Biology subjects

Chakraborty, A.

Publications and source records attributed to Chakraborty, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

LMNA Haploinsufficiency in Human iPSC-Derived Cardiac Organoids Reveals Early Fibrotic Signaling as a Therapeutically Targetable Process

LMNA mutations are a major cause of dilated cardiomyopathy (DCM), with haploinsufficiency representing a common pathogenic mechanism. Yet the earliest disease-initiating events remain poorly defined. Here, we identify a novel intronic splice-site variant, c.937-1G>A, that disrupts pre-mRNA processing and induces nonsense-mediated mRNA decay, resulting in LMNA haploinsufficiency. Using induced pluripotent stem cells (iPSCs) generated from the patients peripheral blood mononuclear cells (PBMCs), we differentiated into self-patterning human cardiac organoids to model early LMNA-DCM in a multicellular human context. Single-nucleus transcriptomics revealed unexpectedly broad remodeling across major cardiac cell types beyond cardiomyocytes. Functionally, LMNA-mutant organoids exhibited impaired contractility, altered calcium handling, and increased arrhythmic activity. These changes were accompanied by early profibrotic activation, including increased reactive oxygen species (ROS), periostin (POSTN) secretion, and CTGF expression. Treatment with the antifibrotic drug nintedanib attenuated this response. Together, these findings show that LMNA haploinsufficiency initiates global pathogenic remodeling at an unexpectedly early developmental stage.

cell biology↗

bioRxiv2026

A systematic analysis of brain tissue response to microelectrode material and size with single-cell spatial transcriptomics

Implantable microelectrode arrays can interface with the central nervous system to record from and/or stimulate neural tissues to treat neurological disease and injury. The chronic tissue response to implanted electrodes is believed to be a driving factor behind microelectrode failure. Next-generation electrodes have been developed to attenuate the tissue response by reducing electrode size and/or incorporating softer materials. In this study, we used single-cell-resolution spatial transcriptomics to quantify the tissue response to implanted electrodes within custom-classified cell types in the rat brain. To test the effects of implant material and size, we assessed polyimide and silicon electrodes of 10 {micro}m and 100 {micro}m cross-sectional dimensions over 6-weeks post-implantation. Our data indicate that implants are associated with upregulation of inflammatory genes in glia that are coupled to damage-initiated losses in synaptic transmission and subsequent engagement of compensatory protective mechanisms (e.g., re-myelination, antioxidant production) to preserve local neurons. While bulk tissue analysis reinforced previously reported observations of glial scar consolidation over time, single cell analysis revealed an unexpected, progressive heightening of the expression of inflammatory genes in individual device-reactive astrocytes. With respect to design features, the impact of device dimensions more heavily influenced responses than material type, particularly by the 6-week time point. Our results add single-cell resolution observations to the growing use of transcriptomics to understand the biocompatibility of devices implanted in the brain.

neuroscience↗

bioRxiv2026

HSPB8 regulates CTP synthase filaments to couple nucleotide metabolism and autophagy in tumors

Metabolic adaptation and proteostasis are essential for tumor survival under nutrient stress, yet how these processes are mechanistically integrated remains unclear. Here, we identify CTP synthase (CTPS) filament dynamics as a regulatory nexus linking nucleotide metabolism to autophagic flux. Under glutamine deprivation--a hallmark of poorly vascularized solid tumors--CTPS undergoes polymerization into filamentous assemblies that exhibit reduced enzymatic activity. We demonstrate that filament formation is driven by intracellular asparagine availability and stabilized by the accumulation of misfolded proteins. Using APEX2-based proximity labeling and proteomics, we identify the small heat shock protein HSPB8 as a filament-associated regulator. HSPB8, acting within the chaperone-assisted selective autophagy (CASA) pathway, antagonizes CTPS polymerization by promoting clearance of misfolded proteins, thereby restoring soluble, catalytically active CTPS. Filament disassembly increases CTP production and enhances synthesis of autophagy-related phospholipids, including phosphatidylinositol and phosphatidylethanolamine, resulting in accelerated autophagic flux. Cells expressing filament-deficient CTPS mutants display elevated autophagosome formation and increased LC3-II accumulation upon lysosomal blockade, confirming enhanced flux. In vivo, disruption of CTPS filament assembly impairs xenograft tumor growth and is associated with excessive autophagy. Analysis of TCGA datasets further reveals that high CTPS and low HSPB8 expression correlate with poor patient survival across multiple cancers. Collectively, our findings establish CTPS filament dynamics as a proteostasis-sensitive metabolic switch that coordinates nucleotide biosynthesis with autophagy, revealing a previously unrecognized vulnerability in tumors adapting to nutrient limitation.

