Biology subjects

Patel, B.

Publications and source records attributed to Patel, B..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

The conserved ATPase PCH-2 controls the number and distribution of crossovers by antagonizing crossover formation in C. elegans

Meiotic crossover recombination is essential for both accurate chromosome segregation and the generation of new haplotypes for natural selection to act upon. This requirement is known as crossover assurance and is one example of crossover control. While the conserved role of the ATPase, PCH-2, during meiotic prophase has been enigmatic, a universal phenotype when pch-2 or its orthologs are mutated is a change in the number and distribution of meiotic crossovers. Here, we show that PCH-2 controls the number and distribution of crossovers by antagonizing their formation. This antagonism produces different effects at different stages of meiotic prophase: early in meiotic prophase, PCH-2 prevents double strand breaks from becoming crossover-eligible intermediates, limiting crossover formation at sites of initial double strand break formation and homolog interactions. Later in meiotic prophase, PCH-2 winnows the number of crossover-eligible intermediates, contributing to the designation of crossovers and ultimately, crossover assurance. We also demonstrate that PCH-2 accomplishes this regulation through the meiotic HORMAD, HIM-3. Our data strongly support a model in which PCH-2s conserved role is to remodel meiotic HORMADs throughout meiotic prophase to destabilize crossover-eligible precursors, coordinate meiotic recombination with synapsis, and contribute to the progressive implementation of meiotic recombination, guaranteeing crossover control.

cell biology↗

bioRxiv2024

LONG-TERM ECOLOGICAL MONITORING IN INDIA: A SYNTHESIS

Long-term ecological monitoring (LTEM) is crucial for understanding ecological processes and responses to environmental change, informing management of natural resources, and biodiversity conservation. Systematic LTEM efforts began in India in the mid-1900s, but there is a lack of comprehensive synthesis of LTEM efforts in the country. Here, we use a wide-ranging questionnaire survey of ecologists coupled with a survey of published literature on LTEM efforts in India to synthesise their thematic and geographical spread, and types of data being collected, and identify key challenges to the establishment and maintenance of LTEM projects in the country. Studies monitor 77 unique subjects across 272 LTEM efforts in India. LTEM efforts are more often located in the Western Ghats and Eastern Himalaya, focused on forest vegetation, and monitoring factors such as abundance, distribution, species richness, and biomass. Regions such as North-Eastern, Eastern, Central, and North-Western India, ecosystems such as grasslands, deserts and wetlands, organisms such as macrofungi, amphibians, and reptiles (other than turtles) are underrepresented. Short turnover times of funding and permits were most frequently reported as hurdles in sustaining LTEM efforts. Data from LTEM efforts have been largely used to produce academic outputs such as journal articles, but have also found use for on-the-ground conservation efforts. Overall, this synthesis can help draw attention to the need for systematic long-term ecological monitoring, help efficient utilisation of existing long-term ecological data, identify regions, species and ecosystem components that are underrepresented in Indian LTEM efforts, foster collaborations, and serve as a starting point to address challenges in sustaining LTEM efforts in India.

ecology↗

bioRxiv2024

PBK/TOPK mediates Ikaros, Aiolos and CTCF displacement from mitotic chromosomes and alters chromatin accessibility at selected C2H2-zinc finger protein binding sites

PBK/TOPK is a mitotic kinase implicated in haematological and non-haematological cancers. Here we show that the key haemopoietic regulators Ikaros and Aiolos require PBK-mediated phosphorylation to dissociate from chromosomes in mitosis. Eviction of Ikaros is rapidly reversed by addition of the PBK-inhibitor OTS514, revealing dynamic regulation by kinase and phosphatase activities. To identify more PBK targets, we analysed loss of mitotic phosphorylation events in Pbk-/-preB cells and performed proteomic comparisons on isolated mitotic chromosomes. Among a large pool of C2H2-zinc finger targets, PBK is essential for evicting the CCCTC-binding protein CTCF and zinc finger proteins encoded by Ikzf1, Ikzf3, Znf131 and Zbtb11. PBK-deficient cells were able to divide but showed altered chromatin accessibility and nucleosome positioning consistent with CTCF retention. Our studies reveal that PBK controls the dissociation of selected factors from condensing mitotic chromosomes and contributes to their compaction.

