The Association of the Vanin-1 N131S Variant with Blood Pressure Is Mediated by Endoplasmic Reticulum-Associated Degradation and Loss of Function

High blood pressure (BP) is the most common cardiovascular risk factor worldwide and a major contributor to heart disease and stroke. We previously discovered a BP-associated missense SNP (single nucleotide polymorphism)–rs2272996–in the gene encoding vanin-1, a glycosylphosphatidylinositol (GPI)-anchored membrane pantetheinase. In the present study, we first replicated the association of rs2272996 and BP traits with a total sample size of nearly 30,000 individuals from the Continental Origins and Genetic Epidemiology Network (COGENT) of African Americans (P = 0.01). This association was further validated using patient plasma samples; we observed that the N131S mutation is associated with significantly lower plasma vanin-1 protein levels. We observed that the N131S vanin-1 is subjected to rapid endoplasmic reticulum-associated degradation (ERAD) as the underlying mechanism for its reduction. Using HEK293 cells stably expressing vanin-1 variants, we showed that N131S vanin-1 was degraded significantly faster than wild type (WT) vanin-1. Consequently, there were only minimal quantities of variant vanin-1 present on the plasma membrane and greatly reduced pantetheinase activity. Application of MG-132, a proteasome inhibitor, resulted in accumulation of ubiquitinated variant protein. A further experiment demonstrated that atenolol and diltiazem, two current drugs for treating hypertension, reduce the vanin-1 protein level. Our study provides strong biological evidence for the association of the identified SNP with BP and suggests that vanin-1 misfolding and degradation are the underlying molecular mechanism.     

Micelle bound structure and DNA interaction of brevinin‐2‐related peptide,an antimicrobial peptide derived from frog skin

Brevinin‐2‐related peptide (BR‐II), a novel antimicrobial peptide isolated from the skin of frog, Rana septentrionalis, shows a broad spectrum of antimicrobial activity with low haemolytic activity. It has also been shown to have antiviral activity, specifically to protect cells from infection by HIV‐1. To understand the active conformation of the BR‐II peptide in membranes, we have investigated the interaction of BR‐II with the prokaryotic and eukaryotic membrane‐mimetic micelles such as sodium dodecylsulfate (SDS) and dodecylphosphocholine (DPC), respectively. The interactions were studied using fluorescence and circular dichroism (CD) spectroscopy. Fluorescence experiments revealed that the N‐terminus tryptophan residue of BR‐II interacts with the hydrophobic core of the membrane mimicking micelles. The CD results suggest that interactions with membrane‐mimetic micelles induce an α‐helix conformation in BR‐II. We have also determined the solution structures of BR‐II in DPC and SDS micelles using NMR spectroscopy. The structural comparison of BR‐II in the presence of SDS and DPC micelles showed significant conformational changes in the residues connecting the N‐terminus and C‐terminus helices. The ability of BR‐II to bind DNA was elucidated by agarose gel retardation and fluorescence experiments. The structural differences of BR‐II in zwitterionic versus anionic membrane mimics and the DNA binding ability of BR‐II collectively contribute to the general understanding of the pharmacological specificity of this peptide towards prokaryotic and eukaryotic membranes and provide insights into its overall antimicrobial mechanism. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

PHYSICO: An UNIX based Standalone Procedure for Computation of Individual and Group Properties of Protein Sequences

In the genomic and proteomic era, efficient and automated analyses of sequence properties of protein have become an important task in bioinformatics. There are general public licensed (GPL) software tools to perform a part of the job. However, computations of mean properties of large number of orthologous sequences are not possible from the above mentioned GPL sets. Further, there is no GPL software or server which can calculate window dependent sequence properties for a large number of sequences in a single run. With a view to overcome above limitations, we have developed a standalone procedure i.e. PHYSICO, which performs various stages of computation in a single run based on the type of input provided either in RAW-FASTA or BLOCK-FASTA format and makes excel output for: a) Composition, Class composition, Mean molecular weight, Isoelectic point, Aliphatic index and GRAVY, b) column based compositions, variability and difference matrix, c) 25 kinds of window dependent sequence properties. The program is fast, efficient, error free and user friendly. Calculation of mean and standard deviation of homologous sequences sets, for comparison purpose when relevant, is another attribute of the program; a property seldom seen in existing GPL softwares.

Availability

PHYSICO is freely available for non-commercial/academic user in formal request to the corresponding author ni.ca.vinurub.hcetoib@eejrenabka     

Predicting genome-wide redundancy using machine learning

Background  

Gene duplication can lead to genetic redundancy, which masks the function of mutated genes in genetic analyses. Methods to increase sensitivity in identifying genetic redundancy can improve the efficiency of reverse genetics and lend insights into the evolutionary outcomes of gene duplication. Machine learning techniques are well suited to classifying gene family members into redundant and non-redundant gene pairs in model species where sufficient genetic and genomic data is available, such as Arabidopsis thaliana, the test case used here.     

