Biology subjects

Maheshwari, A.

Publications and source records attributed to Maheshwari, A..

18 recordsLinked to original sources

bioRxiv2026

Efficient and precise discovery of LTR-retrotransposon families using HiRepEat

Long Terminal Repeat Retrotransposons (LTR-RTs) are mobile genetic elements that replicate within host genomes using an RNA intermediate. Recent high quality genome assemblies provide new opportunities to study these repetitive elements across evolutionary timescales. We adapt the Myers O(Nd) wavefront alignment algorithm to produce a new fast LTR detection, clustering and phylogenetically-informed consensus approach for identifying LTR-RT families in new genome sequences. We present an iterative approach to identifying and removing repeats, initially tandem repeats, that we call TACO (TAndem COmpressor), and a corresponding coordinate mapping system we call SALSA (Sorted Array for Liftover of Sequence Addresses). Together these allow us to read and write in reduced genome space and search for LTR-RTs and tandem repeats in a series of operations. This greatly reduces confounding between different repeat types and allows us to uncover nested insertions. We show results from our clustering and consensus approach across the >500 genomes in the Vertebrate Genomes Project, with analysis completing in most cases in under 60 minutes with 15Gb memory and 16 cores. We also present cross-genome LTR-RT clustering across 30 Drosophila species, as well as across the VGP, providing fine-grained resolution on species-sharing patterns of LTR-RTs and revealing candidates for horizontal transfer.

bioinformatics↗

bioRxiv2026

Convergent Inhibitory Cortical Circuit Disruption Drives Genetically Distinct Absence Seizures

Childhood absence epilepsy is one of the most common pediatric epilepsies, characterized by brief involuntary lapse in consciousness and generalized spike-wave discharges (SWDs) on EEG. Despite a growing list of causative genes, the core cortical circuit abnormalities driving this highly stereotyped SWD phenotype remain elusive. Using two well-established absence epilepsy mouse models carrying point mutations in distinct genes altering pre and postsynaptic transmission, stargazer (Cacng2) and tottering (Cacna1a), we show that a specific translaminar inhibitory microcircuit defined by layer 6 corticothalamic neurons (L6 CT) and a novel Tac1+ Pvalb interneuron subtype is disrupted in both models. This early functional defect was followed by a secondary, marked dysfunction of deep-layer somatostatin-expressing (Sst) interneurons that coincides with the postnatal developmental onset of seizures. Crucially, we established the serial causality of these cascading defects by demonstrating that chemogenetic disruption of the L6 CT-Tac1+ Pvalb microcircuit alone in wild-type mice is sufficient to induce both the secondary Sst interneuron dysfunction and contemporaneous emergence of SWDs. Together, these findings reveal a sequential translaminar synaptic dysfunction or domino effect wherein a primary cell-autonomous defect triggers broader circuit adaptations permitting spike-wave hypersynchrony. Our results thus identify a convergent, causative cortical circuit pathology across two genetically heterogeneous absence epilepsy models, highlighting a common functional target for intervention

neuroscience↗

bioRxiv2026

Electrophysiological features of signals recorded from white matter

Intracranial neurophysiology studies have typically ignored signals from electrodes located in white matter (WM), assuming that their information content is artifactual or related to nearby gray matter (GM). Here, we tested the electrophysiological and functional features of signals recorded from different WM locations. Signals were recorded from 19 patients undergoing intracranial monitoring for drug-resistant epilepsy by means of stereo-electroencephalography (sEEG). Each sEEG electrode was classified into WM or GM based on the surrounding tissue. We obtained recordings from a total of 1,717 sEEG electrode contacts, 36% in WM, while the patients were in awake resting state (5 minutes). For each sEEG electrode, we employed a model-based spectral decomposition to separate periodic and aperiodic components, and we computed signal complexity metrics. For a subset of participants, we computed WM structural information from diffusion-weighted magnetic resonance imaging and we evaluated functional signals during a cognitive control task. Our results show that signals recorded from WM have different spectral features and higher complexity than GM. Complexity correlates positively with fractional anisotropy, and modulations related to behavior during the task were detected in WM. Overall, this indicates that WM signals carry information that may reflect signal propagation across WM fiber tracts.

