Charge block-driven liquid-liquid phase separation - mechanism and biological roles.

Liquid-liquid phase separation (LLPS) has increasingly been found to play pivotal roles in a number of intracellular events and reactions, and has introduced a new paradigm in cell biology to explain protein-protein and enzyme-ligand interactions beyond conventional molecular and biochemical theories. LLPS is driven by the cumulative effects of weak and promiscuous interactions, including electrostatic, hydrophobic and cation-π interactions, among polypeptides containing intrinsically disordered regions (IDRs) and describes the macroscopic behaviours of IDR-containing proteins in an intracellular milieu. Recent studies have revealed that interactions between 'charge blocks' - clusters of like charges along the polypeptide chain - strongly induce LLPS and play fundamental roles in its spatiotemporal regulation. Introducing a new parameter, termed 'charge blockiness', into physicochemical models of disordered polypeptides has yielded a better understanding of how the intrinsic amino acid sequence of a polypeptide determines the spatiotemporal occurrence of LLPS within a cell. Charge blockiness might also explain why some post-translational modifications segregate within IDRs and how they regulate LLPS. In this Review, we summarise recent progress towards understanding the mechanism and biological roles of charge block-driven LLPS and discuss how this new characteristic parameter of polypeptides offers new possibilities in the fields of structural biology and cell biology.

Chromatin Remodeling Due to Transient-Link-and-Pass Activity Enhances Subnuclear Dynamics.

Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus-some of those transiently link and pass two chromatin segments. Here, we study how such an active perturbation affects fluctuating dynamics of an inclusion in the chromatic medium. Using numerical simulations and a versatile effective model, we categorize inclusion dynamics into three distinct modes. The transient-link-and-pass activity speeds up inclusion dynamics by affecting a slow mode related to chromatin remodeling, viz., size and shape of the chromatin meshes.

Coarse Graining DNA: Symmetry, Nonlocal Elasticity, and Persistence Length.

While the behavior of double-stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein interactions and the nucleosome diffusion mechanism. Here, by employing the rigid base-pair model, we connect its microscopic parameters to the persistence length. Combined with all-atom molecular dynamic simulations, our scheme identifies relevant couplings between different degrees of freedom at each coarse-graining step. This allows us to clarify how the scale dependence of the elastic moduli is determined in a systematic way encompassing the role of previously unnoticed off-site couplings between deformations with different parity.

Mechanisms of DNA-Mediated Allostery.

Proteins often regulate their activities via allostery-or action at a distance-in which the binding of a ligand at one binding site influences the affinity for another ligand at a distal site. Although less studied than in proteins, allosteric effects have been observed in experiments with DNA as well. In these experiments two or more proteins bind at distinct DNA sites and interact indirectly with each other, via a mechanism mediated by the linker DNA molecule. We develop a mechanical model of DNA/protein interactions which predicts three distinct mechanisms of allostery. Two of these involve an enthalpy-mediated allostery, while a third mechanism is entropy driven. We analyze experiments of DNA allostery and highlight the distinctive signatures allowing one to identify which of the proposed mechanisms best fits the data.

Nonequilibrium diffusion of active particles bound to a semiflexible polymer network: Simulations and fractional Langevin equation.

In a viscoelastic environment, the diffusion of a particle becomes non-Markovian due to the memory effect. An open question concerns quantitatively explaining how self-propulsion particles with directional memory diffuse in such a medium. Based on simulations and analytic theory, we address this issue with active viscoelastic systems where an active particle is connected with multiple semiflexible filaments. Our Langevin dynamics simulations show that the active cross-linker displays superdiffusive and subdiffusive athermal motion with a time-dependent anomalous exponent α. In such viscoelastic feedback, the active particle always exhibits superdiffusion with α = 3/2 at times shorter than the self-propulsion time (τA). At times greater than τA, the subdiffusive motion emerges with α bounded between 1/2 and 3/4. Remarkably, active subdiffusion is reinforced as the active propulsion (Pe) is more vigorous. In the high Pe limit, athermal fluctuation in the stiff filament eventually leads to α = 1/2, which can be misinterpreted with the thermal Rouse motion in a flexible chain. We demonstrate that the motion of active particles cross-linking a network of semiflexible filaments can be governed by a fractional Langevin equation combined with fractional Gaussian noise and an Ornstein-Uhlenbeck noise. We analytically derive the velocity autocorrelation function and mean-squared displacement of the model, explaining their scaling relations as well as the prefactors. We find that there exist the threshold Pe (Pe∗) and crossover times (τ∗ and τ†) above which active viscoelastic dynamics emerge on timescales of τ∗≲ t ≲ τ†. Our study may provide theoretical insight into various nonequilibrium active dynamics in intracellular viscoelastic environments.

