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Laboratoire Biophysique et Evolution - Paul RAINEY Jérôme BIBETTE Jean BAUDRY Nicolas BREMOND Laurent BOITARD Jairo GARNICA Denis COTTINET
My Science Work - - - 2020
The present invention relates to a method for manipulating the evolution of collectives of self-replicating entities and/or variation between collectives of self-replicating entities, in a high throughput droplet milli-fluidic system.
Experimental manipulation of selfish genetic elements links genes to microbial community function
Laboratoire Biophysique et Evolution - Steven D. Quistad, Guilhem Doulcier and Paul B. Rainey
Philosophical Transactions of the Royal Society - - - 2020
Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose (paper) as sole carbon source. After 1 year of bi-weekly transfer, communities retained hundreds of genera. To connect genes to function, we used a simple experimental manipulation that involved the periodic collection of selfish genetic elements (SGEs) from separate communities, followed by pooling and redistribution across communities. The treatment was predicted to promote amplification and dissemination of SGEs and thus horizontal gene transfer. Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed. Enrichment of genes implicated in nitrogen metabolism, and particularly ammonification, prompted biochemical assays that revealed a measurable impact on community function. Our simple experimental strategy offers a conceptually new approach for unravelling dynamical processes affecting microbial community function.

Toward a dynamical understanding of microbial communities
Laboratoire Biophysique et Evolution - Paul B. Rainey and Steven D. Quistad
Philosophical Transactions of the Royal Society - - - 2020
The challenge of moving beyond descriptions of microbial community composition to the point where understanding underlying eco-evolutionary dynamics emerges is daunting. While it is tempting to simplify through use of model communities composed of a small number of types, there is a risk that such strategies fail to capture processes that might be specific and intrinsic to complexity of the community itself. Here, we describe approaches that embrace this complexity and show that, in combination with metagenomic strategies, dynamical insight is increasingly possible. Arising from these studies is mounting evidence of rapid eco-evolutionary change among lineages and a sense that processes, particularly those mediated by horizontal gene transfer, not only are integral to system function, but are central to long-term persistence. That such dynamic, systems-level insight is now possible, means that the study and manipulation of microbial communities can move to new levels of inquiry.

Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity
Laboratoire Biophysique et Evolution - Guilhem Doulcier, Amaury Lambert, Silvia De Monte, Paul B Rainey
EcologyEvolutionary Biology - - DOI: 10.7554/eLife.53433 - 2020
Interactions among microbial cells can generate new chemistries and functions, but exploitation requires establishment of communities that reliably recapitulate community-level phenotypes. Using mechanistic mathematical models, we show how simple manipulations to population structure can exogenously impose Darwinian-like properties on communities. Such scaffolding causes communities to participate directly in the process of evolution by natural selection and drives the evolution of cell-level interactions to the point where, despite underlying stochasticity, derived communities give rise to offspring communities that faithfully re-establish parental phenotype. The mechanism is akin to a developmental process (developmental correction) that arises from density-dependent interactions among cells. Knowledge of ecological factors affecting evolution of developmental correction has implications for understanding the evolutionary origin of major egalitarian transitions, symbioses, and for top-down engineering of microbial communities.

Ecological scaffolding and the evolution of individuality
Laboratoire Biophysique et Evolution - Andrew J. Black, Pierrick Bourrat & Paul B. Rainey
Nature Ecology & Evolution - 4 426–436 - - 2020
Evolutionary transitions in individuality are central to the emergence of biological complexity. Recent experiments provide glimpses of processes underpinning the transition from single cells to multicellular life and draw attention to the critical role of ecology. Here, we emphasize this ecological dimension and argue that its current absence from theoretical frameworks hampers development of general explanatory solutions. Using mechanistic mathematical models, we show how a minimal ecological structure comprising patchily distributed resources and between-patch dispersal can scaffold Darwinian-like properties on collectives of cells. This scaffolding causes cells to participate directly in the process of evolution by natural selection as if they were members of multicellular collectives, with collectives participating in a death–birth process arising from the interplay between the timing of dispersal events and the rate of resource use by cells. When this timescale is sufficiently long and new collectives are founded by single cells, collectives experience conditions that favour evolution of a reproductive division of labour. Together our simple model makes explicit key events in the major evolutionary transition to multicellularity. It also makes predictions concerning the life history of certain pathogens and serves as an ecological recipe for experimental realization of evolutionary transitions.