molecular biology↗

bioRxiv2024

Diversity and abundance of tree microhabitats in the tropical forests of southern Western Ghats, India

Tree microhabitats (TMHs) are proven tools for assessing and monitoring diversity. These structures on trees are potential indicators of biota, but there is a huge gap in TMH-related knowledge from the tropical regions, the cradles of biodiversity. Thus, an inventory was made to document the TMHs in the tropical forests of southern Western Ghats, India. In evergreen forests, 3,637 TMH host and 450 cavity host trees were identified from the 6,363 trees sampled. The density of TMHs was 972.57{+/-}341.25 ha-1 and cavity density was 63.13{+/-}11.91 ha-1. In moist deciduous forests, out of 1,545 trees sampled, 1,108 hosted TMHs and 212 trees hosted cavities. The density of TMHs was 493.67{+/-}133.28 ha-1 and cavity density was 42.00{+/-}15.01 ha-1. TMHs were categorised into nine categories and 33 sub-categories. The TMH and cavity occurrences were significantly influenced by species richness, stand density, basal area, diameter and height of trees, and density of healthy, unhealthy and dead trees. Dominant and codominant individuals hosted more TMHs and cavities in the deciduous stands while in evergreen, intermediate and overtopped trees had more TMHs and intermediate and codominant had more cavities. In both the habitats the important species of the habitat were also major hosts for TMHs and cavities. HighlightsO_LIPrimary inventory of diversity of TMHs and their host trees in tropical forests C_LIO_LITMH and cavity occurrences are significantly influenced by stand characteristics C_LIO_LIKey species in the habitats also form major hosts for TMHs and cavities C_LIO_LIDominant and codominant individuals host more TMHs and cavities in deciduous stands C_LIO_LIIntermediate and overtopped trees host more TMHs, intermediate and codominant host more cavities in evergreen C_LI

ecology↗

bioRxiv2024

Differentiation marker-negative CD4+ T cells persist after yellow fever virus vaccination and contribute to durable memory

Factors that contribute to durable immunological memory remain incompletely understood. In our longitudinal analyses of CD4+ T cell responses to the yellow fever virus (YFV) vaccine by peptide-MHC tetramers, we unexpectedly found naive phenotype virus-specific CD4+ T cells that persisted months to years after immunization. These Marker negative T cells (TMN) lacked CD95, CXCR3, CD11a, and CD49d surface protein expression, distinguishing them from previously discovered stem-cell memory T cells. Functionally, they resembled genuine naive T cells upon in vitro stimulation. Single-cell TCR sequencing detected expanded clonotypes within the TMN subset and identified a shared repertoire with memory and effector T cells. T cells expressing TMN-associated TCRs were rare before vaccination, suggesting their expansion following vaccination. Longitudinal tracking of YFV-specific responses over the subsequent years revealed superior stability of the TMN subset and their association with the longevity of the overall population. The identification of these long-lived, antigen-experienced T cells may inform the design of durable T cell-based vaccines and engineered T cell therapies.

immunology↗

bioRxiv2023

SODA: Software to Support the Curation and Sharing of FAIR Autonomic Nervous System Data

Since 2014, the National Institutes of Health (NIH)s Stimulating Peripheral Activity to Relieve Conditions (SPARC) Program has been supporting research and development of therapeutic devices that modulate electrical activity in the autonomic nervous system (ANS) to improve organ function, also known as bioelectronic medicine. To optimize the reusability of data resulting from ANS-related research, the SPARC Program also supported the development of guidelines for curating and sharing data in line with the FAIR (Findable, Accessible, Interoperable, Reusable) Principles. These guidelines are exhaustive to maximize FAIRness of data but as a result, they are difficult and time-consuming for researchers to implement. To address these challenges, we developed SODA (Software to Organize Data Automatically), an open source and free cross-platform desktop software that guides researchers step-by-step in preparing and sharing their ANS-related data according to the SPARC guidelines. SODA combines intuitive user interfaces with automation to streamline the process and reduce researchers time, effort, and error in making their data FAIR. We provide in this paper an overview of SODA and results of testing its performance. We also provide an overview of the impact of SODA which is, to our knowledge, the first researcher-oriented tool for making data FAIR.

