Biology subjects

Shinde, P. B.

Publications and source records attributed to Shinde, P. B..

3 recordsLinked to original sources

bioRxiv2025

AntiFP2: Genome and Metagenome-Wide Prediction of Antifungal Proteins

The identification of antifungal proteins (AFPs) is crucial for understanding microbial interactions and facilitating the discovery of antifungals on a large scale from genomic and metagenomic data. Most existing computational tools are developed for predicting antifungal peptides rather than proteins. To address this limitation, we developed AntiFP2. A manually curated dataset of experimentally validated AFPs was used to train and develop prediction models using cross-validation techniques. The ensemble strategy, which combined ESM2, BLAST, and MERCI, achieved the best results across independent validation. Beyond prediction, we implemented a complete pipeline for genome- and metagenome-wide AFP screening. AntiFP2 is freely available as a web server, standalone package, and Docker container, enabling scalable and reproducible antifungal protein discovery.

bioinformatics↗

bioRxiv2021

A Greener Recyclable Process for Extraction of Microbial Melanin using Ionic Liquid

Conventional techniques for the extraction of the melanin encounter several disadvantages such as poor extraction efficiency, excessive use of acid and alkali, and lengthy time duration. To extract melanin in a more sustainable manner, herein suitability of an aqueous solution of quaternary ammonium hydroxide known as tetrabutylammonium hydroxide (40% w/w TBAOH in water) to extract and purify the pigment from the endophyte Streptomyces hyderabadensis 7VPT5-5R was investigated. The solvent could extract 5.54{+/-}0.03 g/L of pure melanin against 3.31{+/-} 0.02 g/L of pure melanin by conventional method from bacterial culture resulting 66% increase in the yield of the pigment. The quaternary ammonium based solvent was further recycled for 5 consecutive cycles and production of melanin with yield ranging from 5.54{+/-}0.03 g/L to 5.47{+/-} 0.02 g/L was obtained. The yield of the pigment was 38-40% higher in the recycled solvent in comparison to the melanin yield extracted by conventional method. Considering the efficiency of the solvent for effective extraction and purification of melanin and its recyclability potential, it can be considered as a sustainable solvent for the extraction of the pigments from bacterial culture. Furthermore, the developed method for extraction of melanin from microorganisms as a sustainable source would help in reducing the cost of melanin leading to its efficient utilization in diverse fields.

microbiology↗

bioRxiv2020

Biodiversity and Antimicrobial Potential of Bacterial Endophytes from Halophyte Salicornia brachiata

Untapped natural habitats like halophytes, marsh land, and marine environment are suitable arena for chemical ecology between plants and microbes having environmental impact. Endophytes constitute an ecofriendly option for the promotion of plant growth and to serve as sustainable resources of novel bioactive natural products. The present study focusing on biodiversity of bacterial endophytes from Salicornia brachiata, led to isolation of around 350 bacterial endophytes. Phylogenetic analysis of 63 endophytes revealed 13 genera with 29 different species, belonging to 3 major groups: Firmicutes, Proteobacteria and Actinobacteria. 30% isolates belonging to various genera demonstrated broad-spectrum antibacterial and antifungal activities against a panel of human, plant, and aquatic infectious agents. An endophytic isolate Bacillus amyloliquefaciens 5NPA-1, exhibited strong in-vitro antibacterial activity against human pathogen S. aureus and phytopathogen X. campestris. Investigation through LC-MS/MS-based molecular networking and bioactivity-guided purification led to the identification of three bioactive compounds belonging to lipopeptide class on the basis of 1H- and 13C-NMR and MS analysis. To our knowledge, this is the first report studying bacterial endophytic biodiversity of Salicornia brachiata and isolation of bioactive compounds from its endophyte. Overall, the present study provides insights into the diversity of endophytes associated with the plants from the extreme environment as rich source of metabolites with remarkable agricultural applications and therapeutic properties.

microbiology↗