Biology subjects

Rathore, D.

Publications and source records attributed to Rathore, D..

11 recordsLinked to original sources

bioRxiv2026

MYH9, a cytosolic myosin protein, binds to dengue virus 3'UTR and facilitates replication and cellular entry

Dengue infections are considered an increasing threat to mankind due to their rapid global spread rate. The development of a widely accepted drug/vaccine is hindered due to an incomplete understanding of the virus lifecycle. Present data suggest that a cytoskeleton protein, called MYH9 binds to the 3UTR, at A4 region, a highly conserved part of the UTR across the serotypes. The levels of this protein were found to be elevated in the cells infected with the virus and the above increase is commensurate with the virus load. This protein is found to accumulate at the endoplasmic reticulum (site of virus replication) and interacts with dsRNA (a replicative intermediate), suggesting its involvement in replication. Inhibition of this proteins expression by its siRNA reduced viral load, supporting its role in viral replication. Immunofluorescence studies indicate that this protein accumulates at the cell periphery and pulldown studies suggest that this protein interacts with the viral envelope protein, suggesting a role in the dengue viruss cellular entry, possibly by acting as a receptor. Use of an anti-MYH9 drug, ML-7 indicated the reduction of the virus load, prevented the accumulation at the periphery and aided in regaining the cell morphology of virus infected cells, confirming its role in replication and entry. Collectively, these studies demonstrate a dual function of MHY9 in the virus life cycle, which may serve as a general paradigm for the other viruses and hence to develop specific drugs.

microbiology↗

bioRxiv2025

Time-dependent processing of dengue virus polyprotein yields multiple capsid forms that disrupt cellular homeostasis

Dengue virus infections spread to new geographical regions every year, cause significant morbidity and mortality, yet the progress in drug/vaccine development is limited due to an incomplete understanding of its life cycle. While a few of the proteins coded by this virus exist in multiple forms, the sequential events of polyprotein processing to yield them and the consequential effects on host cells are unclear. In this study, the virus infected cell culture data suggest that the polyprotein undergoes a time-dependent processing to yield multiple capsid forms, ie, capsid, capsid-anchor, capsid-anchor-pr, capsid-anchor-prM. Among them, the c-anc and c-anc-pr were found to localize to the mitochondria upon transfection into the HEK cells. The transmission electron microscopy studies suggest that c-anc induces mitochondrial fragmentation. Further studies showed that c-anc affects the mitochondrial fusion-related proteins and the genes involved in their functions. The pulldown experiments indicate that c-anc also interacts with 1-syntrophin (SNTA1), a cytoplasmic protein that plays a role in redox potential, oxidative stress and mitochondrial biogenesis. Importantly, the mitostress analyses suggest that c-anc triggers impaired mitochondrial dysfunctions like potential, respiration and ATP generation. In this study, we also identify ursonic acid (UNA) as a c-anc binding compound that restores mitochondrial functions and suppresses virus multiplication in vitro, ex vivo and in mice. The revealed disrupted mitochondrial homeostasis appears to be common to DENV, ZIKV, JEV, YFV, HCV, ASFV and SARS-CoV-2; hence, UNA or its related compounds could be considered as inhibitors for the above virus infections.

microbiology↗

bioRxiv2025

Mitochondrial G4 DNA Cleavage by EndoG Activates a Flexible, Stress-Dependent Repair Response via Double strand break repair pathways

