Common genetic link between metabolic syndrome components and senile cataract

Relationship between cataract and metabolic syndrome (MetS) is well established, but genetic link remains to be explored. D2S439 at 2q37 linked with QTL controlling visceral fat was investigated for its association with senile cataract. Two hundred and twenty-seven subjects including 119 cataract cases were genotyped for D2S439, tetra nucleotide repeat marker. Statistical tools assessed the association of marker's allele with anthropometric, clinical and oxidation stress parameters. Cases with longer allele ≥ (CTAT)(12) repeats, differed significantly from controls (0.77 vs. 0.58, p < 0.0001). Cases with at least one longer allele had higher waist circumference (50% vs. 15%, p = 0.0090), hyper-triglyceridemia (28% vs. 11%), hypo-HDL cholesterolemia (80% vs. 74%) and high diastolic blood pressure (37% vs. 26%) when compared to cases bearing the shorter allele. Cataract subjects with at least one longer allele had significantly raised lipid peroxidation levels (p = 0.0095) and showed an increased risk for cataract (OR = 5.86, CI(95%) = 1.49-23.11, p = 0.0114) after controlling for dependent variables. This exploratory study suggests that presence of even a single longer allele of D2S439 is associated with both cataract and MetS components in Asian Indians, unraveling the existence of a shared genetic locus.     

Identification of Comamonas species using 16S rRNA gene sequence

A bacterial strain Bz02 was isolated from a water sample collected from river Gomti at the Indian city of Lucknow. We characterized the strain using 16S rRNA sequence. Phylogenetic analysis showed that the strain formed a monophyletic clade with members of the genus Comamonas. The closest phylogenetic relative was Comamonas testosteroni with 95% 16S rRNA gene sequence similarity. It is proposed that the identified strain Bz02 be assigned as the type strain of a species of the genus Comamonas (Comamonas sp Bz02) based on 16S rRNA gene sequence search in Ribosomal Database Project, small subunit rRNA and large subunit rRNA databases together with the phylogenetic tree analysis. The sequence is deposted in GenBank with the accession number {"type":"entrez-nucleotide","attrs":{"text":"FJ211417","term_id":"209164434"}}FJ211417.     

Domain-based homology modeling and mapping of the conformational epitopes of envelope glycoprotein of west nile virus

Knowledge-based modeling has proved significantly accurate for generating the quality models for proteins whose sequence identity with the structurally known targets is greater than or equal to 40%. On the other hand, models obtained for low sequence identities are not reliable. Hence, a reliable and alternative strategy that uses knowledge of domains in the protein can be used to improve the quality of the model generated by the homology method. Here, we report a method for developing a 3D-model for the envelope glycoprotein (Egp) of west nile virus (WNV), using knowledge of structurally conserved functional domains amongst the target sequence (Egp of WNV) and its homologous templates belonging to the same protein family, flaviviridae. This strategy is found to be highly effective in reducing the root mean square deviation (RMSD) value at the C positions of the target and its experimental homologues. The 3D structure of a protein is a prerequisite for structure-based drug design as well as for identifying the conformational epitopes that are essential for the designing vaccines. The conformational epitopes are mapped from the 3D structure of Egp of WNV modeled using the concept of an antigenic domain. A total of five such epitope regions/sites have been identified. They have been found distributed in the loop regions (surface) of the whole protein model composed of dimerization, central and immunological domains. These sites are proposed as the binding sites for HLA proteins/B-cell receptors. Binding is required to activate the immune response against WNV.Figure The conformational epitopes that are distributed in all the domains. They are found out by the algorithm by Kolaskar et al.     

A novel approach to study the activity and stoichiometry simultaneously for microsomal pentoxyresorufin-O-dealkylase reaction

A simple approach to study the activity and stoichiometry of cytochrome P-450 IIB1-catalyzed metabolism of pentoxyresorufin (PRF) has been investigated. It involves the continuous spectral analysis of reaction mixture containing PRF, microsomes from phenobarbital-induced rats and NADPH. The kinetics of NADPH consumption, PRF utilization, NADP and resorufin formation was monitored at lambda(max) of 338, 484, 260 and 572 nm, respectively. The stoichiometry of the enzyme reaction tabulated either by specific activity or by V(max) value showed that 10 molecules of NADPH were required for the conversion of one molecule of PRF to one molecule of resorufin along with 10 molecules of NADP. Further, it was observed that almost six molecules of NADPH are consumed in the incubation mixture devoid of PRF indicating the possibility of metabolism of endogenous substrates. Interestingly, the stoichiometry ratio of 1:1 for PRF and resorufin was established even in the presence of P-450 inhibitors with a lower rate of metabolism. However, the ratio of NADPH to PRF was altered in the presence of inhibitors, suggesting that the simultaneous monitoring of the substrate, electron donor and the products could be useful in understanding the modifications of stoichiometry of electron donor and substrate/product.     

