Biology subjects

Mukherjee, M.

Publications and source records attributed to Mukherjee, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Differential Impact of Isoflurane and Propofol on Apoptotic Regulation of Helper T cells

BackgroundAnesthetic agents administered during surgery are one of the key perioperative factors affecting immune modulation in cancer patients. This comparative study elucidated the mechanisms by which the volatile anesthetic, isoflurane and the intravenous anesthetic, propofol impacted apoptosis signaling in CD4+ helper T (Th) cells. MethodsFlow cytometry was used to analyze apoptosis, mitochondrial function and reactive oxygen species (ROS) generation, while Western blotting, ELISA and RT-qPCR were employed to study protein/gene expression in sorted CD4{square} Th cells from perioperative breast cancer female patients (anesthetized with isoflurane or propofol, n=15 per group) and Jurkat T cells. ResultsPatient-derived CD4{square} Th cells and Jurkat T cells exhibited that isoflurane at clinically relevant concentrations triggered apoptosis through mitochondrial depolarization, ROS generation, DNA damage, and activation of caspase-3/7. Specific use of caspase-3/7 inhibitor, Z-DEVD-FMK and antioxidant N-acetyl cysteine rescued isoflurane-induced apoptosis. Further, isoflurane relative to propofol, activated p38 mitogen-activated protein kinase (MAPK), and use of p38 inhibitor, SB203580 suppressed isoflurane-induced apoptosis. Collectively, these findings validated the involvement of the ROS-p38-caspase-3/7 axis in isoflurane-associated apoptosis signaling. On the other hand, propofol conserved mitochondrial integrity, reduced oxidative stress, and maintained higher proliferative capacity. Interestingly, isoflurane-associated apoptosis was transient, with postoperative recovery in patients and similar rescue from apoptosis was evident in Jurkat T cells within 24-48 h of drug removal. ConclusionsBy integrating analyses of patient-derived CD4+ Th cells with mechanistic validations in Jurkat T cells, this study identified the ROS-p38-caspase-3/7 signaling axis and the reversible nature of isoflurane-induced apoptosis.

cancer biology↗

bioRxiv2026

Multicellular Programs Associated with Right Ventricular Adaptation in Pulmonary Arterial Hypertension

