Biology subjects

Sharma, G.

Publications and source records attributed to Sharma, G..

At least 19 recordsLinked to original sources

bioRxiv2026

Biosurfactant polysaccharide drives dispersal of exopolysaccharide-coated myxospores in Myxococcus xanthus

Bacterial spores are highly resilient cell forms, yet the organization of their protective surface layers in diderm species remains largely unexplored. For the social predatory soil bacterium Myxococcus xanthus, myxospore formation within multicellular fruiting body structures is a key ecological adaptation to surviving conditions of nutrient deprivation. These myxospores were long thought to be outwardly coated with so-called major spore coat (MASC) polysaccharide. Using polysaccharide-deficient mutant strains, electron microscopy, surface hydrophobicity assays, dye binding, and functional swarm complementation, we show that MASC instead forms a protective sub-surface outer-cortex layer, while the exopolysaccharide (EPS) glycocalyx inherited from vegetative cells constitutes the true outermost myxospore coat. EPS mediates inter-myxospore adhesion and supports collective behaviors, whereas secretion of biosurfactant polysaccharide (BPS) reduces myxospore surface stickiness, preventing excessive aggregation. BPS-deficient myxospores form persistent clumps, while EPS-deficient myxospores fail to aggregate or restore EPS-dependent swarm motility of vegetative cells. These results reveal a mechanistic interplay in which MASC serves as a sub-surface protective layer, EPS defines the exterior interface, and BPS tunes surface accessibility to regulate dispersal. Our findings overturn long-standing assumptions about myxospore architecture and illustrate a polysaccharide-driven strategy for controlling aggregation and readiness for germination. More broadly, these results highlight how social diderm bacteria leverage inherited and dynamically remodeled polysaccharide surfaces to coordinate multicellular development, in contrast to the rigid protein-based spore surfaces of Gram-positive species.

microbiology↗

bioRxiv2026

Integrated miRNA-protein profiling of small extracellular vesicle cargo reveals dynamic cargo remodelling during tissue repair in UV-C-damaged C. elegans

Ultraviolet-C (UV-C) radiation is a potent environmental stressor that induces DNA damage, accumulation of reactive oxygen species (ROS), and cellular dysfunction. This also initiates coordinated molecular responses to regulate cellular adaptation and recovery. Small extracellular vesicles (sEVs) have emerged as key mediators of intercellular communication through the selective incorporation of microRNAs (miRNAs), proteins, and lipids. However, the temporal changes of sEV-associated cargo during the progression from UV-C-induced damage to recovery remain uncharacterized. We hypothesised that UV-C exposure induces stage-specific changes in sEV cargo (miRNA and proteins) that promote the transition of cells from damage to the response and recovery phases. To examine this, a time-resolved UV-C exposure model was established using Caenorhabditis elegans (C. elegans). In this paper, we studied 2.5 hours of UV-C exposure, including cellular damage, intracellular ROS levels, and DNA integrity, to define the damage and repair state. Based on these temporal variations, samples were collected: i) immediately after exposure, ii) 6 hours post-exposure, and iii) 16 hours post-exposure were designated as damage, response, and recovery conditions, respectively. sEVs isolated from whole-worm preparations were characterised using biophysical and molecular approaches, followed by miRNA sequencing and proteomic analyses. Integrative analysis further identified miRNA-protein associations and associated them with pathways involved in stress adaptation, metabolism, signal transduction, and cellular homeostasis. Collectively, these findings provide a temporal molecular framework of sEV cargo associated with UV-C-induced damage, response, and recovery in C. elegans. Overall, this study identified candidate molecular signatures and miRNA-protein associations that underlie the temporally selective packaging of sEV-associated cargo following UV-C-induced damage, providing a basis for future tissue-specific and mechanistic investigations.

molecular biology↗

bioRxiv2026

Genetically-encoded discovery and development of peptide-macrocycle imaging agents for PD-L1

