Biology subjects

Vats, A.

Publications and source records attributed to Vats, A..

9 recordsLinked to original sources

bioRxiv2026

Single-cell analysis identifies TOP2α as a critical regulator of G2/M entry and differentiation-dependent productive HPV replication

High-risk human papillomaviruses (HPVs) are the etiological agents of over 5% of cancers worldwide including those of the cervix and oropharynx. HPVs infect stratified epithelia and establish latent infections in basal cells but restrict productive replication or amplification to differentiated suprabasal cells. Despite the presence of viral genomes in most differentiated cells, only a subset of cells amplifies genomes as well as express late genes and these correspond to those that have re-entered G2/M, but the factors regulating this selectivity are unknown. To determine the signals that control the productive viral life cycle, single cell RNA seq was performed on cells that stably maintain high-risk HPV genomes following differentiation. Ten populations of undifferentiated and differentiating keratinocytes were identified, however, only one differentiated population had entered G2/M, expressed late genes and amplified viral genomes. One of the highly expressed replication factors in this population was the type II topoisomerase TOP2 while no other topoisomerases were similarly induced. TOP2 was found to bind to viral genomes, and acute depletion in differentiating cells blocked entry into G2/M, impaired genome amplification and abrogated late gene expression. Amplification also requires activation of DNA repair pathways through the induction of high levels of DNA breaks, and TOP2 accounted for more than half of the breaks present in differentiating cells. Increases in levels of TOP2 in differentiating cells were driven by the E7 oncoprotein acting through the transcription factor FOXM1, which also controls expression of G2/M factors suggesting an auto-regulatory loop. These studies identify TOP2 as a critical regulator of HPV genome amplification upon differentiation.

microbiology↗

bioRxiv2026

An Improved Protocol for High-Efficiency and Cost-Effective CRISPR/Cas9-Mediated Knock-ins in C. elegans

CRISPR/Cas9-mediated homology-directed precise genome editing using long single-stranded DNA (ssDNA) donors has expanded the possibilities for generating defined genetic modifications. However, the required ssDNA donor preparation can be technically demanding and often requires extensive locus-specific sequence design. Here, we examined parameters influencing ssDNA donor-mediated genome editing and developed approaches to simplify donor preparation using {lambda}-exonuclease-mediated ssDNA generation. By evaluating donor designs across multiple genomic loci, we found that efficient genome editing can be achieved with relatively short homology regions for a range of insertion sizes. These findings provide a basis for simplifying ssDNA donor preparation and the overall gene-editing pipeline, potentially facilitating its application across species.

molecular biology↗

bioRxiv2026

SureQuant IS-PRM Enables Cross-Species Targeted Quantification of Retinoid Metabolism and Signaling Proteins in the Heart

Retinoic acid signaling is critical for cardiac development and homeostasis. Dysregulation of all-trans retinoic acid metabolism contributes to vascular atherogenesis, restenosis, calcification, and heart failure. Therefore, assessment of proteins involved in retinoid metabolism and signaling has gained interest for identifying potential biomarkers and therapeutic targets in cardiovascular disease. However, quantifying these proteins remains challenging due to limitations of antibody-based methods. We developed a targeted proteomics approach using SureQuant internal standard-triggered parallel reaction monitoring mass spectrometry to profile these proteins. We designed a panel of 80 stable isotope-labeled (heavy) peptides representing proteins involved in retinoid signaling and metabolism, with sequences applicable to human samples and conserved across multiple species. Survey experiments using directed data-dependent acquisition on the Orbitrap Fusion Lumos mass spectrometer determined precursor and product ion masses for each heavy peptide, which were programmed into the SureQuant method for continuous monitoring. Upon detection of these heavy internal standards, the instrument transitions to a targeted PRM acquisition mode in which repeated high-resolution MS/MS spectra of both endogenous (light) and heavy peptides are acquired. Using this method, retinoid pathway-associated proteins were quantified to as low as 10 attomoles for selected targets across multiple tissues and developmental stages. Distinct tissue-specific retinoid metabolic networks were identified across lung, liver, retinal cell lines and cardiac tissues. Developmental profiling of mouse and rat hearts revealed remodeling of retinoid pathway proteins from embryonic to postnatal and adult stages, suggesting a functional transition from retinoid-driven cardiac development toward maintenance of retinoid homeostasis in the mature heart.

biochemistry↗

bioRxiv2026

Distinct Molecular Mechanisms Regulate Feeding State-Dependent CO2 Chemotaxis Plasticity During Different Life Stages in Caenorhabditis elegans

