Biology subjects

Narayanan, S.

Publications and source records attributed to Narayanan, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Open-source virtual reality platform for head-fixed adult zebrafish

Virtual realities (VRs) are powerful tools to study how brains interact with the world through behavior. We present a new platform for closed-loop high-resolution virtual-reality experiments in head-fixed adult zebrafish. The VR is defined using open-source software, projected onto a semi-hexagonal tank by three projectors, and controlled by software allowing for modular trial-and-block experimental designs. Real time VR updates are performed by an optimized algorithm based on infrared tail videos. Two-photon imaging during behavior is achieved by custom gating of VR projectors and coordinated with stimulus triggers by a microcontroller. Using this system we found that fish respond to visual landmarks in virtual corridors with distinct changes in locomotion parameters and body posture. Adding landmarks to a familiar corridor elicited localized behavioral responses that decayed with experience. Restricting the viewing distance by simulating 'murky water' further confirmed that behavioral responses were driven by the visibility of landmarks independent of their position. Our platform provides a user-friendly, versatile VR system for the joint analysis of neuronal activity and behavior in adult zebrafish

neuroscience↗

bioRxiv2026

Verification Debt in Automated Biological Research Workflows: A Proof-of-Concept

Recent biological research has shown significant interest and progress towards adoption of agentic AI systems. Domain specific agentic platforms with access to large collections of biological tools with code generation and/or querying capabilities, such as Biomni (illustrative case in point), are representative of the capability to orchestrate automated research workflows. Such platforms enable collaborative AI workspace for drug discovery, genomics, bioinformatics, literature research, and experimental planning for biologists and researchers. When such platforms are used for the aforementioned workflows, individually validating every agentic decision and the research process by which it was reached becomes challenging due to the scale of decisions involved and oftentimes, insufficient disclosure of assumptions and methodological choices, limited traceability of evidence, and interpretive judgments embedded throughout the workflow, giving rise to verification debt. Verification debt in agentic environments could result in unexpected failures and consequences in downstream experiments. This study focuses on empirical qualitative characterization of verification debt in agentic (prompt to outcomes) workflows. Biomni was chosen the testing AI agentic platform in this study mainly due to the descriptive traces it provides to track every agentic step. Verification debt is examined through two complementary angles: the individual agentic decision steps that carry claims and evidence, and the underlying research process by which the agent arrives at and reports them. This study attempts to characterize verification debt with 10 test cases (covering proteomics, genomics and drug discovery) with varying degree of biological nuance across three identical and independent runs. Verification debt is represented through 9 decision-step metrics and 13 research-process metrics, and also propose the VERIFY framework for evaluating scientific verifiability and validity in agentic workflows.

bioinformatics↗

bioRxiv2026

NANO DOPA MELANIN PIGMENT WITH COSMETIC POTENTIAL PRODUCED BY HALOTOLERANT MARINE CORYNEBACTERIUM AMYCOLATUM

Bacterial melanin are macromolecules found in nature that provide a wide range of biological functions, including pigmentation, resistance to radiation, scavenging of free radicals, thermoregulation and protected from oxidative stress and harmful heavy metals. The melanin is crucial for pathogenesis and bacterial survival in a variety of circumstances, and they can also influence how bacteria interact with other organisms. Usually, bacteria produce the melanin is either black or brown colour. The produced melanin has excellent properties like antimicrobial, antioxidant, photoprotective and antibiofilm. This is a report on Corynebacterium amycolatum melanin-producing bacteria isolated from the marine sediment of Thiruvanmiyur beach in Tamil Nadu, India. Corynebacterium amycolatum was screened using tyrosine basal broth (TBB), and UV-visible spectroscopy, FTIR, and SEM were used to analyse the extracted melanin. The non-pathogenic nature of the Cornynebacterium amycolatum strain was verified through antibiotic sensitivity profiling. The cosmetic potential was evaluated using antioxidant and SPF assays. Corynebacterium amycolatum predominantly uses the DOPA pathway for melanin production, was confirmed using kojic acid inhibitor study. The in vitro studies on mouse fibroblast cell line (L929) and in vivo studies on zebra fish embryos shows non-cytotoxicity using this melanin, even in lower concentration confirms its potential to use in cosmetic formulation. This research aims to demonstrate that bacterial melanin is safe for the environment and has qualities that make it safer and more effective in cosmetics.