The unique cell surface composition of tumor cells forms the molecular basis for many targeting and cell-based therapies. Here, we describe the development of novel peptide-based targeting agents for programmed death ligand 1 (PD-L1). Molecular imaging by peptide agents, coupled with therapeutic intervention using the same modality, represents a critical advancement in cancer management. Whole-body PET imaging of PD-L1 expression offers a superior alternative to traditional immuno-histochemistry, making PD-L1 radiodiagnostic imaging a highly sought-after modality. PD-L1 targeting modalities developed for clinical imaging to date can be divided into antibodies, protein domains, and small macrocyclic peptides with fewer than 20 amino acids. The latter modalities can address many challenges seen in antibody-based targeting vectors. All potent PD-L1 targeting peptide modalities reported to date rely extensively on non-canonical amino acids (ncAAs). Here, we report a comprehensive structure-activity relationship (SAR) analysis of a family of macrocycles discovered from an Sx2Cx8Cx2 phage-display library composed entirely of natural amino acids (x represents 19 natural amino acids excluding Cys). Using >10,000 variants in ''focused'' phage-display libraries, we optimized these macrocycles to achieve single-digit-nanomolar potency in protein- and cell-based assays. En route to this optimization, the activity of 216 synthetic macrocycles towards PD-L1 was measured in five distinct assays; two leads have been evaluated by imaging in tumor xenografts in mice, and the X-ray structure of one advanced lead in complex with PD-L1 has been determined at 2.78 [A] resolution. This publication demonstrates the development potential of PD-L1-targeting macrocycles that do not require extensive incorporation of ncAAs and the democratization of discovery by mapping the optimization path to single-digit-nanomolar assets for targeted radiopharmaceuticals via canonical phage-display technology.

pharmacology and toxicology↗

bioRxiv2026

Male Age and Sexual Maturity: Lipopolysaccharide-induced tumor necrosis factor influences sperm quality and reproduction in Anopheles culicifacies

Elucidating the biological and molecular mechanisms that govern male fertility and mating behavior in mosquitoes is critical for optimizing genetic and sterile insect technique-based vector control strategies. Here, we examined age-related changes in male reproductive capacity in Anopheles culicifacies, using female egg output as an indirect indicator of male fertility. Our results demonstrated that male reproductive age follows a non-linear pattern of fertility. Morphometric analysis from emergence to day 13 post-eclosion revealed a strong correlation between seminal vesicle capacity and female fecundity, suggesting that age-dependent gonadal development directly influences reproductive potential. At the molecular level, we identified AcLITAF6 as a key regulator of male reproductive homeostasis. RNAi-mediated knockdown of AcLITAF6 impaired apoptosis-associated and phagocytic clearance, reduced sperm viability, and decreased female productive outcomes. Conclusively, we reveal a previously unrecognized role of LITAF in sperm quality control and male reproductive fitness, highlighting AcLITAF6 as a potential target for mosquito population suppression strategies.

developmental biology↗

bioRxiv2026

An extended N-terminus restrains the plant cell death-inducing ability of the catalytically competent ribonuclease domain in a pea powdery mildew RALPH effector