BackgroundRight ventricular (RV) adaptation determines outcomes in pulmonary arterial hypertension (PAH), yet multicellular molecular programs associated with adaptive versus maladaptive RV remodeling in living humans remain incompletely defined. MethodsWe collected 32 human RV tissue biopsies from patients with idiopathic PAH, systemic sclerosis-associated PAH (SSc-PAH), systemic sclerosis without pulmonary hypertension, with 24 nonfailing donor RVs serving as controls. We performed single-nucleus RNA sequencing and integrated cell-type specific transcriptional programs with contemporaneously obtained multi-beat pressure-volume loop measurements of RV contractility (Ees, end-systolic elastance) and RV-pulmonary arterial coupling (the ratio of Ees to Ea, the effective arterial load). SSc modification of PAH-associated biology was assessed using interaction terms. Bulk RV proteomic pathway enrichment was performed to assess an orthogonal molecular layer, and exploratory cell-cell communication analyses alongside independent spatial transcriptomic analyses were performed to contextualize key findings. ResultsPAH was associated with broad depletion of biosynthetic, trafficking, and mitochondrial programs across cell types. SSc modified the magnitude of many PAH-associated transcriptional programs while largely preserving pathway directionality. Significant multicellular pathway enrichments were associated with RV-pulmonary arterial coupling. Joint analysis of Ees, Ea, and Ees/Ea identified biologic programs associated with different RV responses to varying loading conditions. Preserved coupling was characterized by enriched extracellular matrix, laminin-integrin, receptor tyrosine kinase, mitochondrial, and translational programs involving fibroblast, endothelial, endocardial, and cardiomyocyte compartments. Cell- cell communication analyses predicted coordinated stromal-vascular signaling networks involving laminin-integrin and endothelial-to-mural signaling in preserved coupling. Proteomic and spatial analyses supported recurrent multicellular themes. ConclusionsRV adaptation in PAH is associated with distinct, coordinated multicellular programs that vary with load and contractile response. RV-PA coupling in PAH is associated with multicellular remodeling that extends beyond cardiomyocytes and reflects organized vascular-stromal support architecture. These findings identify extracellular matrix, laminin- integrin signaling, mitochondrial, and translational programs as associated with adaptive RV remodeling in PAH. Clinical PerspectiveO_ST_ABSWhat is new?C_ST_ABSO_LICell type-resolved molecular profiling of living human RV tissue identifies PAH-associated depletion of biosynthetic, trafficking, mitochondrial, and repair-associated programs across multiple cardiac cell types. C_LIO_LIIntegration with contemporaneously obtained pressure-volume loop physiology demonstrates that preserved RV-pulmonary arterial coupling under lower load was associated predominantly with cardiomyocyte mitochondrial and metabolic competency, whereas preserved coupling under higher load was associated with extracellular matrix remodeling and vascular-stromal signaling. C_LIO_LIProteomic, cell-cell communication, and spatial analyses provided orthogonal support for coordinated extracellular matrix and vascular-stromal programs associated with preserved RV-pulmonary arterial coupling. C_LI What are the clinical implications?O_LIThese findings shift the biology of RV adaptation from a predominantly cardiomyocyte- centered model toward a multicellular tissue model in which metabolic, matrix, and vascular support programs vary according to loading conditions and contractile states. C_LIO_LIExtracellular matrix-integrin signaling, endothelial-mural communication, and mitochondrial competency represent candidate pathways for mechanistic investigation toward RV-directed therapies in PAH. C_LI

molecular biology↗

bioRxiv2026

Metabolomic Network Analysis Reveals Reorganization of Lipid and Steroid Programs Linked to Right Ventricular-Pulmonary Vascular Function in Pulmonary Hypertension

BackgroundPulmonary arterial hypertension (PAH) is characterized by circulating metabolic alterations, but whether these reflect disease-specific metabolic programs or reorganization of normal metabolic architecture, and how they relate to right ventricular-pulmonary vascular function (RV-PV), remains unclear. We hypothesized that the PAH metabolome is organized into biologically coherent, co-regulated metabolic modules whose relationships to RV-PV function would provide insight into known and novel metabolic pathways. MethodsWe applied weighted gene co-expression network analysis (WGCNA) to untargeted metabolomic data from 412 PAH patients enrolled in the multicenter PVDOMICS study. Module preservation analysis was performed in 85 healthy controls, with external replication in an independent single-center pulmonary hypertension cohort of 89 patients. ResultsWGCNA identified 16 distinct metabolic modules organized around biologically coherent programs. A coherent fatty acid axis, spanning substrate pools, {beta}-oxidation intermediates, and conjugated fatty acid disposal products, formed a central organizing structure, with downstream fatty acid oxidation modules strongly associated with adverse hemodynamics and worse RV-pulmonary artery (PA) coupling. Acylcholine-enriched and 5-reduced androgen metabolite modules were associated with favorable hemodynamic indices. Module architecture was largely preserved in healthy controls, with subtle disease-associated modular reorganization, rather than emergence of novel modules, observed in PAH. Core modules were recovered in the replication cohort with conserved hub metabolites. ConclusionsThese findings establish a systems-level framework demonstrating that PAH involves structured intensification and reorganization of interconnected metabolic programs associated with favorable and adverse RV-PV phenotypes. This work provides new insight into the metabolic architecture underlying PAH and identifies coordinated metabolic pathways linked to pulmonary vascular and right ventricular function.

