Search Results (8)

Studying strong interactions at finite temperatures has been a critical topic in high-energy nuclear collisions. Charmonium, as a clear probe of deconfined matter, is believed to be predominantly influenced by the coalescence of off-diagonal charm and anti-charm quarks. The grand canonical ensemble is commonly used to describe the coalescence of charm and anti-charm quarks. In collisions where only one or two charm pairs are produced, the contribution from the coalescence of diagonal charm and anti-charm quarks becomes dominant, a phenomenon known as the canonical effect. This effect is sensitive to the momentum correlation between the heavy quark and anti-quark. In this work, we employ the Langevin model to study the evolutions of correlated charm and anti-charm quarks and their coalescence process. The asymmetry in the momentum of charm and anti-charm quarks play important roles in their coalescence process. In addition, we investigate the impact of this effect on the nuclear modification factor of charmonium, which can be enhanced evidently in semi-central collisions at RHIC Au-Au collisions. The theoretical calculations with canonical effect explain the experimental data well, which helps us to understand the production mechanisms of the quarkonium bound state in the deconfined medium. Full article

Co-varying disturbance and environmental gradients can shape vegetation dynamics and increase the diversity of plant communities and their features. Pinyon–juniper woodlands are widespread in semi-arid climates of western North America, encompassing extensive environmental gradients, and a knowledge gap is how the diversity in features of these communities changes across co-varying gradients in fire history and soil. In pinyon–juniper communities spanning soil parent materials (basalt, limestone) and recent fire histories (0–4 prescribed fires or managed wildfires and 5–43 years since fire) in Grand Canyon-Parashant National Monument (Arizona, USA), we examined variation at 25 sites in three categories of plant community features including fuels, tree structure, and understory vegetation. Based on ordinations, canonical correlation analysis, and permutation tests, plant community features varied primarily with the number of fires, soil coarseness and chemistry, and additionally with tree structure for understory vegetation. Fire and soil variables accounted for 33% of the variance in fuels and tree structure, and together with tree structure, 56% of the variance in understories. The cover of the non-native annual Bromus tectorum was higher where fires had occurred more recently. In turn, B. tectorum was positively associated with the percentage of dead trees and negatively associated with native forb species richness. Based on a dendroecological analysis of 127 Pinus monophylla and Juniperus osteosperma trees, only 18% of trees presently around our study sites originated before the 1870s (Euro-American settlement) and <2% originated before the 1820s. Increasing contemporary fire activity facilitated by the National Park Service since the 1980s corresponded with increasing tree mortality and open-structured stands, apparently more closely resembling pre-settlement conditions. Using physical geography, such as soil parent material, as a landscape template shows promise for (i) incorporating diversity in long-term community change serving as a baseline for vegetation management, (ii) customizing applying treatments to unique conditions on different soil types, and (iii) benchmarking monitoring metrics of vegetation management effectiveness to levels scaled to biophysical variation across the landscape. Full article

(1) Background: Main Protease (Mpro) is an attractive therapeutic target that acts in the replication and transcription of the SARS-CoV-2 coronavirus. Mpro is rich in residues exposed to protonation/deprotonation changes which could affect its enzymatic function. This work aimed to explore the effect of the protonation/deprotonation states of Mpro at different pHs using computational techniques. (2) Methods: The different distribution charges were obtained in all the evaluated pHs by the Semi-Grand Canonical Monte Carlo (SGCMC) method. A set of Molecular Dynamics (MD) simulations was performed to consider the different protonation/deprotonation during 250 ns, verifying the structural stability of Mpro at different pHs. (3) Results: The present findings demonstrate that active site residues and residues that allow Mpro dimerisation was not affected by pH changes. However, Mpro substrate-binding residues were altered at low pHs, allowing the increased pocket volume. Additionally, the results of the solvent distribution around S$\gamma$, H$\gamma$, N$\delta$1 and H$\delta$1 atoms of the catalytic residues Cys145 and His41 showed a low and high-water affinity at acidic pH, respectively. It which could be crucial in the catalytic mechanism of SARS-CoV-2 Mpro at low pHs. Moreover, we analysed the docking interactions of PF-00835231 from Pfizer in the preclinical phase, which shows excellent affinity with the Mpro at different pHs. (4) Conclusion: Overall, these findings indicate that SARS-CoV-2 Mpro is highly stable at acidic pH conditions, and this inhibitor could have a desirable function at this condition. Full article

