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Singh, N. J.

Publications and source records attributed to Singh, N. J..

9 recordsLinked to original sources
bioRxiv2026

Molecular adaptations of activated T-cells in an inflammation-associated schizophrenia sub-group

Thirty-five percent of people with schizophrenia-related disorders (SRD) form a high-inflammation subgroup defined by elevated anti-gliadin antibodies (AGA+) and inflammatory proteins and associated with an increased severity of negative symptoms. However, the immune mechanisms mediating these effects remain poorly defined. Here, we characterized transcriptional signatures of peripheral immune cells in AGA+ SRD (n=7) compared to AGA-negative (AGA-) SRD (n=3) and healthy controls (HC; n=5), using single-cell RNA-sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs). AGA+ SRD was associated with increased abundance of T-helper-17 cells (Th17), T-follicular helper-1 (Tfh1), CD5+ B cells, plasmacytoid dendritic cells (pDCs), and several CD8+ T cell subsets, including memory and Natural Killer-T-like activated subsets. In parallel, AGA-SRD exhibited a higher abundance of several monocyte subsets compared to either AGA+ SRD or HC. Pathway analysis revealed upregulation in AGA+ SRD of JAK/STAT, type I Interferon, and IL-6 signaling pathways in distinct subset of activated T-cells. Collectively, these results define a unique T cell predominant inflammatory signature in AGA+ SRD, as well as potential targets for therapeutic intervention.

genomics↗
bioRxiv2026

The active secretion of a subunit of IL-12 by tissue cells is regulated by Valosin-Containing Protein and intracellular calcium redistribution.

One molecular mechanism for collaboration between innate immune and tissue stromal cells in regulating effector responses is the formation of the innate cytokine IL-12 as a result of the two cell types contributing distinct subunits (p40 and p35) allowing for the localized assembly of the functional IL-12 heterodimer. Dendritic cell activation leads to p40 secretion, but the pathways in stromal cells allowing p35 secretion are unknown. We identify the inhibition of Valosin-Containing Protein (VCP) and increases in intracellular calcium signaling as the key regulators for the secretion of p35 from its homeostatic reservoirs in the endoplasmic reticulum. This p35 secretion, in the absence of co-expression of the p40 subunit, requires active gene expression, is independent of ER stress pathways, and is distinct from passive (cell-death dependent) release processes. Thus, an active sensory apparatus in non-hematopoietic cells contributes to the collaborative control of the trajectory of early immune differentiation. One Sentence SummaryVCP inhibition and calcium flux allows stromal cells to release the p35 subunit of the cytokine IL-12 and regulate localized cytokine activity.

immunology↗
bioRxiv2025

Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments

Minimizing experimental noise is integral to robust data generation in single-cell science. Experimental processing of different samples as a single pool, made possible by hashtag-assisted pooling, helps minimize batch-effects, but the computational demultiplexing of the data can also lead to loss of cells whose hashtags cannot be resolved accurately. Here, we examine four alternate experimental designs that could be used instead of a single-pool approach and quantify the batch effects as well as cell loss in each case. While a reference design offers the best performance, this study can help individual investigators choose one suited for their biological questions.

bioinformatics↗
bioRxiv2024

Kinetic patterns of single cell gene expression discriminate between the murine cellular responses to live attenuated and inactivated Yellow Fever vaccines

The success of the live attenuated Yellow Fever vaccine (YF17D) that elicits immunity lasting over thirty years has made it a widely used model to understand the generation of durable protection. We compare the early single-cell level transcriptional response in mice to YF17D and an adjuvanted-inactivated, but less effective version (InYF). Within the first week, we identify 70 kinetic patterns in 45 cellular clusters, majority of which discriminate between the two formulations, some in a tissue and sex-specific manner. Intriguingly, differential transcripts fall into two categories, one whose association with YF17D or InYF is maintained even when decoupled from their cell-type of expression and the other where such cell-plus-gene pairing is critical to maintain differential marker status. We demonstrate applications of this resource, by identifying B cells with varied interferon and antigen responsiveness in relation to each vaccine. This high-resolution dataset is amenable to further biomarker discovery and hypothesis generation.