microbiology↗

bioRxiv2026

Concurrent AXL inhibition enhances RAS and ERK inhibitor efficacy in KRAS-mutant pancreatic and lung cancer

Resistance limits the clinical efficacy of RAS inhibitors. We applied chemical and genetic screens and identified the AXL receptor tyrosine kinase as a driver of resistance to RAS-ERK inhibition. We determined that combination treatment with the AXL inhibitor bemcentinib (AXLi) together with the RAS(ON) multi-selective tri-complex inhibitor RMC-7977 (RASi) or the ERK-selective inhibitor SCH772984 (ERKi) significantly enhanced growth suppression in human KRAS-mutant pancreatic and lung cancer models. Combined AXLi and RASi treatment of human KRAS-mutant pancreatic cell line-derived xenograft tumors synergistically suppressed ERK activation and MYC expression, and caused tumor regression. Analyses of immunocompetent mouse allograft pancreatic tumor models revealed a largely tumor cell-intrinsic response to inhibitor treatment. We identified an unexpected mechanism whereby KRAS inhibition upregulated the AXL ligand GAS6, activating AXL but inducing an AXL-dependent adaptive resistance mechanism wherein AXL antagonizes RASi efficacy. Our observations support concurrent AXL inhibition as a strategy to enhance RAS inhibitor clinical efficacy. STATEMENT OF SIGNIFICANCEOur findings identify AXL as a driver of resistance to RAS inhibitors, establishing a combination strategy to overcome resistance and enhance RAS inhibitor therapeutic efficacy in KRAS-mutant cancer by maximally inhibiting oncogenic RAS signaling.

cancer biology↗

bioRxiv2026

Dynamic cognitive representations in the dorsal pallium of adult zebrafish

Brains rely on internal models of the world to interpret sensory input and to simulate the future. In the mammalian hippocampal-entorhinal network, environments are represented by cognitive maps that contain spatially selective neurons such as place, grid, head direction and object-vector cells1-6. Neurons with allocentric spatial tuning have recently been discovered also in non-mammalian organisms including larval zebrafish7 but it remains unclear to what extent these neurons establish internal cognitive representations. We measured neuronal activity in telencephalic area Dc of head-fixed adult zebrafish exploring a novel, richly structured virtual reality. Neurons were sharply tuned to one or multiple locations and collectively represented environmental space. Activity fields exhibited neuron-specific associations to visual landmarks, indicating a prominent vectorial component in spatial representations. Population activity evolved and became increasingly informative as fish explored the environment. When landmarks were removed after familiarization, landmark-associated activity partially persisted and subsets of neurons reported prediction errors, implying that activity was in part driven by an internal representation. Strong functional coupling among neuronal ensembles and winner-take-all dynamics suggest that representations evolve by refinements of pre-structured networks. The teleost brain therefore generates internal models of structured environments that are optimized by experience and enable cognitive inference and prediction.