The impact of frost-damage on the quality and quantity of the secreted antigen-specific IgG repertoire
Laboratoire Colloïdes et Matériaux Divisés - Magda Rybczynska, Jean Baudrya, Eyer Klaus
Vaccine - 38(33) 5337-5342 - - 2020
Freezing of alum-based vaccines drastically alters their colloidal composition and leads to irreversible cluster formation. The loss of stability is well described, but the impact of frost damage on the functionality of the induced and secreted antibody repertoire has not been studied in detail. We therefore applied our single-cell measurement platform to extract the frequencies of Immunoglobulin G-secreting cells in combination with individual secretion rates and affinities. We showed that, frost-damaged or not, the tested vaccine was able to generate similar frequencies of total and antigen-affine IgG-secreting cells. Additionally, the frost-damaged vaccine stimulated a similar T-cell cytokine secretion pattern when compared to the regularly stored vaccine. However, frost-damaged vaccines induced no efficient affinity maturation and a complete collapse of the affinity distribution was observed. This study unveiled the impact of frost-damage to alum-based vaccines on the induced secreted antibody repertoire, and illustrated the power of functional single-antibody analysis.

The Quantitative Assessment of the Secreted IgG Repertoire after Recall to Evaluate the Quality of Immunizations
Laboratoire Colloïdes et Matériaux Divisés - Klaus Eyer, Carlos Castrillon, Guilhem Chenon, Jérôme Bibette, Pierre Bruhns, Andrew D. Griffiths and Jean Baudry
The Journal of Immunology - 205 8 - DOI: - 2020
One of the major goals of vaccination is to prepare the body to rapidly secrete specific Abs during an infection. Assessment of the vaccine quality is often difficult to perform, as simple measurements like Ab titer only partly correlate with protection. Similarly, these simple measurements are not always sensitive to changes in the preceding immunization scheme. Therefore, we introduce in this paper a new, to our knowledge, method to assay the quality of immunization schemes for mice: shortly after a recall with pure Ag, we analyze the frequencies of IgG-secreting cells (IgG-SCs) in the spleen, as well as for each cells, the Ag affinity of the secreted Abs. We observed that after recall, appearance of the IgG-SCs within the spleen of immunized mice was fast (<24 h) and this early response was free of naive IgG-SCs. We further confirmed that our phenotypic analysis of IgG-SCs after recall strongly correlated with the different employed immunization schemes. Additionally, a phenotypic comparison of IgG-SCs presented in the spleen during immunization or after recall revealed similarities but also significant differences. The developed approach introduced a novel (to our knowledge), quantitative, and functional highly resolved alternative to study the quality of immunizations.
Quantitative modeling of the effect of antigen dosage on B-cell affinity distributions in maturating germinal centers
Laboratoire Colloïdes et Matériaux Divisés - Marco Molari, Klaus Eyer, Jean Baudry, Simona Cocco, Rémi Monasson
Nature Protocols - 15 2920–2955 - DOI: 10.7554/eLife.55678 - 2020
Affinity maturation is a complex dynamical process allowing the immune system to generate antibodies capable of recognizing antigens. We introduce a model for the evolution of the distribution of affinities across the antibody population in germinal centers. The model is amenable to detailed mathematical analysis and gives insight on the mechanisms through which antigen availability controls the rate of maturation and the expansion of the antibody population. It is also capable, upon maximum-likelihood inference of the parameters, to reproduce accurately the distributions of affinities of IgG-secreting cells we measure in mice immunized against Tetanus Toxoid under largely varying conditions (antigen dosage, delay between injections). Both model and experiments show that the average population affinity depends non-monotonically on the antigen dosage. We show that combining quantitative modeling and statistical inference is a concrete way to investigate biological processes underlying affinity maturation (such as selection permissiveness), hardly accessible through measurements.
Motion of oil in water induced by osmosis in a confined system
Laboratoire Colloïdes et Matériaux Divisés - Erwan Crestel, Anežka Kvasnicková, Enric Santanach-Carreras , Jérôme Bibette, and Nicolas Bremond
Phys. Rev. Fluids - 5 104003 - - 2020
Deep phenotypic characterization of immunization-induced antibacterial IgG repertoires in mice using a single-antibody bioassay
Laboratoire Colloïdes et Matériaux Divisés - Millie Heo, Guilhem Chenon, Carlos Castrillon, Jérôme Bibette, Pierre Bruhns, Andrew D. Griffiths, Jean Baudry & Klaus Eyer
Communications Biology - 614 5337-5342 - - 2020
Antibodies with antibacterial activity need to bind to the bacterial surface with affinity, specificity, and sufficient density to induce efficient elimination. To characterize the anti-bacterial antibody repertoire, we developed an in-droplet bioassay with single-antibody resolution. The assay not only allowed us to identify whether the secreted antibodies recognized a bacterial surface antigen, but also to estimate the apparent dissociation constant (KD app) of the interaction and the density of the recognized epitope on the bacteria. Herein, we found substantial differences within the KD app/epitope density profiles in mice immunized with various species of heat-killed bacteria. The experiments further revealed a high cross-reactivity of the secreted IgG repertoires, binding to even unrelated bacteria with high affinity. This application confirmed the ability to quantify the anti-bacterial antibody repertoire and the utility of the developed bioassay to study the interplay between bacteria and the humoral response.

