Accurate prediction of protein structural classes using functional domains and predicted secondary structure sequences

Protein structural class prediction is one of the challenging problems in bioinformatics. Previous methods directly based on the similarity of amino acid (AA) sequences have been shown to be insufficient for low-similarity protein data-sets. To improve the prediction accuracy for such low-similarity proteins, different methods have been recently proposed that explore the novel feature sets based on predicted secondary structure propensities. In this paper, we focus on protein structural class prediction using combinations of the novel features including secondary structure propensities as well as functional domain (FD) features extracted from the InterPro signature database. Our comprehensive experimental results based on several benchmark data-sets have shown that the integration of new FD features substantially improves the accuracy of structural class prediction for low-similarity proteins as they capture meaningful relationships among AA residues that are far away in protein sequence. The proposed prediction method has also been tested to predict structural classes for partially disordered proteins with the reasonable prediction accuracy, which is a more difficult problem comparing to structural class prediction for commonly used benchmark data-sets and has never been done before to the best of our knowledge. In addition, to avoid overfitting with a large number of features, feature selection is applied to select discriminating features that contribute to achieve high prediction accuracy. The selected features have been shown to achieve stable prediction performance across different benchmark data-sets.     

Scaffolds derived from cancellous bovine bone support mesenchymal stem cells' maintenance and growth

Since bone defects can lead to various disabilities, in recent years, many increasing attempts have been made in bone tissue engineering. In this regard, scaffolds have attracted a lot of attention as three dimensional substrates for cell attachment which improve successful tissue engineering. The aim of the present study was to provide an interconnected porous scaffold to facilitate cell infiltration. To do so, cancellous bone from bovine femur was dissected in fragments and decellularized by physicochemical methods, including snap freeze/thaw, rinsing in hot water and treatment with different solutions of sodium dodecyl sulfate (SDS). Histological analysis and 4′,6-diamidino-2-phenylindole staining revealed that the best results were obtained after treatment with 2.5%, 5%, and 8% SDS for 8, 3, or 1 h respectively, which significantly removed bone cells with intact trabeculae geometry. Further characterization of decellularized scaffolds by the compression tests also revealed no significant difference between elastic modulus values of the three different SDS treatments. Moreover, studying the ratio of bone trabeculae to bone surfaces (BT/BS) as assessed by Clemex vision software 3.5 showed that treatment with 2.5% SDS for 8 h resulted in a BT/BS score in the range of native bone and therefore this treatment was used for further experiments. Histological studies and scanning electron microscopy revealed rat mesenchymal stem cells integration, adhesion, and maintenance during the 2 and 7 d of culture in vitro. In conclusion, the present results support the effective role of SDS in cancellous bovine bone decellularization and also propensity of treated samples in providing a suitable three-dimentional environment to support the maintenance and growth of mesenchymal stem cells.     

Efficacy of Sambiloto Extracts,Andrographis paniculate, (Burm. F) in Inhibiting Diabetic Retinopathy Progression: An in Vivo Study

Background:Diabetic retinopathy (DR) is one of diabetes mellitus complication and occurred in retinal microvascular. This study was aimed to investigate the efficacy of Sambiloto, Andrographis paniculate (A. paniculata) extract on glycemic profile, antioxidant and inflammatory cytokine parameters in diabetic rats, and phytochemical analysis of A. paniculata. Methods:A. paniculata extract (APE) was carried out by maceration with ethanol. Diabetes mellitus in Wistar male rats was induced with streptozotocin. Retinal vessel diameters were estimated using a method by Vucetic. Inflammatory cytokine and antioxidant parameters were evaluated in retinal tissue. The alkaloid and flavonoid contents in extract were analyzed using thin layer chromatography method. Results:Funduscopic examination presented some changes in the diameter of the blood vessels. The vessel diameter in the diabetic retinopathy group with APE in concentration of 100 and 200 mg/kg BW groups was significantly lower than in the DR group (p<0.05). The administration of APE in dosages of 100 and 200 mg/kg BW showed reduced glutathione, SOD, and catalase levels compared to the DR group (p<0.05).Conclusion:A. paniculata extract doses of 100 and 200 mg/kg BW improved diabetic retinopathy in rats through hypoglycemic effects, antioxidant effects, and anti-inflammatory mechanisms.Key Words: Andrographis paniculata, Antioxidants, Diabetic Retinopathy, Plant Extracts, Retinal Vessels     

Interleukin-1 beta induces posttranslational carboxymethylation and alterations in subnuclear distribution of lamin B in insulin-secreting RINm5F cells

We examined the effects of interleukin-1 (IL-1) treatment on the distribution and degradation of lamin B in the nuclear fraction from insulin-secreting RINm5F cells. Western blot analysis indicated that IL-1 treatment caused significant alterations in the redistribution of lamin B, specifically between the Triton X-100-soluble (membrane) and -insoluble (matrix) fractions of the nucleus. IL-1 treatment also increased the lamin carboxymethyltransferase activity and the relative abundance of the carboxymethylated lamin in the nuclear fraction. A significant increase in the relative abundance of lamin B degradation products was also observed in the nuclear fraction from the IL-1-treated cells. These findings are compatible with a measurable increase in the lamin-degrading caspase-6 activity in IL-1-treated cells. Confocal microscopic observation of IL-1-treated cells suggested a significant dissociation of lamin B from the nuclear lamina and its subsequent association with the DNA-rich elements within the nucleus. N^G-monomethyl-L-arginine, a known inhibitor of inducible nitric oxide synthetase (iNOS), markedly inhibited IL-1-induced iNOS gene expression, NO release, caspase-3 and caspase-6 activation, lamin B degradation, and loss of metabolic cell viability, indicating that the observed IL-1-induced effects on nuclear lamin B involve the intermediacy of NO. Together, our data support the hypothesis that IL-1 treatment results in significant increase in the carboxymethylation of lamin B, which would place lamin B in a strategic location for its degradation mediated by caspases. This could possibly lead to dissolution of the nuclear envelope, culminating in the demise of the effete -cell. pancreatic -cell; lamin carboxymethyltransferase; nitric oxide; nuclear matrix; caspases