Slow chromatin dynamics enhances promoter accessibility to transcriptional condensates.

Enhancers are DNA sequences at a long genomic distance from target genes. Recent experiments suggest that enhancers are anchored to the surfaces of condensates of transcription machinery and that the loop extrusion process enhances the transcription level of their target genes. Here, we theoretically study the polymer dynamics driven by the loop extrusion of the linker DNA between an enhancer and the promoter of its target gene to calculate the contact probability of the promoter to the transcription machinery in the condensate. Our theory predicts that when the loop extrusion process is active, the contact probability increases with increasing linker DNA length. This finding reflects the fact that the relaxation time, with which the promoter stays in proximity to the surface of the transcriptional condensate, increases as the length of the linker DNA increases. This contrasts the equilibrium case for which the contact probability between the promoter and the transcription machineries is smaller for longer linker DNA lengths.

Head injuries caused by contact with teeth during sports and exercise activities in Japanese schools during the period 2012-2018.

BACKGROUND/AIM: During sports activities, teeth-related contact can cause injury to both ally and opponent players, which can lead to potential infections and aesthetic problems. However, the extent of such injuries remains unclear. This study aimed to clarify the frequency and situation of head injuries caused by teeth (HICBT) occurring under the supervision of schools in Japan. MATERIAL AND METHODS: HICBT records were extracted from the Japan Sport Council data on head injuries occurring reported during the 7-year period from 2012 to 2018 under the supervision of schools in Japan. RESULTS: Of the total 463,527 head injury cases during the study period, 4495 cases (approximately 1%) were HICBT. Of the HICBT cases, 3650 (81.20%) were related to sports and athletic activity. Such injuries were reported to occur most often during basketball with a rate of 57.07% and 50.43%; soccer/futsal was the next most common sport with a rate of 13.38% and 24.01% in junior high school and high school students. Tag games were responsible for a similar number of HICBT cases at 22.73% and 39.03% in kindergartens and elementary school students. CONCLUSIONS: A total of 4495 cases of HICBT were identified, accounting for about 1% of all head injuries under the supervision of schools in Japan during the study period. This result reminds us that our teeth could be the weapon against the players during sports events. HICBTs occurring during basketball and soccer/futsal, in which mouthguards are not mandatory, were conspicuous among junior and senior high school students. Active use of mouthguards in various sports will protect players as well as their teammates and opponents. Sports dentists should encourage the revision of rules, such as mandating the use of mouthguards, in popular sports with a high incidence of HICBT, such as basketball and soccer/futsal.

Improving light-cured intermediate resin for hard and space mouthguard using a glass fiber.

BACKGROUND/AIMS: A light-cured intermediate material is useful for fabricating a hard insert and a buffer space mouthguard (H&SMG). However, it requires improvement in its mechanical properties and shock-absorbing capacity. The aim of this study was to evaluate the mechanical properties of two prototype light-cured intermediate materials reinforced with glass fibers, and the impact absorption capacity and durability of H&SMGs made with the prototype intermediate materials. MATERIALS AND METHODS: Two prototype materials containing long and microlength glass fibers in a light-cured intermediate material, Innerframe LC®, for H&SMG, were fabricated and tested. A three-point bending test was performed for evaluation of the mechanical properties. In addition, a shock absorption test was conducted using a customized pendulum impact testing machine to evaluate the H&SMGs' impact absorption capacity and durability. RESULTS: Long and microlength glass fibers significantly improved flexural modulus and strength. H&SMGs made with these two glass fiber-containing materials had high impact absorption capacity against both low and high impact forces, while the mouthguards made with long glass fiber materials had the best results. CONCLUSION: Long and microlength glass fibers with the prototype materials improved the mechanical properties of Innerframe LC® and the impact absorption capacity and durability of H&SMGs. H&SMGs made with the long glass fiber prototype materials had the best performance.

Formulation of Chromatin Mobility as a Function of Nuclear Size during C. elegans Embryogenesis Using Polymer Physics Theories.

