Dipak Deka

Proteomic Characterization of Lytic Bacteriophages of Staphylococcus aureus Isolated from Sewage Affluent of India

Staphylococcus aureus is a Gram-positive bacterium that causes a variety of diseases, including bovine mastitis, which has severe economic consequences. Standard antibiotic treatment results in selection of resistant strains, leading to need for an alternative treatment such as bacteriophage therapy. Present study describes isolation and characterization of a staphylococcal phage from sewage samples. S. aureus isolates obtained from microbial type culture collection (MTCC), Chandigarh, India, were used to screen staphylococcal phages. A phage designated as ΦMSP was isolated from sewage samples by soft agar overlay method. It produced clear plaques on tryptone soya agar overlaid with S. aureus. Transmission electron microscopy revealed that the phage had an icosahedral symmetry. It had 5 major proteins and possessed a peptidoglycan hydrolase corresponding to 70 kDa. ΦMSP infection induced 26 proteins to be uniquely expressed in S. aureus. This phage can be proposed as a candidate phage to treat staphylococcal infections.

Sequence analysis of Meq oncogene among Indian isolates of Marek's disease herpesvirus

Mareks disease (MD), caused by Mareks disease virus (MDV), is a highly contagious neoplastic disease of chicken that can be prevented by vaccination. However, in recent years many cases of vaccine failure have been reported worldwide as chickens develop symptoms of MD in spite of proper vaccination. Distinct polymorphism and point mutations in Meq gene of MDV have been reported to be associated with virulence and oncogenicity. The present study was carried out with the objective to isolate and characterize field isolates of MDV on the basis of Meq gene. Twenty five samples of suspected cases of MD were collected and processed for virus isolation in duck embryo fibroblast (DEF) primary culture where 28% (7 of 25) samples showed characteristic cytopathic effects of MDV in the form of plaques and syncytia. Additional evidence of presence of MDV in these samples was confirmed by PCR. To analyze diversity in all seven isolates of MDV, a polymorphism study was carried out by cloning and sequencing of full length of Meq gene (1020 bp). Sequence homology of 7 isolates with 23 reference strains showed 98.10–99.40% similarity in nucleotide and 95.90–98.50% similarity in amino acid sequences. Six isolates revealed 5 repeat sequences of 4 prolines (PPPP) whereas, one isolate revealed only 4 repeats. In phylogenetic analysis, these isolates formed a separate cluster showing close relatedness to the Chinese isolates. The study indicates a high mutation rate in field isolates of MDV that may be probable cause of vaccination failure.

Isolation and phylogenetic characterization of Canine distemper virus from India

Canine distemper (CD), caused by canine distemper virus (CDV) is a highly contagious disease that infects a variety of carnivores. Sequence analysis of CDVs from different geographical areas has shown a lot of variation in the genome of the virus especially in haemagglutinin gene which might be one of the causes of vaccine failure. In this study, we isolated the virus (place: Ludhiana, Punjab; year: 2014) and further cloned, sequenced and analyzed partial haemagglutinin (H) gene and full length genes for fusion protein (F), phosphoprotein (P) and matrix protein (M) from an Indian wild-type CDV. Higher sequence homology was observed with the strains from Switzerland, Hungary, Germany; and lower with the vaccine strains like Ondersteport, CDV3, Convac for all the genes. The multiple sequence alignment showed more variation in partial H (45 nucleotide and 5 amino acid substitutions) and complete F (79 nucleotide and 30 amino acid substitutions) than in complete P (44 nucleotide and 22 amino acid substitutions) and complete M (22 nucleotide and 4 amino acid substitutions) gene/protein. Predicted potential N-linked glycosylation sites in H, F, M and P proteins were similar to the previously known wild-type CDVs but different from the vaccine strains. The Indian CDV formed a distinct clade in the phylogenetic tree clearly separated from the previously known wild-type and vaccine strains.

