Gangopadhyay A.,Jhargram Raj College |
Chakraborty H.J.,Central Inland Fisheries Research Institute |
Datta A.,Jhargram Raj College
Journal of Molecular Graphics and Modelling | Year: 2017
The dengue envelope β-OG pocket is a crucial hinge for mediating virus-host fusion via conformational changes in the envelope to the fusion-competent form. The β-OG pocket is a small molecule target site for inhibition of virus-host fusion. As of date, the only structure of the β-OG pocket known is of serotype 2. Studies of β-OG inhibition by small molecules primarily target viral serotype 2. Envelope and β-OG sequence alignments, reveal dissimilarities across serotypes. In light of protein sequence-structure-function correlation, sequence variations suggest serotypic variations in β-OG druggability. This, together with the fact that dengue viral proteins do have serotype-specific variations of structure and function, lead to the study of the serotype-specificity of the dengue β-OG ligand binding behaviour. β-OG druggability was compared using comparative models of envelope proteins containing the β-OG pocket in four serotypes of the dengue virus. β-OG ligand binding was found to vary with respect to hydrophobicity, hydrophilicity, hydrogen bonding, van der Waals interactions with ligands and tightness of the binding site. The study also reports serotype-specific virtual leads identified from a library of 9175 alkaloids, using a consensus docking and scoring approach. The docking algorithms of Glide SP and XP, together with the Lamarckian genetic algorithm were employed for consensus docking. For consensus scoring, the Glide empirical score was employed along with the scoring function of AutoDock. A multi-dimensional lead optimisation approach was performed for optimising affinity, ligand efficiency, lipophilic ligand efficiency, ADMET and molecular torsional strains. The study proposes the serotype-specific inhibition of the β-OG for an effective inhibition of virus-host fusion, in contrast to a pan inhibitor. © 2017 Elsevier Inc.
Karak T.,Pollution Control Board |
Karak T.,Tea Research Association |
Abollino O.,University of Turin |
Bhattacharyya P.,University of California at Riverside |
And 2 more authors.
Chemosphere | Year: 2011
The distribution pattern and fractionation of arsenic (As) in three soil profiles from tea (Camellia sinensis L.) gardens located in Karbi-Anglong (KA), Cachar (CA) and Karimganj (KG) districts in the state of Assam, India, were investigated depth-wise (0-10, 10-30, 30-60 and 60-100. cm). DTPA-extractable As was primarily restricted to surface horizons. Arsenic speciation study showed the presence of higher As(V) concentrations in the upper horizon and its gradual decrease with the increase in soil depths, following a decrease of Eh. As fractionation by sequential extraction in all the soil profiles showed that arsenic concentrations in the three most labile fractions (i.e., water-soluble, exchangeable and carbonate-bound fractions) were generally low. Most arsenic in soils was nominally associated with the organic and Fe-Mn oxide fractions, being extractable in oxidizing or reducing conditions. DTPA-extractable As (assumed to represent plant-available As) was found to be strongly correlated to the labile pool of As (i.e. the sum of the first three fractions). The statistical comparison of means (two-sample t-test) showed the presence of significant differences between the concentrations of As(III) and As(V) for different soil locations, depths and fractions. The risk assessment code (RAC) was found to be below the pollution level for all soils. The measurement of arsenic uptake by different parts of tea plants corroborated the hypothesis that roots act as a buffer and hold back contamination from the aerial parts. © 2011 Elsevier Ltd.
Sahoo B.R.,Orissa University of Agriculture and Technology |
Sahoo B.R.,Osaka University |
Maharana J.,Orissa University of Agriculture and Technology |
Maharana J.,Central Inland Fisheries Research Institute |
And 7 more authors.
Molecular BioSystems | Year: 2014
Scrutinizing various nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) genes in higher eukaryotes is very important for understanding the intriguing mechanism of the host defense against pathogens. The nucleotide-binding domain (NACHT), leucine-rich repeat (LRR), and pyrin domains (PYD)-containing protein 3 (Nalp3), is an intracellular innate immune receptor and is associated with several immune system related disorders. Despite Nalp3's protective role during a pathogenic invasion, the molecular features and structural organization of this crucial protein is poorly understood. Using comparative modeling and molecular dynamics simulations, we have studied the structural architecture of Nalp3 domains, and characterized the dynamic and energetic parameters of adenosine triphosphate (ATP) binding in NACHT, and pathogen-derived ligands muramyl dipeptide (MDP) and imidazoquinoline with LRR domains. The results suggested that walker A, B and extended walker B motifs were the key ATP binding regions in NACHT that mediate self-oligomerization. The analysis of the binding sites of MDP and imidazoquinoline revealed LRR 7-9 to be the most energetically favored site for imidazoquinoline interaction. However, the binding free energy calculations using the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method indicated that MDP is incompatible for activating the Nalp3 molecule in its monomeric form, and suggest its complex interaction with NOD2 or other NLRs accounts for MDP recognition. The high binding affinity of ATP with NACHT was correlated to the experimental data for human NLRs. Our binding site prediction for imidazoquinoline in LRR warrants further investigation via in vivo models. This is the first study that provides ligand recognition in mouse Nalp3 and its spatial structural arrangements. © 2014 the Partner Organisations.
