Molecular characterization of rare bovine group A rotavirus G15P[11] and G15P[21] strains from eastern India: identification of simian SA11-like VP6 genes in G15P[21] strains
During a surveillance study (November 2001–March 2005), one rare G15P[11] and two rare G15P[21] bovine group A rotavirus strains were detected in diarrhoeic calves in Eastern India. Sequence analysis of the VP8*, VP6, NSP4 and NSP5 genes of the G15P[11] strain confirmed its bovine origin. Although the NSP4 and NSP5 genes of the two G15P[21] strains were of bovine origin, their VP6 genes shared higher nucleotide and amino acid identities with simian strain SA11 (92.5–93.1% and 98.5–98.7%) than bovine strains (88.5–88.9% and 97–97.2%), and by phylogenetic analysis, exhibited clustering with SA11, distantly related to bovine strains. All these pointed towards a possible reassortment event of VP6 gene between bovine and simian (SA11-like) strains. Therefore, the present study provided molecular evidence for bovine origin of G15 strains and revealed a rare instance of genetic diversity in the bovine VP6 gene, otherwise conserved in group A rotavirus strains from cattle.

title: Molecular characterization of a porcine Group A rotavirus strain with G12 genotype specificity
abstract: A porcine Group A rotavirus strain (RU172) was detected and molecularly characterized during a surveillance study conducted for rotavirus infection in a pig farm located in a suburban area of Kolkata City, India. The G12 genotype specificity of RU172 was revealed by PCR-based genotyping assays following addition of a G12 type-specific primer (designed in our laboratory to pick up G12 isolates from field samples) and was confirmed by sequence analysis of the VP7-encoding gene. The RU172 strain exhibited maximum VP7 identities of 93.6% to 94.5% with human G12 strains at the deduced amino acid level. In spite of its G12 genotype nature, RU172 appeared to be distinct from human G12 rotaviruses and, on phylogenetic analysis, formed a separate lineage with human G12 strains. Among the other gene segments analyzed, RU172 belonged to NSP4 genotype B, had a NSP5 and VP6 of porcine origin, and shared maximum VP4 identities with porcine P[7] rotaviruses (94.3%–95.4% at the deduced amino acid level). Therefore, to the best of our knowledge, this is the first report of detection of an animal rotavirus strain with G12 genotype specificity. Detection of strains like RU172 provides vital insights into the genomic diversity of Group A rotaviruses of man and animals.

title: Entero-adherent Escherichia coli is an important diarrhoeagenic agent in infants aged below 6 months in Calcutta, India.
abstract: Escherichia coli adherent to HEp-2 and HeLa cells were isolated from the faeces of 43 (19.7%) of 218 hospitalised infants aged below 6 months with acute diarrhoea. No conventional virulence factors, including enterotoxin production--heat-labile (LT) or heat-stable (ST), the verotoxin (VT) or shiga-like toxin (SLT)--or the invasive phenotype (determined by the Sereny test) could be detected among these isolates. Out of the 43 isolates, 16 (37.2%) were of the known enteropathogenic O:K serogroups--enteropathogenic E. coli (EPEC). The remaining 27 (62.8%) isolates showed different types of adherence to HEp-2 and HeLa cells which was diffuse (40.7%), localised (37.0%), or both (22.3%); they were identified as entero-adherent E. coli (EAEC). The EAEC isolates adhered to HEp-2 and HeLa cells in the presence of mannose, lactose, fucose, galactose, and fetuin, indicating that adhesion was not specific for these sugars or glycoprotein. Haemagglutination and the salt aggregation test (SAT) did not correlate with patterns of adherence. The results of this study indicate that LA-EAEC is an important aetiological agent of acute diarrhoea in infants aged below 6 months in Calcutta.