RALPH (RNase-like proteins associated with haustoria) effectors, which are preferentially expressed in haustoria and structurally resemble fungal T1/F1 RNases, constitute one of the largest effector families in powdery mildew (PM) fungi, yet their functions in dicot-adapted PM species remain poorly understood. Unlike cereal PM RALPHs, which lack the catalytic residues required for RNase activity, some dicot PM RALPHs retain these residues. Here, we performed a comprehensive structural and expression-based characterization of the pea PM Erysiphe pisi RALPH (EpRALPH) repertoire and functionally characterized EpRALPH11, a RALPH effector with partial conservation of the catalytic residues of T1/F1 fungal RNases. Comparative analyses identified multi-RNase-domain RALPHs as a conserved feature of the Erysiphe lineage, while expression profiling showed that many EpRALPHs are preferentially expressed in haustoria during early host colonization. AlphaFold 3-based structural analyses revealed a conserved T1/F1 RNase-like fold despite substantial sequence and surface charge divergence, indicating functional diversification among EpRALPHs. EpRALPH11 enhanced susceptibility to E. pisi in Medicago truncatula, localized to the nucleolus, and induced nucleolar fragmentation when heterologously expressed in Nicotiana benthamiana leaves. Its RNase domain exhibited T1 RNase activity in vitro, supporting the retention of a catalytically competent RNase domain and, together with its nucleolar localization, suggesting that EpRALPH11 targets plant rRNA and disrupts nucleolar functions. The RNase domain induced cell death in N. benthamiana, whereas the full-length protein and catalytic mutants did not. Cell death induction required exclusive nucleolar localization of the RNase domain, and an extended N-terminal intrinsically disordered region suppressed this activity in the full-length protein. Together, our findings reveal a previously unrecognized mechanis regulating RNase activity in a dicot PM RALPH effector and provide new insights into the functional diversification of RALPHs and their adaptation to obligate biotrophy.

plant biology↗

bioRxiv2026

novelBGC: An interactive dual-score framework for biosynthetic gene cluster novelty assessment and candidate prioritisation

Genome mining now yields tens of thousands of putative biosynthetic gene clusters (BGCs) per project, yet, separating genuinely novel candidates from rediscoveries of known compounds remains the rate-limiting step before experimental validation. Single-axis prioritisation tools, antiSMASH similarity, BiG-FAM GCF distance, and self-resistance-enzyme (SRE) filters such as ARTS, each surface a different facet of evidence, yet their isolated use systematically over-ranks rediscovery-prone BGCs and overlooks genuinely orphan clusters. We present novelBGC, a web-hosted framework that converts these disparate outputs into two deliberately non-inverse continuous metrics per BGC, a Novelty (N) and a Reference Similarity (RS) score which together define a 2D decision plane that resolves rediscoveries, divergent family members, contig-edge artefacts, and uncharted chemistry with interactive visualisations, with all component weights user-tuneable at submission. Retrospective validation across three independent experimental datasets demonstrates the utility of the framework for candidate prioritization. Within the first 186-BGC SRE-guided cloning study, every confirmed bioactive product fell within the low-to-mid N band whereas 55 high-N (N [≥] 0.50) BGCs were never selected. Moreover, in the other two studies, it correctly prioritised the fully orphan lariocidin BGC of Paenibacillus sp. M2 and the divergent within-family indanopyrrole-A idp BGC of Streptomyces sp. CNX-425. Together, these case studies demonstrate that the joint (N, RS) space facilitates prioritization decisions that are difficult to achieve using any single criterion alone. from identical input data. novelBGC requires no command-line expertise, no local tool installation, and no manual integration of intermediate output formats, addressing a well-documented accessibility barrier for wet-laboratory researchers engaging with genome-mining workflows. novelBGC is freely available at https://project.iith.ac.in/sharmaglab/novelbgc/.

bioinformatics↗

bioRxiv2026

Astrocytic D1 Dopamine-Signaling Regulates Synaptic Remodeling and Cocaine Seeking

D1-type receptor (D1R)-mediated dopaminergic signaling within the nucleus accumbens shell (NAcSh) is essential for forming adaptive circuit changes that embed persistent memories associated with drug seeking and craving. While D1R is expressed in both NAcSh neurons and astrocytes, the specific contribution of astrocytic D1R to drug-related circuit plasticity remains poorly understood. Here, we demonstrate in mouse NAcSh slices that D1R agonists increase astrocytic Ca2+ activity, an effect that is attenuated by astrocyte-specific D1R knockdown. Furthermore, selective knockdown of astrocytic D1R in the NAcSh prior to cocaine self-administration inhibits cocaine-induced generation of silent synapses, therefore hampering the associated remodeling of NAcSh circuits. Behaviorally, knockdown of NAcSh astrocytic D1R expedites the extinction of cocaine seeking and reduces cue-induced reinstatement. These results identify astrocytic D1R as a fundamental component of NAcSh dopamine signaling during cocaine experience that remodels synaptic connections and neural networks underlying drug seeking and relapse.

