Biology subjects

Bhat, B.

Publications and source records attributed to Bhat, B..

5 recordsLinked to original sources

bioRxiv2025

Chevreul: An R Bioconductor Package for Exploratory Analysis of Full-Length Single Cell Sequencing

Chevreul is an open-source R Bioconductor package and interactive R Shiny app for processing and visualization of single cell RNA sequencing (scRNA-seq) data. It differs from other scRNA- seq analysis packages in its ease of use, its capacity to analyze full-length RNA sequencing data for exon coverage and transcript isoform inference, and its support for batch correction. Chevreul enables exploratory analysis of scRNA-seq data using Bioconductor SingleCellExperiment or Seurat objects. Simple processing functions with sensible default settings enable batch integration, quality control filtering, read count normalization and transformation, dimensionality reduction, clustering at a range of resolutions, and cluster marker gene identification. Processed data can be visualized in an interactive R Shiny app with dynamically linked plots. Expression of gene or transcript features can be displayed on PCA, tSNE, and UMAP embeddings, heatmaps, or violin plots while differential expression can be evaluated with several statistical tests without extensive programming. Existing analysis tools do not provide specialized tools for isoform-level analysis or alternative splicing detection. By enabling isoform-level expression analysis for differential expression, dimensionality reduction and batch integration, Chevreul empowers researchers without prior programming experience to analyze full-length scRNA-seq data. Data availabilityA test dataset formatted as a SingleCellExperiment object can be found at https://github.com/cobriniklab/chevreuldata. Availability & ImplementationChevreul is implemented in R and the R package and integrated Shiny application are freely available at https://github.com/cobriniklab/chevreul.

bioinformatics↗

bioRxiv2023

Community mixing selects for predation resistance in lab-evolved communities of bacterial prey and social predator Myxococcus xanthus

Population mixing, and transmission modes strongly influence social interactions. However, the impact of repeated mixing on the evolutionary dynamics of microbial predator-prey interactions remains underexplored1,2. Hence, we conducted a laboratory evolution experiment with bacterial predator-prey communities under two transfer regimens: repeated mixing (horizontal transfer) versus no mixing (vertical transfer). For this, Myxococcus xanthus served as the generalist predator3,4 and Escherichia coli as prey. We show that prey populations from vertical regimen were less resistant to predation than the ones from horizontal regimen. This was because prey isolates in the vertical treatment showed varying resistance levels relative to ancestors, while those in the horizontal treatment demonstrated less variation. Moreover, analysis of prey populations over evolutionary time revealed that the populations from horizontal treatment showed increasing levels of resistance to predation over time, whereas the ones from vertical treatment did not show similar trend. The differences in the outcomes of the two treatments was because the variants better at intraspecies competition, can only be maintained in the vertical treatment, whereas in horizontal treatment the benefits of superior intraspecies competitive fitness are nullified because of population mixing, as predicted by mathematical modeling approach. These predictions were empirically confirmed. Moreover, contrary to our expectations, predatory efficiency of evolved M. xanthus isolates was either the same or lesser than the ancestor. Together, we demonstrate that mixing affects the evolution of prey bacteria but has little effect on the hunting ability of the social predator M. xanthus.

evolutionary biology↗

bioRxiv2022

Scavenger receptor B1 facilitates the endocytosis of Escherichia coli via TLR4 signaling in mammary gland infection

