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The ring-shaped cohesin complex topologically entraps two DNA molecules to establish sister chromatid cohesion. Cohesin also shapes the interphase chromatin landscape with wide-ranging implications for gene regulation, and cohesin is thought to achieve this by actively extruding DNA loops without topologically entrapping DNA. The 'loop extrusion' hypothesis finds motivation from in vitro observations-whether this process underlies in vivo chromatin loop formation remains untested. Here, using the budding yeast S. cerevisiae, we generate cohesin variants that have lost their ability to extrude DNA loops but retain their ability to topologically entrap DNA. Analysis of these variants suggests that in vivo chromatin loops form independently of loop extrusion. Instead, we find that transcription promotes loop formation, and acts as an extrinsic motor that expands these loops and defines their ultimate positions. Our results necessitate a re-evaluation of the loop extrusion hypothesis. We propose that cohesin, akin to sister chromatid cohesion establishment at replication forks, forms chromatin loops by DNA-DNA capture at places of transcription, thus unifying cohesin's two roles in chromosome segregation and interphase genome organisation., (© 2024. The Author(s).)

Domain decay is at the heart of the so-called evaporation-condensation Ostwald-ripening regime of phase ordering kinetics, where the growth of large domains occurs at the expense of smaller ones, which are expected to "evaporate." We experimentally investigate such decay dynamics at the level of a single spherical domain picked from one phase in coexistence and brought into the other phase by an optomechanical approach, in a near-critical phase-separated binary liquid mixture. We observe that the decay dynamics is generally not compatible with the theoretically expected surface-tension decay laws for conserved order parameters. Using a mean-field description, we quantitatively explain this apparent disagreement by the gradient of solute concentrations induced by gravity close to a critical point. Finally, we determine the conditions for which buoyancy becomes negligible compared to capillarity and perform dedicated experiments that retrieve the predicted surface-tension induced decay exponent. The surface-tension driven decay dynamics of conserved order parameter systems in the presence and the absence of gravity, is thus established at the level of a single domain.

We consider the motion of a harmonically trapped overdamped particle, which is submitted to a self-phoretic force, that is proportional to the gradient of a diffusive field for which the particle itself is the source. In agreement with existing results for free particles or particles in a bounded domain, we find that the system exhibits a transition between an immobile phase, where the particle stays at the center of the trap, and an oscillatory state. We perform an exact analysis giving access to the bifurcation threshold, as well as the frequency of oscillations and their amplitude near the threshold. Our analysis also characterizes the shape of two-dimensional oscillations that take place along a circle or a straight line. Our results are confirmed by numerical simulations.

We study the diffusion of particles confined close to a single wall and in double-wall planar channel geometries where the local diffusivities depend on the distance to the boundaries. Displacement parallel to the walls is Brownian as characterized by its variance, but it is non-Gaussian having a nonzero fourth cumulant. Establishing a link with Taylor dispersion, we calculate the fourth cumulant and the tails of the displacement distribution for general diffusivity tensors along with potentials generated by either the walls or externally, for instance, gravity. Experimental and numerical studies of the motion of a colloid in the direction parallel to the wall give measured fourth cumulants which are correctly predicted by our theory. Interestingly, contrary to models of Brownian-yet-non-Gaussian diffusion, the tails of the displacement distribution are shown to be Gaussian rather than exponential. All together, our results provide additional tests and constraints for the inference of force maps and local transport properties near surfaces.

2021 marked the 80th anniversary of Barbara McClintock's pioneering article on the breakage-fusion-bridge (BFB) cycle. Of the three steps of the BFB cycle, breakage remains the least understood despite its major contribution to mutagenesis. We discuss recent findings shedding light on how chromatin bridges break in yeast and animal cells., Competing Interests: Declaration of interests No interests are declared., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Chemical reactions generically require that particles come into contact. In practice, reaction is often imperfect and can necessitate multiple random encounters between reactants. In confined geometries, despite notable recent advances, there is to date no general analytical treatment of such imperfect transport-limited reaction kinetics. Here, we determine the kinetics of imperfect reactions in confining domains for any diffusive or anomalously diffusive Markovian transport process, and for different models of imperfect reactivity. We show that the full distribution of reaction times is obtained in the large confining volume limit from the knowledge of the mean reaction time only, which we determine explicitly. This distribution for imperfect reactions is found to be identical to that of perfect reactions upon an appropriate rescaling of parameters, which highlights the robustness of our results. Strikingly, this holds true even in the regime of low reactivity where the mean reaction time is independent of the transport process, and can lead to large fluctuations of the reaction time - even in simple reaction schemes. We illustrate our results for normal diffusion in domains of generic shape, and for anomalous diffusion in complex environments, where our predictions are confirmed by numerical simulations., (© 2021. The Author(s).)

