Biology subjects

Roy, S.

Publications and source records attributed to Roy, S..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Distinct mechanisms decommission redundant enhancers to facilitate phenotypic evolution

The evolutionary loss of morphological traits is often driven by changes in gene regulation. Many developmental genes are controlled by multiple, redundant enhancers, raising the question of how robust regulatory systems can be dismantled to permit phenotypic transitions. We show that the loss of larval trichomes in Drosophila sechellia resulted from the independent inactivation of four embryonic enhancers of the shavenbaby gene. Each enhancer was extinguished by a distinct mechanism: (1) a large deletion that removed essential sequences, (2) the loss of activator sites and gain of repressor sites, (3) the acquisition of a long-range silencer, and (4) the unmasking of pre-existing repression. Notably, three of these mechanisms relied on repression, pointing to repression as a rapid route for the evolutionary loss of robust regulatory elements. These results show that robustness in gene regulation does not prevent morphological change but instead provides multiple opportunities for mutations to reduce enhancer activity, giving selection many paths to reshape form.

evolutionary biology↗

bioRxiv2025

Bayesian Cooperative Learning for Multimodal Integration

Bayesian multimodal models that integrate data from multiple sources, studies, or modalities have garnered considerable attention in recent years. However, existing methods either rely on computationally expensive Markov chain Monte Carlo (MCMC) schemes or adopt variational approaches that forgo principled uncertainty quantification. To address this limitation and cater to practical needs, we abandon the MCMC framework and turn to resampling-based posterior inference for multimodal integration. Our method, Bayesian Cooperative Learning (BayesCOOP), embeds fast maximum a posteriori (MAP) estimation within a Bayesian bootstrap, combining a novel jittered group spike-and-slab prior with an efficient expectation-maximization (E M) coordinate descent algorithm under randomly weighted data perturbations. Averaging posterior summaries (MAP estimates) across bootstrap replicates yields approximate posterior samples that retain Bayesian interpretability while avoiding the computational burden of traditional sampling-based inference. We establish theoretical connections between BayesCOOPs pseudo-posterior averaging and posterior contraction principles, demonstrating near-optimal posterior consistency under sparsity. Extensive simulation studies and analyses of pregnancy multi-omics datasets demonstrate that BayesCOOP substantially outperforms state-of-the-art early, intermediate, and late fusion approaches in estimation, prediction, and uncertainty assessment. The open-source implementation of BayesCOOP is available at https://github.com/himelmallick/BayesCOOP.

bioinformatics↗

bioRxiv2025

Forecasting multi-trait resistance evolution under antibiotic stress

Many bacteria rely on efflux pumps to survive antibiotic stress, and exposure to antibiotics often leads to mutations in pump genes or their regulators that increase pump expression. Predicting the spectrum of these mutations is important for designing effective antibiotic treatments, but the underlying regulatory networks are large and complex, making them difficult to map experimentally. To address this challenge, we developed a mathematical framework that integrates dynamical equations for efflux pump regulation with a genetic algorithm for parameter estimation and evolutionary simulations. Using this framework, we simulated in silico evolution of Pseudomonas aeruginosa under exposure to the antibiotics meropenem, tobramycin, and ciprofloxacin. The simulations revealed mutational spectra affecting the expression of four RND efflux pumps and their shared regulatory network. The most frequently mutated genes were single-target regulators that matched well with previous observations in clinical and in vitro studies. The model also showed that the shared use of the OprM protein by two pumps is a key factor shaping their distinct mutational patterns. Mutations often produced multi-trait phenotypes, manifesting as collateral sensitivity or cross-resistance to antibiotics not used for selection. While cross-resistance evolved readily, its extent depended on initial pump expression levels and thus may vary between strains. Finally, simulations of changing environments showed that efflux pump genes tend to be lost in the absence of antibiotics, suggesting a potential strategy to steer bacterial evolution toward reduced capacity to re-evolve resistance.

microbiology↗

bioRxiv2025

Enhancing CRISPR Education: A Plug-And-Play Framework for Teaching Gene Editing in Plant Biology

