RDDSVM: accurate prediction of A-to-I RNA editing sites from sequence using support vector machines

Functional & Integrative Genomics - Adenosine to inosine (A-to-I) editing in RNA is involved in various biological processes like gene expression, alternative splicing, and mRNA degradation...     

Taxonomic study of spongy spumellarian Radiolaria with three and four coplanar spines or arms from the middle Carnian (Late Triassic) of the Köseyahya nappe (Elbistan, SE Turkey) and other Triassic localities

The present article is a taxonomic study of all spongy spumellarian radiolarian taxa with three and four coplanar spines or spongy arms occurring in the middle Carnian from the Köseyahya section, near the town of Elbistan, SE Turkey. This fauna is characteristic of the Tetraporobrachia haeckeli radiolarian Zone, and comes from an 8 m thick succession of clayey-cherty limestones occurring at the lower part of the section. In addition, a few species from the Middle and Upper Triassic from other areas have been also included in this study to improve some generic diagnoses, and to better comprehend the diversity and evolutionary trends of some genera, subfamilies and families. The taxonomy at the generic and suprageneric levels is based primarily on the types of microsphere. This new approach allowed new taxonomic arrangements of genera and suprageneric units, and suggested new phylogenetic relationships among these radiolarians and between them and younger radiolarians. The authors discuss and describe 69 species, of which 37 are new, and 14 genera, of which three are new (Paraparonaella, Pseudangulobracchia, and Ropanaella). The genus Triassoastrum and others are reinterpreted. All genera studied are assigned to five subfamilies, of which two are new (Tetrapaurinellinae and Triassocrucellinae), and two families (Tritrabidae and Veghicycliidae). Nine species in open nomenclature are also illustrated.     

Effects of selenium on altered mechanical and electrical cardiac activities of diabetic rat

Since selenium compounds can restore some metabolic parameters and structural alterations of diabetic rat heart, we were tempted to investigate whether these beneficial effects extend to the diabetic rat cardiac dysfunctions. Diabetes was induced by streptozotocin (50mg/kg body weight) and rats were then treated with sodium selenite (5 micromol/kg body weight/day) for four weeks. Electrically stimulated isometric contraction and intracellular action potential in isolated papillary muscle strips and transient (I(to)) and steady state (I(ss)) outward K(+) currents in isolated cardiomyocytes were recorded. Sodium selenite treatment could reverse the prolongation in both action potential duration and twitch duration of the diabetic rats, and also cause significant increases in the diminished amplitudes of the two K(+) currents. Treatment of rats with sodium selenite also markedly increased the depressed acid-soluble sulfhydryl levels of the hearts. Our data suggest that the beneficial effects of sodium selenite treatment on the mechanical and electrical activities of the diabetic rat heart appear to be due to the restoration of the diminished K(+) currents, partially, related to the restoration of the cell glutathione redox cycle.     

Dihydroisocoumarins and Phenylglycosides from Scorzonera longiana,Their Antimicrobial Activities and Molecular Docking Studies

Five new phenyl dihydroisocoumarin glycosides ( 1 – 5 ) and two known compounds ( 6 – 7 ) were identified from the butanol fraction of Scorzonera longiana. The structures of 1 – 7 were elucidated based on spectroscopic methods. Antimicrobial, antitubercular, and antifungal evaluation of compounds 1 – 7 were carried out using the microdilution method against nine microorganisms. Compound 1 was active only against Mycobacterium smegmatis (Ms) with a MIC value of 14.84 μg/mL. All tested compounds ( 1 – 7 ) were active against Ms but only compounds 3–7 were active against fungi (C. albicans, S. cerevisiae) with MIC values of 25.0–125 μg/mL. In addition, molecular docking studies were conducted against Ms DprE1 (PDB ID: 4F4Q), Mycobacterium tuberculosis (Mbt) DprE1 (PDB ID: 6HEZ), and arabinosyltransferase C (EmbC, PDB ID: 7BVE) enzymes. Compounds 2 , 5 , and 7 are the most effective Ms 4F4Q inhibitors. Compound 4 was the most promising inhibitory activity on Mbt DprE with the lowest binding energy of −9,9 kcal/mol.     