cell biology↗

bioRxiv2026

Epigenetic Programming of Macrophage Phenotypes by STING-IRF3 Drives Inflammation in Ascending Thoracic Aortic Dissection

BackgroundAscending thoracic aortic dissection (ATAD) is characterized by extensive macrophage (M{Phi}) accumulation and profound inflammation; however, the mechanisms sustaining pro-inflammatory M{Phi} activation remain incompletely defined. Emerging evidence indicates that epigenetically generated immune memory drives innate immune cells toward persistent inflammatory states. In this study, we investigated whether epigenetic reprogramming governs M{Phi} phenotypic fate and contributes to ATAD pathogenesis. MethodsWe performed single-cell RNA sequencing of human ascending aortic tissues from controls, patients with ascending thoracic aortic aneurysm (ATAA), and patients with acute ascending thoracic aortic dissection (ATAD). We also performed integrated single-cell RNA sequencing, single-cell ATAC sequencing, and spatial transcriptomics in an angiotensin II (Ang II)-infused mouse model. The role of the STING-IRF3 signaling axis in M{Phi} epigenetic programming was examined using M{Phi}-Sting -/- and M{Phi}-Irf3-/- mice. ResultsIn human and mouse aortic tissues, we identified multiple functional M{Phi} populations including pro-inflammatory, phagocytic/anti-inflammatory, proliferative, and reparative/healing M{Phi}s. Aortic M{Phi}s in both sporadic ATAD patients and Ang II-induced ATAD mice exhibited a pronounced pro-inflammatory bias with enhanced differentiation toward pro-inflammatory M{Phi}s and impaired differentiation toward phagocytic/anti-inflammatory states. Pro-inflammatory M{Phi}s were particularly abundant in dissection sites, whereas phagocytic M{Phi}s were enriched in discrete adventitial niches. Origin analyses revealed a substantial increase in CCR2 recruited M{Phi}s within the aortic wall, which preferentially differentiated into pro-inflammatory M{Phi}s. In contrast, LYVE1 resident M{Phi}s-- predominantly biased toward phagocytic phenotypes--were markedly depleted in ATAD. Single-cell ATAC sequencing identified coordinated chromatin remodeling with increased accessibility at pro-inflammatory gene loci and decreased accessibility at phagocytic gene loci. Among candidate transcriptional regulators identified, IRF family TFs, including IRF3 emerged as unique factors capable of simultaneously promoting pro-inflammatory gene programs while suppressing phagocytic gene expression. Mechanistically, STING-IRF3 signaling orchestrates this biased transcriptional state, likely through coordinated BRG1-dependent chromatin opening at pro-inflammatory gene loci and chromatin closing at phagocytic/anti-inflammatory gene loci. M{Phi} specific Sting -/- and Irf3-/- mice exhibited attenuated inflammatory reprogramming and reduced aortic destruction and dissection. ConclusionsThese findings identify STING-IRF3-mediated epigenetic programming of M{Phi}s as a fundamental mechanism driving aortic inflammation and ATAD development. Targeting M{Phi} epigenetic programming may represent a promising therapeutic strategy to prevent aortic dissection. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=189 HEIGHT=200 SRC="FIGDIR/small/701198v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@c97bcdorg.highwire.dtl.DTLVardef@1df0ca8org.highwire.dtl.DTLVardef@b7fd04org.highwire.dtl.DTLVardef@1443e16_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