neuroscience↗

bioRxiv2025

Calcium Dependent Protein Kinase 3 is not essential for the asexual replication of Plasmodium falciparum

Calcium dependent protein kinases are essential at various stages of malaria parasite development within the vertebrate host and the mosquitoes. In the rodent malaria parasite, Plasmodium berghei, CDPK3 is essential for the sexual stage development of the parasite within mosquitoes. However, the function of CDPK3 in the most lethal human malaria parasite, P. falciparum remains unexplored. Moreover, the calcium dependent kinase activity of CDPK3 has not been experimentally tested. With the aim to biochemically characterize CDPK3 and perform its functional evaluation in the asexual replication of P. falciparum, here we have expressed the full-length CDPK3 in E. coli and demonstrated that it is a bona fide calcium dependent kinase using a luminescence-based assay and a semi-synthetic epitope approach. Complete knock-out of cdpk3 using CRISPR/Cas9 did not show any defect in the asexual replication of the parasite and the knockout parasites look morphologically similar to the wild type. Our study suggests that cdpk3 is not essential for the asexual replication of the parasite under in vitro culture conditions. Perhaps CDPK3 is required for the sexual development of P. falciparum like its ortholog in the rodent malaria parasite. CDPK3 may be a good target for the development of transmission blocking drugs.

microbiology↗

bioRxiv2025

Shared neural geometries for bilingual semantic representations

The human brain has the remarkable ability to comprehend and express similar concepts in multiple languages. To understand how it does so, we examined responses of hippocampal neurons during passive listening, directed speaking, and spontaneous conversation, in both English and Spanish, in a small group of balanced bilinguals. We find a small number of putative cross-language neurons, whose responses to equivalent words (e.g., "tierra" and "earth") are correlated. However, neurons semantic tunings differed substantially by language, suggesting language-specific neural implementations. Instead, the crucial driver of translation was a preserved geometric organization of neural responses between the two languages, one that did not depend on neuron level functional overlap. Indeed, that geometry was implemented by a common set of neurons along distinct readout axes; this difference in readout may help prevent cross-language interference. Together, these results suggest that hippocampus encodes a language-independent internal model for meaning.

neuroscience↗

bioRxiv2025

A semantotopic map in human hippocampus

The hippocampus plays a central role in encoding abstract conceptual and semantic information. However, little is known about the topography of that encoding. We leveraged the rare opportunity to examine neural responses densely along a small portion of the human hippocampus, specifically, the mediolateral axis of the anterior body. We collected responses to passive language listening using Neuropixels probes in three anesthetized patients during clinically indicated neurosurgical procedures. We computed semantic tuning functions for each recording site by regressing threshold crossing events and single unit responses against semantic embeddings from GPT-2, Word2Vec, and SBERT. We find that tuning functions of more distant recording sites are more dissimilar, supporting the hypothesis semantotopic organization. Multiple semantic features showed systematic changes along that axis, including animacy, concreteness, and familiarity; notably, effects were individual-specific. Surprisingly, we also found a small but significant increase in semantic similarity as a function of distance between recording sites, on a shorter spatial scale, suggesting a modest periodic organization. Together, these results demonstrate the presence of a multiscale functional organization of semantics in the hippocampus.

neuroscience↗

bioRxiv2025

Participatory development of innovation and implementation strategy - a practical approach