During early embryogenesis of the nematode, Caenorhabditis elegans, the chromatin motion markedly decreases. Despite its biological implications, the underlying mechanism for this transition was unclear. By combining theory and experiment, we analyze the mean-square displacement (MSD) of the chromatin loci, and demonstrate that MSD-vs-time relationships in various nuclei collapse into a single master curve by normalizing them with the mesh size and the corresponding time scale. This enables us to identify the onset of the entangled dynamics with the size of tube diameter of chromatin polymer in the C. elegans embryo. Our dynamical scaling analysis predicts the transition between unentangled and entangled dynamics of chromatin polymers, the quantitative formula for MSD as a function of nuclear size and timescale, and provides testable hypotheses on chromatin mobility in other cell types and species.

Mechanical properties of nucleic acids and the non-local twistable wormlike chain model.

Mechanical properties of nucleic acids play an important role in many biological processes that often involve physical deformations of these molecules. At sufficiently long length scales (say, above ∼20-30 base pairs), the mechanics of DNA and RNA double helices is described by a homogeneous Twistable Wormlike Chain (TWLC), a semiflexible polymer model characterized by twist and bending stiffnesses. At shorter scales, this model breaks down for two reasons: the elastic properties become sequence-dependent and the mechanical deformations at distal sites get coupled. We discuss in this paper the origin of the latter effect using the framework of a non-local Twistable Wormlike Chain (nlTWLC). We show, by comparing all-atom simulations data for DNA and RNA double helices, that the non-local couplings are of very similar nature in these two molecules: couplings between distal sites are strong for tilt and twist degrees of freedom and weak for roll. We introduce and analyze a simple double-stranded polymer model that clarifies the origin of this universal distal couplings behavior. In this model, referred to as the ladder model, a nlTWLC description emerges from the coarsening of local (atomic) degrees of freedom into angular variables that describe the twist and bending of the molecule. Different from its local counterpart, the nlTWLC is characterized by a length-scale-dependent elasticity. Our analysis predicts that nucleic acids are mechanically softer at the scale of a few base pairs and are asymptotically stiffer at longer length scales, a behavior that matches experimental data.

Jaw-Clenching Intensity Effects on Masseter Oxygen Dynamics and Fatigue: A NIRS Oximetry Study.

The purpose of this study was to clarify the effects of jaw-clenching intensity on masseter muscle oxygen dynamics during clenching and recovery and masseter muscle fatigue using the spatially resolved method of near-infrared spectroscopy. Pulse rate, mean power frequency from electromyography in the masseter and visual analogue scale for masseter fatigue were also examined as related items. The 25% and 50% maximum voluntary contractions were determined using electromyography before the experiment and used as visual feedback on the screen. Twenty-three healthy adult male subjects volunteered for this study. Clenching decreased oxygen and oxygenated haemoglobin, and increased deoxygenated haemoglobin in the masseter muscle. The higher the intensity of clenching, the more prominent the effect. The oxygen dynamics tended to return to normal after clenching, but the change was slower with higher clenching intensity. Pulse rate increased with clenching, and the increment was more prominent with higher clenching intensity. Clenching caused a shift of mean power frequency to a lower range, an increase in subjective fatigue, an early appearance of a breakpoint appearance time and a prolongation of a 1/2 recovery time. All of these effects were more evident with increasing clenching intensity. In conclusion, clenching intensity influenced the oxygen dynamics of the masseter muscle and fatigue state during clenching and recovery. The higher the intensity, the greater the impact.

Twist dynamics and buckling instability of ring DNA: the effect of groove asymmetry and anisotropic bending.

By combining analytical theory and Molecular Dynamics simulations we study the relaxation dynamics of DNA circular plasmids that initially undergo a local twist perturbation. In this process, the twist-bend coupling arising from the groove asymmetry in the DNA double helix clearly shows up. In the two scenarios explored, with/without this coupling, the initial perturbation relaxes diffusively. However, there are some marked differences in the value of the diffusion coefficient and the dynamics in both cases. These differences can be explained by assuming the existence of three distinctive time scales; a rapid relaxation of local bending, the slow twist spreading, and the buckling transition taking place in a much longer time scale. In particular, the separation of time scales allows deducing an effective diffusion equation in stage , with a diffusion coefficient influenced by the twist-bend coupling. We also discuss the mapping of the realistic DNA model to the simpler isotropic twistable worm-like chain using the renormalized bending and twist moduli; although useful in many cases, it fails to make a quantitative prediction on the instability mode of buckling transition.

Transition path times in asymmetric barriers.