immunology↗
bioRxiv2024

CountASAP: A Lightweight, Easy to Use Python Package for Processing ASAPseq Data

Declining sequencing costs coupled with the increasing availability of easy-to-use kits for the isolation of DNA and RNA transcripts from single cells have driven a rapid proliferation of studies centered around genomic and transcriptomic data. Simultaneously, a wealth of new techniques have been developed that utilize single cell technologies to interrogate a broad range of cell-biological processes. One recently developed technique, transposase-accessible chromatin with sequencing (ATAC) with select antigen profiling by sequencing (ASAPseq), provides a combination of chromatin accessibility assessments with measurements of cell-surface marker expression levels. While software exists for the characterization of these datasets, there currently exists no tool explicitly designed to reformat ASAP surface marker FASTQ data into a count matrix which can then be used for these downstream analyses. To address this, we created CountASAP, an easy-to-use Python package purposefully designed to transform FASTQ files from ASAP experiments into count matrices compatible with commonly-used downstream bioinformatic analysis packages. CountASAP takes advantage of the independence of the relevant data structures to perform fully parallelized matches of each sequenced read to user-supplied input ASAP oligos and unique cell-identifier sequences.

bioinformatics↗
bioRxiv2024

Linear infrastructure and associated wildlife accidents create an ecological trap for an apex predator and scavenger

Animals can be caught in an "ecological trap" when they select for seemingly attractive habitats at the expense of their fitness. Such maladaptive behaviour is often a consequence of human induced rapid changes in animals natal environment such as building of energy and transportation infrastructure. We tested the ecological trap hypotheses for human created linear infrastructure on a widely distributed apex predator and a scavenger - the Golden eagle (Aquila chrysaetos), whose range spans across the entire northern hemisphere. Roads and railways create novel and attractive feeding subsidies through traffic induced mortality of other species, while powerline areas provide perching or nesting sites and scavenging opportunities from electrocuted or collision-killed birds. These conditions lead to negative demographic consequences for eagles. We used integrated step selection functions for habitat selection and movement behaviour with ten years of data from 74 GPS-tracked Golden Eagles (36 adult and 38 immature) in Fennoscandia. To measure habitat attractiveness, we use wildlife traffic accident statistics on major wildlife species including the eagles, and mortality of five GPS- tracked eagles to show demographic consequences. Eagles selected for linear features all year round and across entire study region. Individuals also searched and sat alongside roads and railway lines more frequently. Immature eagles selected roads and railway sites more consistently compared to adults and showed learning behaviour with age. We discuss implications of these findings for conservation and population ecology of apex predators and scavengers and their potential evolutionary implications. We suggest that rapid removal of carcasses from roads and tracks is urgently needed to avoid this trap for many raptor and scavenger species throughout the world and develop methods and approaches to reduce wildlife traffic accidents all together.

ecology↗
bioRxiv2023

Airborne eDNA captures three decades of ecosystem biodiversity

Conserving biodiversity is a global imperative, yet our capacity to quantify and understand species occurrences has been limited. To help address this challenge, we develop a novel monitoring approach based on deep sequencing of airborne eDNA. When applied to a 34-year archive of weekly filters from an aerosol sampling station in northern Sweden, our methods enabled robust detection of over 2,700 genera across all domains of life and estimates of eDNA catchment areas. Reconstructed time series revealed regional biodiversity declines consistent with contemporary, large-scale transformations of forest composition and structure. Our results show airborne eDNA can reliably monitor biodiversity and underscore the immense latent potential in the thousands of aerosol monitoring stations deployed worldwide. One-Sentence SummaryDNA captured from air reveals organisms from all domains of life and their long-term trends.

ecology↗
bioRxiv2017

Computational docking reveals evolutionary conservation of a specific interaction between 15d-Prostaglandin-J2 and eIF4A.

15-deoxy-delta 12,14-prostaglandin J2 (15d-PGJ2) is anti-inflammatory/antineoplastic prostaglandin which functions through covalent binding to cysteine residues of various target proteins. We previously showed that 15d-PGJ2 mediated anti-inflammatory responses are dependent on the translational inhibition through its interaction with eIF4A. Binding of 15d-PGJ2 to eIF4A specifically blocks the interaction between eIF4G and eIF4A leads to the formation of stress granules (SGs), which cluster mRNAs with inhibited translation. Here we show that the binding between 15d-PGJ2 and eIF4A specifically blocks the interaction between the MIF4G domain of eIF4G and eIF4A. To reveal the mechanism of this interaction, we used computational simulation-based docking studies and identified that the carboxyl tail of 15d-PGJ2 could stabilize the binding of 15d-PGJ2 to eIF4A through arginine 295 of eIF4A, which is the first suggestion that the 15d-PGJ2 tail play a physiological role. Interestingly, the putative 15d-PGJ2 binding site on eiF4A is conserved across many species, suggesting a biological role. Our data propose that studying 15d-PGJ2 and its targets will may uncover new therapeutic approaches in anti-inflammatory drug discovery.

molecular biology↗