Modern molecular biology tools and technologies such as CRISPR have sped up scientific discovery. From an educational perspective, these advancements are both exciting and overwhelming. Educators shaping these future scientists face the ongoing challenge of staying compliant with the latest developments in molecular biology while finding effective ways to teach these discoveries. As the use of CRISPR gene editing technology continues to expand globally, there is an increasing need for a workforce that is both knowledgeable about its theoretical foundations and trained in its practical use. While advanced, technology-driven STEM courses have the potential to improve student retention, they are often lecture-heavy and lack intentional engagement strategies that support deeper learning. Moreover, agriculture is the second most impacted sector by this technology, yet there is a significant lack of teaching materials focused on CRISPR in plant biology. To address these gaps, we developed a framework for teaching gene editing that incorporates multiple engagement strategies beyond traditional lecture-based instruction. This framework was implemented over two semesters in an Introduction to Gene Editing course at Tennessee State University, offered to both undergraduate and graduate students enrolled in a degree in Agricultural Sciences. This manuscript outlines the various strategies used in the course including active learning, multimodal instructional approaches and experiential learning strategies that can be adopted in other classrooms to effectively teach gene editing. Survey-based results from the course indicate a measurable increase in student comfort with designing and executing CRISPR-Cas based experiments. Societal Impact StatementPlant biology lacks accessible teaching materials for CRISPR, a powerful gene-editing technology widely used to improve agriculture. We developed an engaging framework to teach CRISPR concepts to advanced undergraduates and graduate students in plant sciences, which can be readily adopted by other instructors. The approach increased self-reported confidence in students and comfort in explaining CRISPR. Since instructors often have limited time to design interactive lessons, this framework offers a ready-to-use, effective strategy that makes CRISPR more widely available in classrooms, ultimately strengthening CRISPR literacy in the future agricultural workforce.

scientific communication and education↗

bioRxiv2025

Islet-intrinsic sex differences in inflammatory signaling contribute to autoimmune diabetes susceptibility

Whereas most autoimmune diseases exhibit female predominance, type 1 diabetes (T1D) occurs more frequently in males after puberty, suggesting a role for sex hormones in disease modification. Because islet {beta} cells actively shape local immune responses, we hypothesized that sex-specific islet responses to inflammation contribute to this disparity. Using transcriptomic and proteomic analyses of human islets from male and female donors, we found that male islets exhibit a more aggressive response to proinflammatory cytokines, characterized by greater induction of interferon signaling and suppression of developmental signaling compared to female islets. Treatment of human islets and mouse {beta} cells with the sex hormone 17{beta}-estradiol (E2) suppressed inflammatory signaling and markers of {beta}-cell maturity while enhancing developmental gene programs. Complementary studies in non-obese diabetic (NOD) mice showed that E2 treatment reduces diabetes incidence and limits progression to severe insulitis. Islet single-cell RNA sequencing revealed that E2 treatment of NOD mice suppresses interferon signaling, chemokine production, and antigen presentation in {beta} cells, while reducing activation and cytotoxicity pathways in immune cells. In co-culture studies in vitro, E2 pretreatment of mouse islets reduces subsequent activation of T cells, and in an aggressive adoptive transfer model in vivo, E2 pretreatment of the recipient mice was found to attenuate hyperglycemia. These findings support a model in which E2-mediated {beta}-cell reprogramming reduces {beta}-cell immunogenicity and promotes local immune tolerance, offering mechanistic insight into sex-biased T1D susceptibility.

cell biology↗

bioRxiv2025

CTG clade-specific proteins of the RSC chromatin remodeling complex regulate cell cycle progression of a critical priority fungal pathogen, Candida albicans