BackgroundHealthcare and academic institutions face growing challenges in strategic planning due to rapid advances in medicine and technology, alongside fiscal and workforce constraints that limit traditional consultation. Participatory approaches offer a way to integrate diverse stakeholder perspectives under these constraints, generating contextually relevant strategies that can indicate whether current directions are appropriate or whether priorities have been overlooked. MethodsA structured participatory workshop was conducted at the 10th Grampian Research Conference (June 2025). One hundred seventy-eight participants including National Health Service (NHS) staff, academics, industry partners, patients, and public contributors, engaged in 14 parallel roundtable discussions. Contributions were captured using posters and Post-it notes, collecting 148 written annotations. Data were analysed using thematic and content analysis, supplemented by strategic frameworks including Strengths, Weaknesses, Opportunities and Threats (SWOT/TOWS), and Easy Wins, to identify and prioritise actionable strategies. ResultsFive core themes emerged: (1) access to healthcare and services, (2) patient and public involvement and engagement, (3) digital health and service delivery innovation, (4) data access, integration, and governance, and (5) workforce development and culture. SWOT analysis identified strengths in telemedicine, interdisciplinary student training, and patient and public involvement, alongside weaknesses in fragmented data, referral tracking, and workforce pressures. TOWS matrix produced strategy-oriented recommendations such as AI-enabled scheduling, remote monitoring, and transparent referral systems. Easy Wins framework assessment highlighted immediate, low-cost improvements including identifiable NHS caller identification, automated text message reminders, updated informational videos and multilingual materials. ConclusionBy combining participatory outputs with structured strategy tools, this approach demonstrated a resource-efficient model for adaptive planning. The findings align with and extend current national health policy frameworks, offering a replicable approach for institutions aiming to obtain meaningful stakeholder engagement despite fiscal and temporal constraints.

scientific communication and education↗

bioRxiv2025

Genome-wide CRISPR screens identify PTGES3 as a novel AR modulator

The androgen receptor (AR) is a critical driver of prostate cancer (PCa). To study regulators of AR protein levels and oncogenic activity, we created the first live cell quantitative endogenous AR fluorescent reporters. Leveraging this novel AR reporter, we performed genome-scale CRISPRi flow cytometry sorting screens to systematically identify genes that modulate AR protein levels. We identified and validated known AR protein regulators including HOXB13 and GATA2 and also unexpected top hits including PTGES3, a poorly characterized gene in PCa. PTGES3 repression resulted in loss of AR protein, cell cycle arrest, and cell death in AR-driven PCa models. PTGES3 is not a commonly essential gene, and our data nominate it as a prime PCa therapeutic target. Clinically, analysis of PCa data demonstrate that PTGES3 expression is associated with AR-directed therapy resistance. Mechanistically, we show PTGES3 binds directly to AR, forms a protein complex with AR in the nucleus, regulates AR protein stability in vitro and in vivo and modulates AR function in the nucleus at AR target genes. PTGES3 represents a novel therapeutic target for overcoming known mechanisms of resistance to existing AR-directed therapies in PCa.

cancer biology↗

bioRxiv2025

ralphi: a deep reinforcement learning framework for haplotype assembly

Haplotype assembly is the problem of reconstructing the combination of alleles on the maternally and paternally inherited chromosome copies. Individual haplotypes are essential to our understanding of how combinations of different variants impact phenotype. In this work, we focus on read-based haplotype assembly of individual diploid genomes, which reconstructs the two haplotypes directly from read alignments at variant loci. We introduce ralphi, a novel deep reinforcement learning framework for haplotype assembly, which integrates the representational power of deep learning with reinforcement learning to accurately partition read fragments into their respective haplotype sets. To set the reward objective for reinforcement learning, our approach uses the classic reduction of the problem to the maximum fragment cut formulation on fragment graphs, where nodes correspond to reads and edge weights capture the conflict or agreement of the reads at shared variant sites. We trained ralphi on a diverse dataset of fragment graph topologies derived from genomes in the 1000 Genomes Project. We show that ralphi consistently achieves lower error rates at comparable or longer haplotype block lengths over the state of the art for short and long ONT reads at varying coverage in standard human genome benchmarks. ralphi is available at https://github.com/PopicLab/ralphi.

bioinformatics↗

bioRxiv2025

Resolution of a human super-enhancer by targeted genome randomisation

Human gene expression is controlled from distance via enhancers, which can form longer super-enhancer-regions of intense regulatory activity. Whether super-enhancers constitute a separate regulatory paradigm remains unclear, largely due to the difficulty of dissecting the contributions and interactions of individual elements within their natural chromosomal context. To address this challenge, we developed enhancer scrambling, a high-throughput strategy to generate stochastic inversions and deletions of targeted enhancer regions by combining CRISPR prime editing insertion of symmetrical loxP sites with Cre recombinase-induced rearrangements. We applied our approach to dissect a distal super-enhancer of the OTX2 gene, generating up to 134 alternative regulatory configurations in a single experiment, and establishing how they drive gene expression and chromatin accessibility, as well as the individual contributions of its elements to this activity. Surprisingly, the presence of the sequence containing a single DNase I hypersensitive site predominantly controls OTX2 expression. Our findings highlight that enhancer-driven regulation of some highly expressed, cell-type-specific genes can rely on an individual element within a cluster of non-interacting, dispensable components, and suggest a simple functional core to a subset of super-enhancers. The targeted randomisation method to scramble enhancers can scale to resolve many super-enhancers and human gene regulatory landscapes.