neuroscience↗

bioRxiv2026

Prediction from Statistical Learning Aids Auditory Scene Analysis

Statistical regularities support auditory scene analysis across multiple levels. While acoustic regularities like comodulation and harmonicity aid bottom-up perceptual grouping, higher-level regularities like linguistic or musical structure must be learned to form a mental "schema" of statistical patterns. Although learned schemas may benefit comprehension by helping listeners perceptually separate and/or attend to a target sound stream in an acoustic mixture, the underlying mechanisms are unclear. Here, we used a statistical learning paradigm to expose listeners to sequences of speech syllables with fixed transitional probabilities, forming an artificial "language" of trisyllabic words. Following exposure, participants attended to one of two concurrent syllable streams and detected target syllables. Detection performance improved when the attended stream conformed to the statistical structure learned implicitly during exposure, with a larger benefit in the presence of a competing stream than in quiet. In contrast, predictability of the unattended stream had no effect on performance. Electroencephalography revealed that predictable targets elicited earlier parietal P300 "target-recognition" responses and enhanced neural tracking of the attended stream, with additional signatures of predictive processing observed even in the absence of targets. These findings demonstrate that learned statistical regularities enhance listening in noise by enabling predictive, schema-based selection of relevant input. Rather than facilitating automatic segregation of competing sounds, learned lexical schemas support auditory scene analysis through attentional template matching. Our findings establish a direct mechanistic link to the role of prediction in schema-based listening in noise. SignificanceOur remarkable ability to isolate a target sound source, such as a persons voice, in noisy environments is essential for effective communication. This process--termed auditory scene analysis--is known to rely on low-level acoustic regularities, but it is unclear whether learned higher-level regularities, like linguistic structure, also contribute. Combined electroencephalography and behavioral experiments reveal that statistical prediction of upcoming target syllables based on learned syllable-transition probabilities of an artificial language improves attentional selection to a target sound stream in an acoustic mixture. Prediction enhances neural tracking of the attended stream and speeds neural recognition of auditory targets. These findings have implications for auditory training approaches to rehabilitate hearing-impaired individuals who struggle to understand speech in noise.

neuroscience↗

bioRxiv2026

Synthetic circRNAs employ IRES activity for translation in cells and in cell-free translation systems

Gene regulation through translation is critical for spatiotemporal protein expression. Internal ribosomal entry sites (IRESes) mediate mRNA-specific translation by recruiting ribosomes to 5' untranslated regions. Circular RNAs (circRNAs), naturally occurring and stable RNAs, are increasingly used as synthetic tools for sustained therapeutic protein translation by IRES-driven initiation. However, the functionality of different IRESes in synthetic circRNAs remains sparsely characterized. We systematically examine circRNA reporter translation by viral and cellular IRESes in human cells and in diverse in vitro translation systems. Improved circRNA purification by urea-PAGE and RNase R-treatment removes contaminants that induce RNA sensing. Viral CVB3 and HCV, as well as cellular Hoxa9, Chrdl1, Cofilin and c-Myc IRESes, effectively drive circRNA translation. We also establish circRNA translation in a recently developed human cell-free extract that recapitulates IRES-dependent regulation, and allows for precise engineering of HCV IRES-mediated translation. These findings inform IRES selection for synthetic circRNA translation relevant for circRNA-based medicine. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/715045v2_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1a60d08org.highwire.dtl.DTLVardef@a1a7d6org.highwire.dtl.DTLVardef@112042aorg.highwire.dtl.DTLVardef@1cf6c34_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Machine Learning Ensemble Reveals Distinct Molecular Pathways of Retinal Damage in Spaceflown Mice

BackgroundSpaceflight-associated neuro-ocular syndrome (SANS) poses significant risks to astronaut visual health during long-duration missions, yet its underlying molecular mechanisms remain incompletely understood. Oxidative stress and apoptosis are candidate molecular drivers, but their transcriptomic signatures in spaceflight-exposed retinal tissue have not been systematically characterized. MethodsWe applied a machine learning ensemble of linear regression models to predict two ocular phenotypes: 4-hydroxynonenal (4-HNE) immunostaining as a marker of lipid peroxidation-mediated oxidative damage; and TUNEL positivity as a marker of apoptotic cell death. In this observational study, we use bulk retinal gene expression data obtained from a controlled experiment with ground control and spaceflown mice to predict these phenotypes. Gene Ontology pathway enrichment was performed on the most predictive gene sets for each phenotype. ResultsThe 4-HNE phenotype was predicted by genes that converge on membrane-associated pathways, photoreceptor protein modification, synaptic dysfunction, and extracellular matrix dysregulation, including B2m, Tf, Cnga1, mt-Nd1, Snap25, and Efemp1. The genes predicting the TUNEL phenotype revealed a distinct signature emphasizing stress-induced apoptosis, rod photoreceptor degeneration, and endoplasmic reticulum dysfunction, with Ddit4, Nrl, Rom1, Reep6, and Gabarapl1 emerging as central regulators. ConclusionsOxidative lipid peroxidation and apoptotic cell death represent complementary and molecularly distinct pathological mechanisms in spaceflight-exposed murine retinal tissue. The gene signatures provide a putative molecular framework for developing noninvasive biomarkers and therapeutic targets to monitor and protect astronaut visual health during long-duration and deep-space missions.

