Ref HAL: hal-01881168_v1
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Efficient bacterial chromosome segregation typically requires the coordinated action of a three-component, fueled by adenosine triphosphate machinery called the partition complex. We present a phenomenological model accounting for the dynamic activity of this system that is also relevant for the physics of catalytic particles in active environments. The model is obtained by coupling simple linear reaction-diffusion equations with a proteophoresis, or “volumetric” chemophoresis, force field that arises from protein-protein interactions and provides a physically viable mechanism for complex translocation. This minimal description captures most known experimental observations: dynamic oscillations of complex components, complex separation and subsequent symmetrical positioning. The predictions of our model are in phenomenological agreement with and provide substantial insight into recent experiments. From a non-linear physics view point, this system explores the active separation of matter at micrometric scales with a dynamical instability between static positioning and travelling wave regimes triggered by the dynamical spontaneous breaking of rotational symmetry.

Ref HAL: hal-01926457_v1
PMID 30446599
DOI: 10.15252/msb.20188516
WoS: 000451579500003
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14 Citations
Résumé:

Chromosome and plasmid segregation in bacteria are mostly driven by ParABS systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites (parS). However, the mechanism of how a few parS-bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico-mathematical models. We discriminated between these different models by varying some key parameters in vivo using the plasmid F partition system. We found that ‘Nucleation & caging’ is the only coherent model recapitulating in vivo data. We also showed that the stochastic self-assembly of partition complexes (i) does not directly involve ParA, (ii) results in a dynamic structure of discrete size independent of ParB concentration, and (iii) is not perturbed by active transcription but is by protein complexes. We refined the ‘Nucleation & Caging’ model and successfully applied it to the chromosomally-encoded Par system of Vibrio cholerae, indicating that this stochastic self-assembly mechanism is widely conserved from plasmids to chromosomes.

Ref HAL: hal-01844602_v1
Ref Arxiv: 1712.01055
DOI: 10.1103/PhysRevE.98.012605
WoS: 000439065200005
Ref. & Cit.: NASA ADS
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6 Citations
Résumé:

The number of precise conductance measurements in nanopores is quickly growing. To clarify the dominant mechanisms at play and facilitate the characterization of such systems for which there is still no clear consensus, we propose an analytical approach to the ionic conductance in nanopores that takes into account (i) electro-osmotic effects, (ii) flow slip at the pore surface for hydrophobic nanopores, (iii) a component of the surface charge density that is modulated by the reservoir pH and salt concentration cs using a simple charge regulation model, and (iv) a fixed surface charge density that is unaffected by pH and cs . Limiting cases are explored for various ranges of salt concentration and our formula is used to fit conductance experiments found in the literature for carbon nanotubes. This approach permits us to catalog the different possible transport regimes and propose an explanation for the wide variety of currently known experimental behavior for the conductance versus cs .

Ref HAL: hal-01710924_v1
DOI: 10.1088/1873-7005/aaa739
WoS: 000424711200001
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The Miles' quasi laminar theory of waves generation by wind in finite depth h is presented. In this context, the fully nonlinear Green–Naghdi model equation is derived for the first time. This model equation is obtained by the non perturbative Green–Naghdi approach, coupling a nonlinear evolution of water waves with the atmospheric dynamics which works as in the classic Miles' theory. A depth-dependent and wind-dependent wave growth γ is drawn from the dispersion relation of the coupled Green–Naghdi model with the atmospheric dynamics. Different values of the dimensionless water depth parameter $\delta = \frac{gh}{U_1}$, with g the gravity and $U_1$ a characteristic wind velocity, produce two families of growth rate γ in function of the dimensionless theoretical wave-age $c_0$: a family of γ with h constant and $U_1$ variable and another family of $\gamma$ with $U_1$ constant and $h$ variable. The allowed minimum and maximum values of $\gamma$ in this model are exhibited.

Ref HAL: hal-01561696_v1
Ref Arxiv: 1707.01373
DOI: 10.1088/1367-2630/aaad39
WoS: 000428767700002
Ref. & Cit.: NASA ADS
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4 Citations
Résumé:

The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the Looping and Clustering (LC) model, which employs a statistical physics approach to describe protein-DNA complexes. The LC model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and the configurational and loop entropy of this protein-DNA cluster. Indeed, we show that the protein interaction strength determines the "tightness" of the loopy protein-DNA complex. With this approach we consider the genomic organization of such a protein-DNA cluster around a single high-affinity binding site. Thus, our model provides a theoretical framework to quantitatively compute the binding profiles of ParB-like proteins around a cognate (parS) binding site.

Commentaires: 14 pages, 7 figures

Ref HAL: hal-02090515_v1
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Une méthode permettant la mesure spectrocolorimétrique des solutions opaques très diffusantes, de type jus de fruits, dans leur packaging d'origine. Les appareils courants sur le marché (spectrocolorimètres) ne permettent pas de réaliser cette mesure. La méthode s'affranchit des contraintes présentes dans ces appareils.