Organic Components Modulate the Morphology of Respirable Aerovirology Relevant Aerosols

Airborne transmission of pathogens occurs via aerosol particles, whose morphology provides insights into the microenvironments that pathogens experience. Aerosol morphology includes particle size, shape, phase state, and chemical homogeneity, yet systematic studies remain limited. Here, we characterized model bioaerosol morphologies generated from (1) NaCl-organic two-component mixtures, (2) common cell culture media, and (3) artificial respiratory fluids. Particles were collected using a virtual impactor and Andersen cascade impactor and analyzed by scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDX). Results show that organic components modulate the morphology: dipalmitoylphosphatidylcholine (DPPC) promotes organic-inorganic phase separation while proteins prohibit formation of large crystals and leads to better mixing among components. At 30% RH with a drying period of 10 seconds, most aerosols appeared desiccated, though NaCl-glucose, DMEM-complete-media and artificial saliva with mucin remained semi-solid or gel-like. Among all formulations examined EMEM-complete-media and artificial saliva (non mucin) show a size-dependent morphology. Our study demonstrates how chemical composition and size alters surrogate bioaerosol phase (semi-solid or solid) and morphology and provides new insights into the microenvironment of aerosol particles for aerovirology investigations.

biochemistry↗

bioRxiv2026

Interplay of microRNA-20a and HuR in the regulation of beclin1 during Withaferin-A mediated impaired autophagy in Breast Cancer cell-line, MCF-7

Dysfunctional autophagy is connected to multiple diseases. Withaferin-A, a biologically active withanolide, has been shown to impair autophagy in the breast cancer cell line, MCF-7; however, the underlying mechanism remains unclear. Here while uncovering the mechanism, it was found that treatment of MCF-7 cells with WA declines Beclin1 protein synthesis by restricting association of its mRNA to polysomes with no significant reduction in its mRNA level. Reporter assay established that WA-treatment enhanced the expression level of mature miR-20a which directly interacts with the 3UTR of beclin1 mRNA. RNA affinity chromatography revealed association of mRNA stabilizing protein, HuR with the 3UTR of beclin1 mRNA. Additionally, co-immunoprecipitation assay determined the interactions of GW182, an essential component of GW-body and Ago2, a crucial member of miRNA related silencing complex (RISC) with the 3UTR of beclin1 mRNA. In parallel, it was found that knocking down of HuR eliminates the interaction of GW182 with beclin1 3UTR, while the association of miRNA (Ago2) remains unaffected. These results suggested simultaneous association of HuR, GW182 and microRNA with beclin1 mRNA which could be pivotal for sequestration of beclin1 mRNA in GW-bodies. Thus, our findings culminated in identifying an unconventional mechanism of regulation of Beclin1 expression by the dual interplay between hsa-miR-20a and HuR during WA-induced impaired autophagy in MCF-7 cells.

molecular biology↗

bioRxiv2026

Loss of E3 ligase Ube4A disrupts colon homeostasis and accelerates experimental colitis via altered lipid handling

