An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples

To explore the natural microbial community of any ecosystems by high-resolution molecular approaches including next generation sequencing, it is extremely important to develop a sensitive and reproducible DNA extraction method that facilitate isolation of microbial DNA of sufficient purity and quantity from culturable and uncultured microbial species living in that environment. Proper lysis of heterogeneous community microbial cells without damaging their genomes is a major challenge. In this study, we have developed an improved method for extraction of community DNA from different environmental and human origin samples. We introduced a combination of physical, chemical and mechanical lysis methods for proper lysis of microbial inhabitants. The community microbial DNA was precipitated by using salt and organic solvent. Both the quality and quantity of isolated DNA was compared with the existing methodologies and the supremacy of our method was confirmed. Maximum recovery of genomic DNA in the absence of substantial amount of impurities made the method convenient for nucleic acid extraction. The nucleic acids obtained using this method are suitable for different downstream applications. This improved method has been named as the THSTI method to depict the Institute where the method was developed

Genomic plasticity associated with antimicrobial resistance in Vibrio cholerae.

The Bay of Bengal is known as the epicenter for seeding several devastating cholera outbreaks across the globe. Vibrio cholerae, the etiological agent of cholera, has extraordinary competency to acquire exogenous DNA by horizontal gene transfer (HGT) and adapt them into its genome for structuring metabolic processes, developing drug resistance, and colonizing the human intestine. Antimicrobial resistance (AMR) in V. cholerae has become a global concern. However, little is known about the identity of the resistance traits, source of AMR genes, acquisition process, and stability of the genetic elements linked with resistance genes in V. cholerae Here we present details of AMR profiles of 443 V. cholerae strains isolated from the stool samples of diarrheal patients from two regions of India. We sequenced the whole genome of multidrug-resistant (MDR) and extensively drug-resistant (XDR) V. cholerae to identify AMR genes and genomic elements that harbor the resistance traits. Our genomic findings were further confirmed by proteome analysis. We also engineered the genome of V. cholerae to monitor the importance of the autonomously replicating plasmid and core genome in the resistance profile. Our findings provided insights into the genomes of recent cholera isolates and identified several acquired traits including plasmids, transposons, integrative conjugative elements (ICEs), pathogenicity islands (PIs), prophages, and gene cassettes that confer fitness to the pathogen. The knowledge generated from this study would help in better understanding of V. cholerae evolution and management of cholera disease by providing clinical guidance on preferred treatment regimens.DBT Indi

Comparative evaluation of NBUVB phototherapy and PUVA photochemotherapy in chronic plaque psoriasis

Background: Psoralen UV-A (PUVA) is an established therapy for psoriasis, but there is a well-documenated risk of melanoma and nonmelanoma skin cancer. Narrow-band Ultraviolet-B (NBUVB) therapy has a lower carcinogenic risk, has equal therapeutic potential and is considerably safe in the long term than PUVA. Aim: The aim of present study was to compare the efficacy and side-effects of PUVA and NBUVB in chronic plaque psoriasis. Methods: Sixty patients of chronic plaque psoriasis were taken up for the study and were randomly divided into two groups of 30 each. They were well matched in terms of age, sex, psoriasis extent and pretreatment psoriasis area severity index (PASI) scoring. One group was treated with twice-weekly narrow-band UV-B (TL-01) phototherapy and the other group received twice-weekly oral 8-Methoxsalen PUVA for a period of 3 months. Results: Both the groups achieved >75% reduction in the PASI score or complete clearance at the end of 3 months, but PUVA group patients required significantly fewer number of treatment sessions and fewer number of days to clear the psoriasis as compared to the NBUVB group, while the mean cumulative clearance dose and adverse effects were significantly lower in the NBUVB group. Conclusion: We concluded that PUVA group patients achieved a faster clearance, but the adverse effects were significantly lower in the NBUVB group