A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam.

Metagenomic approach was used to understand the structural and functional diversity present in arsenic contaminated groundwater of the Ganges Brahmaputra Delta aquifer system. A metagene dataset (coded as TTGW1) of 89,171 sequences (totaling 125,449,864 base pairs) with an average length of 1406 bps was annotated. About 74,478 sequences containing 101,948 predicted protein coding regions passed the quality control. Taxonomical classification revealed abundance of bacteria that accounted for 98.3% of the microbial population of the metagenome. Eukaryota had an abundance of 1.1% followed by archea that showed 0.4% abundance. In phylum based classification, Proteobacteria was dominant (62.6%) followed by Bacteroidetes (11.7%), Planctomycetes (7.7%), Verrucomicrobia (5.6%), Actinobacteria (3.7%) and Firmicutes (1.9%). The Clusters of Orthologous Groups (COGs) analysis indicated that the protein regulating the metabolic functions constituted a high percentage (18,199 reads; 39.3%) of the whole metagenome followed by the proteins regulating the cellular processes (22.3%). About 0.07% sequences of the whole metagenome were related to genes coding for arsenic resistant mechanisms. Nearly 50% sequences of these coded for the arsenate reductase enzyme (EC. 1.20.4.1), the dominant enzyme of ars operon. Proteins associated with iron acquisition and metabolism were coded by 2% of the metagenome as revealed through SEED analysis. Our study reveals the microbial diversity and provides an insight into the functional aspect of the genes that might play crucial role in arsenic geocycle in contaminated ground water of Assam.

Enhanced candicidal compound production by a new soil isolate Penicillium verruculosum MKH7 under submerged fermentation.

BACKGROUND: Microorganisms are a rich source of structurally diverse secondary metabolites that exert a major impact on the control of infectious diseases and other medical conditions. The biosynthesis of these metabolites can be improved by manipulating the nutritional or environmental factors. This work evaluates the effects of fermentation parameters on the production of a lactone compound effective against Candida albicans by Penicillium verruculosum MKH7 under submerged fermentation. Design-Expert version8.0 software was used for construction of the experimental design and statistical analysis of the experimental data. RESULTS: The important factors influencing antibiotic production selected in accordance with the Plackett-Burman design were found to be initial pH, temperature, peptone, MgSO4.7H2O. Orthogonal central composite design and response surface methodology were adopted to further investigate the mutual interaction between the variables and identify the optimum values that catalyse maximum metabolite production. The determination coefficient (R2) of the fitted second order model was 0.9852. The validation experiments using optimized conditions of initial pH 7.4, temperature 27 °C, peptone 9.2 g/l and MgSO4.7H2O 0.39 g/l resulted in a significant increase (almost 7 fold from 30 to 205.5 mg/l) in the metabolite production which was in agreement with the prediction (211.24 mg/l). Stability of the compound was also assessed on the basis of its response to physical and chemical stresses. CONCLUSIONS: So far as our knowledge goes, till date there are no reports available on the production of antibiotics by Penicillium verruculosum through media optimization using RSM. Optimization not only led to a 7 fold increase in metabolite yield but the same was achieved at much lesser time (8-10 days compared to the earlier 12-15 days). The enhanced yield of the antibiotic strongly suggests that the fungus P. verruculosum MKH7 can be efficiently used for antibiotic production on a large scale.

Immunogenic potential and protective efficacy of formalin inactivated circulating Indian strain of West Nile virus.