BackgroundUbiquitin-dependent signaling is essential for maintaining intestinal homeostasis and its dysregulation contributes to chronic intestinal disorders, such as Inflammatory Bowel Disease (IBD). Ube4A is a U-box E3/E4 ubiquitin ligase involved in lipid metabolism and insulin signaling in metabolic tissues. Autoantibodies against Ube4A have been identified in patients with IBD and are associated with disease long-term complications. Despite these clinical associations, the physiological role of Ube4A in the gastrointestinal tract remains unknown. This study aimed to define the function of Ube4A in the colon and determine how its loss influences susceptibility to experimental colitis. MethodsUBE4A expression in human colonic tissue from healthy individuals and patients with IBD was analyzed using publicly available single-cell RNA sequencing datasets. The role of Ube4A in colonic homeostasis and colitis pathogenesis was examined using global Ube4A knockout (UKO) mice subjected to dextran sulfate sodium (DSS)-induced colitis. UKO colon phenotypes were characterized using transcriptomic analyses, immunofluorescence, and flow cytometry. ResultsUBE4A is highly expressed in human colonic epithelial cells, and its expression is reduced from healthy to IBD inflamed tissues. In mice, Ube4A deficiency significantly exacerbated DSS-induced colitis, as evidenced by increased weight loss, disease activity scores, shortened colon length, and more severe histological injury. Transcriptomic profiling revealed enhanced inflammatory signaling, alongside dysregulation of lipid transport and storage, as well as antimicrobial defense pathways. DSS-treated UKO mice also exhibited increased mast cell activation and elevated expression of matrix metalloproteinases. Importantly, colons from UKO mice displayed baseline transcriptional alterations indicative of epithelial stress and disrupted lipid metabolic programs, even in the absence of injury. ConclusionsUbe4A is a previously unrecognized regulator of colon homeostasis. Its loss induces existing epithelial stress and metabolic reprogramming that sensitize the colon to exaggerated inflammatory responses during injury such as experimental colitis.

pathology↗

bioRxiv2025

Conformational and Environmental Determinants of RNA Solvation Dynamics: Roles of Intrinsic Flexibility, Allostery, and Protein Binding

Solvation dynamics play a central role in shaping nucleic acid structure, flexibility, and recognition, yet their molecular origins remain poorly understood for RNA, whose diverse architectures and intrinsic conformational plasticity far exceed those of DNA. Here, we present the atomistic, microsecond-scale computational dissection of solvation dynamics in two structurally homologous but functionally distinct viral RNAs--BIV TAR and HIV-2 TAR--in both apo and peptide-bound states mimicking the salt concentration of experimental time-resolved fluorescent spectroscopic measurement. By combining high-temporal-resolution solvation time correlation functions with detailed energy decomposition analyses, we uncover how water, ions, and RNA motions cooperatively shape relaxation across ultrafast to nanosecond timescales. Our results reveal that, unlike DNA, where slow components primarily reflect long-lived hydration and ion condensation, RNA can generate slow solvation decay either through long-lived hydration or through its own internal conformational fluctuations, such as involving spontaneous base-flipping events. Peptide binding modulates this conformational landscape in strikingly system-specific ways: BIV TAR RNA undergoes classical fluctuation quenching, where TAT binding suppresses RNA motions and shifts relaxation toward solvent-RNA compensation, whereas HIV-2 TAR RNA exhibits a non-classical redistribution of solvent-ion-peptide correlations stemming from its weaker and more dynamic binding interface with TAT. The dominant slow decay in HIV-2 apo TAR maps directly onto an allosteric communication channel previously identified from structural analyses, demonstrating that solvation responses can sensitively report on RNA allostery. Together, this study bridges the experimental observations of time resolved fluorescence spectroscopy with mechanistic molecular insight, establishes solvation dynamics as a powerful probe of RNA conformational energetics, and highlights how subtle differences in RNA-protein recognition can imprint distinct signatures on hydration and ion reorganization.

biophysics↗

bioRxiv2025

Metagenomic characterisation of fungal communities associated with Scots pine bark beetles: mechanisms of selective antagonism and monoterpene tolerance