A practical access to four new halogen-substituted pyrrole building blocks was realized in two to five synthetic steps from commercially available starting materials. The target compounds were prepared on a 50 mg to 1 g scale, and their conversion to nanomolar inhibitors of bacterial DNA gyrase B was demonstrated for three of the prepared building blocks to showcase the usefulness of such chemical motifs in medicinal chemistry., Competing Interests: The authors declare no competing financial interest., (© 2021 The Authors. Published by American Chemical Society.)

The synthesis of trifluoromethylthiolated ketenimines is herein described. They are easily synthesized from the corresponding α-trifluoromethylthiolated oximes upon activation with triflic anhydride and a base. The presumed nitrilium ion resulting from the Beckmann rearrangement is deprotonated to lead to the key intermediate, whose stability brought by the fluorinated substituent was unforeseeable. The reaction of these new building blocks with a variety of nucleophiles affords a vast array of cyclic and acyclic products bearing the valuable SCF 3 moiety., (© 2020 Wiley-VCH GmbH.)

Objective: To assess appropriateness of end-of-life treatments provided to actively dying patients attending the emergency department of a primary care hospital., Methods: Retrospective cohort study of patients who died in the emergency department of a French primary care hospital between January 2014 and January 2017. The deceased were identified through the admissions register. Then, electronic medical records were screened for bio-demographic data, data relative to decisions to withhold or withdraw treatments, to diagnosis and to the care provided. Patients were clustered into two categories, actively dying or non-actively dying, using clinical opinion based on their medical records. Appropriateness of care was appraised following French guidelines., Results: One hundred and forty-six deaths were recorded. Actively dying patients mostly suffered from vascular conditions (29.4%). When compared to the overall sample, they were more likely to have decisions to withhold or withdraw treatments (OR = 5.3 [1.56; 20.7], p-value = 0.003), to have strong opioids (OR = 5.32 [2.1; 13.9], p-value <0.0001), hypnotics (OR = 2.6 [0.95; 8.39], p-value = 0.05), and scopolamine (OR = 2.5 [1.1; 6.13], p-value = 0.03). Moreover, they were less likely to have unbeneficial treatments in terminal conditions, such as resuscitation care (OR = 0.06 [0.001; 0.52], p = 0.002) and antibiotics (OR = 0.42 [0.19; 0.92], p-value = 0.022). There were no differences in rate of hydration, venous access and use of tracheal aspirations., Conclusions: Overall, actively dying patients were appropriately supported. However, several issues regarding hydration management, drug administration routes, and broncho-pulmonary secretions management remain to be addressed., (2019 Emergency Medicine Association of Turkey. Production and hosting by Elsevier B. V. on behalf of the Owner.)

In Saccharomyces cerevisiae, dicentric chromosomes stemming from telomere fusions preferentially break at the fusion. This process restores a normal karyotype and protects chromosomes from the detrimental consequences of accidental fusions. Here, we address the molecular basis of this rescue pathway. We observe that tandem arrays tightly bound by the telomere factor Rap1 or a heterologous high-affinity DNA binding factor are sufficient to establish breakage hotspots, mimicking telomere fusions within dicentrics. We also show that condensins generate forces sufficient to rapidly refold dicentrics prior to breakage by cytokinesis and are essential to the preferential breakage at telomere fusions. Thus, the rescue of fused telomeres results from a condensin- and Rap1-driven chromosome folding that favors fusion entrapment where abscission takes place. Because a close spacing between the DNA-bound Rap1 molecules is essential to this process, Rap1 may act by stalling condensins., (Copyright © 2019 Elsevier Inc. All rights reserved.)

The forces acting on optically trapped particles are commonly assumed to be conservative. Nonconservative scattering forces induce toroidal currents in overdamped liquid environments, with negligible effects on position fluctuations. However, their impact in the underdamped regime remains unexplored. Here, we study the effect of nonconservative scattering forces on the underdamped nonlinear dynamics of trapped nanoparticles at various air pressures. These forces induce significant low-frequency position fluctuations along the optical axis and the emergence of toroidal currents in both position and velocity variables. Our experimental and theoretical results provide fundamental insights into the functioning of optical tweezers and a means for investigating nonequilibrium steady states induced by nonconservative forces.