Biomolecular conformational transitions are usually modeled as barrier crossings in a free energy landscape. The transition paths connect two local free energy minima and transition path times (TPT) are the actual durations of the crossing events. The simplest model employed to analyze TPT and to fit empirical data is that of a stochastic particle crossing a parabolic barrier. Motivated by some disagreement between the value of the barrier height obtained from the TPT distributions as compared to the value obtained from kinetic and thermodynamic analyses, we investigate here TPT for barriers which deviate from the symmetric parabolic shape. We introduce a continuous set of potentials, that starting from a parabolic shape, can be made increasingly asymmetric by tuning a single parameter. The TPT distributions obtained in the asymmetric case are very well-fitted by distributions generated by parabolic barriers. The fits, however, provide values for the barrier heights and diffusion coefficients which deviate from the original input values. We show how these findings can be understood from the analysis of the eigenvalues spectrum of the Fokker-Planck equation and highlight connections with experimental results.

Topological free volume and quasi-glassy dynamics in the melt of ring polymers.

Motivated by recent observations that non-concatenated ring polymers in their dense solution exhibit a glass-like dynamics, we propose a free volume description of the motion of such rings based on the notion of topological volume. We first construct a phenomenological free energy which enables one to quantify the degree of topological crowding measured by the coordination number. Then we pinpoint a key role of the cooperative dynamics of neighboring rings, which is responsible for an anomalous dependence of the global structural relaxation (diffusion) time on ring length. Predictions on molecular weight dependence of both static (ring size, coordination number) and dynamic (relaxation time, diffusion coefficient) quantities are in very good agreement with reported numerical simulations. Throughout the discussion, the entanglement length Ne is assumed to be a unique characteristic length for the topological constraint, and hence, all the physical quantities are universally described in terms of the rescaled chain length N/Ne. Finally, we discuss how the dense solution of rings is analogous to yet different from ordinary glassy systems.

Multiple patterns of polymer gels in microspheres due to the interplay among phase separation, wetting, and gelation.

We report the spontaneous patterning of polymer microgels by confining a polymer blend within microspheres. A poly(ethylene glycol) (PEG) and gelatin solution was confined inside water-in-oil (W/O) microdroplets coated with a layer of zwitterionic lipids: dioleoylphosphatidylethanolamine (PE) and dioleoylphosphatidylcholine (PC). The droplet confinement affected the kinetics of the phase separation, wetting, and gelation after a temperature quench, which determined the final microgel pattern. The gelatin-rich phase completely wetted to the PE membrane and formed a hollow microcapsule as a stable state in the PE droplets. Gelation during phase separation varied the relation between the droplet size and thickness of the capsule wall. In the case of the PC droplets, phase separation was completed only for the smaller droplets, wherein the microgel partially wetted the PC membrane and had a hemisphere shape. In addition, the temperature decrease below the gelation point increased the interfacial tension between the PEG/gelatin phases and triggered a dewetting transition. Interestingly, the accompanying shape deformation to minimize the interfacial area was only observed for the smaller PC droplets. The critical size decreased as the gelatin concentration increased, indicating the role of the gel elasticity as an inhibitor of the deformation. Furthermore, variously patterned microgels with spherically asymmetric shapes, such as discs and stars, were produced as kinetically trapped states by regulating the incubation time, polymer composition, and droplet size. These findings demonstrate a way to regulate the complex shapes of microgels using the interplay among phase separation, wetting, and gelation of confined polymer blends in microdroplets.

Active diffusion of model chromosomal loci driven by athermal noise.

Active diffusion, i.e., fluctuating dynamics driven by athermal noise, is found in various out-of-equilibrium systems. Here we discuss the nature of the active diffusion of tagged monomers in a flexible polymer. A scaling argument based on the notion of tension propagation clarifies how the polymeric effect is reflected in the anomalous diffusion exponent, which may be of relevance to the dynamics of chromosomal loci in living cells.

Dynamic compression of single nanochannel confined DNA via a nanodozer assay.

We show that a single DNA molecule confined and extended in a nanochannel can be dynamically compressed by sliding a permeable gasket at a fixed velocity relative to the stationary polymer. The gasket is realized experimentally by optically trapping a nanosphere inside a nanochannel. The trapped bead acts like a "nanodozer," directly applying compressive forces to the molecule without requirement of chemical attachment. Remarkably, these strongly nonequilibrium measurements can be quantified via a simple nonlinear convective-diffusion formalism and yield insights into the local blob statistics, allowing us to conclude that the compressed nanochannel-confined chain exhibits mean-field behavior.

Effect of Vinyl Acetate, Glass Fibers Contents, and Buffer Space on EVA's Mechanical Property and Shock Absorption Ability.

