Biology subjects

Ghosal, R.

Publications and source records attributed to Ghosal, R..

9 recordsLinked to original sources

bioRxiv2026

Pick your battles: competitive strategies of green chromides (Etroplus suratensis) during inter- and intraspecific contests

Competitive ability is a key determinant of organismal fitness, yet high costs of interference competition necessitate strategic behavioural responses. This study investigated how green chromide (GC), a cichlid native to the Indian subcontinent, competes with the globally invasive tilapia species (T, Oreochromis spp.) that has encroached upon its habitats. We staged dyadic feeding competitions between GC and T, and analysed aggression, feeding, and hiding behaviours of both the species and further contrasted them with intraspecific contests in GC. We varied developmental stages, residency status of opponents, and used different combinations of body sizes of competitors to test their effects on the outcome of dyadic contests. We hypothesized that competitors would adjust their strategies based on the context of the competition, and thus, we aimed to identify the factors that contributed to such decision-making. Our findings showed residency as the primary driver of competitive strategy, wherein residents had higher aggression and feeding when compared to intruders. The developmental stage had a significant effect on feeding, increasing from young to older stages, but body size contrasts did not contribute significantly towards the outcome of the contests. For the species effect, T emerged as a winner in most of the interspecific contests, exhibiting a significant amount of total aggression. However, GC showed distinct behavioural strategies when competing against T versus conspecifics, and exhibited higher levels of aggression and reduced hiding during intra- when compared to interspecific trials. Surprisingly, the feeding behaviour of GC was not significantly impacted in the presence of T, possibly because GC used hiding as a defence strategy, emphasizing the context-dependent, strategic thinking of the species. Overall, the variety of behavioural tactics exhibited by GC in staged competitive interactions showcases robust survival skills of the species, a key trait that may help maintain its fitness in challenging ecological habitats.

animal behavior and cognition↗

bioRxiv2026

Empirical Bayes Estimation of Sample-Specific Correlation Networks for Cross-Sectional and Longitudinal Omics Data

Sample-specific molecular networks, which capture how an individual's gene regulatory structure may deviate from the population as a whole, are important tools for understanding heterogeneity in health and disease. However, most existing methods either do not accommodate uncertainty quantification or cannot handle missing data, non-Gaussian modalities, and longitudinal structure common in modern multi-omic studies. For example, copy number alterations in cancer genomic studies are non-Gaussian and often only partially observed, and their regulatory effects on gene expression may vary substantially across patients, variation that a single, population-averaged network cannot capture. To address these challenges, we propose PRISM (Personalized Relational Inference via Sample-specific Modeling), an empirical Bayes framework for estimating sample-specific covariance matrices from cross-sectional and longitudinal multi-omic data. PRISM models each individual sample's covariance matrix as drawn from an inverse-Wishart prior whose parameters are estimated from the data and allowed to vary across subpopulations or evolve over time, yielding a closed-form posterior and edge-level uncertainty quantification, ensuring scalability to high-dimensional omics data. In simulation experiments, PRISM achieves point-estimate accuracy comparable to or better than existing methods, substantially improved uncertainty calibration under non-Gaussian marginals, and lower computational cost, while maintaining robust coverage under moderate missingness. We apply PRISM to a yeast cell-cycle time course dataset, recovering time-varying biologically meaningful regulatory relationships independently documented in literature, and to paired copy number and gene expression data from ovarian cancer patients, identifying copy-number-expression interactions associated with survival, including TFs HNF4G and PAX8 which have independent evidence of clinical relevance in this cancer.

bioinformatics↗

bioRxiv2026

An automated platform for spatial functional modeling and fingerprint analysis of tissue molecular landscapes