We consider a model of a particle trapped in a harmonic optical trap but with the addition of a nonconservative radiation induced force. This model is known to correctly describe experimentally observed trapped particle statistics for a wide range of physical parameters, such as temperature and pressure. We theoretically analyze the effect of nonconservative force on the underlying steady state distribution as well as the power spectrum for the particle position. We compute perturbatively the probability distribution of the resulting nonequilibrium steady states for all dynamical regimes underdamped through to overdamped and give expressions for the associated currents in phase space (position and velocity). We also give the spectral density of the trapped particle's position in all dynamical regimes and for any value of the nonconservative force. Signatures of the presence of nonconservative forces are shown to be particularly strong for the underdamped regime at low frequencies.

Duplication and segregation of chromosomes involves dynamic reorganization of their internal structure by conserved architectural proteins, including the structural maintenance of chromosomes (SMC) complexes cohesin and condensin. Despite active investigation of the roles of these factors, a genome-wide view of dynamic chromosome architecture at both small and large scale during cell division is still missing. Here, we report the first comprehensive 4D analysis of the higher-order organization of the Saccharomyces cerevisiae genome throughout the cell cycle and investigate the roles of SMC complexes in controlling structural transitions. During replication, cohesion establishment promotes numerous long-range intra-chromosomal contacts and correlates with the individualization of chromosomes, which culminates at metaphase. In anaphase, mitotic chromosomes are abruptly reorganized depending on mechanical forces exerted by the mitotic spindle. Formation of a condensin-dependent loop bridging the centromere cluster with the rDNA loci suggests that condensin-mediated forces may also directly facilitate segregation. This work therefore comprehensively recapitulates cell cycle-dependent chromosome dynamics in a unicellular eukaryote, but also unveils new features of chromosome structural reorganization during highly conserved stages of cell division., (© 2017 The Authors. Published under the terms of the CC BY 4.0 license.)

We study the dynamics of local bond orientation in regular hyperbranched polymers modeled by Vicsek fractals. The local dynamics is investigated through the temporal autocorrelation functions of single bonds and the corresponding relaxation forms of the complex dielectric susceptibility. We show that the dynamic behavior of single segments depends on their remoteness from the periphery rather than on the size of the whole macromolecule. Remarkably, the dynamics of the core segments (which are most remote from the periphery) shows a scaling behavior that differs from the dynamics obtained after structural average. We analyze the most relevant processes of single segment motion and provide an analytic approximation for the corresponding relaxation times. Furthermore, we describe an iterative method to calculate the orientational dynamics in the case of very large macromolecular sizes.

We consider the kinetics of first contact between two monomers of the same macromolecule. Relying on a fractal description of the macromolecule, we develop an analytical method to compute the mean first contact time for various molecular sizes. In our theoretical description, the non-Markovian feature of monomer motion, arising from the interactions with the other monomers, is captured by accounting for the nonequilibrium conformations of the macromolecule at the very instant of first contact. This analysis reveals a simple scaling relation for the mean first contact time between two monomers, which involves only their equilibrium distance and the spectral dimension of the macromolecule, independently of its microscopic details. Our theoretical predictions are in excellent agreement with numerical stochastic simulations.

We analyze the mean squared displacement of a Brownian particle in a medium with a spatially varying local diffusivity, which is assumed to be periodic. When the system is asymptotically diffusive, the mean-squared displacement, characterizing the dispersion in the system, is, at late times, a linear function of time. A Kubo-type formula is given for the mean-squared displacement, which allows the recovery of some known results for the effective diffusion constant D(e) in a direct way, but also allows an understanding of the asymptotic approach to the diffusive limit. In particular, as well as as computing the slope of a linear fit to the late-time mean-squared displacement, we find a formula for the constant where the fit intersects the y axis.

Semiflexible polymer rings whose bonds obey both angular and dihedral restrictions [M. Dolgushev and A. Blumen, J. Chem. Phys. 138, 204902 (2013)], are treated under exact closure constraints. This allows us to obtain semianalytic results for their dynamics, based on sets of Langevin equations. The dihedral restrictions clearly manifest themselves in the behavior of the mean-square monomer displacement. The determination of the equilibrium ring conformations shows that the dihedral constraints influence the ring curvature, leading to compact folded structures. The method for imposing such constraints in Gaussian systems is very general and it allows to account for heterogeneous (site-dependent) restrictions. We show it by considering rings in which one site differs from the others.