Validation of immunomodulatory effects of lipopolysaccharide through expression profiling of Th1 and Th2 biased genes in Newcastle disease virus vaccinated indigenous chicken

Background and Aim Newcastle disease (ND) is considered one of the most important poultry diseases with chicken morbidity and mortality rates up to 100%. Current vaccination programs allow the use of live attenuated vaccines in the field to protect against the disease, which alone is inefficient and requires repeat booster doses. Toll-like receptor agonists (e.g., lipopolysaccharide [LPS]) as adjuvants are the ones, most extensively studied and have shown to be very promising in delivering a robust balanced immune response. In the present study, we have evaluated the potential of LPS to elicit a strong immune response with respect to the elicitation of both Th1 (cell-mediated) and Th2 (humoral) immune arms. Materials and Methods A total of 72 apparently healthy 1-day-old indigenous unvaccinated chicks were randomly divided into six experimental Groups A to F (n=12). At 8-week of age chicks in Group A, C, and E were vaccinated with live attenuated La Sota strain ND vaccine along with LPS, bovine serum albumin, and normal saline solution, respectively, and those in Group B, D, and E were kept separately without vaccination. Sampling was done on days 0, 1, 3, 7, 14, 21, 35, and 60 after vaccination. After vaccination and respective adjuvant application, Th1 and Th2 cytokine expression were measured in mRNA of both blood and tissue samples. Results The results were validated by, hemagglutination inhibition and enzyme-linked immunosorbent assay tests, to check for the humoral as well as cell-mediated immune response in blood serum levels. The results showed an increase in mRNA expression of the Th1 biased cytokines in Group A (LPS+NDV) as compared to the control groups. Similar mRNA expression pattern was seen in blood as well as tissue samples. Validation of results also indicates an increase in Cell-mediated Immunity as well as a humoral immune response in Group A (LPS+NDV). Conclusion The results of the study provided enough evidence to consider LPS as a potential vaccine adjuvants candidate against ND in chicken.

Minimization of apoptosis-like changes in cryopreserved buffalo bull sperm by supplementing extender with Bcl-2 protein

Aim: This study was aimed at evaluating the anti-apoptotic effects of Bcl-2 protein in cryopreserved buffalo bull sperm. Materials and Methods: A total 10 ejaculates from two buffalo bulls (5 each) were collected using artificial vagina method, and semen was evaluated using a standard protocol. Semen was extended by Tris egg yolk extender supplemented with Bcl-2 protein at 5, 10, and 15 µM. Semen was cryopreserved at ultra-low temperature using traditional vapor freezing method. Pre-freeze and post-thaw semen samples were evaluated for percent motility, viability, hypo-osmotic swelling test (HOST) reactive sperms; status of mitochondrial membrane activity and status of sperm phospholipase A1 and phospholipase A2 activity. Results: There were no significant effects of Bcl-2 protein supplementation on pre-freeze sperm quality. Percent motility and active mitochondria in post-thaw Bcl-2 supplemented and control groups were also similar. However, viable sperms were significantly (p<0.05) higher (74.29±4.23%) in Bcl-2 supplemented group (5 µM) as compared to control (51.6±5.77%). The proportion of HOST reactive sperms was also higher (63.1±6.73%) in Bcl-2 supplemented (5 µM) group as compared to control (50.7±6.98%). The sperm with low PLA activity (non-apoptotic) was significantly (p<0.05) higher in all the supplemented doses of Bcl-2 protein, i.e., at 5 µM (73.42±5.79%), 10 µM (75.51±6.22%), and 15 µM (74.78±5.89%) as compared to control (60.23±4.45%). We found that Bcl-2 protein supplementation at 5 µM dose improved the post-thaw semen quality indicated by higher viability, HOST reactive sperms, and sperm with low PLA activity (non-apoptotic sperms). Conclusion: Bcl-2 protein supplementation exerts its protective effect on spermatozoa against apoptosis-like changes developed during cryopreservation.

