Biology subjects

Parikh, P.

Publications and source records attributed to Parikh, P..

6 recordsLinked to original sources

bioRxiv2025

Thalamic Interictal Epileptic and Non-Epileptic Events during NREM Sleep in Patients with Focal Epilepsy: a Stereo-EEG Study

BackgroundThalamic recordings are increasingly incorporated into stereo-electroencephalography (SEEG) evaluations of drug-resistant focal epilepsy to guide neuromodulation targeting. Human thalamic electrophysiology, however, is poorly defined, limiting the distinction between pathological and physiological activity. Here, we characterized interictal epileptic and non-epileptic events during non-rapid eye movement (NREM) sleep across multiple thalamic nuclei and examined their relationship to seizure outcomes. MethodsWe analyzed NREM sleep SEEG recordings from 64 patients with drug-resistant focal epilepsy. Electrodes sampled four thalamic nuclei: centromedian (CM), pulvinar (Pu), ventral lateral (VL), and ventral posterolateral (VPL). Patients were classified into three outcome groups: favorable, unfavorable, and surgically non-remediable. Rates of thalamic spikes, high-frequency oscillations (HFOs), spike-fast activity, and sleep spindles were analyzed and compared across nuclei and outcomes. FindingsRecordings of the thalamus revealed both pathological and physiological interictal events. Interictal epileptic events were infrequent. Only [~]0.2% of seizure-onset zone spikes propagated to the thalamus. Thalamic spike-fast activity was indicative of unfavorable surgical outcomes (CM: p = 0.047, d = 0.46) or surgically non-remediable epilepsy (VL: p = 0.002, d = 0.84). In contrast, thalamic sleep spindles were ubiquitous but reduced in surgically non-remediable patients (CM: p = 0.031, d = -0.58; VL: p = 0.005, d = -0.79). Finally, unique thalamic SEEG patterns were identified, including spikes concomitant with spindles, isolated spikes, and physiological fast ripples. InterpretationThis study provides a comprehensive characterization of thalamic interictal events during NREM sleep, enriching our understanding of thalamic pathophysiology and highlighting the value of thalamic recordings in presurgical evaluation.

neuroscience↗

bioRxiv2023

Intermediate CA1 is Required for Object-in-Place Recognition Memory in Mice

Many behaviors that are essential for survival, such as retrieving food, finding shelter and locating predator cues, rely on forming effective associations between the identity and location of spatial elements. This identity-location association is commonly assessed in rodents using spontaneous object-in-place (OiP) recognition memory tasks. OiP recognition memory deficits are seen in autism spectrum disorder, schizophrenia, and are used to detect early onset of Alzheimers disease. These deficits are replicated in animal models of neurodevelopmental, neurodegenerative and chromosomal disorders. Mouse models have been widely adopted in behavioral and systems neuroscience research for their ease of genetic manipulations, and yet very few studies have successfully assessed OiP recognition memory or its neural correlates in mice. To address this limitation, we first established that adult C57/129J and C57BL/6J male and female mice are able to successfully perform the two-object, but not the four-object version of the spontaneous OiP recognition task, with retention intervals of five minutes and one hour. Next, using chemogenetic inhibition, we found that two-object OiP requires the activity of the intermediate CA1 (iCA1) subregion of the hippocampus, but not the medial prefrontal cortex or iCA1-medial prefrontal cortex connections. Our data identify hippocampal subregion specialization in the successful assessment of OiP recognition memory in mice, expanding our understanding of the neural basis of spatial memory processing. Significance StatementAssociations between the identity and location of spatial elements (what-where associations), underlie essential behaviours such as finding food, locating shelter and safely navigating the environment. Deficits in identity-location processing occur in patients with neurodevelopmental and neurodegenerative disorders, and are replicated in rodent models using object-in-place (OiP) recognition tasks. While mice have emerged as a widely used animal model to study the biological mechanisms underlying these disorders, nothing is known about the neural substrates of OiP memory in mice. Here we have established and validated a robust experimental paradigm to assess OiP memory in mice, uncovering a specialized contribution of the hippocampal subregion intermediate CA1 to OiP performance and deepening our understanding of the neural signatures of spatial memory processing.

neuroscience↗

bioRxiv2022

Thyroid Ablation Alters Passive Stiffness and Swimming Kinematics in Zebrafish

Locomotion behavior is ultimately determined by the integration between active and passive tissues of an organism, but little is known about how these properties develop or are maintained. In this study, we used zebrafish (Danio rerio) to address the effects of a developmental hormone on morphogenesis and mechanical integration during swimming. We analyzed common kinematic variables and estimated intervertebral joint (IVJ) stiffness of zebrafish reared under different thyroid hormone profiles (euthyroid and hypothyroid) swimming during two different forward speeds, 5 and 10 BL{middle dot}s-1. We found that zebrafish reared under hypothyroid conditions swam with higher trailing-edge amplitude, a larger amplitude envelope, longer propulsive wavelengths, and lower values of lateral strain in posterior regions at both speeds. IVJ second moment area about the bending axis was greater in the TH-, a result of a change in vertebral shape compared to wildtype fish. We conclude that thyroid hormone contributes to axial design during development and therefore has an important role in determining flexural stiffness and the swimming behaviors that are affected by this important property.

developmental biology↗

bioRxiv2021

Persistence of SARS CoV-2 S1 Protein in CD16+ Monocytes in Post-Acute Sequelae of COVID-19 (PASC) Up to 15 Months Post-Infection