title: Serovars of multi-antibiotic resistant Escherichia coli from the freshwater environs of Calcutta, India.
abstract: For a period of one year (March 1987 to February 1988), the incidence of Escherichia coli was determined in water, sediment and plankton collected from two sampling sites in a freshwater lake extensively used by humans and animals. Densities of E. coli associated with plankton was the lowest while sediments, especially at site 2, harbored high densities of the organism. Correlation coefficients revealed that the density of E. coli in water samples was linearly correlated to temperature, pH of water, sediment and humidity. Stepwise multiple regression analysis, however, showed that sediment temperature was the dominant variable which could explain 27% of the observed variation in the numbers of E. coli in the overlying waters (p = less than 0.001). Of the 150 environmental E. coli strains which were characterized, 31 (20.7%) were found to belong to the classic enteropathogenic E. coli (EPEC) serogroups. Seven of the serogroups among the environmental EPEC strains were also encountered from EPEC strains isolated from human cases during a concurrent clinical study. None of the 150 environmental strains were enterotoxigenic or enteroinvasive but 4 strains possessed HEp-2 cell adhesive factor. With the exception of one, all the EPEC strains isolated were multi-drug resistant. From this study, it was evident that the lake is an important source of infection of EPEC and other related diarrheagenic E. coli.

title: Evidence for independent segregation of the VP6- and NSP4- encoding genes in porcine group A rotavirus G6P[13] strains
abstract: Molecular characterization of two porcine group A rotavirus strains (HP113 and HP140), detected from eastern India, revealed a VP7 closely related to those of human G6P[14] strains, VP4 with a borderline P[13] genotype, and VP6 related to bovine and human SGI strains rather than porcine SGI and/or SGII group A rotaviruses. Both strains had NSP4 and NSP5 of porcine origin. Therefore, to our knowledge, the present study is the first report of detection of group A rotavirus strains with G6P[13] genotype specificities and provides evidence for independent segregation of the VP6- and NSP4-encoding genes in porcine group A rotaviruses.

title: Accuracy of Quadratic Versus Linear Interpolation in Noninvasive Electrocardiographic Imaging (ECGI)
abstract: Electrocardiographic Imaging (ECGI) is a cardiac functional imaging modality, noninvasively reconstructing epicardial potentials, electrograms and isochrones (activation maps) from multi-channel body surface potential recordings. The procedure involves solving Laplace’s equation in the source-free volume conductor between torso and epicardial surfaces, using Boundary Element Method (BEM). Previously, linear interpolation (LI) on three-noded triangular surface elements was used in the BEM formulation. Here, we use quadratic interpolation (QI) for potentials over six-noded linear triangles. The performance of LI and QI in ECGI is evaluated through direct comparison with measured data from an isolated canine heart suspended in a human-torso-shaped electrolyte tank. QI enhances the accuracy and resolution of ECGI reconstructions for two different inverse methods, Tikhonov regularization and Generalized Minimal Residual (GMRes) method, with the QI-GMRes combination providing the highest accuracy and resolution. QI reduces the average relative error (RE) between reconstructed and measured epicardial potentials by 25%. It preserves the amplitude (average RE reduced by 48%) and morphology of electrograms better (average correlation coefficient for QI ∼ 0.97, LI ∼ 0.92). We also applied QI to ECGI reconstructions in human subjects during cardiac pacing, where QI locates ventricular pacing sites with higher accuracy (≤ 10 mm) than LI (≤ 18 mm).