The effect of pH on the supramolecular structure of Helicobacter pylori urease was studied by means of molecular dynamics simulations at seven different pHs. Appropriate urease charge distributions were calculated using a semi-grand canonical Monte Carlo (SGCMC) procedure that assigns each residue’s charge state depending on the assigned individual p$K_{\mathrm{a}}$ obtained by PROPKA. The effect of pH on protein stability has been analyzed through root-mean-square deviation (RMSD), radius of gyration (RG), solvent-accessible surface area (SASA), hydrogen bonds (HB) and salt bridges (SB). Urease catalyses the hydrolysis of urea in 12 active sites that are covered by mobile regions that act like flaps. The mobility of these flaps is increased at acidic pHs. However, extreme acidic conditions cause urease to have the least number of stabilizing interactions. This initiates the process of denaturalization, wherein the four ${\left(\alpha \beta \right)}_3$ subunits of the global structure (($\alpha \beta$)${}_3$)${}_4$ of urease start to separate. Full article

Mesenchymal stromal cells (MSCs) were obtained from human bone marrow and amplified in cultures supplemented with human platelet lysate. Once semi-confluent, cells were seeded in solid collagen scaffolds that were rapidly colonized by the cells generating a 3D cell scaffold. Here, they acquired a myofibroblast phenotype and when exposed to appropriate chemical stimulus, developed tension and cell shortening, similar to those of striated and smooth muscle cells. Myofibroblasts contained a molecular motor—the non-muscle myosin type IIA (NMMIIA) whose crossbridge (CB) kinetics are dramatically slow compared with striated and smooth muscle myosins. Huxley’s equations were used to determine the molecular mechanical properties of NMMIIA. Thank to the great number of NMMIIA molecules, we determined the statistical mechanics (SM) of MSCs, using the grand canonical ensemble which made it possible to calculate various thermodynamic entities such as the chemical affinity, statistical entropy, internal energy, thermodynamic flow, thermodynamic force, and entropy production rate. The linear relationship observed between the thermodynamic force and the thermodynamic flow allowed to establish that MSC-laden in collagen scaffolds were in a near-equilibrium stationary state (affinity ≪ RT), MSCs were also seeded in solid collagen scaffolds functionalized with the tripeptide Arg-Gly-Asp (RGD). This induced major changes in NMMIIA SM particularly by increasing the rate of entropy production. In conclusion, collagen scaffolds laden with MSCs can be viewed as a non-muscle contractile bioengineered tissue operating in a near-equilibrium linear regime, whose SM could be substantially modified by the RGD peptide. Full article

This work addresses the role of charge regulation (CR) and the associated fluctuations in the conformational and mechanical properties of weak polyelectrolytes. Due to CR, changes in the pH-value modifies the average macromolecular charge and conformational equilibria. A second effect is that, for a given average charge per site, fluctuations can alter the intensity of the interactions by means of correlation between binding sites. We investigate both effects by means of Monte Carlo simulations at constant pH-value, so that the charge is a fluctuating quantity. Once the average charge per site is available, we turn off the fluctuations by assigning the same average charge to every site. A constant charge MC simulation is then performed. We make use of a model which accounts for the main fundamental aspects of a linear flexible polyelectrolyte that is, proton binding, angle internal rotation, bond stretching and bending. Steric excluded volume and differentiated treatment for short-range and long-range interactions are also included. This model can be regarded as a kind of “minimal” in the sense that it contains a minimum number of parameters but still preserving the atomistic detail. It is shown that, if fluctuations are activated, gauche state bond probabilities increase and the persistence length decreases, so that the polymer becomes more folded. Macromolecular stretching is also analyzed in presence of CR (the charge depends on the applied force) and without CR (the charge is fixed to the value at zero force). The analysis of the low force scaling behavior concludes that Pincus exponent becomes pH-dependent. Both, with and without CR, a transition from 1/2 at high pH-values (phantom chain) to 3/5 at low pH-values (Pincus regime) is observed. Finally, the intermediate force stretching regime is investigated. It is found that CR induces a moderate influence in the force-extension curves and persistence length (which in this force regime becomes force-dependent). It is thus concluded that the effect of CR on the stretching curves is mainly due to the changes in the average charge at zero force. It is also found that, for the cases studied, the effect of steric excluded volume is almost irrelevant compared to electrostatic interactions. Full article