The recent COVID-19 pandemic is a treatment challenge in the acute infection stage but the recognition of chronic COVID-19 symptoms termed post-acute sequelae SARS-CoV-2 infection (PASC) may affect up to 30% of all infected individuals. The underlying mechanism and source of this distinct immunologic condition three months or more after initial infection remains elusive. Here, we investigated the presence of SARS-CoV-2 S1 protein in 46 individuals. We analyzed T-cell, B-cell, and monocytic subsets in both severe COVID-19 patients and in patients with post-acute sequelae of COVID-19 (PASC). The levels of both intermediate (CD14+, CD16+) and non-classical monocyte (CD14Lo, CD16+) were significantly elevated in PASC patients up to 15 months post-acute infection compared to healthy controls (P=0.002 and P=0.01, respectively). A statistically significant number of non-classical monocytes contained SARS-CoV-2 S1 protein in both severe (P=0.004) and PASC patients (P=0.02) out to 15 months post-infection. Non-classical monocytes were sorted from PASC patients using flow cytometric sorting and the SARS-CoV-2 S1 protein was confirmed by mass spectrometry. Cells from 4 out of 11 severe COVID-19 patients and 1 out of 26 PASC patients contained ddPCR+ peripheral blood mononuclear cells, however, only fragmented SARS-CoV-2 RNA was found in PASC patients. No full length sequences were identified, and no sequences that could account for the observed S1 protein were identified in any patient. Non-classical monocytes are capable of causing inflammation throughout the body in response to fractalkine/CX3CL1 and RANTES/CCR5.

immunology↗

bioRxiv2020

Immune-Based Prediction of COVID-19 Severity and Chronicity Decoded Using Machine Learning

Individuals with systemic symptoms long after COVID-19 has cleared represent approximately ~10% of all COVID-19 infected individuals. Here we present a bioinformatics approach to predict and model the phases of COVID so that effective treatment strategies can be devised and monitored. We investigated 144 individuals including normal individuals and patients spanning the COVID-19 disease continuum. We collected plasma and isolated PBMCs from 29 normal individuals, 26 individuals with mild-moderate COVID-19, 25 individuals with severe COVID-19, and 64 individuals with Chronic COVID-19 symptoms. Immune subset profiling and a 14-plex cytokine panel were run on all patients. Data was analyzed using machine learning methods to predict and distinguish the groups from each other.Using a multi-class deep neural network classifier to better fit our prediction model, we recapitulated a 100% precision, 100% recall and F1 score of 1 on the test set. Moreover, a first score specific for the chronic COVID-19 patients was defined as S1 = (IFN-{gamma} + IL-2)/ CCL4-MIP-1{beta}. Second, a score specific for the severe COVID-19 patients was defined as S2 = (10*IL-10 + IL-6) - (IL-2 + IL-8). Severe cases are characterized by excessive inflammation and dysregulated T cell activation, recruitment, and counteracting activities. While chronic patients are characterized by a profile able to induce the activation of effector T cells with pro-inflammatory properties and the capacity of generating an effective immune response to eliminate the virus but without the proper recruitment signals to attract activated T cells. SummaryImmunologic Modeling of Severity and Chronicity of COVID-19

immunology↗

bioRxiv2017

Redox-Dependent Condensation Of Mycobacterial Genome By WhiB4

Oxidative stress response in bacteria is generally mediated through coordination between the regulators of oxidant-remediation systems (e.g. OxyR, SoxR) and nucleoid condensation (e.g. Dps, Fis). However, these genetic factors are either absent or rendered nonfunctional in the human pathogen Mycobacterium tuberculosis (Mtb). Therefore, how Mtb organizes genome architecture and regulates gene expression to counterbalance oxidative imbalance during infection is not known. Here, we report that an intracellular redox-sensor, WhiB4, dynamically links genome condensation and oxidative stress response in Mtb. Disruption of WhiB4 affects the expression of genes involved in maintaining redox homeostasis, central carbon metabolism (CCM), respiration, cell wall biogenesis, DNA repair and protein quality control under oxidative stress. Notably, disulfide-linked oligomerization of WhiB4 in response to oxidative stress activates the proteins ability to condense DNA in vitro and in vivo. Further, overexpression of WhiB4 led to hypercondensation of nucleoids, redox imbalance and increased susceptibility to oxidative stress, whereas WhiB4 disruption reversed this effect. In accordance with the findings in vitro, ChIP-Seq data demonstrated non-specific binding of WhiB4 to GC-rich regions of the Mtb genome. Lastly, data indicate that WhiB4 deletion affected the expression of only a fraction of genes preferentially bound by the protein, suggesting its indirect effect on gene expression. We propose that WhiB4 is a novel redox-dependent nucleoid condensing protein that structurally couples Mtbs response to oxidative stress with genome organization and transcription.\n\nSignificance StatementMycobacterium tuberculosis (Mtb) needs to adapt in response to oxidative stress encountered inside human phagocytes. In other bacteria, condensation state of nucleoids modulates gene expression to coordinate oxidative stress response. However, this relation remains elusive in Mtb. We performed molecular dissection of a mechanism controlled by an intracellular redox sensor, WhiB4, in organizing both chromosomal structure and selective expression of adaptive traits to counter oxidative stress in Mtb. Using high-resolution sequencing, transcriptomics, imaging, and redox biosensor, we describe how WhiB4 modulates nucleoid condensation, global gene expression, and redox-homeostasis. WhiB4 over-expression hypercondensed nucleoids and perturbed redox homeostasis whereas WhiB4 disruption had an opposite effect. Our study discovered an empirical role for WhiB4 in integrating redox signals with nucleoid condensation in Mtb.

microbiology↗