neuroscience↗

bioRxiv2026

Phylogenomic coupling of F1 chemosensory and archaellum systems across archaea and monoderm bacteria

Archaellum-associated motility has been viewed as solely archaeal, yet new findings in Chloroflexota prompt a broader perspective. By analysing a curated [~]22,000 NCBI reference genomes alongside 2,397 archaeal and 226 archaellum-encoding Chloroflexota genomes, this study systematically characterises the co-distribution of archaellum loci with chemosensory system (CSS) classes. Maximum-likelihood phylogeny of 3,727 F1-type CheA proteins reveals three major clades, with Clade 1 comprising [~]80% monoderm representation, uniting archaeal and monoderm bacterial lineages in a shared evolutionary grouping. Overall, this work shows that not only archaeal-type motility, but also F1-CSS based sensing system, might have been gained from Archaea to Chloroflexota via horizontal gene transfer and both systems shared an evolutionary trajectory altogether.

bioinformatics↗

bioRxiv2026

Chemosensory landscape of order Vibrionales: Genome-scale phylogenomics uncovers four chemosensory architectures driven by bipartite genome organization

Chemosensory systems (CSSs) are multi-protein assemblies regulating bacterial motility and diverse alternative cellular functions. Despite extensive study of chemotaxis in Vibrio cholerae, a comprehensive evolutionary analysis of CSSs across order Vibrionales has been lacking. Using 116 curated representative genomes across 28 Vibrio clades and ~10,000 RefSeq/metagenome-assembled genomes, we characterized the chemosensory toolkit of Vibrionales. CheA-based phylogenetics, CSS architecture, sequence similarity networks, structural comparisons, and synteny analysis identified four discrete CSS types: F6, F7, F9, and an experimentally unexplored F8. F6 is universally conserved on chromosome I and essential for flagellar motility (chemotaxis), while F7, F8, and F9 show patchy, replicon-flexible distributions reflecting lineage-specific retention or horizontal acquisition. F6, F7, and F8 were vertically inherited from Gammaproteobacteria and retained in selected species, whereas F9 was horizontally acquired from Alphaproteobacteria in only selected species. Structural analysis further reveals conserved CheA folds despite sequence divergence, with lineage-specific insertions in F8 and F9 CheA proteins. Collectively, this study reveals a two-tier chemosensory architecture within order Vibrionales: 1) a chromosomally stable F6 motility core under purifying selection, 2) overlaid by dynamically evolving F7, F8, and F9 accessory systems, wherein multipartite genome organization might serve as an evolutionary key for sensory innovation in order Vibrionales, enabling rapid niche adaptation without compromising core chemotactic fidelity.

microbiology↗

bioRxiv2026

Structure-Guided Biochemical Design of DNA Tweezers As A Dual Target of the Primary Glioblastoma Biomarkers S100A4 and Midkine

Glioblastoma multiforme (GBM) is among the most aggressive malignant brain tumors originating from glial cells and characterized by severe infiltration into surrounding brain tissue, rendering early detection difficult with current diagnostic imaging methods. S100A4 has been identified as a biomarker protein associated with glioblastoma invasiveness due to its role in cell motility and tumor metastasis. Similarly, midkine (MDK) poses an optimal biomedical target for identifying GBM invasive phenotypes because of its connection to the tumor microenvironment and infiltrative proliferation. Both proteins notably possess a positive charge that interacts electrostatically with the negatively charged phosphate backbone of DNA. It has been established that early molecular detection remains a critical unmet need. This study investigates a promising strategy for GBM diagnosis based on how S100A4 and MDK can selectively bind with DNA tweezer nanostructures. Computationally predicting eight distinct nucleotide sequences yielded three-stranded, hinge-scaffolded tweezer conformations for each candidate. The target protein and DNA structures, derived from AlphaFold, were paired together by molecular docking simulations conducted with HDOCK. Docking analyses evaluated binding affinity, structural complementarity, and conformational stability of the complexes formed. Among the evaluated candidates, DT3_8 computationally established the most biochemically robust interaction with both biomarker proteins. Selectivity is especially important because many S100 proteins share similar electrostatic profiles, yet DT3_8 indicates stronger selectivity for S100A4 and MDK over other S100 family proteins. These findings establish a biomechanical basis for the development of nanoscale DNA biosensors, which suggests the potential for detecting invasive GBM phenotypes, preceding radiographic manifestation and pending experimental validation.

