Biology subjects

D'Souza, S.

Publications and source records attributed to D'Souza, S..

6 recordsLinked to original sources

bioRxiv2026

A large-scale crowd-sourced annotated acoustic dataset of Indian fauna

Global rates of biodiversity loss warrant conservation action and monitoring at large geographic scales. Conservation technologies such as acoustic monitoring in conjunction with deep learning now enable us to monitor wildlife simultaneously across space and time. However, for a significant proportion of biodiversity in tropical regions, we cannot yet rely on automated recognition approaches because we lack acoustic templates to robustly train deep learning algorithms. In this paper, we relied on a novel participatory approach, enlisting researchers, conservation practitioners, and nature enthusiasts to create a unique crowd-sourced, open-access dataset of acoustic annotations across taxonomic groups for biodiversity in India. Our dataset comprises 3311 minutes of strongly labelled data (bounding boxes or annotations for a species vocalization) and 2504 minutes of weakly labelled data (indicating the presence of a species within an audio file but lacking bounding boxes) for 518 species across India, spanning 25 of 36 states and union territories. We present metadata and code for data processing and highlight the strengths of a participatory approach to biodiversity monitoring.

ecology↗

bioRxiv2026

iAstrocytes model cytokine influences on complement expression and neuronal network synchronization.

Astrocytes play essential roles in neuronal development, function, and disease, yet existing methods to derive astrocytes from human pluripotent stem cells (hPSCs) are complex and can involve months of in vitro maturation. We developed a genomic safe-harbor knock-in system for inducible expression of the astrogenic transcription factors NFIA, NFIB, and SOX9, enabling rapid and robust generation of functional induced astrocytes (iAstrocytes). Across five hPSC lines, NFIB-SOX9 and NFIA-NFIB-SOX9 combinations efficiently generated highly pure populations expressing astrocyte-specific and synaptogenic genes. iAstrocytes displayed cytokine-induced expression of complement factors C3 and C4 and were amenable to CRISPR interference (CRISPRi) gene expression knockdown. Optimization of culture conditions enabled survival of NFIB-SOX9 iAstrocytes in co-culture with human induced neurons (iNeurons). Through pharmacological and genetic perturbations, we uncovered a previously undescribed phenomenon in which co-culture with iAstrocytes promoted the development of synchronized iNeuron network calcium activity mediated by specific gap junction proteins. This rapid and genetically tractable iAstrocyte platform provides a robust model to dissect human genetic and environmental effects on astrocyte-neuron interactions.

neuroscience↗

bioRxiv2023

Multifunctional evolution of palm squirrel coat colour and pattern

Complex colour pattern traits often evolve in response to multiple selective pressures, emphasizing the need for their investigation in an integrative framework. We use museum specimens (n=718) to study the evolution of coat colouration in three palm squirrel species (Funambulus spp.) in the Indian subcontinent, with climate, vegetation, and predators as the potential selective forces. Our results indicate a strong geographical trend in coat colour distribution within and across species, with darker individuals in the southern and lighter individuals in the northern regions. We find significant darkening of coat colouration in more humid, densely vegetated regions with dark soils. Fine-scale intra-specific analyses suggest that species respond differently to multiple abiotic selective pressures. Investigation of stripe pattern elements suggests that the colour-based elements are more visible to raptors, while luminance-based elements are more visible to ferrets. We also find that squirrel species are darker in areas with denser and taller canopies, with low-contrast stripes specific to each predators vision. Overall, squirrel coat colouration evolves in response to multiple abiotic factors, including climate and habitat, and specific stripe elements provide particular visual effects on predators depending on the habitat.

ecology↗

bioRxiv2023

Template-assisted fabrication of moon-shaped channels for protein breakthrough analysis

Cylindrical column with packed stationary phase is the workhorse of liquid chromatography systems. These stationary phases are commonly classified on the basis of different form factors namely, beads and monoliths for protein chromatography. Monolithic rods are one of the important geometries derived from polymers through complex polymerization schemes with additional requirements such as cross-linkers and specific reaction conditions. To address these practical difficulties and enable ease of fabrication at laboratory scale, acrylic copolymers are hypothesized to perform as a monolithic stationary phase suitable for protein chromatography. The present work proposes a rapid fabrication technique to obtain monolithic rods that could be reconditioned without any of the above additional steps. It is characterized with monolith diameter that could be controlled using acrylic copolymer concentration. Formation of the copolymeric stationary phase inside microchannel led to annular geometry and in turn, demonstrated fabrication of moon-shaped channels (MSCs) for the first time in literature. An online monitoring system facilitated tracer breakthrough analysis with MSCs to report sharp peak front and an estimate of channel void volume. Breakthrough curves with single protein validated the selection of blue dextran as tracer and indicated retention of proteins due to electrostatic interactions on the functional copolymer surface.

biochemistry↗

bioRxiv2022

Aging Fly Cell Atlas Identifies Exhaustive Aging Features at Cellular Resolution

Aging is characterized by a decline in tissue function, but the underlying changes at cellular resolution across the organism remain unclear. Here, we present the Aging Fly Cell Atlas, a single-nucleus transcriptomic map of the whole aging Drosophila. We characterize 163 distinct cell types and perform an in-depth analysis of changes in tissue cell composition, gene expression, and cell identities. We further develop aging clock models to predict the fly age and show that ribosomal gene expression is a conserved predictive factor for age. Combining all aging features, we find unique cell type-specific aging patterns. This atlas provides a valuable resource for studying fundamental principles of aging in complex organisms.

developmental biology↗

bioRxiv2019

Adaptive thermogenesis in mice requires adipocyte light-sensing via Opsin 3

Almost all life forms can decode light information for adaptive advantage. Examples include the visual system, where photoreceptor signals are interpreted as images, and the circadian system, where light entrains a physiological clock. Here we describe a local, non-visual light response in mice that employs encephalopsin (OPN3, a 480 nm, blue light responsive opsin) to regulate the function of adipocytes. Germ line null and adipocyte-specific conditional null mice show a deficit in thermogenesis that is phenocopied in mice under blue-light deficient conditions. We show that blue light stimulation of adipocytes activates hormone sensitive lipase, the rate limiting enzyme in the lipolysis pathway, and that this is OPN3-dependent. Opn3 adipocyte conditional null mice also use reduced levels of fat mass when fasted and cold exposed further suggesting a lipolysis deficit. These data suggest the hypothesis that in mice, a local, OPN3-dependent light response in adipocytes is a mechanism for regulation of energy homeostasis.

physiology↗