Physiological role of taurine – from organism to organelle

Taurine is often referred to as a semi‐essential amino acid as newborn mammals have a limited ability to synthesize taurine and have to rely on dietary supply. Taurine is not thought to be incorporated into proteins as no aminoacyl tRNA synthetase has yet been identified and is not oxidized in mammalian cells. However, taurine contributes significantly to the cellular pool of organic osmolytes and has accordingly been acknowledged for its role in cell volume restoration following osmotic perturbation. This review describes taurine homeostasis in cells and organelles with emphasis on taurine biophysics/membrane dynamics, regulation of transport proteins involved in active taurine uptake and passive taurine release as well as physiological processes, for example, development, lung function, mitochondrial function, antioxidative defence and apoptosis which seem to be affected by a shift in the expression of the taurine transporters and/or the cellular taurine content.     

基于改进传染病动力学易感-暴露-感染-恢复（SEIR）模型预测新型冠状病毒肺炎疫情

目的 研究基于传染病动力学易感-暴露-感染-恢复（SEIR）模型对新型冠状病毒肺炎（COVID-19）疫情发展情况的预测效果,为有效应对疫情提供指导。方法 利用Python爬虫自动更新功能获取中华人民共和国国家卫生健康委员会公布的疫情数据,通过改进传染病动力学SEIR模型,自动修正COVID-19基本再生数（R₀）,对中国湖北省和韩国的COVID-19疫情发展趋势进行预测。结果 模型预测的湖北省COVID-19疫情顶点在2020年2月21日,现有确诊病例数约为50 000例（2月19日）,预计疫情将于3月4日回落至30 000例以下,并在5月10日左右结束。中华人民共和国国家卫生健康委员会公布的实际数据显示,确诊人数顶点为53 371例。模型预测的韩国疫情峰值在3月7日,将于4月底结束。结论 改进的传染病动力学SEIR模型在COVID-19疫情早期实现了较准确的数据预测,政府相关部门在疫情中及时、有效的强力干预明显影响了疫情的发展进程,东亚其他国家如韩国的疫情在3月仍处于上升期,提示中国需要提防输入性疫情风险。     

Disentangling the lifespans of hepatitis C virus‐infected cells and intracellular vRNA replication‐complexes during direct‐acting anti‐viral therapy

The decay rate of hepatitis C virus (HCV)‐infected cells during therapy has been used to determine the duration of treatment needed to attain a sustained virologic response, but with direct‐acting anti‐virals (DAA), this rate has been difficult to estimate. Here, we show that it is possible to estimate it, by simultaneously analysing the viral load and alanine aminotransferase (ALT) kinetics during combination DAA therapy. We modelled the HCV RNA and ALT serum kinetics in 26 patients with chronic HCV genotype 1b infection, under four different sofosbuvir‐based combination treatments. In all patients, ALT decayed exponentially to a set point in the normal range by 1‐3 weeks after initiation of therapy. The model indicates that the ALT decay rate during the first few weeks after initiation of therapy reflects the death rate of infected cells, with an estimated median half‐life of 2.5 days in this patient population. This information allows independent estimation of the rate of loss of intracellular replication complexes during therapy. Our model also predicts that the final ALT set point is not related to the release of ALT by dying HCV‐infected cells. Using ALT data, one can separately obtain information about the rate of ‘cure’ of HCV‐infected cells versus their rate of death, something not possible when analysing only HCV RNA data. This information can be used to compare the effects of different DAA combinations and to rationally evaluate their anti‐viral effects.     

Computer-Aided Design of Boron Nitride-Based Membranes with Armchair and Zigzag Nanopores for Efficient Water Desalination

Recent studies have shown that the use of membranes based on artificial nanoporous materials can be effective for desalination and decontamination of water, separation of ions and gases as well as for solutions to other related problems. Before the expensive stages of synthesis and experimental testing, the search of the optimal dimensions and geometry of nanopores for the water desalination membranes can be done using computer-aided design. In the present study, we propose and examine the assumption that rectangular nanopores with a high aspect ratio would demonstrate excellent properties in terms of water permeation rate and ion rejection. Using the non-equilibrium molecular dynamic simulations, the properties of promising hexagonal boron nitride (h-BN) membranes with rectangular nanopores were predicted. It has been found that not only the nanopore width but also its design (“armchair” or “zigzag”) determines the permeability and ion selectivity of the h-BN-based membrane. The results show that membranes with a zigzag-like design of nanopores of ~6.5 Å width and the armchair-like nanopores of ~7.5 Å width possess better efficiency compared with other considered geometries. Moreover, the estimated efficiency of these membranes is higher than that of any commercial membranes and many other previously studied single-layer model membranes with other designs of the nanopores.     

