Biology subjects

Salunke, R. P.

Publications and source records attributed to Salunke, R. P..

3 recordsLinked to original sources

bioRxiv2025

plasmoRUtils: A one-stop R Package for Plasmodium and other Apicomplexan parasite-related Bioinformatics analysis

Bioinformatics analysis of non-model organisms remains challenging due to the limited availability of specialized tools, as most R packages are optimized for well-annotated model species. This problem is exacerbated by genomic and proteomic data being scattered across multiple databases, each employing different identifiers based on varying reference annotations. Comprehensive databases have been developed to disseminate knowledge related to Apicomplexan genomics and proteomics, such as VEupathDB. Several specialised databases, particularly for the malaria parasite Plasmodium, have been developed such as ApicoTFDB, malaria.tools, MPMP, MIIP, Phenoplasm, PlasmoBase, alongside broader resources like HitPredict and TED. However, these platforms often suffer from manual query interfaces, outdated identifiers, and inefficient data retrieval methods, complicating their use for large-scale bioinformatic analyses. To address these limitations, we present plasmoRUtils, an R package designed to streamline database access and data harmonization for Apicomplexan research. plasmoRUtils enables the retrieval of data tables using single-line R functions and standardized Ensembl gene IDs as input. Thanks to the APIs available for some databases such as VEuPathDB, the package also provides functions to build CLI-based queries for VEuPathDBs component databases. Additional support includes performing overrepresentation analyses and estimating parasite transcriptomic age/stage using single-cell or bulk RNA-Seq references. By automating data retrieval and transformation within RStudio, plasmoRUtils eliminates the need for manual database queries, facilitating end-to-end workflow development without leaving the R environment. Available on GitHub https://github.com/Rohit-Satyam/plasmoRUtils, with comprehensive documentation, plasmoRUtils represents a critical step toward efficient and reproducible bioinformatics for Apicomplexan research.

bioinformatics↗

bioRxiv2023

Proteome profiling of nasopharynx reveals pathophysiological signature of COVID-19 disease severity

An aberrant innate immune system caused by the beta coronavirus SARS-CoV-2 is a characteristic manifestation of severe coronavirus disease 2019 (COVID-19). Here, we performed proteome profiling of nasopharyngeal (NP) swabs from 273 hospitalized patients with mild and severe COVID-19 symptoms, including non-survivors. We identified depletion in STAT1-mediated type I interferon response, retinol metabolism and NRF2 antioxidant system that are associated with disease severity in our patient demography. We found that the dysregulation of glucocorticoid signaling and renin-angiotensin-aldosterone system (RAAS) contribute to the pathophysiology of COVID-19 fatality. Hyperactivation of host innate immune system was observed in severe patients, marked by elevated proteins involved in neutrophil degranulation and platelet aggregation. Our study using high-throughput proteomics on the nasopharynx of COVID-19 patients provides additional evidence on the SARS-CoV-2-induced pathophysiological signatures of disease severity and fatality.

immunology↗

bioRxiv2023

PfAP2-MRP DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages

Malaria pathogenicity results from the parasites ability to invade, multiply within and then egress from the host red blood cell (RBC). Infected RBCs are remodeled, expressing antigenic variant proteins (such as PfEMP1, coded by the var gene family) for immune evasion and survival. These processes require the concerted actions of many proteins, but the molecular regulation is poorly understood. We have characterized an essential Plasmodium specific Apicomplexan AP2 (ApiAP2) transcription factor in Plasmodium falciparum (PfAP2-MRP; Master Regulator of Pathogenesis) during the intraerythrocytic developmental cycle (IDC). An inducible gene knockout approach showed that PfAP2-MRP is essential for development during the trophozoite stage, and critical for var gene regulation, merozoite development and parasite egress. ChIP-seq experiments performed at 16 hour post invasion (h.p.i.) and 40 h.p.i. matching the two peaks of PfAP2-MRP expression, demonstrate binding of PfAP2-MRP to the promoters of genes controlling trophozoite development and host cell remodeling at 16 h.p.i. and antigenic variation and pathogenicity at 40 h.p.i. Using single-cell RNA-seq and fluorescence-activated cell sorting, we show de-repression of most var genes in{Delta} pfap2-mrp parasites that express multiple PfEMP1 proteins on the surface of infected RBCs. In addition, the{Delta} pfap2-mrp parasites overexpress several early gametocyte marker genes at both 16 and 40 h.p.i., indicating a regulatory role in the sexual stage conversion. Using the Chromosomes Conformation Capture experiment (Hi-C), we demonstrate that deletion of PfAP2-MRP results in significant reduction of both intra-chromosomal and inter-chromosomal interactions in heterochromatin clusters. We conclude that PfAP2-MRP is a vital upstream transcriptional regulator controlling essential processes in two distinct developmental stages during the IDC that include parasite growth, chromatin structure and var gene expression.

genomics↗