The RSC and the homologous chromatin remodeling complexes are known to regulate cell cycle progression in various organisms, including Saccharomyces cerevisiae, Drosophila, and Homo sapiens. In this work, we characterized the role of two novel CTG clade-specific proteins (Nri1 and Nri2) of the RSC complex in the regulation of cell cycle progression in a critical priority fungal pathogen, Candida albicans. We observed that Nri1, alone or along with Nri2, regulates cell cycle progression at multiple stages. The nri1{Delta}/{Delta} and nri1{Delta}/{Delta} nri2{Delta}/{Delta} mutants exhibited transient cell cycle arrest, defective spindle morphology, and cytokinesis. Transcriptomic analysis supported these mutant phenotypes and indicated a broad role of Nri proteins in the cell cycle. From our results, we conclude that Nri proteins are crucial for C. albicans proliferation and fitness. ImportanceThe composition of the essential RSC chromatin remodeling complex exhibits species-specific divergence, harboring unique subunits with distinct functions. In this study, we report that two fungal CTG clade-specific proteins of the C. albicans RSC complex, namely Nri1 and Nri2 can promote C. albicans fitness through regulating its cell cycle progression at multiple stages. Fitness defect along with stressor sensitivity and differential expression of the genes regulating pathogenesis in the nri mutants indicate potentiality of the Nri proteins as anti-Candida drug targets.

cell biology↗

bioRxiv2025

RNA-Binding moonlighting function of metabolic enzymes reveals deep evolutionary roots in Cyanobacteria

RNA-binding proteins (RBPs) have emerged as key regulators of diverse physiological and metabolic processes in cells. Notably, many metabolic enzymes exhibit moonlighting RNA-binding functions, and a substantial fraction localize to chloroplasts, the primary hub of photosynthesis and cellular metabolic homeostasis. Since chloroplasts originated from free-living cyanobacteria, understanding the RBP repertoire in these ancient phototrophs holds particular evolutionary and functional significance. A comprehensive characterization of the cyanobacterial RBPome is still lacking. Here, we employed Synechococcus elongatus PCC 7942, a model cyanobacterium, to define its RBPome using an RNA-interactome capture approach. We identified 136 RBPs, of which nearly 30% are associated with metabolic pathways, a proportion notably higher than that observed in bacteria, algae, plants, flies, worms, or animals. Strikingly, several enzymes from core metabolic pathways, including glycolysis/gluconeogenesis, the TCA cycle, and the pentose phosphate pathway, that are known RNA binders in humans are also conserved as RBPs in cyanobacteria. We identified a wide array of proteins from the photosynthetic apparatus exhibiting RNA-binding activity, many of which are conserved across the green lineage. In silico structural alignments of RNA-binding metabolic enzymes with their NAD(P)-binding pockets, a potential site for RNA-binding, suggests a broad conservation of RNA-binding capacity of core metabolic enzymes across species. Recent discoveries have revealed that RNA-binding can modulate enzymatic activity. In this context, our findings suggest that RNA-mediated control of core cellular metabolic processes may be widespread in cyanobacteria and riboregulation might be an evolutionarily ancient mechanism, potentially tracing its origins back to cyanobacteria.

plant biology↗

bioRxiv2025

Dynamic expression and differential requirement of the myocyte fusogen Myomixer during distinct myogenic episodes in the zebrafish

Skeletal muscle formation involves the fusion of myocytes into precisely aligned, multinucleated myofibres. These fibres continue to grow through reiterative rounds of myocyte fusion, incorporating new myonuclei and supporting muscle growth, repair and regeneration over organismal life span. The vertebrate-specific myocyte fusogens, Myomaker (Mymk) and Myomixer (Mymx), are crucial for generating multinucleated skeletal muscles. While the role of the transmembrane protein Mymk is well established, expression dynamics of mymx and the function of the Mymx micropeptide is less well understood. Here, using quantitative imaging and a mymx knockout strain, we explored the impact on myogenesis at different life stages of the zebrafish. We demonstrate that during the initial phase of muscle formation, mymx has a spatiotemporally varied expression across all axes of the developing myotome. On Mymx loss, myotome morphogenesis is disrupted, with both cell and tissue structure impacted. Moreover, we could show differential effects of Mymk versus Mymx loss on myocyte fusion and muscle growth. Finally, we report that perturbation to adult muscle multinucleation and size impacted bone development, again with different phenotypic severities among the two fusogen mutants. Together, our work provides key insights into the interplay between myocyte fusion, myotome morphogenesis and acquisition of final adult form.

