Biology subjects

Bagchi, D.

Publications and source records attributed to Bagchi, D..

8 recordsLinked to original sources

bioRxiv2025

Quenching of Chaos in externally driven metacommunities

Population dynamics of different species across food web models of diverse spatial scales have been extensively investigated over the past three decades. Chaotic fluctuations in species populations are generally associated with increased extinction risk due to frequent periods of low species density leading to cascading effects. The existence of a food web where the cohabiting species population oscillates chaotically has been largely attributed to chaos control or death of chaos, mediated either by internal mechanisms, such as the food web favoring parameter values that keep the species population out of the chaotic region, or external mechanisms like environmental forcing. Yet, this picture is not complete, as food webs do not exist in isolation, but are generally connected to each other through dispersal of species, forming a metacommunity. A metacommunity of food webs whose dynamics is that of chaotic attractors can only persist through control and particularly the the quenching of chaos. We claim that habitat heterogeneity in such a metacommunity fulfills this purpose. We address this question by analyzing the dynamics of a drive-response metacommunity composed of five chaotic food webs, each located in a distinct patch. Each patch contains an inherently chaotic tritrophic food web, with habitat heterogeneity present among patches. The first patch functions as the drive, exerting external influence on the dynamics of the remaining four response patches. Our results establish that in a drive-response metacommunity, strong influence from the drive quenches dynamical chaos in both drive and response patches, often leading to steady states. This phenomenon is observed in two distinct metacommunity network structures. The heterogeneity of the response systems (food web models) and the dissimilarity between drive and response systems are found to play significant roles in suppressing chaotic population dynamics. These findings strongly imply that the persistence of such inherently chaotic metacommunities may result from the quenching of chaos through the interplay of chaos, habitat heterogeneity, and to some degree network structure shaped by dispersal. Furthermore, we illustrate that these metacommunities are also susceptible to extinction due to dispersal-induced synchronization. Accordingly, this study also investigates dispersal-induced complete synchronization among the constituent patches.

ecology↗

bioRxiv2025

Asynchronous population dynamics induced by higher-order andnegative asymmetric ecological interactions

Phase synchronized population dynamics of various species constituting a complex ecosystem elevates the risk of their extinction due to both environmental stochasticity and simulateneous low density fluctuations. Therefore, an extremely vital approach to measure the extinction risk of an ecosystem as a whole is to quantify the phase synchrony among the species populations co-habiting and interacting with each other in an ecosystem. Generally, in models describing population dynamics of ecosystems, both trophic and non-trophic inter-species interactions are modelled as interactions between two species. This approach contradicts the fact with such a large number of species living in close proximity, more than two species must partake in the same interaction influencing the population dynamics of each other. To address this, higher-order interactions need to be incorporated in the models describing population dynamics of an ecosystem. Consequently, their effect on phase synchronization of populations also need to be investigated. In this study, we model a species-rich ecosystem as a complex phase oscillator network and examine the phase dynamics of the total population. Each node of this network represents a constituent species, modelled as a Sakugachi-Kuramoto phase oscillator coupled non-linearly to the other nodes through both first-order and higher-order inter-species interactions. These interactions can be both mutualistic (positive) and antagonistic (negative) in nature. Along with the higher-order interactions, we also incorporate inherent asymmetry among the nodes to account for habitat heterogeneity. Further, we investigate the effects of both higher-order coupling and asymmetry on the phase synchronization of the total population. Our findings demonstrate that higher-order interactions above a threshold amplitude enforces a transition from synchronous to asynchronous dynamics of the ecosystem. Further, we find that increase in the size and diversity of the ecosystem leads to an increase in the threshold value of higher order coupling required to reach asynchronous dynamics. We also demonstrate that this higher-order induced asynchrony is further promoted by high asymmetry among the individual nodes. Importantly, negative inter-species interactions, if existing to a high degree also induce asynchrony in the system. Moreover, the size of the network also plays a role in deciding the threshold value of higher order coupling required to induce asynchrony.

ecology↗

bioRxiv2025

Dispersal-induced persistence of chaotic ecosystems under extremeclimatic events

Ecosystems are strongly disrupted by large-scale natural disturbances called extreme events which can potentially lead to their local extinction. In this work, we study one of the most important examples of this, namely, a coastal ecosystem interacting with a tropical cyclone, one of the strongest extreme weather events. We show, that the ecosystem, while perfectly self-sustainable when unperturbed, nevertheless undergoes a reduction in habitat quality when impacted by the extreme event. We show that a certain degree of dispersal between the affected patch and a less affected patch leads to non-zero population density, whereas the population of an uncoupled but affected patch suffers extinction. We also demonstrate that dispersal between two equally affected coastal ecosystems, eventually leads to the extinction of their populations. We show that the critical degree of dispersal for the persistence of the ecosystems under the onslaught of extreme events increases with both damage-susceptibility of the ecosystem and ferocity of the extreme event. We also analyze the dynamical behavior of the affected coastal ecosystem under increasing dispersal.