OBJECTIVES: The aim of the study was to evaluate the mechanical properties and impact absorption capacity of prototype materials comprising ethylene vinyl acetate (EVA) of different hardness reinforced using different amounts of glass fibers (GFs), considering a buffer space. MATERIALS AND METHODS: Six prototype materials were made by adding E-GFs (5 and 10 wt%) to EVA with vinyl acetate (VA) contents of 9.4 wt% ("hard" or HA) and 27.5 wt% ("soft" or SO). Durometer hardness and tensile strength tests were performed to evaluate the mechanical properties of the materials. Moreover, an impact test was conducted using a customized pendulum impact tester to assess the impact absorption capacity (with or without a buffer space) of the specimens. RESULTS: The mechanical properties of the prototypes, namely, durometer hardness, Young's modulus, and tensile strength, were significantly higher in the HA group than in the SO group, regardless of the presence or added amount of GFs. The addition of GFs, particularly in a large amount (10 wt%), significantly increased these values. In terms of the impact absorption capacity, the original hardness of the EVA material, that is, its VA content, had a more substantial effect than the presence or absence of GFs and the added amount of GFs. Interestingly, the HA specimens with the buffer space exhibited significantly higher impact absorption capacities than the SO specimens. Meanwhile, the SO specimens without the buffer space exhibited significantly higher impact absorption capacities than the HA specimens. Moreover, regardless of the sample material and impact distance, the buffer space significantly improved impact absorption. In particular, with the buffer space, the impact absorption capacity increased with the added amount of GFs. CONCLUSION: The basic mechanical properties, including durometer hardness, Young's modulus, and tensile strength, of the EVA prototype were significantly increased by reducing the amount of VA regardless of the presence or added amount of GFs. Adding GFs, particularly in large amounts, significantly increased the values of aforementioned mechanical properties. Impact absorption was significantly affected by the hardness of the original EVA material and enhanced by the addition of the buffer space. The HA specimen had a high shock absorption capacity with the buffer space, and the SO specimen had a high shock absorption capacity without the buffer space. With the buffer space, impact absorption improved with the amount of added GFs.

Hamilton-Jacobi method for molecular distribution function in a chemical oscillator.

Using the Hamilton-Jacobi method, we solve chemical Fokker-Planck equations within the Gaussian approximation and obtain a simple and compact formula for a conditional probability distribution. The formula holds in general transient situations, and can be applied not only to a steady state but also to an oscillatory state. By analyzing the long time behavior of the solution in the oscillatory case, we obtain the phase diffusion constant along the periodic orbit and the steady distribution perpendicular to it. A simple method for numerical evaluation of these formulas are devised, and they are compared with Monte Carlo simulations in the case of Brusselator as an example. Some results are shown to be identical to previously obtained expressions.

Effects of Mouthguards on Skin Damage In Vitro Study.

OBJECTIVE: Mouthguards can prevent and reduce orofacial sports traumas, which occur to the players themselves. However, the effect of mouthguards on skin damage has not been clarified. The present study's purpose was to examine whether the mouthguard can reduce or prevent skin damage caused by teeth (including the difference in mouthguard thickness). MATERIALS AND METHODS: Pigskins, artificial teeth, and Ethylene-vinyl acetate (EVA) mouthguard blanks with 1.5- and 3.0-mm thickness were employed. Each of the two type mouthguards was produced in 10 replicates. Mouthguard incisal thickness and collision touch angle were measured on a PC using imaging software. A pendulum-type machine was used to apply impact. Strain gauges attached to the tooth and impacted plate were used to measure mouthguards' effect on impact stress. Also, a microscope was used to observe the after impacted skin condition, and the extent of damage was assessed as a score. RESULTS: The pigskin was ruptured in without mouthguard (NOMG) with presenting the highest damage score, whereas the complete rupture was not seen in the 1.5 mm MG, but the damage of the skin (defeat) was observed. No tissue change was found with the 3 mmMG. In both the flat plate and impact tooth strain, no significant difference was observed between NOMG and 1.5 mmMG. However, 3 mmMG had a significantly smaller value than the other two conditions. These results are likely to be strongly influenced by the mouthguard incisal thicknesses and collision touch angles differences. CONCLUSION: The present study results clarified that two different thickness mouthguards reduced the skin damage, and the thicker mouthguard showed more effectiveness. Therefore, mouthguards may prevent the wearer's stomatognathic system's trauma and avoid damage to the skin of other athletes they are playing with. This effect seems to be an essential basis for explaining the necessity of using mouthguards for others besides full-contact sports.