developmental biology↗

bioRxiv2025

SMART Sensors for Cell Growth Monitoring in Closed System G-Rex for Scalable, Cost-Conscious Cell and Gene Therapy Manufacturing

Cell and gene-modified cell therapy (CGT), commonly referred to as the fourth pillar of cancer treatment, includes creating advanced cancer killing cells ex vivo and then subsequently putting them into the patients body to selectively attack cancerous cells. Typically, immune cells from a patients body are removed, genetically modified to find and kill cancer, grown to a large army of cancer killing cells, and put back into the patient. This complex process is being simplified through innovation, some of which we describe here. One key innovation is an immune cell manufacturing device configuration called G-Rex (for "gas permeable rapid expansion"), which is now widely used to create armies of cancer killing cells for clinical trials and for commercially approved drug products on a worldwide basis. G-Rex is uniquely simple and popular because it is the only technology that eliminates the need for pumps and flow circuits to deliver oxygen and nutrients. Instead, the material and geometry of G-Rex allow cancer killing cells to get access to oxygen and nutrients on demand. This greatly minimizes complexity and sets the stage for high throughput manufacturing. To further simplify G-Rex relative to all CGT drug product manufacturing alternatives, it would be ideal to eliminate any need of physical intervention to assess cell quantity. With that goal, we conceived a novel approach to determining cell quantity in a non-invasive manner. More specifically, we invented and built a sensor into G-Rex that continuously reports the quantity of cells in G-Rex without any intervention or sampling to an external reader. Herein, we call the sensor a "single-use metabolite absorbing resonant transducer in G-Rex (SMART G-Rex)" and the reader a "SMART Reader." The SMART G-Rex is wirelessly interrogated by the SMART Reader to determine the extent of cell expansion in the G-Rex at any given time. More specifically, as cell quantity increases, the SMART G-Rex absorbs cell secreted metabolites (organic compounds such as eicosanoids) which cause a change in resonant frequency (measured as % of frequency change, or Skroot Growth Index (SGI)). By placing SMART G-Rex in proximity of the SMART Reader, whether in or out of an incubator, changes in resonant frequency are detected and translated into cell quantity with high reliability. For example, using 45 sensors across multiple donor cell samples, we established 99% confidence in SMARTs accuracy at signaling a >60X expansion (3B cells at harvest). The SMART G-Rex provides a non-invasive way of instantly quantifying the number of cells in a CGT drug production process and informing manufacturers when a CGT drug product has reached the desired quantity of cells necessary to proceed with formulation, fill, and finish. By integrating SMART technology, G-Rex is the only technology for CGT manufacturing that can avoid intervention when determining cells quantity or allow real-time knowledge of cell quantity. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/676768v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1557118org.highwire.dtl.DTLVardef@740652org.highwire.dtl.DTLVardef@14b0430org.highwire.dtl.DTLVardef@ac0_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Mesoscopic analysis of GABAergic marker expression in acetylcholine neurons in the whole mouse brain

In the central nervous system, acetylcholine (ACh) neurons coordinate neural network activity required for higher brain functions, such as attention, learning, and memory, as well as locomotion. Disturbances in cholinergic signaling have been described in many diseases of the developing and mature brain. Interestingly, ACh neurons can co-transmit GABA to support essential roles in brain function. However, the contributions of ACh/GABA co-transmission to brain function remain unclear. This underscores the need to better understand the heterogeneity of ACh neurons, particularly the sub-population of ACh neurons co-expressing GABAergic markers. We used various combinations of transgenic mouse lines to systematically label ACh neuron populations positive for different GABAergic markers in the brain. We developed a workflow combining tissue clearing, light-sheet fluorescence microscopy, and machine learning to image entire mouse brain hemispheres followed by quantification of ACh neurons throughout the brain. With this approach, we assessed the role of GABA co-transmission in ACh neuron function and quantified ACh and ACh/GABA neuron sub-populations in the brain. Our results suggest that GABA co-transmission from ACh neurons is not required to maintain the regular ACh neuron count in the brain. Furthermore, we report that a large subset of ACh neurons can potentially synthesize GABA by co-expressing the marker Gad2. However, most of these ACh neurons do not express vGAT, which would enable these neurons to release GABA. Taken together, we conclude that GABA co-transmission likely occurs only from a small population of ACh neurons restricted to few brain nuclei. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/675394v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1dc5915org.highwire.dtl.DTLVardef@15c872borg.highwire.dtl.DTLVardef@1ae3993org.highwire.dtl.DTLVardef@145f32b_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Selective mRNA translation determines adaptative mutability of melanoma cells to anti-BRAF/MEK combination therapy