Bark beetle-associated fungi contribute to beetle nutrition, detoxification, and interactions with conifer hosts; however, their composition and function across development and environments remain poorly understood. We characterised fungal communities of two pine-feeding Ips bark beetles, I. sexdentatus and I. acuminatus, in larval, pupal, and adult stages, and in wild versus laboratory populations, using high-throughput ITS2 amplicon sequencing combined with qPCR and functional assays. Both beetles harboured a stable core mycobiome dominated by Kuraishia, Ogataea, Ophiostoma, Graphilbum and Cyberlindnera, while adults showed species-specific differences and wild beetles, especially I. acuminatus, exhibited greater diversity than laboratory populations. Beetles shared more taxa with unfed control wood than with gallery wood, indicating acquisition during feeding and concurrent restructuring of the wood mycobiome. Monoterpene bioassays on beetle-associated yeasts revealed that mixtures of -pinene, 3-carene and terpinolene suppressed growth more strongly than single compounds, suggesting synergistic inhibition. Yeasts selectively antagonised entomopathogenic fungi and expressed complementary cell-wall-lytic and digestive activities, consistent with combined roles in pathogen suppression and plant-polymer deconstruction. Our results show that Ips mycobiomes are conserved yet dynamic across life stages and environments, and emphasise the importance of multi-terpene and interaction assays for understanding bark beetle-fungus-conifer interactions. ImportanceOur study reveals that pine-feeding bark beetles co-evolved in close association with a stable core mycobiota that supports nutrient acquisition, detoxification, and chemical signalling, while additional fungal partners shift in response to beetle development, environment, and host context. By demonstrating higher mycobiome diversity in beetle larvae and wild populations, substantial overlap between beetle- and wood-associated fungi, differential sensitivity to monoterpene blends and selective antagonism of yeasts towards entomopathogenic fungi, our study unravels key ecological and mechanistic principles shaping beetle-fungus assemblages under conifers, paving the way for more in-depth functional investigations.

microbiology↗

bioRxiv2025

WRN helicase regulates mitophagy by resolving an intricate nexus of G-quadruplexes-R loops-ATG7 pre-mRNA maturation in cancer

Werner syndrome (WS) is a progeroid and cancer-predisposition disorder caused by loss of the Werner RECQ helicase-exonuclease (WRN), a key genome-maintenance enzyme essential for replication-stress signalling and DNA-repair. WS patients also develop metabolic abnormalities, including fatty-liver and diabetes, suggesting a link between WRN-deficiency and mitochondrial-dysfunction. WRN is frequently epigenetically silenced in cancers, yet its precise role in mitochondrial homeostasis in cancer remains unclear. Here, we define a role for WRN in regulating mitophagy and autophagy in cancer. WRN-deficient cells show defective mitochondrial respiration, morphology, and mitophagosome/autophagosome-maturation under basal and cisplatin-induced stress. Mechanistically, WRN-loss causes strong reduction of ATG7-protein, compromising autophagosome-biogenesis. Chromatin immunoprecipitation reveals accumulation of unresolved G-quadruplex structures (G4-DNA) across the ATG7-locus in WRN-deficient cells. Paradoxically, ATG7-mRNA expression is elevated despite reduced ATG7-protein in WRN-deficient cells, indicating a post-transcriptional defect. Further, we show that WRN resolves G4-DNA which prevent R-loops formation and interacts with the mRNA-processing factor U2AF35, independent of its helicase-exonuclease functions, to promote maturation of nascent ATG7 transcripts. In cancer patients, WRN level also inversely correlated with post-transcriptional defects in ATG7 mRNA. Collectively, our findings suggest pivotal association of WRN-loss in autophagy fidelity, which may further contribute to oncogenic transformation in WRN-deficient tissues and exacerbate cancer susceptibility in WS-patients. Significance statementWRN is well recognized for its roles in DNA repair and genome maintenance, which are essential for suppressing tumorigenesis and Werner syndrome (WS)-associated premature-aging. However, its functions in mitochondrial regulation remain underexplored, despite WS patients exhibiting severe metabolic defects and increased cancer risk. Here, we uncover a mechanistic link between WRN and autophagy/mitophagy, showing that WRN resolves G-quadruplexes and R-loops to enable proper post-transcriptional processing and translation of ATG7, a key autophagy enzyme. WRN-loss associated defective-autophagy may heighten the initiation of tumorigenesis in both WS-patients and in normal individual with mutated WRN in different tissue-types. As WRN is actively pursued as a synthetic-lethal target and multiple WRN inhibitors progress through clinical-development, our findings highlight mitochondrial quality-control defects as an additional determinant of WRN-targeted therapeutic-response.