bioinformatics↗

bioRxiv2026

Unrestrained fatty acid oxidation triggers heart failure in mice via cardiolipin loss and mitochondrial dysfunction

Cardiomyocytes primarily rely on fatty acid oxidation (FAO), which provides more than 70% of their energy. However, excessive FAO can disrupt cardiac metabolism by increasing oxygen demand and suppressing glucose utilization through the Randle cycle. Although inhibition of FAO has been investigated in heart failure, its overall therapeutic impact remains uncertain. To determine the consequences of enhanced FAO, we generated cardiomyocyte-specific ACC1 and ACC2 double-knockout (ACC dHKO) mice, which exhibit constitutively elevated FAO. ACC dHKO mice developed dilated cardiomyopathy and heart failure. Lipidomic analysis revealed marked depletion of cardiolipin caused by reduced linoleic acid, a direct consequence of excessive FAO. This cardiolipin deficiency impaired mitochondrial electron transport chain (ETC) activity, leading to mitochondrial dysfunction. Pharmacologic inhibition of FAO with etomoxir or oxfenicine restored cardiolipin levels, normalized ETC activity, and prevented cardiac dysfunction in ACC dHKO mice. These findings demonstrate that unrestrained FAO disrupts both lipid and energy homeostasis, culminating in heart failure in this model. Collectively, these results indicate that although FAO is essential for cardiac energy production, therapeutic strategies aimed at stimulating cardiac FAO may be detrimental rather than beneficial in heart failure.

cell biology↗

bioRxiv2026

Physiological detection of flow states across varied gameplay workloads

Flow is a cognitive state associated with heightened and seemingly effortless behavioral performance. Pioneering research suggests flow is an optimal cognitive mode for demanding tasks but the physiological underpinnings and identification on acute timescales, particularly across task contexts, remains an active area of research. Studies have demonstrated flow experiences are ubiquitous, in that they can arise during nearly any type of activity, suggesting flow represents a fundamental mechanism of skill mastery under which sensory inputs are seamlessly coupled to the necessary motor outputs. Cognitively, flow states are accompanied by a sense of complete task immersion, feelings of control, automatic behavior, decreased self-referential thinking and anxiety, changes in the perception of time, and improved affect to the point that arduous tasks can become autotelic, or self-rewarding. As wearable sensor technology continues to advance, the identification and manipulation of cognitive states in real-time is increasingly becoming a reality, with the potential to revolutionize learning, treatment of neurological disorders, and optimize task performance in domains ranging from professional sports to industry. This study aims to capture flow states from physiological measures so that they might be identified through wearable sensors coupled to machine-learning pipelines. In this work, models are made to predict high behavioral performance across disparately varied task conditions using multimodal physiological data, and these behavioral bouts are loosely correlated to participant responses to traditional flow state survey questions.

neuroscience↗

bioRxiv2025

Modulating p38MAPK recalibrates sensitivity of drug-resistant pancreatic adenoductal carcinoma cells toward chemotherapy and correlate with improved outcome in PDAC patients: Experimental and metadata evidence