During their inevitable evolution towards acquired resistance to anti-cancer targeted therapies, cancer cells adopt distinct gene expression profiles that allow them to transiently adapt to and tolerate the treatment. Similar to bacterial cells that transiently tolerate antibiotics, cancer cells surviving therapy can increase their mutation rate, enhancing the likelihood of acquiring resistance-conferring mutations and evolving into resistant cells. This adaptive mutability has been linked to transcriptional reprogramming of DNA damage repair mechanisms and effective therapeutic strategies to target such mechanisms are currently lacking. Here we show that translational control mediates the adaptive mutability of melanoma drug-tolerant cells by regulating the translation of the error-prone non-homologous end joining (NHEJ) component 53BP1. The specific inhibition of 5UTR-driven 53BP1 mRNA translation was sufficient to impair NHEJ and mutability. We found that the eIF4A RNA helicase, a key component of the eIF4F translation complex, regulates 53BP1 mRNA translation. Consequently, targeting the eIF4A with two small molecule inhibitors significantly delays the acquisition of resistance to combination of BRAF and MEK inhibitors (BRAFi/MEKi) in BRAFV600-mutant melanoma xenograft models and cell lines by reducing the mutability of drug-tolerant cells. Our results demonstrate that a standard-of-care therapy for melanoma, by engaging non-genetic adaptation driven at the translational level, contributes to the evolution of drug-tolerant melanoma cells toward acquired resistance.

cancer biology↗

bioRxiv2025

What Large Language Models Know About Plant Molecular Biology

Large language models (LLMs) are rapidly permeating scientific research, yet their capabilities in plant molecular biology remain largely uncharacterized. Here, we present MOBIPLANT, the first comprehensive benchmark for evaluating LLMs in this domain, developed by a consortium of 112 plant scientists across 19 countries. MOBIPLANT comprises 565 expert-curated multiple-choice questions and 1,075 synthetically generated questions, spanning core topics from gene regulation to plant-environment interactions. We benchmarked seven leading chat-based LLMs using both automated scoring and human evaluation of open-ended answers. Models performed well on multiple-choice tasks (exceeding 75% accuracy), although most of them exhibited a consistent bias towards option A. In contrast, expert reviews exposed persistent limitations, including factual misalignment, hallucinations, and low self-awareness. Critically, we found that model performance strongly correlated with the citation frequency of source literature, suggesting that LLM knowledge inherits the visibility distribution of the underlying scientific corpus. Consequently, models tend to be more reliable on consolidated topics and less reliable on under-cited or recently emerging ones. We also benchmarked agents equipped with web-search and additional tools in more complex tasks involving DNA sequence analysis. These agents were outperformed by domain specific models in sequence classification and regression tasks, indicating an opportunity for joint agentic systems that combine both the reasoning power of LLMs and the dedicated processing of DNA models. This understanding is key to guiding both the development of next-generation models and the informed use of current tools in the everyday work of plant researchers. MOBIPLANT is publicly available online in this link.

plant biology↗

bioRxiv2025

Cytoneme feedback ensures signaling specificity when multiple ligands converge on a common receptor

