Ref HAL: hal-03291847_v1
PMID 31732791
DOI: 10.1007/s00018-019-03372-2
WoS: 000560212600012
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During embryogenesis of all vertebrates, haematopoietic stem/progenitor cells (HSPCs) extrude from the aorta by a complex process named endothelial-to-haematopoietic transition (EHT). HSPCs will then colonize haematopoietic organs allowing haematopoiesis throughout adult life. The mechanism underlying EHT including the role of each aortic endothelial cell (EC) within the global aorta dynamics remains unknown. In the present study, we show for the first time that EHT involves the remodelling of individual cells within a collective migration of ECs which is tightly orchestrated, resulting in HSPCs extrusion in the sub-aortic space without compromising aorta integrity. By performing a cross-disciplinary study which combines high-resolution 4D imaging and theoretical analysis based on the concepts of classical mechanics, we propose that this complex developmental process is dependent on mechanical instabilities of the aorta preparing and facilitating the extrusion of HSPCs.

Commentaires: NOTICE A REPRENDRE PAS DE CLE UT AU 15/07

Ref HAL: hal-03151317_v1
DOI: 10.1103/PhysRevB.102.205305
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Ref HAL: hal-03089688_v1
DOI: 10.5004/dwt.2020.25100
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In response to the fresh water scarcity, Tunisia is utilizing more and more membrane desalination of unconventional resources, including brackish waters and seawater. The widespread reserves of groundwaters and their low salinity make this resource of special interest. Two predominant ionic compositions have been identified depending on their relative proportion of sulfate to chloride ions. The question arising for the decision-makers concerns the choice of membrane technology and, therefore, of membrane. Two nanofiltration (NF) membranes (NF270 and NF90) and a reverse osmosis (RO) one (BW30) were tested in a desalination study of synthetic feeds reproducing the ionic composition of three representative groundwaters. Sulfate/chloride ratio appears to be the key factor for the membrane choice to obtain good quality drinking water meeting the Tunisian standards. Moreover, validation of two prediction tools was investigated: ROSA, software provided by the membrane manufacturer and Nanoflux ® , software specifically designed for NF. The experimental NF results are well fitted by the Nanoflux ® simulations. We concluded that ROSA cannot generally provide good NF predictions because it does not take into account the electric interactions between membrane and feed.

Ref HAL: hal-03052753_v1
DOI: 10.1016/j.isci.2020.101861
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Bacterial ParB partitioning proteins involved in chromosomes and low-copy-number plasmid segregation are CTP-dependent molecular switches. CTP-binding converts ParB dimers to DNA clamps, allowing unidimensional diffusion along the DNA. This sliding property has been proposed to explain the ParB spreading over large distances from parS centromere sites where ParB is specifically loaded. We modeled such a ‘Clamping & sliding’ mechanism as a typical reaction-diffusion system, compared it to the F-plasmid ParB DNA binding pattern, and found that it can account neither for the long range of ParB binding to DNA, nor for the rapid assembly kinetics observed in vivo after parS duplication. Also, it predicts a strong effect on the F-plasmid ParB binding pattern from the presence of a roadblock that is not observed in ChIP-seq. We conclude that although ‘Clamping & sliding’ can occur at short distances from parS, another mechanism must apply for ParB recruitment at larger genomic distances.

Ref HAL: hal-02990631_v1
Ref Arxiv: 2002.00111
Ref. & Cit.: NASA ADS
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We investigate the measurement of DNA supercoiling density ($\sigma$) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in bacteria, to the quantitative modeling of binding properties of ParB proteins around their centromere-like site, {\it parS}. Using this framework, we provide an upper bound for $\sigma$ in the {\it Escherichia coli} chromosome, consistent with plasmid values, and offer a proof of concept for a high accuracy measurement. To reach these conclusions, we revisit the problem of the formation of ParB clusters. We predict, in particular, that they result from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., they behave like liquid-like protein condensates with unconventional ``leaky'' boundaries.

Ref HAL: hal-02957556_v1
DOI: 10.1016/j.jtbi.2020.110370
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The cytoskeleton in eukaryotic cells plays several crucial roles. In terms of intracellular transport, motor proteins use the cytoskeletal filaments as a backbone along which they can actively transport biological cargos such as vesicles carrying biochemical reactants. Crossings between such filaments constitute a key element, as they may serve to alter the destination of such payload. Although motor proteins are known to display a rich behaviour at such crossings, the latter have so far only been modelled as simple branching points. Here we explore a model for a crossing between two microtubules which retains the individual tracks consisting of protofilaments, and we construct a schematic representation of the transport paths. We study collective transport exemplified by the Totally Asymmetric Simple Exclusion Process (TASEP), and provide a full analysis of the transport features and the associated phase diagram, by a generic mean-field approach which we confirm through particle-based stochastic simulations. In particular we show that transport through such a compound crossing cannot be approximated from a coarse-grained structure with a simple branching point. Instead, it gives rise to entirely new and counterintuitive features: the fundamental current-density relation for traffic flow is no longer a single-valued function, and it furthermore differs according to whether it is observed upstream or downstream from the crossing. We argue that these novel features may be directly relevant for interpreting experimental measurements.

Ref HAL: hal-02950974_v1
DOI: 10.1103/PhysRevResearch.2.033377
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The cellular cytoplasm is organized into compartments. Phase separation is a simple manner to create membraneless compartments in order to confine and localize particles like proteins. In many cases, these particles are bound to fluctuating polymers like DNA or RNA. We propose a general theoretical framework for such polymer-bound particles and derive an effective 1D lattice gas model with both nearest-neighbor and emergent long-range interactions arising from looped configurations of the fluctuating polymer. We argue that 1D phase transitions exist in such systems for both Gaussian and self-avoiding polymers and, using a variational method that goes beyond mean-field theory, we obtain the complete mean occupation-temperature phase diagram. To illustrate this model, we apply it to the biologically relevant case of ParABS, a prevalent bacterial DNA segregation system.