bioinformatics↗

bioRxiv2023

NF2 Loss-of-Function and Hypoxia Drive Radiation Resistance in Grade 2 Meningiomas

BackgroundWorld Health Organization Grade 2 meningiomas (G2Ms) exhibit an aggressive natural history characterized by recurrence and therapy resistance. G2Ms with histopathological necrosis have been associated with worse local control (LC) following radiation therapy, but drivers and biomarkers of radiation resistance in these G2Ms remain unknown. MethodsWe performed genetic sequencing and histopathological analysis of 113 G2Ms and investigated the role of intratumoral hypoxia as well as genes of interest through knockdown and clonogenic survival following ionizing radiation. Lastly, we performed transcriptional profiling of our in vitro model and 18 G2M tumors using RNA sequencing. ResultsNF2 loss-of-function (LOF) mutations were associated with necrosis in G2Ms (p=0.0127). Tumors with NF2 mutation and necrosis had worse post-radiation LC compared to NF2 wildtype tumors without necrosis (p=0.035). Under hypoxic conditions, NF2 knockdown increased radiation resistance in vitro (p<0.001). Bulk RNA sequencing of our in vitro model revealed NF2- and hypoxia-specific changes and a 50-gene set signature specific to radiation resistant, NF2 knockdown and hypoxic cells, which could distinguish NF2 mutant and necrotic patient G2Ms by unsupervised clustering. Gene set enrichment analysis of patient tumor and in vitro data revealed downregulation of apoptosis and upregulation of proliferation in NF2-deficient and hypoxic cells, which we validated with functional assays. ConclusionsNF2 LOF in the setting of hypoxia confers radiation resistance through transcriptional programs that reduce apoptosis and promote proliferation. These pathways may identify tumors resistant to radiation and represent therapeutic targets that in the future could improve LC in patients with radiation resistant G2Ms. KEY POINTS1. Spontaneous necrosis with NF2 mutations is associated with radio-resistance in WHO G2Ms. 2. NF2 knockdown in the setting of hypoxia confers radio-resistance to meningioma cells in vitro and is driven by increased cell proliferation and decreased apoptosis. IMPORTANCE OF THE STUDYWorld Health Organization Grade 2 meningiomas (G2M) are often treated with surgical resection followed by radiation, especially in the case of recurrence. However, the mechanisms underlying radiation resistance in G2Ms remain to be identified, and moreover, we lack biomarkers to distinguish G2Ms that will respond to radiotherapy from those that are refractory. In this study we perform histological and molecular analysis of a large cohort of G2Ms to identify predictors of radiation resistance. Using these data and an in vitro model of radiation therapy, we demonstrate that radiation resistance in G2Ms is likely driven by the combination of NF2 gene mutations and the hypoxia that accompanies tumor necrosis. Patients whose tumors bear these two features may therefore benefit from alternative treatments that target specific pathways implicated in radiation resistance.

molecular biology↗

bioRxiv2023

Microglia play beneficial roles in multiple experimental seizure models.

Seizure disorders are common, affecting both the young and the old. Currently available antiseizure drugs are ineffective in a third of patients and have been developed with a focus on known neurocentric mechanisms, raising the need for investigations into alternative and complementary mechanisms that contribute to seizure generation or its containment. Neuroinflammation, broadly defined as the activation of immune cells and molecules in the central nervous system (CNS), has been proposed to facilitate seizure generation, although the specific cells involved in these processes remain inadequately understood. The role of microglia, the primary inflammation-competent cells of the brain, is debated since previous studies were conducted using approaches that were less specific to microglia or had inherent confounds. Using a selective approach to target microglia without such side effects, we show a broadly beneficial role for microglia in limiting chemoconvulsive, electrical, and hyperthermic seizures and argue for a further understanding of microglial contributions to contain seizures.

neuroscience↗

bioRxiv2023

STAT3 protects HSCs from intrinsic interferon signaling and loss of long-term blood-forming activity