Serum interleukin-18 and nitric oxide activity in bladder carcinoma

BACKGROUND: Both interleukin-18 and nitric oxide are multifunctional molecules that are involved in the different steps of carcinogenesis. METHODS: In the present study, we measured serum interleukin-18 and nitric oxide activity in 51 bladder cancer patients with different tumor stage and grade, and in 8 healthy controls. Serum nitrite-nitrate levels were measured as an index of nitric oxide generation. RESULTS: Serum interleukin-18 levels were significantly higher in bladder cancer patients when compared to the control subjects (p > 0.05). Serum interleukin-18 levels were found to be higher in patients with Ta stage than patients with T1 and T2, T3, T4 stages and in patients with grade 1 tumors than patients with grade 2 and grade 3 tumors, but this was not statistically significant (p > 0.05). There was no significant difference in serum nitrite + nitrate levels between bladder cancer patients and control subjects. CONCLUSIONS: Elevated serum interleukin-18 levels in bladder carcinoma patients may be a result of host defence mechanism against the growth and progression of bladder cancer cells.     

Basal metabolic rate and autonomic nervous system dysfunction in men with spinal cord injury

Objectives: The purpose of this study was to determine the relationship between autonomic nervous system dysfunction and basal metabolic rate (BMR), and the effect of spasticity on basal metabolic rate. Research Method and Procedures: Twenty men (11 paraplegic and 9 tetraplegic) with American Spinal Injury Association (ASIA)‐A and ‐B grade chronic spinal cord injury (SCI) participated in this study. Total body fat mass and lean tissue mass were measured in all participants using DXA by standard methods. Patients were allocated into 2 groups to determine the effect of autonomic nervous system dysfunction on BMR: Group I (T6 and upper‐level injuries with history of autonomic dysreflexia) and Group II (T7 and lower‐level injuries without history of autonomic dysreflexia). Measurements of BMR were determined by indirect calorimetry under standardized conditions. Results: There were 13 patients in Group I and 7 patients in Group II and the difference between these two in terms of time since injury, BMI, age, weight, lean tissue mass, BMR, and BMR/kg were not significant. Conclusion: We concluded that autonomic nervous system dysfunction does not affect BMR, and it might be ignored in considering energy needs in spinal cord injury.     

Probing the roles of two tryptophans surrounding the unique zinc coordination site in lipase family I.5

A unique zinc domain found in all of the identified members of the lipase family I.5 is surrounded by two conserved tryptophans (W61 and W212). In this study, we investigated the role of these hydrophobic residues in thermostability and thermoactivity of the lipase from Bacillus thermocatenulatus (BTL2) taken as the representative of the family. Circular dichroism spectroscopy revealed that the secondary structure of BTL2 is conserved by the tryptophan mutations (W61A, W212A, and W61A/W212A), and that W61 is located in a more rigid and less solvent exposed region than is W212. Thermal denaturation and optimal activity analyses pointed out that zinc induces thermostability and thermoactivity of BTL2, in which both tryptophans W61 and W212 play contributing roles. Molecular explanations describing the roles of these tryptophans were pursued by X‐ray crystallography of the open form of the W61A mutant and molecular dynamics simulations which highlighted a critical function for W212 in zinc binding to the coordination site. This study reflects the potential use of hydrophobic amino acids in vicinity of metal coordination sites in lipase biocatalysts design. Proteins 2016; 84:129–142. © 2015 Wiley Periodicals, Inc.     

Twenty-Four-Hour Variations in the Sensitivity of Rat Aorta to Vasoactive Agents

The presence of time-dependent variations in the in vitro sensitivity of aorta preparations to either vasoconstricting or relaxing agents was investigated in rats maintained in light from 08: 00 to 20: 00 and in darkness from 20: 00 to 08: 00. Rat thoracic aorta rings were obtained from animals sacrificed at four different times of the day. The rat aorta was found to be more sensitive to the constricting effect of phenylephrine at 15: 00, and of 5-hydroxytryptamine at 21: 00. On the other hand, both endothelium-dependent and -independent relaxations were more remarkable at 03: 00 than at other times of the day. These variations represented significant circadian rhythms when analyzed by analysis of variance. Different in vitro responsiveness to these agents might reflect changes in the sensitivity and/or number of related receptors in vascular preparations. In conclusion, the circadian time of animal sacrifice to obtain vascular preparations constitutes an important aspect of the research method and a key determinant of findings. (Chronobiology International, 13(6), 465-475, 1996)