bioinformatics↗

bioRxiv2025

Does Fermentation Enhance Beverage Safety? Kombucha's Resistance to Microbial Invasion Suggests a Protective Role

Does fermentation enhance the safety of beverages? This study investigates kombuchas resilience to microbial invasion from human hands. Kombucha, an ancient fermented tea, relies on a biofilm known as a symbiotic community of bacteria and yeast (SCOBY) and a starter culture to ferment sweet tea, producing various metabolites including gluconic acid, acetic acid, ethanol, and carbon dioxide. While fermented foods have been historically associated with potential health benefits, direct evidence comparing the prevalence of human pathogens in fermented versus non-fermented beverages has been lacking. To address this, we conducted a citizen science experiment at Arizona State University, introducing swabs from peoples palms into both kombucha and a sweet tea control. Over 30 days, we monitored the bacterial and fungal composition using 16S and ITS rRNA sequencing. Our findings reveal that kombucha maintained a relatively stable microbial profile and physical appearance, with a typical SCOBY biofilm developing. In stark contrast, the sweet tea experienced a dramatic change in microbial composition and was visibly compromised by rapidly growing microorganisms. Importantly, this suggests that the complex microbial ecosystem of kombucha can limit the growth of foreign microbes introduced from human hands. Given that human pathogens were absent from the kombucha while present in the tea samples, our results indicate that the antimicrobial properties of fermentation byproducts and the physical barrier of the SCOBY may contribute to this resilience. Further research is warranted to fully elucidate the mechanisms underlying kombuchas resistance to microbial invasion.

microbiology↗

bioRxiv2025

HypoxamicroRNA-210 protects against hepatic steatosis by inhibiting CIDEC expression

Background and AimsMetabolic dysfunction-associated steatotic liver disease (MASLD) is a major global health burden. Although hypoxia is known to contribute to MASLD pathogenesis, the role of hypoxia signaling remains poorly defined. We investigated whether HypoxamicroRNA-210 (miR-210), a key hypoxia-inducible microRNA, regulates hepatic lipid metabolism and MASLD development. MethodsSerum miR-210 levels were quantified in MASLD patients and matched controls. Human hepatic spheroids and HepG2 cells were exposed to fatty acids to assess miR-210 induction and lipid accumulation. miR-210 knockout mice were fed a Western diet to evaluate hepatic steatosis and transcriptomic changes using RNA sequencing. RNA pull-down and 3UTR-driven luciferase reporter assays were employed to identify miR-210 targets. Functional effects of miR-210 mimic were examined in knockout mice, db/db mice, and in vitro human hepatic spheroid models. ResultsSerum miR-210 levels were significantly reduced in MASLD patients compared with matched controls. Consistently, human hepatic spheroids did not appropriately increase miR-210 expression in response to fatty acid-induced intracellular hypoxia. This blunted miR-210 response contributed to hepatic lipid accumulation, as loss of miR-210 in a mouse model of MASLD led to increased hepatic lipid deposition and activation of lipid metabolic pathways. We identified CIDEC as a direct miR-210 target mediating its inhibitory effects on hepatic lipid accumulation, and restoring miR-210 expression suppressed CIDEC and reduced hepatic lipid content in knockout mice on a Western diet. Moreover, miR-210 attenuated lipid accumulation in both in vitro human hepatic spheroids and in vivo db/db mice models of MASLD. ConclusionsmiR-210 protects against hepatic steatosis by inhibiting CIDEC expression, suggesting miR-210-CIDEC axis as a promising therapeutic target for reducing hepatic lipid accumulation and preventing MASLD progression. Impact and ImplicationsThis study addresses a critical gap in understanding how hypoxia signaling shapes MASLD and uncovers a novel pathogenic mechanism of hepatic steatosis arising from fatty acids-induced dysregulation of miR-210. Impaired hypoxia responses, via blunted miR-210 induction, contribute to hepatic lipid accumulation through upregulation of CIDEC, a newly identified target of miR-210. These findings establish miR-210 as a novel regulator of hepatic lipid homeostasis and underscore its therapeutic potential. Interventions aimed at restoring miR-210 function in the liver may offer a promising strategy to ameliorate hepatic steatosis and prevent MASLD progression.