STAT3 function in hematopoietic stem and progenitor cells (HSPCs) has been difficult to discern as Stat3 deficiency in the hematopoietic system induces systemic inflammation, which can impact HSPC activity. To address this, we established mixed bone marrow (BM) chimeric mice with CreER-mediated Stat3 deletion in 20% of the hematopoietic compartment. Stat3-deficient HSPCs had impaired hematopoietic activity and failed to undergo expansion in BM in contrast to Stat3-sufficient (CreER) controls. Single-cell RNA sequencing of Lin-ckit+Sca1+ BM cells revealed altered transcriptional responses in Stat3-deficient hematopoietic stem cells (HSCs) and multipotent progenitors, including intrinsic activation of cell cycle, stress response, and interferon signaling pathways. Consistent with their deregulation, Stat3-deficient Lin-ckit+Sca1+ cells accumulated {gamma}H2AX over time. Following secondary BM transplantation, Stat3-deficient HSPCs failed to reconstitute peripheral blood effectively, indicating a severe functional defect in the HSC compartment. Our results reveal essential roles for STAT3 in HSCs and suggest the potential for using targeted synthetic lethal approaches with STAT3 inhibition to remove defective or diseased HSPCs. Key PointsO_LISTAT3 is critical for hematopoietic activity and hematopoietic stem cell maintenance in non-inflammatory conditions C_LIO_LISTAT3 has a cell-intrinsic role in the suppression of interferon signaling and myeloid-skewed transcription in hematopoietic stem cells C_LI

immunology↗

bioRxiv2023

Establishment of beta cell heterogeneity via differential CpG methylation at Nnat

Aims/hypothesisBeta cells within the pancreatic islet represent a heterogenous population wherein individual sub-groups of cells make distinct contributions to the overall control of insulin secretion. These include a subpopulation of highly-connected hub cells, important for the propagation of intercellular Ca2+ waves. Functional subpopulations have also been demonstrated in human beta cells, with an altered subtype distribution apparent in type 2 diabetes. At present, the molecular mechanisms through which beta cell hierarchy is established are poorly understood. Changes at the level of the epigenome provide one such possibility which we explore here by focussing on the imprinted gene neuronatin (Nnat), which is required for normal insulin synthesis and secretion. MethodsSingle cell RNA-seq datasets were examined using Seurat 4.0 and ClusterProfiler running under R. Transgenic mice expressing eGFP under the control of the Nnat enhancer/promoter regions were generated for fluorescence-activated cell (FAC) sorting of beta cells and downstream analysis of CpG methylation by bisulphite and RNA sequencing, respectively. Animals deleted for the de novo methyltransferase, DNMT3A from the pancreatic progenitor stage were used to explore control of promoter methylation. Proteomics was performed using affinity purification mass spectrometry and Ca2+ dynamics explored by rapid confocal imaging of Cal-520 and Cal-590. Insulin secretion was measured using Homogeneous Time Resolved Fluorescence Imaging. ResultsNnat mRNA was differentially expressed in a discrete beta cell population in a developmental stage- and DNA methylation (DNMT3A)-dependent manner. Thus, pseudo-time analysis of embryonic data sets demonstrated the early establishment of Nnat-positive and negative subpopulations during embryogenesis. NNAT expression is also restricted to a subset of beta cells across the human islet that is maintained throughout adult life. NNAT+ beta cells also displayed a discrete transcriptome at adult stages, representing a sub-population specialised for insulin production, reminiscent of recently-described "{beta}HI" cells and were diminished in db/db mice. Hub cells were less abundant in the NNAT+ population, consistent with epigenetic control of this functional specialization. Conclusions/interpretationThese findings demonstrate that differential DNA methylation at Nnat represents a novel means through which beta cell heterogeneity is established during development. We therefore hypothesise that changes in methylation at this locus may thus contribute to a loss of beta cell hierarchy and connectivity, potentially contributing to defective insulin secretion in some forms of diabetes. Research in contextWhat is already known about this subject? - Neuronatin (Nnat/NNAT) is an imprinted gene in humans and mice and is required for glucose-stimulated insulin secretion in vivo - Pancreatic beta cells are functionally heterogeneous with specific highly-connected subpopulations known to coordinate islet wide Ca2+ dynamics - Functional subpopulations have been described in human beta cells and their distribution is altered in type 2 diabetes What is the key question? - Does NNAT mark a discrete subpopulation of functional beta cells and which epigenetic pathways coordinate its formation and maintenance? What are the new findings? - A subpopulation of NNAT+ beta cells is established prior to the first week of postnatal life in mice via de novo DNA methylation at the Nnat promoter - NNAT+ beta cells are transcriptionally highly differentiated and appear to be functionally specialised for insulin production, possibly corresponding to recently-described "{beta}HI" and "CD63hi" beta cells. NNAT is expressed in a subset of beta cells across the human islet, and its deficiency in human beta cells diminishes glucose-stimulated insulin secretion - NNAT+ cells are likelier to belong to the population of follower, rather than hub cells, consistent with a role in insulin production rather than glucose detection How might this impact on clinical practice in the foreseeable future? - Epigenome-modifying compounds may provide a way of enhancing beta cell function and the ensemble behaviour of the islet to stimulate insulin secretion