physiology↗

bioRxiv2025

CircNFATc3 promotes Fetal Hemoglobin induction by regulating let-7b/GATA2 axis

Reactivation of developmentally suppressed fetal hemoglobin (HbF) holds therapeutic promise. However, the post-transcriptional control of regulators that orchestrate {gamma}-globin (HBG1/2) expression is still elusive. This study aims to elucidate the highly understudied role of circular RNA (circRNA), circNFATc3, as post-transcriptional {gamma}-globin regulator. This study evaluates the circNFATc3/let-7b/GATA2 axis and its relationship with HbF induction through computational and experimental molecular and cellular approaches, including gain and loss-of-function studies. These evaluations have revealed that competitive splicing of circNFATc3, at the expense of its linear transcript, sequesters let-7b miRNA, thereby reactivating GATA2-mediated HbF expression. Moreover, transcriptomic profiling of circNFATc3-overexpressed erythroid cells showed that its role is not only restricted to HbF induction but it may play a broader role in erythropoiesis, adding further complexity to the role of this circular transcript. Therefore, our study demonstrates a pivotal role of circNFATc3 as an HbF inducer and places this circRNA as a promising modifier in erythroid transcription programs, opening avenues for novel therapeutic strategies in {beta}-thalassemia.

molecular biology↗

bioRxiv2025

Beyond Temperature: Environmental Filtering and Functional Shifts in Desert Bird Communities Under Climate Change

Deserts present unique opportunities for understanding biodiversity under climate change, yet global-scale assessments remain rare. Birds serve as sensitive ecological indicators of ecosystem health and biodiversity dynamics. In this study, leveraging crowdsourced bird occurrence records (GBIF) and multi-decadal hydro-meteorological datasets (ERA5, GLEAM), and vegetation data (AVHRR), we show how environmental filtering and functional shifts in avian assemblages drive divergent spatial and temporal species richness patterns across ten major deserts. Noteworthy, responses to warming are distinct, wherein temperature alone cannot universally predict community dynamics. Climatic determinants such as precipitation, soil moisture, and NDVI shaped by greening and browning trends, play region-specific roles. Analyses reveal pronounced guild turnover, with notable declines in top avian predators and complex shifts in omnivores and aquatic predators, exposing ecosystem-level vulnerabilities and altered resilience. These findings underscore the need for a paradigm shift from one-dimensional models to integrative, trait-based approaches to conserve desert biodiversity and function under climate change.

ecology↗

bioRxiv2025

SEASONAL PM2.5 DIFFERENTIALLY REGULATES JAK2/STAT3 SIGNALING IN RURAL AND URBAN COHORTS

Ambient particulate matter (PM2.5) is a major environmental carcinogen linked to lung cancer, yet its molecular insights on asymptomatic non-smokers remains unclear. This study examined the effect of seasonal fluctuations of PM2.5 on oxidative stress and pro-oncogenic signaling in rural (RU) and urban (UR) cohorts from West Bengal, India. Environmental monitoring revealed higher PM2.5 and associated benzo[]pyrene in UR, during winter, induced oxidative stress (elevated ROS, 8-OHdG), reduced antioxidants (SOD, catalase, GPx), and promoted airway inflammation. Transcriptomic and bioinformatic analyses identified activation of IL-6/EGFR-driven JAK2/STAT3 signaling and its crosstalk with Ras/Raf/MAPK, leading to increased expression of downstream effectors (BCL-2, MCL-1, c-MYC, cyclin D1) and repression of tumor suppressors (BAX, p21). Notably, downregulation of JAK/STAT inhibitors PIAS2 and SOCS2 suggested persistent activation of oncogenic signaling. Linear mixed-effects models linked winter PM2.5 surges to oxidative stress, inflammation, and altered JAK2/STAT3 signaling, while regression models showed stronger responses in UR. Risk modeling predicted significantly higher lung cancer mortality in UR, underscoring the role of seasonal PM2.5 surges in JAK2/STAT3-driven carcinogenic susceptibility and the urgent need for targeted interventions.

