Prediction of membrane protein types by means of wavelet analysis and cascaded neural networks

In this study, membrane proteins were classified using the information hidden in their sequences. It was achieved by applying the wavelet analysis to the sequences and consequently extracting several features, each of them revealing a proportion of the information content present in the sequence. The resultant features were made normalized and subsequently fed into a cascaded model developed in order to reduce the effect of the existing bias in the dataset, rising from the difference in size of the membrane protein classes. The results indicate an improvement in prediction accuracy of the model in comparison with similar works. The application of the presented model can be extended to other fields of structural biology due to its efficiency, simplicity and flexibility.     

Thermodynamic study of the binding of calcium and magnesium ions with myelin basic protein using the extended solvation theory

The interaction of myelin basic protein (MBP) from the bovine central nervous system with Ca2+ and Mg2+ ions, named as M2+, was studied by isothermal titration calorimetry at 27 degrees C in aqueous solution. The extended solvation model was used to reproduce the enthalpies of MBP+M2+ interactions. The solvation parameters recovered from the extended solvation model were attributed to the structural change of MBP due to the metal ion interaction. It was found that there is a set of two identical and noninteracting binding sites for Ca2+ and Mg2+ ions.     

Calreticulin regulates insulin receptor expression and its downstream PI3 Kinase/Akt signalling pathway

Defects in insulin signalling and glucose metabolism are associated with the development of diabetes. Insulin signalling is initiated by the binding of insulin to its receptor and triggering cascades of events including activation of PI3kinase/Akt signalling pathway. Calreticulin (CRT) is a calcium binding chaperone molecule located in the endoplasmic reticulum. Targeted deletion of CRT in mice is embryonic lethal as a result of developmental and metabolic abnormalities. Rescued CRT null mice develop severe hypoglycemia the reason for which is not known. In addition, ventricular cardiomyocytes isolated from CRT null (crt-/-) mice have increased glycogen deposits. Therefore, the aim of this study was to investigate the changes in the glucose uptake and insulin signalling pathway (mainly PI3 kinase/Akt) in the absence of CRT. Here we show a significant increase in the glucose uptake by the crt-/- cells. This increase was accompanied by a significant increase in both insulin receptor beta expression, Insulin receptor substrate-1 phosphorylation, GLUT-1 expression and in insulin stimulated Akt phosphorylation and kinase activity in the crt-/- cells. Intriguingly, the increased expression of insulin receptor beta in the crt-/- was due to decreased levels of p53 protein. The current study is the first evidence for the up-regulation of insulin receptor density and activity in the absence of CRT function.     

Effects of Water on Enzyme Performance with an Emphasis on the Reactions in Supercritical Fluids

ABSTRACT

Enzymes require a certain level of water in their structures in order to maintain their natural conformation, allowing them to deliver their full functionality. Furthermore, as a modifier of the solvent, up to a certain level, water can modify the solvent properties such as polarity/polarizability as well as the solubility of the reactants and the products. In addition, depending on the type of the reaction, water can be a substrate (e.g., in hydrolysis) or a product (e.g., in esterolysis) of the enzymatic reaction, influencing the enzyme turnover in different ways. It is found that regardless of the type of reaction, the functionality of enzyme itself is maximum at an optimum level of water, beyond which the enzyme performance is declined due to the loss in enzyme stability. Furthermore, mass transfer limitations caused by pathway blockage and/or by reduced solubilities of the reactants and/or products can also affect the enzyme performance at higher water levels. Controlling water content of ingoing CO₂ and substrates as well as precise management of enzyme support and salt hydrates are important strategies to adjust water level in reaction media, especially in supercritical environments.     

Effect of annealing temperature and dopant concentration on the thermoluminescence sensitivity in LiF:Mg,Cu,Ag material

LiF:Mg,Cu,Ag is a new dosimetry material that is similar to LiF:Mg,Cu,P in terms of dosimetric properties. The effect of the annealing temperature in the range of 200 to 350°C on the thermoluminescence (TL) sensitivity and the glow curve structure of this material at different concentrations of silver (Ag) was investigated. It has been demonstrated that the optimum values of the annealing temperature and the Ag concentration are 240°C and 0.1 mol% for better sensitivity, respectively. The TL intensity decreases at annealing temperatures lower than 240°C or higher than 240°C, reaching a minimum at 300°C and then again increases for various Ag concentrations. It was observed that the glow curve structure altered and the area under the low temperature peak as well as the area under the main dosimetric peak decreased with increasing annealing temperature. The position of the main dosimetric peak moved in the direction of higher temperatures, but at 320 and 350°C annealing temperatures, it shifted to lower temperatures. It was also observed that the TL sensitivity could partially be recovered by a combined annealing procedure.     

Effect of landscape features on genetic structure of the goitered gazelle (<Emphasis Type="Italic">Gazella subgutturosa</Emphasis>) in Central Iran

The populations of goitered gazelle suffered significant decline due to natural and anthropogenic factors over the last century. Investigating the effects of barriers on gene flow among the remaining populations is vital for conservation planning. Here we adopted a landscape genetics approach to evaluate the genetic structure of the goitered gazelle in Central Iran and the effects of landscape features on gene flow using 15 polymorphic microsatellite loci. Spatial autocorrelation, isolation by distance (IBD) and isolation by resistance (IBR) models were used to elucidate the effects of landscape features on the genetic structure. Ecological modeling was used to construct landscape permeability and resistance map using 12 ecogeographical variables. Bayesian algorithms revealed three genetically homogeneous groups and restricted dispersal pattern in the six populations. The IBD and spatial autocorrelation revealed a pattern of decreasing relatedness with increasing distance. The distribution of potential habitats was strongly correlated with bioclimatic factors, vegetation type, and elevation. Resistance distances and graph theory were significantly related with variation in genetic structure, suggesting that gazelles are affected by landscape composition. The IBD showed greater impact on genetic structure than IBR. The Mantel and partial Mantel tests indicated low but non-significant effects of anthropogenic barriers on observed genetic structure. We concluded that a combination of geographic distance, landscape resistance, and anthropogenic factors are affecting the genetic structure and gene flow of populations. Future road construction might impede connectivity and gene exchange of populations. Conservation measures on this vulnerable species should consider some isolated population as separate management units.     

The Yin and Yang of carbon nanomaterials in atherosclerosis

With unique characteristics such as high surface area, capacity of various functionalization, low weight, high conductivity, thermal and chemical stability, and free radical scavenging, carbon nanomaterials (CNMs) such as carbon nanotubes (CNTs), fullerene, graphene (oxide), carbon nanohorns (CNHs), and their derivatives have increasingly been utilized in nanomedicine and biomedicine. On the one hand, owing to ever-increasing applications of CNMs in technological and industrial fields as well as presence of combustion-derived CNMs in the ambient air, the skepticism has risen over the adverse effects of CNMs on human being. The influences of CNMs on cardiovascular system and cardiovascular diseases (CVDs) such as atherosclerosis, of which consequences are ischemic heart disease and ischemic stroke, as the main causes of death, is of paramount importance. In this regard, several studies have been devoted to specify the biomedical applications and cardiovascular toxicity of CNMs. Therefore, the aim of this review is to specify the roles and applications of various CNMs in atherosclerosis, and also identify the key role playing parameters in cardiovascular toxicity of CNMs so as to be a clue for prospective deployment of CNMs.