Spatial transcriptomics (ST) enables high-resolution molecular profiling while preserving tissue architecture, creating new opportunities to investigate how disease-associated pathways are organized within tissues. However, existing analytical approaches largely focus on individual pathways or cell types and do not provide a unified framework for modeling spatially varying pathway interactions across tissue sections and anatomical planes. We present an integrative framework, Spatial Fingerprints Analytics (SFinx), that introduces the concept of a spatial fingerprint for representing patterns of molecular signatures, and Spatial Functional Data Analysis for spatial regression and mapping of localized pathway activity and pathway-phenotype interactions in complex tissues. Applying SFinx to ST datasets on murine lupus nephritis, we reconstructed continuous spatial landscapes of pathway activity and disease-associated phenotypes across kidney sections. This approach identified anatomically restricted inflammatory domains characterized by coordinated activation of immune pathways and revealed substantial spatial heterogeneity in pathway crosstalk across renal compartments. Using generalized additive models with tensor-product splines, we quantified spatially varying associations between lupus nephritis and neutrophil activation pathways across tissue sections, uncovering regions with both positive and negative relationships that would be obscured by conventional bulk analyses. Multi-slice integration further demonstrated reproducible spatial interaction patterns while accounting for section-specific variability. Together, SFinx transforms mixed-spot transcriptomic measurements into interpretable spatial pathway landscapes and interaction maps, providing a general framework for identifying localized disease mechanisms. SFinx revealed previously unrecognized spatial organization of inflammatory signaling in lupus nephritis and presents a broadly applicable strategy for studying spatially coordinated biological processes in cancers, autoimmune and neurodegenerative diseases.

bioinformatics↗

bioRxiv2025

Fission or fusion: shoaling adaptations in green chromides (Etroplus suratensis) across multiple manipulations

Collective behaviour contributes towards increased fitness, however, in fission-fusion societies, the decision to participate in a group is based on cost-benefit ratio derived under a given condition. In todays world, this ratio dramatically changes due to increased challenges in degraded habitats, impacting behavioural decisions towards social grouping. In this paper, we used fish shoal as a unit of collective behaviour, and investigated variations in shoaling adaptations across a range of manipulations, mimicking challenges faced by the species under natural conditions. We used green chromides (Etroplus suratensis), a cichlid fish species, and characterised their shoaling behaviour under laboratory conditions for two group sizes, 4 and 8. We then examined the effects of different manipulations, for example, starvation and reduced space (both mimicking resource constrained conditions), and presence of hetero species including tilapia (Oreochromis sp., an alien species widespread within the habitats of E. suratensis) on their shoaling behaviour. Our results showed that E. suratensis formed shoals in both group sizes, 4 and 8. In subsequent analyses, we used group size 8 as a control and demonstrated that space reduction and starvation significantly impacted shoaling, reducing shoal splits and occurrences of solitary fish, while increasing incidences of single, cohesive shoals comprising all individuals. E. suratensis also formed mixed-species shoals with alien Oreochromis spp., but exhibited a large percentage (in absolute terms) of shoal splits. Overall, E. suratensis exhibited plasticity in their shoaling behaviour, and increased fusion of shoals under challenging conditions, which was in contrast to showing more fission in presence of the alien hetero species.

animal behavior and cognition↗

bioRxiv2024

Understanding feeding competition under laboratory conditions: Rohu (Labeo rohita) versus Amazon sailfin catfish (Pterygoplichthys spp.)

Competitive interactions between species is widely prevalent within the animal world. In this manuscript, we attempted to understand feeding competitions between the Amazon sailfin catfish, an invasive species introduced globally, and rohu, a keystone species native to several countries within southeast Asia. We used two different size classes of each species, large-size having total length (TL, from snout tip to caudal fin) of 15-20 cm and fingerling having TL <6 cm, and feeding duration was used as a proxy to understand competition. Our results demonstrated that feeding durations of large-size rohu were either similar or significantly (P<0.05) higher in presence of catfish when compared to trials in presence of conspecifics, indicating that large-size rohu is not a weak competitor. However, feeding durations of fingerling rohu was significantly (P<0.05) reduced in presence of both large-size and fingerling catfish, when compared to trials in presence of conspecifics. Moreover, fingerling rohu also displayed freeze (alarm) behavior in presence of the catfish. Interestingly, presence of rohu had no significant (P>0.05) impact on feeding durations of catfish. Overall, the study demonstrated that invasive catfish may behaviorally outcompete fingerling rohu, thus, threatening the sustenance of a species that is native to several freshwaters around the globe.

ecology↗

bioRxiv2023

Ecological assessment of the Amazon sailfin catfish (Pterygoplichthys species) within the Indian freshwaters: a mesocosm-based approach