13C chemical shift map of the active cofactors in photosynthetic reaction centers of Rhodobacter sphaeroides revealed by photo-CIDNP MAS NMR

13C photo-CIDNP MAS NMR studies have been performed on reaction centers (RCs) of Rhodobacter sphaeroides wild type (WT) that have been selectively labeled with an isotope using [5-13C]-delta-aminolevulinic acid.HCl in all the BChl and BPhe cofactors at positions C-4, C-5, C-9, C-10, C-14, C-15, C-16, and C-20. 13C CP/MAS NMR and 13C-13C dipolar correlation photo-CIDNP MAS NMR provide a chemical shift map of the cofactors involved in the electron transfer process in the RC at the atomic scale. The 13C-13C dipolar correlation photo-CIDNP spectra reveal three strong components, originating from two BChl cofactors, called P1 and P2 and assigned to the special pair, as well as one BPhe, PhiA. In addition, there is a weak component observed that arises from a third BChl cofactor, denoted P3, which appears to originate from the accessory BChl BA. An almost complete set of assignments of all the aromatic carbon atoms in the macrocycles of BChl and BPhe is achieved in combination with previous photo-CIDNP studies on site-directed BChl/BPhe-labeled RCs [Schulten, E. A. M., Matysik, J., Alia, Kiihne, S., Raap, J., Lugtenburg, J., Gast, P., Hoff, A. J., and de Groot, H. J. M. (2002) Biochemistry 41, 8708-8717], allowing a comprehensive map of the ground-state electronic structure of the photochemically active cofactors to be constructed for the first time. The reasons for the anomaly of P2 and the origin of the polarization on P3 are discussed.     

Characterization of the Rust Fungus, Puccinia emaculata, and Evaluation of Genetic Variability for Rust Resistance in Switchgrass Populations

Several fungal pathogens have been identified on ornamental and native stands of switchgrass (Panicum virgatum L.). Diseases of switchgrass, particularly rust, have been largely neglected and are likely to become the major limiting factor to biomass yield and quality, especially when monocultured over a large acreage. Based on teliospore morphology and internal transcribed spacer-based diagnostic primers, the rust pathogen collected from switchgrass research fields in Oklahoma was identified as Puccinia emaculata. Furthermore, to identify genetically diverse source(s) of rust resistance, several switchgrass genotypes from both upland (cv. ‘Summer’ and ‘Cave-in-Rock’) and lowland (cv. ‘Alamo’ and ‘Kanlow’) ecotypes were evaluated in Ardmore, Oklahoma during 2008 and 2009 and in growth chamber assays. Field and growth chamber evaluations revealed a high degree of genetic variation within and among switchgrass cultivars. In general, Alamo and Kanlow showed moderate resistance to P. emaculata, while Summer was highly susceptible. Distinct ecotypic variations for reactions to rust were also prevalent with the lowlands maintaining a high level of resistance. These results suggest the potential for improvement of rust resistance via the selection of resistant individuals from currently available cultivars. Further, the selection pressure on the pathogen would also be reduced by employing several rust resistant cultivars in production-scale situations.     

Synthesis and Biophysical Studies on Fluorescently Labeled Oligodeoxyribonucleotides

Two highly fluorescent compounds, viz. 6-(6-isobutyrylamino-1,3-dioxo-1 H,3H-benzo[de]isoquinolin-2-yl)-hexanoic acid and 6-(6-dimethylamino-1,3-dioxo-1 H,3H-benzo[de]isoqu-inolin-2-yl)-hexanoic acid have been synthesized, characterized, and attached to 12-mer oligodeoxyribonucleotides at their 5′-end using suitable linker molecule. These labeled oligodeoxyribonucleotides have shown appreciable fluorescence even at 0.0019 μM concentrations. Thermal denaturation studies have shown comparatively higher Tm values when oligodeoxyribonucleotides are labeled. These labeled oligodeoxyribonucleotides have been purified on RP-HPLC utilizing their hydrophobicity and on polyacrylamide gel because of their easy detection due to fluorescence.