cell biology↗

bioRxiv2025

A rapid, cost-effective, efficient method for total RNA extraction from pure bacterial cultures and complex microbiomes and its effectiveness in deciphering functionally active microbial populations

Extraction of high-quality RNA from microbial samples, especially complex microbiomes like the gut, remains a significant challenge. The instability of RNA, coupled with the abundance of RNases and difficult-to-lyse microbial cells, often results in degraded or low-yield RNA, hampering downstream applications. To overcome this critical bottleneck, we developed a simple, rapid, cost-effective, and efficient microbial RNA extraction method, which is equally effective for pure cultures and complex microbiomes. The method utilises low pH (4.7) and high temperature to lyse the cells, followed by rapid cooling to induce misfolded renaturation of genomic DNA and proteins. During the phase separation step, RNA remains in the aqueous phase and is subsequently precipitated using chilled isopropanol. The RNA suspended in double-distilled water (pH 6.5) remained stable for six months at -20 {degrees}C. Further, we compared amplicon microbiome profiles generated from metagenomic DNA and cDNA (synthesised from extracted meta-RNA) derived from the broiler gut, taken as a model system. Our findings reveal that the cDNA-based amplicon microbiome composition more accurately deciphers the metabolically active population in gut environments that aligns with culture-based enumeration of viable microbes. This proof-of-concept study underscores the importance of meta-RNA approaches for functional microbiome analysis and provides a reliable RNA isolation method that can be broadly adopted for studies aiming to resolve active microbial community structure.

microbiology↗

bioRxiv2025

CBKMR: A Copula-based Bayesian Kernel Machine Regression Framework for Optimal Marker Detection in Omics Data

High-throughput bulk and single-cell omics technologies enable comprehensive molecular profiling, yet identifying compact, biologically interpretable marker sets that distinguish cell types, conditions, or disease states remains challenging. Standard pipelines rely on univariate differential expression tests, which ignore gene-gene dependencies and nonlinear effects, while multivariate machine-learning (ML) methods often lack principled feature selection and uncertainty quantification. The Bayesian kernel machine regression (BKMR) framework offers an appealing alternative because it (a) captures non-linear gene-outcome relationships and higher-order interactions, and (b) enables automatic relevance determination (ARD) through sparsity-inducing priors. However, we show that the traditional latent Gaussian process (GP) formulation of BKMR is inadequate for discrete outcomes (e.g., cell-type labels), leading to biased inference and unstable variable selection. We propose a copula-based Bayesian kernel machine regression (CBKMR) model that uses outcome-appropriate discrete marginals while a Gaussian copula captures kernel-induced dependence across observations. To ensure scalability to modern single-cell datasets, we further introduce a nearest-neighbor GP-based variant, NNCBKMR, which reduces computational complexity from O(N 3) to nearly linear in N. Simulation studies show that CBKMR more accurately captures nonlinear effects and yields stronger marker-selection performance than BKMR and top ensemble ML methods (e.g., random forests, XGBoost). Applications to multiple scRNA-seq datasets demonstrate that CBKMR identifies concise marker panels that align closely with expert-annotated gene signatures while providingposterior uncertainty for principled decision-making.

bioinformatics↗

bioRxiv2025

Chromosome-level genome assemblies of Nicotiana attenuata and Nicotiana obtusifolia