OBJECTIVE: To assess the best suitable condition for virus inactivation, and to study the immunogenic potential and protective efficacy of a circulating West Nile virus (WNV) strain in Assam. METHODS: Bulk preparation of circulating WNV: WNIRGC07 (GeneBank ID: HQ246154), was undertaken in a bioreactor using cytodex-1. Virus Inactivation was done in three different conditions; 22 °C, 4 °C and room temperature. The virus preparations were evaluated for antigenicity by ELISA and toxicity by cell proliferation kit. Virus efficacy was done in-vivo on swiss albino mice against standard Indian WNV and Japanese encephalitis virus (JEV) strain. Humoral and cell mediated immune response was evaluated in mice sera by ELISA and neutralization assay. RESULTS: Inactivation at 22 °C was found to be more suitable in terms of less toxicity and high antigenicity. The same was selected to study the immune response and efficacy in mice. It induced neutralizing antibody titre of 1: 625 and high IgG response. In vivo experiment showed 100% protective efficacy against WNV and 20.8% cross protective efficacy against JEV. Further assessment of cellular immunity through immunized mice revealed augmentation of high levels of pro-inflammatory cytokines and moderate levels of anti-cytokines indicating a mixed balance of Th1 and Th2 response. CONCLUSIONS: Findings suggest that formalin inactivated Indian WNV strain has a good immunogenic potential. This is the first study on assessment of immunogenic potential of a lineage 5 strain of WNV. Our study reveals that it would be a promising and effective candidate for vaccine studies which warrants further evaluation.

Comparative study of antibiofilm activity of copper oxide and iron oxide nanoparticles against multidrug resistant biofilm forming uropathogens.

The effectiveness of the metal oxide nanoparticles viz. CuO and Fe2O3 as antibacterial agents against multidrug resistant biofilm forming bacteria was evaluated. CuO nanoparticles were also experimented for antibiofilm and time kill assay. The CuO displayed maximum antibacterial activity with zone of inhibition of (22 ± 1) mm against methicillin resistant Staphylococcus aureus (MRSA) followed by Escherichia coli (18 ± 1) mm. The Fe2O3 showed the zone of inhibition against MRSA of (14 ± 1) mm followed by E. coli (12 ± 1) mm. CuO proved to be more toxic than Fe2O3 nanoparticles showing significantly high antibacterial activity and found to possess dose dependent antibiofilm properties.

Insight into structural organization and protein-protein interaction of non structural 3 (NS3) proteins from dengue serotypes.

Dengue infections produce a distinct character of virus-induced intracellular membrane alterations which are associated with the viral replication machinery. Currently, the NS3 protein is being targeted for antiviral therapy against dengue. NS3 protein of dengue virus interacts with nuclear receptor binding protein (NRBP) of human causing cell trafficking between the Endoplasmic Reticulum (ER) and Golgi, which interacts with Rac3, a member of the Rho-GTPase family. No crystal structure of the NRBP is available for any species, thus limiting the complete understanding of structure- function relationships of this protein. The present study deals with the molecular modeling of the viral protein (NS3 of DENV1-4), the host protein (NRBP) and their interactions through protein-protein docking study. Theoretical threedimensional structures of the NRBP and NS3 were modeled using the Modeller 9v8, and the evaluated models were docked using GRAMM-X to study the mode of protein-protein interaction (NRBP as receptor and NS3 as ligand). The docked docking complexes were further evaluated for interaction analysis by the RosettaDock Server. Suface and interface residues were observed along with hydrogen and hydrophobic interaction. The conserved residues forming hydrogen interaction of NRBP with DENV1-4 serotypes were found to be GLN 305, SER 363 and GLN 379.

Association studies of dormancy and cooking quality traits in direct-seeded indica rice.

Association analysis was applied to a panel of accessions of Assam rice (indica) using 98 SSR markers for dormancy-related traits and cooking quality. Analysis of population structure revealed 10 subgroups in the population. The mean r(2) and D' value for all intrachromosomal loci pairs was 0.24 and 0.51, respectively. Linkage disequilibrium between linked markers decreased with distance. Marker-trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). Genome-wide scanning, detected a total of seven significant marker-trait associations (P < 0.01), with the R(2) values ranging from 12.0 to 18.0%. The significant marker associations were for grain dormancy (RM27 on chromosome 2), α-amylase activity (RM27 and RM234 on chromosomes 2 and 7, respectively), germination (RM27 and RM106 on chromosome 2), amylose (RM282 on chromosome 3) and grain length elongation ratio (RM142 on chromosome 4). The present study revealed the association of marker RM27 with traits like dormancy, α-amylase activity and germination. Simple correlation analysis of these traits revealed that these traits were positively correlated with each other and this marker may be useful for simultaneous improvement of these traits. The study indicates the presence of novel QTLs for a few traits under consideration. The study reveals association of traits like dormancy, α-amylase activity, germination, amylose content, grain length elongation ratio with SSR markers indicating the feasibility of undertaking association analysis in conjunction with germplasm characterization.

