Biology subjects

Dubey, R.

Publications and source records attributed to Dubey, R..

8 recordsLinked to original sources

bioRxiv2025

Chronic Dietary Exposure to Methylparaben and Ethyl paraben Induces Developmental, Biochemical, and Behavioural Toxicity in Drosophila melanogaster

Parabens, particularly methylparaben (MP) and ethylparaben (EP), are extensively used preservatives in cosmetics, foods, and pharmaceuticals. Although considered safe at low concentrations, recent evidence questions their biological inertness under chronic exposure. This study evaluated the developmental, biochemical, and behavioral effects of continuous dietary MP and EP exposure in Drosophila melanogaster, an established in vivo model for toxicological screening. Flies were chronically exposed to MP (0.5-2%) or EP (0.5-1.5%) throughout development and adulthood. Developmental timing, lifespan, oxidative-stress markers (MDA, FRAP, total protein), and locomotor performance (negative geotaxis in adults, crawling in larvae) were quantified. Paraben exposure significantly delayed development ([~]15% increase in eclosion time), reduced median lifespan (up to 50% decrease at 2% MP), and elevated oxidative damage ({uparrow}MDA, {downarrow}FRAP) in a dose-dependent manner. Protein content declined more rapidly with age, suggesting oxidative degradation or proteolysis. Both adult climbing and larval crawling performances were impaired, linking biochemical stress to neuromuscular dysfunction. MP produced stronger oxidative and behavioral effects than EP. Feeding controls confirmed that observed deficits were not due to nutritional differences. Chronic MP and EP exposure induces systemic toxicity in D. melanogaster, integrating endocrine disruption and redox imbalance as plausible mechanisms. Given conserved stress and hormonal pathways, these findings reinforce the need to re-evaluate low-dose paraben safety limits and highlight Drosophila as a rapid, ethically viable platform for screening environmental preservatives and safer substitutes.

neuroscience↗

bioRxiv2025

Very long chain fatty acids drive 1-deoxy-Sphingolipid toxicity

1-deoxy-sphingolipids (1-deoxySLs) are atypical sphingolipids synthesized by the serine palmitoyltransferase (SPT) when L-alanine is used instead of its canonical substrate L-serine. Increased 1-deoxySLs are associated with sensory neuropathies such as Hereditary Sensory and Autonomic Neuropathy type 1 (HSAN1) and diabetic polyneuropathy (DPN). Despite their known cellular, mitochondrial, and neurotoxic effects, the mechanisms underlying their toxicity remain poorly understood. Using a CRISPR interference (CRISPRi) screening approach, we identified CERS2, ELOVL1, ACACA, HSD17B12, and PTPLB as key mediators of 1-deoxySL-induced toxicity. All genes are integral to the biosynthesis of very long-chain (VLC) fatty acids and VLC-ceramides. We validated these findings through genetic knockdown experiments, cytotoxicity assays, and stable isotope-resolved lipidomics via LC-MS/MS. Pharmacological inhibition of ELOVL1 using a preclinical tested compound alleviated the cellular, mitochondrial, and neuronal toxicity induced by 1-deoxySLs. Supplementation experiments combining 1-deoxySLs with various VLC fatty acids revealed that 1-deoxyDHceramide conjugated to nervonic acid (m18:0/24:1) is the principal toxic specie. Further mechanistic studies showed that m18:0/24:1 induces apoptosis through the mitochondrial permeability transition pore (mPTP) formation. Inhibition of BAX or blocking mPTP formation with cyclosporin A effectively prevented toxicity. In conclusion, our findings demonstrate that 1-deoxyDHCeramides conjugated to nervonic acid are the primary mediators of 1-deoxySL toxicity, acting through mitochondrial dysfunction and BAX-dependent apoptosis.

biochemistry↗

bioRxiv2024

Substrate-directed control of N-glycosylation in the endoplasmic reticulum calibrates signal reception at the cell-surface