Deformation Behavior of Nanocrystalline Body-Centered Cubic Iron with Segregated,Foreign Interstitial: A Molecular Dynamics Study

In the present work, modified embedded atom potential and large-scale molecular dynamics’ simulations were used to explore the effect of grain boundary (GB) segregated foreign interstitials on the deformation behavior of nanocrystalline (nc) iron. As a case study, carbon and nitrogen (about 2.5 at.%) were added to (nc) iron. The tensile test results showed that, at the onset of plasticity, grain boundary sliding mediated was dominated, whereas both dislocations and twinning were prevailing deformation mechanisms at high strain. Adding C/N into GBs reduces the free excess volume and consequently increases resistance to GB sliding. In agreement with experiments, the flow stress increased due to the presence of carbon or nitrogen and carbon had the stronger impact. Additionally, the simulation results revealed that GB reduction and suppressing GBs’ dislocation were the primary cause for GB strengthening. Moreover, we also found that the stress required for both intragranular dislocation and twinning nucleation were strongly dependent on the solute type.     

The Effects of Grain Boundary Misorientation on the Mechanical Properties and Mechanism of Plastic Deformation of Ni/Ni3Al: A Molecular Dynamics Study

The effects of grain boundary misorientation angle (θ) on mechanical properties and the mechanism of plastic deformation of the Ni/Ni₃Al interface under tensile loading were investigated using molecular dynamics simulations. The results show that the space lattice arrangement at the interface is dependent on grain boundary misorientations, while the interfacial energy is dependent on the arrangement. The interfacial energy varies in a W pattern as the grain boundary misorientation increases from 0° to 90°. Specifically, the interfacial energy first decreases and then increases in both segments of 0–60° and 60–90°. The yield strength, elastic modulus, and mean flow stress decrease as the interfacial energy increases. The mechanism of plastic deformation varies as the grain boundary misorientation angle (θ) increases from 0° to 90°. When θ = 0°, the microscopic plastic deformation mechanisms of the Ni and Ni₃Al layers are both dominated by stacking faults induced by Shockley dislocations. When θ = 30°, 60°, and 80°, the mechanisms of plastic deformation of the Ni and Ni₃Al layers are the decomposition of stacking faults into twin grain boundaries caused by extended dislocations and the proliferation of stacking faults, respectively. When θ = 90°, the mechanisms of plastic deformation of both the Ni and Ni₃Al layers are dominated by twinning area growth resulting from extended dislocations.     

An integrative approach using systems biology,mutational analysis with molecular dynamics simulation to challenge the functionality of a target protein

Visceral leishmaniasis affects millions of people worldwide in areas where Leishmania donovani is endemic. The protozoan species serves a greater threat as it has gradually evolved drug resistance whereby requiring newer approaches to treat the infection. State‐of‐art techniques are mostly directed toward finding better targets extracted from the available proteome data. In light of recent computational advancements, we ascertain and validate one such target, adenylosuccinate lyase (ADSL) by implementation of in‐silico methods which led to the identification of critical amino acid residues that affects its functional attributes. Our target selection was based on comprehensive topological analysis of a knowledge‐based protein–protein interaction network. Subsequently, mutations were incorporated and the dynamic behavior of mutated and native proteins was traced using MD simulations for a total time span of 600 ns. Comparative analysis of the native and mutated structures exhibited perceptible changes in the ligand‐bound catalytic region with respect to time. The unfavorable changes in the orientations of specific catalytic residues, His118 and His196, induced by generated mutations reduce the enzyme specificity. In summary, this integrative approach is able to select a target against pathogen, identify crucial residues, and challenge its functionality through the selected mutations.