Functional assignment to JEV proteins using SVM

Identification of different protein functions facilitates a mechanistic understanding of Japanese encephalitis virus (JEV) infection and opens novel means for drug development. Support vector machines (SVM), useful for predicting the functional class of distantly related proteins, is employed to ascribe a possible functional class to Japanese encephalitis virus protein. Our study from SVMProt and available JE virus sequences suggests that structural and nonstructural proteins of JEV genome possibly belong to diverse protein functions, are expected to occur in the life cycle of JE virus. Protein functions common to both structural and non-structural proteins are iron-binding, metal-binding, lipid-binding, copper-binding, transmembrane, outer membrane, channels/Pores - Pore-forming toxins (proteins and peptides) group of proteins. Non-structural proteins perform functions like actin binding, zinc-binding, calcium-binding, hydrolases, Carbon-Oxygen Lyases, P-type ATPase, proteins belonging to major facilitator family (MFS), secreting main terminal branch (MTB) family, phosphotransfer-driven group translocators and ATP-binding cassette (ABC) family group of proteins. Whereas structural proteins besides belonging to same structural group of proteins (capsid, structural, envelope), they also perform functions like nuclear receptor, antibiotic resistance, RNA-binding, DNA-binding, magnesium-binding, isomerase (intra-molecular), oxidoreductase and participate in type II (general) secretory pathway (IISP).     

Comparison of the properties of active Ca2+ transport by the islet-cell endoplasmic reticulum and plasma membrane

The properties of active or ATP-dependent calcium transport by islet-cell endoplasmic reticulum and plasma membrane-enriched subcellular fractions were directly compared. These studies indicate that the active calcium transport systems of the two membranes are fundamentally distinct. In contrast to calcium uptake by the endoplasmic reticulum-enriched fraction, calcium uptake by islet-cell plasma membrane-enriched vesicles exhibited a different pH optimum, was not sustained by oxalate, and showed an approximate 30-fold greater affinity for ionized calcium. A similar difference in affinity for calcium was exhibited by the Ca²⁺-stimulated ATPase activities which are associated with these islet-cell subcellular fractions. Consistent with the effects of calmodulin on calcium transport, calmodulin stimulated Ca²⁺-ATPase in the plasma membranes, but did not increase calcium-stimulated ATPase activity in the endoplasmic reticulum membranes. The physiological significance of the differences observed in calcium transport by the endoplasmic reticulum and plasma membrane fractions relative to the regulation of insulin secretion by the islets of Langerhans is discussed.     

A medium for enumeration of bacteria in foods containing swarming Bacillus spp.

A new medium containing sodium tripolyphosphate, ethylenediaminetetraacetic acid disodium salt, dihydrate, sodium desoxycholate, supplemented with minerals and nutrient sources was developed, which was very effective in inhibiting swarming of Bacillus spp. This medium polyphosphate-EDTA-desoxycholate agar (PEDA) was compared with tryptone glucose extract agar (Oxoid) for determining the total plate count of various semi-conserved fishery products. While promoting discrete colony formation of Bacillus spp., PEDA provided good bacterial recovery. PEDA is recommended for isolation or enumeration of bacteria in food dominated by swarming Bacillus spp.     

Synergistic interaction between two bacterial isolates in the degradation of carbofuran

The dominant bacteriaPseudomonas sp. andArthrobacter sp. were isolated from the standing water of carbofuran-retreatedAzolla plot.Arthrobacter sp. hydrolysed carbofuran added to the mineral salts medium as a sole source of carbon and nitrogen while no degradation occurred withPseudomonas sp. Interestingly, when the medium containing carbofuran was inoculated with bothArthrobacter sp. andPseudomonas sp., a synergistic increase in its hydrolysis and subsequent release of CO₂ from the side chain was noticed. This synergistic interaction was better expressed at 25° C than at 35° C. Likewise, related carbamates, carbaryl, bendiocarb and carbosulfan were more rapidly degraded in the combined presence of both bacterial isolates.     

Effect of stocking density on growth and survival of Clarias batrachus (Linn.) larvae and fry during hatchery rearing

Experiments were conducted to determine optimum stocking density for Clarias batrachus larvae and fry during hatchery rearing. The increase in stocking density decreased the total weight, specific growth rate (SGR) and percent weight gain of Clarias larvae during a 13‐day experiment. Survival rate was highest at a stocking density of 1000 m^?2 and lowest at 5000 m^?2. Stocking density did not influence the total biomass production of larvae. Clarias batrachus fry performance was studied during a 28‐day hatchery rearing experiment whereby fry stocked at a density of 100 m^?2 attained the highest total body weight (P < 0.05). The survival rate greatly declined to 59–61% by a density increase to 300 m^?2 and above. Stocking density influenced growth and survival of C. batrachus larvae and fry during hatchery rearing. The best performance was obtained when larvae were stocked at 2000 m^?2; survival was highest with C. batrachus fry stocked at 200 m^?2.     

Analysis of the volatile essential oils of Murraya koenigii and Pandanus latifolius

Using well-established techniques, samples were obtained of the volatile essential oils of the two types of curry leaf, Murraya koenigii and Pandanus latifolius. Both contained mainly terpenes, and M. koenigii produced less than 4% of other components with eight monoterpene hydrocarbons (ca 16%) and 17 sesquiterpene hydrocarbons (ca 80%) being obtained. The most important constituents of M. koenigii are β-caryophyllene, β-gurjunene, β-elemene, β-phellandrene and β-thujene. The volatile essential oil of P. latifolius also contained mainly sesquiterpene hydrocarbons (6–42%) but the only monoterpene was linalool (ca 6%). Nearly 2000 times the total quantity of aroma volatiles was produced by M. koenigii compared with P. latifolius, and this partly explains the observed stronger flavour potency of the former.     

Development and characterization of monoclonal antibodies to human type III procollagen

Hybridomas which secrete monoclonal antibodies against human type III procollagen have been developed. By an enzyme-linked immunosorbent assay, three of the monoclonal antibodies have been determined to be against non-helical extensions of the molecules while two of the antibodies are against helical portion of the molecules which is sensitive to bacterial collagenase action. These findings have been further confirmed by carrying out immuno-reaction of the pro α-chains transferred on nitrocellulose paper from sodium dodecyl sulfate polyacrylamide gels. These monoclonal antibodies have been found to be suitable reagents for immunohistochemical studies as well as for immunoassays of type III procollagen and collagen.     

Methotrexate binds in a non-productive orientation to human dihydrofolate reductase in solution, based on NMR spectroscopy

Dihydrofolate reductase (DHFR) is an intracellular target enzyme for folate antagonist drugs, including methotrexate. In order to compare the binding of methotrexate to human DHFR in solution with that observed in the crystalline state, NMR spectroscopy has been used to determine the conformation of the drug bound to human DHFR in solution. In agreement with what has been observed in the crystalline state, NOE's identified protein and methotrexate protons indicate that methotrexate binds in a non-productive orientation. In contrast to what has been reported for E. coli DHFR in solution, only one bound conformation of methotrexate is observed.