cell biology↗

bioRxiv2023

Manipulating mitochondrial dynamics in the NTS prevents diet-induced deficits in brown fat morphology and activity

Brown adipose tissue (BAT) uptakes and metabolises both glucose and triglycerides to produce heat and is activated by the central nervous system (CNS) through direct noradrenergic sympathetic innervation. Dysregulation of signalling modules in selective CNS areas such as the nucleus of tractus solitarius (NTS) are linked with altered BAT activity, obesity and diabetes. High-fat diet (HFD)-feeding increases mitochondrial fragmentation in the NTS triggering insulin resistance, hyperphagia and weight gain. Here we sought to determine whether changes in mitochondrial dynamics in the NTS can affect BAT glucose uptake. Our findings demonstrated that short-term HFD feeding reduces BATs ability to take up glucose, as measured by PET/CT scan. However, inhibiting mitochondrial fragmentation in NTS-astrocytes of HFD-fed rats improved BAT glucose uptake while lowering blood glucose and insulin levels. Compared with HFD-fed rats, HFD fed animals, where mitochondrial fragmentation was inhibited in the NTS-astrocytes, had higher levels of catecholaminergic innervation of BAT, and did not present HFD-dependent infiltration of enlarged white fat droplets in the BAT. In regular chow-fed rats, increasing mitochondrial fragmentation in the NTS-astrocytes reduced BAT glucose uptake, catecholaminergic innervation and {beta}3-adrenergic receptor levels. Our data suggest that targeting mitochondrial dynamics in the NTS-astrocytes could be a beneficial strategy to increase glucose utilization and protect from developing obesity and diabetes.

neuroscience↗

bioRxiv2022

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

Vestibular schwannomas (VS) are benign tumors that lead to significant neurologic and otologic morbidity. How VS heterogeneity and the tumor microenvironment (TME) contribute to the pathogenesis of these tumors remains poorly understood. We performed scRNA-seq on 15 VS samples, with paired scATAC-seq in six samples. We identified diverse Schwann cell (SC), stromal, and immune populations in the VS TME and found that repair-like and MHC-II antigen presenting subtype SCs are associated with increased myeloid cell infiltrate, implicating a nerve injury-like process. Deconvolution analysis of RNA-expression data from 175 tumors revealed Injury-like tumors are associated with larger tumor size, and scATAC-seq identified transcription factors associated with nerve repair among SCs from Injury-like tumors. Ligand-receptor analysis and functional in vitro experiments suggested that SCs recruit monocytes. Our study indicates that Injury-like SCs may cause tumor growth via myeloid cell recruitment and identifies molecular pathways that may be targeted to prevent tumor progression.

cancer biology↗

bioRxiv2022

Making Biomedical Research Software FAIR: Actionable Step-by-step Guidelines with a User-support Tool

