Biology subjects

Krishnan, V.

Publications and source records attributed to Krishnan, V..

27 records · Page 2Linked to original sources

bioRxiv2022

On the Mental Status of Stargazer Mice

In many childhood-onset genetic epilepsies, seizures are accompanied by neurobehavioral impairments and motor disability. In the Stargazer mutant mouse, genetic disruptions of Cacng2 result in absence-like spike-wave seizures, cerebellar gait ataxia and vestibular dysfunction. Here, we combine videotracking and instrumented home-cage monitoring to resolve the neurobehavioral facets of the murine Stargazer syndrome. We find that despite their gait ataxia, stargazer mutants display horizontal hyperactivity and variable rates of repetitive circling behavior. While feeding rhythms, circadian or ultradian oscillations in activity are unchanged, mutants exhibit fragmented sleep bouts, atypical licking dynamics and lowered sucrose preference. Mutants also display an attenuated response to visual and auditory home-cage perturbations, together with profound reductions in voluntary wheel-running. Our results reveal that the seizures and ataxia of Stargazer mutants occur in the context of a more pervasive behavioral syndrome with elements of encephalopathy, repetitive behavior and anhedonia. These findings expand our understanding of the function of Cacng2/CACNG2, variants in which have been identified in patients with bipolar disorder and schizophrenia.

neuroscience↗

bioRxiv2021

Peripheral Coupling Sites Formed by STIM1 Govern the Contractility of Vascular Smooth Muscle Cells

Peripheral coupling between the sarcoplasmic reticulum (SR) and plasma membrane (PM) forms signaling complexes that regulate the membrane potential and contractility of vascular smooth muscle cells (VSMCs), although the mechanisms responsible for these membrane interactions are poorly understood. In many cells, STIM1 (stromal-interaction molecule 1), a single transmembrane-domain protein that resides in the endoplasmic reticulum (ER), transiently moves to ER-PM junctions in response to depletion of ER Ca2+ stores and initiates store-operated Ca2+ entry (SOCE). Fully differentiated VSMCs express STIM1 but exhibit only marginal SOCE activity. We hypothesized that STIM1 is constitutively active in contractile VSMCs and maintains peripheral coupling. In support of this concept, we found that the number and size of SR-PM interacting sites were decreased and SR-dependent Ca2+ signaling processes were disrupted in freshly isolated cerebral artery SMCs from tamoxifen-inducible, SMC-specific STIM1-knockout (Stim1-smKO) mice. VSMCs from Stim1-smKO mice also exhibited a reduction in nanoscale colocalization between Ca2+-release sites on the SR and Ca2+-activated ion channels on the PM, accompanied by diminished channel activity. Stim1-smKO mice were hypotensive and resistance arteries isolated from them displayed blunted contractility. These data suggest that STIM1 - independent of SR Ca2+ store depletion - is critically important for stable peripheral coupling in contractile VSMCs.

physiology↗

bioRxiv2021

Robust clustering and interpretation ofscRNA-seq data using reference componentanalysis

MotivationThe transcriptomic diversity of the hundreds of cell types in the human body can be analysed in unprecedented detail using single cell (SC) technologies. Though clustering of cellular transcriptomes is the default technique for defining cell types and subtypes, single cell clustering can be strongly influenced by technical variation. In fact, the prevalent unsupervised clustering algorithms can cluster cells by technical, rather than biological, variation. ResultsCompared to de novo (unsupervised) clustering methods, we demonstrate using multiple benchmarks that supervised clustering, which uses reference transcriptomes as a guide, is robust to batch effects. To leverage the advantages of supervised clustering, we present RCA2, a new, scalable, and broadly applicable version of our RCA algorithm. RCA2 provides a user-friendly framework for supervised clustering and downstream analysis of large scRNA-seq data sets. RCA2 can be seamlessly incorporated into existing algorithmic pipelines. It incorporates various new reference panels for human and mouse, supports generation of custom panels and uses efficient graph-based clustering and sparse data structures to ensure scalability. We demonstrate the applicability of RCA2 on SC data from human bone marrow, healthy PBMCs and PBMCs from COVID-19 patients. Importantly, RCA2 facilitates cell-type-specific QC, which we show is essential for accurate clustering of SC data from heterogeneous tissues. In the era of cohort-scale SC analysis, supervised clustering methods such as RCA2 will facilitate unified analysis of diverse SC datasets. AvailabilityRCA2 is implemented in R and is available at github.com/prabhakarlab/RCAv2

