Mechanism of action of non-synonymous single nucleotide variations associated with α-carbonic anhydrase II deficiency:

Human carbonic anhydrase II (CA-II) is a Zinc (Zn 2+ ) metalloenzyme responsible for maintenance of acid-base balance within the body through the reversible hydration of CO 2 to produce protons (H + ) and bicarbonate (BCT). Due to its importance, alterations to the amino acid sequence of the protein as a result of single nucleotide variations (nsSNVs) have detrimental effects on homeostasis. Six pathogenic CA-II nsSNVs, K18E, K18Q, H107Y, P236H, P236R and N252D were identified, and variant protein models calculated using homology modeling. The effect of each nsSNV was analyzed using motif analysis, molecular dynamics (MD) simulations, principal component (PCA) and dynamic residue network (DRN) analysis. Motif analysis identified 11 functionally important motifs in CA-II

Acute effects of recreational soccer on inflammatory response and cardiac and skeletal muscle damage indicators

Introduction: Previous studies have indicated that acute bouts of strenuous, long duration exercise induce significant increases in the inflammatory profile and cardiovascular risk markers. Although recreational soccer (RS) is a widespread activity, there are no data on this topic. Thus, the aim of this study was to examine RS-induced changes in inflammatory, cardiac, and skeletal muscle damage indicators in young and middle-aged males

MODE-TASK: large-scale protein motion tools

MODE-TASK, a novel and versatile software suite, comprises Principal Component Analysis, Multidimensional Scaling, and t-Distributed Stochastic Neighbor Embedding techniques using Molecular Dynamics trajectories. MODE-TASK also includes a Normal Mode Analysis tool based on Anisotropic Network Model so as to provide a variety of ways to analyse and compare large-scale motions of protein complexes for which long MD simulations are prohibitive. Beside the command line function, a GUI has been developed as a PyMOL plugin

State-of-the-art process simulations and techno-economic assessments of ionic liquid-based biogas upgrading techniques: Challenges and prospects

Biogas has emerged as an alternative renewable fuel to natural gas. However, the presence of trace contaminants and large quantities of CO2 in biogas necessitates its purification and upgrading to increase its calorific value. Different technologies have been developed to upgrade biogas to biomethane. Among these, chemical absorption is commonly employed due to its high process efficiency and less solvent requirement due to high selectivity compared to physical absorption. However, the chemical decomposition of amine-based solvents, toxicological impact, high plant maintenance costs, high enthalpy of reaction, and corrosivity associated with chemical absorption limit its large-scale application. Recently, ionic liquids (ILs) have garnered attention as alternative absorption media to conventional solvents. ILs have a high CO2 uptake, thermal stability, and negligible vapor pressure. Recent process simulation studies featuring ILs as solvents for biogas upgrading reveal the suitability of these approaches as alternatives to laborious experimental work to assess the practical, technical, and economic viability of ILs. As per the authors' knowledge, this is the first review comparing biogas upgrading technologies from a technical, environmental, and economic perspective. Primarily, studies relating to IL-based biogas upgrading are considered, and challenges associated with the large-scale adoption of ILs as absorption media are discussed. Process simulations and techno-economic assessments of IL-based biogas upgrading techniques are presented. A conceptual design approach is proposed for the successful scale-up of IL-based biogas upgrading. Based on results, deep eutectic solvents are recommended as next-generation solvents for absorption as technical and economic aspects are found superior to conventional amines and ionic liquids

Structure prediction and functional analyses of a thermostable lipase obtained from <i>Shewanella putrefaciens</i>

<p>Previous experimental studies on thermostable lipase from <i>Shewanella putrefaciens</i> suggested the maximum activity at higher temperatures, but with little information on its conformational profile. In this study, the three-dimensional structure of lipase was predicted and a 60 ns molecular dynamics (MD) simulation was carried out at temperatures ranging from 300 to 400 K to better understand its thermostable nature at the molecular level. MD simulations were performed in order to predict the optimal activity of thermostable lipase. The results suggested strong conformational temperature dependence. The thermostable lipase maintained its bio-active conformation at 350 K during the 60 ns MD simulations.</p

Ecological Stoichiometry in Pinus massoniana L. Plantation: Increasing Nutrient Limitation in a 48-Year Chronosequence

Stoichiometric ratios of carbon (C), nitrogen (N), and phosphorus (P) are considered indicators of nutrient status and ultimate ecosystem health. A detailed investigation of these elements in the leaves, branches, forest layer vegetation and soil, depending on stand age, was carried out. We investigated the effects of stand age (9-, 18-, 28-, and 48-year) on the aboveground plant parts (leaf, branch, herb, shrub, plant litter) and belowground pools (soil, roots) of P. massoniana plantations. The CNP stoichiometry of trees was affected by stand age. Mean N content in the aboveground parts in the nine-yr stand was greater than the other stands (18-, 28-, 48-yr), which decreased with increasing stand age. As stands aged, the nutrient demands of the plantations increased as well as their N:P ratios in soil. C content in the soil ranged from 30 to 105, the total N was 0.06 to 1.6, and the total P content ranged from 3.3&ndash;6.4 g kg&minus;1. Soil C, N and P contents were greatly influenced by both stand age and soil depth, because surface soil sequester C and N more actively compared to deeper horizons, and more nutrients are released to the topsoil by the plant litter layer. Similarly, the ratios of other layers had a similar pattern as CNP because more nutrients were taken up by the plantations, decreasing nutrient supply in the deeper soil horizons. The green leaves N:P ratios (16) indicate limited growth of P. massoniana, as the range for global nutrient limitation for woody plants oscillated between 14&ndash;16, indicating N and P limitation. Young stands were observed to have greater P content and P resorption efficiency (56.9%&ndash;67.3%), with lower C:P and N:P ratios (704.4; 14.8). We conclude that with stand development, the nutrient demands of the plantations also increase, and soil N:P stoichiometry shows that these improve soil quality

Genomic Analysis of Waterpipe Smoke-Induced Lung Tumor Autophagy and Plasticity

The role of autophagy in lung cancer cells exposed to waterpipe smoke (WPS) is not known. Because of the important role of autophagy in tumor resistance and progression, we investigated its relationship with WP smoking. We first showed that WPS activated autophagy, as reflected by LC3 processing, in lung cancer cell lines. The autophagy response in smokers with lung adenocarcinoma, as compared to non-smokers with lung adenocarcinoma, was investigated further using the TCGA lung adenocarcinoma bulk RNA-seq dataset with the available patient metadata on smoking status. The results, based on a machine learning classification model using Random Forest, indicate that smokers have an increase in autophagy-activating genes. Comparative analysis of lung adenocarcinoma molecular signatures in affected patients with a long-term active exposure to smoke compared to non-smoker patients indicates a higher tumor mutational burden, a higher CD8+ T-cell level and a lower dysfunction level in smokers. While the expression of the checkpoint genes tested—PD-1, PD-L1, PD-L2 and CTLA-4—remains unchanged between smokers and non-smokers, B7-1, B7-2, IDO1 and CD200R1 were found to be higher in non-smokers than smokers. Because multiple factors in the tumor microenvironment dictate the success of immunotherapy, in addition to the expression of immune checkpoint genes, our analysis explains why patients who are smokers with lung adenocarcinoma respond better to immunotherapy, even though there are no relative differences in immune checkpoint genes in the two groups. Therefore, targeting autophagy in lung adenocarcinoma patients, in combination with checkpoint inhibitor-targeted therapies or chemotherapy, should be considered in smoker patients with lung adenocarcinoma