One-fifth of human proteins are N-glycosylated in the endoplasmic reticulum (ER) by two oligosaccharyltransferases, OST-A and OST-B. Contrary to the prevailing view of N-glycosylation as a housekeeping function, we identified an ER pathway that modulates the activity of OST-A. Genetic analyses linked OST-A to HSP90B1, an ER chaperone for membrane receptors, and CCCD134, an ER protein we identify as the first specificity factor for N-glycosylation. During its translocation into the ER, a N-terminal peptide in HSP90B1 functions as a pseudosubstrate inhibitor of OST-A and templates the assembly of specialized ER translocon complexes containing CCDC134. Unexpectedly, OST-A functions as a scaffold rather than an enzyme in this context, stabilizing HSP90B1 by preventing its hyperglycosylation and degradation. Disruption of this pathway impairs WNT signaling at the cell surface and causes the bone developmental disorder Osteogenesis Imperfecta. Thus, N-glycosylation can be regulated by ER factors to control cell-surface receptor signaling and tissue development. One-Sentence SummaryN-glycosylation of asparagine residues on proteins can be regulated by specificity factors in the endoplasmic reticulum to control cell-surface signaling and tissue development.

cell biology↗

bioRxiv2024

Adapting to loss: A normative account of grief

Grief is a reaction to loss that is observed across human cultures and even in other species. While the particular expressions of grief vary significantly, universal aspects include experiences of emotional pain and frequent remembering of what was lost. Despite its prevalence, and its obvious nature, considering grief from a normative perspective is puzzling: Why do we grieve? Why is it painful? And why is it sometimes prolonged enough to be clinically impairing? Using the framework of reinforcement learning with memory replay, we offer answers to these questions and suggest, counter-intuitively, that grief may have normative value with respect to reward maximization.

neuroscience↗

bioRxiv2022

Having "multiple selves" helps learning agents explore and adapt in complex changing worlds

Satisfying a variety of conflicting needs in a changing environment is a fundamental challenge for any adaptive agent. Here, we show that designing an agent in a modular fashion as a collection of subagents, each dedicated to a separate need, powerfully enhanced the agents capacity to satisfy its overall needs. We used the formalism of deep reinforcement learning to investigate a biologically relevant multi-objective task: continually maintaining homeostasis of a set of physiologic variables. We then conducted simulations in a variety of environments and compared how modular agents performed relative to standard monolithic agents (i.e., agents that aimed to satisfy all needs in an integrated manner using a single aggregate measure of success). Simulations revealed that modular agents: a) exhibited a form of exploration that was intrinsic and emergent rather than extrinsically imposed; b) were robust to changes in non-stationary environments, and c) scaled gracefully in their ability to maintain home-ostasis as the number of conflicting objectives increased. Supporting analysis suggested that the robustness to changing environments and increasing numbers of needs were due to intrinsic exploration and efficiency of representation afforded by the modular architecture. These results suggest that the normative principles by which agents have adapted to complex changing environments may also explain why humans have long been described as consisting of multiple selves. Significance StatementAdaptive agents must continually satisfy a range of distinct and possibly conflicting needs. In most models of learning, a monolithic agent tries to maximize one value that measures how well it balances its needs. However, this task is difficult when the world is changing and needs are many. Here, we considered an agent as a collection of modules each dedicated to a particular need and competing for control of action. Compared to the standard monolithic approach, modular agents were much better at maintaining homeostasis of a set of internal variables in simulated environments, both static and changing. These results suggest that having multiple selves may represent an evolved solution to the universal problem of balancing multiple needs in changing environments.

neuroscience↗

bioRxiv2020

Glibenclamide and Metformin Increases the Expression of Human Bile Salt Export Pump ABCB11