Findable, Accessible, Interoperable, and Reusable (FAIR) guiding principles tailored for research software have been proposed by the FAIR for Research Software (FAIR4RS) Working Group. They provide a foundation for optimizing the reuse of research software. The FAIR4RS principles are, however, aspirational and do not provide practical instructions to the researchers. To fill this gap, we propose in this work the first actionable step-by-step guidelines for biomedical researchers to make their research software compliant with the FAIR4RS principles. We designate them as the FAIR Biomedical Research Software (FAIR-BioRS) guidelines. Our process for developing these guidelines, presented here, is based on an in-depth study of the FAIR4RS principles and a thorough review of current practices in the field. To support researchers, we have also developed a workflow that streamlines the process of implementing these guidelines. This workflow is incorporated in FAIRshare, a free and open-source software application aimed at simplifying the curation and sharing of FAIR biomedical data and software through user-friendly interfaces and automation. Details about this tool are also presented.

scientific communication and education↗

bioRxiv2022

Loss of H3K9 tri-methylation alters chromosome compaction and transcription factor retention during mitosis

Recent studies have shown that repressive chromatin machinery, including DNA methyltransferases (DNMTs) and Polycomb Repressor Complexes (PRCs), bind to chromosomes throughout mitosis and their depletion results in increased chromosome size. Here we show that enzymes that catalyse H3K9 methylation, such as Suv39h1, Suv39h2, G9a and Glp, are also retained on mitotic chromosomes. Surprisingly however, mutants lacking H3K9me3 have unusually small and compact mitotic chromosomes that are associated with increased H3S10ph and H3K27me3 levels. Chromosome size and centromere compaction in these mutants were rescued by providing exogenous Suv39h1, or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wildtype versus Suv39h1/Suv39h2 double-null ESCs revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis, and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.

molecular biology↗

bioRxiv2021

A Spatial Transcriptomics Study of the Brain-Electrode Interface in Rat Motor Cortex

The study of the foreign body reaction to implanted electrodes in the brain is an important area of research for the future development of neuroprostheses and experimental electrophysiology. After electrode implantation in the brain, microglial activation, reactive astrogliosis, and neuronal cell death create an environment immediately surrounding the electrode that is significantly altered from its homeostatic state. To uncover physiological changes potentially affecting device function and longevity, spatial transcriptomics was implemented in this preliminary study to identify changes in gene expression driven by electrode implantation. This RNA-sequencing technique (10x Genomics, Visium) uses spatially coded, RNA-binding oligonucleotides on a microscope slide to spatially identify each sequencing read. For these experiments, sections of rat motor cortex implanted with Michigan-style silicon electrodes were mounted on the Visium slide for processing. Each tissue section was labeled for neurons and astrocytes using immunohistochemistry to provide a spatial reference for mapping each sequencing read relative to the device tract. Results from rat motor cortex at 24 hours, 1 week, and 6 weeks post implantation showed up to 5811 differentially expressed genes between implanted and non-implanted tissue sections. Many of these genes are related to biological mechanisms previously reported in studies of the foreign body response to implanted electrodes, while others are novel to this study. These results will provide a foundation for future work to both improve and measure the effects of gene expression on the long-term stability of recordings from implanted electrodes in the brain. Ongoing work will expand on these initial observations as we gain a better understanding of the dynamic, molecular changes taking place in the brain in response to electrode implantation.

bioengineering↗

bioRxiv2021

Structural Differences In 3C-like protease (Mpro) From SARS-CoV and SARS-CoV-2: Molecular Insights For Drug Repurposing Against COVID-19 Revealed by Molecular Dynamics Simulations.