cancer biology↗

bioRxiv2025

UCA1 lncRNA represses γ-globin expression by sequestering miR-148b, a key post-transcriptional regulator of BCL11A

Fetal hemoglobin (HbF; 2{gamma}2) reactivation is a promising strategy to ameliorate {beta}-hemoglobinopathies. However, limited understanding of {gamma}-globin (HBG1/2) regulation constrains development of therapeutic interventions. BCL11A, a key transcriptional repressor of {gamma}-globin, is central to HbF silencing during adult erythropoiesis. Here, we identify a new post-transcriptional regulatory mechanism involving the lncRNA-UCA1 and miR-148b that modulates BCL11A expression. Using UCA1 knockdown and overexpression strategies, combined with in vivo crosslinking and transcriptomic analyses, we demonstrate that UCA1 functions as a competing endogenous RNA (ceRNA), sequestering miR-148b and thereby attenuating its repressive effect on BCL11A. In the present study, we have elucidated the physiological significance of this interaction in adult erythroid cells, including CD34 HSPCs and HUDEP-2 cells, in which UCA1 depletion led to robust {gamma}-globin induction, a phenotype recapitulated by miR-148b overexpression. These findings uncover a previously unrecognized lncRNA-miRNA-mRNA regulatory axis and highlight the UCA1/miR-148b axis as a potential therapeutic target for HbF reactivation in {beta}-hemoglobinopathies.

genetics↗

bioRxiv2025

Distant Site Mutations in Clinical TEM Beta-Lactamase Variants Enhance Non-Covalent Binding to Ceftazidime: Insights from Spectroscopic and Biophysical Investigations.

{beta}-lactamases retain the central armamentarium against the {beta}-lactams, resulting in surge of antibiotic resistance, primarily due to the hydrolysis of the amide bond of the four-membered ring. This study aimed to investigate the binding interactions of ceftazidime (CAZ) to TEM {beta}- lactamase variants with distant site mutations isolated from clinical setting to explore the cause of their selection and dissemination due to indiscriminate use of {beta}-lactams. Absorbance and fluorescence spectroscopy along with biophysical experimentation indicated facilitated binding of CAZ to the active site of the mutants than the wild type. The CAZ-TEM {beta}-lactamase mutant interactions were predominantly hydrophobic compared to H-bonding and van der Waals forces in the CAZ-wild type complex. Additionally structural alteration to justify more rigid binding of CAZ to the mutants in contrast to the wild type enzyme was established in silico. Therefore, acquisition of distant site mutations with respect to the active site of the {beta}-lactamase variants that rendered conformational flexibility to accommodate CAZ was evidenced. This study provided an insight to the bioactive interaction of CAZ with TEM {beta}-lactamase variants that probably facilitated their selection from clinical settings in response to rampant usage of {beta}-lactams.

microbiology↗

bioRxiv2025

The gut microbiome shapes pharmacology and treatment outcomes for a key anti-inflammatory therapy