Salinity stress limited the production in over 30% of irrigated crops and 7% of dryland agriculture worldwide. The objective was to evaluate the effects of NaCl-stress on the enzymatic activity in tomato. Two experiments were carried out in germination and early vegetative growth stages. The activity of proline and peroxidase of eight varieties (Missouri, Yaqui, Vita, Feroz, Rio Grande, Tropic, Ace, and Floradade) submitted to NaCl concentrations (0, 50, 100, 150 and 200 mM de NaCl) and the semi-quantitative activity of 19 enzymes APY ZYM^® were measured under a completely randomized design with four replications. Data were analyzed using univariate-multivariate analysis of variance, Tukey’s HSD (p = 0.05), canonical discriminant and cluster analysis. The results showed significant differences between varieties and NaCl in proline content. Proline increased as the NaCl concentration increased. Peroxidase did no show significant differences. Eight enzymes were included within the model to properly classify the varieties and NaCl. In shoots, varieties and NaCl showed that enzymatic activity was higher in the order of alkaline-phosphatase > leucine arylamidase > acid phosphatase > naphthol-AS-BI-phosphohydrolase > n-acetyl-β-glucosaminidase > β-galactosidase, while in roots was higher in the order of alkaline-phosphatase > naphthol-AS-BI-phosphohydrolase > acid phosphatase > n-acetyl-β-glucosaminidase. Acid and alkali phosphatase, lipase, esterase, β-galactosidase, and trypsin can be a potential biomarker for NaCl-stress tolerance in tomato. Full article

The classical Rotational Isomeric State (RIS) model, originally proposed by Flory, has been used to rationalize a wide range of physicochemical properties of neutral polymers. However, many weak polyelectrolytes of interest are able to regulate their charge depending on the conformational state of the bonds. Recently, it has been shown that the RIS model can be coupled with the Site Binding (SB) model, for which the ionizable sites can adopt two states: protonated or deprotonated. The resulting combined scheme, the SBRIS model, allows for analyzing ionization and conformational equilibria on the same foot. In the present work, this approach is extended to include pH-dependent electrostatic Long-Range (LR) interactions, ubiquitous in weak polyelectrolytes at moderate and low ionic strengths. With this aim, the original LR interactions are taken into account by defining effective Short-Range (SR) and pH-dependent parameters, such as effective microscopic protonation constants and rotational bond energies. The new parameters are systematically calculated using variational methods. The machinery of statistical mechanics for SR interactions, including the powerful and fast transfer matrix methods, can then be applied. The resulting technique, which we will refer to as the Local Effective Interaction Parameters (LEIP) method, is illustrated with a minimal model of a flexible linear polyelectrolyte containing only one type of rotating bond. LEIP reproduces very well the pH dependence of the degree of protonation and bond probabilities obtained by semi-grand canonical Monte Carlo simulations, where LR interactions are explicitly taken into account. The reduction in the computational time in several orders of magnitude suggests that the LEIP technique could be useful in a range of areas involving linear weak polyelectrolytes, allowing direct fitting of the relevant physical parameters to the experimental quantities. Full article