bioinformatics↗

bioRxiv2021

Revealing the human mucinome

Mucin domains are densely O-glycosylated modular protein domains found in a wide variety of cell surface and secreted proteins. Mucin-domain glycoproteins are key players in a host of human diseases, especially cancer, but the scope of the mucinome remains poorly defined. Recently, we characterized a bacterial mucinase, StcE, and demonstrated that an inactive point mutant retains binding selectivity for mucins. In this work, we leveraged inactive StcE to selectively enrich and identify mucins from complex samples like cell lysate and crude ovarian cancer patient ascites fluid. Our enrichment strategy was further aided by an algorithm to assign confidence to mucin-domain glycoprotein identifications. This mucinomics platform facilitated detection of hundreds of glycopeptides from mucin domains and highly overlapping populations of mucin-domain glycoproteins from ovarian cancer patients. Ultimately, we demonstrate our mucinomics approach can reveal key molecular signatures of cancer from in vitro and ex vivo sources.

biochemistry↗

bioRxiv2020

Single-dose intranasal administration of AdCOVID elicits systemic and mucosal immunity against SARS-CoV-2 in mice

The coronavirus disease 2019 (COVID-19) pandemic has highlighted the urgent need for effective preventive vaccination to reduce burden and spread of severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) in humans. Intranasal vaccination is an attractive strategy to prevent COVID-19 as the nasal mucosa represents the first-line barrier to SARS-CoV-2 entry before viral spread to the lung. Although SARS-CoV-2 vaccine development is rapidly progressing, the current intramuscular vaccines are designed to elicit systemic immunity without conferring mucosal immunity. Here, we show that AdCOVID, an intranasal adenovirus type 5 (Ad5)-vectored vaccine encoding the receptor binding domain (RBD) of the SARS-CoV-2 spike protein, elicits a strong and focused immune response against RBD through the induction of mucosal IgA, serum neutralizing antibodies and CD4+ and CD8+ T cells with a Th1-like cytokine expression profile. Therefore, AdCOVID, which promotes concomitant systemic and local mucosal immunity, represents a promising COVID-19 vaccine candidate.

immunology↗

bioRxiv2020

On the Digital Psychopharmacology of Valproic Acid in Mice

ObjectiveAntiepileptic drugs (AEDs) require daily ingestion for maximal seizure prophylaxis. Adverse psychiatric consequences of AEDs present as: (i) reversible changes in mood, anger, anxiety and/or irritability that often necessitate drug discontinuation, and (ii) autism and/or cognitive/psychomotor developmental delays following fetal exposure. Technical advances in quantifying naturalistic rodent behaviors may provide sensitive preclinical estimates of AED psychiatric tolerability and neuropsychiatric teratogenicity. MethodsUsing instrumented home-cage monitoring, we assessed how valproic acid (VPA, dissolved in sweetened drinking water) alters home-cage behavior in adult C57BL/6J mice and in the adult offspring of VPA-exposed breeder pairs. By utilizing a pup open field assay, we also examined how prenatal VPA exposure impacts early spontaneous exploratory behavior. ResultsAt 500-600mg/kg/d, chronic VPA produced hyperphagia and increased wheel-running without impacting sleep, activity and measures of risk aversion. When applied chronically to breeder pairs of mice, VPA prolonged the latency to viable litters without affecting litter size. Two-week old VPA-exposed pups displayed open field hypoactivity without alterations in thigmotaxis. As adults, prenatal VPA-exposed mice displayed active state fragmentation, hypophagia and increased wheel running, together with subtle alterations in home-cage dyadic behavior. InterpretationThrough automated home-cage assessments of C57BL/6J mice, we capture an ethologically centered psychopharmacological profile of enterally administered VPA that is aligned with human clinical experience. By characterizing the effects of pangestational VPA exposure, we discover novel murine expressions of pervasive neurodevelopment. Incorporating rigorous comprehensive assessments of neuropsychiatric tolerability may inform the design of future AEDs with improved neuropsychiatric safety profiles, both for patients and their offspring.

neuroscience↗

bioRxiv2019

High-resolution MEMRI characterizes laminar specific ascending and descending spinal cord pathways in rats