SCARB1 belongs to class B of Scavenger receptors (SRs) that are known to be involved in binding and endocytosis of various pathogens. SRs have emerging role in regulating innate immunity and host-pathogen interactions by acting in co-ordination with Toll-like receptors. Little is known about the function of SCARB1 in milk-derived mammary epithelial cells (MECs). This study reports the role of SCARB1 in infection and its potential association in TLR4 signaling on bacterial challenge in Goat mammary epithelial cells (GMECs). The novelty in the establishment of MEC culture lies in the method that aims to enhance the viability of the cells with intact characteristics upto a higher passage number. We represent MEC culture to be used as a potential infection model for deeper understanding of animal physiology especially around the mammary gland. On E.coli challenge the expression of SCARB1 was significant in induced GMECs at 6 h. Endoribonuclease-esiRNA based silencing of SCARB1 affects the expression of TLR4 and its pathways i.e. MyD88 and TRIF pathways on infection. Knockdown also affected the endocytosis of E.coli in GMECs demonstrating that E.coli uses SCARB1 function to gain entry in cells. Furthermore, we predict 3 unique protein structures of uncharacterized SCARB1 (Capra hircus) protein. Overall, we highlight SCARB1 as a main participant in host defence and its function in antibacterial advances to check mammary gland infections.

immunology↗

bioRxiv2022

Comparison of co-immunoprecipitation techniques for effective identification of SNTA1 interacting proteins in breast cancer cells

Diverse signal transduction pathways involve thousands of proteins acting in concert that contribute to breast cancer pathology. SNTA1 has emerged as a common link that functions to wire various complex signaling circuits within the cell. In our study we used endogenous SNTA1 protein as bait in pull-down assays to identify SNTA1 interactome from breast cancer cell extract. We compared the utility of two co-immunoprecipitation techniques conventional co-IP and cross-linking co-IP coupled to mass spectrometry (IP-MS) that intriguingly generated valuable inventory of SNTA1 associated proteins in breast cancer cells that may or may not interact physically but contribute to shared functions in breast cancer pathology. We observed that Pierce cross-link IP kit enhanced sensivity of the analysis as it decreased the number of background proteins with a remarkable increase in identified list of proteins. We have also observed that different approaches are able to consistently detect the same signaling outcome as observed by Gene Ontology. Identification of interacting partners of SNTA1 in breast cancer cell lines may depict the possible signaling mechanism of this protein in molecular pathogenesis of breast cancer and its possible use as a therapeutic target.

cancer biology↗

bioRxiv2018

Structural, functional and molecular dynamics analysis of cathepsin B gene SNPs associated with tropical calcific pancreatitis, a rare disease of tropics.

Tropical Calcific Pancreatitis (TCP) is a neglected juvenile form of chronic non-alcoholic pancreatitis. Cathepsin B (CTSB), a lysososmal protease involved in cellular degradation process, is recently been studied as a potential candidate gene in the pathogenesis of TCP. According to cathepsin B hypothesis, mutated CTSB can lead to premature intracellular activation of trypsinogen, which is a key regulatory mechanism in pancreatitis. So far, CTSB mutations have been studied in pancreatitis and neurodegenerative disorders but little is known about the structural and functional effect of variants in CTSB. In this study, we investigated the effect of single nucleotide variants (SNVs) associated with TCP, using molecular dynamics and simulation algorithms. There were two non-synonymous variants in the coding region (L26V and S53G) of CTSB, located in the propeptide region. We tried to predict the effect of these variants on structure and function using multiple algorithms: SIFT, Polyphen2, Panther, SDM sever, i-Mutant2.0 suite, mCSM algorithm and Vadar. Further, using databases like miRdbSNP, PolymiRTS and miRNASNP, two SNPs in 3UTR region were predicted to affect the miRNA binding sites. Structural mutated models of nsSNP mutants (L26V and S53G) were prepared by MODELLER v9.15 and evaluated using TM-Align, Verify 3D, ProSA and Ramachandran plot. The results showed that the models (L26V and S53G) were of high accuracy. The 3D mutated structures were simulated using GROMACS 5.0 to predict the impact of these SNPs on protein stability. The results from in silico analysis and molecular dynamics simulations suggested that these variants in the propeptide region of cathepsin B could lead to structural and functional changes in the protein. Hence, the structural and functional analysis results have given interim conclusions that these variants can have deleterious effect in TCP and thus should be screen in samples from all TCP patients to decipher its distribution in patient population.

bioinformatics↗