Pancreatic cancer is one of the deadliest cancers and has very limited therapeutic options and a dismal prognosis. Among various signaling pathways which are activated during tumor development, hyperactivation of Mitogen-Activated Protein Kinase (MAPK) is responsible for high grade angiogenesis, polarization of Tumor Associated Macrophages, unfolded protein responses and exhaustion of T cells, which together contributes towards this therapeutic resistance. We therefore believe that MAPK targeting is expected to enhance sensitivity of highly resistant PDAC cells toward various cancer directed interventions. In this context, we investigated the impact of modulating p38MAPK on the sensitivity of pancreatic cancer cells towards gemcitabine. Supporting our hypothesis, our results convincely, demonstrated that indeed, p38 inhibition sensitizes both KRAS positive Panc-1 and MiaPaCa2 pancreatic carcinoma cells towards gemcitabine induced death. Interestingly p38MAPK targeting significantly reduced the cell viability, clonogenic potential of these cells and enhanced the early apoptosis. Our in-silico studies, supporting our in vitro data, potentially correlated that that high expression of p38 MAPK14 in PDAC patients is associated with poor prognosis and disease free survival. Deep miming of in silico data further demonstrated that MAPK14, in association with, hypoxia inducible factor-1 alpha and vascular endothelial growth factor signaling pathways promote angiogenic programming of PDAC which render these tumors refractory for cancer directed interventions. Based on our preliminary data, we believe that p38 MAPK based approach is potential approach for changing the faith of PDAC patients toward chemo and immunotherapy and believed to improve PDAC burden effectively in the host. HighlightsO_LIp38 MAPK inhibition enhances the sensitivity of KRAS+ pancreatic cancer cells for Gemcitabine C_LIO_LIP38MAPK knockdown cells are sensitive for Gemcitabine induced death C_LIO_LIMAPK14 (p38) is associated with angiogenesis and poor prognosis in pancreatic cancer C_LIO_LIMAPK14 Regulates Pro-Tumorigenic Pathways and immune infiltration in Pancreatic Cancer C_LI

cancer biology↗

bioRxiv2025

Modeling Human Visuomotor Adaptation with a DisturbanceObserver Framework

A fundamental problem of visuomotor adaptation research is to understand how the brain is capable to asymptotically remove a predictable exogenous disturbance from a visual error signal using limited sensor information by re-calibration of hand movement. From a control theory perspective, the most striking aspect of this problem is that it falls squarely in the realm of the internal model principle of control theory. Despite this fact, the relationship between the internal model principle and models of visuomotor adaptation is currently not well developed. This paper aims to close this gap by proposing an abstract discrete-time state space model of visuomotor adaptation based on the internal model principle. The proposed DO Model, a metonym for its most important component, a disturbance observer, addresses key modeling requirements: modular architecture, physically relevant signals, parameters tied to atomic behaviors, and capacity for abstraction. The two main computational modules are a disturbance observer, a recently developed class of internal models, and a feedforward system that learns from the disturbance observer to improve feedforward motor commands. Author summaryA central research challenge in the field of motor learning is to disentangle the components of motor learning [1-8]. The main hypothesis explored in this paper is that visuomotor rotation experiments in which participants are given distinct instructions to either move the hand or the cursor to the target offer a platform to explore two components of motor learning arising from different computations and possibly different brain regions. The two computations correspond to a disturbance observer whose role is to detect and then eliminate environmental perturbations and a feedforward system whose role is to learn from the disturbance observer to improve feedforward motor commands.

neuroscience↗

bioRxiv2025

Extracellular spike waveform analysis reveals cell type-specific changes in the superior colliculus of fragile X mice