G-quadruplex (G4) structures are non-B DNA elements enriched within the mitochondrial genome and serve as substrates for Endonuclease G (EndoG). Under oxidative stress, endo G relocates from the intermembrane space to the matrix, where it cleaves G4 motifs and generates mitochondrial double-strand breaks (DSBs). Notably, mitochondrial DNA (mtDNA) frequently harbours large deletions flanked by G4 motifs; these deletions are widespread in ageing and mitochondrial disorders, yet the mechanistic basis of their formation remains poorly understood. Here, we identify a damage-specific and stress-responsive mtDNA repair program that resolves EndoG-induced DSBs, using biochemical reconstitution and pharmacological inhibition. We show that these breaks are primarily repaired via microhomology-mediated end joining (MMEJ) and homologous recombination (HR), facilitated by the mitochondrial recruitment of canonical factors, including PARP1, MRE11, and Ligase III. Inhibition of PARP1 or MRE11 significantly impairs repair efficiency, confirming their essential roles in mitochondrial DSB resolution. Interestingly, exposure to ionising radiation (5 Gy) selectively suppresses mitochondrial MMEJ while enhancing HR, revealing a compensatory pathway switch tuned to the nature and severity of genotoxic stress. Classical nonhomologous ending (cNHEJ) remains undetectable under all conditions. Collectively, our findings delineate a flexible, lesion-dependent mitochondrial repair network that resolves DSBs via error-prone or recombinogenic mechanisms. This work provides mechanistic insight into the origin of mtDNA deletions and highlights the adaptive plasticity of mitochondrial genome maintenance under physiological and genotoxic stress.

molecular biology↗

bioRxiv2025

Tissue-Specific Activation of Microhomology-Mediated End Joining with Age Reflects Dynamic Rewiring of DNA Repair in Rats

Genomic instability is a hallmark of ageing, driven by the accumulation of DNA lesions and the decline of high-fidelity repair pathways such as homologous recombination (HR) and classical nonhomologous end joining (c-NHEJ). We hypothesized that ageing cells increasingly rely on microhomology-mediated end joining (MMEJ), an inherently error-prone repair pathway, whose role in ageing remains poorly characterized. Here, we present the first systematic, tissue-wide analysis of MMEJ activity across eight rat organs using an in vitro assay with defined 10-16 nt microhomology substrates and cell-free extracts from rats of different ages. Our results reveal age-associated and tissue-specific reprogramming of MMEJ: activity increased in the testes and liver, newly emerged in kidneys and lungs, and declined in immune tissues such as the spleen and thymus. Strikingly, aged brain extracts exhibited latent MMEJ activity. Repair efficiency was further modulated by microhomology length in a tissue-dependent manner. These functional shifts correlated with altered expression of key MMEJ effectors, including XRCC1, PARP1, Ligase III, and notably FEN1, whose upregulation in aged lungs mirrored robust MMEJ activation. Together, our findings uncover dynamic remodelling of MMEJ during ageing, implicating it in age-related genomic instability and highlighting potential therapeutic targets to mitigate mutation burden in ageing tissues.

molecular biology↗

bioRxiv2025

Context-Dependent Regulation of Microhomology-Mediated End Joining in Normal Tissues: Insights into Tissue-Specific Activation of DNA Repair Pathways

Microhomology-mediated end joining (MMEJ) is a mutagenic DNA double-strand break (DSB) repair pathway, typically regarded as a backup mechanism in cancer, activated when canonical repair pathways such as non-homologous end joining (c-NHEJ) or homologous recombination (HR) are compromised. While MMEJ has been detected in normal tissues, its presence is puzzling given its error-prone nature, and its physiological role remains poorly defined. Recent studies implicating MMEJ in mitosis suggest a potential function in normal proliferative cells. Here, we show that MMEJ is not uniformly active across tissues but is selectively enriched in proliferative tissues, including thymus, spleen, testes, and liver, while markedly reduced in post-mitotic tissues such as brain, heart, kidney, and lung. This differential activity is supported by tissue-specific expression of key MMEJ components (e.g., Ligase III, MRE11, XRCC1, PARP1, Pol {theta}) and inhibitory factors (e.g., WRN, RAD51, ATM). Moreover, proliferative tissues preferentially utilize short microhomologies ([~]10 nt), whereas post-mitotic tissues rely on longer microhomologies ([≥]13 nt), indicating a shift in repair pathway choice. These findings reveal that MMEJ is a tightly regulated, context-dependent repair pathway. Its activity is tolerated in proliferative tissues due to ongoing cell turnover, while its suppression in long-lived, post-mitotic cells is likely essential to preserve genomic stability. This study assigns a physiological role to MMEJ in healthy tissue homeostasis and highlights its relevance for designing targeted DNA repair-based therapeutic strategies across diverse tissue types.