Apollonian packing in polydisperse emulsions
Laboratoire Colloïdes et Matériaux Divisés - Sylvie Kwok, Robert Botet, Lewis Sharpnack and Bernard Cabane
Nature Protocols - 16 2426-2430 - - 2020
We have discovered the existence of polydisperse high internal-phase-ratio emulsions (HIPE) in which the internal-phase droplets, present at 95% volume fraction, remain spherical and organise themselves according to Apollonian packing rules. These polydisperse HIPEs are formed by emulsifying oil dropwise in a surfactant-poor aqueous continuous phase. After stirring has ceased, their droplet size distributions begin to evolve spontaneously and continuously through coalescence towards well-defined power laws with the Apollonian exponent. Small-angle X-ray Scattering performed on aged HIPEs demonstrate that the droplet packing structure agrees with that of a numerically simulated random Apollonian packing. We argue that when such concentrated emulsions are allowed to evolve, the coalescing droplets must obey volume and sphericity conservation. This leads to a mechanism that differs from typical coalescence in dilute emulsions.

Swelling, dewetting and breakup in thin polymer films for cultural heritage
Laboratoire Colloïdes et Matériaux Divisés - Amélie Castel, Philipp Gutfreund, Bernard Cabaned and Yahya Rharbi
Soft Matter - 16 1485-1497 - - 2020
The removal of ultrathin amorphous polymer films in contact with nonsolvent/solvent binary mixtures is addressed by means of neutron reflectometry and atomic force microscopy. The high resolution of neutron scattering makes it possible to resolve the distribution profiles of heavy water and benzyl alcohol inside Laropal®A81, often employed as a protective varnish layer for Culture Heritage in restoration of easel paintings. The swelling kinetics and distribution profiles were recorded as a function of time and increasing benzyl alcohol concentration in water. The varnish film swells by penetration of the good solvent. At higher concentrations water-filled cavities appear inside the varnish and grow with time. Contrary to homogeneous dissolution dewetting is observed at late stages of exposure to the liquid which leads to the Breakup of the film. The high resolution measurements are compared to bulk behaviour characterized by the ternary phase diagram and the Flory–Huggins interaction parameters are calculated and used to predict the swelling and solvent partition in the films. Distinct differences of the thin film to bulk behaviour are found. The expectations made previously for the behaviour of solvent/non-solvent mixtures on the removal of thin layers in the restoration of easel paintings should be revised in view of surface interactions.

Metabolic cost of rapid adaptation of single yeast cells
Laboratoire Colloïdes et Matériaux Divisés - Gabrielle Woronoff, Philippe Nghe, Jean Baudry, Laurent Boitard, Erez Bra
PNAS - 117 (20) 10660-10666 - - 2020
We establish, using single-cell analysis of metabolism and division in a droplet microfluidic system, that yeast can adapt, resuming division, extremely rapidly to an unforeseen environmental challenge, and that adaptation is an active process, requiring the consumption of a characteristic amount energy. The adapted state is stable over at least several days, showing that this is a genuine adaptation process. The adaptation rate (10−3 cells per hour) is orders of magnitude higher than expected based on known mutation rates, suggesting an epigenetic origin, and the tight energetic coupling implies that there is active exploration of different states, and fixation of the solution(s) that allow adaptation.