A long-standing goal of neuroscience has been to elucidate the diverse complement of neurons in the brain, which can be defined by several criteria. Analysis of action potential shape in extracellular recordings has revealed subpopulations in several regions of the brain, allowing for insights into neuronal subtype-specific function in the intact brain. The superior colliculus (SC) is a critical sensorimotor region, integrating visual, somatosensory, auditory, and nociceptive inputs to direct complex behaviors. Recent work suggests that the SC may be adversely impacted in neurodevelopmental disorders (NDDs), underscoring its importance. However, our understanding of cellular diversity in the SC lags in comparison to other regions, limiting our ability to parse circuit changes in NDDs. Here, we utilized semi-automated clustering methods to classify neurons in the mouse SC based on multiple features of extracellularly recorded waveforms to identify five putative cell types. Secondary analysis of firing statistics and visual tuning properties supported the cluster segregation. Interestingly, the proportions of units assigned to each cluster differed in the SC of a mouse model of fragile X syndrome (FXS, Fmr1-/y), with only four of five types identified. Furthermore, we observed changes in waveform properties and firing statistics, but not visual tuning properties, between genotypes in a subtype-specific manner. Taken together, these data add to our understanding of neuronal diversity in the SC and alterations of visual circuit organization and function in NDDs.

neuroscience↗

bioRxiv2025

16S-23S-5S rRNA Database: a comprehensive integrated database of archaeal and bacterial rRNA sequences, alignments, intragenomic heterogeneity, and secondary structures

The 16S-23S-5S ribosomal RNA (rRNA) gene operon is a cornerstone of ribosomal architecture and function, making it an indispensable molecular marker for microbial taxonomy and phylogenetics. Despite the extensive development of 16S rRNA gene databases, a significant void persists in comprehensive resources that integrate all three rRNA genes (16S, 23S, and 5S), their precise alignments, intragenomic heterogeneity, and intricate structural details. To address this critical research gap, we introduce the 16S-23S-5S rRNA Database, a meticulously curated and intuitive platform encompassing around 5000 complete bacterial and archaeal genomes. This database provides granular operon-level annotations, robust alignment data, quantitative copy number statistics, percent identity matrices, and predicted secondary structures for each rRNA component. Our rigorous methodology integrates covariance models from RFAM with BLAST-based analyses for sequence comparisons, Clustal Omega for multiple sequence alignment, and Circos for genomic visualization, thereby elucidating the genomic architecture, sequence diversity, and structural conservation of rRNA genes. Crucially, the database systematically accounts for intragenomic heterogeneity, a factor paramount for accurate microbial classification and the inference of evolutionary trajectories. Our analysis reveals prevalent phyla such as Pseudomonadota (1,891 genomes), Actinomycetota (846 genomes), and Bacillota (773 genomes), with Bacillota exhibiting the highest average rRNA gene copy numbers (e.g., 16S = 6.64 {+/-} 3.3, 23S = 6.63 {+/-} 3.3, and 5S = 6.8 {+/-} 3.3). Across all bacterial genomes, the 16S, 23S, and 5S rRNA genes exhibited average copy numbers of 4.25 {+/-} 2.88, 4.24 {+/-} 2.89, and 4.44 {+/-} 3.08, respectively. The responsive web interface, engineered with HTML5, JavaScript, and Flask, incorporates user feedback mechanisms to enhance usability. By integrating these comprehensive elements, the 16S-23S-5S rRNA Database not only fills a substantial lacuna in the field of rRNA data analysis but also establishes a foundational resource for large-scale investigations in microbial systematics, genome evolution, and ribosomal biology, benefiting taxonomists, microbial genomics, and microbiome researchers alike. Availability and implementation: The 16S-23S-5S rRNA Database is available as an open-access database at https://project.iith.ac.in/sharmaglab/rrnadatabase/. ImportanceUnderstanding the diversity of microbes is essential for research in health, environment, and biotechnology. Ribosomal RNA (rRNA) genes, especially the 16S gene, are commonly used to classify microbes, but studies often ignore the full set of rRNA genes (16S, 23S, and 5S) together. Our work bridges this gap by creating the first comprehensive database that includes all three rRNA genes from around 5,000 microbial genomes. It offers detailed annotations, sequence alignments, intragenomic heterogeneity, and structural insights, helping scientists more accurately classify microbes and trace their evolution. This resource is designed to be easy to use and will support a wide range of microbiological research.

