Biology subjects

Arjyal, R.

Publications and source records attributed to Arjyal, R..

3 recordsLinked to original sources

bioRxiv2025

Comparative analysis of human and mouse ovaries across age

Mouse is a tractable model for human ovarian biology, however its utility is limited by incomplete understanding of how transcription and signaling differ interspecifically and with age. We compared ovaries between species using 3D-imaging, single-cell transcriptomics, and functional studies. In mice, we mapped declining follicle numbers and oocyte competence during aging; in human ovaries, we identified cortical follicle pockets and density changes. Oocytes had species-specific gene expression patterns during growth that converged toward maturity. Age-related transcriptional changes were greater in oocytes than granulosa cells across species, although mature oocytes change more in humans. We identified ovarian sympathetic nerves and glia; nerve density increased in aged human ovaries and, when ablated in mice, perturbed folliculogenesis. This comparative atlas defines shared and species-specific hallmarks of ovarian biology.

genomics↗

bioRxiv2024

Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis

During embryonic development, gene regulatory networks (GRNs) drive molecular differentiation of cell types. However, the temporal dynamics of these networks remain poorly understood. Here, we present Zebrahub-Multiome, a single-cell multiomic atlas that captures chromatin accessibility and gene expression from 94,562 cells across six stages of zebrafish embryogenesis (10-24 hours post-fertilization), capturing key developmental stages from the end of gastrulation to the onset of organogenesis. By measuring regulatory element activity alongside transcriptional output from the same cells, we identify 640,000 cis-regulatory elements organized into 402 hierarchically structured modules corresponding to specific developmental pathways. Early embryonic stages employ broadly shared regulatory programs that progressively fragment into lineage-specific modules. Timeresolved gene regulatory network inference reveals that transcription factors undergo functional transitions - from multilineage regulators to specialized, lineage-committed factors. These quantitative measurements reveal the regulatory network rewiring that drives cell fate specification. Our interactive web portal (zebrahub.org/epigenomics) enables exploration of gene dynamics, regulatory networks, and perturbation predictions, providing a quantitative framework for understanding vertebrate developmental regulation.

developmental biology↗

bioRxiv2024

How Mycobacterium tuberculosis builds a home: Single-cell analysis reveals M. tuberculosis ESX-1-mediated accumulation of anti-inflammatory macrophages in infected mouse lungs.

Mycobacterium tuberculosis (MTB) infects and replicates in lung mononuclear phagocytes (MNPs) with astounding ability to evade elimination. ESX-1, a type VII secretion system, acts as a virulence determinant that contributes to MTBs ability to survive within MNPs, but its effect on MNP recruitment and/or differentiation remains unknown. Here, using single-cell RNA sequencing, we studied the role of ESX-1 in MNP heterogeneity and response in mice and murine bone marrow-derived macrophages (BMDM). We found that ESX-1 is required for MTB to recruit diverse MNP subsets with high MTB burden. Further, MTB induces an anti-inflammatory signature in MNPs and BMDM in an ESX-1 dependent manner. Similarly, spatial transcriptomics revealed an upregulation of anti-inflammatory signals in MTB lesions, where monocyte-derived macrophages concentrate near MTB-infected cells. Together, our findings suggest that MTB ESX-1 mediates the recruitment and differentiation of anti-inflammatory MNPs, which MTB can infect and manipulate for survival.

microbiology↗