title: A multitechnique approach in protein/surfactant interaction study: physicochemical aspects of sodium dodecyl sulfate in the presence of trypsin in aqueous medium.
abstract: Interaction of sodium dodecyl sulfate (SDS) with a globular protein, trypsin, has been physicochemically studied in aqueous medium in detail using tensiometric, conductometric, calorimetric, fluorimetric, viscometric, and circular dichroism techniques. The results indicate that SDS-trypsin aggregates start to form at a surfactant concentration higher than the critical micelle concentration of pure SDS micelle. In contrast, the counterion binding decreases in the presence of trypsin. The free energies and enthalpies of micellization, interfacial adsorption, and entropy of micellization associated with the interaction have also been calculated. The values show that the interaction phenomenon is entropy controlled and endothermic in nature. The increase in viscosity is observed for the system of SDS-trypsin cluster above the critical micelle concentration of SDS micelle only. The aggregation number and interface polarity decrease compared to the values of micelles without protein. Circular dichroism spectra show the high alpha-helical content and unfolded structure of trypsin in the presence of SDS due to strong electrostatic repulsion leading to a probable "necklace and bead" model in the case of biopolymer-surfactant complexes.

title: Two modes of interaction of the single-stranded DNA-binding protein of bacteriophage T7 with the DNA polymerase-thioredoxin complex.
abstract: The DNA polymerase encoded by bacteriophage T7 has low processivity. Escherichia coli thioredoxin binds to a segment of 76 residues in the thumb subdomain of the polymerase and increases the processivity. The binding of thioredoxin leads to the formation of two basic loops, loops A and B, located within the thioredoxin-binding domain (TBD). Both loops interact with the acidic C terminus of the T7 helicase. A relatively weak electrostatic mode involves the C-terminal tail of the helicase and the TBD, whereas a high affinity interaction that does not involve the C-terminal tail occurs when the polymerase is in a polymerization mode. T7 gene 2.5 single-stranded DNA-binding protein (gp2.5) also has an acidic C-terminal tail. gp2.5 also has two modes of interaction with the polymerase, but both involve the C-terminal tail of gp2.5. An electrostatic interaction requires the basic residues in loops A and B, and gp2.5 binds to both loops with similar affinity as measured by surface plasmon resonance. When the polymerase is in a polymerization mode, the C terminus of gene 2.5 protein interacts with the polymerase in regions outside the TBD. gp2.5 increases the processivity of the polymerase-helicase complex during leading strand synthesis. When loop B of the TBD is altered, abortive DNA products are observed during leading strand synthesis. Loop B appears to play an important role in communication with the helicase and gp2.5, whereas loop A plays a stabilizing role in these interactions.

title: A quantile-based method for association mapping of quantitative phenotypes: an application to rheumatoid arthritis phenotypes
abstract: Genetic association of population-based quantitative trait data has traditionally been analyzed using analysis of variance (ANOVA). However, violations of certain statistical assumptions may lead to false-positive association results. In this study, we have explored model-free alternatives to ANOVA using correlations between allele frequencies in the different quantile intervals of the quantitative trait and the quantile values. We performed genome-wide association scans on anti-cyclic citrullinated peptide and rheumatoid factor-immunoglobulin M, two quantitative traits correlated with rheumatoid arthritis, using the data provided in Genetic Analysis Workshop 16. Both the quantitative traits exhibited significant evidence of association on Chromosome 6, although not in the human leukocyte antigen region which is known to harbor a major gene predisposing to rheumatoid arthritis. We found that while a majority of the significant findings using the asymptotic thresholds of ANOVA was not validated using permutations, a relatively higher proportion of the significant findings using the asymptotic cut-offs of the correlation statistic were validated using permutations.

title: Application of rbcL based molecular diversity analysis to algae in wastewater treatment plants.
abstract: The molecular diversity of algae in the final clarifier or denitrification filter outfall from three wastewater treatment plants (WWTPs) with activated sludge based treatment was analyzed using the rbcL gene as a phylogenetic marker. The rbcL gene encodes the large subunit of the CO(2) fixing enzyme RuBisCO. Among algae identified at the WWTPs were diatoms, green algae, cyanobacteria, Eustigmatophyceae, and unknown heterokonts. A high level of diversity was observed within WWTPs with 19-24 unique rbcL sequences detected at each plant. Algae composition also varied between treatment plants. Our results show that the rbcL gene can be used as a phylogenetic marker for algae diversity analysis in a wastewater treatment context.