molecular biology↗

bioRxiv2025

An Oral Combination therapy against SARS-CoV-2 based on Synergistic Action of Auranofin and Remdesivir.

The combination of direct-acting and host-directed antivirals targeting SARS-CoV-2 represents an attractive treatment strategy to combat COVID-19. In our previous work, we showed that the FDA-approved anti-arthritis drug Auranofin restricts SARS-CoV-2 replication and pathology in an animal model. Here, we report that Auranofin inhibits SARS-CoV-2 by targeting viral entry and main protease (Mpro) activity without affecting viral transcription. Time-of-addition studies combined with functional assays of viral entry, protease activity, and cell-cell fusion delineated its inhibitory effects at both early and late stages of the viral life cycle. Molecular docking and isothermal titration calorimetry analyses of Auranofin and the known Mpro inhibitor Nirmatrelvir indicated competitive binding within the Mpro active-site pocket. In addition, Auranofin attenuated NF-{kappa}B-dependent signalling and suppressed proinflammatory cytokine production. Combination studies with SARS-CoV-2 targeting nucleoside analogues, revealed the strongest synergistic antiviral activity with remdesivir in vitro. Comparable synergy was observed between auranofin and GS-621763, the orally bioavailable derivative of remdesivir, and was further validated in a preclinical animal model. Collectively, these findings provide a rationale for the further development of auranofin-nucleoside analog combinations targeting SARS-CoV-2. FundingThis research has been supported by ICMR (IIRPIG-2023-0000978) and BIRAC grant (BT/CS0070/06/22) to ST. We acknowledge the infrastructure and research support provided to IISc by the Crypto Relief Fund, L&T Trust, DST-FIST program, Institute of Eminence Fund, Ministry of Education, and the DBT-IISc partnership program (Phase II). RN acknowledges DBT-RA fellowship, SK acknowledges PMRF fellowship, and RS acknowledges FICCI-PMRF fellowship. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSMultiple previous studies have provided evidence showing that auranofin is an antiviral agent targeting SARS-CoV-2 through a host-targeting mechanism, involving the inhibition of thioredoxin reductase and redox homeostasis. Mixed results have been reported regarding the effect of this drug on inhibiting virus-induced syncytia. A prior study from our lab demonstrated the drugs effectiveness in reducing SARS-CoV-2 viral loads in both cell and animal models. Added value of the studyOur study firmly establishes the synergistic use of Auranofin and Remdesivir GS 621763 in the treatment of SARS-CoV-2 infection.

microbiology↗

bioRxiv2025

Locus coeruleus degeneration is associated with cortical tau deposition and cognitive decline in older adults at familial risk of Alzheimer's disease

INTRODUCTIONThe locus coeruleus (LC) is among the first sites of tau pathology in Alzheimers disease (AD) and may seed neocortical tau. METHODSWe used longitudinal neuromelanin-sensitive MRI to assess LC integrity in vivo in a cohort of cognitively unimpaired older adults with familial risk of AD in relation to tau and amyloid PET and long-term cognitive trajectories. RESULTSWe showed that both LC integrity at baseline and its rate of degeneration over time independently predicted a neocortical pattern of tau deposition. In keeping with the known function of the LC, neuropsychological tests showed that LC integrity at baseline predicted changes in attention. Finally, we found that longitudinal LC degeneration correlated with memory decline in people with elevated neocortical amyloid burden. DISCUSSIONOur findings underscore the importance of LC in AD pathogenesis. Longitudinal measurement of LC degeneration may help distinguish trajectories of age-related cognitive decline and early AD.