The human gut microbiome encodes a formidable metabolic repertoire that harvests nutrients from the diet, but these same pathways may also metabolize medications. Indeed, large screens have revealed extensive microbial metabolism of drugs in vitro, but the pharmacologic and clinical repercussions of microbiota-mediated metabolism in vivo remain to be discerned. As a proof-of-concept, we investigate how human gut microbes contribute to in vivo pharmacology and efficacy of a key anti-inflammatory drug, methotrexate (MTX). Specifically, we demonstrate that the gut microbiome shapes drug pharmacology in vivo in mice, both by directly metabolizing the drug and by inducing host pathways that promote drug metabolism. Moreover, interindividual variation in the human gut microbiome contributes to variation in pharmacokinetic (PK) profiles. When we quantified metabolites produced by microbes, we unexpectedly identified novel MTX metabolites, one of which, p-methylaminobenzoyl-L-glutamic acid (pMABG), was a major byproduct of microbial metabolism both in vitro and in vivo. Further, we find that a large proportion of patient-associated microbes are capable of metabolizing MTX. Finally, we show that microbial metabolism of MTX is linked to PK profiles and disease outcomes in a mouse model of inflammatory arthritis. Taken together, these findings provide evidence that the human gut microbiome causally contributes to drug pharmacology in vivo for a key anti-inflammatory drug through known and novel mechanisms. Our studies provide a framework for elucidating the clinical relevance of drug microbial metabolism in the context of treatment response. These results are a first step towards understanding and manipulating the human gut microbiome in the treatment of autoimmunity and the advancement of precision medicine for millions of patients taking MTX for immune or inflammatory conditions. HighlightsO_LIThe gut microbiome impacts methotrexate (MTX) pharmacology in mice C_LIO_LIThe human gut microbiome contributes to interindividual variation in MTX pharmacology C_LIO_LIHuman gut microbes produce novel MTX metabolites, pMABG and 6-MPDA C_LIO_LIMicrobial metabolism of MTX is linked to treatment outcomes C_LI

pharmacology and toxicology↗

bioRxiv2024

Adaptive Nesting Strategies of Dusky Crag Martins in desert ecoregions: Implications for Conservation and Bioinspired Innovations

Understanding the adaptive strategies of species in extreme environments is crucial for biodiversity conservation. This study is the first to explore the nesting behavior of the Dusky Crag Martin Ptyonoprogne concolor in the Thar Desert, Rajasthan. It examined the birds site selection, nesting frequency, and construction methods. Soil samples from nest sites and source locations were analyzed to identify structural and elemental properties. The bird adopts several strategies, such as aligning its nesting period with the monsoon, reusing nests, and utilizing both macro and micro-level additive construction techniques. Detailed analysis revealed a preference for cohesionless sand with low moisture and higher Soil Organic Carbon (SOC) content. The bird strategically alternates light and dark soil layers in its nest. Structural and elemental analyses using optical microscopy and Scanning Electron Microscopy (SEM), and X-ray Fluorescence (XRF), shows the light layers is rich in calcium oxide and fibrous material, and dark layers containing higher iron oxide and partially decomposed litter from Prosopis cineraria. The study concludes that alternating calcium-rich and iron-rich layers enhances energy efficiency, structural integrity, and pathogen resistance in nest construction. his behavior underscores the evolutionary adaptations of P. concolor to the extreme desert environment. These findings highlight the importance of conserving desert habitats and provide bio-inspired insights for sustainable building and agricultural practices in arid regions.

ecology↗

bioRxiv2024

Avian Atlas: Unveiling the Diversity Divide in Desert Realms between Tropics

Understanding diversity gradients across global deserts remains a significant challenge. The unique characteristics of deserts complicate conservation efforts for these biomes, which are highly affected by climate change. Here, we conduct a comprehensive study of ecological traits to determine the behavior and uniqueness of avian communities in ten major tropical deserts, using crowd-sourced avian diversity data from GBIF.org as a key analytical tool. Our results reveal significant variations in bird diversity among tropical deserts, with heightened diversity in deserts near the Tropic of Cancer (TCan) compared to those near the Tropic of Capricorn (TCap). The analysis of ecological traits indicates that, unlike TCap deserts, TCan deserts have a higher prevalence of migratory species. This is facilitated by a broader niche breadth among sedentary bird species, which reduces niche competition and allows the influx of migratory invertivores. This study is the first to identify a differential avian diversity gradient within tropical deserts, demonstrating that avian species richness in deserts is more closely linked to tropical locations than to realm classifications. Recognizing the vulnerability of TCap deserts and the diverse trophic roles played by avian species, our analysis underscores the need for targeted conservation strategies. Protecting the unique avian diversity in TCan deserts and mitigating extinction risks in TCap deserts are essential steps to ensure the resilience and sustainability of these critical ecosystems.