Highly effective antibiofilm coating of silver-polymer nanocomposite on polymeric medical devices deposited by one step plasma process.

Foley's catheters were coated with Silver (Ag), plasma polymerized aniline (PPAni) and Ag-PPAni composite by plasma based deposition processes which were characterized by XRD, EDX, SEM, and FT-IR spectroscopy and bioassays were performed to validate their efficacies to kill planktonic cells as well as to remove biofilm. The analyses confirmed the formation of Ag nanoparticles (AgNPs), PPAni and Ag-PPAni composite and also corroborated their successful deposition over the catheters. Antibacterial assays showed that coated catheters were capable of killing planktonic cells of most commonly encountered uropathogens and equally capable of eradicating biofilm formation by the uropathogens as evident from the reduced cfu/ml. UV-vis spectroscopy results showed that the nanoparticle coated catheters were capable of gradual release of AgNPs, killing all planktonic cells in solution over the time. Foley's catheters coated with AgNPs and their composites by one step plasma process were non-toxic devices capable of killing planktonic cells and proficient in eradicating biofilm formation which could be used to cutback the likelihood of the catheter related complications.

Design, virtual screening and docking study of novel NS3 inhibitors by targeting protein-protein interacting sites of dengue virus - a novel approach.

Currently dengue is a serious disease which has become a global burden in the last decade. Unfortunately, there are no effective drugs and vaccines against this disease. DENV non-structural protein (NS) 3, which is viral protease which is a potential target for antiviral therapy. Targeting this we performed homology modeling and protein-protein docking study of NS3 with NRBP (Nuclear Receptor Binding Protein) of human as it has been proved that NS3 of DENV interacts with NRBP which causes cellular trafficking in human cell. To carry out search of novel DENV protease inhibitors by in silico screening panduratin molecule was selected. 65 novel compounds were designed which involved substituting positions 1-5 of the benzyl ring A (4hydroxy-panduratinA) with various substituents. The protein-protein docking showed that the aminoacid residues of NS3 which were interacting with NRBP were found to be Ala 325, Asp 324, Phe 326, Asp 335, Glu 336, Glu 328, Asp 485, Gln 478, Arg 459, Gly 446 and Leu 480. These residues were targeted by the ligands which showed excellent binding affinity as binding energy. The ligand PKP10 showed lowest binding energy. It is also observed that the interface residues participated in the protein-protein interaction are being inhibited by the ligands.

Anopheles (Cellia) maculatus group: its spatial distribution and molecular characterization of member species in north-east India.

Anopheles (Cellia) maculatus is considered a group of at least nine formally named species. Faced with the difficulty of correct morphological identification due to overlapping characters, several member species of the An. maculatus group are known to play important role in malaria transmission in the Oriental region. Current assemblage, distribution and vectorial importance of the member species within the Maculatus group is far from clear in the north-eastern region of India. Our study encompassing 410 individuals, collected from 67 geo-referenced spots across the eight north-east Indian states, identified the presence of 6 member species of the Maculatus group using the molecular tools. Anopheles dravidicus and Anopheles rampae were documented for the first time in this part of India with latter forming the new country record. While Anopheles pseudowillmori (59.5%) and An. maculatus (32%) were widely available species in most of the north-eastern states, restricted distribution of Anopheles willmori to Nagaland and that of Anopheles sawadwongporni and An. rampae to Mizoram state was noted. None of the species was found positive for human malaria parasite. While no intraspecific differences existed in the sequences of second internal transcribed spacer (ITS2) region of ribosomal DNA (r-DNA) of the member species of the Maculatus group within north-east India, few differences were detected in the sequences of An. dravidicus, An. maculatus and An. pseudowillmori from north-east India with species from the neighbouring countries.