A recent fatal outbreak of novel coronavirus SARS-CoV-2, identified preliminary as a causative agent for series of unusual pneumonia cases in Wuhan city, China has infected more than 20 million individuals with more than 4 million mortalities. Since, the infection crossed geographical barriers, the WHO permanently named the causing disease as COVID-2019 by declaring it a pandemic situation. SARS-CoV-2 is an enveloped single-stranded RNA virus causing a wide range of pathological conditions from common cold symptoms to pneumonia and fatal severe respiratory syndrome. Genome sequencing of SARS-CoV-2 has revealed 96% identity to the bat coronavirus and 79.6% sequence identity to the previous SARS-CoV. The main protease (known as 3C-like proteinase/ Mpro) plays a vital role during the infection with the processing of replicase polyprotein thus offering an attractive target for therapeutic interventions. SARS-CoV and SARS-CoV-2 Mpro shares 97% sequence identity, with 12 variable residues but none of them present in the catalytic and substrate binding site. With the high level of sequence and structural similarity and absence of any drug/vaccine against SARS-CoV-2, drug repurposing against Mpro is an effective strategy to combat COVID-19. Here, we report a detailed comparison of SARS-CoV-2 Mpro with SARS-CoV Mpro using molecular dynamics simulations to assess the impact of 12 divergent residues on the molecular microenvironment of Mpro. A structural comparison and analysis is made on how these variable residues affects the intra-molecular interactions between key residues in the monomer and biologically active dimer form of Mpro. The present MD simulations study concluded the change in microenvironment of active-site residues at the entrance (T25, T26, M49 and Q189), near the catalytic region (F140, H163, H164, M165 and H172) and other residues in substrate binding site (V35T, N65S, K88R and N180K) due to 12 mutation incorporated in the SARS-CoV-2 Mpro. It is also evident that SARS-CoV-2 dimer is more stable and less flexible state compared to monomer which may be due to these variable residues, mainly F140, E166 and H172 which are involved in dimerization. This also warrants a need for inhibitor design considering the more stable dimer form. The mutation accumulated in SARS-CoV-2 Mpro indirectly reconfigures the key molecular networks around the active site conferring a potential change in SARS-CoV-2, thus posing a challenge in drug repurposing SARS drugs for COVID-19. The new networks and changes in microenvironment identified by our work might guide attempts needed for repurposing and identification of new Mpro inhibitors.

bioinformatics↗

bioRxiv2021

KnowMore: An Automated Knowledge Discovery Tool for the FAIR SPARC Datasets

This manuscript provides the methods and outcomes of KnowMore, the Grand Prize winning automated knowledge discovery tool developed by our team during the 2021 NIH SPARC FAIR Data Codeathon. The National Institutes of Health Stimulating Peripheral Activity to Relieve Conditions (NIH SPARC) program generates rich datasets from neuromodulation researches, curated according to the Findable, Accessible, Interoperable, and Reusable (FAIR) SPARC data standards. These datasets are publicly available through the SPARC Data Portal at sparc.science. Currently, the process of simultaneously comparing and analyzing multiple SPARC datasets is tedious because it requires investigating each dataset of interest individually and downloading all of them to conduct cross-analyses. It is crucial to enhance this process to enable rapid discoveries across SPARC datasets. To fill this need, we created KnowMore, a tool integrated into the SPARC Portal that only requires the user to select their datasets of interest to launch an automated discovery process. KnowMore uses several SPARC resources (Pennsieve, o2S2PARC, SciCrunch, protocols.io, Biolucida), data science methods, and machine learning algorithms in the back end to generate various visualizations in the front end intended to help the user identify potential similarities, differences, and relations across the datasets. These visualizations can lead to a new discovery, new hypothesis, or simply guide the user to the next logical step in their discovery process. The outcome of this project is a SPARC portal-ready code architecture that helps researchers to use SPARC datasets more efficiently and fully leverages their FAIR characteristics. The tool has been built and documented such that more data analysis methods and visualization items could be easily added. The potential for automated discoveries from SPARC datasets is huge given the unique SPARC data ecosystem promoting FAIR data practices, and KnowMore has only demonstrated a small highlight of what could be achieved to speed up discoveries from SPARC datasets.

bioinformatics↗

bioRxiv2021

Single Cell Atlas of Human Dura Reveals Cellular Meningeal Landscape and Insights into Meningioma Immune Response

Recent investigation of the meninges, specifically the dura layer, has highlighted its importance in CNS immune surveillance beyond a purely structural role. However, most of our understanding of the meninges stems from the use of pre-clinical models rather than human samples. In this study, we use single cell RNA-sequencing to perform the first characterization of both non-tumor-associated human dura and meningioma samples. First, we reveal a complex immune microenvironment in human dura that is transcriptionally distinct from that of meningioma. In addition, through T cell receptor sequencing, we show significant TCR overlap between matched dura and meningioma samples. We also identify a functionally heterogeneous population of non-immune cell types and report copy-number variant heterogeneity within our meningioma samples. Our comprehensive investigation of both the immune and non-immune cell landscapes of human dura and meningioma at a single cell resolution provide new insight into previously uncharacterized roles of human dura.

immunology↗