Across developmental stages, animals modulate their behavioural responses to external cues according to intrinsic physiological states. During development, particularly in juvenile stages, nervous systems undergo extensive changes at multiple levels. However, it remains unclear whether nervous systems at different developmental stages employ the same underlying molecular mechanisms to produce equivalent behavioural modulations in response to intrinsic or extrinsic cues. Using the model organism Caenorhabditis elegans, we identify here that animals employ distinct molecular mechanisms to achieve equivalent modulation of CO2-chemosensory behaviour at different developmental stages. Ubiquitin-proteasome-mediated downregulation of the insulin/IGF receptor, DAF-2 by the conserved quality-control ubiquitin ligase CHN-1/CHIP promotes attraction to environmental CO2 during the starvation-induced L1-arrest stage. In contrast, CO2-attaction in dauer animals is independent of CHN-1/CHIP activity. Furthermore, the feeding-induced reversal of CO2-chemotaxis to avoidance during L1-arrest exit requires the insulin/IGF pathway and the conserved CRH-1/CREB1 transcription factor activity in the CO2-sensing BAG neurons. However, induction CO2-avoidance during dauer exit is independent of CRH-1/CREB1 activity. These findings suggest that neural circuits at different life stages may utilize distinct, stage-specific molecular mechanisms to induce identical plasticity in chemosensory behaviour.

neuroscience↗

bioRxiv2025

Molecular Configuration, Regulation and Function of Heterochannel Electrical Synapses

Neuron-specific expression of particular gap junction channel components defines the configuration and functional properties of electrical synapses. However, how a neuron utilises multiple, simultaneously expressed channel proteins - connexins or innexins -to make meaningful connections with distinct synaptic partners remains largely unknown. Using the posterior mechanosensory circuit in C. elegans, we discovered that individual electrical synapses can be formed by clustering together molecularly distinct gap junction channel-types made of three different innexin proteins, INX-1, UNC-7, and UNC-9. In this previously unknown configuration, which we term as heterochannel synapses, molecularly distinct gap junction channel types functionally collaborate to regulate posterior touch sensory behaviour, enhancing functional robustness. We show that the synaptic trafficking of the molecularly different channel types within a heterochannel synapse is independently regulated by discrete and conserved kinesin motor proteins, while distinct molecular pathways involving channel-specific retrograde kinesins regulate their turnover. These independent, channel-specific regulations also make individual synapse-level alterations in the composition of heterochannel synapses possible under altered environmental conditions, providing a novel mechanism for electrical synapse plasticity. Finally, we present evidence of heterochannel electrical synapses in C. elegans locomotory circuits and in the cerebellar Purkinje neurons of zebrafish larvae. Altogether, we demonstrate a novel heterochannel organization of electrical synapses, their regulation, and functional importance, which may be a conserved feature of metazoan nervous system.

neuroscience↗

bioRxiv2025

Recovery of retinal terminal fields after traumatic brain injury: evidence of collateral sprouting and sexual dimorphism

The central nervous system is characterized by its limited regenerative potential, yet striking examples of functional recovery after injury in animal models and humans highlight its capacity for repair. Little is known about repair of pathways/circuits after traumatic brain injury (TBI), which results in disruption of connectivity. Here we utilize a mouse model of diffuse traumatic axonal injury (Impact-acceleration TBI) in order to explore, for the first time, the evolution of structural and functional changes in the terminal fields of the injured visual system. Retinal ganglion cell (RGC) axons and synapses were genetically labeled via AAV transduction, while anterograde and transsynaptic tracers were used to mark terminals and postsynaptic cells. Functional connectivity and visual integrity were assessed by monitoring c-Fos expression following light stimulation and pattern-reversal visual evoked potentials (pVEPs). Our findings demonstrate that, although TAI results in approximately a 50% loss of RGC axons and terminals, surviving RGCs undergo collateral sprouting, a form of compensatory branching of surviving axons, that restores terminal density to pre-injury levels. Transsynaptic tracing and c-Fos mapping confirmed the reestablishment of connectivity, which was also associated with significant improvements in visual function as measured by pVEPs. Interestingly, the recovery process exhibited sexual dimorphism, with female mice showing delayed or incomplete repair. Moreover, collateral sprouting proceeded normally in Sarm1 knockout mice, evidence of some independence from Wallerian degeneration. Our findings show that collateral sprouting may be an important mechanism of circuit repair in TAI and may represent a promising target for therapeutic interventions. SignificanceHomotypic collateral sprouting -the process by which uninjured axons from the same neuronal source extend new branches to reinnervate targets deprived of their original connections- is a fundamental yet understudied mechanism for CNS repair following injury. Unlike heterotypic sprouting, involving sprouting from unrelated pathways, homotypic sprouting offers potential to restore circuit architecture after partial lesions. Here, we employed a model of diffuse axonal injury in the mouse visual system to examine this mechanism. Our research demonstrates surviving retinal ganglion cell axons can re-establish terminal fields, achieving structural and functional connectivity. Importantly, we discovered significant sex differences: female mice showed delayed/incomplete recovery compared to males. These findings provide evidence of repair of brain circuits perturbed by TBI and the role of homotypic sprouting.

