A novel computational and structural analysis of nsSNPs in CFTR gene

Single Nucleotide Polymorphisms (SNPs) are being intensively studied to understand the biological basis of complex traits and diseases. The Genetics of human phenotype variation could be understood by knowing the functions of SNPs. In this study using computational methods, we analyzed the genetic variations that can alter the expression and function of the CFTR gene responsible candidate for causing cystic fibrosis. We applied an evolutionary perspective to screen the SNPs using a sequence homology-based SIFT tool, which suggested that 17 nsSNPs (44%) were found to be deleterious. The structure-based approach PolyPhen server suggested that 26 nsSNPS (66%) may disrupt protein function and structure. The PupaSuite tool predicted the phenotypic effect of SNPs on the structure and function of the affected protein. Structure analysis was carried out with the major mutation that occurred in the native protein coded by CFTR gene, and which is at amino acid position F508C for nsSNP with id (rs1800093). The amino acid residues in the native and mutant modeled protein were further analyzed for solvent accessibility, secondary structure and stabilizing residues to check the stability of the proteins. The SNPs were further subjected to iHAP analysis to identify htSNPs, and we report potential candidates for future studies on CFTR mutations.     

Interactions of tight junctions with membrane channels and transporters

Tight junctions are unique organelles in epithelial cells. They are localized to the apico-lateral region and essential for the epithelial cell transport functions. The paracellular transport process that occurs via tight junctions is extensively studied and is intricately regulated by various extracellular and intracellular signals. Fine regulation of this transport pathway is crucial for normal epithelial cell functions. Among factors that control tight junction permeability are ions and their transporters. However, this area of research is still in its infancy and much more needs to be learned about how these molecules regulate tight junction structure and functions. In this review we have attempted to compile literature on ion transporters and channels involved in the regulation of tight junctions.     

Recurrent heat shock impairs the proliferation and differentiation of C2C12 myoblasts

Heat-related illness and injury are becoming a growing safety concern for the farmers, construction workers, miners, firefighters, manufacturing workers, and other outdoor workforces who are exposed to heat stress in their routine lives. A primary response by a cell to an acute heat shock (HS) exposure is the induction of heat-shock proteins (HSPs), which chaperone and facilitate cellular protein folding and remodeling processes. While acute HS is well studied, the effect of repeated bouts of hyperthermia and the sustained production of HSPs in the myoblast-myotube model system of C2C12 cells are poorly characterized. In C2C12 myoblasts, we found that robust HS (43 °C, dose/time) significantly decreased the proliferation by 50% as early as on day 1 and maintained at the same level on days 2 and 3 of HS. This was accompanied by an accumulation of cells at G2 phase with reduced cell number in G1 phase indicating cell cycle arrest. FACS analysis indicates that there was no apparent change in apoptosis (markers) and cell death upon repeated HS. Immunoblot analysis and qPCR demonstrated a significant increase in the baseline expression of HSP25, 70, and 90 (among others) in cells after a single HS (43 °C) for 60 min as a typical HS response. Importantly, the repeated HS for 60 min each on days 2 and 3 maintained the elevated levels of HSPs compared to the control cells. Further, the continuous HS exposure resulted in significant inhibition of the differentiation of C2C12 myocytes to myotubes and only 1/10th of the cells underwent differentiation in HS relative to control. This was associated with significantly higher levels of HSPs and reduced expression of myogenin and Myh2 (P < 0.05), the genes involved in the differentiation process. Finally, the cell migration (scratch) assay indicated that the wound closure was significantly delayed in HS cells relative to the control cells. Overall, these results suggest that a repeated HS may perturb the active process of proliferation, motility, and differentiation processes in an in vitro murine myoblast-myotube model.     

Physiological significance of proline and glycinebetaine: Maintaining photosynthesis during NaCl stress in wheat

Experiments on the physiological significance of accumulation of proline and glycinebetaine (GB) in sustaining photosynthesis during salt stress in wheat in vivo showed that pre-treatment with GB, but not proline, alleviated NaCl-induced stomatal and non-stomatal inhibition of photosynthesis completely. A permeating and non-dissociating osmoticum, 3-orthomethyl-glucopyranose, also alleviated NaCl-induced perturbations of photosynthesis, suggesting that GB may work by maintaining chloroplast volume and not by specific effects on photosynthetic processes.     

Role of thymine in protein coding frames of mRNA sequences

Distribution of thymine in protein coding mRNA sequences has been studied here. Our study suggest that thymine in protein coding sequences are not randomly distributed but with probability. Frame1 prefers to have definite amount of thymine. It is observed that the thymine content of frame 4 is also involved in protein coding. Frame 3 prefers to have least amount of thymine. However, frame 2 and frame 6 shows a variable degree of thymine content. The mRNA sequences of heterosexual animals, particularly, the human show a different distribution profile (less thymine in frame 1) compared to that of yeast and plants.     

Differential response of antioxidative enzymes to various abiotic stresses in <Emphasis Type="Italic">Pennisetum glaucum</Emphasis> seedlings

Antioxidative enzyme activities and their isozyme patterns under water-deficit, salinity, high and low temperature stresses were studied in the seedlings of Pennisetum glaucum (L.) R.Br. It was observed that under water-deficit stress glutathione reductase (GR) was the key enzyme while in case of high temperature stress, GR along with catalase played a major role. Superoxide dismutase was found to be the main enzyme under low temperature stress. Co-ordinated higher expression of all the antioxidative enzymes was observed under salt stress. This study revealed the operation of different enzymatic antioxidative mechanisms under various abiotic stresses that will aid in understanding the metabolic basis of stress tolerance in pearl millet.     

Chemometric Studies of Multielemental Composition of Few Seagrasses from Gulf of Mannar,India

This paper discusses the determination of minerals content (cadmium, cobalt, chromium, copper, nickel, lead, manganese, magnesium, iron, zinc, sodium, potassium and calcium) of six seagrass samples, Enhalus acoroides, Thalassia hemprichii, Halodule pinifolia, Syringodium isoetifolium, Cymodocea serrulata and Cymodocea rotundata using inductively coupled plasma optical emission spectrophotometry and flame photometer. Principal component analysis (PCA) and hierarchical cluster analysis revealed different mineral compositions of the seagrass samples. Among the 13 elements investigated, Ni 1.513, Na 690.167 and Ca 220.333; Cr 3.957; Mn 23.427, Zn 17.593 and Fe 156.567; Cd 0.357, Co 0.431, Pb 2.040, Mg 912.733 and K 300.9; Cu 7.8 mg/kg dry weight, respectively, were found at high concentrations in E. acoroides; T. hemprichii; H. pinifolia; S. isoetifolium and C. rotundata. PCA analysis confirmed the presence of three components with 91.28% of the total variance. The toxic elements Pb, Cr and Cd were also found in all six seagrasses, although the concentrations were below the permissible limits proposed by the World Health Organization.