Biology subjects

Ranjbaran, A.

Publications and source records attributed to Ranjbaran, A..

3 recordsLinked to original sources

bioRxiv2026

fastdemux: Robust SNP-based demultiplexing of single-cell population genomics data

Sample multiplexing reduces cost and batch effects in population based large-scale single-cell genomics studies but requires accurate and scalable computational demultiplexing. Existing genotype-based methods, such as demuxlet, provide high accuracy but can be computationally slow and memory intensive as the number of cells, donors, and informative variants increases. Here, we introduce fastdemux, a scalable genotype-based demultiplexing framework based on a diagonal linear discriminant analysis (DLDA) model that substantially improves computational efficiency while maintaining accurate donor assignment. Using a pooled single-cell RNA-seq dataset from unrelated donors, we benchmarked fastdemux against demuxlet, vireo, and demuxalot.fastdemux achieved comparable or improved demultiplexing accuracy while reducing runtime and peak memory usage by orders of magnitude relative to alternative methods. Performance remained robust across varying sequencing depths and genotype SNP filtering thresholds. In addition, the DLDA framework naturally extends to doublet and higher-order multiplet detection. We also show thatfastdemux works well with scATAC-seq data where genetic variants are more sparsely covered. Together, these results establish fastdemux as an efficient and scalable solution for genetic demultiplexing of pooled single-cell datasets.

bioinformatics↗

bioRxiv2025

Will they survive? Alarming circumstances of Asiatic cheetah (Acinonyx jubatus venaticus) in Iran's drylands

The Asiatic cheetah (Acinonyx jubatus venaticus), once widespread across West, South, and Central Asia, now survives only in Iran, where its population has declined to the brink of extinction. The current study synthesized 12 years (2012-2024) of monitoring data, including systematic, extensive camera trap surveys across 27 distinct sampling sessions in eight reserves (69,089 trap nights) supplemented by published records of cheetah occurrences on social media to assess the demographic and spatial patterns of this critically endangered subspecies. Our analysis indicates that a total of 24 adult Asiatic cheetahs were identified across the Northern and Southern Landscapes. However, no evidence of reproduction or new individual presence was obtained in the Southern Landscape for over a decade. Meanwhile, the Northern Landscape hosts the remaining population, likely fewer than 30 individuals. Between 2020 and 2024, at least 31 cubs were born in the northern population from six females. However, limited evidence of successful recruitment suggests minimal contribution to population recovery, as only 47.3% of monitored cubs survived beyond their first year. Asiatic cheetahs exhibit extensive mobility across the arid Northern Landscape, frequently traversing unprotected communal lands and a major highway, which increases their vulnerability. While camera trap data have proven effective for individual identification, they are limited in tracking fine-scale movement, emphasizing the urgent need for satellite telemetry. Interventions such as roadside fencing and wildlife underpasses along highways are essential to reduce mortality. These efforts should be complemented by broader conservation measures, including habitat protection and restoration, community-based management of unprotected lands, and enhanced anti-trafficking enforcement. Genetic concerns, especially low effective population size and inbreeding, pose additional threats to viability.

ecology↗

bioRxiv2025

Psychological stress and social support are associated with opposing single-cell pro-inflammatory gene regulatory mechanisms in adults

Psychological stress is linked to elevated markers of chronic inflammation, whereas social support is associated with lower levels; yet, the molecular mechanisms mediating these effects are poorly understood. We investigated gene regulatory variation in peripheral blood mononuclear cells (PBMCs) from 165 self-reported African American adults (aged 50-89 years) using single-cell RNA sequencing (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq). Self-reported psychological stress and social support were associated with differential expression of 1,956 and 1,296 genes, respectively (10% FDR), primarily in CD4+ T cells and monocytes. Interferon signaling genes showed high expression in individuals with high psychological stress and low expression in those with high social support; this pattern mirrored gene expression in individuals with elevated circulating inflammatory markers (IFN-{gamma}, TNF-, IL-6). Genome-wide transcription factor (TF) motif analysis identified stress- and social support-associated changes in motif activity for 70 and 116 TFs, respectively, with 87 motifs enriched near differentially expressed genes. In CD4+ T cells, high psychological stress corresponded to increased IRF and STAT TF motif activity (interferon pathway), while social support was associated with reduced activity and expression in these pathways. We used an immune challenge paradigm (i.e., LPS stimulation), which confirmed the biological pathways of these gene regulatory effects. Our results demonstrate that psychological stress and social support modulate immune gene regulation at the single-cell level, revealing mechanistic links between psychosocial factors and inflammation, and suggesting that social support may promote immunological health.

genomics↗