synthetic biology↗

bioRxiv2024

Plural molecular and cellular mechanisms of pore domain KCNQ2 encephalopathy

KCNQ2 variants in children with neurodevelopmental impairment are difficult to assess due to their heterogeneity and unclear pathogenic mechanisms. We describe a child with neonatal-onset epilepsy, developmental impairment of intermediate severity, and KCNQ2 G256W heterozygosity. Analyzing prior KCNQ2 channel cryoelectron microscopy models revealed G256 as a node of an arch-shaped non-covalent bond network linking S5, the pore turret, and the ion path. Co-expression with G256W dominantly suppressed conduction by wild-type subunits in heterologous cells. Ezogabine partly reversed this suppression. G256W/+ mice have epilepsy leading to premature deaths. Hippocampal CA1 pyramidal cells from G256W/+ brain slices showed hyperexcitability. G256W/+ pyramidal cell KCNQ2 and KCNQ3 immunolabeling was significantly shifted from axon initial segments to neuronal somata. Despite normal mRNA levels, G256W/+ mouse KCNQ2 protein levels were reduced by about 50%. Our findings indicate that G256W pathogenicity results from multiplicative effects, including reductions in intrinsic conduction, subcellular targeting, and protein stability. These studies provide evidence for an unexpected and novel role for the KCNQ2 pore turret and introduce a valid animal model of KCNQ2 encephalopathy. Our results, spanning structure to behavior, may be broadly applicable because the majority of KCNQ2 encephalopathy patients share variants near the selectivity filter.

neuroscience↗

bioRxiv2023

Clinicopathologic Dissociation: Robust Lafora Body Accumulation in Malin KO Mice Without Observable Changes in Home-cage Behavior

Lafora Disease (LD) is a syndrome of progressive myoclonic epilepsy and cumulative neurocognitive deterioration caused by recessively inherited genetic lesions of EPM2A (laforin) or NHLRC1 (malin). Neuropsychiatric symptomatology in LD is thought to be directly downstream of neuronal and astrocytic polyglucosan aggregates, termed Lafora bodies (LBs), which faithfully accumulate in an age-dependent manner in all mouse models of LD. In this study, we applied home-cage monitoring to examine the extent of neurobehavioral deterioration in a model of malin-deficient LD, as a means to identify robust preclinical endpoints that may guide the selection of novel genetic treatments. At 6 weeks, [~]6-7 months and [~]12 months of age, malin deficient mice ("KO") and wild type (WT) littermates underwent a standardized home-cage behavioral assessment designed to non-obtrusively appraise features of rest/arousal, consumptive behaviors, risk aversion and voluntary wheel-running. At all timepoints, and over a range of metrics that we report transparently, WT and KO mice were essentially indistinguishable. In contrast, within WT mice compared across timepoints, we identified age-related nocturnal hypoactivity, diminished sucrose preference and reduced wheel-running. Neuropathological examinations in subsets of the same mice revealed expected age dependent LB accumulation, gliosis and microglial activation in cortical and subcortical brain regions. At 12 months of age, despite the burden of neocortical LBs, we did not identify spontaneous seizures during an electroencephalographic (EEG) survey, and KO and WT mice exhibited similar spectral EEG features. Using an in vitro assay of neocortical function, paroxysmal increases in network activity (UP states) in KO slices were more prolonged at 3 and 6 months of age, but were similar to WT at 12 months. KO mice displayed a distinct response to pentylenetetrazole, with a greater incidence of clonic seizures and a more pronounced post-ictal suppression of movement, feeding and drinking behavior. Together, these results highlight a stark clinicopathologic dissociation in a mouse model of LD, where LBs accrue substantially without clinically meaningful changes in overall wellbeing. Our findings allude to a delay between LB accumulation and neurobehavioral decline: one that may provide a window for treatment, and whose precise duration may be difficult to ascertain within the typical lifespan of a laboratory mouse.