Nicotiana attenuata and Nicotiana obtusifolia are two wild tobacco species from the Solanaceae plant family, which are rich in producing diverse specialized metabolites and have been established as ecological model systems for studying plant-insect interactions. The previously published N. attenuata and N. obtusifolia genomes were draft assemblies and had low assembly contiguity, limiting comparative genomic analysis. Here, we performed chromosome-level genome assemblies and annotations of these two species using long-read sequencing and Hi-C data. Both N. attenuata and N. obutosifolia genomes were anchored to 12 chromosomes, with an assembled genome size of 2.19 Gb and 1.3 Gb, respectively. We achieved high BUSCO completeness at the protein level, with 99.3% for N. attenuata and 97.9% for N. obtusifolia. The reference genomes of N. attenuata and N. obtusifolia presented in this study will advance the understanding of metabolic innovations in Solanaceae plants.

genomics↗

bioRxiv2025

Mapping Allosteric Rewiring in Viral RNA: Sequence-Encoded Control of Protein Binding Mechanisms

RNA recognition by proteins is governed not only by static structure but also by allostery encoded within non-local dynamic motifs. In this study, we systematically identify allosteric communication hubs in RNA and map multiple residue-connected pathways, revealing how these networks are rewired upon mutation and protein binding. To capture these effects under physiological salt conditions, we performed tens of microseconds of atomistic and steered molecular dynamics simulations and computed binding free energies for Tat-TAR complexes across three immunodeficiency virus variants, BIV, HIV-1, and HIV-2. Allosterically coupled sites were identified using contact-based principal component analysis, and communication pathways were traced through an extended graph-network algorithm--the first such application to RNA systems. Two distant motifs--the bulge and the apical loop--emerge as allosteric switches and information hubs: the bulge engages Tat, while the loop interacts with another protein partner, CycT1, both essential for transcriptional activation and antiviral targeting. We find that HIV-2 TAR, with strong loop-bulge coupling and high self-integrity, favour conformational selection and exhibits lower Tat-binding affinity. In contrast, a single C24 insertion in HIV-1 TAR reconfigures communication pathways, enabling an induced-fit mechanism with enhanced affinity. The study not only elucidates an allosteric rewiring between the loop and bulge but also highlights how this communication is dynamically reconfigured upon protein binding. Tat association at the bulge reorganizes and reorients loop residues, thereby promoting the subsequent recruitment of CycT1. This work overall underscores how sequence (even a single mutation) encoded RNA allostery can modulate not only a proteins binding mechanism and affinity but also influence downstream molecular events within transcriptional signalling cascades. STATEMENT OF SIGNIFICANCEIn vitro selection strategies such as SELEX have long underscored the therapeutic relevance of the TAR RNA-Tat protein interface, yet they remain experimentally demanding and often overlook how subtle sequence variations reshape molecular recognition and RNA-protein binding affinity. By integrating atomistic and free-energy simulations with a graph-network-based framework, the study reveals that even a single-nucleotide change can rewire RNAs allosteric communication pathways, switching between conformational selection and induced-fit mechanisms and alter binding affinity. These findings bridge molecular dynamics with experimental selection, offering a predictive, thermodynamics-based framework to rationalize sequence-structure-function relationships and guide the rational design of high-affinity RNA-protein complexes and next-generation RNA therapeutics.

biophysics↗

bioRxiv2025

Disentangling the reproductive and metabolic transcriptional responses to diet in Drosophila melanogaster

Nutrition significantly influences various life-history traits in organisms, impacting decisions about growth, reproduction, and longevity. Previous studies in Drosophila have demonstrated that diet affects gene transcription, with many genes exhibiting altered expression between protein- and carbohydrate-rich diets. Some responses, such as the upregulation of oogenesis-related genes in protein-rich conditions, are physiologically intuitive, yet it remains challenging to distinguish between metabolic adaptations to different diets and regulation pertaining to reproductive investment in response to nutrient availability. In this study, we explore the transcriptomic responses of virgin and mated flies to changes in nutritional environments. We confirm previous phenotypic findings by observing responses to dietary preferences and nutritional needs. Our results indicate that both nutritional conditions and mating status lead to significant changes in gene expression in females. By comparing responses between virgin and mated flies, we differentiate between basal dietary responses and reproductive adaptations, with the latter involving eight times as many genes as the former. Notably, we identify GATA family transcription factors and the heat-shock factor (Hsf) as crucial regulators of diet-dependent reproductive genes. These findings enhance our understanding of the complex interactions between nutrition and reproductive strategies in Drosophila.

