An extrinsic motor directs chromatin loop formation by cohesin.

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.

Condensin-Mediated Chromosome Folding and Internal Telomeres Drive Dicentric Severing by Cytokinesis.

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.

Breakage in breakage-fusion-bridge cycle: an 80-year-old mystery.

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.

Decay Dynamics of a Single Spherical Domain in Near-Critical Phase-Separated Conditions.

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.

Non-Gaussian Diffusion Near Surfaces.

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.

Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle.

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.

Synthesis and Use of Trifluoromethylthiolated Ketenimines.

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 SCF3 moiety.

Nonequilibrium Dynamics Induced by Scattering Forces for Optically Trapped Nanoparticles in Strongly Inertial Regimes.

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.

Contact Kinetics in Fractal Macromolecules.

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.

Gaussian semiflexible rings under angular and dihedral restrictions.

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.

Self-phoretic oscillatory motion in a harmonic trap.

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.

Universal kinetics of imperfect reactions in confinement.

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.

Comparative genomic analysis of obligately piezophilic Moritella yayanosii DB21MT-5 reveals bacterial adaptation to the Challenger Deep, Mariana Trench.

Hadal trenches are the deepest but underexplored ecosystems on the Earth. Inhabiting the trench bottom is a group of micro-organisms termed obligate piezophiles that grow exclusively under high hydrostatic pressures (HHP). To reveal the genetic and physiological characteristics of their peculiar lifestyles and microbial adaptation to extreme high pressures, we sequenced the complete genome of the obligately piezophilic bacterium Moritella yayanosii DB21MT-5 isolated from the deepest oceanic sediment at the Challenger Deep, Mariana Trench. Through comparative analysis against pressure sensitive and deep-sea piezophilic Moritella strains, we identified over a hundred genes that present exclusively in hadal strain DB21MT-5. The hadal strain encodes fewer signal transduction proteins and secreted polysaccharases, but has more abundant metal ion transporters and the potential to utilize plant-derived saccharides. Instead of producing osmolyte betaine from choline as other Moritella strains, strain DB21MT-5 ferments on choline within a dedicated bacterial microcompartment organelle. Furthermore, the defence systems possessed by DB21MT-5 are distinct from other Moritella strains but resemble those in obligate piezophiles obtained from the same geographical setting. Collectively, the intensive comparative genomic analysis of an obligately piezophilic strain Moritella yayanosii DB21MT-5 demonstrates a depth-dependent distribution of energy metabolic pathways, compartmentalization of important metabolism and use of distinct defence systems, which likely contribute to microbial adaptation to the bottom of hadal trench.

Practical Synthesis and Application of Halogen-Doped Pyrrole Building Blocks.

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.

Impact of the PrC-210 Radioprotector Molecule on Cancer Deaths in p53-Deficient Mice.

Radiation-induced cancer is an ongoing and significant problem, with sources that include clinics worldwide in which 3.1 billion radiology exams are performed each year, as well as a variety of other scenarios such as space travel and nuclear cleanup. These radiation exposures are typically anticipated, and the exposure is typically well below 1 Gy. When radiation-induced (actually ROS-induced) DNA mutation is prevented, then so too are downstream radiation-induced cancers. Currently, there is no protection available against the effects of such <1 Gy radiation exposures. In this study, we address whether the new PrC-210 ROS-scavenger is effective in protecting p53-deficient (p53-/-) mice against X-ray-induced accelerated tumor mortality; this is the most sensitive radiation tumorigenesis model currently known. Six-day-old p53-/- pups received a single intraperitoneal PrC-210 dose [0.5 maximum tolerated dose (MTD)] or vehicle, and 25 min later, pups received 4.0 Gy X-ray irradiation. At 5 min postirradiation, blood was collected to quantify white blood cell c-H2AX foci. Over the next 250 days, tumor-associated deaths were recorded. Findings revealed that when administered 25 min before 4 Gy X-ray irradiation, PrC-210 reduced DNA damage (c-H2AX foci) by 40%, and in a notable coincidence, caused a 40% shift in tumor latency/incidence, and the 0.5 MTD PrC210 dose had no discernible toxicities in these p53-/- mice. Essentially, the moles of PrC-210 thiol within a single 0.5 MTD PrC-210 dose suppressed the moles of ROS generated by 40% of the 4 Gy X-ray dose administered to p53-/- pups, and in doing so, eliminated the lifetime leukemia/lymphoma risk normally residing "downstream" of that 40% of the 4 Gy dose. In conclusion: 1. PrC-210 is readily tolerated by the 6-day-old p53-/- mice, with no discernible lifetime toxicities; 2. PrC-210 does not cause the nausea, emesis or hypotension that preclude clinical use of earlier aminothiols; and 3. PrC-210 significantly increased survival after 4 Gy irradiation in the p53-/- mouse model.

Role of nonconservative scattering forces and damping on Brownian particles in optical traps.

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.

Quality of end-of-life care in the emergency department.

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.

Fibro-Neuronal Guidance on Common, 3D-Printed Textured Substrates.

Ability to direct neuronal growth not only carries great potential for treating neural conditions-for example, bridging traumatically shattered connections-but would also be an exquisite tool for bionic applications that require a physical interface between neurons and electronics. A testing platform is needed to better understand axonal guidance in the context of a specific in vivo application. Versatility of 3D printing technology allows tailoring to researcher needs, both in vitro and in vivo. In this paper, we establish a fibro-neuronal co-culture inspired by our neural interface research and demonstrate axon alignment on a textured substrate fabricated with a common, versatile 3D-printing set-up.

Routine use of the Pneumonia Severity Index for guiding the site-of-treatment decision of patients with pneumonia in the emergency department: a multicenter, prospective, observational, controlled cohort study.

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.

Theory of conformational transitions of viral shells.

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.