Cell-cell communication via conserved signaling pathways often involves multiple paracrine ligands that act through shared receptors and/or downstream cascades yet elicit distinct outcomes, raising the question of how specificity is achieved. In the Drosophila adult-muscle-precursor (AMP) niche, the FGF ligands Pyramus and Thisbe both signal through the Heartless (Htl) receptor in isogenic AMPs yet drive divergent responses. In-vivo imaging of endogenous Pyramus:mCherryendo and Thisbe:sfGFPendo knock-ins revealed that the ligands segregate into distinct, receptor-bound territories among isogenic AMPs. This segregation arises as AMPs acquire ligands via polarized, Htl-containing cytonemes that directly contact each ligand source. Cytoneme polarity and target-specificity are position-dependent, enabling ligand distribution to scale with tissue size and AMP organization. A positive feedback loop through the Htl-Pointed axis reinforces cytoneme polarity, amplifying ligand-specific segregation and signaling. These findings establish cell-intrinsic feedback as a general principle for sustaining cytoneme polarity and specificity, and reveal how cytonemes confer signaling specificity to pathways activated by multiple ligands within the same progenitor population.

developmental biology↗

bioRxiv2025

B12 promotes gut dysbiosis and an inflammatory microenvironment that potentiates Tet2-deficient hematopoiesis.

Recent studies have linked elevated vitamin B12 serum levels with the presence of clonal hematopoiesis (CH) and an increased risk of developing myeloid malignancy. High B12 supplementation increases serum levels, alters gut microbial composition, and reduces the production of short-chain fatty acids (SCFAs), which help maintain gut barrier function and mucosal integrity. TET2 mutation is a frequent driver of CH that progresses in a positive feedback loop in response to microbial signals suggesting that B12 may influence CH via the gut microbiome. We evaluated the microenvironmental effects of B12 supplementation in a Tet2-deficient model of CH and found that B12 enhances myelopoiesis, heightens the responses of myeloid cells to bacterial stimuli, and increases the levels of circulating inflammatory cytokines. B12 supplementation also induced gut dysbiosis and reduced the levels of SCFA-producing bacteria in both wild-type and Tet2-deficient mice. Importantly, the effects of excess B12 were reversible upon oral supplementation with the SCFA butyrate. These findings suggest that B12 may promote CH progression by disrupting microbiome-derived SCFA metabolism, highlighting a potential therapeutic role for SCFA supplementation in mitigating CH.

cancer biology↗

bioRxiv2025

Nuclear Fetuin-A Drives Adipocyte Senescence via HIF-1 α During Obesity

Fetuin-A (FetA), a liver derived glycoprotein, has emerged from genome-wide association studies and epidemiological surveillance as a serum biomarker linked to obesity-driven type 2 diabetes mellitus (T2D), primarily due to its contribution to adipose tissue dysfunction. Here, we uncovered an eccentric role of nuclear FetA in visceral white adipocytes of obese T2D conditions. Hypoxia-inducible factor-1 (HIF-1) facilitates the nuclear translocation of FetA via direct interaction, a process that promotes the emergence of a senescence-associated secretory phenotype (SASP). While nuclear co-localization of FetA and HIF-1 strongly promotes adipocyte senescence, silencing FetA alone is sufficient to prevent senescence, even in conditions of HIF-1 overexpression or lipid-rich hypoxic stress. Although nuclear FetA does not directly bind to DNA, it enhances HIF-1 transcriptional activity, potentiating the activation of senescence markers such as {beta}-galactosidase and p53. Selective knockdown of FetA in obese mice notably reduced adipocyte senescence in visceral white adipose tissue (vWAT) and improved fasting glycemic control. Collectively, our findings reveal a previously unrecognized nuclear function for FetA in orchestrating adipocyte senescence in obesity, establishing nuclear FetA as a potential therapeutic target for obesity related metabolic diseases.

cell biology↗

bioRxiv2025

Mapping of genotype-by-environment interaction loci for Metabolic Syndrome-like traits using the multi-parent Drosophila Synthetic Population Resource determines that main genetic effects are distinct from environment dependent plastic loci