genomics↗

bioRxiv2025

Emetine dihydrochloride inhibits Chikungunya virus nsP2 helicase and shows antiviral activity in the cell culture and mouse model of virus infection

Chikungunya virus (CHIKV), a mosquito-borne alphavirus, causes frequent epidemics of chikungunya fever across the world and has become a significant medical challenge, warranting the development of novel antivirals. A cell imaging-based high-content screening of the Spectrum collection of small molecules, containing all the US and international drug molecules, identified Emetine dihydrochloride (ED) as a potent antiviral against CHIKV. ED inhibited CHIKV replication in the C57BL/6 mouse model of chikungunya disease, resulting in significantly lower viremia. Importantly, clinical symptoms of joint swelling were altogether absent in the CHIKV-infected mice treated with ED. In the ERMS cells, ED inhibited the CHIKV uptake, and the virus replication early during the virus life cycle by inhibiting the viral RNA synthesis, resulting in the inhibition of the viral protein synthesis. ED was predicted to bind the helicase domain of the CHIKV non-structural protein nsP2 by in silico methods. The ED binding to the nsP2 protein and its helicase domain was validated in vitro by microscale thermophoresis and isothermal titration calorimetry. Importantly, ED inhibited the CHIKV nsP2 helicase activity in vitro in a dose-dependent manner. These data demonstrate the potential of ED to be repurposed as a novel CHIKV antiviral, warranting clinical development. AUTHOR SUMMARYChikungunya virus (CHIKV) spreads through the bites of the virus-infected Aedes mosquitoes. The virus causes frequent epidemics of chikungunya fever involving severe joint edema and muscle pain. The virus activity has been recorded in more than 100 countries in Asia, Africa, South and Central America, and Europe, and it has become endemic in several regions of the world. In 2024, around 480,000 CHIKV cases and over 200 deaths were reported worldwide. While a CHIKV vaccine was recently approved, no virus-specific antiviral therapy is available. Considering the global medical significance of the virus, the development of effective CHIKV antivirals is a priority. With a view to repurposing an existing drug, we screened a collection of all the approved US and international drug molecules and identified Emetine dihydrochloride (ED) as a potent inhibitor of CHIKV replication in the cell culture model. The CHIKV-infected mice treated with ED showed reduced virus replication and no joint swelling, which is a typical clinical symptom of CHIKV disease. Our studies show that ED binds the CHIKV nsP2, inhibiting its helicase action, which is required for replicating the viral genomic RNA and producing the viral proteins. In the past, emetine has been used in humans to treat amoebiasis. Our work thus shows the potential of the drug emetine to be repurposed for treating CHIKV patients.

microbiology↗

bioRxiv2025

Translation-specific disruption of Col1a1 expression in multiple models of Spinal Muscular Atrophy can be rescued by Risdiplam.

Spinal muscular atrophy (SMA) is a monogenic neurodegenerative disorder caused by decreased levels of Survival of Motor Neuron (SMN) protein. If left untreated, SMA patients have a poor prognosis, marked by the degeneration of motor neurons, progressive muscle weakness and atrophy. The approval of SMN-restoring therapies that improve symptoms and lifespan in patients with SMA has created emerging, non-neuronal phenotypes and an urgent need for deepening our understanding of disease pathogenesis. Leveraging the knowledge that SMN loss drives alterations in translation, we used multiple tissues from a mouse model of SMA to uncover early translational alterations in key mRNAs and proteins, which act as contributors to pathogenesis and hallmarks of the disease. Among hundreds of differentially translated mRNAs, Col1a1 emerged as a translation-specific manifestation of early defects in the mouse model. These findings were confirmed in fibroblasts derived from patients with varying levels of disease severity. Notably, treatment with SMN-restoring therapies rescued COL1A1 protein levels, particularly in fibroblasts from patients with the most severe forms of the disease. Overall, our study identifies COL1A1 as an indicator of disease severity in SMA, which captures early molecular alterations and respond to SMN-modifying therapies.

molecular biology↗