neuroscience↗

bioRxiv2025

Dynamics of mound repair behavior in termites

Termites of the species Odontotermes obesus are found widely across the Indian peninsula. Their presence is visible due to the large over-ground mounds that they build across the landscape. These mounds house their entire colony, including major and minor workers, soldiers, the queen and king, and their brood. In addition, the termites also farm a specific variety of fungus within the mounds, which helps them break down the cellulose-rich food. The precise function of the mound architecture is the subject of some debate, and it has been argued that its structure serves physiological functions including thermoregulation or gas exchange for the entire colony. We hypothesized that if the mound structure indeed serves an important function, termites must be able to sense and repair any injury to their mound structure. To test this hypothesis, we created a hole in the mound wall and observed the dynamics of ensuing breach repair. The breach is quickly detected and repaired by the termites along a consistently sigmodial pattern involving the exponential recruitment of termites during the initial phases of repair, and a derecruitment of termites in the final phases. This behavior provides us with an assay to investigate various phenomena pertaining to mound-building, and to examine the sensory cues involved in detection and repair of the mound. From the basic considerations about the stimuli involved, we developed a logistic model to describe breach repair behavior, highlighting the critical role of a systemic cue in initiating this response. Through a series of experiments utilizing various behavioral assays, we identified the presence of light as this systemic cue that triggers mound repair. When light enters the mound, it triggers construction activity in termites, even though the major and minor workers responsible for repairs do not have image-forming eyes. This suggests that termites detect light through an extraocular mechanism

animal behavior and cognition↗

bioRxiv2021

Baseline cell proliferation rates and response to UV differ in Lymphoblastoid Cell Lines derived from healthy individuals of extreme constitution types

Differences in human phenotypes and susceptibility to complex diseases are an outcome of genetic and environmental interactions. This is evident in diseases that progress through a common set of intermediate patho-endophenotypes. Precision medicine aims to delineate the molecular players for individualized and early interventions. Functional studies in Lymphoblastoid Cell Line (LCL) model of phenotypically well characterized healthy individuals can help deconvolute and validate these molecular mechanisms. We developed LCLs from eight healthy individuals belonging to three extreme constitution types, deep phenotyped on the basis of Ayurveda. LCLs were characterized by karyotyping and immunophenotyping. Growth characteristics and response to UV was studied in these LCLs. We observed significant differences in cell proliferation rates between the contrasting groups such that one type (Kapha) proliferates significantly slower than the other two (Vata, Pitta). In response to UV, one fast growing group (Vata) shows higher cell death but recovers its numbers due to inherent higher rates of proliferation. The baseline differences in cell proliferation are key to understanding the survival of cells in UV stress. Variability in baseline cellular phenotypes not only explains the cellular basis of different constitutions types but can also help set priors during designing an individualized therapy with DNA damaging agents. This is the first study of its kind that shows variability of intermediate patho-phenotypes amongst healthy individuals that have implications in precision medicine.

cell biology↗

bioRxiv2019

pH controlled histone acetylation amplifies melanocyte differentiation program downstream of MITF

Tanning response and melanocyte differentiation are mediated by the central transcription factor MITF. Enigmatically, these involve rapid and selective induction of melanocyte maturation genes, while concomitantly maintaining the expression of other effectors. In this study using cell-based and zebrafish model systems, we elucidate a pH mediated feed-forward mechanism of epigenetic regulation that enables selective amplification of melanocyte maturation program. We demonstrate that MITF activation directly elevates the expression of Carbonic Anhydrase 14 (Ca14) enzyme. Nuclear localized Ca14 increases the intracellular pH, resulting in the activation of histone acetyl transferase activity of p300/CBP. In turn enhanced H3K27 histone acetylation marks of select differentiation genes facilitates their amplified expression by MITF. CRISPR-mediated targeted missense mutation of CA14 in zebrafish results in immature acidic melanocytes with decreased pigmentation, establishing the centrality of this mechanism in rapidly activating melanocyte differentiation. Thereby we reveal a novel epigenetic control through pH modulation that reinforces a deterministic cell fate by altering chromatin dynamics.

cell biology↗