Biocomputational analysis of evolutionary relationship between toll-like receptor and nucleotide-binding oligomerization domain-like receptors genes

Aim: The active domains (TIR and NACHT) of the pattern recognition receptors (PRRs: Toll-like receptors [TLRs] and nucleotide-binding oligomerization domain [NOD]-like receptors [NLR], respectively) are the major hotspots of evolution as natural selection has crafted their final structure by substitution of residues over time. This paper addresses the evolutionary perspectives of the TLR and NLR genes with respect to the active domains in terms of their chronological fruition, functional diversification, and species-specific stipulation. Materials and Methods: A total of 48 full-length cds (and corresponding peptide) of the domains were selected as representatives of each type of PRRs, belonging to divergent animal species, for the biocomputational analyses. The secondary and tertiary structure of the taurine TIR and NACHT domains was predicted to compare the relatedness among the domains under study. Results: Multiple sequence alignment and phylogenetic tree results indicated that these host-specific PRRs formed entirely different clusters, with active domains of NLRs (NACHT) evolved earlier as compared to the active domains of TLRs (TIR). Each type of TLR or NLR shows comparatively less variation among the animal species due to the specificity of action against the type of microbes. Conclusion: It can be concluded from the study that there has been no positive selection acting on the domains associated with disease resistance which is a fitness trait indicating the extent of purifying pressure on the domains. Gene duplication could be a possible reason of genesis of similar kinds of TLRs (virus or bacteria specific).

Detection of Marek's disease virus meq gene in Feather follicle by Loop-mediated Isothermal Amplification

Mareks disease, caused by lymphotropic alphaherpesvirus, is one of the most economically significant diseases of poultry. Despite the ubiquitous use of vaccination to control losses, Mareks disease still affects poultry farming worldwide with an estimated annual loss up to US

Molecular detection of avian oncogenic viruses from apparently healthy chickens

2 billion. There is a need for a simple and rapid diagnostic method for early detection of Mareks disease virus from clinical samples under field conditions. A loop-mediated isothermal amplification assay was developed using a set of six primers in order to detect meq gene segment of oncogenic Mareks disease virus (serotype-1) in feather tips of chickens. Bst polymerase was used for the isothermal amplification of viral DNA at 65 o C for 60 min in a water bath. The fluorescence signal was identified in Mareks disease virus-positive samples after the addition of SYBR Green I under ultraviolet illumination. The loop-mediated isothermal amplification technique was found to be more sensitive as compared to Mareks disease virus-specific PCR for the detection of Mareks disease caused by oncogenic Mareks disease virus. The results demonstrate a significant advantage of loopmediated isothermal amplification in diagnosis of Mareks disease compared to conventional PCR as it can be carried out in most situations where rapid diagnosis is required, like in field conditions.

Data on meq gene sequence analysis of Ludhiana MDV isolates

Neoplastic infections due to oncogenic viruses are one of the major causes of economic problems faced by the poultry industry worldwide and the present study was undertaken in order to establish the prevalence of single or multiple avian oncogenic and associated virus infections in apparently healthy chicken. Mareks disease virus (MDV), reticuloendotheliosis virus (REV) and avian leukosis virus (ALV) could be detected from 9.23%, 95.38% and 93.85% cases, respectively by PCR applied on DNA extracted from blood of apparently healthy chickens. Mixed infection of MDV+REV+ALV and REV+ALV could be detected from 9.23% and 89.23% cases, respectively, indicating that multiple infections of two or more oncoviruses in the same birds was more common than the single virus infection and REV was recorded as the most prevalent oncogenic virus infection in poultry.

Cloning, Expression and Characterisation of Recombinant Outer Membrane Protein 16 from Brucella spp.

The data described are related to the article entitled “Sequence Analysis of Meq oncogene among Indian isolates of Marek׳s Disease Herpesvirus” M. Gupta, D. Deka, Ramneek, 2016. Seven meq genes of Ludhiana Marek׳s disease virus (MDV) field isolates were PCR amplified by using proof reading Platinum Pfx DNA polymerase enzyme, sequenced and then analyzed for the distinct polymorphisms and point mutations. The sequences were named as LDH 1758, LDH 2003, LDH 2483, LDH 2614, LDH 2700, LDH 2929 and LDH 3262. At this point, their deduced Meq amino acid sequences were compared with GenBank available already sequenced meq genes worldwide in their deduced amino acid form to study their identity/similarity with each other.