ecology↗

bioRxiv2024

Microbiota-dependent in vivo biotransformation, accumulation, and excretion of arsenic from arsenobetaine-rich diet

Arsenic (As) is a naturally occurring metalloid that is ubiquitous in the environment. Various chemical forms of As, collectively referred to as "As species", find their way into the food chain, impacting the health of millions globally. Many of these As species are products of bacterial enzymatic transformations in different environments. Yet, the in vivo gut microbial transformation of As and its consequences in the host, especially for less toxic As species like arsenobetaine (AB), remain elusive. Current regulatory assessments regard AB-rich foods, including various seafoods, as safe due to low toxicity and rapid unmodified urinary excretion of the ingested AB. This notion has been challenged by reports of AB metabolism by intestinal bacteria in vitro and by more recent evidence of in vivo AB metabolism in mice. However, these studies did not definitively establish the causal role of intestinal bacteria in AB transformation in vivo. To address this, we employed gnotobiology that allowed us to compare the biotransformation of As from a naturally AB-rich rodent diet in isogenic mice that were either completely germ-free, or colonized with gut microbiota of varying microbial diversity. Additionally, we examined the body distribution, accumulation, and clearance of the ingested As in these mice. Our results confirm the in vivo metabolism of AB in the intestine under chronic dietary exposure. The transformation of ingested As was found to be dependent on the presence/absence and complexity of the gut microbiota. Notably, specific toxic As species were absent under germ-free condition. Furthermore, gut microbial colonization was linked to increased As accumulation in the intestinal lumen as well as systemically, along with delayed clearance from the body. These findings emphasize the mammalian gut microbiota as a critical factor in evaluating the safety of AB-accumulating seafoods.

pharmacology and toxicology↗

bioRxiv2024

Construction of ceRNA networks in endocrine therapy resistance model systems

BackgroundEndocrine therapy resistance (ETR) in breast cancer is achieved via multiple pathways including a decrease in ER, dysregulation of cell cycle genes, and/or mutations in ER/co-activators/co-repressors. We have reported earlier that high expression of Jumonji domaining containing protein 6 (JMJD6) induced ETR by depleting ER expression. In this study, 3 cellular models representing distinct ETR pathways; Tamoxifen resistant (TAMR), Long-term Estrogen deprived (LTEDI), JMJD6 overexpressing (JOE) cells, and parental MCF7 were subjected to RNA-sequencing, CNC, and ceRNA network analysis. We hypothesised that post-comparison RNA regulations that are common to all cell lines, will reveal actionable markers and targets. These will be shared by all patients with ET-resistant disease, independent of the initiating event. Results170 differentially expressed genes were found, of these, 73 maintained the same directionality in expression (ETR cassette genes). These genes segregated TCGA ER+ tumors into two groups, one intermixing with ER-tumors. Pathway-based curation of ETR genes identified 21 genes (7 up- and 14 down-regulated) that participated in multiple cancer hallmark pathways. Genes upregulated in ETR cells were less expressed in ER+ tumors at diagnosis when compared to normal breast samples but their higher expression indicated adverse survival outcomes. Next, these genes were used for CNC and ceRNA network construction and a triad FLT4:MIR503HG:miR-497/195/424 was discovered. The expression levels of miRNAs were predicted via network analysis and quantitative RT-PCR was used to validate the down regulation of miR-497/195/424 and upregulation of their targets, FLT4 and MIR503HG in ETR cells. ConclusionsWe show that total RNA-seq data can be successfully used to predict actionable miRNAs that achieve drug resistance. Re-expression of ETR genes such as FLT4 in tumor cells, that are less expressed at diagnosis, may be indicative of ETR onset. Finally, ETR may arise due to suppression of miR-424/497/195 leading to higher expression of FLT4 and MIR503HG. We posit that FLT4 may be a suitable target and RT-PCR analysis of this RNA triad could be developed as a detection strategy for ETR in ER+ breast cancer.