Amazon sailfin catfish is relatively a recent invader to the open waters of India, and studies on ecological assessment of the species within the Indian freshwaters are lacking. In the present study, to assess the ecological impact of catfish, we established mesocosms mimicking the Indian freshwaters within natural ponds of eastern India using three species of native fish, rohu, catla and mrigal, and for two size classes, small (10-20 cm length) and large (20-30 cm length) native fishes. Mesocosms were maintained with (test) and without the catfish (control), and length and weight of native fish, zooplankton abundance, and several hydrological and soil parameters were measured at a monthly interval for a period of 120-days. The catfish had a significant (P<0.05) negative impact on growth of small-size rohu only. However, we found no significant (P>0.05) differences in abiotic parameters and zooplankton abundance between control and test ponds for the small-size class. We speculate that reduced growth of rohu could be due to competition from catfish in the context of feeding, and not due to modification of abiotic environment. Thus, we emphasize upon the need for behavioral studies to further assess the impact of the catfish.

ecology↗

bioRxiv2022

Genomic and ecologic characteristics of the airway microbial-mucosal complex

SO_SCPLOWUMMARYC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWPARAGRAPHC_SCPLOWLung diseases due to infection and dysbiosis affect hundreds of millions of people world-wide1-4. Microbial communities at the airway mucosal barrier are conserved and highly ordered5, reflecting symbiosis and co-evolution with human host factors6. Freed of selection to digest nutrients for the host, the airway microbiome underpins cognate management of mucosal immunity and pathogen resistance. We show here the results of the first systematic culture and whole-genome sequencing of the principal airway bacterial species, identifying abundant novel organisms within the genera Streptococcus, Pauljensenia, Neisseria and Gemella. Bacterial genomes were enriched for genes encoding antimicrobial synthesis, adhesion and biofilm formation, immune modulation, iron utilisation, nitrous oxide (NO) metabolism and sphingolipid signalling. RNA-targeting CRISPR elements in some taxa suggest the potential to prevent or treat specific viral infections. Homologues of human RO60 present in Neisseria spp. provide a possible respiratory primer for autoimmunity in systemic lupus erythematosus (SLE) and Sjogren syndrome. We interpret the structure and biogeography of airway microbial communities from clinical surveys in the context of whole-genome content, identifying features of airway dysbiosis that may presage breakdown of homeostasis during acute attacks of asthma and chronic obstructive pulmonary disease (COPD). We match the gene content of isolates to human transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways that can sustain host interactions with the microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosal immunity in lung diseases of global significance.

microbiology↗

bioRxiv2021

Effects of active and passive enrichment regimes on fecal glucocorticoid metabolite levels in captive Indian leopards (Panthera pardus fusca)

Environmental enrichment improves health and wellbeing of zoo animals. To test this hypothesis, we used Indian leopards, one of the popular zoo animals, as a model system to understand effects of active (interacting) and passive (noninteracting) enrichment elements on stress hormone levels of captive individuals. We included three enrichment categories, category A (having both active: large size cage, and passive: controlled temperature, playback of forest sounds and sound proof glasses to filter visitors noise, enrichment elements), category B (active enrichment type I, small size cage with air coolers), and category C (active enrichment type II, medium size cage without air coolers) for the leopards (n=14) housed in two Indian zoos. We standardized a non-invasive method to measure fecal glucocorticoid metabolite (fGCM) levels in captive leopards. The standardized fGCM assay was further validated by analysing samples from free-ranging leopards, as well. The fGCM levels (Mean{+/-}SE) were 10.45{+/-}2.01 and 0.95{+/-}0.003g/g dry wt of feces in captive and free-ranging leopards, respectively. Our results demonstrated that fGCM levels of leopards in categories B and C were significantly (P<0.05) different from each other, thus, indicating cage size (an active enrichment element) as an important factor in influencing the physiology of the sampled animals. Overall, the findings of the study will contribute towards informing policies for management of the Indian leopards.

ecology↗

bioRxiv2017

BMP signalling is critical for maintaining homeostasis of hair follicles and intestine in adult mice

BMP signalling play critical roles during embryonic development, however, its roles have not been extensively studied in the maintenance of adult tissue homeostasis. In this study we have used temporal knock out of Bmp2 and Bmp4 to uncover the role of BMP signalling in adult mice. We observed rapid changes in the adult hair follicles and the intestine within two days of depleting BMP signalling, which demonstrates the critical and acute requirement of BMP signalling in maintaining homeostasis in these tissues. In addition, our study demonstrates that while BMP signalling is required for maintenance of quiescence in telogen hair follicles, it is needed for survival and proliferation in late anagen hair follicles. Our study also reveals differential requirement of BMP signalling in differentiation of distinct intestinal cell types. In addition, Loss of BMP signalling rapidly promotes early neoplastic transformations in mouse intestine.

developmental biology↗