Metabolic Syndrome (MetS) risk, driven by genotype-environment interactions like diet, is rising globally. Due to its genetic and environmental complexity, the genetic architecture and interconnected traits underlying MetS is poorly understood. In Drosophila, genotype-by-diet interactions significantly influence MetS-like traits. This study used the Drosophila Synthetic Population Resource to dissect the genetic architecture of both genotypic and genotype-by-diet interaction effects underlying trait variation. The study hypotheses were: 1) Loci responsible for metabolic phenotypic variation should be shared across traits. 2) Genetic loci responsible for plasticity and epistatic interactions for metabolic traits should also be the loci responsible for the main effects. 3) Genes responsible for variation in metabolic traits should share common functions. Using a round-robin crossing scheme and novel analyses, we mapped additive, dominance, and epistatic loci--some diet-specific, others diet-independent. Main-effect and plastic loci were largely distinct, as were epistatic loci from main-effect loci, highlighting that main genetic effects alone will not explain how genetic variants interact with the environment or the genome to influence disease risk. gene-by-diet or gene-by-gene interactions influencing MetS risk. Further, tremendous cryptic genetic variation for metabolic traits is lurking in natural populations. We explored the function of candidate genes from our study empirically and with bioinformatics. While some of the candidate genes might have been expected, most would not have been identified a priori, thus with this study we have identified many new candidate mechanisms contributing to the genetic and genotype-by-diet interaction effects on MetS variance.

genetics↗

bioRxiv2025

Putative MFS transporter Rv1250 of Mycobacterium tuberculosis is involved in multidrug efflux activity

Drug-resistant Mycobacterium tuberculosis is one of the leading causes of global mortality. Mechanisms, such as slow uptake of drugs along with cell wall impermeability and active efflux, are some of the concerning reasons leading to drug resistance. Efflux pumps actively transport a wide variety of drugs and toxins away from the target site, which is considered an emerging cause for the failure of anti-tubercular medications and treatment. In this study, we report that the ability of Rv1250, a probable MFS-type transporter, influences the extrusion of multiple structurally unrelated classes of drugs, enhances the biofilm formation in E. coli and Mycobacterium smegmatis, and facilitates the survival of M. smegmatis cells inside the macrophage during antibiotic stress. Interestingly, in trans, the expression of rv1250 decreased the susceptibility of host cells to several structurally unrelated antibiotics, ranging from fluoroquinolones to aminoglycosides, beta-lactams, and anti-tubercular drugs, thus indicating its involvement in imparting intrinsic drug tolerance. In addition, the increased efflux of EtBr, norfloxacin, and Bocillin FL from host cells expressing rv1250 was revealed by the hosts ability to confer a lower level of antibiotic accumulation. Moreover, the expression of rv1250 resulted in the enhancement of biofilm formation. Overall, we conclude that Rv1250 of Mycobacterium tuberculosis might facilitate the survival of host cells under antimicrobial stress. One sentence summaryRole of Rv1250 as an efflux pump

microbiology↗

bioRxiv2025

Temporal dynamics of RNA metabolic enzyme interactome lay the foundation for riboregulation mediated circadian metabolism

The temporal regulation of the RNA-binding to metabolic enzymes offers a compelling framework to address the open question of whether circadian control of metabolism can be mediated through riboregulation. To advance this understanding, we investigated the time-of-the-day dependent dynamics of RNA-enzymes interactome using a time-resolved RIC approach. 70% of the captured RBPs exhibit differential RNA-binding between subjective day and night, with 27% associated to metabolic pathways, suggesting temporal riboregulation of metabolic enzymes can be widespread. Intriguingly, 63 metabolic enzymes displayed circadian RNA-binding uncoupled from their protein abundance dynamics. This observation suggests that the temporal regulation of their RNA-binding "moonlighting" functions is likely mediated by alternative mechanisms, such as post-translational modifications. Our study presents a catalog of metabolic enzymes localized in mitochondria and chloroplast that exhibit dynamic RNA binding across circadian time, providing a valuable testbed to explore the mechanistic role of riboregulation in driving daily metabolic rhythms across species.

biochemistry↗