cancer biology↗

bioRxiv2024

Component specific responses of the microbiomes to common chemical stressors in the human food chain

Along a food chain, microbiomes occur in each component and often contribute to the functioning or the health of their host or environment. One Health emphasizes the connectivity of each components health. Chemical stress typically causes dysbiotic microbiomes, but it remains unclear whether chemical stressors consistently affect the microbiomes along food chain components. Here, we systematically challenged a model food chain, including water, sediments, soil, plants, and animals, with three chemical stresses consisting of arsenic (a toxic trace element), benzoxazinoids (an abundant bioactive plant metabolites), and terbuthylazine (an herbicide typically found along a human food chain). The analysis of 1,064 microbiome profiles for commonalities and differences in their stress responses indicated that chemical stressors decreased microbiome diversity in soil and animal, but not in the other microbiomes. In response to stress, all food chain communities strongly shifted in their composition, generally becoming compositionally more similar to each other. In addition, we observed stochastic effects in host-associated communities (plant, animal). Dysbiotic microbiomes were characterized by different sets of bacteria, which responded specifically to the three chemical stressors. Microbial co-occurrence patterns significantly shifted with either decreased (water, sediment, plant, animal) or increased (soil) network sparsity and numbers of keystone taxa following stress treatments. This suggested major re-distribution of the roles that specific taxa may have, with the community stability of plant and animal microbiomes being the most affected by chemical stresses. Overall, we observed stress- and component-specific responses to chemical stressors in microbiomes along the model food chain, which could have implications on food chain health.

microbiology↗

bioRxiv2024

Kidney collecting duct cell type composition is regulated by Notch signaling via modulation of mTORC1

The plasticity and diversity of cell types with specialized functions likely defines the capacity of multicellular organisms to adapt to physiologic stressors. The kidney collecting ducts contribute to water, electrolyte, and pH homeostasis and are composed of mature intermingled epithelial cell types that are susceptible to transdifferentiate. The conversion of kidney collecting duct principal cells to intercalated cells is actively inhibited by Notch signaling to ensure urine concentrating capability. Here we identify Hes1, a target of Notch signaling, allows for maintenance of functionally distinct epithelial cell types within the same microenvironment by regulating mechanistic target of rapamycin complex 1 (mTORC1) activity. Hes1 directly represses the expression of insulin receptor substrate 1 (Irs1), an upstream component of mTOR pathway and suppresses mTORC1 activity in principal cells. Genetic inactivation of tuberous sclerosis complex 2 (Tsc2) to increase mTORC1 activity in mature principal cells is sufficient to promote acquisition of intercalated cell properties, while inhibition of mTORC1 in adult kidney epithelia suppresses intercalated cell properties. Considering that mTORC1 integrates environmental cues, the linkage of functionally distinct epithelial cell types to mTORC1 activity levels likely allows for cell plasticity to be regulated by physiologic and metabolic signals and the ability to sense/transduce these signals.

developmental biology↗

bioRxiv2024

Plankton dynamics of Milicz Ponds: indicators ofsustainability and anthropogenic driven threats

Stawy Milickie (Milicz Ponds) is a natural reserve that has a great ecological importance as a Ramsar site and economic importance as one of the largest carp breeding centres in Europe. Continuous anthropogenic pressure on these large ecosystems can lead to a high disturbance on its natural ecology and sustainability. Phytoplankton, one of the most important indicators of any anthropogenic load, especially organic pollution have been studied in the present study. This is the first work ever from Milicz ponds, wherein the diversity, community structure and seasonal variability of phytoplankton with respect to changes in physicochemical parameters and trace metals have been studied. Periodic samples of water and phytoplankton were collected from four selected ponds of various sizes from October 2018 to September 2019. Of the four selected ponds one was unused for carp cultivation. The study reports the presence of 147 phytoplankton species in nine distinct taxonomic groups. The Genera based Algal pollution index indicated presence of organic pollution in both noncultured pond and carp-cultured pond. The heavy metals detected in the concentration order of Cd>Mn>Fe>Zn>Cu>Pb remained much higher than the safe limits of freshwater aquaculture ponds. The probable sources of these pollutants were identified as artificial feed used in the cultivation of carp and inundation from the river basin. This study emphasizes the urgent need for continuous qualitative and quantitative assessment and monitoring of water parameters, including plankton, in these ponds. This study highlights how the structure of microplankton communities, in conjunction with heavy metal analysis, serves as indicators of the spread of organic pollution in non-cultivated aquaculture environments. It strongly advocates for implementing sustainable measures to safeguard this vital ecosystem.