evolutionary biology↗

bioRxiv2025

Parkia javanica extracts exhibits tissue regeneration potential in Zebrafish (Danio rerio)

Parkia javanica is a medicinal plant acknowledged for its diverse pharmacological features, but its biological effects, like regeneration and wound-healing properties, in the zebrafish animal model (Danio rerio) is unexplored. The purpose of this study was to determine the caudal fin tissue regeneration and antioxidant potential in response to Parkia javanica fruit and bark extracts on Danio rerio. The Danio rerio caudal fin was amputated and subsequently was treated with Parkia javanica fruit and bark extracts at 0.346{micro}g/mL and 2.86{micro}g/mL respectively. The regenerative effects of Parkia javanica fruit and bark extracts were evaluated through morphological analysis and dorso-ventral patterning. Additionally, the antioxidant properties of Parkia javanica fruit and bark extracts, along with the mechanistic insights, were evaluated using qRT-PCR. We found that both the Parkia javanica fruit and bark extracts displayed substantial antioxidant capacity with upregulation of key genes like Cat and Sod1. Further, the extracts demonstrated significant fin regeneration compared to the control group. We observed that both the Parkia javanica fruit and bark extracts possess tissue regeneration properties by upregulating key genes, like Anxa2a, Anxa2b, and Wnt3a. All these findings provide novel insights into the molecular mechanisms underlying the tissue repair and regeneration effects of Parkia javanica fruit and bark extracts and may pave the way for the development of novel regenerative therapeutic strategies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/681930v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@9a579org.highwire.dtl.DTLVardef@14edd37org.highwire.dtl.DTLVardef@9d7addorg.highwire.dtl.DTLVardef@ed79da_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Entropy of the resting state cortex in epilepsy

BackgroundEpilepsy has long been conceptualised as a disorder in which aberrant brain dynamics extend beyond the epileptogenic zone. Evidence demonstrates that loss of entropy is a generic feature of pathological dynamics in the brain, including the ictal state. However, the impact of recurrent seizures on entropy in the interictal state remains unknown. MethodsResting state magnetoencephalography (MEG) scans and resection masks of 32 individuals with epilepsy who had Engel I outcome post-surgery were retrospectively retrieved. Using co-registered FreeSurfer parcellations, we reconstructed the source localised MEG time series and computed sample entropy for 114 regions of interest. We then tested the association of entropy with the resected volume of the brain, and additional clinical variables including the age of seizure onset, seizure frequency and duration of epilepsy. To further understand the temporal relationship between seizure onset and entropy in the interictal state, we collected and computed sample entropy for week-long EEG traces from leucine-rich glioma inactivated 1 monoclonal antibody (LGI1-mAb) rodent models of autoimmune encephalitis (n=5) and control rats (n=5). ResultsIn individuals with epilepsy, a lower age of seizure onset was associated with lower mean sample entropy of the whole cortex (Spearmans rho =0.60, p<0.001; partial correlation =0.41, p=0.021). Entropy did not differ between the resected and non-resected regions of the brain. Furthermore, LGI1-mAb treated rodents showed a persistent decrease in sample entropy as compared to control rats, after the onset of seizures, and this difference was greatest during periods of highest seizure frequency (p<0.001). ConclusionRecurrent seizures are associated with a persistent decrease in entropy, even in the interictal state, and this decrease was found to be most profound and affecting the whole cortex in patients who had a lower age of seizure onset.

neuroscience↗

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↗