RNA silencing processes use exogenous or endogenous RNA molecules to specifically and robustly regulate gene expression. In C. elegans, initial mechanistic descriptions of the different silencing processes focused on posttranscriptional regulation. In this review, we discuss recent work showing that, in this model organism, RNA silencing also controls the transcription of target genes by inducing heterochromatin formation. Specifically, it has been shown that ribonucleoprotein complexes containing small RNAs, either processed from exogenous dsRNA or synthesized from the genome itself, and proteins of the Argonaute family, mediate the deposition of repressive histone marks at the targeted loci. Interestingly, the accumulation of repressive marks is required for the inheritance of the silencing effect and the establishment of an epigenetic memory that discriminates self- from non-self-RNAs.

Many cellular processes require molecular motors to produce motion and forces. Single molecule experiments have led to a precise description of how a motor works. Under most physiological conditions, however, molecular motors operate in groups. Interactions between motors yield collective behaviors that cannot be explained only from single molecule properties. The aim of this paper is to review the various theoretical descriptions that explain the emergence of collective effects in molecular motor assemblies. These include bidirectional motion, hysteretic behavior, spontaneous oscillations, and self-organization into dynamical structures. We discuss motors acting on the cytoskeleton both in a prescribed geometry such as in muscles or flagella and in the cytoplasm., (Copyright 2009 Elsevier Ltd. All rights reserved.)

We propose a continuum theory for the conformational transitions of viral shells. Conformational transitions of viral shells, as encountered during viral maturation, are associated with a soft mode instability of the capsid proteins [F. Tama and C. L. Brooks, J. Mol. Biol. 345(2), 299 (2005)]. The continuum theory presented here is an adaptation of the Ginzburg-Landau theory of soft-mode structural phase transitions of solids to viral shells. The theory predicts that the conformational transitions are characterized by a pronounced softening of the shell elasticity in the critical region. We demonstrate that the thermodynamics of the conformational transition can be probed quantitatively by a micromechanical atomic force microscope study. The external force can drive a capsid into a state of phase coexistence characterized by a highly nonlinear force deformation curve.

Background: Although the Pneumonia Severity Index (PSI) has been extensively validated, little is known of the impact of its routine use as an aid to site-of-treatment decisions for patients with pneumonia who present to emergency departments (EDs)., Methods: A prospective, observational, controlled cohort study of patients with pneumonia was conducted in 8 EDs that used the PSI (PSI-user EDs) and 8 EDs that did not use the PSI (PSI-nonuser EDs) in France. The outcomes examined included the proportion of "low-risk" patients (PSI risk classes I-III) treated as outpatients, all-cause 28-day mortality, admission of inpatients to the intensive care unit, and subsequent hospitalization of outpatients., Results: Of the 925 patients enrolled in the study, 472 (51.0%) were treated at PSI-user EDs, and 453 (49.0%) were treated at PSI-nonuser EDs; 449 (48.5%) of all patients were considered to be at low risk. In PSI-user EDs, 92 (42.8%) of 215 patients at low risk were treated as outpatients, compared with 56 (23.9%) of 234 patients at low risk in PSI-nonuser EDs. The adjusted odds ratios for outpatient treatment were higher for patients in PSI risk classes I and II who were treated in PSI-user EDs, compared with PSI-nonuser EDs (adjusted odds ratio, 7.0 [95% confidence interval, 2.0-25.0] and 4.6 [95% confidence interval, 1.3-16.2], respectively), whereas the adjusted odds ratio did not differ by PSI-user status among patients in risk class III or among patients at high risk. After adjusting for pneumonia severity, mortality was lower in patients who were treated in PSI-user EDs; other safety outcomes did not differ between patients treated in PSI-user and PSI-nonuser EDs., Conclusions: The routine use of the PSI was associated with a larger proportion of patients in PSI risk classes I and II who had pneumonia and who were treated in the outpatient environment without compromising their safety.

Chromosome 14 is one of five acrocentric chromosomes in the human genome. These chromosomes are characterized by a heterochromatic short arm that contains essentially ribosomal RNA genes, and a euchromatic long arm in which most, if not all, of the protein-coding genes are located. The finished sequence of human chromosome 14 comprises 87,410,661 base pairs, representing 100% of its euchromatic portion, in a single continuous segment covering the entire long arm with no gaps. Two loci of crucial importance for the immune system, as well as more than 60 disease genes, have been localized so far on chromosome 14. We identified 1,050 genes and gene fragments, and 393 pseudogenes. On the basis of comparisons with other vertebrate genomes, we estimate that more than 96% of the chromosome 14 genes have been annotated. From an analysis of the CpG island occurrences, we estimate that 70% of these annotated genes are complete at their 5' end.