Manganese Enhanced MRI (MEMRI) utilizing different manganese chloride (MnCl2) delivery methods, has yielded valuable architectural, functional and connection information about the brain. MEMRI also has the potential in characterizing neural pathways in the spinal cord. The spinal cord grey matter is anatomically composed of nine distinct cellular laminae, where each of the laminae receives input from a specific type of neuronal population and process or serves as a relay region in a specific sensory or motor pathway. This type of laminar arrangement in the spinal cord is currently only visualized by histological methods. It is of significant interest to determine whether laminar specific enhancement by Mn2+ can be achieved in the spinal cord, as has been reported in the brain and olfactory pathway. Here we focus on using MEMRI to determine the specific laminae of the thoracic region of the spinal cord. We focus on MnCl2 changes in the ascending and descending tracts of the spinal cord. Major factors in applying this technique in the spinal cord are the ability to acquire high-resolution spinal cord images and to determine a noninvasive route of administration which will result in uptake by the central nervous system.\n\nWe have applied the MEMRI approach by intraperitoneal (i.p). delivery of MnCl2 and imaged lumbar and thoracic spinal cord levels in rats to determine whether T1 weighted MRI can detect spinal cord laminae 48 hours following MnCl2 administration. T1 weighted images of the lower lumbar level were obtained from MnCl2 injected and control rats. Here we demonstrate laminar specific signal enhancement in the spinal cord of rats administered with MnCl2 vs. controls in MRI of the cord with ultra-high, 69 m in-plane resolution. We also report reduced T1 values over time in MnCl2 groups across laminae I-IX. The regions with the largest T1 enhancements were observed to correspond to laminae that contain either high cell density or large motor neurons, making MEMRI an excellent tool for studying spinal cord architecture, physiology and function in different animal models.

neuroscience↗

bioRxiv2019

Home-cage Monitoring Ascertains Signatures of Ictal and Interictal Behavior In Mouse Models of Generalized Seizures

Epilepsy is a significant contributor to worldwide disability. In epilepsy, disability has two components: ictal (pertaining to the burden of unpredictable seizures and associated medical complications including death) and interictal (pertaining to more pervasive debilitating changes in cognitive and emotional behavior). In this study, we objectively and noninvasively appraise correlates of ictal and interictal disability in mice using instrumented home-cage chambers designed to assay kinematic and appetitive behavioral measures. We discover that in C57BL/6J mice, intraperitoneal injections of the chemoconvulsant pentylenetetrazole (PTZ) acutely result in complex and dynamic changes in movement and sheltering behavior that evolve (or kindle) with repeated daily injections, and which are separate from the occurrence of convulsions. By closely studying \"interictal\" periods (between PTZ injections), we identify a syndrome of nocturnal hypoactivity and increased sheltering behavior. We observe elements of this interictal behavioral syndrome in seizure-prone DBA/2J mice and in mice with a pathogenic Scn1a mutation (modeling Dravet syndrome). Through analyzing their responses to PTZ, we illustrate how convulsive severity and \"behavioral\" severity are distinct and independent aspects of overall seizure severity. Our results illustrate the utility of an ethologically centered automated approach to quantitatively appraise murine expressions of disability in mouse models of seizures and epilepsy. In doing so, this study highlights the very unique psychopharmacological profile of PTZ.\n\nSignificance StatementEpilepsy is a brain disorder characterized by a pervasively increased risk to develop epileptic seizures. Sadly, patients with epilepsy also experience high rates of anxiety, depression and other psychiatric symptoms that significantly increase overall disability. While many mouse models of seizures and epilepsy exist, we need improved techniques to measure how new treatments impact not only seizure occurrence, but also emotional changes that persist in between seizures. In this study, we apply the technique of home-cage monitoring to clarify precisely how spontaneous mouse behavior is altered in three distinct epilepsy models. Our work illustrates the importance of an ethologically centered appreciation of neuropsychiatric disability in mice and clarifies a new approach to the measurement of \"seizure severity\".

neuroscience↗

bioRxiv2019

Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays.

Benchmarking the performance of complex analytical pipelines is an essential part of developing Laboratory Developed Assays (LDT). Reference samples and benchmark calls published by Genome in a Bottle (GIAB) Consortium have enabled the evaluation of analytical methods. However, the performance of such methods is not uniform across the different regions of the genome/exome and different variant types and lengths. Here we present a scalable and reproducible, cloud-based benchmarking workflow that can be used by clinical laboratories to rapidly access and validate the performance of LDT assays, across their regions of interest and reportable range, using a broad set of benchmarking samples.

bioinformatics↗