Development and Characterization of Mucoadhesive <Emphasis Type="Italic">In Situ</Emphasis> Nasal Gel of Midazolam Prepared with <Emphasis Type="Italic">Ficus carica</Emphasis> Mucilage

The objective of the present study was to prepare mucoadhesive in situ nasal gels with mucilage isolated from fig fruits (Ficus carica, family: Moraceae) containing midazolam hydrochloride. Nasal gels of midazolam were prepared using three different concentrations (0.5%, 1.0% and 1.5% w/v) of F. carica mucilage (FCM) and synthetic polymers (hydroxypropylmethyl cellulose and Carbopol 934). Evaluation of FCM showed that it was as safe as the synthetic polymers for nasal administration. In situ gels were prepared with mixture Pluronic F127 and mucoadhesive agents. Evaluation of the prepared gels was carried out, including determination of viscosity, texture profile analysis and mucoadhesive strength. In vitro drug permeation study was conducted with the gels prepared with and without permeation enhancer (0.5% w/v sodium taurocholate) using excised goat nasal mucosa. In vitro permeation profiles were evaluated, and histological study of nasal mucosae before and after permeation study was also conducted to determine histological change, if any. In vivo experiments conducted in rabbits further confirmed that in situ nasal gels provided better bioavailability of midazolam than the gels prepared from synthetic mucoadhesive polymers. It was observed that the nasal gel containing 0.5% FCM and 0.5% sodium taurocholate exhibited appropriate rheological, mechanical and mucoadhesive properties and showed better drug release profiles. Moreover, this formulation produced no damage to the nasal mucosa that was used for the permeation study, and absolute bioavailability was also higher compared to gels prepared from synthetic polymers.     

Age and sex variation of body mass index and waist circumference among the Santal children of Jharkhand, India

Central body fat (CBF) as measured by waist circumference (WC) etc. has now been considered as risk factor for chronic disease, disability, and death. It has been assumed that one's characteristic level of body fat, as measured by body mass index (BMI), and CBF unfolds during the normal course of growth and development. However, studies of the development of CBF show relatively weak consistency in comparison to body fat. But to the best of our knowledge, no study in this aspect has been undertaken on any Indian population to study the effect of age and sex on body fat and CBF during development. In view of the above consideration, the present work has been undertaken among 179 Santal (a tribal population) children (Boys = 107, Girls = 72) of the Galudih area in East Singbhum, Jharkhand, India. Anthropometric measurements of height, weight, and circumference of waist were taken from each subject using standard procedure. The mean ages of boys and girls were 10.94 years and 9.48 years, respectively. The mean BMI for boys and girls were 14.48 kg/m2 and 13.78 kg/m2 Percent of variance explained by age was much greater for BMI (> 50%) as compared to WC (7-10%) in both sexes. Two way ANOVA showed that BMI had a significant (p < 0.05) effect of age and not of sex, whereas age-sex interaction had a significant impact on WC. The results of the present cross-sectional study indicated that during growth and development unfolding of CBF and BMI is independent of one another. Different set(s) of gene(s), onset of growth hormones during the normal development or their interaction could have been considered for this differentiation.     

Income, birth order, siblings, and anthropometry

The purpose of the present cross-sectional study was to examine the relationship and effect of monthly household income, birth order, and number of siblings on adult body dimensions, adiposity index, and body composition among adult Bengali females. One hundred seventy-one adult Bengali females, age 20.35 +/- 1.51 years (mean +/- SD; range: 18-21 years) from Kolkata (formerly Calcutta) were studied. Anthropometric measures (weight, height, waist circumference, hip circumference, and triceps, biceps, subscapular, suprailiac, and medial calf skinfold thicknesses) were taken from all participants using standard protocols. BMI and log10 of the sum of the five skinfold thicknesses were computed subsequently. Percentage of body fat was estimated from the triceps skinfold thickness following the equation of Durnin and Womersley (1974), and fat mass was then calculated. Results of the correlation analysis revealed that monthly household income had significant (p < 0.05) positive association with all anthropometric variables. Birth order and number of siblings showed significant (p < 0.05) inverse association. The correlation of monthly household income with anthropometric variables was much stronger for number of siblings and birth order. The results of the analysis of variance showed that monthly household income, birth order, and number of siblings (tertiles used to categorize all variables) had significant effects (p < 0.05) on anthropometric variables, indicating differences in adult body dimensions, the adiposity index, and body composition in relation to income, birth order, and number of siblings.