neuroscience↗

bioRxiv2025

Bioenergetic reprogramming of macrophages reduces drug tolerance in Mycobacterium tuberculosis

Eradication of Mycobacterium tuberculosis (Mtb) requires strategies targeting bacteria inside the host. Mtb exhibits heterogeneity in redox metabolism inside macrophages to evade killing by anti-TB drugs. If and how macrophage physiology correlates with bacterial redox heterogeneity and drug tolerance remains unclear. Using a fluorescent reporter of mycobacterial redox potential, flow sorting, and RNA sequencing of infected macrophages, we characterized transcriptional and metabolic responses of macrophages harboring redox-diverse Mtb populations. We found that macrophages with suppressed glycolysis and elevated oxidative phosphorylation (OXPHOS) correlated with Mtb populations exhibiting reductive stress and drug tolerance. Conversely, macrophages with elevated glycolysis and suppressed OXPHOS displayed higher mitochondrial reactive oxygen species through reverse electron transport, resulting in oxidative stress in Mtb and enhancing drug efficacy. Computational and genetic approaches identified Nrf2 as a key regulator of macrophage bioenergetics driving redox heterogeneity and drug tolerance in Mtb. Redirecting macrophage metabolism from OXPHOS to glycolysis using an FDA- approved antiemetic drug, meclizine, subverted redox heterogeneity and diminished drug tolerance in macrophages and mice. The pharmacological profile of meclizine (Cmax and AUClast) indicated no adverse interactions with first-line anti-TB drugs in mice. Our data demonstrate the feasibility of reprogramming macrophage metabolism to reduce drug tolerance in Mtb infection.

microbiology↗

bioRxiv2025

Quantitative evaluation of the role of the microenvironment in the phenotype, metabolism, and drug resistance of PDAC tumor organoids

Tumor organoids are powerful tools to study cancer. However, the clinical translation of organoid-based studies depends on how closely the organoid scaffolding material recapitulates the tumor extracellular matrix (ECM). We present a quantitative analysis of the effect of scaffold composition on the phenotype, tissue remodeling, metabolism, and drug resistance of pancreatic ductal adenocarcinoma (PDAC) organoids. We grew PDAC organoids within hydrogels made of Matrigel, collagen-I, or a mixture of collagen-I and Matrigel. Our results show that 1) PDAC organoids grown in Matrigel-only are phenotypically and metabolically similar to low-physiological two-dimensional PDAC cultures; 2) collagen-containing hydrogels, and especially so those grown in hydrogels of mixed collagen-Matrigel composition, accurately reproduce invasive tumors that underwent epithelial-to-mesenchymal transition (EMT) regarding phenotype, tissue remodeling, metabolic activity, and drug resistance. In summary, our work illustrates the importance of three-dimensional (3D) matrix composition for PDAC growth and postulates that organoids grown in collagen-Matrigel hydrogels are the most adequate for studying the biology of invasive PDAC tumors.

bioengineering↗

bioRxiv2025

Developmental synaptic pruning in the olivo-cerebellar circuit sculpts predictive processing

Developmental synaptic pruning is thought to refine neural circuits by eliminating excess connectivity, but whether this process changes the computations performed by developing circuits remains poorly understood. Here, we show that synaptic pruning sharpens neural representations in the developing zebrafish cerebellum. Climbing fiber (CF) inputs to Purkinje neurons (PNs) progressively transition from poly- to predominantly mono-innervation during the first two weeks of life. In vivo whole-cell recordings reveal that individual CFs convey distinct sensorimotor information, and that convergence of differently tuned CFs degrades the precision of PN representations. As this convergence is reduced during development, PN responses become more selective and temporally precise. Later-stage PNs also exhibit stronger predictive responses to expected sensory events and enhanced responses to violations of those expectations, accompanied by improved behavioral adaptation. These findings suggest that developmental synaptic pruning is not simply a process of reducing excess connectivity, but can contribute to the functional specialization of neural circuits by sharpening neuronal representations and enabling increasingly precise predictive sensorimotor computations.