molecular biology↗

bioRxiv2025

An artefact-resilient wide bandwidth bidirectional graphene neural interface

The ability to simultaneously record and modulate neural activity is critical for next-generation bidirectional neural interfaces aiming to enable adaptive neuromodulation therapies for neurological disorders. Active graphene transistor technologies are particularly promising for neural recordings, as they extend the ability to monitor brain activity at very low frequencies and support multiplexed operation for high-density neural interfaces. However, their limited charge injection capacity makes them unsuitable for stimulation. In this work, we present a bidirectional neural interface that combines nanoporous reduced graphene oxide (rGO) microelectrodes for high charge injection focal stimulation and graphene solution-gated field-effect transistors (gSGFETs) for brain activity monitoring, exploiting the advantages of both technologies in one single device. Using scalable cleanroom microfabrication techniques, we monolithically integrate these two graphene-based technologies into fully flexible probes. We evaluate the performance of the hybrid devices both in saline and in vivo, with a particular focus on transistor performance during stimulation. Our results demonstrate that the recording capability of this bidirectional neural interface, including the monitoring of infraslow and local field potential activity, is not compromised during stimulation. This work highlights the potential of this hybrid neural interface for both basic neurophysiological and clinical translation use.

neuroscience↗

bioRxiv2024

Lifting the degeneracy of optical fiber neural interfaces for optogenetics and electrophysiology by using axialtrodes

Modulating and recording neuronal activity are essential for probing brain function and developing therapies for neurological disorders. However, conventional flat-end optical fibers--widely used for deep brain access-- interact with neural tissue only at their distal tip, limiting spatial resolution across brain layers. To overcome this constraint, we introduce the microfluidic axialtrode: a soft, multimodal neural interface created by controllably angle-cleaving a thermally drawn, multimaterial optical fiber integrated with multiple metal electrodes and microfluidic channels. We demonstrate in vivo that this design enables spatially distributed optogenetics, multisite electrophysiological recording, and targeted drug delivery along the fibers axis, allowing simultaneous interaction with multiple neuronal layers. The axial configuration increases the functional interface with brain tissue, while the soft polymer construction and reduced cross-sectional footprint significantly suppress the inflammatory response compared to conventional silica fibers. Integration with a 3D-printed scaffold, fabricated from FDA-approved biocompatible resin, provides mechanical stability and compatibility with standard experimental hardware. The monolithic integration of these features positions the axialtrode as a scalable and versatile platform for next-generation neural interfacing.

neuroscience↗

bioRxiv2023

VapC12 ribonuclease toxin modulates host immune response during Mycobacterium tuberculosis infection

Mechanistic understanding of antibiotic persistence is a prerequisite in controlling the emergence of MDR cases in Tuberculosis (TB). We have reported that the cholesterol-induced activation of VapC12 ribonuclease is critical for disease persistence in TB. In this study, we observed that relative to the wild type, mice infected with {Delta}vapC12 induced a proinflammatory response, had a higher pathogen load, and responded better to the anti-TB treatment. In a high-dose infection model, all the mice infected with {Delta}vapC12 succumbed early to the disease. Finally, we reported that the above phenotype of {Delta}vapC12 was dependent on the presence of the TLR4 receptor. Overall, the data suggest that the inability of {Delta}vapC12 to resolve neutrophil-mediated inflammation reduced bacterial killing by altering the T-cell response. In conclusion, our findings suggest the role of the VapC12 toxin in modulating the hosts innate immune response in ways that favor the long-term survival of the pathogen inside the host.

microbiology↗

bioRxiv2022

High resolution cryo-EM structures of two potently SARS-CoV-2 neutralizing monoclonal antibodies of same donor origin that vary in neutralizing Omicron variants