Maharana J.,Central Inland Fisheries Research Institute |
Patra M.C.,Orissa University of Agriculture and Technology |
Patra M.C.,National Dairy Research Institute |
De B.C.,Central Inland Fisheries Research Institute |
And 5 more authors.
Journal of Molecular Recognition | Year: 2014
Nucleotide binding and oligomerization domain (NOD2) is a key component of innate immunity that is highly specific for muramyl dipeptide (MDP) - a peptidoglycan component of bacterial cell wall. MDP recognition by NOD2-leucine rich repeat (LRR) domain activates NF-κB signaling through a protein-protein interaction between caspase activating and recruitment domains (CARDs) of NOD2 and downstream receptor interacting and activating protein kinase 2 (RIP2). Due to the lack of crystal/NMR structures, MDP recognition and CARD-CARD interaction are poorly understood. Herein, we have predicted the probable MDP and CARD-CARD binding surfaces in zebrafish NOD2 (zNOD2) using various in silico methodologies. The results show that the conserved residues Phe819, Phe871, Trp875, Trp929, Trp899, and Arg845 located at the concave face of zNOD2-LRR confer MDP recognition by hydrophobic and hydrogen bond (H-bond) interactions. Molecular dynamics simulations reveal a stable association between the electropositive surface on zNOD2-CARDa and the electronegative surface on zRIP2-CARD reinforced mostly by H-bonds and electrostatic interactions. Importantly, a 3.5 Å salt bridge is observed between Arg60 of zNOD2-CARDa and Asp494 of zRIP2-CARD. Arg11 and Lys53 of zNOD2-CARDa and Ser498 and Glu508 of zRIP2-CARD are critical residues for CARD-CARD interaction and NOD2 signaling. The 2.7 Å H-bond between Lys104 of the linker and Glu508 of zRIP2-CARD suggests a possible role of the linker for shaping CARD-CARD interaction. These findings are consistent with existing mutagenesis data. We provide first insight into MDP recognition and CARD-CARD interaction in the zebrafish that will be useful to understand the molecular basis of NOD signaling in a broader perspective. Copyright © 2014 John Wiley & Sons, Ltd.
Dhar A.K.,BrioBiotech Corporation |
Manna S.K.,Central Inland Fisheries Research Institute |
Thomas Allnutt F.C.,BrioBiotech Corporation
VirusDisease | Year: 2014
Over the past decade, aquaculture has grown at an average annual growth rate of approximately 6 % worldwide despite many challenges. Viral diseases are one of the major challenges that are threatening a sustainable growth of finfish farming globally. Vaccination of farmed fish plays an important role in commercial fish farming to mitigate viral diseases. In this review, we summarized the major viral diseases that have caused serious economic losses, and emerging diseases that pose a potential threat to aquaculture. The current status of viral vaccines in farmed fish are discussed, particularly the different types of vaccines that were licensed in recent years and are now commercially available, and the routes of delivery of those vaccines including the merits and demerits of each of these delivery method. Furthermore, the article provides an overview of different experimental vaccines that have been reported in the literatures in recent years besides highlighting the future need for developing cost-effective, oral vaccines that can be easily applicable at farm level. © 2013, Indian Virological Society.
De B.C.,Central Inland Fisheries Research Institute |
De B.C.,Vidyasagar University |
Meena D.K.,Central Inland Fisheries Research Institute |
Behera B.K.,Central Inland Fisheries Research Institute |
And 4 more authors.
Fish Physiology and Biochemistry | Year: 2014
Aquaculture is emerging as one of the most viable and promising enterprises for keeping pace with the surging need for animal protein, providing nutritional and food security to humans, particularly those residing in regions where livestock is relatively scarce. With every step toward intensification of aquaculture practices, there is an increase in the stress level in the animal as well as the environment. Hence, disease outbreak is being increasingly recognized as one of the most important constraints to aquaculture production in many countries, including India. Conventionally, the disease control in aquaculture has relied on the use of chemical compounds and antibiotics. The development of non-antibiotic and environmentally friendly agents is one of the key factors for health management in aquaculture. Consequently, with the emerging need for environmentally friendly aquaculture, the use of alternatives to antibiotic growth promoters in fish nutrition is now widely accepted. In recent years, probiotics have taken center stage and are being used as an unconventional approach that has numerous beneficial effects in fish and shellfish culture: improved activity of gastrointestinal microbiota and enhanced immune status, disease resistance, survival, feed utilization and growth performance. As natural products, probiotics have much potential to increase the efficiency and sustainability of aquaculture production. Therefore, comprehensive research to fully characterize the intestinal microbiota of prominent fish species, mechanisms of action of probiotics and their effects on the intestinal ecosystem, immunity, fish health and performance is reasonable. This review highlights the classifications and applications of probiotics in aquaculture. The review also summarizes the advancement and research highlights of the probiotic status and mode of action, which are of great significance from an ecofriendly, sustainable, intensive aquaculture point of view. © 2014 Springer Science+Business Media Dordrecht.