ecology↗

bioRxiv2022

Supervised Machine Learning Enables Geospatial Microbial Provenance

The recent increase in publicly available metagenomic datasets with geospatial metadata has made it possible to determine location-specific, microbial fingerprints from around the world. Such fingerprints can be useful for comparing microbial niches for environmental research, as well as for applications within forensic science and public health. To determine the regional specificity for environmental metagenomes, we examined 4305 shotgun-sequenced samples from the MetaSUB Consortium dataset - the most extensive public collection of urban microbiomes, spanning 60 different cities, 30 countries, and 6 continents. We were able to identify city-specific microbial fingerprints using supervised machine learning (SML) on the taxonomic classifications, and we also compared the performance of ten SML classifiers. We then further evaluated the five algorithms with the highest accuracy, with the city and continental accuracy ranging from 85-89% to 90-94%, respectively. We then used these results to develop Cassandra, a random-forest-based classifier that identifies indicator species to aid in fingerprinting and can infer higher-order microbial interactions at each site. We further tested the Cassandra algorithm on the Tara Oceans dataset, the largest collection of marine-based microbial genomes, where it classified the oceanic sample locations with 83% accuracy. These results and code show the utility of SML methods and Cassandra to identify bioindicator species across both oceanic and urban environments, which can help guide ongoing efforts in biotracing, environmental monitoring, and microbial forensics (MF).

microbiology↗

bioRxiv2021

Metacommunity stability and persistence for predation turnoff in selective patches

Predation as an important trophic interaction of ecological communities controls the large-scale patterns of species distribution, population abundance and community structure. Numerous studies address that predation can mediate diversity and regulate the ecological community and food web stability through changes in the behaviour, morphology, development, and abundance of prey. Since predation has large effects on persistence and diversity, the local loss or removal of predation in a community can trigger a cascade of extinctions. In ecological theory, the effect of predation removal has been well studied in foodwebs, but it remains unclear in the case of a spatially distributed community connected by dispersal. In this study, the interaction between local and spatial processes is taken into account, we present how a predation turnoff in selective patches affects the stability and persistence of a metacommunity. Using a simple predator-prey metacommunity with a diffusive dispersal, we show the impact of predation on synchronized, asynchronized and source-sink dynamics. Our results reveal that predation turnoff in very few patches alters a perfectly synchronized oscillatory state into multicluster states consisting of various patterns. In a source-sink behaviour, predation turnoff in a source patch reduces the number of sink patches and changes the clusters. In general, predation turnoff in a finite number of patches increases the number of clusters through asynchronized (inhomogeneous) states, whereas predation turnoff in a larger number of patches can lead to the complete extinction of predators. Typically, there exists a critical number of patches below which the predation turnoff results in asynchronized states and above that predation turnoff leads to a synchronized state in prey population with complete extinction of predators. Further, our results identify the network configurations that exhibit a unique number of clusters. Moreover, prey density from the patches where predation is absent goes to a saturating state near the carrying capacity. Thus, this study stresses that predation turnoff in selective patches acts as a stabilizing mechanism that can promote metacommunity persistence.

ecology↗

bioRxiv2021

Knockout of murine Lyplal1 confers sex-specific protection against diet-induced obesity

Human genome-wide association studies found SNPs near LYPLAL1 that have sex-specific effects on fat distribution and metabolic traits. To determine whether altering LYPLAL1 affects obesity and metabolic disease we created and characterized a mouse knockout of Lyplal1. Here we show that CRISPR-Cas9 whole-body Lyplal1 knockout (KO) mice fed a high fat, high sucrose (HFHS) diet showed sex-specific differences in weight gain and fat accumulation. Female, not male, KO mice weighed less than WT mice, had reduced body fat percentage, white fat mass, and adipocyte diameter not accounted for by changes in metabolic rate. Female, but not male, KO mice had increased serum triglycerides, decreased aspartate, and alanine aminotransferase. Lyplal1 KO mice of both sexes have reduced liver triglycerides and steatosis. These diet-specific effects resemble the effects of SNPs near LYPLAL1 in humans, suggesting that LYPLAL1 has an evolutionary conserved sex-specific effect on adiposity. This murine model can be used to study this novel gene-by-sex-by-diet interaction to elucidate the metabolic effects of LYPLAL1 on human obesity.

biochemistry↗

bioRxiv2020

The molecular and metabolic program for adaptation of white adipocytesto cool physiologic temperatures

Although visceral adipocytes located within the bodys central core are maintained at ~37{degrees}C, adipocytes within bone marrow, subcutaneous, and dermal depots are found primarily within the peripheral shell, and generally exist at cooler temperatures. Responses of brown and beige/brite adipocytes to cold stress are well-studied; however, comparatively little is known about mechanisms by white adipocytes adapt to temperatures below 37{degrees}C. Here we report that adaptation of cultured adipocytes to 31{degrees}C, the temperature at which distal marrow adipose tissues and subcutaneous adipose tissues often reside, induces extensive changes in gene expression, increased anabolic and catabolic lipid metabolism, and elevated oxygen consumption with reduced reliance on glucose and preferential use of pyruvate, glutamine and fatty acids as energy sources. Cool temperatures up-regulate stearoyl-CoA desaturase-1 expression and monounsaturated lipid levels in cultured adipocytes and distal bone marrow adipose tissues, and stearoyl-CoA desaturase-1 activity is required for acquisition of maximal oxygen consumption at 31{degrees}C.

physiology↗

bioRxiv2020

The RNA binding protein hnRNP-U is required for physiological hypertrophy of skeletal muscle

Skeletal muscle has the remarkable ability to modulate its mass in response to physiological changes associated with nutritional input, functional utilization, systemic disease, and age. A decreased responsiveness to anabolic stimuli is thought to contribute significantly to the loss of skeletal muscle mass and strength associated with sarcopenia, however the molecular mechanisms precipitating this are unclear. The signal transduction pathways that control the relative balance between anabolic and catabolic processes are tightly regulated at the transcriptional and post-transcriptional levels. Alternative splicing produces multiple protein isoforms from a single gene in a cell-type-specific manner and in response to environmental cues. We show that sustained activation of Akt1 in Hnrnpu deficient mice leads to premature muscle wasting, in part, through impaired autophagy while providing mechanistic insights into the development of anabolic resistance.

cell biology↗