While vaccines have by large been found to effective against the evolving SARS-CoV-2 variants, the profound and rapid effectivity of monoclonal antibodies (mAbs) in significantly reducing hospitalization to severe disease outcomes have also been demonstrated. In the present study, by high resolution cryo-electron microscopy (cryo-EM), we examined the structural insights of two trimeric spike (S) protein bound mAbs isolated from an Indian convalescent individual infected with ancestral SARS-CoV-2 which we recently reported to potently neutralize SARS-CoV-2 from its ancestral form through highly virulent Delta form however different in their ability to neutralize Omicron variants. Our findings showed binding and conformational heterogeneities of both the mAbs (THSC20.HVTR04 and THSC20.HVTR26) bound to S trimer in its apo and hACE-2 bound forms. Additionally, cryo-EM resolved structure assisted modeling highlighted key residues associated with the ability of these two mAbs to neutralize Omicron variants. Our findings highlighted key interacting features modulating antigen-antibody interacting that can further aid in structure guided antibody engineering to enhance their breadth and potency. HighlightsO_LITwo potent human mAbs obtained from a single donor differ binding to Omicron spikes C_LIO_LIPattern of binding and conformation of these mAbs bound to full length spike differs C_LIO_LIAntibody binding alters the conformational states of S trimer in its apo and hACE-2 bound forms. C_LIO_LICryo-EM structure guided modeling highlighted correlates of interacting residues associated with resistance and sensitivity of BA.1, BA.2, BA.4/BA.5 resistance and sensitivity against these mAbs. C_LI

biophysics↗

bioRxiv2022

Differential representation of natural and manmade images in the human ventral visual stream

AO_SCPLOWBSTRACTC_SCPLOWThe human visual cortex processes visual stimuli hierarchically. Early visual areas (V1, V2) of the ventral visual stream feed crude visual features (like orientation and edges) into later visual areas (V4, lateral occipital (Lat Occ), inferior temporal (IT)) that then encode complex visual features (like object form). Previous studies have reported a difference in fMRI responses between natural and urban landscapes in certain parts of the brain. Here we asked if this distinction in the representation of complex natural and man-made visual stimuli extends to the ventral visual stream and if state-of-the-art convolutional neural networks (CNN) provide a map to this categorical distinction. To assess this, we used an open source fMRI data set of V1-4 and LatOcc BOLD responses to 1750 passively viewed natural and man-made grayscale images. The same images were fed into the pre-trained CORnet-S, a CNN designed to model hierarchical human visual processing layer-wise. To identify differences in representations within and between the human visual cortex and the CNN, we computed representational dissimilarity matrices. The BOLD response to the manmade and natural images shows correlation differences for the two categories, which increase across V4 and LatOcc. Such differences were also observed in the model CORnet-S for the layers V4 and IT. Our results suggest that the human visual cortex processes natural and manmade images differently starting from V4 and that this representational difference is modeled in CORnet-S. In both, categorical representation is progressively established in the later processing stages. This might indicate that the brain has perhaps developed two-distinct systems for their representations which can be directed through evolution. Further analysis may elucidate the contributory role of evolution towards this paradigm.

neuroscience↗

bioRxiv2021

Full bandwidth electrophysiology of seizures and epileptiform activity enabled by flexible graphene micro-transistor depth neural probes

Mapping the entire frequency bandwidth of neuronal oscillations in the brain is of paramount importance for understanding physiological and pathological states. The ability to record simultaneously infraslow activity (<0.1 Hz) and higher frequencies (0.1-600 Hz) using the same recording electrode would particularly benefit epilepsy research. However, commonly used metal microelectrode technology is not well suited for recording infraslow activity. Here we use flexible graphene depth neural probes (gDNP), consisting of a linear array of graphene microtransistors, to concurrently record infraslow and high frequency neuronal activity in awake rodents. We show that gDNPs can reliably record and map with high spatial resolution seizures, post-ictal spreading depolarisation, and high frequency epileptic activity through cortical laminae to the CA1 layer of the hippocampus in a mouse model of chemically-induced seizures. We demonstrate functionality of chronically implanted devices over 10 weeks by recording with high fidelity spontaneous spike-wave discharges and associated infraslow activity in a rat model of absence epilepsy. Altogether, our work highlights the suitability of this technology for in vivo electrophysiology research, in particular, to examine the contributions of infraslow activity to seizure initiation and termination.

neuroscience↗