BackgroundBile Salt Export Pump (BSEP/ABCB11) is important in the maintenance of the enterohepatic circulation of bile acids and drugs. Drugs such as rifampicin, glibenclamide inhibit BSEP. Progressive Familial Intrahepatic Cholestasis Type-2, a lethal pediatric disease, some forms of intrahepatic cholestasis of pregnancy, and drug-induced cholestasis are associated with BSEP dysfunction. MethodsWe started with a bioinformatic approach to identify the relationship between ABCB11 and other proteins, microRNAs, and drugs. Microarray data set of the liver samples from ABCB11 knockout mice was analyzed by GEO2R tool. Differentially expressed gene pathway enrichment analysis was done by ClueGo v2.5.5 app from Cytoscape. Protein-protein interaction network was constructed by STRING application in Cytoscape. Networks were analyzed using the Cytoscape software v3.7.1. CyTargetLinker v4.1.0 was used to screen the transcription factors, microRNAs and drugs. Predicted drugs were validated on human liver cell line, HepG2. BSEP expression was quantified by Real Time PCR and Western Blot. ResultsABCB11 knockout in mice was associated with a predominant upregulation and downregulation of genes associated with cellular component movement and sterol metabolism respectively. We further identified the hub genes in the network. Genes related to immune activity, cell signaling and fatty acid metabolism were dysregulated. We further identified drugs (glibenclamide and ATP) and a total of 14 microRNAs targeting the gene. Western Blot and Real Time PCR analysis confirmed the upregulation of BSEP on the treatment of HepG2 cells with glibenclamide, ATP, and metformin. ConclusionThe differential expression of cell signaling genes and those related to immune activity in ABCB11 KO animals may be secondary to cell injury. We have found glibenclamide, ATP, and metformin upregulates BSEP. The mechanisms involved and the clinical relevance of these findings need to be investigated.

molecular biology↗

bioRxiv2018

Advances in Gene Ontology Utilization Improve Statistical Power of Annotation Enrichment

Gene-annotation enrichment is a common method for utilizing ontology-based annotations in these gene and gene-product centric knowledgebases. Effective utilization of these annotations requires inferring semantic linkages by tracing paths through the ontology through edges in the ontological graph, referred to as relations. However, some relations are semantically problematic with respect to scope, necessitating their omission lest erroneous term mappings occur. To address these issues, we present GOcats, a novel tool that organizes the Gene Ontology (GO) into subgraphs representing user-defined concepts, while ensuring that all appropriate relations are congruent with respect to scoping semantics. Here, we demonstrate the improvements in annotation enrichment by re-interpreting edges that would otherwise be omitted by traditional ancestor path-tracing methods.\n\nWe demonstrate that GOcats unique handling of relations improves enrichment over conventional methods in the analysis of two different gene-expression datasets: a breast cancer microarray dataset and several horse cartilage development RNAseq datasets. With the breast cancer microarray dataset, we observed significant improvement (one-sided binomial test p-value=1.86E-25) in 182 of 217 significantly enriched GO terms identified from the conventional path traversal method when GOcats path traversal was used. We also found new significantly enriched terms using GOcats, whose biological relevancy has been experimentally demonstrated elsewhere. Likewise, on the horse RNAseq datasets, we observed a significant improvement in GO term enrichment when using GOcats path traversal: one-sided binomial test p-values range from 1.32E-03 to 2.58E-44.

systems biology↗

bioRxiv2017

Two phosphoglucomutase paralogs regulate triggered secretion of the Toxoplasma micronemes

Parafusin is a phosphoglucomutase (PGM) paralog that acts as a signaling scaffold protein in calcium mediated exocytosis across many eukaryotes. In Toxoplasma gondii the parafusin related protein 1 (PRP1) has been associated in indirect and heterologous studies with the regulated exocytosis of the micronemes, which are required for successful host cell invasion and egress. Here we directly assessed the role of PRP1 by deleting the gene from the parasite. We observed a specific defect in microneme secretion in response to high Ca2+ fluxes, but not to phosphatidic acid fluxes controlling microneme release. We observed no defect in constitutive microneme secretion which was sufficient to support completion of the lytic cycle. Furthermore, deletion of the other PGM in Toxoplasma, PGM2, as well as the double PRP1/PGM2 deletion resulted in a similar phenotype. This suggests a functional interaction between these two genes. Strikingly, tachyzoites without both paralogs are completely viable in vitro and during acute mice infections. This indicates that PGM activity is neither required for glycolysis. In conclusion, the PRP1-PGM2 pair is required for a burst in microneme secretion upon high Ca2+ fluxes, but this burst is not essential to complete the lytic cycle of the parasite.\n\nPlain Language SummaryCalcium mediated control of microneme secretion is essential for host cell invasion and egress of Toxoplasma gondii. Here it is shown that the two phosphoglucomutases in Toxoplasma both function in the translation of a spike in calcium into a burst in microneme secretion.

microbiology↗