neuroscience↗

bioRxiv2022

bII-spectrin is required for synaptic positioning during retinal development

Neural circuit assembly is a multi-step process where synaptic partners are often born at distinct developmental stages, and yet they must find each other and form precise synaptic connections with one another. This developmental process often relies on late-born neurons extending their processes to the appropriate layer to find and make synaptic connections to their early-born targets. The molecular mechanism responsible for the integration of late-born neurons into an emerging neural circuit remains unclear. Here we uncovered a new role for the cytoskeletal protein {beta}II-spectrin in properly positioning pre- and post-synaptic neurons to the developing synaptic layer. Loss of {beta}II-spectrin disrupts retinal lamination, leads to synaptic connectivity defects, and results in impaired visual function. Together, these findings highlight a new function of {beta}II-spectrin in assembling neural circuits in the mouse outer retina. HighlightsO_LIEstablished a new role for {beta}II-spectrin in assembling retinal circuits C_LIO_LI{beta}II-spectrin positions pre- and post-synaptic neurons to the developing synaptic layer C_LIO_LIEarly positioning of processes to the OPL is required for synaptogenesis C_LIO_LILoss of {beta}II-spectrin disrupts synaptic connectivity and impairs visual function C_LI

neuroscience↗

bioRxiv2022

Immune Contexture of Isocitrate Dehydrogenase stratified Human Gliomas

The brain tumor immune microenvironment (TIME) continuously evolves during glioma progression, but only a limited view of a highly complex glioma associated immune contexture across isocitrate dehydrogenase mutation (IDH) classified gliomas is known. Herein, we present an unprecedentedly comprehensive view of myeloid and lymphoid cell type diversity based on our single cell RNA sequencing and spectral cytometry-based interrogation of tumor-associated leukocytes from fifty-five IDH stratified primary and recurrent human gliomas and three non-glioma brains. Our analyses revealed twenty-two myeloid and lymphoid cell types within and across glioma subtypes. Glioma severity correlated with microglial attrition concomitant with a continuum of invading monocyte-derived microglia-like and macrophages amongst other infiltrating conventional T and NK lymphocytes and unconventional mucosa associated invariant T (MAIT) cells. Specifically, certain microglial and monocyte-derived subpopulations were associated with antigen presentation gene modules, akin to cross-presenting dendritic cells (DCs). Furthermore, we identified phagocytosis and antigen presentation gene modules enriched in Triggering receptor expressed on myeloid (TREM)-2+ cells as a putative anti-glioma axis. Accelerated glioma growth was observed in Trem2 deficient mice implanted with CT2A glioma cells affirming the anti-glioma role of TREM2+ myeloid cells. In addition to providing a comprehensive landscape of glioma-specific immune contexture, our investigations discover TREM2 as a novel immunotherapy target for brain malignancies.

immunology↗

bioRxiv2022

Intracranial EEG spectral feature analysis and focal brain stimulation reveal affective specialization within dorsal anterior cingulate cortex

Emotion is represented in several limbic and prefrontal cortical brain areas herein referred to as the Affective Salience Network (ASN). Within this network, less is known about how valence and intensity are processed in the dorsal anterior cingulate (dACC), and how affective processes in dACC compare to activity in other nodes within the ASN. Using a novel spectral feature approach to analyze intracranial electrophysiological data, we discover hemispheric specialization in the dACC such that the right hemisphere is sensitive to intensity while the left hemisphere is sensitive to valence and negative affective bias. We further applied 130 Hz continuous stimulation to the anterior cingulum bundle while patients viewed emotional faces. Faces were rated happier in all patients, an effect modulated by baseline affective bias, suggesting a causal role for the dACC during the processing of external affective stimuli.

neuroscience↗

bioRxiv2020

Removal of KCNQ2 from Parvalbumin-expressing Interneurons Improves Anti-Seizure Efficacy of Retigabine