ecology↗

bioRxiv2024

Wastelands or Preferred-lands? Indicators for redefining Desert conservation

Desert ecosystems though crucial in shaping global climate, are often perceived to have limited function and are frequently designated as wastelands due to low biotic diversity and abundance. We explore the functional properties of desert through assessment of spatio-temporal variations of avian species richness and insect abundance of the relatively understudied Thar in Rajasthan. The study was conducted across four contrasting ecoregions (Western Thar (WT), Eastern Thar (ET), Transitional Zone (TZ), and Cultivated Zone (CZ) spanning 33 counties of Rajasthan. Monthly avian diversity were obtained from crowdsourced eBird data. Insect diversity and abundance accross the ecoregions were curated from the annual surveys of ZSI, India. The leads were corroborated with five years feeding behaviour observational data recorded from a representative site spanning 852 acres. There was a significant seasonal differences in bird species richness between the ecoregions with the most pronounced variations between summer and winter and CZ exhibiting the highest spatial variability followed by WT. WT also recorded the highest insect diversity and abundance, especially the orders Orthoptera, Hymenoptera, Coleoptera, Lepidotera and Diptera. The correlation matrix between bird and insect abundance and Kernel Density Estimation (KDE) plot indicated the relation between diverse dietary preferences and migratory patterns. These observations challenge the conventional notion that resource-limited environments harbour lesser biodiversity especially in arid environments. The dominance of insectivory among winter migrants aligns with the higher density of resident arthropods and emphasizes the pivotal role of insects as a food source during the migratory period. The adaptability of resident species to varied food sources, particularly arthropods, provides a means to strategically navigate during resource constraints. This study thus provides a unique framework to (a) redefine the functional importance of desert using migratory birds as prominent ecological indicators. (b) include an ecological criteria during policy formulation for biodiversity conservation. It also emphasizes reevaluation of deserts during designation of wastelands especially in the unique WT eco-regions when evolving developmental as well as ecological restoration strategies.

ecology↗

bioRxiv2023

NPZfc: An ecological relation based fish catch prediction model using Artificial Neural Network

Quantifying interactions of organisms of the various trophic levels is very important in understanding the dynamics of aquatic ecosystems. With regards to fish, as both ecologically and commercially important parts of an ecosystem, predicting their catch in relation to primary producers provides insight into sustainable management. The present paper describes a novel model NPZfc, for nutrients, phytoplankton, zooplankton and fishes, which can predict planktivorous fish catch. Unlike the existing models which deal with the interactions within the system through mathematical equilibrium, the proposed model uses artificial neural network (ANN) to automatically learn inter-dependencies between different related variables and predict the fish catch of a water body. The efficiency of the model was increased by refining the input variables. Here biomass of plankton species population (phyto-plankton and zooplankton) were specifically selected from feeding ecology studies of target fish species as input variable. The study of two of the commercially important fish species, Etroplus suratensis and Nematalosa nasus in Chilika lagoon showed that the model can predict with high accuracy from limited input data. The root mean square error (RMSE) is found to be very satisfactory, ranging from 3.53% to 11.5% for E. suratensis and from 1.63% to 2.22% for N. nasus. Higher accuracy and better predictive ability with a smaller dataset makes this ANN-based NPZfc model more conducive.

ecology↗