Optimised hyperbolic microchannels for the mechanical characterisation of bio-particles
Laboratoire Complex Suspensions - Yanan Liu, Konstantinos Zografos, Joana Fidalgo, Charles Duchene, Clement Quintard, Thierry Darnige, Vasco Filipe, Sylvain Huille, Olivia du Roure, Monica S. N. Oliveira and Anke Lindner
Soft Matter - 16 9844 - DOI: 10.1039/d0sm01293a - 2020
The transport of bio-particles in viscous flows exhibits a rich variety of dynamical behaviour, such as
morphological transitions, complex orientation dynamics or deformations. Characterising such complex
behaviour under well controlled flows is key to understanding the microscopic mechanical properties of
biological particles as well as the rheological properties of their suspensions. While generating regions of
simple shear flow in microfluidic devices is relatively straightforward, generating straining flows in which
the strain rate is maintained constant for a sufficiently long time to observe the objects’ morphologic
evolution is far from trivial. In this work, we propose an innovative approach based on optimised design
of microfluidic converging–diverging channels coupled with a microscope-based tracking method to
characterise the dynamic behaviour of individual bio-particles under homogeneous straining flow.
The tracking algorithm, combining a motorised stage and a microscopy imaging system controlled by
external signals, allows us to follow individual bio-particles transported over long-distances with highquality
images. We demonstrate experimentally the ability of the numerically optimised microchannels
to provide linear velocity streamwise gradients along the centreline of the device, allowing for extended
consecutive regions of homogeneous elongation and compression. We selected three test cases (DNA,
actin filaments and protein aggregates) to highlight the ability of our approach for investigating dynamics
of objects with a wide range of sizes, characteristics and behaviours of relevance in the biological world
Self-Similar Relaxation of Confined Microfluidic Droplets
Laboratoire INDYSOFT - Margaux Kerdraon1, Joshua D. McGraw1, Benjamin Dollet2, and Marie-Caroline Jullien
Phys. Rev. Lett. - 123 24501 - - 2020
We report an experimental study concerning the capillary relaxation of a confined liquid droplet in a microscopic channel with a rectangular cross section. The confinement leads to a droplet that is extended along the direction normal to the cross section. These droplets, found in numerous microfluidic applications, are pinched into a peanutlike shape thanks to a localized, reversible deformation of the channel. Once the channel deformation is released, the droplet relaxes back to a pluglike shape. During this relaxation, the liquid contained in the central pocket drains towards the extremities of the droplet. Modeling such viscocapillary droplet relaxation requires considering the problem as 3D due to confinement. This 3D consideration yields a scaling model incorporating dominant dissipation within the droplet menisci. As such, the self-similar droplet dynamics is fully captured.
Natural Abundance Oxygen-17 Solid-State NMR of Metal Organic Frameworks Enhanced by Dynamic Nuclear Polarization
Laboratoire Institut des Matériaux Poreux de Paris - Carnevale D, Mouchaham G, Wang S, Baudin M, Serre C, Bodenhausen G, Abergel D
ChemRxiv - - DOI: 10.26434/chemrxiv.12477449.v1 - 2020
The 17O resonances of Zirconium-oxo clusters that can be found in porous Zr carboxylate metal-organic frameworks (MOFs) have been investigated by magic-angle spinning (MAS) NMR spectroscopy enhanced by dynamic nuclear polarization (DNP). High-resolution 17O spectra at 0.037 % natural abundance could be obtained in 48 hours, thanks to DNP enhancement of the 1H polarization by factors e(1H) = Swith/Swithout = 28, followed by 1H®17O cross-polarization, allowing a saving in experimental time by a factor of ca. 800. The distinct 17O sites from the oxo-clusters can be resolved at 18.8 T. Their assignment is supported by density functional theory (DFT) calculations of chemical shifts and quadrupolar parameters.
One‐step versatile room temperature synthesis of metal(IV) carboxylate MOFs
Laboratoire Institut des Matériaux Poreux de Paris - Shan Dai, Farid Nouar, Sanjun Zhang, Antoine Tissot, and Christian Serre
Angew. Chem. Int. Ed - - : - 2020
This manuscript has been accepted after peer review and appears as an Accepted Article online prior to editing, proofing, and formal publication of the final Version of Record (VoR). This work is currently citable by using the Digital Object Identifier (DOI) given below. The VoR will be published online in Early View as soon as possible and may be different to this Accepted Article as a result of editing. Readers should obtain
the VoR from the journal website shown below when it is published to ensure accuracy of information. The authors are responsible for the content of this Accepted Article.
Principal Component Analysis (PCA) for Powder Diffraction Data: Towards Unblinded Applications
Laboratoire Institut des Matériaux Poreux de Paris - Dmitry Chernyshov, Iurii Dovgaliuk, Vadim Dyadkin and Wouter van Beek
CRYSTALS - 10 7 - - 2020
