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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Genome Sequence of Piezophilic Bacterium Desulfovibrio profundus Strain 500-1, Isolated from a Deep Sediment Layer in the Japan Sea.

Piezophilic Desulfovibrio profundus strain 500-1 was isolated in the Japan Sea from a sediment layer at 500-m depth under a water column of 1,000 m. Here, we report the genome sequence of this strain, which includes a 4,168,905-bp circular chromosome and two plasmids of 42,836 bp and 6,167 bp.

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.

Local orientational mobility in regular hyperbranched polymers.

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.

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.

Transgenerational functions of small RNA pathways in controlling gene expression in C. elegans.

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.

Approach to asymptotically diffusive behavior for Brownian particles in media with periodic diffusivities.

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.

Coordination and collective properties of molecular motors: theory.

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.