast-developing field of synthetic biology enables broad applications of programmed microorganisms including the development of whole-cell biosensors, delivery vehicles for therapeutics, or diagnostic agents. However, the lack of spatial control required for localizing microbial functions could limit their use and induce their dilution leading to ineffective action or dissemination. To overcome this limitation, the integration of magnetic properties into living systems enables a contact-less and orthogonal method for spatiotemporal control. Here, we generated a magnetic-sensing Escherichia coli by driving the formation of iron-rich bodies into bacteria. We found that these bacteria could be spatially controlled by magnetic forces and sustained cell growth and division, by transmitting asymmetrically their magnetic properties to one daughter cell. We combined the spatial control of bacteria with genetically encoded-adhesion properties to achieve the magnetic capture of specific target bacteria as well as the spatial modulation of human cell invasions.



An Epigenetic Priming Mechanism Mediated by Nutrient Sensing Regulates Transcriptional Output
Laboratoire pour la biologie quantitative du développement - Natalia Stec, Katja Doerfel, Kelly Hills-Muckey, Victoria M. Ettorre, Sevinc Ercan, Wolfgang Keil, C. M. Hammell
bioRxiv - - doi.org/10.1101/2020.09.01.278127 - 2020
While precise tuning of gene expression levels is critical for most developmental pathways, the mechanisms by which the transcriptional output of dosage-sensitive molecules is established or modulated by the environment remain poorly understood. Here, we provide a mechanistic framework for how the conserved transcription factor BLMP-1/Blimp1 operates as a pioneer factor to decompact chromatin near its target loci hours before transcriptional activation and by doing so, regulates both the duration and amplitude of subsequent target gene transcription. This priming mechanism is genetically separable from the mechanisms that establish the timing of transcriptional induction and functions to canalize aspects of cell-fate specification, animal size regulation, and molting. A key feature of the BLMP-1-dependent transcriptional priming mechanism is that chromatin decompaction is initially established during embryogenesis and maintained throughout larval development by nutrient sensing. This anticipatory mechanism integrates transcriptional output with environmental conditions and is essential for resuming normal temporal patterning after animals exit nutrient-mediated developmental arrests.
Electrocatalytic behaviour of CeZrOx-supported Ni catalysts in plasma assisted CO2 methanation
Laboratoire Procédés - Plasmas - Microsystèmes - Maria Mikhail, Patrick Da Costa, Jacques Amouroux, Siméon Cavadias, Michael Tatoulian, Stéphanie Ognier and María Elena Gálvez
Catalys Science & Technology - 10 4532-4543 - https://doi.org/10.1039/D0CY00312C - 2020
Plasma-catalytic and thermo-catalytic methanation were assayed in the presence of a CeZrOx-supported Ni catalyst, proving that high CO2 conversions and high methane yields can be obtained under dielectric barrier discharge (DBD) plasma conditions and that they are maintained with time-on-stream over 100 h operating time. The characterization of the spent catalysts through TPD-MS, ATR-FTIR, TEM and HR-TEM and XRD evidenced the coexistence of a Ni0/NiO phase together with an increased presence of Ce3+ cations and oxygen vacancies, on the surface of the catalyst submitted to plasma catalytic operation. The different facts collected through physicochemical characterization point to our catalyst behaving like a PN junction, or like a fuel cell, with a P-side, the anode, i.e. the Ni-side releasing electrodes, while the CeZrOx support, N-side and cathode, acts as an acceptor. The DBD plasma, rich in ionic species and free electrodes, acts as the electrolyte, conducting the electrodes in the right direction. Oxygen accumulation on the surface of the catalyst during thermo-catalytic methanation leads to the formation of non-reactive adsorbed species, whereas Ni-sintering is favored. Under DBD plasma conditions, electron transfer is guaranteed and the adsorption–desorption of reactants and products is favored.
Coupling experiment and simulation analysis to investigate physical parameters of CO2 methanation in a plasma catalytic hybrid process
Laboratoire Procédés - Plasmas - Microsystèmes - Bo Wang Maria Mikhail Maria Elena Galvez Simeon Cavadias Michael Tatoulian Patrick Da Costa Stéphanie Ognier
First published - 17 9 - https://doi.org/10.1002/ppap.201900261 - 2020
This study focuses on the use of a heterogeneous catalyst Ni/Ce0.58Zr0.42O2 to study the Sabatier reaction in conventional catalytic thermal heating and the dielectric barrier discharge plasma‐catalytic process. Its aim is to study the threshold temperature of the Sabatier reaction in plasma conditions. A set of experiments with different inlet flow rates is carried out in a plasma reactor to investigate the steady‐state temperature of the reaction. To estimate the threshold temperature of the Sabatier reaction more accurately, the temperature difference between the catalytic bed and the external surface of the reactor is calculated and simulated in COMSOL Multiphysics® software. Finally, the threshold temperature of the Sabatier reaction during plasma processing is assumed to be 116°C, based on the experimental data and simulation analysis.

635 publications.