We analyze the application of Principal Component Analysis (PCA) for untangling the main contributions to changing diffracted intensities upon variation of site occupancy and lattice dimensions induced by external stimuli. The information content of the PCA output consists of certain functions of Bragg angles (loadings) and their evolution characteristics that depend on external variables like pressure or temperature (scores). The physical meaning of the PCA output is to date not well understood. Therefore, in this paper, the intensity contributions are first derived analytically, then compared with the PCA components for model data; finally PCA is applied for the real data on isothermal gas uptake by nanoporous framework γ –Mg(BH 4 ) 2 . We show that, in close agreement with previous analysis of modulation diffraction, the variation of intensity of Bragg lines and the displacements of their positions results in a series of PCA components. Every PCA extracted component may be a mixture of terms carrying information on the average structure, active sub-structure, and their cross-term. The rotational ambiguities, that are an inherently part of PCA extraction, are at the origin of the mixing. For the experimental case considered in the paper, the extraction of the physically meaningful loadings and scores can only be achieved with a rotational correction. Finally, practical recommendations for non-blind applications, i.e., what boundary conditions to apply for the the rotational correction, of PCA for diffraction data are given.
Non-Isothermal Kinetics of Kr Adsorption by Nanoporous γ-Mg(BH4)2 from in Situ Synchrotron Powder Diffraction
Laboratoire Institut des Matériaux Poreux de Paris - Iurii Dovgaliuk*, Vadim Dyadkin, Mathieu Vander Donckt, Yaroslav Filinchuk*, and Dmitry Chernyshov
ACS Publications - 12(6) 7710–7716 - - 2020
Crystalline materials with pore dimensions comparable to the kinetic diameters of the guest molecules are attractive for their potential use in adsorption and separation applications. The nanoporous γ-Mg(BH4)2 features one-dimensional channels matching this criterion for Kr uptake, which has been probed using synchrotron powder diffraction at various pressures and temperatures. It results in two coexisting crystalline phases with the limiting composition Mg(BH4)2·0.66Kr expecting the highest Kr content (50.7 wt % in the crystalline phase) reported for porous materials. Quasi-equilibrium isobars built from Rietveld refinements of Kr site occupancies were rationalized with a noncooperative lattice gas model, yielding the values of the thermodynamic parameters. The latter were independently confirmed from Kr fluorescence. We have also parameterized the pronounced kinetic hysteresis with a modified mean-field model adopted for the Arrhenius kinetics.
Factors Determining Microporous Material Stability in Water: The Curious Case of SAPO-37
Laboratoire Institut des Matériaux Poreux de Paris - Georgios N. Kalantzopoulos, Fredrik Lundvall, Knut Thorshaug, Anna Lind, Ponniah Vajeeston, Iurii Dovgaliuk, Bjørnar Arstad, David S. Wragg, and Helmer Fjellvåg
ACS Publications - 32(4) 1495–1505 - - 2020
Silicoaluminophosphates (SAPOs) are a special class of zeolites that, due to their acidic and shape-selective properties, play a major role in ion exchange and separation processes and in crude oil cracking. SAPO-37 has the faujasite (FAU) topology same as zeolites X and Y, which are involved in more than 40% of the total crude oil conversion worldwide. A critical parameter that promotes detrimental structural transformations in SAPOs during real-life applications is the presence of humidity. In this study, we employ a multidisciplinary approach combining in situ synchrotron radiation powder X-ray diffraction (SR-PXRD), water adsorption, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), and density functional theory (DFT) calculations to describe the mechanism and reveal the reasons why SAPO-37 collapses upon contact with humidity below 345 K. SR-PXRD revealed that the sodalite (SOD) cages (subunits of the FAU structure) have the strongest affinity to water during hydration below 345 K. Furthermore, below 345 K, the faujasite framework takes up an order of magnitude more water molecules than at temperatures above 345 K. DRIFTS confirmed the presence of Si–OH and P–OH surface structural defects that act as hydration centers, accelerating the loss of a long-range order. Finally, DFT calculations showed that the enthalpy of water adsorption in the sodalite cage and the faujasite supercage is −212 and −13 kJ/mol, respectively. The results presented in this work are highly topical for understanding the effect of water on the frameworks of the SAPO microporous catalysts family. The notorious instability of SAPO-37 is the result of the accumulative contribution of topological, physical, and chemical effects, leading to an array of rapidly evolving cascading effects. Our work shows how advancements in SR-PXRD methodology and hardware give new insight into highly dynamic features previously difficult to observe. In addition, this work introduces the conceptual insight that nonhomogeneous sorption of molecular species will induce dynamic features with dramatic consequences at both molecular and atomic levels. This is a highly impactful factor opening research paths for further work within catalysis, porous material design and chemistry, and sorption reactions and processes.


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