Anti-seizure drug (ASD) targets are widely expressed in both excitatory and inhibitory neurons. It remains unknown if the action of an ASD upon inhibitory neurons could counteract its beneficial effects on excitatory neurons (or vice versa), thereby reducing the efficacy of the ASD. Here, we examine whether the efficacy of the ASD retigabine (RTG) is altered after removal of the Kv7 potassium channel subunit KCNQ2, one of its drug targets, from parvalbumin-expressing interneurons (PV-INs). Parvalbumin-Cre (PV-Cre) mice were crossed with Kcnq2-floxed (Kcnq2fl/fl) mice to conditionally delete Kcnq2 from PV-INs. In these conditional knockout mice (cKO, PV-Kcnq2fl/fl), RTG (10 mg/kg, i.p.) significantly delayed the onset of either picrotoxin (PTX, 10 mg/kg, i.p)- or kainic acid (KA, 30mg/kg, i.p.)-induced convulsive seizures compared to vehicle, while RTG was not effective in wild-type littermates (WT). Immunostaining for KCNQ2 and KCNQ3 revealed that both subunits were enriched at axon initial segments (AISs) of hippocampal CA1 PV-INs, and their specific expression was selectively abolished in cKO mice. Accordingly, the M-currents recorded from CA1 PV-INs and their sensitivity to RTG were significantly reduced in cKO mice. While the ability of RTG to suppress CA1 excitatory neurons in hippocampal slices was unchanged in cKO mice, its suppressive effect on the spike activity of CA1 PV-INs was significantly reduced compared with WT mice. In addition, the RTG-induced suppression on intrinsic membrane excitability of PV-INs in WT mice was significantly reduced in cKO mice. These findings suggest that preventing RTG from suppressing PV-INs improves its anticonvulsant effect. Significance StatementOne out of three patients with epilepsy remain resistant to anti-seizure drugs (ASD). Therefore, strategies that can enhance the efficacy of current ASDs or aid in the development of novel ASDs are in high demand. Here we show that by sparing a subset of inhibitory neurons, the ASD retigabine becomes more efficacious. These findings indicate that developing the ASDs that have relatively greater effects on excitatory over inhibitory neurons may be an effective strategy to improve the efficacy of ASDs.

neuroscience↗

bioRxiv2020

Right lateralized posterior parietal theta-gamma coupling during sustained attention in mice

Sustained attention is supported by circuits in the frontoparietal attention network. In human and primate studies, the right posterior parietal cortex (PPC) shows dominance for sustained attention, and phase-amplitude coupling (PAC) throughout the frontoparietal network correlates with performance on attention tasks. Here we evaluate oscillatory dynamics of bilateral PPC in mice during the 5-Choice Serial Reaction Time Task (5-CSRTT). Right PPC theta-gamma PAC (TG-PAC) and gamma power were independently elevated to a greater degree than the left PPC during the period prior to a correct response and were significantly correlated with accuracy in both simple and difficult tasks. Greater task difficulty was also associated with greater hemispheric asymmetry in TG-PAC, favoring the right PPC. These findings highlight the engagement of PPC with sustained attention in mice, reflected by increases in TG-PAC and gamma power, with maximal expression in the right hemisphere.

neuroscience↗

bioRxiv2018

Asynchronous suppression of visual cortex during absence seizures

Absence epilepsy is a common childhood disorder featuring frequent cortical spike-wave seizures with a loss of awareness and behavior. Using the calcium indicator GCaMP6 with in vivo 2-photon cellular microscopy and simultaneous electrocorticography, we examined the collective activity profiles of individual neurons and surrounding neuropil across all layers in V1 during spike-wave seizure activity over prolonged periods in stargazer mice. We show that most ([~]80%) neurons in all cortical layers reduce their activity during seizures, whereas a smaller pool activates or remains neutral. Unexpectedly, ictal participation of identified single unit activity is not fixed, but fluctuates on a flexible time scale across seizures. Pairwise correlation analysis of calcium activity reveals a surprising lack of synchrony among neurons and neuropil patches in all layers during seizures. Our results demonstrate an asynchronous suppression of visual cortex during absence seizures, with major implications for understanding cortical network function during EEG states of reduced awareness.

neuroscience↗