Bhattacharjee S.,Central Inland Fisheries Research Institute |
Mohanty S.,KIIT University |
Sharma A.P.,Central Inland Fisheries Research Institute |
Mohanty B.P.,Central Inland Fisheries Research Institute
Proteomics - Clinical Applications | Year: 2011
Purpose: To study the effect of storage temperature on lens crystallins quality for proteomic analysis, using αA-crystallins as internal marker. Experimental design: Lenses were stored at -40°C, -10°C and ice for up to 10 days. Protein extracts were prepared from samples stored at -40°C and -10°C on completion of 10 days; for samples kept under ice-storage, lenses were taken out at every 24h, extracts prepared and stored. Fresh lens extracts served as the control. Results: SDS-PAGE analysis of proteins from lens stored at -40°C and -10°C for 10 days did not show any appreciable change in profiles; however, two protein bands of 27 and 29kDa disappeared from lens stored in ice. A time-course analysis showed that such changes in ice-stored lens occurred beyond six days of storage. Appearance of additional αA-crystallin fragments on 1-D and 2-D immunoblots confirmed degradation of αA-crystallins. Protein spots altered in abundance and identified by peptide mass fingerprinting include αA-, αB-, βB1-, βB2- and γ-crystallins. Conclusions and clinical relevance: For proteomic studies, quality of the starting material must be ensured to avoid erroneous and misleading interpretation of results. Under field conditions where deep freezing or immediate preparations of samples are not the options, eye lens can be transported under ice-storage for about six days without deterioration in protein quality. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Manna Ranjan K.,Regional Center |
Das Archan K.,Central Inland Fisheries Research Institute |
Krishna Rao D.S.,Hessarghata Lake Post |
Karthikeyan M.,Hessarghata Lake Post |
Singh D.N.,4 Pannalal Road
Indian Journal of Traditional Knowledge | Year: 2011
Fisheries ecology of entire stretch of river Krishna was investigated during 2001-02 along with the status of fish and fisheries. Documentation of crafts and gears in freshwater sector of India is scanty. This paper is an attempt to record the fishery related indigenous technological knowledge in terms of fishing crafts and gear used in river Krishna. As many as 6 different types of crafts and 10 different gear were encountered during the monsoon survey of the river. The crafts were coracle, plank-built boat, palm-canoe, thermocol raft, rubber tube platform and banana stem raft. The gears were gill net, cast net, drag net, push net (triangular), scoop net, ring net, hook and line, lantern net (light trap), box trap and cradle trap.
Kumar A.,Central Institute for Research on Goats |
Rout P.K.,Central Institute for Research on Goats |
Mohanty B.P.,Central Inland Fisheries Research Institute
Journal of Proteomics and Bioinformatics | Year: 2013
Analysis of casein and whey protein was carried out in six Indian goats by both SDS-PAGE and 2-DE analysis. The variation was observed mainly in αs 1, αs2, β, κ-casein and β-lacto globulin locus in these breeds. Proteome analysis showed the presence of high number of spots in αs1 -casein, and κ-casein showed highest number of spots in all the goat breeds. The gels were showing remarkably both variability and similarity suggesting that the heterogeneity in protein forms in individual milk samples exist, and milk protein represents a common pattern of post-translational modification. © 2013 Kumar A, et al.
Samanta S.,Central Inland Fisheries Research Institute
Aquatic Ecosystem Health and Management | Year: 2013
The River Ganga passes through a large number of cities, towns, villages and agricultural fields. A sizable fraction of effluents and sewages generated from all these diverse sectors enters into the river. The incoming water is, therefore, carrying huge amounts of organic substances, residues of the used pesticides and metals along with other contaminants. Review of the pesticide residue studies indicate that hexachlorocyclohexane (HCH), dichlorodiphenyltrichloroethane (DDT) and endosulfan were the major contaminants in water and biota while HCH, DDT, aldrin and dieldrin dominate the sediment phase. In water the residues are frequently crossing the permissible limits of US EPA standards for aquatic organisms and their consumers, indicating various levels of risk. In fishes, the permissible limits for HCH, endosulfan and DDT are exceed only in some occasions, signifying minor risks on human consumption. Regarding metal contaminations, the uppermost stretch, up to Haridwar, is relatively free from pollutions. The middle stretch, receiving diverse kinds of effluents, is markedly polluted. Although a significant stretch of the estuarine zone is densely industrialized and regularly receives effluents, the tidal action is maintaining the metals in lower level than the middle stretch. However, in majority of the cases the reported levels in water were much higher than the US EPA permissible limits for aquatic organisms. With respect to the metal contaminations in sediments, the river is found moderately polluted. In some fishes, contamination of Pb, Hg and Cr crosses the limits. However, the alkaline pH, high sediment transportation and rigorous flushing during monsoons are protecting the river from accumulation of these toxic contaminants. With respect to aquatic health, it is anticipated that the metal and pesticide contaminations might have adversely affected fish health. Systematic studies are, however, lacking on this aspect. © 2013 Copyright Taylor and Francis Group, LLC.