neuroscience↗

bioRxiv2024

Notch signaling stabilizes lengths of motile cilia in multiciliated cells in the lung

Airway multiciliated cells (MCs) maintain respiratory health by clearing mucus and trapped particles through the beating of motile cilia. While it is known that ciliary lengths decrease along the proximal-distal (P-D) axis of the tracheobronchial tree, how this is regulated is unclear. Here, we demonstrate that canonical Notch signaling in MCs plays a critical role in stabilizing ciliary length. Inhibition of Notch signaling in MCs results in ciliary shortening in the trachea, lengthening in the distal airway, and to region-specific alterations in gene expression. We probe how environmental challenges impact MC homeostasis using germ-free and Mycobacterium tuberculosis (M. tb) infection models. While germ-free conditions do not perturb ciliary lengths, M. tb infection leads to lengthening of distal airway cilia, correlating with a downregulation of Notch signaling. These findings reveal that ciliary length and the P-D gradient in the airways are actively regulated, with Notch signaling serving as a stabilizing mechanism.

cell biology↗

bioRxiv2024

XRN1 supplies free nucleotides to feed alphavirus replication

Several RNA viruses induce widespread degradation of cellular mRNAs upon infection; however, the biological significance and mechanistic details of this phenomenon remain unknown. Here, we make use of a model alphavirus, Sindbis virus (SINV), to fill this knowledge gap. We found that SINV triggers cellular RNA decay through the exonuclease XRN1 and the 5-to-3 degradation machinery (5-3DM). These proteins accumulate at viral replication organelles (VROs) and interact with the non-structural protein 1 (nsP1), bringing mRNA degradation into proximity with vRNA synthesis. Our data suggest that monophosphate nucleotides released by cellular RNA decay are recycled through the salvage pathway to feed viral replications. Our work thus reveals a fundamental connection between cellular mRNA degradation and viral replication via nucleotides repurposing. Research highlightsO_LI5-3 RNA decay is essential for the replication of a wide range of viruses. C_LIO_LIXRN1 directly interacts with transcripts which are degraded during infection. C_LIO_LIRNA decay factors and salvage pathway members localise to viral factories. C_LIO_LISupplying nucleosides to several 5-3DM deficient cells facilitates SINV infection. C_LI

biochemistry↗

bioRxiv2024

Immunogenicity and protection efficacy of self-amplifying and circular mRNA vaccines for SARS-CoV-2

Recent advances in vaccine technology have positioned messenger RNA (mRNA) vaccines as safe and reliable options for human use. Conventionally, mRNA vaccines were designed using linear or self-amplifying mRNA (SAM), the latter considered to be superior. However, limited success was achieved with SAM vaccines during the COVID-19 pandemic. Further, studies on Circular mRNA (Circ-RNA) vaccines against the SARS-CoV-2, Ebola and monkey pox proved their efficacy. Circ-RNAs are highly stable, neither they induce inflammatory response nor require any extracellular protein for their function. Here, we compared the efficacy of SAM- and Circ-RNA vaccines using the SARS-CoV-2-RBD (receptor binding domain) as the antigen. Both SAM-RBD and Circ-RBD induced a comparable anti-RBD IgG titer and virus-neutralizing antibody titer. However, the latter induced a significantly higher memory T-cell response. Immunization with SAM- and Circ-RBD showed no mortality and improved lung pathophysiology against acute SARS-CoV-2 infection in mice. The Circ-RBD vaccine is stable for 4 weeks at 40C. A bivalent vaccine containing Circ-RBD of both delta and omicron SARS-CoV-2 variants potently neutralized these viruses. These findings demonstrate Circ-RNA-RBD as an excellent vaccine candidate against COVID-19 and also provide a platform for developing bivalent Circ-RNA vaccine candidates against SARS-CoV-2 or other viruses with rapidly emerging variants.

microbiology↗